Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion.
Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion.
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患者模型中的多模式合并Perturb-CITE-seq筛选定义了癌症免疫逃避的机制。
DOI：
10.1038/s41588-021-00779-1
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发表时间：
2021-03
期刊：
影响因子：
30.8
通讯作者：
Izar B
中科院分区：
文献类型：
--
作者：
Frangieh CJ;Melms JC;Thakore PI;Geiger-Schuller KR;Ho P;Luoma AM;Cleary B;Jerby-Arnon L;Malu S;Cuoco MS;Zhao M;Ager CR;Rogava M;Hovey L;Rotem A;Bernatchez C;Wucherpfennig KW;Johnson BE;Rozenblatt-Rosen O;Schadendorf D;Regev A;Izar B
对免疫检查点抑制剂（ICR）的耐药性是癌症治疗中的一个关键挑战。为了阐明潜在的机制，我们开发了Perturb-CITE-seq，使合并的CRISPR-Cas9扰动与单细胞转录组和蛋白质读出成为可能。在患者来源的黑色素瘤细胞和自体肿瘤浸润淋巴细胞（TIL）共培养物中，我们在约750次与癌细胞内在ICR相关的扰动下分析了约218，000个细胞中的转录组和20种蛋白质。我们恢复了已知的耐药机制，包括IFNγ-JAK/STAT和RNA、蛋白质和扰动空间中的抗原呈递途径的缺陷，以及新的机制，包括CD 58的丢失/下调。CD 58的缺失在多种共培养模型中赋予免疫逃避，并且在患有ICR的黑色素瘤患者的肿瘤中下调。CD 58的表达不受IFNγ的显著调节，CD 58的缺失导致免疫逃避而不影响MHC的表达，这表明其作用与ICR的已知机制正交。这项工作为通过具有多模式单细胞读数的大规模扰动筛选来破译复杂机制提供了框架，并发现了潜在的临床相关免疫逃避机制。
Resistance to immune checkpoint inhibitors (ICR) is a key challenge in cancer therapy. To elucidate underlying mechanisms, we developed Perturb-CITE-seq, enabling pooled CRISPR-Cas9 perturbations with single-cell transcriptome and protein read-outs. In patient-derived melanoma cells and autologous tumor infiltrating lymphocyte (TIL) co-cultures, we profiled transcriptomes and 20 proteins in ~218,000 cells under ~750 perturbations associated with cancer cell-intrinsic ICR. We recover known mechanisms of resistance, including defects in the IFNγ-JAK/STAT and antigen-presentation pathways in RNA, protein and perturbation space, and novel ones, including loss/downregulation of CD58. Loss of CD58 conferred immune evasion in multiple co-culture models and was downregulated in tumors of melanoma patients with ICR. CD58 expression was not significantly regulated by IFNγ and CD58 loss conferred immune evasion without compromising MHC expression, suggesting that it acts orthogonal to known mechanisms of ICR. This work provides framework for deciphering complex mechanisms by large-scale perturbation screens with multi-modal single-cell readouts, and discovers potentially clinically relevant mechanisms of immune evasion.
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影响因子：
64.5
作者：
Jaitin, Diego Adhemar;Weiner, Assaf;Amit, Ido
通讯作者：
Amit, Ido
影响因子：
64.8
作者：
Manguso RT;Pope HW;Zimmer MD;Brown FD;Yates KB;Miller BC;Collins NB;Bi K;LaFleur MW;Juneja VR;Weiss SA;Lo J;Fisher DE;Miao D;Van Allen E;Root DE;Sharpe AH;Doench JG;Haining WN
通讯作者：
Haining WN
影响因子：
28.2
作者：
Peng W;Chen JQ;Liu C;Malu S;Creasy C;Tetzlaff MT;Xu C;McKenzie JA;Zhang C;Liang X;Williams LJ;Deng W;Chen G;Mbofung R;Lazar AJ;Torres-Cabala CA;Cooper ZA;Chen PL;Tieu TN;Spranger S;Yu X;Bernatchez C;Forget MA;Haymaker C;Amaria R;McQuade JL;Glitza IC;Cascone T;Li HS;Kwong LN;Heffernan TP;Hu J;Bassett RL Jr;Bosenberg MW;Woodman SE;Overwijk WW;Lizée G;Roszik J;Gajewski TF;Wargo JA;Gershenwald JE;Radvanyi L;Davies MA;Hwu P
通讯作者：
Hwu P
DOI：
10.1038/nrc3239
发表时间：
2012-03-22
期刊：
Nature reviews. Cancer
影响因子：
--
作者：
Pardoll DM
通讯作者：
Pardoll DM
DOI：
10.1038/nri3191
发表时间：
2012-03-22
期刊：
Nature reviews. Immunology
影响因子：
--
作者：
Restifo NP;Dudley ME;Rosenberg SA
通讯作者：
Rosenberg SA