JP2021191298A - アデノウイルスの複製動態を測定するための高スループットアッセイ - Google Patents
アデノウイルスの複製動態を測定するための高スループットアッセイ Download PDFInfo
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Abstract
Description
この出願は、2016年2月23日に出願された米国仮出願第62/298,649号(これは、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。
本開示は、組換えアデノウイルス構築物における外因性オープンリーディングフレームの最適な配置、およびアデノウイルスの複製動態を測定するためのアッセイにおける組換えウイルスの使用に関する。
添付の配列表に列挙されている核酸配列およびアミノ酸配列は、37 C.F.R.1.822に定義されるように、ヌクレオチド塩基の標準的な略字およびアミノ酸の3文字コードを使用して示されている。それぞれの核酸配列の一方の鎖のみが示されているが、相補鎖は、提示された鎖に対する任意の参照により含まれると理解される。配列表は、2017年2月21日に作成された609KBのASCIIテキストファイルとして提出されており、参照により本明細書に組み込まれる。添付の配列表においては、以下の通りである。
Ad アデノウイルス
ADP アデノウイルス死タンパク質
BFP 青色蛍光タンパク質
DBP DNA結合タンパク質
E2A ウマ鼻炎Aウイルス2A
ELISA 酵素結合免疫吸着法
ERAV ウマ鼻炎Aウイルス
F2A 口蹄疫ウイルス2A
FACS 蛍光活性化細胞分取
FMDV 口蹄疫ウイルス(food and mouth disease virus)
GFP 緑色蛍光タンパク質
MOI 感染多重度
OD 光学密度
ORF オープンリーディングフレーム
P2A ブタテッショウウイルス−1 2A
pIX タンパク質IX
PTV1 ブタテッショウウイルス−1
RFP 赤色蛍光タンパク質
SLIC 配列およびライゲーション非依存性クローニング
T2A Thosea asignaウイルス2A
TaV Thosea asignaウイルス
YFP 黄色蛍光タンパク質
別途注記されない限り、技術用語は、従来の使用法に従って使用される。分子生物学における一般用語の定義は、Oxford University Pressによって1994年に刊行されたBenjamin Lewin、Genes V(ISBN 0−19−854287−9);Blackwell Science Ltd.によって1994年に刊行されたKendrewら(編)、The Encyclopedia of Molecular Biology(ISBN 0−632−02182−9);およびVCH Publishers, Inc.によって1995年に刊行されたRobert A. Meyers(編)、Molecular Biology and Biotechnology: a Comprehensive Desk Reference(ISBN 1−56081−569−8)に見出すことができる。
Sci. USA、85巻、2444頁、1988年;HigginsおよびSharp、Gene、73巻、237〜44頁、1988年;HigginsおよびSharp、CABIOS、5巻、151〜3頁、1989年;Corpetら、Nuc. Acids Res.、16巻、10881〜90頁、1988年;Huangら、Computer Appls. in the Biosciences、8巻、155〜65頁、1992年;ならびにPearsonら、Meth. Mol. Bio.、24巻、307〜31頁、1994年。Altschulら、J. Mol. Biol.、215巻、403〜10頁、1990年は、配列アラインメント方法および相同性の計算に関する詳細な考察を提示している。
異種オープンリーディングフレーム(ORF)および自己切断ペプチドコーディング配列を含む、組換えアデノウイルスゲノムが、本明細書において開示される。組換えアデノウイルスゲノムおよび開示されるゲノムによって産生される組換えアデノウイルスは、例えば、ウイルス複製動態を測定するための高スループットアッセイにおいて使用することができる。
BFP−EBFP、EBFP2、Sapphire、T−Sapphire、Azurite、mTagBFP、
シアン蛍光タンパク質−ECFP、mECFP、Cerulean、CyPet、AmCyan1、Midori−Ishi Cyan、mTurquoise、mTFP1、
GFP−GFP、EGFP、AcGFP1、Emerald、Superfolder GFP、Azami Green、mWasabi、TagGFP、TurboGFP、ZsGreen、
YFP−EYFP、Topaz、Venus、mCitrine、YPet、TagYFP、PhiYFP、ZsYellow1、mBanana、
橙色蛍光タンパク質−Kusabira Orange、Kusabira Orange2、mOrange、mOrange2、mTangerine、
橙色または赤色蛍光タンパク質−dTomato、dTomato−Tandem、TagRFP、TagRFP−T、DsRed、DsRed2、DsRed−Express(T1)、DsRed−Monomer、および
RFP−mRuby、mApple、mStrawberry、AsRed2、mRFP1、JRed、mCherry、HcRed1、mRaspberry、dKeima−Tandem、HcRed−Tandem、mPlum、AQ143、tdTomato、E2−Crimson。
36kbのアデノウイルスゲノムは、小型であり、様々な遺伝子のコーディングにトップストランド(top strand)とボトムストランド(bottom strand)の両方を使用する。アデノウイルスゲノム内の多数の位置において、トップストランドとボトムストランドとの両方が、別個の遺伝子のコーディングに同時に使用される。ゲノムのサイズは、そのキャプシドへの挿入に最適となるように進化してきた。結果として、外因性遺伝子の挿入は、キャプシドのサイズ容量によって制限されるが、これは、外因性核酸の過剰な追加により、キャプシドへのゲノムローディング(genome loading)が不完全となり、ウイルス動態が低減されるためである。
E1B−55k−SC−異種ORF
異種ORF−SC−(DNAポリメラーゼ)
DBP−SC−異種ORF
異種ORF−SC−ADP
E3−14.7k−SC−異種ORF
異種ORF−SC−E4−ORF2
自己切断ペプチドは、リボソームがC末端におけるペプチド結合の合成をスキップするように誘導し、そのペプチド配列と下流のポリペプチドとの分離をもたらす、ペプチドである。自己切断ペプチドの使用により、単一のORFから、自己切断ペプチドに隣接する複数のタンパク質の発現が可能となる。ウイルスによってコードされる2Aペプチドは、自己切断ペプチドの一種である。
asignaウイルス(TaV)、ウマ鼻炎Aウイルス(ERAV)、ブタテッショウウイルス−1(PTV1)、および口蹄疫ウイルス(FMDV)によってコードされる2Aペプチド、またはそれらの修飾バージョンが挙げられるが、これらに限定されない。
P2A:ATNFSLLKQAGDVEENPGP(配列番号12)
F2A:VKQTLNFDLLKLAGDVESNPGP(配列番号13)
E2A:QCTNYALLKLAGDVESNPGP(配列番号14)
T2A:EGRGSLLTCGDVEENPGP(配列番号15)
修飾されたP2A:GSGATNFSLLKQAGDVEENPGP(配列番号16)
修飾されたF2A:GSGVKQTLNFDLLKLAGDVESNPGP(配列番号17)
修飾されたE2A:GSGQCTNYALLKLAGDVESNPGP(配列番号18)
修飾されたT2A:GSGEGRGSLLTCGDVEENPGP(配列番号19)
選択的に複製するウイルスの評価のための重要な基準は、複数回の複製にわたり、がん細胞と正常細胞との間で、ウイルス増殖動態を比較することである。ウイルス複製におけるわずかな差は、高いMOIではマスクされ得る。複数回のウイルス複製を測定することにより、この問題を克服することができる。
アデノウイルスゲノムは、E1、E2、E3、E4、およびL1−5とラベル付けされた複数の機能的な群に組織化される。E1領域は、すべての他のウイルス遺伝子の転写を調節するタンパク質をコードし、宿主細胞にS期を誘導する。E2領域は、ウイルスDNA複製を駆動させるタンパク質をコードする。E3領域のタンパク質は、宿主細胞の免疫応答をモジュレートし、細胞培養においては必須ではない。E4領域は、異なる機能セットの遺伝子を含有する。そしてL1−5領域は、ウイルス粒子の構造タンパク質をコードする。
この実施例では、ウイルス動態を破壊することなく、自己切断ペプチド配列とともに、外因性ORFを挿入することができる、アデノウイルスゲノム内での特異的な位置の特定について記載する。
蛍光タンパク質をアデノウイルスORFに直接的に融合したいくつかの構築物を、生成した。具体的には、以下の直接的融合体を、生成した:YPet−E1A、YPet(DNAポリメラーゼ)、およびmCherry−ADP。
図7は、5種類の異なる構築物の自然対数スロープの比較を示す:YPet−E1A、YPet−P2A−E1A、E1A−P2A−mCherry、E1B−55k−P2A−YPet、およびYPet−P2A−ADP。上述のように、YPetのE1Aへの直接的な融合により、有意に減損された動態を有するウイルスが産生され、P2A部位をN末端(YPet−P2A−E1A)またはC末端(E1A−P2A−mCherry)のいずれかに付加することにより、ウイルス動態は改善されたが、野生型レベルには至らなかった。しかしながら、P2A部位および異種ORFを、E1B−55kのC末端(E1B−55k−P2A−YPet)またはADPのN末端(YPet−P2A−ADP)に挿入することにより、野生型ウイルス動態を有する組換えウイルスが生成された。
E1B−55k−SC−異種ORF
異種ORF−SC−(DNAポリメラーゼ)
DBP−SC−異種ORF
異種ORF−SC−ADP
E3−14.7k−SC−異種ORF
異種ORF−SC−E4−ORF2
これまでに説明されているウイルス動態を測定する方法は、すべて、細胞型特異的アッセイに高度に依存し、したがって、それぞれのアデノウイルス血清型の多様な親和性に起因して、血清型特異的である。本明細書において開示されるアデノウイルス動態アッセイは、いずれか1つの細胞型に依存するものではなく、そのため、Ad5以外の血清型に拡張することが可能である。すべてのアデノウイルス血清型は、Ad5 E3−14.7kと同等のORFを含有する。したがって、Ad9(E3−15kを含有する)およびAd34(E3−14.8kを含有する)を使用して、Ad5 E3−14.7k−P2A−YPet(PCMN−887、配列番号9)と同等のウイルスを生成した:PCMN−888(Ad9 E3−15k−P2A−YPet、配列番号20)およびPCMN−889(Ad34 E3−14.8k−P2A−YPet、配列番号21)。Ad5コア、ならびにAd9またはAd34のいずれかに由来するファイバーシャフトおよびノブを含有するキメラウイルスもまた、生成した。次いで、4つの組換えウイルスを、293細胞(図9A)、A549細胞(図9B)、およびU2OS細胞(図9C)を使用して、FBVKアッセイにおいて試験した。4つすべての組換えウイルスは、高いレベルのYPet発現を呈し、外因性ORFの挿入によって生じるウイルス動態への影響は最小限であった。
組換えアデノウイルスをアセンブリするためのAdsembly方法およびAdSLIC方法は、短時間で、多数の組換えウイルスゲノムおよびウイルスを生成するための手段を提供する。しかしながら、臨床上および治療上の使用のために設計された組換えアデノウイルスの複製動態を評価する高速かつ高スループットな方法に対する必要性が存在する。この実施例では、組換えアデノウイルスのウイルス複製動態を試験するために使用することができる、蛍光に基づくウイルス動態アッセイについて説明する(図3)。このアッセイは、組換えアデノウイルスゲノムプラスミドまたは組換えアデノウイルス粒子のいずれかを出発材料として用いて、行うことができる。
対数スロープを測定するために、時間に対する蛍光強度の線形プロットを、それぞれの時点で測定した蛍光強度の自然対数を取得することによって、片対数プロットに変換する。蛍光強度は、ウイルス複製時には指数関数的増殖を呈するため、この変換は、時間に対する自然対数(蛍光強度)をプロットすると直線となる。次いで、この直線を、標準的な最小二乗法を使用して当てはめる。この当てはめにより産生された結果として得られるスロープは、時間に対する蛍光の自然対数スロープであり、したがって、時間に対するウイルス増殖の自然対数スロープである。式を、以下に示す。
両側の自然対数を取得すると:
本発明は、例えば以下の項目を提供する。
(項目1)
異種オープンリーディングフレーム(ORF)および自己切断ペプチドコーディング配列を、いずれも内因性アデノウイルスORFと同じリーディングフレーム内に、それと作動可能に連結した状態で含む、組換えアデノウイルスゲノムであって、前記自己切断ペプチドコーディング配列が、前記異種ORFと前記内因性ORFとの間に位置し、かつ
前記内因性ORFが、E1B−55kであり、前記異種ORFが、E1B−55kの3’にあるか、
前記内因性ORFが、DNAポリメラーゼであり、前記異種ORFが、DNAポリメラーゼの5’にあるか、
前記内因性ORFが、DNA結合タンパク質(DBP)であり、前記異種ORFが、DBPの3’にあるか、
前記内因性ORFが、アデノウイルス死タンパク質(ADP)であり、前記異種ORFが、ADPの5’にあるか、
前記内因性ORFが、E3−14.7kであり、前記異種ORFが、E3−14.7kの3’にあるか、または
前記内因性ORFが、E4−ORF2であり、前記異種ORFが、E4−ORF2の5’にある、組換えアデノウイルスゲノム。
(項目2)
前記自己切断ペプチドが、2Aペプチドまたはそのバリアントである、項目1に記載の組換えアデノウイルスゲノム。
(項目3)
前記2Aペプチドが、ブタテッショウウイルス−1(PTV1)2A(P2A)ペプチド、口蹄疫ウイルス(FMDV)2A(F2A)ペプチド、ウマ鼻炎Aウイルス(ERAV)2A(E2A)ペプチド、またはThosea asignaウイルス(TaV)2A(T2A)ペプチド、またはそれらのバリアントを含む、項目2に記載の組換えアデノウイルスゲノム。
(項目4)
前記自己切断ペプチドのアミノ酸配列が、配列番号12〜19のうちのいずれか1つのアミノ酸配列に対して、少なくとも80%、少なくとも85%、少なくとも90%、または少なくとも95%同一である、項目3に記載の組換えアデノウイルスゲノム。
(項目5)
前記自己切断ペプチドが、配列番号12〜19のうちのいずれか1つのアミノ酸配列を含む、項目3に記載の組換えアデノウイルスゲノム。
(項目6)
前記異種ORFが、蛍光タンパク質をコードする、項目1から5のいずれか一項に記載の組換えアデノウイルスゲノム。
(項目7)
前記蛍光タンパク質が、緑色蛍光タンパク質(GFP)、黄色蛍光タンパク質(YFP)、赤色蛍光タンパク質(RFP)、または青色蛍光タンパク質(BFP)である、項目6に記載の組換えアデノウイルスゲノム。
(項目8)
前記YFPが、YPetであるか、または前記RFPが、mCherryである、項目7に記載の組換えアデノウイルスゲノム。
(項目9)
5’から3’の方向に、
E1B−55K−P2A−YPet、
E1B−55K−P2A−mCherry、
YPet−P2A−(DNAポリメラーゼ)、
DBP−P2A−YPet、
YPet−P2A−ADP、
E3−14.7k−P2A−YPet、
YPet−P2A−E4−ORF2、または
mCherry−P2A−E4−ORF2を含む、項目1から8のいずれか一項に記載の組換えアデノウイルスゲノム。
(項目10)
配列番号3〜7、9〜11、20、および21のうちのいずれか1つのヌクレオチド配列を含む、項目1から9のいずれか一項に記載の組換えアデノウイルスゲノム。
(項目11)
項目1から10のいずれか一項に記載の組換えアデノウイルスゲノムを含む、組換えアデノウイルス。
(項目13)
項目1に記載の組換えアデノウイルスゲノムを含む組換えアデノウイルスの複製動態を測定するための方法であって、前記異種ORFが、蛍光タンパク質をコードし、前記方法は、以下:
(i)細胞に、前記組換えアデノウイルスのゲノムをトランスフェクトするか、または細胞に、前記組換えアデノウイルスの粒子を感染させるステップと、
(ii)トランスフェクトした前記細胞または感染させた前記細胞を、少なくとも2日間培養するステップと、
(iii)前記培養期間の間、規則的な間隔で、蛍光を測定するステップと、
(iv)前記蛍光測定値から対数スロープを計算し、それによって、前記組換えアデノウイルスの複製動態を測定するステップとを含む、方法。
(項目14)
前記組換えアデノウイルスが、第2の異種ORFをさらに含む、項目13に記載の方法。
(項目15)
前記細胞が、マルチウェルプレートにおいて培養される、項目13または項目14に記載の方法。
(項目16)
前記組換えアデノウイルスの複製動態が、第1の細胞型および第2の細胞型において測定される、項目13から15のいずれか一項に記載の方法。
(項目17)
前記第1の細胞型が、腫瘍細胞であり、前記第2の細胞型が、非腫瘍細胞である、項目16に記載の方法。
(項目18)
蛍光が、およそ10分ごと、15分ごと、30分ごと、60分ごと、または120分ごとに測定される、項目13から17のいずれか一項に記載の方法。
(項目19)
蛍光が、TECAN(商標)蛍光プレートリーダーにおいて測定される、項目13から18のいずれか一項に記載の方法。
(項目20)
細胞に、前記組換えアデノウイルスのゲノムをトランスフェクトするステップを含む、項目13から19のいずれか一項に記載の方法。
(項目21)
トランスフェクションにより、細胞のおよそ5〜10%がトランスフェクトされる、項目20に記載の方法。
(項目22)
細胞に、前記組換えアデノウイルスの粒子を感染させるステップを含む、項目13から19のいずれか一項に記載の方法。
(項目23)
前記細胞に、前記組換えアデノウイルス粒子の連続希釈物を感染させる、項目22に記載の方法。
(項目24)
1:100、1:300、1:900、1:2700、1:8100、1:24,300、1:72,900、および1:218,700の希釈物を含む、項目23に記載の方法。
(項目25)
(i)項目1から10のいずれか一項に記載の組換えアデノウイルスゲノムまたは項目11に記載の組換えアデノウイルスと、
(ii)細胞、細胞培養培地、および/またはマルチウェルプレートと
を含む、キット。
Claims (1)
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