JP7227619B2 - ヌクレアーゼプロファイリングシステム - Google Patents
ヌクレアーゼプロファイリングシステム Download PDFInfo
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Description
本願は、2014年6月30日出願の米国出願USSN14/320,370および2014年6月30日出願の米国出願USSN14/320,413の米国特許法第365条(c)の下における優先権を主張し、2013年8月9日出願の米国仮特許出願USSN61/864,289の米国特許法第119条(e)の下における優先権をもまた主張し、そのそれぞれは参照によって本明細書に組み込まれる。
本発明は、国防高等研究計画局によって授与された助成金HR0011-11-2-0003号およびN66001-12-C-4207号の下で米国政府の援助によってなされた。米国政府は本発明にある権利を有する。
本明細書および請求項において用いられる場合には、単数形「a」、「an」、および「the」は、文脈が別様に明確に示さない限り、単数および複数の参照を包含する。それゆえに、例えば「薬剤」の参照は単一の薬剤および複数個のかかる薬剤を包含する。
ATGGATAAGAAATACTCAATAGGCTTAGATATCGGCACAAATAGCGTCGGATGGGCGGTGATCACTGATGATTATAAGGTTCCGTCTAAAAAGTTCAAGGTTCTGGGAAATACAGACCGCCACAGTATCAAAAAAAATCTTATAGGGGCTCTTTTATTTGGCAGTGGAGAGACAGCGGAAGCGACTCGTCTCAAACGGACAGCTCGTAGAAGGTATACACGTCGGAAGAATCGTATTTGTTATCTACAGGAGATTTTTTCAAATGAGATGGCGAAAGTAGATGATAGTTTCTTTCATCGACTTGAAGAGTCTTTTTTGGTGGAAGAAGACAAGAAGCATGAACGTCATCCTATTTTTGGAAATATAGTAGATGAAGTTGCTTATCATGAGAAATATCCAACTATCTATCATCTGCGAAAAAAATTGGCAGATTCTACTGATAAAGCGGATTTGCGCTTAATCTATTTGGCCTTAGCGCATATGATTAAGTTTCGTGGTCATTTTTTGATTGAGGGAGATTTAAATCCTGATAATAGTGATGTGGACAAACTATTTATCCAGTTGGTACAAATCTACAATCAATTATTTGAAGAAAACCCTATTAACGCAAGTAGAGTAGATGCTAAAGCGATTCTTTCTGCACGATTGAGTAAATCAAGACGATTAGAAAATCTCATTGCTCAGCTCCCCGGTGAGAAGAGAAATGGCTTGTTTGGGAATCTCATTGCTTTGTCATTGGGATTGACCCCTAATTTTAAATCAAATTTTGATTTGGCAGAAGATGCTAAATTACAGCTTTCAAAAGATACTTACGATGATGATTTAGATAATTTATTGGCGCAAATTGGAGATCAATATGCTGATTTGTTTTTGGCAGCTAAGAATTTATCAGATGCTATTTTACTTTCAGATATCCTAAGAGTAAATAGTGAAATAACTAAGGCTCCCCTATCAGCTTCAATGATTAAGCGCTACGATGAACATCATCAAGACTTGACTCTTTTAAAAGCTTTAGTTCGACAACAACTTCCAGAAAAGTATAAAGAAATCTTTTTTGATCAATCAAAAAACGGATATGCAGGTTATATTGATGGGGGAGCTAGCCAAGAAGAATTTTATAAATTTATCAAACCAATTTTAGAAAAAATGGATGGTACTGAGGAATTATTGGTGAAACTAAATCGTGAAGATTTGCTGCGCAAGCAACGGACCTTTGACAACGGCTCTATTCCCCATCAAATTCACTTGGGTGAGCTGCATGCTATTTTGAGAAGACAAGAAGACTTTTATCCATTTTTAAAAGACAATCGTGAGAAGATTGAAAAAATCTTGACTTTTCGAATTCCTTATTATGTTGGTCCATTGGCGCGTGGCAATAGTCGTTTTGCATGGATGACTCGGAAGTCTGAAGAAACAATTACCCCATGGAATTTTGAAGAAGTTGTCGATAAAGGTGCTTCAGCTCAATCATTTATTGAACGCATGACAAACTTTGATAAAAATCTTCCAAATGAAAAAGTACTACCAAAACATAGTTTGCTTTATGAGTATTTTACGGTTTATAACGAATTGACAAAGGTCAAATATGTTACTGAGGGAATGCGAAAACCAGCATTTCTTTCAGGTGAACAGAAGAAAGCCATTGTTGATTTACTCTTCAAAACAAATCGAAAAGTAACCGTTAAGCAATTAAAAGAAGATTATTTCAAAAAAATAGAATGTTTTGATAGTGTTGAAATTTCAGGAGTTGAAGATAGATTTAATGCTTCATTAGGCGCCTACCATGATTTGCTAAAAATTATTAAAGATAAAGATTTTTTGGATAATGAAGAAAATGAAGATATCTTAGAGGATATTGTTTTAACATTGACCTTATTTGAAGATAGGGGGATGATTGAGGAAAGACTTAAAACATATGCTCACCTCTTTGATGATAAGGTGATGAAACAGCTTAAACGTCGCCGTTATACTGGTTGGGGACGTTTGTCTCGAAAATTGATTAATGGTATTAGGGATAAGCAATCTGGCAAAACAATATTAGATTTTTTGAAATCAGATGGTTTTGCCAATCGCAATTTTATGCAGCTGATCCATGATGATAGTTTGACATTTAAAGAAGATATTCAAAAAGCACAGGTGTCTGGACAAGGCCATAGTTTACATGAACAGATTGCTAACTTAGCTGGCAGTCCTGCTATTAAAAAAGGTATTTTACAGACTGTAAAAATTGTTGATGAACTGGTCAAAGTAATGGGGCATAAGCCAGAAAATATCGTTATTGAAATGGCACGTGAAAATCAGACAACTCAAAAGGGCCAGAAAAATTCGCGAGAGCGTATGAAACGAATCGAAGAAGGTATCAAAGAATTAGGAAGTCAGATTCTTAAAGAGCATCCTGTTGAAAATACTCAATTGCAAAATGAAAAGCTCTATCTCTATTATCTACAAAATGGAAGAGACATGTATGTGGACCAAGAATTAGATATTAATCGTTTAAGTGATTATGATGTCGATCACATTGTTCCACAAAGTTTCATTAAAGACGATTCAATAGACAATAAGGTACTAACGCGTTCTGATAAAAATCGTGGTAAATCGGATAACGTTCCAAGTGAAGAAGTAGTCAAAAAGATGAAAAACTATTGGAGACAACTTCTAAACGCCAAGTTAATCACTCAACGTAAGTTTGATAATTTAACGAAAGCTGAACGTGGAGGTTTGAGTGAACTTGATAAAGCTGGTTTTATCAAACGCCAATTGGTTGAAACTCGCCAAATCACTAAGCATGTGGCACAAATTTTGGATAGTCGCATGAATACTAAATACGATGAAAATGATAAACTTATTCGAGAGGTTAAAGTGATTACCTTAAAATCTAAATTAGTTTCTGACTTCCGAAAAGATTTCCAATTCTATAAAGTACGTGAGATTAACAATTACCATCATGCCCATGATGCGTATCTAAATGCCGTCGTTGGAACTGCTTTGATTAAGAAATATCCAAAACTTGAATCGGAGTTTGTCTATGGTGATTATAAAGTTTATGATGTTCGTAAAATGATTGCTAAGTCTGAGCAAGAAATAGGCAAAGCAACCGCAAAATATTTCTTTTACTCTAATATCATGAACTTCTTCAAAACAGAAATTACACTTGCAAATGGAGAGATTCGCAAACGCCCTCTAATCGAAACTAATGGGGAAACTGGAGAAATTGTCTGGGATAAAGGGCGAGATTTTGCCACAGTGCGCAAAGTATTGTCCATGCCCCAAGTCAATATTGTCAAGAAAACAGAAGTACAGACAGGCGGATTCTCCAAGGAGTCAATTTTACCAAAAAGAAATTCGGACAAGCTTATTGCTCGTAAAAAAGACTGGGATCCAAAAAAATATGGTGGTTTTGATAGTCCAACGGTAGCTTATTCAGTCCTAGTGGTTGCTAAGGTGGAAAAAGGGAAATCGAAGAAGTTAAAATCCGTTAAAGAGTTACTAGGGATCACAATTATGGAAAGAAGTTCCTTTGAAAAAAATCCGATTGACTTTTTAGAAGCTAAAGGATATAAGGAAGTTAAAAAAGACTTAATCATTAAACTACCTAAATATAGTCTTTTTGAGTTAGAAAACGGTCGTAAACGGATGCTGGCTAGTGCCGGAGAATTACAAAAAGGAAATGAGCTGGCTCTGCCAAGCAAATATGTGAATTTTTTATATTTAGCTAGTCATTATGAAAAGTTGAAGGGTAGTCCAGAAGATAACGAACAAAAACAATTGTTTGTGGAGCAGCATAAGCATTATTTAGATGAGATTATTGAGCAAATCAGTGAATTTTCTAAGCGTGTTATTTTAGCAGATGCCAATTTAGATAAAGTTCTTAGTGCATATAACAAACATAGAGACAAACCAATACGTGAACAAGCAGAAAATATTATTCATTTATTTACGTTGACGAATCTTGGAGCTCCCGCTGCTTTTAAATATTTTGATACAACAATTGATCGTAAACGATATACGTCTACAAAAGAAGTTTTAGATGCCACTCTTATCCATCAATCCATCACTGGTCTTTATGAAACACGCATTGATTTGAGTCAGCTAGGAGGTGACTGA(配列番号1)
MDKKYSIGLDIGTNSVGWAVITDDYKVPSKKFKVLGNTDRHSIKKNLIGALLFGSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLADSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQIYNQLFEENPINASRVDAKAILSARLSKSRRLENLIAQLPGEKRNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNSEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGAYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDRGMIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGHSLHEQIANLAGSPAIKKGILQTVKIVDELVKVMGHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSFIKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGD(配列番号2)
序論
部位特異的ヌクレアーゼは、インビトロまたはインビボのターゲティングされたゲノム改変に強力なツールである。いくつかの部位特異的ヌクレアーゼは、いずれかの他のゲノム部位に影響すること無しに、切断のためにゲノム中の単一のユニークな部位をターゲティングすることを可能にするであろうターゲット切断部位に対する特異性のレベルを理論上は達成し得る。生細胞内でのヌクレアーゼ切断がDNA修復機構を誘発し、これが、切断された修復されたゲノム配列の改変を(例えば相同組み換えによって)高頻度にもたらすということが報告されている。従って、ゲノム中の特異的なユニークな配列のターゲティングされた切断は、生細胞(従来の遺伝子ターゲティング法によって操作することが難しい細胞、例えば多くのヒト体性または胚性幹細胞を包含する)における遺伝子ターゲティングおよび遺伝子改変に新たな道を開く。疾患関連配列(例えば、HIV/AIDS患者のCCR-5アレル、または腫瘍の血管新生に必要な遺伝子)のヌクレアーゼによって媒介される改変は臨床的な文脈中で用いられ得、2つの部位特異的ヌクレアーゼが現在治験中である。
本開示のいくつかの側面は、いずれかの部位特異的ヌクレアーゼによって切断される核酸ターゲット部位を決定するための改善された方法および試薬を提供する。本明細書において提供される方法は、平滑末端を生ずるヌクレアーゼおよび粘着末端を生ずるヌクレアーゼ両方のターゲット部位選好性および特異性の評価のために用いられ得る。一般的に、かかる方法は、ヌクレアーゼがターゲット部位に結合して切断するのに好適な条件下でターゲット部位のライブラリーと所与のヌクレアーゼを接触させることと、どのターゲット部位をヌクレアーゼが実際に切断するのかを決定することとを含む。実際の切断に基づくヌクレアーゼのターゲット部位プロファイルの決定は、部位特異的ヌクレアーゼの望まれないオフターゲット効果を媒介することにより関係するパラメータを測定するという点において、結合に依存する方法に優る利点を有する。一般的に、本明細書において提供される方法は、5’リン酸依存的なライゲーションによって、目的のヌクレアーゼによって切断された核酸分子に既知の配列のアダプターをライゲーションすることを含む。従って、本明細書において提供される方法は、それらのターゲット部位を切断するときに切断された核酸鎖の5’末端にリン酸部分を残すヌクレアーゼによって切断されるターゲット部位を同定することに、特に有用である。切断された核酸鎖の5’末端にアダプターをライゲーション後に、切断された鎖は、シーケンシングリンカーとしてアダプターを用いて直接的にシーケンシングされ得る。または、切断されたターゲット部位と同一の無傷のターゲット部位を含む切断されたライブラリーメンバーコンカテマーの一部がPCRによって増幅され得、増幅産物はそれからシーケンシングされ得る。
本開示のいくつかの態様は、ヌクレアーゼターゲット部位プロファイリングのための核酸分子のライブラリーを提供する。いくつかの態様において、ライブラリーの候補核酸分子は構造R1-[(NZ)-(PAM)-(定常領域)]X-R2を含み、R1およびR2は、独立して、[(NZ)-(PAM)-(定常領域)]リピート単位の断片を含み得る核酸配列であり、各Nは独立していずれかのヌクレオチドをあらわし、Zは1~50の整数であり、Xは2~yの整数である。いくつかの態様において、yは少なくとも101、少なくとも102、少なくとも103、少なくとも104、少なくとも105、少なくとも106、少なくとも107、少なくとも108、少なくとも109、少なくとも1010、少なくとも1011、少なくとも1012、少なくとも1013、少なくとも1014、または少なくとも1015である。いくつかの態様において、yは102よりも少し、103よりも少し、104よりも少し、105よりも少し、106よりも少し、107よりも少し、108よりも少し、109よりも少し、1010よりも少し、1011よりも少し、1012よりも少し、1013よりも少し、1014よりも少し、または1015よりも少しである。いくつかの態様において、Zは少なくとも2、少なくとも3、少なくとも4、少なくとも5、少なくとも6、少なくとも7、少なくとも8、少なくとも9、少なくとも10、少なくとも11、少なくとも12、少なくとも13、少なくとも14、少なくとも15、少なくとも16、少なくとも17、少なくとも18、少なくとも19、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、または少なくとも50である。いくつかの態様において、Zは20である。各Nは独立していずれかのヌクレオチドをあらわす。従って、Z=2を有するNZとして提供される配列はNNであり、各Nは独立してA、T、G、またはCをあらわすであろう。従って、Z=2を有するNZはAA、AT、AG、AC、TA、TT、TG、TC、GA、GT、GG、GC、CA、CT、CG、およびCCをあらわし得る。
本開示のいくつかの側面は、複雑なゲノムの文脈中で単一のユニークな部位のターゲティングされた切断を可能にする、部位特異的ヌクレアーゼを選択および設計するための方法および戦略を提供する。いくつかの態様において、方法が提供され、同じコンセンサス配列を切断するように設計されたかまたは切断することが既知である複数個の候補ヌクレアーゼを提供することと、各候補ヌクレアーゼによって実際に切断されたターゲット部位をプロファイリングし、それゆえにいずれかの切断されたオフターゲット部位(コンセンサスターゲット部位とは異なるターゲット部位)を検出することと、そのように同定されたオフターゲット部位(単数または複数)に基づいて候補ヌクレアーゼを選択することとを含む。いくつかの態様において、この方法は、候補ヌクレアーゼの群から最も特異的なヌクレアーゼ(例えば、最高の特異性でコンセンサスターゲット部位を切断するヌクレアーゼ、最低数のオフターゲット部位を切断するヌクレアーゼ、ターゲットゲノムの文脈中で最低数のオフターゲット部位を切断するヌクレアーゼ、またはコンセンサスターゲット部位以外のいずれのターゲット部位も切断しないヌクレアーゼ)を選択するために用いられる。いくつかの態様において、この方法は、ヌクレアーゼの治療有効濃度よりも高いかまたはそれに等しい濃度で、対象のゲノムの文脈中のいずれのオフターゲット部位も切断しないヌクレアーゼを選択するために用いられる。
本開示のいくつかの態様は、ゲノム中のヌクレアーゼターゲット部位を選択するための方法を提供する。本明細書において他所でより詳細に記載される通り、所与のヌクレアーゼによって切断されるオフターゲット部位が、典型的にはコンセンサスターゲット部位に高度に類似であり、例えばコンセンサスターゲット部位とは1のみ、2のみ、3のみ、4のみ、または5ヌクレオチド残基のみが異なるということが驚くべきことに発見された。この発見に基づいて、ゲノム中のヌクレアーゼターゲット部位は、この部位をターゲティングするヌクレアーゼが、ゲノム中のいずれのオフターゲット部位も切断しない見込みを増大させるように選択され得る。例えば、いくつかの態様において、方法が提供され、候補ヌクレアーゼターゲット部位を同定することと、ゲノム中の他の配列と候補ヌクレアーゼターゲット部位を比較することとを含む。ゲノム中の他の配列と候補ヌクレアーゼターゲット部位を比較するための方法は当業者に周知であり、例えば配列アラインメント法を包含し、これは例えば配列アラインメントソフトウェアまたはアルゴリズム(例えばBLAST)を汎用コンピュータ上で用いる。好適なユニークなヌクレアーゼターゲット部位は、それから配列比較の結果に基づいて選択され得る。いくつかの態様において、候補ヌクレアーゼターゲット部位がゲノム中のいずれかの他の配列とは少なくとも3、少なくとも4、少なくとも5、少なくとも6、少なくとも7、少なくとも8、少なくとも9、または少なくとも10ヌクレオチドだけ異なる場合には、ヌクレアーゼターゲット部位はゲノム中のユニークな部位として選択され、しかし部位がこの基準にかなっていない場合には、部位は捨てられ得る。いくつかの態様において、上で略説された通り、ひとたび部位が配列比較に基づいて選択されたら、選択された部位をターゲティングする部位特異的ヌクレアーゼが設計される。例えば、ジンクフィンガーヌクレアーゼは、ターゲット部位に結合するジンクフィンガーアレイを構築することと、ジンクフィンガーアレイをDNA切断ドメインにコンジュゲーションすることとによって、いずれかの選択されたヌクレアーゼターゲット部位をターゲティングするように設計され得る。DNA切断ドメインがDNAを切断するために二量体化する必要がある態様においては、ジンクフィンガーアレイが設計され、それぞれはヌクレアーゼターゲット部位のハーフ部位に結合し、それぞれは切断ドメインにコンジュゲーションされるであろう。いくつかの態様において、ヌクレアーゼ設計および/または生成は組み換え技術によってなされる。好適な組み換え技術は当業者に周知であり、開示はこの点に関して限定されない。
本開示のいくつかの側面は、本明細書に記載される方法および戦略を用いて設計される向上した特異性を有する単離された部位特異的ヌクレアーゼを提供する。本開示のいくつかの態様は、かかるヌクレアーゼをコードする核酸を提供する。本開示のいくつかの態様は、かかるコードする核酸を含む発現コンストラクトを提供する。例えば、いくつかの態様においては、単離されたヌクレアーゼが提供され、これはゲノム中の望まれるターゲット部位を切断するように操作されており、ヌクレアーゼがその目指すターゲット部位を切断するのに有効な濃度で1個よりも少し、2個よりも少し、3個よりも少し、4個よりも少し、5個よりも少し、6個よりも少し、7個よりも少し、8個よりも少し、9個よりも少し、または10個よりも少しのオフターゲット部位を切断すると、本明細書において提供される方法に従って評価されている。いくつかの態様において、単離されたヌクレアーゼが提供され、これは、ゲノム中のいずれかの他の部位とは少なくとも3、少なくとも4、少なくとも5、少なくとも6、少なくとも7、少なくとも8、少なくとも9、または少なくとも10ヌクレオチド残基だけ異なるように選択された望まれるユニークなターゲット部位を切断するように操作されている。いくつかの態様において、単離されたヌクレアーゼは、RNAによってプログラム可能なヌクレアーゼ、例えばCas9ヌクレアーゼ、ジンクフィンガーヌクレアーゼ(ZFN)、もしくは転写活性化因子様エフェクターヌクレアーゼ(TALEN)、ホーミングエンドヌクレアーゼ、有機化合物ヌクレアーゼ、またはエンジイン抗生物質(例えば、ダイネミシン、ネオカルジノスタチン、カリケアミシン、エスペラミシン、ブレオマイシン)である。いくつかの態様において、単離されたヌクレアーゼは、疾患または障害と関連したアレル内のターゲット部位を切断する。いくつかの態様において、単離されたヌクレアーゼはターゲット部位を切断し、その切断は疾患または障害の処置または予防をもたらす。いくつかの態様において、疾患はHIV/AIDSまたは増殖性疾患である。いくつかの態様において、アレルはCCR5(HIV/AIDSを処置するため)またはVEGFAアレル(増殖性疾患を処置するため)である。
オリゴヌクレオチド.本研究に用いられた全てのオリゴヌクレオチドはIntegrated DNA Technologiesから購入した。オリゴヌクレオチド配列は表9に列挙されている。
全てのスクリプトはC++で書いた。本研究に用いられたアルゴリズムは以前の報告された(参照)通りであり、改変を有する。
例のリード:
例:ACTTGCAGATGTAGTCTTTCCACATGGGTCGACACAAACACAA(配列番号49)-CLTA4
iii)バーコードの前の配列は、完全な選択後ライブラリーメンバーである(最初の4および最後の4ヌクレオチドは、完全にランダム化された隣接配列である)
例:ACTT GCAGATGTAGTCTTTCCACATGG GTCG(配列番号50)
iv)23ヌクレオチドの選択後ライブラリーメンバーに対応する位置について、品質スコアをパースする
例のリード:
AACACATGGGTCGACACAAACACAACTCGGCAGGTACTTGCAGATGTAGTCTTTCCACATGGGTCGACACAAACACAACTCGGCAGGTATCTCGTATGCC(配列番号51)
CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJGIJJJJIJIJJJIIIHIIJJJHHHGHAEFCDDDDDDDDDDDDDDDDDDDDDDD?CDDEDD@DCCCD
v)配列の対応する品質スコアストリング(下線付き)FASTQ品質キャラクターがASCIIコードで「?」であるかまたはより高い(Phred品質スコア>=30)場合にのみ、配列をキープする
例のリード:
例の隣接配列:GCTGGTGCACTGAAGAGCCA(配列番号53)
AATATCTTAATCCTACTCAG(配列番号54)
2)隣接配列について全ての配列リードを検索し、潜在的なオフターゲット部位(隣接配列間の配列)を同定する
例の潜在的なオフターゲット部位長=22
例の対応するFASTQ品質キャラクター:HHGHHHHHHHHHHHHHHHHHHH
4)ステップ2および3をパスする全ての配列をビニングおよびマニュアル検査し、それらが、位置16、17、もしくは18(非PAM末端からカウントして20のうち)が関与する少なくとも1つの欠失を有する場合、または、それらが位置17および18間に挿入を有する場合に、潜在的な改変された配列として配列をキープする。これは、目指すターゲット部位について観察された最も高頻度の改変と一致している(図3)
例の潜在的なオフターゲット部位(逆相補。位置が標識されている)と参照配列:
11111111112222
非PAM末端 12345678901234567890123 PAM末端
GCAGATGTAGTGTTTC-ACAGGG(配列番号56)
GCAGATGTAGTGTTTCCACAGGG(配列番号57)
4)ステップ1~3をリード2について繰り返し、配列が同じである場合にのみキープする
5)Cas9単独サンプルとCas9+sgRNAによって処置されたサンプルにおける総合的なカウントを比較して、改変された部位を同定する
1)(最初の定常配列の前の)バーコードの後のシーケンシングリード中の最初の位置と同一である、(2つの定常配列間の)完全なシーケンシングされた認識部位内の最初の位置を同定することによって、認識部位を通して切断部位箇所を集計する。
2)集計後にステップ1を繰り返し、シーケンシングリードの少なくとも5%に存在する切断部位箇所を有する配列のみをキープする。
広範囲なオフターゲットDNA切断プロファイリングは、RNAによってプログラムされるCas9ヌクレアーゼ特異性を明らかにする。
ジンクフィンガーヌクレアーゼ(ZFN)および転写活性化因子様エフェクターヌクレアーゼ(TALEN)を包含する配列特異的エンドヌクレアーゼは、人工多能性幹細胞(iPSC)1~3、多細胞生物4~8、およびエクスビボの遺伝子治療治験9、10において遺伝子を改変するための重要なツールになった。ZFNおよびTALENはかかる遺伝子操作に有効だと判明しているが、新たなZFNまたはTALEN蛋白質は各DNAターゲット部位について生成しなければならない。対照的に、RNAガイドCas9エンドヌクレアーゼはRNA:DNAハイブリダイゼーションを用いてターゲットDNA切断部位を決定しており、単一の単量体蛋白質がガイドRNAによって規定されるいずれかの配列を原理的には切断することを可能にする11。
当業者は、本明細書に記載される本発明の具体的な態様の多くの均等物を認識するか、または慣例以下の実験法を用いて確認する能力があるであろう。本発明の範囲は上の記載に限定されることを目指されているのではなく、添付の請求項において示される通りとする。
表1.Cas9:CLTA4 sgRNAによって誘導された細胞の改変。酵素制限または酵素飽和条件下でのCas9:CLTA4 v2.1 sgRNAインビトロ選択において濃縮された、33個のヒトゲノムDNA配列が同定された。下線によって示されている部位は、HEK293T細胞におけるかなりのCas9:sgRNAによって媒介される改変と一致する挿入または欠失(インデル)を含有する。Cas9:CLTA4 v1.0 sgRNAまたはCas9:CLTA4 v2.1 sgRNAによる選択のインビトロ濃縮値は、3つまたは2つ以下の変異を有する配列について示されている。インビトロ選択配列カウントの少数のため、濃縮値は、4つまたは5つ以上の変異を有する配列については算出しなかった。sgRNA無しのCas9(「sgRNA無し」)、CLTA4 v1.0 sgRNA有りのCas9、またはCLTA4 v2.1 sgRNA有りのCas9によって処置されたHEK293T細胞における改変頻度(合計の配列数によって除算されたインデルを有する配列数)。P値が、sgRNA無しのCas9によって処置した細胞と比較してv1.0 sgRNAまたはv2.1 sgRNAによって処置された細胞においてかなりの改変を示す部位について列挙されている。「試験せず(n.t.)」は、ゲノム配列のPCRが特異的な増幅産物を提供できなかったということを示す。
Claims (35)
- ヌクレアーゼのターゲット部位を同定するための方法であって、
(a)二本鎖核酸ターゲット部位を切断するヌクレアーゼを提供し、ターゲット部位の切断が、切断された核酸鎖をもたらすこと;
(b)ヌクレアーゼが候補ヌクレアーゼターゲット部位において候補核酸分子を切断し、切断された核酸鎖を形成するのに好適な条件下で、候補核酸分子のライブラリーと(a)のヌクレアーゼを接触させること、ここで各候補核酸分子は、候補ヌクレアーゼターゲット部位と定常挿入配列とを含む配列のコンカテマーを含む、
(c)候補核酸分子上の切断された末端に核酸アダプターをライゲーションすること、および
(d)切断された末端に隣接する未切断のヌクレアーゼターゲット部位を、単一のリードスルーにおいて、核酸アダプターから直接シーケンシングし、それによってヌクレアーゼのターゲット部位を同定すること、
を含む、前記方法。 - ヌクレアーゼのターゲット部位を同定することが、切断されたハーフ部位の配列からターゲット部位のコンピュータによる再構築を要求しない、請求項1に記載の方法。
- 切断された末端が、平滑に切断された末端である、請求項1に記載の方法。
- 切断された末端が、5’オーバーハングを有するスタッガードに切断された末端である、請求項1に記載の方法。
- ライゲーションが、5’リン酸依存的なライゲーション反応である、請求項1に記載の方法。
- 5’オーバーハングを埋めて、平滑末端を形成することをさらに含む、請求項4に記載の方法。
- 候補核酸分子のライブラリーが、少なくとも108、少なくとも109、少なくとも1010、少なくとも1011、または少なくとも1012個の異なる候補ヌクレアーゼ切断部位を含む、請求項1~6のいずれか一項に記載の方法。
- ヌクレアーゼが、疾患と関連した遺伝子内の特異的なヌクレアーゼターゲット部位を切断する治療用ヌクレアーゼである、請求項1~7のいずれか一項に記載の方法。
- 治療用ヌクレアーゼが特異的なヌクレアーゼターゲット部位を切断し、かつ10よりも多く、5よりも多く、4よりも多く、3よりも多く、2よりも多く、1よりも多く、または全く追加のヌクレアーゼターゲット部位を切断しない治療用ヌクレアーゼの最大濃度を決定することをさらに含む、請求項8に記載の方法。
- ステップ(a)のヌクレアーゼが、RNA分子との複合体を形成するRNAによってプログラム可能なヌクレアーゼであり、ヌクレアーゼ:RNA複合体が、RNA分子の配列に相補的な核酸配列に特異的に結合し、任意にヌクレアーゼがCas9ヌクレアーゼである、請求項1~9のいずれか一項に記載の方法。
- RNA分子が、シングルガイドRNA(sgRNA)であり、任意に、sgRNAが、ターゲット部位に相補的である15~25、19~21、または20ヌクレオチドを含む、請求項10に記載の方法。
- ヌクレアーゼターゲット部位が、[sgRNA相補配列]-[プロトスペーサー隣接モチーフ(PAM)]構造を含み、ヌクレアーゼはターゲット部位をsgRNA相補配列内で切断し、任意に、sgRNA相補配列が、10、11、12、13、14、15、16、17、18、19、20、21、22、23、24、25、26、27、28、29、または30ヌクレオチドを含む、請求項10または11に記載の方法。
- ヌクレアーゼが非特異的核酸切断ドメインを含む、請求項1~9のいずれか一項に記載の方法。
- ヌクレアーゼが、切断ドメイン二量体化時にターゲット配列を切断する核酸切断ドメインを含む、請求項1~9および13のいずれか一項に記載の方法。
- ヌクレアーゼが、核酸配列に特異的に結合する結合ドメインを含む、請求項1~9、13および14のいずれか一項に記載の方法。
- ヌクレアーゼが、FokI切断ドメインを含む、請求項1~9および13~15のいずれか一項に記載の方法。
- 結合ドメインが、ジンクフィンガーを含む、請求項15に記載の方法。
- 結合ドメインが、少なくとも2、少なくとも3、少なくとも4、または少なくとも5つのジンクフィンガーを含む、請求項17に記載の方法。
- 結合ドメインが、転写活性化因子様エレメント(TALE)を含む、請求項15に記載の方法。
- ヌクレアーゼが転写活性化因子様エレメントヌクレアーゼ(TALEN)である、請求項1~9および13~15のいずれか一項に記載の方法。
- ヌクレアーゼが有機化合物を含み、任意に有機化合物が抗生物質である、請求項1~9のいずれか一項に記載の方法。
- 有機化合物が、ダイネミシン、ネオカルジノスタチン、カリケアミシン、エスペラミシン、ブレオマイシン、エンジイン、またはそれらの誘導体である、請求項21に記載の方法。
- ヌクレアーゼがホーミングエンドヌクレアーゼである、請求項1~9のいずれか一項に記載の方法。
- 複数個のヌクレアーゼからコンセンサスターゲット部位を特異的に切断するヌクレアーゼを選択する方法であって、
(a)同じコンセンサス配列を切断する複数個の候補ヌクレアーゼを提供すること;
(b)ステップ(a)の候補ヌクレアーゼのそれぞれについて、請求項1~23のいずれか一項に記載の方法を用いて、コンセンサスターゲット部位とは異なる候補ヌクレアーゼによって切断されたヌクレアーゼターゲット部位を同定すること;および
(c)ステップ(b)において同定されたヌクレアーゼターゲット部位に基づいてヌクレアーゼを選択すること、
を含む、前記方法。 - ステップ(c)において選択されたヌクレアーゼが、最高の特異性でコンセンサスターゲット部位を切断するヌクレアーゼである、請求項24に記載の方法。
- (i)最高の特異性でコンセンサスターゲット部位を切断するヌクレアーゼが、コンセンサス部位とは異なる最低数のターゲット部位を切断する候補ヌクレアーゼである、または
(ii)最高の特異性でコンセンサスターゲット部位を切断する候補ヌクレアーゼが、ターゲットゲノムの文脈中で、コンセンサス部位とは異なる最低数のターゲット部位を切断する候補ヌクレアーゼである、
請求項25に記載の方法。 - 候補ヌクレアーゼが、コンセンサスターゲット部位以外のいずれのターゲット部位も切断しない、請求項24~26のいずれか一項に記載の方法。
- ステップ(c)において選択された候補ヌクレアーゼが、ヌクレアーゼの治療有効濃度で対象のゲノム中のコンセンサスターゲット部位以外のいずれのターゲット部位も切断しないヌクレアーゼである、請求項24~27のいずれか一項に記載の方法。
- ステップ(c)において選択されたヌクレアーゼとゲノムを接触させることをさらに含み、任意にゲノムが、脊椎動物、哺乳類、ヒト、非ヒト霊長類、げっ歯類、マウス、ラット、ハムスター、ヤギ、ヒツジ、ウシ、イヌ、ネコ、爬虫類、両生類、魚類、線虫、昆虫、またはハエのゲノムである、請求項24~28のいずれか一項に記載の方法。
- ゲノムが生細胞内にあり、任意にゲノムが対象内にある、請求項24~29のいずれか一項に記載の方法。
- コンセンサスターゲット部位が、疾患または障害と関連したアレル内にある、請求項24~30のいずれか一項に記載の方法。
- コンセンサスターゲット部位の切断が、疾患または障害の処置または予防をもたらす、請求項31に記載の方法。
- コンセンサスターゲット部位の切断が、疾患または障害の症状の緩和をもたらす、請求項31に記載の方法。
- 疾患がHIV/AIDSであり、およびアレルが任意にCCR5アレルである;または疾患が増殖性疾患であり、およびアレルが任意にVEGFAアレルである、請求項31~33のいずれか一項に記載の方法。
- ステップ(c)の前に、アダプターにハイブリダイゼーションするPCRプライマーおよび定常挿入配列にハイブリダイゼーションするPCRプライマーを用いるPCR反応によって、切断された核酸鎖の断片を増幅することをさらに含む、請求項1に記載の方法。
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