RNA interference for the treatment of gain-of-function disorders

• US 9,434,943 B2
• Filed: 01/22/2014
• Issued: 09/06/2016
• Est. Priority Date: 09/12/2003
• Status: Active Grant

• Current Assignee: University Of Massachusetts
• Original Assignee: University Of Massachusetts
• Inventors: Aronin, Neil, Zamore, Phillip D.
• Primary Examiner(s): ZARA, JANE J
• Application Number:
  US14/161,266
• Publication Number:
  US 20140370597A1
• Time in Patent Office: 958 Days
• Field of Search: 435/6.1, 435/91.1, 435/9, 435/1.31, 435/455, 435/91.31, 435/325, 435/320.1, 435/458, 435/366, 514/44, 536/23.1, 536/24.5
• US Class Current: 1/1
• CPC Class Codes: A61K 48/005 characterised by an aspect of the 'active' part of the composition delivered, i.e. the nucleic acid delivered
• CPC Class Codes: A61P 25/00 Drugs for disorders of the nervous system
• 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: C07H 21/02 with ribosyl as saccharide radical
• 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 2310/531 Stem-loop; Hairpin
• CPC Class Codes: C12N 2320/30 Special therapeutic applications
• CPC Class Codes: C12N 2320/34 Allele or polymorphism specific uses
• CPC Class Codes: C12N 5/06 Animal cells or tissues; Human cells or tissues preservation of living cells or tissues A01N1/02

Abstract

The present invention relates to the discovery of an effective treatment for a variety of gain-of-function diseases, in particular, Huntington'"'"'s disease (HD). The present invention utilizes RNA Interference technology (RNAi) against polymorphic regions in the genes encoding various gain-of-function mutant proteins resulting in an effective treatment for the gain-of-function disease.

Claims

1. A composition for treating a subject having or at risk for Huntington'"'"'s disease caused by a mutation within the htt gene encoding a gain-of-function mutant huntingtin protein, comprising:

a vector that expresses an effective amount of an siRNA or an shRNA targeting a non-disease causing heterozygous single nucleotide polymorphism (SNP) within a gene encoding said mutant huntingtin protein located at a site distinct from the expanded CAG region mutation within the htt gene encoding the mutant huntingtin protein.

2. The composition of claim 1, wherein said siRNA or shRNA comprises a first strand comprising about 16-25 nucleotides homologous to a region of the gene comprising the polymorphism and a second strand comprising about 16-25 nucleotides substantially complementary to the first strand such that the first and second strands are capable of annealing together.

4. The composition of claim 1, wherein the vector is a viral vector, retroviral vector, expression cassette, or plasmid.

5. The composition of claim 1, wherein the vector further comprises an RNA Polymerase III or RNA Polymerase II promoter.

6. The composition of claim 5, wherein the RNA Polymerase III promoter is the U6 or H1 promoter.

7. An isolated host cell comprising the vector of claim 4.

8. The isolated host cell of claim 7, which is a mammalian host cell.

9. The isolated host cell of claim 8, which is a non-human mammalian cell.

10. The isolated host cell of claim 8, which is a human cell.

3. A composition for treating a subject having or at risk for Huntington'"'"'s disease caused by a mutation within the htt gene encoding a gain-of-function mutant huntingtin protein, comprising a vector that expresses an effective amount of a siRNA or shRNA targeting a heterozygous SNP within a gene encoding said mutant huntingtin protein, wherein the SNP has an allelic frequency of at least 10% in a sample population and is present at a genomic site selected from the group consisting of RS362331, RS4690077, RS363125, RS363075, RS362268, RS362267, RS362307, RS362306, RS362305, RS362304, and RS362303.

11. A composition for treating a subject having or at risk for Huntington'"'"'s disease characterized or caused by a mutant huntingtin (htt) protein, comprising a vector that expresses an effective amount of a siRNA targeting a heterozygous single nucleotide polymorphism (SNP) within a gene encoding the mutant htt protein, such that RNA silencing of said gene occurs, wherein the siRNA comprises

(i) an antisense strand or a variant thereof having sufficient complementarity to the SNP at genomic site RS362307 to direct target-specific RNA interference of the gene encoding the mutant htt protein;

and

(ii) a sense strand or a variant thereof that is substantially complementary to the antisense strand, such that the sense and antisense strands are capable of annealing together.

12. A composition for treating a subject having or at risk for Huntington'"'"'s disease characterized or caused by a mutant huntingtin (htt) protein, comprising a vector that expresses an effective amount of a siRNA targeting a heterozygous single nucleotide polymorphism (SNP) within a gene encoding the mutant htt protein, such that RNA silencing of said gene occurs, wherein the siRNA comprises

(i) an antisense strand or a variant thereof having sufficient complementarity to the SNP at genomic site RS362331 or RS363125 to direct target-specific RNA interference of the gene encoding the mutant htt protein;

and

(ii) a sense strand or a variant thereof that is substantially complementary to the antisense strand, such that the sense and antisense strands are capable of annealing together.