Selective reduction of allelic variants

• US 9,006,198 B2
• Filed: 02/08/2011
• Issued: 04/14/2015
• Est. Priority Date: 02/08/2010
• Status: Active Grant

• Current Assignee: Ionis Pharmaceuticals, Inc., University of British Columbia
• Original Assignee: ISIS Pharmaceuticals Incorporated, University of British Columbia
• Inventors: Bennett, C. Frank, Hayden, Michael, Freier, Susan M., Greenlee, Sarah, Carroll, Jeffrey, Warby, Simon, Swayze, Eric E.
• Primary Examiner(s): Vivlemore, Tracy
• Assistant Examiner(s): POLIAKOVA-GEORGA, EKATERINA
• Application Number:
  US13/577,622
• Publication Number:
  US 20130046008A1
• Time in Patent Office: 1,526 Days
• US Class Current: 514/44.A
• 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. A method of selectively reducing the expression of a mutant huntingtin allele in a cell, tissue, or animal comprising administering to the cell, tissue, or animal a compound comprising a modified, single-stranded antisense oligonucleotide complementary to the mutant huntingtin allele at a position comprising a single nucleotide polymorphism, wherein the modified oligonucleotide consists of 12 to 30 linked nucleosides and comprises a wing-gap-wing motif with a 5′

wing region positioned at the 5′

end of a deoxynucleoside gap, and a 3′

wing region positioned at the 3′

end of the deoxynucleoside gap, wherein position 8, 9, or 10 of the modified oligonucleotide, as counted from the 5′

terminus of the modified oligonucleotide, aligns with the single nucleotide polymorphism, wherein the expression of the mutant huntingtin allele is selectively reduced, and wherein the single nucleotide polymorphism is rs362306, rs362331, rs2298969, rs7685686, rs4690072, rs2024115, or rs363088.

2. The method of claim 1, wherein at least one nucleoside comprises a modified sugar.

3. The method of claim 2, wherein the modified sugar is a high-affinity sugar modification.

4. The method of claim 3, wherein the high-affinity sugar is a bicyclic sugar.

5. The method of claim 4, wherein each bicyclic sugar comprises a 4′

-CH(CH₃)—

O-2′

bridge.

6. The method of claim 3, wherein the at least one modified sugar comprises a 2′

-O-methoxyethyl.

7. The method of claim 1, wherein the wing-gap-wing motif is any of the group consisting of 2-9-6, 3-9-3, 3-9-4, 3-9-5, 4-7-4, 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.

8. The method of claim 7, wherein each nucleoside positioned in the wing segment of the modified oligonucleotide comprises a 2′

-O-methoxyethyl modification.

9. The method of claim 7, wherein at least one of the wing regions comprises a 4′

to 2′

bicyclic nucleoside and at least one of the remaining wing nucleosides is a non-bicyclic 2′

-modified nucleoside.

10. The method of claim 9, wherein the non-bicyclic 2′

-modified nucleoside is a 2′

-O-methoxyethyl nucleoside.

11. The method of claim 9, wherein the 4′

to 2′

bicyclic nucleoside is a 4′

-CH(CH₃)—

O-2′

bicyclic nucleoside.

12. The method of claim 1, wherein at least one nucleoside comprises a modified nucleobase.

13. The method of claim 12, wherein the at least one modified nucleobase is a 5′

-methylcytosine.

14. The method of claim 1, wherein the modified oligonucleotide is 95% complementary to the mutant huntingtin allele.

15. The method of claim 1, wherein the modified oligonucleotide is 100% complementary to the mutant huntingtin allele.

16. The method of claim 7, wherein at least one internucleoside linkage is a modified internucleoside linkage.

17. The method of claim 16, wherein each internucleoside linkage is a phosphorothioate internucleoside linkage.

19. The method of claim 1, wherein the single nucleotide polymorphism is rs2298969, rs7685686, rs4690072, rs2024115, or rs363088.

18. A method of treating, ameliorating, or slowing the onset or progression of Huntington'"'"'s Disease, comprising administering to an animal a compound comprising a modified, single-stranded antisense oligonucleotide complementary to a mutant huntingtin allele at a position on the allele comprising a single nucleotide polymorphism site, wherein the modified oligonucleotide consists of 12 to 30 linked nucleosides and comprises a wing-gap-wing motif with a 5′

wing region positioned at the 5′

end of a deoxynucleoside gap, and a 3′

wing region positioned at the 3′

end of the deoxynucleoside gap, wherein position 8, 9, or 10 of the modified oligonucleotide, as counted from the 5′

terminus of the modified oligonucleotide, aligns with the single nucleotide polymorphism, wherein the compound administered to the animal treats, ameliorates or slows the onset or progression Huntington'"'"'s Disease by selectively reducing the mutant huntingtin allele, and wherein the single nucleotide polymorphism site is rs362306, rs362331, rs2298969, rs7685686, rs4690072, rs2024115, or rs363088.

20. The method of claim 18, wherein the single nucleotide polymorphism is rs2298969, rs7685686, rs4690072, rs2024115, or rs363088.