51. Discovering dominant tumor immune archetypes in a pan-cancer census
- Author
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Combes, Alexis J, Samad, Bushra, Tsui, Jessica, Chew, Nayvin W, Yan, Peter, Reeder, Gabriella C, Kushnoor, Divyashree, Shen, Alan, Davidson, Brittany, Barczak, Andrea J, Adkisson, Michael, Edwards, Austin, Naser, Mohammad, Barry, Kevin C, Courau, Tristan, Hammoudi, Taymour, Argüello, Rafael J, Rao, Arjun Arkal, Olshen, Adam B, Consortium, The Immunoprofiler, Spitzer, Matthew, Fong, Lawrence, Nelson, Amanda, Kumar, Raj, Lee, Justin, Burra, Arun, Hsu, Joy, Hackett, Caroline, Tolentino, Karen, Sjarif, Jasmine, Johnson, Peter, Shao, Evans, Abrau, Darrell, Lupin, Leonard, Shaw, Cole, Collins, Zachary, Lea, Tasha, Corvera, Carlos, Nakakura, Eric, Carnevale, Julia, Alvarado, Michael, Loo, Kimberley, Chen, Lawrence, Chow, Melissa, Grandis, Jennifer, Ryan, Will, El-Sayed, Ivan, Jablons, David, Woodard, Gavitt, Meng, Maxwell W, Porten, Sima P, Okada, Hideho, Tempero, Margaret, Ko, Andrew, Kirkwood, Kim, Vandenberg, Scott, Guevarra, Denise, Oropeza, Erica, Cyr, Chris, Glenn, Pat, Bolen, Jennifer, Morton, Amanda, Eckalbar, Walter, Cai, Cathy, Zhan, Jenny, Davis, Katelyn C, Kelley, Robin K, Chapman, Jocelyn S, Atreya, Chloe E, Patel, Amar, Daud, Adil I, Ha, Patrick, Diaz, Aaron A, Kratz, Johannes R, Collisson, Eric A, Fragiadakis, Gabriela K, Erle, David J, Boissonnas, Alexandre, Asthana, Saurabh, Chan, Vincent, and Krummel, Matthew F
- Subjects
Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Immunology ,Genetics ,Cancer ,Cancer Genomics ,Human Genome ,Biomarkers ,Tumor ,Censuses ,Cluster Analysis ,Cohort Studies ,Computational Biology ,Flow Cytometry ,Gene Expression Regulation ,Neoplastic ,Humans ,Neoplasms ,RNA-Seq ,San Francisco ,Transcriptome ,Tumor Microenvironment ,Universities ,Immunoprofiler Consortium ,Pan Cancer analysis ,immune profiling ,solid tumor microenvironement ,system immunology ,tumor immunology ,unsupervised clustering ,Biological Sciences ,Medical and Health Sciences ,Developmental Biology ,Biological sciences ,Biomedical and clinical sciences - Abstract
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.
- Published
- 2022