WO2016138278A2 - Compositions for inhibiting checkpoint gene expression and uses thereof - Google Patents

Compositions for inhibiting checkpoint gene expression and uses thereof Download PDF

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WO2016138278A2
WO2016138278A2 PCT/US2016/019584 US2016019584W WO2016138278A2 WO 2016138278 A2 WO2016138278 A2 WO 2016138278A2 US 2016019584 W US2016019584 W US 2016019584W WO 2016138278 A2 WO2016138278 A2 WO 2016138278A2
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seq
certain embodiments
independently
human
gene silencing
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WO2016138278A3 (en
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Sudhir Agrawal
Wayne JIANG
Daqing Wang
Jessica SEITZER
Fu-Gang Zhu
Xianzhi Mao
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Idera Pharmaceuticals, Inc.
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Publication of WO2016138278A3 publication Critical patent/WO2016138278A3/en

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    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/11DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00Medicinal preparations containing organic active ingredients
    • A61K31/70Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7088Compounds having three or more nucleosides or nucleotides
    • A61K31/7105Natural ribonucleic acids, i.e. containing only riboses attached to adenine, guanine, cytosine or uracil and having 3'-5' phosphodiester links
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K45/00Medicinal preparations containing active ingredients not provided for in groups A61K31/00 - A61K41/00
    • A61K45/06Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
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    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/11DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • C12N15/1138Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing against receptors or cell surface proteins
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    • C12N2310/00Structure or type of the nucleic acid
    • C12N2310/10Type of nucleic acid
    • C12N2310/11Antisense
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    • C12N2310/00Structure or type of the nucleic acid
    • C12N2310/30Chemical structure
    • C12N2310/31Chemical structure of the backbone
    • C12N2310/314Phosphoramidates
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    • C12N2310/00Structure or type of the nucleic acid
    • C12N2310/50Physical structure
    • C12N2310/51Physical structure in polymeric form, e.g. multimers, concatemers

Definitions

  • the immune system is a hosts defense against foreign antigens; however, in order to function properly a variety of checks and balances are required to protect against self-antigens (i.e., autoimmunity) and, at the same time, provide an appropriate response against foreign.
  • Immune-activating and immune-suppressive receptors and ligands provide these regulatory checks and balances (see Pardoll et al, The blockade of immune checkpoints in cancer immunotherapy, Nat. Rev. Cane. 12, 252 (2012)).
  • Immune checkpoints refer to a group of endogenous immune-suppressive ligands and receptors that are crucial for the maintenance of self-tolerance and the protection of tissues from damage when the immune system is responding to an infection, (see Y.L. Wu, et al, Immunotherapies: The Blockade of Inhibitory Signals, Int. J. Biol. Sci. 8, 1420 (2012)) In response to the induction of an immune response expression of checkpoints increases. These checkpoints act as regulatory feedback to maintain immune homeostasis.
  • tumor mutations give rise to tumor-specific antigens that can be recognized by the immune system, particularly T-cells, leading to elimination of cancer cells.
  • T-cells can co-opt immune checkpoint pathways to suppress the immune response in the tumor microenvironment and evade the host immune system by inhibiting T cells that might otherwise attack the tumor cells, (see J.F. Grosso & M.N. Jure-Kunkel; CTLA-4 blockade in tumor models: an overview of preclinical and translational research, Cancer Immun. 13, 5 (2013); M.E. Turnis, et al; Combinatorial immunotherapy: PD-1 may not be LAG-ing behind any more, Oncolmmunology 1, 1172 (2012)).
  • the present invention is directed to compounds, compositions, and methods useful for modulating PDl, PDL1, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAMl, OX40, and/or OX40L mRNA or protein expression using gene silencing compounds comprising two or more single stranded antisense oligonucleotides that are linked through their 5 '-ends to allow the presence of two or more accessible 3 '-ends.
  • the gene silencing compounds according to the invention effectively inhibit or decrease PDl, PDL1, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAMl, OX40, and/or OX40L mRNA or protein expression.
  • kits for modulating expression of PDl, PDL1, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAMl, OX40, and/or OX40L mRNA and protein are gene silencing compounds.
  • diseases, disorders, and conditions are hyperproliferative diseases, disorders, and conditions.
  • hyperproliferative diseases, disorders, and conditions include cancer as well as associated malignancies and metastases.
  • methods of treatment include administering a PDl
  • the invention relates to the therapeutic and prophylactic use of gene silencing compounds, also referred to as 3 rd generation antisense (3GA) compounds, to down-regulate checkpoint mRNA or protein expression.
  • gene silencing compounds also referred to as 3 rd generation antisense (3GA) compounds
  • 3GA 3 rd generation antisense
  • Such molecules are useful, for example, in providing compositions for modulation of checkpoint gene expression or for treating and/or preventing diseases and/or conditions that are capable of responding to modulation of checkpoint gene expression in patients, subjects, animals or organisms.
  • NCBI National Center for Biotechnology Information
  • the term "2'-0-substituted” means substitution of the 2' position of the pentose moiety with an -O- lower alkyl group containing 1-6 saturated or unsaturated carbon atoms (for example, but not limited to, 2'-0-methyl), or with an -O-aryl or allyl group having 2-6 carbon atoms, wherein such alkyl, aryl or allyl group may be unsubstituted or may be substituted, (for example, with 2'-0-methoxyethyl, ethoxy, methoxy, halo, hydroxy 1, trifluoromethyl, cyano, nitro, acyl, acyloxy, alkoxy, carboxyl, carbalkoxyl, or amino groups); or with a hydroxyl, an amino or a halo group, but not with a 2'-H group.
  • an -O- lower alkyl group containing 1-6 saturated or unsaturated carbon atoms for example, but not limited to, 2
  • the oligonucleotides of the invention include four or five 2'-0-alky nucleotides at their 5' terminus, and/or four or five 2'-0-alky nucleotides at their 3' terminus.
  • the term "3"' when used directionally, generally refers to a region or position in a polynucleotide or oligonucleotide 3' (toward the 3 'end of the nucleotide) from another region or position in the same polynucleotide or oligonucleotide.
  • the term "3' end” generally refers to the 3' terminal nucleotide of the component oligonucleotides.
  • “Two or more oligonucleotides linked at their 3' ends” generally refers to a linkage between the 3' terminal nucleotides of the oligonucleotides which may be directly via 5', 3' or 2' hydroxyl groups, or indirectly, via a non-nucleotide linker. Such linkages may also be via a nucleoside, utilizing both 2' and 3' hydroxyl positions of the nucleoside. Such linkages may also utilize a functionalized sugar or nucleobase of a 3 'terminal nucleotide.
  • the term "5' end” generally refers to the 5' terminal nucleotide of the component oligonucleotides.
  • "Two or more single-stranded antisense oligonucleotides linked at their 5' ends” generally refers to a linkage between the 5' terminal nucleotides of the oligonucleotides which may be directly via 5', 3' or 2' hydroxyl groups, or indirectly, via a non-nucleotide linker. Such linkages may also be via a nucleoside, utilizing both 2' and 3' hydroxyl positions of the nucleoside. Such linkages may also utilize a functionalized sugar or nucleobase of a 5 'terminal nucleotide.
  • the term "accessible” generally means when related to a compound according to the invention, that the relevant portion of the molecule is able to be recognized by the cellular components necessary to elicit an intended response to the compound.
  • agonist generally refers to a substance that binds to a receptor of a cell and induces a response.
  • An agonist can be a naturally occurring substance such as bacterial DNA or a synthetic composition.
  • a synthetic agonist often mimics the action of a naturally occurring substance such as a ligand.
  • GSO Gene silencing oligonucleotide
  • GSO Gene silencing compound
  • 3GA 3 rd generation antisense
  • Antisense oligonucleotide means a single-stranded oligonucleotide having a nucleobase sequence that permits hybridization to a corresponding region or segment of a target nucleic acid.
  • cancer generally refers to, without limitation, any malignant growth or tumor caused by abnormal or uncontrolled cell proliferation and/or division.
  • co-administration or “co-administered” generally refers to the administration of at least two different substances. Co-administration refers to simultaneous administration, as well as temporally spaced order of up to several days apart, of at least two different substances in any order, either in a single dose or separate doses.
  • CEACAM1 nucleic acid means any nucleic acid encoding CEACAM1.
  • a CEACAM1 nucleic acid includes a DNA sequence encoding CEACAM1, an RNA sequence transcribed from DNA encoding CEACAM1 (including genomic DNA comprising introns and exons), and an mRNA sequence encoding CEACAM1.
  • CEACAM1 mRNA means an mRNA encoding a CEACAM1 protein.
  • linear synthesis generally refers to a synthesis that starts at one end of an oligonucleotide and progresses linearly to the other end. Linear synthesis permits incorporation of either identical or non-identical (in terms of length, base composition and/or chemical modifications incorporated) monomeric units into an oligonucleotide.
  • nucleoside generally refers to compounds consisting of a sugar, usually ribose, deoxyribose, pentose, arabinose or hexose, and a purine or pyrimidine base.
  • a base is considered to be non-natural if it is not guanine, cytosine, adenine, thymine or uracil and a sugar is considered to be non-natural if it is not ⁇ -ribo-furanoside or 2'-deoxyribo-furanoside.
  • oligonucleotide in which at least two of its nucleotides are covalently linked via a synthetic linkage, i.e., a linkage other than a phosphodiester linkage between the 5' end of one nucleotide and the 3' end of another nucleotide in which the 5' nucleotide phosphate has been replaced with any number of chemical groups.
  • a synthetic linkage i.e., a linkage other than a phosphodiester linkage between the 5' end of one nucleotide and the 3' end of another nucleotide in which the 5' nucleotide phosphate has been replaced with any number of chemical groups.
  • modified oligonucleotide also encompasses 2'-0,4'-C-methylene-b-D-ribofuranosyl nucleic acids, arabinose nucleic acids, substituted arabinose nucleic acids, hexose nucleic acids, peptide nucleic acids, morpholino, and oligonucleotides having at least one nucleotide with a modified base and/or sugar, such as a 2'-0-substituted, a 5- methylcytosine and/or a 3 '-0-substituted ribonucleotide.
  • nucleic acid encompasses a genomic region or an RNA molecule transcribed therefrom.
  • the nucleic acid is mRNA.
  • Such linker can be either a non-nucleotide linker or a nucleoside linker.
  • nucleotide linkage generally refer to a chemical linkage to join two nucleosides through their sugars (e.g. 3 '-3 ', 2'-3', 2'-5 ', 3 '-5', 5'-5') consisting of a phosphorous atom and a charged, or neutral group (e.g., phosphodiester, phosphorothioate, phosphorodithioate or methylphosphonate) between adjacent nucleosides.
  • sugars e.g. 3 '-3 ', 2'-3', 2'-5 ', 3 '-5', 5'-5'
  • neutral group e.g., phosphodiester, phosphorothioate, phosphorodithioate or methylphosphonate
  • oligonucleotide refers to a polynucleoside formed from a plurality of linked nucleoside units, which may include, for example, deoxyribonucleotides or ribonucleotides, synthetic or natural nucleotides, phosphodiester or modified linkages, natural bases or modified bases natural sugars or modified sugars, or combinations of these components.
  • the nucleoside units may be part of viruses, bacteria, cell debris or
  • oligonucleotide-based compositions for example, siRNA and microRNA.
  • each nucleoside unit includes a heterocyclic base and a pentofuranosyl, trehalose, arabinose, 2'- deoxy-2'-substituted nucleoside, 2'-deoxy-2'-substituted arabinose, 2'-0- substitutedarabinose or hexose sugar group.
  • the nucleoside residues can be coupled to each other by any of the numerous known intemucleoside linkages.
  • intemucleoside linkages include, without limitation, phosphodiester, phosphorothioate, phosphorodithioate, methylphosphonate, alkylphosphonate, alkylphosphonothioate, phosphotriester,
  • oligonucleotide also encompasses polynucleosides having one or more stereospecific intemucleoside linkage (e.g., (Rp)- or (Sp)-phosphorothioate, alkylphosphonate, or phosphotriester linkages).
  • the phosphorothioate linkages may be mixed Rp and Sp enantiomers, or they may be stereoregular or substantially stereoregular in either Rp or Sp form (see Iyer et al. (1995) Tetrahedron Asymmetry 6: 1051 -1054).
  • one or more of the oligonucleotides within the antisense compositions of the invention contain one or more 2'- 0,4'-C-methylene-b-D-ribofuranosyl nucleic acids, wherein the ribose is modified with a bond between the 2' and 4' carbons, which fixes the ribose in the 3'-endo structural conformation.
  • OX40 nucleic acid means any nucleic acid encoding OX40.
  • a OX40 nucleic acid includes a DNA sequence encoding OX40, an RNA sequence transcribed from DNA encoding OX40 (including genomic DNA comprising introns and exons), and an mRNA sequence encoding OX40.
  • OX40 mRNA means an mRNA encoding an OX40 protein.
  • OX40L nucleic acid means any nucleic acid encoding OX40L.
  • a OX40L nucleic acid includes a DNA sequence encoding OX40L, an RNA sequence transcribed from DNA encoding OX40L (including genomic DNA comprising introns and exons), and an mRNA sequence encoding OX40L.
  • OX40L mRNA means an mRNA encoding an OX40L protein.
  • PD1 nucleic acid means any nucleic acid encoding PD1.
  • a PD1 nucleic acid includes a DNA sequence encoding PD1, an RNA sequence transcribed from DNA encoding PDl (including genomic DNA comprising introns and exons), and an mRNA sequence encoding PDl .
  • PDl mRNA means an mRNA encoding a PDl protein.
  • PDLl nucleic acid means any nucleic acid encoding PDLl .
  • a PDLl nucleic acid includes a DNA sequence encoding PDLl, an RNA sequence transcribed from DNA encoding PDLl (including genomic DNA comprising introns and exons), and an mRNA sequence encoding PDLl .
  • PDLl mRNA means an mRNA encoding a PDLl protein.
  • peptide generally refers to oligomers or polymers of amino acids that are of sufficient length and composition to affect a biological response, for example, antibody production or cytokine activity whether or not the peptide is a hapten.
  • peptide may include modified amino acids (whether or not naturally or non-naturally occurring), where such modifications include, but are not limited to, phosphorylation, glycosylation, pegylation, lipidization, and methylation.
  • pharmaceutically acceptable means a non-toxic material that does not interfere with the effectiveness of a compound according to the invention or the biological activity of a compound according to the invention.
  • physiologically acceptable refers to a non-toxic material that is compatible with a biological system such as a cell, cell culture, tissue, or organism.
  • the biological system is a living organism, such as a mammal, particularly a human.
  • prophylactically effective amount generally refers to an amount sufficient to prevent or reduce the development of an undesired biological effect.
  • Portion means a defined number of contiguous (i.e., linked) nucleobases of a nucleic acid. In certain embodiments, a portion is a defined number of contiguous nucleobases of a target nucleic acid. In certain embodiments, a portion is a defined number of contiguous nucleobases of an antisense compound.
  • Single-stranded oligonucleotide means an oligonucleotide which is not hybridized to a complementary strand.
  • Specifically hybridizable refers to a gene silencing compound having a sufficient degree of complementarity between an antisense oligonucleotide and a target nucleic acid to induce a desired effect, while exhibiting minimal or no effects on non-target nucleic acids under conditions in which specific binding is desired, i.e., under physiological conditions in the case of in vivo assays and therapeutic treatments.
  • Targeting or “targeted” means the process of design and selection of a gene silencing compound that will specifically hybridize to a target nucleic acid and induce a desired effect.
  • Target nucleic acid refers to a nucleic acid capable of being targeted by gene silencing compounds.
  • Target segment means the sequence of nucleotides of a target nucleic acid to which a gene silencing compound is targeted.
  • 5' target site refers to the 5'-most nucleotide of a target segment.
  • 3' target site refers to the 3'-most nucleotide of a target segment.
  • TIM3 nucleic acid means any nucleic acid encoding TIM3.
  • a TIM3 nucleic acid includes a DNA sequence encoding TIM3, an RNA sequence transcribed from DNA encoding TIM3 (including genomic DNA comprising introns and exons), and an mRNA sequence encoding TIM3.
  • TIM3 mRNA means an mRNA encoding a TIM3 protein.
  • treatment generally refers to an approach intended to obtain a beneficial or desired result, which may include alleviation of symptoms, or delaying or ameliorating a disease progression.
  • gene silencing compounds according to the invention comprise two or more single-stranded antisense oligonucleotides linked at their 5' ends, wherein the compounds have two or more accessible 3' ends.
  • the general structure of the oligonucleotide-based compounds of the invention may be described by the following formula I:
  • mouse PD1 nucleic acid is the sequence set forth in GENBANK Accession No. NM_008798 (incorporated herein as SEQ ID NO: 387) or the human PD1 nucleic acid is the sequence set forth in GENBANK Accession No. NM_005018 (incorporated herein as SEQ ID NO: 388).
  • gene silencing compounds targeted to a mouse or human PDLl nucleic acid are provided.
  • the mouse PDLl nucleic acid is the sequence set forth in GENBANK Accession No. NM_021893 (incorporated herein as SEQ ID NO: 389) or the human PDLl nucleic acid is the sequence set forth in GENBANK Accession No. NM_014143 (incorporated herein as SEQ ID NO: 390).
  • gene silencing compounds targeted to a mouse or human IDOl nucleic acid are provided.
  • the mouse IDOl nucleic acid is the sequence set forth in GENBANK Accession No. NM_008324 (incorporated herein as SEQ ID NO: 391) or the human IDOl nucleic acid is the sequence set forth in GENBANK Accession No. NM_002164 (incorporated herein as SEQ ID NO: 392).
  • mouse TIM3 nucleic acid is the sequence set forth in GENBANK Accession No. NM_134250 (incorporated herein as SEQ ID NO: 395) or the human TIM3 nucleic acid is the sequence set forth in GENBANK Accession No. NM_032782 (incorporated herein as SEQ ID NO: 396).
  • gene silencing compounds targeted to a mouse or human ID02 nucleic acid are provided.
  • the mouse ID02 nucleic acid is the sequence set forth in GENBANK Accession No. NM_145949 (incorporated herein as SEQ ID NO: 399) or the human ID02 nucleic acid is the sequence set forth in GENBANK Accession No. NM_194294 (incorporated herein as SEQ ID NO: 400).
  • gene silencing compounds targeted to a mouse or human CEACAM1 nucleic acid are provided.
  • the mouse CEACAM1 nucleic acid is the sequence set forth in GENBANK Accession No. NM_001039187
  • Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 387, SEQ ID NO: 388, SEQ ID NO: 389, SEQ ID NO: 390, SEQ ID NO: 391, SEQ ID NO: 392, SEQ ID NO: 393, SEQ ID NO: 394, SEQ ID NO: 395, SEQ ID NO: 396, SEQ ID NO: 397, SEQ ID NO: 398, SEQ ID NO: 399, SEQ ID NO: 400, SEQ ID NO: 401, SEQ ID NO: 402, SEQ ID NO: 403, SEQ ID NO: 404, SEQ ID NO: 405, or SEQ ID NO:
  • the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 387, SEQ ID NO: 388, SEQ ID NO: 389, SEQ ID NO: 390, SEQ ID NO: 391, SEQ ID NO: 392, SEQ ID NO: 393, SEQ ID NO: 394, SEQ ID NO: 395, SEQ ID NO: 396, SEQ ID NO: 397, SEQ ID NO: 398, SEQ ID NO: 399, SEQ ID NO: 400, SEQ ID NO: 401, SEQ ID NO: 402, SEQ ID NO: 403, SEQ ID NO: 404, SEQ ID NO: 405, or SEQ ID NO: 406.
  • Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 387, SEQ ID NO: 389, SEQ ID NO: 391, SEQ ID NO: 393, SEQ ID NO: 395, SEQ ID NO: 397, SEQ ID NO: 399, SEQ ID NO: 401, SEQ ID NO:
  • Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 387, SEQ ID NO: 389, SEQ ID NO: 391, SEQ ID NO: 393, SEQ ID NO: 395, SEQ ID NO: 397, SEQ ID NO: 399, SEQ ID NO: 401, SEQ ID NO: 403, or SEQ ID NO: 405.
  • the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 387, SEQ ID NO: 389, SEQ ID NO: 391, SEQ ID NO: 393, SEQ ID NO: 395, SEQ ID NO: 397, SEQ ID NO: 399, SEQ ID NO: 401, SEQ ID NO: 403, or SEQ ID NO: 405.
  • Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 388, SEQ ID NO: 390, SEQ ID NO: 392, SEQ ID NO: 394, SEQ ID NO: 396, SEQ ID NO: 398, SEQ ID NO: 400, SEQ ID NO: 402, SEQ ID NO:
  • Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 388, SEQ ID NO: 390, SEQ ID NO: 392, SEQ ID NO: 394, SEQ ID NO: 396, SEQ ID NO: 398, SEQ ID NO: 400, SEQ ID NO: 402, SEQ ID NO: 404, or SEQ ID NO: 406.
  • Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 388, SEQ ID NO: 390, SEQ ID NO: 392, SEQ ID NO: 394, SEQ ID NO: 396, SEQ ID NO: 398, SEQ ID NO: 400, SEQ ID NO: 402, SEQ ID NO: 404, or SEQ ID NO: 406.
  • the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 388, SEQ ID NO: 390, SEQ ID NO: 392, SEQ ID NO: 394, SEQ ID NO: 396, SEQ ID NO: 398, SEQ ID NO: 400, SEQ ID NO: 402, SEQ ID NO: 404, or SEQ ID NO: 406.
  • Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 387. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 387.
  • Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 387.
  • the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 387.
  • Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 388. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 388.
  • Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 388.
  • the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 388.
  • Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 389. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 389.
  • Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 389.
  • the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 389.
  • Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 392. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 392.
  • Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 392.
  • the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 392.
  • Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 393. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 393.
  • Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 394. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 394.
  • Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 394.
  • the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 394.
  • Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 398.
  • the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 398.
  • Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 399. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 399.
  • Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 399.
  • the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 399.
  • Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 400.
  • the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 400.
  • Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 401.
  • the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 401.
  • Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 402. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 402.
  • Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 402.
  • the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 402.
  • Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 403. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 403.
  • Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 403.
  • the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 403.
  • Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 404. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 404.
  • Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 404.
  • the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 404.
  • Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 405.
  • the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 405.
  • Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 406. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 406.
  • Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 406.
  • the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 406.
  • the nucleobase sequence of the oligonucleotides of the gene silencing compound are, independently, at least 95% complementary over its entire length to a nucleobase sequence of SEQ ID NO: 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, or 406.
  • the oligonucleotides of the gene silencing compound are, independently, 12 to 30 nucleotides in length. In other words, the oligonucleotides are from 12 to 30 linked nucleobases. In other embodiments, the oligonucleotides,
  • compositions comprising a 3GA compound as described herein, or a salt thereof, and a pharmaceutically acceptable carrier or diluent.
  • compositions comprising two or more 3GA compounds as described herein, or a salt thereof, and a pharmaceutically acceptable carrier or diluent.
  • the two or more 3GA compounds can inhibit the mRNA or protein expression of the same target or can inhibit the mRNA or protein expression of different targets.
  • the linker is small molecule linker such as glycerol or a glycerol homolog of the formula
  • a and/or Domain B and/or Domain C and/or Domain D are antisense oligonucleotides that are designed to selectively hybridize to the same target RNA sequence or different target RNA sequences.
  • Domain A and/or Domain B and/or Domain C of Formulas II and/or III are antisense oligonucleotides that are designed to selectively hybridize to the same target RNA sequence.
  • Domain A and/or Domain B and/or Domain C can be designed to hybridize to the same region on the target RNA sequence or to different regions of the same target RNA sequence.
  • genes silencing compounds of the invention can be prepared by the art recognized methods such as phosphoramidate or H-phosphonate chemistry which can be carried out manually or by an automated synthesizer.
  • the synthetic antisense oligonucleotides of the invention may comprise combinations of intemucleotide linkages.
  • U.S. Pat. No. 5,149,797 describes traditional chimeric oligonucleotides having a phosphorothioate core region interposed between methylphosphonate or phosphoramidate flanking regions.
  • U.S. Pat. No. 5,652,356 discloses "inverted" chimeric oligonucleotides comprising one or more nonionic oligonucleotide region (e.g.
  • intemucleotide linkages can be prepared according to standard methods.
  • the phosphorothioate linkages may be mixed Rp and Sp enantiomers, or they may be made stereoregular or substantially stereoregular in either Rp or Sp form.
  • modifications of gene silencing compounds of the invention include those that are internal or at the end(s) of the oligonucleotide molecule and include additions to the molecule of the intemucleoside phosphate linkages, such as cholesterol, cholesteryl, or diamine compounds with varying numbers of carbon residues between the amino groups and terminal ribose, deoxyribose and phosphate modifications which cleave, or crosslink to the opposite chains or to associated enzymes or other proteins which bind to the genome.
  • intemucleoside phosphate linkages such as cholesterol, cholesteryl, or diamine compounds with varying numbers of carbon residues between the amino groups and terminal ribose, deoxyribose and phosphate modifications which cleave, or crosslink to the opposite chains or to associated enzymes or other proteins which bind to the genome.
  • modified oligonucleotides include oligonucleotides with a modified base and/or sugar such as 2'-0,4'-C-methylene-b-D-ribofuranosyl, or arabinose instead of ribose, or a 3', 5 '-substituted oligonucleotide having a sugar which, at both its 3' and 5' positions, is attached to a chemical group other than a hydroxyl group (at its 3' position) and other than a phosphate group (at its 5' position).
  • a modified base and/or sugar such as 2'-0,4'-C-methylene-b-D-ribofuranosyl, or arabinose instead of ribose
  • modifications to sugars of the oligonucleoti de-based compounds of the invention include modifications to the 2' position of the ribose moiety which include but are not limited to 2'-0-substituted with an -O-alkyl group containing 1-6 saturated or unsaturated carbon atoms, or with an -O-aryl, or -O-allyl group having 2-6 carbon atoms wherein such -O-alkyl, -O-aryl or -O-allyl group may be unsubstituted or may be substituted, for example with halo, hydroxyl, trifiuoromethyl, cyano, nitro, acyl, acyloxy, alkoxy, carboxy, carbalkoxyl or amino groups. None of these substitutions are intended to exclude the presence of other residues having native 2'-hydroxyl group in the case of ribose or 2' H- in the case of deoxyribose.
  • the gene silencing compounds according to the invention can comprise one or more ribonucleotides.
  • US Pat No. 5,652,355 discloses traditional hybrid oligonucleotides having regions of 2 '-0 -substituted ribonucleotides flanking a DNA core region.
  • 5,652,356 discloses an "inverted" hybrid oligonucleotide that includes an oligonucleotide comprising a 2'-0-substituted (or 2' OH, unsubstituted) RNA region which is in between two oligodeoxyribonucleotide regions, a structure that "inverted relative to the "traditional" hybrid oligonucleotides.
  • Non-limiting examples of particularly useful oligonucleotides of the invention have 2'-0-alkylated ribonucleotides at their 3', 5', or 3' and 5' termini, with at least four, and in some exemplary embodiments five, contiguous nucleotides being so modified.
  • Non-limiting examples of 2'-0-alkylated groups include 2'- O-methyl, 2'-0-ethyl, 2'-0-propyl, 2'-0-butyls and 2'-0-methoxy-ethyl.
  • the oligonucleotide-based compounds of the invention may conveniently be deprotected with concentrated ammonia solution or as recommended by the phosphoramidite supplier, if a modified nucleoside is incorporated.
  • the product oligonucleotide-based compounds is preferably purified by reversed phase HPLC, detritylated, desalted and dialyzed.
  • the oligonucleotides of the gene silencing compound according to the invention are selected from the non-limiting list of the oligonucleotides shown in Table 3 below.
  • the oligonucleotides shown in Table 3 have phosphorothioate (PS) linkages, but may also include phosphodiester linkages. Those skilled in the art will recognize, however, that other linkages, based on phosphodiester or non-phosphodiester moieties may be included.
  • PS phosphorothioate
  • CTLA4 Human 1537 CCTTGTGTTCTACCTGGTG 221 CTLA4 Human 1570 CCTC ATCCAGTTTCCAAG C
  • 3 rd generation antisense (3GA) compounds according to the invention are based on the target and oligonucleotide target site(s) as depicted Table 3.
  • 3GA 384" comprises two copies of Oligo # 384 linked at their 5' ends (e.g., 3 -CCACGAGTGAGCGAAACCC-5 -X-5'-
  • a 3GA compound comprising two different oligonucleotides such as Oligo # 385 and Oligo # 386 (e.g., 3 ' - ACCGGACGAGAAGGGTAC A-5 ' -X-5 ' - GGTGGAGTGAGGCTGGTGC-3', wherein X represents a non-nucleotidic linker) will be referred to herein, for example, as "3GA 385/386”.
  • Oligo # 385 and Oligo # 386 e.g., 3 ' - ACCGGACGAGAAGGGTAC A-5 ' -X-5 ' - GGTGGAGTGAGGCTGGTGC-3', wherein X represents a non-nucleotidic linker
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NO: 1 , 2, 3, 4, 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, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99,
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1, 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, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91 , 92, 93, 94, 95, 96, 97
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 1, 2, 3, 4, 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, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102,
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 1, 2, 3, 4, 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, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102,
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 49, 50, 51, 52, 53, 54, 75, 76, 77, 78, 79, 80, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204
  • the gene silencing compounds comprise two oligonucleot des each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 49, 50, 51, 52, 53, 54, 75, 76, 77, 78, 79, 80,101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205,
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 49, 50, 51, 52, 53, 54, 75, 76, 77, 78, 79, 80,101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205,
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 49, 50, 51, 52, 53, 54, 75, 76, 77, 78, 79, 80,101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206,
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137,
  • SEQ ID NO: 388 complimentary to its target site within SEQ ID NO: 388, SEQ ID NO: 390, SEQ ID NO: 392, SEQ ID NO: 394, SEQ ID NO: 396, SEQ ID NO: 398, SEQ ID NO: 400, SEQ ID NO: 402, SEQ ID NO: 404, or SEQ ID NO: 406.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, or 8, and is at least 80% complimentary to SEQ ID NO: 387. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, or 8, and is at least 85% complimentary to SEQ ID NO: 387.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, or 8, and is at least 90% complimentary to SEQ ID NO: 387. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, or 8, and is at least 95% complimentary to SEQ ID NO: 387.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 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, and is at least 80% complimentary to SEQ ID NO: 388.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 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, and is at least 85% complimentary to SEQ ID NO: 388.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 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, and is at least 90% complimentary to SEQ ID NO: 388.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 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, and is at least 95% complimentary to SEQ ID NO: 388.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 49, 50, 51, 52, 53, 54, and is at least 80% complimentary to SEQ ID NO: 389. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 49, 50, 51, 52, 53, 54, and is at least 85% complimentary to SEQ ID NO: 389.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 49, 50, 51, 52, 53, 54, and is at least 90% complimentary to SEQ ID NO: 389.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 49, 50, 51, 52, 53, 54, and is at least 95% complimentary to SEQ ID NO: 389.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, and is at least 80% complimentary to SEQ ID NO: 390.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, and is at least 85%
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, and is at least 90% complimentary to SEQ ID NO: 390.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, and is at least 95% complimentary to SEQ ID NO: 390.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 75, 76, 77, 78, 79, 80, and is at least 80% complimentary to SEQ ID NO: 391.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 75, 76, 77, 78, 79, 80, and is at least 85% complimentary to SEQ ID NO: 391.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 75, 76, 77, 78, 79, 80, and is at least 90% complimentary to SEQ ID NO: 391.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 75, 76, 77, 78, 79, 80, and is at least 95% complimentary to SEQ ID NO: 391.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, and is at least 80% complimentary to SEQ ID NO: 392.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, and is at least 85%
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, and is at least 90% complimentary to SEQ ID NO: 392.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, and is at least 95% complimentary to SEQ ID NO: 392.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, and is at least 80%
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, and is at least 85% complimentary to SEQ ID NO: 393.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, and is at least 90% complimentary to SEQ ID NO: 393.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, and is at least 95% complimentary to SEQ ID NO: 393.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, and is at least 80%
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, and is at least 85% complimentary to SEQ ID NO: 394.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, and is at least 90% complimentary to SEQ ID NO: 394.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, and is at least 95% complimentary to SEQ ID NO: 394.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, and is at least 80% complimentary to SEQ ID NO: 395.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165,
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166,
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, and is at least 95% complimentary to SEQ ID NO: 395.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, and is at least 80% complimentary to SEQ ID NO: 396.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185,
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186,
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 169, 170, 171,
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, and is at least 85% complimentary to SEQ ID NO: 397.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, and is at least 90% complimentary to SEQ ID NO: 397.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, and is at least 95% complimentary to SEQ ID NO: 397.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, and is at least 80% complimentary to SEQ ID NO:
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NO: 1
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226,
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, and is at least 95% complimentary to SEQ ID NO: 398.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, and is at least 80% complimentary to SEQ ID NO: 399.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245,
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246,
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, and is at least 95% complimentary to SEQ ID NO: 399.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, and is at least 80% complimentary to SEQ ID NO: 400.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, and is at least 85% complimentary to SEQ ID NO: 400.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, and is at least 90% complimentary to SEQ ID NO: 400.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, and is at least 95% complimentary to SEQ ID NO: 400.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, and is at least 80% complimentary to SEQ ID NO: 401.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, and is at least 85% complimentary to SEQ ID NO: 401.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, and is at least 90% complimentary to SEQ ID NO: 401.
  • the gene silencing compounds comprise two
  • oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, and is at least 95% complimentary to SEQ ID NO: 401.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, and is at least 80% complimentary to SEQ ID NO: 402.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304,
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305,
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, and is at least 95% complimentary to SEQ ID NO: 402.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, and is at least 80% complimentary to SEQ ID NO: 403.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, and is at least 85% complimentary to SEQ ID NO: 403.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, and is at least 90% complimentary to SEQ ID NO: 403.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, and is at least 95% complimentary to SEQ ID NO: 403.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, and is at least 80% complimentary to SEQ ID NO: 404.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345,
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, and is at least 90% complimentary to SEQ ID NO: 404.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, and is at least 95% complimentary to SEQ ID NO: 404.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, and is at least 80% complimentary to SEQ ID NO: 405.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs:
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, and is at least 90% complimentary to SEQ ID NO: 405.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, and is at least 95% complimentary to SEQ ID NO: 405.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, or 386, and is at least 80% complimentary to SEQ ID NO: 406.
  • the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, or 386, and is at least 80% complimentary to SEQ ID NO: 406.
  • the gene silencing compounds comprise two
  • oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, or 386, and is at least 85% complimentary to SEQ ID NO: 406.
  • the gene silencing compounds comprise two
  • oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, or 386, and is at least 90% complimentary to SEQ ID NO: 406.
  • the gene silencing compounds comprise two
  • oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, or 386, and is at least 95% complimentary to SEQ ID NO: 406.
  • the invention provides a composition comprising a 3GA compound according to the invention and one or more vaccines, antigens, antibodies, cytotoxic agents, chemotherapeutic agents (both traditional chemotherapy and modem targeted therapies), kinase inhibitors, allergens, antibiotics, agonist, antagonist, antisense oligonucleotides, ribozymes, RNAi molecules, siRNA molecules, miRNA molecules, aptamers, proteins, gene therapy vectors, DNA vaccines, adjuvants, co-stimulatory molecules or combinations thereof.
  • chemotherapeutic agents both traditional chemotherapy and modem targeted therapies
  • kinase inhibitors include kinase inhibitors, allergens, antibiotics, agonist, antagonist, antisense oligonucleotides, ribozymes, RNAi molecules, siRNA molecules, miRNA molecules, aptamers, proteins, gene therapy vectors, DNA vaccines, adjuvants, co-stimulatory molecules or combinations thereof.
  • the invention provides a method for inhibiting PD1,
  • the method comprising contacting a cell with a gene silencing compound according to the invention.
  • the cell can be contacted with two or more gene silencing compounds targeting different regions of the same checkpoint.
  • the cell can be contacted with two or more gene silencing compounds targeting different checkpoints.
  • Certain embodiments further provide a method to reduce PD 1 , PDL 1 , IDO 1 ,
  • LAG3, TIM3, CTLA4, ID02, CEACAM1, OX40, and/or or OX40L mRNA or protein expression in an animal comprising administering to the animal a gene silencing compound or composition as described herein to reduce PD1, PDL1, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAM1, OX40, or OX40L mRNA or protein expression in the animal.
  • the animal is a human.
  • reducing PD1, PDL1, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAM1, OX40, or OX40L mRNA or protein expression prevents, treats, ameliorates, or slows progression of disease.
  • reducing PD1, PDL1, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAM1, OX40, or OX40L mRNA or protein expression inhibits immune system tolerance.
  • two or more gene silencing compounds targeting different regions of the same checkpoint can be administered.
  • two or more gene silencing compounds targeting different checkpoints can be administered.
  • kits for inhibiting immune system tolerance to tumors comprising administering to the animal a gene silencing compound or composition as described herein to reduce PD1, PDL1, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAM1, OX40, and/or OX40L mRNA or protein expression in the animal.
  • the animal is a human.
  • the gene silencing compound or composition as described herein is administered intratumorally.
  • the inhibition of PD1, PDL1, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAM1, OX40, or OX40L mRNA or protein expression may provide a potentially useful immunotherapy strategy for patients with cancer.
  • two or more gene silencing compounds targeting different regions of the same checkpoint can be administered.
  • two or more gene silencing compounds targeting different checkpoints can be administered.
  • PDl PDl, PDLl, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAMl, OX40, or
  • OX40L associated diseases, disorders, and conditions include hyperproliferative diseases, e.g., cancer, carcinomas, sarcomas, lymphomas, and leukemias as well as associated malignancies and metastases.
  • PDl, PDLl, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAMl, OX40, or OX40L associated diseases, disorders, and conditions can also include autoimmune diseases and disorders.
  • PDl In certain embodiments provided are PDl, PDLl, IDOl, LAG3, TIM3,
  • CTLA4, ID02, CEACAMl, OX40, or OX40L gene silencing compounds for use in treating, preventing, or ameliorating a PDl, PDLl, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAMl, OX40, or OX40L associated disease.
  • TIM3, CTLA4, ID02, CEACAMl, OX40, or OX40L gene silencing compounds are capable of inhibiting the expression of PDl, PDLl, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAMl, OX40, or OX40L mRNA and/or PDl, PDLl, IDOl, LAG3, TIM3, CTLA4, ID02,
  • CEACAMl, OX40, or OX40L protein in a cell, tissue, or animal in a cell, tissue, or animal.
  • Certain embodiments provide methods comprising administering to an animal a gene silencing compounds as described herein. In certain embodiments two or more gene silencing compounds targeting different regions of the same checkpoint can be administered. In certain embodiments two or more gene silencing compounds targeting different checkpoints can be administered.
  • Certain embodiments provide gene silencing compounds as described herein for use in treating, preventing, or ameliorating disease as described herein by combination therapy with an additional agent or therapy as described herein.
  • Agents or therapies can be co-administered or administered concomitantly.
  • Certain embodiments provide the use of a gene silencing compound as described herein in the manufacture of a medicament for treating, preventing, or ameliorating disease as described herein by combination therapy with an additional agent or therapy as described herein.
  • Agents or therapies can be co-administered or administered concomitantly.
  • Certain embodiments provide the use of a gene silencing compound as described herein in the manufacture of a medicament for treating, preventing, or ameliorating disease as described herein in a patient who is subsequently administered an additional agent or therapy as described herein.
  • the gene silencing compound according to the invention can variously act by producing direct gene expression modulation effects alone and/or in combination with any other agent useful for treating or preventing the disease or condition that does not diminish the gene expression modulation effect of the gene silencing compound according to the invention.
  • the agent(s) useful for treating or preventing the disease or condition includes, but is not limited to, vaccines, antigens, antibodies, preferably
  • TLR antagonist e.g. antagonists of TLR3 and/or TLR7 and/or antagonists of TLR8 and/or antagonists of TLR9
  • chemotherapeutic agents both traditional chemotherapy and modem targeted therapies
  • targeted therapeutic agents activated cells, peptides, proteins, gene therapy vectors, peptide vaccines, protein vaccines, DNA vaccines, adjuvants, and co-stimulatory molecules (e.g. cytokines, chemokines, protein ligands, trans-activating factors, peptides or peptides comprising modified amino acids), or combinations thereof.
  • the oligonucleotide-based compound according to the invention may be administered in combination with one or more chemotherapeutic compound, targeted therapeutic agent and/or monoclonal antibody.
  • the agent can include DNA vectors encoding for antigen or allergen.
  • the gene silencing compound according to the invention can be administered in combination with other compounds (for example lipids or liposomes) to enhance the specificity or magnitude of the gene expression modulation of the
  • administration of gene silencing compounds according to the invention, alone or in combination with any other agent can be by any suitable route, including, without limitation, parenteral, mucosal, oral, sublingual, intratumoral, transdermal, topical, inhalation, intrathecal, intranasal, aerosol, intraocular, intratracheal, intrarectal, vaginal, by gene gun, dermal patch or in eye drop or mouthwash form.
  • administration of gene silencing compounds according to the invention, alone or in combination with any other agent can be directly to a tissue or organ such as, but not limited to, the bladder, liver, lung, kidney or lung.
  • administration of gene silencing compounds according to the invention, alone or in combination with any other agent is by intratumoral administration. In certain embodiments, administration of gene silencing compounds according to the invention, alone or in combination with any other agent, is by mucosal administration. In certain embodiments, administration of gene silencing compounds according to the invention, alone or in combination with any other agent, is by oral administration. In certain embodiments, administration of gene silencing compounds according to the invention, alone or in combination with any other agent, is by intrarectal administration. In certain embodiments, administration of gene silencing compounds according to the invention, alone or in combination with any other agent, is by intrathecal administration.
  • administration of gene silencing compounds according to the invention, alone or in combination with any other agent is directly to the bladder. In certain embodiments, administration of gene silencing compounds according to the invention, alone or in combination with any other agent, is directly to the lung.
  • an effective amount of a gene silencing compound according to the invention for treating a disease and/or disorder could be that amount necessary to alleviate or reduce the symptoms, or delay or ameliorate the disease and/or disorder.
  • an effective amount of a gene silencing compound according to the invention is an amount sufficient to achieve the desired modulation as compared to the gene expression in the absence of the gene silencing compound according to the invention.
  • the effective amount for any particular application can vary depending on such factors as the disease or condition being treated, the particular compound being administered, the size of the subject, or the severity of the disease or condition.
  • One of ordinary skill in the art can empirically determine the effective amount of a particular compound without necessitating undue experimentation.
  • the therapeutic composition is preferably administered at a sufficient dosage to attain a blood level of gene silencing compound according to the invention from about 0.0001 micromolar to about 10 micromolar. For localized administration, much lower concentrations than this may be effective, and much higher concentrations may be tolerated.
  • a total dosage of gene silencing compound according to the invention ranges from about 0.001 mg per patient per day to about 200 mg per kg body weight per day. In certain embodiments, the total dosage may be 0.08, 0.16, 0.32, 0.48, 0.32, 0.64, 1, 10 or 30 mg/kg body weight administered daily, twice weekly or weekly. It may be desirable to administer simultaneously, or sequentially a therapeutically effective amount of one or more of the therapeutic compositions of the invention to an individual as a single treatment episode.
  • the methods according to this aspect of the invention are useful for model studies of gene expression.
  • the methods are also useful for the prophylactic or therapeutic treatment of human or animal disease.
  • the methods are useful for pediatric and veterinary inhibition of gene expression applications.
  • oligonucleotide-based compounds of the invention were chemically synthesized using phosphoramidite chemistry on automated DNA/RNA synthesizer.
  • TAC protected (Except U) 2'-0-TBDMS RNA monomers, A, G, C and U, were purchased from Sigma- Aldrich. 7-deaza-G, inosine and loxoribine monomers were purchased from ChemGenes Corporation. 0.25M 5-ethylthio-lH-tetrazole, PAC- anhydride Cap A and Cap B were purchased from Glen Research.
  • Oligonucleotide-based compounds of the invention were synthesized at 1-2 ⁇ scale using a standard RNA synthesis protocol.
  • Oligonucleotide-based compounds of the invention were cleaved from solid support and the solution was further heated at 65 °C to removing protecting groups of exo cyclic-amines. The resulting solution was dried completely in a SpeedVac.
  • Oligonucleotide-based compounds of the invention were purified by ion exchange HPLC.
  • Buffer A 20 mM Tris-HCl, pH 7.0, 20% acetinitrile
  • Buffer B 3.0 M NaCl, 20 mM Tris-HCl, pH 7.0, 20% acetonitrile
  • the solution is placed in SpeedVac for 30 minutes. The remaining solution was filter through a 0.2 micro filter and then was lyophilized to dryness. The solid was then re-dissolved in water to make the desired concentration.
  • Oligonucleotide-based compounds of the invention were analyzed by capillary electrophoresis according to the following conditions.
  • Capillary 62cm ssDNA capillary
  • Sample preparation 0.2 OD of oligonucleotide-based composition according to the invention was dissolved in 200ul of RNAse-free water.
  • Injection electro-kinetic injection at 5KV for 5 seconds.
  • Running condition 14KV for 50 minutes at 30 °C.
  • Oligonucleotide-based compounds of the invention were analyzed by ion exchange HPLC according to the following conditions:
  • Buffer A 100 mM Tris-HCl, pH 8.0, 20% acetinitrile
  • Buffer B 2.0 M LiCl, 100 mM Tris-HCl, pH 8.0, 20% acetonitrile
  • Hepa 1-6 cells are co-transfected with GSO and target plasmid simultaneously using LIP OFECTAMINE® 2000 on day one (20,000 c/well).
  • RLuc siRNA was used as the positive control and GSO mu/hu universal control was used as the negative control.
  • luminescence measurements for both reporter genes are taken separately: Firefly luciferase: expression serves as the normalizer for the assay; Renilla luciferase: substrate includes a "stop" reagent to quench luminescence from firefly. Separate luminescence measurements are taken to correspond to renilla-target transcript expression. Substrate includes DTT to lyse cells. Results are shown in Table 4A and Table 4B.
  • glycerol is the non- nucleotidic linker.
  • Resuspended cell suspensions in the flow cytometry staining buffer were run on BD Accuri C6 to acquire data and analyzed by FLOWJO (TreeStar).
  • Hepa 1-6 cells are co-transfected with 3GA and target plasmid simultaneously using LIPOFECTAMINE® 2000 on day one (20,000 c/well). Concentration of 3GAs were ranging from 0.019 to 41.7 nM with a 3-fold increment. RLuc siRNA was used as the positive control and 3GA mu/hu universal control was used as the negative control. On day two (24 hours post-transfection), luminescence measurements for both reporter genes are taken separately: Firefly luciferase: expression serves as the normalizer for the assay; Renilla luciferase: substrate includes a "stop" reagent to quench luminescence from firefly. Separate luminescence measurements are taken to correspond to renilla-target transcript expression. Substrate includes DTT to lyse cells. IC50 of 3GAs was calculated using GraphPad Prism 6. Results are shown in Table 5.
  • Colon tumor can be implanted in BALB/c mice by subcutaneous injection of
  • Treatment can be initiated on day 6 or when tumor size reached to 70 to 80 mm 3 by intra-tumor injection of gene silencing compound according to the invention at various dosages (e.g., 2 mg/kg, 5 mg/kg, 12.5 mg/kg, or 25 mg/kg) on day 6, 10, 13, 16, 20, and 22.
  • dosages e.g., 2 mg/kg, 5 mg/kg, 12.5 mg/kg, or 25 mg/kg
  • T lymphocyte population in blood and spleen samples were detected and analyzed by flow cytometry.
  • Spleen IFN-y-producing cells were detected with ELISPOT assay after culture of spleen cells for 24 hours with tumor antigen beta-gal or AH1 peptide.
  • Tumor tissues were analyzed for gene expression by RT-PCR.
  • oligonucleotides may be used. Such equivalents are considered to be within the scope of this invention, and are covered by the following claims.

Abstract

The present invention is directed to compounds, compositions, and methods useful for modulating PD1, PDL1, IDO1, LAG3, TIM3, CTLA4, ID02, CEACAM1, OX40, and/or OX40L mRNA or protein expression using gene silencing compounds comprising two or more single stranded antisense oligonucleotides that are linked through their 5 '-ends to allow the presence of two or more accessible 3 '-ends.

Description

COMPOSITIONS FOR INHIBITING CHECKPOINT GENE EXPRESSION AND USES
THEREOF
BACKGROUND OF THE INVENTION
Related Applications
[0001] This application claims the benefit of U.S. provisional patent application serial number 62/126,368, filed on February 27, 2015, the contents of which are incorporated herein by reference in its entirety. Field of the invention
[0002] The present invention relates to compounds, compositions, and methods of use for the inhibition of checkpoint gene expression or for diagnosing, treating and/or preventing diseases and/or conditions that respond to the inhibition of checkpoint gene expression. Summary of the related art
[0003] The immune system is a hosts defense against foreign antigens; however, in order to function properly a variety of checks and balances are required to protect against self-antigens (i.e., autoimmunity) and, at the same time, provide an appropriate response against foreign. Immune-activating and immune-suppressive receptors and ligands provide these regulatory checks and balances (see Pardoll et al, The blockade of immune checkpoints in cancer immunotherapy, Nat. Rev. Cane. 12, 252 (2012)).
[0004] Immune checkpoints refer to a group of endogenous immune-suppressive ligands and receptors that are crucial for the maintenance of self-tolerance and the protection of tissues from damage when the immune system is responding to an infection, (see Y.L. Wu, et al, Immunotherapies: The Blockade of Inhibitory Signals, Int. J. Biol. Sci. 8, 1420 (2012)) In response to the induction of an immune response expression of checkpoints increases. These checkpoints act as regulatory feedback to maintain immune homeostasis.
[0005] In patients with cancer, tumor mutations give rise to tumor-specific antigens that can be recognized by the immune system, particularly T-cells, leading to elimination of cancer cells. However, to defend themselves, tumor cells can co-opt immune checkpoint pathways to suppress the immune response in the tumor microenvironment and evade the host immune system by inhibiting T cells that might otherwise attack the tumor cells, (see J.F. Grosso & M.N. Jure-Kunkel; CTLA-4 blockade in tumor models: an overview of preclinical and translational research, Cancer Immun. 13, 5 (2013); M.E. Turnis, et al; Combinatorial immunotherapy: PD-1 may not be LAG-ing behind any more, Oncolmmunology 1, 1172 (2012)).
[0006] Many previous cancer immunotherapies have likely been limited by these suppressive mechanisms. Thus there is a need to over these immunosuppressive
mechanisms in order to enhance antitumor immunotherapy applications.
BRIEF SUMMARY OF THE INVENTION
[0007] The present invention is directed to compounds, compositions, and methods useful for modulating PDl, PDL1, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAMl, OX40, and/or OX40L mRNA or protein expression using gene silencing compounds comprising two or more single stranded antisense oligonucleotides that are linked through their 5 '-ends to allow the presence of two or more accessible 3 '-ends. The gene silencing compounds according to the invention effectively inhibit or decrease PDl, PDL1, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAMl, OX40, and/or OX40L mRNA or protein expression.
[0008] Provided herein are methods, compounds, and compositions for modulating expression of PDl, PDL1, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAMl, OX40, and/or OX40L mRNA and protein. In certain embodiments, compounds useful for modulating expression of PDl, PDL1, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAMl, OX40, and/or OX40L mRNA and protein are gene silencing compounds.
[0009] In certain embodiments, modulation can occur in a cell or tissue. In certain embodiments the cell is a tumor cell. In certain embodiments, the tissue is a tumor. In certain embodiments, the cell or tissue is in an animal. In certain embodiments, the animal is a human. In certain embodiments, PDl, PDL1, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAMl, OX40, and/or OX40L mRNA levels are reduced. In certain embodiments, PDl, PDL1, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAMl, OX40, and/or OX40L protein levels are reduced. Such reduction can occur in a time-dependent manner or in a dose- dependent manner.
[0010] Also provided are methods, compounds, and compositions useful for preventing, treating, and ameliorating diseases, disorders, and conditions. In certain embodiments, such diseases, disorders, and conditions are hyperproliferative diseases, disorders, and conditions. In certain embodiments such hyperproliferative diseases, disorders, and conditions include cancer as well as associated malignancies and metastases.
[0011] In certain embodiments, methods of treatment include administering a PDl,
PDL1, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAMl, OX40, and/or OX40L gene silencing compound or composition to an individual in need thereof. In certain embodiments, the gene silencing compound or composition is administered intratumorally.
DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
[0012] The invention relates to the therapeutic and prophylactic use of gene silencing compounds, also referred to as 3rd generation antisense (3GA) compounds, to down-regulate checkpoint mRNA or protein expression. Such molecules are useful, for example, in providing compositions for modulation of checkpoint gene expression or for treating and/or preventing diseases and/or conditions that are capable of responding to modulation of checkpoint gene expression in patients, subjects, animals or organisms.
[0013] The objects of the present invention, the various features thereof, as well as the invention itself may be more fully understood from the following description, when read together with the accompanying drawings in which the following terms have the ascribed meaning. Unless specific definitions are provided, the nomenclature utilized in connection with, and the procedures and techniques of, analytical chemistry, synthetic organic chemistry, and medicinal and pharmaceutical chemistry described herein are those well-known and commonly used in the art. Standard techniques may be used for chemical synthesis, and chemical analysis. Where permitted, all patents, applications, published applications and other publications, GENBANK Accession Numbers and associated sequence information obtainable through databases such as National Center for Biotechnology Information (NCBI) and other data referred to throughout in the disclosure herein are incorporated by reference for the portions of the document discussed herein, as well as in their entirety.
[0014] The term "2'-0-substituted" means substitution of the 2' position of the pentose moiety with an -O- lower alkyl group containing 1-6 saturated or unsaturated carbon atoms (for example, but not limited to, 2'-0-methyl), or with an -O-aryl or allyl group having 2-6 carbon atoms, wherein such alkyl, aryl or allyl group may be unsubstituted or may be substituted, (for example, with 2'-0-methoxyethyl, ethoxy, methoxy, halo, hydroxy 1, trifluoromethyl, cyano, nitro, acyl, acyloxy, alkoxy, carboxyl, carbalkoxyl, or amino groups); or with a hydroxyl, an amino or a halo group, but not with a 2'-H group. In some
embodiments the oligonucleotides of the invention include four or five 2'-0-alky nucleotides at their 5' terminus, and/or four or five 2'-0-alky nucleotides at their 3' terminus.
[0015] The term "3"', when used directionally, generally refers to a region or position in a polynucleotide or oligonucleotide 3' (toward the 3 'end of the nucleotide) from another region or position in the same polynucleotide or oligonucleotide. [0016] The term "3' end" generally refers to the 3' terminal nucleotide of the component oligonucleotides. "Two or more oligonucleotides linked at their 3' ends" generally refers to a linkage between the 3' terminal nucleotides of the oligonucleotides which may be directly via 5', 3' or 2' hydroxyl groups, or indirectly, via a non-nucleotide linker. Such linkages may also be via a nucleoside, utilizing both 2' and 3' hydroxyl positions of the nucleoside. Such linkages may also utilize a functionalized sugar or nucleobase of a 3 'terminal nucleotide.
[0017] The term "5"', when used directionally, generally refers to a region or position in a polynucleotide or oligonucleotide 5' (toward the 5 'end of the nucleotide) from another region or position in the same polynucleotide or oligonucleotide.
[0018] The term "5' end" generally refers to the 5' terminal nucleotide of the component oligonucleotides. "Two or more single-stranded antisense oligonucleotides linked at their 5' ends" generally refers to a linkage between the 5' terminal nucleotides of the oligonucleotides which may be directly via 5', 3' or 2' hydroxyl groups, or indirectly, via a non-nucleotide linker. Such linkages may also be via a nucleoside, utilizing both 2' and 3' hydroxyl positions of the nucleoside. Such linkages may also utilize a functionalized sugar or nucleobase of a 5 'terminal nucleotide.
[0019] The term "about" generally means that the exact number is not critical. Thus, oligonucleotides having one or two fewer nucleoside residues, or from one to several additional nucleoside residues are contemplated as equivalents of each of the embodiments described above.
[0020] The term "accessible" generally means when related to a compound according to the invention, that the relevant portion of the molecule is able to be recognized by the cellular components necessary to elicit an intended response to the compound.
[0021] The term "agonist" generally refers to a substance that binds to a receptor of a cell and induces a response. An agonist can be a naturally occurring substance such as bacterial DNA or a synthetic composition. A synthetic agonist often mimics the action of a naturally occurring substance such as a ligand.
[0022] The term "antigen" generally refers to a substance that is recognized and selectively bound by an antibody or by a T cell antigen receptor. Antigens may include but are not limited to peptides, proteins, lipids, carbohydrates, nucleosides, nucleotides, nucleic acids, and combinations thereof. Antigens may be natural or synthetic and generally induce an immune response that is specific for that antigen. [0023] "Antisense activity" means any detectable or measurable activity attributable to the hybridization of a gene silencing compound to its target nucleic acid. In certain embodiments, antisense activity is a decrease in the amount or expression of a target nucleic acid or protein encoded by such target nucleic acid.
[0024] As used herein, "Gene silencing oligonucleotide (GSO)", "Gene silencing compound", or "3rd generation antisense (3GA)" compound are used interchangeably to refer to an oligomeric compound comprising two or more single stranded antisense
oligonucleotides that are linked through their 5 '-ends to allow the presence of two or more accessible 3 '-ends. Gene silencing compounds are capable of undergoing hybridization to a target nucleic acid through hydrogen bonding.
[0025] "Antisense inhibition" means reduction of target nucleic acid levels or target protein levels in the presence of a gene silencing compound complementary to a target nucleic acid as compared to target nucleic acid levels or target protein levels in the absence of the gene silencing compound.
[0026] "Antisense oligonucleotide" means a single-stranded oligonucleotide having a nucleobase sequence that permits hybridization to a corresponding region or segment of a target nucleic acid.
[0027] The term "biologic instability" generally refers to a molecule's ability to be degraded and subsequently inactivated in vivo. For oligonucleotides, such degradation results from exonuclease activity and/or endonuclease activity, wherein exonuclease activity refers to cleaving nucleotides from the 3' or 5' end of an oligonucleotide, and endonuclease activity refers to cleaving phosphodi ester bonds at positions other than at the ends of the
oligonucleotide.
[0028] The term "cancer" generally refers to, without limitation, any malignant growth or tumor caused by abnormal or uncontrolled cell proliferation and/or division.
Cancers may occur in humans and/or mammals and may arise in any and all tissues. Treating a patient having cancer may include administration of a compound, pharmaceutical formulation or vaccine according to the invention such that the abnormal or uncontrolled cell proliferation and/or division, or metastasis is affected.
[0029] The term "carrier" generally encompasses any excipient, diluent, filler, salt, buffer, stabilizer, solubilizer, oil, lipid, lipid containing vesicle, microspheres, liposomal encapsulation, or other material for use in pharmaceutical formulations. It will be understood that the characteristics of the carrier, excipient or diluent will depend on the route of administration for a particular application. The preparation of pharmaceutically acceptable formulations containing these materials is described in, for example, Remington 's
Pharmaceutical Sciences, 18th Edition, ed. A. Gennaro, Mack Publishing Co., Easton, PA, 1990.
[0030] The term "co-administration" or "co-administered" generally refers to the administration of at least two different substances. Co-administration refers to simultaneous administration, as well as temporally spaced order of up to several days apart, of at least two different substances in any order, either in a single dose or separate doses.
[0031] The term "in combination with" generally means administering two or more agents (e.g., a gene silencing compound according to the invention and another agent) such that there is an overlap of an effect of each agent on the patient. Such administration may be done in any order, including simultaneous administration, as well as temporally spaced order from a few seconds up to several days apart. In some embodiments, the administration of the agents are spaced sufficiently close together such that a combinatorial effect is achieved. Such combination treatment may also include more than a single administration of the compound according to the invention and/or independently the other agent. The
administration of the compound according to the invention and the other agent may be by the same or different routes. In some embodiments, administration of at least one agent is made while the other agent is still present at a therapeutic level in the subject.
[0032] The term "complementary" is intended to mean the capacity for pairing between nucleobases of a first nucleic acid and a second nucleic acid.
[0033] "Contiguous nucleobases" means nucleobases immediately adjacent to each other.
[0034] The term "individual" or "subject" or "patient" generally refers to a mammal, such as a human.
[0035] "CEACAM1 nucleic acid" means any nucleic acid encoding CEACAM1. For example, in certain embodiments, a CEACAM1 nucleic acid includes a DNA sequence encoding CEACAM1, an RNA sequence transcribed from DNA encoding CEACAM1 (including genomic DNA comprising introns and exons), and an mRNA sequence encoding CEACAM1. "CEACAM1 mRNA" means an mRNA encoding a CEACAM1 protein.
[0036] "CTLA4 nucleic acid" means any nucleic acid encoding CTLA4. For example, in certain embodiments, a CTLA4 nucleic acid includes a DNA sequence encoding CTLA4, an RNA sequence transcribed from DNA encoding CTLA4 (including genomic DNA comprising introns and exons), and an mRNA sequence encoding CTLA4. "CTLA4 mRNA" means an mRNA encoding a CTLA4 protein.
[0037] "Fully complementary" or " 100% complementary" means each nucleobase of a first nucleic acid has a complementary nucleobase in a second nucleic acid. In certain embodiments, a first nucleic acid is an antisense compound and a target nucleic acid is a second nucleic acid.
[0038] "Hybridization" means the annealing of complementary nucleic acid molecules. In certain embodiments, complementary nucleic acid molecules include an antisense compound and a target nucleic acid.
[0039] "IDOl nucleic acid" means any nucleic acid encoding IDOl . For example, in certain embodiments, a IDOl nucleic acid includes a DNA sequence encoding IDOl, an RNA sequence transcribed from DNA encoding IDOl (including genomic DNA comprising introns and exons), and an mRNA sequence encoding IDOl. "IDOl mRNA" means an mRNA encoding an IDOl protein.
[0040] "ID02 nucleic acid" means any nucleic acid encoding ID02. For example, in certain embodiments, a ID02 nucleic acid includes a DNA sequence encoding ID02, an RNA sequence transcribed from DNA encoding ID02 (including genomic DNA comprising introns and exons), and an mRNA sequence encoding ID02. "ID02 mRNA" means an mRNA encoding an ID02 protein.
[0041] "Inhibiting PDl, PDLl, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAMl,
OX40, and/or OX40L mRNA or protein expression" means reducing expression of PDl, PDLl, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAMl, OX40, and/or OX40L mRNA and/or protein levels in the presence of a gene silencing compound according to the invention as compared to expression of PDl, PDLl, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAMl, OX40, and/or OX40L mRNA and/or protein levels in the absence of a gene silencing compound according to the invention.
[0042] The term "kinase inhibitor" generally refers to molecules that antagonize or inhibit phosphorylation-dependent cell signaling and/or growth pathways in a cell. Kinase inhibitors may be naturally occurring or synthetic and include small molecules that have the potential to be administered as oral therapeutics. Kinase inhibitors have the ability to rapidly and specifically inhibit the activation of the target kinase molecules. Protein kinases are attractive drug targets, in part because they regulate a wide variety of signaling and growth pathways and include many different proteins. As such, they have great potential in the treatment of diseases involving kinase signaling, including cancer, cardiovascular disease, inflammatory disorders, diabetes, macular degeneration and neurological disorders. A non- limiting example of a kinase inhibitor is sorafenib.
[0043] "LAG3 nucleic acid" means any nucleic acid encoding LAG3. For example, in certain embodiments, a LAG3 nucleic acid includes a DNA sequence encoding LAG3, an RNA sequence transcribed from DNA encoding LAG3 (including genomic DNA comprising introns and exons), and an mRNA sequence encoding LAG3. "LAG3 mRNA" means an mRNA encoding a LAG3 protein.
[0044] The term "linear synthesis" generally refers to a synthesis that starts at one end of an oligonucleotide and progresses linearly to the other end. Linear synthesis permits incorporation of either identical or non-identical (in terms of length, base composition and/or chemical modifications incorporated) monomeric units into an oligonucleotide.
[0045] The term "mammal" is expressly intended to include warm blooded, vertebrate animals, including, without limitation, humans, non-human primates, rats, mice, cats, dogs, horses, cattle, cows, pigs, sheep and rabbits.
[0046] The term "nucleoside" generally refers to compounds consisting of a sugar, usually ribose, deoxyribose, pentose, arabinose or hexose, and a purine or pyrimidine base.
[0047] The term "nucleotide" generally refers to a nucleoside comprising a phosphorous-containing group attached to the sugar.
[0048] The term "modified nucleoside" or "nucleotide derivative" generally is a nucleoside that includes a modified heterocyclic base, a modified sugar moiety, or any combination thereof. In some embodiments, the modified nucleoside or nucleotide derivative is a non-natural pyrimidine or purine nucleoside, as herein described. For purposes of the invention, a modified nucleoside or nucleotide derivative, a pyrimidine or purine analog or non-naturally occurring pyrimidine or purine can be used interchangeably and refers to a nucleoside that includes a non-naturally occurring base and/or non-naturally occurring sugar moiety. For purposes of the invention, a base is considered to be non-natural if it is not guanine, cytosine, adenine, thymine or uracil and a sugar is considered to be non-natural if it is not β-ribo-furanoside or 2'-deoxyribo-furanoside.
[0049] The term "modified oligonucleotide" as used herein describes an
oligonucleotide in which at least two of its nucleotides are covalently linked via a synthetic linkage, i.e., a linkage other than a phosphodiester linkage between the 5' end of one nucleotide and the 3' end of another nucleotide in which the 5' nucleotide phosphate has been replaced with any number of chemical groups. The term "modified oligonucleotide" also encompasses 2'-0,4'-C-methylene-b-D-ribofuranosyl nucleic acids, arabinose nucleic acids, substituted arabinose nucleic acids, hexose nucleic acids, peptide nucleic acids, morpholino, and oligonucleotides having at least one nucleotide with a modified base and/or sugar, such as a 2'-0-substituted, a 5- methylcytosine and/or a 3 '-0-substituted ribonucleotide.
[0050] The term "nucleic acid" encompasses a genomic region or an RNA molecule transcribed therefrom. In some embodiments, the nucleic acid is mRNA.
[0051] The term "linker" generally refers to any moiety that can be attached to an oligonucleotide by way of covalent or non-covalent bonding through a sugar, a base, or the backbone. The non-covalent linkage may be, without limitation, electrostatic interactions, hydrophobic interactions, π-stacking interactions, hydrogen bonding and combinations thereof. Non-limiting examples of such non-covalent linkage includes Watson-Crick base pairing, Hoogsteen base pairing, and base stacking. The linker can be used to attach two or more nucleosides or can be attached to the 5 ' and/or 3 ' terminal nucleotide in the
oligonucleotide. Such linker can be either a non-nucleotide linker or a nucleoside linker.
[0052] The term "non-nucleotide linker" generally refers to a chemical moiety, other than a linkage directly between two nucleotides that can be attached to an oligonucleotide by way of covalent or non-covalent bonding. Preferably such non-nucleotide linker is from about 2 angstroms to about 200 angstroms in length, and may be either in a cis or trans orientation.
[0053] The term "internucleotide linkage" generally refer to a chemical linkage to join two nucleosides through their sugars (e.g. 3 '-3 ', 2'-3', 2'-5 ', 3 '-5', 5'-5') consisting of a phosphorous atom and a charged, or neutral group (e.g., phosphodiester, phosphorothioate, phosphorodithioate or methylphosphonate) between adjacent nucleosides.
[0054] The term "oligonucleotide" refers to a polynucleoside formed from a plurality of linked nucleoside units, which may include, for example, deoxyribonucleotides or ribonucleotides, synthetic or natural nucleotides, phosphodiester or modified linkages, natural bases or modified bases natural sugars or modified sugars, or combinations of these components. The nucleoside units may be part of viruses, bacteria, cell debris or
oligonucleotide-based compositions (for example, siRNA and microRNA). Such
oligonucleotides can also be obtained from existing nucleic acid sources, including genomic or cDNA, but are preferably produced by synthetic methods. In certain embodiments each nucleoside unit includes a heterocyclic base and a pentofuranosyl, trehalose, arabinose, 2'- deoxy-2'-substituted nucleoside, 2'-deoxy-2'-substituted arabinose, 2'-0- substitutedarabinose or hexose sugar group. The nucleoside residues can be coupled to each other by any of the numerous known intemucleoside linkages. Such intemucleoside linkages include, without limitation, phosphodiester, phosphorothioate, phosphorodithioate, methylphosphonate, alkylphosphonate, alkylphosphonothioate, phosphotriester,
phosphoramidate, siloxane, carbonate, carboalkoxy, acetamidate, carbamate, morpholino, borano, thioether, bridged phosphoramidate, bridged methylene phosphonate, bridged phosphorothioate, and sulfone intemucleoside linkages. The term "oligonucleotide" also encompasses polynucleosides having one or more stereospecific intemucleoside linkage (e.g., (Rp)- or (Sp)-phosphorothioate, alkylphosphonate, or phosphotriester linkages). As used herein, the terms "oligonucleotide" and "dinucleotide" are expressly intended to include polynucleosides and dinucleosides having any such intemucleoside linkage, whether or not the linkage comprises a phosphate group. In certain exemplary embodiments, these intemucleoside linkages may be phosphodiester, phosphorothioate or phosphorodithioate linkages, or combinations thereof. In exemplary embodiments, the nucleotides of the synthetic oligonucleotides are linked by at least one phosphorothioate intemucleotide linkage. The phosphorothioate linkages may be mixed Rp and Sp enantiomers, or they may be stereoregular or substantially stereoregular in either Rp or Sp form (see Iyer et al. (1995) Tetrahedron Asymmetry 6: 1051 -1054). In certain embodiments, one or more of the oligonucleotides within the antisense compositions of the invention contain one or more 2'- 0,4'-C-methylene-b-D-ribofuranosyl nucleic acids, wherein the ribose is modified with a bond between the 2' and 4' carbons, which fixes the ribose in the 3'-endo structural conformation.
[0055] "OX40 nucleic acid" means any nucleic acid encoding OX40. For example, in certain embodiments, a OX40 nucleic acid includes a DNA sequence encoding OX40, an RNA sequence transcribed from DNA encoding OX40 (including genomic DNA comprising introns and exons), and an mRNA sequence encoding OX40. "OX40 mRNA" means an mRNA encoding an OX40 protein.
[0056] "OX40L nucleic acid" means any nucleic acid encoding OX40L. For example, in certain embodiments, a OX40L nucleic acid includes a DNA sequence encoding OX40L, an RNA sequence transcribed from DNA encoding OX40L (including genomic DNA comprising introns and exons), and an mRNA sequence encoding OX40L. "OX40L mRNA" means an mRNA encoding an OX40L protein.
[0057] "PD1 nucleic acid" means any nucleic acid encoding PD1. For example, in certain embodiments, a PD1 nucleic acid includes a DNA sequence encoding PD1, an RNA sequence transcribed from DNA encoding PDl (including genomic DNA comprising introns and exons), and an mRNA sequence encoding PDl . "PDl mRNA" means an mRNA encoding a PDl protein.
[0058] "PDLl nucleic acid" means any nucleic acid encoding PDLl . For example, in certain embodiments, a PDLl nucleic acid includes a DNA sequence encoding PDLl, an RNA sequence transcribed from DNA encoding PDLl (including genomic DNA comprising introns and exons), and an mRNA sequence encoding PDLl . "PDLl mRNA" means an mRNA encoding a PDLl protein.
[0059] The term "peptide" generally refers to oligomers or polymers of amino acids that are of sufficient length and composition to affect a biological response, for example, antibody production or cytokine activity whether or not the peptide is a hapten. The term
"peptide" may include modified amino acids (whether or not naturally or non-naturally occurring), where such modifications include, but are not limited to, phosphorylation, glycosylation, pegylation, lipidization, and methylation.
[0060] The term "pharmaceutically acceptable" means a non-toxic material that does not interfere with the effectiveness of a compound according to the invention or the biological activity of a compound according to the invention.
[0061] The term "physiologically acceptable" refers to a non-toxic material that is compatible with a biological system such as a cell, cell culture, tissue, or organism.
Preferably, the biological system is a living organism, such as a mammal, particularly a human.
[0062] The term "prophylactically effective amount" generally refers to an amount sufficient to prevent or reduce the development of an undesired biological effect.
[0063] "Portion" means a defined number of contiguous (i.e., linked) nucleobases of a nucleic acid. In certain embodiments, a portion is a defined number of contiguous nucleobases of a target nucleic acid. In certain embodiments, a portion is a defined number of contiguous nucleobases of an antisense compound.
[0064] "Single-stranded oligonucleotide" means an oligonucleotide which is not hybridized to a complementary strand.
[0065] "Specifically hybridizable" refers to a gene silencing compound having a sufficient degree of complementarity between an antisense oligonucleotide and a target nucleic acid to induce a desired effect, while exhibiting minimal or no effects on non-target nucleic acids under conditions in which specific binding is desired, i.e., under physiological conditions in the case of in vivo assays and therapeutic treatments. [0066] "Targeting" or "targeted" means the process of design and selection of a gene silencing compound that will specifically hybridize to a target nucleic acid and induce a desired effect.
[0067] "Target nucleic acid," "target RNA," "target mRNA," and "target RNA transcript" all refer to a nucleic acid capable of being targeted by gene silencing compounds.
[0068] "Target segment" means the sequence of nucleotides of a target nucleic acid to which a gene silencing compound is targeted. "5' target site" refers to the 5'-most nucleotide of a target segment. "3' target site" refers to the 3'-most nucleotide of a target segment.
[0069] The term "therapeutically effective amount" or "pharmaceutically effective amount" generally refers to an amount sufficient to affect a desired biological effect, such as a beneficial result, including, without limitation, prevention, diminution, amelioration or elimination of signs or symptoms of a disease or disorder. Thus, the total amount of each active component of the pharmaceutical composition or method is sufficient to show a meaningful patient benefit, for example, but not limited to, healing of chronic conditions characterized by immune stimulation. Thus, a "pharmaceutically effective amount" will depend upon the context in which it is being administered. A pharmaceutically effective amount may be administered in one or more prophylactic or therapeutic administrations. When applied to an individual active ingredient, administered alone, the term refers to that ingredient alone. When applied to a combination, the term refers to combined amounts of the active ingredients that result in the therapeutic effect, whether administered in combination, serially or simultaneously.
[0070] "TIM3 nucleic acid" means any nucleic acid encoding TIM3. For example, in certain embodiments, a TIM3 nucleic acid includes a DNA sequence encoding TIM3, an RNA sequence transcribed from DNA encoding TIM3 (including genomic DNA comprising introns and exons), and an mRNA sequence encoding TIM3. "TIM3 mRNA" means an mRNA encoding a TIM3 protein.
[0071] The term "treatment" generally refers to an approach intended to obtain a beneficial or desired result, which may include alleviation of symptoms, or delaying or ameliorating a disease progression.
[0072] The term "gene expression" generally refers to process by which information from a gene is used in the synthesis of a functional gene product, which may be a protein. The process may involve transcription, RNA splicing, translation, and post-translational modification of a protein, and may include mRNA, preRNA, ribosomal RNA, and other templates for protein synthesis. [0073] In certain embodiments provided are methods, compounds, and compositions for inhibiting PD1, PDLl, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAM1, OX40, or OX40L mRNA or protein expression. In certain embodiments the compounds are antisense oligonucleotides, double stranded or single-stranded siRNA compounds, or gene silencing compounds.
[0074] As used herein, gene silencing compounds according to the invention comprise two or more single-stranded antisense oligonucleotides linked at their 5' ends, wherein the compounds have two or more accessible 3' ends. The general structure of the oligonucleotide-based compounds of the invention may be described by the following formula I:
3 ' -Nn... N1N2N3N4-5 '-L-5 ' -N8N7N6N5...Nm-3 ' (Formula I), wherein L is a nucleotide linker or non-nucleotide linker; N1-N8, at each occurrence, is independently a nucleotide or nucleotide derivative; Nm and Nn, at each occurrence, are independently a nucleotide or nucleotide derivative; and wherein m and n are independently numbers from 0 to about 40.
[0075] The linkage at the 5' ends of the component oligonucleotides is independent of the other oligonucleotide linkages and may be directly via 5', 3' or 2' hydroxy 1 groups, or indirectly, via a non-nucleotide linker or a nucleoside, utilizing either the 2' or 3' hydroxyl positions of the nucleoside. Linkages may also utilize a functionalized sugar or nucleobase of a 5' terminal nucleotide.
[0076] In certain embodiments provided are gene silencing compounds targeted to a mouse or human PD1 nucleic acid. In certain embodiments, the mouse PD1 nucleic acid is the sequence set forth in GENBANK Accession No. NM_008798 (incorporated herein as SEQ ID NO: 387) or the human PD1 nucleic acid is the sequence set forth in GENBANK Accession No. NM_005018 (incorporated herein as SEQ ID NO: 388).
[0077] In certain embodiments provided are gene silencing compounds targeted to a mouse or human PDLl nucleic acid. In certain embodiments, the mouse PDLl nucleic acid is the sequence set forth in GENBANK Accession No. NM_021893 (incorporated herein as SEQ ID NO: 389) or the human PDLl nucleic acid is the sequence set forth in GENBANK Accession No. NM_014143 (incorporated herein as SEQ ID NO: 390).
[0078] In certain embodiments provided are gene silencing compounds targeted to a mouse or human IDOl nucleic acid. In certain embodiments, the mouse IDOl nucleic acid is the sequence set forth in GENBANK Accession No. NM_008324 (incorporated herein as SEQ ID NO: 391) or the human IDOl nucleic acid is the sequence set forth in GENBANK Accession No. NM_002164 (incorporated herein as SEQ ID NO: 392).
[0079] In certain embodiments provided are gene silencing compounds targeted to a mouse or human LAG3 nucleic acid. In certain embodiments, the mouse LAG3 nucleic acid is the sequence set forth in GENBANK Accession No. NM_008479 (incorporated herein as SEQ ID NO: 393) or the human LAG3 nucleic acid is the sequence set forth in GENBANK Accession No. NM_002286 (incorporated herein as SEQ ID NO: 394).
[0080] In certain embodiments provided are gene silencing compounds targeted to a mouse or human TIM3 nucleic acid. In certain embodiments, the mouse TIM3 nucleic acid is the sequence set forth in GENBANK Accession No. NM_134250 (incorporated herein as SEQ ID NO: 395) or the human TIM3 nucleic acid is the sequence set forth in GENBANK Accession No. NM_032782 (incorporated herein as SEQ ID NO: 396).
[0081] In certain embodiments provided are gene silencing compounds targeted to a mouse or human CTLA4 nucleic acid. In certain embodiments, the mouse CTLA4 nucleic acid is the sequence set forth in GENBANK Accession No. NM_009843 (incorporated herein as SEQ ID NO: 397) or the human CTLA4 nucleic acid is the sequence set forth in
GENBANK Accession No. NM_005214 (incorporated herein as SEQ ID NO: 398).
[0082] In certain embodiments provided are gene silencing compounds targeted to a mouse or human ID02 nucleic acid. In certain embodiments, the mouse ID02 nucleic acid is the sequence set forth in GENBANK Accession No. NM_145949 (incorporated herein as SEQ ID NO: 399) or the human ID02 nucleic acid is the sequence set forth in GENBANK Accession No. NM_194294 (incorporated herein as SEQ ID NO: 400).
[0083] In certain embodiments provided are gene silencing compounds targeted to a mouse or human CEACAM1 nucleic acid. In certain embodiments, the mouse CEACAM1 nucleic acid is the sequence set forth in GENBANK Accession No. NM_001039187
(incorporated herein as SEQ ID NO: 401) or the human CEACAM1 nucleic acid is the sequence set forth in GENBANK Accession No. NM_001205344 (incorporated herein as SEQ ID NO: 402).
[0084] In certain embodiments provided are gene silencing compounds targeted to a mouse or human OX40 nucleic acid. In certain embodiments, the mouse OX40 nucleic acid is the sequence set forth in GENBANK Accession No. NM_011659 (incorporated herein as SEQ ID NO: 403) or the human OX40 nucleic acid is the sequence set forth in GENBANK Accession No. NM_003327 (incorporated herein as SEQ ID NO: 404). [0085] In certain embodiments provided are gene silencing compounds targeted to a mouse or human OX40L nucleic acid. In certain embodiments, the mouse OX40L nucleic acid is the sequence set forth in GENBANK Accession No. NM_009452 (incorporated herein as SEQ ID NO: 405) or the human OX40L nucleic acid is the sequence set forth in
GENBANK Accession No. NM_003326 (incorporated herein as SEQ ID NO: 406).
[0086] Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 387, SEQ ID NO: 388, SEQ ID NO: 389, SEQ ID NO: 390, SEQ ID NO: 391, SEQ ID NO: 392, SEQ ID NO: 393, SEQ ID NO: 394, SEQ ID NO: 395, SEQ ID NO: 396, SEQ ID NO: 397, SEQ ID NO: 398, SEQ ID NO: 399, SEQ ID NO: 400, SEQ ID NO: 401, SEQ ID NO: 402, SEQ ID NO: 403, SEQ ID NO: 404, SEQ ID NO:
405, or SEQ ID NO: 406. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 387, SEQ ID NO: 388, SEQ ID NO: 389, SEQ ID NO: 390, SEQ ID NO: 391, SEQ ID NO: 392, SEQ ID NO: 393, SEQ ID NO: 394, SEQ ID NO: 395, SEQ ID NO: 396, SEQ ID NO: 397, SEQ ID NO: 398, SEQ ID NO: 399, SEQ ID NO: 400, SEQ ID NO: 401, SEQ ID NO: 402, SEQ ID NO: 403, SEQ ID NO: 404, SEQ ID NO: 405, or SEQ ID NO: 406. Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 387, SEQ ID NO: 388, SEQ ID NO: 389, SEQ ID NO: 390, SEQ ID NO: 391, SEQ ID NO: 392, SEQ ID NO: 393, SEQ ID NO: 394, SEQ ID NO: 395, SEQ ID NO: 396, SEQ ID NO: 397, SEQ ID NO: 398, SEQ ID NO: 399, SEQ ID NO: 400, SEQ ID NO: 401, SEQ ID NO: 402, SEQ ID NO: 403, SEQ ID NO: 404, SEQ ID NO: 405, or SEQ ID NO:
406. In certain embodiments, the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 387, SEQ ID NO: 388, SEQ ID NO: 389, SEQ ID NO: 390, SEQ ID NO: 391, SEQ ID NO: 392, SEQ ID NO: 393, SEQ ID NO: 394, SEQ ID NO: 395, SEQ ID NO: 396, SEQ ID NO: 397, SEQ ID NO: 398, SEQ ID NO: 399, SEQ ID NO: 400, SEQ ID NO: 401, SEQ ID NO: 402, SEQ ID NO: 403, SEQ ID NO: 404, SEQ ID NO: 405, or SEQ ID NO: 406. [0087] Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 387, SEQ ID NO: 389, SEQ ID NO: 391, SEQ ID NO: 393, SEQ ID NO: 395, SEQ ID NO: 397, SEQ ID NO: 399, SEQ ID NO: 401, SEQ ID NO: 403, or SEQ ID NO: 405. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 387, SEQ ID NO: 389, SEQ ID NO: 391, SEQ ID NO: 393, SEQ ID NO: 395, SEQ ID NO: 397, SEQ ID NO: 399, SEQ ID NO: 401, SEQ ID NO:
403, or SEQ ID NO: 405. Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 387, SEQ ID NO: 389, SEQ ID NO: 391, SEQ ID NO: 393, SEQ ID NO: 395, SEQ ID NO: 397, SEQ ID NO: 399, SEQ ID NO: 401, SEQ ID NO: 403, or SEQ ID NO: 405. In certain embodiments, the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 387, SEQ ID NO: 389, SEQ ID NO: 391, SEQ ID NO: 393, SEQ ID NO: 395, SEQ ID NO: 397, SEQ ID NO: 399, SEQ ID NO: 401, SEQ ID NO: 403, or SEQ ID NO: 405.
[0088] Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 388, SEQ ID NO: 390, SEQ ID NO: 392, SEQ ID NO: 394, SEQ ID NO: 396, SEQ ID NO: 398, SEQ ID NO: 400, SEQ ID NO: 402, SEQ ID NO:
404, or SEQ ID NO: 406. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 388, SEQ ID NO: 390, SEQ ID NO: 392, SEQ ID NO: 394, SEQ ID NO: 396, SEQ ID NO: 398, SEQ ID NO: 400, SEQ ID NO: 402, SEQ ID NO: 404, or SEQ ID NO: 406. Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 388, SEQ ID NO: 390, SEQ ID NO: 392, SEQ ID NO: 394, SEQ ID NO: 396, SEQ ID NO: 398, SEQ ID NO: 400, SEQ ID NO: 402, SEQ ID NO: 404, or SEQ ID NO: 406. In certain embodiments, the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 388, SEQ ID NO: 390, SEQ ID NO: 392, SEQ ID NO: 394, SEQ ID NO: 396, SEQ ID NO: 398, SEQ ID NO: 400, SEQ ID NO: 402, SEQ ID NO: 404, or SEQ ID NO: 406.
[0089] Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 387. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 387. Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 387. In certain embodiments, the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 387.
[0090] Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 388. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 388. Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 388. In certain embodiments, the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 388.
[0091] Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 389. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 389. Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 389. In certain embodiments, the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 389.
[0092] Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 390. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 390. Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 390. In certain embodiments, the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 390.
[0093] Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 391. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 391. Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 391. In certain embodiments, the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 391.
[0094] Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 392. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 392. Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 392. In certain embodiments, the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 392.
[0095] Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 393. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 393. Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 393. In certain embodiments, the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 393.
[0096] Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 394. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 394. Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 394. In certain embodiments, the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 394.
[0097] Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 395. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 395. Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 395. In certain embodiments, the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 395.
[0098] Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 396. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 396. Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 396. In certain embodiments, the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 396.
[0099] Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 397. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 397. Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 397. In certain embodiments, the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 397.
[00100] Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 398. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 398. Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 398. In certain embodiments, the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 398.
[00101] Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 399. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 399. Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 399. In certain embodiments, the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 399.
[00102] Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 400. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 400. Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 400. In certain embodiments, the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 400. [00103] Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 401. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 401. Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 401. In certain embodiments, the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 401.
[00104] Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 402. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 402. Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 402. In certain embodiments, the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 402.
[00105] Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 403. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 403. Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 403. In certain embodiments, the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 403.
[00106] Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 404. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 404. Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 404. In certain embodiments, the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 404.
[00107] Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 405. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 405. Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 405. In certain embodiments, the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 405.
[00108] Certain embodiments provide gene silencing compounds comprising two oligonucleotides each, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 406. Certain embodiments provide compounds comprising two oligonucleotides each, independently, consisting of 15 to 25 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 406. Certain embodiments provide compounds comprising a modified oligonucleotide consisting of 18 to 21 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 406. In certain embodiments, the two oligonucleotide of the gene silencing compound each, independently, comprise at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 406.
[00109] In certain embodiments, the nucleobase sequence of the oligonucleotides of the gene silencing compound are, independently, at least 90% complementary over its entire length to a nucleobase sequence of SEQ ID NO: 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, or 406. In certain embodiments, the nucleobase sequence of the oligonucleotides of the gene silencing compound are, independently, at least 95% complementary over its entire length to a nucleobase sequence of SEQ ID NO: 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, or 406. In certain embodiments, the oligonucleotides of the gene silencing compound are at least 99% complementary over its entire length to SEQ ID NO: 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, or 406. In certain embodiments, the nucleobase sequence of the oligonucleotides of the gene silencing compound are 100% complementary over its entire length to a nucleobase sequence of SEQ ID NO: 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, or 406.
[00110] In certain embodiments, the oligonucleotides of the gene silencing compound are, independently, 12 to 30 nucleotides in length. In other words, the oligonucleotides are from 12 to 30 linked nucleobases. In other embodiments, the oligonucleotides,
independently, consist of 15 to 28, 18 to 24, 19 to 22, or 20 linked nucleobases. In certain such embodiments, the oligonucleotides, independently, consist of 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 linked nucleobases in length, or a range defined by any two of the above values.
[00111] In certain embodiments, a target region is a structurally defined region of the target nucleic acid. For example, a target region may encompass a 3' UTR, a 5' UTR, an exon, an intron, an exon/intron junction, a coding region, a translation initiation region, translation termination region, or other defined nucleic acid region. The structurally defined regions for PD1, PDL1, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAMl, OX40, or OX40L can be obtained by accession number from sequence databases such as NCBI and such information is incorporated herein by reference. In certain embodiments, a target region may encompass the sequence from a 5' target site of one target segment within the target region to a 3' target site of another target segment within the same target region.
[00112] Certain embodiments provide a composition comprising a 3GA compound as described herein, or a salt thereof, and a pharmaceutically acceptable carrier or diluent.
Certain embodiments provide a composition comprising two or more 3GA compounds as described herein, or a salt thereof, and a pharmaceutically acceptable carrier or diluent. The two or more 3GA compounds can inhibit the mRNA or protein expression of the same target or can inhibit the mRNA or protein expression of different targets.
[00113] In certain embodiments, the 3GA compounds according to the invention comprise two identical or different sequences linked at their 5 '-5' ends via a phosphodi ester, phosphorothioate or non-nucleoside linker. 3GA compounds according to the invention that comprise identical sequences are able to bind to a specific mRNA via Watson-Crick hydrogen bonding interactions and inhibit mRNA and protein expression. Gene silencing compounds according to the invention that comprise different sequences are able to bind to two or more different regions of one or more mRNA target and inhibit mRNA and protein expression. Such compounds are comprised of heteronucleotide sequences complementary to target mRNA and form stable duplex structures through Watson-Crick hydrogen bonding.
[00114] In certain embodiments, gene silencing compounds according to the invention are useful in treating and/or preventing diseases wherein inhibiting PD1, PDL1, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAMl, OX40, or OX40L expression would be beneficial. Gene silencing compounds according to the invention include, but are not limited to, antisense oligonucleotides comprising naturally occurring nucleotides, modified nucleotides, modified oligonucleotides and/or backbone modified oligonucleotides. [00115] The oligonucleotides of the 3GA compounds are linked through their 5'-ends to allow the presence of two or more accessible 3 '-ends. In certain embodiments, the oligonucleotides are linked through one or more of the non-nucleotide linkers listed in Table 1. In certain embodiments, a single linker listed in Table 1 is used to link the
oligonucleotides of the gene silencing compounds. In certain embodiments, the linker is small molecule linker such as glycerol or a glycerol homolog of the formula
HO-(CH2)0-CH(OH)-(CH2)i.-OH, wherein o and p independently are integers from 1 to about 6, from 1 to about 4 or from 1 to about 3. In some other embodiments, the small molecule linker is a derivative of l,3-diamino-2-hydroxypropane. Some such derivatives have the formula HO-(CH2)m-C(0)NH-CH2-CH(OH)-CH2-NHC(0)-(CH2)m-OH, wherein m is an integer from 0 to about 10, from 0 to about 6, from 2 to about 6 or from 2 to about 4.
Representative non-nucleotide linkers are set forth in Table 1.
Table 1: Representative Non-Nucleotide Linkers
HO OH
Figure imgf000029_0001
OH 1,1,1 -Tris(hy droxy methy l)nitro methane
Glycerol (1,2,3-Propanetriol)
Figure imgf000029_0002
l)propane
1,2,4-Butanetriol
Figure imgf000029_0003
2 - Amino -2 -(hydroxy methy 1) - 1 , 3 -propane dio 1
1,1,1 -Tris(hy droxymethyl)ethane
Figure imgf000029_0004
N- [Tris (hy dro xy methy 1) me thy 1] ac ry lamide Table 1: Continued
Figure imgf000030_0001
cis-l,3,5-Tri(hydroxymethyl)cyclohexane
Figure imgf000030_0002
3 ,5 ,-Di(hydroxymethyl)phenol
Figure imgf000030_0003
l,3,5,-Tri(hydroxymethyl)benzene Table 1: Continued
Figure imgf000031_0001
l,6-anhydro-P-D-Glucose 4,6-Nitropyrogallol
Figure imgf000031_0002
l,3,5-Tris(2-hydroxyethyl)-Cyanuric acid
Figure imgf000031_0003
Figure imgf000031_0004
3,5,7-Trihydroxyflavone Table 1: Continued
HO' v ^ "OH
,OH 1.5-Pentanediol
HO
Ethylene glycol
OH OH
1.3-Propanediol
2.4-Pentanediol
HO
OH
1,2 -Propanediol
1,6-Hexanediol
Figure imgf000032_0001
2,5-Hexanediol
Figure imgf000032_0002
Table 1: Continued
Figure imgf000033_0001
2-( 1 - Aminopropy 1)- 1 , 3 -propanediol
1,8-Octanediol
Figure imgf000033_0002
HO' "" '" ""' "OH 1,2-Dideoxyribose
1,9-Nonanediol
1,12-Dodecanediol
Triethylene glycol
Tetraethylene glycol
Hexaethylene glycol
[00116] In some embodiments, the small molecule linker is glycerol or a glycerol homolog of the formula HO-(CH2)0-CH(OH)-(CH2)i.-OH, wherein o and p independently are integers from 1 to about 6, from 1 to about 4 or from 1 to about 3. In some other embodiments, the small molecule linker is a derivative of l,3-diamino-2-hydroxypropane. Some such derivatives have the formula
HO-(CH2)m-C(0)NH-CH2-CH(OH)-CH2-NHC(0)-(CH2)m-OH, wherein m is an integer from 0 to about 10, from 0 to about 6, from 2 to about 6 or from 2 to about 4.
[00117] In certain embodiments, the two or more oligonucleotides of the gene silencing compounds of the invention can be linked as shown in Table 2.
Table 2: Oligoribonucleotide Formulas II - - V
Domain A Domain B
Formula II 3' 5' 1 5' 3'
Formula III
Figure imgf000034_0001
Formula IV
Formula V
Figure imgf000035_0001
[00118] In certain embodiments of Formulas II and/or V, L is a linker or a nucleotide linkage and Domain A and/or Domain B are antisense oligonucleotides that are designed to selectively hybridize to the same target RNA sequence or different target RNA sequences.
[00119] In certain embodiments of Formulas II, III, IV or V, L is a linker and Domain
A and/or Domain B and/or Domain C and/or Domain D are antisense oligonucleotides that are designed to selectively hybridize to the same target RNA sequence or different target RNA sequences. For example, in one embodiment, Domain A and/or Domain B and/or Domain C of Formulas II and/or III are antisense oligonucleotides that are designed to selectively hybridize to the same target RNA sequence. In this embodiment, Domain A and/or Domain B and/or Domain C can be designed to hybridize to the same region on the target RNA sequence or to different regions of the same target RNA sequence.
[00120] In a further embodiment of this aspect of the invention, Domain A, Domain B,
Domain C, and Domain D are independently RNA or DNA-based oligonucleotides. In certain aspects of this embodiment, the oligonucleotides comprise mixed backbone oligonucleotides. [00121] In another embodiment, one or more of Domain A and/or Domain B and/or
Domain C and/or Domain D is an antisense oligonucleotide that is designed to selectively hybridize to one target RNA sequence and one or more of the remaining Domain A and/or Domain B and/or Domain C and/or Domain D is an antisense oligonucleotide that is designed to selectively hybridized to a different target RNA sequence.
[00122] In another embodiment, one or more of Domain A and/or Domain B and/or
Domain C and/or Domain D is an RNA-based oligonucleotide hybridized to a complimentary RNA-based oligonucleotide such that the domain comprises an siRNA molecule.
[00123] These gene silencing compounds of the invention can be prepared by the art recognized methods such as phosphoramidate or H-phosphonate chemistry which can be carried out manually or by an automated synthesizer. The synthetic antisense
oligonucleotides of the invention may also be modified in a number of ways without compromising their ability to hybridize to mRNA. Such modifications may include at least one intemucleotide linkage of the oligonucleotide being an alkylphosphonate,
phosphorothioate, phosphorodithioate, methylphosphonate, phosphate ester,
alkylphosphonothioate, phosphoramidate, carbamate, carbonate, phosphate hydroxyl, acetamidate or carboxymethyl ester or a combination of these and other intemucleotide linkages between the 5' end of one nucleotide and the 3' end of another nucleotide in which the 5' nucleotide phosphodiester linkage has been replaced with any number of chemical groups.
[00124] The synthetic antisense oligonucleotides of the invention may comprise combinations of intemucleotide linkages. For example, U.S. Pat. No. 5,149,797 describes traditional chimeric oligonucleotides having a phosphorothioate core region interposed between methylphosphonate or phosphoramidate flanking regions. Additionally, U.S. Pat. No. 5,652,356 discloses "inverted" chimeric oligonucleotides comprising one or more nonionic oligonucleotide region (e.g. alkylphosphonate and/or phosphoramidate and/or phosphotriester internucleoside linkage) flanked by one or more region of oligonucleotide phosphorothioate. Various synthetic antisense oligonucleotides with modified
intemucleotide linkages can be prepared according to standard methods. In certain embodiments, the phosphorothioate linkages may be mixed Rp and Sp enantiomers, or they may be made stereoregular or substantially stereoregular in either Rp or Sp form.
[00125] Other modifications of gene silencing compounds of the invention include those that are internal or at the end(s) of the oligonucleotide molecule and include additions to the molecule of the intemucleoside phosphate linkages, such as cholesterol, cholesteryl, or diamine compounds with varying numbers of carbon residues between the amino groups and terminal ribose, deoxyribose and phosphate modifications which cleave, or crosslink to the opposite chains or to associated enzymes or other proteins which bind to the genome.
Examples of such modified oligonucleotides include oligonucleotides with a modified base and/or sugar such as 2'-0,4'-C-methylene-b-D-ribofuranosyl, or arabinose instead of ribose, or a 3', 5 '-substituted oligonucleotide having a sugar which, at both its 3' and 5' positions, is attached to a chemical group other than a hydroxyl group (at its 3' position) and other than a phosphate group (at its 5' position).
[00126] Other examples of modifications to sugars of the oligonucleoti de-based compounds of the invention include modifications to the 2' position of the ribose moiety which include but are not limited to 2'-0-substituted with an -O-alkyl group containing 1-6 saturated or unsaturated carbon atoms, or with an -O-aryl, or -O-allyl group having 2-6 carbon atoms wherein such -O-alkyl, -O-aryl or -O-allyl group may be unsubstituted or may be substituted, for example with halo, hydroxyl, trifiuoromethyl, cyano, nitro, acyl, acyloxy, alkoxy, carboxy, carbalkoxyl or amino groups. None of these substitutions are intended to exclude the presence of other residues having native 2'-hydroxyl group in the case of ribose or 2' H- in the case of deoxyribose.
[00127] The gene silencing compounds according to the invention can comprise one or more ribonucleotides. For example, US Pat No. 5,652,355 discloses traditional hybrid oligonucleotides having regions of 2 '-0 -substituted ribonucleotides flanking a DNA core region. U.S. Pat. No. 5,652,356 discloses an "inverted" hybrid oligonucleotide that includes an oligonucleotide comprising a 2'-0-substituted (or 2' OH, unsubstituted) RNA region which is in between two oligodeoxyribonucleotide regions, a structure that "inverted relative to the "traditional" hybrid oligonucleotides. Non-limiting examples of particularly useful oligonucleotides of the invention have 2'-0-alkylated ribonucleotides at their 3', 5', or 3' and 5' termini, with at least four, and in some exemplary embodiments five, contiguous nucleotides being so modified. Non-limiting examples of 2'-0-alkylated groups include 2'- O-methyl, 2'-0-ethyl, 2'-0-propyl, 2'-0-butyls and 2'-0-methoxy-ethyl.
[00128] The oligonucleotide-based compounds of the invention may conveniently be synthesized using an automated synthesizer and phosphoramidite approach further described in Example 1. In some embodiments, the oligonucleotide-based compounds of the invention are synthesized by a linear synthesis approach. [00129] An alternative mode of synthesis is "parallel synthesis", in which synthesis proceeds outward from a central linker moiety. A solid support attached linker can be used for parallel synthesis, as is described in U. S. Patent No. 5,912,332. Alternatively, a universal solid support (such as phosphate attached controlled pore glass) support can be used.
[00130] Parallel synthesis of the oligonucleotide-based compounds of the invention has several advantages over linear synthesis: (1) parallel synthesis permits the incorporation of identical monomeric units; (2) unlike in linear synthesis, both (or all) the monomeric units are synthesized at the same time, thereby the number of synthetic steps and the time required for the synthesis is the same as that of a monomeric unit; and (3) the reduction in synthetic steps improves purity and yield of the final immune modulatory oligoribonucleotide product.
[00131] At the end of the synthesis by either linear synthesis or parallel synthesis protocols, the oligonucleotide-based compounds of the invention may conveniently be deprotected with concentrated ammonia solution or as recommended by the phosphoramidite supplier, if a modified nucleoside is incorporated. The product oligonucleotide-based compounds is preferably purified by reversed phase HPLC, detritylated, desalted and dialyzed.
[00132] In certain embodiments, the oligonucleotides of the gene silencing compound according to the invention are selected from the non-limiting list of the oligonucleotides shown in Table 3 below. The oligonucleotides shown in Table 3 have phosphorothioate (PS) linkages, but may also include phosphodiester linkages. Those skilled in the art will recognize, however, that other linkages, based on phosphodiester or non-phosphodiester moieties may be included.
Table 3
Figure imgf000039_0001
PD1 Human 1896 TACCTTCCCACCCAGGCCC
PD1 Human 1898 TGTACCTTCCCACCCAGGC
PD1 Human 1900 CCTGTACCTTCCCACCCAG
PD1 Human 1996 CTG G ATG CTG GTG G CCCTG
PD1 Human 1997 CCTG G ATG CTG GTG G CCCT
PD1 Human 2024 CCCAGCCACTCAGGTGCCT
PD1 Human 2032 TCCCTTGTCCCAG CCACTC
PD1 Human 2034 GATCCCTTGTCCCAGCCAC
PDL1 Mouse 219 CAAGCAGGTCCAGCTCCCG
PDL1 Mouse 316 CTCCCCCTGAAGTTGCTGT
PDL1 Mouse 436 TTGTAGTCCGCACCACCGT
PDL1 Mouse 1399 GGTGACCTCTGTGTTCCCT
PDL1 Mouse 2152 G CCTG CCTCTG CCTCCCTA
PDL1 Mouse 3311 G CCCAG CCTGTTCCTTCAG
PDL1 Human 571 GGTAGCCCTCAGCCTGACA
PDL1 Human 892 CCA I CA I I C I CCC I 1 M C I
PDL1 Human 1075 ATTG CCTG C ATCCC ACG G G
PDL1 Human 1080 CCCACATTGCCTGCATCCC
PDL1 Human 1103 TTC AGTG CTTG G G CCTTTT
PDL1 Human 1163 G G CTCCCTGTTTG ACTCC A
PDL1 Human 1182 GTATCAAGGTCTCCCTCCA
PDL1 Human 1230 TCCTTTCTCCCTGTCACAG
PDL1 Human 1296 ATTCTCAACCCGTCTTCCT
PDL1 Human 1855 TCTGTTTGCTTCCTCAGCT
PDL1 Human 1904 G G GTG G CAGTCTG AG GTCT
PDL1 Human 1911 GGACAGTGGGTGGCAGTCT
PDL1 Human 2142 TTCCCCTCG CATCATCCTT
PDL1 Human 2192 TCCCAGACCACATTGGCCT
PDL1 Human 2901 TG C ACCCTG G AG AG CCC AT
PDL1 Human 3128 G CTG GTG G C ATTC A AG G GT
PDL1 Human 3173 CG AAACCTCCAG G A AG CCT
PDL1 Human 3196 G ATCTCCC AG G G C ATCTG A
PDL1 Human 3397 G CCTTG CTC AG CC AC A ATT
PDL1 Human 3402 TATGTGCCTTGCTCAGCCA
ID01 Mouse 138 CTAG CCACA AG G ACCCAGG
ID01 Mouse 264 ATGTACCCCAG GG CCAG GT
ID01 Mouse 295 ATCCCCTCG GTTCCACAC A
ID01 Mouse 492 CCCTTGTCG CAGTCCCCAC
ID01 Mouse 817 GAAGATGCTGCTCTGGCCT
ID01 Mouse 1145 CAG I CCC I C I GC I 1 I CCAC
ID01 Human 172 G C AG AG C A A AG CCC ACTTC
ID01 Human 184 CCTGTGGATTTGGCAGAGC
ID01 Human 388 C I CA I ACC I 1 I CCCCA
ID01 Human 507 C I 1 1 1 I C I I CA I 1 I GCC
ID01 Human 619 CAGCTGCTATTTCCACCAA 86 IDOl Human 816 GTTGCL I 1 I CCAGCCAGAC
87 IDOl Human 823 GU GGGG I I CC I 1 I CA
88 IDOl Human 849 CCCTTC ATAC ACC AG ACCG
89 IDOl Human 956 TGTCCTCCACCAG CAGTCT
90 IDOl Human 1138 GCAGATGGTAGCTCCTCAG
91 IDOl Human 1187 I CU 1 I GU GU GGU I G
92 IDOl Human 1239 GCU CCA I I CU 1 I GGU
93 IDOl Human 1246 AATCAGTGCCTCCAGTTCC
94 IDOl Human 1327 GTG CTCTTGTTG G GTTACA
95 IDOl Human 1627 G CCTCG GCCTCCCA AAGTG
96 IDOl Human 1745 TAGCTGGGACTACAGGTGC
97 IDOl Human 1767 TCTCCTGCCTCAGCCTCCC
98 IDOl Human 1774 ACGCCATTCTCCTGCCTCA
99 IDOl Human 1792 G CTCCG CCTCCCAG GTTC A
100 IDOl Human 1815 G G C AC A ATCTTG G CTC ACT
101 LAG 3 Mouse 25 GCTCCTCCAGACCCAGTCC
102 LAG 3 Mouse 321 G G CCTCCCC AG CCCTCC A A
103 LAG 3 Mouse 355 G G AG C AG GTCCTCCCTC AT
104 LAG 3 Mouse 422 AG CTCTTTCCC AG GCCCTG
105 LAG 3 Mouse 585 CCCCTG GTG AAGGTCAAG G
106 LAG 3 Mouse 590 GGCATCCCCTGGTGAAGGT
107 LAG 3 Mouse 601 GTCTAGGCGAGGGCATCCC
108 LAG 3 Mouse 953 G G C ACTCG GTTCTG GCCCT
109 LAG 3 Mouse 1044 GACACAGCCCCAGGTCCCA
110 LAG 3 Mouse 1108 GCTCCAGACCCAGAACCTT
111 LAG 3 Mouse 1161 GGGCAGCTCCACCCTAGAA
112 LAG 3 Mouse 1260 G CCACTCTTTCCAG CCACG
113 LAG 3 Mouse 1295 GCCAGACCCACAG CCTCAA
114 LAG 3 Mouse 1316 CAGGTGTAGGTCCCAGCCT
115 LAG 3 Mouse 1349 G C ATTG AG CTG CTGTCCCT
116 LAG 3 Mouse 1524 G G CCTCCTG A ATCTCCAG C
117 LAG 3 Mouse 1573 G CCTCTG GCCCTCGTACAG
118 LAG 3 Mouse 1819 CCAGCTCCTCTATCTTCCT
119 LAG 3 Mouse 1918 CTGCCTCGGCTCCAGGTCA
120 LAG 3 Mouse 1936 GCTGCTGAGACCTGCTGGC
121 LAG 3 Mouse/Human 1315 AGGTGTAGGTCCCAGCCTG
122 LAG 3 Mouse/Human 1822 G CTCC AG CTCCTCTATCTT
123 LAG 3 Mouse/Human 1062 G CCATCTCTGTAG GTG AG G
124 LAG 3 Mouse/Human 1356 GACAGTGGCATTGAGCTGC
125 LAG 3 Human 3 TCTCTG G G CCTTC ACCCCT
126 LAG 3 Human 123 CTGGGCAGATCAGGCAGCC
127 LAG 3 Human 167 GGGAGGGATGACCAGAGGC
128 LAG 3 Human 229 GGGAGGTGGAGGAAGGGGT
129 LAG 3 Human 346 CTGAGCCTCCCACATCTCT
130 LAG 3 Human 395 G CTTCACTG G AG CC ACCC A 131 LAG 3 Human 494 GGCTGAGATCCTGGAGGGG
132 LAG 3 Human 524 G CTG CCAAGTG ACCCCTG C
133 LAG 3 Human 648 G G ACCCACG CTCAG CACCG
134 LAG 3 Human 736 CCATAGCGAGAAGTCCCCG
135 LAG 3 Human 834 TGGCCCAGGCGCAGACGGA
136 LAG 3 Human 1034 CC ATG G G G CTG ACTTG G G G
137 LAG 3 Human 1359 TTG AG CTG CTGTTCCTG C A
138 LAG 3 Human 1433 G CAG CTTCCCCAG GGATCC
139 LAG 3 Human 1499 GGGATGGGGTGTCCAGAGA
140 LAG 3 Human 1554 TGGGAAAGGAGCTGGGCCT
141 LAG 3 Human 1593 AGAAGCCTCTCCCCCTGGT
142 LAG 3 Human 1636 G G C ACCTG G G CTAG AC AG C
143 LAG 3 Human 1848 G GTTCTTG CTCC AG CTCCT
144 LAG 3 Human 1940 GCTGAGATCTGCTGGCTGC
145 LAG 3 Human/Mouse 1972 GCTGCTGACAGGGAGTTTA
146 LAG 3 Human/Mouse 642 ACGCTCAG CACCGTGTAG C
147 LAG 3 Human/Mouse 1234 AG G AG G AGTCCACTTG G CA
148 LAG 3 Human/Mouse 1366 AGTGGCATTGAGCTGCTGT
149 TIM3 Mouse 222 AATCCCTTGCCCCAGCACA
150 TIM3 Mouse 319 GAGA I GCCC I 1 I AGC I G
151 TIM3 Mouse 386 TG CAG CAGTAG GTCCCATG
152 TIM3 Mouse 462 GGAGTGACCTTGGCTGCTT
153 TIM3 Mouse 661 CCCAGCAGAGACTCCCACT
154 TIM3 Mouse 782 C ATTTG CC A ACCCTCCTG G
155 TIM3 Mouse 887 GCTGGCTGTTGACGTAGCA
156 TIM3 Mouse 1273 1 I AGCCC I 1 I A I I CCCCC I
157 TIM3 Mouse 1416 CCTCCTGCCTAAGGTTCCC
158 TIM3 Mouse 1425 ACTTATCACCCTCCTGCCT
159 TIM3 Mouse 1517 GAG CCTC ATCTCC AG CCTC
160 TIM3 Mouse 1526 TCACTGTCCGAGCCTCATC
161 TIM3 Mouse 1668 CTG ACTG CACG C A AG CCCC
162 TIM3 Mouse 1767 GAGCAGAGGACAACCCCCA
163 TIM3 Mouse 1953 CTG CTCTG CC ATG CTCCC A
164 TIM3 Mouse 2138 GTCAGTTCCCCTTGAGCAC
165 TIM3 Mouse 2220 CTGCCTTCGTATGTCCCAG
166 TIM3 Mouse 2461 CACAGTTGCTCCCCAATGC
167 TIM3 Mouse 2570 AG CC AG G ACCTCC AC AG CT
168 TIM3 Mouse 2596 GTCTCCCTTCCATACCCAC
169 TIM3 Human 59 CTG CCAG GTCTACAGTCAC
170 TIM3 Human 281 CAG CAG CAG CAG CAG G AC A
171 TIM3 Human 338 GGCATTCTGACCG ACCTCC
172 TIM3 Human 457 I CCC I 1 I CA I A I CC I GA
173 TIM3 Human 740 G AG G CTCCCCAGTGTCTGT
174 TIM3 Human 803 G G CCAATCTAG AGTCCCGT
175 TIM3 Human 1110 GTGAGGGTTGCTGCCTGCT 176 TIM3 Human 1235 G CAGTG G ACAG A ACCTCCA
177 TIM3 Human 1304 CAGTG CAG GTCCCAGTTCA
178 TIM3 Human 1442 GAGCTCCAGAGACCCCACG
179 TIM3 Human 1456 GCCCGAATTTCCTGGAGCT
180 TIM3 Human 1506 CAGCACCCA I 11 ICCCIA
181 TIM3 Human 1549 GCCCCI 1 IAGACI 1 ICIGI
182 TIM3 Human 1640 TG CCATTG C ACTCC AG CCT
183 TIM3 Human 1716 ATCCCAGCCACTCAGGAGG
184 TIM3 Human 1725 ATGCCTGTAATCCCAGCCA
185 TIM3 Human 1863 G CTCACG CCTGTAATCCC A
186 TIM3 Human 1877 GGCTGGATGTGGTGGCTCA
187 TIM3 Human 2053 G CC AC ATCTC AG CCCTG C A
188 TIM3 Human 2246 GCCI 1 I CCI Id 1 ICCAC
189 CTLA4 Mouse 106 GGTCCTCAGGGAGCAGAGT
190 CTLA4 Mouse 191 AGGCCAAGTCCTAGAAGGC
191 CTLA4 Mouse 253 TG G GTCACCTGTATG G CTT
192 CTLA4 Mouse 344 AGTCACCCGGACCTCATCA
193 CTLA4 Mouse 416 G CCCACTGTATTCTTCTCT
194 CTLA4 Mouse 497 GTCAACAGCTCTCAGTCCT
195 CTLA4 Mouse 563 GTTGCCCATGCCCACAAAG
196 CTLA4 Mouse 567 TCCCGTTG CCCATG CCCAC
197 CTLA4 Mouse 647 CCCCAAG CTAACTG CG ACA
198 CTLA4 Mouse 735 TCACATAGACCCCTGTTGT
199 CTLA4 Mouse 760 C ATTCTG G CTCTGTTG G G G
200 CTLA4 Mouse 1084 CCTTGACCCCACACCATAA
201 CTLA4 Mouse 1135 CTCTTCCTTCACCCCCTTC
202 CTLA4 Mouse 1434 CTCCCCAGCCAAACCTCCC
203 CTLA4 Mouse 1436 AGCTCCCCAGCCAAACCTC
204 CTLA4 Mouse 1470 G ACCTCG AGTCC A ACCTG A
205 CTLA4 Mouse 1484 GCCAGTTGGTGCAGGACCT
206 CTLA4 Mouse 1542 ACTCCATCACCATCG GTTT
207 CTLA4 Mouse 1552 CCCAGTTTACACTCCATCA
208 CTLA4 Mouse 1794 TCCC ATCCTACC ATCTG CT
209 CTLA4 Human 129 GGGAGCGGTGTTCAGGTCT
210 CTLA4 Human 211 AGGAGAGTGCAGGGCCAGG
211 CTLA4 Human 346 CG G ACCTC AGTG G CTTTG C
212 CTLA4 Human 504 CCATGGCCCTCAGTCCTTG
213 CTLA4 Human 574 CCGTTG CCTATG CCCAGGT
214 CTLA4 Human 953 GG I I CGCAI CAACI 11
215 CTLA4 Human 1007 CAICCCAGCI I I I 1 IC
216 CTLA4 Human 1067 G C ATCCCC ATATT A ATCCC
217 CTLA4 Human 1136 LI LLC 1 GCCI 11 ICCI ICI
218 CTLA4 Human 1308 ACCI 1 IAGCAICACI GCI
219 CTLA4 Human 1514 AGTGTCCTGAGCTCCTCCA
220 CTLA4 Human 1537 CCTTGTGTTCTACCTGGTG 221 CTLA4 Human 1570 CCTC ATCCAGTTTCCAAG C
222 CTLA4 Human 1606 CTCAGCACAATTCCACGCA
223 CTLA4 Human 1632 AG CCCC A A AG C AC ATGTC A
224 CTLA4 Human 1747 ATACCTGTG G GTCTCCTG G
225 CTLA4 Human 1822 G CCTTCTTCTGTCC ATG G C
226 CTLA4 Human 1844 GCACCCCATTCTGCCACCT
227 CTLA4 Human/Mouse 744 TCACATAGACCCCTGTTGT
228 CTLA4 Human/Mouse 1117 TTG G G CTGTG CC ATTCCCT
229 ID02 Mouse 49 TGCCCCAGAGGAATGCCCA
230 ID02 Mouse 127 GTGGTATCTCCCCAAGGAC
231 ID02 Mouse 279 CAGTCCAGGAGAGGCATCC
232 ID02 Mouse 440 GGAGTCCCAAGTTCCTGGA
233 ID02 Mouse 510 TCCAACGGTCCTTCTGGGT
234 ID02 Mouse 639 G CCTCCATTCCCTG AACC A
235 ID02 Mouse 801 GGATTGTCCTTCCACCCAG
236 ID02 Mouse 873 G CTG C ACTTCCTCC AG AGT
237 ID02 Mouse 971 G CG G CATGTAGTCCCTCAT
238 ID02 Mouse 1047 CCAG G ACCAG AG G CCAGTA
239 ID02 Mouse 1215 GTACCCCCAGTG CCCCTGT
240 ID02 Mouse 1280 CACCAGGACACAGGAGGGC
241 ID02 Mouse 1617 GCTCCCACGGGACCTGACT
242 ID02 Mouse 1782 TGAGGAGGTCATGGCTGCA
243 ID02 Mouse 1911 GGGACGAGGGAGGTAGGGA
244 ID02 Mouse 2058 GTTTGAGGCCCATCAGACC
245 ID02 Mouse 2345 G CTCAGTGG CTCATCCCTG
246 ID02 Mouse 2638 GGCTGTCCCAGGTCACAGA
247 ID02 Mouse 2748 G GTG ACTTCC AGGTCTG CA
248 ID02 Mouse 2756 CCCGTG CTG GTG ACTTCCA
249 ID02 Human 156 G GTGTCCATTG CCTTCTGT
250 ID02 Human 214 G CCTG GTG G GTG AAGTGTC
251 ID02 Human 222 TTGTGGTGGCCTGGTGGGT
252 ID02 Human 284 ATTCG GTCTGTG GG G CTCC
253 ID02 Human 561 CTCCTTCCTG CCAG AC ATA
254 ID02 Human 633 G CCCCAAGTTCCTG G AG AC
255 ID02 Human 713 CCC A ATTTCC AG G A ATCCG
256 ID02 Human 722 CTCCAGGTTCCCAATTTCC
257 ID02 Human 757 TG C AG G CTCTCTCCCCC AG
258 ID02 Human 802 GGCAC I GC I I C I 1 I C I C I A
259 ID02 Human 1137 AG I CACCAC I 1 I CC I I GC I
260 ID02 Human 1207 GGTGCTGAGTGGATGTCTT
261 ID02 Human 1253 CAGCAAGTGGTCCTGTCCA
262 ID02 Human 1363 GGCTTCCCATG CTTTG CCT
263 ID02 Human 1415 TCCACCTGTG CCCCTGTCT
264 ID02 Human 1464 ACTCCAAG GTCTTATCCCT
265 ID02 Human 1573 TGATCCCAGGCAGAACCCT 266 ID02 Human 1593 G G G CTG AG ATCCTTCCTG G
267 ID02 Human 1745 TG G G G GTTCTG C ATG AG G A
268 ID02 Human 1752 ACTCCTCTGGGGGTTCTGC
269 ID02 Human 1837 AGTAATGTATCCCCAG G CA
270 ID02 Human 1945 AAGAGGGCTGGTCTGGGAC
271 CEACAM1 Mouse 291 GTAGTGTTTCCCTTGTACC
272 CEACAM1 Mouse 294 GCCGTAGTGTTTCCCTTGT
273 CEACAM1 Mouse 299 CTATAGCCGTAGTGTTTCC
274 CEACAM1 Mouse 1110 GTGAGGAACAGAATCCGGG
275 CEACAM1 Mouse 1526 TTCCTGCTTCTGGTTTGTT
276 CEACAM1 Mouse 1530 CCATTTCCTGCTTCTGGTT
277 CEACAM1 Mouse 1531 G CCATTTCCTG CTTCTGGT
278 CEACAM1 Mouse 2474 CC ATG CTG G A ACTCTGTCT
279 CEACAM1 Mouse 2485 CTG C AC AG G CTCC ATG CTG
280 CEACAM1 Mouse 2486 CCTG C AC AG G CTCC ATG CT
281 CEACAM1 Mouse 2500 CTGTGGGATTGAAACCTGC
282 CEACAM1 Mouse 2507 GGTGTTACTGTGGGATTGA
283 CEACAM1 Mouse 2513 G C AG A AG GTGTTACTGTG G
284 CEACAM1 Mouse 2533 GTCTGAGCAGGTGGGGTGC
285 CEACAM1 Mouse 2536 GCAGTCTGAGCAGGTGGGG
286 CEACAM1 Mouse 2568 TGTCCAG GTAGCCAG G CCT
287 CEACAM1 Mouse 2570 A ATGTCCAGGTAG CCAG G C
288 CEACAM1 Human 103 G CCCTGTCTTCACCTGTG G
289 CEACAM1 Human 111 TCCTG CTG G CCCTGTCTTC
290 CEACAM1 Human 126 GTG CCCCATG GTGTCTCCT
291 CEACAM1 Human 1021 TGGCGTGGCAGGTATAGGA
292 CEACAM1 Human 1403 GCCCCAGGTGAGAGGCCAT
293 CEACAM1 Human 1440 AACCAG GG CCACTACTCCA
294 CEACAM1 Human 1463 G CC AG G G CTACTG CTATC A
295 CEACAM1 Human 1851 G GTTTCCTACAG ACTCCCA
296 CEACAM1 Human 1908 GTTCTG GTCCCTCTTTCCC
297 CEACAM1 Human 2230 G GTG CTTAG ACCCTG ATCC
298 CEACAM1 Human 2396 CTG CCTTG A AC AG AG CCC A
299 CEACAM1 Human 2414 A ACCCCTCCCTCTC AG C AC
300 CEACAM1 Human 2436 G CTG GTTCCCTCCTG A AG C
301 CEACAM1 Human 2473 C I 1 I CCAA I I I AGC
302 CEACAM1 Human 2489 G G G C AG CTCTCTG ATTCCT
303 CEACAM1 Human 2700 GCTCCTGACCAAGGGACCT
304 CEACAM1 Human 2894 AG C AG AG G CCA AG GTTTCC
305 CEACAM1 Human 2924 CTCCCACTTCTCA AG G ACC
306 CEACAM1 Human 3019 TCACAGCCCCATTTCCCCA
307 CEACAM1 Human 3323 G CACAGTCCGTGTCAG GGT
308 OX40 Mouse 20 GTATGCAGAGTCCCATGAT
309 OX40 Mouse 121 CCTTG C AG G GTGTG G CTAT
310 OX40 Mouse 161 CCTTGTCTGCTTTCTGCCT 311 OX40 Mouse 270 TGTGACCACTGGGGTAGGT
312 OX40 Mouse 495 GAG GTTG G GTG CCTG GTCT
313 OX40 Mouse 509 GCCGCTGTCCTGCCGAGGT
314 OX40 Mouse 544 GGAGGGCAGGGAACACAGT
315 OX40 Mouse 572 CTG GTTGTTG CCTG G AG A A
316 OX40 Mouse 593 ATTG GTCC AG G G CTTG C AG
317 OX40 Mouse 642 CCA AG CTGTC ACTG G CTG G
318 OX40 Mouse 693 GGGTCTCCCAGAGCAGTGT
319 OX40 Mouse 845 AGTCAAGGGAGCCAGCAGG
320 OX40 Mouse 904 GGTTTGGGAGTGTTAGGCA
321 OX40 Mouse 941 CTCCTG G ATCG G G GTCCTG
322 OX40 Mouse 1010 G CCCCATA AAATCCACTCC
323 OX40 Mouse 1021 G G GTTGTCCGTG CCCCATA
324 OX40 Mouse 1038 G G C AG G CATC AG GAT ATG G
325 OX40 Mouse 1069 G CCCAG CACCTAG A ACG GT
326 OX40 Mouse 1080 GCCCAGAGCCAGCCCAGCA
327 OX40 Mouse 1126 TTAGGAGCACCACCAGGCA
328 OX40 Human 82 CCCAGGAGGAGCAGAGCCG
329 OX40 Human 192 TG C AG CG G CTC ACCATCCC
330 OX40 Human 273 AGGGCTTGCACGGCTTGGA
331 OX40 Human 300 TCCCACTTCTGAGGTTACA
332 OX40 Human 312 G CTTCCG CTCACTCCCACT
333 OX40 Human 342 AGACTGTGTCCTGTGTGGC
334 OX40 Human 347 GCGGCAGACTGTGTCCTGT
335 OX40 Human 401 G G CACAGTCAACTCCAG GC
336 OX40 Human 462 AGTTGGTCCAGGG CTTG CA
337 OX40 Human 485 GGTGTG CTTCCCAG CCAAG
338 OX40 Human 746 CCGGAGCAGGTACAGGGCC
339 OX40 Human 762 G CAG CCTCTG GTCCCTCCG
340 OX40 Human 763 G G C AG CCTCTG GTCCCTCC
341 OX40 Human 823 TG CTCCTCTTG G ATG G G G G
342 OX40 Human 865 G G CCCAG GTCAG ATCTTG G
343 OX40 Human 967 GTTGGCCCAGGAGCGTGGC
344 OX40 Human 1036 G C AG G AG GTATG C ATG G C A
345 OX40 Human 1058 G l 1 1 1 I A I I G I GG I CCCGC
346 OX40 Human 1075 G ACTCCCGTCTG CCAAG GT
347 OX40L Mouse 141 CCCTTCCCCTTCCATCTCT
348 OX40L Mouse 167 TCCAGATTCTCATCCAGGG
349 OX40L Mouse 182 GGCC I I GA I CCG I 1 1 I CCA
350 OX40L Mouse 218 ACCACCAG CCTTAG CGTCT
351 OX40L Mouse 226 TCCCAGAGACCACCAGCCT
352 OX40L Mouse 240 CCCTGCTCCCTTGATCCCA
353 OX40L Mouse 303 1 GAGG 1 I 1 1 CCGGA
354 OX40L Mouse 399 GTTCTG CACCTCCATAGTT
355 OX40L Mouse 454 AGGAGCCCTTCAGGTAGAT 356 OX40L Mouse 565 CCAAAGAGGCCACCACAGT
357 OX40L Mouse 650 ACAATCAG CTCCCCATCAT
358 OX40L Mouse 753 CCTGTGTCCCGTCCACCCT
359 OX40L Mouse 817 AGGGTAGGCTCTGCATTCA
360 OX40L Mouse 895 G C AG G CTC A AG G CAATCCT
361 OX40L Mouse 1069 TGGACACCACCCTTTCCAT
362 OX40L Mouse 1157 CCCCCATGAGATGAGAGAC
363 OX40L Mouse 1173 AA I U I d 1 1 (_(_ A AG (_(_(_(_
364 OX40L Mouse 1193 AG I CC I GC I 1 1 CCACGGGG
365 OX40L Mouse 1298 G GTGG GTATCATAGTCCCT
366 OX40L Mouse 1439 CC I I C I I GGCC I 1 l A I CC I
367 OX40L Human 494 G G G CTCCTC ATC CTTCTG G
368 OX40L Human 712 GTTCATG CTGGTG CCTGGT
369 OX40L Human 814 GGGAGGGCCAGGATCTGCT
370 OX40L Human 1104 CCTTCACTCCTTG CTCCTC
371 OX40L Human 1120 GATTCATAACCCCACTCCT
372 OX40L Human 1139 GTTCATACCACCTTTG G CA
373 OX40L Human 1276 GGCTCTCTTCAAGTCCTGA
374 OX40L Human 1378 CACATCCCCAGACAGTTCT
375 OX40L Human 1383 AGCATCACATCCCCAGACA
376 OX40L Human 1492 GTCCAGTTCCCTG CTATCC
377 OX40L Human 1569 I GC I 1 I GCC I G I C I G I GGC
378 OX40L Human 1577 GCA I G I G I I GC I 1 I GCC I G
379 OX40L Human 1828 ATTCCATTG A AG CCCTGGC
380 OX40L Human 2127 C AG CCCTCC ACCTTTCTG G
381 OX40L Human 2367 GTCCACAGTAGGCCCTCCA
382 OX40L Human 2376 CAGTG CCTG GTCCACAGTA
383 OX40L Human 2387 AGTATTTAGCCCAGTGCCT
384 OX40L Human 2729 CCCAAAGCGAGTGAGCACC
385 OX40L Human 2754 AC ATG G G A AG AG C AG G CC A
386 OX40L Human 2808 GGTGGAGTGAGGCTGGTGC
[00133] Compound names for the 3rd generation antisense (3GA) compounds according to the invention are based on the target and oligonucleotide target site(s) as depicted Table 3. For example, "3GA 384" comprises two copies of Oligo # 384 linked at their 5' ends (e.g., 3 -CCACGAGTGAGCGAAACCC-5 -X-5'-
CCC AAAGCGAGTGAGC ACC-3 ' , wherein X represents a non-nucleotidic linker). Alternatively, a 3GA compound comprising two different oligonucleotides such as Oligo # 385 and Oligo # 386 (e.g., 3 ' - ACCGGACGAGAAGGGTAC A-5 ' -X-5 ' - GGTGGAGTGAGGCTGGTGC-3', wherein X represents a non-nucleotidic linker) will be referred to herein, for example, as "3GA 385/386". [00134] Certain embodiments provide gene silencing compounds comprising two oligonucleotides independently selected from the oligonucleotides listed in Table 3. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NO: 1 , 2, 3, 4, 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, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 1 10, 1 11 , 1 12, 1 13, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161 , 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181 , 182, 183, 184, 185, 186, 187, 188, 189, 190, 191 , 192, 193, 194, 195, 196, 197, 198, 199, 200, 201 , 202, 203, 204, 205, 206, 207, 208, 209, 210, 21 1, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251 , 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271 , 272, 273, 274, 275, 276, 277, 278, 279, 280, 281 , 282, 283, 284, 285, 286, 287, 288, 289, 290, 291 , 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 31 1, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341 , 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361 , 362, 363, 364, 365, 366, 367, 368, 369, 370, 371 , 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, or 386, or combinations thereof. In certain embodiments, the oligonucleotides of the gene silencing compound are the same. In certain embodiments, the oligonucleotides of the gene silencing compounds are different.
[00135] In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1, 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, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 1 10, 11 1, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, or 386,and is at least 80% complimentary to its target site with SEQ ID NO: 387, SEQ ID NO: 388, SEQ ID NO: 389, SEQ ID NO: 390, SEQ ID NO: 391, SEQ ID NO: 392, SEQ ID NO: 393, SEQ ID NO: 394, SEQ ID NO: 395, SEQ ID NO: 396, SEQ ID NO: 397, SEQ ID NO: 398, SEQ ID NO: 399, SEQ ID NO: 400, SEQ ID NO: 401, SEQ ID NO: 402, SEQ ID NO: 403, SEQ ID NO: 404, SEQ ID NO: 405, or SEQ ID NO: 406. In certain
embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 1, 2, 3, 4, 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, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, or 386, and is at least 85% complimentary to its target site with SEQ ID NO: 387, SEQ ID NO: 388, SEQ ID NO: 389, SEQ ID NO: 390, SEQ ID NO: 391, SEQ ID NO: 392, SEQ ID NO: 393, SEQ ID NO: 394, SEQ ID NO: 395, SEQ ID NO: 396, SEQ ID NO: 397, SEQ ID NO: 398, SEQ ID NO: 399, SEQ ID NO: 400, SEQ ID NO: 401, SEQ ID NO: 402, SEQ ID NO: 403, SEQ ID NO: 404, SEQ ID NO: 405, or SEQ ID NO: 406. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 1, 2, 3, 4, 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, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, or 386, and is at least 90% complimentary to its target site with SEQ ID NO: 387, SEQ ID NO: 388, SEQ ID NO: 389, SEQ ID NO: 390, SEQ ID NO: 391, SEQ ID NO: 392, SEQ ID NO: 393, SEQ ID NO: 394, SEQ ID NO: 395, SEQ ID NO: 396, SEQ ID NO: 397, SEQ ID NO: 398, SEQ ID NO: 399, SEQ ID NO: 400, SEQ ID NO: 401, SEQ ID NO: 402, SEQ ID NO: 403, SEQ ID NO: 404, SEQ ID NO: 405, or SEQ ID NO: 406. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 1, 2, 3, 4, 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, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, or 386,and is at least 95% complimentary to its target site with SEQ ID NO: 387, SEQ ID NO: 388, SEQ ID NO: 389, SEQ ID NO: 390, SEQ ID NO: 391, SEQ ID NO: 392, SEQ ID NO: 393, SEQ ID NO: 394, SEQ ID NO: 395, SEQ ID NO: 396, SEQ ID NO: 397, SEQ ID NO: 398, SEQ ID NO: 399, SEQ ID NO: 400, SEQ ID NO: 401, SEQ ID NO: 402, SEQ ID NO: 403, SEQ ID NO: 404, SEQ ID NO: 405, or SEQ ID NO: 406.
[00136] In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 49, 50, 51, 52, 53, 54, 75, 76, 77, 78, 79, 80, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, or 365, and is at least 80% complimentary to its target site with SEQ ID NO: 387, SEQ ID NO: 389, SEQ ID NO: 391, SEQ ID NO: 393, SEQ ID NO: 395, SEQ ID NO: 397, SEQ ID NO: 399, SEQ ID NO: 401, SEQ ID NO: 403, or SEQ ID NO: 405. In certain embodiments, the gene silencing compounds comprise two oligonucleot des each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 49, 50, 51, 52, 53, 54, 75, 76, 77, 78, 79, 80,101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, or 365, and is at least 85% complimentary to its target site with SEQ ID NO: 387, SEQ ID NO: 389, SEQ ID NO: 391, SEQ ID NO: 393, SEQ ID NO: 395, SEQ ID NO: 397, SEQ ID NO: 399, SEQ ID NO: 401, SEQ ID NO: 403, or SEQ ID NO: 405. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 49, 50, 51, 52, 53, 54, 75, 76, 77, 78, 79, 80,101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, or 365, and is at least 90% complimentary to its target site with SEQ ID NO: 387, SEQ ID NO: 389, SEQ ID NO: 391, SEQ ID NO: 393, SEQ ID NO: 395, SEQ ID NO: 397, SEQ ID NO: 399, SEQ ID NO: 401, SEQ ID NO: 403, or SEQ ID NO: 405. In certain
embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 49, 50, 51, 52, 53, 54, 75, 76, 77, 78, 79, 80,101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, or 365, and is at least 95% complimentary to its target site with SEQ ID NO: 387, SEQ ID NO: 389, SEQ ID NO: 391, SEQ ID NO: 393, SEQ ID NO: 395, SEQ ID NO: 397, SEQ ID NO: 399, SEQ ID NO: 401, SEQ ID NO: 403, or SEQ ID NO: 405.
[00137] In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, or 386, and is at least 80%
complimentary to its target site within SEQ ID NO: 388, SEQ ID NO: 390, SEQ ID NO: 392, SEQ ID NO: 394, SEQ ID NO: 396, SEQ ID NO: 398, SEQ ID NO: 400, SEQ ID NO: 402, SEQ ID NO: 404, or SEQ ID NO: 406. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, or 386, and is at least 85% complimentary to its target site within SEQ ID NO: 388, SEQ ID NO: 390, SEQ ID NO: 392, SEQ ID NO: 394, SEQ ID NO: 396, SEQ ID NO: 398, SEQ ID NO: 400, SEQ ID NO: 402, SEQ ID NO: 404, or SEQ ID NO: 406. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, or 386, and is at least 90% complimentary to its target site within SEQ ID NO: 388, SEQ ID NO: 390, SEQ ID NO: 392, SEQ ID NO: 394, SEQ ID NO: 396, SEQ ID NO: 398, SEQ ID NO: 400, SEQ ID NO: 402, SEQ ID NO: 404, or SEQ ID NO: 406. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, or 386, and is at least 95% complimentary to its target site within SEQ ID NO: 388, SEQ ID NO: 390, SEQ ID NO: 392, SEQ ID NO: 394, SEQ ID NO: 396, SEQ ID NO: 398, SEQ ID NO: 400, SEQ ID NO: 402, SEQ ID NO: 404, or SEQ ID NO: 406.
[00138] In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, or 8, and is at least 80% complimentary to SEQ ID NO: 387. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, or 8, and is at least 85% complimentary to SEQ ID NO: 387. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, or 8, and is at least 90% complimentary to SEQ ID NO: 387. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, or 8, and is at least 95% complimentary to SEQ ID NO: 387.
[00139] In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 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, and is at least 80% complimentary to SEQ ID NO: 388. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 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, and is at least 85% complimentary to SEQ ID NO: 388. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 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, and is at least 90% complimentary to SEQ ID NO: 388. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 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, and is at least 95% complimentary to SEQ ID NO: 388.
[00140] In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 49, 50, 51, 52, 53, 54, and is at least 80% complimentary to SEQ ID NO: 389. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 49, 50, 51, 52, 53, 54, and is at least 85% complimentary to SEQ ID NO: 389. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 49, 50, 51, 52, 53, 54, and is at least 90% complimentary to SEQ ID NO: 389. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 49, 50, 51, 52, 53, 54, and is at least 95% complimentary to SEQ ID NO: 389.
[00141] In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, and is at least 80% complimentary to SEQ ID NO: 390. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, and is at least 85%
complimentary to SEQ ID NO: 390. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, and is at least 90% complimentary to SEQ ID NO: 390. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, and is at least 95% complimentary to SEQ ID NO: 390.
[00142] In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 75, 76, 77, 78, 79, 80, and is at least 80% complimentary to SEQ ID NO: 391. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 75, 76, 77, 78, 79, 80, and is at least 85% complimentary to SEQ ID NO: 391. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 75, 76, 77, 78, 79, 80, and is at least 90% complimentary to SEQ ID NO: 391. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 75, 76, 77, 78, 79, 80, and is at least 95% complimentary to SEQ ID NO: 391.
[00143] In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, and is at least 80% complimentary to SEQ ID NO: 392. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, and is at least 85%
complimentary to SEQ ID NO: 392. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, and is at least 90% complimentary to SEQ ID NO: 392. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, and is at least 95% complimentary to SEQ ID NO: 392. [00144] In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, and is at least 80%
complimentary to SEQ ID NO: 393. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, and is at least 85% complimentary to SEQ ID NO: 393. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, and is at least 90% complimentary to SEQ ID NO: 393. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, and is at least 95% complimentary to SEQ ID NO: 393.
[00145] In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, and is at least 80%
complimentary to SEQ ID NO: 394. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, and is at least 85% complimentary to SEQ ID NO: 394. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, and is at least 90% complimentary to SEQ ID NO: 394. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, and is at least 95% complimentary to SEQ ID NO: 394. [00146] In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, and is at least 80% complimentary to SEQ ID NO: 395. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165,
166, 167, 168, and is at least 85% complimentary to SEQ ID NO: 395. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166,
167, 168, and is at least 90% complimentary to SEQ ID NO: 395. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, and is at least 95% complimentary to SEQ ID NO: 395.
[00147] In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, and is at least 80% complimentary to SEQ ID NO: 396. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185,
186, 187, 188, and is at least 85% complimentary to SEQ ID NO: 396. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186,
187, 188, and is at least 90% complimentary to SEQ ID NO: 396. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 169, 170, 171,
172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, and is at least 95% complimentary to SEQ ID NO: 396.
[00148] In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, and is at least 80% complimentary to SEQ ID NO:
397. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, and is at least 85% complimentary to SEQ ID NO: 397. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, and is at least 90% complimentary to SEQ ID NO: 397. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, and is at least 95% complimentary to SEQ ID NO: 397.
[00149] In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, and is at least 80% complimentary to SEQ ID NO:
398. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID
NOs: 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225,
226, 227, 228, and is at least 85% complimentary to SEQ ID NO: 398. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226,
227, 228, and is at least 90% complimentary to SEQ ID NO: 398. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, and is at least 95% complimentary to SEQ ID NO: 398.
[00150] In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, and is at least 80% complimentary to SEQ ID NO: 399. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245,
246, 247, 248, and is at least 85% complimentary to SEQ ID NO: 399. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246,
247, 248, and is at least 90% complimentary to SEQ ID NO: 399. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, and is at least 95% complimentary to SEQ ID NO: 399.
[00151] In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, and is at least 80% complimentary to SEQ ID NO: 400. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, and is at least 85% complimentary to SEQ ID NO: 400. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, and is at least 90% complimentary to SEQ ID NO: 400. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, and is at least 95% complimentary to SEQ ID NO: 400.
[00152] In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, and is at least 80% complimentary to SEQ ID NO: 401. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, and is at least 85% complimentary to SEQ ID NO: 401. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, and is at least 90% complimentary to SEQ ID NO: 401. In certain embodiments, the gene silencing compounds comprise two
oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, and is at least 95% complimentary to SEQ ID NO: 401.
[00153] In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, and is at least 80% complimentary to SEQ ID NO: 402. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304,
305, 306, 307, and is at least 85% complimentary to SEQ ID NO: 402. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305,
306, 307, and is at least 90% complimentary to SEQ ID NO: 402. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, and is at least 95% complimentary to SEQ ID NO: 402.
[00154] In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, and is at least 80% complimentary to SEQ ID NO: 403. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, and is at least 85% complimentary to SEQ ID NO: 403. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, and is at least 90% complimentary to SEQ ID NO: 403. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, and is at least 95% complimentary to SEQ ID NO: 403.
[00155] In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, and is at least 80% complimentary to SEQ ID NO: 404. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345,
346, and is at least 85% complimentary to SEQ ID NO: 404. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, and is at least 90% complimentary to SEQ ID NO: 404. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, and is at least 95% complimentary to SEQ ID NO: 404.
[00156] In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, and is at least 80% complimentary to SEQ ID NO: 405. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs:
347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, and is at least 85% complimentary to SEQ ID NO: 405. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, and is at least 90% complimentary to SEQ ID NO: 405. In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, and is at least 95% complimentary to SEQ ID NO: 405.
[00157] In certain embodiments, the gene silencing compounds comprise two oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, or 386, and is at least 80% complimentary to SEQ ID NO: 406. In certain embodiments, the gene silencing compounds comprise two
oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, or 386, and is at least 85% complimentary to SEQ ID NO: 406. In certain embodiments, the gene silencing compounds comprise two
oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, or 386, and is at least 90% complimentary to SEQ ID NO: 406. In certain embodiments, the gene silencing compounds comprise two
oligonucleotides each, independently, comprising a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, or 386, and is at least 95% complimentary to SEQ ID NO: 406.
[00158] In certain embodiments, the invention provides a composition comprising a 3GA compound according to the invention and one or more vaccines, antigens, antibodies, cytotoxic agents, chemotherapeutic agents (both traditional chemotherapy and modem targeted therapies), kinase inhibitors, allergens, antibiotics, agonist, antagonist, antisense oligonucleotides, ribozymes, RNAi molecules, siRNA molecules, miRNA molecules, aptamers, proteins, gene therapy vectors, DNA vaccines, adjuvants, co-stimulatory molecules or combinations thereof.
[00159] In certain embodiments, the invention provides a method for inhibiting PD1,
PDL1, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAM1, OX40, and/or OX40L mRNA or protein expression, the method comprising contacting a cell with a gene silencing compound according to the invention. In certain embodiments, the cell can be contacted with two or more gene silencing compounds targeting different regions of the same checkpoint. In certain embodiments, the cell can be contacted with two or more gene silencing compounds targeting different checkpoints.
[00160] Certain embodiments further provide a method to reduce PD 1 , PDL 1 , IDO 1 ,
LAG3, TIM3, CTLA4, ID02, CEACAM1, OX40, and/or or OX40L mRNA or protein expression in an animal comprising administering to the animal a gene silencing compound or composition as described herein to reduce PD1, PDL1, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAM1, OX40, or OX40L mRNA or protein expression in the animal. In certain embodiments, the animal is a human. In certain embodiments, reducing PD1, PDL1, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAM1, OX40, or OX40L mRNA or protein expression prevents, treats, ameliorates, or slows progression of disease. In certain embodiments reducing PD1, PDL1, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAM1, OX40, or OX40L mRNA or protein expression inhibits immune system tolerance. In certain embodiments two or more gene silencing compounds targeting different regions of the same checkpoint can be administered. In certain embodiments two or more gene silencing compounds targeting different checkpoints can be administered.
[00161] In certain embodiments provided are methods for inhibiting immune system tolerance to tumors comprising administering to the animal a gene silencing compound or composition as described herein to reduce PD1, PDL1, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAM1, OX40, and/or OX40L mRNA or protein expression in the animal. In certain embodiments, the animal is a human. In certain embodiments, the gene silencing compound or composition as described herein is administered intratumorally. Thus, the inhibition of PD1, PDL1, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAM1, OX40, or OX40L mRNA or protein expression may provide a potentially useful immunotherapy strategy for patients with cancer. In certain embodiments two or more gene silencing compounds targeting different regions of the same checkpoint can be administered. In certain embodiments two or more gene silencing compounds targeting different checkpoints can be administered.
[00162] In certain embodiments provided are methods for preventing tumor growth and tumor volume. In certain embodiments provided are methods for reducing tumor growth and tumor volume. [00163] In certain embodiments provided are methods, compounds, and compositions for the treatment, prevention, or amelioration of diseases, disorders, and conditions associated with PDl, PDLl, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAMl, OX40, or OX40L in an individual in need thereof. Also contemplated are methods and compounds for the preparation of a medicament for the treatment, prevention, or amelioration of a disease, disorder, or condition associated with PDl, PDLl, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAMl, OX40, or OX40L. In certain embodiments two or more gene silencing compounds targeting different regions of the same checkpoint can be administered. In certain embodiments two or more gene silencing compounds targeting different checkpoints can be administered.
[00164] PDl, PDLl, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAMl, OX40, or
OX40L associated diseases, disorders, and conditions include hyperproliferative diseases, e.g., cancer, carcinomas, sarcomas, lymphomas, and leukemias as well as associated malignancies and metastases. PDl, PDLl, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAMl, OX40, or OX40L associated diseases, disorders, and conditions can also include autoimmune diseases and disorders.
[00165] In certain embodiments provided are PDl, PDLl, IDOl, LAG3, TIM3,
CTLA4, ID02, CEACAMl, OX40, or OX40L gene silencing compounds for use in treating, preventing, or ameliorating a PDl, PDLl, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAMl, OX40, or OX40L associated disease. In certain embodiments, PDl, PDLl, IDOl, LAG3,
TIM3, CTLA4, ID02, CEACAMl, OX40, or OX40L gene silencing compounds are capable of inhibiting the expression of PDl, PDLl, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAMl, OX40, or OX40L mRNA and/or PDl, PDLl, IDOl, LAG3, TIM3, CTLA4, ID02,
CEACAMl, OX40, or OX40L protein in a cell, tissue, or animal.
[00166] Certain embodiments provide methods comprising administering to an animal a gene silencing compounds as described herein. In certain embodiments two or more gene silencing compounds targeting different regions of the same checkpoint can be administered. In certain embodiments two or more gene silencing compounds targeting different checkpoints can be administered.
[00167] Also provided are methods and gene silencing compounds for the preparation of a medicament for the treatment, prevention, or amelioration of disease. [00168] Certain embodiments provide the use of gene silencing compounds as described herein in the manufacture of a medicament for treating, ameliorating, or preventing disease.
[00169] Certain embodiments provide gene silencing compounds as described herein for use in treating, preventing, or ameliorating disease as described herein by combination therapy with an additional agent or therapy as described herein. Agents or therapies can be co-administered or administered concomitantly.
[00170] Certain embodiments provide the use of a gene silencing compound as described herein in the manufacture of a medicament for treating, preventing, or ameliorating disease as described herein by combination therapy with an additional agent or therapy as described herein. Agents or therapies can be co-administered or administered concomitantly.
[00171] Certain embodiments provide the use of a gene silencing compound as described herein in the manufacture of a medicament for treating, preventing, or ameliorating disease as described herein in a patient who is subsequently administered an additional agent or therapy as described herein.
[00172] In any of the methods according to the invention, the gene silencing compound according to the invention can variously act by producing direct gene expression modulation effects alone and/or in combination with any other agent useful for treating or preventing the disease or condition that does not diminish the gene expression modulation effect of the gene silencing compound according to the invention. In any of the methods according to the invention, the agent(s) useful for treating or preventing the disease or condition includes, but is not limited to, vaccines, antigens, antibodies, preferably
monoclonal antibodies, cytotoxic agents, kinase inhibitors, allergens, antibiotics, siRNA molecules, antisense oligonucleotides, TLR antagonist (e.g. antagonists of TLR3 and/or TLR7 and/or antagonists of TLR8 and/or antagonists of TLR9), chemotherapeutic agents (both traditional chemotherapy and modem targeted therapies), targeted therapeutic agents, activated cells, peptides, proteins, gene therapy vectors, peptide vaccines, protein vaccines, DNA vaccines, adjuvants, and co-stimulatory molecules (e.g. cytokines, chemokines, protein ligands, trans-activating factors, peptides or peptides comprising modified amino acids), or combinations thereof. For example, in the treatment of cancer, it is contemplated that the oligonucleotide-based compound according to the invention may be administered in combination with one or more chemotherapeutic compound, targeted therapeutic agent and/or monoclonal antibody. Alternatively, the agent can include DNA vectors encoding for antigen or allergen. Alternatively, the gene silencing compound according to the invention can be administered in combination with other compounds (for example lipids or liposomes) to enhance the specificity or magnitude of the gene expression modulation of the
oligonucleotide-based compound according to the invention.
[00173] In any of the methods according to the invention, administration of gene silencing compounds according to the invention, alone or in combination with any other agent, can be by any suitable route, including, without limitation, parenteral, mucosal, oral, sublingual, intratumoral, transdermal, topical, inhalation, intrathecal, intranasal, aerosol, intraocular, intratracheal, intrarectal, vaginal, by gene gun, dermal patch or in eye drop or mouthwash form. In any of the methods according to the invention, administration of gene silencing compounds according to the invention, alone or in combination with any other agent, can be directly to a tissue or organ such as, but not limited to, the bladder, liver, lung, kidney or lung. In certain embodiments, administration of gene silencing compounds according to the invention, alone or in combination with any other agent, is by intratumoral administration. In certain embodiments, administration of gene silencing compounds according to the invention, alone or in combination with any other agent, is by mucosal administration. In certain embodiments, administration of gene silencing compounds according to the invention, alone or in combination with any other agent, is by oral administration. In certain embodiments, administration of gene silencing compounds according to the invention, alone or in combination with any other agent, is by intrarectal administration. In certain embodiments, administration of gene silencing compounds according to the invention, alone or in combination with any other agent, is by intrathecal administration. In certain embodiments, administration of gene silencing compounds according to the invention, alone or in combination with any other agent, is directly to the bladder. In certain embodiments, administration of gene silencing compounds according to the invention, alone or in combination with any other agent, is directly to the lung.
[00174] Administration of the therapeutic compositions of gene silencing compounds according to the invention can be carried out using known procedures using an effective amount and for periods of time effective to reduce symptoms or surrogate markers of the disease. For example, an effective amount of a gene silencing compound according to the invention for treating a disease and/or disorder could be that amount necessary to alleviate or reduce the symptoms, or delay or ameliorate the disease and/or disorder. In the context of administering a composition that modulates gene expression, an effective amount of a gene silencing compound according to the invention is an amount sufficient to achieve the desired modulation as compared to the gene expression in the absence of the gene silencing compound according to the invention. The effective amount for any particular application can vary depending on such factors as the disease or condition being treated, the particular compound being administered, the size of the subject, or the severity of the disease or condition. One of ordinary skill in the art can empirically determine the effective amount of a particular compound without necessitating undue experimentation.
[00175] When administered systemically, the therapeutic composition is preferably administered at a sufficient dosage to attain a blood level of gene silencing compound according to the invention from about 0.0001 micromolar to about 10 micromolar. For localized administration, much lower concentrations than this may be effective, and much higher concentrations may be tolerated. Preferably, a total dosage of gene silencing compound according to the invention ranges from about 0.001 mg per patient per day to about 200 mg per kg body weight per day. In certain embodiments, the total dosage may be 0.08, 0.16, 0.32, 0.48, 0.32, 0.64, 1, 10 or 30 mg/kg body weight administered daily, twice weekly or weekly. It may be desirable to administer simultaneously, or sequentially a therapeutically effective amount of one or more of the therapeutic compositions of the invention to an individual as a single treatment episode.
[00176] The methods according to this aspect of the invention are useful for model studies of gene expression. The methods are also useful for the prophylactic or therapeutic treatment of human or animal disease. For example, the methods are useful for pediatric and veterinary inhibition of gene expression applications.
[00177] The examples below are intended to further illustrate certain preferred embodiments of the invention, and are not intended to limit the scope of the invention.
Example 1 :
Preparation of Oligonucleotide-based compounds
[00178] The oligonucleotide-based compounds of the invention were chemically synthesized using phosphoramidite chemistry on automated DNA/RNA synthesizer. TAC protected (Except U) 2'-0-TBDMS RNA monomers, A, G, C and U, were purchased from Sigma- Aldrich. 7-deaza-G, inosine and loxoribine monomers were purchased from ChemGenes Corporation. 0.25M 5-ethylthio-lH-tetrazole, PAC- anhydride Cap A and Cap B were purchased from Glen Research. 3% trichloroacetic acid (TCA) in dichloromethane (DCM) and 5% 3H-l,2-Benzodithiole-3-one-l,l-dioxide (Beaucage reagent) were made in house.
[00179] Oligonucleotide-based compounds of the invention were synthesized at 1-2 μΜ scale using a standard RNA synthesis protocol.
Cleavage and base deprotection
[00180] Oligonucleotide-based compounds of the invention were cleaved from solid support and the solution was further heated at 65 °C to removing protecting groups of exo cyclic-amines. The resulting solution was dried completely in a SpeedVac.
IE HPLC Purification
[00181] Oligonucleotide-based compounds of the invention were purified by ion exchange HPLC.
Column: Dionex DNAPac 100 column (22X250)
Column Heater: ChromTech TL-105 HPLC column heater, temperature is set to 80 °C.
Buffer A: 20 mM Tris-HCl, pH 7.0, 20% acetinitrile
Buffer B: 3.0 M NaCl, 20 mM Tris-HCl, pH 7.0, 20% acetonitrile
Flow rate: lOml/min
Gradient:
0-2 min: 0% B
2-11 min: 0% B to 35% B
11-41 min: 35% B to 90% B
41-45 min: 100% B
[00182] Crude solution of oligonucleotide-based compounds of the invention was injected into HPLC. Above gradient is performed and the fractions were collected. All fractions containing more than 90% desired product were mixed, and then the solution was concentrated to almost dry by RotoVap. RNAse-free water was added to make final volume of 10ml. C-18 Reversed Phase Desalting
[00183] CC-18 Sep-Pak cartridge purchased from Waters was first conditioned with
10ml of acetonitrile followed by 10 ml of 0.5 M sodium acetate. 10 ml of the solution of oligonucleotide-based compounds of the invention was loaded. 15 ml of water was then used to wash out the salt. The oligonucleotide-based compounds of the invention was eluted out by 1 ml of 50% acetonitrile in water.
[00184] The solution is placed in SpeedVac for 30 minutes. The remaining solution was filter through a 0.2 micro filter and then was lyophilized to dryness. The solid was then re-dissolved in water to make the desired concentration.
[00185] The final solution was stored below 0 °C.
Capillary Electrophoresis
[00186] Oligonucleotide-based compounds of the invention were analyzed by capillary electrophoresis according to the following conditions.
Instrument: Beckman 5010
Capillary: 62cm ssDNA capillary
Sample preparation: 0.2 OD of oligonucleotide-based composition according to the invention was dissolved in 200ul of RNAse-free water.
Injection: electro-kinetic injection at 5KV for 5 seconds.
Running condition: 14KV for 50 minutes at 30 °C.
Ion Exchange HPLC analysis
[00187] Oligonucleotide-based compounds of the invention were analyzed by ion exchange HPLC according to the following conditions:
Column: Dionex DNAPac guard column (22X250)
Column Heater: ChromTech TL-105 HPLC column heater, temperature is set to 80
°C.
Buffer A: 100 mM Tris-HCl, pH 8.0, 20% acetinitrile
Buffer B: 2.0 M LiCl, 100 mM Tris-HCl, pH 8.0, 20% acetonitrile
Flow rate: 2ml/min
Gradient:
0-2 min: 0% B
2-10 min: 0% B to 100% B
10-15 min: 100% B PAGE analysis
[00188] 0.3 OD of oligonucleoti de-based compounds of the invention was loaded on
20% polyacrylamide gel and was running at constant power of 4 watts for approximately 5 hours. The gel was viewed under short wavelength UV light.
Dual Luciferase Reporter System Assay
[00189] Hepa 1-6 cells are co-transfected with GSO and target plasmid simultaneously using LIP OFECTAMINE® 2000 on day one (20,000 c/well). RLuc siRNA was used as the positive control and GSO mu/hu universal control was used as the negative control. On day two (24 hours post-transfection), luminescence measurements for both reporter genes are taken separately: Firefly luciferase: expression serves as the normalizer for the assay; Renilla luciferase: substrate includes a "stop" reagent to quench luminescence from firefly. Separate luminescence measurements are taken to correspond to renilla-target transcript expression. Substrate includes DTT to lyse cells. Results are shown in Table 4A and Table 4B.
Table 4A
Figure imgf000072_0001
21 3'-CCTCTTCGTCCGTCCCACG-5'-X-5'-GCACCCTGCCTGCTTCTCC-3' 68.62
22 3 '-TCTTCGTCCGTCCCACGTC-5 '-X-5 '-CTG CACCCTG CCTG CTTCT-3 ' 73.88
23 3'-GGGTCCGTCGTCCACAGTG-5'-X-5'-GTGACACCTGCTGCCTGGG-3' 61.92
24 3'-GGATGTCCCTCCCGGTCTA-5'-X-5'-ATCTGGCCCTCCCTGTAGG-3' 40.93
25 3'-ATGTCCCTCCCGGTCTACG-5'-X-5'-GCATCTGGCCCTCCCTGTA-3' 41.82
26 3'-GTCCCTCCCGGTCTACGTC-5'-X-5'-CTGCATCTGGCCCTCCCTG-3' 57.94
27 3'-CCCTCCCGGTCTACGTCAG-5'-X-5'-GACTGCATCTGGCCCTCCC-3' 58.14
28 3'-CTCCCGGTCTACGTCAGTG-5'-X-5'-GTGACTGCATCTGGCCCTC-3' 63.13
29 3'-G GTTCTG ACCCGTGTCCTC-5 '-X-5 '-CTCCTGTGCCCAGTCTTG G-3 ' 59.63
30 3'-TCG AG G ACCG ACACCACCC-5 '-X-5 '-CCCACCACAGCCAG G AGCT-3 ' 77.64
31 3'-CGAGGACCGACACCACCCG-5'-X-5'-GCCCACCACAGCCAGGAGC-3' 80.53
32 3'-GGGTCCGTCGTGGAGTCCG-5'-X-5'-GCCTGAGGTGCTGCCTGGG-3' 62.62
33 3'-CCGTCCCTTCGACTCCGTC-5'-X-5'-CTGCCTCAGCTTCCCTGCC-3' 73.27
34 3'-CGTCCCTTCGACTCCGTCA-5'-X-5'-ACTGCCTCAGCTTCCCTGC-3' 78.22
35 3'-CCCGTCCGTCTCGACCTCC-5'-X-5'-CCTCCAGCTCTGCCTGCCC-3' 60.58
36 3'-CCGTCCGTCTCGACCTCCG-5'-X-5'-GCCTCCAGCTCTGCCTGCC-3' 54.52
37 3'-CAGGGTTCCAGTCCTCCCG-5'-X-5'-GCCCTCCTGACCTTGGGAC-3' 71.63
38 3'-GG GTTCCAGTCCTCCCGTC-5 '-X-5'-CTG CCCTCCTG ACCTTG GG-3 ' 69.94
39 3'-GTTCCAGTCCTCCCGTCCC-5 '-X-5 '-CCCTG CCCTCCTG ACCTTG-3 ' 71.58
40 3'-GTCCCG G ACCCACCCTTCC-5 '-X-5 '-CCTTCCCACCCAGG CCCTG-3 ' 57.15
41 3'-CCCGGACCCACCCTTCCAT-5'-X-5'-TACCTTCCCACCCAGGCCC-3' 51.93
42 3'-CGGACCCACCCTTCCATGT-5'-X-5'-TGTACCTTCCCACCCAGGC-3' 31.04
43 3'GACCCACCCTTCCATGTCC-5'-X-5'-CCTGTACCTTCCCACCCAG-3' 44.89
44 3'-GTCCCGGTGGTCGTAGGTC-5'-X-5'-CTGGATGCTGGTGGCCCTG-3' 61.72
45 3'-TCCCGGTGGTCGTAGGTCC-5'-X-5'-CCTGGATGCTGGTGGCCCT-3' 52.12
46 3'TCCGTGGACTCACCGACCC-5'-X-5'-CCCAGCCACTCAGGTGCCT-3' 76.87
47 3'-CTCACCGACCCTGTTCCCT-5'-X-5'-TCCCTTGTCCCAGCCACTC-3' 68.50
48 3'-CACCGACCCTGTTCCCTAG-5'-X-5'-GATCCCTTGTCCCAGCCAC-3' 74.30
49 3'-GCCCTCGACCTGGACGAAC-5'-X-5'-CAAGCAGGTCCAGCTCCCG-3' 67.80
50 3'-TGTCGTTG AAGTCCCCCTC-5 '-X-5 '-CTCCCCCTG AAGTTG CTGT-3 ' 76.40
51 3'-TGCCACCACGCCTGATGTT-5'-X-5'-TTGTAGTCCGCACCACCGT-3' 84.40
52 3'-TCCCTTGTGTCTCCAGTG G-5 '-X-5 '-GGTG ACCTCTGTGTTCCCT-3 ' 58.30
53 3'-ATCCCTCCGTCTCCGTCCG-5'-X-5'-GCCTGCCTCTGCCTCCCTA-3' 76.10
54 3'-GACTTCCTTGTCCGACCCG-5'-X-5'-GCCCAGCCTGTTCCTTCAG-3' 70.30
Where X is glycerol Table 4B
Figure imgf000073_0001
58 82.08 224 70.29
59 64.04 225 69.92
60 61.19 226 81.70
61 55.65 227 59.46
62 29.88 228 81.39
63 44.00 229 88.01
64 73.27 230 75.84
65 69.04 231 58.18
66 76.39 232 29.33
67 67.30 233 61.77
68 84.30 234 72.38
69 61.65 235 45.83
70 59.28 236 39.94
71 60.44 237 66.24
72 49.61 238 49.78
73 65.21 239 23.03
74 52.34 240 59.57
75 82.43 241 41.65
76 68.25 242 44.50
77 83.97 243 18.23
78 82.25 244 37.51
79 67.84 245 58.43
80 41.54 246 70.66
81 80.09 247 74.80
82 53.95 248 70.32
83 74.05 249 90.70
84 2.78 250 73.19
85 53.89 251 81.50
86 53.70 252 87.92
87 34.15 253 76.82
88 77.07 254 55.60
89 23.27 255 42.30
90 41.99 256 44.52
91 41.36 257 81.17
92 60.45 258 64.45
93 58.99 259 79.46
94 74.51 260 41.81
95 10.33 261 46.85
96 9.46 262 83.04
97 42.36 263 78.00
98 27.05 264 69.88
99 24.30 265 59.09
100 10.54 266 39.05 101 85.55 267 34.97
102 60.69 268 83.20
103 63.04 269 86.16
104 59.83 270 49.03
105 57.80 271 70.17
106 71.35 272 86.40
107 74.39 273 67.96
108 74.04 274 44.65
109 80.27 275 65.68
110 89.98 276 66.68
111 86.33 277 76.67
112 88.35 278 39.46
113 84.67 279 69.63
114 57.13 280 68.44
115 56.03 281 57.77
116 77.36 282 67.85
117 72.63 283 61.74
118 74.24 284 69.87
119 79.93 285 58.11
120 86.42 286 41.07
121 57.13 287 42.40
122 49.63 288 42.09*
123 65.62 289 61.77*
124 72.63 290 33.46*
125 96.00 291 49.08*
126 71.45 292 43.43*
127 -0.08 293 40.08*
128 4.49 294 57.06*
129 60.37 295 87.34*
130 67.01 296 76.54*
131 10.42 297 36.96*
132 72.11 298 96.71*
133 66.46 299 70.53*
134 58.22 300 88.21*
135 40.56 301 76.86*
136 75.82 302 85.21*
137 69.22 303 74.25*
138 69.06 304 70.61*
139 79.03 305 83.52*
140 10.17 306 65.18*
141 25.50 307 84.36*
142 84.19 308 91.72
143 81.61 309 93.78 144 70.57 310 86.49
145 78.67 311 79.67
146 66.46 312 78.18
147 58.98 313 68.73
148 69.06 314 49.06
149 97.18 315 51.92
150 81.25 316 64.80
151 30.14 317 49.86
152 73.42 318 60.88
153 79.87 319 54.14
154 63.67 320 54.27
155 71.18 321 64.20
156 64.26 322 57.54
157 84.39 323 64.73
158 91.96 324 24.73
159 87.62 325 -3.86
160 85.37 326 58.29
161 90.51 327 85.58
162 90.48 328 38.27
163 88.20 329 54.35
164 82.16 330 37.69
165 79.86 331 42.71
166 88.55 332 77.86
167 91.35 333 34.95
168 81.98 334 29.20
169 94.67 335 41.76
170 84.41 336 55.25
171 82.59 337 56.23
172 31.12 338 44.34
173 67.25 339 42.26
174 36.58 340 33.54
175 55.38 341 32.88
176 73.10 342 46.91
177 77.05 343 25.39
178 91.25 344 53.54
179 83.86 345 68.08
180 85.21 346 65.26
181 72.85 347 70.49
182 61.27 348 33.62
183 81.35 349 78.29
184 68.97 350 87.30
185 67.13 351 92.56
186 57.30 352 82.30 187 79.41 353 62.64
188 41.38 354 84.10
189 50.80 355 72.48
190 52.18 356 87.25
191 63.14 357 68.93
192 82.52 358 77.23
193 41.99 359 74.70
194 73.39 360 43.71
195 76.17 361 86.31
196 85.66 362 52.57
197 98.60 363 38.62
198 47.11 364 64.49
199 42.47 365 66.70
200 87.17 366 77.24
201 74.36 367 89.81
202 58.24 368 77.82
203 59.21 369 62.31
204 42.36 370 80.21
205 74.17 371 58.76
206 76.54 372 71.34
207 30.41 373 65.23
208 68.55 374 65.58
209 69.73 375 78.67
210 59.73 376 67.01
211 54.92 377 32.15
212 56.90 378 49.07
213 69.09 379 53.07
214 77.40 380 58.24
215 39.73 381 72.09
216 39.23 382 63.90
217 41.13 383 68.54
218 23.48 384 15.69
219 79.92 385 25.43
220 29.57 386 40.49
For 3GA compounds numbers 55 through 386 listed in Table 4B, glycerol is the non- nucleotidic linker. Flow cytometric analysis
[00190] Whole blood samples with anticoagulant EDTA from mice in study were stained for 30 minutes in the dark at room temperature with the following labeled antibodies from BD Biosciences in the presence of mouse Fc blocker (Affymetrix eBioscience, 14- 0161): rat anti-mouse CD3-Alexa Fluor 647 (557869), rat anti-mouse CD4-Alexa Fluor 647 (557681), rat anti-mouse CD8-Alexa Fluor 488 (557668) or the corresponding isotype controls. Red blood cells were lysed with freshly prepared lx RBC lysis buffer (eBioscience, 00-4300) and washed with flow cytometry staining buffer (BD Biosciences, 554657).
Resuspended cell suspensions in the flow cytometry staining buffer were run on BD Accuri C6 to acquire data and analyzed by FLOWJO (TreeStar).
IC50 Analysis
[00191] Hepa 1-6 cells are co-transfected with 3GA and target plasmid simultaneously using LIPOFECTAMINE® 2000 on day one (20,000 c/well). Concentration of 3GAs were ranging from 0.019 to 41.7 nM with a 3-fold increment. RLuc siRNA was used as the positive control and 3GA mu/hu universal control was used as the negative control. On day two (24 hours post-transfection), luminescence measurements for both reporter genes are taken separately: Firefly luciferase: expression serves as the normalizer for the assay; Renilla luciferase: substrate includes a "stop" reagent to quench luminescence from firefly. Separate luminescence measurements are taken to correspond to renilla-target transcript expression. Substrate includes DTT to lyse cells. IC50 of 3GAs was calculated using GraphPad Prism 6. Results are shown in Table 5.
Table 5
Figure imgf000078_0001
180 1506 CAGCACCCAG I 1 1 I CCCTA 6.10
183 1716 ATCCCAG CCACTCAG G AG G 32.7
110 mLAG3 1108 G CTCCAG ACCCAG AACCTT 6.49
124 1356/1369 G ACAGTG G CATTG AG CTG C 11.9
122 h LAG3 1822/1841 G CTCCAG CTCCTCTATCTT 9.10
143 1848 G GTTCTTG CTCCAG CTCCT 5.03
195 mCTLA4 563 GTTG CCCATG CCCACAAAG 19.6
225 hCTLA4 1822 GCCTTCTTCTGTCCATGGC 1.71
247 m lD02 2748 GGTGACTTCCAGGTCTGCA 0.247
249 156 G GTGTCCATTG CCTTCTGT 2.73
259 h l D02 1137 AG I ACCAC I 1 I C I I GC I 3.36
262 1363 GG I I CCA I G I 1 I GC I 1.28
361 mOX40L 1069 1 GGACACCACC 1 1 1 CCA 1 0.673
368 712 TGGTCCGTGGTCGTACTTG 0.553 hOX40L
370 1104 CTCCTCGTTCCTCACTTCC 5.01
In Vivo Mouse Tumor Model
[00192] Colon tumor can be implanted in BALB/c mice by subcutaneous injection of
106 CT26.WT cells at right flank (Tumor 1) and 106 CT26.CL25 cells at left flank (Tumor 2) on day 0. Treatment can be initiated on day 6 or when tumor size reached to 70 to 80 mm3 by intra-tumor injection of gene silencing compound according to the invention at various dosages (e.g., 2 mg/kg, 5 mg/kg, 12.5 mg/kg, or 25 mg/kg) on day 6, 10, 13, 16, 20, and 22.
[00193] Tumor growth can be monitored twice per week throughout the study period.
The study can be terminated with blood, spleen and tumor tissues collected for further evaluation. T lymphocyte population in blood and spleen samples were detected and analyzed by flow cytometry. Spleen IFN-y-producing cells were detected with ELISPOT assay after culture of spleen cells for 24 hours with tumor antigen beta-gal or AH1 peptide. Tumor tissues were analyzed for gene expression by RT-PCR. EQUIVALENTS
[00194] Those skilled in the art will recognize, or be able to ascertain, using no more than routine experimentation, numerous equivalents to the specific substances and procedures described herein. For example, antisense oligonucleotides that overlap with the
oligonucleotides may be used. Such equivalents are considered to be within the scope of this invention, and are covered by the following claims.

Claims

CLAIMS What is claimed is:
1. A 3rd generation antisense (3GA) compound comprising two oligonucleotides linked at their 5' ends, each oligonucleotide, independently, consists of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 387, SEQ ID NO: 388, SEQ ID NO: 389, SEQ ID NO: 390, SEQ ID NO: 391, SEQ ID NO: 392, SEQ ID NO: 393, SEQ ID NO: 394, SEQ ID NO: 395, SEQ ID NO: 396, SEQ ID NO: 397, SEQ ID NO: 398, SEQ ID NO: 399, SEQ ID NO: 400, SEQ ID NO: 401, SEQ ID NO: 402, SEQ ID NO: 403, SEQ ID NO: 404, SEQ ID NO: 405, or SEQ ID NO: 406.
2. The 3GA compound according to claim 1, wherein each oligonucleotide, independently, consisting of 12 to 30 nucleotides having a nucleobase sequence comprising a portion of at least 12 contiguous nucleobases complementary to an equal length portion of SEQ ID NO: 388, SEQ ID NO: 390, SEQ ID NO: 392, SEQ ID NO: 394, SEQ ID NO: 396, SEQ ID NO: 398, SEQ ID NO: 400, SEQ ID NO: 402, SEQ ID NO: 404, or SEQ ID NO: 406.
3. The 3GA compound according to claim 1, wherein the nucleobase sequence of each oligonucleotide is, independently, at least 90% complementary over its entire length to a nucleobase sequence of SEQ ID NO: 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, or 406.
4. The 3GA compound according to claim 3, wherein the nucleobase sequence of each oligonucleotide is, independently, at least 90% complementary over its entire length to a nucleobase sequence of SEQ ID NO: 388, 390, 392, 394, 396, 398, 400, 402, 404, or 406. 5. The 3GA compound according to claim 1, wherein each oligonucleotide, independently, comprises a portion of at least 12 contiguous nucleobases of SEQ ID NO: 1,
2, 3, 4,
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, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161 , 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181 , 182, 183, 184, 185, 186, 187, 188, 189, 190, 191 , 192, 193, 194, 195, 196, 197, 198, 199, 200, 201 , 202, 203, 204, 205, 206, 207, 208, 209, 210, 21 1, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251 , 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271 , 272, 273, 274, 275, 276, 277, 278, 279, 280, 281 , 282, 283, 284, 285, 286, 287, 288, 289, 290, 291 , 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 31 1, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341 , 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361 , 362, 363, 364, 365, 366, 367, 368, 369, 370, 371 , 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, or 386, or combinations thereof.
6. The 3GA compound according to claim 5, wherein each oligonucleotide, independently, comprises a portion of least 12 contiguous nucleobases of SEQ ID NOs: 1 , 2,
3, 4, 5, 6, 7, 8, 9, 10, 1 1 , 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, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99, 100, 101 , 102, 103, 104, 105, 106, 107, 108, 109, 1 10, 1 11 , 1 12, 1 13, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161 , 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181 , 182, 183, 184, 185, 186, 187, 188, 189, 190, 191 , 192, 193, 194, 195, 196, 197, 198, 199, 200, 201 , 202, 203, 204, 205, 206, 207, 208, 209, 210, 21 1, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251 , 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271 , 272, 273, 274, 275, 276, 277, 278, 279, 280, 281 , 282, 283, 284, 285, 286, 287, 288, 289, 290, 291 , 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 31 1, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, or 386, and is at least 80% complimentary to its target site with SEQ ID NO: 387, SEQ ID NO: 388, SEQ ID NO: 389, SEQ ID NO: 390, SEQ ID NO: 391, SEQ ID NO: 392, SEQ ID NO: 393, SEQ ID NO: 394, SEQ ID NO: 395, SEQ ID NO: 396, SEQ ID NO: 397, SEQ ID NO: 398, SEQ ID NO: 399, SEQ ID NO: 400, SEQ ID NO: 401, SEQ ID NO: 402, SEQ ID NO: 403, SEQ ID NO: 404, SEQ ID NO: 405, or SEQ ID NO: 406.
7. The 3GA compound according to claim 6, wherein each oligonucleotide, independently, comprises a portion of at least 12 contiguous nucleobases of SEQ ID NOs: 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, or 386, and is at least 80% complimentary to its target site within SEQ ID NO: 388, SEQ ID NO: 390, SEQ ID NO: 392, SEQ ID NO: 394, SEQ ID NO: 396, SEQ ID NO: 398, SEQ ID NO: 400, SEQ ID NO: 402, SEQ ID NO: 404, or SEQ ID NO: 406.
8. A composition comprising a 3GA compound according to claim 1 and a
pharmaceutically acceptable carrier.
9. The composition according to claim 8, further one or more vaccines, antigens, antibodies, cytotoxic agents, chemotherapeutic agents, kinase inhibitors, allergens, antibiotics, agonist, antagonist, antisense oligonucleotides, ribozymes, RNAi molecules, siRNA molecules, miRNA molecules, aptamers, proteins, gene therapy vectors, DNA vaccines, adjuvants, co-stimulatory molecules or combinations thereof.
10. A method for inhibiting PD1, PDLl, IDOl, LAG3, TIM3, CTLA4, ID02,
CEACAMl, OX40, and/or OX40L mRNA or protein expression, the method comprising contacting a cell with at least one 3GA compound according to claim 1.
11. The method according to claim 10, wherein the cell is contacted with two or more 3GA compounds targeting different regions of the same checkpoint.
12. The method according to claim 10, wherein the cell is contacted with two or more 3GA compounds targeting different checkpoints.
13. A method for inhibiting immune system tolerance to tumors comprising administering to an animal at least one 3GA compound according to claim 1 or composition according to claim 8 to reduce PD1, PDLl, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAMl, OX40, and/or OX40L mRNA or protein expression.
14. A method for the treatment of a disease, disorder, or condition associated with PD1, PDLl, IDOl, LAG3, TIM3, CTLA4, ID02, CEACAMl, OX40, or OX40L in an individual in need thereof, the method comprising administering at least one 3GA compound according to claim 1.
15. The method according to claim 1, wherein the disease, disorder, or condition is a hyperproliferative disease or an autoimmune disease.
16. The method according to claim 2, wherein the hyperproliferative disease is cancer, carcinomas, sarcomas, lymphomas, leukemias and associated malignancies and metastases.
17. The method according to claim 3, wherein the 3GA compound is administered intratumorally.
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