Gene therapy for treating propionic acidemia

Patent metadata

Field	Value
Publication number	US-12472268-B2
Application number	US-201917278847-A
Country	US
Kind code	B2
Filing date	Oct 1, 2019
Priority date	Oct 1, 2018
Publication date	Nov 18, 2025
Grant date	Nov 18, 2025

Abstract

This present disclosure provides adeno-associated viral vectors, recombinant adeno-associated virus (rAAV), and methods of their use in gene therapy for treating propionic acidemia (PA). Also provided are pharmaceutical compositions comprising a recombinant adeno-associated virus of the invention and a pharmaceutically acceptable carrier or excipient. These pharmaceutical (compositions may be useful in gene therapy for the treatment of PA caused by mutations in propionyl-CoA carboxylase α-subunit (PCCA) or mutations in propionyl-CoA carboxylase β-subunit (PCCB).

First claim

What is claimed is:

1 . A recombinant adeno-associated virus (rAAV), said rAAV comprising an AAV capsid, and a vector genome packaged therein, said vector genome comprising in 5′ to 3′ order:
(a) a 5′-inverted terminal repeat sequence (5′-ITR) sequence;
(b) a promoter sequence;
(c) a human beta globin IVS2 intron sequence;
(d) a wild type coding sequence for propionyl-CoA carboxylase B (PCCB) according to SEQ ID NO: 7; and
(e) a 3′-inverted terminal repeat sequence (3′-ITR) sequence.

2 . The rAAV according to claim 1 , wherein the AAV capsid is from an AAV of serotype 9, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, rh10, or hu37.

3 . The rAAV according to claim 1 , wherein the promoter sequence is selected from a chicken β-actin (CBA) promoter sequence, a cytomegalovirus (CMV) immediate early gene promoter sequence, a transthyretin (TTR) promoter sequence, a thyroxine binding globulin (TBG) promoter sequence, an alpha-1 anti-trypsin (A1AT) promoter sequence, a CAG promoter sequence, and a PCCB gene-specific endogenous promoter sequence.

4 . The rAAV according to claim 3 , wherein the promoter sequence is:
a) the PCCB gene-specific endogenous promoter sequence comprising a nucleotide sequence of at least 15 continuous nucleotides, which is at least 95% identical to an equal length region of SEQ ID NO: 36; or b) the CBA promoter sequence.

5 . The rAAV according to claim 1 , wherein:
a) the 5′-ITR sequence and/or the 3′-ITR sequence are from AAV2; and/or b) the 5′-ITR sequence and the 3′-ITR sequence comprises or consists of SEQ ID NO: 15.

6 . The rAAV according to claim 1 , wherein the 5′-ITR sequence and/or the 3′-ITR sequence are from a non-AAV2 source.

7 . The rAAV according to claim 1 , wherein the vector genome further comprises a truncated or complete nucleotide sequence of a human PCCB 5′-untranslated region (UTR) and/or a 3′-UTR.

8 . The rAAV according to claim 7 , wherein:
a) the complete nucleotide sequence of the human PCCB 5′-UTR comprises SEQ ID NO: 32; and/or b) the truncated nucleotide sequence of the human PCCB 5′-UTR comprises a nucleotide sequence of at least 100 continuous nucleotides, which is at least 95% identical to an equal length region of SEQ ID NO: 32.

9 . The rAAV according to claim 1 , wherein the vector genome further comprises:
a) a polyadenylation signal sequence; and/or b) one or more enhancer sequences.

10 . The rAAV according to claim 9 , wherein:
a) the polyadenylation signal sequence:
i. is selected from an SV40 polyadenylation signal sequence, a bovine growth hormone (BGH) polyadenylation signal sequence, a rabbit beta globin polyadenylation signal sequence, and a PCCB gene-specific endogenous polyadenylation signal sequence;
ii. is a bovine growth hormone (BGH) polyadenylation signal sequence comprising SEQ ID NO: 22;
iii. is an SV40 polyadenylation signal sequence comprising SEQ ID NO: 23; or
iv. comprises the PCCB gene-specific endogenous polyadenylation signal sequence; and/or
b) the one or more enhancer sequences:
i. is selected from a cytomegalovirus (CMV) immediate early gene enhancer sequence, a transthyretin enhancer (enTTR) sequence, a chicken β-actin (CBA) enhancer sequence, an En34 enhancer sequence, and an apolipoprotein E (ApoE) enhancer sequence;
ii. comprises or consists of SEQ ID NO: 19; and/or
iii. is located upstream of the promoter sequence.

11 . The rAAV according to claim 10 , wherein the PCCB gene-specific endogenous polyadenylation signal sequence comprises a nucleotide sequence of at least 15 continuous nucleotides, which is at least 95% identical to an equal length region of SEQ ID NO: 37.

12 . A recombinant adeno-associated virus (rAAV), said rAAV comprising an AAV capsid, and a vector genome packaged therein, said vector genome comprising in 5′ to 3′ order:
(a) a 5′-ITR sequence;
(b) an enhancer sequence;
(c) a promoter sequence;
(d) a human beta globin IVS2 intron sequence;
(e) wild type coding sequence for propionyl-CoA carboxylase B (PCCB) according to SEQ ID NO: 7;
(f) a polyadenylation signal sequence; and
(g) a 3′-ITR sequence.

13 . The rAAV according to claim 12 , wherein the AAV capsid is from an AAV of serotype 9, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, rh10, or hu37.

14 . The rAAV according to claim 12 , wherein:
a) the promoter sequence is selected from a chicken β-actin (CBA) promoter sequence, a cytomegalovirus (CMV) immediate early gene promoter sequence, a transthyretin (TTR) promoter sequence, a thyroxine binding globulin (TBG) promoter sequence, an alpha-1 anti-trypsin (A1AT) promoter sequence, a CAG promoter sequence, and a PCCB gene-specific endogenous promoter sequence; b) the polyadenylation signal sequence is selected from a bovine growth hormone (BGH) polyadenylation signal sequence, an SV40 polyadenylation signal sequence, a rabbit beta globin polyadenylation signal sequence, and a PCCB gene-specific endogenous polyadenylation signal sequence; c) the enhancer sequence is selected from a cytomegalovirus (CMV) immediate early gene enhancer sequence, a transthyretin enhancer (enTTR) sequence, a chicken β-actin (CBA) enhancer sequence, an En34 enhancer sequence, and an ApoE enhancer sequence; d) the 5′-ITR sequence and/or the 3′-ITR sequence are from AAV2 or from a non-AAV2 source; and/or e) the 5′-ITR sequence and the 3′-ITR sequence comprises or consists of SEQ ID NO: 15.

15 . The rAAV according to claim 14 , wherein the promoter sequence is:
a) the PCCB gene-specific endogenous promoter sequence comprising a nucleotide sequence of at least 15 continuous nucleotides, which is at least 95% identical to an equal length region of SEQ ID NO: 36; or b) the CBA promoter sequence.

16 . The rAAV according to claim 14 , wherein:
a) the polyadenylation signal sequence:
i. is a bovine growth hormone (BGH) polyadenylation signal sequence comprising SEQ ID NO: 22;
ii. is an SV40 polyadenylation signal sequence comprising SEQ ID NO: 23; or
iii. comprises the PCCB gene-specific endogenous polyadenylation signal sequence; and/or
b) the enhancer sequence is the CMV immediate early gene enhancer sequence.

17 . The rAAV according to claim 16 , wherein the PCCB gene-specific endogenous polyadenylation signal sequence comprises a nucleotide sequence of at least 15 continuous nucleotides, which is at least 95% identical to an equal length region of SEQ ID NO: 37.

18 . The rAAV according to claim 12 , wherein the vector genome further comprises a truncated or complete nucleotide sequence of a human PCCB 5′-untranslated region (UTR), located between vector genome elements (d) and (e).

19 . The rAAV according to claim 18 , wherein:
a) the complete nucleotide sequence of the human PCCB 5′-UTR comprises SEQ ID NO: 32; and/or b) the truncated nucleotide sequence of the human PCCB 5′-UTR comprises a nucleotide sequence of at least 100 continuous nucleotides, which is at least 95% identical to an equal length region of SEQ ID NO: 32.

20 . The rAAV according to claim 12 , wherein the vector genome further comprises a truncated or complete nucleotide sequence of a human PCCB 3′-untranslated region (UTR), located between vector genome elements (f) and (g).

21 . The rAAV according to claim 20 , wherein:
a) the complete nucleotide sequence of the human PCCB 3′-UTR comprises SEQ ID NO: 33; and/or b) the truncated nucleotide sequence of the human PCCB 3′-UTR comprises a nucleotide sequence of at least 15 continuous nucleotides, which is at least

Assignees

• Ultragenyx Pharmaceutical Inc

Inventors

• Fuller Matthew Scott
• Wadsworth Samuel
• Clark Kelly Reed
• Daugherty Sean Christopher
• Craig Stewart

Classifications

• C12N2830/50

  regulating RNA stability, not being an intron, e.g. poly A signal · CPC title

• C12N2830/008

  cell type or tissue specific enhancer/promoter combination · CPC title

• C12N2750/14143

  viral genome or elements thereof as genetic vector · CPC title

• C12N15/86 Primary

  Viral vectors · CPC title

• A61K48/0091

  Purification or manufacturing processes for gene therapy compositions · CPC title