JP2020510439A - シトシンからグアニンへの塩基編集因子 - Google Patents
シトシンからグアニンへの塩基編集因子 Download PDFInfo
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Abstract
Description
核酸配列の標的編集(例えば、標的切断またはゲノムDNA中への特異的改変の標的導入)は、遺伝子機能の研究にとって極めて有望なアプローチであり、またヒト遺伝子疾患のための新しい治療(therapies)を提供する見込みも有している。多くの遺伝子疾患は原理上、ゲノム中の特定の場所での特定のヌクレオチド変化をもたらすこと(例えば、疾患に関連する遺伝子の特定のコドンにおけるC→G変化またはG→C変化)によって処置され得るところ、かかる精密な遺伝子編集を達成するためのプログラム可能なやり方の開発は、強力で新しい研究ツールならびに遺伝子編集ベースの治療法(therapeutics)に対して見込みのある新しいアプローチの両方に代表される。
本明細書におよびクレームに使用されるとき、単数形「a」、「an」、および「the」は、文脈上明白に他に示される場合を除き、単数または複数を含む。よって、例えば、「薬剤(an agent)」への言及は、単数の剤および複数のかかる剤を含む。
例示的な触媒不活性型Cas9(dCas9):
例示的な触媒不活性型Cas9(dCas9):
核酸プログラム可能なDNA結合蛋白質(napDNAbp)
本開示のいくつかの側面は、塩基編集因子などの蛋白質を、特定の核酸(例えばDNAまたはRNA)配列へとガイドするために用いられ得る、核酸プログラム可能なDNA結合蛋白質を提供する。核酸プログラム可能なDNA結合蛋白質は、Cas9(例えば、dCas9およびnCas9)、CasX、CasY、Cpf1、C2c1、C2c2、C2C3、およびアルゴノートを包含するが、これに限定されない。Cas9とは異なるPAM特異性を有する核酸プログラム可能なDNA結合蛋白質の一例は、プレボテラ属(Prevotella)およびフランシセラ1(Francisella)由来のクラスター化され、規則的に間隔が空いている短い回分配列リピート(Cpf1)である。Cas9と同様に、Cpf1もまたクラス2CRISPRエフェクターである。Cpf1が、Cas9とは別個の特徴との強固なDNA干渉を仲介することが示されている。Cpf1は、tracrRNAを欠く単一RNA−誘導型エンドヌクレアーゼであり、T−リッチプロトスペーサー隣接モチーフ(TTN、TTTN、またはYTN)を利用する。さらに、Cpf1はねじれ型DNAの二本鎖切断を介してDNAを切断する。16のCpf1−ファミリー蛋白質の中で、AcidaminococcusおよびLachnospiraceae由来の2つの酵素がヒト細胞において効率的なゲノム編集活性を有することが示されている。Cpf1蛋白質は、当分野において公知であり、例えば以前に、Yamano et al., “Crystal stucture of Cpf1 in complex with guide RNA and target DNA.” Cell (165) 2016, p. 949-962に記載されており、その内容全体は参照として本明細書に組み込まれる。
いくつかの側面において、核酸プログラム可能なDNA結合蛋白質(napDNAbp)は、Cas9ドメインである。非限定的な、例示的なCas9ドメインは、本明細書において提供される。Cas9ドメインは、ヌクレアーゼ活性Cas9ドメイン、ヌクレアーゼ不活性Cas9ドメイン、またはCas9ニッカーゼであってもよい。 いくつかの態様において、Cas9ドメインは、ヌクレアーゼ活性ドメインである。例えば、Cas9ドメインは、二本鎖核酸の両方の鎖を切る(例えば二本鎖DNA分子の両方の鎖)、Cas9ドメインであってもよい。いくつかの態様において、Cas9ドメインは、配列番号4〜29に提示される、いずれか1つのアミノ酸配列を含む。いくつかの態様において、Cas9ドメインは、本明細書に提供されるいずれかのCas9または配列番号4〜29において提示される1つのアミノ酸配列に、少なくとも60%、少なくとも65%、少なくとも70%、少なくとも75%、少なくとも80%、少なくとも85%、少なくとも90%、少なくとも95%、少なくとも96%、少なくとも97%、少なくとも98%、少なくとも99%、または少なくとも99.5%、同一であるアミノ酸配列を含む。いくつかの態様において、Cas9ドメインは、本明細書に提供されるいずれかのCas9または配列番号4〜29において提示されるいずれか1つのアミノ酸配列と比較して、1、2、3、4、5、6、7、8、9、10、11、12、13、14、15、16、17、18、19、20、21、22、21、24、25、26、27、28、29、30、31、32、33、34、35、36、37、38、39、40、41、42、43、44、45、46、47、48、49、50またはより多くの変異を有するアミノ酸配列を含む。いくつかの態様において、Cas9ドメインは、本明細書に提供される任意のCas9または配列番号4〜29において提示されるいずれか1つのアミノ酸配列と比較して、少なくとも10、少なくとも15、少なくとも20、少なくとも30、少なくとも40、少なくとも50、少なくとも 60、少なくとも70、少なくとも80、少なくとも90、少なくとも100、少なくとも150、少なくとも200、少なくとも250、少なくとも300、少なくとも350、少なくとも400、少なくとも500、少なくとも600、少なくとも700、少なくとも800、少なくとも900、少なくとも1000、少なくとも1100、または少なくとも1200同一である近接しているアミノ酸残基を有するアミノ酸配列を含む。
開示のいくつかの側面は、異なるPAM特異性を有するCas9ドメインを提供する。典型的に、S.pyogenes(SpCas9)からのCas9などのCas9蛋白質は、特定の核酸領域に結合するのに、古典的なNGGPAM配列を要求し、そこで、「NGG」における「N」は、アデニン(A)、チミン(T)、グアニン(G)、またはシトシン(C)、およびGは、グアニンである。これは、ゲノム内の所望される塩基を編集する能力を限定することがある。いくつかの態様において、本明細書に提供される融合蛋白質を編集する、塩基は、正確な場所に位置することが必要であり、例えば、PAMの上流のおよそ15塩基である領域(例えば、「脱アミノ化するウィンドウ」)の4塩基内に標的塩基が存在する。Komor, A.C., et al., “Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage” Nature 533, 420-424 (2016)、を参照、その内容全体は、参照によって本明細書に組み込まれる。いくつかの態様において、脱アミノ化ウィンドウは、2、3、4、5、6、7、8、9、または10塩基領域内である。いくつかの態様において、脱アミノ化ウィンドウは、PAMの5、6、7、8、9、10、11、12、13、14、15、16、17、18、19、20、21、22、23、24、または25塩基上流である。よって、いくつかの態様において、本明細書に提供される任意の融合蛋白質は、古典的な(例えば、NGG)PAM配列を含有しないヌクレオチド配列に結合することが可能であるCas9ドメインを含有することがある。非古典的なPAM配列に結合するCas9ドメインは、当該技術分野において記載されてきており、および当業者に明らかであるだろう。例えば、非古典的なPAM配列に結合するCas9ドメインは、Kleinstiver, B. P., et al., “Engineered CRISPR-Cas9 nucleases with altered PAM specificities” Nature 523, 481-485 (2015); and Kleinstiver, B. P., et al., “Broadening the targetting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition” Nature Biotechnology 33, 1293-1298 (2015)、に記載されており;各々の全体の内容は、参照によって本明細書に組み込まれる。
本開示のいくつかの側面は、本明細書に提供される核酸塩基編集因子の高いフィデリティCas9ドメインを提供する。いくつかの態様において、高いフィデリティのCas9ドメインは、対応する野生型Cas9ドメインと比較して、Cas9ドメインとDNAの糖リン酸バックボーンとの間の静電気の相互作用を減少させる1つ以上の変異を含む、操作されたCas9ドメインである。特定の理論に束縛されることを望まないが、DNAの糖リン酸バックボーンとの減少した静電気の相互作用を有する高いフィデリティのCas9ドメインは、より少ないオフターゲット効果を有する。いくつかの態様において、Cas9ドメイン(例えば、野生型Cas9ドメイン)は、Cas9ドメインとDNAの糖リン酸バックボーンとの間の会合を減少させる1つ以上の変異を有する。いくつかの態様において、Cas9ドメインは、Cas9ドメインとDNAの糖リン酸バックボーンとの間の会合を、少なくとも1%、少なくとも2%、少なくとも3%、少なくとも4%、少なくとも5%、少なくとも10%、少なくとも15%、少なくとも20%、少なくとも25%、少なくとも30%、少なくとも35%、少なくとも40%、少なくとも45%、少なくとも50%、少なくとも55%、少なくとも60%、少なくとも65%、少なくとも70%、またはより多くの程度減少させる1つ以上の変異を含む。
ウラシル結合蛋白質またはUBPは、ウラシルに結合することが可能である蛋白質を指す。いくつかの態様において、ウラシル結合蛋白質は、ウラシル修飾酵素である。いくつかの態様において、ウラシル結合蛋白質は、ウラシル塩基除去酵素である。いくつかの態様において、ウラシル結合蛋白質は、ウラシルDNAグルコシラーゼ(UDG)である。いくつかの態様において、ウラシル結合蛋白質は、野生型UDG(例えば、ヒトUDG)がウラシルに結合する親和性の、少なくとも1%、2%、3%、5%、10%、15%、20%、30%、40%、50%、60%、70%、80%、90%、または少なくとも95%である親和性で、ウラシルに結合する。いくつかの態様において、ウラシル結合蛋白質は、ウラシルに結合する野生型UDG(例えば、ヒトUDG)などの、野生型ウラシル結合蛋白質と比較して、1、2、3、4、5、6、7、8、9、10、11、12、13、14、15、16、17、18、19、20、21、22、21、24、25、26、27、28、29、30、31、32、33、34、35、36、37、38、39、40、41、42、43、44、45、46、47、48、49、50、またはより多くのアミノ酸変化を有することがある。
UDG
核酸ポリメラーゼ、またはNAPは、ヌクレオチド(例えば、デオキシリボヌクレオチドおよびリボヌクレオチド)から核酸分子(例えばDNAおよびRNA)を合成する酵素を指す。いくつかの態様において、NAPは、DNAポリメラーゼである。いくつかの態様において、NAPは、損傷乗り越えポリメラーゼである。損傷乗り越えポリメラーゼは、例えば、複製フォークをリスタートすること、またはDNA損傷の存在によるゲノムにおいて残存するギャップを満たすことによって、変異誘発において役割を担う。例示的な損傷乗り越えポリメラーゼは、Polベータ、Polラムダ、Polエタ、Polミュ―、Polイオタ、Polカッパ、Polアルファ、Polデルタ、Polガンマ、およびPolニューを包含する。
Polベータ
塩基除去酵素、またはBEEは、核酸分子(例えば、DNAまたはRNA)から塩基(例えば、A、T、C、G、またはU)を除去することが可能である、蛋白質を指す。いくつかの態様において、BEEは、DNAからシトシンを除去することが可能である。いくつかの態様において、BEEは、DNAからチミンを除去することが可能である。例示的なBEEは、限定されることなしに、Sang et al., “A Unique uracil-DNA binding protein of the uracil DNA glycosylase superfamily,” Nucleic Acids Research, Vol. 43, No. 17 2015、において記載されるように、UDG Tyr147AlaおよびUDG Asn204Aspを包含し;その内容全体は、参照によって本明細書に組み込まれる。
UDG(Tyr147Ala)−変異された残基は、太字および下線付きによって示される。
いくつかの態様において、本明細書に提供される任意の融合蛋白質または塩基編集因子は、シチジンデアミナーゼドメインを含む。いくつかの態様において、シチジンデアミナーゼドメインは、CからUへの塩基変化を触媒し得る。いくつかの態様において、シチジンデアミナーゼドメインは、アポリポ蛋白質B mRNA編集複合体(APOBEC)ファミリーデアミナーゼである。いくつかの態様において、シチジンデアミナーゼドメインは、APOBEC1デアミナーゼである。いくつかの態様において、シチジンデアミナーゼドメインは、APOBEC2デアミナーゼである。いくつかの態様において、シチジンデアミナーゼドメインは、APOBEC3デアミナーゼである。いくつかの態様において、シチジンデアミナーゼドメインは、APOBEC3Aデアミナーゼである。いくつかの態様において、シチジンデアミナーゼドメインは、APOBEC3Bデアミナーゼである。いくつかの態様において、シチジンデアミナーゼドメインは、APOBEC3Cデアミナーゼである。いくつかの態様において、シチジンデアミナーゼドメインは、APOBEC3Dデアミナーゼである。いくつかの態様において、シチジンデアミナーゼドメインは、APOBEC3Eデアミナーゼである。いくつかの態様において、シチジンデアミナーゼドメインは、APOBEC3Fデアミナーゼである。いくつかの態様において、シチジンデアミナーゼドメインは、APOBEC3Gデアミナーゼである。いくつかの態様において、シチジンデアミナーゼドメインは、APOBEC3Hデアミナーゼである。いくつかの態様において、シチジンデアミナーゼドメインは、APOBEC4デアミナーゼである。いくつかの態様において、シチジンデアミナーゼドメインは、活性化誘導 デアミナーゼ(AID)である。いくつかの態様において、シチジンデアミナーゼドメインは、脊椎動物のデアミナーゼである。いくつかの態様において、シチジンデアミナーゼドメインは、非脊椎動物のデアミナーゼである。いくつかの態様において、シチジンデアミナーゼドメインは、ヒト、チンパンジー、ゴリラ、サル、ウシ、イヌ、ラット、マウスのデアミナーゼである。いくつかの態様において、シチジンデアミナーゼドメインは、ヒトデアミナーゼである。いくつかの態様において、シチジンデアミナーゼドメインは、ラットデアミナーゼ、例えばrAPOBEC1である。いくつかの態様において、シチジンデアミナーゼドメインは、Petromyzon marinusシチジンデアミナーゼ1(pmCDA1)である。いくつかの態様において、シチジンデアミナーゼドメインは、ヒトAPOBEC3G(配列番号77)である。いくつかの態様において、シチジンデアミナーゼドメインは、ヒトAPOBEC3Gのフラグメントである(配列番号100)。いくつかの態様において、シチジンデアミナーゼドメインは、D316R_D317R変異(配列番号99)を含むヒトAPOBEC3Gのバリアントである。いくつかの態様において、シチジンデアミナーゼドメインは、ヒトAPOBEC3Gのフラグメントであり、および配列番号77(配列番号101)におけるD316R_D317R変異に対応する変異を含む。
本開示のいくつかの側面は、本明細書に提供される任意の融合蛋白質のデアミナーゼドメインの触媒活性を調節すること、例えば、デアミナーゼドメインにおいて点変異を作製することによって、融合蛋白質(例えば、塩基編集因子)の加工性に影響を与えるという認識に基づく。例えば、塩基編集融合蛋白質内のデアミナーゼドメインの触媒活性を減らす、しかし除かない変異は、デアミナーゼドメインが標的残基に隣接する残基の脱アミノ化を触媒するだろうことの可能性をより低くし得、これにより脱アミノ化ウィンドウを狭める。脱アミノ化ウィンドウを狭める能力は、特定の標的残基に隣接する残基の望まれない脱アミノ酸を防止してもよく、それは、オフターゲット効果を減少させるか、または防止する。
本開示のいくつかの側面は、核酸プログラム可能なDNA結合蛋白質(napDNAbp)、シチジンデアミナーゼ、およびウラシル結合蛋白質(UBP)を含む融合蛋白質を提供する。いくつかの態様において、本明細書に提供される任意の融合蛋白質は、塩基編集因子である。いくつかの態様において、UBPは、ウラシル修飾酵素である。いくつかの態様において、UBPは、ウラシル塩基除去酵素である。いくつかの態様において、UBPは、ウラシルDNAグリコシラーゼである。いくつかの態様において、UBPは、本明細書に提供される任意のウラシル結合蛋白質である。例えば、UBPは、UDG、UdgX、UdgX*、UdgX_On、またはSMUG1であってもよい。いくつかの態様において、UBPは、ウラシル結合蛋白質、ウラシル塩基除去酵素またはウラシルDNAグルコシラーゼ(UDG)酵素に、少なくとも75%、80%、85%、90%、95%、96%、97%、98%、99%、または99.5%同一であるアミノ酸配列を含む。いくつかの態様において、UBPは、本明細書に提供される任意のウラシル結合蛋白質に、少なくとも75%、80%、85%、90%、95%、96%、97%、98%、99%、または99.5%同一であるアミノ酸配列を含む。例えば、UBPは、配列番号48〜53のいずれか1つに、少なくとも75%、80%、85%、90%、95%、96%、97%、98%、99%、または99.5%同一であるアミノ酸配列を含んでもよい。いくつかの態様において、UBPは、配列番号48〜53のいずれか1つのアミノ酸配列を含む。
NH2−[シチジンデアミナーゼ]−[napDNAbp]−[UBP]−COOH;
NH2−[シチジンデアミナーゼ]−[UBP]−[napDNAbp]−COOH;
NH2−[UBP]−[シチジンデアミナーゼ]−[napDNAbp]−COOH;
NH2−[UBP]−[napDNAbp]−[シチジンデアミナーゼ]−COOH;
NH2−[napDNAbp]−[UBP]−[シチジンデアミナーゼ]−COOH;または
NH2−[napDNAbp]−[シチジンデアミナーゼ]−[UBP]−COOH
を含む。
SGSETPGTSESATPES(配列番号102)、
SGGS(配列番号103)、
SGGSSGSETPGTSESATPESSGGS(配列番号107)、
SGGSSGGSSGSETPGTSESATPESSGGSSGGS(配列番号108)、
GGSGGSPGSPAGSPTSTEEGTSESATPESGPGTSTEPSEGSAPGSPAGSPTSTEEGTSTEPSEGSAPGTSTEPSEGSAPGTSESATPESGPGSEPATSGGSGGS(配列番号109)、または
SGGSGGSGGS(配列番号120)
のアミノ酸配列を含むリンカーを介して融合される。いくつかの態様において、シチジンデアミナーゼとnapDNAbp、シチジンデアミナーゼとUBP、および/またはnapDNAbpとUBPは、アミノ酸配列SGSETPGTSESATPES(配列番号102)を含むリンカーを介して融合され、それはまた、XTENリンカーとしても言及される。
本開示のいくつかの側面は、核酸プログラム可能なDNA結合蛋白質(napDNAbp)、シチジンデアミナーゼおよび核酸ポリメラーゼ(NAP)ドメインを含む融合蛋白質を提供する。いくつかの態様において、本明細書に提供される任意の融合蛋白質は、塩基編集因子である。いくつかの態様において、NAPは、真核生物の核酸ポリメラーゼである。いくつかの態様において、NAPは、DNAポリメラーゼである。いくつかの態様において、NAPは、損傷乗り越えポリメラーゼ活性を有する。いくつかの態様において、NAPは、損傷乗り越えDNAポリメラーゼである。いくつかの態様において、NAPは、Rev7、Rev1複合体、ポリメラーゼイオタ、ポリメラーゼカッパ、またはポリメラーゼエタである。いくつかの態様において、NAPは、真核生物のポリメラーゼアルファ、ベータ、ガンマ、デルタ、イプシロン、ガンマ、エタ、イオタ、カッパ、ラムダ、ミュー、またはニューである。いくつかの態様において、NAPは、核酸ポリメラーゼ(例えば、損傷乗り越えDNAポリメラーゼ)に少なくとも75%、80%、85%、90%、95%、96%、97%、98%、99%、または99.5%同一であるアミノ酸配列を含む。いくつかの態様において、NAPは、本明細書に提供される任意の核酸ポリメラーゼ配列に少なくとも75%、80%、85%、90%、95%、96%、97%、98%、99%、または99.5%同一であるアミノ酸配列を含む。例えば、NAPは、配列番号54〜64のいずれか1つに、少なくとも75%、80%、85%、90%、95%、96%、97%、98%、99%、または99.5%同一であるアミノ酸配列を含む。いくつかの態様において、NAPは、配列番号54〜64のいずれか1つのアミノ酸配列を含む。
NH2−[シチジンデアミナーゼ]−[napDNAbp]−[NAP]−COOH;
NH2−[シチジンデアミナーゼ]−[NAP]−[napDNAbp]−COOH;
NH2−[NAP]−[シチジンデアミナーゼ]−[napDNAbp]−COOH;
NH2−[NAP]−[napDNAbp]−[シチジンデアミナーゼ]−COOH;
NH2−[napDNAbp]−[NAP]−[シチジンデアミナーゼ]−COOH;または
NH2−[napDNAbp]−[シチジンデアミナーゼ]−[NAP]−COOH
を含む。
GSETPGTSESATPES(配列番号102)、
SGGS(配列番号103)、
SGGSSGSETPGTSESATPESSGGS(配列番号107)、
SGGSSGGSSGSETPGTSESATPESSGGSSGGS(配列番号108)、
GGSGGSPGSPAGSPTSTEEGTSESATPESGPGTSTEPSEGSAPGSPAGSPTSTEEGTSTEPSEGSAPGTSTEPSEGSAPGTSESATPESGPGSEPATSGGSGGS(配列番号109)、または
SGGSGGSGGS(配列番号120)のアミノ酸配列を含む、リンカーを介して融合される。いくつかの態様において、シチジンデアミナーゼとnapDNAbp、シチジンデアミナーゼとNAP、および/またはnapDNAbpとNAPは、アミノ酸配列SGSETPGTSESATPES(配列番号102)を含むリンカーを介して融合され、それは、XTENリンカーとしてもまた言及されてもよい。
本開示のいくつかの側面は、核酸プログラム可能なDNA結合蛋白質(napDNAbp)、シチジンデアミナーゼ、ウラシル結合蛋白質(UBP)、および核酸ポリメラーゼ(NAP)ドメインを含む、融合蛋白質を提供する。いくつかの態様において、本明細書に提供される任意の融合蛋白質は、塩基編集因子である。いくつかの態様において、NAPは、真核生物の核酸ポリメラーゼである。いくつかの態様において、NAPは、DNAポリメラーゼである。いくつかの態様において、NAPは、損傷乗り越えポリメラーゼ活性を有する。いくつかの態様において、NAPは、損傷乗り越えDNAポリメラーゼである。いくつかの態様において、NAPは、Rev7、Rev1複合体、ポリメラーゼイオタ、ポリメラーゼカッパ、またはポリメラーゼエタである。いくつかの態様において、NAPは、真核生物のポリメラーゼアルファ、ベータ、ガンマ、デルタ、イプシロン、ガンマ、エタ、イオタ、カッパ、ラムダ、ミュー、またはニューである。いくつかの態様において、NAPは、核酸ポリメラーゼ(例えば、損傷乗り越えDNAポリメラーゼ)に少なくとも75%、80%、85%、90%、95%、96%、97%、98%、99%、または99.5%同一である、アミノ酸配列を含む。いくつかの態様において、NAPは、本明細書に提供される任意の核酸ポリメラーゼに、少なくとも75%、80%、85%、90%、95%、96%、97%、98%、99%、または99.5%同一であるアミノ酸配列を含む。例えば、NAPは、配列番号54〜64のいずれか1つに少なくとも75%、80%、85%、90%、95%、96%、97%、98%、99%、または99.5% 同一であるアミノ酸配列を含んでもよい。いくつかの態様において、NAPは、配列番号54〜64のいずれか1つのアミノ酸配列を含む。
NH2−[NAP]−[シチジンデアミナーゼ]−[napDNAbp]−[UBP]−COOH;
NH2−[シチジンデアミナーゼ]−[NAP]−[napDNAbp]−[UBP]−COOH;
NH2−[シチジンデアミナーゼ]−[napDNAbp]−[NAP]−[UBP]−COOH;
NH2−[シチジンデアミナーゼ]−[napDNAbp]−[UBP]−[NAP]−COOH;
NH2−[NAP]−[シチジンデアミナーゼ]−[UBP]−[napDNAbp]−COOH;
NH2−[シチジンデアミナーゼ]−[NAP]−[UBP]−[napDNAbp]−COOH;
NH2−[シチジンデアミナーゼ]−[UBP]−[NAP]−[napDNAbp]−COOH;
NH2−[シチジンデアミナーゼ]−[UBP]−[napDNAbp]−[NAP]−COOH;
NH2−[NAP]−[UBP]−[シチジンデアミナーゼ]−[napDNAbp]−COOH;
NH2−[UBP]−[NAP]−[シチジンデアミナーゼ]−[napDNAbp]−COOH;
NH2−[UBP]−[シチジンデアミナーゼ]−[NAP]−[napDNAbp]−COOH;
NH2−[UBP]−[シチジンデアミナーゼ]−[napDNAbp]−[NAP]−COOH;
NH2−[NAP]−[UBP]−[napDNAbp]−[シチジンデアミナーゼ]−COOH;
NH2−[UBP]−[NAP]−[napDNAbp]−[シチジンデアミナーゼ]−COOH;
NH2−[UBP]−[napDNAbp]−[NAP]−[シチジンデアミナーゼ]−COOH;
NH2−[UBP]−[napDNAbp]−[シチジンデアミナーゼ]−[NAP]−COOH;
NH2−[NAP]−[napDNAbp]−[UBP]−[シチジンデアミナーゼ]−COOH;
NH2−[napDNAbp]−[NAP]−[UBP]−[シチジンデアミナーゼ]−COOH;
NH2−[napDNAbp]−[UBP]−[NAP]−[シチジンデアミナーゼ]−COOH;
NH2−[napDNAbp]−[UBP]−[シチジンデアミナーゼ]−[NAP]−COOH;
NH2−[NAP]−[napDNAbp]−[シチジンデアミナーゼ]−[UBP]−COOH;
NH2−[napDNAbp]−[NAP]−[シチジンデアミナーゼ]−[UBP]−COOH;
NH2−[napDNAbp]−[シチジンデアミナーゼ]−[NAP]−[UBP]−COOH;または
NH2−[napDNAbp]−[シチジンデアミナーゼ]−[UBP]−[NAP]−COOH
を含む。
いくつかの態様において、
SGSETPGTSESATPES(配列番号102)、SGGS(配列番号103)、
SGGSSGSETPGTSESATPESSGGS(配列番号107)、
SGGSSGGSSGSETPGTSESATPESSGGSSGGS(配列番号108)、
GGSGGSPGSPAGSPTSTEEGTSESATPESGPGTSTEPSEGSAPGSPAGSPTSTEEGTSTEPSEGSAPGTSTEPSEGSAPGTSESATPESGPGSEPATSGGSGGS(配列番号109)、
またはSGGSGGSGGS(配列番号120)
のアミノ酸配列を含むリンカー。
いくつかの態様において、リンカーは、アミノ酸配列SGSETPGTSESATPES(配列番号102)を含み、それはXTENリンカーとしてもまた言及されることがある。
本開示のいくつかの側面は、核酸プログラム可能なDNA結合蛋白質(napDNAbp)、および塩基除去酵素を含む、融合蛋白質を提供する。いくつかの態様において、本明細書に提供される任意の融合蛋白質は、塩基編集因子である。いくつかの態様において、塩基除去酵素(BEE)は、シトシン、チミン、アデニン、グアニン、またはウラシル塩基除去酵素である。いくつかの態様において、塩基除去酵素(BEE)は、シトシン塩基除去酵素である。いくつかの態様において、BEEはチミン塩基除去酵素である。いくつかの態様において、塩基除去酵素は、天然に生じるBEEに少なくとも75%、80%、85%、90%、95%、96%、97%、98%、99%、または99.5%同一であるアミノ酸配列を含む。いくつかの態様において、塩基除去酵素は、配列番号65または66のいずれか1つに少なくとも75%、80%、85%、90%、95%、96%、97%、98%、99%、または99.5%同一であるアミノ酸配列を含む。いくつかの態様において、塩基除去酵素は、配列番号65または66のいずれか1つのアミノ酸配列を含む。
NH2−[BEE]−[napDNAbp]−COOH;または
NH2−[napDNAbp]−[BEE]−COOH;
を含む。
いくつかの態様において、NAPは、DNAポリメラーゼである。いくつかの態様において、NAPは、損傷乗り越えポリメラーゼ活性を有する。いくつかの態様において、NAPは、損傷乗り越えDNAポリメラーゼである。いくつかの態様において、NAPは、Rev7、Rev1複合体、ポリメラーゼイオタ、ポリメラーゼカッパ、またはポリメラーゼエタである。いくつかの態様において、NAPは、真核生物のポリメラーゼアルファ、ベータ、ガンマ、デルタ、イプシロン、ガンマ、エタ、イオタ、カッパ、ラムダ、ミュー、またはニューである。いくつかの態様において、NAPは、核酸ポリメラーゼ(例えば、損傷乗り越えDNAポリメラーゼ)に、少なくとも75%、80%、85%、90%、95%、96%、97%、98%、99%、または99.5%同一であるアミノ酸配列を含む。いくつかの態様において、NAPは、本明細書に提供される任意の核酸ポリメラーゼに少なくとも75%、80%、85%、90%、95%、96%、97%、98%、99%、または99.5%同一であるアミノ酸配列を含む。例えば、NAPは、配列番号54〜64のいずれか1つに少なくとも75%、80%、85%、90%、95%、96%、97%、98%、99%、または99.5%同一であるアミノ酸配列を含んでもよい。いくつかの態様において、NAPは、配列番号54〜64のいずれか1つのアミノ酸配列を含む。いくつかの態様において、融合蛋白質は、構造:
NH2−[BEE]−[napDNAbp]−[NAP]−COOH;
NH2−[BEE]−[NAP]−[napDNAbp]−COOH;
NH2−[NAP]−[BEE]−[napDNAbp]−COOH;
NH2−[NAP]−[napDNAbp]−[BEE]−COOH;
NH2−[napDNAbp]−[NAP]−[BEE]−COOH;または
NH2−[napDNAbp]−[BEE]−[NAP]−COOH
を含む。
SGSETPGTSESATPES(配列番号102)、SGGS(配列番号103)、
SGGSSGSETPGTSESATPESSGGS(配列番号107)、
SGGSSGGSSGSETPGTSESATPESSGGSSGGS(配列番号108)、
GGSGGSPGSPAGSPTSTEEGTSESATPESGPGTSTEPSEGSAPGSPAGSPTSTEEGTSTEPSEGSAPGTSTEPSEGSAPGTSESATPESGPGSEPATSGGSGGS(配列番号109)、または
SGGSGGSGGS(配列番号120)
のアミノ酸配列を含むリンカー。いくつかの態様において、リンカーは、XTENリンカーとしてもまた言及されてもよい、アミノ酸配列SGSETPGTSESATPES(配列番号102)を含む。
いくつかの態様において、本明細書において提供される融合蛋白質は、1つ以上の核標的配列、例えば、核局在配列(NLS)をさらに含む。いくつかの態様において、NLSは、NLSを含む、細胞核への蛋白質の移入を促進する(例えば、核輸送により)アミノ酸配列を含む。いくつかの態様において、本明細書において提供される任意の融合蛋白質は、核局在配列(NLS)さらに含む。いくつかの態様において、NLSは融合蛋白質のN末端に融合されている。いくつかの態様において、NLSは融合蛋白質のC末端に融合されている。いくつかの態様において、NLSはnapDNAbpのN末端に融合されている。いくつかの態様において、NLSはnapDNAbpのC末端に融合されている。いくつかの態様において、NLSはNAPのN末端に融合されている。いくつかの態様において、NLSはNAPのC末端に融合されている。いくつかの態様において、NLSはシチジンデアミナーゼのN末端に融合されている。いくつかの態様において、NLSはシチジンデアミナーゼのC末端に融合されている。いくつかの態様において、NLSはUBPのN末端に融合されている。いくつかの態様において、NLSはUBPのC末端に融合されている。いくつかの態様において、NLSはBEEのN末端に融合されている。いくつかの態様において、NLSはBEEのC末端に融合されている。いくつかの態様において、NLSは1つ以上のリンカーを介して融合蛋白質に融合されている。いくつかの態様において、NLSはリンカーを用いないで融合蛋白質に融合されている。いくつかの態様において、NLSは本明細書において提供される、または参照されるNLS配列のいずれか1つのアミノ酸配列を含む。いくつかの態様において、NLSは配列番号41または配列番号42で示されるアミノ酸配列を含む。追加の核局在配列は当分野において知られており、当業者にとって明らかであるだろう。例えば、NLS配列はPlank et al.,PCT/EP2000/011690において記載されており、その内容は例示的な核局在配列の開示についての参照により本明細書に組み込まれる。いくつかの態様において、NLSは、アミノ酸配列PKKKRKV(配列番号41)、MDSLLMNRRKFLYQFKNVRWAKGRRETYLC(配列番号42)、KRTADGSEFESPKKKRKV(配列番号43)、KRGINDRNFWRGENGRKTR(配列番号44)、KKTGGPIYRRVDGKWRR(配列番号45)、RRELILYDKEEIRRIWR(配列番号46)、またはAVSRKRKA(配列番号47)を含む。
ある種の態様においては、リンカーが、本明細書に記載の蛋白質または蛋白質ドメインのいずれかをリンクするために用いられ得る。リンカーは共有結合ほども単純であり得、または、これは長さが多くの原子であるポリマーリンカーであり得る。ある種の態様において、リンカーはポリペプチド(polypeptide)であるか、またはアミノ酸に基づく。他の態様において、リンカーはペプチド様ではない。ある種の態様において、リンカーは共有結合である(例えば、炭素−炭素結合、ジスルフィド結合、炭素−ヘテロ原子結合など)。ある種の態様において、リンカーはアミド結合の炭素−窒素結合である。ある種の態様において、リンカーは、環状または非環状の、置換または無置換の、分岐または非分岐の、脂肪族またはヘテロ脂肪族リンカーである。ある種の態様において、リンカーはポリマー性である(例えば、ポリエチレン、ポリエチレングリコール、ポリアミド、ポリエステルなど)。ある種の態様において、リンカーはアミノアルカン酸のモノマー、二量体、またはポリマーを含む。ある種の態様において、リンカーはアミノアルカン酸を含む(例えば、グリシン、エタン酸、アラニン、ベータ−アラニン、3−アミノプロパン酸、4−アミノ酪酸、5−ペンタン酸など)。ある種の態様において、リンカーはアミノヘキサン酸(Ahx)のモノマー、二量体、またはポリマーを含む。ある種の態様において、リンカーは炭素環部分に基づく(例えば、シクロペンタン、シクロヘキサン)。他の態様において、リンカーはポリエチレングリコール部分(PEG)を含む。他の態様において、リンカーはアミノ酸を含む。ある種の態様において、リンカーはペプチドを含む。ある種の態様において、リンカーはアリールまたはヘテロアリール部分を含む。ある種の態様において、リンカーはフェニル環に基づく。リンカーは、ペプチドからリンカーへの求核剤の取り付けを促すための官能部分(例えば、チオール、アミノ)を包含し得る。いずれかの求電子剤がリンカーの一部として用いられ得る。例示的な求電子剤は、活性エステル、活性アミド、マイケルアクセプター、ハロゲン化アルキル、ハロゲン化アリール、ハロゲン化アシルおよびイソチオシアネートを包含し、しかしこれらに限定されない。
本開示のいくつかの側面は、本明細書において提供される融合蛋白質のいずれか、および融合蛋白質のnapDNAbpに結合したガイド核酸を含む複合体を提供する。本開示のいくつかの側面は、本明細書において提供される、任意の融合蛋白質、および融合蛋白質のCas9ドメイン(例えば、dCas9、ヌクレアーゼ活性型Cas9、またはCas9ニッカーゼ)に結合したガイドRNAを含む複合体を提供する。
本開示の、いくつかの側面は、本明細書に提供される任意の融合蛋白質(例えば塩基編集因子)、またはガイド核酸(例えば、gRNA)および本明細書に提供される融合蛋白質(例えば、塩基編集因子)を含む、複合体を使用する方法を提供する。例えば、本開示のいくつかの側面は、DNAまたはRNA分子を、本明細書において提供される融合蛋白質または塩基編集因子のいずれかと、および、少なくとも1つのガイド核酸(e.g.ガイドRNA)と接触させる方法を提供し、ここにおいて、該ガイド核酸(例えば、ガイドRNA)は、約15〜100ヌクレオチド長であり、標的配列に対して相補的である、少なくとも10の一続きのヌクレオチドを含む。いくつかの態様において、標的配列の3’末端は、古典的なspCas9PAM配列(NGG)に、直ちに隣接する。いくつかの態様において、標的配列の3’末端は、古典的なspCas9PAM配列(NGG)に、直ちに隣接しない。いくつかの態様において、標的配列の3’末端は、AGC、GAG、TTT、GTG、またはCAA配列に、直ちに隣接する。
症候群;デスモステロール症;DFNA2非症候性難聴;糖尿病2型;糖尿病、インスリン依存性、20;Digitorenocerebral症候群;拡張型心筋症1FF;拡張型心筋症1G;拡張型心筋症1S;拡張型心筋症1X;拡張型心筋症3B;シトクロムp450酸化還元酵素欠損によるステロイド生成障害;遠位遺伝性運動神経障害2B型;口内炎−リンパ浮腫症候群;ダッシュ症候群;デュシェンヌ型筋ジストロフィー;ディスケラット症先天性常染色体優性;先天性ディスケラット症X連鎖;先天性ディスケラット症、常染色体優性、2;先天性ディスケラット症、常染色体劣性、5;ジストニア1;ジストニア27;ジストニア5、ドーパ反応型;高フェニルアラニン血症を伴うまたは伴わないジストニア、ドーパ反応性、常染色体劣性;早期乳児てんかん性脳症13;早期乳児てんかん性脳症2;早期乳児てんかん性脳症8;早期乳児てんかん性脳症9;早期筋クローヌス脳症;外胚葉異形成合指症候群1;欠指症、外胚葉異形成、および口唇/口蓋裂症候群3;エーラース・ダンロス症候群、古典型;エーラース・ダンロス症候群、ヒドロキシリジン欠乏症;エーラース・ダンロス症候群、筋収縮型;エーラース・ダンロス症候群、4型;アイヒスフェルト型先天性筋ジストロフィー;エリプトサイトーシス3;子宮内膜癌;終板アセチルコリンエステラーゼ欠損症;前庭水道肥大症候群;エンテロキナーゼ欠損症;単純性表皮水疱症、ケブナー型;てんかん、夜間前頭葉、3型;てんかん、進行性筋クローヌス1A(UnverrichtおよびLundborg);てんかん、進行性筋クローヌス2b;てんかん性脳症、早期乳児、1;てんかん性脳症、早期乳児、24;てんかん性脳症、早期乳児、28;てんかん性脳症、早期乳児、31;骨端軟骨異形成、ミウラ型;突発性運動失調1型;突発性運動失調、6型;突発性疼痛症候群、家族性、3;赤血球増加症、家族性、2;赤血球増加症、家族性、3;運動失調を伴うエリスロケラット皮膚炎;滲出性硝子体網膜症1;滲出性硝子体網膜症5;Fabry疾患;Fabry疾患、心臓バリアント;第V因子および第VIII因子、複合欠損症、2;蕁麻疹と難聴を伴う家族性アミロイド腎症;家族性乳がん;家族性寒冷蕁麻疹;家族性熱性けいれん8;家族性片麻痺片頭痛3型;家族性肥大型心筋症1;家族性肥大型心筋症10;家族性肥大型心筋症11;家族性肥大型心筋症20;家族性肥大型心筋症23;家族性肥大型心筋症4;家族性肥大型心筋症6;家族性形成不全、糸球体嚢胞腎;家族性乳児筋無力症;家族性若年性痛風;家族性地中海熱;骨髄性悪性腫瘍を伴う家族性血小板障害;家族性孔脳症;家族性皮膚ポルフィリン症;家族性内臓アミロイドーシス、オスタータグ型;ファンコニ貧血、補完グループC;ファンコニ貧血、補完グループF;ファンコニ貧血、補完グループG;ファンコニ貧血、補完グループJ;ファンコニ貧血、補完グループT;ファーバー脂肪肉芽腫症;胎児ヘモグロビン量的形質遺伝子座1;胎児ヘモグロビン量的形質遺伝子座6;線維軟骨形成;精神遅滞を伴うまたは伴わない言語障害を伴う焦点てんかん;限局性糸球体硬化症6;中心窩形成不全および初老性白内障症候群;前鼻異形成1;前鼻異形成2;前頭側頭型認知症;フルクトースビホスファターゼ欠損症;フマラーゼ欠損症;ガラクトシルセラミドベータ−ガラクトシダーゼ欠損症;胆嚢疾患4;Gamstorp-Wohlfart症候群;ガングリオシドシアリダーゼ欠損症;ガングリオシドーシスGM1 3型;ガードナー症候群;赤血球生成異常を伴うGATA−1関連血小板減少症;Gaucher疾患;Gaucher疾患3C型;ゴーシェ病、周産期致死;Gaucher疾患、1型;熱性けいれんを伴う全身性てんかん、1型;熱性けいれんを伴う全身性てんかん、2型;熱性けいれんを伴う全身性てんかん、9型;ゲルストマン・シュトラウスラー・シャインカー症候群;グランツマン血栓症;緑内障1、開放隅角、F;緑内障、先天性;全体(global)発達遅延;グルココルチコイド欠乏症4;グルタル酸尿症、1型;グリコーゲン貯蔵疾患IIIa;グリコーゲン貯蔵疾患IV、先天性神経筋;グリコーゲン貯蔵疾患IXB;グリコーゲン貯蔵心臓の疾患、先天致死性;グリコーゲン貯蔵疾患、II型;グリコーゲン貯蔵疾患、IV型;グリコーゲン貯蔵疾患、V型;グリコーゲン貯蔵疾患、VI型;グリコシルホスファチジルイノシトール欠乏症;灰色の血小板症候群;グリス細胞I症候群2型;発育と精神遅滞、下顎顔面骨異形成症、小頭症、口蓋裂;免疫不全を伴う成長ホルモン非感受性;ヘモクロマトーシス1型;ヘモクロマトーシス3型;ヘキソキナーゼ欠損による溶血性貧血;グルコースリン酸イソメラーゼ欠損による溶血性貧血、非球状赤血球症;アセルロプラスミン血症による全身性ヘモジデローシス;ヘンネカムリンパ管拡張症−リンパ浮腫症候群;遺伝性先天性末端皮膚炎;遺伝性血管浮腫1型;遺伝性乳がんおよび卵巣がん症候群;遺伝性がん素因症候群;遺伝性びまん性胃がん;スフェロイドを伴う遺伝性びまん性白質脳症;遺伝性第II因子欠乏症;遺伝性第IX因子欠乏症;遺伝性第VIII因子欠乏症;遺伝性第XI因子欠乏症;遺伝性フルクトスリア;遺伝性平滑筋腫症および腎細胞がん;I型遺伝性リンパ浮腫;遺伝性神経痛性筋萎縮症;遺伝性非ポリポーシス大腸がん5型;遺伝性非ポリポーシス大腸腫瘍;遺伝性膵炎;遺伝性傍神経節腫−褐色細胞腫症候群;遺伝性パイロポイキロサイトーシス;遺伝性感覚神経障害1D型;遺伝性鉄芽球性貧血;ヘテロタキシー、内臓、X連鎖;異所形成;ヒルシュスプルング疾患神経節芽細胞腫;組織球性骨髄性網状赤血球症;全前脳症11;全前脳症2;全前脳症3;全前脳症4;MTHFR欠乏によるホモシステイン血症;CBS欠乏によるホモシスチン尿症;ハーラー症候群;甲状腺好酸性細胞癌;ハッチンソン・ギルフォード症候群;高カルシウム尿症、小児期、自然治癒;高コレステロール血症;過剰驚愕症3;遺伝性ハイパーエクプレシア;高フェリチン血症白内障症候群;高リポ蛋白質血症、I型;高リポ蛋白質血症、ID型;高リジン血症;高オルニチン血症−高アンモニア血症−ホモシトルリン尿症症候群;高プロインスリン血症;顔面中央部の突出、近視、精神遅滞、および骨の脆弱性を伴う重度の両眼隔離症;肥大型心筋症;低カルシウム血症、常染色体優性1;低カルシウム血症、常染色体優性1、バーター症候群;軟骨形成不全;鉄過剰を伴う低色素性小球性貧血;肝臓グリコーゲン合成酵素の欠損を伴う低血糖;嗅覚低下を伴うまたは伴わない性腺機能低下性性腺機能低下症13;脱汗性X連鎖外胚葉形成異常;低カリウム血症の定期的な麻痺1;低マグネシウム血症1、腸;眼球の関与を伴う低マグネシウム血症5、腎;低マグネシウム血症、発作、および精神遅滞;低髄鞘形成性白質ジストロフィー7;乏歯症および/または低ゴナドトロピン性性腺機能低下症を伴うまたは伴わない、低髄鞘形成性白質ジストロフィー8;低蛋白質血症、異化亢進性;甲状腺機能低下症、先天性、非甲状腺腫、1;甲状腺機能低下症、先天性、非甲状腺腫性、5;甲状腺機能低下症、先天性、非甲状腺腫性、6;貧毛症6;貧毛症−リンパ浮腫−毛細血管拡張症症候群;I細胞疾患; 尋常性魚鱗癬;特発性大脳基底核石灰化5;免疫不全12;免疫不全23;免疫不全24;免疫不全30;免疫不全31a;免疫不全31C;高IgM1型の免疫不全;封入体ミオパチー2;乳児小脳網膜の変性;乳児GM1ガングリオシドーシス;乳児の低ホスファターゼ症;乳児眼振、X連鎖;インスリン抵抗性糖尿病および黒皮症;知的障害;中間型メープルシロップ尿疾患2型;侵襲性肺炎球菌感染症、再発性孤立、2;虹彩−角膜−線維柱形成不全;脳内の鉄蓄積;ジャクソン・ワイス症候群;ヤコブ・クロイツフェルト病;ジュベール症候群23;若年性GM>1<ガングリオシドーシス;若年性ポリポーシス症候群;歌舞伎メイクアップ症候群;カルマン症候群3;カルマン症候群4;カルマン症候群5;カルマン症候群6;円錐角膜1;コールシュッター症候群;クーゲルベルク・ヴェランダー病;ラフォラ病;ランガー中等度異形成症候群;ラロン型孤立性ソマトトロピン欠損;ラーセン症候群、優性型;妊娠の母体急性脂肪肝を伴うLchad欠乏症;レーバー先天性黒内障13;レーバー先天性黒内障4;レーバー先天性黒内障9;リー病;レオパード症候群;レオパード症候群1;レオパード症候群2;レプラショーニズム症候群;レリ・ヴァイル異軟骨症;レッシュ・ナイハン症候群;白質ジストロフィー、低髄鞘形成、6;運動失調を伴う白質脳症;脳幹および脊髄の関与および乳酸上昇を伴う白質脳症;白質消失を伴う白質脳症;ライディッヒ細胞無形成;リー・フラウメニ症候群1;肢帯型筋ジストロフィー;肢帯型筋ジストロフィー、1B型;肢帯型筋ジストロフィー、1C型;肢帯型筋ジストロフィー、1E型;肢帯型筋ジストロフィー、2A型;肢帯型筋ジストロフィー、2B型;肢帯型筋ジストロフィー、2E型;肢帯型筋ジストロフィー、2F型;肢帯型筋ジストロフィー、2L型;肢帯筋ジストロフィー−ジストログリカノパチー、C1型;肢帯型筋ジストロフィー−ジストログリカノパチー、C14型;肢帯型筋ジストロフィー−ジストログリカノパチー、C2型;肢帯型筋ジストロフィー−ジストログリカノパチー、C7型;滑脳症1;QT延長症候群1;QT延長症候群13;QT延長症候群15;QT延長症候群2;QT延長症候群9;QT延長症候群、LQT1サブタイプ;長鎖3−ヒドロキシアシルCoA脱水素酵素欠損症;ロウ症候群;黄体形成ホルモン抵抗性、女性;リンパ増殖性症候群1;リンパ増殖性症候群1、X連鎖;リンチ症候群I;リンチ症候群II;マクロ血小板減少症、家族性、バーナード・スリエ型;中心錐体に関与する黄斑ジストロフィー;マジード症候群;食道の悪性腫瘍;前立腺の悪性腫瘍;下顎骨異形成症;メープルシロップ尿疾患;メープルシロップ尿疾患1A型;メープルシロップ尿疾患2型;マルファン症候群;マリー・ウンナの遺伝性貧毛症1;若年者の成人発症型2型糖尿病;若年者の成人発症型3型糖尿病;中鎖アシルCoA脱水素酵素;マイヤー・ゴーリン症候群5;メルニック・フレーザー症候群;MEN2表現型:未分類;MEN2表現型:不明;メンケス癖髪症候群;閉経期、自然、年齢、量的形質遺伝子座3;精神遅滞30、X連鎖;橋と小脳の形成不全を伴う精神遅滞と小頭症;精神遅滞、常染色体優性13;精神遅滞、常染色体優性16;精神遅滞、常染色体優性29;精神遅滞、常染色体優性38;精神遅滞、常染色体優性7;精神遅滞、常染色体劣性34;精神遅滞、常染色体劣性49;精神遅滞、ステレオタイプ運動、てんかん、および/または脳奇形;精神遅滞、症候性、Claes-Jensen型、X連鎖;精神遅滞、X連鎖、症候群13;精神遅滞、X連鎖、症候群32;精神遅滞、X連鎖、症候群、レイモンド型;精神遅滞、X連鎖、症候群、wuタイプ;精神遅滞−低張相症候群X連鎖、1;メロシン欠損先天性筋ジストロフィー;メタクロマチック白質ジストロフィー;骨幹端軟骨異形成症、シュミット型;メチルコバラミン欠乏症、cblgタイプ;メチルマロン酸尿症、mut(0)タイプ;小頭症および絨毛網膜症、常染色体劣性、2;絨毛網膜症、リンパ浮腫、または精神遅滞を伴うまたは伴わない小頭症;小球性貧血;陰茎;微小眼球症候群3;微小眼球症症候群5;分離した小眼球症3;分離した小眼球症6;孤立性小眼球症、コロボーマ7;糖尿病の微小血管合併症7;軽度の非PKU高フェニルアラニン血症;ミトコンドリア複合体I欠損症;ミトコンドリア複合体II欠損症;ミトコンドリア複合体III欠損症;ミトコンドリアDNA枯渇症候群13(脳筋障害型);ミトコンドリアDNA枯渇症候群2;ミトコンドリアDNA枯渇症候群9(メチルマロン酸尿症を伴う脳筋障害);ミトコンドリア短鎖エノイルCoAヒドラターゼ欠損症;ミトコンドリア三機能性蛋白質欠損症;三好筋ジストロフィー1;三好筋ジストロフィー3;モール・トラネビャエル症候群;多彩異数性モザイク症候群;モワット・ウィルソン症候群;ムコリピドーシスIIIガンマ;ムコ多糖症VI型;ムコ多糖症、MPS−II;ムコ多糖症、MP
S−III−B;ムコ多糖症、MPS−I−S;ムコ多糖症、MPS−IV−A;ムコ多糖症、MPS−IV−B;ムンケ症候群;ムリブリーナニズム症候群;複数の先天異常;多発性内分泌腫瘍、1型;多発性内分泌腫瘍、2型;多発性内分泌腫瘍、2a型;多発性骨端異形成1;多発性骨端異形成症5;複数の外骨腫2型;多発性翼状片症候群エスコバール型;複数のスルファターゼ欠損症;角膜真皮の切断;筋無力症、肢帯、家族性;アセチルコリン受容体欠損症に関連する先天性筋無力症候群、9;アセチルコリン受容体欠損症に関連する、先天性筋無力症候群、9;シナプス前およびシナプス後欠損を伴う先天性筋無力症候群;先天性筋無力症候群、尿細管凝集2;筋無力症候群、先天性スローチャネル型;筋クローヌスてんかんミオパチー感覚性運動失調;筋クローヌス、家族性皮質;筋原線維性ミオパチー1;ミオキミア1;姿勢筋萎縮を伴う筋障害、X連鎖;ミオパチー、アクチン、先天性、過剰な細い筋フィラメント;ミオパチー、中心核の;ミオパチー、遠位、1;ミオパチー、分離したミトコンドリアの、常染色体優性;ミオパチー、体重の減少、X連鎖、早期発症、重度;先天性筋強直症;爪疾患、非症候性先天性、8;小眼球症4;ナルコレプシー7;ネイティブアメリカンミオパチー;ナバホ神経肝障害;ネマリンミオパチー3;新生児低血圧症;新生児のインスリン依存性糖尿病;シトリン欠乏による新生児肝内胆汁うっ滞;卵巣の腫瘍;腎結石/骨粗鬆症、低リン血症、2;ネフロン癆16;ネフロン癆18;ネフローゼ症候群、10型;Neu-Laxova症候群1;脳鉄蓄積を伴う神経変性5;脳下垂体糖尿病尿崩症;ニコライデス・バライサー症候群;ニーマン・ピック病C1型;ニーマン・ピック病、A型;ニーマン・ピック病、B型;ニーマン・ピック病、c1型、少年型;埜中ミオパチー;非ケトン性高グリシン血症;ヌーナン症候群1;ヌーナン症候群5;ヌーナン症候群7;ヌーナン症候群8;提供されない;指定されていない;眼皮膚白皮症3型;眼咽頭筋ジストロフィー;眼異形成症;視神経萎縮9;視神経萎縮および白内障、常染色体優性;視神経低形成および中枢神経系の異常;口腔顔面デジタル症候群;オルニチンアミノトランスフェラーゼ欠損症;オルニチンカルバモイルトランスフェラーゼ欠損症;口腔顔面裂溝11;オロファシオデジタル症候群6;オロト酸尿症;骨形成不全症12型;骨形成不全症13型;骨形成不全症III型;正常な強膜を伴う骨形成不全、優性型;骨形成不全、劣性周産期致死;大理石骨病常染色体優性タイプ1;大理石骨病常染色体劣性7;耳口蓋デジタル症候群、I型;厚皮骨膜症症候群;パリスター・ホール症候群;パピヨン−レフ\ xc3 \ xa8vre症候群;傍神経節腫1;傍神経節腫4;副甲状腺癌;頭頂孔2;パーキンソン病1;パーキンソン病7;パーキンソン病9;発作性夜間ヘモグロビン尿症1;部分ヒポキサンチン−グアニンホスホリボシルトランスフェラーゼ欠損症;剥離性皮膚症候群、先端部タイプ;Pelger-Hu \ xc3 \ xabtの異常;ペリツェウス・メルツバッハ病;ペンドレッド症候群;永久的な新生児糖尿病;ペルオキシソーム生合成障害6B;ペルオキシソーム生合成障害9B;ポイツ・ジェガーズ症候群;ファイファー症候群;フェニルケトン尿症;褐色細胞腫;ホスホグリセリン酸キナーゼ1欠損症;ホスホリボシルピロリン酸シンテターゼ超活性;感光性トリコチオジストロフィー;ピアソン症候群;色素性淡蒼球変性;ピットホプキンス症候群;ピットホプキンス様症候群2;下垂体依存性副腎皮質機能亢進症;下垂体ホルモン欠乏症、複合型1;下垂体ホルモン欠乏症、複合型4;下垂体ホルモン欠乏症,複合型5;血小板型出血障害16;凝集性赤血球症候群;結節性多発動脈炎;多発性嚢胞腎疾患、乳児型;ポリグルコサン体ミオパチー2;多小脳回、両側前頭頭頂;多発神経障害、難聴、運動失調、網膜色素変性、白内障;先天性小脳形成不全、1B型;先天性小脳形成不全、1c型;先天性小脳形成不全、9型;ポレッティボルトシャウザー症候群;軸前多指症2;早期の染色分体分離特性;早発性卵巣障害5;早発性卵巣不全7;早発性卵巣障害9;原発性常染色体劣性小頭症1;原発性常染色体劣性小頭症2;原発性常染色体劣性小頭症5;原発性常染色体劣性小頭症6;原発性毛様体ジスキネジア;原発性拡張型心筋症;原発性家族性肥大型心筋症;原発性高シュウ酸尿症、I型;原発性高シュウ酸尿症、III型;原発性限局性皮膚アミロイドーシス1;原発性開放隅角緑内障若年発症1;原発性肺高血圧;原発性肺高血圧4;プリムローズ症候群;進行性骨化性筋炎;進行性硬化性ポリジストロフィー;増殖性血管障害および水頭症−水頭症症候群;X連鎖のプロペルジン欠乏症;プロピオン酸血症;疑似ハーラー多発性ジストロフィー;偽性低アルドステロン症1型常染色体優性;偽性低アルドステロン症2B型;偽性低アルドステロン症、2型;偽性副甲状腺機能低下症1A型;弾性線維性仮性黄色腫;多発性凝固因子欠乏症を伴う弾性線維性仮性黄色腫;遺伝性出血性毛細血管拡張症に関する肺動脈高血圧;肺線維症および/または骨髄機能不全、テロメアに関する、2;濃化異骨症;ピリドキシン依存性てんかん;ピルビン酸デヒドロゲナーゼE1−アルファ欠損症;橈骨形成不全−血小板減少症候群;レイン症候群;ラソパシー;劣性ジストロフィー表皮水疱症;ライフェンシュタイン症候群;腎カルニチン輸送障害;腎細胞癌、乳頭、1;腎異形成;腎低尿酸血症2;溶血性貧血を伴う腎尿細管性アシドーシス;網膜錐体ジストロフィー3A;色素性網膜炎;網膜色素変性症10;網膜色素変性症11;網膜色素変性症14;色素性網膜炎2;網膜色素変性症25;網膜色素変性症33;網膜色素変性症35;色素性網膜炎4;網膜色素変性症43;網膜色素変性症50;網膜色素変性症56;色素性網膜炎73;色素性網膜炎74;網膜芽細胞腫;レット障害;レット症候群、先天性バリアント;レット症候群、zappellaバリアント;ラブドイド腫瘍素因症候群2;根粒性軟骨異形成症1型;リエンホフ症候群;ロバーツ−SC恐怖症症候群;ロビノー症候群;RRM2B関連ミトコンドリア疾患;ルビンシュタイン・タイビ症候群;セートレ・ヒョツェン症候群;肩甲骨筋障害、X連鎖優性;シンドラー病、1型;シンドラー病、3型;シュナイダー結晶性角膜ジストロフィー;セッケル症候群1;発作;選択的歯非形成1(selective tooth agenesis 1);シニア・ローケン症候群8;感覚性運動失調性ニューロパシー、構音障害、および眼不全麻痺;セサミ(SeSAME)症候群;アデノシンデアミナーゼ欠損症による重度の複合型免疫不全;重度の複合型免疫不全と小頭症、発育異常、電離放射線に対する感受性;重度の先天性好中球減少症;重度の先天性好中球減少症4、常染色体劣性;乳児期の重度の筋クローヌスてんかん;重度のX連鎖筋管ミオパチー;QT短縮症候群;QT短縮症候群2;非特異的骨格異常を伴う低身長;低身長、外耳道閉鎖、下顎形成不全、骨格異常;低身長、特発性、常染色体;低身長、特発性、X連鎖;多指症を伴う、または伴わない短指胸部形成異常13;多指症を伴う短胸部形成異常14;多指症を伴うまたは伴わない仮肋骨胸部形成異常3;シュプリンツェン症候群;シュプリンツェン・ゴールドバーグ症候群;シュワックマン症候群;シアル酸貯蔵疾患、重度の乳児性型;シアリドーシス、II型;洞機能不全症候群2、常染色体優性;B細胞免疫不全、周期性発熱、および発達遅延を伴う鉄芽球性貧血;シトステロール血症;Sj \ xc3 \ xb6gren-Larsson症候群;スミス・レムリ・オピッツ症候群;ソースビー眼底変性症;ソトス症候群1;ソトス症候群2;痙性運動失調Charlevoix-Saguenay型;痙性対麻痺11、常染色体劣性;痙性対麻痺30、常染色体劣性;痙性対麻痺4、常染色体優性;痙性対麻痺54、常染色体劣性;痙性対麻痺6;痙性対麻痺7;痙性対麻痺8;精子形成不全8;球状赤血球症4型;スフィンゴ脂質活性化剤蛋白質1欠乏症;スフィンゴミエリン/コレステロールリピドーシス;脊髄性筋萎縮症、下肢優位2、常染色体優性;脊髄性筋萎縮症、II型;脊髄小脳失調症14;脊髄小脳性運動失調21;脊髄小脳性運動失調35;脊髄小脳性運動失調38;脊髄小脳性運動失調、常染色体劣性12;脊椎肋骨異骨症2;関節弛緩を伴う骨幹端異形成;脊椎骨幹端骨異形成、パキスタン型;先天性脊椎骨端異形成症;錐体杆体ジストロフィーを伴う脊椎骨幹端骨異形成;頭頸部の扁平上皮癌;シュタルガルト病1;シュタルガルト病3;スチール症候群;スティックラー症候群1型;硬い皮膚症候群(Stiff skin syndrome);刺痛関連脈管障害、乳児発症;亜急性神経障害性ゴーシェ病;スクシニルCoAアセトアセテートトランスフェラーゼ欠損症;スーパーオキシドジスムターゼ、細胞外の上昇;弁上大動脈狭窄;指節癒合症−短指症症候群;合指症9型;タンジール病;足根手根連合症候群;テイ・サックス疾患;テイ・サックス疾患、B1バリアント;T細胞前リンパ球性白血病;テンプル・バライサー症候群;腹部前軸短指症症候群;ファロー四徴;胸部大動脈瘤および大動脈解離;血小板減少症2;血小板減少症、X連鎖;血小板減少症、X連鎖、間欠性;活性化された蛋白質C耐性による血栓症;血栓症、遺伝性、蛋白質C欠乏、常染色体優性による;血栓症、遺伝性、蛋白質C欠乏、常染色体劣性による;甲状腺がん、非髄質、4;甲状腺機能障害1;甲状腺毒性の定期的な麻痺;ティーツ症候群;歯の無形成、選択的、3;歯の無形成、選択的、X連鎖、1;一過性新生児糖尿病1;一過性新生児糖尿病2;トリーチャーコリンズ症候群2;毛状指節異形成症I型;魚鱗癬を伴うトリグリセリド貯蔵疾患;トリオースリン酸イソメラーゼ欠損症;三指節親指;結節性硬化症1;結節性硬化症2;結節性硬化症候群;チロシナーゼ陰性眼皮膚白皮症;チロシナーゼ陽性の眼皮膚白皮症;チロシン血症2型;ウルリッヒ型先天性筋ジストロフィー;未分類;ウンフェルリヒト・ルントボルク症候群;アップショー・シュルマン症候群;ウリジン−5‘−一リン酸ヒドロラーゼ欠損症による、溶血性貧血;アッシャー症候群、1D型;アッシャー症候群、1F型;アッシャー症候群、2A型;ファンデルワーデ症候群;多彩なポルフィリン症;大頭症と脳室肥大を有するベイター症候群(vater association);心室中隔欠損3;ビタミンD依存性くる病、1型;ビタミンD依存性くる病、2型;ビタミンk依存性凝固因子、複合欠乏症、1;卵形ジストロフィー;フォン・ヒッペル・リンダウ症候群;フォン・ヴィルブランド病、2b型;ワールデンブルグ症候群1型;ワールデンブルグ症候群2E型、神経学的関与なし;ワールデンブルグ症候群4A型;ワールデンブルグ症候群4B型;ワールデンブルグ症候群4C型;ウォーカー・ワールブルグ先天性筋ジストロフィー;ウォーバーグマイクロ症候群3;いぼ、低ガンマグロブリン血症、感染症、および骨髄性細胞貯留;ウェルドニッヒ・ホフマン病;ウェルナー症候群;ウィアッカー症候群;ヴィーデマン・シュタイナー症候群;ウィンチェスター症候群;ウルフラム症候群2;遺伝性乾燥有口赤血球症(Xerocytosis);色素性乾皮症、グループD;色素性乾皮症、グループG;X連鎖ガンマグロブリン血症;X連鎖遺伝性運動神経および感覚神経症;ステリルスルファターゼ欠損症を伴うX連鎖魚鱗癬;X連鎖精神遅滞41;X連鎖精神遅滞90;X連鎖脳室周囲の異所形成;Zimmermann-Laband症候群;またはZimmermann-Laband症候群2である。
本開示のいくつかの側面は、ここで提供される塩基編集因子のいずれかが、インデルの有意な割合を生成することなしに特定のヌクレオチド塩基を改変することができるという認識に基づく。ここで用いられる「インデル」は、核酸へのヌクレオチド塩基の挿入または欠失を言う。かかる挿入または欠失は、遺伝子のコード領域内のフレームシフト変異に至り得る。いくつかの態様においては、核酸中に多数の挿入または欠失(すなわちインデル)を生成することなしに、核酸中の特定のヌクレオチドを効率的に改変する(例えば変異させるかまたは脱アミノ化する)塩基編集因子を創ることが望ましい。ある種の態様において、ここで提供される塩基編集因子のいずれかは、インデルと比べて、意図される改変(例えば、点変異または脱アミノ化)のより高い割合を生成することができる。いくつかの態様において、ここで提供される塩基編集因子は、1:1超である意図される点変異対インデルの比を生成することができる。いくつかの態様において、ここで提供される塩基編集因子は、少なくとも1.5:1、少なくとも2:1、少なくとも2.5:1、少なくとも3:1、少なくとも3.5:1、少なくとも4:1、少なくとも4.5:1、少なくとも5:1、少なくとも5.5:1、少なくとも6:1、少なくとも6.5:1、少なくとも7:1、少なくとも7.5:1、少なくとも8:1、少なくとも10:1、少なくとも12:1、少なくとも15:1、少なくとも20:1、少なくとも25:1、少なくとも30:1、少なくとも40:1、少なくとも50:1、少なくとも100:1、少なくとも200:1、少なくとも300:1、少なくとも400:1、少なくとも500:1、少なくとも600:1、少なくとも700:1、少なくとも800:1、少なくとも900:1、もしくは少なくとも1000:1、またはより多くである意図される点変異対インデルの比を生成することができる。意図される変異およびインデルの数は、いずれかの好適な方法、例えば下の例に用いられている方法を用いて決定され得る。いくつかの態様において、インデル頻度を計算するために、インデルが生じる可能性があるウインドウの両側に隣接する2つの10bp配列に対する正確な一致について、配列決定リードがスキャンされる。正確に一致するものが見つからない場合、リードは分析から除外される。このインデルウインドウの長さが参照配列と正確に一致する場合、リードはインデルを含まないものとして分類される。インデルウインドウが参照配列より2塩基以上長いかまたは短い場合、配列決定のリードはそれぞれ挿入または欠失として分類される。
本開示のいくつかの側面は、核酸を編集するための方法を提供する。いくつかの態様において、方法は、核酸の核酸塩基(例えば、二本鎖DNA配列の塩基対)を編集するための方法である。いくつかの態様において、方法は、a)核酸(例えば、二本鎖DNA配列)の標的領域を、塩基編集因子(例えば、シチジンデアミナーゼおよびウラシル結合蛋白質に融合したCas9ドメイン)およびガイド核酸(例えばgRNA)を含む複合体と接触させ、標的領域が標的の核酸塩基対を含むステップと、b)前記標的領域において鎖分離を誘導するステップと、c)標的領域の単一鎖上の前記標的核酸塩基対の第1の核酸塩基を第2の核酸塩基に変換するステップと、d)第2の核酸塩基を切除し、それにより脱塩基部位を創り出すステップと、e)第1の核酸塩基に対して相補的な第3の核酸塩基を、シトシン(C)である第4の核酸塩基によって置き換るステップを含む。いくつかの態様において、方法は、核酸中における20%未満のインデル形成をもたらす。いくつかの態様においてステップbが省かれるということは理解されるはずである。いくつかの態様において、第1の核酸塩基はシトシン(C)である。いくつかの態様において、第2の核酸塩基は脱アミノ化されたシトシンまたはウラシルである。いくつかの態様において、第3の核酸塩基はグアニンである。いくつかの態様において、第4の核酸塩基はシトシン(C)である。いくつかの態様において、第5の核酸塩基は、ステップ(d)において、生成された脱塩基部位の中へ連結される。いくつかの態様において第5の核酸塩基はグアニン(G)である。いくつかの態様において、方法は、19%、18%、16%、14%、12%、10%、8%、6%、4%、2%、1%、0.5%、0.2%未満、または0.1%未満のインデル形成をもたらす。いくつかの態様においては、意図される塩基対の少なくとも5%が編集される。いくつかの態様においては、意図される塩基対の少なくとも10%、15%、20%、25%、30%、35%、40%、45%、または50%が編集される。
本開示の他の側面は、ここに記載の、塩基編集因子、融合蛋白質、または融合蛋白質−gRNA複合体のいずれかを含む医薬組成物に関する。ここで使用される用語「医薬組成物」は、医薬用途のために処方された組成物を指す。いくつかの態様において、医薬組成物は薬学的に許容可能な担体をさらに含む。いくつかの態様において、医薬組成物は追加の薬剤(例えば、特異的送達、半減期の延長、または他の治療用化合物用)を含む。
この開示のいくつかの側面は、(a)本明細書に提供される任意の融合タンパク質をコードする核酸配列、および(b)(a)の配列の発現を駆動する異種プロモーターを含む核酸コンストラクトを含むキットを提供する。いくつかの態様において、キットは、ガイドRNAバックボーンをコードする発現コンストラクトをさらに含み、ここでコンストラクトは、標的配列と同一または相補的な核酸配列のガイドRNAバックボーンへのクローニングを可能にするように位置するクローニング部位を含む。
脱塩基部位の生成を介するシトシン(C)→グアニン(G)塩基編集因子および操作された特異的な修復
HEK2、RNF2、およびFANCF部位についてのシーケンシングデータは、下に与えられる。表示されるデータは、ウィンドウにおいて最も編集されたCについての塩基編集値を表す。これはHEK2についてのC6、RNF2についてのC6、およびFANCFについてのC6である。塩基編集の前および後の3つの異なる部位についての配列は、以下の通りである:
BE_完全長−これは、シチジンデアミナーゼ、nCas9、およびウラシルグリコシラーゼ阻害剤(UGI)ドメインを含む、C→T塩基編集因子コンストラクトである。
脱塩基部位が、より効率的に生成される場合、C→G塩基編集経路を介するフラックスの合計は、増加するだろう。このアプローチにおいて使用される塩基編集因子の模式図表示が、図3および4に示される。UdgXを使用し、最小のウラシル切除活性でウラシルにきつく結合すると同定されるUDGの相同分子種は、C→G編集の量を増加する。特定の理論に束縛されることを望まないが、Uにほぼ共有結合するUdgXは、損傷乗り越えポリメラーゼタイプの修復を扇動する傷害を擬態する。さらに、UdgXは、低いレベルの触媒活性を有し、それはきつい結合と組み合わせて、Uを切除しおよび脱塩基部位形成をもたらす。脱塩基部位形成は、オフターゲット生成物を許容し、およびこの損傷の優先的な生成は、より多くの生成物をもたらす。これは、異なる実験および塩基編集因子を介して指示され、そして図5および6において説明される。
脱塩基部位の反対へのC組み込みについての優先性の増加は、全体のC→G塩基編集の増加をもたらすはずである。このアプローチについての模式図およびこのアプローチに使用される塩基編集因子は、図33および34において説明される。C→G塩基編集のためのこのアプローチに使用され得る種々のポリメラーゼは、図35において示される。簡単には、脱塩基部位の生成は、Cから非T生成物の形成をもたらす。Rev1はdCトランスフェラーゼ活性を有する。この経路を除くこと、またはどのように脱塩基傷害が修復されるかを変えることは、新しい塩基編集因子をもたらすはずである。この経路がこの生成物の形成を単独で担う場合、Rev1−/−ノックアウト細胞株は、C→G編集を欠損するはずである。種々のポリメラーゼの融合は、脱塩基部位へ反対の修復についてのポリメラーゼ優先性に基づき、反対の鎖の修復をもたらし、C→G塩基編集を増加することをもたらすはずである。例示的な塩基編集因子は、図36において説明される。
増加されるC→G塩基編集のために脱塩基形成およびC組み込みの両方を増加するための塩基編集因子の模式図が、図40において説明される。コンストラクトに繋ぎ留められるポリメラーゼの追加、特にPolカッパは、C→G塩基編集を増加する。PolカッパまたはPolイオタのいずれかにより繋ぎ留められるコンストラクトを使用する、HEK2、RNF2およびFANCF部位での塩基編集の結果は、図41に示される。WT細胞におけるシトシン残基での、HEK2、RNF2、およびFACF部位における、追加のポリメラーゼに繋ぎ留められるコンストラクトを使用する塩基編集の結果が、図42〜47において示される。UDG147は、Tを直接的に除去し、およびC→G塩基編集を増加する酵素である(図42〜44)、一方で、UDG204は、Cを直接的に除去し、およびC→G塩基編集を増加する酵素(図45〜47)である。
C→G編集を改善する1つの方法は、代わりの修復の経路を除くまたは下方調節することである。1つの例として、タンパク質MSH2−/−修復経路を除くことは、C→G塩基編集の増加をもたらすことがあることが、図48に示される。種々の塩基編集因子(BE3;BE3_UdgX;BE2_UdgX_On;BE3_UdgX_On;BE2_UDG;およびBE3_UDG)を使用するMSH2−/−細胞におけるHEK2、RNF2、およびFANCF部位でのC→G塩基編集の結果は、図49〜51に示される。
一緒に機能する塩基編集因子構成要素を同定するための1つのアプローチは、それらの構成要素を、細胞において、トランスで一緒に発現することである。C→G変異を誘導する塩基編集因子構成要素(例えば、ポリメラーゼ、ウラシル結合蛋白質、塩基除去酵素、シチジンデアミナーゼ、および/または核酸プログラム可能なDNA結合蛋白質)が同定されれば、それらは、繋ぎ留められ、塩基編集因子を生成し得る。APOBEC−Cas9ニッカーゼに融合され発現されるUDGおよびUdgXバリアントおよびトランスに同時に過剰発現されるTLSポリメラーゼは、RNF2部位でのC→G編集をもたらす。構成要素のトランスでの発現を説明する模式図は、図52において示される。
参考文献
本開示は、Cas9バリアント、例えば1つ以上の生物からのCas9蛋白質を提供し、これは1つ以上の変異を含み得る(例えば、dCas9またはCas9ニッカーゼを創るため)。いくつかの態様において、下でアステリスク(asterek)によって同定されているCas9蛋白質のアミノ酸残基の1つ以上は、変異させられ得る。いくつかの態様において、配列番号6によって提供されるアミノ酸配列のD10および/またはH840残基、または配列番号4〜26によって提供されるアミノ酸配列のいずれか1つなどにおける、本明細書に提供される任意のCas9における対応する変異は、変異している。いくつかの態様において、配列番号6によって提供されるアミノ酸配列のD10残基、または配列番号4〜26によって提供されるアミノ酸配列のいずれか1つなどにおける、本明細書に提供される任意のCas9における対応する変異は、Dを除く任意のアミノ酸残基に変異している。いくつかの態様において、配列番号6によって提供されるアミノ酸配列のD10残基、または配列番号4〜26によって提供されるアミノ酸配列のいずれか1つなどにおける、本明細書に提供される任意のCas9における対応する変異は、Aに変異している。いくつかの態様において、配列番号6によって提供されるアミノ酸配列のH840残基、または配列番号4〜26によって提供される任意のアミノ酸配列などの任意のCas9における対応する残基は、Hである。いくつかの態様において、配列番号6によって提供されるアミノ酸配列のH840残基、または配列番号4〜26によって提供される任意のアミノ酸配列などの任意のCas9における対応する変異は、Hを除くいずれかのアミノ酸残基に変異している。いくつかの態様において、配列番号6によって提供されるアミノ酸配列のH840残基、または配列番号4〜26によって提供される任意のアミノ酸配列などの、任意のCas9における対応する変異は、Aに変異している。いくつかの態様において、配列番号6によって提供されるアミノ酸配列のD10残基、または配列番号4〜26によって提供される任意のアミノ酸配列などの、任意のCas9における対応する残基は、Dである。
当業者は、ここに記載されている発明の特定の態様に対する多くの均等物を認識し、または日常的な実験のみを用いて確かめることができるであろう。本発明の範囲は、上記の説明に限定されることを意図するものではなく、むしろ添付の請求項に記載の通りである。
Claims (181)
- (i)核酸プログラム可能なDNA結合蛋白質(napDNAbp)、および(ii)シチジンデアミナーゼドメイン、および(iii)ウラシル結合蛋白質(UBP)を含む、融合蛋白質。
- ウラシル結合蛋白質が、ウラシル修飾酵素である、請求項1に記載の融合蛋白質。
- ウラシル結合蛋白質が、ウラシル塩基除去酵素である、請求項1または2に記載の融合蛋白質。
- ウラシル結合蛋白質が、ウラシルDNAグルコシラーゼ(UDG)酵素である、請求項1〜3のいずれか一項に記載の融合蛋白質。
- ウラシルDNAグルコシラーゼ(UDG)酵素が、ヒト、マウス、ラット、イヌ、サル、ウシ、アカゲザル、チンパンジー、ゴリラ、ヤツメウナギ、またはウラシルDNAグルコシラーゼ(UDG)活性を有する、それらの任意の変異型からである、請求項4に記載の融合蛋白質。
- ウラシル結合蛋白質が、配列番号49(UdgX)のアミノ酸配列に少なくとも80%、85%、90%、95%、98%または99%同一であるアミノ酸配列を含むUdgXである、請求項1〜5のいずれか一項に記載の融合蛋白質。
- ウラシル結合蛋白質が、配列番号49(UdgX)のアミノ酸配列を含む、請求項6に記載の融合蛋白質。
- ウラシル結合蛋白質が、配列番号48(UDG)のアミノ酸配列と少なくとも80%、85%、90%、95%、98%または99%同一であるアミノ酸配列を含む、UDGである、請求項1〜5のいずれか一項に記載の融合蛋白質。
- ウラシル結合蛋白質が、配列番号48(UDG)のアミノ酸配列を含む、請求項8に記載の融合蛋白質。
- ウラシル結合蛋白質が、配列番号50(UdgX*)のアミノ酸配列と少なくとも80%、85%、90%、95%、98%または99%同一であるアミノ酸配列を含む、UdgX*である、請求項1〜5のいずれか一項に記載の融合蛋白質。
- ウラシル結合蛋白質が、配列番号50(UdgX*)のアミノ酸配列を含む、請求項10に記載の融合蛋白質。
- ウラシル結合蛋白質が、配列番号51(UdgX_Оn)のアミノ酸配列と少なくとも80%、85%、90%、95%、98%または99%同一であるアミノ酸配列を含むUdgX_Оnである、請求項1〜5のいずれか一項に記載の融合蛋白質。
- ウラシル結合蛋白質が、配列番号51(UdgX_Оn)のアミノ酸配列を含む、請求項12に記載の融合蛋白質。
- ウラシル結合蛋白質が、配列番号53(SMUG1)のアミノ酸配列と少なくとも80%、85%、90%、95%、98%または99%同一であるアミノ酸配列を含む、SMUG1である、請求項1〜5のいずれか一項に記載の融合蛋白質。
- ウラシル結合蛋白質が、配列番号53(SMUG1)のアミノ酸配列を含む、請求項14に記載の融合蛋白質。
- 融合蛋白質が、構造:[シチジンデアミナーゼ]−[napDNAbp]−[UBP]を含み、ここで各々の「 ]−[ 」の例が、任意のリンカーを含む、請求項1〜15のいずれか一項に記載の融合蛋白質。
- シチジンデアミナーゼおよびnapDNAbpが、リンカーを介して融合される、請求項1〜16のいずれか一項に記載の融合蛋白質。
- シチジンデアミナーゼおよびnapDNAbpが、配列番号102〜109のいずれか1つのアミノ酸配列を含むリンカーを介して融合されている、請求項17に記載の融合蛋白質。
- napDNAbpおよびUBPが、リンカーを介して融合されている、請求項1〜18いずれか一項のいずれかの融合蛋白質。
- napDNAbpおよびUBPが、配列番号102〜109のいずれか1つのアミノ酸配列を含むリンカーを介して融合されている、請求項19に記載の融合蛋白質。
- 融合蛋白質が、(iv)核酸ポリメラーゼドメイン(NAP)を、さらに含む、請求項1〜20のいずれか一項に記載の融合蛋白質。
- 核酸ポリメラーゼドメインが、真核生物の核酸ポリメラーゼドメインである、請求項21に記載の融合蛋白質。
- 核酸ポリメラーゼドメインが、DNAポリメラーゼドメインである、請求項21または22に記載の融合蛋白質。
- 核酸ポリメラーゼドメインが、損傷乗り越えポリメラーゼ活性を有する、請求項21〜23のいずれか一項に記載の融合蛋白質。
- 核酸ポリメラーゼドメインが、損傷乗り越えDNAポリメラーゼである、請求項21〜24いずれか一項に記載の融合蛋白質。
- 核酸ポリメラーゼドメインが、Rev7、Rev1複合体、ポリメラーゼイオタ、ポリメラーゼカッパ、およびポリメラーゼエタからである、請求項21〜25のいずれか一項に記載の融合蛋白質。
- 核酸ポリメラーゼドメインが、アルファ、ベータ、ガンマ、デルタ、イプシロン、ガンマ、エタ、イオタ、カッパ、ラムダ、ミューおよびニューからなる真核生物のポリメラーゼの群から選択される、請求項21〜25いずれか一項に記載の融合蛋白質。
- 核酸ポリメラーゼドメインが、配列番号54〜64のいずれか1つのアミノ酸配列と少なくとも80%、85%、90%、95%、98%または99%同一であるアミノ酸配列を含む、請求項21〜27のいずれか一項に記載の融合蛋白質。
- 核酸ポリメラーゼドメインが、配列番号54〜64のいずれか1つのアミノ酸配列を含む、請求項21〜28のいずれか一項に記載の融合蛋白質。
- 融合蛋白質が、構造:
[シチジンデアミナーゼ]−[napDNAbp]−[UBP]−[NAP];
[シチジンデアミナーゼ]−[napDNAbp]−[NAP]−[UBP];
[シチジンデアミナーゼ]−[NAP]−[napDNAbp]−[UBP];または、
[NAP]−[シチジンデアミナーゼ]−[napDNAbp]−[UBP];を含み、ここで、「 ]−[ 」のどの場合も、任意のリンカーを含む、請求項21〜29のいずれか一項に記載の前記融合蛋白質。 - NAPおよびUBPが、リンカーを介して融合されている、請求項21〜30いずれか一項に記載の融合蛋白質。
- NAPおよびUBPが、配列番号102〜109のいずれか1つのアミノ酸配列を含むリンカーを介して融合されている、請求項31の融合蛋白質。
- NAPおよびnapDNAbpが、リンカーを介して融合されている、請求項21〜32いずれか一項に記載の融合蛋白質。
- NAPおよびnapDNAbpが、配列番号102〜109のいずれか1つのアミノ酸配列を含むリンカーを介して融合される、請求項33に記載の融合蛋白質。
- NAPおよびシチジンデアミナーゼが、リンカーを介して融合されている、請求項21〜34いずれか一項に記載のいずれかの融合蛋白質。
- NAPおよびシチジンデアミナーゼが、配列番号102〜109のいずれか1つのアミノ酸配列を含むリンカーを介して融合されている、請求項35に記載の融合蛋白質。
- napDNAbpが、Cas9ドメインを含む、請求項1〜36のいずれか一項に記載の融合蛋白質。
- Cas9ドメインが、配列番号4〜26のいずれか1つのアミノ酸配列と少なくとも85%同一であるアミノ酸配列を含む、請求項37に記載の融合蛋白質。
- Cas9ドメインが、配列番号4〜26のいずれか1つのアミノ酸配列を含む、請求項37または38に記載の融合蛋白質。
- Cas9ドメインが、Cas9ニッカーゼ(nCas9)である、請求項37に記載の融合蛋白質。
- Cas9ニッカーゼ(nCas9)が、配列番号10、13、16または21のいずれか1つに少なくとも85%同一であるアミノ酸配列を含む、請求項40に記載の融合蛋白質。
- nCas9が、配列番号10、13、16または21のいずれか1つのアミノ酸配列を含む、請求項40または41に記載の融合蛋白質。
- Cas9ドメインがヌクレアーゼ不活性Cas9(dCas9)である、請求項37に記載の融合蛋白質。
- ヌクレアーゼ不活性Cas9(dCas9)が、配列番号7、8、9または22のいずれか1つに少なくとも85%同一であるアミノ酸配列を含む、請求項43に記載の融合蛋白質。
- dCas9が、配列番号7、8、9または22のいずれか1つのアミノ酸配列を含む、請求項43または44に記載の融合蛋白質。
- (i)核酸プログラム可能なDNA結合蛋白質(napDNAbp)、および(ii)シチジンデアミナーゼドメイン、および(iii)核酸ポリメラーゼ(NAP)ドメインを含む融合蛋白質。
- 核酸ポリメラーゼドメインが、真核生物の核酸ポリメラーゼドメインである、請求項46に記載の融合蛋白質。
- 核酸ポリメラーゼドメインが、DNAポリメラーゼドメインである、請求項46または47に記載の融合蛋白質。
- 核酸ポリメラーゼドメインが、損傷乗り越えポリメラーゼ活性を有する、請求項46〜48のいずれか一項に記載の融合蛋白質。
- 核酸ポリメラーゼドメインが、損傷乗り越えDNAポリメラーゼである、請求項46〜49のいずれか一項に記載の融合蛋白質。
- 核酸ポリメラーゼドメインが、Rev7、Rev1複合体、ポリメラーゼイオタ、ポリメラーゼカッパおよびポリメラーゼエタからである、請求項46〜50のいずれか一項に記載の融合蛋白質。
- 核酸ポリメラーゼドメインが、アルファ、ベータ、ガンマ、デルタ、イプシロン、ガンマ、エタ、イオタ、カッパ、ラムダ、ミューおよびニューからなる真核生物の ポリメラーゼの群から選択される、請求項46〜51のいずれか一項に記載の融合蛋白質。
- 核酸 ポリメラーゼドメインが、配列番号54〜64のいずれか1つのアミノ酸配列に少なくとも80%、85%、90%、95%、98%、または99%同一であるアミノ酸配列を含む、請求項46〜52のいずれか一項に記載の融合蛋白質。
- 核酸ポリメラーゼドメインが、配列番号54〜64のいずれか1つのアミノ酸配列を含む、請求項46〜53のいずれか一項に記載の融合蛋白質。
- シチジンデアミナーゼドメインが、アポリポ蛋白質B mRNA編集複合体(APOBEC)ファミリーデアミナーゼからのデアミナーゼである、請求項1〜54のいずれか一項に記載の融合蛋白質。
- APOBECファミリーデアミナーゼが、APOBEC1デアミナーゼ、APOBEC2デアミナーゼ、APOBEC3Aデアミナーゼ、APOBEC3Bデアミナーゼ、APOBEC3Cデアミナーゼ、APOBEC3Dデアミナーゼ、APOBEC3Fデアミナーゼ、APOBEC3Gデアミナーゼ、およびAPOBEC3Hデアミナーゼからなる群から選択される、請求項55に記載の融合蛋白質。
- シチジンデアミナーゼドメインが、配列番号67〜101のいずれか1つのアミノ酸配列に少なくとも85%同一であるアミノ酸配列を含む、請求項1〜56のいずれか一項に記載の融合蛋白質。
- シチジンデアミナーゼドメインが、配列番号67〜101のいずれか1つのアミノ酸配列を含む、請求項1〜57のいずれか一項に記載の融合蛋白質。
- シチジンデアミナーゼドメインが、配列番号93のW90Y、R126E、およびR132Eからなる群から選択される1つ以上の変異、または別のAPOBECデアミナミナーゼにおける1つ以上の対応する変異、を含むラットAPOBEC1(rAPOBEC1)デアミナーゼである、請求項1〜57のいずれか一項に記載の融合蛋白質。
- シチジンデアミナーゼドメインが、配列番号91のW90Y、Q126E、およびR132Eからなる群から選択される1つ以上の変異、または別のAPOBECデアミナミナーゼにおける1つ以上の対応する変異、を含むヒトAPOBEC1(hAPOBEC1)デアミナーゼである、請求項1〜57のいずれか一項に記載の融合蛋白質。
- シチジンデアミナーゼドメインが、配列番号77のW285Y、R320E、およびR326Eからなる群から選択される1つ以上の変異、または別のAPOBECデアミナミナーゼにおける1つ以上の対応する変異、を含むヒトAPOBEC3G(hAPOBEC3G)デアミナーゼである、請求項1〜57のいずれか一項に記載の融合蛋白質。
- シチジンデアミナーゼドメインが、活性化誘導デアミナーゼ(AID)である、請求項1〜54のいずれか一項に記載の融合蛋白質。
- シチジンデアミナーゼドメインが、Petromyzon marinusからのシチジンデアミナーゼ1(pmCDA1)である、請求項1〜54のいずれか一項に記載の融合蛋白質。
- napDNAbpが、Cas9ドメインである、請求項46〜63のいずれか一項に記載の融合蛋白質。
- Cas9ドメインが、配列番号4〜26のいずれか1つに少なくとも85%同一であるアミノ酸配列を含む、請求項64に記載の融合蛋白質。
- Cas9ドメインが、配列番号4〜26のいずれか1つのアミノ酸配列を含む、請求項64または65に記載の融合蛋白質。
- Cas9ドメインが、Cas9ニッカーゼ(nCas9)である、請求項64に記載の融合蛋白質。
- Cas9ニッカーゼ(nCas9)が、配列番号10、13、16、または21に少なくとも85%同一であるアミノ酸配列を含む、請求項67に記載の融合蛋白質。
- nCas9が、配列番号10、13、16、または21のアミノ酸配列を含む、請求項67または68に記載の融合蛋白質。
- Cas9ドメインが、ヌクレアーゼ不活性Cas9(dCas9)である、請求項64に記載の融合蛋白質。
- ヌクレアーゼ不活性Cas9(dCas9)が、配列番号7、8、9、または22に少なくとも85%同一であるアミノ酸配列を含む、請求項70に記載の融合蛋白質。
- ヌクレアーゼ不活性Cas9(dCas9)が、配列番号7、8、9、または22のアミノ酸配列を含む請求項70または71に記載の融合蛋白質。
- 融合蛋白質が、構造:[シチジンデアミナーゼ]−[napDNAbp]−[NAP]を含み、ここで、「 ]−[ 」のどの場合も、任意のリンカーを含む、請求項46〜72のいずれか一項に記載の融合蛋白質。
- シチジンデアミナーゼおよびnapDNAbpが、リンカーを介して融合されている、請求項46〜73のいずれか一項に記載の融合蛋白質。
- シチジンデアミナーゼおよびnapDNAbpが、配列番号102〜109のいずれか1つのアミノ酸配列を含むリンカーを介して融合されている、請求項74に記載の融合蛋白質。
- napDNAbpおよびNAPが、リンカーを介して融合されている、請求項46〜75のいずれか一項に記載の融合蛋白質。
- napDNAbおよびNAPが、配列番号102〜109のいずれか1つのアミノ酸配列を含むリンカーを介して融合される、請求項76に記載の融合蛋白質。
- (i)核酸プログラム可能なDNA結合蛋白質(napDNAbp)、および(ii)塩基除去酵素(BEE)を含む、融合蛋白質。
- 塩基除去酵素が、シトシン(C)またはチミン(T)塩基除去酵素である、請求項78に記載の融合蛋白質。
- 塩基除去酵素が、シトシン(C)塩基除去酵素である、請求項78または79に記載の融合蛋白質。
- 塩基除去酵素が、配列番号48に少なくとも85%同一であるアミノ酸配列を含み、および配列番号48のアミノ酸残基156においてAを含む、請求項79または80に記載の融合蛋白質。
- 塩基除去酵素が、配列番号65のアミノ酸配列を含む、請求項80または81に記載の融合蛋白質。
- 塩基除去酵素が、チミン(T)塩基除去酵素である、請求項78または79の融合蛋白質。
- 塩基除去酵素が、配列番号48に少なくとも85%同一であるアミノ酸配列を含み、および配列番号48のアミノ酸残基213においてDを含む、請求項83に記載の融合蛋白質。
- 塩基除去酵素が、配列番号66のアミノ酸配列を含む、請求項B6またはB7に記載の融合蛋白質。
- 融合蛋白質が、構造:[napDNAbp]−[BEE]、または[BEE]−[napDNAbp]を含み、ここで、「 ]−[ 」のどの場合も、任意のリンカーを含む、請求項78〜85のいずれか一項に記載の融合蛋白質。
- BEEおよびnapDNAbpが、リンカーを介して融合されている、請求項78〜86のいずれか一項に記載の融合蛋白質。
- BEEおよびnapDNAbpが、配列番号102〜109のいずれか1つのアミノ酸配列を含むリンカーを介して融合されている、請求項86または87に記載の融合蛋白質。
- 融合蛋白質が、(iii)核酸ポリメラーゼドメイン(NAP)をさらに含む、請求項78〜88のいずれか一項に記載の融合蛋白質。
- 核酸ポリメラーゼドメインが、真核生物の核酸ポリメラーゼドメインである、請求項89に記載の融合蛋白質。
- 核酸ポリメラーゼドメインが、DNAポリメラーゼドメインである、請求項89または90に記載の融合蛋白質。
- 核酸ポリメラーゼドメインが、損傷乗り越えポリメラーゼ活性を有する、請求項89〜91のいずれか一項に記載の融合蛋白質。
- 核酸ポリメラーゼドメインが、損傷乗り越えDNAポリメラーゼである、請求項89〜92のいずれか一項に記載の融合蛋白質。
- 核酸ポリメラーゼドメインが、Rev7、Rev1複合体、ポリメラーゼイオタ、ポリメラーゼカッパ、およびポリメラーゼエタからである、請求項89〜93のいずれか一項に記載の融合蛋白質。
- 核酸ポリメラーゼドメインが、アルファ、ベータ、ガンマ、デルタ、イプシロン、ガンマ、エタ、イオタ、カッパ、ラムダ、ミューおよびニューからなる真核生物の核酸ポリメラーゼの群から選択される、請求項89〜94のいずれか一項に記載の融合蛋白質。
- 核酸ポリメラーゼドメインが、配列番号54〜64のいずれか1つのアミノ酸配列に、少なくとも80%、85%、90%、95%、98%、または99%同一であるアミノ酸配列を含む、請求項89〜95のいずれか一項に記載の融合蛋白質。
- 核酸ポリメラーゼドメインが、配列番号54〜64のいずれか1つのアミノ酸配列を含む、請求項89〜96に記載の融合蛋白質。
- 融合蛋白質が、構造:
「napDNAbp」−[BEE]−[NAP];
[napDNAbp]−[NAP]−[BEE];
[NAP]−[napDNAbp]−[BEE];
[NAP]−[BEE]−[napDNAbp];
[BEE]−[napDNAbp]−[NAP];または
[BEE]−[NAP]−[napDNAbp]を含み、
ここで、「 ]−[ 」のどの場合も、任意のリンカーを含む、請求項89〜97のいずれか一項に記載の融合蛋白質。 - NAPとBEEが、リンカーを介して融合されている、請求項89〜98のいずれか一項に記載の融合蛋白質。
- NAPとBEEが、配列番号102〜109のいずれか1つのアミノ酸配列を含むリンカーを介して融合されている、請求項99に記載の融合蛋白質。
- BEEとnapDNAbpが、リンカーを介して融合されている、請求項89〜100のいずれか一項のいずれかに記載の融合蛋白質。
- BEEとnapDNAbpが、配列番号102〜109のいずれか1つのアミノ酸を含むリンカーを介して融合されている、請求項101に記載の融合蛋白質。
- BEEとnapDNAbpが、リンカーを介して融合されている、請求項89〜102のいずれか一項に記載の融合蛋白質。
- BEEとnapDNAbpが、配列番号102〜109のいずれか1つのアミノ酸を含むリンカーを介して融合される、請求項103に記載の融合蛋白質。
- napDNAbpが、Cas9ドメインを含む、請求項78〜104のいずれか一項に記載の融合蛋白質。
- Cas9ドメインが、配列番号4〜26のいずれか1つに少なくとも85%同一であるアミノ酸配列を含む、請求項105に記載の融合蛋白質。
- Cas9ドメインが、配列番号4〜26のいずれか1つのアミノ酸配列を含む、請求項105または106に記載の融合蛋白質。
- Cas9ドメインが、Cas9ニッカーゼ(nCas9)である、請求項105に記載の融合蛋白質。
- Cas9ニッカーゼ(nCas9)が、配列番号10、13、16、または21に少なくとも85%同一であるアミノ酸配列を含む、請求項108に記載の融合蛋白質。
- nCas9が、配列番号10、13、16、または21のアミノ酸配列を含む、請求項108または109に記載の融合蛋白質。
- Cas9ドメインが、ヌクレアーゼ不活性Cas9(dCas9)である、請求項105に記載の融合蛋白質。
- ヌクレアーゼ不活性Cas9(dCas9)が、配列番号7、8、9、または22に少なくとも85%同一であるアミノ酸配列を含む、請求項111に記載の融合蛋白質。
- dCas9が、配列番号7、8、9、または22のアミノ酸配列を含む、請求項B34またはB35に記載の融合蛋白質。
- 以下:
(i)配列番号4〜40のいずれか1つのアミノ酸配列に少なくとも80%同一である第1のアミノ酸配列;
(ii)配列番号67〜101のいずれか1つのアミノ酸配列に少なくとも80%同一である第2のアミノ酸配列;および
(iii)配列番号48〜53のいずれか1つのアミノ酸配列に少なくとも80%同一である第3のアミノ酸配列を含む、融合蛋白質。 - (iv)配列番号54〜64のいずれか1つのアミノ酸配列に少なくとも80%同一である第4のアミノ酸配列をさらに含む、請求項114に記載の前記融合蛋白質。
- 第1アミノ酸配列が、配列番号4〜40のいずれか1つのアミノ酸配列に少なくとも85%、90%、95%、98%、または99%同一である、請求項114または115に記載の融合蛋白質。
- 第2のアミノ酸配列が、配列番号67〜101のいずれか1つのアミノ酸配列に少なくとも85%、90%、95%、98%、または99%同一である、請求項114〜116のいずれか一項に記載の融合蛋白質。
- 第3のアミノ酸配列が、配列番号48〜53のいずれか1つのアミノ酸配列に少なくとも85%、90%、95%、98%、または99%同一である、請求項114〜117のいずれか一項に記載の融合蛋白質。
- 第4のアミノ酸配列が、配列番号54〜64のいずれか1つのアミノ酸配列に少なくとも85%、90%、95%、98%、または99%同一である、請求項115〜118のいずれか一項に記載の融合蛋白質。
- 融合蛋白質が、構造:
NH2-[第2のアミノ酸配列]−[第1のアミノ酸配列]−[第3のアミノ酸配列]−COOH;
NH2−[第2のアミノ酸配列]−[第3のアミノ酸配列]−[第1のアミノ酸配列]−COOH;
NH2−[第1のアミノ酸配列]−[第2のアミノ酸配列]−[第3のアミノ酸配列]−COOH;
NH2−[第1のアミノ酸配列]−[第3のアミノ酸配列]−[第2のアミノ酸配列]−COOH;
NH2−[第3のアミノ酸配列]−[第1のアミノ酸配列]−[第2のアミノ酸配列]−COOH;
NH2−[第3のアミノ酸配列]−[第2のアミノ酸配列]−[第1のアミノ酸配列]−COOH;を含み、ここで「−」の各々が、任意のリンカーを含む、請求項114〜119のいずれか一項に記載の融合蛋白質。 - 融合蛋白質が、構造:
NH2−[第4のアミノ酸配列]−[第2のアミノ酸配列]−[第1のアミノ酸配列]−[第3のアミノ酸配列]−COOH;
NH2−[第2のアミノ酸配列]−[第4のアミノ酸配列]−[第1のアミノ酸配列]−[第3のアミノ酸配列]−COOH;
NH2−[第2のアミノ酸配列]−[第1のアミノ酸配列]−[第4のアミノ酸配列]−[第3のアミノ酸配列]−COOH;
NH2−[第2のアミノ酸配列]−[第1のアミノ酸配列]−[第3のアミノ酸配列]−[第4のアミノ酸配列]−COOH;
NH2−[第4のアミノ酸配列]−[第2のアミノ酸配列]−[第3のアミノ酸配列]−[第1のアミノ酸配列]−COOH;
NH2−[第2のアミノ酸配列]−[第4のアミノ酸配列]−[第3のアミノ酸配列]−[第1のアミノ酸配列]−COOH;
NH2−[第2のアミノ酸配列]−[第3のアミノ酸配列]−[第4のアミノ酸配列]−[第1のアミノ酸配列]−COOH;
NH2−[第2のアミノ酸配列]−[第3のアミノ酸配列]−[第1のアミノ酸配列]−[第4のアミノ酸配列]−COOH;
NH2−[第4のアミノ酸配列]−[第1のアミノ酸配列]−[第2のアミノ酸配列]−[第3のアミノ酸配列]−COOH;
NH2−[第1のアミノ酸配列]−[第4のアミノ酸配列]−[第2のアミノ酸配列]−[第3のアミノ酸配列]−COOH;
NH2−[第1のアミノ酸配列]−[第2のアミノ酸配列]−[第4のアミノ酸配列]−[第3のアミノ酸配列]−COOH;
NH2−[第1のアミノ酸配列]−[第2のアミノ酸配列]−[第3のアミノ酸配列]−[第4のアミノ酸配列]−COOH;
NH2−[第4のアミノ酸配列]−[第1のアミノ酸配列]−[第3のアミノ酸配列]−[第2のアミノ酸配列]−COOH;
NH2−[第1のアミノ酸配列]−[第4のアミノ酸配列]−[第3のアミノ酸配列]−[第2のアミノ酸配列]−COOH;
NH2−[第1のアミノ酸配列]−[第3のアミノ酸配列]−[第4のアミノ酸配列]−[第2のアミノ酸配列]−COOH;
NH2−[第1のアミノ酸配列]−[第3のアミノ酸配列]−[第2のアミノ酸配列]−[第4のアミノ酸配列]−COOH;
NH2−[第4のアミノ酸配列]−[第3のアミノ酸配列]−[第1のアミノ酸配列]−[第2のアミノ酸配列]−COOH;
NH2−[第3のアミノ酸配列]−[第4のアミノ酸配列]−[第1のアミノ酸配列]−[第2のアミノ酸配列]−COOH;
NH2−[第3のアミノ酸配列]−[第1のアミノ酸配列]−[第4のアミノ酸配列]−[第2のアミノ酸配列]−COOH;
NH2−[第3のアミノ酸配列]−[第1のアミノ酸配列]−[第2のアミノ酸配列]−[第4のアミノ酸配列]−COOH;
NH2−[第4のアミノ酸配列]−[第3のアミノ酸配列]−[第2のアミノ酸配列]−[第1のアミノ酸配列]−COOH;
NH2−[第3のアミノ酸配列]−[第4のアミノ酸配列]−[第2のアミノ酸配列]−[第1のアミノ酸配列]−COOH;
NH2−[第3のアミノ酸配列]−[第2のアミノ酸配列]−[第4のアミノ酸配列]−[第1のアミノ酸配列]−COOH;
NH2−[第3のアミノ酸配列]−[第2のアミノ酸配列]−[第1のアミノ酸配列]−[第4のアミノ酸配列]−COOH;
を含み、ここで、「−」の各々が、任意のリンカーを含む、請求項115〜119のいずれか一項に記載の融合蛋白質。 - 以下:
(i)配列番号4〜40のいずれか1つのアミノ酸配列に少なくとも80%同一である第1のアミノ酸配列;
(ii)配列番号67〜101のいずれか1つのアミノ酸配列に少なくとも80%同一である第2のアミノ酸配列;および
(iii)配列番号54〜64のいずれか1つのアミノ酸配列に少なくとも80%同一である第3のアミノ酸配列、
を含む、融合蛋白質。 - 第1のアミノ酸配列が、配列番号4〜40のいずれか1つのアミノ酸配列に少なくとも85%、90%、95%、98%、または99%同一である、請求項122に記載の融合蛋白質。
- 第2のアミノ酸配列が、配列番号67〜101のいずれか1つのアミノ酸配列に少なくとも85%、90%、95%、98%、または99%同一である、請求項122〜123のいずれか一項に記載の融合蛋白質。
- 第3のアミノ酸配列が、配列番号54〜64のいずれか1つのアミノ酸配列に少なくとも85%、90%、95%、98%、または99%同一である、請求項122〜124のいずれか一項に記載の融合蛋白質。
- 融合蛋白質が、構造:
NH2−[第2のアミノ酸配列]−[第1のアミノ酸配列]−[第3のアミノ酸配列]−COOH;
NH2−[第2のアミノ酸配列]−[第3のアミノ酸配列]−[第1のアミノ酸配列]−COOH;
NH2−[第1のアミノ酸配列]−[第2のアミノ酸配列]−[第3のアミノ酸配列]−COOH;
NH2−[第1のアミノ酸配列]−[第3のアミノ酸配列]−[第2のアミノ酸配列]−COOH;
NH2−[第3のアミノ酸配列]−[第1のアミノ酸配列]−[第2のアミノ酸配列]−COOH;
NH2−[第3のアミノ酸配列]−[第2のアミノ酸配列]−[第1のアミノ酸配列]−COOH;
を含み、ここで「−」の各々が任意のリンカーを含む、請求項122〜125のいずれか一項に記載の前記融合蛋白質。 - 以下:
(i)配列番号4〜40のいずれか1つのアミノ酸配列に少なくとも80%同一である第1のアミノ酸配列;
(ii)配列番号65または66のアミノ酸配列に少なくとも80%同一である、第2のアミノ酸配列;
を含む融合蛋白質。 - (iii)配列番号54〜64のいずれか1つのアミノ酸配列に少なくとも80%同一である第3のアミノ酸配列をさらに含む、請求項127に記載の融合蛋白質。
- 第1のアミノ酸配列が、配列番号4〜40のいずれか1つのアミノ酸配列に少なくとも85%、90%、95%、98%、または99%同一である、請求項127または128に記載の融合蛋白質。
- 第2のアミノ酸配列が、配列番号65または66のアミノ酸配列に少なくとも85%、90%、95%、98%、または99%同一である、請求項127〜129のいずれか一項に記載の融合蛋白質。
- 第3のアミノ酸配列が、配列番号54〜64のいずれか1つのアミノ酸配列に少なくとも85%、90%、95%、98%、または99%同一である、請求項128〜130のいずれか一項に記載の融合蛋白質。
- 融合蛋白質が、構造:
NH2−[第2のアミノ酸配列]−[第1のアミノ酸配列]−COOH;または
NH2−[第1のアミノ酸配列]−[第2のアミノ酸配列]−COOH;
を含み、ここで「−」の各々が、任意のリンカーを含む、請求項127〜131のいずれか一項に記載の融合蛋白質。 - 融合蛋白質が、構造:
NH2−[第2のアミノ酸配列]−[第1のアミノ酸配列]−[第3のアミノ酸配列]−COOH;
NH2−[第2のアミノ酸配列]−[第3のアミノ酸配列]−[第1のアミノ酸配列]−COOH;
NH2−[第1のアミノ酸配列]−[第2のアミノ酸配列]−[第3のアミノ酸配列]−COOH;
NH2−[第1のアミノ酸配列]−[第3のアミノ酸配列]−[第2のアミノ酸配列]−COOH;
NH2−[第3のアミノ酸配列]−[第1のアミノ酸配列]−[第2のアミノ酸配列]−COOH;
NH2−[第3のアミノ酸配列]−[第2のアミノ酸配列]−[第1のアミノ酸配列]−COOH;
を含み、ここで「−」の各々が、任意のリンカーを含む、請求項128〜131のいずれか一項に記載の融合蛋白質。 - 核酸分子および請求項1〜133のいずれか一項に記載の融合蛋白質を含む、複合体。
- 核酸分子が、RNAである、請求項134に記載の複合体。
- 核酸分子が、gRNAである、請求項134または135に記載の複合体。
- 核酸分子が、sgRNAである、請求項134〜136のいずれか一項に記載の複合体。
- 請求項1〜133のいずれか一項に記載の融合蛋白質を含む、医薬組成物。
- 請求項134〜137のいずれか一項に記載の複合体を含む、医薬組成物。
- 薬学的に許容し得る賦形剤をさらに含む、請求項138または139に記載の医薬組成物。
- 核酸分子を請求項1〜133のいずれか一項に記載の融合蛋白質に、または請求項134〜137のいずれか一項の複合体に接触することを含む、方法。
- 核酸分子が、DNAである、請求項141に記載の方法。
- 核酸分子が、ゲノムのDNAである、請求項141または142に記載の方法。
- 二本鎖DNA配列の核酸塩基対を編集する方法であって、方法が:
a)二本鎖DNA配列の標的領域を、核塩基編集因子およびガイド核酸を含む複合体と接触すること、ここで、標的領域が、標的核酸塩基対を含み;
b)前記標的領域の鎖分離を誘導すること;および
c)標的領域の単一鎖において、シトシンまたはチミンを切除すること、を含む前記方法。 - ステップcが、標的領域の単一鎖においてシトシンを切除することを含む、請求項144に記載の方法。
- 二本鎖DNA配列の核酸塩基対を編集するための方法で、方法が:
a)二本鎖DNA配列の標的領域を核酸プログラム可能なDNA結合蛋白質と接触させること、ここで、標的領域は、標的核酸塩基対を含み;
b)標的領域の前記標的核酸塩基対の第1核酸塩基を切除すること;および
c)第1核酸塩基を、第1核酸塩基とは異なる第2核酸塩基と置き換えること;を含む前記方法。 - 核酸コンストラクトを含むキットであって:
(a)請求項1〜133のいずれか一項に記載の融合蛋白質をコードする核酸配列;および
(b)(a)の発現を駆動する、異種プロモーター
を含む、前記キット。 - 請求項1〜133のいずれか一項に記載の融合蛋白質をコードするポリヌクレオチド。
- 請求項148に記載のポリヌクレオチドを含む、ベクター。
- 請求項1〜133のいずれか一項に記載の融合蛋白質を含む、細胞。
- 請求項134〜137のいずれか一項に記載の複合体を含む、細胞。
- 請求項1〜133のいずれか一項に記載の融合蛋白質をコードする核酸分子を含む、細胞。
- 細胞が、in vitroに存在する、請求項150〜152のいずれか一項に記載の細胞。
- 細胞が、in vivoに存在する、請求項150〜152のいずれか一項に記載の細胞。
- 疾患または障害を有するまたは有することが疑われる対象を処置する方法で、請求項1〜133のいずれか一項に記載の融合蛋白質、134〜137のいずれか一項に記載の複合体、請求項148に記載のポリヌクレオチド、または請求項149に記載のベクターを、対象へ投与することを含む、前記方法。
- 二本鎖DNA配列の核酸塩基対を編集するための方法で、方法が:
a.二本鎖DNA配列の標的領域を核酸塩基編集因子およびガイド核酸を含む複合体に接触させること、ここで、標的領域が標的核酸塩基対を含む;
b.前記標的領域の鎖分離を誘導すること;
c.標的領域の単一鎖における前記標的核酸塩基対の第1の核酸塩基を第2の核酸塩基へ変換すること;
d.二本鎖のDNA配列から前記第2核酸塩基を切除して、脱塩基の部位を産生すること;および
e.前記標的領域の1つの鎖だけを切ること;
ここで、脱塩基の部位に反対の第3の核酸塩基が、第4の核酸塩基によって置き換えられること;を含む、前記方法。 - 20%未満から1%未満までのインデル形成を引き起こす、請求項156に記載の方法。
- 第4の核酸塩基に相補的な第5の核酸塩基を、脱塩基の部位の中へ挿入することをさらに含み、それにより意図される編集された塩基対を生成する、請求項156に記載の方法。
- 意図される編集された塩基対を生成する効率が、少なくとも5%である、請求項158に記載の方法。
- 効率が、少なくとも10%から少なくとも50%にわたる、請求項159に記載の方法。
- 意図される編集された塩基対に対する意図されない編集された塩基対の比が2:1から10:1である、請求項158に記載の方法。
- 意図される編集された塩基対に対するインデル形成の比が、2:1から200:1にわたる、請求項158に記載の方法。
- 切断される鎖が、ガイド核酸にハイブリダイゼーションされる、請求項156に記載の方法。
- 切断された単一鎖が、第一核酸塩基を含む鎖に反対である、請求項156に記載の方法。
- 第1核酸塩基が、シトシンである、請求項156に記載の方法。
- 第2の核酸塩基が、ウラシルである、請求項156に記載の方法。
- 核酸塩基編集因子が、ウラシル結合蛋白質を含む、請求項156に記載の方法。
- 核酸塩基編集因子が、ニッカーゼ活性を含む、請求項156に記載の方法。
- 意図される編集された塩基対が、PAM部位の上流である、請求項159に記載の方法。
- 意図される編集された塩基対が、PAM部位の1、2、3、4、5、6、7、8、9、10、11、12、13、14、15、16、17、18、19、または20ヌクレオチド上流である、請求項169に記載の方法。
- 意図される編集された塩基対が、PAM部位の下流である、請求項158に記載の方法。
- 意図される編集された塩基対が、PAM部位の1、2、3、4、5、6、7、8、9、10、11、12、13、14、15、16、17、18、19、または20ヌクレオチド下流である、請求項171に記載の方法。
- 核酸塩基編集因子が、リンカーを含む、請求項156に記載の方法。
- リンカーが1〜25アミノ酸長である、請求項173に記載の方法。
- リンカーが5〜20アミノ酸長である、請求項173に記載の方法。
- リンカーが、10、11、12、13、14、15、16、17、18、19、または20アミノ酸長である、請求項173に記載の方法。
- 標的領域が標的ウインドウを含み、標的ウインドウが標的核酸塩基対を含む、請求項156に記載の方法。
- 標的ウインドウが1〜10のヌクレオチドを含む、請求項177に記載の方法。
- 標的ウインドウが、1〜9、1〜8、1〜7、1〜6、1〜5、1〜4、1〜3、1〜2、または1ヌクレオチド長である、請求項177に記載の方法。
- 標的ウインドウが、1、2、3、4、5、6、7、8、9、10、11、12、13、14、15、16、17、18、19、または20ヌクレオチド長である、請求項177に記載の方法。
- 標的ウインドウが、意図される編集された塩基対を含む、請求項177〜180のいずれか一項に記載の方法。
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