Literature DB >> 36151395

In vivo CRISPR screens reveal the landscape of immune evasion pathways across cancer.

Juan Dubrot1,2,3,4, Peter P Du1,5, Sarah Kate Lane-Reticker1, Emily A Kessler1, Audrey J Muscato1, Arnav Mehta1,2,3, Samuel S Freeman1,2,3, Peter M Allen1, Kira E Olander1, Kyle M Ockerman1, Clara H Wolfe1, Fabius Wiesmann1, Nelson H Knudsen1,2,3, Hsiao-Wei Tsao1, Arvin Iracheta-Vellve1, Emily M Schneider1, Andrea N Rivera-Rosario1, Ian C Kohnle1, Hans W Pope1, Austin Ayer1, Gargi Mishra1, Margaret D Zimmer1, Sarah Y Kim1, Animesh Mahapatra1, Hakimeh Ebrahimi-Nik1, Dennie T Frederick2,3,6, Genevieve M Boland2,3,6, W Nicholas Haining1,7,8, David E Root1, John G Doench1, Nir Hacohen1,2,3, Kathleen B Yates9,10,11, Robert T Manguso12,13,14.   

Abstract

The immune system can eliminate tumors, but checkpoints enable immune escape. Here, we identify immune evasion mechanisms using genome-scale in vivo CRISPR screens across cancer models treated with immune checkpoint blockade (ICB). We identify immune evasion genes and important immune inhibitory checkpoints conserved across cancers, including the non-classical major histocompatibility complex class I (MHC class I) molecule Qa-1b/HLA-E. Surprisingly, loss of tumor interferon-γ (IFNγ) signaling sensitizes many models to immunity. The immune inhibitory effects of tumor IFN sensing are mediated through two mechanisms. First, tumor upregulation of classical MHC class I inhibits natural killer cells. Second, IFN-induced expression of Qa-1b inhibits CD8+ T cells via the NKG2A/CD94 receptor, which is induced by ICB. Finally, we show that strong IFN signatures are associated with poor response to ICB in individuals with renal cell carcinoma or melanoma. This study reveals that IFN-mediated upregulation of classical and non-classical MHC class I inhibitory checkpoints can facilitate immune escape.
© 2022. Springer Nature America, Inc.

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Year:  2022        PMID: 36151395     DOI: 10.1038/s41590-022-01315-x

Source DB:  PubMed          Journal:  Nat Immunol        ISSN: 1529-2908            Impact factor:   31.250


  67 in total

1.  Nivolumab in previously untreated melanoma without BRAF mutation.

Authors:  Caroline Robert; Georgina V Long; Benjamin Brady; Caroline Dutriaux; Michele Maio; Laurent Mortier; Jessica C Hassel; Piotr Rutkowski; Catriona McNeil; Ewa Kalinka-Warzocha; Kerry J Savage; Micaela M Hernberg; Celeste Lebbé; Julie Charles; Catalin Mihalcioiu; Vanna Chiarion-Sileni; Cornelia Mauch; Francesco Cognetti; Ana Arance; Henrik Schmidt; Dirk Schadendorf; Helen Gogas; Lotta Lundgren-Eriksson; Christine Horak; Brian Sharkey; Ian M Waxman; Victoria Atkinson; Paolo A Ascierto
Journal:  N Engl J Med       Date:  2014-11-16       Impact factor: 91.245

2.  A major chromatin regulator determines resistance of tumor cells to T cell-mediated killing.

Authors:  Deng Pan; Aya Kobayashi; Peng Jiang; Lucas Ferrari de Andrade; Rong En Tay; Adrienne M Luoma; Daphne Tsoucas; Xintao Qiu; Klothilda Lim; Prakash Rao; Henry W Long; Guo-Cheng Yuan; John Doench; Myles Brown; X Shirley Liu; Kai W Wucherpfennig
Journal:  Science       Date:  2018-01-04       Impact factor: 47.728

3.  Identification of essential genes for cancer immunotherapy.

Authors:  Shashank J Patel; Neville E Sanjana; Rigel J Kishton; Arash Eidizadeh; Suman K Vodnala; Maggie Cam; Jared J Gartner; Li Jia; Seth M Steinberg; Tori N Yamamoto; Anand S Merchant; Gautam U Mehta; Anna Chichura; Ophir Shalem; Eric Tran; Robert Eil; Madhusudhanan Sukumar; Eva Perez Guijarro; Chi-Ping Day; Paul Robbins; Steve Feldman; Glenn Merlino; Feng Zhang; Nicholas P Restifo
Journal:  Nature       Date:  2017-08-07       Impact factor: 49.962

4.  In vivo screens using a selective CRISPR antigen removal lentiviral vector system reveal immune dependencies in renal cell carcinoma.

Authors:  Juan Dubrot; Sarah Kate Lane-Reticker; Emily A Kessler; Austin Ayer; Gargi Mishra; Clara H Wolfe; Margaret D Zimmer; Peter P Du; Animesh Mahapatra; Kyle M Ockerman; Thomas G R Davis; Ian C Kohnle; Hans W Pope; Peter M Allen; Kira E Olander; Arvin Iracheta-Vellve; John G Doench; W Nicholas Haining; Kathleen B Yates; Robert T Manguso
Journal:  Immunity       Date:  2021-01-25       Impact factor: 31.745

5.  Pembrolizumab versus Chemotherapy for PD-L1-Positive Non-Small-Cell Lung Cancer.

Authors:  Martin Reck; Delvys Rodríguez-Abreu; Andrew G Robinson; Rina Hui; Tibor Csőszi; Andrea Fülöp; Maya Gottfried; Nir Peled; Ali Tafreshi; Sinead Cuffe; Mary O'Brien; Suman Rao; Katsuyuki Hotta; Melanie A Leiby; Gregory M Lubiniecki; Yue Shentu; Reshma Rangwala; Julie R Brahmer
Journal:  N Engl J Med       Date:  2016-10-08       Impact factor: 91.245

6.  In vivo CRISPR screening identifies Ptpn2 as a cancer immunotherapy target.

Authors:  Robert T Manguso; Hans W Pope; Margaret D Zimmer; Flavian D Brown; Kathleen B Yates; Brian C Miller; Natalie B Collins; Kevin Bi; Martin W LaFleur; Vikram R Juneja; Sarah A Weiss; Jennifer Lo; David E Fisher; Diana Miao; Eliezer Van Allen; David E Root; Arlene H Sharpe; John G Doench; W Nicholas Haining
Journal:  Nature       Date:  2017-07-19       Impact factor: 49.962

7.  Nivolumab versus Everolimus in Advanced Renal-Cell Carcinoma.

Authors:  Robert J Motzer; Bernard Escudier; David F McDermott; Saby George; Hans J Hammers; Sandhya Srinivas; Scott S Tykodi; Jeffrey A Sosman; Giuseppe Procopio; Elizabeth R Plimack; Daniel Castellano; Toni K Choueiri; Howard Gurney; Frede Donskov; Petri Bono; John Wagstaff; Thomas C Gauler; Takeshi Ueda; Yoshihiko Tomita; Fabio A Schutz; Christian Kollmannsberger; James Larkin; Alain Ravaud; Jason S Simon; Li-An Xu; Ian M Waxman; Padmanee Sharma
Journal:  N Engl J Med       Date:  2015-09-25       Impact factor: 91.245

8.  Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion.

Authors:  Chris J Frangieh; Johannes C Melms; Pratiksha I Thakore; Kathryn R Geiger-Schuller; Patricia Ho; Adrienne M Luoma; Brian Cleary; Livnat Jerby-Arnon; Shruti Malu; Michael S Cuoco; Maryann Zhao; Casey R Ager; Meri Rogava; Lila Hovey; Asaf Rotem; Chantale Bernatchez; Kai W Wucherpfennig; Bruce E Johnson; Orit Rozenblatt-Rosen; Dirk Schadendorf; Aviv Regev; Benjamin Izar
Journal:  Nat Genet       Date:  2021-03-01       Impact factor: 38.330

9.  In vivo CRISPR screens identify the E3 ligase Cop1 as a modulator of macrophage infiltration and cancer immunotherapy target.

Authors:  Xiaoqing Wang; Collin Tokheim; Shengqing Stan Gu; Binbin Wang; Qin Tang; Yihao Li; Nicole Traugh; Zexian Zeng; Yi Zhang; Ziyi Li; Boning Zhang; Jingxin Fu; Tengfei Xiao; Wei Li; Clifford A Meyer; Jun Chu; Peng Jiang; Paloma Cejas; Klothilda Lim; Henry Long; Myles Brown; X Shirley Liu
Journal:  Cell       Date:  2021-09-27       Impact factor: 66.850

10.  Functional genomic landscape of cancer-intrinsic evasion of killing by T cells.

Authors:  Keith A Lawson; Cristovão M Sousa; Xiaoyu Zhang; Eiru Kim; Rummy Akthar; Joseph J Caumanns; Yuxi Yao; Nicholas Mikolajewicz; Catherine Ross; Kevin R Brown; Abdelrahman Abou Zid; Zi Peng Fan; Shirley Hui; Jordan A Krall; Donald M Simons; Chloe J Slater; Victor De Jesus; Lujia Tang; Richa Singh; Joshua E Goldford; Sarah Martin; Qian Huang; Elizabeth A Francis; Andrea Habsid; Ryan Climie; David Tieu; Jiarun Wei; Ren Li; Amy Hin Yan Tong; Michael Aregger; Katherine S Chan; Hong Han; Xiaowei Wang; Patricia Mero; John H Brumell; Antonio Finelli; Laurie Ailles; Gary Bader; Gromoslaw A Smolen; Gillian A Kingsbury; Traver Hart; Charles Kung; Jason Moffat
Journal:  Nature       Date:  2020-09-23       Impact factor: 69.504

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