Compositions and methods for treating Huntington's disease

1. A modulatory polynucleotide comprising the nucleotide sequence of SEQ ID NO: 349.

2. An adeno-associated viral (AAV) vector genome comprising a nucleic acid sequence positioned between two inverted terminal repeats (ITRs), wherein the nucleic acid sequence encodes a modulatory polynucleotide comprising the nucleotide sequence of SEQ ID NO: 349.

3. The AAV vector genome of claim 2 , which further comprises:

(i) a promoter operably linked to the nucleic acid sequence encoding the modulatory polynucleotide;

(ii) an enhancer;

(iii) an intron region; and/or

(iii) a poly A signal region.

4. The AAV vector genome of claim 3 , wherein:

(i) the promoter comprises a CBA promoter, a CMV promoter, a PGK promoter, an H1 promoter, a UBC promoter, a GUSB promoter, an NSE promoter, a synapsin promoter, a MeCP2 promoter, or a GFAP promoter;

(ii) the enhancer comprises a CMV enhancer; and/or

(iii) the intron comprises an SV40 intron.

5. A recombinant AAV (rAAV) viral particle comprising the AAV vector genome of claim 2 , and a capsid protein.

6. The rAAV viral particle of claim 5 , wherein the capsid protein comprises an AAV1 capsid protein or a variant thereof, an AAV5 capsid protein or a variant thereof, or an AAV9 capsid protein or a variant thereof.

7. A vector comprising the AAV vector genome of claim 2 .

8. An isolated cell comprising the AAV vector genome of claim 2 , which is a mammalian cell, a medium spiny neuron, a cortical neuron, or an astrocyte.

9. A pharmaceutical composition comprising the AAV vector genome of claim 2 , and a pharmaceutically acceptable excipient.

10. A pharmaceutical composition comprising the rAAV viral particle of claim 5 , and a pharmaceutically acceptable excipient.

11. A method of inhibiting a huntingtin (HTT) gene, mRNA, and/or protein expression in a cell, comprising contacting the cell with an AAV vector genome comprising a nucleic acid sequence positioned between two inverted terminal repeats (ITRs), wherein the nucleic acid sequence encodes a modulatory polynucleotide comprising the nucleotide sequence of SEQ ID NO: 349,

thereby inhibiting expression of the HTT gene, mRNA, and/or protein in the cell.

12. The method of claim 11 , wherein the AAV vector genome is present in an rAAV viral particle.

13. The method of claim 12 , wherein the rAAV viral particle further comprises a capsid protein, wherein the capsid protein comprises an AAV1 capsid protein or variant thereof, an AAV5 capsid or variant thereof, or an AAV9 capsid or variant thereof.

14. The method of claim 11 , wherein the cell comprises a medium spiny neuron, a cortical neuron, or an astrocyte.

15. The method of claim 11 , wherein the cell is in a subject, wherein the subject has Huntingtin's disease (HD).

16. The method of claim 11 , wherein expression of the HTT mRNA is inhibited by at least 45%, 50%, 55%, 60%, 65%, 70%, 75%, or 80%.

17. A method of treating Huntington's Disease (HD) in a subject, comprising administering to the subject an effective amount of an AAV vector genome comprising a nucleic acid sequence positioned between two inverted terminal repeats (ITRs), wherein the nucleic acid sequence encodes a modulatory polynucleotide comprising the nucleotide sequence of SEQ ID NO: 349,

thereby treating HD in the subject.

18. The method of claim 17 , wherein the AAV vector genome is present in an rAAV viral particle.

19. The method of claim 18 , wherein the rAAV viral particle further comprises a capsid protein, wherein the capsid protein comprises an AAV1 capsid protein or variant thereof, an AAV5 capsid or variant thereof, or an AAV9 capsid or variant thereof.

20. The method of claim 18 , wherein the AAV vector genome or the rAAV viral particle is present in a pharmaceutical composition, which further comprises a pharmaceutically acceptable excipient.

21. The method of claim 17 , wherein the expression of an HTT gene, mRNA, and/or protein is inhibited in a CNS cell or a CNS region, wherein:

(i) the CNS cell comprises a neuron, a medium spiny neuron, an astrocyte, or a combination thereof;

(ii) the CNS region is a forebrain region, a midbrain region, a putamen region, a striatum region, a cortex region, a motor cortex region, a somatosensory cortex region, a temporal cortex region, or a combination thereof; or

(iii) the CNS region is a putamen region.

22. The method of claim 21 , wherein the HTT gene, mRNA, and/or protein comprises:

an HTT gene, mRNA, and/or protein comprising a CAG repeat.

23. The method of claim 22 , wherein the HTT gene, mRNA, and/or protein comprising a CAG repeat is a CAG-expanded HTT, comprising at least 36-40 CAG repeats.

24. The method of claim 17 , wherein the HD is:

(i) a juvenile form HD, wherein a subject having HD is 2 to 20 years of age;

(ii) an early stage HD;

(iii) a late stage HD;

(iv) a fully penetrant HD, wherein an HTT gene has least 41 or more CAG repeats;

(v) an incomplete penetrance HD, wherein an HTT gene has 36-40 CAG repeats; and/or

(vi) an asymptomatic HD.

25. The method of claim 17 , wherein treatment comprises amelioration of a symptom of HD in the subject, wherein the symptom comprises apathy or lack of initiative, dysphoria, irritability, agitation or anxiety, poor self-care, poor judgment, inflexibility, disinhibition, depression, suicidal ideation euphoria, aggression, delusions, compulsions, hypersexuality, hallucinations, dystonia, speech deterioration, slurred speech, difficulty swallowing, weight loss, bradykinesia, incoordination, cognitive dysfunction, unsteady gait and involuntary movements, or CNS deterioration.

26. The method of claim 17 , wherein the AAV vector genome is administered via intravenous administration, intracisternal administration, or both.

27. The method of claim 17 , wherein the AAV vector genome is administered to the subject in combination with an additional therapeutic agent suitable for treatment of HD, wherein the additional therapeutic agent comprises a neuroprotective agent, a dopamine-depleting agent, a benzodiazepine, an anticonvulsant, an amino acid precursor of dopamine, a skeletal muscle relaxant, an inhibitor for acetylcholine release at the neuromuscular junction, an atypical neuroleptic, an agent to increase ATP/cellular energetics, a selective serotonin reuptake inhibitor (SSRI), a mood stabilizer, or a combination thereof.

28. The method of claim 27 , wherein the additional therapeutic agent comprises tetrabenazine, clonazepam, sodium valproate, levetiracetam, levodopa, baclofen, tizanidine, botulinum toxin, olanzapine, quetiapine, risperidone, sulpiride, haloperidol, clozapine, aripiprazole, creatine, citalopram, fluoxetine, paroxetine, sertraline, mirtazapine, venlafaxine, xopiclone and/or zolpidem, odium valproate, carbamazepine, IGF-I, GDNF, BDNF, CTNF, VEGF, Colivelin, Xaliproden, Thyrotrophin-releasing hormone and ADNF, or a combination thereof.

29. A method of making the rAAV particle of claim 5 , comprising:

(i) providing a cell comprising the AAV vector genome and a nucleic acid encoding a capsid protein; and

(ii) purifying the rAAV viral particle from the cell;

thereby making the rAAV viral particle.