RNA SILENCING COMPOSITIONS AND METHODS FOR THE TREATMENT OF HUNTINGTON'S DISEASE

• US 20090186410A1
• Filed: 01/05/2009
• Published: 07/23/2009
• Est. Priority Date: 07/07/2006
• Status: Abandoned Application

• Current Assignee: University Of Massachusetts
• Original Assignee: University Of Massachusetts
• Inventors: Zamore, Phillip D., Aronin, Neil
• Application Number:
  US12/348,794
• Publication Number:
  US 20090186410A1
• Time in Patent Office: Days
• US Class Current: 435/375
• CPC Class Codes: C12N 15/111 General methods applicable to biologically active non-coding nucleic acids
• 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 2310/14 interfering N.A.
• CPC Class Codes: C12N 2310/3515 Lipophilic moiety, e.g. cholesterol
• CPC Class Codes: C12N 2320/34 Allele or polymorphism specific uses

Abstract

The present invention relates to the discovery of an effective treatment for a variety of Huntington'"'"'s disease (HD). The present invention utilizes RNA silencing technology (e.g. RNAi) against single nucleotide polymorphisms (SNPs) in the Huntingtin (htt) gene encoding the dominant, gain-of-function mutant Huntington protein, thereby resulting in an effective treatment for the gain-of-function disease.

Claims

1. A method of silencing a target mRNA encoding a mutant huntingtin (htt) protein in a cell, comprising contacting the cell with effective amount of a RNA silencing agent targeting a heterozygous single nucleotide polymorphism (SNP) within the target mRNA, such that RNA silencing of said mRNA occurs, wherein the SNP has an allelic frequency of at least 35% in a sample population.

2. The method of claim 1, wherein the SNP is present at genomic site RS362331.

3. The method of claim 3, wherein the target mRNA comprises the sequence set forth as SEQ ID NO:

5.

4. The method of claim 3, wherein the target mRNA comprises the sequence set forth as SEQ ID NO:

6.

5. The method of claim 3, wherein the RNA silencing agent is capable of inducing discriminatory RNA silencing.

6. The method of claim 3, wherein the antisense strand of said RNA silencing agent is complementary to the SNP and wherein said RNA silencing agent is capable of substantially silencing the mutant huntingtin protein without substantially silencing the corresponding wild-type huntingtin protein.

7. The method of claim 3, wherein the sample population is of Western European origin.

9. The method of any of claim 7, wherein the siRNA comprises a lipophilic moiety.

10. The method of claim 9, wherein the lipophilic moiety is a cholesterol moiety.

8. A method of silencing a target mRNA encoding a mutant huntingtin (htt) protein in a cell, comprising contacting the cell with effective amount of a siRNA targeting a heterozygous single nucleotide polymorphism (SNP) within the target mRNA, such that RNA silencing of said mRNA occurs, wherein the siRNA is selected from the group consisting of:

a. an siRNA comprising (i) a sense strand comprising the sequence set forth as SEQ ID NO;

3 or a variant thereof; and

(ii) an antisense strand comprising the sequence set forth as SEQ ID NO;

4 or a variant thereof, said variant comprising at least one nucleotide analog or backbone modification;

b. an siRNA comprising (i) a sense strand comprising the sequence set forth as SEQ ID NO;

7 or a variant thereof; and

(ii) an antisense strand comprising the sequence set forth as SEQ ID NO;

8 or a variant thereof, said variant comprising at least one nucleotide analog or backbone modification,

c. an siRNA comprising (i) a sense strand comprising the sequence set forth as SEQ ID NO;

9 or a variant thereof; and

(ii) an antisense strand comprising the sequence set forth as SEQ ID NO;

10 or a variant thereof, said variant comprising at least one nucleotide analog or backbone modification, and

d. an siRNA comprising (i) a sense strand comprising the sequence set forth as SEQ ID NO;

13 or a variant thereof; and

(ii) an antisense strand comprising the sequence set forth as SEQ ID NO;

14 or a variant thereof, said variant comprising at least one nucleotide analog or backbone modification.

11. An RNA silencing agent comprising an antisense strand comprising about 16-25 nucleotides homologous to a region of an mRNA encoding a mutant huntingtin (htt) protein, said region comprising a heterozygous single nucleotide polymorphism (SNP) having an allelic frequency of at least 35% in a sample population, wherein the RNA silencing agent is capable of directing RNA silencing of said mRNA.

12. The RNA silencing agent of claim 11, wherein the SNP is present at genomic site RS362331.

13. The RNA silencing agent of claim 11, wherein the target mRNA comprises the sequence set forth as SEQ ID NO:

5.

14. The RNA silencing agent of claim 11, wherein the target mRNA comprises the sequence set forth as SEQ ID NO:

6.

15. The RNA silencing agent of claim 11, which is capable of inducing discriminatory RNA silencing.

16. The RNA silencing agent of claim 11, which is capable of substantially silencing the mutant huntingtin protein without substantially silencing the corresponding wild-type huntingtin protein.

17. The RNA silencing agent of claim 11, wherein the RNA silencing agent is an siRNA.

18. The siRNA of claim 17, comprising a sense strand having a nucleotide sequence identical to the sequence of the SNP.

19. The siRNA of claim 11, wherein the sense strand of the siRNA is identical to the polymorphism at a nucleotide position that is 10 nucleotides from the 5′

end of the sense strand.

20. The siRNA of claim 11, wherein the sense strand of the siRNA is identical to the polymorphism at a nucleotide position that is 16 nucleotides from the 5′

end of the sense strand.

21. An siRNA is selected from the group consisting of:

a. an siRNA comprising (i) a sense strand comprising the sequence set forth as SEQ ID NO;

3 or a variant thereof; and

(ii) an antisense strand comprising the sequence set forth as SEQ ID NO;

4 or a variant thereof, said variant comprising at least one nucleotide analog or backbone modification;

b. an siRNA comprising (i) a sense strand comprising the sequence set forth as SEQ ID NO;

7 or a variant thereof; and

(ii) an antisense strand comprising the sequence set forth as SEQ ID NO;

8 or a variant thereof, said variant comprising at least one nucleotide analog or backbone modification,

c. an siRNA comprising (i) a sense strand comprising the sequence set forth as SEQ ID NO;

9 or a variant thereof; and

(ii) an antisense strand comprising the sequence set forth as SEQ ID NO;

10 or a variant thereof, said variant comprising at least one nucleotide analog or backbone modification, and

d. an siRNA comprising (i) a sense strand comprising the sequence set forth as SEQ ID NO;

13 or a variant thereof; and

(ii) an antisense strand comprising the sequence set forth as SEQ ID NO;

14 or a variant thereof, said variant comprising at least one nucleotide analog or backbone modification.

22. The siRNA of claim 21, wherein the siRNA comprises a lipophilic moiety.

23. The siRNA of claim 22, wherein the lipophilic moiety is a cholesterol moiety.