{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Huang C"],"funding":["NIEHS NIH HHS","National Cancer Institute","NCI NIH HHS","Cancer Prevention and Research Institute of Texas"],"pagination":["361-379.e16"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC7946781"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["39(3)"],"pubmed_abstract":["We present a proteogenomic study of 108 human papilloma virus (HPV)-negative head and neck squamous cell carcinomas (HNSCCs). Proteomic analysis systematically catalogs HNSCC-associated proteins and phosphosites, prioritizes copy number drivers, and highlights an oncogenic role for RNA processing genes. Proteomic investigation of mutual exclusivity between FAT1 truncating mutations and 11q13.3 amplifications reveals dysregulated actin dynamics as a common functional consequence. Phosphoproteomics characterizes two modes of EGFR activation, suggesting a new strategy to stratify HNSCCs based on EGFR ligand abundance for effective treatment with inhibitory EGFR monoclonal antibodies. Widespread deletion of immune modulatory genes accounts for low immune infiltration in immune-cold tumors, whe"],"journal":["Cancer cell"],"pubmed_title":["Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma."],"pmcid":["PMC7946781"],"funding_grant_id":["U24 CA210954","T32 CA203690","U24 CA210985","U24 CA210986","U24 CA210972","U24 CA210993","P30 ES010126","U01 CA214125","U24 CA210967","U24 CA210979"],"pubmed_authors":["Hu Y","Jewell SD","Traer E","Calinawan AP","Lei JT","Heiman D","Kinsinger CR","Suh J","Bathe OF","Newton CJ","Xu M","Maunganidze N","Paulovich AG","McDermott JE","Carr SA","Borate U","D'Angelo F","Krug K","Fenyo D","Sikora AG","Cao L","Qi L","Clauser KR","Vatanian N","Yu F","Anurag M","Valley DR","Hannick LI","Hiltke T","Zhao G","Roche N","Placantonakis D","Marrero-Oliveras A","Mareedu S","Chinnaiyan AM","Hayes DN","Vats P","Zhu J","Hindenach B","Cieslik M","Bocik WE","Pazardzhikliev DD","Colaprico A","Agarwal A","Tabor D","Skelly T","Omenn GS","Wiznerowicz M","Mieczkowski P","Chen L","Francis A","Li K","Thangudu RR","Ketchum KA","Cerda S","Li Y","Birger C","Goldthwaite CA","Birrer MJ","Eguez RV","Dhanasekaran SM","Kumar-Sinha C","Liu H","Cai S","Liu T","Migliozzi S","Ma W","Zhou DC","Gillette MA","Zelt R","Jiang W","Kothadia RB","Petralia F","Petrenko L","Clark DJ","Polonskaya L","Thiagarajan M","Mani DR","Chang HY","Savage SR","Domagalski MJ","Cho KC","Blumenberg L","Ermakova TS","Zhang Z","Yoo S","Mesri M","Burke MC","Culpepper H","Dort JC","Stein SE","Wyczalkowski MA","Zhang H","Miles G","Shi Z","Lubinski J","Shi Y","Um KS","Dou Y","Duffy E","Robles AI","Zakhartsev Y","Chen XS","Montgomery R","Velvulou U","Zhang B","Tsang S","Wendl M","Li QK","Teo GC","Pico AR","An E","Boja ES","Dyer M","Potapova O","Rykunov D","Satpathy S","Nesvizhskii AI","Zaalishvili K","Krek A","Ozbek U","Yi X","Chan DW","Druker B","Ramkissoon S","Demir E","Day J","Westbrook TF","Vasilev LV","Vernon M","Reva B","Qu N","Karz A","Hariharan P","Whiteaker JR","Qian J","Borucki M","Edwards NJ","Jones CD","Rohrer DC","De Young S","Schadt EE","Elburn K","Shutack Y","da Veiga Leprevost F","Malc E","El-Naggar AK","Huang C","Chen LS","Richey S","Wierzbicka M","Payne SH","Wang P","Szopa W","Gabriel S","Wen B","Wang Y","Avtonomov D","Singh S","Wu Y","Yao L","Liao Y","Garofano L","Stawicki J","Sokoll LJ","Tan D","Ponomareva EV","Markey SP","Charamut A","Avanessian SC","Clinical Proteomic Tumor Analysis Consortium","Hostetter G","Tognon C","Jaehnig EJ","Ding F","Tansil D","Tyner J","Geffen Y","Perou AM","Rodriguez H","Getz G","Hoadley KA","Liang WW","Weaver AM","Chowdhury S","McGarvey PB","Ding L","Anderson ML","Piehowski PD","Kane MH","Song X","McGee J","Robinson K","Ji J","Schnaubelt M","Hyrcza M","Rodland K","Pan J","Malovannaya A","Ferrarotto R","Czernicki T","Smith R","Ellis MJ"],"additional_accession":[]},"is_claimable":false,"name":"Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma.","description":"We present a proteogenomic study of 108 human papilloma virus (HPV)-negative head and neck squamous cell carcinomas (HNSCCs). Proteomic analysis systematically catalogs HNSCC-associated proteins and phosphosites, prioritizes copy number drivers, and highlights an oncogenic role for RNA processing genes. Proteomic investigation of mutual exclusivity between FAT1 truncating mutations and 11q13.3 amplifications reveals dysregulated actin dynamics as a common functional consequence. Phosphoproteomics characterizes two modes of EGFR activation, suggesting a new strategy to stratify HNSCCs based on EGFR ligand abundance for effective treatment with inhibitory EGFR monoclonal antibodies. Widespread deletion of immune modulatory genes accounts for low immune infiltration in immune-cold tumors, whe","dates":{"release":"2021-01-01T00:00:00Z","publication":"2021 Mar","modification":"2026-05-31T19:52:11.56Z","creation":"2025-04-05T22:20:15.239Z"},"accession":"S-EPMC7946781","cross_references":{"pubmed":["33417831"],"doi":["10.1016/j.ccell.2020.12.007"]}}