WO2010138806A2 - Treatment of antiviral gene related diseases by inhibition of natural antisense transcript to an antiviral gene - Google Patents

Treatment of antiviral gene related diseases by inhibition of natural antisense transcript to an antiviral gene Download PDF

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Publication number
WO2010138806A2
WO2010138806A2 PCT/US2010/036558 US2010036558W WO2010138806A2 WO 2010138806 A2 WO2010138806 A2 WO 2010138806A2 US 2010036558 W US2010036558 W US 2010036558W WO 2010138806 A2 WO2010138806 A2 WO 2010138806A2
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WIPO (PCT)
Prior art keywords
oligonucleotide
antiviral gene
antisense
nucleic acid
expression
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PCT/US2010/036558
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French (fr)
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WO2010138806A8 (en
WO2010138806A3 (en
Inventor
Joseph Collard
Olga Khorkova Sherman
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Curna, Inc.
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority to EP10781271.1A priority Critical patent/EP2435571B1/en
Priority to KR1020167034817A priority patent/KR101704988B1/en
Priority to JP2012513290A priority patent/JP5960049B2/en
Priority to CN201080036011.5A priority patent/CN103221541B/en
Priority to CA 2764683 priority patent/CA2764683A1/en
Priority to ES10781271.1T priority patent/ES2618576T3/en
Application filed by Curna, Inc. filed Critical Curna, Inc.
Priority to US13/321,996 priority patent/US8791085B2/en
Publication of WO2010138806A2 publication Critical patent/WO2010138806A2/en
Publication of WO2010138806A3 publication Critical patent/WO2010138806A3/en
Publication of WO2010138806A8 publication Critical patent/WO2010138806A8/en
Priority to US14/297,101 priority patent/US9133456B2/en
Priority to US14/814,833 priority patent/US9512427B2/en

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Definitions

  • Embodiments of the invention comprise oligonucleotides modulating expression and/or function of an Antiviral gene and associated molecules.
  • DNA-RNA and RNA-RNA hybridization arc important to many aspects of nucleic acid function including DNA replication, transcription, and translation. Hybridization is also central to a variety of technologies that either detect a particular nucleic acid or alter its expression. Antiscnsc nucleotides, for example, disrupt gene expression by hybridizing to target RNA, thereby interfering with RNA splicing, transcription, translation, and replication. Antisensc DNA has the added feature that DNA-RNA hybrids serve as a substrate for digestion by ribonuclease H, an activity that is present in most cell types.
  • Antisensc molecules can be delivered into cells, as is the case for oligodcoxynucleotides (ODNs), or they can be expressed from endogenous genes as RNA molecules.
  • ODNs oligodcoxynucleotides
  • V1TRAVENETM for treatment of cytomegalovirus retinitis
  • the invention provides methods for inhibiting the action of a natural antiscnsc transcript by using antiscnsc oligonucleotide(s) targeted to any region of the natural antiscnsc transcript resulting in up-rcgulation of the corresponding sense gene. It is also contemplated herein that inhibition of the natural antisense transcript can be achieved by siRNA, ribozymes and small molecules, which are considered to be within the scope of the present invention.
  • One embodiment provides a method of modulating function and/or expression of an Antiviral gene polynucleotide in patient cells or tissues in vivo or in vitro comprising contacting said cells or tissues with an antiscnsc oligonucleotide 5 to 30 nucleotides in length wherein said oligonucleotide has at least 50% sequence identity to a reverse complement of a polynucleotide comprising 5 to 30 consecutive nucleotides within nucleotides I to 1267 of SEQ ID SEQ ID NO: 4, 1 to 586 of SEQ ID NO: 5, 1 to 741 of SEQ ID SEQ ID NO: 6, I to 251 of SEQ ID NO: 7, 1 to 681 of SEQ ID NO: 8, and 1 to 580 of SEQ ID NO: 9 thereby modulating function and/or expression of the Antiviral gene polynucleotide in patient cells or tissues in vivo or in vitro.
  • an oligonucleotide targets a natural antisense sequence of an Antiviral gene polynucleotide, for example, nucleotides set forth in SEQ ID NO: 4 to 9, and any variants, alleles, homologs, mutants, derivatives, fragments and complementary sequences thereto.
  • antisense oligonucleotides are set forth as SEQ ID NOS: 10 to 30.
  • Another embodiment provides a method of modulating function and/or expression of an Antiviral gene polynucleotide in patient cells or tissues in vivo or in vitro comprising contacting said cells or tissues with an antisense oligonucleotide 5 to 30 nucleotides in length wherein said oligonucleotide has at least 50% sequence identity to a reverse complement of the an antisense of the Antiviral gene polynucleotide; thereby modulating function and/or expression of the Antiviral gene polynucleotide in patient cells or tissues in vivo or in vitro.
  • Another embodiment provides a method of modulating function and/or expression of an Antiviral gene polynucleotide in patient cells or tissues in vivo or in vitro comprising contacting said cells or tissues with an antisense oligonucleotide 5 to 30 nucleotides in length wherein said oligonucleotide has at least 50% sequence identity to an antisense oligonucleotide to an Antiviral gene antisense polynucleotide; thereby modulating function and/or expression of the Antiviral gene polynucleotide in patient cells or tissues in vivo or in vitro.
  • a composition comprises one or more antisense oligonucleotides which bind to sense and/or antisense Antiviral gene polynucleotides.
  • the oligonucleotides comprise one or more modified or substituted nucleotides.
  • the oligonucleotides comprise one or more modified bonds.
  • the modified nucleotides comprise modified bases comprising phosphorothioatc, mcthylphosphonatc, peptide nucleic acids, 2'-O-mcthyl, fluoro- or carbon, methylene or other locked nucleic acid (LNA) molecules.
  • the modified nucleotides arc locked nucleic acid molecules, including ⁇ -L-LNA.
  • the oligonucleotides are administered to a patient subcutancously, intramuscularly, int ⁇ n'cnously or intraperitoneal Iy.
  • the oligonucleotides arc administered in a pharmaceutical composition.
  • a treatment regimen comprises administering the antisense compounds at least once to patient; however, this treatment can be modified to include multiple doses over a period of time.
  • the treatment can be combined with one or more other types of therapies.
  • the oligonucleotides arc encapsulated in a liposome or attached to a carrier molecule (e.g. cholesterol, TAT peptide).
  • a carrier molecule e.g. cholesterol, TAT peptide.
  • Figure 1 is a graph of real time PCR results showing the fold change + standard deviation in RIG 1 mRNA after treatment of HcpG2 cells with phosphorothioatc oligonucleotides introduced using Lipofcctaminc 2000, as compared to control.
  • Real Time PCR results show that levels of RIG I mRNA in HcpG2 cells arc significantly increased 48h after treatment with siRNAs to RIG l antisense hs.6OI664 and AK300104. Bars denoted as CUR- 0544, CUR-0546.
  • CUR-0548, CUR-O55O, CUR-0552, CUR-0554, CUR-0556, CUR-0558 and CUR-0560 correspond to samples treated with SEQ ID NOS: 10 to 18 respectively.
  • Figure 2 is a graph of real time PCR results showing the fold change + standard deviation in MDA5 mRNA after treatment of HcpG2 cells with phosphorothioatc oligonucleotides introduced using Lipofectaminc 2000, as compared to control.
  • Real time PCR results show that the levels of MDA5 mRNA in HcpG2 cells are significantly increased 48h after treatment with two of the oligos designed to MDA5 anriscnsc BU663736.
  • FIG. 3 is a graph of real time PCR results showing the fold change + standard deviation in IFNA I mRNA after treatment of HcpG2 cells with phosphorothioate oligonucleotides introduced using Lipofcctamine 2000, as compared to control.
  • Real time PCR results show that the levels of IFNAI mRNA in HepG2 cells are significantly increased 48h after treatment with one oligo designed to IFNAI antiscnsc DA393812.
  • FIG. 4 is a graph of real time PCR results showing the fold change + standard deviation in IFNAl mRNA after treatment of ZR75 cells with phosphorothioatc oligonucleotides introduced using Lipofectaminc 2000, as compared to control.
  • Real time PCR results show that the levels of IFNAI mRNA in ZR75 cells are significantly increased 48h after treatment with one oligo designed to IFNAI antiscnsc DA393812.
  • Bars denoted as CUR-0916, CUR-0919, CUR-0918 and CUR-0917 and correspond to samples treated with SEQ ID NOS: 27, 30, 29 and 28 respectively.
  • Figure 5 is a graph of real time PCR results showing the fold change + standard deviation in IFNA I mRNA after treatment of HUVEC cells with phosphorothioate oligonucleotides introduced using Lipofectaminc 2000, as compared to control.
  • Real time PCR results show that the levels of IFNAJ mRNA in HUVEC cells are significantly increased 48h after treatment with one oligo designed to IFNAI antisensc DA393812. Bars denoted as CUR-0916, CUR-09I 7, CUR-0918 and CUR-0919 correspond to samples treated with SEQ ID NOS: 27 to 30 respectively.
  • FIG. 6 ELISA Assay results show that IFNA protein was uprcgulated in extracts from MCF7 cells which were treated with oligos designed to IFNAl antisensc DA393812. Bars denoted as CUR-0916, CUR-0919. CUR-0918 and CUR-0917 and correspond to samples treated with SEQ ID NOS: 27, 30, 29 and 28 respectively. [0023] Sequence Listing Description
  • SEQ ID NO: 1 Homo sapiens atonal homolog 1 (Drosophila) (ATOH l ), mRNA (NCBI Accession No.:
  • SEQ ID NO: 2 Homo sapiens interferon induced with helicase C domain I (IFlH l ), mRNA (NCBI Accession
  • SEQ ID NO: 3 NM_0240l 3.1
  • SEQ ID NOs: 4 to 9 SEQ ID NO: 4: Natural RIGl antisense sequence (AK300104); SEQ ID NO: 5: Natural RJG l antisensc sequence (hs.601664); SEQ ID NO: 6: Natural RIGl antisense sequence (hs.104091); SEQ ID NO: 7: Natural MDA5 antisense sequence (Hs.692345); SEQ ID NO: 8: Natural MDA5 antisense sequence (BU663736) and SEQ ID NO: 9: Natural IFNA 1 antisense sequence (DA393812) SEQ ID NOs: IO to 30: Antisense oligonucleotides. V indicates RNA and * indicates phosphothioatc bond. SEQ ID NO: 31 and 39 arc the reverse complements of the antisense oligonucleotides SEQ ID NO: I O and 18 respectively. V indicates RNA. DETAILED DESCRIPTION
  • genes, gene names, and gene products disclosed herein arc intended to correspond to homologs from any species for which the compositions and methods disclosed herein are applicable.
  • the terms include, but arc not limited to genes and gene products from humans and mice. It is understood that when a gene or gene product from a particular species is disclosed, this disclosure is intended to be exemplary only, and is not to be interpreted as a limitation unless the context in which il appears clearly indicates.
  • the genes disclosed herein which in some embodiments relate to mammalian nucleic acid and amino acid sequences arc intended to encompass homologous and/or orthologous genes and gene products from other animals including, but not limited to other mammals, fish, amphibians, reptiles, and birds.
  • the genes or nucleic acid sequences are human. Definitions
  • "about” can mean a range of up to 20%, preferably up to 10%, more preferably up to 5%, and more preferably still up to 1% of a given value.
  • the term can mean within an order of magnitude, preferably within 5-fold, and more preferably within 2-fold, of a value.
  • mRNA means the presently known mRNA transcript(s) of a targeted gene, and any further transcripts which may be elucidated.
  • antisense oligonucleotides or “antisense compound” is meant an RNA or DNA molecule that binds to another RNA or DNA (target RNA, DNA). For example, if it is an RNA oligonucleotide it binds to another RNA target by means of RNA-RNA interactions and alters the activity of the target RNA.
  • An antisense oligonucleotide can uprcgulatc or downrcgulatc expression and/or function of a particular polynucleotide.
  • RNA or DNA molecules which is useful from a therapeutic, diagnostic, or other viewpoint.
  • molecules include, for example, antisense RNA or DNA molecules, interference RNA (RNAi), micro RNA, decoy RNA molecules, siRNA, enzymatic RNA, therapeutic editing RNA and agonist and antagonist RNA, antisense oligomeric compounds, antisense oligonucleotides, external guide sequence (EGS) oligonucleotides, alternate splicers, primers, probes, and other oligomeric compounds that hybridize to at least a portion of the target nucleic acid.
  • RNAi interference RNA
  • micro RNA decoy RNA molecules
  • siRNA siRNA
  • enzymatic RNA therapeutic editing RNA and agonist and antagonist RNA
  • antisense oligomeric compounds antisense oligonucleotides
  • EGS external guide sequence oligonucleotides
  • alternate splicers primers, probes, and other oligomeric compounds that hybridize to at
  • oligonucleotide refers to an oligomer or polymer of ribonucleic acid (RNA) or deoxyribonucleic acid (DNA) or mimctics thereof.
  • oligonucleotide also includes linear or circular oligomers of natural and/or modified monomers or linkages, including deoxyribonuclcosidcs, ribonuclcosidcs, substituted and alpha-anomeric forms thereof, peptide nucleic acids (PNA), locked nucleic acids (LNA), phosphorothioatc, mcthylphosphonatc, and the like.
  • Oligonucleotides arc capable of specifically binding to a target polynucleotide by way of a regular pattern of monomcr-to-monomer interactions, such as Watson-Crick type of base pairing, Hoogstecn or reverse Hoogsteen types of base pairing, or the like.
  • the oligonucleotide may be "chimeric", that is, composed of different regions.
  • "chimeric" compounds arc oligonucleotides, which contain two or more chemical regions, for example, DNA rcgion(s), RNA rcgion(s), PNA region(s) etc.
  • Each chemical region is made up of at least one monomer unit, i.e., a nucleotide in the case of an oligonucleotides compound.
  • These oligonucleotides typically comp ⁇ sc at least one region wherein the oligonucleotide is modified in order to exhibit one or more desired properties.
  • the desired properties of the oligonucleotide include, but arc not limited, for example, to increased resistance to nuclease degradation, increased cellular uptake, and/or increased binding affinity for the target nucleic acid. Different regions of the oligonucleotide may therefore have different properties.
  • the chimeric oligonucleotides of the present invention can be formed as mixed structures of two or more oligonucleotides, modified oligonucleotides, oligonucleotides and/or oligonucleotide analogs as described above.
  • the oligonucleotide can be composed of regions that can be linked in "register” that is, when the monomers arc linked consecutively, as in native DNA, or linked via spacers.
  • the spacers arc intended to constitute a covalcnt "bridge” between the regions and have in cases a length not exceeding about 100 carbon atoms.
  • the spacers may carry different functionalities, for example, having positive or negative charge, carry special nucleic acid binding properties (intcrcalators, groove binders, toxins, fluorophors etc.), being lipophilic, inducing special secondary structures like, for example, alanine containing peptides that induce alpha-helices.
  • Antiviral genes and “Antiviral gene” are inclusive of all family members, mutants, alleles, fragments, species, coding and noncoding sequences, sense and antisense polynucleotide strands, etc.
  • the words RlG l , RIG-I , RIG-I, DEAD box protein 58, DKFZp434Jl l 11 , DKJFZp686N 19181 , FLJ 13599, Rctinoic acid-induciblc gene 1 protein, Retinoic acid-induciblc gene 1 protein, arc considered the same in the literature and are used interchangeably in the present application.
  • RNA helicase-DEAD box protein 1 16 are considered the same in the literature and are used interchangeably in the present application.
  • the words IFNAl , IFNAI l , G lOPl , GARG- 16, IFI56, IFI-56, IFI-56K, IFIT-I v Interferon- induced 56 kDa protein, Intcrfcron-induccd protein with tctratricopcptide repeats 1 , 1SG56, RNM561 arc considered the same in the literature and arc used interchangeably in the present application.
  • oligonucleotide specific for or "oligonucleotide which targets” refers to an oligonucleotide having a sequence (i) capable of forming a stable complex with a portion of the targeted gene, or (ii) capable of forming a stable duplex with a portion of a mRNA transcript of the targeted gene. Stability of the complexes and duplexes can be determined by theoretical calculations and/or in vitro assays. Exemplary assays for determining stability of hybridization complexes and duplexes arc described in the Examples below.
  • target nucleic acid encompasses DNA, RNA (comprising prcmRNA and mRNA) transcribed from such DNA, and also cDNA derived from such RNA, coding, noncoding sequences, sense or antisense polynucleotides.
  • RNA comprising prcmRNA and mRNA
  • cDNA derived from such RNA
  • coding, noncoding sequences sense or antisense polynucleotides.
  • antisense The functions of DNA to be interfered include, for example, replication and transcription.
  • RNA to be interfered include all vital functions such as, for example, translocation of the RNA to the site of protein translation, translation of protein from the RNA, splicing of the RNA to yield one or more mRNA species, and catalytic activity which may be engaged in or facilitated by the RNA.
  • the overall effect of such interference with target nucleic acid function is modulation of the expression of an encoded product or oligonucleotides.
  • RNA interference "RNAi” is mediated by double stranded RNA (dsRNA) molecules that have scqucncc- specific homology to their "target" nucleic acid sequences.
  • the mediators arc 5-25 nucleotide "small interfering" RNA duplexes (siRNAs).
  • siRNAs arc derived from the processing of dsRNA by an RNasc enzyme known as Dicer.
  • siRNA duplex products arc recruited into a multi- protein siRNA complex termed RISC (RNA Induced Silencing Complex).
  • a RISC is then believed to be guided to a target nucleic acid (suitably mRNA), where the siRNA duplex interacts in a sequence-specific way to mediate cleavage in a catalytic fashion.
  • mRNA target nucleic acid
  • Small interfering RNAs that can be used in accordance with the present invention can be synthesized and used according to procedures that are well known in the art and that will be familiar to the ordinarily skilled artisan.
  • Small interfering RNAs for use in the methods of the present invention suitably comprise between about 1 to about 50 nucleotides (nt).
  • siRNAs can comprise about 5 to about 40 nt, about 5 to about 30 nt, about 10 to about 30 nt, about 15 to about 25 nt, or about 20-25 nucleotides.
  • Selection of appropriate oligonucleotides is facilitated by using computer programs that automatically align nucleic acid sequences and indicate regions of identity or homology. Such programs are used to compare nucleic acid sequences obtained, for example, by searching databases such as GcnBank or by sequencing PCR products. Comparison of nucleic acid sequences from a range of species allows the selection of nucleic acid sequences that display an appropriate degree of identity between species. In the case of genes that have not been sequcnccd, Southern blots arc performed to allow a determination of the degree of identity between genes in target species and other species. By performing Southern blots at varying degrees of stringency, as is well known in the art, it is possible to obtain an approximate measure of identity.
  • enzymatic RNA an RNA molecule with enzymatic activity.
  • Enzymatic nucleic acids act by first binding to a target RNA. Such binding occurs through the target binding portion of an enzymatic nucleic acid which is held in close proximity to an enzymatic portion of the molecule that acts to cleave the target RNA. Thus, the enzymatic nucleic acid first recognizes and then binds a target RNA through base pairing, and once bound to the correct site, acts cnzymatically to cut the target RNA.
  • decoy RNA is meant an RNA molecule that mimics the natural binding domain for a ligand.
  • the decoy RNA therefore competes with natural binding target for the binding of a specific ligand.
  • TAR HIV trans-activation response
  • TAR HIV trans-activation response
  • RNA can act as a "decoy” and efficiently binds HIV tat protein, thereby preventing it from binding to TAR sequences encoded in the HIV RNA.
  • This is meant to be a specific example. Those in the art will recognize that this is but one example, and other embodiments can be readily generated using techniques generally known in the art.
  • the term "monomers” typically indicates monomers linked by phosphodiester bonds or analogs thereof to form oligonucleotides ranging in size from a few monomelic units, e.g., from about 3-4, to about several hundreds of monomeric units. Analogs of phosphodiester linkages include: phosphorothioatc, phosphorodithioate, mcthylphosphomates, phosphorosclenoate, phosphoramidatc, and the like, as more fully described below. [0044] The term “nucleotide” covers naturally occurring nucleotides as well as nonnaturally occurring nucleotides.
  • nucleotides includes not only the known purine and pyrimidinc hctcrocyclcs-containing molecules, but also heterocyclic analogues and tautomers thereof
  • nucleotides include molecules containing adenine, guanine, thymine, cytosinc, uracil, purine, xanthine, diaminopurine, 8-oxo- N6-methyladenine, 7-dcazaxanthinc, 7- deazaguanine, N4,N4-ethanocytosin, N6,N6-ethano-2,6- diaminopurine, 5-methylcytosine, 5-(C3-C6)- alkynylcytosinc, 5-fluorouracil, 5-bromouracil, pseudoisocyto
  • nucleotide is intended to cover every and all of these examples as well as analogues and tautomers thereof.
  • Especially interesting nucleotides arc those containing adenine, guanine, thymine, cytosinc, and uracil, which are considered as the naturally occurring nucleotides in relation to therapeutic and diagnostic application in humans.
  • Nucleotides include the natural 2'-deoxy and 2'- hydroxyl sugars, e.g., as described in Romberg and Baker, DNA Replication, 2nd Ed. (Freeman, San Francisco, 1992) as well as their analogs.
  • nucleotides in reference to nucleotides includes synthetic nucleotides having modified base moieties and/or • modified sugar moieties. Such analogs include synthetic nucleotides designed to enhance binding properties, e.g., duplex or triplex stability, specificity, or the like.
  • hybridization means the pai ⁇ ng of substantially complementary strands of oligomcric compounds.
  • One mechanism of pairing involves hydrogen bonding, which may be Watson-Crick, Hoogstccn or reversed Hoogsteen hydrogen bonding, between complementary nucleoside or nucleotide bases (nucleotides) of the strands of oligomcric compounds.
  • hydrogen bonding may be Watson-Crick, Hoogstccn or reversed Hoogsteen hydrogen bonding, between complementary nucleoside or nucleotide bases (nucleotides) of the strands of oligomcric compounds.
  • adenine and thymine arc complementary nucleotides which pair through the formation of hydrogen bonds.
  • Hybridization can occur under varying circumstances.
  • An antiscnsc compound is "specifically hybridizablc" when binding of the compound to the target nucleic acid interferes with the normal function of the target nucleic acid to cause a modulation of function and/or activity, and there is a sufficient degree of complementarity to avoid non-specific binding of the antisense compound to non-target nucleic acid sequences under conditions in which specific binding is desired, i.e., under physiological conditions in the case of in vivo assays or therapeutic treatment, and under conditions in which assays arc performed in the case of in vitro assays.
  • stringent hybridization conditions refers to conditions under which a compound of the invention will hybridize to its target sequence, but to a minimal number of other sequences. Stringent conditions arc sequence-dependent and will be different in different circumstances and in the context of this invention, "stringent conditions" under which oligomeric compounds hybridize to a target sequence are determined by the nature and composition of the oligomeric compounds and the assays in which they are being investigated. In general, stringent hybridization conditions comprise low concentrations ( ⁇ 0.15M) of salts with inorganic cations such as Na++ or K++ (i.e., low ionic strength), temperature higher than 2()°C - 25° C.
  • the hybridization rate decreases 1.1% for each 1% formamide.
  • An example of a high stringency hybridization condition is 0.1 X sodium chloride-sodium citrate buffer (SSQ/0.1 % (w/v) SDS at 60° C. for 30 minutes.
  • a nucleobase at a certain position of an antisense compound is capable of hydrogen bonding with a nucleobase at a certain position of a target nucleic acid, said target nucleic acid being a DNA, RNA, or oligonucleotide molecule
  • the position of hydrogen bonding between the oligonucleotide and the target nucleic acid is considered to be a complementary position.
  • the oligomeric compound and the further DNA, RNA, or oligonucleotide molecule arc complementary to each other when a sufficient number of complementary positions in each molecule are occupied by nucleotides which can hydrogen bond with each other.
  • oligomeric compound need not be 100% complementary to that of its target nucleic acid to be specifically hybridizable.
  • an oligonucleotide may hybridize over one or more segments such that intervening or adjacent segments arc not involved in the hybridization event (e.g., a loop structure, mismatch or hairpin structure).
  • the oligomeric compounds of the present invention comprise at least about 70%, or at least about 75%, or at least about 80%, or at least about 85%, or at least about 90%, or at least about 95%, or at least about 99% sequence complementarity to a target region within the target nucleic acid sequence to which they arc targeted.
  • an antisense compound in which 18 of 20 nucleotides of the antisense compound arc complementary to a target region, and would therefore specifically hybridize would represent 90 percent complementarity.
  • the remaining noncomplementary nucleotides may be clustered or interspersed with complementary nucleotides and need not be contiguous to each other or to complementary nucleotides.
  • an antisense compound which is 18 nucleotides in length having 4 (four) noncomplementary nucleotides which arc flanked by two regions of complete complementarity with the target nucleic acid would have 77.8% overall complementarity with the target nucleic acid and would thus fall within the scope of the present invention.
  • Percent complementarity of an antisense compound with a region of a target nucleic acid can be determined routinely using BLAST programs (basic local alignment search tools) and PowcrBLAST programs known in the art.
  • Percent homology, sequence identity or complementarity can be determined by, for example, the Gap program (Wisconsin Sequence Analysis Package, Version 8 for Unix, Genetics Computer Group, University Research Park, Madison Wis.), using default settings, which uses the algorithm of Smith and Waterman (Adv. Appl. Math., (1981 ) 2, 482-489).
  • Thermal Melting Point refers to the temperature, under defined ionic strength, pH, and nucleic acid concentration, at which 50% of the oligonucleotides complementary to the target sequence hybridize to the target sequence at equilibrium.
  • stringent conditions will be those in which the salt concentration is at least about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30 0 C for short oligonucleotides (e.g., IO to 50 nucleotide). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide.
  • modulation means either an increase (stimulation) or a decrease (inhibition) in die expression of a gene.
  • variants when used in the context of a polynucleotide sequence, may encompass a / polynucleotide sequence related to a wild type gene. This definition may also include, for example, "allelic,” “splice,” “species,” or “polymorphic” variants.
  • a splice variant may have significant identity to a reference molecule, but will generally have a greater or lesser number of polynucleotides due to alternate splicing of cxons during mRNA processing.
  • the corresponding polypeptide may possess additional functional domains or an absence of domains.
  • Species variants arc polynucleotide sequences that vary from one species to another.
  • variants of wild type gene products may result from at least one mutation in the nucleic acid sequence and may result in altered mRNAs or in polypeptides whose structure or function may or may not be altered. Any given natural or recombinant gene may have none, one, or many allelic forms. Common mutational changes that give rise to variants are generally ascribed to natural deletions, additions, or substitutions of nucleotides. Each of these types of changes may occur alone, or in combination with the others, one or more times in a given sequence. [0054] The resulting polypeptides generally will have significant amino acid identity relative to each other.
  • a polymo ⁇ hic variant is a variation in the polynucleotide sequence of a particular gene between individuals of a given species.
  • Polymo ⁇ hic variants also may encompass "single nucleotide polymo ⁇ hisms" (SNPs,) or single base mutations in which the polynucleotide sequence varies by one base. The presence of SNPs may be indicative of, for example, a certain population with a propensity for a disease state, that is susceptibility versus resistance.
  • Derivative polynucleotides include nucleic acids subjected to chemical modification, for example, replacement of hydrogen by an alkyl, acyl, or amino group.
  • Derivatives e.g., derivative oligonucleotides
  • Derivative nucleic acids may also contain labels, including radionuclcotidcs, enzymes, fluorescent agents, chcmi luminescent agents, chromogcnic agents, substrates, cofactors, inhibitors, magnetic particles, and the like.
  • a “derivative" polypeptide or peptide is one that is modified, for example, by glycosylation, pcgylation, phosphorylation, sulfation, rcduction/alkylation, acylation, chemical coupling, or mild formalin treatment.
  • a derivative may also be modified to contain a detectable label, either directly or indirectly, including, but not limited to, a radioisotope, fluorescent, and enzyme label.
  • animal or “patient” is meant to include, for example, humans, sheep, elks, deer, mule deer, minks, mammals, monkeys, horses, cattle, pigs, goats, dogs, cats, rats, mice, birds, chicken, reptiles, fish, insects and arachnids.
  • "Mammal” covers warm blooded mammals that arc typically under medical care (e.g., humans and domesticated animals). Examples include feline, canine, equine, bovine, and human, as well as just human.
  • Treating covers the treatment of a disease-state in a mammal, and includes: (a) preventing the disease-state from occurring in a mammal, in particular, when such mammal is predisposed to the disease-state but has not yet been diagnosed as having it; (b) inhibiting the disease-state, e.g., arresting it development: and/or (c) relieving the discasc-statc, e.g., causing regression of the disease state until a desired cndpoint is reached.
  • Treating also includes the amelioration of a symptom of a disease (e.g., lessen the pain or discomfort), wherein such amelioration may or may not be directly affecting the disease (e.g., cause, transmission, expression, etc.).
  • cancer refers to all types of cancer or neoplasm or malignant tumors found in mammals, including, but not limited to: leukemias, lymphomas, melanomas, carcinomas and sarcomas. The cancer manifests itself as a "tumor” or tissue comprising malignant cells of the cancer.
  • tumors include sarcomas and carcinomas such as, but not limited to: fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, chordoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma, lymphangioendotheliosarcoma, synovioma, mesothelioma, Ewing's tumor, leiomyosarcoma, rhabdomyosarcoma, colon carcinoma, pancreatic cancer, breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous gland carcinoma, papillary carcinoma, papillary adenocarcinomas, cystadcnocarcinoma, medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma, hepatoma, bile duct carcinoma, choriocar
  • acoustic neuroma oligodendroglioma, meningioma, melanoma, neuroblastoma, and retinoblastoma.
  • Additional cancers which can be treated by the disclosed composition according to the invention include but not limited to, for example, Hodgkin's Disease, Non-Hodgkin's Lymphoma, multiple myeloma, neuroblastoma, breast cancer, ovarian cancer, lung cancer, rhabdomyosarcoma, primary thrombocytosis, primary macroglobulincmia, small-cell lung tumors, primary brain tumors, stomach cancer, colon cancer, malignant pancreatic insulanoma, malignant carcinoid, urinary bladder cancer, prcmalignant skin lesions, testicular cancer, lymphomas, thyroid cancer, neuroblastoma, esophageal cancer, genitourinary tract cancer, malignant hypercalcemia, cervical cancer, endometrial cancer, adrenal cortical cancer, and
  • Neurological disease or disorder refers to any disease or disorder of the nervous system and/or visual system.
  • Neurological disease or disorder include disease or disorders that involve the central nervous system (brain, brainstem and cerebellum), the peripheral nervous system (including cranial nerves), and the autonomic nervous system (parts of which are located in both central and peripheral nervous system).
  • Examples of neurological disorders include but arc not limited to, headache, stupor and coma, dementia, seizure, sleep disorders, trauma, infections, neoplasms, ncuroopthalmology, movement disorders, dcmyclinating diseases, spinal cord disorders, and disorders of peripheral nerves, muscle and neuromuscular junctions.
  • Addiction and mental illness include, but are not limited to, bipolar disorder and schizophrenia, are also included in the definition of neurological disorder.
  • An "Inflammation” refers to systemic inflammatory conditions and conditions associated locally with migration and attraction of monocytes, leukocytes and/or neutrophils.
  • inflammation include, but arc not limited to, Inflammation resulting from infection with pathogenic organisms (including gram-positive bacteria, gram-ncgativc bacteria, viruses, fungi, and parasites such as protozoa and helminths), transplant rejection (including rejection of solid organs such as kidney, liver, heart, lung or cornea, as well as rejection of bone marrow transplants including graft-versus-host disease (GVHD)), or from localized chronic or acute autoimmune or allergic reactions.
  • pathogenic organisms including gram-positive bacteria, gram-ncgativc bacteria, viruses, fungi, and parasites such as protozoa and helminths
  • transplant rejection including rejection of solid organs such as kidney, liver, heart, lung or cornea, as well as rejection of bone marrow transplants including graft-versus-host disease (GVHD)
  • Autoimmune diseases include acute glomerulonephritis; rheumatoid or reactive arthritis: chronic glomerulonephritis; inflammatory bowel diseases such as Crohn's disease, ulcerative colitis and necrotizing enterocolitis; granulocyte transfusion associated syndromes; inflammatory dermatoses such as contact dermatitis, atopic dermatitis, psoriasis; systemic lupus erythematosus (SLE), autoimmune thyroiditis, multiple sclerosis, and some forms of diabetes, or any other autoimmune state where attack by the subject's own immune system results in pathologic tissue destruction.
  • Allergic reactions include allergic asthma, chronic bronchitis, acute and delayed hypersensitivity.
  • Systemic inflammatory disease states include inflammation associated with trauma, bums, repcrfusion following ischemic events (e.g. thrombotic events in heart, brain, intestines or peripheral vasculature, including myocardial infarction and stroke), sepsis, ARDS or multiple organ dysfunction syndrome. Inflammatory cell recruitment also occurs in atherosclerotic plaques.
  • Inflammation includes, but is not limited to, Non-Hodgkin's lymphoma, Wegener's granulomatosis, Hashimoto's thyroiditis, hepatocellular carcinoma, thymus atrophy, chronic pancreatitis, rheumatoid arthritis, reactive lymphoid hyperplasia, osteoarthritis, ulcerative colitis, papillary carcinoma, Crohn's disease, ulcerative colitis, acute cholecystitis, chronic cholecystitis, cirrhosis, chronic sialadenitis, peritonitis, acute pancreatitis, chronic pancreatitis, chronic Gastritis, adcnomyosis, endometriosis, acute cci ⁇ 'icitis, chronic cervicitis, lymphoid hyperplasia, multiple sclerosis, hypertrophy secondary to idiopathic thrombocytopenic purpura, primary IgA nephropathy, systemic lupus ery
  • a cardiovascular disease or disorder includes those disorders that can either cause ischemia or are caused by rcpcrfusion of the heart. Examples include, but arc not limited to, atherosclerosis, coronary artery disease, granulomatous myocarditis, chronic myocarditis (non-granulomatous), primary hypertrophic cardiomyopathy, peripheral artery disease (PAD), stroke, angina pectoris, myocardial infarction, cardiovascular tissue damage caused by cardiac arrest, cardiovascular tissue damage caused by cardiac bypass, cardiogenic shock, and related conditions that would be known by those of ordinary skill in the art or which involve dysfunction of or tissue damage to the heart or vasculature, especially, but not limited to, tissue damage related to an Antiviral gene activation.
  • CVS diseases include, but arc not limited to, atherosclerosis, granulomatous myocarditis, myocardial infarction, myocardial fibrosis secondary to valvular heart disease, myocardial fibrosis without infarction, primary hypertrophic cardiomyopathy, and chronic myocarditis (non-granulomatous).
  • viruses or viruses causing patient diseases comprise: Herpesviruses, such as for example, Alpha-herpesviruses (e.g. Herpes simplex virus 1 (HSV-I); Herpes simplex virus 2 (HSV-2); Varicella Zoster virus (VZV)), Bcta-hcrpesvi ruses (e.g.
  • Cytomegalovirus CMV
  • Herpes virus 6 HHV-6
  • Gamma-herpesviruses e.g. Epstcin-Barr virus (EBV); Herpes virus 8 (HHV-8)
  • Hepatitis viruses e.g. Hepatitis A virus; Hepatitis B virus; Hepatitis C virus; Hepatitis D virus; Hepatitis E virus
  • Rctrovimscs e.g. Human Immunodeficiency 1 (HIV-I)
  • Orthomyxoviruses e.g. Influenza viruses A, B and C
  • Paramyxoviruses Respiratory Syncytial virus (RSV), Parainfluenza viruses (Pl)
  • RSV Human Immunodeficiency 1
  • Mumps virus Measles virus
  • Togaviruses e.g. Rubella virus
  • Picomaviruscs e.g. Enteroviruses, Rhinoviruses; Coronaviruses
  • Papovaviruscs e.g. Human papilloma viruses (HPV); Polyomaviruscs (BKV and ICV); Gastroenteritis viruses), Filoviridae, Bunyaviridae, Rhabdoviridac, Flaviviridac.
  • bacteria causing bacterial diseases comprise: Staphylococcus aureus: strains include mcthicillin resistant (MRSA), methicillin-vancomycin resistant (VMRSA) and vancomycin intermediate resistant (VISA); Staphylococcus epidcrmidis; Entcrococcus faecalis and E. faecium: strains include vancomycin resistant (VRE); Streptococcus pneumoniae; Pseudomonas aeruginosa; Burkholdia cepacia; Xanthomonas maltophila; Escherichia coli; Enterobactcr spp.; Klebsiella pneumoniae; Salmonella spp. Polynucleotide and Oligonucleotide Compositions and Molecules Targets
  • the targets comprise nucleic acid sequences of an Antiviral gene, including without limitation sense and/or antisense noncoding and/or coding sequences associated with an Antiviral gene.
  • the targets comprise nucleic acid sequences of RIG l , including without limitation sense and/or antisense honcoding and/or coding sequences associated with RIG I gene.
  • the targets comprise nucleic acid sequences of MDA5, including without limitation sense and/or antisensc noncoding and/or coding sequences associated with MDA5 gene.
  • the targets comprise nucleic acid sequences of IFNA l , including without limitation sense and/or antisensc noncoding and/or coding sequences associated with IFNA 1 gene.
  • RIG-I retinoic acid-inducible gene 1 product
  • IFN-B beta interferon
  • many viruses arc known to encode viral products that inhibit IFN-B production.
  • the viral nonstructural protein 1 (NS 1 ) prevents the induction of the IFN-B promoter by inhibiting the activation of transcription factors, including IRF-3, involved in IFN-B transcriptional activation.
  • the inhibitory properties of NSl appear to be due at least in part to its binding to double-stranded RNA (dsRNA), resulting in the sequestration of this viral mediator of RIG-I activation.
  • Retinoic acid-induciblc gene I (RlG-I) and melanoma differentiation-associated gene 5 (MDA5) arc cytoplasmic DEx(D/H) box helicases that can detect intracellular viral products such as genomic RNA (vRNA) to signal IFN-/- production in infected cells.
  • vRNA genomic RNA
  • IPS-I interferon promoter-stimulating factor 1
  • IRFs interferon-reg ⁇ latory factors
  • RIG-I Signaling by RIG-I is triggered during infection by a number of RNA viruses and by the presence of synthetic RNA transcribed in vitro. More recently, RIG-I has been implicated in the recognition ofRNA moieties that harbor 5' triphosphate ends or of RNAs that assume complex secondary structures. In contrast, signaling by MDA5 is uniquely triggered during picornavirus infections or in the presence of a synthetic RNA polymer consisting of annealing strands of inosine and cytosine, poly(I:C). [0072] Human melanoma cells can be reprogrammed to terminally differentiate and irreversibly lose proliferative capacity by appropriate pharmacological manipulation.
  • melanoma differentiation-associated genc-5 (mda-5) as a gene induced during differentiation, cancer reversion, and programmed cell death (apoptosis).
  • This gene contains both a caspase recruitment domain and putative DExH group RNA helicasc domains.
  • Atypical helicase motifs ofMDA-5 deviate from consensus sequences but arc well conserved in a potentially new group of cloned and hypothetical proteins, mda-5 is an early response gene inducible by IFN and tumor necrosis factor-a, responding predominantly to IFN-. Protein kinase C activation by mczcrcin further augments mda-5 expression induced by IFN-.
  • mda-5 is controlled transcriptionally by IFN-, and the MDA-5 protein localizes in the cytoplasm, mda-5 displays RNA-dcpcndcnt ATPasc activity, and ectopic expression of mda5 in human melanoma cells inhibits colony formation.
  • mda-5 may function as a mediator oflFN-induced growth inhibition and/or apoptosis.
  • MDA-5 is a double-stranded RNA- dependent ATPasc that contains both a caspase recruitment domain and RNA hclicasc motifs, with a confirmed association with growth and differentiation in human melanoma cells.
  • IFNs interferons
  • Strategies evolved by viruses to antagonize the actions of IFNs have contributed significantly to our understanding in multiple areas of virology and molecular cell biology, ranging from pathways of signal transduction to the biochemical mechanisms of transcriptional and translational control to die molecular basis of viral pathogenesis.
  • IFNs arc approved therapeutics and have moved from the basic research laboratory to the clinic.
  • RNA-dependent protein kinase PLR
  • OAS 2',5'-oligoadenylate synthetase
  • RNase L the Mx protein GTPases.
  • Double stranded RNA plays a central role in modulating protein phosphorylation and RNA degradation catalyzed by the IFN-inducible PKR kinase and the 2'- 5'-oligoadcnylate-dcpcndcnt RNase L, respectively, and also in RNA editing by the IFN-induciblc RNA-spccific adenosine deaminase (ADARl).
  • ADARl IFN-induciblc RNA-spccific adenosine deaminase
  • IFN also induces a form of inducible nitric oxide synthase (iNOS2) and the major histocompatibility complex class I and II proteins, all of which play important roles in immune response to infections.
  • iNOS2 inducible nitric oxide synthase
  • INOS2 major histocompatibility complex class I and II proteins
  • IFN-alpha IFN-alpha
  • IFN-bcta IFN-gamma
  • IFN-gamma receptors
  • Jak and Stat and IRF signal transduction components proteins
  • proteins such as PKR, 2',5'-OAS, Mx, and ADAR, whose expression bombard is regulated by IFNs, has permitted the generation of mutant proteins, cells that overexpress different forms of the proteins, and animals in which their expression has been disrupted by targeted gene disruption.
  • IFN system reagents both in cell culture and in whole animals, continues to provide important contributions to our understanding of the virus-host interaction and cellular antiviral response.
  • Interferons are involved in numerous immune interactions during viral infections and contribute to both induction and regulation of innate and adaptive antiviral mechanisms. IFNs playa pivotaJ rule in the outcome of a viral infection, as demonstrated by the impaired resistance against different viruses in mice deficient for the receptors 1FNAR-2 and IFNGR. During viral infections, IFNs are involved in numerous immune interactions as inducers, regulators, and effectors of both innate and adaptive antiviral mechanisms.
  • IFN-alpha/bcta is produced rapidly when viral factors, such as envelope glycoproteins, CpG DNA, or dsRNA, interact with cellular pattern- recognition receptors (PRRs), such as mannosc receptors, toll-like receptors (TLRs), and cytosolic receptors.
  • PRRs cellular pattern- recognition receptors
  • TLRs toll-like receptors
  • cytosolic receptors cellular pattern- recognition receptors
  • These host-virus interactions signal downstream to activate transcription factors needed to achieve expression from IFN- alpha/bcta genes.
  • IRF-3 IFN regulatory factor-3
  • 1RF-5 1RF-5
  • 1RF-7 c-Jun/ATF-2
  • NF-kappaB NF-kappaB.
  • IFN-gamma is induced by receptor-mediated stimulation or in response to early produced cytokines, including interleukin-2 (IL- 12), IL- 18, and IFN-alpha/beta, or by stimulation through T cell receptors (TCRs) or natural killer (NK) cell receptors.
  • IFNs signal through transmembrane receptors, activating mainly Jak- Stat pathways but also other signal transduction pathways.
  • Cytokine and TCR-induced IFN-gamma expression uses distinct signal transduction pathways involving such transcription factors as NFAT, Stats and NF-kappaB.
  • RNA-activatcd protein kinase PLR
  • Mx proteins Mx proteins
  • IFNs modulate distinct aspects of both innate and adaptive immunity.
  • IFNalpha/ beta and IFN-gamma affect activities of macrophages, NK cells, dendritic cells (DC), and T cells by enhancing antigen presentation, cell trafficking, and cell differentiation and expression profiles, ultimately resulting in enhanced antiviral effector functions.
  • antiscnsc oligonucleotides are used to prevent or treat diseases or disorders associated with Antiviral gene family members.
  • Exemplary Antiviral gene mediated diseases and disorders which can be treated with cell/tissues regenerated from stem cells obtained using the antiscnse compounds comprise: cancer, an inflammatory disease, a disease, disorder or a condition caused by an infectious agent (e.g., including, viral, bacterial, fungal, protozoan etc.), a viral disease, inflammation, arthritis, psoriasis, a neurological disease or disorder, an immune system disease or disorder, an autoimmune disease or disorder, an immunodeficiency disease, an allergy, psoriasis, neurological diseases, a renal disease or disorder, a cardiovascular disease or disorder, a muscular disease or disorder, atherosclerosis, diabetes, a hepatic disease or disorder and a communicable disease.
  • an infectious agent e.g., including, viral, bacterial, fungal, protozoan etc.
  • a viral disease e.g., including, viral, bacterial, fungal, protozoan etc.
  • a viral disease e.g.
  • the antisensc oligonucleotides modulate the expression, in vivo amounts and/or function of an Antiviral gene in patients suffering from or at risk of developing diseases or disorders associated with Antiviral genes.
  • HMPV Human mctapncumovirus
  • Modulation of RIG-I expression and/or function modulate viral infection by various mechanisms, including for example, viral genomic sequence destruction.
  • RJG-I antiscnsc oligonucleotides would thus be of great therapeutic value in the development of anti- viral agents.
  • modulation of retinoic acid inducible gene I detects and destroys viral genomes. In another embodiment, modulation of retinoic acid inducible gene I (RIG-I) prevents or treats against viral infections in patients.
  • the oligonucleotides arc specific for polynucleotides of an Antiviral gene, which includes, without limitation noncoding regions.
  • the Antiviral gene targets comprise variants of an Antiviral gene; mutants of an Antiviral gene, including SNPs; noncoding sequences of an Antiviral gene; alleles, fragments and the like.
  • the oligonucleotide is an antiscnsc RNA molecule.
  • the target nucleic acid molecule is not limited to an Antiviral gene polynucleotides alone but extends to any of the isoforms, receptors, homologs, non-coding regions and the like of an Antiviral gene.
  • an oligonucleotide targets a natural antisensc sequence (natural antiscnsc to the coding and non-coding regions) of an Antiviral gene targets, including, without limitation, variants, alleles, homologs, mutants, derivatives, fragments and complementary sequences thereto.
  • the oligonucleotide is an antiscnsc RNA or DNA molecule.
  • the oligomeric compounds of the present invention also include variants in which a different base is present at one or more of the nucleotide positions in the compound.
  • the first nucleotide is an adenine
  • variants may be produced which contain thymidine, guanosinc, cytidinc or other natural or unnatural nucleotides at this position. This may be done at any of the positions of the antiscnsc compound.
  • homology, sequence identity or complementarity, between the antiscnsc compound and target is from about 50% to about 60%. In some embodiments, homology, sequence identity or complementarity, is from about 60% to about 70%.
  • homology, sequence identity or complementarity is from about 70% to about 80% In some embodiments, homology, sequence identity or complementarity, is from about 80% to about 90%. In some embodiments, homology, sequence identity or complementarity, is about 90%, about 92%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99% or about 100%
  • An antisense compound is specifically hybridizablc when binding of the compound to the target nucleic acid interferes with the normal function of the target nucleic acid to cause a loss of activity, and there is a sufficient degree of complementarity to avoid non-specific binding of the antisense compound to non-target nucleic acid sequences under conditions in which specific binding is desired.
  • Such conditions include, i.c , physiological conditions in the case of in vivo assays or therapeutic treatment, and conditions in which assays arc performed in the case of in vitro assays.
  • An antiscnsc compound whether DNA, RNA. chimeric, substituted etc, is specifically hybridizablc when binding of the compound to the target DNA or RNA molecule interferes with the normal function of the target DNA or RNA to cause a loss of utility, and there is a sufficient degree of complementarity to avoid non-specific binding of the antisense compound to non-target sequences under conditions in which specific binding is desired, i.e., under physiological conditions in the case of in vivo assays or therapeutic treatment, and in the case of in vitro assays, under conditions in which the assays are performed.
  • targeting of an Antiviral gene including without limitation, antiscnsc sequences which are identified and expanded, using for example. PCR, hybridization etc., one or more of the sequences set forth as SEQ ID NO: 4 to 9, and the like, modulate the expression or function of an Antiviral gene.
  • expression or function is up-rcgulatcd as compared to a control.
  • expression or function is down-regulated as compared to a control.
  • oligonucleotides comprise nucleic acid sequences set forth as SEQ ID NOS: 10 to 30 including antisense sequences which are identified and expanded, using for example, PCR, hybridization etc. These oligonucleotides can comprise one or more modified nucleotides, shorter or longer fragments, modified bonds and the like. Examples of modified bonds or intemucleotidc linkages comprise phosphorothioate, phosphorodithioate or the like. In another embodiment, the nucleotides comprise a phosphorus derivative.
  • the phosphorus derivative (or modified phosphate group) which may be attached to the sugar or sugar analog moiety in the modified oligonucleotides of the present invention may be a monophosphate, diphosphate, triphosphate, alkylphosphatc, alkancphosphatc, phosphorothioate and the like.
  • the preparation of the above-noted phosphate analogs, and their incorporation into nucleotides, modified nucleotides and oligonucleotides, per se, is also known and need not be described here. [0090]
  • the specificity and sensitivity of antisense is also harnessed by those of skill in the art for therapeutic uses.
  • Antisense oligonucleotides have been employed as therapeutic moieties in the treatment of disease states in animals and man. Antisense oligonucleotides have been safely and effectively administered to humans and numerous clinical trials arc presently underway. It is thus established that oligonucleotides can be useful therapeutic modalities that can be configured to be useful in treatment regimes for treatment of cells, tissues and animals, especially humans. [0091 ] In embodiments of the present invention oligomeric antisense compounds, particularly oligonucleotides, bind to target nucleic acid molecules and modulate the expression and/or function of molecules encoded by a target gene. The functions of DNA to be interfered comprise, for example, replication and transcription.
  • RNA to be interfered comprise all vital functions such as, for example, translocation of the RNA to the site of protein translation, translation of protein from the RNA, splicing of the RNA to yield one or more mRNA species, and catalytic activity which may be engaged in or facilitated by the RNA.
  • the functions may be up-rcgulatcd or inhibited depending on the functions desired.
  • the antisense compounds include, antisense oligomeric compounds, antisense oligonucleotides, external guide sequence (EGS) oligonucleotides, alternate splicers, primers, probes, and other oligomeric compounds that hybridize to at least a portion of the target nucleic acid. As such, these compounds may be introduced in the form of single-stranded, double-stranded, partially single-stranded, or circular oligomeric compounds.
  • EGS external guide sequence
  • Targeting an antisense compound to a particular nucleic acid molecule can be a multistcp process.
  • the process usually begins with the identification of a target nucleic acid whose function is to be modulated.
  • This target nucleic acid may be, for example, a cellular gene (or mRNA transcribed from the gene) whose expression is associated with a particular disorder or disease state, or a nucleic acid molecule from an infectious agent.
  • the target nucleic acid encodes an Antiviral gene.
  • the targeting process usually also includes determination of at least one target region, segment, or site within the target nucleic acid for the antisense interaction to occur such that the desired effect, e.g., modulation of expression, will result.
  • region is defined as a portion of the target nucleic acid having at least one identifiable structure, function, or characteristic.
  • regions of target nucleic acids arc segments.
  • Segments arc defined as smaller or sub-portions of regions within a target nucleic acid.
  • Sites as used in the present invention, are defined as positions within a target nucleic acid.
  • the antisensc oligonucleotides bind to the natural antiscnsc sequences of an Antiviral gene and modulate the expression and/or Junction of an Antiviral gene (SEQ ID NO: 1 to 3).
  • antisensc sequences include SEQ ID NOS: 4 to 30.
  • the antisense oligonucleotides bind to one or more segments of an Antiviral gene polynucleotide and modulate the expression and/or function of an Antiviral gene.
  • the segments comprise at least five consecutive nucleotides of an Antiviral gene sense or antiscnsc polynucleotides.
  • the antiscnsc oligonucleotides arc specific for natural antisense sequences of an Antiviral gene wherein binding of the oligonucleotides to the natural antisensc sequences of an Antiviral gene modulate expression and/or function of an Antiviral gene.
  • oligonucleotide compounds comprise sequences set forth as SEQ ID NOS: 10 to 30, antiscnsc sequences which arc identified and expanded, using for example, PCR, hybridization etc
  • These oligonucleotides can comprise one or more modified nucleotides, shorter or longer fragments, modified bonds and the like. Examples of modified bonds or intcrnucleotidc linkages comprise phosphorothioate, phosphorodithioatc or the like.
  • the nucleotides comprise a phosphorus derivative.
  • the phosphorus derivative (or modified phosphate group) which may be attached to the sugar or sugar analog moiety in the modified oligonucleotides of the present invention may be a monophosphate, diphosphate, triphosphate, alkylphosphate, alkancphosphatc, phosphorothioate and the like.
  • the preparation of the above-noted phosphate analogs, and their incorporation into nucleotides, modified nucleotides and oligonucleotides, per sc, is also known and need not be described here.
  • the translation initiation codon is typically 5'-AUG (in transcribed mRNA molecules; 5'-ATG in the corresponding DNA molecule), the translation initiation codon is also referred to as the "AUG codon,” the “start codon” or the “AUG start codon”.
  • a minority of genes has a translation initiation codon having the RNA sequence 5'-GUG, 5'-UUG or 5'-CUG; and 5'-AUA, 5'-ACG and 5'-CUG have been shown to function in vivo.
  • translation initiation codon and “start codon” can encompass many codon sequences, even though the initiator amino acid in each instance is typically methionine (in eukaryotes) or formylmethionine (in prokaryotes).
  • Eukaryotic and prokaryotic genes may have two or more alternative start codons, any one of which may be preferentially utilized for translation initiation in a particular cell type or tissue, or under a particular set of conditions.
  • start codon and “translation initiation codon” refer to the codon or codons that are used in vivo to initiate translation of an mRNA transcribed from a gene encoding an Antiviral gene, regardless of the scqucnce(s) of such codons.
  • a translation termination codon (or "stop codon") of a gene may have one of three sequences, i.e., 5'-UAA, 5'-UAG and 5'-UGA (the corresponding DNA sequences are 5'-TAA, 5'- TAG and 5'-TGA, respectively).
  • start codon region and “translation initiation codon region” refer to a portion of such an mRN A or gene that encompasses from about 25 to about 50 contiguous nucleotides in cither direction (i.e., 5' or 3') from a translation initiation codon.
  • stop codon region and “translation termination codon region” refer to a portion of such an mRNA or gene that encompasses from about 25 to about 50 contiguous nucleotides in cither direction (i.c., 5' or 3') from a translation termination codon.
  • a targeted region is the intragenic region encompassing the translation initiation or termination codon of the open reading frame (ORF) of a gene.
  • Another target region includes the 5' untranslated region (5'UTR), known in the art to refer to the portion of an mRNA in the 5' direction from the translation initiation codon, and thus including nucleotides between the 5' cap site and the translation initiation codon of an mRNA (or corresponding nucleotides on the gene).
  • Still another target region includes the 3' untranslated region (3'UTR), known in the art to refer to the portion of an mRNA in the 3' direction from the translation termination codon, and thus including nucleotides between the translation termination codon and 3' end of an mRNA (or corresponding nucleotides on the gene).
  • the 5' cap site of an mRNA comprises an N7-mcthylated guanosinc residue joined to the 5'-most residue of the mRNA via a 5'-5' triphosphate linkage.
  • the 5' cap region of an mRNA is considered to include the 5' cap structure itself as well as the first 50 nucleotides adjacent to the cap site.
  • Another target region for this invention is the 5' cap region.
  • mRNA transcripts are directly translated, many contain one or more regions, known as "introns," which arc excised from a transcript before it is translated. The remaining (and therefore translated) regions are known as “cxons" and are spliced together to form a continuous mRNA sequence.
  • targeting splice sites i.e., intron-cxon junctions or exon-intron junctions, is particularly useful in situations where aberrant splicing is implicated in disease, or where an overproduction of a particular splice product is implicated in disease.
  • An aberrant fusion junction due to rearrangement or deletion is another embodiment of a target site.
  • fusion transcripts mRNA transcripts produced via the process of splicing of two (or more) mRN As from different gene sources are known as "fusion transcripts". Introns can be effectively targeted using antisense compounds targeted to, for example, DNA or prc-mRNA.
  • the antisense oligonucleotides bind to coding and/or non-coding regions of a target polynucleotide and modulate the expression and/or function of the target molecule.
  • the antisense oligonucleotides bind to natural antisense polynucleotides and modulate the expression and/or function of the target molecule.
  • the antiscnsc oligonucleotides bind to sense polynucleotides and modulate the expression and/or function of the target molecule.
  • RNA transcripts can be produced from the same genomic region of DNA. These alternative transcripts are generally known as "variants”. More specifically, “pre-mRNA variants” are transcripts produced from the same genomic DNA that differ from other transcripts produced from the same genomic DNA in either their start or stop position and contain both intronic and cxonic sequence.
  • pre-mRNA variants Upon excision of one or more exon or intron regions, or portions thereof during splicing, pre-mRNA variants produce smaller "mRNA variants". Consequently, mRNA variants are processed pre-mRNA variants and each unique pre-mRNA variant must always produce a unique mRNA variant as a result of splicing. These mRNA variants are also known as "alternative splice variants". If no splicing of the pre-mRNA variant occurs then the pre- mRNA variant is identical to the mRNA variant.
  • Variants can be produced through the use of alternative signals to start or stop transcription.
  • Pre-mRN As and mRNAs can possess more than one start codon or stop codon.
  • Variants that originate from a pre-mRNA or mRNA that use alternative start codons arc known as "alternative start variants" of that pre-mRNA or mRNA.
  • Those transcripts that use an alternative stop codon arc known as "alternative stop variants" of that pre-mRNA or mRNA.
  • One specific type of alternative stop variant is the "polyA variant” in which the multiple transcripts produced result from the alternative selection of one of the "polyA stop signals" by the transcription machinery, thereby producing transcripts that terminate at unique polyA sites.
  • the types of variants described herein arc also embodiments of target nucleic acids.
  • the locations on the target nucleic acid to which the antiscnsc compounds hybridize arc defined as at least a 5-nuclcotidc long portion of a target region to which an active antiscnsc compound is targeted.
  • Target segments 5- 100 nucleotides in length comprising a stretch of at least five (5) consecutive nucleotides selected from within the illustrative target segments arc considered to be suitable for targeting as well.
  • Target segments can include DNA or RNA sequences that comprise at least the 5 consecutive nucleotides from the 5'-terminus of one of the illustrative target segments (the remaining nucleotides being a consecutive stretch of the same DNA or RNA beginning immediately upstream of the 5'-terminus of the target segment and continuing until the DNA or RNA contains about 5 to about 100 nucleotides).
  • target segments arc represented by DNA or RNA sequences that comprise at least the 5 consecutive nucleotides from the 3'-terminus of one of the illustrative target segments (the remaining nucleotides being a consecutive stretch of the same DNA or RNA beginning immediately downstream of the 3'-terminus of the target segment and continuing until the DNA or RNA contains about 5 to about 100 nucleotides).
  • target segments arc represented by DNA or RNA sequences that comprise at least the 5 consecutive nucleotides from the 3'-terminus of one of the illustrative target segments (the remaining nucleotides being a consecutive stretch of the same DNA or RNA beginning immediately downstream of the 3'-terminus of the target segment and continuing until the DNA or RNA contains about 5 to about 100 nucleotides).
  • antiscnsc compounds arc chosen which are sufficiently complementary to the target, i.e., hybridize sufficiently well and with sufficient specificity, to give the desired effect.
  • the oligonucleotides bind to an antisense strand of a particular target.
  • the oligonucleotides arc at least 5 nucleotides in length and can be synthesized so each oligonucleotide targets overlapping sequences such that oligonucleotides arc synthesized to cover the entire length of the target polynucleotide.
  • the targets also include coding as well as non coding regions.
  • specific nucleic acids arc targeted by antisense oligonucleotides. Targeting an antisense compound to a particular nucleic acid, is a multistep process.
  • RNAs can be classified into ( 1 ) messenger RNAs (mRNAs), which arc translated into proteins,' and (2) non-protein-coding RNAs (ncRNAs). ncRNAs comprise microRNAs, antisense transcripts and other Transcriptional Units (TU) containing a high density of stop codons and lacking any extensive "Open Reading Frame”.
  • mRNAs messenger RNAs
  • ncRNAs non-protein-coding RNAs
  • ncRNAs comprise microRNAs, antisense transcripts and other Transcriptional Units (TU) containing a high density of stop codons and lacking any extensive "Open Reading Frame”.
  • ncRNAs appear to start from initiation sites in 3' untranslated regions (3'UTRs) of protein-coding loci. ncRNAs arc often rare and at least half of the ncRNAs that have been scqucnccd by the FANTOM consortium seem not to be polyadcnylatcd. Most researchers have for obvious reasons focused on polyadcnylated mRNAs that arc processed and exported to the cytoplasm. Recently, it was shown that the set of non-polyadcnylated nuclear RNAs may be very large, and that many such transcripts arise from intcrgcnic regions. The mechanism by which ncRNAs may regulate gene expression is by base pai ⁇ ng with target transcripts.
  • RNAs that function by base pairing can be grouped into ( I) cis encoded RNAs that arc encoded at the same genetic location, but on the opposite strand to the RNAs they act upon and therefore display perfect complementarity to their target, and (2) trans-encoded RNAs that are encoded at a chromosomal location distinct from the RNAs they act upon and generally do not exhibit perfect base-pairing potential with their targets.
  • perturbation of an antisense polynucleotide by the antisense oligonucleotides described herein can alter the expression of the corresponding sense messenger RNAs.
  • this regulation can either be discordant (antisense knockdown results in messenger RNA elevation) or concordant (antisense knockdown results in concomitant messenger RNA reduction).
  • antisense oligonucleotides can be targeted to overlapping or non-overlapping parts of the antisense transcript resulting in its knockdown or sequestration.
  • Coding as well as non-coding antisense can be targeted in an identical manner and that either category is capable of regulating the corresponding sense transcripts - either in a concordant or disconcordant manner.
  • the strategics that are employed in identifying new oligonucleotides for use against a target can be based on the knockdown of antiscnse RNA transcripts by antisense oligonucleotides or any other means of modulating the desired target.
  • Strategy 2 In the case of concordant regulation, one could concomitantly knock down both antisense and sense transcripts and thereby achieve synergistic reduction of the conventional (sense) gene expression. If, for example, an antisense oligonucleotide is used to achieve knockdown, then this strategy can be used to apply one antisense oligonucleotide targeted to the sense transcript and another antisense oligonucleotide to the corresponding antisense transcript, or a single energetically symmetric antisense oligonucleotide that simultaneously targets overlapping sense and antisense transcripts.
  • antisense compounds include antisense oligonucleotides, ribozymes, external guide sequence (EGS) oligonucleotides, siRNA compounds, single- or double-stranded RNA interference (RNAi) compounds such as siRNA compounds, and other oligomeric compounds which hybridize to at least a portion of the target nucleic acid and modulate its function.
  • GCS external guide sequence
  • siRNA compounds single- or double-stranded RNA interference (RNAi) compounds such as siRNA compounds, and other oligomeric compounds which hybridize to at least a portion of the target nucleic acid and modulate its function.
  • RNAi RNA interference
  • they may be DNA, RNA, DNA-like, RNA- likc, or mixtures thereof, or may be mimctics of one or more of these.
  • Antisense compounds may be singlc-strandcd, doublcstrandcd, circular or hairpin oligomeric compounds and may contain structural elements such as internal or terminal bulges, mismatches or loops.
  • Antisense compounds arc routinely prepared linearly but can be joined or otherwise prepared to be circular and/or branched.
  • Antisense compounds can include constructs such as, for example, two strands hybridized to form a wholly or partially doublc-strandcd compound or a single strand with sufficient self-complcmcntarity to allow for hybridization and formation of a fully or partially doublc-strandcd compound.
  • the two strands can be linked internally leaving free 3' or 5' termini or can be linked to form a continuous hairpin structure or loop.
  • the hairpin structure may contain an overhang on cither the 5' or 3' terminus producing an extension of single stranded character.
  • the double stranded compounds optionally can include overhangs on the ends. Further modifications can include conjugate groups attached to one of the termini, selected nucleotide positions, sugar positions or to one of the intcmuclcosidc linkages. Alternatively, the two strands can be linked via a non-nucleic acid moiety or linker group.
  • dsRNA can take the form of a sclf-complcmcntary hairpin-type molecule that doubles back on itself to form a duplex.
  • the dsRNAs can be fully or partially double stranded. Specific modulation of gene expression can be achieved by stable expression of dsRNA hairpins in transgenic cell lines, however, in some embodiments, the gene expression or function is up regulated.
  • the gene expression or function is up regulated.
  • the two strands are complementary RNA strands that base pair in Watson-Crick fashion.
  • nucleic acids including oligonucleotides
  • DNA- likc i.e., generally having one or more 2'-dcoxy sugars and, generally, T rather than U bases
  • RNA-likc i.e., generally having one or more 2'- hydroxyl or 2'-modificd sugars and, generally U rather than T bases.
  • Nucleic acid helices can adopt more than one type of structure, most commonly the A- and B-forms.
  • an antisense compound may contain both A- and B- form regions.
  • the desired oligonucleotides or antisense compounds comprise at least one of: antisense RNA, antisense DNA, chimeric antisense oligonucleotides, antisense oligonucleotides comprising modified linkages, interference RNA (RNAi), short interfering RNA (siRN A); a micro, interfering RNA (miRNA); a small, temporal RNA (stRNA); or a short, hairpin RNA (shRNA): small RNA-induccd gene activation (RNAa); small activating RNAs (saRNAs), or combinations thereof.
  • RNAi interference RNA
  • siRN A micro, interfering RNA
  • miRNA micro, interfering RNA
  • stRNA small, temporal RNA
  • shRNA short, hairpin RNA
  • RNAa small RNA-induccd gene activation
  • saRNAs small activating RNAs
  • dsRNA can also activate gene expression, a mechanism that has been termed “small RNA-induccd gene activation” or RNAa. dsRNAs targeting gene promoters induce potent transcriptional activation of associated genes. RNAa was demonstrated in human cells using synthetic dsRNAs, termed “small activating RNAs" (saRNAs).
  • dsRNA small double-stranded RNA
  • siRNA small interfering RNA
  • miRNA microRNA
  • RMAi RNA interference
  • oligonucleotides arc shown to increase the expression and/or function of the Antiviral gene polynucleotides and encoded products thereof.
  • dsRNAs may also act as small activating RNAs (saRNA).
  • RNAa dsRNA-induced transcriptional activation
  • the "target segments” identified herein may be employed in a screen for additional compounds that modulate the expression of an Antiviral gene polynucleotide.
  • “Modulators” are those compounds that decrease or increase the expression of a nucleic acid molecule encoding an Antiviral gene and which comprise at least a 5-nuclcotidc portion that is complementary to a target segment.
  • the screening method comprises the steps of contacting a target segment of a nucleic acid molecule encoding sense or natural antisense polynucleotides of an Antiviral gene with one or more candidate modulators, and selecting for one or more candidate modulators which decrease or increase the expression of a nucleic acid molecule encoding an Antiviral gene polynucleotide, e.g. SEQ ID NOS: 10 to 30.
  • the candidate modulator or modulators arc capable of modulating (e.g.
  • the modulator may then be employed in further investigative studies of the function of an Antiviral gene polynucleotide, or for use as a research, diagnostic, or therapeutic agent in accordance with the present invention.
  • Targeting the natural antisensc sequence modulates the function of the target gene.
  • the Antiviral gene e.g. accession numbers NM 014314, NM_022168, NM 024013.
  • the target is an antisensc polynucleotide of the Antiviral gene.
  • an antisense oligonucleotide targets sense and/or natural antisense sequences of an Antiviral gene polynucleotide (e.g. accession numbers NM 014314, NM_( ) 22168, NM_024013), variants, alleles, isoforms, homologs, mutants, derivatives, fragments and complementary sequences thereto.
  • the oligonucleotide is an antisense molecule and the targets include coding and noncoding regions of antisense and/or sense Antiviral gene polynucleotides.
  • target segments of the present invention may be also be combined with their respective complementary antisense compounds of the present invention to form stabilized double-stranded (duplexed) oligonucleotides.
  • double stranded oligonucleotide moieties have been shown in the art to modulate target expression and regulate translation as well as RNA processing via an antisense mechanism. Moreover, the double-stranded moieties may be subject to chemical modifications. For example, such double-stranded moieties have been shown to inhibit the target by the classical hybridization of antisense strand of the duplex to the target, thereby triggering enzymatic degradation of the target.
  • an antisense oligonucleotide targets Antiviral gene polynucleotides (e.g. accession numbers NMJ) 14314, NM_022168, NM_024013), ⁇ ariants, alleles, isoforms, homologs, mutants, derivatives, fragments and complementary sequences thereto.
  • the oligonucleotide is an antisense molecule.
  • the target nucleic acid molecule is not limited to Antiviral gene alone but extends to any of the isoforms, receptors, homologs and the like of an Antiviral gene molecule.
  • an oligonucleotide targets a natural antisense sequence of an Antiviral gene polynucleotide, for example, polynucleotides set forth as SEQ ID NO: 4 to 9, and any variants, alleles, homologs, mutants, derivatives, fragments and complementary sequences thereto.
  • antisense oligonucleotides are set forth as SEQ ID NOS: 10 to 30.
  • the oligonucleotides are complementary to or bind to nucleic acid sequences of an Antiviral gene antisensc, including without limitation noncoding sense and/or antisense sequences associated with an Antiviral gene polynucleotide and modulate expression and/or function of an Antiviral gene molecule.
  • the oligonucleotides arc complementary to or bind to nucleic acid sequences of an Antiviral gene natural antiscnsc, set forth as SEQ ID NO: 4 to 9 and modulate expression and/or function of an Antiviral gene molecule.
  • oligonucleotides comprise sequences of at least 5 consecutive nucleotides of SEQ ID NOS: 10 to 30 and modulate expression and/or function of an Antiviral gene molecule.
  • the polynucleotide targets comprise Antiviral gene, including family members thereof, variants of an Antiviral gene; mutants of an Antiviral gene, including SNPs; noncoding sequences of an Antiviral gene; alleles of an Antiviral gene; species variants, fragments and the like.
  • the oligonucleotide is an antiscnse molecule.
  • the oligonucleotide targeting Antiviral gene polynucleotides comprise: antiscnsc RNA, interference RNA (RNAi), short interfering RNA (siRNA); micro interfering RNA (miRNA); a small, temporal RNA (stRNA); or a short, hairpin RNA (shRNA); small RNA-induccd gene activation (RNAa); or, small activating RNA (saRNA).
  • RNAi interference RNA
  • siRNA short interfering RNA
  • miRNA micro interfering RNA
  • shRNA small, temporal RNA
  • shRNA small RNA-induccd gene activation
  • RNAa small activating RNA
  • targeting of an Antiviral gene polynucleotide e.g. SEQ ID NO: 4 to 9 modulate the expression or function of these targets.
  • expression or function is up-regulated as compared to a control.
  • expression or function is down-regulated as compared to a control.
  • antisensc compounds comprise sequences set forth as SEQ ID NOS: 10 to 30. These oligonucleotides can comprise one or more modified nucleotides, shorter or longer fragments, modified bonds and the like. [00140] In another embodiment, SEQ ID NOS: 10 to 30 comprise one or more LNA nucleotides. [00141] The modulation of a desired target nucleic acid can be carried out in several ways known in the art. For example, antiscnsc oligonucleotides, siRNA etc.
  • Enzymatic nucleic acid molecules arc nucleic acid molecules capable of catalyzing one or more of a variety of reactions, including the ability to repeatedly cleave other separate nucleic acid molecules in a nucleotide base sequence-specific manner. Such enzymatic nucleic acid molecules can be used, for example, to target virtually any RNA transcript. [00142] Because of their sequence-specificity, trans-cleaving enzymatic nucleic acid molecules show promise as therapeutic agents for human disease. Enzymatic nucleic acid molecules can be designed to cleave specific RNA targets within the background of cellular RNA. Such a cleavage event renders the mRNA non-functional and abrogates protein expression from that RNA.
  • enzymatic nucleic acids with RNA cleaving activity act by first binding to a target RNA. Such binding occurs through the target binding portion of a enzymatic nucleic acid which is held in close proximity to an enzymatic portion of the molecule that acts to cleave the target RNA.
  • the enzymatic nucleic acid first recognizes and then binds a target RNA through complementary base pairing, and once bound to the correct site, acts cnzymatically to cut the target RNA. Strategic cleavage of such a target RNA will destroy its ability to direct synthesis of an encoded protein.
  • RNA target After an enzymatic nucleic acid has bound and cleaved its RNA target, it is released from that RNA to search for another target and can repeatedly bind and cleave new targets.
  • in vitro selection (evolution) strategics have been used to evolve new nucleic acid catalysts capable of catalyzing a variety of reactions, such as cleavage and ligation of phosphodiestcr linkages and amide linkages.
  • RNA-clcaving ribozymcs for the purpose of regulating gene expression.
  • the hammerhead ribozymc functions with a catalytic rate (kcat) of about 1 min-1 in the presence of saturating ( 10 mM) concentrations of Mg2+ cofactor.
  • An artificial "RNA ligase" ribozyme has been shown to catalyze the corresponding self-modification reaction with a rate of about 100 min-l .
  • RNA phosphodiestcr cleavage of an RNA substrate by an RNA catalyst that fits the "hammerhead" model was first shown in 1987. The RNA catalyst was recovered and reacted with multiple RNA molecules, demonstrating that it was truly catalytic.
  • Catalytic RNAs designed based on the "hammerhead” motif have been used to cleave specific target sequences by making appropriate base changes in the catalytic RNA to maintain necessary base pairing with the target sequences. This has allowed use of the catalytic RNA to cleave specific target sequences and indicates that catalytic RNAs designed according to the "hammerhead” model may possibly cleave specific substrate RNAs in vivo.
  • RNA interference has become a powerful tool for modulating gene expression in mammals and mammalian cells.
  • This approach requires the delivery of small interfering RNA (siRNA) either as RNA itself or as DNA, using an expression plasmid or virus and the coding sequence for small hairpin RNAs that are processed to siRNAs.
  • siRNA small interfering RNA
  • This system enables efficient transport of the prc-siRNAs to the cytoplasm where they arc active and permit the use of regulated and tissue specific promoters for gene expression.
  • an oligonucleotide or antiscnse compound comprises an oligomer or polymer of ribonucleic acid (RNA) and/or deoxyribonucleic acid (DNA), or a mimetic, chimera, analog or homolog thereof.
  • RNA ribonucleic acid
  • DNA deoxyribonucleic acid
  • mimetic, chimera analog or homolog thereof.
  • This term includes oligonucleotides composed of naturally occurring nucleotides, sugars and covalent intcrnuclcosidc (backbone) linkages as well as oligonucleotides having non-naturally occurring portions which function similarly.
  • oligonucleotides or "antisense compounds” include antisense oligonucleotides (e.g.
  • RNA DNA, mimetic, chimera, analog or homolog thereof
  • ribozymcs external guide sequence (EGS) oligonucleotides
  • siRNA compounds single- or double-stranded RNA interference (RNAi) compounds
  • RNAi RNA interference
  • siRNA compounds single- or double-stranded RNA interference (RNAi) compounds
  • siRNA compounds single- or double-stranded RNA interference (RNAi) compounds
  • siRNA compounds single- or double-stranded RNA interference (RNAi) compounds
  • siRNA compounds single- or double-stranded RNA interference (RNAi) compounds
  • siRNA compounds single- or double-stranded RNA interference (RNAi) compounds
  • siRNA compounds single- or double-stranded RNA interference (RNAi) compounds
  • siRNA compounds single- or double-stranded RNA interference (RNAi) compounds
  • saRNA, aRNA single- or double-stranded RNA interference (RNAi) compounds
  • siRNA compounds single- or double-strand
  • Antisense compounds may be single- stranded, double-stranded, circular or hairpin oligomeric compounds and may contain structural elements such as internal or terminal bulges, mismatches or loops.
  • Antisense compounds arc routinely prepared linearly but can be joined or otherwise prepared to be circular and/or branched.
  • Antisense compounds can include constructs such as, for example, two strands hybridized to form a wholly or partially double-stranded compound or a single strand with sufficient self-complementarity to allow for hybridization and formation of a fully or partially double-stranded compound.
  • the two strands can be linked internally leaving free 3' or 5' termini or can be linked to form a continuous hairpin structure or loop.
  • the hairpin structure may contain an overhang on cither the 5' or 3' terminus producing an extension of single stranded character.
  • the double stranded compounds optionally can include overhangs on the ends. Further modifications can include conjugate groups attached to one of the termini, selected nucleotide positions, sugar positions or to one of the intemuclcosidc linkages. Alternatively, the two strands can be linked via a non-nucleic acid moiety or linker group.
  • dsRNA can take the form of a self-complementary hairpin-type molecule that doubles back on itself to form a duplex. Thus, the dsRNAs can be fully or partially double stranded.
  • dsRNA hai ⁇ ins can be achieved by stable expression of dsRNA hai ⁇ ins in transgenic cell lines.
  • the two strands are complementary RNA strands that base pair in Watson-Crick fashion.
  • the compounds of the invention may elicit the action of one or more enzymes or structural proteins to effect cleavage or other modification of the target nucleic acid or may work via occupancy-based mechanisms.
  • nucleic acids may be described as "DNA- like” (i.e., generally having one or more 2'-dcoxy sugars and, generally, T rather than U bases) or "RNA-likc” (i.e., generally having one or more 2'- hydroxyl or 2'-modificd sugars and, generally U rather than T bases).
  • DNA- like i.e., generally having one or more 2'-dcoxy sugars and, generally, T rather than U bases
  • RNA-likc i.e., generally having one or more 2'- hydroxyl or 2'-modificd sugars and, generally U rather than T bases.
  • Nucleic acid helices can adopt more than one type of structure, most commonly the A- and B-forms.
  • an antisense compound may contain both A- and B- form regions.
  • the antisense compounds in accordance with this invention can comprise an antisense portion from about 5 to about 80 nucleotides (i.e. from about 5 to about 80 linked nucleosides) in length. This refers to the length of the antisense strand or portion of the antisense compound.
  • a single-stranded antisense compound of the invention comprises from 5 to about 80 nucleotides
  • a double-stranded antisense compound of the invention (such as a dsRNA, for example) comprises a sense and an antisense strand or portion of 5 to about 80 nucleotides in length.
  • the antisense compounds of the invention have antisense portions of 10 to 50 nucleotides in length.
  • the oligonucleotides are 15 nucleotides in length.
  • the antisense or oligonucleotide compounds of the invention have antisense portions of 12 or 13 to 30 nucleotides in length.
  • antisense compounds having antisense portions of 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29 or 30 nucleotides in length, or any range thcrcwithi ⁇
  • the oligomc ⁇ c compounds of the present invention also include variants in which a different base is present at one or more of the nucleotide positions in the compound.
  • variants may be produced which contain thymidine, guanosine or cytidine at this position. This may be done at any of the positions of the antisense or dsRNA compounds. These compounds are then tested using the methods described herein to determine their ability to inhibit expression of a target nucleic acid.
  • homology, sequence identity or complementarity, between the antisense compound and target is from about 40% to about 60%. In some embodiments, homology, sequence identity or complementarity, is from about 60% to about 70%. In some embodiments, homology, sequence identity or complementarity, is from about 70% to about 80%. In some embodiments, homology, sequence identity or complementarity, is from about 80% to about 90%. In some embodiments, homology, sequence identity or complementarity, is about 90%, about 92%, about 94%, about 95%, about 96%. about 97%, about 98%, about 99% or about 100%.
  • the antisensc oligonucleotides such as for example, nucleic acid molecules set forth in SEQ ID NOS: 4 to 30 comprise one or more substitutions or modifications.
  • the nucleotides arc substituted with locked nucleic acids (LNA).
  • the oligonucleotides target one or more regions of the nucleic acid molecules sense and/or antisense of coding and/or non-coding sequences associated with Antiviral gene and the sequences set forth as SEQ ID NOS: I to 9.
  • the oligonucleotides are also targeted to overlapping regions of SEQ ID NOS: 1 to 9.
  • oligonucleotides of this invention are chimeric oligonucleotides.
  • "Chimeric oligonucleotides” or “chimeras,” in the context of this invention, are oligonucleotides which contain two or more chemically distinct regions, each made up of at least one nucleotide. These oligonucleotides typically contain at least one region of modified nucleotides that confers one or more beneficial properties (such as, for example, increased nuclease resistance, increased uptake into cells, increased binding affinity for the target) and a region that is a substrate for enzymes capable of cleaving RNA:DNA or RNA:RNA hybrids.
  • RNasc H is a cellular
  • RNA target which cleaves the RNA strand of an RNA:DNA duplex.
  • Activation of RNase H therefore, results in cleavage of the RNA target, thereby greatly enhancing the efficiency of antisense modulation of gene expression. Consequently, comparable results can often be obtained with shorter oligonucleotides when chimeric oligonucleotides are used, compared to phosphorothioate deoxyoligoniiclcotides hybridizing to the same target region.
  • Cleavage of the RNA target can be routinely detected by gel electrophoresis and, if necessary, associated nucleic acid hybridization techniques known in the art.
  • a chimeric oligonucleotide comprises at least one region modified to increase target binding affinity, and, usually, a region that acts as a substrate for RNAsc H.
  • Affinity of an oligonucleotide for its target is routinely determined by measuring the Tm of an oligonuclcotidc/targct pair, which is the temperature at which the oligonucleotide and target dissociate; dissociation is detected spcctrophotometrically. The higher the Tm, the greater is the affinity of the oligonucleotide for the target.
  • Chimeric antisense compounds of the invention may be formed as composite structures of two or more oligonucleotides, modified oligonucleotides, oligonuclcosides and/or oligonucleotides mimctics as described above. Such; compounds have also been referred to in the art as hybrids or gapmcrs. Representative United States patents that teach the preparation of such hybrid structures comprise, but are not limited to, US patent nos.
  • the region of the oligonucleotide which is modified comprises at least one nucleotide modified at the 2' position of the sugar, most preferably a 2'-Oalkyl, 2'-0-alkyl-0-alkyl or 2'-fluoro- modificd nucleotide.
  • RNA modifications include 2'-fluoro, 2'-amino and 2' O-mcthyl modifications on the ribosc of pyrimidines, abasic residues or an inverted base at the 3' end of the RNA.
  • RNAsc H is a cellular cndonuclcasc that cleaves the RNA strand of RNAiDNA duplexes; activation of this enzyme therefore results in cleavage of the RNA target, and thus can greatly enhance the efficiency of RNAi inhibition. Cleavage of the RNA target can be routinely demonstrated by gel electrophoresis.
  • the chimeric oligonucleotide is also modified to enhance nuclease resistance.
  • Cells contain a variety of cxo- and cndo-nuclcascs which can degrade nucleic acids. A number of nucleotide and nucleoside modifications have been shown to make the oligonucleotide into which they arc incorporated more resistant to nuclease digestion than the native oligodcoxynucleotidc.
  • Nuclease resistance is routinely measured by incubating oligonucleotides with cellular extracts or isolated nuclease solutions and measuring the extent of intact oligonucleotide remaining over time, usually by gel electrophoresis.
  • Oligonucleotides which have been modified to enhance their nuclease resistance survive intact for a longer time than unmodified oligonucleotides.
  • a variety of oligonucleotide modifications have been demonstrated to enhance or confer nuclease resistance.
  • Oligonucleotides which contain at least one phosphorothioate modification are presently more preferred.
  • oligonucleotide modifications which enhance target binding affinity are also, independently, able to enhance nuclease resistance.
  • oligonucleotides envisioned for this invention include those comprising modified backbones, for example, phosphorothioatcs, phosphotricstcrs, methyl phosphonatcs, short chain alkyl or cycloalkyl intcrsugar linkages or short chain hctcroatomic or heterocyclic intersugar linkages.
  • modified backbones for example, phosphorothioatcs, phosphotricstcrs, methyl phosphonatcs, short chain alkyl or cycloalkyl intcrsugar linkages or short chain hctcroatomic or heterocyclic intersugar linkages.
  • oligonucleotides having morpholino backbone structures (Summerton and Wcller, U.S. Pat. No. 5,034,506).
  • PNA peptide nucleic acid
  • the phosphodiester backbone of the oligonucleotide is replaced with a polyamidc backbone, the nucleotides being bound directly or indirectly to the aza nitrogen atoms of the polyamidc backbone.
  • Oligonucleotides may also comprise one or more substituted sugar moieties, oligonucleotides comprise one of the following at the T position: OH 1 SH, SCH3, F, OCN, 0CH3 OCH3, OCH3 O(CH2)n CH3, O(CH2)n NH2 or O(CH2)n CH3 where n is from 1 to about 10; C l to ClO lower alkyl, alkoxyalkoxy, substituted lower alkyl, alkaryl or aralkyl; Cl; Br; CN; CF3 ; OCF3; O-, S-, or N-alkyl; O-, S-, or N-alkenyl; SOCH3; SO2 CH3; ONO2; NO2; N3; NH2; heterocycloalkyl; heterocycloalkaryl; aminoalkylamino; polyalkylamino; substituted silyl; an RNA cleaving group; a reporter group; an intercalator; a group for improving the
  • a modification includes 2'-methoxyethoxy
  • Other modifications include 2'-mcthoxy (2'-O-CH3), 2'- propoxy (2'-OCH2 CH2CH3) and 2'-fluoro (2'-F).
  • Similar modifications may also be made at other positions on the oligonucleotide, particularly the 3' position of the sugar on the 3' terminal nucleotide and the 5' position of 5' terminal nucleotide.
  • Oligonucleotides may also have sugar mimctics such as cyclobutyls in place of the pcntofuranosyl group.
  • Oligonucleotides may also include, additionally or alternatively, nucleobase (often referred to in the art simply as “base”) modifications or substitutions.
  • nucleobase often referred to in the art simply as “base”
  • “unmodified” or “natural” nucleotides include adenine (A), guanine (G), thymine (T), cytosine (C) and uracil (U).
  • Modified nucleotides include nucleotides found only infrequently or transiently in natural nucleic acids, e.g., hypoxanthine, 6-methyladcnine, 5-Me pyrimidines, particularly 5-methylcytosine (also referred to as 5-methyl-2' deoxycytosine and often referred to in the art as 5- Mc-C), 5- hydroxymcthylcytosinc (HMC), glycosyl HMC and gcntobiosyl HMC, as well as synthetic nucleotides, e.g., 2-aminoadcninc, 2-(methylamino)adcninc, 2-(imidazolylalkyl)adcninc, 2- (aminoalklyamino)adcninc or other heterosubstituted alkyladenines, 2-thiouracil, 2-thiothymine, 5- bromouracil, 5-hydroxymethyluracil, 8-azaguanine, 7-
  • a "universal" base known in the art e.g., inosinc, may be included.
  • 5-Mc-C substitutions have been shown to increase nucleic acid duplex stability by 0.6- 1.2 0 C. (Sanghvi, Y. S., in Crookc, S. T. and Lcbleu, B., cds., Antiscnsc Research and Applications, CRC Press, Boca Raton, 1993, pp. 276-278) and are presently base substitutions.
  • Another modification of the oligonucleotides of the invention involves chemically linking to the oligonucleotide one or more moieties or conjugates which enhance the activity or cellular uptake of the oligonucleotide.
  • Such moieties include but arc not limited to lipid moieties such as a cholesterol moiety, a cholcstcryl moiety, a thiocther, e.g., hcxyl-S-tritylthioL, a thiocholesterol, an aliphatic chain, e.g., dodecandiol or undccyl residues, a phospholipid, e.g., di-hcxadccyl-rac-glyccrol or tricthylammonium 1 ,2-di-O-hexadccyl-rac- glyccro- 3-H-phosphonate, a polyaminc or a polyethylene glycol chain, or adamantanc acetic acid .
  • lipid moieties such as a cholesterol moiety, a cholcstcryl moiety, a thiocther, e.g., hcxy
  • Oligonucleotides comprising lipophilic moieties, and methods for preparing such oligonucleotides are known in the art, for example, U.S. PaL Nos. 5, 138,045, 5,218, 105 and 5,459,255.
  • oligonucleotides which arc chimeric oligonucleotides as hereinbefore defined.
  • the nucleic acid molecule of the present invention is conjugated with another moiety including but not limited to abasic nucleotides, polycthcr, polyamine, polyamidcs, peptides, carbohydrates, lipid, or polyhydrocarbon compounds.
  • abasic nucleotides polycthcr, polyamine, polyamidcs, peptides, carbohydrates, lipid, or polyhydrocarbon compounds.
  • these molecules can be linked to one or more of any nucleotides comprising the nuclesc acid molecule at several positions on the sugar, base or phosphate group.
  • oligonucleotides used in accordance with this invention may be conveniently and routinely made through the well-known technique of solid phase synthesis. Equipment for such synthesis is sold by several vendors including Applied Biosystems. Any other means for such synthesis may also be employed; the actual synthesis of the oligonucleotides is well within the talents of one of ordinary skill in the art. It is also well known to use similar techniques to prepare other oligonucleotides such as the phosphorothioatcs and alkylated derivatives.
  • CPG controlled-porc glass
  • LNA monomers to enhance the potency, specificity and duration of action and broaden the routes of administration of oligonucleotides comprised of current chemistries such as MOE, ANA, FANA, PS etc. This can be achieved by substituting some of the monomers in the current oligonucleotides by LNA monomers.
  • the LNA modified oligonucleotide may have a size similar to the parent compound or may be larger or preferably smaller.
  • LNA-modified oligonucleotides contain less than about 70%, more preferably less than about 60%, most preferably less than about 50% LNA monomers and that their sizes arc between about 5 and 25 nucleotides, more preferably between about 12 and 20 nucleotides.
  • Modified oligonucleotide backbones comprise, but arc not limited to, phosphorothioatcs, chiral phosphorothioatcs, phosphorodithioatcs, phosphotricsters, aminoalkylphosphotricstcrs, methyl and other alkyl phosphonatcs comprising 3'alkylcnc phosphonates and chiral phosphonatcs, phosphinates, phosphoramidatcs comprising 3'-amino phosphoramidate and aminoalkylphosphoramidatcs, thionophosphoramidatcs, thionoalkylphosphonates, thionoalkylphosphotriesters, and boranophosphatcs having normal 3'-5 * linkages, 2'-5' linked analogs of these, and those having inverted polarity wherein the adjacent pairs of nucleoside units arc linked 3'-5' to 5'-3' or 2'-5' to 5 -2
  • Modified oligonucleotide backbones that do not include a phosphorus atom therein have backbones that arc formed by short chain alkyl or cycloalkyl intemucleoside linkages, mixed hcteroatom and alkyl or cycloalkyl intemucleoside linkages, or one or more short chain heteroatomic or heterocyclic intemucleoside linkages.
  • These comprise those having morpholino linkages (formed in part from the sugar portion of a nucleoside); siloxanc backbones; sulfide, sulfoxide and sulfone backbones; formacctyl and thioformacetyl backbones; methylene formacetyl and thioformacetyl backbones; alkcnc containing backbones; sulfamatc backbones; mcthylcneimino and mcthylcnehydrazino backbones; sulfonate and sulfonamide backbones; amide backbones; and others having mixed N 1 0, S and CH2 component parts.
  • siloxanc backbones siloxanc backbones
  • sulfide, sulfoxide and sulfone backbones formacctyl and thioformacetyl backbones
  • Representative United States patents that teach the preparation of the above oligonuclcosidcs comprise, but arc not limited to, US patent nos. 5,034,506; 5,166,315; 5,185,444; 5,214,134; 5,216,141 ; 5,235,033; 5,264, 562; 5, 264,564; 5,405,938; 5,434,257; 5,466,677; 5,470,967; 5,489,677; 5,541 ,307; 5,561 ,225; 5,596, 086; 5,602,240; 5,610,289; 5,602,240; 5,608,046; 5,610,289; 5,618,704; 5,623, 070; 5,663,312; 5,633,360; 5,677,437; and 5,677,439, each of which is herein incorporated by reference.
  • both the sugar and the intemucleoside linkage, i.e., the backbone, of the nucleotide units arc replaced with novel groups.
  • the base units arc maintained for hybridization with an appropriate nucleic acid target compound.
  • One such oligomcric compound an oligonucleotide mimetic that has been shown to have excellent hybridization properties, is referred to as a peptide nucleic acid (PNA)
  • PNA peptide nucleic acid
  • the sugar-backbone of an oligonucleotide is replaced with an amide containing backbone, in particular an aminoethylglycine backbone.
  • nucleobases are retained and are bound directly or indirectly to aza nitrogen atoms of the amide portion of the backbone.
  • Representative United States patents that teach the preparation of PNA compounds comprise, but arc not limited to, US patent nos. 5,539,082; 5,714,331 ; and 5,719,262, each of which is herein incorporated by reference . Further teaching of PNA compounds can be found in Nielsen, el al. (1991) Science 254, 1497- 1500.
  • the oligonucleotides with phosphorothioatc backbones and oligonuclcosidcs with hcteroatom backbones and in particular- CH2-NH-O-CH2-,-CH2-N (CH3)-O-CH2-known as a methylene (mcthylimino) or MMI backbone,- CH2-O-N (CH3)-CH2-,-CH2N(CH3)-N(CH3) CH2-and-O- N(CH3)-CH2-CH2- wherein the native phosphodicstcr backbone is represented as-O-P-O-CH2- of the above referenced US patent no. 5,489,677, and the amide backbones of the above referenced US patent no. 5,602,240. Also arc oligonucleotides having morpholino backbone structures of the above-referenced US patent no. 5,034,506.
  • Modified oligonucleotides may also contain one or more substituted sugar moieties, oligonucleotides comprise one of the following at the 2' position: OH; F; O-, S-, or N-alkyl; O-, S-, or N-alkcnyl; O-, S-or N- alkynyl; or O alkyl-O-alkyl, wherein the alkyl, alkcnyl and alkynyl may be substituted or unsubstitutcd C to CO alkyl or C2 to CO alkcnyl and alkynyl. Particularly arc O (CH2)n 0mCH3, O(CH2)n,OCH3, O(CH2)nNH2.
  • oligonucleotides comprise one of the following at the 2' position: C to CO, (lower alkyl, substituted lower alkyl, alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH3, OCN, Cl, Br, CN, CF3, OCF3, SOCH3, SO2CH3, ONO2, NO2, N3, NH2, hetcrocycloalkyl, hcterocycloalkaryl, aminoalkylamino, polyalkylamino, substituted silyl, an RNA cleaving group, a reporter group, an intercalator, a group for improving the pharmacokinetic properties of an oligonucleotide, or a group for improving the pharmacodynamic properties of an oligonucleotide, and other substituents having similar properties.
  • a modification comprises 2'-mcthoxycthoxy (2 -O-CH2CH2OCH3, also known as 2'-O-(2- mcthoxyethyl) or 2'-MOE) i.e., an alkoxyalkoxy group.
  • a further modification comprises 2'- dimcthylaminooxyethoxy, i.e. , a O(CH2)2ON(CH3)2 group, also known as 2'-DMAOE, as described in examples herein below, and 2'- dimcthylaminocthoxycthoxy (also known in the art as 2'-O-dimcthylaminoethoxycthyl or 2'- DMAEOE).
  • modifications comprise 2'-methoxy (2'-0 CH3), 2'-aminopropoxy (2'-0 CH2CH2CH2NH2) and 2'-fluoro (2'-F). Similar modifications may also be made at other positions on the oligonucleotide, particularly the 3' position of the sugar on the 3' terminal nucleotide or in 2'-5' linked oligonucleotides and the 5' position of 5' terminal nucleotide. Oligonucleotides may also have sugar mimctics such as cyclobutyl moieties in place of the pcntofuranosyl sugar.
  • Oligonucleotides may also comprise nucleobase (often referred to in the art simply as “base”) modifications or substitutions.
  • nucleobase often referred to in the art simply as “base”
  • “unmodified” or “natural” nucleotides comprise the purine bases adenine (A) and guanine (G), and the pyrimidinc bases thymine (T), cytosinc (C) and uracil (U)- Modified nucleotides comprise other synthetic and natural nucleotides such as 5-mcthylcytosinc (5-mc-C), 5-hydroxymcthyl cytosinc, xanthine, hypoxanthinc, 2- aminoadeninc, 6-mcthyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosinc
  • nucleotides comprise those disclosed in United States Patent No. 3,687,808, those disclosed in The Concise Encyclopedia of Polymer Science And Engineering', pages 858-859, Kroschwitz, J.I., cd. John Wiley & Sons, 1990, those disclosed by Englisch el a!., 'Angcwandlc Chcmic, International Edition', 1991 , 30, page 613, and those disclosed by Sanghvi, Y.S., Chapter 15, 'Antiscnsc Research and Applications', pages 289-302, Crookc, ST. and Lcblcu, B. ca., CRC Press, 1993.
  • nucleotides arc particularly useful for increasing the binding affinity of the oligomeric compounds of the invention.
  • These comprise 5-substituted pyrimidines, 6- azapyrimidincs and N-2, N-6 and 0-6 substituted purines, comprising 2-aminopropyladenine, 5- propynyluracil and 5-propynylcytosinc.
  • 5-methylcytosine substitutions have been shown to increase nucleic acid duplex stability by 0.6-1.2 0 C (Sanghvi, Y.S., Crookc, S.T. and Lebleu, B., eds, 'Antiscnsc Research and Applications', CRC Press, Boca Raton, 1993, pp.
  • Another modification of the oligonucleotides of the invention involves chemically linking to the oligonucleotide one or more moieties or conjugates, which enhance the activity, cellular distribution, or cellular uptake of the oligonucleotide.
  • Such moieties comprise but arc not limited to, lipid moieties such as a cholesterol moiety, cholic acid, a thioether, e.g., hexyl-S-tritylthiol, a thiocholesterol , an aliphatic chain, e.g., dodccandiol or undecyl residues , a phospholipid, e.g., di-hexadecyl-rac-glycerol or triethylammonium l ,2-di-O-hexadecyl-rac-glyccro-3-H- phosphonate , a polyamine or a polyethylene glycol chain , or adamantane acetic acid , a palmityl moiety , or an octadecylaminc or hexylamino-carbonyl-t oxycholesterol moiety .
  • lipid moieties such as a cholesterol mo
  • Drug discovery The compounds of the present invention can also be applied in the areas of drug discovery and target validation.
  • the present invention comprehends the use of the compounds and target segments identified herein in drug discovery efforts to elucidate relationships that exist between an Antiviral gene polynucleotide and a disease state, phenotypc, or condition.
  • These methods include detecting or modulating an Antiviral gene polynucleotide comprising contacting a sample, tissue, cell, or organism with the compounds of the present invention, measuring the nucleic acid or protein level of an Antiviral gene polynucleotide and/or a related phcnotypic or chemical cndpoint at some time after treatment, and optionally comparing the measured value to a non-treated sample or sample treated with a further compound of the invention.
  • These methods can also be performed in parallel or in combination with other experiments to determine the function of unknown genes for the process of target validation or to determine the validity of a particular gene product as a target for treatment or prevention of a particular disease, condition, or phenotype. Assessing Up-reg ⁇ lation or Inhibition of Gene Expression:
  • Transfer of an exogenous nucleic acid into a host cell or organism can be assessed by directly detecting the presence of the nucleic acid in the cell or organism. Such detection can be achieved by several methods well known in the art. For example, the presence of the exogenous nucleic acid can be detected by Southern blot or by a polymerase chain reaction (PCR) technique using primers that specifically amplify nucleotide sequences associated with the nucleic acid. Expression of the exogenous nucleic acids can also be measured using conventional methods including gene expression analysis. For instance, mRNA produced from an exogenous nucleic acid can be detected and quantified using a Northern blot and reverse transcription PCR (RT-PCR).
  • RT-PCR Northern blot and reverse transcription PCR
  • RNA from the exogenous nucleic acid can also be detected by measuring an enzymatic activity or a reporter protein activity.
  • antiscnsc modulatory activity can be measured indirectly as a decrease or increase in target nucleic acid expression as an indication that the exogenous nucleic acid is producing the effector RNA.
  • primers can be designed and used to amplify coding regions of the target genes. Initially, the most highly expressed coding region from each gene can be used to build a model control gene, although any coding or non coding region can be used. Each control gene is assembled by inserting each coding region between a reporter coding region and its poly(A) signal.
  • plasmids would produce an mRNA with a reporter gene in the upstream portion of the gene and a potential RNAi target in the 3' non-coding region.
  • the effectiveness of individual antisensc oligonucleotides would be assayed by modulation of the reporter gene.
  • Reporter genes useful in the methods of the present invention include acctohydroxyacid synthase (AHAS) 1 alkaline phosphatase (AP), beta galactosidase (LacZ), beta glucoronidasc (GUS), chloramphenicol acctyltransferase (CAT), green fluorescent protein (GFP), red fluorescent protein (RFP), yellow fluorescent protein (YFP), cyan fluorescent protein (CFP), horseradish peroxidase (HRP), lucifcrasc (Luc), nopalinc synthase (NOS), octopinc synthase (OCS), and derivatives thereof.
  • AHAS acctohydroxyacid synthase
  • AP alkaline phosphatase
  • LacZ beta galactosidase
  • GUS beta glucoronidasc
  • CAT chloramphenicol acctyltransferase
  • GFP green fluorescent protein
  • RFP red fluorescent protein
  • YFP yellow fluorescent protein
  • Multiple selectable markers arc available that confer resistance to ampicillin, bleomycin, chloramphenicol, gcntamycin, hygromycin, kanamycin, lincomycin, methotrexate, phosphinothricin, puromycin, and tetracycline.
  • Methods to determine modulation of a reporter gene include, but arc not limited to, fluoromctric methods (e.g. fluorescence spectroscopy, Fluorescence Activated Cell Sorting (FACS), fluorescence microscopy), antibiotic resistance determination.
  • RlG l , MDA5, IFNAl proteins and mRNA expression can be assayed using methods known to those of skill in the art and described elsewhere herein.
  • immunoassays such as the ELISA can be used to measure protein levels.
  • Antiviral gene antibodies for ELISAs arc available commercially, e.g., from R&D Systems (Minneapolis, MN), Abeam, Cambridge, MA.
  • RlGl, MDA5, IFNAl expression (e.g., mRNA or protein) in a sample (e.g., cells or tissues in vivo or in vitro) treated using an antisense oligonucleotide of the invention is evaluated by comparison with Antiviral gene expression in a control sample.
  • expression of the protein or nucleic acid can be compared using methods known to those of skill in the art with that in a mock-treated or untreated sample.
  • comparison with a sample treated with a control antiscnse oligonucleotide e.g., one having an altered or different sequence
  • a difference in the expression of the Antiviral gene protein or nucleic acid in a treated vs. an untreated sample can be compared with the difference in expression of a different nucleic acid (including any standard deemed appropriate by the researcher, e.g., a housekeeping gene) in a treated sample vs. an untreated sample.
  • the level of an Antiviral gene mRNA or protein, in a sample treated with an antisense oligonucleotide of the present invention is increased or decreased by about 1.25-fold to about 10- fold or more relative to an untreated sample or a sample treated with a control nucleic acid.
  • the level of an Antiviral gene mRNA or protein is increased or decreased by at least about 1.25-fold, at least about 1.3- fold, at least about 1.4-fold, at least about 1.5-fold, at least about 1.6-fold, at least about 1.7-fold, at least about 1.8- fold, at least about 2-fold, at least about 2.5-fold, at least about 3-fold, at least about 3.5-fold, at least about 4-fold, at least about 4.5-fold, at least about 5-fold, at least about 5.5-fold, at least about 6-fold, at least about 6.5-fold, at least about 7-fold, at least about 7.5-fold, at least about 8-fold, at least about 8.5-fold, at least about 9-fold, at least about 9.5-fold, or at least about 10-fold or more.
  • kits, Research Reagents, Diagnostics, and Therapeutics can be utilized for diagnostics, therapeutics, and prophylaxis, and as research reagents and components of kits.
  • antisense oligonucleotides which arc able to inhibit gene expression with exquisite specificity, are often used by those of ordinary skill to elucidate the function of particular genes or to distinguish between functions of various members of a biological pathway.
  • the compounds of the present invention are useful as tools in differential and/or combinatorial analyses to elucidate expression patterns of a portion or the entire complement of genes expressed within cells and tissues.
  • biological system or “system” is defined as any organism, cell, cell culture or tissue that expresses, or is made competent to express products of the Antiviral genes. These include, but arc not limited to, humans, transgenic animals, cells, cell cultures, tissues, xenografts, transplants and combinations thereof.
  • expression patterns within cells or tissues treated with one or more antisense compounds are compared to control cells or tissues not treated with antisense compounds and the patterns produced are analyzed for differential levels of gene expression as they pertain, for example, to disease association, signaling pathway, cellular localization, expression level, size, structure or function of the genes examined. These analyses can be performed on stimulated or unstimulated cells and in the presence or absence of other compounds that affect expression patterns.
  • Examples of methods of gene expression analysis known in the art include DNA arrays or microarrays (Brazma and ViIo, (2000) I EBS Lett., 480, 17-24; Cclis, el ai, (2000) FEBS Lett., 480, 2-16), SAGE (serial analysis of gene expression) (Madden, el ai, (2(XK)) Drug Discov.
  • the compounds of the invention are useful for research and diagnostics, because these compounds hybridize to nucleic acids encoding an Antiviral gene.
  • oligonucleotides that hybridize with such efficiency and under such conditions as disclosed herein as to be effective Antiviral gene modulators arc effective primers or probes under conditions favoring gene amplification or detection, respectively.
  • These primers and probes arc useful in methods requiring the specific detection of nucleic acid molecules encoding an Antiviral gene and in the amplification of said nucleic acid molecules for detection or for use in further studies of an Antiviral gene.
  • Hybridization of the antisensc oligonucleotides, particularly the primers and probes, of the invention with a nucleic acid encoding an Antiviral gene can be detected by means known in the art.
  • Such means may include conjugation of an enzyme to the oligonucleotide, radiolabcling of the oligonucleotide, or any other suitable detection means. Kits using such detection means for detecting the level of an Antiviral gene in a sample may also be prepared.
  • antisensc compounds have been employed as therapeutic moieties in the treatment of disease states in animals, including humans.
  • Antisensc oligonucleotide drugs have been safely and effectively administered to humans and numerous clinical trials arc presently underway. It is thus established that antisensc compounds can be useful therapeutic modalities that can be configured to be useful in treatment regimes for the treatment of cells, tissues and animals, especially humans.
  • an animal preferably a human, suspected of having a disease or disorder which can be treated by modulating the expression of an Antiviral gene polynucleotide is treated by administering antiscnse compounds in accordance with this invention.
  • the methods comprise the step of administering to the animal in need of treatment, a therapeutically effective amount of an Antiviral gene modulator.
  • the Antiviral gene modulators of the present invention effectively modulate the activity of an Antiviral gene or modulate the expression of an Antiviral gene protein.
  • the activity or expression of an Antiviral gene in an animal is inhibited by about 10% as compared to a control.
  • the activity or expression of an Antiviral gene in an animal is inhibited by about 30%. More preferably, the activity or expression of an Antiviral gene in an animal is inhibited by 50% or more.
  • the oligomcric compounds modulate expression of an Antiviral gene mRNA by at least 10%, by at least 50%, by at least 25%, by at least 30%, by at least 40%, by at least 50%, by at least 60%, by at least 70%, by at least 75%, by at least 80%, by at least 85%, by at least 90%, by at least 95%, by at least 98%, by at ieast 99%, or by 100% as compared to a control.
  • the activity or expression of an Antiviral gene and/or in an animal is increased by about 10% as compared to a control.
  • the activity or expression of an Antiviral gene in an animal is increased by about 30%. More preferably, the activity or expression of an Antiviral gene in an animal is increased by 50% or more.
  • the oligomeric compounds modulate expression of an Antiviral gene mRNA by at least 10%, by at least 50%, by at least 25%, by at least 30%, by at least 40%, by at least 50%, by at least 60%, by at least 70%, by at least 75%, by at least 80%, by at least 85%, by at least 90%, by at least 95%, by at least 98%, by at least 99%, or by 100% as compared to a control.
  • the reduction of the expression of an Antiviral gene may be measured in scrum, blood, adipose tissue, liver or any other body fluid, tissue or organ of the animal.
  • the cells contained within said fluids, tissues or organs being analyzed contain a nucleic acid molecule encoding Antiviral gene peptides and/or the Antiviral gene protein itself.
  • the compounds of the invention can be utilized in pharmaceutical compositions by adding an effective amount of a compound to a suitable pharmaceutically acceptable diluent or carrier. Use of the compounds and methods of the invention may also be useful prophylactically.
  • Conjugates Another modification of the oligonucleotides of the invention involves chemically linking to the oligonucleotide one or more moieties or conjugates that enhance the activity, cellular distribution or cellular uptake of the oligonucleotide. These moieties or conjugates can include conjugate groups covalcntly bound to functional groups such as primary or secondary hydroxyl groups.
  • Conjugate groups of the invention include intcrcalators, reporter molecules, polyamines, polyamidcs, polyethylene glycols, polycthcrs, groups that enhance the pharmacodynamic properties of oligomers, and groups that enhance the pharmacokinetic properties of oligomers.
  • Typicalconjugatc groups include cholcstcrols, lipids, phospholipids, biotin, phcnazinc, folate, phcnanthridinc, anthraquinonc, acridine, fluoresceins, rhodamincs, coumarins, and dyes.
  • Groups that enhance the pharmacodynamic properties include groups that improve uptake, enhance resistance to degradation, and/or strengthen sequence-specific hybridization with the target nucleic acid.
  • Groups that enhance the pharmacokinetic properties include groups that improve uptake, distribution, metabolism or excretion of the compounds of the present invention.
  • Representative conjugate groups arc disclosed in International Patent Application No. PCT/US92/09196, filed Oct. 23, 1992, and U.S. Pat. No. 6,287,860, which arc incorporated herein by reference.
  • Conjugate moieties include, but arc not limited to, lipid moieties such as a cholesterol moiety, cholic acid, a thiocthcr, e.g., hcxyl-5- tritylthiol, a thiocholcsterol, an aliphatic chain, e.g., dodccandiol or undccyl residues, a phospholipid, e.g., di-hcxadccyl-rac-glyccrol or tricthylammonium 1 ,2-di-O-hexadccyl-rac-glyccro-3-Hphosphonatc, a polyaminc or a polyethylene glycol chain, or adamantane acetic acid, a palmityl moiety, or an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety.
  • lipid moieties such as
  • Oligonucleotides of the invention may also be conjugated to active drug substances, for example, aspirin, warfarin, phenylbutazone, ibuprofen, suprofcn, fcnbufen, ketoprofen, (S)-(+)-pranoprofen, carprofcn, dansylsarcosine, 2,3,5- triiodobenzoic acid, flufenamic acid, folinic acid, a benzothiadiazide, chlorothiazide, a diazepine, indomethicin, a barbiturate, a cephalosporin, a sulfa drug, an antidiabetic, an antibacterial or an antibiotic.
  • active drug substances for example, aspirin, warfarin, phenylbutazone, ibuprofen, suprofcn, fcnbufen, ketoprofen, (S)-(+)-pranoprofen
  • Representative United States patents that teach the preparation of such oligonucleotides conjugates include, but are not limited to, U.S. Pat. Nos. 4,828,979; 4,948,882; 5,218,105; 5,525,465; 5,541 ,313; 5,545,730; 5,552,538; 5,578,717, 5,580,731 ; 5,580,731 ; 5,591 ,584; 5,109,124; 5,1 18,802; 5,138,045; 5,414,077; 5,486,603; 5,512,439; 5,578,718; 5,608,046; 4,587,044; 4,605,735; 4,667,025; 4,762,779; 4,789,737; 4,824,941 ; 4,835,263; 4,876,335; 4,904,582; 4,958.013; 5,082,830; 5, 1 12,963; 5,214, 136; 5,082,830; 5, 1 12,963; 5,214
  • F ⁇ nmtlations The compounds of the invention may also be admixed, encapsulated, conjugated or otherwise associated with other molecules, molecule structures or mixtures of compounds, as forexamplc, liposomes, receptor-targeted molecules, oral, rectal, topical or other formulations, for assisting in uptake, distribution and/or absorption.
  • Representative United States patents that teach the preparation of such uptake, distribution and/or absorption-assisting formulations include, but arc not limited to, U.S. Pat. Nos.
  • antiscnsc oligonucleotides do not need to be administered in the context of a vector in order to modulate a target expression and/or function
  • embodiments of the invention relates to expression vector constructs for the expression of antiscnsc oligonucleotides, comprising promoters, hybrid promoter gene sequences and possess a strong constitutive promoter activity, or a promoter activity which can be induced in the desired case.
  • invention practice involves administering at least one of the foregoing antiscnsc oligonucleotides with a suitable nucleic acid delivery system.
  • that system includes a non-viral vector opcrably linked to the polynucleotide.
  • nonviral vectors include the oligonucleotide alone (e.g. any one or more of SEQ ID NOS: 10 to 30) or in combination with a suitable protein, polysaccharide or lipid formulation.
  • suitable nucleic acid delivery systems include viral vector, typically sequence from at least one of an adenovirus, adcnovirus-associatcd virus (AAV), helper-dependent adenovirus, retrovirus, or hcmagglutinatin virus of Japan-liposomc (HVJ) complex.
  • the viral vector comprises a strong cukaryotic promoter operably linked to the polynucleotide e.g., a cytomegalovirus (CMV) promoter.
  • CMV cytomegalovirus
  • retroviral vectors include Moloney murine leukemia viruses and HIV-based viruses.
  • One HIV-based viral vector comprises at least two vectors wherein the gag and pol genes arc from an HIV genome and the cnv gene is from another vims. DNA viral vectors arc preferred. These vectors include pox vectors such as orthopox or avipox vectors, herpesvirus vectors such as a herpes simplex I virus (HSV) vector, Adenovirus Vectors and Adeno-associated Virus Vectors).
  • the antisensc compounds of the invention encompass any pharmaceutically acceptable salts, esters, or salts of such esters, or any other compound which, upon administration to an animal, including a human, is capable of providing (directly or indirectly) the biologically active metabolite or residue thereof.
  • pharmaceutically acceptable salts refers to physiologically and pharmaceutically acceptable salts of Ac compounds of the invention: i.e., salts that retain the desired biological activity of the parent compound and do not impart undcsircd toxicological effects thereto.
  • examples of pharmaceutically acceptable salts and their uses arc further described in U.S. Pat. No. 6,287,860, which is incorporated herein by reference.
  • the present invention also includes pharmaceutical compositions and formulations that include the antiscnsc compounds of the invention.
  • the pharmaceutical compositions of the present invention may be administered in a number of ways depending upon whether local or systemic treatment is desired and upon the area to be treated. Administration may be topical (including ophthalmic and to mucous membranes including vaginal and rectal delivery), pulmonary, e.g., by inhalation or insufflation of powders or aerosols, including by nebulizer; intratracheal, intranasal, epidermal and transdermal), oral or parenteral. Parenteral administration includes intravenous, intraarterial, subcutaneous, intraperitoneal or intramuscular injection or infusion; or intracranial, e.g., intrathecal or intraventricular, administration.
  • administration can be made by, e.g., injection or infusion into the cerebrospinal fluid.
  • Administration of antisense RNA into cerebrospinal fluid is described, e.g., in U.S. Pat. App. Pub. No. 2007/01 17772, "Methods for slowing familial ALS disease progression," incorporated herein by reference in its entirety.
  • administration can be with one or more agents capable of promoting penetration of the subject antiscnse oligonucleotide across the blood-brain barrier.
  • Injection can be made, e.g., in the cntorhinal cortex or hippocampus.
  • Delivery of neurotrophic factors by administration of an adenovirus vector to motor neurons in muscle tissue is described in, e.g., U.S. Pat. No. 6,632,427, "Adcnoviral-vector-mcdiatcd gene transfer into medullary motor neurons," incorporated herein by reference.
  • Delivery of vectors directly to the brain e.g., the striatum, the thalamus, the hippocampus, or the substantia nigra, is known in the art and described, e.g., in U.S. Pat. No.
  • Administration can be rapid as by injection or made over a period of time as by slow infusion or administration of slow release formulations.
  • the subject antisense oligonucleotides can also be linked or conjugated with agents that provide desirable pharmaceutical or pharmacodynamic properties.
  • the antiscnse oligonucleotide can be coupled to any substance, known in the art to promote penetration or transport across the blood-brain barrier, such as an antibody to the transferrin receptor, and administered by intravenous injection
  • the antisense compound can be linked with a viral vector, for example, that makes the antisense compound more effective and/or increases the transport of the antisense compound across the blood-brain barrier.
  • Osmotic blood brain barrier disruption can also be accomplished by, e.g., infusion of sugars including, but not limited to, meso erythritol, xylitol, D(+) galactose, D(+) lactose, D(+) xylose, dulcitol, myo-inositol, L(-) fructose, D(-) mannitol, D(+) glucose, D(+) arabinosc, D(-) arabinosc, cellobiosc, D(+) maltose, D(+) raffinosc, L(+) rhamnosc, D(+) melibiosc, D(-) ribosc, adonitol, D(+) arabitol, L(-) arabitol, D(+) fucosc, L(-) fucosc, D(-) lyxose, L(+) lyxo
  • the subject antiscnse compounds may be admixed, encapsulated, conjugated or otherwise associated with other molecules, molecule structures or mixtures of compounds, for example, liposomes, rcccptor-targctcd molecules, oral, rectal, topical or other formulations, for assisting in uptake, distribution and/or absorption.
  • cationic lipids may be included in the formulation to facilitate oligonucleotide uptake.
  • One such composition shown to facilitate uptake is LIPOFECTFN (available from GIBCO-BRL, Bcthcsda, MD).
  • Oligonucleotides with at least one 2'-0-mcthoxycthyl modification arc believed to be particularly useful for oral administration.
  • Pharmaceutical compositions and formulations for topical administration may include transdermal patches, ointments, lotions, creams, gels, drops, suppositories, sprays, liquids and powders.
  • Conventional pharmaceutical carriers, aqueous, powder or oily bases, thickeners and the like may be necessary or desirable.
  • Coated condoms, gloves and the like may also be useful.
  • the pharmaceutical formulations of the present invention may be prepared according to conventional techniques well known in the pharmaceutical industry. Such techniques include the step of bringing into association the active ingredients with the pharmaceutical carricr(s) or cxcipicnt(s). In general, the formulations arc prepared by uniformly and intimately bringing into association the active ingredients with liquid carriers or finely divided solid carriers or both, and then, if necessary, shaping the product
  • compositions of the present invention may be formulated into any of many possible dosage forms such as, but not limited to, tablets, capsules, gel capsules, liquid syrups, soft gels, suppositories, and enemas.
  • the compositions of the present invention may also be formulated as suspensions in aqueous, non-aqueous or mixed media.
  • Aqueous suspensions may further contain substances that increase the viscosity of the suspension including, for example, sodium carboxymethylccllulose, sorbitol and/or dcxtran.
  • the suspension may also contain stabilizers.
  • compositions of the present invention include, but are not limited to, solutions, emulsions, foams and liposome-containing formulations.
  • the pharmaceutical compositions and formulations of the present invention may comprise one or more penetration enhancers, carriers, excipicnts or other active or inactive ingredients.
  • Emulsions are typically heterogeneous systems of one liquid dispersed in another in the form of droplets usually exceeding 0.1 ⁇ m in diameter. Emulsions may contain additional components in addition to the dispersed phases, and the active drug that may be present as a solution in cither the aqueous phase, oily phase or itself as a separate phase. Microcmulsions arc included as an embodiment of the present invention. Emulsions and their uses arc well known in the art and arc further described in U.S. Pat. No. 6,287,860.
  • Formulations of the present invention include liposomal formulations.
  • liposome means a vesicle composed of amphiphilic lipids arranged in a spherical bilayer or bilayers. Liposomes are unilamellar or multilamellar vesicles which have a membrane formed from a lipophilic material and an aqueous interior that contains the composition to be delivered. Cationic liposomes are positively charged liposomes that arc believed to interact with negatively charged DNA molecules to form a stable complex.
  • Liposomes that are pH-sensitive or negatively-charged are believed to entrap DNA rather than complex with it.
  • Liposomes also include "sterically stabilized" liposomes, a term which, as used herein, refers to liposomes comprising one or more specialized lipids. When incorporated into liposomes, these specialized lipids result in liposomes with enhanced circulation lifetimes relative to liposomeslacking such specialized lipids.
  • sterically stabilized liposomes are those in which part of the vesicle-forming lipid portion of the liposome comprises one or more glycolipids or is dcrivatized with one or more hydrophilic polymers, such as a polyethylene glycol (PEG) moiety.
  • PEG polyethylene glycol
  • Liposomes and their uses are further described in U.S. Pat. No. 6,287,860.
  • the pharmaceutical formulations and compositions of the present invention may also include surfactants.
  • the use of surfactants in drug products, formulations and in emulsions is well known in the art.
  • Surfactants and their uses are further described in U.S. Pat. No. 6,287,860, which is incorporated herein by reference.
  • the present invention employs various penetration enhancers to effect the efficient delivery of nucleic acids, particularly oligonucleotides.
  • penetration enhancers also enhance the permeability of lipophilic drugs.
  • Penetration enhancers may be classified as belonging to one of five broad categories, i.e., surfactants, fatty acids, bile salts, chelating agents, and non-chclating nonsurfactants. Penetration enhancers and their uses are further described in U.S. Pat. No. 6,287,860, which is incorporated herein by reference.
  • formulations for topical administration include those in which the oligonucleotides of the invention are in admixture with a topical delivery agent such as lipids, liposomes, fatty acids, fatty acid esters, steroids, chelating agents and surfactants, lipids and liposomes • include neutral (e.g. dioleoyl-phosphatidyl DOPE ethanolaminc, dimyristoylphosphatidyl choline DMPC, distearolyphosphatidyl choline) negative (e.g.
  • oligonucleotides of the invention may be encapsulated within liposomes or may form complexes thereto, in particular to cationic liposomes.
  • oligonucleotides may be complcxcd to lipids, in particular to cationic lipids, fatty acids and esters, pharmaceutically acceptable salts thereof, and their uses arc further described in U.S. Pat. No.
  • compositions and formulations for oral administration include powders or granules, microparticulatcs, nanoparticulates, suspensions or solutions in water or non-aqueous media, capsules, gel capsules, sachets, tablets or minitablcts.
  • Thickeners, flavoring agents, diluents, cmulsifiers, dispersing aids or binders may be desirable, oral formulations arc those in which oligonucleotides of the invention arc administered in conjunction with one or more penetration enhancers surfactants and chelators, surfactants include fatty acids and/or esters or salts thereof, bile acids and/or salts thereof, bile acids/salts and fatty acids and their uses arc further described in U.S. Pat. No. 6,287,860, which is incorporated herein by reference. Also are combinations of penetration enhancers, for example, fatty acids/salts in combination with bile acids/salts.
  • a particularly combination is the sodium salt of lauric acid, capric acid and UDCA.
  • Further penetration enhancers include polyoxycthylcnc-9-lauryl ether, polyoxycthylcnc- 20-cetyl ether.
  • Oligonucleotides of the invention may be delivered orally, in granular form including sprayed dried particles, or complexed to form micro or nanoparticles. Oligonucleotide complcxing agents and their uses are further described in U.S. Pat. No. 6,287,860, which is incorporated herein by reference.
  • compositions and formulations for parenteral, intrathecal or intraventricular administration may include sterile aqueous solutions that may also contain buffers, diluents and other suitable additives such as, but not limited to, penetration enhancers, carrier compounds and other pharmaceutically acceptable carriers or excipients.
  • Certain embodiments of the invention provide pharmaceutical compositions containing one or more oligomeric compounds and one or more other chcmothcrapcutic agents that function by a non-antisensc mechanism.
  • chcmothcrapcutic agents include but arc not limited to cancer chcmothcrapcutic drugs such as daunorubicin, daunomycin, dactinomycin, doxorubicin, epirubicin, idarubicin, esorubicin, bleomycin, mafosfamide, ifosfamide, cytosine arabinoside, bischloroethyl- nitrosurea, busulfan, mitomycin C, actinomycin D, mithramycin, prednisone, hydroxyprogesterone, testosterone, tamoxifen, dacarbazine, procarbazine, hcxamethylmclamine, pcntamethylmclaminc, mito
  • chemotherapeutic agents When used with the compounds of the invention, such chemotherapeutic agents may be used individually (e.g., 5-FU and oligonucleotide), sequentially (e.g., 5-FU and oligonucleotide for a period of time followed by MTX and oligonucleotide), or in combination with one or more other such chemotherapeutic agents (e.g., 5-FU, MTX and oligonucleotide, or 5-FU, radiotherapy and oligonucleotide).
  • chemotherapeutic agents may be used individually (e.g., 5-FU and oligonucleotide), sequentially (e.g., 5-FU and oligonucleotide for a period of time followed by MTX and oligonucleotide), or in combination with one or more other such chemotherapeutic agents (e.g., 5-FU, MTX and oligonucleotide, or 5-FU, radiotherapy and oligon
  • Anti-inflammatory drugs including but not limited to nonsteroidal anti-inflammatory drugs and corticosteroids, and antiviral drugs, including but not limited to ribivirin, vidarabinc, acyclovir and ganciclovir, may also be combined in compositions of the invention. Combinations of antisensc compounds and other non-antiscnsc drugs arc also within the scope of this invention. Two or more combined compounds may be used together or sequentially. [00229] In another related embodiment, compositions of the invention may contain one or more antisense compounds, particularly oligonucleotides, targeted to a first nucleic acid and one or more additional antisense compounds targeted to a second nucleic acid target.
  • the first target may be a particular antisense sequence of an Antiviral gene
  • the second target may be a region from another nucleotide sequence.
  • compositions of the invention may contain two or more antisensc compounds targeted to different regions of the same Antiviral gene nucleic acid target. Numerous examples of antisense compounds arc illustrated herein and others may be selected from among suitable compounds known in the art. Two or more combined compounds may be used together or sequentially.
  • Dosing [00230] The formulation of therapeutic compositions and their subsequent administration (dosing) is believed to be within the skill of those in the art.
  • Dosing is dependent on severity and responsiveness of the disease state to be treated, with the course of treatment lasting from several days to several months, or until a cure is effected or a diminution of the disease state is achieved.
  • Optimal dosing schedules can be calculated from measurements of drug accumulation in the body of the patient. Persons of ordinary skill can easily determine optimum dosages, dosing methodologies and repetition rates. Optimum dosages may vary depending on the relative potency of individual oligonucleotides, and can generally be estimated based on EC50s found to be effective in in vitro and in vivo animal models.
  • dosage is from 0.01 ⁇ g to 100 g per kg of body weight, and may be given once or more daily, weekly, monthly or yearly, or even once every 2 to 20 years. Persons of ordinary skill in the art can easily estimate repetition rates for dosing based on measured residence times and concentrations of the drug in bodily fluids or tissues. Following successful treatment, it may be desirable to have the patient undergo maintenance therapy to prevent the recurrence of the disease state, wherein the oligonucleotide is administered in maintenance doses, ranging from 0.01 ⁇ g to 100 g per kg of body weight, once or more daily, to once every 20 years.
  • a patient is treated with a dnsage of drug that is at least about I , at least about 2, at least about 3, at least about 4, at least about 5, at least about 6, at least about 7, at least about 8, at least about 9, at least about 10, at least about 15, at least about 20, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, at least about 50, at least about 60, at least about 70, at least about 80, at least about 90, or at least about 100 mg/kg body weight.
  • Certain injected dosages of antiscnse oligonucleotides arc described, e.g., in U.S. Pat. No.
  • lixample 1 Design ofanfisen.se oligonucleotides specific for a nucleic acid molecule a ⁇ tisense to an Antiviral gene and/or a sense strand of an Antiviral gene polynucleotide
  • oligonucleotide specific for or “oligonucleotide targets” refers to an oligonucleotide having a sequence (i) capable of forming a stable complex with a portion of the targeted gene, or (ii) capable of forming a stable duplex with a portion of an mRNA transcript of the targeted gene.
  • oligonucleotides are facilitated by using computer programs that automatically align nucleic acid sequences and indicate regions of identity or homology. Such programs arc used to compare nucleic acid sequences obtained, for example, by searching databases such as GcnBank or by sequencing PCR products. Comparison of nucleic acid sequences from a range of species allows the selection of nucleic acid sequences that display an appropriate degree of identity between species. In the case of genes that have not been sequenced. Southern blots are performed to allow a determination of the degree of identity between genes in target species and other species. By performing Southern blots at varying degrees of stringency, as is well known in the art, it is possible to obtain an approximate measure of identity.
  • An antiscnsc compound is "specifically hybridizablc" when binding of the compound to the target nucleic acid interferes with the normal function of the target nucleic acid to cause a modulation of function and/or activity, and there is a sufficient degree of complementarity to avoid non-specific binding of the antiscnsc compound to non-target nucleic acid sequences under conditions in which specific binding is desired, i.e., under physiological conditions in the case of in vivo assays or therapeutic treatment, and under conditions in which assays are performed in the case of in vitro assays [00238]
  • the hybridization properties of the oligonucleotides described herein can be determined by one or more in vitro assays as known in the art. For example, the properties of the oligonucleotides described herein can be obtained by determination of binding strength between the target natural antisensc and a potential drug molecules using melting curve assay.
  • Tlic binding strength between the target natural antiscnsc and a potential drug molecule can be estimated using any of the established methods of measuring the strength of intermolecular interactions, for example, a melting curve assay.
  • Melting curve assay determines the temperature at which a rapid transition from double-stranded to single-stranded conformation occurs for the natural antiscnse/MoIeculc complex. This temperature is widely accepted as a reliable measure of the interaction strength between the two molecules.
  • a melting curve assay can be performed using a cDNA copy of the actual natural antiscnsc RNA molecule or a synthetic DNA or RNA nucleotide corresponding to the binding site of the Molecule. Multiple kits containing all necessary reagents to perform this assay arc available (e.g. Applied Biosystcms Inc. McltDoctor kit).
  • kits include a suitable buffer solution containing one of the double strand DNA (dsDNA) binding dyes (such as ABI HRM dyes, SYBR Green, SYTO, etc.).
  • dsDNA double strand DNA
  • ABI HRM dyes such as ABI HRM dyes, SYBR Green, SYTO, etc.
  • the properties of the dsDNA dyes arc such that they emit almost no fluorescence in free form, but arc highly fluorescent when bound to dsDN A.
  • the cDNA or a corresponding oligonucleotide are mixed with Molecule in concentrations defined by the particular manufacturer's protocols.
  • the mixture is heated to 95 0 C to dissociate all pre-formcd dsDNA complexes, then slowly cooled to room temperature or other lower temperature defined by the kit manufacturer to allow the DNA molecules to anneal.
  • the newly formed complexes are then slowly heated to 95 0 C with simultaneous continuous collection of data on the amount of fluorescence that is produced by the reaction.
  • the fluorescence intensity is inversely proportional to the amounts of dsDNA present in the reaction.
  • the data can be collected using a real time PCR instrument compatible with the kit (e.g.ABI's StcpOnc Plus Real Time PCR System or LightTyper instrument, Roche Diagnostics, Lewes, UK) [00243] Melting peaks are constructed by plotting the negative derivative of fluorescence with respect to temperature (-d( Fluorescence )/dT) on the y-axis) against temperature (x-axis) using appropriate software (for example LightTyper (Roche) or SDS Dissociation Curve, ABI). The data is analyzed to identify the temperature of the rapid transition from dsDNA complex to single strand molecules. This temperature is called Tm and is directly proportional to the strength of interaction between the two molecules. Typically, Tm will exceed 40 0 C.
  • Example 2 Modulation of an Antiviral gene polynucleotide Treatment ofHepG2 cells with antisense oligonucleotides
  • HcpG2 cells from ATCC (cat# HB-8065) were grown in growth media (MEM/EBSS (Hyclonc cat #SH30024, " or Mediatech cat # MT-IO-OlO-CV) +10% FBS (Mediatech cat# MT35- OH-CV)+ penicillin/streptomycin (Mediatech cat# MT3O-OO2-CI)) at 37°C and 5% CO2.
  • MEM/EBSS Hyclonc cat #SH30024, " or Mediatech cat # MT-IO-OlO-CV) +10% FBS (Mediatech cat# MT35- OH-CV)+ penicillin/streptomycin (Mediatech cat# MT3O-OO2-CI)
  • MEM/EBSS Hyclonc cat #SH30024, " or Mediatech cat # MT-IO-OlO-CV) +10% FBS (Mediatech cat# MT35- OH-CV)+ penicillin/streptomycin (Mediatech cat#
  • All antiscnsc oligonucleotides were diluted to the concentration of 20 ⁇ M. Two ⁇ l of this solution was incubated with 400 ⁇ l of Opti-MEM media (Gibco cat#31985-070) and 4 ⁇ l of Lipofectamine 2000 (Invitrogen cat# 1 1668019) at room temperature for 20 min and applied to each well of the 6 well plates with HcpG2 cells. A Similar mixture including 2 ⁇ l of water instead of the oligonucleotide solution was used for the mock-transfcctcd controls. After 3-18 h of incubation at 37°C and 5% CO2 the media was changed to fresh growth media.
  • the cDNA from this reverse transcription reaction was used to monitor gene expression by real time PCR using ABI Taqman Gene Expression Mix (cat#4369510) and primers/probes designed by ABI (Applied Biosystcms Taqman Gene Expression Assay: Hs0O204833_ml , HsOO22342O_m 1 , HsOO85547l_j>l by Applied Biosystcms Inc., Foster City CA).
  • the following PCR cycle was used: 50 0 C for 2 min, 95°C for 10 min, 40 cycles of (95°C for 15 seconds, 60 0 C for 1 min) using Mx4000 thermal cycler (Stratagcnc).
  • ZR75 cells from ATCC (Cat# CRL-15 ( K ) were grown in growth media (MEM/EBSS (Hyclone cat #SH3()O24, or Mcdiatcch cat # MT-I O-OlO-C V) +10% FBS (Mcdiatcch cat# MT35- O H-CV)+ penicillin/streptomycin (Mcdiatcch cat# MT30-002-CI)) at 37°C and 5% CO;.
  • MCM/EBSS Hyclone cat #SH3()O24, or Mcdiatcch cat # MT-I O-OlO-C V
  • FBS Fediatcch cat# MT35- O H-CV
  • penicillin/streptomycin Mcdiatcch cat# MT30-002-CI
  • the cDNA from this reverse transcription reaction was used to monitor gene expression by real time PCR using ABI Taqman Gene Expression Mix (cat#4369510) and primers/probes designed by ABI (Applied Biosystems Taqman Gene Expression Assay: HsO0855471_gl .
  • the following PCR cycle was used: 50 0 C for 2 min, 95°C for 10 min, 40 cycles of (95°C for 15 seconds, 60 0 C for 1 min) using StepOnc Plus Real Time PCR Machine (Applied Biosystems).
  • HUVEC cells from ATCC (Promo Cell cat# C- 12253) were grown in Epithelial Growth Media (Promo Cell cat #C-22010) at 37oC and 5% CO2.
  • Epithelial Growth Media Promo Cell cat #C-22010
  • One day before the experiment the cells were replated using Promo Cell Detach Kit (cat#C-41200) at the density of 1.5xl0 ⁇ 5/ml into 6 well plates and incubated at 37oC and 5% CO2.
  • the media in the 6 well plates was changed to fresh Epithelial Growth Media. All antiscnsc oligonucleotides were diluted to the concentration of 20 ⁇ M.
  • the cDNA from this reverse transcription reaction was used to monitor gene expression by real time PCR using ABI Taqman gene Expression Mix (cat#4369510) and primers/probes designed by ABI (Applied Biosystems Taqman Gene Expression Assays: HsOO15334O_ml and HsOO855471_gl by Applied Biosystems Inc., Foster City CA).
  • the following PCR cycle was used: 50 0 C for 2 min, 95°C for 10 min, 40 cycles of (95°C for 15 seconds, 6O 0 C for 1 min) using StepOnc Plus Real Time PCR Machine (Applied Biosystems Inc.) or Mx4000 thermal cycler (Stratagene).
  • MCF-7 cells from ATCC (cat# HTB-22) were grown in growth media (MEM/EBSS (Hyclone cat #SH30024, or Mediatech cat # MT-IO-OlO-CV) +10% FBS (Mediatech cat# MT35- OH-CV)+ penicillin/streptomycin (Mediatech cat# MT3O-OO2-CI)) at 37°C and 5% CO 2 .
  • MEM/EBSS Hyclone cat #SH30024, or Mediatech cat # MT-IO-OlO-CV
  • FBS Mediatech cat# MT35- OH-CV
  • penicillin/streptomycin Mediatech cat# MT3O-OO2-CI
  • All antisense oligonucleotides were diluted to the concentration of 20 ⁇ M. Two ⁇ l of this solution was incubated with 400 ⁇ l of Opti-MEM media (Gibco cat#31985-070) and 4 ⁇ l of Lipofcctamine 2000 (Invitrogen car# 1 1668019) at room temperature for 20 min and applied to each well of the 6 well plates with MCF-7 cells. Similar mixture including 2 ⁇ l of water instead of the oligonucleotide solution was used for the mock-transfectcd controls. After 3-18 h of incubation at 37°C and 5% CO2 the media was changed to fresh growth media.
  • the cDNA from this reverse transcription reaction was used to monitor gene expression by real time PCR using ABI Taqman Gene Expression Mix (cat#4369510) and primers/probes designed by ABI (Applied Biosystems Taqman Gene Expression Assay: Hs00855471_gl .
  • the following PCR cycle was used: 5O 0 C for 2 min, 95°C for 10 min, 40 cycles of (95 0 C for 15 seconds, 60 0 C for 1 min) using StepOne Plus Real Time PCR Machine (Applied Biosystems).

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Abstract

The present invention relates to antisense oligonucleotides that modulate the expression of and/or function of an Antiviral gene, in particular, by targeting natural antisense polynucleotides of an Antiviral gene. The invention also relates to the identification of these antisense oligonucleotides and their use in treating diseases and disorders associated with the expression of Antiviral genes.

Description

TREATMENT OF ANTIVIRAL GENE RELATED DISEASES BY INHIBITION OF NATURAL
ANTISENSE TRANSCRIPT TO AN ANTIVIRAL GENE
FIELD OF THE INVENTION
[0001 ] The present application claims the priority of U.S. provisional patent application 61/181 ,773 filed May 28, 2009, No. 61/231.458 filed August 5, 2009 and U.S. provisional patent application No. 61/237,886 filed Aug 28, 2009 which arc incorporated herein by reference in their entireties.
[0002] Embodiments of the invention comprise oligonucleotides modulating expression and/or function of an Antiviral gene and associated molecules.
BACKGROUND [0003] DNA-RNA and RNA-RNA hybridization arc important to many aspects of nucleic acid function including DNA replication, transcription, and translation. Hybridization is also central to a variety of technologies that either detect a particular nucleic acid or alter its expression. Antiscnsc nucleotides, for example, disrupt gene expression by hybridizing to target RNA, thereby interfering with RNA splicing, transcription, translation, and replication. Antisensc DNA has the added feature that DNA-RNA hybrids serve as a substrate for digestion by ribonuclease H, an activity that is present in most cell types. Antisensc molecules can be delivered into cells, as is the case for oligodcoxynucleotides (ODNs), or they can be expressed from endogenous genes as RNA molecules. The FDA recently approved an antisense drug, V1TRAVENE™ (for treatment of cytomegalovirus retinitis), reflecting that antiscnsc has therapeutic utility.
SUMMARY [0004] In one embodiment, the invention provides methods for inhibiting the action of a natural antiscnsc transcript by using antiscnsc oligonucleotide(s) targeted to any region of the natural antiscnsc transcript resulting in up-rcgulation of the corresponding sense gene. It is also contemplated herein that inhibition of the natural antisense transcript can be achieved by siRNA, ribozymes and small molecules, which are considered to be within the scope of the present invention. [0005] One embodiment provides a method of modulating function and/or expression of an Antiviral gene polynucleotide in patient cells or tissues in vivo or in vitro comprising contacting said cells or tissues with an antiscnsc oligonucleotide 5 to 30 nucleotides in length wherein said oligonucleotide has at least 50% sequence identity to a reverse complement of a polynucleotide comprising 5 to 30 consecutive nucleotides within nucleotides I to 1267 of SEQ ID SEQ ID NO: 4, 1 to 586 of SEQ ID NO: 5, 1 to 741 of SEQ ID SEQ ID NO: 6, I to 251 of SEQ ID NO: 7, 1 to 681 of SEQ ID NO: 8, and 1 to 580 of SEQ ID NO: 9 thereby modulating function and/or expression of the Antiviral gene polynucleotide in patient cells or tissues in vivo or in vitro. [0006] In another embodiment, an oligonucleotide targets a natural antisense sequence of an Antiviral gene polynucleotide, for example, nucleotides set forth in SEQ ID NO: 4 to 9, and any variants, alleles, homologs, mutants, derivatives, fragments and complementary sequences thereto. Examples of antisense oligonucleotides are set forth as SEQ ID NOS: 10 to 30.
[0007] Another embodiment provides a method of modulating function and/or expression of an Antiviral gene polynucleotide in patient cells or tissues in vivo or in vitro comprising contacting said cells or tissues with an antisense oligonucleotide 5 to 30 nucleotides in length wherein said oligonucleotide has at least 50% sequence identity to a reverse complement of the an antisense of the Antiviral gene polynucleotide; thereby modulating function and/or expression of the Antiviral gene polynucleotide in patient cells or tissues in vivo or in vitro. [0008] Another embodiment provides a method of modulating function and/or expression of an Antiviral gene polynucleotide in patient cells or tissues in vivo or in vitro comprising contacting said cells or tissues with an antisense oligonucleotide 5 to 30 nucleotides in length wherein said oligonucleotide has at least 50% sequence identity to an antisense oligonucleotide to an Antiviral gene antisense polynucleotide; thereby modulating function and/or expression of the Antiviral gene polynucleotide in patient cells or tissues in vivo or in vitro. [0009] In one embodiment, a composition comprises one or more antisense oligonucleotides which bind to sense and/or antisense Antiviral gene polynucleotides. [0010] In another embodiment, the oligonucleotides comprise one or more modified or substituted nucleotides. [001 1 ] In another embodiment, the oligonucleotides comprise one or more modified bonds. [0012] In yet another embodiment, the modified nucleotides comprise modified bases comprising phosphorothioatc, mcthylphosphonatc, peptide nucleic acids, 2'-O-mcthyl, fluoro- or carbon, methylene or other locked nucleic acid (LNA) molecules. Preferably, the modified nucleotides arc locked nucleic acid molecules, including α-L-LNA.
[0013] In another embodiment, the oligonucleotides are administered to a patient subcutancously, intramuscularly, intπn'cnously or intraperitoneal Iy.
[0014] In another embodiment, the oligonucleotides arc administered in a pharmaceutical composition. A treatment regimen comprises administering the antisense compounds at least once to patient; however, this treatment can be modified to include multiple doses over a period of time. The treatment can be combined with one or more other types of therapies.
[0015] In another embodiment, the oligonucleotides arc encapsulated in a liposome or attached to a carrier molecule (e.g. cholesterol, TAT peptide). [0016] Other aspects are described infra. BRIEF DESCRIPTION OF THE DRAWINGS
[0017] Figure 1 is a graph of real time PCR results showing the fold change + standard deviation in RIG 1 mRNA after treatment of HcpG2 cells with phosphorothioatc oligonucleotides introduced using Lipofcctaminc 2000, as compared to control. Real Time PCR results show that levels of RIG I mRNA in HcpG2 cells arc significantly increased 48h after treatment with siRNAs to RIG l antisense hs.6OI664 and AK300104. Bars denoted as CUR- 0544, CUR-0546. CUR-0548, CUR-O55O, CUR-0552, CUR-0554, CUR-0556, CUR-0558 and CUR-0560 correspond to samples treated with SEQ ID NOS: 10 to 18 respectively.
[0018] Figure 2 is a graph of real time PCR results showing the fold change + standard deviation in MDA5 mRNA after treatment of HcpG2 cells with phosphorothioatc oligonucleotides introduced using Lipofectaminc 2000, as compared to control. Real time PCR results show that the levels of MDA5 mRNA in HcpG2 cells are significantly increased 48h after treatment with two of the oligos designed to MDA5 anriscnsc BU663736. Bars denoted as CUR-0908, CUR-0909, CUR-0910, CUR-091 1, CUR-0912, CUR-0913, CUR-0914 and CUR-0915 correspond to samples treated with SEQ ID NOS: 19 to 26 respectively. [0019] Figure 3 is a graph of real time PCR results showing the fold change + standard deviation in IFNA I mRNA after treatment of HcpG2 cells with phosphorothioate oligonucleotides introduced using Lipofcctamine 2000, as compared to control. Real time PCR results show that the levels of IFNAI mRNA in HepG2 cells are significantly increased 48h after treatment with one oligo designed to IFNAI antiscnsc DA393812. Bars denoted as CUR-0916, CUR-0917, CUR-0918 and CUR-0919 correspond to samples treated with SEQ ID NOS: 27 to 30 respectively. [0020] Figure 4 is a graph of real time PCR results showing the fold change + standard deviation in IFNAl mRNA after treatment of ZR75 cells with phosphorothioatc oligonucleotides introduced using Lipofectaminc 2000, as compared to control. Real time PCR results show that the levels of IFNAI mRNA in ZR75 cells are significantly increased 48h after treatment with one oligo designed to IFNAI antiscnsc DA393812. Bars denoted as CUR-0916, CUR-0919, CUR-0918 and CUR-0917 and correspond to samples treated with SEQ ID NOS: 27, 30, 29 and 28 respectively.
[0021 ] Figure 5 is a graph of real time PCR results showing the fold change + standard deviation in IFNA I mRNA after treatment of HUVEC cells with phosphorothioate oligonucleotides introduced using Lipofectaminc 2000, as compared to control. Real time PCR results show that the levels of IFNAJ mRNA in HUVEC cells are significantly increased 48h after treatment with one oligo designed to IFNAI antisensc DA393812. Bars denoted as CUR-0916, CUR-09I 7, CUR-0918 and CUR-0919 correspond to samples treated with SEQ ID NOS: 27 to 30 respectively.
[0022] Figure 6: ELISA Assay results show that IFNA protein was uprcgulated in extracts from MCF7 cells which were treated with oligos designed to IFNAl antisensc DA393812. Bars denoted as CUR-0916, CUR-0919. CUR-0918 and CUR-0917 and correspond to samples treated with SEQ ID NOS: 27, 30, 29 and 28 respectively. [0023] Sequence Listing Description
SEQ ID NO: 1 : Homo sapiens atonal homolog 1 (Drosophila) (ATOH l ), mRNA (NCBI Accession No.:
NM_OO5172).
SEQ ID NO: 2: Homo sapiens interferon induced with helicase C domain I (IFlH l ), mRNA (NCBI Accession
No.: NM_022168.2). SEQ ID NO: 3: NM_0240l 3.1 | Homo sapiens interferon, alpha I (IFNA l), mRNA (NCBI Accession No.: NM_005 l72).
SEQ ID NOs: 4 to 9: SEQ ID NO: 4: Natural RIGl antisense sequence (AK300104); SEQ ID NO: 5: Natural RJG l antisensc sequence (hs.601664); SEQ ID NO: 6: Natural RIGl antisense sequence (hs.104091); SEQ ID NO: 7: Natural MDA5 antisense sequence (Hs.692345); SEQ ID NO: 8: Natural MDA5 antisense sequence (BU663736) and SEQ ID NO: 9: Natural IFNA 1 antisense sequence (DA393812) SEQ ID NOs: IO to 30: Antisense oligonucleotides. V indicates RNA and * indicates phosphothioatc bond. SEQ ID NO: 31 and 39 arc the reverse complements of the antisense oligonucleotides SEQ ID NO: I O and 18 respectively. V indicates RNA. DETAILED DESCRIPTION
[0024] Several aspects of the invention are described below with reference to example applications for illustration. It should be understood that numerous specific details, relationships, and methods arc set forth to provide a full understanding of the invention. One having ordinary skill in the relevant art, however, will readily recognize that the invention can be practiced without one or more of the specific details or with other methods. The present invention is not limited by the ordering of acts or events, as some acts may occur in different orders and/or concurrently with other acts or events. Furthermore, not all illustrated acts or events are required to implement a methodology in accordance with the present invention.
[0025] All genes, gene names, and gene products disclosed herein arc intended to correspond to homologs from any species for which the compositions and methods disclosed herein are applicable. Thus, the terms include, but arc not limited to genes and gene products from humans and mice. It is understood that when a gene or gene product from a particular species is disclosed, this disclosure is intended to be exemplary only, and is not to be interpreted as a limitation unless the context in which il appears clearly indicates. Thus, for example, for the genes disclosed herein, which in some embodiments relate to mammalian nucleic acid and amino acid sequences arc intended to encompass homologous and/or orthologous genes and gene products from other animals including, but not limited to other mammals, fish, amphibians, reptiles, and birds. In embodiments, the genes or nucleic acid sequences are human. Definitions
[0026] The terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting of the invention. As used herein, the singular forms "a", "an" and "the" arc intended to include the plural forms as well, unless the context clearly indicates otherwise. Furthermore, to the extent that the terms "including", "includes", "having", "has", "with", or variants thereof arc used in cither the detailed description and/or the claims, such terms arc intended to be inclusive in a manner similar to the term "comprising." [0027] The term "about" or "approximately" means within an acceptable error range for the particular value as determined by one of ordinary skill in the art, which will depend in part on how the value is measured or determined, i.e., the limitations of the measurement system. For example, "about" can mean within 1 or more than I standard deviation, per the practice in the art. Alternatively, "about" can mean a range of up to 20%, preferably up to 10%, more preferably up to 5%, and more preferably still up to 1% of a given value. Alternatively, particularly with respect to biological systems or processes, the term can mean within an order of magnitude, preferably within 5-fold, and more preferably within 2-fold, of a value. Where particular values arc described in the application and claims, unless otherwise stated the term "about" meaning within an acceptable error range for the particular value should be assumed.
[0028] As used herein, the term "mRNA" means the presently known mRNA transcript(s) of a targeted gene, and any further transcripts which may be elucidated. [0029] By "antisense oligonucleotides" or "antisense compound" is meant an RNA or DNA molecule that binds to another RNA or DNA (target RNA, DNA). For example, if it is an RNA oligonucleotide it binds to another RNA target by means of RNA-RNA interactions and alters the activity of the target RNA. An antisense oligonucleotide can uprcgulatc or downrcgulatc expression and/or function of a particular polynucleotide. The definition is meant to include any foreign RNA or DNA molecule which is useful from a therapeutic, diagnostic, or other viewpoint. Such molecules include, for example, antisense RNA or DNA molecules, interference RNA (RNAi), micro RNA, decoy RNA molecules, siRNA, enzymatic RNA, therapeutic editing RNA and agonist and antagonist RNA, antisense oligomeric compounds, antisense oligonucleotides, external guide sequence (EGS) oligonucleotides, alternate splicers, primers, probes, and other oligomeric compounds that hybridize to at least a portion of the target nucleic acid. As such, these compounds may be introduced in the form of single-stranded, double-stranded, partially single-stranded, or circular oligomeric compounds.
[0030] In the context of this invention, the term "oligonucleotide" refers to an oligomer or polymer of ribonucleic acid (RNA) or deoxyribonucleic acid (DNA) or mimctics thereof. The term "oligonucleotide", also includes linear or circular oligomers of natural and/or modified monomers or linkages, including deoxyribonuclcosidcs, ribonuclcosidcs, substituted and alpha-anomeric forms thereof, peptide nucleic acids (PNA), locked nucleic acids (LNA), phosphorothioatc, mcthylphosphonatc, and the like. Oligonucleotides arc capable of specifically binding to a target polynucleotide by way of a regular pattern of monomcr-to-monomer interactions, such as Watson-Crick type of base pairing, Hoogstecn or reverse Hoogsteen types of base pairing, or the like.
[0031 ] The oligonucleotide may be "chimeric", that is, composed of different regions. In the context of this invention "chimeric" compounds arc oligonucleotides, which contain two or more chemical regions, for example, DNA rcgion(s), RNA rcgion(s), PNA region(s) etc. Each chemical region is made up of at least one monomer unit, i.e., a nucleotide in the case of an oligonucleotides compound. These oligonucleotides typically compπsc at least one region wherein the oligonucleotide is modified in order to exhibit one or more desired properties. The desired properties of the oligonucleotide include, but arc not limited, for example, to increased resistance to nuclease degradation, increased cellular uptake, and/or increased binding affinity for the target nucleic acid. Different regions of the oligonucleotide may therefore have different properties. The chimeric oligonucleotides of the present invention can be formed as mixed structures of two or more oligonucleotides, modified oligonucleotides, oligonucleotides and/or oligonucleotide analogs as described above.
[0032] The oligonucleotide can be composed of regions that can be linked in "register" that is, when the monomers arc linked consecutively, as in native DNA, or linked via spacers. The spacers arc intended to constitute a covalcnt "bridge" between the regions and have in cases a length not exceeding about 100 carbon atoms. The spacers may carry different functionalities, for example, having positive or negative charge, carry special nucleic acid binding properties (intcrcalators, groove binders, toxins, fluorophors etc.), being lipophilic, inducing special secondary structures like, for example, alanine containing peptides that induce alpha-helices. [0033] As used herein "Antiviral genes" and "Antiviral gene" are inclusive of all family members, mutants, alleles, fragments, species, coding and noncoding sequences, sense and antisense polynucleotide strands, etc. [0034] As used herein, the words RlG l , RIG-I , RIG-I, DEAD box protein 58, DKFZp434Jl l 11 , DKJFZp686N 19181 , FLJ 13599, Rctinoic acid-induciblc gene 1 protein, Retinoic acid-induciblc gene 1 protein, arc considered the same in the literature and are used interchangeably in the present application. [0035] As used herein, the words MDA5, MDA-5, Melanoma differentiation-associated protein 5, Hclicard, Helicase with 2 CARD domains, Hied, IDDM 19, Interferon-induced helicase C domain-containing protein I , Interferon-induced with helicase C domain protein 1 , MGC133047, Murabutide down-regulated protein, RH I 16, RNA helicase-DEAD box protein 1 16 are considered the same in the literature and are used interchangeably in the present application. [0036] As used herein, the words IFNAl , IFNAI l , G lOPl , GARG- 16, IFI56, IFI-56, IFI-56K, IFIT-I v Interferon- induced 56 kDa protein, Intcrfcron-induccd protein with tctratricopcptide repeats 1 , 1SG56, RNM561 arc considered the same in the literature and arc used interchangeably in the present application. [0037] As used herein, the term "oligonucleotide specific for" or "oligonucleotide which targets" refers to an oligonucleotide having a sequence (i) capable of forming a stable complex with a portion of the targeted gene, or (ii) capable of forming a stable duplex with a portion of a mRNA transcript of the targeted gene. Stability of the complexes and duplexes can be determined by theoretical calculations and/or in vitro assays. Exemplary assays for determining stability of hybridization complexes and duplexes arc described in the Examples below. [0038] As used herein, the term "target nucleic acid" encompasses DNA, RNA (comprising prcmRNA and mRNA) transcribed from such DNA, and also cDNA derived from such RNA, coding, noncoding sequences, sense or antisense polynucleotides. The specific hybridization of an oligomeric compound with its target nucleic acid interferes with the normal function of the nucleic acid. This modulation of function of a target nucleic acid by compounds, which specifically hybridize to it, is generally referred to as "antisense". The functions of DNA to be interfered include, for example, replication and transcription. The functions of RNA to be interfered, include all vital functions such as, for example, translocation of the RNA to the site of protein translation, translation of protein from the RNA, splicing of the RNA to yield one or more mRNA species, and catalytic activity which may be engaged in or facilitated by the RNA. The overall effect of such interference with target nucleic acid function is modulation of the expression of an encoded product or oligonucleotides.
[0039] RNA interference "RNAi" is mediated by double stranded RNA (dsRNA) molecules that have scqucncc- specific homology to their "target" nucleic acid sequences. In certain embodiments of the present invention, the mediators arc 5-25 nucleotide "small interfering" RNA duplexes (siRNAs). The siRNAs arc derived from the processing of dsRNA by an RNasc enzyme known as Dicer. siRNA duplex products arc recruited into a multi- protein siRNA complex termed RISC (RNA Induced Silencing Complex). Without wishing to be bound by any particular theory, a RISC is then believed to be guided to a target nucleic acid (suitably mRNA), where the siRNA duplex interacts in a sequence-specific way to mediate cleavage in a catalytic fashion. Small interfering RNAs that can be used in accordance with the present invention can be synthesized and used according to procedures that are well known in the art and that will be familiar to the ordinarily skilled artisan. Small interfering RNAs for use in the methods of the present invention suitably comprise between about 1 to about 50 nucleotides (nt). In examples of non limiting embodiments, siRNAs can comprise about 5 to about 40 nt, about 5 to about 30 nt, about 10 to about 30 nt, about 15 to about 25 nt, or about 20-25 nucleotides.
[0040] Selection of appropriate oligonucleotides is facilitated by using computer programs that automatically align nucleic acid sequences and indicate regions of identity or homology. Such programs are used to compare nucleic acid sequences obtained, for example, by searching databases such as GcnBank or by sequencing PCR products. Comparison of nucleic acid sequences from a range of species allows the selection of nucleic acid sequences that display an appropriate degree of identity between species. In the case of genes that have not been sequcnccd, Southern blots arc performed to allow a determination of the degree of identity between genes in target species and other species. By performing Southern blots at varying degrees of stringency, as is well known in the art, it is possible to obtain an approximate measure of identity. These procedures allow the selection of oligonucleotides that exhibit a high degree of complementarity to target nucleic acid sequences in a subject to be controlled and a lower degree of complementarity to corresponding nucleic acid sequences in other species. One skilled in the art will realize that there is considerable latitude in selecting appropriate regions of genes for use in the present invention.
[0041] By "enzymatic RNA" is meant an RNA molecule with enzymatic activity. Enzymatic nucleic acids (ribozymcs) act by first binding to a target RNA. Such binding occurs through the target binding portion of an enzymatic nucleic acid which is held in close proximity to an enzymatic portion of the molecule that acts to cleave the target RNA. Thus, the enzymatic nucleic acid first recognizes and then binds a target RNA through base pairing, and once bound to the correct site, acts cnzymatically to cut the target RNA.
[0042] By "decoy RNA" is meant an RNA molecule that mimics the natural binding domain for a ligand. The decoy RNA therefore competes with natural binding target for the binding of a specific ligand. For example, it has been shown that over-expression of HIV trans-activation response (TAR) RNA can act as a "decoy" and efficiently binds HIV tat protein, thereby preventing it from binding to TAR sequences encoded in the HIV RNA. This is meant to be a specific example. Those in the art will recognize that this is but one example, and other embodiments can be readily generated using techniques generally known in the art. [0043] As used herein, the term "monomers" typically indicates monomers linked by phosphodiester bonds or analogs thereof to form oligonucleotides ranging in size from a few monomelic units, e.g., from about 3-4, to about several hundreds of monomeric units. Analogs of phosphodiester linkages include: phosphorothioatc, phosphorodithioate, mcthylphosphomates, phosphorosclenoate, phosphoramidatc, and the like, as more fully described below. [0044] The term "nucleotide" covers naturally occurring nucleotides as well as nonnaturally occurring nucleotides. It should be clear to the person skilled in the art that various nucleotides which previously have been considered "non-natural Iy occurring" have subsequently been found in nature. Thus, "nucleotides" includes not only the known purine and pyrimidinc hctcrocyclcs-containing molecules, but also heterocyclic analogues and tautomers thereof Illustrative examples of other types of nucleotides are molecules containing adenine, guanine, thymine, cytosinc, uracil, purine, xanthine, diaminopurine, 8-oxo- N6-methyladenine, 7-dcazaxanthinc, 7- deazaguanine, N4,N4-ethanocytosin, N6,N6-ethano-2,6- diaminopurine, 5-methylcytosine, 5-(C3-C6)- alkynylcytosinc, 5-fluorouracil, 5-bromouracil, pseudoisocytosine, 2-hydroxy-5-methyl-4-triazolopyridin, isocytosinc, isoguanin, inosinc and the "non-narurally occurring" nucleotides described in U.S. Pat No. 5,432,272. The term "nucleotide" is intended to cover every and all of these examples as well as analogues and tautomers thereof. Especially interesting nucleotides arc those containing adenine, guanine, thymine, cytosinc, and uracil, which are considered as the naturally occurring nucleotides in relation to therapeutic and diagnostic application in humans. Nucleotides include the natural 2'-deoxy and 2'- hydroxyl sugars, e.g., as described in Romberg and Baker, DNA Replication, 2nd Ed. (Freeman, San Francisco, 1992) as well as their analogs. [0045] "Analogs" in reference to nucleotides includes synthetic nucleotides having modified base moieties and/or • modified sugar moieties. Such analogs include synthetic nucleotides designed to enhance binding properties, e.g., duplex or triplex stability, specificity, or the like.
[0046] As used herein, "hybridization" means the paiπng of substantially complementary strands of oligomcric compounds. One mechanism of pairing involves hydrogen bonding, which may be Watson-Crick, Hoogstccn or reversed Hoogsteen hydrogen bonding, between complementary nucleoside or nucleotide bases (nucleotides) of the strands of oligomcric compounds. For example, adenine and thymine arc complementary nucleotides which pair through the formation of hydrogen bonds. Hybridization can occur under varying circumstances. [0047] An antiscnsc compound is "specifically hybridizablc" when binding of the compound to the target nucleic acid interferes with the normal function of the target nucleic acid to cause a modulation of function and/or activity, and there is a sufficient degree of complementarity to avoid non-specific binding of the antisense compound to non-target nucleic acid sequences under conditions in which specific binding is desired, i.e., under physiological conditions in the case of in vivo assays or therapeutic treatment, and under conditions in which assays arc performed in the case of in vitro assays.
[0048] As used herein, the phrase "stringent hybridization conditions" or "stringent conditions" refers to conditions under which a compound of the invention will hybridize to its target sequence, but to a minimal number of other sequences. Stringent conditions arc sequence-dependent and will be different in different circumstances and in the context of this invention, "stringent conditions" under which oligomeric compounds hybridize to a target sequence are determined by the nature and composition of the oligomeric compounds and the assays in which they are being investigated. In general, stringent hybridization conditions comprise low concentrations (<0.15M) of salts with inorganic cations such as Na++ or K++ (i.e., low ionic strength), temperature higher than 2()°C - 25° C. below the Tm of the oligomeric compound:target sequence complex, and the presence of denaturants such as formamide, dimethylformamidc, dimethyl sulfoxide, or the detergent sodium dodccyl sulfate (SDS). For example, the hybridization rate decreases 1.1% for each 1% formamide. An example of a high stringency hybridization condition is 0.1 X sodium chloride-sodium citrate buffer (SSQ/0.1 % (w/v) SDS at 60° C. for 30 minutes. [0049] "Complementary," as used herein, refers to the capacity for precise pairing between two nucleotides on one or two oligomeric strands. For example, if a nucleobase at a certain position of an antisense compound is capable of hydrogen bonding with a nucleobase at a certain position of a target nucleic acid, said target nucleic acid being a DNA, RNA, or oligonucleotide molecule, then the position of hydrogen bonding between the oligonucleotide and the target nucleic acid is considered to be a complementary position. The oligomeric compound and the further DNA, RNA, or oligonucleotide molecule arc complementary to each other when a sufficient number of complementary positions in each molecule are occupied by nucleotides which can hydrogen bond with each other. Thus, "specifically hybridizable" and "complementary" are terms which arc used to indicate a sufficient degree of precise pairing or complementarity over a sufficient number of nucleotides such that stable and specific binding occurs between the oligomeric compound and a target nucleic acid. [0050] It is understood in the art that the sequence of an oligomeric compound need not be 100% complementary to that of its target nucleic acid to be specifically hybridizable. Moreover, an oligonucleotide may hybridize over one or more segments such that intervening or adjacent segments arc not involved in the hybridization event (e.g., a loop structure, mismatch or hairpin structure). The oligomeric compounds of the present invention comprise at least about 70%, or at least about 75%, or at least about 80%, or at least about 85%, or at least about 90%, or at least about 95%, or at least about 99% sequence complementarity to a target region within the target nucleic acid sequence to which they arc targeted. For example, an antisense compound in which 18 of 20 nucleotides of the antisense compound arc complementary to a target region, and would therefore specifically hybridize, would represent 90 percent complementarity. In this example, the remaining noncomplementary nucleotides may be clustered or interspersed with complementary nucleotides and need not be contiguous to each other or to complementary nucleotides. As such, an antisense compound which is 18 nucleotides in length having 4 (four) noncomplementary nucleotides which arc flanked by two regions of complete complementarity with the target nucleic acid would have 77.8% overall complementarity with the target nucleic acid and would thus fall within the scope of the present invention. Percent complementarity of an antisense compound with a region of a target nucleic acid can be determined routinely using BLAST programs (basic local alignment search tools) and PowcrBLAST programs known in the art. Percent homology, sequence identity or complementarity, can be determined by, for example, the Gap program (Wisconsin Sequence Analysis Package, Version 8 for Unix, Genetics Computer Group, University Research Park, Madison Wis.), using default settings, which uses the algorithm of Smith and Waterman (Adv. Appl. Math., (1981 ) 2, 482-489). [0051] As used herein, the term "Thermal Melting Point (Tm)" refers to the temperature, under defined ionic strength, pH, and nucleic acid concentration, at which 50% of the oligonucleotides complementary to the target sequence hybridize to the target sequence at equilibrium. Typically, stringent conditions will be those in which the salt concentration is at least about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 300C for short oligonucleotides (e.g., IO to 50 nucleotide). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide.
[0052] As used herein, "modulation" means either an increase (stimulation) or a decrease (inhibition) in die expression of a gene.
[0053] The term "variant," when used in the context of a polynucleotide sequence, may encompass a / polynucleotide sequence related to a wild type gene. This definition may also include, for example, "allelic," "splice," "species," or "polymorphic" variants. A splice variant may have significant identity to a reference molecule, but will generally have a greater or lesser number of polynucleotides due to alternate splicing of cxons during mRNA processing. The corresponding polypeptide may possess additional functional domains or an absence of domains. Species variants arc polynucleotide sequences that vary from one species to another. Of particular utility in the invention arc variants of wild type gene products. Variants may result from at least one mutation in the nucleic acid sequence and may result in altered mRNAs or in polypeptides whose structure or function may or may not be altered. Any given natural or recombinant gene may have none, one, or many allelic forms. Common mutational changes that give rise to variants are generally ascribed to natural deletions, additions, or substitutions of nucleotides. Each of these types of changes may occur alone, or in combination with the others, one or more times in a given sequence. [0054] The resulting polypeptides generally will have significant amino acid identity relative to each other. A polymoφhic variant is a variation in the polynucleotide sequence of a particular gene between individuals of a given species. Polymoφhic variants also may encompass "single nucleotide polymoφhisms" (SNPs,) or single base mutations in which the polynucleotide sequence varies by one base. The presence of SNPs may be indicative of, for example, a certain population with a propensity for a disease state, that is susceptibility versus resistance. [0055] Derivative polynucleotides include nucleic acids subjected to chemical modification, for example, replacement of hydrogen by an alkyl, acyl, or amino group. Derivatives, e.g., derivative oligonucleotides, may comprise non-naturally-occurring portions, such as altered sugar moieties or intcr-sugar linkages. Exemplary among these arc phosphorothioatc and other sulfur containing species which arc known in the art. Derivative nucleic acids may also contain labels, including radionuclcotidcs, enzymes, fluorescent agents, chcmi luminescent agents, chromogcnic agents, substrates, cofactors, inhibitors, magnetic particles, and the like. [0056] A "derivative" polypeptide or peptide is one that is modified, for example, by glycosylation, pcgylation, phosphorylation, sulfation, rcduction/alkylation, acylation, chemical coupling, or mild formalin treatment. A derivative may also be modified to contain a detectable label, either directly or indirectly, including, but not limited to, a radioisotope, fluorescent, and enzyme label.
[0057] As used herein, the term "animal" or "patient" is meant to include, for example, humans, sheep, elks, deer, mule deer, minks, mammals, monkeys, horses, cattle, pigs, goats, dogs, cats, rats, mice, birds, chicken, reptiles, fish, insects and arachnids. [0058] "Mammal" covers warm blooded mammals that arc typically under medical care (e.g., humans and domesticated animals). Examples include feline, canine, equine, bovine, and human, as well as just human.
[0059] "Treating" or "treatment" covers the treatment of a disease-state in a mammal, and includes: (a) preventing the disease-state from occurring in a mammal, in particular, when such mammal is predisposed to the disease-state but has not yet been diagnosed as having it; (b) inhibiting the disease-state, e.g., arresting it development: and/or (c) relieving the discasc-statc, e.g., causing regression of the disease state until a desired cndpoint is reached. Treating also includes the amelioration of a symptom of a disease (e.g., lessen the pain or discomfort), wherein such amelioration may or may not be directly affecting the disease (e.g., cause, transmission, expression, etc.). [0060] As used herein, "cancer" refers to all types of cancer or neoplasm or malignant tumors found in mammals, including, but not limited to: leukemias, lymphomas, melanomas, carcinomas and sarcomas. The cancer manifests itself as a "tumor" or tissue comprising malignant cells of the cancer. Examples of tumors include sarcomas and carcinomas such as, but not limited to: fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, chordoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma, lymphangioendotheliosarcoma, synovioma, mesothelioma, Ewing's tumor, leiomyosarcoma, rhabdomyosarcoma, colon carcinoma, pancreatic cancer, breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous gland carcinoma, papillary carcinoma, papillary adenocarcinomas, cystadcnocarcinoma, medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma, hepatoma, bile duct carcinoma, choriocarcinoma, seminoma, embryonal carcinoma, Wilms' tumor, cervical cancer, testicular tumor, lung carcinoma, small cell lung carcinoma, bladder carcinoma, epithelial carcinoma, glioma, astrocytoma, mcdulloblastoma, craniopharyngioma, ependymoma, pinealoma, hcmangioblastoma. acoustic neuroma, oligodendroglioma, meningioma, melanoma, neuroblastoma, and retinoblastoma. Additional cancers which can be treated by the disclosed composition according to the invention include but not limited to, for example, Hodgkin's Disease, Non-Hodgkin's Lymphoma, multiple myeloma, neuroblastoma, breast cancer, ovarian cancer, lung cancer, rhabdomyosarcoma, primary thrombocytosis, primary macroglobulincmia, small-cell lung tumors, primary brain tumors, stomach cancer, colon cancer, malignant pancreatic insulanoma, malignant carcinoid, urinary bladder cancer, prcmalignant skin lesions, testicular cancer, lymphomas, thyroid cancer, neuroblastoma, esophageal cancer, genitourinary tract cancer, malignant hypercalcemia, cervical cancer, endometrial cancer, adrenal cortical cancer, and prostate cancer.
[0061 ] "Neurological disease or disorder" refers to any disease or disorder of the nervous system and/or visual system. "Neurological disease or disorder" include disease or disorders that involve the central nervous system (brain, brainstem and cerebellum), the peripheral nervous system (including cranial nerves), and the autonomic nervous system (parts of which are located in both central and peripheral nervous system). Examples of neurological disorders include but arc not limited to, headache, stupor and coma, dementia, seizure, sleep disorders, trauma, infections, neoplasms, ncuroopthalmology, movement disorders, dcmyclinating diseases, spinal cord disorders, and disorders of peripheral nerves, muscle and neuromuscular junctions. Addiction and mental illness, include, but are not limited to, bipolar disorder and schizophrenia, are also included in the definition of neurological disorder. The following is a list of several neurological disorders, symptoms, signs and syndromes that can be treated using compositions and methods according to the present invention: acquired epileptiform aphasia; acute disseminated encephalomyelitis; adrcnolcukodystrophy; age-related macular degeneration; agenesis of the coφus callosum; agnosia; Aicardi syndrome; Alexander disease; Alpcrs' disease; alternating hemiplegia; Vascular dementia; amyotrophic lateral sclerosis; ancnccphaly; Angelman syndrome; angiomatosis; anoxia; aphasia; apraxia; arachnoid cysts; arachnoiditis; Anronl-Chiari malformation; arteriovenous malformation; Asperger syndrome; ataxia telcgiectasia; attention deficit hyperactivity disorder; autism; autonomic dysfunction; back pain; Batten disease; Behcet's disease; Bell's palsy; benign essential blepharospasm; benign focal; amyotrophy; benign intracranial hypertension;
Figure imgf000013_0001
disease; blepharospasm; Bloch Sulzberger syndrome; brachial plexus injury; brain abscess; brain injury; brain rumors (including glioblastoma multiforme); spinal tumor; Brown- Sequard syndrome; Canavan disease; carpal tunnel syndrome; causalgia; central pain syndrome; central pontine myelinolysis; cephalic disorder; cerebral aneurysm; cerebral arteriosclerosis; cerebral atrophy; cerebral gigantism; cerebral palsy; Charcot-Maric-Tooth disease; chemotherapy-induced neuropathy and neuropathic pain; Chiari malformation; chorea; chronic inflammatory dcmyclinating polyneuropathy; chronic pain; chronic regional pain syndrome; Coffin Lowry syndrome; coma, including persistent vegetative state; congenital facial diplegia; corticobasal degeneration; cranial arteritis; craniosynostosis; Crcutzfcldt-Jakob disease; cumulative trauma disorders; Cushing's syndrome; cytomegalic inclusion body disease; cytomegalovirus infection; dancing cycs- dancing feet syndrome; DandyWalker syndrome; Dawson disease; De Morsier's syndrome; Dejerine-Klumke palsy; dementia; dermatomyositis; diabetic neuropathy; diffuse sclerosis; dysautonomia; dysgraphia: dyslexia; dystonias; early infantile epileptic encephalopathy, empty sella syndrome; encephalitis: cncephaloccles; encephalotrigeminal angiomatosis; epilepsy; Erb's palsy; essential tremor, Fabry's disease; Fahr's syndrome; fainting; familial spastic paralysis; febrile seizures; Fisher syndrome; Friedreich's ataxia; fronto-tcmporal dementia and other "tauopathics"; Gauchcr's disease; Gcrstmanns syndrome; giant cell arteritis; giant cell inclusion disease; globoid cell leukodystrophy, Guillain-Barrc syndrome; HTLV-I -associated myelopathy; Hallcrvordcn-Spatz disease; head injury; headache; hemifacial spasm; hereditary spastic paraplegia; heredopathia atactic a polyncuritiformis; herpes zoster oticus; herpes zoster; Hirayama syndrome; HlVassociatcd dementia and neuropathy (also neurological manifestations of AIDS); holoprosencephaly; Huntington's disease and other polyglutaminc repeat diseases; hydranencephaly; hydrocephalus; hypercortisolism; hypoxia; immune-mediated encephalomyelitis; inclusion body myositis; incontinentia pigmenti; infantile phytanic acid storage disease; infantile refsum disease; infantile spasms; inflammatory myopathy; intracranial cyst; intracranial hypertension; Joubcrt syndrome; Kcams-Sayrc syndrome; Kennedy disease Kinsboumc syndrome; Klippcl Fcil syndrome; Krabbe disease; Kugelberg-Welander disease; kuru. Lafora disease; Lambert-Eaton myasthenic syndrome; Landau-Klcfther syndrome; lateral medullary (Wallenberg) syndrome; learning disabilities; Leigh's disease; Lennox-Gustaut syndrome; Lesch-Nyhan syndrome, leukodystrophy; Lewy body dementia; Lissenccphaly; locked-in syndrome; Lou Gehrig's disease (i.e., motor neuron disease or amyotrophic lateral sclerosis); lumbar disc disease; Lyme disease— neurological sequelae; Machado-Joscph disease; macrcncephaly; megalencephaly; Melkersson-Rosenthal syndrome; Menieres disease; meningitis; Menkes disease; metachromatic leukodystrophy; microcephaly; migraine; Miller Fisher syndrome; mini-strokes; mitochondrial myopathies; Mobius syndrome; monomelic amyotrophy: motor neuron disease; Moyamoya disease; mucopolysaccharidoses; milti-iπfarct dementia; multifocal motor neuropathy; multiple sclerosis and other demyelinating disorders; multiple system atrophy with postural hypotension; p muscular dystrophy; myasthenia gravis; myclinoclastic diffuse sclerosis; myoclonic encephalopathy of infants; myoclonus; myopathy; myotonia congenital; narcolepsy; neurofibromatosis; neuroleptic malignant syndrome; neurological manifestations of AIDS; neurological sequelae oflupus; neuromyotonia; neuronal ceroid lipofuscinosis; neuronal migration disorders; Nicmann-Pick disease; O'Sullivan- McLeod syndrome; occipital neuralgia; occult spinal dysraphism sequence; Ohtahara syndrome; olivopontocerebellar atrophy; opsoclonus myoclonus; optic neuritis; orthostatic hypotension; overuse syndrome: paresthesia; Neurodegenerative disease or disorder (Parkinson's disease, Huntington's disease, Alzheimer's disease, amyotrophic lateral sclerosis (ALS), dementia, multiple sclerosis and other diseases and disorders associated with neuronal cell death); paramyotonia congenital; paraneoplastic diseases; paroxysmal attacks; Parry Romberg syndrome; Pelizaeus-Merzbacher disease; periodic paralyses; peripheral neuropathy; painful neuropathy and neuropathic pain; persistent vegetative state; pervasive developmental disorders; photic sneeze reflex; phytanic acid storage disease; Pick's disease; pinched nerve; pituitary tumors; polymyositis; porencephaly; post-polio syndrome; postherpetic neuralgia; postinfectious encephalomyelitis; postural hypotension; Prader- Willi syndrome; primary lateral sclerosis; prion diseases; progressive hemifacial atrophy; progressive multifocallcukoencephalopathy; progressive sclerosing poliodystrophy; progressive supranuclear palsy; pseudotumor cerebri; Ramsay-Hunt syndrome (types I and 1 1); Rasmusscn's encephalitis; reflex sympathetic dystrophy syndrome; Refsum disease; repetitive motion disorders; repetitive stress injuries; restless legs syndrome; rctrovirus-associatcd myelopathy; Rett syndrome; Rcyc's syndrome; Saint Vitus dance; Sandhoff disease; Schildc^s disease; schizenccphaly; scpto-optic dysplasia; shaken baby syndrome; shingles; Shy-Dragcr syndrome; Sjogren's syndrome; sleep apnea; Soto's syndrome; spasticity; spina bifida; spinal cord injury; spinal cord tumors; spinal muscular atrophy; Stiff-Person syndrome; stroke; Sturge-Weber syndrome; subacute sclerosing panencephalitis; subcortical arteriosclerotic encephalopathy; Sydenham chorea; syncope; syringomyelia; tardive dyskinesia; Tay-Sachs disease; temporal arteritis; tethered spinal cord syndrome; Thomsen disease; thoracic outlet syndrome; Tic Douloureux; Todd's paralysis; Tourette syndrome; transient ischemic attack; transmissible spongiform encephalopathies; transverse myelitis; traumatic brain injury; tremor; trigeminal neuralgia; tropical spastic paraparesis; tuberous sclerosis; vascular dementia (multi-infarct dementia); vasculitis including temporal arteritis; Von Hippel-Lindau disease; Wallenberg's syndrome; Werdnig-Hoffman disease; West syndrome; whiplash; Williams syndrome; Wildon's disease; and Zellweger syndrome.
[0062] An "Inflammation" refers to systemic inflammatory conditions and conditions associated locally with migration and attraction of monocytes, leukocytes and/or neutrophils. Examples of inflammation include, but arc not limited to, Inflammation resulting from infection with pathogenic organisms (including gram-positive bacteria, gram-ncgativc bacteria, viruses, fungi, and parasites such as protozoa and helminths), transplant rejection (including rejection of solid organs such as kidney, liver, heart, lung or cornea, as well as rejection of bone marrow transplants including graft-versus-host disease (GVHD)), or from localized chronic or acute autoimmune or allergic reactions. Autoimmune diseases include acute glomerulonephritis; rheumatoid or reactive arthritis: chronic glomerulonephritis; inflammatory bowel diseases such as Crohn's disease, ulcerative colitis and necrotizing enterocolitis; granulocyte transfusion associated syndromes; inflammatory dermatoses such as contact dermatitis, atopic dermatitis, psoriasis; systemic lupus erythematosus (SLE), autoimmune thyroiditis, multiple sclerosis, and some forms of diabetes, or any other autoimmune state where attack by the subject's own immune system results in pathologic tissue destruction. Allergic reactions include allergic asthma, chronic bronchitis, acute and delayed hypersensitivity. Systemic inflammatory disease states include inflammation associated with trauma, bums, repcrfusion following ischemic events (e.g. thrombotic events in heart, brain, intestines or peripheral vasculature, including myocardial infarction and stroke), sepsis, ARDS or multiple organ dysfunction syndrome. Inflammatory cell recruitment also occurs in atherosclerotic plaques. Inflammation includes, but is not limited to, Non-Hodgkin's lymphoma, Wegener's granulomatosis, Hashimoto's thyroiditis, hepatocellular carcinoma, thymus atrophy, chronic pancreatitis, rheumatoid arthritis, reactive lymphoid hyperplasia, osteoarthritis, ulcerative colitis, papillary carcinoma, Crohn's disease, ulcerative colitis, acute cholecystitis, chronic cholecystitis, cirrhosis, chronic sialadenitis, peritonitis, acute pancreatitis, chronic pancreatitis, chronic Gastritis, adcnomyosis, endometriosis, acute cciΛ'icitis, chronic cervicitis, lymphoid hyperplasia, multiple sclerosis, hypertrophy secondary to idiopathic thrombocytopenic purpura, primary IgA nephropathy, systemic lupus erythematosus, psoriasis, pulmonary emphysema, chronic pyelonephritis, and chronic cystitis. [0063] A cardiovascular disease or disorder includes those disorders that can either cause ischemia or are caused by rcpcrfusion of the heart. Examples include, but arc not limited to, atherosclerosis, coronary artery disease, granulomatous myocarditis, chronic myocarditis (non-granulomatous), primary hypertrophic cardiomyopathy, peripheral artery disease (PAD), stroke, angina pectoris, myocardial infarction, cardiovascular tissue damage caused by cardiac arrest, cardiovascular tissue damage caused by cardiac bypass, cardiogenic shock, and related conditions that would be known by those of ordinary skill in the art or which involve dysfunction of or tissue damage to the heart or vasculature, especially, but not limited to, tissue damage related to an Antiviral gene activation. CVS diseases include, but arc not limited to, atherosclerosis, granulomatous myocarditis, myocardial infarction, myocardial fibrosis secondary to valvular heart disease, myocardial fibrosis without infarction, primary hypertrophic cardiomyopathy, and chronic myocarditis (non-granulomatous). [0064] Examples of viruses or viruses causing patient diseases comprise: Herpesviruses, such as for example, Alpha-herpesviruses (e.g. Herpes simplex virus 1 (HSV-I); Herpes simplex virus 2 (HSV-2); Varicella Zoster virus (VZV)), Bcta-hcrpesvi ruses (e.g. Cytomegalovirus (CMV); Herpes virus 6 (HHV-6)), Gamma-herpesviruses (e.g. Epstcin-Barr virus (EBV); Herpes virus 8 (HHV-8)), Hepatitis viruses (e.g. Hepatitis A virus; Hepatitis B virus; Hepatitis C virus; Hepatitis D virus; Hepatitis E virus), Rctrovimscs (e.g. Human Immunodeficiency 1 (HIV-I)), Orthomyxoviruses (e.g. Influenza viruses A, B and C), Paramyxoviruses, Respiratory Syncytial virus (RSV), Parainfluenza viruses (Pl) (e.g. Mumps virus. Measles virus), Togaviruses (e.g. Rubella virus), Picomaviruscs (e.g. Enteroviruses, Rhinoviruses; Coronaviruses), Papovaviruscs (e.g. Human papilloma viruses (HPV); Polyomaviruscs (BKV and ICV); Gastroenteritis viruses), Filoviridae, Bunyaviridae, Rhabdoviridac, Flaviviridac. [0065] Examples of bacteria causing bacterial diseases comprise: Staphylococcus aureus: strains include mcthicillin resistant (MRSA), methicillin-vancomycin resistant (VMRSA) and vancomycin intermediate resistant (VISA); Staphylococcus epidcrmidis; Entcrococcus faecalis and E. faecium: strains include vancomycin resistant (VRE); Streptococcus pneumoniae; Pseudomonas aeruginosa; Burkholdia cepacia; Xanthomonas maltophila; Escherichia coli; Enterobactcr spp.; Klebsiella pneumoniae; Salmonella spp. Polynucleotide and Oligonucleotide Compositions and Molecules Targets
[0066] In one embodiment, the targets comprise nucleic acid sequences of an Antiviral gene, including without limitation sense and/or antisense noncoding and/or coding sequences associated with an Antiviral gene. [0067] In one embodiment, the targets comprise nucleic acid sequences of RIG l , including without limitation sense and/or antisense honcoding and/or coding sequences associated with RIG I gene. [0068] In one embodiment, the targets comprise nucleic acid sequences of MDA5, including without limitation sense and/or antisensc noncoding and/or coding sequences associated with MDA5 gene.
[0069] In one embodiment, the targets comprise nucleic acid sequences of IFNA l , including without limitation sense and/or antisensc noncoding and/or coding sequences associated with IFNA 1 gene. [0070] The retinoic acid-inducible gene 1 product (RIG-I) has been identified as a cellular sensor of RNA virus infection resulting in beta interferon (IFN-B) induction. However, many viruses arc known to encode viral products that inhibit IFN-B production. In the case of influenza A virus, the viral nonstructural protein 1 (NS 1 ) prevents the induction of the IFN-B promoter by inhibiting the activation of transcription factors, including IRF-3, involved in IFN-B transcriptional activation. The inhibitory properties of NSl appear to be due at least in part to its binding to double-stranded RNA (dsRNA), resulting in the sequestration of this viral mediator of RIG-I activation.
[0071 ] Retinoic acid-induciblc gene I (RlG-I) and melanoma differentiation-associated gene 5 (MDA5) arc cytoplasmic DEx(D/H) box helicases that can detect intracellular viral products such as genomic RNA (vRNA) to signal IFN-/- production in infected cells. Signaling by each occurs through homotypic caspasc activation and recruitment domain (CARD) interactions with the interferon promoter-stimulating factor 1 (IPS-I) adaptor protein, which recruits RIG-I and MDA5 to the outer membrane of the mitochondria as part of a macromolecular signaling complex that serves to activate downstream interferon-regύlatory factors (IRFs) and other transcription factors that induce IFN-/~ and ISG expression. Although RIG-I and MDA5 may share similar signaling features and structural homology, accumulating evidence suggests that the two helicases may discriminate among different ligands to trigger the innate immune response to RNA viruses. Signaling by RIG-I is triggered during infection by a number of RNA viruses and by the presence of synthetic RNA transcribed in vitro. More recently, RIG-I has been implicated in the recognition ofRNA moieties that harbor 5' triphosphate ends or of RNAs that assume complex secondary structures. In contrast, signaling by MDA5 is uniquely triggered during picornavirus infections or in the presence of a synthetic RNA polymer consisting of annealing strands of inosine and cytosine, poly(I:C). [0072] Human melanoma cells can be reprogrammed to terminally differentiate and irreversibly lose proliferative capacity by appropriate pharmacological manipulation. Subtraction hybridization identified melanoma differentiation-associated genc-5 (mda-5) as a gene induced during differentiation, cancer reversion, and programmed cell death (apoptosis). This gene contains both a caspase recruitment domain and putative DExH group RNA helicasc domains. Atypical helicase motifs ofMDA-5 deviate from consensus sequences but arc well conserved in a potentially new group of cloned and hypothetical proteins, mda-5 is an early response gene inducible by IFN and tumor necrosis factor-a, responding predominantly to IFN-. Protein kinase C activation by mczcrcin further augments mda-5 expression induced by IFN-. Expression ofmda-5 is controlled transcriptionally by IFN-, and the MDA-5 protein localizes in the cytoplasm, mda-5 displays RNA-dcpcndcnt ATPasc activity, and ectopic expression of mda5 in human melanoma cells inhibits colony formation. In these contexts, mda-5 may function as a mediator oflFN-induced growth inhibition and/or apoptosis. MDA-5 is a double-stranded RNA- dependent ATPasc that contains both a caspase recruitment domain and RNA hclicasc motifs, with a confirmed association with growth and differentiation in human melanoma cells.
[0073] Progress has been made in understanding the molecular basis of the antiviral actions of interferons (IFNs), as well as strategies evolved by viruses to antagonize the actions of IFNs. Furthermore, advances made while elucidating the IFN system have contributed significantly to our understanding in multiple areas of virology and molecular cell biology, ranging from pathways of signal transduction to the biochemical mechanisms of transcriptional and translational control to die molecular basis of viral pathogenesis. IFNs arc approved therapeutics and have moved from the basic research laboratory to the clinic. Among the IFN-induced proteins important in the antiviral actions of IFNs are the RNA-dependent protein kinase (PKR), the 2',5'-oligoadenylate synthetase (OAS) and RNase L, and the Mx protein GTPases. Double stranded RNA plays a central role in modulating protein phosphorylation and RNA degradation catalyzed by the IFN-inducible PKR kinase and the 2'- 5'-oligoadcnylate-dcpcndcnt RNase L, respectively, and also in RNA editing by the IFN-induciblc RNA-spccific adenosine deaminase (ADARl). IFN also induces a form of inducible nitric oxide synthase (iNOS2) and the major histocompatibility complex class I and II proteins, all of which play important roles in immune response to infections. Several additional genes whose expression profiles arc altered in response to IFN treatment and virus infection have been identified by microarray analyses. The availability of cDNA and genomic clones for many of the components of the IFN system, including IFN-alpha, IFN-bcta, and IFN-gamma, their receptors, Jak and Stat and IRF signal transduction components, and proteins such as PKR, 2',5'-OAS, Mx, and ADAR, whose expression „ is regulated by IFNs, has permitted the generation of mutant proteins, cells that overexpress different forms of the proteins, and animals in which their expression has been disrupted by targeted gene disruption. The use of these IFN system reagents, both in cell culture and in whole animals, continues to provide important contributions to our understanding of the virus-host interaction and cellular antiviral response.
[0074] Interferons (IFN)s are involved in numerous immune interactions during viral infections and contribute to both induction and regulation of innate and adaptive antiviral mechanisms. IFNs playa pivotaJ rule in the outcome of a viral infection, as demonstrated by the impaired resistance against different viruses in mice deficient for the receptors 1FNAR-2 and IFNGR. During viral infections, IFNs are involved in numerous immune interactions as inducers, regulators, and effectors of both innate and adaptive antiviral mechanisms. IFN-alpha/bcta is produced rapidly when viral factors, such as envelope glycoproteins, CpG DNA, or dsRNA, interact with cellular pattern- recognition receptors (PRRs), such as mannosc receptors, toll-like receptors (TLRs), and cytosolic receptors. These host-virus interactions signal downstream to activate transcription factors needed to achieve expression from IFN- alpha/bcta genes. These include IFN regulatory factor-3 (IRF-3), 1RF-5, 1RF-7, c-Jun/ATF-2, and NF-kappaB. In [0075] contrast, IFN-gamma is induced by receptor-mediated stimulation or in response to early produced cytokines, including interleukin-2 (IL- 12), IL- 18, and IFN-alpha/beta, or by stimulation through T cell receptors (TCRs) or natural killer (NK) cell receptors. IFNs signal through transmembrane receptors, activating mainly Jak- Stat pathways but also other signal transduction pathways. Cytokine and TCR-induced IFN-gamma expression uses distinct signal transduction pathways involving such transcription factors as NFAT, Stats and NF-kappaB. This [0076] results in induction and activation of numerous intrinsic antiviral factors, such as RNA-activatcd protein kinase (PKR), the 2-5A system, Mx proteins, and several apoptotic pathways. In addition, IFNs modulate distinct aspects of both innate and adaptive immunity. Thus.IFNalpha/ beta and IFN-gamma affect activities of macrophages, NK cells, dendritic cells (DC), and T cells by enhancing antigen presentation, cell trafficking, and cell differentiation and expression profiles, ultimately resulting in enhanced antiviral effector functions. [0077] In some embodiments, antiscnsc oligonucleotides are used to prevent or treat diseases or disorders associated with Antiviral gene family members. Exemplary Antiviral gene mediated diseases and disorders which can be treated with cell/tissues regenerated from stem cells obtained using the antiscnse compounds comprise: cancer, an inflammatory disease, a disease, disorder or a condition caused by an infectious agent (e.g., including, viral, bacterial, fungal, protozoan etc.), a viral disease, inflammation, arthritis, psoriasis,a neurological disease or disorder, an immune system disease or disorder, an autoimmune disease or disorder, an immunodeficiency disease, an allergy, psoriasis, neurological diseases, a renal disease or disorder, a cardiovascular disease or disorder, a muscular disease or disorder, atherosclerosis, diabetes, a hepatic disease or disorder and a communicable disease. [0078] In another embodiment, the antisensc oligonucleotides modulate the expression, in vivo amounts and/or function of an Antiviral gene in patients suffering from or at risk of developing diseases or disorders associated with Antiviral genes. [0079] In another example, Human mctapncumovirus (HMPV) is a recently discovered pathogen that causes a significant proportion of respiratory infections in young infants, the elderly and immunocompromised patients. Modulation of RIG-I expression and/or function modulate viral infection by various mechanisms, including for example, viral genomic sequence destruction. RJG-I antiscnsc oligonucleotides would thus be of great therapeutic value in the development of anti- viral agents. [0080] In one embodiment, modulation of retinoic acid inducible gene I (RIG-I) detects and destroys viral genomes. In another embodiment, modulation of retinoic acid inducible gene I (RIG-I) prevents or treats against viral infections in patients.
[0081 ] In one embodiment, the oligonucleotides arc specific for polynucleotides of an Antiviral gene, which includes, without limitation noncoding regions. The Antiviral gene targets comprise variants of an Antiviral gene; mutants of an Antiviral gene, including SNPs; noncoding sequences of an Antiviral gene; alleles, fragments and the like. Preferably the oligonucleotide is an antiscnsc RNA molecule.
[0082] In accordance with embodiments of the invention, the target nucleic acid molecule is not limited to an Antiviral gene polynucleotides alone but extends to any of the isoforms, receptors, homologs, non-coding regions and the like of an Antiviral gene. [0083] In another embodiment, an oligonucleotide targets a natural antisensc sequence (natural antiscnsc to the coding and non-coding regions) of an Antiviral gene targets, including, without limitation, variants, alleles, homologs, mutants, derivatives, fragments and complementary sequences thereto. Preferably the oligonucleotide is an antiscnsc RNA or DNA molecule. [0084] In another embodiment, the oligomeric compounds of the present invention also include variants in which a different base is present at one or more of the nucleotide positions in the compound. For example, if the first nucleotide is an adenine, variants may be produced which contain thymidine, guanosinc, cytidinc or other natural or unnatural nucleotides at this position. This may be done at any of the positions of the antiscnsc compound. [0085] In some embodiments, homology, sequence identity or complementarity, between the antiscnsc compound and target is from about 50% to about 60%. In some embodiments, homology, sequence identity or complementarity, is from about 60% to about 70%. In some embodiments, homology, sequence identity or complementarity, is from about 70% to about 80% In some embodiments, homology, sequence identity or complementarity, is from about 80% to about 90%. In some embodiments, homology, sequence identity or complementarity, is about 90%, about 92%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99% or about 100%
[0086] An antisense compound is specifically hybridizablc when binding of the compound to the target nucleic acid interferes with the normal function of the target nucleic acid to cause a loss of activity, and there is a sufficient degree of complementarity to avoid non-specific binding of the antisense compound to non-target nucleic acid sequences under conditions in which specific binding is desired. Such conditions include, i.c , physiological conditions in the case of in vivo assays or therapeutic treatment, and conditions in which assays arc performed in the case of in vitro assays.
[0087] An antiscnsc compound, whether DNA, RNA. chimeric, substituted etc, is specifically hybridizablc when binding of the compound to the target DNA or RNA molecule interferes with the normal function of the target DNA or RNA to cause a loss of utility, and there is a sufficient degree of complementarity to avoid non-specific binding of the antisense compound to non-target sequences under conditions in which specific binding is desired, i.e., under physiological conditions in the case of in vivo assays or therapeutic treatment, and in the case of in vitro assays, under conditions in which the assays are performed.
[0088] In another embodiment, targeting of an Antiviral gene including without limitation, antiscnsc sequences which are identified and expanded, using for example. PCR, hybridization etc., one or more of the sequences set forth as SEQ ID NO: 4 to 9, and the like, modulate the expression or function of an Antiviral gene. In one embodiment, expression or function is up-rcgulatcd as compared to a control. In another embodiment, expression or function is down-regulated as compared to a control.
[0089] In another embodiment, oligonucleotides comprise nucleic acid sequences set forth as SEQ ID NOS: 10 to 30 including antisense sequences which are identified and expanded, using for example, PCR, hybridization etc. These oligonucleotides can comprise one or more modified nucleotides, shorter or longer fragments, modified bonds and the like. Examples of modified bonds or intemucleotidc linkages comprise phosphorothioate, phosphorodithioate or the like. In another embodiment, the nucleotides comprise a phosphorus derivative. The phosphorus derivative (or modified phosphate group) which may be attached to the sugar or sugar analog moiety in the modified oligonucleotides of the present invention may be a monophosphate, diphosphate, triphosphate, alkylphosphatc, alkancphosphatc, phosphorothioate and the like. The preparation of the above-noted phosphate analogs, and their incorporation into nucleotides, modified nucleotides and oligonucleotides, per se, is also known and need not be described here. [0090] The specificity and sensitivity of antisense is also harnessed by those of skill in the art for therapeutic uses. Antisense oligonucleotides have been employed as therapeutic moieties in the treatment of disease states in animals and man. Antisense oligonucleotides have been safely and effectively administered to humans and numerous clinical trials arc presently underway. It is thus established that oligonucleotides can be useful therapeutic modalities that can be configured to be useful in treatment regimes for treatment of cells, tissues and animals, especially humans. [0091 ] In embodiments of the present invention oligomeric antisense compounds, particularly oligonucleotides, bind to target nucleic acid molecules and modulate the expression and/or function of molecules encoded by a target gene. The functions of DNA to be interfered comprise, for example, replication and transcription. The functions of RNA to be interfered comprise all vital functions such as, for example, translocation of the RNA to the site of protein translation, translation of protein from the RNA, splicing of the RNA to yield one or more mRNA species, and catalytic activity which may be engaged in or facilitated by the RNA. The functions may be up-rcgulatcd or inhibited depending on the functions desired.
[0092] The antisense compounds, include, antisense oligomeric compounds, antisense oligonucleotides, external guide sequence (EGS) oligonucleotides, alternate splicers, primers, probes, and other oligomeric compounds that hybridize to at least a portion of the target nucleic acid. As such, these compounds may be introduced in the form of single-stranded, double-stranded, partially single-stranded, or circular oligomeric compounds.
[0093] Targeting an antisense compound to a particular nucleic acid molecule, in the context of this invention, can be a multistcp process. The process usually begins with the identification of a target nucleic acid whose function is to be modulated. This target nucleic acid may be, for example, a cellular gene (or mRNA transcribed from the gene) whose expression is associated with a particular disorder or disease state, or a nucleic acid molecule from an infectious agent. In the present invention, the target nucleic acid encodes an Antiviral gene.
[0094] The targeting process usually also includes determination of at least one target region, segment, or site within the target nucleic acid for the antisense interaction to occur such that the desired effect, e.g., modulation of expression, will result. Within the context of the present invention, the term "region" is defined as a portion of the target nucleic acid having at least one identifiable structure, function, or characteristic. Within regions of target nucleic acids arc segments. "Segments" arc defined as smaller or sub-portions of regions within a target nucleic acid. "Sites," as used in the present invention, are defined as positions within a target nucleic acid. [0095] In one embodiment, the antisensc oligonucleotides bind to the natural antiscnsc sequences of an Antiviral gene and modulate the expression and/or Junction of an Antiviral gene (SEQ ID NO: 1 to 3). Examples of antisensc sequences include SEQ ID NOS: 4 to 30.
[0096] In another embodiment, the antisense oligonucleotides bind to one or more segments of an Antiviral gene polynucleotide and modulate the expression and/or function of an Antiviral gene. The segments comprise at least five consecutive nucleotides of an Antiviral gene sense or antiscnsc polynucleotides. [0097] In another embodiment, the antiscnsc oligonucleotides arc specific for natural antisense sequences of an Antiviral gene wherein binding of the oligonucleotides to the natural antisensc sequences of an Antiviral gene modulate expression and/or function of an Antiviral gene.
[0098] In another embodiment, oligonucleotide compounds comprise sequences set forth as SEQ ID NOS: 10 to 30, antiscnsc sequences which arc identified and expanded, using for example, PCR, hybridization etc These oligonucleotides can comprise one or more modified nucleotides, shorter or longer fragments, modified bonds and the like. Examples of modified bonds or intcrnucleotidc linkages comprise phosphorothioate, phosphorodithioatc or the like. In another embodiment, the nucleotides comprise a phosphorus derivative. The phosphorus derivative (or modified phosphate group) which may be attached to the sugar or sugar analog moiety in the modified oligonucleotides of the present invention may be a monophosphate, diphosphate, triphosphate, alkylphosphate, alkancphosphatc, phosphorothioate and the like. The preparation of the above-noted phosphate analogs, and their incorporation into nucleotides, modified nucleotides and oligonucleotides, per sc, is also known and need not be described here.
[0099] Since, as is known in the art, the translation initiation codon is typically 5'-AUG (in transcribed mRNA molecules; 5'-ATG in the corresponding DNA molecule), the translation initiation codon is also referred to as the "AUG codon," the "start codon" or the "AUG start codon". A minority of genes has a translation initiation codon having the RNA sequence 5'-GUG, 5'-UUG or 5'-CUG; and 5'-AUA, 5'-ACG and 5'-CUG have been shown to function in vivo. Thus, the terms "translation initiation codon" and "start codon" can encompass many codon sequences, even though the initiator amino acid in each instance is typically methionine (in eukaryotes) or formylmethionine (in prokaryotes). Eukaryotic and prokaryotic genes may have two or more alternative start codons, any one of which may be preferentially utilized for translation initiation in a particular cell type or tissue, or under a particular set of conditions. In the context of the invention, "start codon" and "translation initiation codon" refer to the codon or codons that are used in vivo to initiate translation of an mRNA transcribed from a gene encoding an Antiviral gene, regardless of the scqucnce(s) of such codons. A translation termination codon (or "stop codon") of a gene may have one of three sequences, i.e., 5'-UAA, 5'-UAG and 5'-UGA (the corresponding DNA sequences are 5'-TAA, 5'- TAG and 5'-TGA, respectively). [00100] The terms "start codon region" and "translation initiation codon region" refer to a portion of such an mRN A or gene that encompasses from about 25 to about 50 contiguous nucleotides in cither direction (i.e., 5' or 3') from a translation initiation codon. Similarly, the terms "stop codon region" and "translation termination codon region" refer to a portion of such an mRNA or gene that encompasses from about 25 to about 50 contiguous nucleotides in cither direction (i.c., 5' or 3') from a translation termination codon. Consequently, the "start codon region" (or "translation initiation codon region") and the "stop codon region" (or "translation termination codon region") arc all regions that may be targeted effectively with the antiscnsc compounds of the present invention. [00101 ] The open reading frame (ORF) or "coding region," which is known in the art to refer to the region between the translation initiation codon and the translation termination codon, is also a region which may be targeted effectively. Within the context of the present invention, a targeted region is the intragenic region encompassing the translation initiation or termination codon of the open reading frame (ORF) of a gene. [00102] Another target region includes the 5' untranslated region (5'UTR), known in the art to refer to the portion of an mRNA in the 5' direction from the translation initiation codon, and thus including nucleotides between the 5' cap site and the translation initiation codon of an mRNA (or corresponding nucleotides on the gene). Still another target region includes the 3' untranslated region (3'UTR), known in the art to refer to the portion of an mRNA in the 3' direction from the translation termination codon, and thus including nucleotides between the translation termination codon and 3' end of an mRNA (or corresponding nucleotides on the gene). The 5' cap site of an mRNA comprises an N7-mcthylated guanosinc residue joined to the 5'-most residue of the mRNA via a 5'-5' triphosphate linkage. The 5' cap region of an mRNA is considered to include the 5' cap structure itself as well as the first 50 nucleotides adjacent to the cap site. Another target region for this invention is the 5' cap region.
[00103] Although some cukaryotic mRNA transcripts are directly translated, many contain one or more regions, known as "introns," which arc excised from a transcript before it is translated. The remaining (and therefore translated) regions are known as "cxons" and are spliced together to form a continuous mRNA sequence. In one embodiment, targeting splice sites, i.e., intron-cxon junctions or exon-intron junctions, is particularly useful in situations where aberrant splicing is implicated in disease, or where an overproduction of a particular splice product is implicated in disease. An aberrant fusion junction due to rearrangement or deletion is another embodiment of a target site. mRNA transcripts produced via the process of splicing of two (or more) mRN As from different gene sources are known as "fusion transcripts". Introns can be effectively targeted using antisense compounds targeted to, for example, DNA or prc-mRNA. [00104] In another embodiment, the antisense oligonucleotides bind to coding and/or non-coding regions of a target polynucleotide and modulate the expression and/or function of the target molecule.
[00105] In another embodiment, the antisense oligonucleotides bind to natural antisense polynucleotides and modulate the expression and/or function of the target molecule. [00106] In another embodiment, the antiscnsc oligonucleotides bind to sense polynucleotides and modulate the expression and/or function of the target molecule.
[00107] Alternative RNA transcripts can be produced from the same genomic region of DNA. These alternative transcripts are generally known as "variants". More specifically, "pre-mRNA variants" are transcripts produced from the same genomic DNA that differ from other transcripts produced from the same genomic DNA in either their start or stop position and contain both intronic and cxonic sequence.
[00108] Upon excision of one or more exon or intron regions, or portions thereof during splicing, pre-mRNA variants produce smaller "mRNA variants". Consequently, mRNA variants are processed pre-mRNA variants and each unique pre-mRNA variant must always produce a unique mRNA variant as a result of splicing. These mRNA variants are also known as "alternative splice variants". If no splicing of the pre-mRNA variant occurs then the pre- mRNA variant is identical to the mRNA variant.
[00109] Variants can be produced through the use of alternative signals to start or stop transcription. Pre-mRN As and mRNAs can possess more than one start codon or stop codon. Variants that originate from a pre-mRNA or mRNA that use alternative start codons arc known as "alternative start variants" of that pre-mRNA or mRNA. Those transcripts that use an alternative stop codon arc known as "alternative stop variants" of that pre-mRNA or mRNA. One specific type of alternative stop variant is the "polyA variant" in which the multiple transcripts produced result from the alternative selection of one of the "polyA stop signals" by the transcription machinery, thereby producing transcripts that terminate at unique polyA sites. Within the context of the invention, the types of variants described herein arc also embodiments of target nucleic acids. [001 10] The locations on the target nucleic acid to which the antiscnsc compounds hybridize arc defined as at least a 5-nuclcotidc long portion of a target region to which an active antiscnsc compound is targeted. [001 1 1 ] While the specific sequences of certain exemplary target segments arc set forth herein, one of skill in the art will recognize that these serve to illustrate and describe particular embodiments within the scope of the present invention. Additional target segments arc readily identifiable by one having ordinary skill in the art in view of this disclosure.
[001 12] Target segments 5- 100 nucleotides in length comprising a stretch of at least five (5) consecutive nucleotides selected from within the illustrative target segments arc considered to be suitable for targeting as well. [001 13] Target segments can include DNA or RNA sequences that comprise at least the 5 consecutive nucleotides from the 5'-terminus of one of the illustrative target segments (the remaining nucleotides being a consecutive stretch of the same DNA or RNA beginning immediately upstream of the 5'-terminus of the target segment and continuing until the DNA or RNA contains about 5 to about 100 nucleotides). Similarly target segments arc represented by DNA or RNA sequences that comprise at least the 5 consecutive nucleotides from the 3'-terminus of one of the illustrative target segments (the remaining nucleotides being a consecutive stretch of the same DNA or RNA beginning immediately downstream of the 3'-terminus of the target segment and continuing until the DNA or RNA contains about 5 to about 100 nucleotides). One having skill in the art armed with the target segments illustrated herein will be able, without undue experimentation, to identify further target segments. [001 14] Once one or more target regions, segments or sites have been identified, antiscnsc compounds arc chosen which are sufficiently complementary to the target, i.e., hybridize sufficiently well and with sufficient specificity, to give the desired effect.
[001 15] In embodiments of the invention the oligonucleotides bind to an antisense strand of a particular target. The oligonucleotides arc at least 5 nucleotides in length and can be synthesized so each oligonucleotide targets overlapping sequences such that oligonucleotides arc synthesized to cover the entire length of the target polynucleotide. The targets also include coding as well as non coding regions. [001 16] In one embodiment, specific nucleic acids arc targeted by antisense oligonucleotides. Targeting an antisense compound to a particular nucleic acid, is a multistep process. The process usually begins with the identification of a nucleic acid sequence whose function is to be modulated. This may be, for example, a cellular gene (or mRNA transcribed from the gene) whose expression is associated with a particular disorder or disease state, or a non coding polynucleotide such as for example, non coding RNA (ncRNA). [001 17] RNAs can be classified into ( 1 ) messenger RNAs (mRNAs), which arc translated into proteins,' and (2) non-protein-coding RNAs (ncRNAs). ncRNAs comprise microRNAs, antisense transcripts and other Transcriptional Units (TU) containing a high density of stop codons and lacking any extensive "Open Reading Frame". Many ncRNAs appear to start from initiation sites in 3' untranslated regions (3'UTRs) of protein-coding loci. ncRNAs arc often rare and at least half of the ncRNAs that have been scqucnccd by the FANTOM consortium seem not to be polyadcnylatcd. Most researchers have for obvious reasons focused on polyadcnylated mRNAs that arc processed and exported to the cytoplasm. Recently, it was shown that the set of non-polyadcnylated nuclear RNAs may be very large, and that many such transcripts arise from intcrgcnic regions. The mechanism by which ncRNAs may regulate gene expression is by base paiπng with target transcripts. The RNAs that function by base pairing can be grouped into ( I) cis encoded RNAs that arc encoded at the same genetic location, but on the opposite strand to the RNAs they act upon and therefore display perfect complementarity to their target, and (2) trans-encoded RNAs that are encoded at a chromosomal location distinct from the RNAs they act upon and generally do not exhibit perfect base-pairing potential with their targets.
[001 18] Without wishing to be bound by theory, perturbation of an antisense polynucleotide by the antisense oligonucleotides described herein can alter the expression of the corresponding sense messenger RNAs. However, this regulation can either be discordant (antisense knockdown results in messenger RNA elevation) or concordant (antisense knockdown results in concomitant messenger RNA reduction). In these cases, antisense oligonucleotides can be targeted to overlapping or non-overlapping parts of the antisense transcript resulting in its knockdown or sequestration. Coding as well as non-coding antisense can be targeted in an identical manner and that either category is capable of regulating the corresponding sense transcripts - either in a concordant or disconcordant manner. The strategics that are employed in identifying new oligonucleotides for use against a target can be based on the knockdown of antiscnse RNA transcripts by antisense oligonucleotides or any other means of modulating the desired target.
[001 19] Strategy I: In the case of discordant regulation, knocking down the antisense transcript elevates the expression of the conventional (sense) gene. Should that latter gene encode for a known or putative drug target, then knockdown of its antisense counterpart could conceivably mimic the action of a receptor agonist or an enzyme stimulant.
[00120] Strategy 2: In the case of concordant regulation, one could concomitantly knock down both antisense and sense transcripts and thereby achieve synergistic reduction of the conventional (sense) gene expression. If, for example, an antisense oligonucleotide is used to achieve knockdown, then this strategy can be used to apply one antisense oligonucleotide targeted to the sense transcript and another antisense oligonucleotide to the corresponding antisense transcript, or a single energetically symmetric antisense oligonucleotide that simultaneously targets overlapping sense and antisense transcripts. [00121 ] According to the present invention, antisense compounds include antisense oligonucleotides, ribozymes, external guide sequence (EGS) oligonucleotides, siRNA compounds, single- or double-stranded RNA interference (RNAi) compounds such as siRNA compounds, and other oligomeric compounds which hybridize to at least a portion of the target nucleic acid and modulate its function. As such, they may be DNA, RNA, DNA-like, RNA- likc, or mixtures thereof, or may be mimctics of one or more of these. These compounds may be singlc-strandcd, doublcstrandcd, circular or hairpin oligomeric compounds and may contain structural elements such as internal or terminal bulges, mismatches or loops. Antisense compounds arc routinely prepared linearly but can be joined or otherwise prepared to be circular and/or branched. Antisense compounds can include constructs such as, for example, two strands hybridized to form a wholly or partially doublc-strandcd compound or a single strand with sufficient self-complcmcntarity to allow for hybridization and formation of a fully or partially doublc-strandcd compound. The two strands can be linked internally leaving free 3' or 5' termini or can be linked to form a continuous hairpin structure or loop. The hairpin structure may contain an overhang on cither the 5' or 3' terminus producing an extension of single stranded character. The double stranded compounds optionally can include overhangs on the ends. Further modifications can include conjugate groups attached to one of the termini, selected nucleotide positions, sugar positions or to one of the intcmuclcosidc linkages. Alternatively, the two strands can be linked via a non-nucleic acid moiety or linker group. When formed from only one strand, dsRNA can take the form of a sclf-complcmcntary hairpin-type molecule that doubles back on itself to form a duplex. Thus, the dsRNAs can be fully or partially double stranded. Specific modulation of gene expression can be achieved by stable expression of dsRNA hairpins in transgenic cell lines, however, in some embodiments, the gene expression or function is up regulated. When formed from two strands, or a single strand that takes the form of a self-complementary hairpin- type molecule doubled back on itself to form a duplex, the two strands (or duplex-forming regions of a single strand) are complementary RNA strands that base pair in Watson-Crick fashion.
[00122] Once introduced to a system, the compounds of the invention may elicit the action of one or more enzymes or structural proteins to effect cleavage or other modification of the target nucleic acid or may work via occupancy-based mechanisms. In general, nucleic acids (including oligonucleotides) may be described as "DNA- likc" (i.e., generally having one or more 2'-dcoxy sugars and, generally, T rather than U bases) or "RNA-likc" (i.e., generally having one or more 2'- hydroxyl or 2'-modificd sugars and, generally U rather than T bases). Nucleic acid helices can adopt more than one type of structure, most commonly the A- and B-forms. It is believed that, in general, oligonucleotides which have B-form-like structure are "DNA-like" and those which have A-formlike structure are "RNA-like." In some (chimeric) embodiments, an antisense compound may contain both A- and B- form regions.
[00123] In another embodiment, the desired oligonucleotides or antisense compounds, comprise at least one of: antisense RNA, antisense DNA, chimeric antisense oligonucleotides, antisense oligonucleotides comprising modified linkages, interference RNA (RNAi), short interfering RNA (siRN A); a micro, interfering RNA (miRNA); a small, temporal RNA (stRNA); or a short, hairpin RNA (shRNA): small RNA-induccd gene activation (RNAa); small activating RNAs (saRNAs), or combinations thereof.
[00124] dsRNA can also activate gene expression, a mechanism that has been termed "small RNA-induccd gene activation" or RNAa. dsRNAs targeting gene promoters induce potent transcriptional activation of associated genes. RNAa was demonstrated in human cells using synthetic dsRNAs, termed "small activating RNAs" (saRNAs).
[00125] Small double-stranded RNA (dsRNA), such as small interfering RNA (siRNA) and microRNA (miRNA), have been found to be the trigger of an evolutionary conserved mechanism known as RNA interference (RNAi). RMAi invariably leads to gene silencing. However, in instances described in detail in the examples section which follows, oligonucleotides arc shown to increase the expression and/or function of the Antiviral gene polynucleotides and encoded products thereof. dsRNAs may also act as small activating RNAs (saRNA). Without wishing to be bound by theory, by targeting sequences in gene promoters, saRNAs would induce target gene expression in a phenomenon referred to as dsRNA-induced transcriptional activation (RNAa). [00126] In a further embodiment, the "target segments" identified herein may be employed in a screen for additional compounds that modulate the expression of an Antiviral gene polynucleotide. "Modulators" are those compounds that decrease or increase the expression of a nucleic acid molecule encoding an Antiviral gene and which comprise at least a 5-nuclcotidc portion that is complementary to a target segment. The screening method comprises the steps of contacting a target segment of a nucleic acid molecule encoding sense or natural antisense polynucleotides of an Antiviral gene with one or more candidate modulators, and selecting for one or more candidate modulators which decrease or increase the expression of a nucleic acid molecule encoding an Antiviral gene polynucleotide, e.g. SEQ ID NOS: 10 to 30. Once it is shown that the candidate modulator or modulators arc capable of modulating (e.g. cither decreasing or increasing) the expression of a nucleic acid molecule encoding an Antiviral gene polynucleotide, the modulator may then be employed in further investigative studies of the function of an Antiviral gene polynucleotide, or for use as a research, diagnostic, or therapeutic agent in accordance with the present invention.
[00127] Targeting the natural antisensc sequence modulates the function of the target gene. For example, the Antiviral gene (e.g. accession numbers NM 014314, NM_022168, NM 024013). In a embodiment, the target is an antisensc polynucleotide of the Antiviral gene. In a embodiment, an antisense oligonucleotide targets sense and/or natural antisense sequences of an Antiviral gene polynucleotide (e.g. accession numbers NM 014314, NM_()22168, NM_024013), variants, alleles, isoforms, homologs, mutants, derivatives, fragments and complementary sequences thereto. Preferably the oligonucleotide is an antisense molecule and the targets include coding and noncoding regions of antisense and/or sense Antiviral gene polynucleotides.
[00128] The target segments of the present invention may be also be combined with their respective complementary antisense compounds of the present invention to form stabilized double-stranded (duplexed) oligonucleotides.
[00129] Such double stranded oligonucleotide moieties have been shown in the art to modulate target expression and regulate translation as well as RNA processing via an antisense mechanism. Moreover, the double-stranded moieties may be subject to chemical modifications. For example, such double-stranded moieties have been shown to inhibit the target by the classical hybridization of antisense strand of the duplex to the target, thereby triggering enzymatic degradation of the target.
[00130] In a embodiment, an antisense oligonucleotide targets Antiviral gene polynucleotides (e.g. accession numbers NMJ) 14314, NM_022168, NM_024013), \ariants, alleles, isoforms, homologs, mutants, derivatives, fragments and complementary sequences thereto. Preferably the oligonucleotide is an antisense molecule. [00131 ] In accordance with embodiments of the invention, the target nucleic acid molecule is not limited to Antiviral gene alone but extends to any of the isoforms, receptors, homologs and the like of an Antiviral gene molecule.
[00132] In another embodiment, an oligonucleotide targets a natural antisense sequence of an Antiviral gene polynucleotide, for example, polynucleotides set forth as SEQ ID NO: 4 to 9, and any variants, alleles, homologs, mutants, derivatives, fragments and complementary sequences thereto. Examples of antisense oligonucleotides are set forth as SEQ ID NOS: 10 to 30.
[00133] In one embodiment, the oligonucleotides are complementary to or bind to nucleic acid sequences of an Antiviral gene antisensc, including without limitation noncoding sense and/or antisense sequences associated with an Antiviral gene polynucleotide and modulate expression and/or function of an Antiviral gene molecule. [00134] In another embodiment, the oligonucleotides arc complementary to or bind to nucleic acid sequences of an Antiviral gene natural antiscnsc, set forth as SEQ ID NO: 4 to 9 and modulate expression and/or function of an Antiviral gene molecule.
[00135] In a embodiment, oligonucleotides comprise sequences of at least 5 consecutive nucleotides of SEQ ID NOS: 10 to 30 and modulate expression and/or function of an Antiviral gene molecule.
[00136] The polynucleotide targets comprise Antiviral gene, including family members thereof, variants of an Antiviral gene; mutants of an Antiviral gene, including SNPs; noncoding sequences of an Antiviral gene; alleles of an Antiviral gene; species variants, fragments and the like. Preferably the oligonucleotide is an antiscnse molecule. [00137] In another embodiment, the oligonucleotide targeting Antiviral gene polynucleotides, comprise: antiscnsc RNA, interference RNA (RNAi), short interfering RNA (siRNA); micro interfering RNA (miRNA); a small, temporal RNA (stRNA); or a short, hairpin RNA (shRNA); small RNA-induccd gene activation (RNAa); or, small activating RNA (saRNA).
[00138] In another embodiment, targeting of an Antiviral gene polynucleotide, e.g. SEQ ID NO: 4 to 9 modulate the expression or function of these targets. In one embodiment, expression or function is up-regulated as compared to a control. In another embodiment, expression or function is down-regulated as compared to a control.
[00139] In another embodiment, antisensc compounds comprise sequences set forth as SEQ ID NOS: 10 to 30. These oligonucleotides can comprise one or more modified nucleotides, shorter or longer fragments, modified bonds and the like. [00140] In another embodiment, SEQ ID NOS: 10 to 30 comprise one or more LNA nucleotides. [00141] The modulation of a desired target nucleic acid can be carried out in several ways known in the art. For example, antiscnsc oligonucleotides, siRNA etc. Enzymatic nucleic acid molecules (e.g., ribozymcs) arc nucleic acid molecules capable of catalyzing one or more of a variety of reactions, including the ability to repeatedly cleave other separate nucleic acid molecules in a nucleotide base sequence-specific manner. Such enzymatic nucleic acid molecules can be used, for example, to target virtually any RNA transcript. [00142] Because of their sequence-specificity, trans-cleaving enzymatic nucleic acid molecules show promise as therapeutic agents for human disease. Enzymatic nucleic acid molecules can be designed to cleave specific RNA targets within the background of cellular RNA. Such a cleavage event renders the mRNA non-functional and abrogates protein expression from that RNA. In this manner, synthesis of a protein associated with a disease state can be selectively inhibited. [00143] In general, enzymatic nucleic acids with RNA cleaving activity act by first binding to a target RNA. Such binding occurs through the target binding portion of a enzymatic nucleic acid which is held in close proximity to an enzymatic portion of the molecule that acts to cleave the target RNA. Thus, the enzymatic nucleic acid first recognizes and then binds a target RNA through complementary base pairing, and once bound to the correct site, acts cnzymatically to cut the target RNA. Strategic cleavage of such a target RNA will destroy its ability to direct synthesis of an encoded protein. After an enzymatic nucleic acid has bound and cleaved its RNA target, it is released from that RNA to search for another target and can repeatedly bind and cleave new targets. [00144] Several approaches such as in vitro selection (evolution) strategics have been used to evolve new nucleic acid catalysts capable of catalyzing a variety of reactions, such as cleavage and ligation of phosphodiestcr linkages and amide linkages.
[00145] The development of ribozymcs that are optimal for catalytic activity would contribute significantly to any strategy that employs RNA-clcaving ribozymcs for the purpose of regulating gene expression. The hammerhead ribozymc, for example, functions with a catalytic rate (kcat) of about 1 min-1 in the presence of saturating ( 10 mM) concentrations of Mg2+ cofactor. An artificial "RNA ligase" ribozyme has been shown to catalyze the corresponding self-modification reaction with a rate of about 100 min-l . In addition, it is known that certain modified hammerhead ribozymes that have substrate binding arms made of DNA catalyze RNA cleavage with multiple turn-over rates that approach 100 min- 1. Finally, replacement of a specific residue within the catalytic core of the hammerhead with certain nucleotide analogues gives modified ribozymcs that show as much as a 10-fold improvement in catalytic rate These findings demonstrate that ribozymes can promote chemical transformations with catalytic rates that are significantly greater than those displayed in vitro by most natural self-cleaving ribozymes. It is then possible that the structures of certain selfcleaving ribozymes may be optimized to give maximal catalytic activity, or that entirely new RNA motifs can be made that display significantly faster rates for RNA phosphodiestcr cleavage. [00146] Intcrmolccular cleavage of an RNA substrate by an RNA catalyst that fits the "hammerhead" model was first shown in 1987. The RNA catalyst was recovered and reacted with multiple RNA molecules, demonstrating that it was truly catalytic.
[00147] Catalytic RNAs designed based on the "hammerhead" motif have been used to cleave specific target sequences by making appropriate base changes in the catalytic RNA to maintain necessary base pairing with the target sequences. This has allowed use of the catalytic RNA to cleave specific target sequences and indicates that catalytic RNAs designed according to the "hammerhead" model may possibly cleave specific substrate RNAs in vivo.
[00148] RNA interference (RNAi) has become a powerful tool for modulating gene expression in mammals and mammalian cells. This approach requires the delivery of small interfering RNA (siRNA) either as RNA itself or as DNA, using an expression plasmid or virus and the coding sequence for small hairpin RNAs that are processed to siRNAs. This system enables efficient transport of the prc-siRNAs to the cytoplasm where they arc active and permit the use of regulated and tissue specific promoters for gene expression.
[00149] In one embodiment, an oligonucleotide or antiscnse compound comprises an oligomer or polymer of ribonucleic acid (RNA) and/or deoxyribonucleic acid (DNA), or a mimetic, chimera, analog or homolog thereof. This term includes oligonucleotides composed of naturally occurring nucleotides, sugars and covalent intcrnuclcosidc (backbone) linkages as well as oligonucleotides having non-naturally occurring portions which function similarly. Such modified or substituted oligonucleotides arc often desired over native forms because of desirable properties such as, for example, enhanced cellular uptake, enhanced affinity for a target nucleic acid and increased stability in the presence of nucleases. [00150] According to the present invention, the oligonucleotides or "antisense compounds" include antisense oligonucleotides (e.g. RNA, DNA, mimetic, chimera, analog or homolog thereof), ribozymcs, external guide sequence (EGS) oligonucleotides, siRNA compounds, single- or double-stranded RNA interference (RNAi) compounds such as siRNA compounds, saRNA, aRNA, and other oligomcric compounds which hybridize to at least a portion of the target nucleic acid and modulate its function. As such, they may be DNA, RNA, DNA-like, RNA-like, or mixtures thereof, or may be mimetics of one or more of these. These compounds may be single- stranded, double-stranded, circular or hairpin oligomeric compounds and may contain structural elements such as internal or terminal bulges, mismatches or loops. Antisense compounds arc routinely prepared linearly but can be joined or otherwise prepared to be circular and/or branched. Antisense compounds can include constructs such as, for example, two strands hybridized to form a wholly or partially double-stranded compound or a single strand with sufficient self-complementarity to allow for hybridization and formation of a fully or partially double-stranded compound. The two strands can be linked internally leaving free 3' or 5' termini or can be linked to form a continuous hairpin structure or loop. The hairpin structure may contain an overhang on cither the 5' or 3' terminus producing an extension of single stranded character. The double stranded compounds optionally can include overhangs on the ends. Further modifications can include conjugate groups attached to one of the termini, selected nucleotide positions, sugar positions or to one of the intemuclcosidc linkages. Alternatively, the two strands can be linked via a non-nucleic acid moiety or linker group. When formed from only one strand, dsRNA can take the form of a self-complementary hairpin-type molecule that doubles back on itself to form a duplex. Thus, the dsRNAs can be fully or partially double stranded. Specific modulation of gene expression can be achieved by stable expression of dsRNA haiφins in transgenic cell lines. When formed from two strands, or a single strand that takes the form of a self-complementary hairpin-typc molecule doubled back on itself to form a duplex, the two strands (or duplex- forming regions of a single strand) are complementary RNA strands that base pair in Watson-Crick fashion. [00151 ] Once introduced to a system, the compounds of the invention may elicit the action of one or more enzymes or structural proteins to effect cleavage or other modification of the target nucleic acid or may work via occupancy-based mechanisms. In general, nucleic acids (including oligonucleotides) may be described as "DNA- like" (i.e., generally having one or more 2'-dcoxy sugars and, generally, T rather than U bases) or "RNA-likc" (i.e., generally having one or more 2'- hydroxyl or 2'-modificd sugars and, generally U rather than T bases). Nucleic acid helices can adopt more than one type of structure, most commonly the A- and B-forms. It is believed that, in general, oligonucleotides which have B-form-like structure are "DNA-like" and those which have A-formlikc structure arc "RNA-like." In some (chimeric) embodiments, an antisense compound may contain both A- and B- form regions.
[001 52] The antisense compounds in accordance with this invention can comprise an antisense portion from about 5 to about 80 nucleotides (i.e. from about 5 to about 80 linked nucleosides) in length. This refers to the length of the antisense strand or portion of the antisense compound. In other words, a single-stranded antisense compound of the invention comprises from 5 to about 80 nucleotides, and a double-stranded antisense compound of the invention (such as a dsRNA, for example) comprises a sense and an antisense strand or portion of 5 to about 80 nucleotides in length. One of ordinary skill in the art will appreciate that this comprehends antisense portions of 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 , 32, 33, 34, 35, 36, 37, 38, 39, 40, 41 , 42, 43, 44, 45, 46, 47, 48, 49, 50, 51 , 52, 53. 54, 55, 56, 57, 58. 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68. 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, or 80 nucleotides in length, or any range therewithin. [00153] In one embodiment, the antisense compounds of the invention have antisense portions of 10 to 50 nucleotides in length. One having ordinary skill in the art will appreciate that this embodies oligonucleotides having antisense portions of 10, N , 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 , 32, 33, 34, 35, 36, 37, 38, 39, 40, 41 , 42, 43, 44, 45, 46, 47, 48, 49, or 50 nucleotides in length, or any range therewithin. In some embodiments, the oligonucleotides are 15 nucleotides in length.
[00154] In one embodiment, the antisense or oligonucleotide compounds of the invention have antisense portions of 12 or 13 to 30 nucleotides in length. One having ordinary skill in the art will appreciate that this embodies antisense compounds having antisense portions of 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29 or 30 nucleotides in length, or any range thcrcwithiα
[00155] In another embodiment, the oligomcπc compounds of the present invention also include variants in which a different base is present at one or more of the nucleotide positions in the compound. For example, if the first nucleotide is an adenosine, variants may be produced which contain thymidine, guanosine or cytidine at this position. This may be done at any of the positions of the antisense or dsRNA compounds. These compounds are then tested using the methods described herein to determine their ability to inhibit expression of a target nucleic acid.
[00156] In some embodiments, homology, sequence identity or complementarity, between the antisense compound and target is from about 40% to about 60%. In some embodiments, homology, sequence identity or complementarity, is from about 60% to about 70%. In some embodiments, homology, sequence identity or complementarity, is from about 70% to about 80%. In some embodiments, homology, sequence identity or complementarity, is from about 80% to about 90%. In some embodiments, homology, sequence identity or complementarity, is about 90%, about 92%, about 94%, about 95%, about 96%. about 97%, about 98%, about 99% or about 100%. [00157] In another embodiment, the antisensc oligonucleotides, such as for example, nucleic acid molecules set forth in SEQ ID NOS: 4 to 30 comprise one or more substitutions or modifications. In one embodiment, the nucleotides arc substituted with locked nucleic acids (LNA).
[00158] In another embodiment, the oligonucleotides target one or more regions of the nucleic acid molecules sense and/or antisense of coding and/or non-coding sequences associated with Antiviral gene and the sequences set forth as SEQ ID NOS: I to 9. The oligonucleotides are also targeted to overlapping regions of SEQ ID NOS: 1 to 9.
[001 59] Certain oligonucleotides of this invention are chimeric oligonucleotides. "Chimeric oligonucleotides" or "chimeras," in the context of this invention, are oligonucleotides which contain two or more chemically distinct regions, each made up of at least one nucleotide. These oligonucleotides typically contain at least one region of modified nucleotides that confers one or more beneficial properties (such as, for example, increased nuclease resistance, increased uptake into cells, increased binding affinity for the target) and a region that is a substrate for enzymes capable of cleaving RNA:DNA or RNA:RNA hybrids. By way of example, RNasc H is a cellular
, endonuclease which cleaves the RNA strand of an RNA:DNA duplex. Activation of RNase H, therefore, results in cleavage of the RNA target, thereby greatly enhancing the efficiency of antisense modulation of gene expression. Consequently, comparable results can often be obtained with shorter oligonucleotides when chimeric oligonucleotides are used, compared to phosphorothioate deoxyoligoniiclcotides hybridizing to the same target region. Cleavage of the RNA target can be routinely detected by gel electrophoresis and, if necessary, associated nucleic acid hybridization techniques known in the art. In one embodiment, a chimeric oligonucleotide comprises at least one region modified to increase target binding affinity, and, usually, a region that acts as a substrate for RNAsc H. Affinity of an oligonucleotide for its target (in this case, a nucleic acid encoding ras) is routinely determined by measuring the Tm of an oligonuclcotidc/targct pair, which is the temperature at which the oligonucleotide and target dissociate; dissociation is detected spcctrophotometrically. The higher the Tm, the greater is the affinity of the oligonucleotide for the target. [00160] Chimeric antisense compounds of the invention may be formed as composite structures of two or more oligonucleotides, modified oligonucleotides, oligonuclcosides and/or oligonucleotides mimctics as described above. Such; compounds have also been referred to in the art as hybrids or gapmcrs. Representative United States patents that teach the preparation of such hybrid structures comprise, but are not limited to, US patent nos. 5,013,830; 5, 149,797; 5, 220,007; 5,256,775; 5,366,878; 5,403,71 1 ; 5.491 , 133; 5,565,350; 5,623,065; 5,652,355; 5,652,356; and 5,700,922, each of which is herein incorporated by reference.
[00161 ] In another embodiment, the region of the oligonucleotide which is modified comprises at least one nucleotide modified at the 2' position of the sugar, most preferably a 2'-Oalkyl, 2'-0-alkyl-0-alkyl or 2'-fluoro- modificd nucleotide. In other embodiments, RNA modifications include 2'-fluoro, 2'-amino and 2' O-mcthyl modifications on the ribosc of pyrimidines, abasic residues or an inverted base at the 3' end of the RNA. Such modifications arc routinely incorporated into oligonucleotides and these oligonucleotides have been shown to have a higher Tm (i.e., higher target binding affinity) than; 2'-dcoxyoligonucleotides against a given target. The effect of such increased affinity is to greatly enhance RNAi oligonucleotide inhibition of gene expression. RNAsc H is a cellular cndonuclcasc that cleaves the RNA strand of RNAiDNA duplexes; activation of this enzyme therefore results in cleavage of the RNA target, and thus can greatly enhance the efficiency of RNAi inhibition. Cleavage of the RNA target can be routinely demonstrated by gel electrophoresis. In another embodiment, the chimeric oligonucleotide is also modified to enhance nuclease resistance. Cells contain a variety of cxo- and cndo-nuclcascs which can degrade nucleic acids. A number of nucleotide and nucleoside modifications have been shown to make the oligonucleotide into which they arc incorporated more resistant to nuclease digestion than the native oligodcoxynucleotidc. Nuclease resistance is routinely measured by incubating oligonucleotides with cellular extracts or isolated nuclease solutions and measuring the extent of intact oligonucleotide remaining over time, usually by gel electrophoresis. Oligonucleotides which have been modified to enhance their nuclease resistance survive intact for a longer time than unmodified oligonucleotides. A variety of oligonucleotide modifications have been demonstrated to enhance or confer nuclease resistance. Oligonucleotides which contain at least one phosphorothioate modification are presently more preferred. In some cases, oligonucleotide modifications which enhance target binding affinity are also, independently, able to enhance nuclease resistance. Some desirable modifications can be found in Dc Mesmacker el al. (1995) Ace. Chem. Res., 28:366-374.
[00162] Specific examples of some oligonucleotides envisioned for this invention include those comprising modified backbones, for example, phosphorothioatcs, phosphotricstcrs, methyl phosphonatcs, short chain alkyl or cycloalkyl intcrsugar linkages or short chain hctcroatomic or heterocyclic intersugar linkages. Most arc oligonucleotides with phosphorothioate backbones and those with heteroatom backbones, particularly CH2 -NH-- O-CH2, CH,-N(CH3)~O-CH2 Iknown as a methylenc(methylimino) or MMI backbone], CH2 -O--N (CH3)~ CH2, CH2 -N (CH3)-N (CH3>-CH2 and O~N (CH3)-CH2 -CH2 backbones, wherein the native phosphodicstcr backbone is represented as O--P--O-CH,). The amide backbones disclosed by Dc Mcsmaekcr el al. (1995) Ace. Chem. Res. 28:366-374 arc also preferred. Also arc oligonucleotides having morpholino backbone structures (Summerton and Wcller, U.S. Pat. No. 5,034,506). In other embodiments, such as the peptide nucleic acid (PNA) backbone, the phosphodiester backbone of the oligonucleotide is replaced with a polyamidc backbone, the nucleotides being bound directly or indirectly to the aza nitrogen atoms of the polyamidc backbone. Oligonucleotides may also comprise one or more substituted sugar moieties, oligonucleotides comprise one of the following at the T position: OH1 SH, SCH3, F, OCN, 0CH3 OCH3, OCH3 O(CH2)n CH3, O(CH2)n NH2 or O(CH2)n CH3 where n is from 1 to about 10; C l to ClO lower alkyl, alkoxyalkoxy, substituted lower alkyl, alkaryl or aralkyl; Cl; Br; CN; CF3 ; OCF3; O-, S-, or N-alkyl; O-, S-, or N-alkenyl; SOCH3; SO2 CH3; ONO2; NO2; N3; NH2; heterocycloalkyl; heterocycloalkaryl; aminoalkylamino; polyalkylamino; substituted silyl; an RNA cleaving group; a reporter group; an intercalator; a group for improving the pharmacokinetic properties of an oligonucleotide; or a group for improving the pharmacodynamic properties of an oligonucleotide and other substituents having similar properties. A modification includes 2'-methoxyethoxy |2'-O-CH2 CH2 OCH3, also known as 2'-O-(2-mcthoxyethyl)]. Other modifications include 2'-mcthoxy (2'-O-CH3), 2'- propoxy (2'-OCH2 CH2CH3) and 2'-fluoro (2'-F). Similar modifications may also be made at other positions on the oligonucleotide, particularly the 3' position of the sugar on the 3' terminal nucleotide and the 5' position of 5' terminal nucleotide. Oligonucleotides may also have sugar mimctics such as cyclobutyls in place of the pcntofuranosyl group. [00163] Oligonucleotides may also include, additionally or alternatively, nucleobase (often referred to in the art simply as "base") modifications or substitutions. As used herein, "unmodified" or "natural" nucleotides include adenine (A), guanine (G), thymine (T), cytosine (C) and uracil (U). Modified nucleotides include nucleotides found only infrequently or transiently in natural nucleic acids, e.g., hypoxanthine, 6-methyladcnine, 5-Me pyrimidines, particularly 5-methylcytosine (also referred to as 5-methyl-2' deoxycytosine and often referred to in the art as 5- Mc-C), 5- hydroxymcthylcytosinc (HMC), glycosyl HMC and gcntobiosyl HMC, as well as synthetic nucleotides, e.g., 2-aminoadcninc, 2-(methylamino)adcninc, 2-(imidazolylalkyl)adcninc, 2- (aminoalklyamino)adcninc or other heterosubstituted alkyladenines, 2-thiouracil, 2-thiothymine, 5- bromouracil, 5-hydroxymethyluracil, 8-azaguanine, 7-dcazaguaninc, N6 (6-aminohcxyl)adeninc and 2,6-diaminopurine.. A "universal" base known in the art, e.g., inosinc, may be included. 5-Mc-C substitutions have been shown to increase nucleic acid duplex stability by 0.6- 1.20C. (Sanghvi, Y. S., in Crookc, S. T. and Lcbleu, B., cds., Antiscnsc Research and Applications, CRC Press, Boca Raton, 1993, pp. 276-278) and are presently base substitutions. [00164] Another modification of the oligonucleotides of the invention involves chemically linking to the oligonucleotide one or more moieties or conjugates which enhance the activity or cellular uptake of the oligonucleotide. Such moieties include but arc not limited to lipid moieties such as a cholesterol moiety, a cholcstcryl moiety, a thiocther, e.g., hcxyl-S-tritylthioL, a thiocholesterol, an aliphatic chain, e.g., dodecandiol or undccyl residues, a phospholipid, e.g., di-hcxadccyl-rac-glyccrol or tricthylammonium 1 ,2-di-O-hexadccyl-rac- glyccro- 3-H-phosphonate, a polyaminc or a polyethylene glycol chain, or adamantanc acetic acid . Oligonucleotides comprising lipophilic moieties, and methods for preparing such oligonucleotides are known in the art, for example, U.S. PaL Nos. 5, 138,045, 5,218, 105 and 5,459,255.
[00165] It is not necessary for all positions in a given oligonucleotide to be uniformly modified, and in fact more than one of the aforementioned modifications may be incorporated in a single oligonucleotide or even at within a single nucleoside within an oligonucleotide. The present invention also includes oligonucleotides which arc chimeric oligonucleotides as hereinbefore defined.
[00166] In another embodiment, the nucleic acid molecule of the present invention is conjugated with another moiety including but not limited to abasic nucleotides, polycthcr, polyamine, polyamidcs, peptides, carbohydrates, lipid, or polyhydrocarbon compounds. Those skilled in the art will recognize that these molecules can be linked to one or more of any nucleotides comprising the nuclesc acid molecule at several positions on the sugar, base or phosphate group.
[00167] The oligonucleotides used in accordance with this invention may be conveniently and routinely made through the well-known technique of solid phase synthesis. Equipment for such synthesis is sold by several vendors including Applied Biosystems. Any other means for such synthesis may also be employed; the actual synthesis of the oligonucleotides is well within the talents of one of ordinary skill in the art. It is also well known to use similar techniques to prepare other oligonucleotides such as the phosphorothioatcs and alkylated derivatives. It is also well known to use similar techniques and commercially available modified amidites and controlled-porc glass (CPG) products such as biotin, fluorescein, acridine or psoralen-modified amidites and/or CPG (available from Glen Research, Sterling VA) to synthesize fluorescently labeled, biotinylated or other modified oligonucleotides such as cholesterol-modified oligonucleotides.
[00168] In accordance with the invention, use of modifications such as the use of LNA monomers to enhance the potency, specificity and duration of action and broaden the routes of administration of oligonucleotides comprised of current chemistries such as MOE, ANA, FANA, PS etc. This can be achieved by substituting some of the monomers in the current oligonucleotides by LNA monomers. The LNA modified oligonucleotide may have a size similar to the parent compound or may be larger or preferably smaller. It is that such LNA-modified oligonucleotides contain less than about 70%, more preferably less than about 60%, most preferably less than about 50% LNA monomers and that their sizes arc between about 5 and 25 nucleotides, more preferably between about 12 and 20 nucleotides. [00169] Modified oligonucleotide backbones comprise, but arc not limited to, phosphorothioatcs, chiral phosphorothioatcs, phosphorodithioatcs, phosphotricsters, aminoalkylphosphotricstcrs, methyl and other alkyl phosphonatcs comprising 3'alkylcnc phosphonates and chiral phosphonatcs, phosphinates, phosphoramidatcs comprising 3'-amino phosphoramidate and aminoalkylphosphoramidatcs, thionophosphoramidatcs, thionoalkylphosphonates, thionoalkylphosphotriesters, and boranophosphatcs having normal 3'-5* linkages, 2'-5' linked analogs of these, and those having inverted polarity wherein the adjacent pairs of nucleoside units arc linked 3'-5' to 5'-3' or 2'-5' to 5 -2'. Various salts, mixed salts and free acid forms arc also included. [00170] Representative United States patents that teach the preparation of the above phosphorus containing linkages comprise, but arc not limited to, US patent nos. 3,687.808; 4,469,863; 4,476,301 ; 5,023,243; 5, 177, 196; 5, 188,897; 5,264,423; 5,276,019; 5,278,302; 5,286,7P; 5,321 , 131 ; 5,399,676; 5,405,939; 5,453,496; 5,455, 233; 5,466,677; 5,476,925; 5,519, 126; 5,536,821 ; 5,541 ,306; 5,550.1 1 1 ; 5,563, 253; 5,571 ,799; 5,587,361 ; and 5,625,050, each of which is herein incorporated by reference.
[00171] Modified oligonucleotide backbones that do not include a phosphorus atom therein have backbones that arc formed by short chain alkyl or cycloalkyl intemucleoside linkages, mixed hcteroatom and alkyl or cycloalkyl intemucleoside linkages, or one or more short chain heteroatomic or heterocyclic intemucleoside linkages. These comprise those having morpholino linkages (formed in part from the sugar portion of a nucleoside); siloxanc backbones; sulfide, sulfoxide and sulfone backbones; formacctyl and thioformacetyl backbones; methylene formacetyl and thioformacetyl backbones; alkcnc containing backbones; sulfamatc backbones; mcthylcneimino and mcthylcnehydrazino backbones; sulfonate and sulfonamide backbones; amide backbones; and others having mixed N1 0, S and CH2 component parts.
[00172] Representative United States patents that teach the preparation of the above oligonuclcosidcs comprise, but arc not limited to, US patent nos. 5,034,506; 5,166,315; 5,185,444; 5,214,134; 5,216,141 ; 5,235,033; 5,264, 562; 5, 264,564; 5,405,938; 5,434,257; 5,466,677; 5,470,967; 5,489,677; 5,541 ,307; 5,561 ,225; 5,596, 086; 5,602,240; 5,610,289; 5,602,240; 5,608,046; 5,610,289; 5,618,704; 5,623, 070; 5,663,312; 5,633,360; 5,677,437; and 5,677,439, each of which is herein incorporated by reference.
[001 73] In other oligonucleotide mimetics, both the sugar and the intemucleoside linkage, i.e., the backbone, of the nucleotide units arc replaced with novel groups. The base units arc maintained for hybridization with an appropriate nucleic acid target compound. One such oligomcric compound, an oligonucleotide mimetic that has been shown to have excellent hybridization properties, is referred to as a peptide nucleic acid (PNA) In PNA compounds, the sugar-backbone of an oligonucleotide is replaced with an amide containing backbone, in particular an aminoethylglycine backbone. The nucleobases are retained and are bound directly or indirectly to aza nitrogen atoms of the amide portion of the backbone. Representative United States patents that teach the preparation of PNA compounds comprise, but arc not limited to, US patent nos. 5,539,082; 5,714,331 ; and 5,719,262, each of which is herein incorporated by reference . Further teaching of PNA compounds can be found in Nielsen, el al. (1991) Science 254, 1497- 1500.
[00174] In another embodiment of the invention the oligonucleotides with phosphorothioatc backbones and oligonuclcosidcs with hcteroatom backbones, and in particular- CH2-NH-O-CH2-,-CH2-N (CH3)-O-CH2-known as a methylene (mcthylimino) or MMI backbone,- CH2-O-N (CH3)-CH2-,-CH2N(CH3)-N(CH3) CH2-and-O- N(CH3)-CH2-CH2- wherein the native phosphodicstcr backbone is represented as-O-P-O-CH2- of the above referenced US patent no. 5,489,677, and the amide backbones of the above referenced US patent no. 5,602,240. Also arc oligonucleotides having morpholino backbone structures of the above-referenced US patent no. 5,034,506.
[00175] Modified oligonucleotides may also contain one or more substituted sugar moieties, oligonucleotides comprise one of the following at the 2' position: OH; F; O-, S-, or N-alkyl; O-, S-, or N-alkcnyl; O-, S-or N- alkynyl; or O alkyl-O-alkyl, wherein the alkyl, alkcnyl and alkynyl may be substituted or unsubstitutcd C to CO alkyl or C2 to CO alkcnyl and alkynyl. Particularly arc O (CH2)n 0mCH3, O(CH2)n,OCH3, O(CH2)nNH2. O(CH2)nCH3, O(CH2)nONH2, and O(CH2nON(CH2)nCH3)2 where n and m can be from 1 to about 10. Other oligonucleotides comprise one of the following at the 2' position: C to CO, (lower alkyl, substituted lower alkyl, alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH3, OCN, Cl, Br, CN, CF3, OCF3, SOCH3, SO2CH3, ONO2, NO2, N3, NH2, hetcrocycloalkyl, hcterocycloalkaryl, aminoalkylamino, polyalkylamino, substituted silyl, an RNA cleaving group, a reporter group, an intercalator, a group for improving the pharmacokinetic properties of an oligonucleotide, or a group for improving the pharmacodynamic properties of an oligonucleotide, and other substituents having similar properties. A modification comprises 2'-mcthoxycthoxy (2 -O-CH2CH2OCH3, also known as 2'-O-(2- mcthoxyethyl) or 2'-MOE) i.e., an alkoxyalkoxy group. A further modification comprises 2'- dimcthylaminooxyethoxy, i.e. , a O(CH2)2ON(CH3)2 group, also known as 2'-DMAOE, as described in examples herein below, and 2'- dimcthylaminocthoxycthoxy (also known in the art as 2'-O-dimcthylaminoethoxycthyl or 2'- DMAEOE). i.e., 2'-O-CH2-O-CH2-N (CH2)2. [00176] Other modifications comprise 2'-methoxy (2'-0 CH3), 2'-aminopropoxy (2'-0 CH2CH2CH2NH2) and 2'-fluoro (2'-F). Similar modifications may also be made at other positions on the oligonucleotide, particularly the 3' position of the sugar on the 3' terminal nucleotide or in 2'-5' linked oligonucleotides and the 5' position of 5' terminal nucleotide. Oligonucleotides may also have sugar mimctics such as cyclobutyl moieties in place of the pcntofuranosyl sugar. Representative United States patents that teach the preparation of such modified sugar structures comprise, but are not limited to, US patent nos. 4,981 ,957; 5, 1 18,8(M); 5.319,080; 5,359,044; 5,393,878; 5,446,137; 5,466,786; 5,514, 785; 5,519,134; 5,567,811 ; 5,576,427; 5,591 ,722; 5,597,909; 5,610,300; 5,627,053; 5,639,873; 5,646, 265; 5,658,873; 5,670,633; and 5,700,920, each of which is herein incorporated by reference. [00177] Oligonucleotides may also comprise nucleobase (often referred to in the art simply as "base") modifications or substitutions. As used herein, "unmodified" or "natural" nucleotides comprise the purine bases adenine (A) and guanine (G), and the pyrimidinc bases thymine (T), cytosinc (C) and uracil (U)- Modified nucleotides comprise other synthetic and natural nucleotides such as 5-mcthylcytosinc (5-mc-C), 5-hydroxymcthyl cytosinc, xanthine, hypoxanthinc, 2- aminoadeninc, 6-mcthyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosinc, 5- halouracil and cytosinc, 5-propynyl uracil and cytosinc, 6-azo uracil, cytosinc and thymine, 5-uracil (pscudo- uracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substitutcd adenines and guanines, 5-halo particularly 5-bromo, 5-trifluoromethyl and other 5-substituted uracils and cytosincs, 7- mcthylquanine and 7-methyladenine, 8-azaguanine and 8-azaadenine, 7-deazaguaninc and 7-dcazaadeninc and 3- deazaguaninc and 3-dcazaadcninc.
[001 78] Further, nucleotides comprise those disclosed in United States Patent No. 3,687,808, those disclosed in The Concise Encyclopedia of Polymer Science And Engineering', pages 858-859, Kroschwitz, J.I., cd. John Wiley & Sons, 1990, those disclosed by Englisch el a!., 'Angcwandlc Chcmic, International Edition', 1991 , 30, page 613, and those disclosed by Sanghvi, Y.S., Chapter 15, 'Antiscnsc Research and Applications', pages 289-302, Crookc, ST. and Lcblcu, B. ca., CRC Press, 1993. Certain of these nucleotides arc particularly useful for increasing the binding affinity of the oligomeric compounds of the invention. These comprise 5-substituted pyrimidines, 6- azapyrimidincs and N-2, N-6 and 0-6 substituted purines, comprising 2-aminopropyladenine, 5- propynyluracil and 5-propynylcytosinc. 5-methylcytosine substitutions have been shown to increase nucleic acid duplex stability by 0.6-1.20C (Sanghvi, Y.S., Crookc, S.T. and Lebleu, B., eds, 'Antiscnsc Research and Applications', CRC Press, Boca Raton, 1993, pp. 276-278) and are presently base substitutions, even more particularly when combined with 2'-Omethoxycthyl sugar modifications. [001 79] Representative United States patents that teach the preparation of the above noted modified nucleotides as well as other modified nucleotides comprise, but arc not limited to, US patent nos. 3,687,808, as well as 4,845,205; 5,130,302; 5,134,066; 5,175, 273; 5, 367,066; 5,432,272; 5,457, 187; 5,459,255; 5,484,908; 5,502, 177; 5.525,71 1 ; 5,552,540; 5,587,469; 5,596,091 ; 5,614.617; 5,750,692, and 5,681 ,941 , each of which is herein incorporated by reference. [001 80] Another modification of the oligonucleotides of the invention involves chemically linking to the oligonucleotide one or more moieties or conjugates, which enhance the activity, cellular distribution, or cellular uptake of the oligonucleotide.
[001 81 ] Such moieties comprise but arc not limited to, lipid moieties such as a cholesterol moiety, cholic acid, a thioether, e.g., hexyl-S-tritylthiol, a thiocholesterol , an aliphatic chain, e.g., dodccandiol or undecyl residues , a phospholipid, e.g., di-hexadecyl-rac-glycerol or triethylammonium l ,2-di-O-hexadecyl-rac-glyccro-3-H- phosphonate , a polyamine or a polyethylene glycol chain , or adamantane acetic acid , a palmityl moiety , or an octadecylaminc or hexylamino-carbonyl-t oxycholesterol moiety .
[00182] Representative United States patents that teach the preparation of such oligonucleotides conjugates comprise, but arc not limited to, US patent nos. 4,828,979; 4,948,882; 5.218.105; 5,525,465; 5.541.313; 5.545.730; 5,552, 538; 5,578,717, 5,580,731 ; 5,580,731 ; 5,591 ,584; 5,109,124; 5, 1 18,802; 5,138,045; 5,414,077; 5,486, 603; 5,512,439; 5,578,718; 5,608,046; 4,587,044; 4,605,735; 4,667.025; 4,762, 779; 4,789,737; 4,824,941 ; 4,835,263; 4,876,335; 4.904,582; 4,958,013; 5,082, 830; 5, 112,963; 5,214,136; 5,082,830; 5, 1 12,963; 5,214, 136; 5, 245,022, 5,254,469; 5,258,506; 5,262,536; 5,272,250; 5,292,873; 5,317,098; 5,371,241, 5,391, 723; 5,416,203, 5,451,463; 5,510,475; 5,512,667; 5,514,785; 5, 565,552; 5,567,810; 5,574, 142; 5,585,481 ; 5,587,371 ; 5,595,726; 5,597,696; 5,599,923; 5,599, 928 and 5,688,941 , each of which is herein incorporated by reference.
[00183] Drug discovery: The compounds of the present invention can also be applied in the areas of drug discovery and target validation. The present invention comprehends the use of the compounds and target segments identified herein in drug discovery efforts to elucidate relationships that exist between an Antiviral gene polynucleotide and a disease state, phenotypc, or condition. These methods include detecting or modulating an Antiviral gene polynucleotide comprising contacting a sample, tissue, cell, or organism with the compounds of the present invention, measuring the nucleic acid or protein level of an Antiviral gene polynucleotide and/or a related phcnotypic or chemical cndpoint at some time after treatment, and optionally comparing the measured value to a non-treated sample or sample treated with a further compound of the invention. These methods can also be performed in parallel or in combination with other experiments to determine the function of unknown genes for the process of target validation or to determine the validity of a particular gene product as a target for treatment or prevention of a particular disease, condition, or phenotype. Assessing Up-regιιlation or Inhibition of Gene Expression:
[00184] Transfer of an exogenous nucleic acid into a host cell or organism can be assessed by directly detecting the presence of the nucleic acid in the cell or organism. Such detection can be achieved by several methods well known in the art. For example, the presence of the exogenous nucleic acid can be detected by Southern blot or by a polymerase chain reaction (PCR) technique using primers that specifically amplify nucleotide sequences associated with the nucleic acid. Expression of the exogenous nucleic acids can also be measured using conventional methods including gene expression analysis. For instance, mRNA produced from an exogenous nucleic acid can be detected and quantified using a Northern blot and reverse transcription PCR (RT-PCR).
[00185] Expression of RNA from the exogenous nucleic acid can also be detected by measuring an enzymatic activity or a reporter protein activity. For example, antiscnsc modulatory activity can be measured indirectly as a decrease or increase in target nucleic acid expression as an indication that the exogenous nucleic acid is producing the effector RNA. Based on sequence conservation, primers can be designed and used to amplify coding regions of the target genes. Initially, the most highly expressed coding region from each gene can be used to build a model control gene, although any coding or non coding region can be used. Each control gene is assembled by inserting each coding region between a reporter coding region and its poly(A) signal. These plasmids would produce an mRNA with a reporter gene in the upstream portion of the gene and a potential RNAi target in the 3' non-coding region. The effectiveness of individual antisensc oligonucleotides would be assayed by modulation of the reporter gene. Reporter genes useful in the methods of the present invention include acctohydroxyacid synthase (AHAS)1 alkaline phosphatase (AP), beta galactosidase (LacZ), beta glucoronidasc (GUS), chloramphenicol acctyltransferase (CAT), green fluorescent protein (GFP), red fluorescent protein (RFP), yellow fluorescent protein (YFP), cyan fluorescent protein (CFP), horseradish peroxidase (HRP), lucifcrasc (Luc), nopalinc synthase (NOS), octopinc synthase (OCS), and derivatives thereof. Multiple selectable markers arc available that confer resistance to ampicillin, bleomycin, chloramphenicol, gcntamycin, hygromycin, kanamycin, lincomycin, methotrexate, phosphinothricin, puromycin, and tetracycline. Methods to determine modulation of a reporter gene are well known in the art, and include, but arc not limited to, fluoromctric methods (e.g. fluorescence spectroscopy, Fluorescence Activated Cell Sorting (FACS), fluorescence microscopy), antibiotic resistance determination. [00186] RlG l , MDA5, IFNAl proteins and mRNA expression can be assayed using methods known to those of skill in the art and described elsewhere herein. For example, immunoassays such as the ELISA can be used to measure protein levels. Antiviral gene antibodies for ELISAs arc available commercially, e.g., from R&D Systems (Minneapolis, MN), Abeam, Cambridge, MA.
[00187] In embodiments, RlGl, MDA5, IFNAl expression (e.g., mRNA or protein) in a sample (e.g., cells or tissues in vivo or in vitro) treated using an antisense oligonucleotide of the invention is evaluated by comparison with Antiviral gene expression in a control sample. For example, expression of the protein or nucleic acid can be compared using methods known to those of skill in the art with that in a mock-treated or untreated sample. Alternatively, comparison with a sample treated with a control antiscnse oligonucleotide (e.g., one having an altered or different sequence) can be made depending on the information desired. In another embodiment, a difference in the expression of the Antiviral gene protein or nucleic acid in a treated vs. an untreated sample can be compared with the difference in expression of a different nucleic acid (including any standard deemed appropriate by the researcher, e.g., a housekeeping gene) in a treated sample vs. an untreated sample.
[00188] Observed differences can be expressed as desired, e.g., in the form of a ratio or fraction, for use in a comparison with control. In embodiments, the level of an Antiviral gene mRNA or protein, in a sample treated with an antisense oligonucleotide of the present invention, is increased or decreased by about 1.25-fold to about 10- fold or more relative to an untreated sample or a sample treated with a control nucleic acid. In embodiments, the level of an Antiviral gene mRNA or protein is increased or decreased by at least about 1.25-fold, at least about 1.3- fold, at least about 1.4-fold, at least about 1.5-fold, at least about 1.6-fold, at least about 1.7-fold, at least about 1.8- fold, at least about 2-fold, at least about 2.5-fold, at least about 3-fold, at least about 3.5-fold, at least about 4-fold, at least about 4.5-fold, at least about 5-fold, at least about 5.5-fold, at least about 6-fold, at least about 6.5-fold, at least about 7-fold, at least about 7.5-fold, at least about 8-fold, at least about 8.5-fold, at least about 9-fold, at least about 9.5-fold, or at least about 10-fold or more. Kits, Research Reagents, Diagnostics, and Therapeutics [00189] The compounds of the present invention can be utilized for diagnostics, therapeutics, and prophylaxis, and as research reagents and components of kits. Furthermore, antisense oligonucleotides, which arc able to inhibit gene expression with exquisite specificity, are often used by those of ordinary skill to elucidate the function of particular genes or to distinguish between functions of various members of a biological pathway. [00190] For use in kits and diagnostics and in various biological systems, the compounds of the present invention, either alone or in combination with other compounds or therapeutics, are useful as tools in differential and/or combinatorial analyses to elucidate expression patterns of a portion or the entire complement of genes expressed within cells and tissues.
[00191 ] As used herein the term "biological system" or "system" is defined as any organism, cell, cell culture or tissue that expresses, or is made competent to express products of the Antiviral genes. These include, but arc not limited to, humans, transgenic animals, cells, cell cultures, tissues, xenografts, transplants and combinations thereof.
[00192] As one non limiting example, expression patterns within cells or tissues treated with one or more antisense compounds are compared to control cells or tissues not treated with antisense compounds and the patterns produced are analyzed for differential levels of gene expression as they pertain, for example, to disease association, signaling pathway, cellular localization, expression level, size, structure or function of the genes examined. These analyses can be performed on stimulated or unstimulated cells and in the presence or absence of other compounds that affect expression patterns.
[00193] Examples of methods of gene expression analysis known in the art include DNA arrays or microarrays (Brazma and ViIo, (2000) I EBS Lett., 480, 17-24; Cclis, el ai, (2000) FEBS Lett., 480, 2-16), SAGE (serial analysis of gene expression) (Madden, el ai, (2(XK)) Drug Discov. Today, 5, 415- 425), READS (restriction enzyme amplification of digested cDNAs) (Prashar and Wcissman, (1999) Methods Enzymoi, 303, 258-72), TOGA (total gene expression analysis) (Sutcliffc, el ai, (2000) Proc. Nail. Acad Sd. U.S.A., 97, 1976-81 ), protein arrays and proteomics (Celis, el ai, (2000) FEBS Lett., 480, 2-16; Jungblut. ct al., Electrophoresis, 1999, 20, 2100- 10), expressed sequence tag (EST) sequencing (Celis, et al., FEBS Lett., 2000, 480, 2-16; Larsson, et al., J. Biotechnol., 2000, 80, 143-57), sυbtractive RNA fingerprinting (SuRF) (Fuchs. et ai, (2000) Anal. Biochcm. 286, 91 -98; Larson, et ai, (2000) Cytometry 41 , 203-208), subtractive cloning, differential display (DD) (Jurecic and Bclmont. (2000) Cun: Opin. Microbiol. 3, 316-21), comparative genomic hybridization (Carulli, el ai, (1998) J. Cell Biυchem. Suppi, 31 , 286-96), FISH (fluorescent in situ hybridization) techniques (Going and Gustcrson, ( 1999) Eur. J. Cancer. 35, 1895-904) and mass spectrometry methods (To, Comb. (2000) Chem. High Throughput Screen, 3, 235-41).
[00194] The compounds of the invention are useful for research and diagnostics, because these compounds hybridize to nucleic acids encoding an Antiviral gene. For example, oligonucleotides that hybridize with such efficiency and under such conditions as disclosed herein as to be effective Antiviral gene modulators arc effective primers or probes under conditions favoring gene amplification or detection, respectively. These primers and probes arc useful in methods requiring the specific detection of nucleic acid molecules encoding an Antiviral gene and in the amplification of said nucleic acid molecules for detection or for use in further studies of an Antiviral gene. Hybridization of the antisensc oligonucleotides, particularly the primers and probes, of the invention with a nucleic acid encoding an Antiviral gene can be detected by means known in the art. Such means may include conjugation of an enzyme to the oligonucleotide, radiolabcling of the oligonucleotide, or any other suitable detection means. Kits using such detection means for detecting the level of an Antiviral gene in a sample may also be prepared.
[00195] The specificity and sensitivity of antisensc arc also harnessed by those of skill in the art for therapeutic uses. Antisensc compounds have been employed as therapeutic moieties in the treatment of disease states in animals, including humans. Antisensc oligonucleotide drugs have been safely and effectively administered to humans and numerous clinical trials arc presently underway. It is thus established that antisensc compounds can be useful therapeutic modalities that can be configured to be useful in treatment regimes for the treatment of cells, tissues and animals, especially humans.
[00196] For therapeutics, an animal, preferably a human, suspected of having a disease or disorder which can be treated by modulating the expression of an Antiviral gene polynucleotide is treated by administering antiscnse compounds in accordance with this invention. For example, in one non-limiting embodiment, the methods comprise the step of administering to the animal in need of treatment, a therapeutically effective amount of an Antiviral gene modulator. The Antiviral gene modulators of the present invention effectively modulate the activity of an Antiviral gene or modulate the expression of an Antiviral gene protein. In one embodiment, the activity or expression of an Antiviral gene in an animal is inhibited by about 10% as compared to a control. Preferably, the activity or expression of an Antiviral gene in an animal is inhibited by about 30%. More preferably, the activity or expression of an Antiviral gene in an animal is inhibited by 50% or more. Thus, the oligomcric compounds modulate expression of an Antiviral gene mRNA by at least 10%, by at least 50%, by at least 25%, by at least 30%, by at least 40%, by at least 50%, by at least 60%, by at least 70%, by at least 75%, by at least 80%, by at least 85%, by at least 90%, by at least 95%, by at least 98%, by at ieast 99%, or by 100% as compared to a control.
[00197] In one embodiment, the activity or expression of an Antiviral gene and/or in an animal is increased by about 10% as compared to a control. Preferably, the activity or expression of an Antiviral gene in an animal is increased by about 30%. More preferably, the activity or expression of an Antiviral gene in an animal is increased by 50% or more. Thus, the oligomeric compounds modulate expression of an Antiviral gene mRNA by at least 10%, by at least 50%, by at least 25%, by at least 30%, by at least 40%, by at least 50%, by at least 60%, by at least 70%, by at least 75%, by at least 80%, by at least 85%, by at least 90%, by at least 95%, by at least 98%, by at least 99%, or by 100% as compared to a control.
[00198] For example, the reduction of the expression of an Antiviral gene may be measured in scrum, blood, adipose tissue, liver or any other body fluid, tissue or organ of the animal. Preferably, the cells contained within said fluids, tissues or organs being analyzed contain a nucleic acid molecule encoding Antiviral gene peptides and/or the Antiviral gene protein itself.
[00199] The compounds of the invention can be utilized in pharmaceutical compositions by adding an effective amount of a compound to a suitable pharmaceutically acceptable diluent or carrier. Use of the compounds and methods of the invention may also be useful prophylactically. [00200] Conjugates: Another modification of the oligonucleotides of the invention involves chemically linking to the oligonucleotide one or more moieties or conjugates that enhance the activity, cellular distribution or cellular uptake of the oligonucleotide. These moieties or conjugates can include conjugate groups covalcntly bound to functional groups such as primary or secondary hydroxyl groups. Conjugate groups of the invention include intcrcalators, reporter molecules, polyamines, polyamidcs, polyethylene glycols, polycthcrs, groups that enhance the pharmacodynamic properties of oligomers, and groups that enhance the pharmacokinetic properties of oligomers. Typicalconjugatc groups include cholcstcrols, lipids, phospholipids, biotin, phcnazinc, folate, phcnanthridinc, anthraquinonc, acridine, fluoresceins, rhodamincs, coumarins, and dyes. Groups that enhance the pharmacodynamic properties, in the context of this invention, include groups that improve uptake, enhance resistance to degradation, and/or strengthen sequence-specific hybridization with the target nucleic acid. Groups that enhance the pharmacokinetic properties, in the context of this invention, include groups that improve uptake, distribution, metabolism or excretion of the compounds of the present invention. Representative conjugate groups arc disclosed in International Patent Application No. PCT/US92/09196, filed Oct. 23, 1992, and U.S. Pat. No. 6,287,860, which arc incorporated herein by reference. Conjugate moieties include, but arc not limited to, lipid moieties such as a cholesterol moiety, cholic acid, a thiocthcr, e.g., hcxyl-5- tritylthiol, a thiocholcsterol, an aliphatic chain, e.g., dodccandiol or undccyl residues, a phospholipid, e.g., di-hcxadccyl-rac-glyccrol or tricthylammonium 1 ,2-di-O-hexadccyl-rac-glyccro-3-Hphosphonatc, a polyaminc or a polyethylene glycol chain, or adamantane acetic acid, a palmityl moiety, or an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety. Oligonucleotides of the invention may also be conjugated to active drug substances, for example, aspirin, warfarin, phenylbutazone, ibuprofen, suprofcn, fcnbufen, ketoprofen, (S)-(+)-pranoprofen, carprofcn, dansylsarcosine, 2,3,5- triiodobenzoic acid, flufenamic acid, folinic acid, a benzothiadiazide, chlorothiazide, a diazepine, indomethicin, a barbiturate, a cephalosporin, a sulfa drug, an antidiabetic, an antibacterial or an antibiotic.
[00201] Representative United States patents that teach the preparation of such oligonucleotides conjugates include, but are not limited to, U.S. Pat. Nos. 4,828,979; 4,948,882; 5,218,105; 5,525,465; 5,541 ,313; 5,545,730; 5,552,538; 5,578,717, 5,580,731 ; 5,580,731 ; 5,591 ,584; 5,109,124; 5,1 18,802; 5,138,045; 5,414,077; 5,486,603; 5,512,439; 5,578,718; 5,608,046; 4,587,044; 4,605,735; 4,667,025; 4,762,779; 4,789,737; 4,824,941 ; 4,835,263; 4,876,335; 4,904,582; 4,958.013; 5,082,830; 5, 1 12,963; 5,214, 136; 5,082,830; 5, 1 12,963; 5,214,136; 5,245,022; 5,254,469; 5,258,506; 5,262,536; 5,272,250; 5,292,873; 5,317,098; 5,371 ,241 , 5,391 ,723; 5,416,203, 5,451 ,463; 5,510,475; 5,512,667; 5,514,785; 5,565,552; 5,567,810; 5,574, 142; 5,585,481 ; 5,587,371 ; 5,595,726; 5,597,696; 5,599,923; 5,599,928 and 5,688,941.
[00202] Fυnmtlations: The compounds of the invention may also be admixed, encapsulated, conjugated or otherwise associated with other molecules, molecule structures or mixtures of compounds, as forexamplc, liposomes, receptor-targeted molecules, oral, rectal, topical or other formulations, for assisting in uptake, distribution and/or absorption. Representative United States patents that teach the preparation of such uptake, distribution and/or absorption-assisting formulations include, but arc not limited to, U.S. Pat. Nos. 5, 108,921 ; 5,354,844; 5,416,016; 5,459, 127; 5,521 ,291 ; 5,543, 165; 5,547,932; 5,583,020; 5,591 ,721 ; 4,426,330; 4,534,899; 5,013,556; 5, 108,921 ; 5,213,804; 5,227,170; 5,264,221 ; 5,356,633; 5,395,619; 5,416,016; 5,417,978; 5,462,854; 5,469,854; 5,512,295; 5,527,528; 5,534,259; 5,543, 152; 5,556,948; 5,580,575; and 5,595,756, each of which is herein incorporated by reference. [00203] Although, the antiscnsc oligonucleotides do not need to be administered in the context of a vector in order to modulate a target expression and/or function, embodiments of the invention relates to expression vector constructs for the expression of antiscnsc oligonucleotides, comprising promoters, hybrid promoter gene sequences and possess a strong constitutive promoter activity, or a promoter activity which can be induced in the desired case. [00204] In an embodiment, invention practice involves administering at least one of the foregoing antiscnsc oligonucleotides with a suitable nucleic acid delivery system. In one embodiment, that system includes a non-viral vector opcrably linked to the polynucleotide. Examples of such nonviral vectors include the oligonucleotide alone (e.g. any one or more of SEQ ID NOS: 10 to 30) or in combination with a suitable protein, polysaccharide or lipid formulation.
[00205] Additionally suitable nucleic acid delivery systems include viral vector, typically sequence from at least one of an adenovirus, adcnovirus-associatcd virus (AAV), helper-dependent adenovirus, retrovirus, or hcmagglutinatin virus of Japan-liposomc (HVJ) complex. Preferably, the viral vector comprises a strong cukaryotic promoter operably linked to the polynucleotide e.g., a cytomegalovirus (CMV) promoter. [00206] Additionally vectors include viral vectors, fusion proteins and chemical conjugates. Retroviral vectors include Moloney murine leukemia viruses and HIV-based viruses. One HIV-based viral vector comprises at least two vectors wherein the gag and pol genes arc from an HIV genome and the cnv gene is from another vims. DNA viral vectors arc preferred. These vectors include pox vectors such as orthopox or avipox vectors, herpesvirus vectors such as a herpes simplex I virus (HSV) vector, Adenovirus Vectors and Adeno-associated Virus Vectors). [00207] The antisensc compounds of the invention encompass any pharmaceutically acceptable salts, esters, or salts of such esters, or any other compound which, upon administration to an animal, including a human, is capable of providing (directly or indirectly) the biologically active metabolite or residue thereof.
[00208] The term "pharmaceutically acceptable salts" refers to physiologically and pharmaceutically acceptable salts of Ac compounds of the invention: i.e., salts that retain the desired biological activity of the parent compound and do not impart undcsircd toxicological effects thereto. For oligonucleotides, examples of pharmaceutically acceptable salts and their uses arc further described in U.S. Pat. No. 6,287,860, which is incorporated herein by reference.
[00209] The present invention also includes pharmaceutical compositions and formulations that include the antiscnsc compounds of the invention. The pharmaceutical compositions of the present invention may be administered in a number of ways depending upon whether local or systemic treatment is desired and upon the area to be treated. Administration may be topical (including ophthalmic and to mucous membranes including vaginal and rectal delivery), pulmonary, e.g., by inhalation or insufflation of powders or aerosols, including by nebulizer; intratracheal, intranasal, epidermal and transdermal), oral or parenteral. Parenteral administration includes intravenous, intraarterial, subcutaneous, intraperitoneal or intramuscular injection or infusion; or intracranial, e.g., intrathecal or intraventricular, administration.
[00210] For treating tissues in the central nervous system, administration can be made by, e.g., injection or infusion into the cerebrospinal fluid. Administration of antisense RNA into cerebrospinal fluid is described, e.g., in U.S. Pat. App. Pub. No. 2007/01 17772, "Methods for slowing familial ALS disease progression," incorporated herein by reference in its entirety. [0021 1 ] When it is intended that the antiscnsc oligonucleotide of the present invention be administered to cells in the central nervous system, administration can be with one or more agents capable of promoting penetration of the subject antiscnse oligonucleotide across the blood-brain barrier. Injection can be made, e.g., in the cntorhinal cortex or hippocampus. Delivery of neurotrophic factors by administration of an adenovirus vector to motor neurons in muscle tissue is described in, e.g., U.S. Pat. No. 6,632,427, "Adcnoviral-vector-mcdiatcd gene transfer into medullary motor neurons," incorporated herein by reference. Delivery of vectors directly to the brain, e.g., the striatum, the thalamus, the hippocampus, or the substantia nigra, is known in the art and described, e.g., in U.S. Pat. No. 6,756,523, "Adenovirus vectors for the transfer of foreign genes into cells of the central nervous system particularly in brain," incorporated herein by reference. Administration can be rapid as by injection or made over a period of time as by slow infusion or administration of slow release formulations.
[00212] The subject antisense oligonucleotides can also be linked or conjugated with agents that provide desirable pharmaceutical or pharmacodynamic properties. For example, the antiscnse oligonucleotide can be coupled to any substance, known in the art to promote penetration or transport across the blood-brain barrier, such as an antibody to the transferrin receptor, and administered by intravenous injection The antisense compound can be linked with a viral vector, for example, that makes the antisense compound more effective and/or increases the transport of the antisense compound across the blood-brain barrier. Osmotic blood brain barrier disruption can also be accomplished by, e.g., infusion of sugars including, but not limited to, meso erythritol, xylitol, D(+) galactose, D(+) lactose, D(+) xylose, dulcitol, myo-inositol, L(-) fructose, D(-) mannitol, D(+) glucose, D(+) arabinosc, D(-) arabinosc, cellobiosc, D(+) maltose, D(+) raffinosc, L(+) rhamnosc, D(+) melibiosc, D(-) ribosc, adonitol, D(+) arabitol, L(-) arabitol, D(+) fucosc, L(-) fucosc, D(-) lyxose, L(+) lyxosc, and L(-) lyxosc, or amino acids including, but not limited to, glutamine, lysine, argininc, asparagine, aspartic acid, cysteine, glutamic acid, glycine, histidinc, leucine, methionine, phenylalanine, proline, serine, threonine, tyrosine, valine, and taurine. Methods and materials for enhancing blood brain barrier penetration arc described, e.g., in U. S. Patent No. 4,866,042, "Method for the delivery of genetic material across the blood brain barrier," 6,294,520, "Material for passage through the blood-brain barrier," and 6,936,589, "Parenteral delivery systems," all incorporated herein by reference in their entirety.
[00213] The subject antiscnse compounds may be admixed, encapsulated, conjugated or otherwise associated with other molecules, molecule structures or mixtures of compounds, for example, liposomes, rcccptor-targctcd molecules, oral, rectal, topical or other formulations, for assisting in uptake, distribution and/or absorption. For example, cationic lipids may be included in the formulation to facilitate oligonucleotide uptake. One such composition shown to facilitate uptake is LIPOFECTFN (available from GIBCO-BRL, Bcthcsda, MD). [00214] Oligonucleotides with at least one 2'-0-mcthoxycthyl modification arc believed to be particularly useful for oral administration. Pharmaceutical compositions and formulations for topical administration may include transdermal patches, ointments, lotions, creams, gels, drops, suppositories, sprays, liquids and powders. Conventional pharmaceutical carriers, aqueous, powder or oily bases, thickeners and the like may be necessary or desirable. Coated condoms, gloves and the like may also be useful.
[00215] The pharmaceutical formulations of the present invention, which may conveniently be presented in unit dosage form, may be prepared according to conventional techniques well known in the pharmaceutical industry. Such techniques include the step of bringing into association the active ingredients with the pharmaceutical carricr(s) or cxcipicnt(s). In general, the formulations arc prepared by uniformly and intimately bringing into association the active ingredients with liquid carriers or finely divided solid carriers or both, and then, if necessary, shaping the product
[00216] The compositions of the present invention may be formulated into any of many possible dosage forms such as, but not limited to, tablets, capsules, gel capsules, liquid syrups, soft gels, suppositories, and enemas. The compositions of the present invention may also be formulated as suspensions in aqueous, non-aqueous or mixed media. Aqueous suspensions may further contain substances that increase the viscosity of the suspension including, for example, sodium carboxymethylccllulose, sorbitol and/or dcxtran. The suspension may also contain stabilizers.
[00217] Pharmaceutical compositions of the present invention include, but are not limited to, solutions, emulsions, foams and liposome-containing formulations. The pharmaceutical compositions and formulations of the present invention may comprise one or more penetration enhancers, carriers, excipicnts or other active or inactive ingredients.
[00218] Emulsions are typically heterogeneous systems of one liquid dispersed in another in the form of droplets usually exceeding 0.1 μm in diameter. Emulsions may contain additional components in addition to the dispersed phases, and the active drug that may be present as a solution in cither the aqueous phase, oily phase or itself as a separate phase. Microcmulsions arc included as an embodiment of the present invention. Emulsions and their uses arc well known in the art and arc further described in U.S. Pat. No. 6,287,860.
[00219] Formulations of the present invention include liposomal formulations. As used in the present invention, the term "liposome" means a vesicle composed of amphiphilic lipids arranged in a spherical bilayer or bilayers. Liposomes are unilamellar or multilamellar vesicles which have a membrane formed from a lipophilic material and an aqueous interior that contains the composition to be delivered. Cationic liposomes are positively charged liposomes that arc believed to interact with negatively charged DNA molecules to form a stable complex.
Liposomes that are pH-sensitive or negatively-charged are believed to entrap DNA rather than complex with it.
Both cationic and noncationic liposomes have been used to deliver DNA to cells. [00220] Liposomes also include "sterically stabilized" liposomes, a term which, as used herein, refers to liposomes comprising one or more specialized lipids. When incorporated into liposomes, these specialized lipids result in liposomes with enhanced circulation lifetimes relative to liposomeslacking such specialized lipids.
Examples of sterically stabilized liposomes are those in which part of the vesicle-forming lipid portion of the liposome comprises one or more glycolipids or is dcrivatized with one or more hydrophilic polymers, such as a polyethylene glycol (PEG) moiety. Liposomes and their uses are further described in U.S. Pat. No. 6,287,860. [00221 ] The pharmaceutical formulations and compositions of the present invention may also include surfactants. The use of surfactants in drug products, formulations and in emulsions is well known in the art. Surfactants and their uses are further described in U.S. Pat. No. 6,287,860, which is incorporated herein by reference.
[00222] In one embodiment, the present invention employs various penetration enhancers to effect the efficient delivery of nucleic acids, particularly oligonucleotides. In addition to aiding the diffusion of non-lipophilic drugs across cell membranes, penetration enhancers also enhance the permeability of lipophilic drugs. Penetration enhancers may be classified as belonging to one of five broad categories, i.e., surfactants, fatty acids, bile salts, chelating agents, and non-chclating nonsurfactants. Penetration enhancers and their uses are further described in U.S. Pat. No. 6,287,860, which is incorporated herein by reference.
[00223] One of skill in the art will recognize that formulations arc routinely designed according to their intended use, i.e. route of administration. [00224] formulations for topical administration include those in which the oligonucleotides of the invention are in admixture with a topical delivery agent such as lipids, liposomes, fatty acids, fatty acid esters, steroids, chelating agents and surfactants, lipids and liposomes • include neutral (e.g. dioleoyl-phosphatidyl DOPE ethanolaminc, dimyristoylphosphatidyl choline DMPC, distearolyphosphatidyl choline) negative (e.g. dimyristoylphosphatidyl glycerol DMPG) and cationic (e.g. dioleoyltetramcthylaminopropyl DOTAP and dioleoyl-phosphatidyl ethanolaminc DOTMA). [00225] For topical or other administration, oligonucleotides of the invention may be encapsulated within liposomes or may form complexes thereto, in particular to cationic liposomes. Alternatively, oligonucleotides may be complcxcd to lipids, in particular to cationic lipids, fatty acids and esters, pharmaceutically acceptable salts thereof, and their uses arc further described in U.S. Pat. No. 6,287,860. [00226] Compositions and formulations for oral administration include powders or granules, microparticulatcs, nanoparticulates, suspensions or solutions in water or non-aqueous media, capsules, gel capsules, sachets, tablets or minitablcts. Thickeners, flavoring agents, diluents, cmulsifiers, dispersing aids or binders may be desirable, oral formulations arc those in which oligonucleotides of the invention arc administered in conjunction with one or more penetration enhancers surfactants and chelators, surfactants include fatty acids and/or esters or salts thereof, bile acids and/or salts thereof, bile acids/salts and fatty acids and their uses arc further described in U.S. Pat. No. 6,287,860, which is incorporated herein by reference. Also are combinations of penetration enhancers, for example, fatty acids/salts in combination with bile acids/salts. A particularly combination is the sodium salt of lauric acid, capric acid and UDCA. Further penetration enhancers include polyoxycthylcnc-9-lauryl ether, polyoxycthylcnc- 20-cetyl ether. Oligonucleotides of the invention may be delivered orally, in granular form including sprayed dried particles, or complexed to form micro or nanoparticles. Oligonucleotide complcxing agents and their uses are further described in U.S. Pat. No. 6,287,860, which is incorporated herein by reference.
[00227] Compositions and formulations for parenteral, intrathecal or intraventricular administration may include sterile aqueous solutions that may also contain buffers, diluents and other suitable additives such as, but not limited to, penetration enhancers, carrier compounds and other pharmaceutically acceptable carriers or excipients.
[00228] Certain embodiments of the invention provide pharmaceutical compositions containing one or more oligomeric compounds and one or more other chcmothcrapcutic agents that function by a non-antisensc mechanism. Examples of such chcmothcrapcutic agents include but arc not limited to cancer chcmothcrapcutic drugs such as daunorubicin, daunomycin, dactinomycin, doxorubicin, epirubicin, idarubicin, esorubicin, bleomycin, mafosfamide, ifosfamide, cytosine arabinoside, bischloroethyl- nitrosurea, busulfan, mitomycin C, actinomycin D, mithramycin, prednisone, hydroxyprogesterone, testosterone, tamoxifen, dacarbazine, procarbazine, hcxamethylmclamine, pcntamethylmclaminc, mitoxantrone, amsacrine, chlorambucil, mcthylcyclohcxylnitrosurca, nitrogen mustards, mclphalan, cyclophosphamide, 6-mcrcaptopurinc, 6-thioguaninc, cytarabine, 5- azacytidine, hydroxyurea, deoxycoformycin, 4-hydroxyperoxycyclo-phosphoramide, 5-fluorouracil (5-FU), 5-fluorodeoxyuridine (5-FUdR), methotrexate (MTX), colchicine, taxol, vincristine, vinblastine, ctoposidc (VP- 16), trimetrexate, irinotecan, topotecan, gemcitabine, teniposide, cisplatin and diethylstilbestrol (DES). When used with the compounds of the invention, such chemotherapeutic agents may be used individually (e.g., 5-FU and oligonucleotide), sequentially (e.g., 5-FU and oligonucleotide for a period of time followed by MTX and oligonucleotide), or in combination with one or more other such chemotherapeutic agents (e.g., 5-FU, MTX and oligonucleotide, or 5-FU, radiotherapy and oligonucleotide). Anti-inflammatory drugs, including but not limited to nonsteroidal anti-inflammatory drugs and corticosteroids, and antiviral drugs, including but not limited to ribivirin, vidarabinc, acyclovir and ganciclovir, may also be combined in compositions of the invention. Combinations of antisensc compounds and other non-antiscnsc drugs arc also within the scope of this invention. Two or more combined compounds may be used together or sequentially. [00229] In another related embodiment, compositions of the invention may contain one or more antisense compounds, particularly oligonucleotides, targeted to a first nucleic acid and one or more additional antisense compounds targeted to a second nucleic acid target. For example, the first target may be a particular antisense sequence of an Antiviral gene, and the second target may be a region from another nucleotide sequence. Alternatively, compositions of the invention may contain two or more antisensc compounds targeted to different regions of the same Antiviral gene nucleic acid target. Numerous examples of antisense compounds arc illustrated herein and others may be selected from among suitable compounds known in the art. Two or more combined compounds may be used together or sequentially. Dosing: [00230] The formulation of therapeutic compositions and their subsequent administration (dosing) is believed to be within the skill of those in the art. Dosing is dependent on severity and responsiveness of the disease state to be treated, with the course of treatment lasting from several days to several months, or until a cure is effected or a diminution of the disease state is achieved. Optimal dosing schedules can be calculated from measurements of drug accumulation in the body of the patient. Persons of ordinary skill can easily determine optimum dosages, dosing methodologies and repetition rates. Optimum dosages may vary depending on the relative potency of individual oligonucleotides, and can generally be estimated based on EC50s found to be effective in in vitro and in vivo animal models. In general, dosage is from 0.01 μg to 100 g per kg of body weight, and may be given once or more daily, weekly, monthly or yearly, or even once every 2 to 20 years. Persons of ordinary skill in the art can easily estimate repetition rates for dosing based on measured residence times and concentrations of the drug in bodily fluids or tissues. Following successful treatment, it may be desirable to have the patient undergo maintenance therapy to prevent the recurrence of the disease state, wherein the oligonucleotide is administered in maintenance doses, ranging from 0.01 μg to 100 g per kg of body weight, once or more daily, to once every 20 years. [00231 ] In embodiments, a patient is treated with a dnsage of drug that is at least about I , at least about 2, at least about 3, at least about 4, at least about 5, at least about 6, at least about 7, at least about 8, at least about 9, at least about 10, at least about 15, at least about 20, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, at least about 50, at least about 60, at least about 70, at least about 80, at least about 90, or at least about 100 mg/kg body weight. Certain injected dosages of antiscnse oligonucleotides arc described, e.g., in U.S. Pat. No. 7,563,884, "Antiscnse modulation of PTPlB expression," incorporated herein by reference in its entirety. [00232] While various embodiments of the present invention have been described above, it should be understood that they have been presented by way of example only, and not limitation. Numerous changes to the disclosed embodiments can be made in accordance with the disclosure herein without departing from the spirit or scope of the invention. Thus, the breadth and scope of the present invention should not be limited by any of the above described embodiments. [00233] All documents mentioned herein are incorporated herein by reference. All publications and patent documents cited in this application arc incorporated by reference for all purposes to the same extent as if each individual publication or patent document were so individually denoted. By their citation of various references in this document, Applicants do not admit any particular reference is "prior art" to their invention. Embodiments of inventive compositions and methods arc illustrated in the following examples. EXAMPLES
[00234] The following non-limiting Examples serve to illustrate selected embodiments of the invention. It will be appreciated that variations in proportions and alternatives in elements of the components shown will be apparent to those skilled in the art and are within the scope of embodiments of the present invention. lixample 1 : Design ofanfisen.se oligonucleotides specific for a nucleic acid molecule aπtisense to an Antiviral gene and/or a sense strand of an Antiviral gene polynucleotide
[00235] As indicated above the term "oligonucleotide specific for" or "oligonucleotide targets" refers to an oligonucleotide having a sequence (i) capable of forming a stable complex with a portion of the targeted gene, or (ii) capable of forming a stable duplex with a portion of an mRNA transcript of the targeted gene.
[00236] Selection of appropriate oligonucleotides is facilitated by using computer programs that automatically align nucleic acid sequences and indicate regions of identity or homology. Such programs arc used to compare nucleic acid sequences obtained, for example, by searching databases such as GcnBank or by sequencing PCR products. Comparison of nucleic acid sequences from a range of species allows the selection of nucleic acid sequences that display an appropriate degree of identity between species. In the case of genes that have not been sequenced. Southern blots are performed to allow a determination of the degree of identity between genes in target species and other species. By performing Southern blots at varying degrees of stringency, as is well known in the art, it is possible to obtain an approximate measure of identity. These procedures allow the selection of oligonucleotides that exhibit a high degree of complementarity to target nucleic acid sequences in a subject to be controlled and a lower degree of complementarity to corresponding nucleic acid sequences in other species. One skilled in the art will realize that there is considerable latitude in selecting appropriate regions of genes for use in the present invention.
[00237] An antiscnsc compound is "specifically hybridizablc" when binding of the compound to the target nucleic acid interferes with the normal function of the target nucleic acid to cause a modulation of function and/or activity, and there is a sufficient degree of complementarity to avoid non-specific binding of the antiscnsc compound to non-target nucleic acid sequences under conditions in which specific binding is desired, i.e., under physiological conditions in the case of in vivo assays or therapeutic treatment, and under conditions in which assays are performed in the case of in vitro assays [00238] The hybridization properties of the oligonucleotides described herein can be determined by one or more in vitro assays as known in the art. For example, the properties of the oligonucleotides described herein can be obtained by determination of binding strength between the target natural antisensc and a potential drug molecules using melting curve assay.
[00239] Tlic binding strength between the target natural antiscnsc and a potential drug molecule (Molecule) can be estimated using any of the established methods of measuring the strength of intermolecular interactions, for example, a melting curve assay.
[00240] Melting curve assay determines the temperature at which a rapid transition from double-stranded to single-stranded conformation occurs for the natural antiscnse/MoIeculc complex. This temperature is widely accepted as a reliable measure of the interaction strength between the two molecules. [00241 ] A melting curve assay can be performed using a cDNA copy of the actual natural antiscnsc RNA molecule or a synthetic DNA or RNA nucleotide corresponding to the binding site of the Molecule. Multiple kits containing all necessary reagents to perform this assay arc available (e.g. Applied Biosystcms Inc. McltDoctor kit). These kits include a suitable buffer solution containing one of the double strand DNA (dsDNA) binding dyes (such as ABI HRM dyes, SYBR Green, SYTO, etc.). The properties of the dsDNA dyes arc such that they emit almost no fluorescence in free form, but arc highly fluorescent when bound to dsDN A.
[00242] To perform the assay the cDNA or a corresponding oligonucleotide are mixed with Molecule in concentrations defined by the particular manufacturer's protocols. The mixture is heated to 95 0C to dissociate all pre-formcd dsDNA complexes, then slowly cooled to room temperature or other lower temperature defined by the kit manufacturer to allow the DNA molecules to anneal. The newly formed complexes are then slowly heated to 95 0C with simultaneous continuous collection of data on the amount of fluorescence that is produced by the reaction. The fluorescence intensity is inversely proportional to the amounts of dsDNA present in the reaction. The data can be collected using a real time PCR instrument compatible with the kit (e.g.ABI's StcpOnc Plus Real Time PCR System or LightTyper instrument, Roche Diagnostics, Lewes, UK) [00243] Melting peaks are constructed by plotting the negative derivative of fluorescence with respect to temperature (-d( Fluorescence )/dT) on the y-axis) against temperature (x-axis) using appropriate software (for example LightTyper (Roche) or SDS Dissociation Curve, ABI). The data is analyzed to identify the temperature of the rapid transition from dsDNA complex to single strand molecules. This temperature is called Tm and is directly proportional to the strength of interaction between the two molecules. Typically, Tm will exceed 40 0C. Example 2: Modulation of an Antiviral gene polynucleotide Treatment ofHepG2 cells with antisense oligonucleotides
[00244] HcpG2 cells from ATCC (cat# HB-8065) were grown in growth media (MEM/EBSS (Hyclonc cat #SH30024, " or Mediatech cat # MT-IO-OlO-CV) +10% FBS (Mediatech cat# MT35- OH-CV)+ penicillin/streptomycin (Mediatech cat# MT3O-OO2-CI)) at 37°C and 5% CO2. One day before the experiment the cells were replatcd at the density of 1.5 * 105/ml into 6 well plates and incubated at 37°C and 5% CO2. On the day of the experiment the media in the 6 well plates was changed to fresh growth media. All antiscnsc oligonucleotides were diluted to the concentration of 20 μM. Two μl of this solution was incubated with 400 μl of Opti-MEM media (Gibco cat#31985-070) and 4 μl of Lipofectamine 2000 (Invitrogen cat# 1 1668019) at room temperature for 20 min and applied to each well of the 6 well plates with HcpG2 cells. A Similar mixture including 2 μl of water instead of the oligonucleotide solution was used for the mock-transfcctcd controls. After 3-18 h of incubation at 37°C and 5% CO2 the media was changed to fresh growth media. 48 h after addition of antiscnsc oligonucleotides the media was removed and RNA was extracted from the cells using SV Total RNA Isolation System from Promcga (cat # Z3105) or RNcasy Total RNA Isolation kit from Qiagen (cat# 74181) following the manufacturers' instructions. 600 ng of RNA was added to the reverse transcription reaction performed using Verso cDNA kit from Thermo Scientific (cat#AB 1453B) or High Capacity cDNA Reverse Transcription Kit (cat# 4368813) as described in the manufacturer's protocol. The cDNA from this reverse transcription reaction was used to monitor gene expression by real time PCR using ABI Taqman Gene Expression Mix (cat#4369510) and primers/probes designed by ABI (Applied Biosystcms Taqman Gene Expression Assay: Hs0O204833_ml , HsOO22342O_m 1 , HsOO85547l_j>l by Applied Biosystcms Inc., Foster City CA). The following PCR cycle was used: 500C for 2 min, 95°C for 10 min, 40 cycles of (95°C for 15 seconds, 600C for 1 min) using Mx4000 thermal cycler (Stratagcnc).
[00245] Fold change in gene expression after treatment with antisense oligonucleotides was calculated based on the difference in ISS-normalized dCt values between treated and mock-transfected samples. Results
[00246] Real Time PCR results show that levels of RIG l mRNA in HcpG2 cells are significantly increased 48h after treatment with siRNAs to RIG I antisense hs.601664 and AK300104 (Fig 1 ).
[00247] Real time PCR results show that the levels of MDA5 mRNA in HcpG2 cells arc significantly increased 48h after treatment with two of the oligos designed to MDA5 antisense BU663736. (Fig 2). [00248] Real time PCR results show that the levels of IFNAI mRNA in HepG2 cells arc significantly increased 48h after treatment with one oligo designed to IFNAI antisense DA393812 (Fig 3). Treatment ofZR75 cells with antisense oligonucleotides:
[00249] ZR75 cells from ATCC (Cat# CRL-15(K)) were grown in growth media (MEM/EBSS (Hyclone cat #SH3()O24, or Mcdiatcch cat # MT-I O-OlO-C V) +10% FBS (Mcdiatcch cat# MT35- O H-CV)+ penicillin/streptomycin (Mcdiatcch cat# MT30-002-CI)) at 37°C and 5% CO;. One day before the experiment the cells were rcplatcd at the density of 1.5 * lOVml into 6 well plates and incubated at 370C and 5% CO2. On the day of the experiment the media in the 6 well plates was changed to fresh growth media. All antisense oligonucleotides were diluted to the concentration of 20 μM. Two μl of this solution was incubated with 400 μl of Opti-MEM media (Gibco cat#31985-070) and 4 μl of Lipofectamine 2000 (Invitrogen cat# 1 1668019) at room temperature for 20 min and applied to each well of the 6 well plates with ZR75 cells. Similar mixture including 2 μl of water instead of the oligonucleotide solution was used for the mock-transfcctcd controls. After 3- 18 h of incubation at 37°C and 5% CO2 the media was changed to fresh growth media. 48 h after addition of antisense oligonucleotides the media was removed and RNA was extracted from the cells using SV Total RNA Isolation System from Promega (cat # Z3105) or RNcasy Total RNA Isolation kit from Qiagcn (cat# 74181 ) following the manufacturers' instructions. 6(H) ng of RNA was added to the reverse transcription reaction performed using Verso cDNA kit from Thermo Scientific (cat#AB 1453B) or High Capacity cDNA Reverse Transcription Kit (cat# 4368813) as described in the manufacturer's protocol. The cDNA from this reverse transcription reaction was used to monitor gene expression by real time PCR using ABI Taqman Gene Expression Mix (cat#4369510) and primers/probes designed by ABI (Applied Biosystems Taqman Gene Expression Assay: HsO0855471_gl . The following PCR cycle was used: 500C for 2 min, 95°C for 10 min, 40 cycles of (95°C for 15 seconds, 600C for 1 min) using StepOnc Plus Real Time PCR Machine (Applied Biosystems).
[00250] Fold change in gene expression after treatment with antiscnsc oligonucleotides was calculated based on the difference in 18S-normalizcd dCt values between treated and mock-transfected samples. Results: Real time PCR results show that the levels of IFNAI mRNA in ZR75 cells are significantly increased 48h after treatment with one oligo designed to IFNAl antiscnse DA393812 (Fig. 4). ■ Treatment of HVVEC cells with antisense oligonucleotides
[00251] HUVEC cells from ATCC (Promo Cell cat# C- 12253) were grown in Epithelial Growth Media (Promo Cell cat #C-22010) at 37oC and 5% CO2. One day before the experiment the cells were replated using Promo Cell Detach Kit (cat#C-41200) at the density of 1.5xl0Λ5/ml into 6 well plates and incubated at 37oC and 5% CO2. On the day of the experiment the media in the 6 well plates was changed to fresh Epithelial Growth Media. All antiscnsc oligonucleotides were diluted to the concentration of 20 μM. Two μl of this solution was incubated with 400 μl of Opti-MEM media (Gibco cat#31985-070) and 4 μl of Lipofcctaminc 2000 (Invitrogcn cat# 1 1668019) at room temperature for 20 min and applied to each well of the 6 well plates with HlWEC cells. Similar mixture including 2 μl of water instead of the oligonucleotide solution was used for the mock-transfected controls. After 3- 18 h of incubation at 37°C and 5% CO2 the media was changed to fresh growth media. 48 h after addition of antiscnse oligonucleotides the media was removed and RNA was extracted from the cells using SV Total RNA Isolation System from Promcga (cat # Z3105) or RNeasy Total RNA Isolation kit from Qiagcn (cat# 74181) following the manufacturers' instructions. 600 ng of RNA was added to the reverse transcription reaction performed using Verso cDNA kit from Thermo Scientific (cat#AB1453B) as described in the manufacturer's protocol. The cDNA from this reverse transcription reaction was used to monitor gene expression by real time PCR using ABI Taqman gene Expression Mix (cat#4369510) and primers/probes designed by ABI (Applied Biosystems Taqman Gene Expression Assays: HsOO15334O_ml and HsOO855471_gl by Applied Biosystems Inc., Foster City CA). The following PCR cycle was used: 500C for 2 min, 95°C for 10 min, 40 cycles of (95°C for 15 seconds, 6O0C for 1 min) using StepOnc Plus Real Time PCR Machine (Applied Biosystems Inc.) or Mx4000 thermal cycler (Stratagene).
[00252] Fold change in gene expression after treatment with antiscnse oligonucleotides was calculated based on the difference in 18S-normaIized dCt values between treated and mock-transfected samples. Results: Real time PCR results show that the levels of IFNAI mRNA in HUVEC cells arc significantly increased 48h after treatment with one oligo designed to IFNAl antiscnsc DA393812 (Fig. 5). Treatment ofMCF-7 cells with antisense oligonucleotides:
[00253] MCF-7 cells from ATCC (cat# HTB-22) were grown in growth media (MEM/EBSS (Hyclone cat #SH30024, or Mediatech cat # MT-IO-OlO-CV) +10% FBS (Mediatech cat# MT35- OH-CV)+ penicillin/streptomycin (Mediatech cat# MT3O-OO2-CI)) at 37°C and 5% CO2. One day before the experiment the cells were rcplatcd at the density of 1.5 x 105ZmI into 6 well plates and incubated at 37°C and 5% CO2. On the day of the experiment the media in the 6 well plates was changed to fresh growth media. All antisense oligonucleotides were diluted to the concentration of 20 μM. Two μl of this solution was incubated with 400 μl of Opti-MEM media (Gibco cat#31985-070) and 4 μl of Lipofcctamine 2000 (Invitrogen car# 1 1668019) at room temperature for 20 min and applied to each well of the 6 well plates with MCF-7 cells. Similar mixture including 2 μl of water instead of the oligonucleotide solution was used for the mock-transfectcd controls. After 3-18 h of incubation at 37°C and 5% CO2 the media was changed to fresh growth media. 48 h after addition of antisense oligonucleotides the media was removed and RNA was extracted from the cells using SV Total RNA Isolation System from Promega (cat # Z3105) or RNeasy Total RNA Isolation kit from Qiagen (cat# 74181) following the manufacturers' instructions. 600 ng of RNA was added to the reverse transcription reaction performed using Verso cDNA kit from Thermo Scientific (cat#AB1453B) or High Capacity cDNA Reverse Transcription Kit (cat# 4368813) as described in the manufacturer's protocol. The cDNA from this reverse transcription reaction was used to monitor gene expression by real time PCR using ABI Taqman Gene Expression Mix (cat#4369510) and primers/probes designed by ABI (Applied Biosystems Taqman Gene Expression Assay: Hs00855471_gl . The following PCR cycle was used: 5O0C for 2 min, 95°C for 10 min, 40 cycles of (950C for 15 seconds, 600C for 1 min) using StepOne Plus Real Time PCR Machine (Applied Biosystems).
[00254] Fold change in gene expression after treatment with antisense oligonucleotides was calculated based on the difference in 18S-normalizcd dCt values between treated and mock-transfccted samples. Results: ELlSA Assay results show that IFNA protein was upregulatcd in extracts from MCF7 cells which were treated with oligos designed to IFNAI antisense DA39381 (Fig. 6).
[00255] Although the invention has been illustrated and described with respect to one or more implementations, equivalent alterations and modifications will occur to others skilled in the art upon the reading and understanding of this specification and the annexed drawings. In addition, while a particular feature of the invention may have been disclosed with respect to only one of several implementations, such feature may be combined with one or more other features of the other implementations as may be desired and advantageous for any given or particular application.
[00256] The Abstract of the disclosure will allow the reader to quickly ascertain the nature of the technical disclosure. It is submitted with the understanding that it will not be used to interpret or limit the scope or meaning of the following claims.

Claims

CLAIMSWhat is claimed is:
1. A method of modulating a function of and/or the expression of an Antiviral gene polynucleotide in patient cells or tissues in vivo or in vitro comprising: contacting said cells or tissues with at least one antiscnse oligonucleotide 5 to 30 nucleotides in length wherein said at least one oligonucleotide has at least 50% sequence identity to a reverse complement of a polynucleotide comprising 5 to 30 consecutive nucleotides within nucleotides I to 1267 of SEQ ID SEQ ID NO: 4, 1 to 586 of SEQ ID NO: 5, 1 to 741 of SEQ ID SEQ ID NO: 6, 1 to 251 of SEQ ID NO: 7, 1 to 681 of SEQ ID NO: 8, and 1 to 580 of SEQ ID NO: 9; thereby modulating a function of and/or the expression of the Antiviral gene polynucleotide in patient cells or tissues in vivo or in vitro.
2. A method of modulating a function of and/or the expression of an Antiviral gene polynucleotide in patient cells or tissues in vivo or in vitro comprising: contacting said cells or tissues with at least one antisensc oligonucleotide 5 to 30 nucleotides in length wherein said at least one oligonucleotide has at least 50% sequence identity to a reverse complement of a natural antisense of an Antiviral gene polynucleotide; thereby modulating a function of and/or the expression of the
Antiviral gene polynucleotide in patient cells or tissues in vivo or in vitm.
3. A method of modulating a function of and/or the expression of an Antiviral gene polynucleotide in patient cells or tissues in vivo or in vitro comprising: contacting said cells or tissues with at least one antisense oligonucleotide 5 to 30 nucleotides in length wherein said oligonucleotide has at least 50% sequence identity to an antisense oligonucleotide to the Antiviral gene polynucleotide; thereby modulating a function of and/or the expression of the Antiviral gene polynucleotide in patient cells or tissues in vivo or in vitro.
4. A method of modulating a function of and/or the expression of an Antiviral gene polynucleotide in patient cells or tissues in vivo or in vitro comprising: contacting said cells or tissues with at least one antisense oligonucleotide that targets a region of a natural antisense oligonucleotide of the Antiviral gene polynucleotide; thereby modulating a function of and/or the expression of the Antiviral gene polynucleotide in patient cells or tissues in vivo or in vitm.
5. The method of claim 4, wherein a function of and/or the expression of the Antiviral gene is increased in vivo or in vitm with respect to a control. 6. The method of claim 4, wherein the at least one antisense oligonucleotide targets a natural antisense sequence of an Antiviral gene polynucleotide.
7. The method of claim 4, wherein the at least one antisense oligonucleotide targets a nucleic acid sequence comprising coding and/or non-coding nucleic acid sequences of an Antiviral gene polynucleotide.
8. The method of claim 4, wherein the at least one antiscnsc oligonucleotide targets overlapping and/or non- overlapping sequences of an Antiviral gene polynucleotide.
9. The method of claim 4, wherein the at least one antisense oligonucleotide comprises one or more modifications selected from: at least one modified sugar moiety, at least one modified intcmuclcosidc linkage, at least one modified nucleotide, and combinations thereof.
10. The method of claim 9, wherein the one or more modifications comprise at least one modified sugar moiety selected from: a 2'-O-mcthoxycthyl modified sugar moiety, a 2'-mcthoxy modified sugar moiety, a 2'-0-alkyl modified sugar moiety, a bicyclic sugar moiety, and combinations thereof.
1 1. The method of claim 9, wherein the one or more modifications comprise at least one modified internucleoside linkage selected from: a phosphorothioate, 2'- Omethoxyethyl (MOE), 2'-fluoro, alkylphosphonate, phosphorodithioate, alkylphosphonothioate, phosphoramidate, carbamate, carbonate, phosphate triester, acctamidatc, carboxymethyl ester, and combinations thereof.
12. The method of claim 9, wherein the one or more modifications comprise at least one modified nucleotide selected from: a peptide nucleic acid (PNA), a locked nucleic acid (LNA), an arabino-nucleic acid (FANA), an analogue, a derivative, and combinations thereof.
13. The method of claim 1, wherein the at least one oligonucleotide comprises at least one oligonucleotide sequences set forth as SEQ ID NOS: 10 to 30.
14. A method of modulating a function of and/or the expression of an Antiviral gene in mammalian cells or tissues in vivo or in vitro comprising: contacting said cells or tissues with at least one short interfering RNA (siRNA) oligonucleotide 5 to 30 nucleotides in length, said at least one siRNA oligonucleotide being specific for an antisense polynucleotide of an Antiviral gene polynucleotide, wherein said at least one siRNA oligonucleotide has at least 50% sequence identity to a complementary sequence of at least about five consecutive nucleic acids of the antisense and/or sense nucleic acid molecule of the Antiviral gene polynucleotide; and, modulating a function of and/or the expression of an Antiviral gene in mammalian cells or tissues in vivo or in vitro,
15. The method of claim 14, wherein said oligonucleotide has at least 80% sequence identity to a sequence of at least about five consecutive nucleic acids that is complementary to the antisense and/or sense nucleic acid molecule of the Antiviral gene polynucleotide.
16. A method of modulating a function of and/or the expression of an Antiviral gene in mammalian cells or tissues in vivo or in vitm comprising: contacting said cells or tissues with at least one antisense oligonucleotide of about 5 to 30 nucleotides in length specific for noncoding and/or coding sequences of a sense and/or natural antisense strand of an Antiviral gene polynucleotide wherein said at least one antisense oligonucleotide has at least 50% sequence identity to at least one nucleic acid sequence set forth as SEQ ID NOS: 1 to 9; and, modulating the function and/or expression of the Antiviral gene in mammalian cells or tissues in vivo or in vitro.
17. A synthetic, modified oligonucleotide comprising at least one modification wherein the at least one modification is selected from: at least one modified sugar moiety; at least one modified intcrnucleotidc linkage; at least one modified nucleotide, and combinations thereof; wherein said oligonucleotide is an antiscnsc compound which hybridizes to and modulates the function and/or expression of an Antiviral gene in vivo or in vitm as compared to a normal control.
18. The oligonucleotide of claim 17, wherein the at least one modification comprises an internucleotide linkage selected from the group consisting of: phosphorothioate, alkylphosphonate, phosphorodithioate, alkylphosphonothioate, phosphoramidate, carbamate, carbonate, phosphate triester, acetamidate, carboxymethyl ester, and combinations thereof.
19. The oligonucleotide of claim 17, wherein said oligonucleotide comprises at least one phosphorothioate internucleotide linkage.
20. The oligonucleotide of claim 17, wherein said oligonucleotide comprises a backbone of phosphorothioate internucleotide linkages.
21. The oligonucleotide of claim 17, wherein the oligonucleotide comprises at least one modified nucleotide, said modified nucleotide selected from: a peptide nucleic acid, a locked nucleic acid (LNA). analogue, derivative, and a combination thereof.
22. The oligonucleotide of claim 17, wherein the oligonucleotide comprises a plurality of modifications, wherein said modifications comprise modified nucleotides selected from: phosphorothioate, alkylphosphonate, phosphorodithioate, alkylphosphonothioate, phosphoramidate, carbamate, carbonate, phosphate triester, acetamidate, carboxymethyl ester, and a combination thereof.
23. The oligonucleotide of claim 17, wherein the oligonucleotide comprises a plurality of modifications, wherein said modifications comprise modified nucleotides selected from: peptide nucleic acids, locked nucleic acids (LNA), analogues, derivatives, and a combination thereof.
24. The oligonucleotide of claim 17, wherein the oligonucleotide comprises at least one modified sugar moiety selected from: a 2'-O-methoxyethyl modified sugar moiety, a 2'-methoxy modified sugar moiety, a 2'-0-alkyl modified sugar moiety, a bicyclic sugar moiety, and a combination thereof.
25. The oligonucleotide of claim 17, wherein the oligonucleotide comprises a plurality of modifications, wherein said modifications comprise modified sugar moieties selected from: a 2'-O-mcthoxycthyl modified sugar moiety, a 2'-mcthoxy modified sugar moiety, a 2'-0-alkyl modified sugar moiety, a bicyclic sugar moiety, and a combination thereof.
26. The oligonucleotide of claim 17, wherein the oligonucleotide is of at least about 5 to 30 nucleotides in length and hybridizes to an antisense and/or sense strand of an Antiviral gene polynucleotide wherein said oligonucleotide has at least about 20% sequence identity to a complementary sequence of at least about five consecutive nucleic acids of the antisense and/or sense coding and/or noncoding nucleic acid sequences of the Antiviral gene polynucleotide.
27. The oligonucleotide of claim 17, wherein the oligonucleotide has at least about 80% sequence identity to a complementary sequence of at least about five consecutive nucleic acids of the antisense and/or sense coding and/or noncoding nucleic acid sequence of the Antiviral gene polynucleotide.
28. The oligonucleotide of claim 17, wherein said oligonucleotide hybridizes to and modulates expression and/or function of at least one Antiviral gene polynucleotide in vivo or in vitro, as compared to a normal control.
29. The oligonucleotide of claim 17, wherein the oligonucleotide comprises the sequences set forth as SEQ ID NOS: IO to 30.
30. A composition comprising one or more oligonucleotides specific for one or more Antiviral gene polynucleotides, said polynucleotides comprising antisense sequences, complementary sequences, alleles, homologs, isoforms, variants, derivatives, mutants, fragments, or combinations thereof.
31. The composition of claim 30, wherein the oligonucleotides have at least about 40% sequence identity as compared to any one of the nucleotide sequences set forth as SEQ ID NOS: 10 to 30.
32. The composition of claim 30, wherein the oligonucleotides comprise nucleotide sequences set forth as SEQ ID NOS: 10 to 30.
33. The composition of claim 32, wherein the oligonucleotides set forth as SEQ ID NOS: 10 to 30 comprise one or more modifications or substitutions. 34. The composition of claim 33, wherein the one or more modifications are selected from: phosphorothioate, mcthylphosphonate, peptide nucleic acid, locked nucleic acid (LNA) molecules, and combinations thereof.
35. A method of preventing or treating a disease associated with at least one Antiviral gene polynucleotide and/or at least one encoded product thereof, comprising: administering to a patient a therapeutically effective dose of at least one antisense oligonucleotide that binds to a natural antisense sequence of said at least one Antiviral gene polynucleotide and modulates expression of said at least one Antiviral gene polynucleotide; thereby preventing or treating the disease associated with the at least one Antiviral gene polynucleotide and/or at least one encoded product thereof.
36. The method of claim 35, wherein a disease associated with the at least one Antiviral gene polynucleotide is selected from: cancer, an inflammatory disease, a disease, disorder or a condition caused by an infectious agent (e.g., including, viral, bacterial, fungal, protozoan etc.), a viral disease, inflammation, arthritis, psoriasis,a neurological disease or disorder, an immune system disease or disorder, an autoimmune disease or disorder, an immunodeficiency disease, an allergy, psoriasis, neurological diseases, a renal disease or disorder, a cardiovascular disease or disorder, a muscular disease or disorder, atherosclerosis, diabetes, a hepatic disease or disorder and a communicable disease.
7. A method of identifying and selecting at least one oligonucleotide for in vivo administration comprising: selecting a target polynucleotide associated with a disease state; identifying at least one oligonucleotide comprising at least five consecutive nucleotides which are complementary to the selected target polynucleotide or to a polynucleotide that is antisensc to the selected target polynucleotide; measuring the thermal melting point of a hybrid of an antiscnse oligonucleotide and the target polynucleotide or the polynucleotide that is antisensc to the selected target polynucleotide under stringent hybridization conditions; and selecting at least one oligonucleotide for in vivo administration based on the information obtained.
PCT/US2010/036558 2009-05-28 2010-05-28 Treatment of antiviral gene related diseases by inhibition of natural antisense transcript to an antiviral gene WO2010138806A2 (en)

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JP2012513290A JP5960049B2 (en) 2009-05-28 2010-05-28 Treatment of antiviral gene-related diseases by suppression of natural antisense transcripts against antiviral genes
CN201080036011.5A CN103221541B (en) 2009-05-28 2010-05-28 Antiviral gene relevant disease is treated by the natural antisense transcript suppressing antiviral gene
CA 2764683 CA2764683A1 (en) 2009-05-28 2010-05-28 Treatment of antiviral gene related diseases by inhibition of natural antisense transcript to an antiviral gene
ES10781271.1T ES2618576T3 (en) 2009-05-28 2010-05-28 Treatment of diseases related to an antiviral gene by inhibiting a natural antisense transcript to an antiviral gene
EP10781271.1A EP2435571B1 (en) 2009-05-28 2010-05-28 Treatment of antiviral gene related diseases by inhibition of natural antisense transcript to an antiviral gene
US13/321,996 US8791085B2 (en) 2009-05-28 2010-05-28 Treatment of antiviral gene related diseases by inhibition of natural antisense transcript to an antiviral gene
US14/297,101 US9133456B2 (en) 2009-05-28 2014-06-05 Treatment of antiviral gene related diseases by inhibition of natural antisense transcript to an antiviral gene
US14/814,833 US9512427B2 (en) 2009-05-28 2015-07-31 Treatment of antiviral gene related diseases by inhibition of natural antisense transcript to an antiviral gene

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US9816094B2 (en) 2010-11-12 2017-11-14 The General Hospital Corporation Polycomb-associated non-coding RNAs
US9920317B2 (en) 2010-11-12 2018-03-20 The General Hospital Corporation Polycomb-associated non-coding RNAs
US10058623B2 (en) 2012-05-16 2018-08-28 Translate Bio Ma, Inc. Compositions and methods for modulating UTRN expression
US10059941B2 (en) 2012-05-16 2018-08-28 Translate Bio Ma, Inc. Compositions and methods for modulating SMN gene family expression
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* Cited by examiner, † Cited by third party
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Citations (181)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US3687808A (en) 1969-08-14 1972-08-29 Univ Leland Stanford Junior Synthetic polynucleotides
US4426330A (en) 1981-07-20 1984-01-17 Lipid Specialties, Inc. Synthetic phospholipid compounds
US4469863A (en) 1980-11-12 1984-09-04 Ts O Paul O P Nonionic nucleic acid alkyl and aryl phosphonates and processes for manufacture and use thereof
US4476301A (en) 1982-04-29 1984-10-09 Centre National De La Recherche Scientifique Oligonucleotides, a process for preparing the same and their application as mediators of the action of interferon
US4534899A (en) 1981-07-20 1985-08-13 Lipid Specialties, Inc. Synthetic phospholipid compounds
US4587044A (en) 1983-09-01 1986-05-06 The Johns Hopkins University Linkage of proteins to nucleic acids
US4605735A (en) 1983-02-14 1986-08-12 Wakunaga Seiyaku Kabushiki Kaisha Oligonucleotide derivatives
US4667025A (en) 1982-08-09 1987-05-19 Wakunaga Seiyaku Kabushiki Kaisha Oligonucleotide derivatives
US4762779A (en) 1985-06-13 1988-08-09 Amgen Inc. Compositions and methods for functionalizing nucleic acids
US4824941A (en) 1983-03-10 1989-04-25 Julian Gordon Specific antibody to the native form of 2'5'-oligonucleotides, the method of preparation and the use as reagents in immunoassays or for binding 2'5'-oligonucleotides in biological systems
US4828979A (en) 1984-11-08 1989-05-09 Life Technologies, Inc. Nucleotide analogs for nucleic acid labeling and detection
US4835263A (en) 1983-01-27 1989-05-30 Centre National De La Recherche Scientifique Novel compounds containing an oligonucleotide sequence bonded to an intercalating agent, a process for their synthesis and their use
US4845205A (en) 1985-01-08 1989-07-04 Institut Pasteur 2,N6 -disubstituted and 2,N6 -trisubstituted adenosine-3'-phosphoramidites
US4866042A (en) 1987-11-18 1989-09-12 Neuwelt Edward A Method for the delivery of genetic material across the blood brain barrier
US4876335A (en) 1986-06-30 1989-10-24 Wakunaga Seiyaku Kabushiki Kaisha Poly-labelled oligonucleotide derivative
US4904582A (en) 1987-06-11 1990-02-27 Synthetic Genetics Novel amphiphilic nucleic acid conjugates
US4948882A (en) 1983-02-22 1990-08-14 Syngene, Inc. Single-stranded labelled oligonucleotides, reactive monomers and methods of synthesis
US4958013A (en) 1989-06-06 1990-09-18 Northwestern University Cholesteryl modified oligonucleotides
US4981957A (en) 1984-07-19 1991-01-01 Centre National De La Recherche Scientifique Oligonucleotides with modified phosphate and modified carbohydrate moieties at the respective chain termini
US5013556A (en) 1989-10-20 1991-05-07 Liposome Technology, Inc. Liposomes with enhanced circulation time
US5013830A (en) 1986-09-08 1991-05-07 Ajinomoto Co., Inc. Compounds for the cleavage at a specific position of RNA, oligomers employed for the formation of said compounds, and starting materials for the synthesis of said oligomers
US5023243A (en) 1981-10-23 1991-06-11 Molecular Biosystems, Inc. Oligonucleotide therapeutic agent and method of making same
US5034506A (en) 1985-03-15 1991-07-23 Anti-Gene Development Group Uncharged morpholino-based polymers having achiral intersubunit linkages
US5082830A (en) 1988-02-26 1992-01-21 Enzo Biochem, Inc. End labeled nucleotide probe
US5109124A (en) 1988-06-01 1992-04-28 Biogen, Inc. Nucleic acid probe linked to a label having a terminal cysteine
US5108921A (en) 1989-04-03 1992-04-28 Purdue Research Foundation Method for enhanced transmembrane transport of exogenous molecules
US5112963A (en) 1987-11-12 1992-05-12 Max-Planck-Gesellschaft Zur Foerderung Der Wissenschaften E.V. Modified oligonucleotides
US5118802A (en) 1983-12-20 1992-06-02 California Institute Of Technology DNA-reporter conjugates linked via the 2' or 5'-primary amino group of the 5'-terminal nucleoside
US5118800A (en) 1983-12-20 1992-06-02 California Institute Of Technology Oligonucleotides possessing a primary amino group in the terminal nucleotide
US5130302A (en) 1989-12-20 1992-07-14 Boron Bilogicals, Inc. Boronated nucleoside, nucleotide and oligonucleotide compounds, compositions and methods for using same
US5134066A (en) 1989-08-29 1992-07-28 Monsanto Company Improved probes using nucleosides containing 3-dezauracil analogs
US5138045A (en) 1990-07-27 1992-08-11 Isis Pharmaceuticals Polyamine conjugated oligonucleotides
US5149797A (en) 1990-02-15 1992-09-22 The Worcester Foundation For Experimental Biology Method of site-specific alteration of rna and production of encoded polypeptides
US5166315A (en) 1989-12-20 1992-11-24 Anti-Gene Development Group Sequence-specific binding polymers for duplex nucleic acids
US5175273A (en) 1988-07-01 1992-12-29 Genentech, Inc. Nucleic acid intercalating agents
US5177196A (en) 1990-08-16 1993-01-05 Microprobe Corporation Oligo (α-arabinofuranosyl nucleotides) and α-arabinofuranosyl precursors thereof
US5185444A (en) 1985-03-15 1993-02-09 Anti-Gene Deveopment Group Uncharged morpolino-based polymers having phosphorous containing chiral intersubunit linkages
US5188897A (en) 1987-10-22 1993-02-23 Temple University Of The Commonwealth System Of Higher Education Encapsulated 2',5'-phosphorothioate oligoadenylates
US5214136A (en) 1990-02-20 1993-05-25 Gilead Sciences, Inc. Anthraquinone-derivatives oligonucleotides
US5214134A (en) 1990-09-12 1993-05-25 Sterling Winthrop Inc. Process of linking nucleosides with a siloxane bridge
US5216141A (en) 1988-06-06 1993-06-01 Benner Steven A Oligonucleotide analogs containing sulfur linkages
US5218105A (en) 1990-07-27 1993-06-08 Isis Pharmaceuticals Polyamine conjugated oligonucleotides
US5220007A (en) 1990-02-15 1993-06-15 The Worcester Foundation For Experimental Biology Method of site-specific alteration of RNA and production of encoded polypeptides
US5227170A (en) 1989-06-22 1993-07-13 Vestar, Inc. Encapsulation process
US5235033A (en) 1985-03-15 1993-08-10 Anti-Gene Development Group Alpha-morpholino ribonucleoside derivatives and polymers thereof
US5245022A (en) 1990-08-03 1993-09-14 Sterling Drug, Inc. Exonuclease resistant terminally substituted oligonucleotides
US5254469A (en) 1989-09-12 1993-10-19 Eastman Kodak Company Oligonucleotide-enzyme conjugate that can be used as a probe in hybridization assays and polymerase chain reaction procedures
US5256775A (en) 1989-06-05 1993-10-26 Gilead Sciences, Inc. Exonuclease-resistant oligonucleotides
US5258506A (en) 1984-10-16 1993-11-02 Chiron Corporation Photolabile reagents for incorporation into oligonucleotide chains
US5262536A (en) 1988-09-15 1993-11-16 E. I. Du Pont De Nemours And Company Reagents for the preparation of 5'-tagged oligonucleotides
US5264423A (en) 1987-03-25 1993-11-23 The United States Of America As Represented By The Department Of Health And Human Services Inhibitors for replication of retroviruses and for the expression of oncogene products
US5264564A (en) 1989-10-24 1993-11-23 Gilead Sciences Oligonucleotide analogs with novel linkages
US5264221A (en) 1991-05-23 1993-11-23 Mitsubishi Kasei Corporation Drug-containing protein-bonded liposome
US5264562A (en) 1989-10-24 1993-11-23 Gilead Sciences, Inc. Oligonucleotide analogs with novel linkages
US5272250A (en) 1992-07-10 1993-12-21 Spielvogel Bernard F Boronated phosphoramidate compounds
US5276019A (en) 1987-03-25 1994-01-04 The United States Of America As Represented By The Department Of Health And Human Services Inhibitors for replication of retroviruses and for the expression of oncogene products
US5278302A (en) 1988-05-26 1994-01-11 University Patents, Inc. Polynucleotide phosphorodithioates
US5292873A (en) 1989-11-29 1994-03-08 The Research Foundation Of State University Of New York Nucleic acids labeled with naphthoquinone probe
US5317098A (en) 1986-03-17 1994-05-31 Hiroaki Shizuya Non-radioisotope tagging of fragments
US5319080A (en) 1991-10-17 1994-06-07 Ciba-Geigy Corporation Bicyclic nucleosides, oligonucleotides, process for their preparation and intermediates
US5321131A (en) 1990-03-08 1994-06-14 Hybridon, Inc. Site-specific functionalization of oligodeoxynucleotides for non-radioactive labelling
US5354844A (en) 1989-03-16 1994-10-11 Boehringer Ingelheim International Gmbh Protein-polycation conjugates
US5356633A (en) 1989-10-20 1994-10-18 Liposome Technology, Inc. Method of treatment of inflamed tissues
US5359044A (en) 1991-12-13 1994-10-25 Isis Pharmaceuticals Cyclobutyl oligonucleotide surrogates
US5367066A (en) 1984-10-16 1994-11-22 Chiron Corporation Oligonucleotides with selectably cleavable and/or abasic sites
US5371241A (en) 1991-07-19 1994-12-06 Pharmacia P-L Biochemicals Inc. Fluorescein labelled phosphoramidites
US5391723A (en) 1989-05-31 1995-02-21 Neorx Corporation Oligonucleotide conjugates
US5395619A (en) 1993-03-03 1995-03-07 Liposome Technology, Inc. Lipid-polymer conjugates and liposomes
US5399676A (en) 1989-10-23 1995-03-21 Gilead Sciences Oligonucleotides with inverted polarity
US5403711A (en) 1987-11-30 1995-04-04 University Of Iowa Research Foundation Nucleic acid hybridization and amplification method for detection of specific sequences in which a complementary labeled nucleic acid probe is cleaved
US5405939A (en) 1987-10-22 1995-04-11 Temple University Of The Commonwealth System Of Higher Education 2',5'-phosphorothioate oligoadenylates and their covalent conjugates with polylysine
US5405938A (en) 1989-12-20 1995-04-11 Anti-Gene Development Group Sequence-specific binding polymers for duplex nucleic acids
US5414077A (en) 1990-02-20 1995-05-09 Gilead Sciences Non-nucleoside linkers for convenient attachment of labels to oligonucleotides using standard synthetic methods
US5417978A (en) 1993-07-29 1995-05-23 Board Of Regents, The University Of Texas System Liposomal antisense methyl phosphonate oligonucleotides and methods for their preparation and use
US5432272A (en) 1990-10-09 1995-07-11 Benner; Steven A. Method for incorporating into a DNA or RNA oligonucleotide using nucleotides bearing heterocyclic bases
US5434257A (en) 1992-06-01 1995-07-18 Gilead Sciences, Inc. Binding compentent oligomers containing unsaturated 3',5' and 2',5' linkages
US5446137A (en) 1993-12-09 1995-08-29 Syntex (U.S.A.) Inc. Oligonucleotides containing 4'-substituted nucleotides
US5451463A (en) 1989-08-28 1995-09-19 Clontech Laboratories, Inc. Non-nucleoside 1,3-diol reagents for labeling synthetic oligonucleotides
US5455233A (en) 1989-11-30 1995-10-03 University Of North Carolina Oligoribonucleoside and oligodeoxyribonucleoside boranophosphates
US5457187A (en) 1993-12-08 1995-10-10 Board Of Regents University Of Nebraska Oligonucleotides containing 5-fluorouracil
US5459255A (en) 1990-01-11 1995-10-17 Isis Pharmaceuticals, Inc. N-2 substituted purines
US5459127A (en) 1990-04-19 1995-10-17 Vical, Inc. Cationic lipids for intracellular delivery of biologically active molecules
US5462854A (en) 1993-04-19 1995-10-31 Beckman Instruments, Inc. Inverse linkage oligonucleotides for chemical and enzymatic processes
US5466677A (en) 1993-03-06 1995-11-14 Ciba-Geigy Corporation Dinucleoside phosphinates and their pharmaceutical compositions
US5466786A (en) 1989-10-24 1995-11-14 Gilead Sciences 2'modified nucleoside and nucleotide compounds
US5470967A (en) 1990-04-10 1995-11-28 The Dupont Merck Pharmaceutical Company Oligonucleotide analogs with sulfamate linkages
US5469854A (en) 1989-12-22 1995-11-28 Imarx Pharmaceutical Corp. Methods of preparing gas-filled liposomes
US5476925A (en) 1993-02-01 1995-12-19 Northwestern University Oligodeoxyribonucleotides including 3'-aminonucleoside-phosphoramidate linkages and terminal 3'-amino groups
US5484908A (en) 1991-11-26 1996-01-16 Gilead Sciences, Inc. Oligonucleotides containing 5-propynyl pyrimidines
US5486603A (en) 1990-01-08 1996-01-23 Gilead Sciences, Inc. Oligonucleotide having enhanced binding affinity
US5489677A (en) 1990-07-27 1996-02-06 Isis Pharmaceuticals, Inc. Oligonucleoside linkages containing adjacent oxygen and nitrogen atoms
US5491133A (en) 1987-11-30 1996-02-13 University Of Iowa Research Foundation Methods for blocking the expression of specifically targeted genes
US5502177A (en) 1993-09-17 1996-03-26 Gilead Sciences, Inc. Pyrimidine derivatives for labeled binding partners
US5510475A (en) 1990-11-08 1996-04-23 Hybridon, Inc. Oligonucleotide multiple reporter precursors
US5512295A (en) 1994-11-10 1996-04-30 The Board Of Trustees Of The Leland Stanford Junior University Synthetic liposomes for enhanced uptake and delivery
US5512439A (en) 1988-11-21 1996-04-30 Dynal As Oligonucleotide-linked magnetic particles and uses thereof
US5512667A (en) 1990-08-28 1996-04-30 Reed; Michael W. Trifunctional intermediates for preparing 3'-tailed oligonucleotides
US5514785A (en) 1990-05-11 1996-05-07 Becton Dickinson And Company Solid supports for nucleic acid hybridization assays
US5519134A (en) 1994-01-11 1996-05-21 Isis Pharmaceuticals, Inc. Pyrrolidine-containing monomers and oligomers
US5519126A (en) 1988-03-25 1996-05-21 University Of Virginia Alumni Patents Foundation Oligonucleotide N-alkylphosphoramidates
US5521291A (en) 1991-09-30 1996-05-28 Boehringer Ingelheim International, Gmbh Conjugates for introducing nucleic acid into higher eucaryotic cells
US5525711A (en) 1994-05-18 1996-06-11 The United States Of America As Represented By The Secretary Of The Department Of Health And Human Services Pteridine nucleotide analogs as fluorescent DNA probes
US5525465A (en) 1987-10-28 1996-06-11 Howard Florey Institute Of Experimental Physiology And Medicine Oligonucleotide-polyamide conjugates and methods of production and applications of the same
US5527528A (en) 1989-10-20 1996-06-18 Sequus Pharmaceuticals, Inc. Solid-tumor treatment method
US5534259A (en) 1993-07-08 1996-07-09 Liposome Technology, Inc. Polymer compound and coated particle composition
US5539082A (en) 1993-04-26 1996-07-23 Nielsen; Peter E. Peptide nucleic acids
US5541307A (en) 1990-07-27 1996-07-30 Isis Pharmaceuticals, Inc. Backbone modified oligonucleotide analogs and solid phase synthesis thereof
US5543165A (en) 1995-06-06 1996-08-06 Hill; Julie B. Process of making a soluble tea product with champagne-like properties
US5543152A (en) 1994-06-20 1996-08-06 Inex Pharmaceuticals Corporation Sphingosomes for enhanced drug delivery
US5545730A (en) 1984-10-16 1996-08-13 Chiron Corporation Multifunctional nucleic acid monomer
US5547932A (en) 1991-09-30 1996-08-20 Boehringer Ingelheim International Gmbh Composition for introducing nucleic acid complexes into higher eucaryotic cells
US5550111A (en) 1984-07-11 1996-08-27 Temple University-Of The Commonwealth System Of Higher Education Dual action 2',5'-oligoadenylate antiviral derivatives and uses thereof
US5552540A (en) 1987-06-24 1996-09-03 Howard Florey Institute Of Experimental Physiology And Medicine Nucleoside derivatives
US5556948A (en) 1993-01-22 1996-09-17 Mitsubishi Chemical Corporation Phospholipid derivatized with PEG bifunctional linker and liposome containing it
US5561225A (en) 1990-09-19 1996-10-01 Southern Research Institute Polynucleotide analogs containing sulfonate and sulfonamide internucleoside linkages
US5565552A (en) 1992-01-21 1996-10-15 Pharmacyclics, Inc. Method of expanded porphyrin-oligonucleotide conjugate synthesis
US5565350A (en) 1993-12-09 1996-10-15 Thomas Jefferson University Compounds and methods for site directed mutations in eukaryotic cells
US5567811A (en) 1990-05-03 1996-10-22 Amersham International Plc Phosphoramidite derivatives, their preparation and the use thereof in the incorporation of reporter groups on synthetic oligonucleotides
US5571799A (en) 1991-08-12 1996-11-05 Basco, Ltd. (2'-5') oligoadenylate analogues useful as inhibitors of host-v5.-graft response
US5574142A (en) 1992-12-15 1996-11-12 Microprobe Corporation Peptide linkers for improved oligonucleotide delivery
US5576427A (en) 1993-03-30 1996-11-19 Sterling Winthrop, Inc. Acyclic nucleoside analogs and oligonucleotide sequences containing them
US5578718A (en) 1990-01-11 1996-11-26 Isis Pharmaceuticals, Inc. Thiol-derivatized nucleosides
US5580575A (en) 1989-12-22 1996-12-03 Imarx Pharmaceutical Corp. Therapeutic drug delivery systems
US5580731A (en) 1994-08-25 1996-12-03 Chiron Corporation N-4 modified pyrimidine deoxynucleotides and oligonucleotide probes synthesized therewith
US5583020A (en) 1992-11-24 1996-12-10 Ribozyme Pharmaceuticals, Inc. Permeability enhancers for negatively charged polynucleotides
US5585481A (en) 1987-09-21 1996-12-17 Gen-Probe Incorporated Linking reagents for nucleotide probes
US5587361A (en) 1991-10-15 1996-12-24 Isis Pharmaceuticals, Inc. Oligonucleotides having phosphorothioate linkages of high chiral purity
US5587371A (en) 1992-01-21 1996-12-24 Pharmacyclics, Inc. Texaphyrin-oligonucleotide conjugates
US5591722A (en) 1989-09-15 1997-01-07 Southern Research Institute 2'-deoxy-4'-thioribonucleosides and their antiviral activity
US5591721A (en) 1994-10-25 1997-01-07 Hybridon, Inc. Method of down-regulating gene expression
US5595726A (en) 1992-01-21 1997-01-21 Pharmacyclics, Inc. Chromophore probe for detection of nucleic acid
US5596086A (en) 1990-09-20 1997-01-21 Gilead Sciences, Inc. Modified internucleoside linkages having one nitrogen and two carbon atoms
US5595756A (en) 1993-12-22 1997-01-21 Inex Pharmaceuticals Corporation Liposomal compositions for enhanced retention of bioactive agents
US5596091A (en) 1994-03-18 1997-01-21 The Regents Of The University Of California Antisense oligonucleotides comprising 5-aminoalkyl pyrimidine nucleotides
US5597909A (en) 1994-08-25 1997-01-28 Chiron Corporation Polynucleotide reagents containing modified deoxyribose moieties, and associated methods of synthesis and use
US5597696A (en) 1994-07-18 1997-01-28 Becton Dickinson And Company Covalent cyanine dye oligonucleotide conjugates
US5599928A (en) 1994-02-15 1997-02-04 Pharmacyclics, Inc. Texaphyrin compounds having improved functionalization
US5602240A (en) 1990-07-27 1997-02-11 Ciba Geigy Ag. Backbone modified oligonucleotide analogs
US5608046A (en) 1990-07-27 1997-03-04 Isis Pharmaceuticals, Inc. Conjugated 4'-desmethyl nucleoside analog compounds
US5610289A (en) 1990-07-27 1997-03-11 Isis Pharmaceuticals, Inc. Backbone modified oligonucleotide analogues
US5610300A (en) 1992-07-01 1997-03-11 Ciba-Geigy Corporation Carbocyclic nucleosides containing bicyclic rings, oligonucleotides therefrom, process for their preparation, their use and intermediates
US5614617A (en) 1990-07-27 1997-03-25 Isis Pharmaceuticals, Inc. Nuclease resistant, pyrimidine modified oligonucleotides that detect and modulate gene expression
US5618704A (en) 1990-07-27 1997-04-08 Isis Pharmacueticals, Inc. Backbone-modified oligonucleotide analogs and preparation thereof through radical coupling
US5623070A (en) 1990-07-27 1997-04-22 Isis Pharmaceuticals, Inc. Heteroatomic oligonucleoside linkages
US5623065A (en) 1990-08-13 1997-04-22 Isis Pharmaceuticals, Inc. Gapped 2' modified oligonucleotides
US5625050A (en) 1994-03-31 1997-04-29 Amgen Inc. Modified oligonucleotides and intermediates useful in nucleic acid therapeutics
US5627053A (en) 1994-03-29 1997-05-06 Ribozyme Pharmaceuticals, Inc. 2'deoxy-2'-alkylnucleotide containing nucleic acid
US5633360A (en) 1992-04-14 1997-05-27 Gilead Sciences, Inc. Oligonucleotide analogs capable of passive cell membrane permeation
US5639873A (en) 1992-02-05 1997-06-17 Centre National De La Recherche Scientifique (Cnrs) Oligothionucleotides
US5646265A (en) 1990-01-11 1997-07-08 Isis Pharmceuticals, Inc. Process for the preparation of 2'-O-alkyl purine phosphoramidites
US5652356A (en) 1995-08-17 1997-07-29 Hybridon, Inc. Inverted chimeric and hybrid oligonucleotides
US5652355A (en) 1992-07-23 1997-07-29 Worcester Foundation For Experimental Biology Hybrid oligonucleotide phosphorothioates
US5658873A (en) 1993-04-10 1997-08-19 Degussa Aktiengesellschaft Coated sodium percarbonate particles, a process for their production and detergent, cleaning and bleaching compositions containing them
US5663312A (en) 1993-03-31 1997-09-02 Sanofi Oligonucleotide dimers with amide linkages replacing phosphodiester linkages
US5670633A (en) 1990-01-11 1997-09-23 Isis Pharmaceuticals, Inc. Sugar modified oligonucleotides that detect and modulate gene expression
US5677437A (en) 1990-07-27 1997-10-14 Isis Pharmaceuticals, Inc. Heteroatomic oligonucleoside linkages
US5677439A (en) 1990-08-03 1997-10-14 Sanofi Oligonucleotide analogues containing phosphate diester linkage substitutes, compositions thereof, and precursor dinucleotide analogues
US5681941A (en) 1990-01-11 1997-10-28 Isis Pharmaceuticals, Inc. Substituted purines and oligonucleotide cross-linking
US5688941A (en) 1990-07-27 1997-11-18 Isis Pharmaceuticals, Inc. Methods of making conjugated 4' desmethyl nucleoside analog compounds
US5700922A (en) 1991-12-24 1997-12-23 Isis Pharmaceuticals, Inc. PNA-DNA-PNA chimeric macromolecules
US5714331A (en) 1991-05-24 1998-02-03 Buchardt, Deceased; Ole Peptide nucleic acids having enhanced binding affinity, sequence specificity and solubility
US5719262A (en) 1993-11-22 1998-02-17 Buchardt, Deceased; Ole Peptide nucleic acids having amino acid side chains
US5750692A (en) 1990-01-11 1998-05-12 Isis Pharmaceuticals, Inc. Synthesis of 3-deazapurines
WO2000058512A1 (en) 1999-03-26 2000-10-05 Isis Pharmaceuticals, Inc. Antisense modulation of interleukin-5 signal transduction
US6287860B1 (en) 2000-01-20 2001-09-11 Isis Pharmaceuticals, Inc. Antisense inhibition of MEKK2 expression
US6294520B1 (en) 1989-03-27 2001-09-25 Albert T. Naito Material for passage through the blood-brain barrier
WO2002048314A2 (en) 2000-11-01 2002-06-20 Isis Pharmaceuticals, Inc. Antisense modulation of raidd expression
US6632427B1 (en) 1994-12-13 2003-10-14 Aventis Pharma S.A. Adenoviral-vector-mediated gene transfer into medullary motor neurons
US20030225256A1 (en) 2002-05-31 2003-12-04 Isis Pharmaceuticals Inc. Antisense modulation of pctaire protein kinase 2 expression
US20040023906A1 (en) 2002-08-01 2004-02-05 Isis Pharmaceuticals Inc. Antisense modulation of phosphotyrosyl phosphatase activator expression
US6756523B1 (en) 1992-09-25 2004-06-29 Aventis Pharma S.A. Adenovirus vectors for the transfer of foreign genes into cells of the central nervous system particularly in brain
WO2005013901A2 (en) 2003-07-31 2005-02-17 Isis Pharmaceuticals, Inc. Oligomeric compounds and compositions for use in modulation of small non-coding rnas
US20050186594A1 (en) 2002-05-31 2005-08-25 Bennett C. F. Compositions and their uses directed to cell growth and maintenance proteins
US6936589B2 (en) 2001-09-28 2005-08-30 Albert T. Naito Parenteral delivery systems
CN1904900A (en) 2005-07-28 2007-01-31 中国科学院生物物理研究所 Human autogenous siRNA sequence, its application and screening method
US20070117772A1 (en) 2001-06-21 2007-05-24 Bennett C F Methods for slowing familial ALS disease progression
WO2007087113A2 (en) 2005-12-28 2007-08-02 The Scripps Research Institute Natural antisense and non-coding rna transcripts as drug targets
WO2009046397A2 (en) 2007-10-04 2009-04-09 Board Of Regents, The University Of Texas System Modulating gene expression with agrna and gapmers targeting antisense transcripts
US7517644B1 (en) 1991-08-23 2009-04-14 Larry J. Smith Method and compositions for cellular reprogramming
US7563884B2 (en) 2000-01-18 2009-07-21 Isis Pharmaceuticals, Inc. Antisense modulation of PTP1B expression
US9209196B2 (en) 2011-11-30 2015-12-08 Sharp Kabushiki Kaisha Memory circuit, method of driving the same, nonvolatile storage device using the same, and liquid crystal display device

Family Cites Families (213)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
NZ207394A (en) 1983-03-08 1987-03-06 Commw Serum Lab Commission Detecting or determining sequence of amino acids
US4754065A (en) 1984-12-18 1988-06-28 Cetus Corporation Precursor to nucleic acid probe
US5506337A (en) 1985-03-15 1996-04-09 Antivirals Inc. Morpholino-subunit combinatorial library and method
US4683195A (en) 1986-01-30 1987-07-28 Cetus Corporation Process for amplifying, detecting, and/or-cloning nucleic acid sequences
US4683202A (en) 1985-03-28 1987-07-28 Cetus Corporation Process for amplifying nucleic acid sequences
US4800159A (en) 1986-02-07 1989-01-24 Cetus Corporation Process for amplifying, detecting, and/or cloning nucleic acid sequences
US5288512A (en) 1987-12-15 1994-02-22 The Procter & Gamble Company Reduced calorie fats made from triglycerides containing medium and long chain fatty acids
NL8800756A (en) 1988-03-25 1989-10-16 Vereniging Voor Christelijk Wetenschappelijk Onderwijs GENETICALLY MANUFACTURED PLANT CELLS AND PLANTS AND USEABLE RECOMBINANT DNA.
US6203976B1 (en) 1989-07-18 2001-03-20 Osi Pharmaceuticals, Inc. Methods of preparing compositions comprising chemicals capable of transcriptional modulation
US5457189A (en) 1989-12-04 1995-10-10 Isis Pharmaceuticals Antisense oligonucleotide inhibition of papillomavirus
US5852188A (en) 1990-01-11 1998-12-22 Isis Pharmaceuticals, Inc. Oligonucleotides having chiral phosphorus linkages
US6034233A (en) 1990-05-04 2000-03-07 Isis Pharmaceuticals Inc. 2'-O-alkylated oligoribonucleotides and phosphorothioate analogs complementary to portions of the HIV genome
IE66205B1 (en) 1990-06-14 1995-12-13 Paul A Bartlett Polypeptide analogs
US5650489A (en) 1990-07-02 1997-07-22 The Arizona Board Of Regents Random bio-oligomer library, a method of synthesis thereof, and a method of use thereof
CA2096222C (en) 1990-11-13 1998-12-29 Stephen D. Lupton Bifunctional selectable fusion genes
US6307040B1 (en) 1992-03-05 2001-10-23 Isis Pharmaceuticals, Inc. Sugar modified oligonucleotides that detect and modulate gene expression
US5474796A (en) 1991-09-04 1995-12-12 Protogene Laboratories, Inc. Method and apparatus for conducting an array of chemical reactions on a support surface
US5661134A (en) 1991-10-15 1997-08-26 Isis Pharmaceuticals, Inc. Oligonucleotides for modulating Ha-ras or Ki-ras having phosphorothioate linkages of high chiral purity
US5576302A (en) 1991-10-15 1996-11-19 Isis Pharmaceuticals, Inc. Oligonucleotides for modulating hepatitis C virus having phosphorothioate linkages of high chiral purity
US6335434B1 (en) 1998-06-16 2002-01-01 Isis Pharmaceuticals, Inc., Nucleosidic and non-nucleosidic folate conjugates
US5605662A (en) 1993-11-01 1997-02-25 Nanogen, Inc. Active programmable electronic devices for molecular biological analysis and diagnostics
US5573905A (en) 1992-03-30 1996-11-12 The Scripps Research Institute Encoded combinatorial chemical libraries
IL101600A (en) 1992-04-15 2000-02-29 Yissum Res Dev Co Synthetic partially phosphorothioated antisense oligodeoxynucleotides and pharmaceutical compositions containing them
US5288514A (en) 1992-09-14 1994-02-22 The Regents Of The University Of California Solid phase and combinatorial synthesis of benzodiazepine compounds on a solid support
US6710174B2 (en) 2001-09-13 2004-03-23 Isis Pharmaceuticals, Inc. Antisense inhibition of vascular endothelial growth factor receptor-1 expression
EP1138766A3 (en) 1992-10-15 2003-05-02 Toray Industries, Inc. Process for preparing major histocompatibility antigen class II protein and materials having the same immobilized thereon
JPH08510130A (en) 1993-05-11 1996-10-29 ザ・ユニヴァーシティ・オヴ・ノース・キャロライナ・アト・チャペル・ヒル Antisense oligonucleotides that inhibit aberrant splicing and methods of using the same
CA2163427A1 (en) 1993-05-21 1994-12-08 Stephen D. Lupton Bifunctional selectable fusion genes based on the cytosine deaminase (cd) gene
ATE247128T1 (en) 1993-09-03 2003-08-15 Isis Pharmaceuticals Inc AMINODERIVATIZED NUCLEOSIDES AND OLIGONUCLEOSIDES
US5491084A (en) 1993-09-10 1996-02-13 The Trustees Of Columbia University In The City Of New York Uses of green-fluorescent protein
WO1995015373A2 (en) 1993-11-30 1995-06-08 Mcgill University Inhibition of dna methyltransferase
US5908779A (en) 1993-12-01 1999-06-01 University Of Connecticut Targeted RNA degradation using nuclear antisense RNA
US5593853A (en) 1994-02-09 1997-01-14 Martek Corporation Generation and screening of synthetic drug libraries
EP0745134A1 (en) 1994-02-22 1996-12-04 Danafarber Cancer Institute Nucleic acid delivery system, method of synthesis and uses thereof
US5902880A (en) 1994-08-19 1999-05-11 Ribozyme Pharmaceuticals, Inc. RNA polymerase III-based expression of therapeutic RNAs
US5539083A (en) 1994-02-23 1996-07-23 Isis Pharmaceuticals, Inc. Peptide nucleic acid combinatorial libraries and improved methods of synthesis
US6551618B2 (en) 1994-03-15 2003-04-22 University Of Birmingham Compositions and methods for delivery of agents for neuronal regeneration and survival
US6015880A (en) 1994-03-16 2000-01-18 California Institute Of Technology Method and substrate for performing multiple sequential reactions on a matrix
US5807522A (en) 1994-06-17 1998-09-15 The Board Of Trustees Of The Leland Stanford Junior University Methods for fabricating microarrays of biological samples
US5525735A (en) 1994-06-22 1996-06-11 Affymax Technologies Nv Methods for synthesizing diverse collections of pyrrolidine compounds
US5549974A (en) 1994-06-23 1996-08-27 Affymax Technologies Nv Methods for the solid phase synthesis of thiazolidinones, metathiazanones, and derivatives thereof
US6645943B1 (en) 1994-10-25 2003-11-11 Hybridon, Inc. Method of down-regulating gene expression
GB9501465D0 (en) 1995-01-25 1995-03-15 King S College London Nucleoside phosphorothioate derivatives,synthesis and use thereof
DE19502912A1 (en) 1995-01-31 1996-08-01 Hoechst Ag G-Cap Stabilized Oligonucleotides
IT1275862B1 (en) 1995-03-03 1997-10-24 Consiglio Nazionale Ricerche ANTI-SENSE TRANSCRIPT ASSOCIATED WITH SOME TYPES OF TUMOR CELLS AND SYNTHETIC OLIGODEOXYNUCLEOTIDES USEFUL IN DIAGNOSIS AND TREATMENT
IT1276642B1 (en) 1995-03-03 1997-11-03 Consiglio Nazionale Ricerche ANTI-SENSE TRANSCRIPT PRESENT IN B LYMPHOCYTES AND SYNTHETIC OLIGODEOXYNUCLEOTIDES USEFUL FOR INHIBIRING THEIR ACTION
US5739311A (en) 1995-06-07 1998-04-14 Gen-Probe Incorporated Enzymatic synthesis of phosphorothioate oligonucleotides using restriction endonucleases
US5569588A (en) 1995-08-09 1996-10-29 The Regents Of The University Of California Methods for drug screening
WO1997030067A1 (en) 1996-02-14 1997-08-21 Isis Pharmaceuticals, Inc. Sugar-modified gapped oligonucleotides
CA2246768C (en) 1996-03-14 2013-12-31 Genentech, Inc. Uses of gdnf and gdnf receptor
EP0910634A2 (en) 1996-04-17 1999-04-28 Hoechst Marion Roussel Deutschland GmbH ANTISENSE INHIBITORS OF VASCULAR ENDOTHELIAL GROWTH FACTOR (VEgF/VPF) EXPRESSION
US5786213A (en) 1996-04-18 1998-07-28 Board Of Regents, The University Of Texas System Inhibition of endogenous gastrin expression for treatment of colorectal cancer
US5756710A (en) 1996-06-05 1998-05-26 The Trustees Of Columbia University In City Of New York Phosphorothioate oligonucleotides that bind to the V3-loop and uses thereof
US5898031A (en) 1996-06-06 1999-04-27 Isis Pharmaceuticals, Inc. Oligoribonucleotides for cleaving RNA
US5849902A (en) 1996-09-26 1998-12-15 Oligos Etc. Inc. Three component chimeric antisense oligonucleotides
US5739119A (en) 1996-11-15 1998-04-14 Galli; Rachel L. Antisense oligonucleotides specific for the muscarinic type 2 acetylcholine receptor MRNA
US7008776B1 (en) 1996-12-06 2006-03-07 Aventis Pharmaceuticals Inc. Compositions and methods for effecting the levels of high density lipoprotein (HDL) cholesterol and apolipoprotein AI very low density lipoprotein (VLDL) cholesterol and low density lipoprotein (LDL) cholesterol
US7235653B2 (en) 1996-12-31 2007-06-26 Isis Pharmaceuticals, Inc. Oligonucleotide compositions and methods for the modulation of the expression of B7 protein
JP3756313B2 (en) 1997-03-07 2006-03-15 武 今西 Novel bicyclonucleosides and oligonucleotide analogues
US6013786A (en) 1997-08-22 2000-01-11 Hybridon, Inc. MDM2-specific antisense oligonucleotides
US6794499B2 (en) 1997-09-12 2004-09-21 Exiqon A/S Oligonucleotide analogues
US7572582B2 (en) 1997-09-12 2009-08-11 Exiqon A/S Oligonucleotide analogues
ATE293123T1 (en) 1997-09-12 2005-04-15 Exiqon As BI- AND TRI-CYCLIC - NUCLEOSIDE, NUCLEOTIDE AND OLIGONUCLEOTIDE ANALOGS
US7285288B1 (en) 1997-10-03 2007-10-23 Board Of Regents, The University Of Texas System Inhibition of Bcl-2 protein expression by liposomal antisense oligodeoxynucleotides
US6034883A (en) 1998-01-29 2000-03-07 Tinney; Charles E. Solid state director for beams
US6175409B1 (en) 1999-04-02 2001-01-16 Symyx Technologies, Inc. Flow-injection analysis and variable-flow light-scattering methods and apparatus for characterizing polymers
US7321828B2 (en) 1998-04-13 2008-01-22 Isis Pharmaceuticals, Inc. System of components for preparing oligonucleotides
US20040186071A1 (en) 1998-04-13 2004-09-23 Bennett C. Frank Antisense modulation of CD40 expression
US6221587B1 (en) 1998-05-12 2001-04-24 Isis Pharmceuticals, Inc. Identification of molecular interaction sites in RNA for novel drug discovery
US6833361B2 (en) 1998-05-26 2004-12-21 Ribapharm, Inc. Nucleosides having bicyclic sugar moiety
SK17432000A3 (en) 1998-05-26 2001-07-10 Icn Pharmaceuticals, Inc. Novel nucleosides having bicyclic sugar moiety
US6100090A (en) 1999-06-25 2000-08-08 Isis Pharmaceuticals Inc. Antisense inhibition of PI3K p85 expression
US20030139359A1 (en) 2001-12-04 2003-07-24 Isis Pharmaceuticals Inc. Antisense modulation of phospholipid scramblase 3 expression
US6867294B1 (en) 1998-07-14 2005-03-15 Isis Pharmaceuticals, Inc. Gapped oligomers having site specific chiral phosphorothioate internucleoside linkages
US6242589B1 (en) 1998-07-14 2001-06-05 Isis Pharmaceuticals, Inc. Phosphorothioate oligonucleotides having modified internucleoside linkages
US6214986B1 (en) 1998-10-07 2001-04-10 Isis Pharmaceuticals, Inc. Antisense modulation of bcl-x expression
AU1607100A (en) 1998-11-06 2000-05-29 Alcon Laboratories, Inc. Upregulation of endogenous prostaglandins to lower intraocular pressure
US5985663A (en) 1998-11-25 1999-11-16 Isis Pharmaceuticals Inc. Antisense inhibition of interleukin-15 expression
EP1146908B1 (en) 1999-01-27 2005-08-03 Becker, David, Dr. Formulations comprising antisense nucleotides to connexins
AU758956B2 (en) 1999-02-12 2003-04-03 Daiichi Sankyo Company, Limited Novel nucleosides and oligonucleotide analogues
ATE385237T1 (en) 1999-02-26 2008-02-15 Univ British Columbia ANTISENSE THERAPY FOR TRPM-2
JP4726302B2 (en) 1999-03-15 2011-07-20 ユニバーシティ オブ ブリティッシュ コロンビア Methods and reagents for regulating ABC1 polypeptide and cholesterol levels
US20040137423A1 (en) 1999-03-15 2004-07-15 Hayden Michael R. Compositions and methods for modulating HDL cholesterol and triglyceride levels
US7084125B2 (en) 1999-03-18 2006-08-01 Exiqon A/S Xylo-LNA analogues
CN1361829A (en) 1999-03-18 2002-07-31 埃克西库恩公司 Detection of mutations in genes by specific LNA primers
ES2269113T3 (en) 1999-03-24 2007-04-01 Exiqon A/S IMPROVED SYNTHESIS OF -2.2.1 / BICICLO-NUCLEOSIDOS.
US6734291B2 (en) 1999-03-24 2004-05-11 Exiqon A/S Synthesis of [2.2.1]bicyclo nucleosides
IL145526A0 (en) 1999-03-26 2002-06-30 Aventis Pharm Prod Inc Compositions and methods for effecting the levels of high density lipoprotein (hdl) chloesterol and apolipoprotein ai, very low density lipopritein (vldl) cholesterol and low density lipoprotein (ldl) cholesterol
WO2000061770A2 (en) 1999-04-08 2000-10-19 Chiron Corporation Enhancement of the immune response for vaccine and gene therapy applications
WO2000063365A1 (en) 1999-04-21 2000-10-26 Pangene Corporation Locked nucleic acid hybrids and methods of use
NZ514348A (en) 1999-05-04 2004-05-28 Exiqon As L-ribo-LNA analogues
US6525191B1 (en) 1999-05-11 2003-02-25 Kanda S. Ramasamy Conformationally constrained L-nucleosides
DE19925073C2 (en) 1999-06-01 2001-07-19 Stefan Weiss Nucleic acid molecules with specific recognition of native PrP · S ·· c ·, production and use
US6656730B1 (en) 1999-06-15 2003-12-02 Isis Pharmaceuticals, Inc. Oligonucleotides conjugated to protein-binding drugs
AU781437B2 (en) 1999-06-25 2005-05-26 Serono Genetics Institute S.A. A novel BAP28 gene and protein
US20040006031A1 (en) 2002-07-02 2004-01-08 Isis Pharmaceuticals Inc. Antisense modulation of HMG-CoA reductase expression
US6147200A (en) 1999-08-19 2000-11-14 Isis Pharmaceuticals, Inc. 2'-O-acetamido modified monomers and oligomers
WO2001021631A2 (en) 1999-09-20 2001-03-29 Millennium Pharmaceuticals, Inc. Secreted proteins and uses thereof
US6617442B1 (en) 1999-09-30 2003-09-09 Isis Pharmaceuticals, Inc. Human Rnase H1 and oligonucleotide compositions thereof
US6986988B2 (en) 1999-10-06 2006-01-17 Quark Biotech, Inc. Method for enrichment of natural antisense messenger RNA
IL148922A0 (en) 1999-10-06 2002-09-12 Quark Biotech Inc Method for enrichment of natural antisense messenger rna
WO2001051630A1 (en) 2000-01-07 2001-07-19 Baylor University Antisense compositions and methods
AU3091301A (en) 2000-01-14 2001-07-24 Us Health Methanocarba cycloalkyl nucleoside analogues
US6303374B1 (en) 2000-01-18 2001-10-16 Isis Pharmaceuticals Inc. Antisense modulation of caspase 3 expression
JP2001247459A (en) 2000-03-03 2001-09-11 Oakland Uniservices Ltd Combination therapy for cancer
OA12240A (en) 2000-03-27 2006-05-10 Univ Delaware Targeted chromosomal genomic alterations with modified single stranded oligonucleotides.
US6936467B2 (en) 2000-03-27 2005-08-30 University Of Delaware Targeted chromosomal genomic alterations with modified single stranded oligonucleotides
US7402434B2 (en) 2000-05-08 2008-07-22 Newman Stuart A Splice choice antagonists as therapeutic agents
JP2004530420A (en) 2000-06-29 2004-10-07 ファーマ パシフィック プロプライエタリー リミテッド Interferon-α inducible gene
EP1311262A4 (en) 2000-07-28 2005-06-01 Cancer Rec Tech Ltd Cancer treatment by combination therapy
EP1314734A1 (en) 2000-08-29 2003-05-28 Takeshi Imanishi Novel nucleoside analogs and oligonucleotide derivatives containing these analogs
EP1313768B1 (en) 2000-09-02 2008-02-06 Grünenthal GmbH Antisense oligonucleotides against vr1
US6444464B1 (en) 2000-09-08 2002-09-03 Isis Pharmaceuticals, Inc. Antisense modulation of E2F transcription factor 2 expression
WO2002024717A1 (en) 2000-09-20 2002-03-28 Isis Pharmaceuticals, Inc. Antisense modulation of flip-c expression
CA2422934A1 (en) 2000-10-13 2002-04-18 Institut De Cardiologie De Montreal Antisense oligonucleotides directed toward mammalian vegf receptor genes and uses thereof
US20030228618A1 (en) 2000-11-24 2003-12-11 Erez Levanon Methods and systems for identifying naturally occurring antisense transcripts and methods, kits and arrays utilizing same
US20050222029A1 (en) 2001-01-04 2005-10-06 Myriad Genetics, Incorporated Compositions and methods for treating diseases
US7423142B2 (en) 2001-01-09 2008-09-09 Alnylam Pharmaceuticals, Inc. Compositions and methods for inhibiting expression of anti-apoptotic genes
US20020147165A1 (en) 2001-02-22 2002-10-10 Isis Pharmaceuticals, Inc. Antisense modulation of calreticulin expression
AU2002234755A1 (en) 2001-02-26 2002-09-12 Pharma Pacific Pty Ltd Interferon-alpha induced gene
AUPR497101A0 (en) 2001-05-14 2001-06-07 Queensland University Of Technology Polynucleotides and polypeptides linked to cancer and/or tumorigenesi
IL143379A (en) 2001-05-24 2013-11-28 Yissum Res Dev Co Antisense oligonucleotide against the r isophorm of human ache and uses thereof
US7053195B1 (en) 2001-06-12 2006-05-30 Syngenta Participatious Ag Locked nucleic acid containing heteropolymers and related methods
US7153954B2 (en) 2001-07-12 2006-12-26 Santaris Pharma A/S Method for preparation of LNA phosphoramidites
EP2345720A3 (en) 2001-07-12 2012-01-25 University of Massachusetts In vivo production of small interfering RNAs that mediate gene silencing
US7425545B2 (en) 2001-07-25 2008-09-16 Isis Pharmaceuticals, Inc. Modulation of C-reactive protein expression
US20030096772A1 (en) 2001-07-30 2003-05-22 Crooke Rosanne M. Antisense modulation of acyl CoA cholesterol acyltransferase-2 expression
US7259150B2 (en) 2001-08-07 2007-08-21 Isis Pharmaceuticals, Inc. Modulation of apolipoprotein (a) expression
WO2003020739A2 (en) 2001-09-04 2003-03-13 Exiqon A/S Novel lna compositions and uses thereof
WO2003023015A2 (en) * 2001-09-13 2003-03-20 California Institute Of Technology Method for expression of small antiviral rna molecules within a cell
US20040214766A1 (en) 2001-10-01 2004-10-28 Kari Alitalo VEGF-C or VEGF-D materials and methods for treatment of neuropathologies
BR0213180A (en) 2001-10-10 2004-09-14 Nestle Sa Coffee plant with reduced alpha-d-galactosidase activity
AR037699A1 (en) 2001-12-04 2004-12-01 Monsanto Technology Llc TRANSGENIC CORN WITH IMPROVED PHENOTYPE
US7125982B1 (en) 2001-12-05 2006-10-24 Frayne Consultants Microbial production of nuclease resistant DNA, RNA, and oligo mixtures
US6965025B2 (en) 2001-12-10 2005-11-15 Isis Pharmaceuticals, Inc. Antisense modulation of connective tissue growth factor expression
CA2365811A1 (en) 2001-12-21 2003-06-21 Institut De Cardiologie A new gene therapy using antisense strategy to estrogen receptors (er .alpha. and/or er .beta.) to optimize vascular healing and cardioprotection after vascular injury
KR20030056538A (en) 2001-12-28 2003-07-04 주식회사 웰진 EFFECTIVE INHIBITION OF TRANSFORMING GROWTH FACTOR-β1 BY A RIBBON-TYPE ANTISENSE OLIGONUCLEOTIDE
US20030191075A1 (en) 2002-02-22 2003-10-09 Cook Phillip Dan Method of using modified oligonucleotides for hepatic delivery
US20050143357A1 (en) 2002-02-25 2005-06-30 Ake Pousette Vitamin d upregulated protein 1 (vdup-) methods and uses thereof
AU2003225701A1 (en) 2002-03-08 2003-09-22 Glen Research Corporation Fluorescent nitrogenous base and nucleosides incorporating same
GB2386836B (en) 2002-03-22 2006-07-26 Cancer Res Ventures Ltd Anti-cancer combinations
US7169916B2 (en) 2002-04-01 2007-01-30 Isis Pharmaceuticals, Inc. Chloral-free DCA in oligonucleotide synthesis
US20050215504A1 (en) 2002-04-02 2005-09-29 Bennett C F Antisense modulation of sterol regulatory element-binding protein-1 expression
ES2649817T3 (en) 2002-04-05 2018-01-15 Roche Innovation Center Copenhagen A/S Oligomeric compounds for modulation of the expression of HIF-1¿Á
US6808906B2 (en) 2002-05-08 2004-10-26 Rigel Pharmaceuticals, Inc. Directionally cloned random cDNA expression vector libraries, compositions and methods of use
US7569575B2 (en) 2002-05-08 2009-08-04 Santaris Pharma A/S Synthesis of locked nucleic acid derivatives
US7199107B2 (en) 2002-05-23 2007-04-03 Isis Pharmaceuticals, Inc. Antisense modulation of kinesin-like 1 expression
US7148342B2 (en) 2002-07-24 2006-12-12 The Trustees Of The University Of Pennyslvania Compositions and methods for sirna inhibition of angiogenesis
US20040033480A1 (en) 2002-08-15 2004-02-19 Wong Norman C.W. Use of resveratrol to regulate expression of apolipoprotein A1
EP1555870A4 (en) 2002-09-10 2006-11-02 Samuel Roberts Noble Found Inc METHODS AND COMPOSITIONS FOR GENERATING NUTRACEUTICAL PRODUCTS CONTAINING FLAVONOIDS AND ISOFLAVONOIDS
EP1549387A1 (en) 2002-09-25 2005-07-06 Pharmacia Corporation Antisense modulation of farnesoid x receptor expression
WO2004031350A2 (en) 2002-09-26 2004-04-15 Amgen, Inc. Modulation of forkhead box o1a expression
GB2394658A (en) 2002-11-01 2004-05-05 Cancer Rec Tech Ltd Oral anti-cancer composition
JP5449639B2 (en) 2002-11-01 2014-03-19 ザ トラスティーズ オブ ザ ユニバーシティ オブ ペンシルバニア Compositions and methods for siRNA inhibition of HIF-1 alpha
US20040152651A1 (en) 2002-11-01 2004-08-05 Rana Tariq M. Regulation of transcription elongation factors
EP1562971B1 (en) 2002-11-05 2014-02-12 Isis Pharmaceuticals, Inc. Polycyclic sugar surrogate-containing oligomeric compounds and compositions for use in gene modulation
AU2003290596B2 (en) 2002-11-05 2011-05-12 Isis Pharmaceuticals, Inc. Sugar surrogate-containing oligomeric compounds and compositions for use in gene modulation
US20060009410A1 (en) 2002-11-13 2006-01-12 Crooke Rosanne M Effects of apolipoprotein B inhibition on gene expression profiles in animals
CA2506576C (en) 2002-11-18 2018-03-06 Santaris Pharma A/S Antisense gapmer oligonucleotides
US7144999B2 (en) 2002-11-23 2006-12-05 Isis Pharmaceuticals, Inc. Modulation of hypoxia-inducible factor 1 alpha expression
US7713738B2 (en) 2003-02-10 2010-05-11 Enzon Pharmaceuticals, Inc. Oligomeric compounds for the modulation of survivin expression
US7598227B2 (en) 2003-04-16 2009-10-06 Isis Pharmaceuticals Inc. Modulation of apolipoprotein C-III expression
US7339051B2 (en) 2003-04-28 2008-03-04 Isis Pharmaceuticals, Inc. Compositions and methods for the treatment of severe acute respiratory syndrome (SARS)
WO2004108081A2 (en) 2003-06-02 2004-12-16 Isis Pharmaceuticals, Inc. Oligonucleotide synthesis with alternative solvents
AU2004253455B2 (en) 2003-06-03 2011-03-03 Eli Lilly And Company Modulation of survivin expression
US7825235B2 (en) 2003-08-18 2010-11-02 Isis Pharmaceuticals, Inc. Modulation of diacylglycerol acyltransferase 2 expression
EP1668130A2 (en) 2003-09-18 2006-06-14 Isis Pharmaceuticals, Inc. Modulation of eif4e expression
US8258105B2 (en) 2003-10-07 2012-09-04 Isis Pharmaceuticals, Inc. Antisense oligonucleotides optimized for kidney targeting
EP1675948A2 (en) 2003-10-23 2006-07-05 Sirna Therapeutics, Inc. RNA INTERFERENCE MEDIATED TREATMENT OF PARKINSON DISEASE USING SHORT INTERERING NUCLEIC ACID (siNA)
JP4642775B2 (en) 2003-12-23 2011-03-02 サンタリス ファーマ アー／エス Oligomer compounds for modulation of BCL-2
JP4801802B2 (en) 2004-01-12 2011-10-26 ザ・トラスティーズ・オブ・ザ・ユニバーシティ・オブ・ペンシルバニア Systems and methods for upregulating bone morphogenetic protein (BMP) gene expression in bone cells via application of electric fields generated by specific selective electrical and electromagnetic signals
JPWO2005071085A1 (en) * 2004-01-22 2007-09-06 株式会社ディナベック研究所 Method for producing viral vector
US7468431B2 (en) 2004-01-22 2008-12-23 Isis Pharmaceuticals, Inc. Modulation of eIF4E-BP2 expression
GB0403041D0 (en) 2004-02-11 2004-03-17 Milner Anne J Induction of apoptosis
EP1566202A1 (en) 2004-02-23 2005-08-24 Sahltech I Göteborg AB Use of resistin antagonists in the treatment of rheumatoid arthritis
US7402574B2 (en) 2004-03-12 2008-07-22 Avi Biopharma, Inc. Antisense composition and method for treating cancer
US8394947B2 (en) 2004-06-03 2013-03-12 Isis Pharmaceuticals, Inc. Positionally modified siRNA constructs
WO2006085987A2 (en) 2004-07-09 2006-08-17 University Of Iowa Research Foundation Rna interference in respiratory epitheial cells
WO2006023880A2 (en) 2004-08-23 2006-03-02 Isis Pharmaceuticals, Inc. Compounds and methods for the characterization of oligonucleotides
JP4825807B2 (en) 2004-11-09 2011-11-30 サンタリス ファーマ アー／エス Powerful LNA oligonucleotides for inhibition of HIF-1a expression
US7220549B2 (en) 2004-12-30 2007-05-22 Helicos Biosciences Corporation Stabilizing a nucleic acid for nucleic acid sequencing
EP1846034A4 (en) * 2005-02-02 2010-11-10 Uab Research Foundation AGENTS AND METHODS FOR REDUCING AGONIST RESISTANCE OF APOPTOSIS-INDUCING DEATH RECEPTORS
US8333971B2 (en) * 2006-05-15 2012-12-18 Immunomedics, Inc. Methods and compositions for treatment of human immunodeficiency virus infection with conjugated antibodies or antibody fragments
AU2006261732B2 (en) 2005-06-27 2011-09-15 Alnylam Pharmaceuticals, Inc. RNAi modulation of HIF-1 and theraputic uses thereof
US20070213292A1 (en) 2005-08-10 2007-09-13 The Rockefeller University Chemically modified oligonucleotides for use in modulating micro RNA and uses thereof
WO2007028065A2 (en) 2005-08-30 2007-03-08 Isis Pharmaceuticals, Inc. Chimeric oligomeric compounds for modulation of splicing
US7320965B2 (en) 2005-10-28 2008-01-22 Alnylam Pharmaceuticals, Inc. Compositions and methods for inhibiting expression of Huntingtin gene
US7582745B2 (en) 2005-11-04 2009-09-01 Alnylam Pharmaceuticals, Inc. Compositions and methods for inhibiting expression of Nav1.8 gene
CA2629664A1 (en) 2005-11-17 2007-08-02 Board Of Regents, The University Of Texas System Modulation of gene expression by oligomers targeted to chromosomal dna
WO2007102861A2 (en) 2005-12-02 2007-09-13 Sirtris Pharmaceuticals, Inc. Modulators of cdc2-like kinases (clks) and methods of use thereof
US20070231816A1 (en) 2005-12-09 2007-10-04 Baylor Research Institute Module-Level Analysis of Peripheral Blood Leukocyte Transcriptional Profiles
WO2007071824A1 (en) 2005-12-20 2007-06-28 Oy Jurilab Ltd Novel genes and markers associated with high-density lipoprotein -cholesterol (hdl-c)
CN100356377C (en) 2005-12-20 2007-12-19 无锡永中科技有限公司 Document display method
DK1984381T3 (en) 2006-01-27 2010-11-01 Isis Pharmaceuticals Inc 6-modified bicyclic nucleic acid analogues
US7569686B1 (en) 2006-01-27 2009-08-04 Isis Pharmaceuticals, Inc. Compounds and methods for synthesis of bicyclic nucleic acid analogs
US7718629B2 (en) 2006-03-31 2010-05-18 Alnylam Pharmaceuticals, Inc. Compositions and methods for inhibiting expression of Eg5 gene
EP2023939B1 (en) 2006-05-05 2012-06-27 Isis Pharmaceuticals, Inc. Compounds and methods for modulating expression of pcsk9
EP3578656B1 (en) 2006-05-11 2021-01-06 Alnylam Pharmaceuticals, Inc. Compositions and methods for inhibiting expression of the pcsk9 gene
US7547684B2 (en) 2006-05-11 2009-06-16 Isis Pharmaceuticals, Inc. 5′-modified bicyclic nucleic acid analogs
US7666854B2 (en) 2006-05-11 2010-02-23 Isis Pharmaceuticals, Inc. Bis-modified bicyclic nucleic acid analogs
EP1867338A1 (en) 2006-05-30 2007-12-19 Université Libre De Bruxelles Pharmaceutical composition comprising apolipoproteins for the treatment of human diseases
WO2008066672A2 (en) 2006-11-06 2008-06-05 Beth Israel Deaconess Medical Center Identification and use of small molecules to modulate transcription factor function and to treat transcription factor associated diseases
WO2008057556A2 (en) 2006-11-06 2008-05-15 Beth Israel Deaconess Medical Center Identification and use of small molecules to modulate ese-1 transcription factor function and to treat ese-1 transcription factor associated diseases
US8093222B2 (en) 2006-11-27 2012-01-10 Isis Pharmaceuticals, Inc. Methods for treating hypercholesterolemia
US20100169996A1 (en) 2007-01-19 2010-07-01 Lionel Navarro Methods and compositions for modulating the sirna and rna-directed-dna methylation pathways
US20090053145A1 (en) * 2007-01-26 2009-02-26 University Of Georgia Research Foundation, Inc. Anti-viral compositions and methods of use in cattle
US20100255117A1 (en) 2007-04-06 2010-10-07 The Johns Hopkins University Methods and compositions for the treatment of cancer
US20080293142A1 (en) 2007-04-19 2008-11-27 The Board Of Regents For Oklahoma State University Multiple shRNA Expression Vectors and Methods of Construction
CA2729713C (en) 2008-07-01 2020-07-28 Monsanto Technology Llc Recombinant dna constructs and methods for modulating expression of a target gene
MX339820B (en) 2008-10-03 2016-06-13 Curna Inc Treatment of apolipoprotein-a1 related diseases by inhibition of natural antisense transcript to apolipoprotein-a1.
EP2177615A1 (en) 2008-10-10 2010-04-21 Fraunhofer-Gesellschaft zur Förderung der angewandten Forschung e.V. Method for a genome wide identification of expression regulatory sequences and use of genes and molecules derived thereof for the diagnosis and therapy of metabolic and/or tumorous diseases
US8606289B2 (en) 2008-11-10 2013-12-10 Qualcomm Incorporated Power headroom-sensitive scheduling
JP2012509306A (en) 2008-11-22 2012-04-19 ザ ユニバーシティ オブ ブリストル New use of VEGFxxxb

Patent Citations (202)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US3687808A (en) 1969-08-14 1972-08-29 Univ Leland Stanford Junior Synthetic polynucleotides
US4469863A (en) 1980-11-12 1984-09-04 Ts O Paul O P Nonionic nucleic acid alkyl and aryl phosphonates and processes for manufacture and use thereof
US4426330A (en) 1981-07-20 1984-01-17 Lipid Specialties, Inc. Synthetic phospholipid compounds
US4534899A (en) 1981-07-20 1985-08-13 Lipid Specialties, Inc. Synthetic phospholipid compounds
US5023243A (en) 1981-10-23 1991-06-11 Molecular Biosystems, Inc. Oligonucleotide therapeutic agent and method of making same
US4476301A (en) 1982-04-29 1984-10-09 Centre National De La Recherche Scientifique Oligonucleotides, a process for preparing the same and their application as mediators of the action of interferon
US4789737A (en) 1982-08-09 1988-12-06 Wakunaga Seiyaku Kabushiki Kaisha Oligonucleotide derivatives and production thereof
US4667025A (en) 1982-08-09 1987-05-19 Wakunaga Seiyaku Kabushiki Kaisha Oligonucleotide derivatives
US4835263A (en) 1983-01-27 1989-05-30 Centre National De La Recherche Scientifique Novel compounds containing an oligonucleotide sequence bonded to an intercalating agent, a process for their synthesis and their use
US4605735A (en) 1983-02-14 1986-08-12 Wakunaga Seiyaku Kabushiki Kaisha Oligonucleotide derivatives
US5541313A (en) 1983-02-22 1996-07-30 Molecular Biosystems, Inc. Single-stranded labelled oligonucleotides of preselected sequence
US4948882A (en) 1983-02-22 1990-08-14 Syngene, Inc. Single-stranded labelled oligonucleotides, reactive monomers and methods of synthesis
US4824941A (en) 1983-03-10 1989-04-25 Julian Gordon Specific antibody to the native form of 2'5'-oligonucleotides, the method of preparation and the use as reagents in immunoassays or for binding 2'5'-oligonucleotides in biological systems
US4587044A (en) 1983-09-01 1986-05-06 The Johns Hopkins University Linkage of proteins to nucleic acids
US5118800A (en) 1983-12-20 1992-06-02 California Institute Of Technology Oligonucleotides possessing a primary amino group in the terminal nucleotide
US5118802A (en) 1983-12-20 1992-06-02 California Institute Of Technology DNA-reporter conjugates linked via the 2' or 5'-primary amino group of the 5'-terminal nucleoside
US5550111A (en) 1984-07-11 1996-08-27 Temple University-Of The Commonwealth System Of Higher Education Dual action 2',5'-oligoadenylate antiviral derivatives and uses thereof
US4981957A (en) 1984-07-19 1991-01-01 Centre National De La Recherche Scientifique Oligonucleotides with modified phosphate and modified carbohydrate moieties at the respective chain termini
US5545730A (en) 1984-10-16 1996-08-13 Chiron Corporation Multifunctional nucleic acid monomer
US5258506A (en) 1984-10-16 1993-11-02 Chiron Corporation Photolabile reagents for incorporation into oligonucleotide chains
US5367066A (en) 1984-10-16 1994-11-22 Chiron Corporation Oligonucleotides with selectably cleavable and/or abasic sites
US5552538A (en) 1984-10-16 1996-09-03 Chiron Corporation Oligonucleotides with cleavable sites
US5578717A (en) 1984-10-16 1996-11-26 Chiron Corporation Nucleotides for introducing selectably cleavable and/or abasic sites into oligonucleotides
US4828979A (en) 1984-11-08 1989-05-09 Life Technologies, Inc. Nucleotide analogs for nucleic acid labeling and detection
US4845205A (en) 1985-01-08 1989-07-04 Institut Pasteur 2,N6 -disubstituted and 2,N6 -trisubstituted adenosine-3'-phosphoramidites
US5034506A (en) 1985-03-15 1991-07-23 Anti-Gene Development Group Uncharged morpholino-based polymers having achiral intersubunit linkages
US5235033A (en) 1985-03-15 1993-08-10 Anti-Gene Development Group Alpha-morpholino ribonucleoside derivatives and polymers thereof
US5185444A (en) 1985-03-15 1993-02-09 Anti-Gene Deveopment Group Uncharged morpolino-based polymers having phosphorous containing chiral intersubunit linkages
US4762779A (en) 1985-06-13 1988-08-09 Amgen Inc. Compositions and methods for functionalizing nucleic acids
US5317098A (en) 1986-03-17 1994-05-31 Hiroaki Shizuya Non-radioisotope tagging of fragments
US4876335A (en) 1986-06-30 1989-10-24 Wakunaga Seiyaku Kabushiki Kaisha Poly-labelled oligonucleotide derivative
US5013830A (en) 1986-09-08 1991-05-07 Ajinomoto Co., Inc. Compounds for the cleavage at a specific position of RNA, oligomers employed for the formation of said compounds, and starting materials for the synthesis of said oligomers
US5286717A (en) 1987-03-25 1994-02-15 The United States Of America As Represented By The Department Of Health And Human Services Inhibitors for replication of retroviruses and for the expression of oncogene products
US5276019A (en) 1987-03-25 1994-01-04 The United States Of America As Represented By The Department Of Health And Human Services Inhibitors for replication of retroviruses and for the expression of oncogene products
US5264423A (en) 1987-03-25 1993-11-23 The United States Of America As Represented By The Department Of Health And Human Services Inhibitors for replication of retroviruses and for the expression of oncogene products
US4904582A (en) 1987-06-11 1990-02-27 Synthetic Genetics Novel amphiphilic nucleic acid conjugates
US5552540A (en) 1987-06-24 1996-09-03 Howard Florey Institute Of Experimental Physiology And Medicine Nucleoside derivatives
US5585481A (en) 1987-09-21 1996-12-17 Gen-Probe Incorporated Linking reagents for nucleotide probes
US5188897A (en) 1987-10-22 1993-02-23 Temple University Of The Commonwealth System Of Higher Education Encapsulated 2',5'-phosphorothioate oligoadenylates
US5405939A (en) 1987-10-22 1995-04-11 Temple University Of The Commonwealth System Of Higher Education 2',5'-phosphorothioate oligoadenylates and their covalent conjugates with polylysine
US5525465A (en) 1987-10-28 1996-06-11 Howard Florey Institute Of Experimental Physiology And Medicine Oligonucleotide-polyamide conjugates and methods of production and applications of the same
US5112963A (en) 1987-11-12 1992-05-12 Max-Planck-Gesellschaft Zur Foerderung Der Wissenschaften E.V. Modified oligonucleotides
US4866042A (en) 1987-11-18 1989-09-12 Neuwelt Edward A Method for the delivery of genetic material across the blood brain barrier
US5491133A (en) 1987-11-30 1996-02-13 University Of Iowa Research Foundation Methods for blocking the expression of specifically targeted genes
US5403711A (en) 1987-11-30 1995-04-04 University Of Iowa Research Foundation Nucleic acid hybridization and amplification method for detection of specific sequences in which a complementary labeled nucleic acid probe is cleaved
US5082830A (en) 1988-02-26 1992-01-21 Enzo Biochem, Inc. End labeled nucleotide probe
US5519126A (en) 1988-03-25 1996-05-21 University Of Virginia Alumni Patents Foundation Oligonucleotide N-alkylphosphoramidates
US5278302A (en) 1988-05-26 1994-01-11 University Patents, Inc. Polynucleotide phosphorodithioates
US5453496A (en) 1988-05-26 1995-09-26 University Patents, Inc. Polynucleotide phosphorodithioate
US5109124A (en) 1988-06-01 1992-04-28 Biogen, Inc. Nucleic acid probe linked to a label having a terminal cysteine
US5216141A (en) 1988-06-06 1993-06-01 Benner Steven A Oligonucleotide analogs containing sulfur linkages
US5175273A (en) 1988-07-01 1992-12-29 Genentech, Inc. Nucleic acid intercalating agents
US5262536A (en) 1988-09-15 1993-11-16 E. I. Du Pont De Nemours And Company Reagents for the preparation of 5'-tagged oligonucleotides
US5512439A (en) 1988-11-21 1996-04-30 Dynal As Oligonucleotide-linked magnetic particles and uses thereof
US5599923A (en) 1989-03-06 1997-02-04 Board Of Regents, University Of Tx Texaphyrin metal complexes having improved functionalization
US5354844A (en) 1989-03-16 1994-10-11 Boehringer Ingelheim International Gmbh Protein-polycation conjugates
US6294520B1 (en) 1989-03-27 2001-09-25 Albert T. Naito Material for passage through the blood-brain barrier
US5416016A (en) 1989-04-03 1995-05-16 Purdue Research Foundation Method for enhancing transmembrane transport of exogenous molecules
US5108921A (en) 1989-04-03 1992-04-28 Purdue Research Foundation Method for enhanced transmembrane transport of exogenous molecules
US5391723A (en) 1989-05-31 1995-02-21 Neorx Corporation Oligonucleotide conjugates
US5256775A (en) 1989-06-05 1993-10-26 Gilead Sciences, Inc. Exonuclease-resistant oligonucleotides
US5416203A (en) 1989-06-06 1995-05-16 Northwestern University Steroid modified oligonucleotides
US4958013A (en) 1989-06-06 1990-09-18 Northwestern University Cholesteryl modified oligonucleotides
US5227170A (en) 1989-06-22 1993-07-13 Vestar, Inc. Encapsulation process
US5451463A (en) 1989-08-28 1995-09-19 Clontech Laboratories, Inc. Non-nucleoside 1,3-diol reagents for labeling synthetic oligonucleotides
US5134066A (en) 1989-08-29 1992-07-28 Monsanto Company Improved probes using nucleosides containing 3-dezauracil analogs
US5254469A (en) 1989-09-12 1993-10-19 Eastman Kodak Company Oligonucleotide-enzyme conjugate that can be used as a probe in hybridization assays and polymerase chain reaction procedures
US5591722A (en) 1989-09-15 1997-01-07 Southern Research Institute 2'-deoxy-4'-thioribonucleosides and their antiviral activity
US5213804A (en) 1989-10-20 1993-05-25 Liposome Technology, Inc. Solid tumor treatment method and composition
US5356633A (en) 1989-10-20 1994-10-18 Liposome Technology, Inc. Method of treatment of inflamed tissues
US5527528A (en) 1989-10-20 1996-06-18 Sequus Pharmaceuticals, Inc. Solid-tumor treatment method
US5013556A (en) 1989-10-20 1991-05-07 Liposome Technology, Inc. Liposomes with enhanced circulation time
US5399676A (en) 1989-10-23 1995-03-21 Gilead Sciences Oligonucleotides with inverted polarity
US5264562A (en) 1989-10-24 1993-11-23 Gilead Sciences, Inc. Oligonucleotide analogs with novel linkages
US5466786A (en) 1989-10-24 1995-11-14 Gilead Sciences 2'modified nucleoside and nucleotide compounds
US5466786B1 (en) 1989-10-24 1998-04-07 Gilead Sciences 2' Modified nucleoside and nucleotide compounds
US5264564A (en) 1989-10-24 1993-11-23 Gilead Sciences Oligonucleotide analogs with novel linkages
US5292873A (en) 1989-11-29 1994-03-08 The Research Foundation Of State University Of New York Nucleic acids labeled with naphthoquinone probe
US5455233A (en) 1989-11-30 1995-10-03 University Of North Carolina Oligoribonucleoside and oligodeoxyribonucleoside boranophosphates
US5130302A (en) 1989-12-20 1992-07-14 Boron Bilogicals, Inc. Boronated nucleoside, nucleotide and oligonucleotide compounds, compositions and methods for using same
US5405938A (en) 1989-12-20 1995-04-11 Anti-Gene Development Group Sequence-specific binding polymers for duplex nucleic acids
US5166315A (en) 1989-12-20 1992-11-24 Anti-Gene Development Group Sequence-specific binding polymers for duplex nucleic acids
US5580575A (en) 1989-12-22 1996-12-03 Imarx Pharmaceutical Corp. Therapeutic drug delivery systems
US5469854A (en) 1989-12-22 1995-11-28 Imarx Pharmaceutical Corp. Methods of preparing gas-filled liposomes
US5486603A (en) 1990-01-08 1996-01-23 Gilead Sciences, Inc. Oligonucleotide having enhanced binding affinity
US5750692A (en) 1990-01-11 1998-05-12 Isis Pharmaceuticals, Inc. Synthesis of 3-deazapurines
US5646265A (en) 1990-01-11 1997-07-08 Isis Pharmceuticals, Inc. Process for the preparation of 2'-O-alkyl purine phosphoramidites
US5587469A (en) 1990-01-11 1996-12-24 Isis Pharmaceuticals, Inc. Oligonucleotides containing N-2 substituted purines
US5459255A (en) 1990-01-11 1995-10-17 Isis Pharmaceuticals, Inc. N-2 substituted purines
US5681941A (en) 1990-01-11 1997-10-28 Isis Pharmaceuticals, Inc. Substituted purines and oligonucleotide cross-linking
US5578718A (en) 1990-01-11 1996-11-26 Isis Pharmaceuticals, Inc. Thiol-derivatized nucleosides
US5670633A (en) 1990-01-11 1997-09-23 Isis Pharmaceuticals, Inc. Sugar modified oligonucleotides that detect and modulate gene expression
US5220007A (en) 1990-02-15 1993-06-15 The Worcester Foundation For Experimental Biology Method of site-specific alteration of RNA and production of encoded polypeptides
US5366878A (en) 1990-02-15 1994-11-22 The Worcester Foundation For Experimental Biology Method of site-specific alteration of RNA and production of encoded polypeptides
US5149797A (en) 1990-02-15 1992-09-22 The Worcester Foundation For Experimental Biology Method of site-specific alteration of rna and production of encoded polypeptides
US5214136A (en) 1990-02-20 1993-05-25 Gilead Sciences, Inc. Anthraquinone-derivatives oligonucleotides
US5414077A (en) 1990-02-20 1995-05-09 Gilead Sciences Non-nucleoside linkers for convenient attachment of labels to oligonucleotides using standard synthetic methods
US5541306A (en) 1990-03-08 1996-07-30 Worcester Foundation For Biomedical Research Aminoalkylphosphotriester oligonucleotide derivatives
US5536821A (en) 1990-03-08 1996-07-16 Worcester Foundation For Biomedical Research Aminoalkylphosphorothioamidate oligonucleotide deratives
US5563253A (en) 1990-03-08 1996-10-08 Worcester Foundation For Biomedical Research Linear aminoalkylphosphoramidate oligonucleotide derivatives
US5321131A (en) 1990-03-08 1994-06-14 Hybridon, Inc. Site-specific functionalization of oligodeoxynucleotides for non-radioactive labelling
US5470967A (en) 1990-04-10 1995-11-28 The Dupont Merck Pharmaceutical Company Oligonucleotide analogs with sulfamate linkages
US5459127A (en) 1990-04-19 1995-10-17 Vical, Inc. Cationic lipids for intracellular delivery of biologically active molecules
US5567811A (en) 1990-05-03 1996-10-22 Amersham International Plc Phosphoramidite derivatives, their preparation and the use thereof in the incorporation of reporter groups on synthetic oligonucleotides
US5514785A (en) 1990-05-11 1996-05-07 Becton Dickinson And Company Solid supports for nucleic acid hybridization assays
US5614617A (en) 1990-07-27 1997-03-25 Isis Pharmaceuticals, Inc. Nuclease resistant, pyrimidine modified oligonucleotides that detect and modulate gene expression
US5610289A (en) 1990-07-27 1997-03-11 Isis Pharmaceuticals, Inc. Backbone modified oligonucleotide analogues
US5138045A (en) 1990-07-27 1992-08-11 Isis Pharmaceuticals Polyamine conjugated oligonucleotides
US5677437A (en) 1990-07-27 1997-10-14 Isis Pharmaceuticals, Inc. Heteroatomic oligonucleoside linkages
US5688941A (en) 1990-07-27 1997-11-18 Isis Pharmaceuticals, Inc. Methods of making conjugated 4' desmethyl nucleoside analog compounds
US5602240A (en) 1990-07-27 1997-02-11 Ciba Geigy Ag. Backbone modified oligonucleotide analogs
US5218105A (en) 1990-07-27 1993-06-08 Isis Pharmaceuticals Polyamine conjugated oligonucleotides
US5623070A (en) 1990-07-27 1997-04-22 Isis Pharmaceuticals, Inc. Heteroatomic oligonucleoside linkages
US5489677A (en) 1990-07-27 1996-02-06 Isis Pharmaceuticals, Inc. Oligonucleoside linkages containing adjacent oxygen and nitrogen atoms
US5608046A (en) 1990-07-27 1997-03-04 Isis Pharmaceuticals, Inc. Conjugated 4'-desmethyl nucleoside analog compounds
US5541307A (en) 1990-07-27 1996-07-30 Isis Pharmaceuticals, Inc. Backbone modified oligonucleotide analogs and solid phase synthesis thereof
US5618704A (en) 1990-07-27 1997-04-08 Isis Pharmacueticals, Inc. Backbone-modified oligonucleotide analogs and preparation thereof through radical coupling
US5677439A (en) 1990-08-03 1997-10-14 Sanofi Oligonucleotide analogues containing phosphate diester linkage substitutes, compositions thereof, and precursor dinucleotide analogues
US5567810A (en) 1990-08-03 1996-10-22 Sterling Drug, Inc. Nuclease resistant compounds
US5245022A (en) 1990-08-03 1993-09-14 Sterling Drug, Inc. Exonuclease resistant terminally substituted oligonucleotides
US5623065A (en) 1990-08-13 1997-04-22 Isis Pharmaceuticals, Inc. Gapped 2' modified oligonucleotides
US5177196A (en) 1990-08-16 1993-01-05 Microprobe Corporation Oligo (α-arabinofuranosyl nucleotides) and α-arabinofuranosyl precursors thereof
US5512667A (en) 1990-08-28 1996-04-30 Reed; Michael W. Trifunctional intermediates for preparing 3'-tailed oligonucleotides
US5214134A (en) 1990-09-12 1993-05-25 Sterling Winthrop Inc. Process of linking nucleosides with a siloxane bridge
US5561225A (en) 1990-09-19 1996-10-01 Southern Research Institute Polynucleotide analogs containing sulfonate and sulfonamide internucleoside linkages
US5596086A (en) 1990-09-20 1997-01-21 Gilead Sciences, Inc. Modified internucleoside linkages having one nitrogen and two carbon atoms
US5432272A (en) 1990-10-09 1995-07-11 Benner; Steven A. Method for incorporating into a DNA or RNA oligonucleotide using nucleotides bearing heterocyclic bases
US5510475A (en) 1990-11-08 1996-04-23 Hybridon, Inc. Oligonucleotide multiple reporter precursors
US5264221A (en) 1991-05-23 1993-11-23 Mitsubishi Kasei Corporation Drug-containing protein-bonded liposome
US5714331A (en) 1991-05-24 1998-02-03 Buchardt, Deceased; Ole Peptide nucleic acids having enhanced binding affinity, sequence specificity and solubility
US5371241A (en) 1991-07-19 1994-12-06 Pharmacia P-L Biochemicals Inc. Fluorescein labelled phosphoramidites
US5571799A (en) 1991-08-12 1996-11-05 Basco, Ltd. (2'-5') oligoadenylate analogues useful as inhibitors of host-v5.-graft response
US7517644B1 (en) 1991-08-23 2009-04-14 Larry J. Smith Method and compositions for cellular reprogramming
US5521291A (en) 1991-09-30 1996-05-28 Boehringer Ingelheim International, Gmbh Conjugates for introducing nucleic acid into higher eucaryotic cells
US5547932A (en) 1991-09-30 1996-08-20 Boehringer Ingelheim International Gmbh Composition for introducing nucleic acid complexes into higher eucaryotic cells
US5587361A (en) 1991-10-15 1996-12-24 Isis Pharmaceuticals, Inc. Oligonucleotides having phosphorothioate linkages of high chiral purity
US5319080A (en) 1991-10-17 1994-06-07 Ciba-Geigy Corporation Bicyclic nucleosides, oligonucleotides, process for their preparation and intermediates
US5393878A (en) 1991-10-17 1995-02-28 Ciba-Geigy Corporation Bicyclic nucleosides, oligonucleotides, process for their preparation and intermediates
US5484908A (en) 1991-11-26 1996-01-16 Gilead Sciences, Inc. Oligonucleotides containing 5-propynyl pyrimidines
US5359044A (en) 1991-12-13 1994-10-25 Isis Pharmaceuticals Cyclobutyl oligonucleotide surrogates
US5700922A (en) 1991-12-24 1997-12-23 Isis Pharmaceuticals, Inc. PNA-DNA-PNA chimeric macromolecules
US5565552A (en) 1992-01-21 1996-10-15 Pharmacyclics, Inc. Method of expanded porphyrin-oligonucleotide conjugate synthesis
US5595726A (en) 1992-01-21 1997-01-21 Pharmacyclics, Inc. Chromophore probe for detection of nucleic acid
US5587371A (en) 1992-01-21 1996-12-24 Pharmacyclics, Inc. Texaphyrin-oligonucleotide conjugates
US5639873A (en) 1992-02-05 1997-06-17 Centre National De La Recherche Scientifique (Cnrs) Oligothionucleotides
US5633360A (en) 1992-04-14 1997-05-27 Gilead Sciences, Inc. Oligonucleotide analogs capable of passive cell membrane permeation
US5434257A (en) 1992-06-01 1995-07-18 Gilead Sciences, Inc. Binding compentent oligomers containing unsaturated 3',5' and 2',5' linkages
US5610300A (en) 1992-07-01 1997-03-11 Ciba-Geigy Corporation Carbocyclic nucleosides containing bicyclic rings, oligonucleotides therefrom, process for their preparation, their use and intermediates
US5700920A (en) 1992-07-01 1997-12-23 Novartis Corporation Carbocyclic nucleosides containing bicyclic rings, oligonucleotides therefrom, process for their preparation, their use and intermediates
US5272250A (en) 1992-07-10 1993-12-21 Spielvogel Bernard F Boronated phosphoramidate compounds
US5652355A (en) 1992-07-23 1997-07-29 Worcester Foundation For Experimental Biology Hybrid oligonucleotide phosphorothioates
US6756523B1 (en) 1992-09-25 2004-06-29 Aventis Pharma S.A. Adenovirus vectors for the transfer of foreign genes into cells of the central nervous system particularly in brain
US5583020A (en) 1992-11-24 1996-12-10 Ribozyme Pharmaceuticals, Inc. Permeability enhancers for negatively charged polynucleotides
US5574142A (en) 1992-12-15 1996-11-12 Microprobe Corporation Peptide linkers for improved oligonucleotide delivery
US5556948A (en) 1993-01-22 1996-09-17 Mitsubishi Chemical Corporation Phospholipid derivatized with PEG bifunctional linker and liposome containing it
US5476925A (en) 1993-02-01 1995-12-19 Northwestern University Oligodeoxyribonucleotides including 3'-aminonucleoside-phosphoramidate linkages and terminal 3'-amino groups
US5395619A (en) 1993-03-03 1995-03-07 Liposome Technology, Inc. Lipid-polymer conjugates and liposomes
US5466677A (en) 1993-03-06 1995-11-14 Ciba-Geigy Corporation Dinucleoside phosphinates and their pharmaceutical compositions
US5576427A (en) 1993-03-30 1996-11-19 Sterling Winthrop, Inc. Acyclic nucleoside analogs and oligonucleotide sequences containing them
US5663312A (en) 1993-03-31 1997-09-02 Sanofi Oligonucleotide dimers with amide linkages replacing phosphodiester linkages
US5658873A (en) 1993-04-10 1997-08-19 Degussa Aktiengesellschaft Coated sodium percarbonate particles, a process for their production and detergent, cleaning and bleaching compositions containing them
US5462854A (en) 1993-04-19 1995-10-31 Beckman Instruments, Inc. Inverse linkage oligonucleotides for chemical and enzymatic processes
US5539082A (en) 1993-04-26 1996-07-23 Nielsen; Peter E. Peptide nucleic acids
US5534259A (en) 1993-07-08 1996-07-09 Liposome Technology, Inc. Polymer compound and coated particle composition
US5417978A (en) 1993-07-29 1995-05-23 Board Of Regents, The University Of Texas System Liposomal antisense methyl phosphonate oligonucleotides and methods for their preparation and use
US5502177A (en) 1993-09-17 1996-03-26 Gilead Sciences, Inc. Pyrimidine derivatives for labeled binding partners
US5719262A (en) 1993-11-22 1998-02-17 Buchardt, Deceased; Ole Peptide nucleic acids having amino acid side chains
US5457187A (en) 1993-12-08 1995-10-10 Board Of Regents University Of Nebraska Oligonucleotides containing 5-fluorouracil
US5446137A (en) 1993-12-09 1995-08-29 Syntex (U.S.A.) Inc. Oligonucleotides containing 4'-substituted nucleotides
US5446137B1 (en) 1993-12-09 1998-10-06 Behringwerke Ag Oligonucleotides containing 4'-substituted nucleotides
US5565350A (en) 1993-12-09 1996-10-15 Thomas Jefferson University Compounds and methods for site directed mutations in eukaryotic cells
US5595756A (en) 1993-12-22 1997-01-21 Inex Pharmaceuticals Corporation Liposomal compositions for enhanced retention of bioactive agents
US5519134A (en) 1994-01-11 1996-05-21 Isis Pharmaceuticals, Inc. Pyrrolidine-containing monomers and oligomers
US5599928A (en) 1994-02-15 1997-02-04 Pharmacyclics, Inc. Texaphyrin compounds having improved functionalization
US5596091A (en) 1994-03-18 1997-01-21 The Regents Of The University Of California Antisense oligonucleotides comprising 5-aminoalkyl pyrimidine nucleotides
US5627053A (en) 1994-03-29 1997-05-06 Ribozyme Pharmaceuticals, Inc. 2'deoxy-2'-alkylnucleotide containing nucleic acid
US5625050A (en) 1994-03-31 1997-04-29 Amgen Inc. Modified oligonucleotides and intermediates useful in nucleic acid therapeutics
US5525711A (en) 1994-05-18 1996-06-11 The United States Of America As Represented By The Secretary Of The Department Of Health And Human Services Pteridine nucleotide analogs as fluorescent DNA probes
US5543152A (en) 1994-06-20 1996-08-06 Inex Pharmaceuticals Corporation Sphingosomes for enhanced drug delivery
US5597696A (en) 1994-07-18 1997-01-28 Becton Dickinson And Company Covalent cyanine dye oligonucleotide conjugates
US5580731A (en) 1994-08-25 1996-12-03 Chiron Corporation N-4 modified pyrimidine deoxynucleotides and oligonucleotide probes synthesized therewith
US5597909A (en) 1994-08-25 1997-01-28 Chiron Corporation Polynucleotide reagents containing modified deoxyribose moieties, and associated methods of synthesis and use
US5591584A (en) 1994-08-25 1997-01-07 Chiron Corporation N-4 modified pyrimidine deoxynucleotides and oligonucleotide probes synthesized therewith
US5591721A (en) 1994-10-25 1997-01-07 Hybridon, Inc. Method of down-regulating gene expression
US5512295A (en) 1994-11-10 1996-04-30 The Board Of Trustees Of The Leland Stanford Junior University Synthetic liposomes for enhanced uptake and delivery
US6632427B1 (en) 1994-12-13 2003-10-14 Aventis Pharma S.A. Adenoviral-vector-mediated gene transfer into medullary motor neurons
US5543165A (en) 1995-06-06 1996-08-06 Hill; Julie B. Process of making a soluble tea product with champagne-like properties
US5652356A (en) 1995-08-17 1997-07-29 Hybridon, Inc. Inverted chimeric and hybrid oligonucleotides
WO2000058512A1 (en) 1999-03-26 2000-10-05 Isis Pharmaceuticals, Inc. Antisense modulation of interleukin-5 signal transduction
US7563884B2 (en) 2000-01-18 2009-07-21 Isis Pharmaceuticals, Inc. Antisense modulation of PTP1B expression
US6287860B1 (en) 2000-01-20 2001-09-11 Isis Pharmaceuticals, Inc. Antisense inhibition of MEKK2 expression
WO2002048314A2 (en) 2000-11-01 2002-06-20 Isis Pharmaceuticals, Inc. Antisense modulation of raidd expression
US20070117772A1 (en) 2001-06-21 2007-05-24 Bennett C F Methods for slowing familial ALS disease progression
US6936589B2 (en) 2001-09-28 2005-08-30 Albert T. Naito Parenteral delivery systems
US20030225256A1 (en) 2002-05-31 2003-12-04 Isis Pharmaceuticals Inc. Antisense modulation of pctaire protein kinase 2 expression
US20050186594A1 (en) 2002-05-31 2005-08-25 Bennett C. F. Compositions and their uses directed to cell growth and maintenance proteins
US20040023906A1 (en) 2002-08-01 2004-02-05 Isis Pharmaceuticals Inc. Antisense modulation of phosphotyrosyl phosphatase activator expression
WO2005013901A2 (en) 2003-07-31 2005-02-17 Isis Pharmaceuticals, Inc. Oligomeric compounds and compositions for use in modulation of small non-coding rnas
CN1904900A (en) 2005-07-28 2007-01-31 中国科学院生物物理研究所 Human autogenous siRNA sequence, its application and screening method
WO2007087113A2 (en) 2005-12-28 2007-08-02 The Scripps Research Institute Natural antisense and non-coding rna transcripts as drug targets
WO2009046397A2 (en) 2007-10-04 2009-04-09 Board Of Regents, The University Of Texas System Modulating gene expression with agrna and gapmers targeting antisense transcripts
US9209196B2 (en) 2011-11-30 2015-12-08 Sharp Kabushiki Kaisha Memory circuit, method of driving the same, nonvolatile storage device using the same, and liquid crystal display device

Non-Patent Citations (23)

* Cited by examiner, † Cited by third party
Title
"Antisense Research and Applications", 1993, CRC PRESS, pages: 276 - 278
"The Concise Encyclopedia of Polymer Science And Engineering", 1990, JOHN WILEY & SONS, pages: 858 - 859
BRAZMA; VILO, FEBS LETT., vol. 480, 2000, pages 17 - 24
CARULLI ET AL., J CELL BIOCHEM., vol. 31, 1998, pages 286 - 296
CELIS ET AL., FEBS LETT., vol. 480, 2000, pages 2 - 16
DE MESMAEKER ET AL., ACC. CHEM. RES., vol. 28, 1995, pages 366 - 374
ENGLISCH ET AL., ANGEWANDLE CHEMIE, INTERNATIONAL EDITION, vol. 30, 1991, pages 613
FUCHS ET AL., ANAL. BIOCHEM., vol. 286, 2000, pages 91 - 98
GOING; GUSTERSON, EUR. J CANCER, vol. 35, 1999, pages 1895 - 1904
JUNGBLUT ET AL., ELECTROPHORESIS, vol. 20, 1999, pages 2100 - 2110
JURECIC; BELMONT, CURR. OPIN. MICROBIOL., vol. 3, 2000, pages 316 - 321
KOMBERG; BAKER: "DNA Replication", 1992, FREEMAN
LARSON ET AL., CYTOMETRY, vol. 41, 2000, pages 203 - 208
LARSSON ET AL., J. BIOTECHNOL., vol. 80, 2000, pages 143 - 157
MADDEN ET AL., DRUG DISCOV. TODAY, vol. 5, 2000, pages 415 - 425
NIELSEN ET AL., SCIENCE, vol. 254, 1991, pages 1497 - 1500
PRASHAR; WEISSMAN, METHODS ENZYMOL., vol. 303, 1999, pages 258 - 272
SALAH ET AL., MOLECULAR CELL, vol. 33, no. 4, 2009, pages 462 - 471
SANGHVI, Y.S.; CROOKE, S.T.; LEBLEU, B. EA.: "Antisense Research and Applications", 1993, CRC PRESS, pages: 289 - 302
SMITH; WATERMAN, ADV. APPL. MATH., vol. 2, 1981, pages 482 - 489
SUTCLIFFE ET AL., PROC. NATL. ACAD. SCI. U.S.A., vol. 97, 2000, pages 1976 - 1981
TO, COMB., CHEM. HIGH THROUGHPUT SCREEN, vol. 3, 2000, pages 235 - 241
WAHLESTEDT ET AL., DRUG DISCOVERY TODAY, vol. 11, no. 11-12, 2006, pages 503 - 508

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US10058623B2 (en) 2012-05-16 2018-08-28 Translate Bio Ma, Inc. Compositions and methods for modulating UTRN expression
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