SINGLE NUCLEOTIDE POLYMORPHISM (SNP) TARGETING THERAPIES FOR THE TREATMENT OF HUNTINGTON'S DISEASE

• US 20120136039A1
• Filed: 04/08/2010
• Published: 05/31/2012
• Est. Priority Date: 04/08/2009
• Status: Active Grant

• Current Assignee: University Of Massachusetts
• Original Assignee: University Of Massachusetts
• Inventors: Aronin, Neil, Zamore, Phillip D., Pfister, Edith
• Granted Patent: US 8,987,222 B2
• Time in Patent Office: Days
• US Class Current: 514/44.A
• CPC Class Codes: A61K 31/713 Double-stranded nucleic acids or oligonucleotides
• 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 2320/34 Allele or polymorphism specific uses

Abstract

The present invention relates to the discovery of (SNPs) significantly associated with Huntington'"'"'s disease (HD). The present invention utilizes RNA silencing technology (e.g. RNAi) against such SNPs optimally combined with select additional SNP targeting silencing agents, thereby resulting in an effective treatment of significantly-sized patient populations. Silencing agents having enhanced discriminatory properties are also featured.

Claims

1. A method of silencing mutant huntingtin (htt) mRNA in a HD patient population, comprising administering to said patient population an effective amount of a first RNA silencing agent targeting a HD-associated htt single nucleotide polymorphism (SNP) in combination with one or more RNA silencing agents targeting other htt SNPs, such that RNA silencing of said mRNA occurs, said one or more other htt SNPs having frequency of heterozygosity of at least 20%, 30%, 35% or more in a sample population.

2. The method of claim 1, wherein the HD-associated htt SNP is present at genomic site RS362307.

3. The method of claim 1, wherein the other htt SNPs are as set forth in any of Tables 1, 2, 5 and 6.

4. The method of claim 1, wherein the other htt SNPs are selected from the group consisting of rs4690074, rs362336, rs362331, rs362373, rs362272, rs362306, rs362268, and rs362267.

5. The method of claim 3, wherein the patient population is of US or Western European origin.

12. The method of claim 1, wherein a nucleotide complementary to the SNP in the mutant htt mRNA is located at position 10 relative to the 5′

end of the antisense strand of the RNA silencing agent.

13. The method of claim 12, wherein the RNA silencing agent further comprises a mismatch with respect to both the mutant htt mRNA and the wild-type htt mRNA at one or more positions located within the seed sequence of the RNA silencing agent.

14. The method of claim 13, wherein said one or more positions are selected from the group consisting of position 2, position 3, position 4, position 5, position 6, and position 7 relative to the 5′

end of the antisense strand of the RNA silencing agent.

15. The method of claim 14, wherein said position is position 5.

16. The method of claim 14, wherein said position is position 6.

6. A method of silencing mutant htt mRNA in 70% or more HD patients in a HD patient population, comprising administering to said patients in the HD patient population one or more RNA silencing agents, wherein each RNA silencing agent targets a htt single nucleotide polymorphism (SNP) having a frequency of heterozygosity of at least 20% or more in a sample HD patient population, such that RNA silencing of said mRNA occurs in 70% or more patients in the HD patient population.

7. The method of claim 6, further comprising identifying the sequence of the nucleotide located at one or more SNPs selected from the group consisting of rs362307, rs363125 and rs362273 in the mutant htt mRNA of the HD patients in the HD patient population.

8. The method of claim 6, wherein the RNA silencing agents target SNP1, SNP2, and SNP3 as set forth in Table 2.

9. The method of claim 6 wherein each RNA silencing agent targets a htt single nucleotide polymorphism (SNP) selected from the group consisting of rs362307, rs363125 and rs362273.

10. The method of claim 6, wherein the RNA silencing agent is a siRNA or a shRNA.

17. The method of claim 6, comprising administering to said patients in the HD patient population one or more siRNAs each comprising a guide strand and a complementary strand, wherein the guide strand is selected from the group consisting of SEQ ID NO:

210, SEQ ID NO;

211, SEQ ID NO;

220, SEQ ID NO;

230, and SEQ ID NO;

233.

18. The method of claim 6, comprising administering to said patients in the HD patient population one or more siRNAs each comprising a guide strand and a complementary strand, wherein the guide strand is selected from the group consisting of SEQ ID NO:

210, SEQ ID NO;

211, SEQ ID NO;

219, SEQ ID NO;

230, and SEQ ID NO;

233.

11. (canceled)

19. A kit comprising:

(a) a first RNA silencing agent targeting a HD-associated htt single nucleotide polymorphism (SNP);

(b) one or more additional RNA silencing agents targeting other htt SNPs having a frequency of heterozygosity of at least 20%, 30%, 35% or more in a sample population; and

(c) instructions for administration of one or more of the RNA silencing agents to a subject having Huntington'"'"'s disease.

21. The kit of claim 19, wherein the first silencing agent targets htt SNP rs362307, and the additional RNA silencing agents target htt SNPs rs363125 and rs362273.

20. A kit comprising:

(a) one or more siRNAs comprising a guide strand and a complementary strand, wherein said guide strand has a nucleotide sequence set forth in Table 6 (SEQ ID NOs;

208-233); and

(b) instructions for use thereof for silencing mutant huntingtin (htt) mRNA in a subject having Huntington'"'"'s disease.

22. An siRNA comprising a guide strand and a complementary strand, wherein said guide strand has a nucleotide sequence set forth in Table 6 (SEQ ID NOs:

208-233).

23. The siRNA of claim 22, wherein the guide strand has the nucleotide sequence of SEQ ID NO:

219 or SEQ ID NO;

220.

24. The siRNA of claim 22, wherein the guide strand has the nucleotide sequence of SEQ ID NO:

210 or SEQ ID NO;

211.

25. The siRNA of claim 22, wherein the guide strand has the nucleotide sequence of SEQ ID NO:

230 or SEQ ID NO;

228