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CN-121986107-A - Compositions and methods for treating diseases associated with ataxin (FRATAXIN) deficiency

CN121986107ACN 121986107 ACN121986107 ACN 121986107ACN-121986107-A

Abstract

The present disclosure relates to compositions and methods for altering, e.g., enhancing, the level of ataxin via the use of adeno-associated virus (AAV) capsid variants. The compositions and methods of the present disclosure are useful for treating a subject suffering from, having been diagnosed with, or at risk of suffering from a disorder associated with deficiency of ataxin (FXN), such as friedel Lai Xixing ataxia.

Inventors

  • M, E, Nen, Maher
  • A.Z.Ren
  • MORA DIEGO
  • W.WANG

Assignees

  • 沃雅戈治疗公司

Dates

Publication Date
20260505
Application Date
20240815
Priority Date
20230816

Claims (20)

  1. 1. An adeno-associated virus (AAV) particle comprising an AAV capsid variant and a viral genome, wherein the viral genome comprises an ataxin (FXN) coding sequence, and the AAV capsid variant comprises an amino acid sequence having the formula [ N2] - [ N3], wherein: (i) [ N2] comprises X 1 、X 2 、X 3 、X 4 and X 5 , wherein: (a) X 1 is Y, N or C; (b) X 2 is P, K, T or Q; (c) X 3 is A or P; (d) X 4 is E, S or A (E) X 5 is V, L or E, and (Ii) [ N3] comprises the amino acid sequence VQK, EQK, VKK, VHK, VQQ or LQK, and Wherein the AAV capsid variant comprises the amino acid sequence of SEQ ID NO. 739 or an amino acid sequence at least 95% identical thereto.
  2. 2. The AAV particle of claim 1, wherein [ N2] - [ N3] is present in loop VIII, wherein loop VIII is present at an amino acid comprising amino acids corresponding to positions 571-599 of the amino acid sequence of SEQ ID No. 982.
  3. 3. The AAV particle of claim 1 or claim 2, wherein [ N2] - [ N3] is present immediately after the amino acid corresponding to position 576 of the amino acid sequence of SEQ ID No. 982.
  4. 4. The AAV particle of any one of claims 1-3, wherein the AAV capsid variant is an AAV5 capsid variant comprising [ N2] - [ N3] in place of an amino acid corresponding to T577 of the amino acid sequence of SEQ ID No. 138.
  5. 5. The AAV particle of any one of claims 1-4, wherein [ N2] comprises amino acid sequence YP, YPA, YPAE (SEQ ID NO: 21) or YPAEV (SEQ ID NO: 1).
  6. 6. The AAV particle of any one of claims 1-5, wherein [ N3] comprises amino acid sequence VQK.
  7. 7. The AAV particle of any one of claims 1-6, wherein [ N2] - [ N3] comprises amino acid sequence AEVVQK (SEQ ID NO: 36) or PAEVVQK (SEQ ID NO: 20).
  8. 8. The AAV particle of any one of claims 1-7, wherein [ N2] - [ N3] comprises amino acid sequence YPAEVVQK (SEQ ID NO: 943).
  9. 9. The AAV particle of any one of claims 1-8, wherein the AAV capsid variant further comprises [ N1], comprising X D 、X E and X F , wherein: (a) X D of [ N1] is Q, T, S, A, I, L or H; (b) X E of [ N1] is S, G, A or R, and (C) X F of [ N1] is S, K, L, R, A or T; Wherein [ N1] immediately precedes [ N2] - [ N3 ].
  10. 10. The AAV particle of claim 9, wherein [ N1] comprises the amino acid sequence QS, SS, or QSs.
  11. 11. The AAV particle of claim 9 or claim 10, wherein [ N1] - [ N2] comprises amino acid sequence QSSYPAEV (SEQ ID NO: 96).
  12. 12. The AAV particle of any one of claims 9-11, wherein [ N1] - [ N2] - [ N3] comprises amino acid sequence SSYPAEVVQ (SEQ ID NO: 121) or QSSYPAEVVQK (SEQ ID NO: 150).
  13. 13. The AAV particle of any one of claims 9-12, wherein the AAV capsid variant further comprises [ N0], comprising X A 、X B and X C , wherein: (a) X A of [ N0] is T, I or N; (b) X B of [ N0] is N, and (C) X C of [ N0] is N, T, S or K; Wherein [ N0] immediately precedes [ N1 ].
  14. 14. The AAV particle of claim 13, wherein [ N0] comprises the amino acid sequence TN, NN, or TNN.
  15. 15. The AAV particle of claim 13 or claim 14, wherein [ N0] - [ N1] comprises amino acid sequence TNNQSS (SEQ ID NO: 183).
  16. 16. The AAV particle of any one of claims 13-15, wherein [ N0] - [ N1] - [ N2] - [ N3] comprises amino acid sequence TNNQSSYPAEVVQK (SEQ ID NO: 500).
  17. 17. The AAV particle of any one of claims 13-16, wherein the AAV capsid variant further comprises [ N4], comprising X G and X H , wherein: (a) [ N4] X G is T, P or N, and (B) X H of [ N4] is A; wherein [ N4] is present immediately after [ N3 ].
  18. 18. The AAV particle of claim 17, wherein [ N4] comprises the amino acid sequence TA.
  19. 19. The AAV particle of claim 17 or claim 18, wherein [ N0] - [ N1] - [ N2] - [ N3] - [ N4] comprises amino acid sequence TNNQSSYPAEVVQKTA (SEQ ID NO: 1533).
  20. 20. The AAV particle of any one of claims 16-18, wherein [ N0] - [ N1] - [ N2] - [ N3] - [ N4] is present in loop VIII, wherein loop VIII is present at an amino acid comprising an amino acid corresponding to positions 571-599 of the amino acid sequence of SEQ ID No. 982.

Description

Compositions and methods for treating diseases associated with ataxin (FRATAXIN) deficiency RELATED APPLICATIONS The present application claims the benefit and priority of U.S. provisional application No. 63/519,952 filed on 8/16 of 2023. Sequence listing The present application is presented with a sequence listing in electronic format. A sequence table file named 14640_0092-00304_sl.xml was created at month 6 of 2024, 21 and its size was 1,753,602 bytes. The information in the sequence listing in electronic format is incorporated herein by reference in its entirety. Technical Field Described herein are compositions and methods relating to adeno-associated virus (AAV) viral particles for delivering polynucleotides, e.g., polynucleotide encoding ataxin (FXN) for treating Friedreich's Ataxia, FA. In some embodiments, the compositions described herein can be used to treat a subject in need thereof, such as a human subject diagnosed with FA, or as a research tool to study a disease or condition in a cell or animal model of FA. Background Friedel Lai Xixing ataxia (FA) is an autosomal recessive genetic disease that causes progressive damage to the nervous system. See Parkinson et al, journal of Neurochemistry, 2013, 126 (journal 1), 103-117, the contents of which are incorporated herein by reference in their entirety. FA is typically caused by degeneration of neural tissue in the spinal cord, which results from reduced expression of mitochondrial protein ataxin (FXN; also known as, for example CyaY, FA, FARR, FRDA and X25) in sensory neurons that direct muscle movement of the arms and legs. See Koeppen, arnulf; J Neurol Sci.15, 2011, 4, 303 (1-2): 1-12. Attacks usually occur during puberty or before the age of 25 years. See Campuzano et al, science, 271.5254 (1996, 3, 8) 1423. Initial symptoms of FA include dyscoordination (such as gait disorder), poor balance, leg weakness, reduced walking, impaired coordination, dysarthria, nystagmus, impaired sensation, kyphosis, lateral curvature, and foot deformity. See Parkinson et al Journal of Neurochemistry, 2013, 126 (journal 1), 103-117. FA is also associated with scoliosis, heart disease, and diabetes. The disease generally progresses until a wheelchair is needed for movement. The incidence of FA in the Caucasian population (Caucasian populations) is between about 1/20,000 and about 1/50,000, and the carrier frequency in the European population is inferred to be about 1/120. See NAGESHWARAN and FESTENSTEIN, frontiers in Neurology, volume 6, article 262 (2015), campuzano et al, science, 271.5254 (8, 3, 1996): 1423, the contents of each of which are incorporated herein by reference in their entirety. Amplification of the intron GAA trinucleotide repeat in the FXN gene is the genetic cause leading to reduced expression of FXN in FA. See Parkinson et al Journal of Neurochemistry, 2013, 126 (journal 1), 103-117. Over time, this deficiency can lead to the aforementioned symptoms, as well as frequent fatigue due to effects on cellular metabolism. Currently, the only FDA approved therapeutic agent for FA is the ox Ma Suolong (omaveloxolone) (SKYCLARYS) cube. And the ao Ma Suolong is a semisynthetic oleanane triterpene compound which activates a main transcription factor Nrf2 for regulating genes with antioxidant, anti-inflammatory and mitochondrial bioenergy characteristics. See Reisman et al (2019) Drug Des development Ther.13:1259-1270. While gene therapy constructs for delivery of ataxin have been described in the panel, there remains a need to develop improved constructs to better target appropriate tissues in the body. Adeno-associated viruses (AAV) have been presented as viral particles that are widely studied and utilized for delivering therapeutically effective polypeptides to mammalian cells. See, for example, TRATSCHIN et al, mol. Cell biol., 5 (11): 3251-3260 (1985) and Grimm et al, hum. Gene Ther., 10 (15): 2445-2450 (1999), the contents of each of which are incorporated herein by reference in their entirety. There remains a need for effective therapeutic methods using AAV capsids capable of delivering FXN to a cell or tissue of interest (e.g., CNS cells or tissue). Disclosure of Invention The present disclosure addresses these challenges by providing AAV-based compositions, AAV-based compositions for use in methods of treating friedel Lai Xixing ataxia (FA) in a subject, and methods of treating FA in a subject. Disclosed herein are compositions and methods for AAV-based gene delivery of FXN (e.g., human FXN) to mitigate loss of function and improve FXN expression (e.g., expression in the brain, e.g., in neurons). In some embodiments, the compositions and methods can be used to slow, stop, or reverse FA symptoms. In some aspects, the disclosure provides an AAV particle comprising an AAV capsid and a nucleotide sequence encoding FXN protein (also referred to herein as FXN coding sequence or FXN protein coding sequence). In some embodiments, the nucleotide