SELECTIVE REDUCTION OF ALLELIC VARIANTS

• US 20150292015A1
• Filed: 03/03/2015
• Published: 10/15/2015
• Est. Priority Date: 02/08/2010
• Status: Abandoned Application

• Current Assignee: Ionis Pharmaceuticals, Inc.
• Original Assignee: ISIS Pharmaceuticals Incorporated (Ionis Pharmaceuticals, Inc.)
• Inventors: Bennett, C. Frank, Hayden, Michael, Freier, Susan M., Greenlee, Sarah, Carroll, Jeffrey, Warby, Simon, Swayze, Eric E.
• Application Number:
  US14/636,960
• Publication Number:
  US 20150292015A1
• Time in Patent Office: Days
• US Class Current: 1/1
• CPC Class Codes: A61P 25/14 for treating abnormal movements, e.g. chorea, dyskinesia
• CPC Class Codes: A61P 25/28 for treating neurodegenerative disorders of the central nervous system, e.g. nootropic agents, cognition enhancers, drugs for treating Alzheimer's disease or other forms of dementia
• CPC Class Codes: C12N 15/113 Non-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 when used in plants C12N15/8218
• CPC Class Codes: C12N 2310/11 Antisense
• CPC Class Codes: C12N 2320/34 Allele or polymorphism specific uses
• CPC Class Codes: C12Q 1/6811 Selection methods for production or design of target specific oligonucleotides or binding molecules
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 1/6897 involving reporter genes operably linked to promoters
• CPC Class Codes: C12Q 2521/327 RNAse, e.g. RNAseH
• CPC Class Codes: C12Q 2525/121 incorporating both deoxyribonucleotides and ribonucleotides
• CPC Class Codes: C12Q 2525/185 incorporating bases where the precise position of the bases in the nucleic acid string is important
• CPC Class Codes: C12Q 2525/207 siRNA, miRNA
• CPC Class Codes: C12Q 2535/131 Allele specific probes
• CPC Class Codes: C12Q 2539/107 Representational Difference Analysis [RDA]
• CPC Class Codes: C12Q 2600/136 Screening for pharmacological compounds
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/158 Expression markers

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).

Claims

1-97. -97. (canceled)

98. 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.

99. The method of claim 98, further comprising the step of contacting a third cell, tissue, or animal with said agent at one or more concentrations, wherein said third 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 and has a different genotype than said first cell, tissue, or animal and said second cell, tissue, or animal.

100. The method of claim 98, wherein said first allelic variant is a mutant allele and said second allelic variant is a wild-type allele.

101. The method of claim 98, wherein said first allelic variant is a wild-type allele and said second allelic variant is a mutant allele.

102. The method of claim 101, wherein said mutant allelic variant is associated with disease.

103. The method of claim 102, wherein said disease is Huntington'"'"'s Disease.

104. The method of claim 98, wherein said first nucleotide is in linkage disequilibrium with a disease associated mutation.

105. The method of claim 98, wherein said second nucleotide is in linkage disequilibrium with a disease associated mutation.

106. The method of claim 105, wherein said disease associated mutation is a tri-nucleotide repeat expansion.

107. The method of claim 106, wherein said tri-nucleotide repeat expansion is a CAG expansion.

108. The method of claim 107, wherein said CAG expansion is in a HTT gene.

109. The method of claim 98, wherein said first nucleotide is A.

110. The method of claim 109, wherein said second nucleotide is any of C, G, or T.

111. The method of claim 109, wherein said second nucleotide is any of A, G, or T.

112. The method of claim 98, wherein said agent is an antisense compound.

113. The method of claim 112, said antisense compound is an antisense oligonucleotide.

114. The method of claim 113, wherein said antisense oligonucleotide is a gapmer.

115. The method of claim 113, wherein said gapmer has a wing-gap-wing motif.

116. The method of claim 115, wherein the wing-gap-wing motif is any one of the group consisting of 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.

117. The method of claim 98, 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, rs362331, 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.