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US 2026/0224748 A1Published application
Methods and compositions for treating alpha-1 antitrypsin deficiency
AssigneeBeam Therapeutics Inc.
InventorsMichael Packer, Brian Cafferty, Yi Yu
Life of this patent
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Abstract
Compositions and methods for editing deleterious mutations associated with Alpha-1 Antitrypsin Deficiency (A1AD). In particular embodiments, the invention provides methods for treating A1AD using a modified adenosine base editor with improved on-target editing and decreased off-target editing to correct mutations associated with A1AD.
Claims30
A nucleic acid encoding a base editor comprising a nucleic acid programmable DNA binding protein (napDNAbp) domain and an adenosine deaminase domain, wherein the napDNAbp domain comprises an alteration selected from the group consisting of M1135L, E1250K, A1283D, Q1136Y, R1337K, R765A, and Q768A of an amino acid sequence, or a fragment thereof lacking an N-terminal methionine, that is at least 90% identical to:
- (SEQ ID NO:
- 554)
- MDKKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGA
- LLFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHR
- LEESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKAD
- LRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENP
- INASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTP
- NFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAI
- LLSDILRVNTEITKAPLSASMVKRYDEHHQDLTLLKALVRQQLPEKYKEI
- FFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLR
- KQRTFDNGIIPHQIHLGELHAILRRQGDFYPFLKDNREKIEKILTFRIPY
- YVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDK
- NLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVD
- LLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKI
- IKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQ
- LKRLRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDD
- SLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKVVDELVKV
- MGGHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHP
- VENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSFLKDD
- SIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNL
- TKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLI
- REVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKK
- YPKLESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEI
- TLANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEV
- QTGGFSKESILPKGNSDKLIARKKDWDPKKYGGFMQPTVAYSVLVVAKVE
- KGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPK
- YSLFELENGRKRMLASAKFLQKGNELALPSKYVNFLYLASHYEKLKGSPE
- DNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDK
- PIREQAENIIHLFTLTNLGAPRAFKYFDTTIARKEYRSTKEVLDATLIHQ
- SITGLYETRIDLSQLGGD.
27 more elements
A base editor system comprising a nucleic acid encoding a base editor comprising (i) a nucleic acid programmable DNA binding protein (napDNAbp) domain and an adenosine deaminase domain and (ii) a guide polynucleotide,
- wherein the napDNAbp domain comprises an alteration selected from the group consisting of M1135L, E1250K, A1283D, Q1136Y, R1337K, R765A, and Q768A of an amino acid sequence, or a fragment thereof lacking an N-terminal methionine, that is at least 90% identical to:
- (SEQ ID NO:
- 554)
- MDKKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETAEAT
- RLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNIVD
- EVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFI
- QLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGL
- TPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNT
- EITKAPLSASMVKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEF
- YKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGIIPHQIHLGELHAILRRQGDFYPFLK
- DNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMT
- NFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRK
- VTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIV
- LTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRLRYTGWGRLSRKLINGIRDKQSGKTILDF
- LKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKVV
- DELVKVMGGHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHPVENTQL
- QNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSFLKDDSIDNKVLTRSDKNRGKSD
- NVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKH
- VAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAV
- VGTALIKKYPKLESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLAN
- GEIRKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKGNS
- DKLIARKKDWDPKKYGGFMQPTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNP
- IDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASAKFLQKGNELALPSKYVNFLYLAS
- HYEKLKGSPEDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPI
- REQAENIIHLFTLTNLGAPRAFKYFDTTIARKEYRSTKEVLDATLIHQSITGLYETRIDLSQ
- LGGD.
23 more elements
A guide RNA comprising a nucleotide sequence, from 5′ to 3′, selected from the group consisting of:
- (SEQ ID NO:
- 569)
- mAsmUsmCsGACAAGAAAGGGACUGAGUUUUAGAGCUAGAAAUAGCAAGU
- UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU
- GCmUsmUsmUsU;
- (SEQ ID NO:
- 570)
- mAsmUsmCsGACAAGAAAGGGACUGAGUUUUAGAGCUAGAAAUAGCAAGU
- UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU
- GCUsmUsmUsmU,
- wherein the guide is covalently linked at the 3′ end to a peptide with the amino acid sequence CKRTADGSEFESPKKKRKV (SEQ ID NO:
- 543);
- (SEQ ID NO:
- 571)
- mAsmUsmCsmGmAmCmAmAmGmAfAfAfGIGGsAsfCfUGsmAmGUsUsUsfUfAmGmAmGm
- CmUmAmGmAmAmAmUmAmGmCmAmAmGUUmAAmAmAUmAmAmGmGCUmAGUCmCGUUmAmUm
- CmAmAmCmUmUmGmAmAmAmAmAmGmUmGmGmCmAmCmCmGmAmGmUmCmGmGmUmGmCsmU
- smUsmU;
- (SEQ ID NOs:
- 572)
- mAsmUsmCsGACAAGAAAGGGACUGAmGUUUUAGmAmGmCmUmAmGmAmAmAmUmAmGmCmA
- mAGUUmAAmAAmUAmAmGmGmCmUmAGUmCmCGUUAmUmCAAmCmUmUmGmAmAmAmAmAmG
- mUmGGmCmAmCmCmGmAmGmUmCmGmGmUmGmCmUsmUsmUsmU;
- (SEQ ID NOs:
- 573)
- mCsmAsmUsCGACAAGAAAGGGACUGAGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGC
- UAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCmUsmUsmUsU;
- (SEQ ID NOs:
- 574)
- mAsmUsmCsmGmAmCmAmAmGmAfAfAfGIGGsAsfCUGmAmGUSUUfUfAmGmAmGmCmUm
- AmGmAmAmAmUmAmGmCmAmAmGUUmAAmAmAUmAmAmGmGCUmAGUCmCGUUmAmUmCmAm
- AmCmUmUmGmAmAmAmAmAmGUGmGmCmAmCmCmGmAmGmUmCmGmGmUmGmCsmUsmUsmU;
- (SEQ ID NOs:
- 575)
- mAsmUsmCsGACAAGAAAGGGACUGAmGUUUUAGmAmGmCmUmAmGmAmAmAmUmAmGmCmA
- mAGUUmAAmAAmUAmAmGmGmCmUmAGUmCmCGUUAmUmCAAmCmUmUmGmAmAmAmAmAmG
- UGGmCmAmCmCmGmAmGmUmCmGmGmUmGmCmUsmUsmUsmU;
- (SEQ ID NOs:
- 576)
- mAsmUsmCsmGmAmCmAmAmGmAAAGGGACUGmAmGUUUUAmGmAmGmCmUmAmGmAmAmAm
- UmAmGmCmAmAmGUUmAAmAmAUmAmAmGmGCUmAGUCmCGUUmAmUmCmAmAmCmUmUmGm
- AmAmAmAmAmGUGmGmCmAmCmCmGmAmGmUmCmGmGmUmGmCsmUsmUsmU;
- (SEQ ID NOs:
- 577)
- mAsmUsmCsmGmAmCmAmAmGmAAAGGGACUGAmGUUUUAGmAmGmCmUmAmGmAmAmAmUm
- AmGmCmAmAGUUmAAmAAmUAmAmGmGmCmUmAGUmCmCGUUAmUmCAAmCmUmUmGmAmAm
- AmAmAmGUGGmCmAmCmCmGmAmGmUmCmGmGmUmGmCmUsmUsmUsmU;
- (SEQ ID NOs:
- 578)
- mCsmAsmUsmCmGmAmCmAmAmGmAAAGGGACUGAmGUUUUAGmAmGmCmUmAmGmAmAmAm
- UmAmGmCmAmAGUUmAAmAAmUAmAmGmGmCmUmAGUmCmCGUUAmUmCAAmCmUmUmGmAm
- AmAmAmAmGUGGmCmAmCmCmGmAmGmUmCmGmGmUmGmCmUsmUsmUsmU;
- (SEQ ID NOs:
- 579)
- mAsmUsmCsmGmAmCmAmAmGmAmAAmGmGGAmCUGmAmGUUUUAGmAmGmCmUmAmGmAmA
- mAmUmAmGmCmAmAGUUmAAmAAmUAmAmGmGmCmUmAGUmCmCGUUAmUmCAAmCmUmUmG
- mAmAmAmAmAmGUGGmCmAmCmCmGmAmGmUmCmGmGmUmGmCmUsmUsmUsmU;
- (SEQ ID NOs:
- 580)
- mCsmAsmUsmCmGmAmCmAmAmGmAmAAmGmGGAmCUGmAmGUUUUAGmAmGmCmUmAmGmA
- mAmAmUmAmGmCmAmAGUUmAAmAAmUAmAmGmGmCmUmAGUmCmCGUUAmUmCAAmCmUmU
- mGmAmAmAmAmAmGUGGmCmAmCmCmGmAmGmUmCmGmGmUmGmCmUsmUsmUsmU;
- (SEQ ID NOs:
- 581)
- mCsmAsmUsCGACAAGAAAGGGACUGAmGUUUUAGmAmGmCmUmAmGmAmAmAmUmAmGmCm
- AmAGUUmAAmAAmUAmAmGmGmCmUmAGUmCmCGUUAmUmCAAmCmUmUmGmAmAmAmAmAm
- GUGGmCmAmCmCmGmAmGmUmCmGmGmUmGmCmUsmUsmUsmU;
- and
- (SEQ ID NOs:
- 582)
- mAsmUsmCsGACAAGAAAGGGACUGAGUUUUAGAmGmCmCmGmGmCmGmGmAmAmAmCmGmC
- mCmGmGmCAAGUUAAAAUAAGGCUAGUCCGUUAUCAmAmCmUmUmGmAmAmAmAmAmGmUmG
- mGmCmAmCmCmGmAmGmUmCmGmGmUmGmCmUsmUsmUsmU;
- (SEQ ID NOs:
- 583)
- mAsmUsmCsmGmAmCmAmAmGmAAAGGGACUGAGUUUUAGAmGmCmCmGmGmCmGmGmAmAm
- AmCmGmCmCmGmGmCAAGUUAAAAUAAGGCUAGUCCGUUAUCAmAmCmUmUmGmAmAmAmAm
- AmGmUmGmGmCmAmCmCmGmAmGmUmCmGmGmUmGmCmUsmUsmUsmU;
- (SEQ ID NOs:
- 584)
- mAsmUsmCsGACAAGAAAGGGACUGAGUUUUAGAmGmCmUmAmGmAmAmAmUmAmGmCAAGU
- UAAAAUAAGGCUAGUCCGUUAmUmCAAmCmUmUGGACUUCGGUCCmAmAmGmUmGGmCmAmC
- mCmGmAmGmUmCmGmGmUmGmCmUsmUsmUsmU;
- or
- (SEQ ID NO:
- 585)
- mAsmUsmCsGACAAGAAAGGGACUGAGUUUUAGAmGmCmCmGmGmCmGmGmAmAmAmCmGmC
- mCmGmGmCAAGUUAAAAUAAGGCUAGUCCGUUAmUmCAAmCmUmUGGACUUCGGUCCmAmAm
- GmUmGGmCmAmCmCmGmAmGmUmCmGmGmUmGmCmUmUmUmU;
- wherein “N” represents any nucleotide, “mN” indicates a 2′-OMe modification of the nucleotide “N”, fN indicates a 2′-fluoro (F) modification of the nucleotide “N,” and “Ns” indicates that the nucleotide “N” is linked to the following nucleotide by a phosphorothioate. sgRNA modified sequence here.
87 more elements
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 a guide RNA, and a base editor comprising a nucleic acid programmable DNA binding protein (napDNAbp) domain and an adenosine deaminase domain, wherein the napDNAbp domain comprises an alteration selected from the group consisting of M1135L, E1250K, A1283D, Q1136Y, R1337K, R765A, and Q768A of an amino acid sequence, or a fragment thereof lacking an N-terminal methionine, that is at least 90% identical to:
- (SEQ ID NO:
- 554)
- MDKKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETAEAT
- RLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNIVD
- EVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFI
- QLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGL
- TPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNT
- EITKAPLSASMVKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEF
- YKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGIIPHQIHLGELHAILRRQGDFYPFLK
- DNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMT
- NFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRK
- VTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIV
- LTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRLRYTGWGRLSRKLINGIRDKQSGKTILDF
- LKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKVV
- DELVKVMGGHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHPVENTQL
- QNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSFLKDDSIDNKVLTRSDKNRGKSD
- NVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKH
- VAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAV
- VGTALIKKYPKLESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLAN
- GEIRKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKGNS
- DKLIARKKDWDPKKYGGFMQPTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNP
- IDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASAKFLQKGNELALPSKYVNFLYLAS
- HYEKLKGSPEDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPI
- REQAENIIHLFTLTNLGAPRAFKYFDTTIARKEYRSTKEVLDATLIHQSITGLYETRIDLSQ
- LGGD,
- and wherein said guide RNA targets said base editor to effect an alteration of the SNP associated with alpha-1 antitrypsin deficiency.
23 more elements
Dependencies are inferred from the claim text.