COMPOSITIONS FOR MODULATING C9ORF72 EXPRESSION

• US 20160251655A1
• Filed: 10/11/2014
• Published: 09/01/2016
• Est. Priority Date: 10/11/2013
• Status: Active Grant

• Current Assignee: Ionis Pharmaceuticals, Inc.
• Original Assignee: Ionis Pharmaceuticals, Inc.
• Inventors: Singh, Priyam, Freier, Susan M., Rigo, Frank
• Granted Patent: US 10,221,414 B2
• Time in Patent Office: Days
• US Class Current: 1/1
• CPC Class Codes: A61P 25/00 Drugs for disorders of the nervous system
• CPC Class Codes: A61P 25/16 Anti-Parkinson drugs
• 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 2310/315 Phosphorothioates
• 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 2310/341 Gapmers, i.e. of the type ===---===
• CPC Class Codes: C12N 2310/343 having patterns, e.g. ==--==--==--
• CPC Class Codes: G01N 33/6896 Neurological disorders, e.g. Alzheimer's disease

Abstract

Disclosed herein are compositions and methods for reducing expression of C90RF72 mRNA and protein in an animal with C90RF72 specific inhibitors. Also disclosed herein are compositions and methods of selectively inhibiting a C90RF72 pathogenic associated mRNA variant by administering an antisense compound targeting the region beginning at the start site of exon 1A to the start site of exon 1B of a C90RF72 pre-mRNA. Such methods are useful to treat, prevent, or ameliorate neurodegenerative diseases in an individual in need thereof. Such C90RF72 specific inhibitors include antisense compounds.

Claims

1. A compound, comprising a modified oligonucleotide consisting of 12 to 30 linked nucleosides and having a nucleobase sequence comprising at least 8, 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, or at least 20 consecutive nucleobases of any of the nucleobase sequences of SEQ ID NOs:

20-401 and 441-1545.

14. The compound of any preceding claim, consisting of a single-stranded modified oligonucleotide.

15. The compound of any preceding claim, wherein at least one internucleoside linkage is a modified internucleoside linkage.

18. The compound of any preceding claim, wherein at least one internucleoside linkage is a phosphodiester internucleoside linkage.

19. The compound of any preceding claim, wherein at least one internucleoside linkage is a phosphorothioate linkage and at least one internucleoside linkage is a phosphodiester linkage.

20. The compound of any preceding claim, wherein at least one nucleoside comprises a modified nucleobase.

22. The compound of any preceding claim, wherein at least one nucleoside of the modified oligonucleotide comprises a modified sugar.

23. The compound of claim 15, wherein the at least one modified sugar is a bicyclic sugar.

26. The compound of claim 15, wherein at least one modified sugar comprises a 2′

-O-methoxyethyl group.

27. The compound of claim 15, wherein the modified sugar comprises a 2′

-O(CH₂)₂—

OCH₃ group.

28. The compound of any preceding claim, wherein the modified oligonucleotide comprises:

a gap segment consisting of 10 linked deoxynucleosides;

a 5′

wing segment consisting of 5 linked nucleosides; and

a 3′

wing segment consisting of 5 linked nucleosides;

wherein the gap segment is positioned between the 5′

wing segment and the 3′

wing segment and wherein each nucleoside of each wing segment comprises a modified sugar.

29. The compound of any preceding claim, wherein the modified oligonucleotide comprises:

a gap segment consisting of 8 linked deoxynucleosides;

a 5′

wing segment consisting of 5 linked nucleosides; and

a 3′

wing segment consisting of 5 linked nucleosides;

wherein the gap segment is positioned between the 5′

wing segment and the 3′

wing segment and wherein each nucleoside of each wing segment comprises a modified sugar.

32. The compound of any preceding claim, wherein the modified oligonucleotide consists of 20 linked nucleosides.

33. The compound of any preceding claim, wherein the modified oligonucleotide consists of 19 linked nucleosides.

34. The compound of any preceding claim, wherein the modified oligonucleotide consists of 18 linked nucleosides.

35. The compound of any preceding claim, wherein the modified oligonucleotide consists of 17 linked nucleosides.

36. A composition comprising the compound of any preceding claim or salt thereof and at least one of a pharmaceutically acceptable carrier or diluent.

37. A method comprising administering to an animal the compound or composition of any preceding claim.

38. The method of claim 37, wherein the animal is a human.

39. The method of claim 38, wherein administering the compound prevents, treats, ameliorates, or slows progression of a C9ORF72 associated disease, disorder or condition.

40. The method of claim 38, wherein administering the compound prevents, treats, ameliorates, or slows progression of a C9ORF72 hexanucleotide repeat expansion associated disease, disorder or condition.

41. The method of claim 39 or 40, wherein the disease, disorder or condition is amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), corticalbasal degeneration syndrome (CBD), atypical Parkinsonian syndrome, and olivopontocerellar degeneration (OPCD).

42. The method of claim 37, wherein the administering reduces nuclear foci.

43. The method of claim 37, wherein the administering reduces expression of C9ORF72 associated RAN translation products.

44. The method claim 43, wherein the C9ORF72 associated RAN translation products are any of poly-(glycine-proline), poly-(glycine-alanine), and poly-(glycine-arginine).

45. Use of the compound or composition of any preceding claim for the manufacture of a medicament for treating a neurodegenerative disorder.

2. A compound, comprising a modified oligonucleotide consisting of 12 to 30 linked nucleosides and comprising a nucleobase sequence comprising at least 8, 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, or at least 20 consecutive nucleobases complementary to an equal length portion of nucleobases 1107-1520 of SEQ ID NO:

2.

13. The compound of claims 2-5, wherein the nucleobase sequence of the modified oligonucleotide is at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% complementary to SEQ ID NO:

1.

21. The compound of claim 13, wherein the modified nucleobase is a 5-methylcytosine.

3. A compound, comprising a modified oligonucleotide consisting of 12 to 30 linked nucleosides and comprising a nucleobase sequence comprising at least 8, 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, or at least 20 consecutive nucleobases complementary to an equal length portion of nucleobases 1111-1200 of SEQ ID NO:

2.

4. A compound, comprising a modified oligonucleotide consisting of 12 to 30 linked nucleosides and comprising a nucleobase sequence comprising at least 8, 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, or at least 20 consecutive nucleobases complementary to an equal length portion of nucleobases 1211-1318 of SEQ ID NO:

2.

5. A compound, comprising a modified oligonucleotide consisting of 12 to 30 linked nucleosides and comprising a nucleobase sequence comprising at least 8, 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, or at least 20 consecutive nucleobases complementary to an equal length portion of nucleobases 1326-1540 of SEQ ID NO:

2.

6. A compound, comprising a modified oligonucleotide consisting of 12 to 30 linked nucleosides and comprising a nucleobase sequence comprising at least 8, 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, or at least 20 consecutive nucleobases complementary to an equal length portion of nucleobases 1331-1375 of SEQ ID NO:

2.

7. A compound, comprising a modified oligonucleotide consisting of 12 to 30 linked nucleosides and comprising a nucleobase sequence comprising at least 8, 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, or at least 20 consecutive nucleobases complementary to an equal length portion of nucleobases 1368-1391 of SEQ ID NO:

2.

8. A compound, comprising a modified oligonucleotide consisting of 12 to 30 linked nucleosides and comprising a nucleobase sequence comprising at least 8, 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, or at least 20 consecutive nucleobases complementary to an equal length portion of nucleobases 1398-1424 of SEQ ID NO:

2.

16. The compound of claim 8, wherein at least one modified internucleoside linkage is a phosphorothioate internucleoside linkage.

17. The compound of claim 8, wherein each modified internucleoside linkage is a phosphorothioate internucleoside linkage.

24. The compound of claim 16, wherein the bicyclic sugar comprises a chemical link between the 2′

and 4′

position of the sugar 4′

-CH2-N(R)—

O-2′

bridge wherein R is, independently, H, C1-C12 alkyl, or a protecting group.

25. The compound of claim 16, wherein the bicyclic sugar comprises a 4′

-CH2-N(R)—

O-2′

bridge wherein R is, independently, H, C1-C12 alkyl, or a protecting group.

9. A compound, comprising a modified oligonucleotide consisting of 12 to 30 linked nucleosides and comprising a nucleobase sequence comprising at least 8, 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, or at least 20 consecutive nucleobases complementary to an equal length portion of nucleobases 1411-1440 of SEQ ID NO:

2.

10. A compound, comprising a modified oligonucleotide consisting of 12 to 30 linked nucleosides and comprising a nucleobase sequence comprising at least 8, 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, or at least 20 consecutive nucleobases complementary to an equal length portion of nucleobases 1429-1481 of SEQ ID NO:

2.

11. A compound, comprising a modified oligonucleotide consisting of 12 to 30 linked nucleosides and comprising a nucleobase sequence comprising at least 8, 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, or at least 20 consecutive nucleobases complementary to an equal length portion of nucleobases 1502-1539 of SEQ ID NO:

2.

12. A compound, comprising a modified oligonucleotide consisting of 12 to 30 linked nucleosides and comprising a nucleobase sequence comprising at least 8, 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, or at least 20 consecutive nucleobases complementary to an equal length portion of nucleobases 1508-1539 of SEQ ID NO:

2.

30. The compound of any preceeding claim, wherein the modified oligonucleotide comprises sugar modifications in any of the following patterns:

eeekkdddddddkkeee, eekkddddddddkkeee, ekddddddddekekeee, kekeddddddddekeke, and ekekddddddddkekee;

wherein,

e=a 2′

-O-methoxyethyl modified nucleoside

d=a 2′

-deoxynucleoside, and

k=a cEt nucleoside.

31. The compound of any preceeding claim, wherein the modified oligonucleotide comprises internucleoside linkages in any of the following patterns:

soooossssssssssooss, sooosssssssssooss, soosssssssssooss, and sosssssssssoooss;

wherein,

s=a phosphorothioate linkage, and

o=a phosphodiester linkage.

46. A method of selectively inhibiting a C9ORF72 pathogenic associated mRNA variant by administering an antisense compound targeting the region beginning at the start site of exon 1A to the start site of exon 1B of a C9ORF72 pre-mRNA.