@article{6b5a8782b91e42aa93223ea326997ee3,
title = "Pan-cancer proteogenomics connects oncogenic drivers to functional states",
abstract = "Cancer driver events refer to key genetic aberrations that drive oncogenesis; however, their exact molecular mechanisms remain insufficiently understood. Here, our multi-omics pan-cancer analysis uncovers insights into the impacts of cancer drivers by identifying their significant cis-effects and distal trans-effects quantified at the RNA, protein, and phosphoprotein levels. Salient observations include the association of point mutations and copy-number alterations with the rewiring of protein interaction networks, and notably, most cancer genes converge toward similar molecular states denoted by sequence-based kinase activity profiles. A correlation between predicted neoantigen burden and measured T cell infiltration suggests potential vulnerabilities for immunotherapies. Patterns of cancer hallmarks vary by polygenic protein abundance ranging from uniform to heterogeneous. Overall, our work demonstrates the value of comprehensive proteogenomics in understanding the functional states of oncogenic drivers and their links to cancer development, surpassing the limitations of studying individual cancer types.",
keywords = "CPTAC, cancer hallmark, oncogenic driver, pan-cancer, phosphoproteomics, protein complex, proteogenomics, proteomics, therapeutic target",
author = "{Clinical Proteomic Tumor Analysis Consortium} and Yize Li and Eduard Porta-Pardo and Collin Tokheim and Bailey, {Matthew H.} and Yaron, {Tomer M.} and Vasileios Stathias and Yifat Geffen and Imbach, {Kathleen J.} and Song Cao and Shankara Anand and Yo Akiyama and Wenke Liu and Wyczalkowski, {Matthew A.} and Yizhe Song and Storrs, {Erik P.} and Wendl, {Michael C.} and Wubing Zhang and Mustafa Sibai and Victoria Ruiz-Serra and Liang, {Wen Wei} and Terekhanova, {Nadezhda V.} and Rodrigues, {Fernanda Martins} and Clauser, {Karl R.} and Heiman, {David I.} and Qing Zhang and Francois Aguet and Calinawan, {Anna P.} and Dhanasekaran, {Saravana M.} and Chet Birger and Shankha Satpathy and Zhou, {Daniel Cui} and Wang, {Liang Bo} and Jessika Baral and Johnson, {Jared L.} and Huntsman, {Emily M.} and Pietro Pugliese and Antonio Colaprico and Antonio Iavarone and Chheda, {Milan G.} and Ricketts, {Christopher J.} and David Feny{\"o} and Payne, {Samuel H.} and Henry Rodriguez and Robles, {Ana I.} and Gillette, {Michael A.} and Chandan Kumar-Sinha and Lazar, {Alexander J.} and Cantley, {Lewis C.} and Gad Getz and Li Ding and Eunkyung An and Meenakshi Anurag and Jasmin Bavarva and Birrer, {Michael J.} and Anna Calinawan and Michele Ceccarelli and Chan, {Daniel W.} and Chinnaiyan, {Arul M.} and Hanbyul Cho and Shrabanti Chowdhury and Cieslik, {Marcin P.} and {da Veiga Leprevost}, Felipe and Corbin Day and Domagalski, {Marcin J.} and Yongchao Dou and Druker, {Brian J.} and Nathan Edwards and Ellis, {Matthew J.} and Selvan, {Myvizhi Esai} and Foltz, {Steven M.} and Alicia Francis and {Gonzalez Robles}, {Tania J.} and Gosline, {Sara J.C.} and G{\"u}m{\"u}{\c s}, {Zeynep H.} and Tara Hiltke and Runyu Hong and Galen Hostetter and Yingwei Hu and Chen Huang and Emily Huntsman and Jaehnig, {Eric J.} and Jewel, {Scott D.} and Jiayi Ji and Wen Jiang and Lizabeth Katsnelson and Ketchum, {Karen A.} and Iga Kolodziejczak and Lei, {Jonathan T.} and Yuxing Liao and Lindgren, {Caleb M.} and Tao Liu and Weiping Ma and Wilson McKerrow and Nesvizhskii, {Alexey I.} and Chelsea Newton and Robert Oldroyd and Omenn, {Gilbert S.} and Paulovich, {Amanda G.} and Francesca Petralia and Boris Reva and Rodland, {Karin D.} and Ruggles, {Kelly V.} and Dmitry Rykunov and Savage, {Sara R.} and Schadt, {Eric E.} and Michael Schnaubelt and Tobias Schraink and Zhiao Shi and Smith, {Richard D.} and Xiaoyu Song and Jimin Tan and Thangudu, {Ratna R.} and Nicole Tignor and Wang, {Joshua M.} and Pei Wang and Wang, {Ying (Cindy)} and Bo Wen and Maciej Wiznerowicz and Xinpei Yi and Bing Zhang and Hui Zhang and Xu Zhang and Zhen Zhang",
note = "Publisher Copyright: {\textcopyright} 2023 The Authors",
year = "2023",
month = aug,
day = "31",
doi = "10.1016/j.cell.2023.07.014",
language = "English",
volume = "186",
pages = "3921--3944.e25",
journal = "Cell",
issn = "0092-8674",
number = "18",
}