@article{d94f5b59cd3b4a16a3b04c0161cec3c7,
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 Shrabanti Chowdhury and G{\"u}m{\"u}{\c s}, {Zeynep H.} and Francesca Petralia and Boris Reva and Pei Wang",
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",
publisher = "Elsevier B.V.",
number = "18",
}