JP7381476B2 - 希少疾患の処置のための方法および組成物 - Google Patents
希少疾患の処置のための方法および組成物 Download PDFInfo
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Description
本出願は、その開示が、参照によりその全体が本明細書に組み込まれる2017年10月24日に出願された米国特許仮出願第62/576,584号の利益を主張する。
本明細書において開示される、方法の実施ならびに組成物の調製および使用は、特に断りのない限り、当該技術分野内のもののような、分子生物学、生化学、クロマチン構造および解析、コンピュータ化学、細胞培養、組換えDNAおよび関連分野における従来技術を用いる。これらの技術は、文献に十分に説明されている。例えば、Sambrook et al. MOLECULAR CLONING: A LABORATORY MANUAL, Second edition, Cold Spring Harbor Laboratory Press, 1989および Third edition, 2001;Ausubel et al., CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, New York, 1987および定期的更新物;the series METHODS IN ENZYMOLOGY, Academic Press, San Diego; Wolffe, CHROMATIN STRUCTURE AND FUNCTION, Third edition, Academic Press, San Diego, 1998;METHODS IN ENZYMOLOGY, Vol. 304, “Chromatin” (P.M. Wassarman and A. P. Wolffe, eds.), Academic Press, San Diego, 1999;およびMETHODS IN MOLECULAR BIOLOGY, Vol. 119, “Chromatin Protocols” (P.B. Becker, ed.) Humana Press, Totowa, 1999を参照のこと。
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、同義的に使用され、直鎖状または環状コンホメーションの、一本鎖または二本鎖形態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ポリマーを指す。本開示の目的上、これらの用語は、ポリマーの長さに関して制限すると解釈されてはならない。この用語は、天然ヌクレオチドの公知類似体ならびに塩基、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)において修飾されている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類似体は、同一塩基対合特異性を有する、すなわち、Aの類似体は、Tと塩基対合する。
(i)特に、このような哺乳動物が状態になりやすいが、それを有するとまだ診断されていない場合に哺乳動物において疾患もしくは状態を発生から妨げること、
(ii)疾患もしくは状態を阻害すること、すなわち、その発生を停止すること、
(iii)疾患もしくは状態を軽減すること、すなわち、疾患または状態の退縮を引き起こすことならびに/または
(iv)疾患もしくは状態に起因する症状を軽減もしくは排除すること、すなわち、根底にある疾患もしくは状態に対処してもしくは対処せずに疼痛を軽減すること
を含む。
本明細書において記載される方法は、内因性DUX4、C9orf72、SMN1、SMN2、UBE34またはUbe34-ATS遺伝子中の標的配列(例えば、9~20以上の連続または非連続ヌクレオチドの標的部位)と特異的に結合するDNA結合ドメインを含む組成物、例えば、遺伝子調節性転写因子を使用する。任意のポリヌクレオチドまたはポリペプチドDNA結合ドメイン、例えば、DNA結合タンパク質(例えば、ZFPまたはTALE)またはDNA結合ポリヌクレオチド(例えば、シングルガイドRNA)は、本明細書において開示される組成物および方法において使用され得る。したがって、DUX4、C9orf72、SMN1、SMN2、UBE34またはUbe34-ATS遺伝子の遺伝子リプレッサーが記載されている。
種 PAM
S.ピオゲネス NGG
S.ピオゲネス NAG
S.ミュータンス NGG
S.サーモフィルス NGGNG
S.サーモフィルス NNAAAW
S.サーモフィルス NNAGAA
S.サーモフィルス NNNGATT
C.ジェジュニ NNNNACA
N.メニンギチデス NNNNGATT
P.マルトシダ GNNNCNNA
F.ノビシダ NG
DNA結合ドメインは、本明細書において記載される方法において使用するために、任意のさらなる分子(例えば、ポリペプチド)に融合され得る、そうでなければそれと会合する。ある特定の実施形態では、方法は、少なくとも1つのDNA結合分子(例えば、ZFP、TALEまたはシングルガイドRNA)および異種調節(機能的)ドメイン(またはその機能的断片)、例えば、希少疾患関連遺伝子中の標的部位と結合するDNA結合ドメインおよび転写調節ドメインを含む人工転写因子(アクチベーターまたはリプレッサー)を含む融合分子を用いる。
本明細書において記載される転写因子、ヌクレアーゼおよび/またはポリヌクレオチド(例えば、遺伝子モジュレーター)ならびにタンパク質および/またはポリヌクレオチドを含む組成物は、例えば、タンパク質の注射によって、mRNAを介して、および/または発現コンストラクト(例えば、プラスミド、レンチウイルスベクター、AAVベクター、Adベクターなど)を使用して、を含む任意の好適な手段によって標的細胞にデリバリーされ得る。好ましい実施形態では、遺伝子モジュレーター(例えば、リプレッサー)は、それだけには限らないが、米国特許第9,585,971号に記載されるようなAAV9ベクター[またはその偽型(pseuotyped)ベクター](米国特許7,198,951を参照のこと)またはAAVベクターを含む、AAVベクターを使用してデリバリーされる。
CNS障害の研究は、非ヒト霊長類などの動物モデル系において実施され得る[例えば、パーキンソン病(Johnston and Fox (2015) Curr Top Behav Neurosci 22: 221-35]、筋萎縮性側索硬化症[Jackson et al, (2015) J. Med Primatol: 44(2):66-75]、ハンチントン舞踏病[Yang et al (2008) Nature 453(7197):921-4]、アルツハイマー病[Park et al (2015) Int J Mol Sci 16(2):2386-402]、てんかん発作[Hsiao et al (2016) EBioMed 9:257-77]、イヌ[例えば、MPS VII(Gurda et al (2016) Mol Ther 24(2):206-216]、アルツハイマー病[Schutt et al (J Alzheimers Dis 52(2):433-49]、てんかん発作[Varatharajah et al (2017) Int J Neural Syst 27(1):1650046]およびマウス[例えば、てんかん発作(Kadiyala et al (2015) Epilepsy Res 109:183-96]、アルツハイマー病[Li et al (2015) J Alzheimers Dis Parkin 5(3) doi 10:4172/2161-0460]、[概説:Webster et al (2014) Front Genet 5 art 88, doi:10.3389f/Gene.2014.00088]。これらのモデルは、CNS疾患を完全に再現する動物モデルがない場合でさえ、疾患の特異的症状のセットを調べるために有用であり得るので使用され得る。モデルは、本明細書において記載される治療方法および組成物(遺伝子リプレッサー)の有効性および安全性プロファイルの決定において役立ち得る。
本明細書において記載されるようなDUX4、C9orf72、UBE34、Ube3a-ATS、SMN1またはSMN2結合分子(例えば、ZFP、TALE、CRISPR/Cas系、Ttagoなど)を含む本明細書において記載されるような遺伝子モジュレーターおよびそれらをコードする核酸は、種々の適用のために使用され得る。これらの適用は、DUX4、C9orf72、UBE34、Ube3a-ATS、SMN1またはSMN2結合分子(DNA結合タンパク質をコードする核酸を含む)が、ウイルス(例えば、AAV)または非ウイルスベクターを使用して対象に投与され、対象内で標的遺伝子の発現を調節するために使用される治療方法を含む。調節は、抑制、例えば、ALSまたはFTD病状に寄与しているC9orf72(例えば、突然変異体)発現の抑制またはAS病状に寄与しているUbe3a-ATS発現の抑制の形態であり得る。あるいは、調節は、内因性細胞性遺伝子の発現の活性化または発現の増大が、罹患状態を寛解させ得る場合には活性化の形態であり得る。なおさらなる実施形態では、調節は、例えば、DUX4、C9orf72、UBE34、Ube3a-ATS、SMN1またはSMN2遺伝子の不活性化のための、切断(例えば、1つまたは複数のヌクレアーゼによる)による抑制であり得る。上記で記載したように、このような適用のために、標的結合分子またはより通常は、それらをコードする核酸は薬学的に許容される担体とともに医薬組成物として製剤化される。
DUX4、C9orf72、UBE34、Ube3a-ATS、SMN1またはSMN2を標的とするジンクフィンガータンパク質、TALEおよびsgRNAを、本質的に米国特許第6,534,261号、同第8,586,526号および米国特許公開第20150056705号、同第20110082093号、同第20130253040号および同第20150335708号に記載されるとおりに遺伝子操作する。リプレッサーのセットも、マウスおよびヒト両方においてDUX4、C9orf72、UBE34、Ube3a-ATS、SMN1またはSMN2配列を標的とするように作製する。リプレッサーを、標準SELEX解析によって評価し、その標的部位と結合すると示される。リンカーを使用して、ZFP DNA結合ドメインを転写リプレッサーと連結させ、リンカーは以下のアミノ酸配列:LRQKDAARGS(配列番号33)を有していた。C9orf72を標的とする例示的ZFPが、以下に表1中に示されており、すべてその標的部位と結合すると示された。
表1に示されるZFP-TFの全体的な特異性を、C9021細胞においてマイクロアレイ解析によって評価した。手短には、100ngのZFP-TFをコードするmRNAを、生物学的に4連で150,000個のC9021細胞にトランスフェクトした。24時間後、全RNAを抽出し、製造業者のプロトコール(Affymetrix Genechip MTA1.0)によって処理した。ロバストマルチアレイ平均(RMA)を使用して、各プローブセットからの生シグナルを正規化した。解析は、「遺伝子レベル差次的発現解析」オプションを備えたトランスクリプトーム解析コンソール3.0(Affymetrix)を使用して実施した。ZFPがトランスフェクトされたサンプルを、無関係のZFP-TF(C9orf72標的部位と結合しない)を用いて処理されているサンプルと比較した。変化呼び出しは、対照に対して平均シグナルにおいて>2倍の相違およびP値<0.05(各プローブセットについて一元ANOVA解析、独立T検定)を有する転写物(プローブセット)について報告される。
マウスDUX4、C9orf72またはUbe3a-ATSを標的とするすべてのリプレッサーを、発現を駆動するためのCMVプロモーターを使用してrAAV2/9ベクターにクローニングする。ウイルスは、当技術分野で公知の方法に従って、HEK293T細胞において産生され、CsCl密度勾配を使用して精製され、リアルタイムqPCRによって力価測定される。3E5、1E5、3E4および1E4VG/細胞で培養一次マウス皮質ニューロンに感染させるために精製ウイルスが使用される。7日後、全RNAを抽出し、DUX4、C9orf72またはUbe3a-ATSおよび2種の参照遺伝子(ATP5b、EIF4a2)の発現を、リアルタイムRT-qPCRを使用してモニタリングした。
TFを、マウス海馬にデリバリーし、インビボでDUX4、C9orf72またはUbe3a-ATSの抑制を評価する。手短には、半球あたりrAAV2/9-CMV-ZFP-TFの8E9VGの総用量を、二重両側性2μL注射による定位的注射によって投与する。注射の5週間後に動物を犠牲にし、各半球を解析のために3片に切開する。DUX4、C9orf72またはUbe3a-ATSおよびZFP-TF発現をリアルタイムRT-qPCRによって解析し、3種のハウスキーピング遺伝子(ATP5b、EIF4a2およびGAPDH)の幾何平均に対して正規化する。
Claims (18)
- C9orf72遺伝子の遺伝子モジュレーターであって、
C9orf72遺伝子中の標的部位と結合するジンクフィンガータンパク質(ZFP)DNA結合ドメインであって、ZFP DNA結合ドメインは、配列の配列番号が括弧内に示される以下の表の単一列に示される認識ヘリックス領域を含み、そして、それぞれの標的部位は、以下の表の配列番号1および2の大文字によって示される、ZFP DNA結合ドメインと、
転写調節ドメインまたはヌクレアーゼドメインと
を含む、遺伝子モジュレーター。 - 転写調節ドメインが、抑制ドメインまたは活性化ドメインを含む、請求項1に記載の遺伝子モジュレーター。
- 遺伝子モジュレーターが、遺伝子の突然変異体アレルの発現を、未処置対照と比較して少なくとも50%抑制することができる、請求項1または2に記載の遺伝子モジュレーター。
- ZFP DNA結合ドメインと抑制ドメインが、配列番号33を含むリンカーによって連結される、請求項2または3に記載の遺伝子モジュレーター。
- 請求項1から4のいずれかに記載の遺伝子モジュレーターをコードするポリヌクレオチド。
- 請求項5に記載のポリヌクレオチドを含む遺伝子デリバリーベクター。
- AAVベクターを含む、請求項6に記載の遺伝子デリバリーベクター。
- 請求項5に記載の1つもしくは複数のポリヌクレオチドまたは請求項6もしくは7に記載の1つもしくは複数の遺伝子デリバリーベクターを含む医薬組成物。
- 遺伝子モジュレーターがヌクレアーゼドメインを含み、遺伝子モジュレーターがC9orf72遺伝子を切断する、請求項8に記載の医薬組成物。
- 切断されたC9orf72遺伝子中に組み込まれるドナー分子をさらに含む、請求項9に記載の医薬組成物。
- 請求項1から4のいずれかに記載の1つもしくは複数の遺伝子モジュレーター、請求項5に記載の1つもしくは複数のポリヌクレオチド、請求項6もしくは7に記載の1つもしくは複数の遺伝子デリバリーベクターおよび/または請求項8から10のいずれかに記載の1つもしくは複数の医薬組成物を含む単離細胞。
- 細胞においてC9orf72遺伝子発現を調節する方法において使用するための医薬組成物であって、方法が、請求項1から4のいずれかに記載の1つもしくは複数の遺伝子モジュレーター、請求項5に記載の1つもしくは複数のポリヌクレオチド、請求項6もしくは7に記載の1つもしくは複数の遺伝子デリバリーベクターおよび/または請求項8から10のいずれかに記載の1つもしくは複数の医薬組成物を投与することを含む、医薬組成物。
- C9orf72遺伝子発現が抑制される、請求項12に記載の医薬組成物。
- C9orf72センスおよびアンチセンス両方の遺伝子発現が抑制される、請求項13に記載の医薬組成物。
- 投与が、脳室内、くも膜下腔内、頭蓋内、後眼窩(RO)、静脈内、鼻腔内または大槽内である、請求項12から14のいずれかに記載の医薬組成物。
- 対象において筋萎縮性側索硬化症(ALS)または前頭側頭型認知症(FTD)を処置および/または予防する方法において使用するための医薬組成物であって、方法が、請求項8から10のいずれかに記載の医薬組成物によってC9orf72発現を抑制することを含む、医薬組成物。
- 請求項1から4のいずれかに記載の1つもしくは複数の遺伝子モジュレーター、請求項5に記載の1つもしくは複数のポリヌクレオチド、請求項6もしくは7に記載の1つもしくは複数の遺伝子デリバリーベクターおよび/または請求項8から10のいずれかに記載の1つもしくは複数の医薬組成物および適宜、使用のための説明書を含む、キット。
- 対象における筋萎縮性側索硬化症(ALS)または前頭側頭型認知症(FTD)の処置および/または予防のための、請求項1から4のいずれかに記載の1つもしくは複数の遺伝子モジュレーター、請求項5に記載の1つもしくは複数のポリヌクレオチド、請求項6もしくは7に記載の1つもしくは複数の遺伝子デリバリーベクターおよび/または請求項8から10のいずれかに記載の1つもしくは複数の医薬組成物を含む、医薬組成物。
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