Selective Reduction of Allelic Variants

Abstract

Disclosed herein are antisense compounds and methods for selectively reducing expression of an allelic variant of a huntingtin gene containing a single nucleotide polymorphism (SNP). Such methods, compounds, and composition are useful to treat, prevent, or ameliorate Huntington's Disease (HD).

1 . A method for determining whether an agent selectively inhibits expression of a first allelic variant of a gene relative to a second allelic variant of said gene wherein said first allelic variant comprises a first nucleotide at a SNP position and said second allelic variant comprises a second nucleotide at said SNP position, comprising:
 contacting a first cell, tissue or animal with said agent at one or more concentrations, wherein said first cell, tissue or animal is homozygous for said first nucleotide at said SNP position;   contacting a second cell, tissue or animal with said agent at one or more concentrations, wherein said second cell, tissue or animal is homozygous for said second nucleotide at said SNP position or is heterozygous for said first and said second nucleotides at said SNP position;   measuring inhibition of expression of said allelic variant in each of said cell, tissue or animal for each of said one or more concentrations of said agent; and   comparing said inhibition of expression in each of said cell, tissue or animal for each of said one or more concentrations of said agent to determine whether said agent selectively inhibits expression of said first allelic variant of said gene relative to said second allelic variant of said gene.   
     
     
         2 . (canceled) 
     
     
         3 . The method of  claim 1 , wherein said first allelic variant is a mutant allele and said second allelic variant is a wild-type allele, or said first allelic variant is a wild-type allele and said second allelic variant is a mutant allele. 
     
     
         4 . (canceled) 
     
     
         5 . The method of  claim 3 , wherein said mutant allelic variant is associated with disease. 
     
     
         6 . (canceled) 
     
     
         7 . The method of  claim 5 , wherein said disease is Huntington's Disease. 
     
     
         8 . The method of  claim 1 , wherein said first nucleotide or said second nucleotide is in linkage disequilibrium with a disease associated mutation. 
     
     
         9 . (canceled) 
     
     
         10 . The method of  claim 8 , wherein said disease associated mutation is a tri-nucleotide repeat expansion. 
     
     
         11 . The method of  claim 10 , wherein said tri-nucleotide repeat expansion is a CAG expansion. 
     
     
         12 . The method of  claim 11 , wherein said CAG expansion is in a HTT gene. 
     
     
         13 .- 25 . (canceled) 
     
     
         26 . The method of  claim 1 , wherein said agent is an antisense oligonucleotide. 
     
     
         27 .- 41 . (canceled) 
     
     
         42 . The method of  claim 1 , wherein said first cell and/or said second cell is any of the group consisting of fibroblast cell line, neuronal cell line, or lymphoblast cell line. 
     
     
         43 .- 46 . (canceled) 
     
     
         47 . The method of  claim 1 , wherein said SNP position is any of the group consisting of rs6446723, rs3856973, rs2285086, rs363092, rs916171, rs6844859, rs7691627, rs4690073, rs2024115, rs11731237, rs362296, rs10015979, rs7659144,
 rs363096, rs362273, rs16843804, rs362271, rs362275, rs3121419, rs362272, rs3775061, rs34315806, rs363099, rs2298967, rs363088, rs363064, rs363102, rs2798235, rs363080, rs363072, rs363125, rs362303, rs362310, rs10488840, rs362325, rs35892913, rs363102, rs363096, rs11731237, rs10015979, rs363080, rs2798235, rs1936032, rs2276881, rs363070, rs35892913, rs12502045, rs6446723, rs7685686, rs3733217, rs6844859,   rs1143646, rs2285086, rs2298969, rs4690072, rs916171, rs3025849, rs7691627, rs4690073, rs3856973, rs363092, rs362310, rs362325, rs363144, rs362303, rs34315806, rs363099, rs363081, rs3775061, rs2024115, rs10488840, rs363125, rs362296, rs2298967, rs363088, rs363064, rs362275, rs3121419, rs3025849, rs363070, rs362273, rs362272, rs362306, rs362271, rs363072, rs16843804, rs7659144, rs363120, and rs12502045.   
     
     
         48 .- 81 . (canceled) 
     
     
         82 . A method of treating Huntington's Disease, comprising selectively reducing expression of a mutant huntingtin allele in an animal in need thereof, comprising administering to the animal a compound, comprising a modified oligonucleotide consisting of 15 to 20 linked nucleosides and fully complementary to the mutant huntingtin allele, wherein position 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 of the modified oligonucleotide, as counted from the 5′ terminus of the modified oligonucleotide, aligns with any of the SNP sites in the group consisting of rs6446723, rs3856973, rs2285086, rs363092, rs916171, rs6844859, rs7691627, rs4690073, rs2024115,rs1731237, rs362296, rs10015979, rs7659144, rs363096, rs362273, rs16843804, rs362271, rs362275, rs3121419, rs362272, rs3775061, rs34315806, rs363099, rs2298967, rs363088, rs363064, rs363102, rs2798235, rs363080, rs363072, rs363125, rs362303, rs362310, rs10488840, rs362325, rs35892913, rs1936032, rs2276881, rs363070, rs12502045, rs7685686, rs3733217, rs2857936, rs12506200, rs762855, rs4690072, rs363081, rs363075, rs3025849, rs6855981, rs363144, rs3025838, rs2298969, rs362322, rs362306, and rs1006798. 
     
     
         83 . (canceled) 
     
     
         84 . A compound comprising a modified oligonucleotide 15 to 20 linked nucleosides in length, targeted to a huntingtin single nucleotide polymorphism, comprising a 12 nucleobase portion of the nucleobase sequence of any one of SEQ ID NO: 6 to 285, wherein position 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 of the modified oligonucleotide, as counted from the 5′ terminus of the modified oligonucleotide, aligns with the huntingtin single nucleotide polymorphism. 
     
     
         85 . The compound of  claim 84 , wherein the modified oligonucleotide comprises awing-gap-wing motif selected from 5-10-5, 2-9-6, 3-9-3, 3-9-4, 3-9-5, 4-7-4, 4-9-3, 4-9-4, 4-9-5, 4-10-5, 4-11-4, 4-11-5, 5-7- 5, 5-8-6, 5-9-3, 5-9-5, 5-10-4, 5-10-5, 6-7-6, 6-8-5, and 6-9-2. 
     
     
         86 .- 95 . (canceled) 
     
     
         96 . A method of selectively reducing mutant huntingtin, comprising administering the compound of  claim 84 . 
     
     
         97 . (canceled)