@article{d084e6b3aa4b40809fa7c40a30b1bb54,
title = "A proteogenomic portrait of lung squamous cell carcinoma",
abstract = "Lung squamous cell carcinoma (LSCC) remains a leading cause of cancer death with few therapeutic options. We characterized the proteogenomic landscape of LSCC, providing a deeper exposition of LSCC biology with potential therapeutic implications. We identify NSD3 as an alternative driver in FGFR1-amplified tumors and low-p63 tumors overexpressing the therapeutic target survivin. SOX2 is considered undruggable, but our analyses provide rationale for exploring chromatin modifiers such as LSD1 and EZH2 to target SOX2-overexpressing tumors. Our data support complex regulation of metabolic pathways by crosstalk between post-translational modifications including ubiquitylation. Numerous immune-related proteogenomic observations suggest directions for further investigation. Proteogenomic dissection of CDKN2A mutations argue for more nuanced assessment of RB1 protein expression and phosphorylation before declaring CDK4/6 inhibition unsuccessful. Finally, triangulation between LSCC, LUAD, and HNSCC identified both unique and common therapeutic vulnerabilities. These observations and proteogenomics data resources may guide research into the biology and treatment of LSCC.",
keywords = "CPTAC, acetylation, genomics, lung cancer, phosphorylation, protein, proteogenomics, proteomics, squamous, ubiquitylation",
author = "{Clinical Proteomic Tumor Analysis Consortium} and Shankha Satpathy and Karsten Krug and {Jean Beltran}, {Pierre M.} and Savage, {Sara R.} and Francesca Petralia and Chandan Kumar-Sinha and Yongchao Dou and Boris Reva and Kane, {M. Harry} and Avanessian, {Shayan C.} and Vasaikar, {Suhas V.} and Azra Krek and Lei, {Jonathan T.} and Jaehnig, {Eric J.} and Tatiana Omelchenko and Yifat Geffen and Bergstrom, {Erik J.} and Vasileios Stathias and Christianson, {Karen E.} and Heiman, {David I.} and Cieslik, {Marcin P.} and Song Cao and Xiaoyu Song and Jiayi Ji and Wenke Liu and Kai Li and Bo Wen and Yize Li and G{\"u}m{\"u}{\c s}, {Zeynep H.} and Selvan, {Myvizhi Esai} and Rama Soundararajan and Visal, {Tanvi H.} and Raso, {Maria G.} and Parra, {Edwin Roger} and {\"O}zg{\"u}n Babur and Pankaj Vats and Shankara Anand and Tobias Schraink and MacIntosh Cornwell and Rodrigues, {Fernanda Martins} and Houxiang Zhu and Mo, {Chia Kuei} and Yuping Zhang and {da Veiga Leprevost}, Felipe and Chen Huang and Chinnaiyan, {Arul M.} and Wyczalkowski, {Matthew A.} and Omenn, {Gilbert S.} and Newton, {Chelsea J.} and Stephan Schurer and Ruggles, {Kelly V.} and David Feny{\"o} and Jewell, {Scott D.} and Mathangi Thiagarajan and Mehdi Mesri and Henry Rodriguez and Mani, {Sendurai A.} and Udeshi, {Namrata D.} and Gad Getz and James Suh and Li, {Qing Kay} and Galen Hostetter and Paik, {Paul K.} and Dhanasekaran, {Saravana M.} and Ramaswamy Govindan and Li Ding and Robles, {Ana I.} and Clauser, {Karl R.} and Nesvizhskii, {Alexey I.} and Pei Wang and Carr, {Steven A.} and Bing Zhang and Mani, {D. R.} and Gillette, {Michael A.} and Alex Green and Alfredo Molinolo and Alicia Francis and Paulovich, {Amanda G.} and Andrii Karnuta and Antonio Colaprico and Barbara Hindenach and Pruetz, {Barbara L.} and Bartosz Kubisa and Druker, {Brian J.} and Carissa Huynh and Goldthwaite, {Charles A.} and Chet Birger and Kinsinger, {Christopher R.} and Jones, {Corbin D.} and Dan Rohrer and Valley, {Dana R.} and Chan, {Daniel W.} and David Chesla and Donna Hansel and Ponomareva, {Elena V.} and Elizabeth Duffy and Eric Burks and Schadt, {Eric E.} and Fedorov, {Eugene S.} and Eunkyung An and Fei Ding and Wilson, {George D.} and Harsh Batra and Hui Zhang and Maas, {Jennifer E.} and Jennifer Eschbacher and Ketchum, {Karen A.} and Rodland, {Karin D.} and Hoadley, {Katherine A.} and Kei Suzuki and Um, {Ki Sung} and Liqun Qi and Lori Bernard and Maciej Wiznerowicz and Ma{\l}gorzata Wojty{\'s} and Domagalski, {Marcin J.} and Ellis, {Matthew J.} and Dyer, {Maureen A.} and Melissa Borucki and Meenakshi Anurag and Birrer, {Michael J.} and Midie Xu and Mikhail Krotevich and Nancy Roche and Edwards, {Nathan J.} and Negin Vatanian and Mucci, {Neil R.} and Nicollette Maunganidze and Nikolay Gabrovski and Olga Potapova and Oluwole Fadare and Pamela Grady and McGarvey, {Peter B.} and Pushpa Hariharan and Thangudu, {Ratna R.} and Rebecca Montgomery and Renganayaki Pandurengan and Smith, {Richard D.} and Welsh, {Robert J.} and Sailaja Mareedu and Payne, {Samuel H.} and Sandra Cottingham and Shilpi Singh and Tsang, {Shirley X.} and Shuang Cai and Stacey Gabriel and Tao Liu and Tara Hiltke and Tanmayi Vashist and Thomas Bauer and Volodymyr Sovenko and Tourtellotte, {Warren G.} and Weiping Ma and William Bocik and Wohaib Hasan and Xiaojun Jing and Ximing Tang and Yuxing Liao and Yvonne and Shutack and Zhen Zhang and Ziad Hanhan",
note = "Publisher Copyright: {\textcopyright} 2021 The Author(s)",
year = "2021",
month = aug,
day = "5",
doi = "10.1016/j.cell.2021.07.016",
language = "English",
volume = "184",
pages = "4348--4371.e40",
journal = "Cell",
issn = "0092-8674",
number = "16",
}