METHODS AND COMPOUNDS USEFUL IN CONDITIONS RELATED TO REPEAT EXPANSION

• US 20160159846A1
• Filed: 07/31/2014
• Published: 06/09/2016
• Est. Priority Date: 07/31/2013
• Status: Active Grant

• Current Assignee: Board of Regents of the University of Texas System (University of Texas System)
• Original Assignee: ISIS Pharmaceuticals Incorporated, Board of Regents of the University of Texas System (University of Texas System)
• Inventors: Prakash, Thazha P., Hu, Jiaxin, Liu, Jing, Yu, Dongbo, Corey, David, Swayze, Eric E.
• Granted Patent: US 10,435,430 B2
• Time in Patent Office: Days
• CPC Class Codes: C07H 21/02 with ribosyl as saccharide radical
• 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 2310/32 of the sugar
• CPC Class Codes: C12N 2320/34 Allele or polymorphism specific uses

Abstract

Described are compounds and methods useful for the treatment and investigation of diseases and disorders associated with expanded repeat-containing RNA molecules. In certain embodiments, compounds and methods useful for the modulation of ATXN-3 pre-mRNA are described. In certain embodiments, compounds and methods useful for the modulation of ATN-1 mRNA are described.

Claims

1. A compound comprising a single-stranded oligonucleotide consisting of 13 to 30 linked nucleosides and having a nucleobase sequence complementary to a repeat region of an expanded repeat-containing target RNA, wherein the 5′

-terminal nucleoside of the single-stranded oligonucleotide comprises a phosphate moiety and an internucleoside linking group linking the 5′

-terminal nucleoside to the remainder of the oligonucleotide.

2. The compound of claim 1, wherein the 5′

-terminal nucleoside of the single-stranded oligonucleotide has Formula I;

3. The compound of claim 2, wherein M₃ is selected from among:

O, CH═

CH, OCH₂, and OC(H)(Bx₂).

4. The compound of claim 2, wherein M₃ is O.

5. The compound of any of claims 2-4, wherein each of J₄, J₅, J₆ and J₇ is H.

6. The compound of any of claims 2-5, wherein J₄ forms a bridge with either J₅ or J₇.

7. The compound of any of claims 2-6, wherein A has the formula:

8. The compound of claim 7, wherein each of Q₁ and Q₂ is H.

9. The compound of claim 7, wherein Q₁ and Q₂ are each independently selected from among:

H and a halogen.

10. The compound of claim 7, wherein one of Q₁ and Q₂ is H and the other of Q₁ and Q₂ is F, CH₃ or OCH₃.

11. The compound of any of claims 2 to 10, wherein T₁ has the formula:

12. The compound of claim 11, wherein R_b is O and R_a and R_c are each, independently selected from among:

OCH₃, OCH₂CH₃, OCH(CH₃)₂.

13. The compound of any of claims 2 to 12, wherein G is selected from among:

a halogen, OCH₃, OCH₂F, OCHF₂, OCF₃, OCH₂CH₃, O(CH₂)₂F, OCH₂CHF₂, OCH₂CF₃, OCH₂—

CH═

CH₂, O(CH₂)₂—

OCH₃, O(CH₂)₂—

SCH₃, O(CH₂)₂—

OCF₃, O(CH₂)₃—

N(R₁₀)(R₁₁), O(CH₂)₂—

ON(R₁₀)(R₁₁), O(CH₂)₂—

O(CH₂)₂—

N(R₁₀)(R₁₁), OCH₂C(═

O)—

N(R₁₀)(R₁₁), OCH₂C(═

O)—

N(R₁₂)—

(CH₂)₂—

N(R₁₀)(R₁₁), and O(CH₂)₂—

N(R₁₂)—

C(═

NR₁₃)[N(R₁₀)(R₁₁)];

wherein R₁₀, R₁₁, R₁₂ and R₁₃ are each, independently, H or C₁-C₆ alkyl.

14. The compound of any of claims 2-13, wherein G is selected from among:

a halogen, OCH₃, OCF₃, OCH₂CH₃, OCH₂CF₃, OCH₂—

CH—

CH₂, O(CH₂)₂—

OCH₃, O(CH₂)₂—

O(CH₂)₂—

N(CH₃)₂, OCH₂C(═

O)—

N(H)CH₃, OCH₂C(═

O)—

N(H)—

(CH₂)₂—

N(CH₃)₂, and OCH₂—

N(H)—

C(═

NH)NH₂.

15. The compound of any of claims 2-14, wherein G is selected from among:

F, OCH₃, and O(CH₂)₂—

OCH₃.

16. The compound of claim 15, wherein G is O(CH₂)₂—

OCH₃.

17. The compound of any of claims 2-13, wherein G is a conjugate group.

18. The compound of claim 17, wherein the conjugate of the conjugate group is selected from among:

an intercalator, a polyamine, a polyamide, a polyethylene glycol, a thioether, a polyether, a cholesterol, a thiocholesterol, a cholic acid moiety, a folate, a lipid, a phospholipid, biotin, phenazine, phenanthridine, anthraquinone, adamantane, acridine, a fluorescein, a rhodamine, and a coumarin.

19. The compound of claim 17 or 18, wherein the conjugate of the conjugate group is selected from among:

cholesterol, palmityl, stearoyl, lithocholic-oleyl, C₂₂ alkyl, C₂₀ alkyl, C₁₆ alkyl, C₁₈ alkyl, and C₁₀ alkyl.

20. The compound of any of claims 17-19, wherein the conjugate group comprises a linker.

21. The compound of claim 20, wherein the linker is selected from among:

hexanamide, 8-amino-3,6-dioxaoctanoic acid (ADO), succinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SMCC), 6-aminohexanoic acid (AHEX or AHA), substituted C₁-C₁₀ alkyl, substituted or unsubstituted C₂-C₁₀ alkenyl, and substituted or unsubstituted C₂-C₁₀ alkynyl.

22. The compound of any of claims 2-21, wherein the nucleobase is a modified nucleobase.

23. The compound of any of claims 2-22, wherein the nucleobase is a pyrimidine, substituted pyrimidine, purine or substituted purine.

24. The compound of any of claims 2-23, wherein the nucleobase is uracil, thymine, cytosine, 5-methylcytosine, adenine or guanine.

25. The compound of any of claims 2-24, wherein the 5′

-terminal nucleoside of the single-stranded oligonucleotide has Formula III;

26. The compound of claim 25, wherein A has the formula:

27. The compound of claim 26, wherein Q₁ and Q₂ are each independently selected from among:

H, F, CH₃, and OCH₃.

28. The compound of any of claims 2-27, wherein the 5′

-terminal nucleoside has Formula V;

29. The compound of any of claims 1-28, wherein the remainder of the oligonucleotide comprises at least one RNA or RNA-like nucleoside.

30. The compound of claim 29, wherein essentially each nucleoside of the remainder of the oligonucleotide is an RNA-like nucleoside.

31. The compound of claim 30, wherein each nucleoside of the remainder of the oligonucleotide is an RNA or RNA-like nucleoside.

32. The compound of any of claims 29-31, wherein each RNA-like nucleoside is independently selected from among:

a 2′

-endo furanosyl nucleoside and an RNA-surrogate nucleoside.

33. The compound of claim 32, wherein each RNA-like nucleoside is a 2′

-endo furanosyl nucleoside.

34. The compound of claim 33, wherein each RNA-like nucleoside is selected from among:

2′

-F, 2′

-MOE, 2′

-OMe, LNA, F-HNA, and cEt.

35. The compound of any of claims 1-34, wherein the remainder of the oligonucleotide comprises at least one region having sugar motif:

-[(A)_x-(B)_y-(A)_z]_q-

wherein

A is a modified nucleoside of a first type,

B is a modified nucleoside of a second type;

each x and each y is independently 1 or 2;

z is 0 or 1;

q is 1-15;

36. The compound of claim 35, wherein the modifications of the first type and the modifications of the second type are selected from among:

2′

-F, 2′

-OMe, and F-HNA.

37. The compound of claim 35, wherein the modifications of the first type are 2′

-F and the modifications of the second type are 2′

-OMe.

38. The compound of claim 35, wherein the modifications of the first type are 2′

-OMe and the modifications of the second type are 2′

-F.

39. The compound of any of claims 35-38, wherein each x and each y is 1.

40. The compound of any of claims 1-39, wherein the remainder of the oligonucleotide comprises 1-4 3′

terminal nucleosides, each comprising the same sugar modification, wherein the sugar modification of the 1-4 3′

terminal nucleosides is different from the sugar modification of the immediately adjacent nucleoside.

41. The compound of claim 40, wherein the 3′

-terminal nucleosides are each 2′

-MOE nucleosides.

42. The compound of claim 40 or 41 comprising two 3′

-terminal nucleosides.

43. The compound of any of claims 1-42, comprising at least one modified internucleoside linkage.

44. The compound of claim 43, wherein each internucleoside linkage is selected from phosphorothioate and phosphodiester.

45. The compound of claim 43 or 44, wherein each of the 6-10 3′

-most internucleoside linkages is phosphorothioate linkage.

46. The compound of any of claims 43-45, wherein the 5′

-most internucleoside linkage is a phosphorothioate linkage.

47. The compound of any of claims 43-46, comprising a region of alternating linkages.

48. The compound of any of claims 1-47, comprising a 5′

region having the motif;

(Nucleoside of Formula I, III, or V)-s-(A-s-B-o-A)_x(-s-B)_Y

wherein;

A is a nucleoside of a first type;

B is a nucleoside of a second type;

s is a phosphorothioate linkage;

o is a phosphodiester linkage;

X is 1-8; and

Y is 1 or O.

49. The compound of any of claims 1-48, comprising a 3′

region having the motif;

-(A-s-B-s-A)_z(-s-B)_q-s-(D)-(s-D)_r

wherein;

s is a phosphorothioate linkage;

A is a nucleoside of a first type;

B is a nucleoside of a second type;

D is a nucleoside of a third type;

Z is 1-5;

q is 1 or 0; and

and r is 0-3.

50. The compound claim 48 or 49, wherein A is a 2′

-F nucleoside.

51. The compound of any of claims 48-50, wherein B is a 2′

-OMe nucleoside.

52. The compound of any of claims 49-51, wherein D is a 2′

-MOE nucleoside.

53. The compound of any of claims 49-52, wherein the oligonucleotide comprises a hybridizing region and a 3′

-terminal region, wherein the hybridizing region comprises nucleosides A and B and the terminal region comprising nucleosides D, wherein the hybridizing region is complementary to the repeat region of the expanded repeat-containing target RNA.

54. The compound of any of claims 1-48, comprising the motif:

(Nucleoside of Formula V)-s-A-s-B-o-A-s-B-o-A-s-B-o-A-s-B-o-A-s-B-o-A-s-B-o-A-s-B-s-A-s-B-s-A-s-B-s-D- s-D-s

wherein;

s is a phosphorothioate linkage;

A is a nucleoside of a first type;

B is a nucleoside of a second type; and

D is a nucleoside of a third type.

55. The compound of any of claims 1-48, consisting of the motif:

(Nucleoside of Formula V)-s-A-s-B-o-A-s-B-o-A-s-B-o-A-s-B-o-A-s-B-o-A-s-B-o-A-s-B-s-A-s-B-s-A-s-B-s-D- s-D-s

wherein;

s is a phosphorothioate linkage;

A is a nucleoside of a first type;

B is a nucleoside of a second type; and

D is a nucleoside of a third type.

56. The compound of any of claims 1-48, consisting of the motif:

(Nucleoside of Formula V)-s-C-o-C-o-C-o-B-o-A-s-B-o-A-s-B-o-A-s-B-o-A-s-B-o-A-s-B-s-A-s-B-s-A-s-B-s-D- s-D-s

wherein;

s is a phosphorothioate linkage;

A is a nucleoside of a first type;

B is a nucleoside of a second type; and

D is a nucleoside of a third type.

57. The compound of any of claims 1-48, consisting of the motif:

(Nucleoside of Formula V)-s-A-o-B-o-A-o-C-o-C-o-C-o-A-s-B-o-A-s-B-o-A-s-B-o-A-s-B-s-A-s-B-s-A-s-B-s-D- s-D-s

wherein;

s is a phosphorothioate linkage;

A is a nucleoside of a first type;

B is a nucleoside of a second type; and

D is a nucleoside of a third type.

58. The compound of any of claims 1-48, consisting of the motif:

(Nucleoside of Formula V)-s-A-s-B-o-A-s-B-o-A-s-B-o-C-o-C-o-C-o-B-o-A-s-B-o-A-s-B-s-A-s-B-s-A-s-B-s-D- s-D-s

wherein;

s is a phosphorothioate linkage;

A is a nucleoside of a first type;

B is a nucleoside of a second type; and

D is a nucleoside of a third type.

59. The compound of any of claims 1-48, consisting of the motif:

(Nucleoside of Formula V)-s-C-o-C-o-C-o-C-o-C-o-C-o-C-o-C-o-C-o-B-o-A-s-B-o-A-s-B-s-A-s-B-s-A-s-B-s-D- s-D-s

wherein;

s is a phosphorothioate linkage;

A is a nucleoside of a first type;

B is a nucleoside of a second type; and

D is a nucleoside of a third type.

60. The compound of claims 54 to 59, wherein A is a 2′

-F nucleoside.

61. The compound of any of claims 54-60, wherein B is a 2′

-OMe nucleoside.

62. The compound of any of claims 54-61, wherein D is a 2′

-MOE nucleoside.

63. The compound of any of claims 54-61, wherein C is a ribonucleoside.

64. The compound of any of claims 1-63, wherein the remainder of the oligonucleotide comprises at least one conjugate group.

65. The compound of claim 64, wherein the conjugate of the conjugate group is selected from among:

an intercalator, a polyamine, a polyamide, a polyethylene glycol, a thioether, a polyether, a cholesterol, a thiocholesterol, a cholic acid moiety, a folate, a lipid, a phospholipid, biotin, phenazine, phenanthridine, anthraquinone, adamantane, acridine, a fluorescein, a rhodamine, and a coumarin.

66. The compound of claim 64 or 65, wherein the conjugate of the conjugate group is selected from among:

cholesterol, palmityl, stearoyl, lithocholic-oleyl, C₂₂ alkyl, C₂₀ alkyl, C₁₆ alkyl, C₁₈ alkyl, and C₁₀ alkyl.

67. The compound of any of claims 64-66, wherein the conjugate group comprises a linker.

68. The compound of claim 67, wherein the linker is selected from among:

hexanamide, 8-amino-3,6-dioxaoctanoic acid (ADO), succinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SMCC), 6-aminohexanoic acid (AHEX or AHA), substituted C₁-C₁₀ alkyl, substituted or unsubstituted C₂-C₁₀ alkenyl, and substituted or unsubstituted C₂-C₁₀ alkynyl.

69. The compound of any of claims 1-68, wherein the oligonucleotide is 100% complementary to the repeat region of the expanded repeat-containing target RNA.

70. The compound of any of claims 1-68, wherein the oligonucleotide has one mismatch relative to the repeat region of the expanded repeat-containing target RNA.

71. The compound of any of claims 1-68, wherein the oligonucleotide has two mismatches relative to the repeat region of the expanded repeat-containing target RNA.

72. The compound of any of claims 1-68, wherein the oligonucleotide has three mismatches relative to the repeat region of the expanded repeat-containing target RNA.

73. The compound of any of claims 1-68, wherein the oligonucleotide has four mismatches relative to the repeat region of the expanded repeat-containing target RNA.

74. The compound of any of claims 1-68, wherein the oligonucleotide has five mismatches relative to the repeat region of the expanded repeat-containing target RNA.

75. The compound of any of claims 1-74, wherein the oligonucleotide comprises a hybridizing region and 0-4 3′

-terminal nucleosides.

76. The compound of any of claims 1-74, wherein the oligonucleotide comprises a hybridizing region and 1-4 3′

-terminal nucleosides.

77. The compound of claim 75 or 76, wherein the hybridizing region is 100% complementary to the repeat region of the expanded repeat-containing target RNA.

78. The compound of claim 75 or 76, wherein the hybridizing region has one mismatch relative to the repeat region of the expanded repeat-containing target RNA.

79. The compound of claim 75 or 76, wherein the hybridizing region has two mismatches relative to the repeat region of the expanded repeat-containing target RNA.

80. The compound of claim 75 or 76 wherein the hybridizing region has three mismatches relative to the repeat region of the expanded repeat-containing target RNA.

81. The compound of claim 75 or 76 wherein the hybridizing region has four mismatches relative to the repeat region of the expanded repeat-containing target RNA.

82. The compound of claim 75 or 76 wherein the hybridizing region has five mismatches relative to the repeat region of the expanded repeat-containing target RNA.

83. The compound of any of claims 70-82, having a mismatch at the eighth nucleobase from the 5′

-end of the hybridizing region.

84. The compound of any of claims 70-83, having a mismatch at the ninth nucleobase from the 5′

-end of the hybridizing region.

85. The compound of any of claims 70-84, having a mismatch at the tenth nucleobase from the 5′

-end of the hybridizing region.

86. The compound of any of claims 70-85, having a mismatch at the ninth nucleobase from the 3′

-end of the hybridizing region.

87. The compound of any of claims 70-86, having a mismatch at the tenth nucleobase from the 3′

-end of the hybridizing region.

88. The compound of any of claims 70-87, having a mismatch at the eleventh nucleobase from the 3′

-end of the hybridizing region.

89. The compound of any of claims 1-68, wherein the oligonucleotide comprises a hybridizing region having two or more mismatches relative to the repeat region of the expanded repeat-containing target RNA, and wherein each of the mismatches is adjacent to one another.

90. The compound of any of claims 1-68, wherein the oligonucleotide comprises a hybridizing region having three or more mismatches relative to the repeat region of the expanded repeat-containing target RNA, and wherein each of the mismatches is adjacent to one another.

91. The compound of any of claims 1-68, wherein the oligonucleotide comprises a hybridizing region having two mismatches relative to the repeat region of the expanded repeat-containing target RNA, and wherein each of the mismatches is adjacent to one another.

92. The compound of claim 86, wherein the mismatches are located at the 9^th and 10^th nucleobases from the 5′

-terminal nucleoside of the compound.

93. The compound of claim 86, wherein the mismatches are located at the 10^th and 11^th nucleobases from the 5′

-terminal nucleoside of the compound.

94. The compound of claim 86, wherein the mismatches are located at the 8^th and 9^th nucleobases from the 5′

-terminal nucleoside of the compound.

95. The compound of any of claims 1-68, wherein the oligonucleotide comprises a hybridizing region having three mismatches relative to the repeat region of the expanded repeat-containing target RNA, and wherein each of the mismatches is adjacent to one another.

96. The compound of claim 95, wherein the mismatches are located at the 9^th, 10^th, and 11^th nucleobases from the 5′

-terminal nucleoside of the compound.

97. The compound of claim 95, wherein the mismatches are located at the 10^th, 11^th and 12^th nucleobases from the 5′

-terminal nucleoside of the compound.

98. The compound of claim 95, wherein the mismatches are located at the 8^th, 9^th, and 10^th nucleobases from the 5′

-terminal nucleoside of the compound.

99. The compound of any of claims 1-68, wherein the oligonucleotide comprises a hybridizing region having four mismatches relative to the repeat region of the expanded repeat-containing target RNA, and wherein each of the mismatches is adjacent to one another.

100. The compound of claim 99, wherein the mismatches are located at the 8^th, 9^th, 10^th, and 11^th nucleobases from the 5′

-terminal nucleoside of the compound.

101. The compound of claim 99, wherein the mismatches are located at the 9^th, 10^th, 11^th and 12^th nucleobases from the 5′

-terminal nucleoside of the compound.

102. The compound of claim 99, wherein the mismatches are located at the 7^th, 8^th, 9^th, and 10^th nucleobases from the 5′

-terminal nucleoside of the compound.

103. The compound of any of claims 1-68, having a mismatch at ninth and 10^th nucleobase from the 5′

-terminal nucleoside of the compound.

104. The compound of any of claims 1-68, having a mismatch at ninth and 11^th nucleobase from the 5′

-terminal nucleoside of the compound.

105. The compound of any of claims 1-68, having a mismatch at ninth and 12^th nucleobase from the 5′

-terminal nucleoside of the compound.

106. The compound of any of claims 1-68, having a mismatch at ninth and 13^th nucleobase from the 5′

-terminal nucleoside of the compound.

107. The compound of any of claims 1-68, having a mismatch at ninth and 14^th nucleobase from the 5′

-terminal nucleoside of the compound.

108. The compound of any of claims 1-68, having a mismatch at ninth and 15^th nucleobase from the 5′

-terminal nucleoside of the compound.

109. The compound of any of claims 1-68, having a mismatch at ninth and 16^th nucleobase from the 5′

-terminal nucleoside of the compound.

110. The compound of any of claims 1-68, having a mismatch at ninth and 17^th nucleobase from the 5′

-terminal nucleoside of the compound.

111. The compound of any of claims 1-68, having a mismatch at ninth and 18^th nucleobase from the 5′

-terminal nucleoside of the compound.

112. The compound of any of claims 1-68, having a mismatch at ninth, 10^th, and 11^th nucleobase from the 5′

-terminal nucleoside of the compound.

113. The compound of any of claims 1-68, having a mismatch at 8^th, 9th, 10^th, and 11^th nucleobase from the 5′

-terminal nucleoside of the compound.

114. The compound of any of claims 1-68, having a mismatch at 4th, 10^th, and 11^th nucleobase from the 5′

-terminal nucleoside of the compound.

115. The compound of any of claims 1-68, having a mismatch at 3rd, 8^th, 13^th, and 17^th nucleobase from the 5′

-terminal nucleoside of the compound.

116. The compound of any of claims 69-115, wherein one or more of the 3′

-terminal nucleosides is not complementary to the target RNA.

117. The compound of any of claims 69-116, wherein the nucleobase of each 3′

-terminal nucleoside is a purine.

118. The compound of claim 117, wherein the nucleobase of each 3′

-terminal nucleoside is an adenine.

119. The compound of any of claims 1-118, wherein the repeat region of the expanded repeat-containing RNA consists of a repeating triplet.

120. The compound of claim 119, wherein the repeating triplet is CAG.

121. The compound of claim 119, wherein the repeating triplet is CUG.

122. The compound of any of claims 1-121 wherein the expanded repeat-containing RNA is associated with spinocerebellar ataxia.

123. The compound of any of claims 1-121 wherein the expanded repeat-containing RNA is associated with spinocerebellar ataxia 3.

124. The compound of any of claims 1-121 wherein the expanded repeat-containing RNA is associated with spinocerebellar ataxia 10.

125. The compound of any of claims 1-121 wherein the expanded repeat-containing RNA is associated with Dentatorubral-pallidoluysian atrophy.

126. The compound of any of claims 1-125, wherein the compound is a mutant selective compound.

127. The compound of claim 126, wherein the compound is capable of reducing the activity or amount of an expanded repeat-containing RNA at least ten fold more than it reduces the activity or amount of a corresponding wild type RNA.

128. The compound of claim 126 or 127, wherein the compound is capable of reducing the activity or amount of a protein encoded by an expanded repeat-containing RNA at least ten fold more than it reduces the activity or amount of a corresponding wild type protein.

129. The compound of claim 126, wherein the compound is capable of reducing the activity or amount of an expanded repeat-containing RNA at least five fold more than it reduces the activity or amount of a corresponding wild type RNA.

130. The compound of claim 126 or 127, wherein the compound is capable of reducing the activity or amount of a protein encoded by an expanded repeat-containing RNA at least five fold more than it reduces the activity or amount of a corresponding wild type protein.

131. The compound of claim 126 or 127, wherein the compound is capable of distribution throughout the ipsilateral striatum, contralateral cortex, contralateral striatum, thalamus, cerebellum, and brainstem.

132. The compound of claim 125 or 126, wherein a single dose of the compound is capable of reducing the activity or amount of mutant ATXN-3 expression for up to 5 days.

133. The compound of claim 125 or 126, wherein a single dose of the compound is capable of reducing the activity or amount of mutant ATXN-3 expression for up to 8 days.

135. A method of selectively reducing the activity or amount of an expanded repeat-containing RNA in a cell, comprising contacting a cell having an expanded repeat-containing RNA with at least one compound of any of claims 1 to 134;

and thereby selectively reducing the activity or amount of the expanded repeat-containing RNA in the cell.

136. The method of claim 135, wherein the amount or activity of the expanded repeat-containing RNA is reduced at least ten-fold more than that of a corresponding wild-type RNA.

140. A method of selectively reducing the amount or activity of a protein encoded by an expanded repeat-containing RNA in a cell, comprising contacting a cell having an expanded repeat-containing RNA with at least one compound of any of claims 1 to 134;

and thereby selectively reducing the activity or amount of the protein encoded by the expanded repeat-containing RNA in the cell.

146. A pharmaceutical composition comprising at least one compound of any of claims 1-133 and a pharmaceutical carrier or diluents.

147. A method of treating a patient having a disease associated with an expanded repeat-containing RNA comprising administering to the patient the pharmaceutical composition of claim 146.

148. The method of claim 147, wherein the disease is selected from among:

spinocerebellar ataxia 10 or spinocerebellar ataxia 3.

149. The method of claim 147, wherein the disease is Dentatorubral-pallidoluysian atrophy.

150. The method of claim 147, wherein the disease is spinocerebellar ataxia.

151. The method of any of claims 147-150, wherein the pharmaceutical composition is administered by injection.

152. The method of any of claims 147-150, wherein the pharmaceutical composition is adminstered into the central nervous system.

153. The method of any of claims 147-150, wherein the pharmaceutical composition is adminstered into the cerebrospinal fluid.

154. The method of any of claims 147-150, wherein the pharmaceutical composition is adminstered by intracerebroventricular administration.

155. The method of any of claims 147-150, wherein the pharmaceutical composition is administered intrathecally.

156. The method of any of claims 147-150, wherein the pharmaceutical composition is administered into the brain.

157. The method of any of claims 147-156, wherein the administration comprises a bolus injection.

158. The method of any of claims 147-157, wherein the administration comprises an infusion.

159. The method of claim 158, wherein the administration comprises an infusion by infusion pump.

160. A method of modulating the splicing of a pre-mRNA, comprising contacting a cell with a compound of any of claims 1 to 134.

161. A method of modulating the splicing of a pre-mRNA containing an expanded CAG repeat, comprising contacting a cell with a compound of any of claims 1 to 134.

162. A method of modulating the splicing of an ATXN-3 pre-mRNA, comprising contacting a cell with a compound of any of claims 1 to 134.

163. A method of modulating the splicing of a mutant ATXN-3 pre-mRNA, comprising contacting a cell with a compound of any of claims 1 to 134.

164. A method of modulating the splicing of a mutant ATXN-3 pre-mRNA containing an expanded CAG repeat, comprising contacting a cell with a compound of any of claims 1 to 134.

165. A method of increasing the exclusion of exon 10 of ATXN-3, comprising contacting a cell with a compound of any of claims 1 to 134.

168. Use of a compound according to any of claims 1-134 or the pharmaceutical composition of claim 146 for the preparation of a medicament for use in the treatment of Spinocerebellar ataxia type 3.

169. Use of a compound according to any of claims 1-134 or the pharmaceutical composition of claim 146 for modulating the splicing of ATXN-3 pre-mRNA.

134. The compound of any of 1-133, wherein the oligonucleotide comprises at least one modified nucleobase.

137. The method of claim 134 or 135, wherein the cell is in vitro.

138. The method of claim 134 or 135, wherein the cell is in an animal.

139. The method of claim 134 or 135, wherein the expanded repeat-containing RNA is ATXN-3 RNA.

141. The method of claim 139, wherein the amount or activity of the protein encoded by the expanded repeat-containing RNA is reduced at least ten-fold more than that of a corresponding wild-type protein.

142. The method of claim 139 or 140, wherein the cell is in vitro.

143. The method of claim 139 or 140, wherein the cell is in an animal.

144. The method of claim 134 or 135, wherein the protein encoded by an expanded repeat-containing RNA is ATXN-3.

145. The method of claim 134 or 135, wherein the protein encoded by an expanded repeat-containing RNA is ATN-1.

166. A method of modulating the splicing of a ATXN-3 pre-mRNA, comprising contacting a cell with an ss-siRNA compound targeted to a repeat region.

167. A method of modulating the splicing of a mutant ATXN-3 pre-mRNA containing an expanded CAG repeat, comprising contacting a cell with an ss-siRNA compound targeted to a repeat region.