JP2021512956A - 腫瘍免疫応答のバイオマーカーとしてのリピートrna - Google Patents
腫瘍免疫応答のバイオマーカーとしてのリピートrna Download PDFInfo
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Abstract
Description
本出願は、2018年2月6日に出願された米国仮特許出願第62/627,151号の利益を主張する。前述の全内容は、参照により本明細書に組み込まれる。
本発明は、国立衛生研究所によって付与された助成金番号CA087497、および全米科学財団によって付与された助成金番号1545935の政府支援により行われた。政府は、本発明において一定の権利を有する。
がん由来の細胞を含む試料を提供すること;
細胞中のリピートRNA(例えば、HSATII、LINE−1、HERV−K、HERV−H)のレベルを検出すること;
試料中のリピートRNAのレベルを参照レベルと比較すること;および
参照レベルを上回るリピートRNAのレベルを有するがんを有する対象に対して、(i)リピートRNAの排出のレベルを低減させるか、もしくは細胞中のリピートRNAのレベルを増加させる処置、または(ii)腫瘍保護的免疫抑制を低減する免疫療法の1つまたは両方を含む処置を選択し、任意選択で行うこと
を含む。いくつかの実施形態において、リピートRNAはHSATIIである。
出願人は、がん細胞中のリピートRNA、例えば、HSATII、LINE−1、HERV−K、HERV−H RNAのレベルの間の相関、および免疫細胞の特定の集団の存在を特定した。本明細書に記載されるように、高レベルのHSATII RNAを有するがん細胞は、CD163+腫瘍関連マクロファージの存在と正に相関する。理論に縛られることを望まないが、腫瘍中の高レベルのHSATII RNAは、マクロファージを引き寄せ、次いで保護効果を発揮し、抗腫瘍免疫応答を抑制する、腫瘍環境に存在する高レベルのHSATII RNA(例えば、エキソソーム)をもたらすHSATII RNAの排出(例えば、エキソソームによる)と関連すると考えられる。これらのがんは、マクロファージを標的にする療法、またはエキソソームによるHSATII RNA輸送のレベルを低減する療法に応答し、細胞中のHSATIIの増加、およびネクロトーシスによる細胞死をもたらすことが予想される。次いで、これは、マクロファージに排出されたHSATII RNAの量を減少させて、それらに影響を及ぼす。このため、本明細書に記載の方法は、高レベルのHSATII RNA(すなわち、選択された閾値を上回るHSATII RNAのレベル)を有するがんを有するとして特定された対象に、マクロファージを標的にする療法を行うことを含み得る。いくつかの実施形態において、本方法は、HSATII RNAの排出のレベルを低減させる/細胞中のHSATII RNAのレベルを増加させる処置、例えば、1つまたは複数の、HSATII阻害性核酸;逆転写阻害剤;DNMT阻害剤などのDNA低メチル化剤;ヒストンデアセチラーゼ(HDAC)阻害剤;またはブロモドメインおよび末端外モチーフ(BET)阻害剤;またはマクロファージを標的にする処置、例えば、CD11b、CSF−1R、CCL2、ニューロピリン−1、ANG2、IL−4、IL−4Rアルファ、IL−13、Fc−ガンマR、IL−6、IL−6R、TNF−アルファ、CD40を対象に投与することを含み得る。任意のこれらの処置は、単独で、一緒に、または互いもしくは別の抗がん療法、例えば、細胞傷害性化学療法の適用と同時にまたは前に、行うことができる。いくつかの実施形態において、対象が(例えば、本明細書に記載のアッセイを使用して)高レベルのHSATII RNAを有するがんを有するとして特定された後、がん細胞から排出されたHSATII RNAのレベルを低減させる処置および/またはマクロファージのレベルを低減させるか、もしくはマクロファージの活性をモジュレートする処置は、HSATII RNAのレベルを変える(例えば、HSATII RNAの排出のレベルを低減させる/細胞中のHSATII RNAのレベルを増加させる)および/またはマクロファージのレベルを増加させるのに十分な時間、例えば、少なくとも2日間、5日間、7日間、10日間、14日間、18日間、21日間、28日間、30日間、またはそれよりも長く行われる。任意選択で、HSATII RNAのレベルおよび/またはマクロファージのレベルは、再び決定される。細胞中のHSATIIのレベルが増加し、腫瘍環境におけるエキソソーム中のHSATIIのレベルが低減され、またはマクロファージのレベルが低減されると(すなわち、閾値を上回るまたは下回る)、本方法は、HSATII低がん(すなわち、閾値を下回るHSATIIレベルを有するがん)を有する対象に対して、本明細書に記載の処置を行うことを含み得る。
出願人は、驚くべきことに、抗腫瘍応答を増強する免疫療法による処置に抵抗性のHSATII高がん細胞が、免疫抑制を低減する処置を使用した場合により感受性になることを発見した。いくつかの実施形態において、処置は、逆転写酵素阻害剤(RTI)、例えば、ヌクレオシドアナログ逆転写酵素阻害剤(NRTI)、ヌクレオチドアナログ逆転写酵素阻害剤または非ヌクレオシド逆転写酵素阻害剤(NNRTI)の投与を含む。いくつかの実施形態において、処置は、ヌクレオシドアナログ逆転写酵素阻害剤、ヌクレオチドアナログ逆転写酵素阻害剤および/または非ヌクレオシド逆転写酵素阻害剤の組合せを含む。いくつかの実施形態において、処置はNRTIを含まない。
いくつかの実施形態において、本方法は、HDAC阻害剤の投与を含み、いくつかのHDAC阻害剤が、当技術分野において公知であり、スベロイルアニリドヒドロキサム酸(SAHA/ボリノスタット/ゾリンザ)、トリコスタチンA(TSA)、およびPXD−101(ヒドロキサム酸系の汎HDAC阻害剤である);デプシペプチド(FK228/ロミデプシン/ISTODAX(登録商標))(HDAC1/2の天然の環状ペプチド阻害剤である);MS−275およびMGCD0103(合成ベンズアミド誘導体である);ならびにバルプロ酸およびフェニル酪酸ナトリウム(比較的低い効力の脂肪酸である)を含む。例えば、Kim and Bae, Am J Transl Res. 2011 Jan 1; 3(2): 166-179を参照されたい。
いくつかの実施形態において、本方法は、BET阻害剤の投与を含み、いくつかのBET阻害剤は、当技術分野において公知であり、(+)−JQ1、I−BET762、OTX015、I−BET151、CPI203、PFI−1、MS436、CPI−0610、RVX2135、FT−1101、BAY1238097、INCB054329、TEN−010、GSK2820151、ZEN003694、BAY−299、BMS−986158、ABBV−075、GS−5829およびPLX51107を含み、例えば、Perez-Salvia and Esteller, Epigenetics. 2017; 12(5): 323-339を参照されたい。
いくつかの実施形態において、本明細書に記載の方法は、DNA低メチル化剤を対象に投与することをさらに含む。DNAメチル化は、遺伝子の転写のサイレンシングを調節するエピジェネティック修飾である。ゲノムのメチル化パターンは、腫瘍中で変化し得(Smet et al. (2010) Epigenetics 5(3): 206-13)、B細胞悪性腫瘍において重要であり得る(Debatin et al. (2007) Cell 129(5): 853-5;Martin-Subero (2006) Leukemia 20(10): 1658-60)。下記に記載するように、例えば、DNA低メチル化剤(例えば、5−アザシチジン)による処置。任意の特定の理論に縛られることを望まないが、DNA低メチル化剤による処置は、HSATIIの転写を活性化すると考えられ、NRTIによる処置に感受性の細胞にする。
いくつかの実施形態において、本明細書に記載の方法は、HSATIIを特異的に標的にする阻害性核酸(例えば、LNA分子)を対象に投与することをさらに含む。HSATIIを標的にする阻害性核酸はおよびそれを使用する方法は、例えば、米国特許出願公開第2017/0198288号明細書に開示されており、この全内容は参照によって本明細書に明示的に組み込まれる。
いくつかの実施形態において、本方法は、免疫療法剤を、本明細書に記載の方法を使用して特定された対象に投与することを含む。免疫療法剤は、腫瘍が誘導する免疫抑制を標的にする療法を含み、例えば、Stewart and Smyth (2011) Cancer Metastasis Rev. 30(1): 125-40を参照されたい。
いくつかの実施形態において、本方法は、抗腫瘍免疫応答を増強する療法を選択および/または行うことを含む。CD8+細胞応答を増強する免疫療法の例としては、限定されるものではないが、養子T細胞療法またはがん細胞を認識するTリンパ球を誘導するように設計されたがんワクチン調製物、ならびに抗CD137抗体(例えば、BMS−663513)、抗PD1抗体(例えば、ニボルマブ、ペムブロリズマブ/MK−3475、ピディリズマブ(CT−011))、抗PDL1抗体(例えば、BMS−936559、MPDL3280A)または抗CTLA−4抗体(例えば、イピリムマブ(ipilumimab)、例えば、Kruger et al. (2007) Histol Histopathol. 22(6): 687-96;Eggermont et al. (2010) Semin Oncol. 37(5): 455-9;Klinke (2010) Mol. Cancer. 9: 242;Alexandrescu et al. (2010) J. Immunother. 33(6): 570-90;Moschella et al. (2010) Ann N Y Acad Sci. 1194: 169-78;Ganesan and Bakhshi (2010) Natl. Med. J. India 23(1): 21-7;およびGolovina and Vonderheide (2010) Cancer J. 16(4): 342-7を参照されたい)などのチェックポイント阻害剤が挙げられる。
いくつかの実施形態において、本方法は、腫瘍保護的免疫抑制を低減する療法を選択および/または行うことを含み、これらの療法は、例えば、数を低減すること、機能を変更すること、または免疫調節性細胞型の腫瘍局在化を予防することによって、調節性T細胞(Treg)またはM2極性化マクロファージなどの免疫調節性細胞型を主に標的にし得る。例えば、Treg標的化療法としては、抗GITRモノクローナル抗体(TRX518)、シクロホスファミド(例えば、メトロノミック用量)、三酸化ヒ素、パクリタキセル、スニチニブ、オキサリプラチン、PLX4720、アントラサイクリン系化学療法、ダクリズマブ(抗CD25);免疫毒素、例えば、Ontak(デニロイキンジフチトクス);リンパ切除(例えば、化学または照射リンパ切除)、ならびにVEGF遮断抗体(例えば、ベバシズマブ)などのVEGF−VEGFRシグナル伝達軸を選択的に標的にする薬剤、またはVEGFRチロシンキナーゼ活性(例えば、レンバチニブ)もしくはATP加水分解の阻害剤(例えば、エクトヌクレオチダーゼ阻害剤、例えば、ARL67156(6−N,N−ジエチル−D−β,γ−ジブロモメチレンATP三ナトリウム塩)、8−(4−クロロフェニルチオ)cAMP(pCPT−cAMP)および関連する環状ヌクレオチドアナログ(8−[4−クロロフェニルチオ]cGMP;pCPT−cGMP)、および国際公開第2007/135195号パンフレットに記載のもの、ならびにCD73またはCD39に対するモノクローナル抗体(mAb)を使用する)が挙げられる。ドセタキセルもM2マクロファージに対して効果を有する。例えば、Zitvogel et al. (2013) Immunity 39: 74-88を参照されたい。
本明細書に記載の方法は、本明細書に記載の治療剤を含む医薬組成物および製剤の投与を含み得る。
すべてのRNA−ISHおよびIHCアッセイの組合せは以下の通り行われる。免疫細胞(T細胞サブセットのCD3、CD4、CD8、FOXP3;マクロファージのCD68、CD163;B細胞のCD20;NK細胞のCD16、CD56)のためのモノクローナル抗体、およびリピートRNA(HSATII、HERV−K、HERV−H、LINE1)のためのRNA ISHプローブを、単一の組織学スライド上に連続して適用し、対照的な色素原を使用して、抗体:免疫マーカーについて茶色(ジアミノベンジジン[DAB])、およびRNA:リピートRNAについて赤(ファストレッド)を視覚化した。パラフィン包埋した切片を、コーティングされたスライド上に載せ、60℃で60分間にわたってオーブンに置いた。連続した二重染色プロトコールは、Leica Bond Rx自動免疫染色装置を使用して行った。脱パラフィン化(View RNA Dewax1プロトコール)および行われた抗原回復は、EDTA系の独自のLeica溶液(pH8.0〜8.5)であるHIER2試薬を用いて、およそ100℃で20分間行った。それぞれの免疫細胞のサブセットに対するモノクローナル抗体を、プロトコールに従って、Leica抗体希釈溶液に希釈した。ISH部分について、View−RNA eZL検出キット(Affymetrix)を、Bond RX免疫組織化学的検査およびBDZ6.0ソフトウェア(Leica Biosystems)を用いるISH染色システムにおいて使用した。部分2についてのBond Rxユーザーが選択可能なセッティングは以下の通りであった:ViewRNA eZ−l検出1−plex(赤)プロトコール;ViewRNA Dewax1調製プロトコール;ViewRNA酵素2(10);これらのセッティングでViewRNAプローブのハイブリダイゼーションを3時間、FFPE組織についてのRNA脱マスキング条件は以下で構成された:Bond Enzyme PretreatmentキットからのプロテイナーゼKとともに、1:1000希釈で10分のインキュベーション(Leica Biosystems)。RNAリピートEzプローブを、ViewRNAプローブ希釈液(Affymetrix)に1:40で希釈した。実行後、スライドを水ですすぎ、室温で30分間風乾し、Dako Ultramount(Dako、Carpinteria、CA)を使用して載せ、標準的な明視野顕微鏡を使用して可視化した。リピートRNAおよびリンパ球における褐色細胞質反応性に対する陽性シグナルとして定義される細胞の細胞質および核における点状のような赤色のハイブリダイゼーションシグナルは、免疫マーカーに対して陽性と見なした。
免疫療法の分野は、CD8+T細胞浸潤物が、一般に、免疫療法(CTLA4またはPD1/PDL1)に対する応答と相関することを示している(Taube JM et al. Mod Pathol. 2017 Dec 1. doi: 10.1038/modpathol.2017.156)。FOXP3+調節性T細胞は、抗腫瘍T細胞応答を遮断すると考えられるが、このデータはさらに矛盾している(例えば、Manjili and Butler, Immunol Invest. 2016 Nov;45(8):759-766;Ward-Hartstonge and Kemp, Clin Transl Immunology. 2017 Sep 15;6(9):e154を参照されたい)。
HSATIIおよびCD163+マクロファージは、膵管腺癌(PDAC)において正に相関した。HSATII高発現は、より高いCD163+マクロファージに関連した。したがって、腫瘍細胞中のHSATIIは、腫瘍免疫微小環境においてマクロファージを標的にする薬物について患者を選択するために使用することができるマクロファージ浸潤物の代理マーカーである。この知見は、図6および7における結腸がんについてのデータと一致した。
HSATIIおよびCD8+T細胞は、膵管腺癌(図9)、肝内胆管癌(図11)および肝細胞癌(図12)において負に相関し、このマーカーの細胞溶解性免疫細胞浸潤物の代理としての有用性を実証し、これは、免疫チェックポイント阻害(抗CTLA4および/または抗PD1/PDL1)を受け入れることができる腫瘍の決定において有用であろう。これは、公開された結腸がんにおけるデータを拡張した(Solovyov A et al. Cell Reports 2018)。
実験手順
本発明者らは、総RNA凍結固形腫瘍のRNA配列データを有するTCGAから38個の試料を選択した。これらの試料は、12個のLUAD腫瘍、10個のCOAD腫瘍、5個のBRCA腫瘍、4個のKIRC腫瘍、4個のUCEC腫瘍、3個のBLCA腫瘍で構成された。これらの38個の試料のうち、29個の試料は、マッチングするポリ(A)RNA配列データを有していた。アリコートを調製する総RNAおよびポリ(A)は、同じ身体試料に由来していた。これらの試料は、11個のLUAD腫瘍、6個のCOAD腫瘍、5個のBRCA腫瘍、4個のKIRC腫瘍、3個のBLCA腫瘍で構成された。このような対を成す試料の存在は、シークエンシングプロトコールおよびコンピューターで計算された遺伝子発現におけるそれらの効果の技術的比較を行うことを可能にした。
ERVクラス発現は、陽性の抗PD−L1免疫療法の応答と関連し得る。
本発明をその詳細な説明と併せて説明してきたが、前述の説明は例示を意図するものであり、添付の特許請求の範囲によって定義される本発明の範囲を限定するものではないことが理解されるべきである。他の態様、利点および改変は、以下の特許請求の範囲の範囲内である。
Claims (19)
- 対象においてがんを有する対象を処置する方法であって、
前記がん由来の細胞を含む試料を提供すること;
前記細胞中のリピートRNA(例えば、HSATII、LINE−1、HERV−K、HERV−H)のレベルを検出すること;
前記試料中の前記リピートRNAのレベルを参照レベルと比較すること;および
参照レベルを上回るリピートRNAのレベルを有するがんを有する対象に対して、(i)前記細胞において、リピートRNAの排出のレベルを低減させるか、もしくはリピートRNAのレベルを増加させる処置、または(ii)腫瘍保護的免疫抑制を低減する免疫療法の1つまたは両方を含む処置を選択し、任意選択で行うこと
を含む、方法。 - 前記細胞において、リピートRNAの排出のレベルを低減させるか、またはリピートRNAのレベルを増加させる前記処置が、リピートRNAを標的にする阻害性核酸であり、好ましくは、ロックド核酸(LNA)分子、短ヘアピンRNA(shRNA)分子、小阻害性RNA(siRNA)分子、アンチセンス核酸分子、ペプチド核酸分子およびモルホリノからなる群から選択される阻害性核酸である、請求項1に記載の方法。
- 前記細胞において、リピートRNAの排出のレベル、またはリピートRNAのレベルを増加させる前記処置が、ヌクレオシドアナログ逆転写酵素阻害剤、ヌクレオチドアナログ逆転写酵素阻害剤、非ヌクレオシド逆転写酵素阻害剤およびこれらの組合せからなる群から選択される逆転写酵素阻害剤(RTI)である、請求項1に記載の方法。
- 前記ヌクレオシドアナログ逆転写酵素阻害剤が、ラミブジン、アバカビル、ジドブジン、エムトリシタビン、ジダノシン、スタブジン、エンテカビル、アプリシタビン、センサブジン、ザルシタビン、デキセルブシタビン、アムドキソビル、エルブシタビン、フェスチナビル、ラシビル、スタムピジンまたはこれらの組合せを含む、請求項3に記載の方法。
- 前記非ヌクレオシド逆転写酵素阻害剤が、レルシビリン、リルピビリン、エファビレンツ、エトラビリン、ドラビリン、ダピビリンもしくはこれらの組合せを含むか、または前記ヌクレオチドアナログ逆転写酵素阻害剤が、テノホビルアラフェナミドフマル酸塩、テノホビルジソプロキシルフマル酸塩、アデホビルもしくはこれらの組合せを含む、請求項3に記載の方法。
- 前記細胞において、リピートRNAの排出のレベルを低減させるか、またはリピートRNAのレベルを増加させる前記処置が、シチジンアナログまたはグアノシンアナログを含む、請求項1に記載の方法。
- 前記細胞において、リピートRNAの排出のレベルを低減させるか、またはリピートRNAのレベルを増加させる前記処置が、HDAC阻害剤、BET阻害剤またはDNA低メチル化剤を含む、請求項1に記載の方法。
- 前記DNA低メチル化剤が、アザシチジン、デシタビン、クラドリビンまたはこれらの組合せであり、前記HDAC阻害剤が、スベロイルアニリドヒドロキサム酸(SAHA/ボリノスタット/ゾリンザ)、トリコスタチンA(TSA)、PXD−101、デプシペプチド、MS−275、MGCD0103、バルプロ酸またはフェニル酪酸ナトリウムであるか、または前記BET阻害剤が、(+)−JQ1、I−BET762、OTX015、I−BET151、CPI203、PFI−1、MS436、CPI−0610、RVX2135、FT−1101、BAY1238097、INCB054329、TEN−010、GSK2820151、ZEN003694、BAY−299、BMS−986158、ABBV−075、GS−5829またはPLX51107である、請求項7に記載の方法。
- 後続の参照レベルを下回るまでリピートのレベルを低減させるために十分な時間、(i)前記細胞において、リピートRNAの排出のレベルを低減させるか、もしくはリピートRNAのレベルを増加させる処置、または(ii)腫瘍保護的免疫抑制を低減する免疫療法の1つまたは両方を含む前記処置を行うこと、および次いで、前記対象に抗腫瘍免疫を増強する免疫療法を含む処置を行うことを含み、最初および後続の参照レベルが、同一または異なり得る、請求項1に記載の方法。
- 前記抗腫瘍免疫を増強する免疫療法が、抗PD−1抗体、抗PD−L1抗体、抗CD137抗体、抗CTLA4抗体、抗CD40抗体、抗IL10抗体、抗TGF−β抗体および抗IL−6抗体からなる群から選択される免疫療法剤を含む、請求項9に記載の方法。
- 前記処置を行うことが、前記対象における腫瘍量の低減をもたらす、請求項1から10のいずれか一項に記載の方法。
- 前記がんが、上皮がんである、請求項1から11のいずれか一項に記載の方法。
- 前記上皮がんが、メラノーマ、膵臓がん、結腸直腸がん、乳がん、前立腺がん、腎臓がん、卵巣がん、肺がん、膵臓がん、肝臓がんまたは尿路上皮がんである、請求項12に記載の方法。
- 前記がんが、腫瘍タンパク質p53(TP53)における変異を含む、請求項1から13のいずれか一項に記載の方法。
- がんが、抗腫瘍免疫を増強する免疫療法を含む処置に応答するか否かを予測する方法であって、
前記がん由来の細胞を含む試料を提供すること;
前記細胞中のリピートRNAのレベルを検出すること;および
前記試料中の前記リピートRNAのレベルを参照レベルと比較すること
を含み、
前記参照レベルを下回るリピートRNAのレベルを有するがんが、抗腫瘍免疫を増強する免疫療法を含む処置に応答する可能性がある、方法。 - がんが、腫瘍保護的免疫抑制を低減する免疫療法を含む処置に応答するか否かを予測する方法であって、
前記がん由来の細胞を含む試料を提供すること;
前記細胞中のリピートRNAのレベルを検出すること;および
前記試料中の前記リピートRNAのレベルを参照レベルと比較すること
を含み、
前記参照レベルを上回るリピートRNAのレベルを有するがんが、腫瘍保護的免疫抑制を低減する免疫療法、リピートRNAを標的にする阻害性核酸、またはヌクレオシドアナログ逆転写酵素阻害剤、ヌクレオチドアナログ逆転写酵素阻害剤、非ヌクレオシド逆転写酵素阻害剤およびこれらの組合せからなる群から選択される逆転写酵素阻害剤(RTI)を含む処置に応答する可能性がある、方法。 - がん中の免疫細胞のレベルを決定する方法であって、
前記がん由来の細胞を含む試料を提供すること;
前記細胞中のHSATIIおよび/またはHERV−HリピートRNAのレベルを検出すること;および
前記試料中の前記HSATIIおよび/またはHERV−HリピートRNAのレベルを参照レベル(例えば、正常な隣接細胞または組織中のレベル)と比較すること
を含み、
前記参照レベルを上回るHSATIIリピートRNAのレベルを有するがんが、前記がん中にCD8T細胞を有し、
前記参照レベルのHSATIIリピートRNAのレベルまたは前記参照レベルを下回るHSATIIリピートRNAのレベルを有するがんが、CD163マクロファージを有し、
前記参照レベルを上回るHERV−HリピートRNAのレベルを有するがんが、FOXP3T細胞を有する、方法。 - 前記がんを、前記細胞中のHSATIIおよび/またはHERV−Hのレベルに基づいて、CD8+、CD163+またはFOXP3+として分類することをさらに含む、請求項17に記載の方法。
- 前記上皮がんが、膵管腺癌、肝内胆管癌または肝細胞癌である、請求項13に記載の方法。
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EP3749330A1 (en) | 2020-12-16 |
AU2019217875A1 (en) | 2020-08-20 |
EP4317972A2 (en) | 2024-02-07 |
EP4317972A3 (en) | 2024-03-13 |
WO2019157087A1 (en) | 2019-08-15 |
CN112533613A (zh) | 2021-03-19 |
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