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


Journal

Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462

Informations de publication

Date de publication:
10 2020
Historique:
received: 09 09 2019
accepted: 30 06 2020
pubmed: 25 9 2020
medline: 12 1 2021
entrez: 24 9 2020
Statut: ppublish

Résumé

The genetic circuits that allow cancer cells to evade destruction by the host immune system remain poorly understood

Identifiants

pubmed: 32968282
doi: 10.1038/s41586-020-2746-2
pii: 10.1038/s41586-020-2746-2
pmc: PMC9014559
mid: NIHMS1791173
doi:

Substances chimiques

NF-kappa B 0
Interferon-gamma 82115-62-6

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

120-126

Subventions

Organisme : NCI NIH HHS
ID : P30 CA016672
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM130119
Pays : United States

Commentaires et corrections

Type : CommentIn

Références

Chen, D. S. & Mellman, I. Elements of cancer immunity and the cancer-immune set point. Nature 541, 321–330 (2017).
doi: 10.1038/nature21349 pubmed: 28102259
Hegde, P. S. & Chen, D. S. Top 10 challenges in cancer immunotherapy. Immunity 52, 17–35 (2020).
pubmed: 31940268 doi: 10.1016/j.immuni.2019.12.011
Binnewies, M. et al. Understanding the tumor immune environment (TIME) for effective therapy. Nat. Med. 24, 541–550 (2018).
pubmed: 29686425 pmcid: 5998822 doi: 10.1038/s41591-018-0014-x
Hugo, W. et al. Genomic and transcriptomic features of response to anti-pd-1 therapy in metastatic melanoma. Cell 165, 35–44 (2016).
pubmed: 26997480 pmcid: 4808437 doi: 10.1016/j.cell.2016.02.065
Rooney, M. S., Shukla, S. A., Wu, C. J., Getz, G. & Hacohen, N. Molecular and genetic properties of tumors associated with local immune cytolytic activity. Cell 160, 48–61 (2015).
pubmed: 25594174 pmcid: 4856474 doi: 10.1016/j.cell.2014.12.033
Zaretsky, J. M. et al. Mutations associated with acquired resistance to PD-1 blockade in melanoma. N. Engl. J. Med. 375, 819–829 (2016).
pubmed: 27433843 pmcid: 5007206 doi: 10.1056/NEJMoa1604958
Kearney, C. J. et al. Tumor immune evasion arises through loss of TNF sensitivity. Sci. Immunol. 3, eaar3451 (2018).
pubmed: 29776993 doi: 10.1126/sciimmunol.aar3451
Manguso, R. T. et al. In vivo CRISPR screening identifies Ptpn2 as a cancer immunotherapy target. Nature 547, 413–418 (2017).
pubmed: 28723893 pmcid: 5924693 doi: 10.1038/nature23270
Pan, D. et al. A major chromatin regulator determines resistance of tumor cells to T cell-mediated killing. Science 359, 770–775 (2018).
pubmed: 29301958 pmcid: 5953516 doi: 10.1126/science.aao1710
Patel, S. J. et al. Identification of essential genes for cancer immunotherapy. Nature 548, 537–542 (2017).
pubmed: 28783722 pmcid: 5870757 doi: 10.1038/nature23477
Vredevoogd, D. W. et al. Augmenting immunotherapy impact by lowering tumor TNF cytotoxicity threshold. Cell 178, 585–599 (2019).
pubmed: 31303383 doi: 10.1016/j.cell.2019.06.014
Hart, T. et al. Evaluation and design of genome-wide CRISPR/SpCas9 knockout screens. G3 7, 2719–2727 (2017).
pubmed: 28655737 doi: 10.1534/g3.117.041277 pmcid: 5555476
Hart, T., Brown, K. R., Sircoulomb, F., Rottapel, R. & Moffat, J. Measuring error rates in genomic perturbation screens: gold standards for human functional genomics. Mol. Syst. Biol. 10, 733 (2014).
pubmed: 24987113 pmcid: 4299491 doi: 10.15252/msb.20145216
Hart, T. et al. High-resolution CRISPR screens reveal fitness genes and genotype-specific cancer liabilities. Cell 163, 1515–1526 (2015).
pubmed: 26627737 doi: 10.1016/j.cell.2015.11.015
Hart, T. & Moffat, J. BAGEL: a computational framework for identifying essential genes from pooled library screens. BMC Bioinformatics 17, 164 (2016).
pubmed: 27083490 pmcid: 4833918 doi: 10.1186/s12859-016-1015-8
Li, B. et al. A comprehensive mouse transcriptomic BodyMap across 17 tissues by RNA-seq. Sci. Rep. 7, 4200 (2017).
pubmed: 28646208 pmcid: 5482823 doi: 10.1038/s41598-017-04520-z
Söllner, J. F. et al. An RNA-seq atlas of gene expression in mouse and rat normal tissues. Sci. Data 4, 170185 (2017).
pubmed: 29231921 pmcid: 5726313 doi: 10.1038/sdata.2017.185
Zimmermann, M. et al. CRISPR screens identify genomic ribonucleotides as a source of PARP-trapping lesions. Nature 559, 285–289 (2018).
pubmed: 29973717 pmcid: 6071917 doi: 10.1038/s41586-018-0291-z
Costanzo, M. et al. A global genetic interaction network maps a wiring diagram of cellular function. Science 353, aaf1420 (2016).
pubmed: 27708008 pmcid: 5661885 doi: 10.1126/science.aaf1420
Weichhart, T. & Säemann, M. D. The multiple facets of mTOR in immunity. Trends Immunol. 30, 218–226 (2009).
pubmed: 19362054 doi: 10.1016/j.it.2009.02.002
Gerlinger, M. et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N. Engl. J. Med. 366, 883–892 (2012).
pubmed: 22397650 pmcid: 4878653 doi: 10.1056/NEJMoa1113205
Thorsson, V. et al. The immune landscape of cancer. Immunity 48, 812–830.e14 (2018).
pubmed: 29628290 pmcid: 5982584 doi: 10.1016/j.immuni.2018.03.023
Smith, C. C. et al. Endogenous retroviral signatures predict immunotherapy response in clear cell renal cell carcinoma. J. Clin. Invest. 128, 4804–4820 (2018).
pubmed: 30137025 pmcid: 6205406 doi: 10.1172/JCI121476
Liddicoat, B. J. et al. RNA editing by ADAR1 prevents MDA5 sensing of endogenous dsRNA as nonself. Science 349, 1115–1120 (2015).
pubmed: 26275108 pmcid: 5444807 doi: 10.1126/science.aac7049
Starr, R. et al. A family of cytokine-inducible inhibitors of signalling. Nature 387, 917–921 (1997).
pubmed: 9202125 doi: 10.1038/43206
Ishizuka, J. J. et al. Loss of ADAR1 in tumours overcomes resistance to immune checkpoint blockade. Nature 565, 43–48 (2019).
pubmed: 30559380 doi: 10.1038/s41586-018-0768-9
Miranda, D. A. et al. Fat storage-inducing transmembrane protein 2 is required for normal fat storage in adipose tissue. J. Biol. Chem. 289, 9560–9572 (2014).
pubmed: 24519944 pmcid: 3975007 doi: 10.1074/jbc.M114.547687
Becuwe, M. et al. FIT2 is a lipid phosphate phosphatase crucial for endoplasmic reticulum homeostasis. Preprint at bioRxiv https://doi.org/10.1101/291765 (2018).
Robke, L. et al. Phenotypic identification of a novel autophagy inhibitor chemotype targeting lipid kinase VPS34. Angew. Chem. Int. Edn Engl. 56, 8153–8157 (2017).
doi: 10.1002/anie.201703738
Tan, J. M. J., Mellouk, N. & Brumell, J. H. An autophagy-independent role for ATG16L1: promoting lysosome-mediated plasma membrane repair. Autophagy 15, 932–933 (2019).
pubmed: 30806149 pmcid: 6526803 doi: 10.1080/15548627.2019.1586261
Diebold, S. S., Cotten, M., Koch, N. & Zenke, M. MHC class II presentation of endogenously expressed antigens by transfected dendritic cells. Gene Ther. 8, 487–493 (2001).
pubmed: 11313828 doi: 10.1038/sj.gt.3301433
Mair, B. et al. Essential gene profiles for human pluripotent stem cells identify uncharacterized genes and substrate dependencies. Cell Rep. 27, 599–615 (2019).
pubmed: 30970261 doi: 10.1016/j.celrep.2019.02.041
Colic, M. et al. Identifying chemogenetic interactions from CRISPR screens with drugZ. Genome Med. 11, 52 (2019).
pubmed: 31439014 pmcid: 6706933 doi: 10.1186/s13073-019-0665-3
Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545–15550 (2005).
pubmed: 16199517 doi: 10.1073/pnas.0506580102 pmcid: 1239896
Michailidou, K. et al. Association analysis identifies 65 new breast cancer risk loci. Nature 551, 92–94 (2017).
pubmed: 29059683 pmcid: 5798588 doi: 10.1038/nature24284
Lee, I., Date, S. V., Adai, A. T. & Marcotte, E. M. A probabilistic functional network of yeast genes. Science 306, 1555–1558 (2004).
pubmed: 15567862 doi: 10.1126/science.1099511
Kanehisa, M., Furumichi, M., Tanabe, M., Sato, Y. & Morishima, K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 45, D353–D361 (2017).
pubmed: 27899662 doi: 10.1093/nar/gkw1092
Giurgiu, M. et al. CORUM: the comprehensive resource of mammalian protein complexes-2019. Nucleic Acids Res. 47, D559–D563 (2019).
pubmed: 30357367 doi: 10.1093/nar/gky973
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
doi: 10.1093/bioinformatics/bts635 pubmed: 23104886
Seki, A. & Rutz, S. Optimized RNP transfection for highly efficient CRISPR/Cas9-mediated gene knockout in primary T cells. J. Exp. Med. 215, 985–997 (2018).
pubmed: 29436394 pmcid: 5839763 doi: 10.1084/jem.20171626
Yoshihara, K. et al. Inferring tumour purity and stromal and immune cell admixture from expression data. Nat. Commun. 4, 2612 (2013).
pubmed: 24113773 doi: 10.1038/ncomms3612
Langfelder, P., Zhang, B. & Horvath, S. Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. Bioinformatics 24, 719–720 (2008).
pubmed: 18024473 doi: 10.1093/bioinformatics/btm563

Auteurs

Keith A Lawson (KA)

Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.
Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
Division of Urology, Department of Surgery, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.

Cristovão M Sousa (CM)

Agios Pharmaceuticals, Cambridge, MA, USA.

Xiaoyu Zhang (X)

Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.
Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.

Eiru Kim (E)

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Rummy Akthar (R)

Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.
Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.

Joseph J Caumanns (JJ)

Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.

Yuxi Yao (Y)

Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.
Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.

Nicholas Mikolajewicz (N)

Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.

Catherine Ross (C)

Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.

Kevin R Brown (KR)

Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.

Abdelrahman Abou Zid (AA)

Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.
Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.

Zi Peng Fan (ZP)

Agios Pharmaceuticals, Cambridge, MA, USA.

Shirley Hui (S)

Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.

Jordan A Krall (JA)

Agios Pharmaceuticals, Cambridge, MA, USA.

Donald M Simons (DM)

Agios Pharmaceuticals, Cambridge, MA, USA.

Chloe J Slater (CJ)

Agios Pharmaceuticals, Cambridge, MA, USA.

Victor De Jesus (V)

Agios Pharmaceuticals, Cambridge, MA, USA.

Lujia Tang (L)

Agios Pharmaceuticals, Cambridge, MA, USA.

Richa Singh (R)

Agios Pharmaceuticals, Cambridge, MA, USA.

Joshua E Goldford (JE)

Agios Pharmaceuticals, Cambridge, MA, USA.

Sarah Martin (S)

Agios Pharmaceuticals, Cambridge, MA, USA.

Qian Huang (Q)

Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.

Elizabeth A Francis (EA)

Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.

Andrea Habsid (A)

Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.

Ryan Climie (R)

Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.

David Tieu (D)

Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.

Jiarun Wei (J)

Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.

Ren Li (R)

Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.

Amy Hin Yan Tong (AHY)

Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.

Michael Aregger (M)

Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.

Katherine S Chan (KS)

Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.

Hong Han (H)

Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.

Xiaowei Wang (X)

Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.

Patricia Mero (P)

Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.

John H Brumell (JH)

Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.

Antonio Finelli (A)

Division of Urology, Department of Surgery, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.

Laurie Ailles (L)

Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
Ontario Institute for Cancer Research, Toronto, Ontario, Canada.

Gary Bader (G)

Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.
Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.

Gromoslaw A Smolen (GA)

Agios Pharmaceuticals, Cambridge, MA, USA.
Celsius Therapeutics, Cambridge, MA, USA.

Gillian A Kingsbury (GA)

Agios Pharmaceuticals, Cambridge, MA, USA.

Traver Hart (T)

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Charles Kung (C)

Agios Pharmaceuticals, Cambridge, MA, USA.

Jason Moffat (J)

Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. j.moffat@utoronto.ca.
Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. j.moffat@utoronto.ca.
Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada. j.moffat@utoronto.ca.

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