JP7170328B2 - スイッチ可能cas9ヌクレアーゼおよびその使用 - Google Patents
スイッチ可能cas9ヌクレアーゼおよびその使用 Download PDFInfo
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- JP7170328B2 JP7170328B2 JP2019221158A JP2019221158A JP7170328B2 JP 7170328 B2 JP7170328 B2 JP 7170328B2 JP 2019221158 A JP2019221158 A JP 2019221158A JP 2019221158 A JP2019221158 A JP 2019221158A JP 7170328 B2 JP7170328 B2 JP 7170328B2
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Description
本出願は、2014年7月8日に出願された米国特許出願第14/326,329号、2014年7月8日に出願された米国特許出願第14/326,340号、2014年7月8日に出願された米国特許出願第14/326,361号に対して、米国特許法第365条(c)に基づく優先権の利益を主張し、また、2013年9月6日に出願された米国特許仮出願第61/874,682号に対して、米国特許法第119条(e)に基づく優先権の利益を主張し、その全開示を参照により本明細書に組み込むものである。
本明細書および請求の範囲で使用される、単数型の「a」、「an」、および「the」は、文脈から明らかに判別されない限り、単数型および複数型を含むものである。従って、例えば、「薬剤」という場合には、単一の薬剤および複数の薬剤を含む。
部位特異的ヌクレアーゼは、in vitroおよびin vivoでの標的ゲノム修飾のための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、理論的には、他のゲノムの部位に影響を与えずに、ゲノム中の単一の特有な部位を切断の標的とすることを可能とするレベルの標的切断部位特異性を達成することが可能である。生細胞中でのヌクレアーゼ切断が、例えば相同組換えまたは非相同末端結合により切断・修復されたゲノム配列の修飾を頻繁にもたらすDNA修復機構を誘発することが報告されている。従って、ゲノム内のある特定の配列の標的切断は、多くのヒト体細胞または胚性幹細胞など、従来の標的遺伝子組換え法での操作が困難である細胞などの生細胞中での標的遺伝子組換えおよび遺伝子修飾のための新しい道を開くものである。例えばHIV/AIDS患者におけるCCR-5アレルなどの疾患関連配列または腫瘍血管新生に必要な遺伝子のヌクレアーゼ仲介修飾は臨床の環境においても使用可能であり、2つの部位特異的ヌクレアーゼが現在臨床試験中である(Perez, E.E. et al., "Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases." Nature Biotechnology. 26, 808-816 (2008); ClinicalTrials.gov identifiers: NCT00842634, NCT01044654, NCT01252641, NCT01082926)。部位特異的ヌクレアーゼを使用して処置可能な他の疾患としては、例えば、トリプレット病と関連する疾患(例、ハンチントン病、筋緊張性ジストロフィー、脊髄小脳失調症など)、嚢胞性線維症(CFTR遺伝子を標的とすることによる)、がん、自己免疫疾患、およびウイルス感染症が挙げられる。
本開示のいくつかの側面は、「オン」および「オフ」状態の両方を有するように操作されているgRNAを提供する。そして、いくつかの側面では、これらのgRNAは、「スイッチ可能gRNA」と総称できる。例えば、スイッチ可能gRNAは、gRNAの標的核酸への結合を阻止する構造状態にあるとき「オフ」状態であると言われる。いくつかの側面では、「オフ」状態のgRNAは、それと同種のRNA誘導型ヌクレアーゼ(例、Cas9)に結合可能であるが、ヌクレアーゼ:gRNA複合体(gRNAが「オフ」状態にあるとき)は、標的核酸を結合して切断を仲介することはできない。他の側面では、「オフ」状態のgRNAは、標的配列またはCas9などのRNA誘導型ヌクレアーゼに結合できない。逆に、スイッチ可能gRNAは、gRNAが、(例、Cas9などのRNA誘導型ヌクレアーゼとの複合体として)gRNAの標的核酸への結合を可能とする構造状態であるとき「オン」状態であると言われる。本開示のいくつかの実施態様では、Cas9などのRNA誘導型ヌクレアーゼと関連する本発明のgRNAを含む複合体、およびそれらの使用方法が提供される。本開示のいくつかの実施態様は、そのようなgRNAおよび/またはRNA誘導型ヌクレアーゼ(例、Cas9)をコードする核酸を提供する。本開示のいくつかの実施態様は、そのようなコードする核酸を含む発現構築物を提供する。
1つの実施態様では、アプタマーを含むgRNAが提供される。例えば、図1を参照。例えば、いくつかの実施態様では、gRNAは、本明細書で記載されるように、ヌクレオチドリンカーを介してアプタマーに連結している。アプタマーは、通常、例えば抗体抗原相互作用に競合する親和性で特異的リガンドを結合するRNAまたはペプチドに基づいた分子である。いくつかの実施態様では、アプタマーは、約1nM~10μM、約1nM~1μM、約1nM~500nM、または約1nM~100nMのKdでリガンドを結合する。RNAに基づいたアプタマー、例えば、mRNAのリボスイッチ中にあるものに関しては、リガンドのアプタマードメインへの結合により、mRNAの発現(例、翻訳)を調節する立体構造的変化をもたらす。RNAアプタマーは、例えば遺伝子発現を調節するために他の分子にクローン化・適応されていたり、またはSELEXを使用して特定のリガンドに対して操作・選択されている(例えば、Dixon et al., "Reengineering orthogonally selective riboswitches." PNAS 2010; 107 (7): 2830-2835; Suess et al., "A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo." Nucleic Acids Res. 2004; 32(4): 1610-1614; Ellington and Szostak, "In vitro selection of RNA molecules that bind specific ligands." Nature. 1990; 346:818-822; Tuerk and Gold, "Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase." Science. 1990; 249:505-510; Burke and Gold, "RNA aptamers to the adenosine moiety of S-adenosyl methionine: structural inferences from variations on a theme and the reproducibility of SELEX." Nucleic Acids Res. 1997; 25(10):2020-4; Ulrich et al., "DNA and RNA aptamers: from tools for basic research towards therapeutic applications." Comb Chem High Throughput Screen. 2006; 9(8):619-32; Svobodova et al., "Comparison of different methods for generation of single-stranded DNA for SELEX processes. Anal Bioanal Chem. 2012; 404:835-842を参照、それらの全内容を参照により本明細書に取り込むものである)。アプタマーを結合するリガンドとしては、限定されるものではないが、小分子、代謝産物、炭水化物、タンパク質、ペプチド、または核酸が挙げられる。図1に示されるように、アプタマーに連結したgRNAは、アプタマーを結合する特異的リガンドの非存在下で「オフ」状態で存在する。通常、「オフ」状態は、標的核酸とハイブリダイズするgRNAの配列の全部または一部が標的核酸に自由にハイブリダイズするのを阻止する構造的特徴により仲介される。例えば、いくつかの側面では、アプタマーを含むgRNAは、アプタマー配列の一部が、標的とハイブリダイズするgRNAの配列の一部または全部とハイブリダイズするように設計されている。標的を結合するgRNAの配列(例、図1Cおよび図1Dに「標的切断ガイド」として示す、本明細書では「ガイド」配列と呼ぶ)は、任意の所望の核酸標的を標的とする配列を含むように、当分野で公知の方法を使用して操作可能であり、従って、図に示す配列は例示の目的であって限定するものではない。同様に、任意の好適なアプタマーは、gRNA配列に5’または3’側で連結することが可能であり、当分野の常法を使用してgRNA中の特定のガイド配列にハイブリダイズするであろうヌクレオチドを含むように修飾することが可能である。いくつかの実施態様では、本明細書で提供される任意のgRNAに連結するアプタマーは、本明細書で記載されるようなRNAアプタマーである。いくつかの実施態様では、RNAアプタマーは、リボスイッチに由来する(例えばそれからクローンされる)。任意のリボスイッチをRNAアプタマーに使用することができる。リボスイッチの例としては、限定されるものではないが、テオフィリンリボスイッチ、チアミンピロリン酸エステル(TPP)リボスイッチ、アデノシンコバラミン(AdoCbl)リボスイッチ、S-アデノシルメチオニン(SAM)リボスイッチ、SAHリボスイッチ、フラビンモノヌクレオチド(FMN)リボスイッチ、テトラヒドロ葉酸リボスイッチ、リジンリボスイッチ、グリシンリボスイッチ、プリンリボスイッチ、GlmSリボスイッチ、およびプレケオシン1(PreQ1)リボスイッチが挙げられる。いくつかの実施態様では、RNAアプタマーは、テオフィリンリボスイッチに由来する。いくつかの実施態様では、テオフィリンリボスイッチに由来するアプタマーは、配列番号3を含む。いくつかの実施態様では、配列番号3の太字の下線部分を、そこにある任意のヌクレオチドを他の任意のヌクレオチドで置換するように修飾可能であり、および/または1つ以上のヌクレオチドを付加または欠失することにより修飾可能である。例えば、太字の下線部分は、標的核酸とハイブリダイズするgRNAの配列の一部または全部とハイブリダイズする配列を含むように修飾可能である。例えば、図1Cを参照。いくつかの実施態様では、RNAアプタマーは、配列番号3と、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98%、または少なくとも99%同一である。
5’-GGUGAUACCAGCAUCGUCUUGAUGCCCUUGGCAGCACC-3’(配列番号3)
他の実施態様によれば、ある条件下で(例、代謝産物、小分子、核酸などの存在下で)標的核酸を結合するgRNAが提供される。いくつかの実施態様では、gRNAは、他の分子がgRNAに結合(例、ハイブリダイズ)して、「オン」状態に対応する構造再構成をもたらさない限り、構造的に、標的と結合する(例、ハイブリダイズする)ことから阻止されている(例えば、「オフ」状態にある)。いくつかの実施態様では、特定の転写物(例、mRNA)のgRNAへの結合は、gRNAを「オフ」状態から「オン」状態へ移行させる。例えば、図2を参照。そのようなgRNAは、「mRNAをセンスする」gRNAと呼ばれる。例えば、いくつかの側面では、(i)標的核酸の領域とハイブリダイズする領域(例、「ガイド」配列)と;(ii)領域(i)の配列と部分的にまたは完全にハイブリダイズする他の領域(例、「ガイドブロック」配列)と;(iii)転写物(mRNA)の領域とハイブリダイズする領域(例、「転写物センサー」)とを含むgRNAが提供される。いくつかの実施態様では、各領域(例、i~iii)は、少なくとも5、少なくとも10、少なくとも15、少なくとも20、または少なくとも25個のヌクレオチドを含む。いくつかの実施態様では、gRNAは、ステム・ループ構造を形成する。いくつかの実施態様では、ステムが、領域(ii)の配列の一部または全部とハイブリダイズした領域(i)の配列を含み、ループが領域(iii)の配列の一部または全部からなる。いくつかの実施態様では、領域(ii)および領域(iii)の両方が、領域(i)に対して5’または3’側のいずれかにある。例えば、図2A対図2Cを参照。標的を結合するgRNAの配列(例、「ガイド」配列)は、当分野で公知の方法を使用して、任意の所望の核酸標的を標的とする任意の配列を含むよう操作することが可能であり、従って、例として図に示す配列に限定されるものではない。同様に、領域(iii)(例、転写物センサー)は、当分野の常法を使用して、目的のmRNAとハイブリダイズする任意の配列を含むよう操作することが可能である。同様に、領域(ii)は、当分野の常法を使用して、「ガイド」配列の一部または全部とハイブリダイズする配列を含むよう操作可能である。例えば、いくつかの側面では、mRNAは、細胞中で発現されるとき、標的核酸(例、遺伝子)のゲノム修飾が望まれるものである。このように、mRNAの非存在下で、細胞へ送達される(または、発現される)と、gRNAは「オフ」状態のままである。mRNAが存在する(例、発現される)と、それはgRNAの転写物センサーを結合して、「ガイド」配列の標的核酸へのハイブリダイゼーションを阻止していたステム・ループ構造のアンフォールディングをもたらし、それによってgRNAを「オン」とする。例えば、図2Bおよび2Dを参照。提供された「オン」状態のgRNAは、RNA誘導型ヌクレアーゼ(例、Cas9タンパク質)と会合して、標的核酸の結合をガイドすることができる。
他の実施態様によれば、gRNAが少なくとも2つの異なる領域で標的核酸とハイブリダイズしない限り「オフ」状態のままでいる修飾したgRNAが提供される。例えば、図3を参照。そのようなgRNAは、特定のgRNA/標的相互作用の認識配列を効果的に延長するので、RNA誘導型ヌクレアーゼ(例、Cas9)への特異性が改善されている。そのようなgRNAは、「xDNAをセンスする」gRNA(「x」は、「伸長」DNA認識の略語である)と呼ばれる。例えば、(i)標的核酸の領域とハイブリダイズする領域(例、「ガイド」配列)と;(ii)領域(i)の配列と部分的にまたは完全にハイブリダイズする他の領域(例、「ガイドブロック」)と;(iii)標的核酸の他の領域とハイブリダイズする領域(例、「xDNAセンサー」)とを含むgRNAが提供される。いくつかの実施態様では、xDNAセンサーは、ガイド配列が標的に結合できる前に、まず標的核酸を結合しなくてはならない。いくつかの実施態様では、xDNAセンサーは、ガイド配列を結合する標的の同一の鎖を結合する。いくつかの実施態様では、xDNAセンサーおよびガイド配列は、標的核酸の異なる鎖を結合する。いくつかの実施態様では、領域(i)および領域(ii)の配列が、少なくとも5、少なくとも10、少なくとも15、少なくとも20、または少なくとも25個のヌクレオチドを含む。いくつかの実施態様では、領域(iii)の配列は、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40、少なくとも50、少なくとも75、または少なくとも100個のヌクレオチドを含む。いくつかの実施態様では、gRNAは、ステム・ループ構造を形成する。例えば、いくつかの実施態様では、ステムが領域(ii)の配列の一部または全部とハイブリダイズした領域(i)の配列を含み、ループが領域(iii)の配列の一部または全部からなる。いくつかの実施態様では、領域(i)および領域(iii)は、gRNA中で隣接する配列を含む。いくつかの実施態様では、領域(ii)および領域(iii)の両方が、領域(i)に対して5’または3’側のいずれかにある。例えば、図3A対図3Cを参照。いくつかの実施態様では、領域(ii)は、領域(i)と領域(iii)の間に配置されている。標的を結合するgRNAの配列(例、「ガイド」配列)は、当分野で公知の方法を使用して任意の所望の核酸標的を標的とする任意の配列を含むように操作可能であり、従って図に例として示す配列に限定するものではない。同様に、領域(iii)(例、xDNAセンサー)は、当分野の常法を使用して、標的核酸の他の領域(例、「ガイド」配列により標的とされる領域と異なる領域)とハイブリダイズする任意の配列を含むように操作可能である。同様に、領域(ii)は、当分野の常法を使用して、「ガイド」配列の一部または全部とハイブリダイズする配列を含むように操作してもよい。従って、適正な標的核酸(例、gRNAがハイブリダイズするよう設計された両方の領域を含む標的)の非存在下では、gRNAは、細胞へ送達される(またはそこで発現される)と、「オフ」状態のままである。特定の理論に束縛されるものではないが、gRNAが(例、Cas9と会合して)標的核酸と接触すると、xDNAセンサーが標的とハイブリダイズし、それは次に「ガイド」配列をブロックするステム・ループ構造をほどき、gRNAを「オン」にすると考えられる。それが適正な標的核酸であれば、ガイド配列は標的にハイブリダイズし、複合体は任意に標的核酸を切断するであろう。例えば、図3Bおよび図3Dを参照。
いくつかの実施態様では、本明細書で記載される任意のRNA/gRNA(例、アプタマーに連結したgRNA、mRNAをセンスするgRNA、またはxDNAセンサーを含むgRNAを含むRNA)を含む複合体が提供される。いくつかの側面では、RNA誘導型ヌクレアーゼと会合する、提供されたRNA/gRNAを含む複合体が提供される。いくつかの実施態様では、RNA誘導型ヌクレアーゼは、例えば本明細書で記載されるCas9、Cas9の変異体、またはCas9の断片である。いくつかの実施態様では、RNA誘導型ヌクレアーゼは、全内容を参照により本明細書に取り込む、2013年9月6日に出願された米国特許仮出願第61/874,609号名称「Cas9変異体およびその使用」、および2014年9月6日に出願された米国特許仮出願第61/874,746号名称「機能性ヌクレアーゼの送達システム」に提供されるCas9タンパク質の任意の形態である。
いくつかの実施態様では、本明細書に記載される任意のgRNAが、医薬組成物の一部として提供される。いくつかの実施態様では、医薬組成物は、本発明のgRNAと複合体を形成するRNA誘導型ヌクレアーゼ(例、Cas9)を更に含む。例えば、いくつかの実施態様は、本明細書で提供されるgRNAおよびRNA誘導型ヌクレアーゼ、またはそのようなgRNAおよび/またはヌクレアーゼをコードする核酸と、医薬的に許容される賦形剤とを含む医薬組成物を提供する。医薬組成物は、更に治療的に活性のある物質を1つ以上任意に含むことができる。
本開示の他の実施態様では、部位特異的核酸(例、DNA)切断方法が提供される。いくつかの実施態様では、この方法は、DNAを本明細書に記載の任意のCas9:RNA複合体に接触させることを含む。例えば、いくつかの実施態様では、この方法は、(i)DNAの部分に結合する配列を含み、本明細書で記載されるアプタマーに連結したgRNAと;(ii)gRNAのアプタマーに結合したリガンドと;(iii)RNA誘導型ヌクレアーゼ(例、Cas9タンパク質)とを含む複合体に、Cas9ヌクレアーゼがDNAを切断するのに好適な条件下でDNAを接触させることを含む。
本開示の他の実施態様では、本明細書に記載のいずれかのgRNA(および任意にいずれかのCas9タンパク質)をコードするポリヌクレオチドが提供される。例えば、本明細書に記載のいずれかのgRNAおよび/またはCas9タンパク質をコードするポリヌクレオチドは、本発明のgRNA、またはそれを含む複合体、例えば本発明のgRNAおよびRNA誘導型ヌクレアーゼ(例、Cas9タンパク質)を含む複合体などの組換え発現および精製のために提供される。いくつかの実施態様では、提供されるポリヌクレオチドは、gRNAをコードする1つ以上の配列を、単独で、または本明細書に記載のいずれかのCas9タンパク質をコードする配列との組み合わせで含む。
当業者は、本明細書に記載の本発明の具体的な実施態様の多くの等価物を認識可能であるか、または単に通常の実験により確認可能であろう。本発明の範囲は、上記の記述に限定されることを意図するものではなく、添付の請求の範囲に記載されるものである。
Claims (18)
- (i)少なくとも10個のヌクレオチドの配列を含む領域であって、標的核酸配列の領域にハイブリダイズする前記領域;(ii)少なくとも10個のヌクレオチドの配列を含む他の領域であって、領域(ii)の配列が領域(i)の配列とハイブリダイズされるとステムが形成される場合にステム・ループ構造が形成されるように、領域(i)の配列とハイブリダイズする、前記領域;および(iii)少なくとも10個のヌクレオチドの配列を含む領域であって、転写物(mRNA)の領域にハイブリダイズする前記領域、
を含む、シングルガイドRNA(sgRNA)であって、
領域(i)の配列が領域(ii)の配列とハイブリダイズするとステム・ループ構造のループが領域(iii)の配列の一部または全部から形成され;
領域(iii)の配列とハイブリダイズする転写物の非存在下でステム・ループ構造が形成され;
転写物が領域(iii)の配列とハイブリダイズすることにより、領域(ii)の配列が領域(i)の配列とハイブリダイズしないように、ステム・ループ構造がアンフォールドされるか、またはステム・ループ構造の形成が阻止され;および
sgRNAは、Cas9タンパク質を結合するドメインをさらに含む、
前記sgRNA。 - 領域(i)、領域(ii)、および領域(iii)の各配列が、少なくとも15個、少なくとも20個、または少なくとも25個のヌクレオチドを含む、請求項1に記載のsgRNA。
- 領域(ii)および領域(iii)の両方が、領域(i)に対して5’または3’側のいずれかにある、請求項1または2に記載のsgRNA。
- 領域(iii)の配列が転写物とハイブリダイズすると領域(i)の配列が標的核酸とハイブリダイズする、請求項1~3のいずれか一項に記載のsgRNA。
- Cas9タンパク質と請求項1~4のいずれか一項に記載のsgRNAとを含む、複合体。
- DNAを請求項5に記載の複合体と接触させることを含む、in vitroでの部位特異的DNA切断方法。
- DNAが細胞中にある、請求項6に記載の方法。
- 細胞が真核細胞である、請求項7に記載の方法。
- 真核細胞が個体に由来する、請求項8に記載の方法。
- 個体がヒトである、請求項9に記載の方法。
- 請求項1~4のいずれか一項に記載のsgRNAをコードするポリヌクレオチド。
- 請求項11に記載のポリヌクレオチドを含むベクター。
- 請求項1~4のいずれか一項に記載のsgRNAをコードするポリヌクレオチドを含む、組換え発現用ベクター。
- Cas9タンパク質をコードするポリヌクレオチドをさらに含む、請求項12または13に記載のベクター。
- 請求項1~4のいずれか一項に記載のsgRNAおよび任意にCas9タンパク質を発現するポリヌクレオチドを含む、細胞。
- 細胞が真核細胞である、請求項15に記載の細胞。
- 請求項1~4のいずれか一項に記載のsgRNA、請求項11に記載の単離されたポリヌクレオチド、請求項12~14のいずれか一項に記載のベクター、および/または請求項15または16に記載の細胞を含む、キット。
- 1つ以上のCas9タンパク質または1つ以上のCas9タンパク質を発現するベクターをさらに含む、請求項17に記載のキット。
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