Compositions and methods for modulating Ataxin 3 expression

• US 10,533,175 B2
• Filed: 09/23/2016
• Issued: 01/14/2020
• Est. Priority Date: 09/25/2015
• Status: Active Grant

• Current Assignee: Ionis Pharmaceuticals, Inc.
• Original Assignee: Ionis Pharmaceuticals, Inc.
• Inventors: Rigo, Frank, Prakash, Thazha P., Van Roon-Mom, Wilhelmina Maria Clasina, Toonen, Lodewijk Julius Anton
• Primary Examiner(s): Vivlemore, Tracy
• Application Number:
  US15/761,964
• Publication Number:
  US 20180258425A1
• Time in Patent Office: 1,208 Days
• Field of Search: None
• CPC Class Codes: A61K 31/712 Nucleic acids or oligonucleotides having modified sugars, i.e. other than ribose or 2'-deoxyribose
• 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 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/3231 having an additional ring, e.g. LNA, ENA
• CPC Class Codes: C12N 2310/3341 5-Methylcytosine
• CPC Class Codes: C12N 2310/3525 MOE, methoxyethoxy
• CPC Class Codes: C12N 9/485 Exopeptidases (3.4.11-3.4.19)
• CPC Class Codes: C12Y 304/19012 Ubiquitinyl hydrolase 1 (3.4.19.12)

Abstract

Disclosed are methods for modulating splicing of Ataxin 3 mRNA in an animal with modified oligonucleotides. Such compounds and methods are useful to treat, prevent, or ameliorate spinocerebellar ataxia type 3 (SCA3) in an individual in need thereof.

Claims

1. An oligomeric compound comprising a modified oligonucleotide consisting of 15-25 linked nucleosides, wherein the oligonucleotide has a nucleobase sequence comprising at least 15, 16, 17, or 18 contiguous nucleobases of any one of SEQ ID NO:

9 or 10, wherein at least one nucleoside of the modified oligonucleotide comprises a modified sugar.

2. The oligomeric compound of claim 1, consisting of the modified oligonucleotide.

3. The oligomeric compound of claim 1, wherein the modified oligonucleotide is single-stranded.

4. The oligomeric compound of claim 1, wherein at least one internucleoside linkage of the modified oligonucleotide is a modified internucleoside linkage.

5. The oligomeric compound of claim 1, wherein each internucleoside linkage of the modified oligonucleotide is a modified internucleoside linkage.

6. The oligomeric compound of claim 4, wherein the modified internucleoside linkage is a phosphorothioate internucleoside linkage.

7. The oligomeric compound of claim 1, wherein at least one nucleobase of the modified oligonucleotide is a modified nucleobase.

8. The oligomeric compound of claim 7, wherein the modified nucleobase is a 5-methylcytosine.

9. The oligomeric compound of claim 1, wherein each nucleobase of each nucleoside of the modified oligonucleotide is either an unmodified nucleobase or is a 5-methylcytosine.

10. The oligomeric compound of claim 1, wherein at least one modified sugar is a bicyclic sugar.

11. The oligomeric compound of claim 10, wherein the bicyclic sugar comprises a chemical bridge between the 4′

and 2′

positions of the sugar, wherein the chemical bridge is selected from;

4′

-CH(R)—

O-2′ and

4′

-(CH₂)₂—

O-2′

, wherein R is independently H, C₁-C₆ alkyl, and C₁-C₆ alkoxy.

12. The oligomeric compound of claim 11, wherein the chemical bridge is 4′

-CH(R)—

O-2′ and

wherein R is H, methyl, or —

CH₂—

O—

CH₃.

13. The oligomeric compound of claim 1, wherein the modified sugar comprises a T-O-methoxyethyl group or a 2′

-O-methyl group.

14. The oligomeric compound of claim 1, wherein the modified sugar is a morpholino.

15. A composition comprising the oligomeric compound of claim 1, or a salt thereof, and a pharmaceutically acceptable carrier or diluent.

22. A method comprising administering to an animal having or at risk for developing SCA3 a therapeutically effective amount of an oligomeric compound of claim 1, wherein the administering reduces the number and/or volume of aggregates in brain tissue.

23. The method of claim 22, wherein the brain tissue is selected from the group consisting of brainstem, cerebellum, or cortex.

24. The oligomeric compound of claim 1, wherein each nucleoside of the modified oligonucleotide comprises a modified sugar.

25. The oligomeric compound of claim 24, wherein each nucleoside comprises a 2′

-O-methoxyethyl group.

26. The oligomeric compound of claim 24, wherein each nucleoside comprises a 2′

-O-methyl group.

27. The oligomeric compound of claim 1, wherein at least one nucleoside of the modified oligonucleotide is a 2′

-deoxynucleoside.

16. A method of modulating splicing of Ataxin-3 pre-mRNA in a cell comprising contacting a cell with an oligomeric compound wherein the oligomeric compound comprises a modified oligonucleotide consisting of 15-25 linked nucleosides and has a nucleobase sequence comprising at least 15, 16, 17, or 18 contiguous nucleobases of any one of SEQ ID NO:

9 or 10, wherein at least one nucleoside of the modified oligonucleotide comprises a modified sugar.

17. The method of claim 16, wherein each nucleoside of the modified oligonucleotide comprises a modified sugar.

18. The method of claim 16, wherein at least one nucleoside of the modified oligonucleotide is a 2′

-deoxynucleoside.

19. The method of claim 16, wherein the modified oligonucleotide comprises at least one nucleoside comprising a modified sugar selected from among:

2′

-O-methoxyethyl group, 2′

-O-methyl group, morpholino, and a bicyclic sugar.

20. The method of claim 16, wherein the cell is in vitro.

21. The method of claim 16, wherein the cell is in an animal.

28. An oligomeric compound comprising a modified oligonucleotide consisting of 18, 19, 20, 21, or 22 linked nucleosides, wherein the oligonucleotide has a nucleobase sequence comprising at least 18 contiguous nucleobases of any one of SEQ ID NO:

4 or 5, wherein each nucleoside of the modified oligonucleotide comprises a 2′

-O-methoxyethyl group.

29. The oligomeric compound of claim 28, consisting of the modified oligonucleotide.

30. The oligomeric compound of claim 28, wherein at least one internucleoside linkage of the modified oligonucleotide is a modified internucleoside linkage.

31. The oligomeric compound of claim 30, wherein the modified internucleoside linkage is a phosphorothioate internucleoside linkage.

32. The oligomeric compound of claim 28, wherein at least one nucleobase of the modified oligonucleotide is a modified nucleobase.

33. The oligomeric compound of claim 32, wherein the modified nucleobase is a 5-methylcytosine.

37. The oligomeric compound of claim 30, wherein the modified internucleoside linkage is a phosphorothioate internucleoside linkage.

34. An oligomeric compound comprising a modified oligonucleotide consisting of 18, 19, 20, or 21 linked nucleosides, wherein the oligonucleotide has a nucleobase sequence comprising at least 18 contiguous nucleobases of SEQ ID NO:

7, wherein each nucleoside of the modified oligonucleotide comprises a 2′

-O-methoxyethyl group.

35. The oligomeric compound of claim 34, consisting of the modified oligonucleotide.

36. The oligomeric compound of claim 34, wherein at least one internucleoside linkage of the modified oligonucleotide is a modified internucleoside linkage.

38. The oligomeric compound of claim 34, wherein at least one nucleobase of the modified oligonucleotide is a modified nucleobase.

39. The oligomeric compound of claim 38, wherein the modified nucleobase is a 5-methylcytosine.

40. An oligomeric compound comprising a modified oligonucleotide consisting of 18, 19, or 20 linked nucleosides, wherein the oligonucleotide has a nucleobase sequence comprising at least 18 contiguous nucleobases of SEQ ID NO:

8, wherein at least one nucleoside of the modified oligonucleotide comprises a modified sugar.

41. The oligomeric compound of claim 40, consisting of the modified oligonucleotide.

42. The oligomeric compound of claim 40, wherein at least one internucleoside linkage of the modified oligonucleotide is a modified internucleoside linkage.

43. The oligomeric compound of claim 42, wherein the modified internucleoside linkage is a phosphorothioate internucleoside linkage.

44. The oligomeric compound of claim 40, wherein at least one nucleobase of the modified oligonucleotide is a modified nucleobase.

45. The oligomeric compound of claim 44, wherein the modified nucleobase is a 5-methylcytosine.

46. The oligomeric compound of claim 40, wherein at least one modified sugar is a bicyclic sugar.

47. The oligomeric compound of claim 46, wherein the bicyclic sugar comprises a chemical bridge between the 4′

and 2′

positions of the sugar, wherein the chemical bridge is selected from;

4′

-CH(R)—

O-2′ and

4′

-(CH₂)₂-O-2′

, wherein R is independently H, C₁-C₆ alkyl, and C₁-C₆ alkoxy.

48. The oligomeric compound of claim 47, wherein the chemical bridge is 4′

-CH(R)—

O-2′ and

wherein R is H, methyl, or —

CH₂—

O—

CH₃.

49. The oligomeric compound of claim 40, wherein the modified sugar comprises a 2′

-O-methoxyethyl group or a 2′

-O-methyl group.

50. The oligomeric compound of claim 40, wherein the modified sugar is a morpholino.

51. The oligomeric compound of claim 40, wherein each nucleoside of the modified oligonucleotide comprises a modified sugar.

52. The oligomeric compound of claim 51, wherein each nucleoside comprises a 2′

-O-methoxyethyl group.

53. The oligomeric compound of claim 51, wherein each nucleoside comprises a 2′

-O-methyl group.

54. The oligomeric compound of claim 40, wherein at least one nucleoside of the modified oligonucleotide is a 2′

-deoxynucleoside.