Pan-cancer proteogenomics characterization of tumor immunity

Petralia, Francesca; Ma, Weiping; Yaron, Tomer M.; Caruso, Francesca Pia; Tignor, Nicole; Wang, Joshua M.; Charytonowicz, Daniel; Johnson, Jared L.; Huntsman, Emily M.; Marino, Giacomo B.; Calinawan, Anna; Evangelista, John Erol; Selvan, Myvizhi Esai; Chowdhury, Shrabanti; Rykunov, Dmitry; Krek, Azra; Song, Xiaoyu; Turhan, Berk; Christianson, Karen E.; Lewis, David A.; Deng, Eden Z.; Clarke, Daniel J.B.; Whiteaker, Jeffrey R.; Kennedy, Jacob J.; Zhao, Lei; Segura, Rossana Lazcano; Batra, Harsh; Raso, Maria Gabriela; Parra, Edwin Roger; Soundararajan, Rama; Tang, Ximing; Li, Yize; Yi, Xinpei; Satpathy, Shankha; Wang, Ying; Wiznerowicz, Maciej; González-Robles, Tania J.; Iavarone, Antonio; Gosline, Sara J.C.; Reva, Boris; Robles, Ana I.; Nesvizhskii, Alexey I.; Mani, D. R.; Gillette, Michael A.; Klein, Robert J.; Cieslik, Marcin; Zhang, Bing; Paulovich, Amanda G.; Sebra, Robert; Gümüş, Zeynep H.; Hostetter, Galen; Fenyö, David; Omenn, Gilbert S.; Cantley, Lewis C.; Ma'ayan, Avi; Lazar, Alexander J.; Ceccarelli, Michele; Wang, Pei; Abelin, Jennifer; Aguet, François; Akiyama, Yo; An, Eunkyung; Anand, Shankara; Anurag, Meenakshi; Babur, Özgün; Bavarva, Jasmin; Birger, Chet; Birrer, Michael J.; Cao, Song; Carr, Steven A.; Chan, Daniel W.; Chinnaiyan, Arul M.; Cho, Hanbyul; Clauser, Karl; Colaprico, Antonio; Zhou, Daniel Cui; da Veiga Leprevost, Felipe; Day, Corbin; Dhanasekaran, Saravana M.; Ding, Li; Domagalski, Marcin J.; Dou, Yongchao; Druker, Brian J.; Edwards, Nathan; Ellis, Matthew J.; Foltz, Steven M.; Francis, Alicia; Geffen, Yifat; Getz, Gad; Heiman, David I.; Hong, Runyu; Hu, Yingwei; Huang, Chen; Jaehnig, Eric J.; Jewell, Scott D.; Ji, Jiayi; Jiang, Wen; Katsnelson, Lizabeth; Ketchum, Karen A.; Kolodziejczak, Iga; Krug, Karsten; Kumar-Sinha, Chandan; Lei, Jonathan T.; Liang, Wen-Wei; Liao, Yuxing; Lindgren, Caleb M.; Liu, Tao; Liu, Wenke; McDermott, Jason; McKerrow, Wilson; Mesri, Mehdi; Mumphrey, Michael Brodie; Newton, Chelsea J.; Oldroyd, Robert; Payne, Samuel H.; Pugliese, Pietro; Rodland, Karin D.; Rodrigues, Fernanda Martins; Ruggles, Kelly V.; Savage, Sara R.; Schadt, Eric E.; Schnaubelt, Michael; Schraink, Tobias; Schürer, Stephan; Shi, Zhiao; Smith, Richard D.; Song, Feng; Song, Yizhe; Stathias, Vasileios; Storrs, Erik P.; Tan, Jimin; Terekhanova, Nadezhda V.; Thangudu, Ratna R.; Thiagarajan, Mathangi; Wang, Liang-Bo; Wen, Bo; Wu, Yige; Wyczalkowski, Matthew A.; Yao, Lijun; Li, Qing Kay; Zhang, Hui; Zhang, Qing; Zhang, Xu; Zhang, Zhen

doi:10.1016/j.cell.2024.01.027

Pan-cancer proteogenomics characterization of tumor immunity

Journal Article · Wed Feb 14 00:00:00 EST 2024 · Cell

DOI:https://doi.org/10.1016/j.cell.2024.01.027· OSTI ID:2406480

; Ma, Weiping; Yaron, Tomer M.; Caruso, Francesca Pia; Tignor, Nicole; Wang, Joshua M.; Charytonowicz, Daniel; Johnson, Jared L.; Huntsman, Emily M.; Marino, Giacomo B.; Calinawan, Anna; Evangelista, John Erol; Selvan, Myvizhi Esai; Chowdhury, Shrabanti; Rykunov, Dmitry; Krek, Azra; Song, Xiaoyu; Turhan, Berk; Christianson, Karen E.; Lewis, David A. more »

Despite the successes of immunotherapy in cancer treatment over recent decades, less than <10%–20% cancer cases have demonstrated durable responses from immune checkpoint blockade. To enhance the efficacy of immunotherapies, combination therapies suppressing multiple immune evasion mechanisms are increasingly contemplated. To better understand immune cell surveillance and diverse immune evasion responses in tumor tissues, we comprehensively characterized the immune landscape of more than 1,000 tumors across ten different cancers using CPTAC pan-cancer proteogenomic data. We identified seven distinct immune subtypes based on integrative learning of cell type compositions and pathway activities. We then thoroughly categorized unique genomic, epigenetic, transcriptomic, and proteomic changes associated with each subtype. Further leveraging the deep phosphoproteomic data, we studied kinase activities in different immune subtypes, which revealed potential subtype-specific therapeutic targets. Insights from this work will facilitate the development of future immunotherapy strategies and enhance precision targeting with existing agents.

View Accepted Manuscript (DOE)

Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE

Contributing Organization:: Clinical Proteomic Tumor Analysis Consortium

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 2406480

Report Number(s):: PNNL-SA--188762

Journal Information:: Cell, Journal Name: Cell Journal Issue: 5 Vol. 187; ISSN 0092-8674

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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