Compositions and methods for treating alpha-1 antitrypsin deficiency
AssigneeBeam Therapeutics Inc.
InventorsNicole Gaudelli, Michael Packer, Bernd Zetsche, Ian Slaymaker, Yi Yu, David A. Born, Seung-Joo Lee
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Abstract
The present invention features compositions and methods for editing deleterious mutations associated with alpha-1 anti-trypsin (A1AT) deficiency. In particular embodiments, the invention provides methods for correcting mutations in an A1AT polynucleotide using an adenosine deaminase base editor. ABE8, having unprecedented levels of efficiency.
Claims21
A method of editing an alpha-1 antitrypsin polynucleotide comprising a single nucleotide polymorphism (SNP) associated with alpha-1 antitrypsin deficiency, the method comprising contacting the polynucleotide with one or more guide RNAs and a base editor comprising a polynucleotide programmable DNA binding domain and at least one base editor domain that comprises an adenosine deaminase variant comprising an amino acid sequence that is at least 90% identical to the following TadA*7.10 amino acid sequence and that further comprises an arginine or a threonine at amino acid position 147 compared to the TadA*7.10 amino acid sequence:
- (SEQ ID NO:
- 3)
- MSEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVLNNRVIGEGWNRAIG
- LHDPTAHAEIMALRQGGLVMQNYRLIDATLYVTFEPCVMCAGAMIHSRIG
- RVVFGVRNAKTGAAGSLMDVLHYPGMNHRVEITEGILADECAALLCYFFR
- MPRQVFNAQKKAQSSTD,
- wherein said guide RNA targets said base editor to effect an alteration of the SNP associated with alpha-1 antitrypsin deficiency.
A method of editing an alpha-1 antitrypsin polynucleotide comprising a single nucleotide polymorphism (SNP) associated with alpha-1 antitrypsin deficiency, the method comprising contacting an alpha-1 antitrypsin polynucleotide with one or more guide RNAs and a fusion protein comprising a polynucleotide programmable DNA binding domain comprising an amino acid sequence with at least 90% identity to SEQ ID NO:
- 13, and at least one base editor domain comprising an adenosine deaminase variant comprising an amino acid sequence that is at least 90% identical to the following TadA*7.10 amino acid sequence and that further comprises an arginine or a threonine at amino acid position 147 compared to the TadA*7.10 amino acid sequence:
- (SEQ ID NO:
- 3)
- MSEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVLNNRVIGEGWNRAIGL
- HDPTAHAEIMALRQGGLVMQNYRLIDATLYVTFEPCVMCAGAMIHSRIGRV
- VFGVRNAKTGAAGSLMDVLHYPGMNHRVEITEGILADECAALLCYFFRMPR
- QVFNAQKKAQSSTD.
A base editor system comprising:
- a) a base editor comprising a polynucleotide programmable DNA binding domain and at least one base editor domain that comprises an adenosine deaminase variant comprising an amino acid sequence that is at least 90% identical to the following TadA*7.10 amino acid sequence and that further comprises an arginine or a threonine at amino acid position 147 compared to the TadA*7.10 amino acid sequence:
- MSEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVLNNRVIGEGWNRAIGLHDPTAHAEIMALRQGG LVMQNYRLIDATLYVTFEPCVMCAGAMIHSRIGRVVFGVRNAKTGAAGSLMDVLHYPGMNHRVEITE GILADECAALLCYFFRMPRQVFNAQKKAQSSTD (SEQ ID NO:
- 3);
- and
- b) a guide RNA comprising a nucleic acid sequence selected from the group consisting of
- (SEQ ID NO:
- 5)
- 5′-ACCAUCGACAAGAAAGGGACUGA GUUUUAGAGC UAGAAAUAGC AAGUUAAAAU
- AAGGCUAGUC CGUUAUCAAC UUGAAAAAGU GGCACCGAGU CGGUGCUUUU-3′;
- (SEQ ID NO:
- 6)
- 5′-CCAUCGACAAGAAAGGGACUGA GUUUUAGAGC UAGAAAUAGC AAGUUAAAAU
- AAGGCUAGUC CGUUAUCAAC UUGAAAAAGU GGCACCGAGU CGGUGCUUUU-3′;
- (SEQ ID NO:
- 7)
- 5′-CAUCGACAAGAAAGGGACUGA GUUUUAGAGC UAGAAAUAGC AAGUUAAAAU
- AAGGCUAGUC CGUUAUCAAC UUGAAAAAGU GGCACCGAGU CGGUGCUUUU-3′;
- (SEQ ID NO:
- 8)
- 5′-AUCGACAAGAAAGGGACUGA GUUUUAGAGC UAGAAAUAGC AAGUUAAAAU
- AAGGCUAGUC CGUUAUCAAC UUGAAAAAGU GGCACCGAGU CGGUGCUUUU-3′;
- (SEQ ID NO:
- 9)
- 5′-UCGACAAGAAAGGGACUGA GUUUUAGAGC UAGAAAUAGC AAGUUAAAAU
- AAGGCUAGUC CGUUAUCAAC UUGAAAAAGU GGCACCGAGU CGGUGCUUUU-3′;
- (SEQ ID NO:
- 10)
- 5′-CGACAAGAAAGGGACUGA GUUUUAGAGC UAGAAAUAGC AAGUUAAAAU AAGGCUAGUC
- CGUUAUCAAC UUGAAAAAGU GGCACCGAGU CGGUGCUUUU-3′.
A pharmaceutical composition or a kit comprising a base editor system comprising:
- a) a base editor comprising a polynucleotide programmable DNA binding domain and at least one base editor domain that comprises an adenosine deaminase variant comprising an amino acid sequence that is at least 90% identical to the following TadA*7.10 amino acid sequence and that further comprises an arginine or a threonine at amino acid position 147 compared to the TadA*7.10 amino acid sequence:
- (SEQ ID NO:
- 3)
- MSEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVLNNRVIGEGWNRAI
- GLHDPTAHAEIMALRQGGLVMQNYRLIDATLYVTFEPCVMCAGAMIHSR
- IGRVVFGVRNAKTGAAGSLMDVLHYPGMNHRVEITEGILADECAALLCY
- FFRMPRQVFNAQKKAQSSTD;
- and
- b) a guide RNA comprising a nucleic acid sequence selected from the group consisting of
- (SEQ ID NO:
- 5)
- 5′-ACCAUCGACAAGAAAGGGACUGA GUUUUAGAGC UAGAAAUAGC
- AAGUUAAAAU AAGGCUAGUC CGUUAUCAAC UUGAAAAAGU
- GGCACCGAGU CGGUGCUUUU-3′;
- (SEQ ID NO:
- 6)
- 5′-CCAUCGACAAGAAAGGGACUGA GUUUUAGAGC UAGAAAUAGC
- AAGUUAAAAU AAGGCUAGUC CGUUAUCAAC UUGAAAAAGU
- GGCACCGAGU CGGUGCUUUU-3′;
- (SEQ ID NO:
- 7)
- 5′-CAUCGACAAGAAAGGGACUGA GUUUUAGAGC UAGAAAUAGC
- AAGUUAAAAU AAGGCUAGUC CGUUAUCAAC UUGAAAAAGU
- GGCACCGAGU CGGUGCUUUU-3′;
- (SEQ ID NO:
- 8)
- 5′-AUCGACAAGAAAGGGACUGA GUUUUAGAGC UAGAAAUAGC
- AAGUUAAAAU AAGGCUAGUC CGUUAUCAAC UUGAAAAAGU
- GGCACCGAGU CGGUGCUUUU-3′;
- (SEQ ID NO:
- 9)
- 5′-UCGACAAGAAAGGGACUGA GUUUUAGAGC UAGAAAUAGC
- AAGUUAAAAU AAGGCUAGUC CGUUAUCAAC UUGAAAAAGU
- GGCACCGAGU CGGUGCUUUU-3′;
- and
- (SEQ ID NO:
- 10)
- 5′-CGACAAGAAAGGGACUGA GUUUUAGAGC UAGAAAUAGC
- AAGUUAAAAU AAGGCUAGUC CGUUAUCAAC UUGAAAAAGU
- GGCACCGAGU CGGUGCUUUU-3′;
- wherein the pharmaceutical composition further comprises a pharmaceutically acceptable carrier, vehicle, or excipient.
A base editor system comprising a polynucleotide programmable DNA binding domain and at least one base editor domain that comprises an adenosine deaminase variant comprising an amino acid sequence that is at least 90% identical to the following TadA*7.10 amino acid sequence and that further comprises an arginine or a threonine at amino acid position 147 of the TadA*7.10 amino acid sequence:
- (SEQ ID NO:
- 3)
- MSEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVLNNRVIGEGWNRAIGL
- HDPTAHAEIMALRQGGLVMQNYRLIDATLYVTFEPCVMCAGAMIHSRIGRV
- VFGVRNAKTGAAGSLMDVLHYPGMNHRVEITEGILADECAALLCYFFRMPR
- QVFNAQKKAQSSTD
- and a guide RNA, wherein said guide RNA targets said base editor to effect an alteration of a SNP associated with alpha-1 antitrypsin deficiency.
A base editor system comprising one or more guide RNAs comprising a nucleic acid sequence complementary to an alpha-1 antitrypsin nucleic acid sequence containing a SNP associated with alpha-1 antiytrypsin deficiency, and a fusion protein comprising a polynucleotide programmable DNA binding domain comprising an amino acid sequence with at least 90% identity to SEQ ID NO:
- 13, and at least one base editor domain comprising an adenosine deaminase variant comprising an amino acid sequence that is at least 90% identical to the following TadA*7.10 amino acid sequence and that further comprises an arginine or a threonine at amino acid position 147 of the TadA*7.10 amino acid sequence:
- (SEQ ID NO:
- 3)
- MSEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVLNNRVIGEGWNRAIGL
- HDPTAHAEIMALRQGGLVMQNYRLIDATLYVTFEPCVMCAGAMIHSRIGRV
- VFGVRNAKTGAAGSLMDVLHYPGMNHRVEITEGILADECAALLCYFFRMPR
- QVFNAQKKAQSSTD.
Dependencies are inferred from the claim text.