{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Kolodziejczak-Guglas I"],"funding":["Instituto Nacional do Câncer, Ministério da Saúde","NCI NIH HHS","National Institutes of Health","State of Sao Paulo Research Foundation"],"pagination":["100851"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12230239"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["5(6)"],"pubmed_abstract":["Cancer progression and therapeutic resistance are closely linked to a stemness phenotype. Here, we introduce a protein-expression-based stemness index (PROTsi) to evaluate oncogenic dedifferentiation in relation to histopathology, molecular features, and clinical outcomes. Utilizing datasets from the Clinical Proteomic Tumor Analysis Consortium across 11 tumor types, we validate PROTsi's effectiveness in accurately quantifying stem-like features. Through integration of PROTsi with multi-omics, including protein post-translational modifications, we identify molecular features associated with stemness and proteins that act as active nodes within transcriptional networks, driving tumor aggressiveness. Proteins highly correlated with stemness were identified as potential drug targets, both sha"],"journal":["Cell genomics"],"pubmed_title":["Proteomic-based stemness score measures oncogenic dedifferentiation and enables the identification of druggable targets."],"pmcid":["PMC12230239"],"funding_grant_id":["U24 CA210967","U24 CA210985","U24CA210967","U24 CA210986","U24CA210986","U24CA210985","U01CA214116","U01 CA214125","U01CA214114","2018/00583-0","2022/16350-0","U24 CA210979","U24CA210955","U24 CA210954","U24 CA210955","U24CA210954","U24CA210979","U01 CA214116","U24 CA210972","U24CA210972","U24 CA210993","U24CA210993","U01 CA214114","U01CA214125","U24 CA271012"],"pubmed_authors":["Wyczalkowski MA","Hu Y","Akiyama Y","Malta TM","Zhang H","Jewell SD","Lubinski J","Yaron TM","Shi Z","Zhang Q","Dou Y","Calinawan AP","Robles AI","Lei JT","Schraink T","Katsnelson L","Zhang B","Kolodziejczak-Guglas I","Newton CJ","Paulovich AG","Rodland KD","Simoes RLS","An E","Edwards N","Carr SA","Rykunov D","Satpathy S","Stathias V","Foltz SM","Krug K","Nesvizhskii AI","Fenyo D","Terekhanova NV","Yi X","Chan DW","Clauser KR","Smith RD","Anurag M","Druker BJ","McKerrow W","Reva B","Gonzalez Robles TJ","Aguet F","Schurer S","Wang JM","Ruggles KV","Selvan ME","Gumus ZH","Bavarva J","Lazcano Segura RN","Chinnaiyan AM","Schadt EE","Storrs E","Kurzawa P","Day C","da Veiga Leprevost F","Cantley LC","Cao S","Hong R","Huang C","Payne SH","Ceccarelli M","Pugliese P","Lindgren CM","Colaprico A","Wang LB","Babur O","Wang P","Wen B","Omenn GS","Wang Y","Wu Y","Yao L","Johnson JL","Liao Y","Wiznerowicz M","Tan J","Francis A","Anand S","Noushmehr H","Thangudu RR","Ketchum KA","Huntsman E","Li Y","Kaminska B","Birger C","Priebe W","Clinical Proteomic Tumor Analysis Consortium","Hostetter G","Birrer MJ","Kumar-Sinha C","Dhanasekaran SM","Jaehnig EJ","Lazar AJ","Geffen Y","Iavarone A","Getz G","Chowdhury S","Liang WW","Liu T","Ding L","Ma W","Rodrigues FM","Gosline SJC","Liu W","Zhou DC","Gillette MA","Cho H","Jiang W","Petralia F","de Souza Santos E","Thiagarajan M","Mani DR","Tignor N","Song X","Song Y","Oldroyd R","Savage SR","Ji J","Domagalski MJ","Schnaubelt M","Zhang Z","Demicco EG","Ellis MJ","Zhang X","Cieslik MP","Heiman DI","Mesri M"],"additional_accession":[]},"is_claimable":false,"name":"Proteomic-based stemness score measures oncogenic dedifferentiation and enables the identification of druggable targets.","description":"Cancer progression and therapeutic resistance are closely linked to a stemness phenotype. Here, we introduce a protein-expression-based stemness index (PROTsi) to evaluate oncogenic dedifferentiation in relation to histopathology, molecular features, and clinical outcomes. Utilizing datasets from the Clinical Proteomic Tumor Analysis Consortium across 11 tumor types, we validate PROTsi's effectiveness in accurately quantifying stem-like features. Through integration of PROTsi with multi-omics, including protein post-translational modifications, we identify molecular features associated with stemness and proteins that act as active nodes within transcriptional networks, driving tumor aggressiveness. Proteins highly correlated with stemness were identified as potential drug targets, both sha","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Jun","modification":"2026-06-06T15:09:33.74Z","creation":"2026-06-01T03:10:56.786Z"},"accession":"S-EPMC12230239","cross_references":{"pubmed":["40250426"],"doi":["10.1016/j.xgen.2025.100851"]}}