JP2017532955A - 造血幹細胞におけるヌクレアーゼ媒介性ゲノム工学および補正のための方法および組成物 - Google Patents
造血幹細胞におけるヌクレアーゼ媒介性ゲノム工学および補正のための方法および組成物 Download PDFInfo
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Abstract
Description
この出願は、2014年9月16日に出願された米国仮出願第62/051,159号(この開示は、その全体が参考として本明細書に援用される)の利益を主張する。
鎌状赤血球患者の処置および管理は、急性エピソードにおける抗生物質処置、疼痛管理および輸血に関与する一生の命題である。アプローチの1つは、一部にはγグロビンの産生を増加させることによりその効果を発揮する、ヒドロキシ尿素の使用である。慢性ヒドロキシ尿素療法の長期副作用は未だ不明であるが、処置は、望まれない副作用を生じ、患者毎に可変的な有効性を有する場合がある。鎌状赤血球処置の有効性の増加にもかかわらず、患者の平均余命は依然として、50代半ばから後半でしかなく、疾患の関連する罹患率は、患者のクオリティオブライフに著明な影響を有する。
本明細書に開示される方法、ならびに組成物の調製および使用の実施は、特に示さない限り、本技術分野の技術範囲内の、分子生物学、生化学、クロマチン構造および分析、計算機化学、細胞培養、組換えDNAならびに関連分野における従来の技術を用いる。これらの技術は、文献中に完全に説明されている。例えば、SambrookらMOLECULAR CLONING: A LABORATORY MANUAL、第2版、Cold Spring Harbor Laboratory Press、1989年および第3版、2001年;Ausubelら、CURRENT PROTOCOLS IN MOLECULAR BIOLOGY、John Wiley & Sons、New York、1987年および定期的更新;シリーズMETHODS IN ENZYMOLOGY、Academic Press、San Diego;Wolffe、CHROMATIN STRUCTURE AND FUNCTION、第3版、Academic Press、San Diego、1998年;METHODS IN ENZYMOLOGY、304巻、「Chromatin」(P.M. WassarmanおよびA. P. Wolffe編)、Academic Press、San Diego、1999年;ならびにMETHODS IN MOLECULAR BIOLOGY、119巻、「Chromatin Protocols」(P.B. Becker編)Humana Press、Totowa、1999年を参照されたい。
用語「核酸」、「ポリヌクレオチド」および「オリゴヌクレオチド」は、相互交換可能に使用され、直鎖状または環状コンフォメーションの、一本鎖形態または二本鎖形態のいずれかの、デオキシリボヌクレオチドまたはリボヌクレオチドのポリマーを指す。本開示の目的のため、これらの用語は、ポリマーの長さに関して限定的であると解釈すべきではない。これらの用語は、天然ヌクレオチドの公知のアナログ、ならびに塩基、糖および/またはリン酸部分(例えば、ホスホロチオエート骨格)において修飾されたヌクレオチドを包含し得る。一般に、特定のヌクレオチドのアナログは、同じ塩基対合特異性を有する;即ち、Aのアナログは、Tと塩基対合する。
幹細胞増大および/または分化を増強するいずれかの因子(単数または複数)を、本発明の実施において使用することができる。因子は、細胞へと直接的に導入することができる(例えば、因子をコードする遺伝子として)、および/または周囲の培養培地(フィーダー層および他の固体培養基を含む)へと導入して、細胞に影響を与えることができる。例えば、ヌクレアーゼ媒介性改変が誘導される前、その間またはその後の、培養条件におけるこのような因子の使用は、幹細胞のヌクレアーゼ媒介性改変の率を増加させる。
細胞、特に、幹細胞における選択された標的遺伝子の開裂に有用な組成物、例えば、ヌクレアーゼが、本明細書に記載されている。ある特定の実施形態では、融合分子の1種または複数の構成成分(例えば、ヌクレアーゼ)は、天然起源である。他の実施形態では、融合分子の構成成分のうち1種または複数(例えば、ヌクレアーゼ)は、非天然起源である、すなわち、DNA結合ドメインおよび/または開裂ドメインにおいて操作されている。例えば、天然起源のヌクレアーゼのDNA結合ドメインは、選択された標的部位に結合するように変更され得る(例えば、同族結合部位とは異なる部位に結合するように操作されたメガヌクレアーゼ)。他の実施形態では、ヌクレアーゼは、異種のDNA結合ドメインおよび開裂ドメイン(例えば、異種開裂ドメインを有する、ジンクフィンガーヌクレアーゼ;TALエフェクタードメインDNA結合タンパク質;メガヌクレアーゼDNA結合ドメイン)を含む。
ある特定の実施形態では、本明細書に記載されている組成物および方法は、ドナー分子に結合するために、および/または細胞のゲノム中の目的の領域に結合するために、メガヌクレアーゼ(ホーミングエンドヌクレアーゼ)DNA結合分子(DNA結合ドメインとも称される)を用いる。天然起源のメガヌクレアーゼは、15〜40塩基対の開裂部位を認識し、一般的に、4種のファミリーへとグループ化される:LAGLIDADGファミリー、GIY−YIGファミリー、His−CystボックスファミリーおよびHNHファミリー。例示的なホーミングエンドヌクレアーゼには、I−SceI、I−CeuI、PI−PspI、PI−Sce、I−SceIV、I−CsmI、I−PanI、I−SceII、I−PpoI、I−SceIII、I−CreI、I−TevI、I−TevIIおよびI−TevIIIが含まれる。それらの認識配列は公知である。米国特許第5,420,032号;米国特許第6,833,252号;Belfortら(1997年)Nucleic Acids Res. 25巻:3379〜3388頁;Dujonら(1989年)Gene 82巻:115〜118頁;Perlerら(1994年)Nucleic Acids Res. 22巻、1125〜1127頁;Jasin(1996年)Trends Genet. 12巻:224〜228頁;Gimbleら(1996年)J. Mol. Biol. 263巻:163〜180頁;Argastら(1998年)J. Mol. Biol. 280巻:345〜353頁およびNew England Biolabsカタログもまた参照されたい。加えて、ホーミングエンドヌクレアーゼおよびメガヌクレアーゼのDNA結合特異性は、非天然標的部位に結合するように操作することができる。例えば、Chevalierら(2002年)Molec. Cell 10巻:895〜905頁;Epinatら(2003年)Nucleic Acids Res.31巻:2952〜2962頁;Ashworthら(2006年)Nature 441巻:656〜659頁;Paquesら(2007年)Current Gene Therapy 7巻:49〜66頁;米国特許出願公開第20070117128号を参照されたい。ホーミングエンドヌクレアーゼおよびメガヌクレアーゼのDNA結合ドメインは、全体としてヌクレアーゼに関して変更され得(即ち、ヌクレアーゼが同族開裂ドメインを含むように)、または異種開裂ドメインに融合され得る。
いずれか適した開裂ドメインをDNA結合ドメインに操作可能に連結して、ヌクレアーゼを形成することができる。例えば、ZFP DNA結合ドメインがヌクレアーゼドメインに融合されて、ZFN(種々の生物におけるゲノム改変における使用のためを含む、その操作された(ZFP)DNA結合ドメインによりその意図される核酸標的を認識し、ヌクレアーゼ活性によりZFP結合部位付近でDNAをカットすることができる機能的な実体)を作製した。例えば、米国特許出願公開第20030232410号;同第20050208489号;同第20050026157号;同第20050064474号;同第20060188987号;同第20060063231号;および国際公開WO07/014275を参照されたい。同様に、TALE DNA結合ドメインがヌクレアーゼドメインに融合されて、TALENを作製した。例えば、米国特許第8.586,526号を参照されたい。標的化開裂を誘導するための、DNAに結合し、開裂ドメイン(例えば、Casドメイン)に会合する単一ガイドRNA(sgRNA)を含む、CRISPR/Casヌクレアーゼ系についても記載されている。例えば、米国特許第8,697,359号および同第8,932,814号および米国特許出願公開第20150056705号を参照されたい。
上で詳細に記載されるように、DNA結合ドメインは、任意の選択した配列に結合するように操作され得る。操作されたDNA結合ドメインは、天然に存在するDNA結合ドメインと比較して新規の結合特異性を有し得る。
ある特定の実施形態では、本開示は、幹細胞のゲノムのヌクレアーゼ媒介性改変に関する。上に記す通り、外因性配列(「ドナー配列」または「ドナー」または「導入遺伝子」とも呼ばれる)の挿入は、例えば、指定の領域の欠失のため、および/または変異体遺伝子の補正のため、または野生型遺伝子の発現増加のためになされる。ドナー配列が、典型的には、これが配置されるゲノム配列と同一ではないことが容易に明らかとなるであろう。ドナー配列は、目的の位置における効率的HDRを可能にするため、2個の相同性領域に挟まれた非相同配列を含有することができる、または非相同性誘導型修復機構により組み込むことができる。その上、ドナー配列は、細胞クロマチンにおける目的の領域と相同ではない配列を含有するベクター分子を含むことができる。ドナー分子は、細胞クロマチンと相同性のいくつかの不連続領域を含有することができる。さらに、目的の領域に通常存在しない配列の標的化挿入のため、前記配列は、ドナー核酸分子に存在して、目的の領域における配列と相同性の領域に挟まれることができる。
よって、本明細書に記載されている方法によって産生される細胞を含む、不活性化された遺伝子および/または導入遺伝子を含む遺伝子改変された細胞、例えば、幹細胞が本明細書に提供される。導入遺伝子は、1種または複数のヌクレアーゼを使用して、細胞のゲノムへと標的化様式で組み込まれる。ランダムな組込みとは異なり、標的化組込みは、導入遺伝子が、指定の遺伝子へと組み込まれることを確実にする。導入遺伝子は、標的遺伝子におけるいずれの箇所にも組み込むことができる。ある特定の実施形態では、導入遺伝子は、ヌクレアーゼ結合および/または開裂部位にまたはその付近に、例えば、開裂部位および/または結合部位の上流または下流の1〜300(またはその間のいずれかの数の塩基対)塩基対以内に、より好ましくは、開裂および/または結合部位のいずれか一方の側の1〜100塩基対(またはその間のいずれかの数の塩基対)以内に、さらにより好ましくは、開裂および/または結合部位のいずれか一方の側の1〜50塩基対(またはその間のいずれかの数の塩基対)以内に組み込まれる。ある特定の実施形態では、組み込まれた配列は、いかなるベクター配列(例えば、ウイルスベクター配列)も含まない。ある特定の実施形態では、細胞は、改変が、ベータ−グロビン遺伝子のエクソン内、例えば、エクソン1、2または3内に存在するような、本明細書に記載されているヌクレアーゼによって作製される改変(例えば、挿入および/または欠失)を含む。ある特定の実施形態では、改変は、ベータグロビン遺伝子のエクソン1における鎌状赤血球変異を補正する。ある特定の実施形態では、改変は、配列番号23または24にまたはその付近(例えば、1〜300塩基対またはその間のいずれかの数の塩基対)に存在する。他の実施形態では、改変は、配列番号23または24の1〜100塩基対(またはその間のいずれかの数の塩基対)である。ある特定の実施形態では、改変は、配列番号23および/または配列番号24内に存在する、例えば、配列番号23または24のいずれかにおける1または複数塩基対の改変である。
ヌクレアーゼ、これらのヌクレアーゼをコードするポリヌクレオチド、ドナーポリヌクレオチド、ならびに本明細書に記載されているタンパク質および/またはポリヌクレオチドを含む組成物を、任意の適当な手段によって送達してもよい。ある特定の実施形態では、ヌクレアーゼおよび/またはドナーは、in vivoで送達される。他の実施形態では、ヌクレアーゼおよび/またはドナーは、患者へのex vivo送達において有用な改変された細胞の提供のために、単離された細胞(例えば、自家または異種幹細胞)へと送達される。
上述の方法のいずれかを行うためのキットも提供される。キットは、典型的に、1種もしくは複数のヌクレアーゼをコードするポリヌクレオチド、幹細胞増大に影響を与える1種もしくは複数の因子、および/または本明細書に記載されているドナーポリヌクレオチド、ならびに幹細胞に影響を与える因子を、ヌクレアーゼおよび/またはドナーポリヌクレオチドが導入される細胞(または周囲の培地)へと投与するための指示を含有する。キットは、細胞、細胞の形質転換のためのバッファー、細胞のための培養培地および/またはアッセイを行うためのバッファーを含有することもできる。典型的には、キットは、キットの他の構成成分に添付または他の仕方で添えられた指示、包装または広告チラシ等、いずれかの材料を含むラベルも含有する。
基本的にUrnovら(2005年)Nature 435巻(7042号):646〜651頁、Perezら(2008年)Nature Biotechnology 26巻(7号):808〜816頁に記載され、米国特許第6,534,261号に記載されている通りにジンクフィンガータンパク質を設計し、プラスミド、AAVまたはアデノウイルスベクターに取り込み、結合に関して検査した。ヒトベータグロビン遺伝子座に特異的なZFNおよびTALENに関しては、共有の米国特許第7,888,121号ならびに米国特許出願公開第20130137104号および同第20130122591号を参照されたい。
ヒトグロビン遺伝子座を標的化するZFN対を使用して、特異的標的部位においてDSBを誘導するこのようなZFNの能力を検査した。示されているZFNの各フィンガーの認識ヘリックス領域のアミノ酸配列を下表1に示す。標的部位(DNA標的部位を大文字で示し;非接触ヌクレオチドを小文字で示す)を表2に示す。
標的化されたベータ−グロビン遺伝子座における開裂が成功した後に、本発明者らは、相同ドナー鋳型を使用して、この部位における鎌状塩基の補正が可能であるか決定することを試みた。この目的のため、2種類の遺伝子補正鋳型を並行して設計し、検査した:短いDNAオリゴおよびIDLV。IDLVへとクローニングされた1.1kbのヒトベータ−グロビン遺伝子断片ドナー鋳型は、鎌状変異に補正的変化を含むと共に、相同組換えの代替解析のためのHhaI制限部位を作製するためのサイレント制限断片長多型(RFLP)を含むように設計した(図1C)。IDLVによりドナー鋳型を送達し(図2Dを参照)、最小の細胞傷害性でのCD34+HSPCの効率的形質導入を可能にし、最小のゲノム組込みでの高い鋳型コピー数を一過的に産生する。
ベータ−グロビンは、他のグロビン遺伝子(デルタ−、イプシロン−、Aガンマ−、Gガンマ−およびシュード−ベータ−グロビン)に対し高い相同性を有するため、これらの領域における開裂を回避するようにZFNを設計した(図6A)。33488/33501対を使用した相同グロビン遺伝子における開裂率を、Surveyorヌクレアーゼアッセイを使用して、また、ハイスループットDNA配列決定によりアッセイした。これらの領域のそれぞれの解析は、mPB、CBおよびSCD BM CD34+細胞における高度に相同なデルタ−グロビン遺伝子のみにおけるオフターゲット改変を明らかにした(図6B、表3)。本発明者らは、より網羅的な不偏ゲノムワイドアプローチにより、オフターゲットZFN開裂のこのような直接的検査を補完して、オフターゲット部位を同定した。このアッセイは、二本鎖切断の部位において捕捉される非相同IDLVの傾向に基づき、IDLV捕捉に対するその寛容性のために選択されたK562細胞における組込みの下流クラスター化組込み部位解析(CLIS)を使用する。用いた手順について、下に概要を述べる:
遺伝子改変されたHSPCが、正常な広範囲の赤芽球および骨髄系分化が可能であることを確実にするために、処理された細胞を単一細胞としておよびバルク培養においての両方でアッセイした。HSPC分化を促進するサイトカインを含有するメチルセルロース培地におけるコロニー形成能に関して単一細胞をモニターした。簡潔に説明すると、エレクトロポレーション1日後に、MethoCult(商標)Optimumメチルセルロースに基づく培地(Stem Cell Technologies)において、35mm細胞培養皿毎に100および300個の生細胞を二連で蒔いた。オリゴヌクレオチドドナーによる実験に関して、エレクトロポレーション5日後に細胞を蒔いた。5%CO2、37℃および加湿雰囲気下の培養における2週間後に、その形態に基づき、異なる種類のコロニーを特徴付け、数え上げた。ZFN単独(対33488/33501)で処理したまたはZFNおよびオリゴヌクレオチドドナーで処理したHSPCは、同様の数およびパターンの赤芽球および骨髄系クローンを生成した。
ZFN改変された細胞が、その造血再増殖能を維持するか決定するために、ZFNおよびドナー処理したまたは偽処理したCB由来HSPCを、免疫不全NSGマウスに異種移植した。
鎌状赤血球症患者は、G−CSFによる幹細胞動員の候補ではないため、本発明者らは、これらの患者のBM吸引液からCD34+HSPCを得た。ZFN mRNAおよびIDLVドナーを使用して、部位特異的遺伝子補正を行った。細胞を赤芽球増大培地に置き、その後に確立された方法を使用して分化させた(Romeroら、前記箇所、Giarratanaら、前記箇所)。加えて、細胞の一部をそのコロニー形成能に関して評価した。ZFN+IDLV(対33488/33501)で処理した細胞は、偽、非エレクトロポレーション対照試料と比較して、やや低い(35%)コロニー形成能力を示した(図15)。
Claims (26)
- 内在性ヒトベータ−ヘモグロビン(Hbb)遺伝子の配列番号23または配列番号24にまたはその付近にゲノム改変を含む、遺伝子改変された細胞であって、前記ゲノム改変が、挿入、欠失およびこれらの組合せからなる群から選択される、遺伝子改変された細胞。
- 幹細胞である、請求項1に記載の遺伝子改変された細胞。
- 前記幹細胞が、造血幹細胞である、請求項2に記載の遺伝子改変された細胞。
- 前記造血幹細胞が、CD34+細胞である、請求項3に記載の遺伝子改変された細胞。
- 請求項1〜4のいずれかに記載の幹細胞に由来する遺伝子改変された分化細胞。
- 赤血球細胞(RBC)である、請求項5に記載の遺伝子改変された細胞。
- 前記遺伝子改変が、ヌクレアーゼを使用してなされる、請求項1〜6のいずれかに記載の遺伝子改変された細胞。
- 前記ヌクレアーゼが、ジンクフィンガーヌクレアーゼである、請求項7に記載の遺伝子改変された細胞。
- 前記ヌクレアーゼが、ジンクフィンガーヌクレアーゼを含み、前記ジンクフィンガーヌクレアーゼが、認識ヘリックスを含む5または6個のジンクフィンガードメインを含み、さらに、前記ジンクフィンガータンパク質が、表1の単一の行に示す順序で前記認識ヘリックス領域を含む、請求項8に記載の遺伝子改変された細胞。
- 前記挿入が、導入遺伝子をコードするドナーポリヌクレオチドの組込みを含む、請求項1〜9のいずれかに記載の遺伝子改変された細胞。
- 前記ドナーポリヌクレオチドが、鎌状赤血球変異を補正する、請求項10に記載の遺伝子改変された細胞。
- 請求項1〜11のいずれかに記載の遺伝子改変された細胞を含む医薬組成物。
- 認識ヘリックス領域を含む5または6個のジンクフィンガードメインを含むジンクフィンガータンパク質であって、表1の単一の行に示す順序で前記認識ヘリックス領域を含む、ジンクフィンガータンパク質。
- 請求項13に記載のジンクフィンガータンパク質と、野生型または操作された開裂ハーフドメインとを含む融合タンパク質。
- 請求項13または請求項14に記載の1種または複数のタンパク質をコードするポリヌクレオチド。
- 請求項14に記載の1種もしくは複数の融合タンパク質または請求項15に記載の1種もしくは複数のポリヌクレオチドを含む単離された細胞。
- 赤血球細胞(RBC)または前駆体細胞(例えば、CD4+造血幹細胞)からなる群から選択される、請求項16に記載の細胞。
- i)請求項15に記載のタンパク質をコードするポリヌクレオチドまたはii)請求項13もしくは請求項14に記載のタンパク質のうち少なくとも1種を含むキット。
- 細胞におけるHbb発現を変更する方法であって、
請求項15に記載の1種または複数のポリヌクレオチドを、1種または複数のタンパク質が発現され、Hbb遺伝子の発現が変更されるような条件下で、前記細胞に導入するステップを含む、方法。 - 前記Hbb遺伝子の発現が増加される、請求項19に記載の方法。
- 前記細胞のゲノムにドナー配列を組み込むステップをさらに含む、請求項19または請求項20に記載の方法。
- 前記細胞が、赤血球細胞(RBC)前駆体細胞および造血幹細胞からなる群から選択される、請求項19〜21のいずれかに記載の方法。
- 前記ドナー配列が、前記Hbb遺伝子のmRNAプロセシングのためのスプライスドナー部位を変更する変異を補正するオリゴヌクレオチドを含む、請求項19〜22のいずれかに記載の方法。
- 内在性Hbb遺伝子内にゲノム改変を含む遺伝子改変された細胞を産生する方法であって、
a)請求項14に記載の融合タンパク質をコードするポリヌクレオチドと細胞を接触させるステップと、
b)前記ポリヌクレオチドからの前記融合タンパク質の発現を促進する条件に前記細胞を供するステップと、
c)前記遺伝子改変された細胞の産生に十分な発現された前記融合タンパク質により前記内在性Hbb遺伝子を改変するステップと
を含む、方法。 - 少なくとも1種のサイトカインで前記細胞を刺激するステップをさらに含む、請求項24に記載の方法。
- β−サラセミアを有する患者を処置する方法であって、前記患者におけるHbb遺伝子発現を増加させるのに十分な量の請求項12に記載の医薬組成物を前記患者に投与するステップを含む、方法。
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