METHODS FOR MODULATING C9ORF72 EXPRESSION

• US 20150267197A1
• Filed: 10/15/2013
• Published: 09/24/2015
• Est. Priority Date: 10/15/2012
• Status: Active Grant

• Current Assignee: Ionis Pharmaceuticals, Inc.
• Original Assignee: ISIS Pharmaceuticals Incorporated (Ionis Pharmaceuticals, Inc.), Ludwig Institute for Cancer Research, Ltd., Regents of the University of California (University of California)
• Inventors: Bennett, C. Frank, Freier, Susan M., Rigo, Frank, Cleveland, Don W., Lagier-Tourenne, Clotilde, Ravits, John M., Baughn, Michael W.
• Granted Patent: US 9,963,699 B2
• Time in Patent Office: Days
• US Class Current: 1/1
• 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 2310/14 interfering N.A.
• CPC Class Codes: C12N 2310/315 Phosphorothioates
• CPC Class Codes: C12N 2310/3181 Peptide nucleic acid, PNA
• 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 2310/3233 Morpholino-type ring
• CPC Class Codes: C12N 2310/3341 5-Methylcytosine
• CPC Class Codes: C12N 2310/341 Gapmers, i.e. of the type ===---===
• CPC Class Codes: C12N 2310/3525 MOE, methoxyethoxy

Abstract

Disclosed herein are methods for reducing expression of C90RF72 mRNA and protein in an animal with C90RF72 specific inhibitors. Such methods are useful to treat, prevent, or ameliorate neurodegenerative diseases in an individual in need thereof. Such C90RF72 specific inhibitors include antisense compounds. Examples of neurodegenerative diseases that can be treated, prevented, and ameliorated with the administration C90RF72 specific inhibitors include amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), corticalbasal degeneration syndrome (CBD), atypical Parkinsonian syndrome, and olivopontocerellar degeneration (OPCD).

Claims

1. A method comprising administering a C9ORF72 specific inhibitor or a C9ORF72 homolog specific inhibitor to an animal.

3. The method of claims 1-2, wherein the animal is a human.

4. The method of claims 1-3, wherein the C9ORF72 specific inhibitor is any of an antisense compound, an aptamer, an antibody, a peptide, or a small molecule.

5. The method of claim 4, wherein the antisense compound comprises a single-stranded antisense oligonucleotide complementary to a C9ORF72 nucleic acid.

6. The method of claim 5, wherein the C9ORF72 nucleic acid is a human C9ORF72 nucleic acid.

7. The method of claim 1, wherein the animal has a C9ORF72 associated disease.

46. The method of any preceding claim, wherein expression of C9ORF72 RNA is reduced.

47. The method of claim 46, wherein expression of C9ORF72 RNA is reduced in a nucleus.

48. The method of any preceding claim, wherein expression of C9ORF72 protein is reduced.

49. The method of claim 48, wherein expression of C9ORF72 protein is reduced in a nucleus.

50. The method of claims 46-49, wherein expression is reduced in any of fibroblasts, immortalized lymphoblasts, spinal motor neurons, purkinje and granular cells in the cerebellum, cortical neurons, astrocytes, or microglia.

51. The method of claims 46-47 and 50, wherein expression of C9ORF72 isoform V1 RNA is reduced.

52. The method of claims 48-50, wherein expression of C9ORF72 isoform V1 protein is reduced.

53. The method of claims 46-47 and 50, wherein expression of C9ORF72 isoform V2 RNA is reduced.

54. The method of claims 48-50, wherein expression of C9ORF72 isoform V2 protein is reduced.

55. The method of claims 46-47 and 50, wherein expression of C9ORF72 isoform V3 RNA is reduced.

56. The method of claims 48-50, wherein expression of C9ORF72 isoform V3 protein is reduced.

57. The method of claims 46-47 and 50, wherein expression of C9ORF72 isoform V2 RNA and expression of C9ORF72 isoform V3 RNA is reduced and C9ORF72 isoform V1 RNA is not reduced.

58. The method of claim 48-50, wherein expression of C9ORF72 isoform V2 protein and expression of C9ORF72 isoform V3 protein is reduced and C9ORF72 isoform V1 protein is not reduced.

59. The method of any preceding claim, wherein C9ORF72 RNA foci are reduced.

60. The method of claim 59, wherein C9ORF72 RNA foci are reduced in a nucleus.

61. The method of any preceding claim, wherein the administering is parenteral administration.

62. The method of claim 61, wherein the parenteral administration is any of injection or infusion.

63. The method of claims 61-62, wherein the parenteral administration is any of intrathecal administration or intracerebroventricular administration.

2. A method comprising:

identifying an animal having a C9ORF72 associated disease; and

administering a C9ORF72 specific inhibitor.

8. The method of claims 2-7, wherein the C9ORF72 associated disease is a C9ORF72 hexanucleotide repeat expansion associated disease.

9. The method of claims 2-7, wherein C9ORF72 associated disease is amyotrophic lateral sclerosis (ALS) or frontotemporal dementia (FTD).

10. The method of claim 8, wherein the C9ORF72 hexanucleotide repeat expansion associated disease is amyotrophic lateral sclerosis (ALS) or frontotemporal dementia (FTD).

11. The method of claims 9-10, wherein the amyotrophic lateral sclerosis (ALS) is familial ALS or sporadic ALS.

12. The method of claims 5-11, wherein the single-stranded antisense oligonucleotide comprises at least one modification.

13. The method of claims 5-12, wherein the single-stranded antisense oligonucleotide is specifically hybridizable to a human C9ORF72 nucleic acid.

14. The method of claims 5-13, wherein the single-stranded antisense oligonucleotide is at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% complementary to an equal length portion of a human C9ORF72 nucleic acid.

15. The method of claims 5-14, wherein the single-stranded antisense oligonucleotide is 100% complementary to an equal length portion of a human C9ORF72 nucleic acid.

16. The method of claims 12-15, wherein the single-stranded antisense oligonucleotide comprises at least one modified internucleoside linkage.

17. The method of claim 16, wherein each internucleoside linkage of the single-stranded antisense oligonucleotide is a modified internucleoside linkage.

18. The method of claims 16-17, wherein the modified internucleoside linkage is a phosphorothioate internucleoside linkage.

19. The method of claims 12-18, comprising at least one modified nucleoside.

20. The method of claims 12-19, wherein the single-stranded antisense oligonucleotide comprises at least one modified nucleoside having a modified sugar.

21. The method of claim 20, wherein the single-stranded antisense oligonucleotide comprises at least one modified nucleoside comprising a bicyclic sugar.

22. The method of claim 21, wherein the bicyclic sugar comprises a 4′

to 2′

bridge selected from among;

4′

-(CH₂)_n—

O-2′

bridge, wherein n is 1 or 2; and

4′

-CH₂—

O—

CH₂-2′

.

23. The method of claim 22, wherein the bicyclic sugar comprises a 4′

-CH(CH₃)—

O-2′

bridge.

24. The method of claim 20, wherein the at least one modified nucleoside having a modified sugar comprises a non-bicyclic 2′

-modified modified sugar moiety.

25. The method of claim 24, wherein the 2′

-modified sugar moiety comprises a 2′

-O-methoxyethyl group.

26. The method of claim 24, wherein the 2′

-modified sugar moiety comprises a 2′

-O-methyl group.

27. The method of claim 20, wherein the at least one modified nucleoside having a modified sugar comprises a sugar surrogate.

28. The method of claim 27, wherein the sugar surrogate is a morpholino.

29. The method of claim 27, wherein the sugar surrogate is a peptide nucleic acid.

30. The method of claims 19-29, wherein each nucleoside is modified.

31. The method of claims 5-30, wherein the single-stranded antisense oligonucleotide comprises at least one modified nucleobase.

32. The method of claim 31, wherein the modified nucleobase is a 5′

-methylcytosine.

33. The method of claim 12-32, wherein the single-stranded antisense oligonucleotide comprises:

a gap segment consisting of linked deoxynucleosides;

a 5′

wing segment consisting of linked nucleosides;

a 3′

wing segment consisting of linked nucleosides;

wherein the gap segment is positioned immediately adjacent to and between the 5′

wing segment and the 3′

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

34. The method of claim 33, wherein the single-stranded antisense oligonucleotide comprises:

a gap segment consisting of ten linked deoxynucleosides;

a 5′

wing segment consisting of five linked nucleosides;

a 3′

wing segment consisting of five linked nucleosides;

wherein the gap segment is positioned immediately adjacent and between the 5′

wing segment and the 3′

wing segment, wherein each nucleoside of each wing segment comprises a 2′

-O-methoxyethyl sugar; and

wherein each internucleoside linkage is a phosphorothioate linkage.

35. The method of claims 5-33, wherein the single-stranded antisense oligonucleotide consists of 15 linked nucleosides.

36. The method of claims 5-33, wherein the single-stranded antisense oligonucleotide consists of 16 linked nucleosides.

37. The method of claims 5-33, wherein the single-stranded antisense oligonucleotide consists of 17 linked nucleosides.

38. The method of claims 5-33, wherein the single-stranded antisense oligonucleotide consists of 18 linked nucleosides.

39. The method of claims 5-33, wherein the single-stranded antisense oligonucleotide consists of 19 linked nucleosides.

40. The method of claims 5-34, wherein the single-stranded antisense oligonucleotide consists of 20, 21, 22, 23, 24, or 25 linked nucleosides.

41. The method of claims 5-40, wherein the single-stranded antisense oligonucleotide complementary to a C9ORF72 nucleic acid is complementary to any of an intron, an exon, a splice junction, an exon:

exon junction, a repeat, the 3′

UTR, or the 5′

UTR of the C9ORF72 nucleic acid.

42. The method of claim 41, wherein the intron is any of introns 1, intron 2, intron 3, intron 4, intron 5, intron 6, intron 7, intron 8, intron 9, or intron 10.

43. The method of claim 41, wherein the exon is any of exon 1a, exon 1b, exon 1c, exon 1d, exon 1d, exon 2, exon 3, exon 4, exon 5, exon 6, exon 7, exon 8, exon 9, exon 10, or exon 11.

44. The method of claim 41, wherein the repeat is a hexanucleotide repeat.

45. The method of claim 44, wherein the hexanucleotide repeat is any of GGGGCC, GGGGGG, GGGGCG, or GGGGGC.

64. The method of claims 2-63, wherein at least one symptom of a C9ORF72 associated disease is ameliorated or prevented.

65. The method of claims 8-63, wherein at least one symptom of a C9ORF72 hexanucleotide repeat expansion associated disease is ameliorated or prevented.

66. The method of claims 2-63, wherein progression of at least one symptom of a C9ORF72 associated disease is slowed.

67. The method of claims 8-63, wherein progression of at least one symptom of a C9ORF72 hexanucleotide repeat expansion associated disease is slowed.

68. The method of claims 64-67, wherein the at least one symptom is any of motor function, respiration, muscle weakness, fasciculation and cramping of muscles, difficulty in projecting the voice, shortness of breath, difficulty in breathing and swallowing, inappropriate social behavior, lack of empathy, distractibility, changes in food preferences, agitation, blunted emotions, neglect of personal hygiene, repetitive or compulsive behavior, and decreased energy and motivation.