Discovering dominant tumor immune archetypes in a pan-cancer census

被引：89

作者：

Combes, Alexis J. ^{[1
,2
,3
,4
]}

Samad, Bushra ^{[1
,2
,3
,4
]}

Tsui, Jessica ^{[1
,2
,3
,4
]}

Chew, Nayvin W. ^{[1
,2
,3
,4
]}

Yan, Peter ^{[1
,2
,3
,4
]}

Reeder, Gabriella C. ^{[1
,2
,3
,4
]}

Kushnoor, Divyashree ^{[1
,2
,3
,4
]}

Shen, Alan ^{[1
,2
,3
,4
]}

Davidson, Brittany ^{[2
,3
,4
]}

Barczak, Andrea J. ^{[3
,4
]}

Adkisson, Michael ^{[3
,4
]}

Edwards, Austin ^{[1
,2
,3
,4
]}

Naser, Mohammad ^{[1
,2
,3
,4
]}

Barry, Kevin C. ^{[5
]}

Courau, Tristan ^{[1
,2
,3
,4
]}

Hammoudi, Taymour ^{[1
,2
,3
,4
]}

Arguello, Rafael J. ^{[6
]}

Rao, Arjun Arkal ^{[1
,2
,3
,4
]}

Olshen, Adam B. ^{[3
,7
,8
]}

Cai, Cathy ^{[1
,2
,3
,4
]}

Zhan, Jenny ^{[1
,2
,3
,4
]}

Davis, Katelyn C. ^{[1
,2
,3
,4
]}

Kelley, Robin K. ^{[7
]}

Chapman, Jocelyn S. ^{[3
,9
,10
,11
]}

Atreya, Chloe E. ^{[3
,7
,12
]}

Patel, Amar ^{[3
,12
]}

Daud, Adil, I ^{[12
,13
]}

Ha, Patrick ^{[14
]}

Diaz, Aaron A. ^{[15
]}

Kratz, Johannes R. ^{[2
,16
]}

Collisson, Eric A. ^{[3
,7
,12
]}

Fragiadakis, Gabriela K. ^{[2
,3
,4
,17
]}

Erle, David J. ^{[2
,3
,4
,18
,19
]}

Boissonnas, Alexandre ^{[20
]}

Asthana, Saurabh ^{[3
,8
]}

Chan, Vincent ^{[2
,3
,21
]}

Krummel, Matthew F. ^{[1
,2
,3
]}

机构：

[1] Univ Calif San Francisco, Dept Pathol, San Francisco, CA 94143 USA

[2] Univ Calif San Francisco, ImmunoX Initiat, San Francisco, CA 94143 USA

[3] Univ Calif San Francisco, UCSF Immunoprofiler Initiat, San Francisco, CA 94143 USA

[4] Univ Calif San Francisco, UCSF CoLabs, San Francisco, CA 94143 USA

[5] Fred Hutchinson Canc Res Ctr, Publ Hlth Sci Div, Translat Res Program, 1124 Columbia St, Seattle, WA 98104 USA

[6] Aix Marseille Univ, Ctr Immunol Marseille Luminy, CIML, CNRS,INSERM, Marseille, France

[7] Univ Calif San Francisco, Helen Diller Family Comprehens Canc Ctr, San Francisco, CA 94143 USA

[8] Univ Calif San Francisco, Dept Epidemiol & Biostat, San Francisco, CA 94143 USA

[9] Univ Calif San Francisco, Dept Obstet, San Francisco, CA 94143 USA

[10] Univ Calif San Francisco, Dept Gynecol, San Francisco, CA 94143 USA

[11] Univ Calif San Francisco, Dept Reprod Sci, Med, San Francisco, CA 94143 USA

[12] Univ Calif San Francisco, Div Hematol & Oncol, Dept Med, San Francisco, CA 94143 USA

[13] Univ Calif San Francisco, Dept Dermatol, San Francisco, CA 94143 USA

[14] Univ Calif San Francisco, Dept Otolaryngol, San Francisco, CA 94143 USA

[15] Univ Calif San Francisco, Dept Neurol Surg, San Francisco, CA 94143 USA

[16] Univ Calif San Francisco, Dept Surg, San Francisco, CA 94143 USA

[17] Univ Calif San Francisco, Div Rheumatol, Dept Med, San Francisco, CA 94143 USA

[18] Univ Calif San Francisco, Dept Med, Lung Biol Ctr, San Francisco, CA 94143 USA

[19] Univ Calif San Francisco, Cardiovasc Res Inst, San Francisco, CA 94143 USA

[20] Sorbonne Univ, INSERM, CNRS, Ctr Immunol & Malad Infect CIMI, Paris, France

[21] Univ Calif San Francisco, Dept Microbiol & Immunol, San Francisco, CA 94143 USA

来源：

CELL | 2022年 / 185卷 / 01期

关键词：

T-CELL SUBSETS; SINGLE-CELL; GENE-EXPRESSION; LANDSCAPE; REVEALS; MICROENVIRONMENT; IMMUNOTHERAPY; FEATURES; THERAPY; MACROPHAGES;

D O I：

10.1016/j.cell.2021.12.004

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Cancers display significant heterogeneity with respect to tissue of origin, driver mutations, and other features of the surrounding tissue. It is likely that individual tumors engage common patterns of the immune system-here "archetypes"-creating prototypical non-destructive tumor immune microenvironments (TMEs) and modulating tumor-targeting. To discover the dominant immune system archetypes, the University of California, San Francisco (UCSF) Immunoprofiler Initiative (IPI) processed 364 individual tumors across 12 cancer types using standardized protocols. Computational clustering of flow cytometry and transcriptomic data obtained from cell sub-compartments uncovered dominant patterns of immune composition across cancers. These archetypes were profound insofar as they also differentiated tumors based upon unique immune and tumor gene expression patterns. They also partitioned well-established classifications of tumor biology. The IPI resource provides a template for understanding cancer immunity as a collection of dominant patterns of immune organization and provides a rational path forward to learn how to modulate these to improve therapy.

引用

页码：184 / +

页数：40

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