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US-12617821-B2 - Engineered viral capsid polypeptides and uses thereof

US12617821B2US 12617821 B2US12617821 B2US 12617821B2US-12617821-B2

Abstract

The technology described herein provides variant adeno-associated viral capsid polypeptides and viruses comprising the same. Such variant viral capsid polypeptides bear a mutation relative to SEQ ID NO: 2 (WT AAV2) in a region corresponding to amino acids 561-588, wherein the region corresponding to amino acids 561-588 comprises a sequence selected from SEQ ID NO: 4-41,337. Further provided herein are methods for delivering a viral payload using viruses comprising variant capsid polypeptides described herein.

Inventors

  • Eric Kelsic
  • Sam Sinai
  • Pierce OGDEN
  • George M. Church

Assignees

  • PRESIDENT AND FELLOWS OF HARVARD COLLEGE

Dates

Publication Date
20260505
Application Date
20201106

Claims (18)

  1. 1 . A viral capsid polypeptide bearing a mutation relative to SEQ ID NO: 2 (WT AAV2) in a region corresponding to amino acids 561-588, wherein the region corresponding to amino acids 561-588 comprises a sequence selected from SEQ ID NO: 4-41,337.
  2. 2 . The viral capsid polypeptide of claim 1 , which is an AAV capsid polypeptide.
  3. 3 . The viral capsid polypeptide of claim 2 , wherein the AAV capsid polypeptide is an AAV2 capsid polypeptide.
  4. 4 . The viral capsid polypeptide of claim 1 , wherein the viral capsid polypeptide is an AAV VP1 capsid polypeptide.
  5. 5 . The viral capsid polypeptide of claim 4 , wherein the region corresponding to amino acids 561-588 of SEQ ID NO: 2 comprises a sequence selected from SEQ ID NO: 4-41,337.
  6. 6 . The viral capsid polypeptide of claim 4 , which is an AAV2 capsid polypeptide.
  7. 7 . The viral capsid polypeptide of claim 1 , comprising a sequence of SEQ ID NO: 2, wherein the region of amino acids 561-588 of SEQ ID NO: 2 comprises a variant sequence selected from SEQ ID NO: 4-41,337.
  8. 8 . An AAV2 capsid polypeptide comprising a sequence of SEQ ID NO: 2, wherein the region of amino acids 561-588 of SEQ ID NO: 2 comprises a variant sequence selected from SEQ ID NO: 4-41,337.
  9. 9 . A nucleic acid encoding the capsid polypeptide of claim 1 .
  10. 10 . An engineered AAV vector having at least a capsid comprising the capsid polypeptide of claim 1 .
  11. 11 . A viral particle comprising the capsid polypeptide of claim 1 .
  12. 12 . A method for delivering a payload, the method comprising contacting a cell with the engineered AAV vector of claim 10 .
  13. 13 . A method for delivering a payload, the method comprising contacting a cell with viral particle of claim 11 .
  14. 14 . The method of claim 13 , wherein the contacting is sufficient to allow for expression of the payload in the cell.
  15. 15 . A method for administering a payload, the method comprising administering to a subject the engineered AAV vector of claim 10 .
  16. 16 . A method for administering a payload, the method comprising administering to a subject the viral particle of claim 11 .
  17. 17 . The method of claim 16 , wherein the administering is sufficient to allow for expression of the payload in the cell.
  18. 18 . The method of claim 16 , wherein the payload is selected from the group consisting of: a nucleic acid, a polypeptide, an inhibitory RNA, an antibody or antibody reagent, an oligonucleotide, and a miRNA.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS This application is a 35 U.S.C. § 371 National Phase Entry Application of International Application No. PCT/US2020/059294 filed Nov. 6, 2020, which designates the U.S. and claims benefit under 35 U.S.C. § 119 (e) of U.S. Provisional Application No. 62/932,646 filed Nov. 8, 2019, the content of which is incorporated herein by reference in their entirety. GOVERNMENT SUPPORT This invention was made with government support under HG008525 and HG005550 awarded by National Institutes of Health. The government has certain rights in the invention. SEQUENCE LISTING The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Oct. 30, 2019, is named 002806-096400PL01_SL.txt and is 16,548,992 bytes in size. TECHNICAL FIELD OF THE INVENTION This invention is related to engineering viral vectors. BACKGROUND OF THE INVENTION Adeno-associated virus (AAV) is an attractive agent for use as gene delivery vector. Its simple structure also makes it an attractive target for genetic improvement programs. Nonetheless, there is a continuing need in the art to improve delivery of DNA using AAV and other viral vectors. SUMMARY OF THE INVENTION Described herein are viral vectors comprising a variant sequence of the capsid gene, VP1. Such vectors provide, e.g., an improvement in the degree of tissue targeting, payload packaging, delivery efficiency, etc., attainable with such vectors. In particular, viral vectors with capsid polypeptide mutations that modify tropism of the viral particles relative to particles with wild-type capsid polypeptide are described. Accordingly, one aspect provided herein is a viral capsid polypeptide bearing a mutation relative to SEQ ID NO: 2 (WT AAV2) in a region corresponding to amino acids 561-588. In one embodiment of any aspect provided herein, the region corresponding to amino acids 561-588 comprises a sequence selected from SEQ ID NO: 4-41,337. In one embodiment of any aspect provided herein, the capsid is an AAV capsid. In one embodiment of any aspect provided herein, the capsid is an AAV2 capsid. In one embodiment of any aspect provided herein, the only variation relative to a wild-type AAV viral capsid is in the region corresponding to amino acids 561-588 of SEQ ID NO: 2. Another aspect described herein provides an AAV VP1 capsid polypeptide bearing a mutation in the region corresponding to amino acids 561-588 of SEQ ID NO: 2. In one embodiment of any aspect provided herein, the region corresponding to amino acids 561-588 of SEQ ID NO: 2 comprises a sequence selected from SEQ ID NO: 4-41,337. In one embodiment of any aspect provided herein, the AAV VP1 polypeptide described herein is an AAV2 capsid polypeptide. Another aspect described herein provides a viral capsid polypeptide comprising a sequence of SEQ ID NO: 2, wherein the region of amino acids 561-588 of SEQ ID NO: 2 comprises a variant sequence selected from SEQ ID NO: 4-41,337. Another aspect described herein provides a variant of the viral capsid polypeptide of SEQ ID NO: 2, wherein the region of amino acids 561-588 comprises a sequence selected from SEQ ID NO: 4-41,337. Another aspect described herein provides an AAV2 capsid polypeptide comprising a sequence of SEQ ID NO: 2, wherein the region of amino acids 561-588 of SEQ ID NO: 2 comprises a variant sequence selected from SEQ ID NO: 4-41,337. Another aspect described herein provides an engineered AAV vector having at least one viral capsid polypeptide comprising any of the capsid polypeptides described herein. Another aspect described herein provides a nucleic acid encoding any of the capsid polypeptide described herein. Another aspect described herein provides a viral particle comprising any of the capsid polypeptide described herein. Another aspect described herein provides a method for delivering a payload, the method comprising contacting a cell with any of the engineered AAV vectors described herein, or any of the viral particles described herein. In one embodiment of any aspect provided herein, the contacting is sufficient to allow for expression of the payload in the cell. Another aspect described herein provides a method for administering a payload, the method comprising administering to a subject any of the engineered AAV vectors described herein, or any of the viral particles described herein. In one embodiment of any aspect provided herein, the administering is sufficient to allow for expression of the payload in the cell. In one embodiment of any aspect provided herein, the payload is selected from the group consisting of: a nucleic acid, a polypeptide, an inhibitory RNA, an antibody or antibody reagent, an oligonucleotide, and an miRNA. In yet another aspect, provided herein is a cell comprising a variant capsid polypeptide described herein or a polynucleotide encoding same. For example, a cell comprising