{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T23:06:59Z","timestamp":1788217619940,"version":"build-2803163510"},"reference-count":102,"publisher":"American Association for Cancer Research (AACR)","issue":"9","funder":[{"name":"TargetCancer Foundation","award":["TargetCancer Foundation Cholangiocarcinoma Cell Line Project"],"award-info":[{"award-number":["TargetCancer Foundation Cholangiocarcinoma Cell Line Project"]}]},{"DOI":"10.13039\/100011475","name":"Cholangiocarcinoma Foundation","doi-asserted-by":"publisher","award":["C2T2 Precision Oncology Award"],"award-info":[{"award-number":["C2T2 Precision Oncology Award"]}],"id":[{"id":"10.13039\/100011475","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100011475","name":"Cholangiocarcinoma Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100011475","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100011475","name":"Cholangiocarcinoma Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100011475","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100011475","name":"Cholangiocarcinoma Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100011475","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014042","name":"DOD Peer Reviewed Cancer Research Program","doi-asserted-by":"publisher","award":["CA160216"],"award-info":[{"award-number":["CA160216"]}],"id":[{"id":"10.13039\/100014042","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014042","name":"DOD Peer Reviewed Cancer Research Program","doi-asserted-by":"publisher","award":["CA210849"],"award-info":[{"award-number":["CA210849"]}],"id":[{"id":"10.13039\/100014042","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["P50CA127003"],"award-info":[{"award-number":["P50CA127003"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["1R01CA280085-01"],"award-info":[{"award-number":["1R01CA280085-01"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["K08 CA260442"],"award-info":[{"award-number":["K08 CA260442"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["1K99CA245194-01"],"award-info":[{"award-number":["1K99CA245194-01"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["aacrjournals.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2025,9,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>Biliary tract cancers (BTC) are aggressive malignancies encompassing intrahepatic and extrahepatic cholangiocarcinoma, gallbladder carcinoma, and ampullary carcinoma. Here, we report integrative analysis of 63 BTC cell lines via multi-omics and genome-scale CRISPR screens. We identify widespread EGFR dependency in BTC, alongside dependencies selective to anatomic subtypes. Additionally, we delineate strategies to overcome therapeutic resistance, with combined EGFR inhibition potentiating targeting of KRAS-mutant and FGFR2 fusion\u2013driven models and SHP2 inhibition effective in the latter context. Clustering RNA\/protein expression and dependencies data revealed functional relationships transcending single-gene alterations, with biliary, squamous, or dual biliary\/hepatocyte lineage signatures stratifying BTC models. These subtypes exhibit distinct dependency profiles\u2014including cell fate transcription factors GRHL2, TP63, and HNF1B, respectively\u2014and demonstrate prognostic significance in patient samples. Potential subtype-specific targetable vulnerabilities include integrin\u03b13 and the detoxification enzyme UXS1. This cell line atlas reveals therapeutic targets in molecularly defined BTCs, unveils disease subtypes, and provides a resource for therapeutic development.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Significance:<\/jats:title>\n                    <jats:p>This integrative analysis of BTC cell lines defines the landscape of vulnerabilities across BTCs, stratifying distinct subtypes, and provides a key resource for studying disease heterogeneity. The findings highlight strategies for targeting BTCs with specific genomic alterations, as well as broader approaches based on shared molecular programs and essential pathways.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1158\/2159-8290.cd-24-1383","type":"journal-article","created":{"date-parts":[[2025,5,12]],"date-time":"2025-05-12T11:01:56Z","timestamp":1747047716000},"page":"1858-1882","update-policy":"https:\/\/doi.org\/10.1158\/crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["Generation of a Biliary Tract Cancer Cell Line Atlas Identifies Molecular Subtypes and Therapeutic Targets"],"prefix":"10.1158","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7886-7443","authenticated-orcid":false,"given":"Vindhya","family":"Vijay","sequence":"first","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"2Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"3Department of Medicine, Harvard Medical School, Boston, Massachusetts."},{"name":"4Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9858-5654","authenticated-orcid":false,"given":"Negin","family":"Karisani","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"4Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1149-0474","authenticated-orcid":false,"given":"Lei","family":"Shi","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"2Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"3Department of Medicine, Harvard Medical School, Boston, Massachusetts."},{"name":"4Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3278-3201","authenticated-orcid":false,"given":"Yu-Han","family":"Hung","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"2Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"3Department of Medicine, Harvard Medical School, Boston, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-3846-3002","authenticated-orcid":false,"given":"Phuong","family":"Vu","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"2Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"3Department of Medicine, Harvard Medical School, Boston, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-3099-0780","authenticated-orcid":false,"given":"Prabhat","family":"Kattel","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"2Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"3Department of Medicine, Harvard Medical School, Boston, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-4969-8000","authenticated-orcid":false,"given":"Lauren","family":"Kenney","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"2Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"3Department of Medicine, Harvard Medical School, Boston, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-1306-7791","authenticated-orcid":false,"given":"Joshua","family":"Merritt","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"2Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"3Department of Medicine, Harvard Medical School, Boston, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-3986-6819","authenticated-orcid":false,"given":"Ramzi","family":"Adil","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"2Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"3Department of Medicine, Harvard Medical School, Boston, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-5445-5201","authenticated-orcid":false,"given":"Qibiao","family":"Wu","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"2Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"3Department of Medicine, Harvard Medical School, Boston, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9383-9117","authenticated-orcid":false,"given":"Yuanli","family":"Zhen","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"2Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"3Department of Medicine, Harvard Medical School, Boston, Massachusetts."},{"name":"4Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1615-5915","authenticated-orcid":false,"given":"Robert","family":"Morris","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4716-2843","authenticated-orcid":false,"given":"Johannes","family":"Kreuzer","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-6673-8733","authenticated-orcid":false,"given":"Meena","family":"Kathiresan","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-6226-8082","authenticated-orcid":false,"given":"Xcanda Ixchel","family":"Herrera Lopez","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4915-9640","authenticated-orcid":false,"given":"Haley","family":"Ellis","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"2Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"3Department of Medicine, Harvard Medical School, Boston, Massachusetts."},{"name":"4Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7313-0450","authenticated-orcid":false,"given":"Ilaria","family":"Gritti","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"2Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"3Department of Medicine, Harvard Medical School, Boston, Massachusetts."},{"name":"4Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-0218-1654","authenticated-orcid":false,"given":"Lilian","family":"Lecorgne","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"2Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"3Department of Medicine, Harvard Medical School, Boston, Massachusetts."},{"name":"4Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-5236-3819","authenticated-orcid":false,"given":"Ines","family":"Farag","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"2Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"3Department of Medicine, Harvard Medical School, Boston, Massachusetts."},{"name":"4Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7156-272X","authenticated-orcid":false,"given":"Alexandra","family":"Popa","sequence":"additional","affiliation":[{"name":"5Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4394-7099","authenticated-orcid":false,"given":"William","family":"Shen","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"3Department of Medicine, Harvard Medical School, Boston, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0655-1519","authenticated-orcid":false,"given":"Hiroyuki","family":"Kato","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"2Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"3Department of Medicine, Harvard Medical School, Boston, Massachusetts."},{"name":"4Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5860-8225","authenticated-orcid":false,"given":"Qin","family":"Xu","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"2Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"3Department of Medicine, Harvard Medical School, Boston, Massachusetts."},{"name":"4Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5491-3089","authenticated-orcid":false,"given":"Eranga R.","family":"Balasooriya","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"2Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"3Department of Medicine, Harvard Medical School, Boston, Massachusetts."},{"name":"4Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6847-7065","authenticated-orcid":false,"given":"Meng-Ju","family":"Wu","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"2Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"3Department of Medicine, Harvard Medical School, Boston, Massachusetts."},{"name":"4Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6736-0332","authenticated-orcid":false,"given":"Jinkai","family":"Wan","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"2Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"3Department of Medicine, Harvard Medical School, Boston, Massachusetts."},{"name":"4Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0001-9492","authenticated-orcid":false,"given":"Hiroshi","family":"Kondo","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"2Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"3Department of Medicine, Harvard Medical School, Boston, Massachusetts."},{"name":"4Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0350-6974","authenticated-orcid":false,"given":"Saireudee","family":"Chaturantabut","sequence":"additional","affiliation":[{"name":"4Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5374-9918","authenticated-orcid":false,"given":"Srivatsan","family":"Raghavan","sequence":"additional","affiliation":[{"name":"3Department of Medicine, Harvard Medical School, Boston, Massachusetts."},{"name":"4Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts."},{"name":"6Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5073-442X","authenticated-orcid":false,"given":"Matthew D.","family":"Hall","sequence":"additional","affiliation":[{"name":"7National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4265-7620","authenticated-orcid":false,"given":"Samarjit","family":"Patnaik","sequence":"additional","affiliation":[{"name":"7National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8218-0433","authenticated-orcid":false,"given":"Min","family":"Shen","sequence":"additional","affiliation":[{"name":"7National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1984-2430","authenticated-orcid":false,"given":"Robin K.","family":"Kelley","sequence":"additional","affiliation":[{"name":"8Division of Hematology-Oncology, Department of Medicine, University of California San Francisco, San Francisco, California."},{"name":"9Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7213-3951","authenticated-orcid":false,"given":"James M.","family":"Cleary","sequence":"additional","affiliation":[{"name":"3Department of Medicine, Harvard Medical School, Boston, Massachusetts."},{"name":"7National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1307-459X","authenticated-orcid":false,"given":"Michael S.","family":"Lawrence","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"2Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"3Department of Medicine, Harvard Medical School, Boston, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5122-861X","authenticated-orcid":false,"given":"David E.","family":"Root","sequence":"additional","affiliation":[{"name":"4Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2386-6435","authenticated-orcid":false,"given":"Krushna C.","family":"Patra","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"10Department of Cancer Biology, University of Cincinnati, Cincinnati, Ohio."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5633-9490","authenticated-orcid":false,"given":"Vanessa S.","family":"Silveira","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"2Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"3Department of Medicine, Harvard Medical School, Boston, Massachusetts."},{"name":"4Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8751-9707","authenticated-orcid":false,"given":"Cyril H.","family":"Benes","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4230-9308","authenticated-orcid":false,"given":"Vikram","family":"Deshpande","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"11Department of Pathology, Harvard Medical School, Boston, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2983-7704","authenticated-orcid":false,"given":"Dejan","family":"Juric","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3539-9803","authenticated-orcid":false,"given":"William R.","family":"Sellers","sequence":"additional","affiliation":[{"name":"3Department of Medicine, Harvard Medical School, Boston, Massachusetts."},{"name":"4Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts."},{"name":"6Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6295-1085","authenticated-orcid":false,"given":"Cristina R.","family":"Ferrone","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8225-9099","authenticated-orcid":false,"given":"Wilhelm","family":"Haas","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2857-4685","authenticated-orcid":false,"given":"Francisca","family":"Vazquez","sequence":"additional","affiliation":[{"name":"4Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0936-0753","authenticated-orcid":false,"given":"Gad","family":"Getz","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"3Department of Medicine, Harvard Medical School, Boston, Massachusetts."},{"name":"4Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts."},{"name":"11Department of Pathology, Harvard Medical School, Boston, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3867-0416","authenticated-orcid":false,"given":"Nabeel","family":"Bardeesy","sequence":"additional","affiliation":[{"name":"1Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"2Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts."},{"name":"3Department of Medicine, Harvard Medical School, Boston, Massachusetts."},{"name":"4Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts."}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1086","published-online":{"date-parts":[[2025,5,12]]},"reference":[{"key":"2025090403075024400_bib1","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1016\/S0140-6736(21)00153-7","article-title":"Biliary tract cancer","volume":"397","author":"Valle","year":"2021","journal-title":"Lancet"},{"key":"2025090403075024400_bib2","doi-asserted-by":"crossref","first-page":"2666","DOI":"10.1002\/cncr.32803","article-title":"Global trends in intrahepatic and extrahepatic cholangiocarcinoma incidence from 1993 to 2012","volume":"126","author":"Florio","year":"2020","journal-title":"Cancer"},{"key":"2025090403075024400_bib3","doi-asserted-by":"crossref","first-page":"2238","DOI":"10.1002\/cncr.33476","article-title":"The global, regional, and national burden of gallbladder and biliary tract cancer and its attributable risk factors in 195 countries and territories, 1990 to 2017: a systematic analysis for the Global Burden of Disease Study 2017","volume":"127","author":"Ouyang","year":"2021","journal-title":"Cancer"},{"key":"2025090403075024400_bib4","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1038\/s41571-023-00770-1","article-title":"Cholangiocarcinoma - novel biological insights and therapeutic strategies","volume":"20","author":"Ilyas","year":"2023","journal-title":"Nat Rev Clin Oncol"},{"key":"2025090403075024400_bib5","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1038\/s41698-022-00327-y","article-title":"Comprehensive clinicopathological and genomic profiling of gallbladder cancer reveals actionable targets in half of patients","volume":"6","author":"de Bitter","year":"2022","journal-title":"NPJ Precis Oncol"},{"key":"2025090403075024400_bib6","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1038\/s41416-019-0415-8","article-title":"Can we classify ampullary tumours better? Clinical, pathological and molecular features. Results of an AGEO study","volume":"120","author":"Perkins","year":"2019","journal-title":"Br J Cancer"},{"key":"2025090403075024400_bib7","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1038\/s41575-020-0310-z","article-title":"Cholangiocarcinoma 2020: the next horizon in mechanisms and management","volume":"17","author":"Banales","year":"2020","journal-title":"Nat Rev Gastroenterol Hepatol"},{"key":"2025090403075024400_bib8","doi-asserted-by":"crossref","first-page":"2488","DOI":"10.1158\/2159-8290.CD-20-1669","article-title":"FGFR2 extracellular domain in-frame deletions are therapeutically targetable genomic alterations that function as oncogenic drivers in cholangiocarcinoma","volume":"11","author":"Cleary","year":"2021","journal-title":"Cancer Discov"},{"key":"2025090403075024400_bib9","doi-asserted-by":"crossref","first-page":"1116","DOI":"10.1158\/2159-8290.CD-17-0368","article-title":"Whole-genome and epigenomic landscapes of etiologically distinct subtypes of cholangiocarcinoma","volume":"7","author":"Jusakul","year":"2017","journal-title":"Cancer Discov"},{"key":"2025090403075024400_bib10","doi-asserted-by":"crossref","first-page":"1003","DOI":"10.1038\/ng.3375","article-title":"Genomic spectra of biliary tract cancer","volume":"47","author":"Nakamura","year":"2015","journal-title":"Nat Genet"},{"key":"2025090403075024400_bib11","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1016\/j.celrep.2015.12.005","article-title":"Ampullary cancers harbor ELF3 tumor suppressor gene mutations and exhibit frequent WNT dysregulation","volume":"14","author":"Gingras","year":"2016","journal-title":"Cell Rep"},{"key":"2025090403075024400_bib12","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1016\/j.ccell.2015.12.012","article-title":"Genomic sequencing identifies ELF3 as a driver of ampullary carcinoma","volume":"29","author":"Yachida","year":"2016","journal-title":"Cancer Cell"},{"key":"2025090403075024400_bib13","doi-asserted-by":"crossref","first-page":"22087","DOI":"10.1038\/s41598-020-77939-6","article-title":"Genomic profiling reveals high frequency of DNA repair genetic aberrations in gallbladder cancer","volume":"10","author":"Abdel-Wahab","year":"2020","journal-title":"Sci Rep"},{"key":"2025090403075024400_bib14","doi-asserted-by":"crossref","first-page":"4154","DOI":"10.1158\/1078-0432.CCR-18-0078","article-title":"Comprehensive molecular profiling of intrahepatic and extrahepatic cholangiocarcinomas: potential targets for intervention","volume":"24","author":"Lowery","year":"2018","journal-title":"Clin Cancer Res"},{"key":"2025090403075024400_bib15","doi-asserted-by":"crossref","first-page":"2716","DOI":"10.1200\/JCO.21.02576","article-title":"Precision medicine in biliary tract cancer","volume":"40","author":"Scott","year":"2022","journal-title":"J Clin Oncol"},{"key":"2025090403075024400_bib16","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1038\/s41586-019-1186-3","article-title":"Next-generation characterization of the cancer cell line encyclopedia","volume":"569","author":"Ghandi","year":"2019","journal-title":"Nature"},{"key":"2025090403075024400_bib17","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1038\/ng.2764","article-title":"The cancer genome atlas pan-cancer analysis project","volume":"45","author":"Weinstein","year":"2013","journal-title":"Nat Genet"},{"key":"2025090403075024400_bib18","doi-asserted-by":"crossref","first-page":"2780","DOI":"10.1016\/j.celrep.2017.02.033","article-title":"Integrative genomic analysis of cholangiocarcinoma identifies distinct IDH-mutant molecular profiles","volume":"18","author":"Farshidfar","year":"2017","journal-title":"Cell Rep"},{"key":"2025090403075024400_bib19","doi-asserted-by":"crossref","first-page":"4097","DOI":"10.1200\/JCO.23.00434","article-title":"Adagrasib in advanced solid tumors harboring a KRASG12C mutation","volume":"41","author":"Bekaii-Saab","year":"2023","journal-title":"J Clin Oncol"},{"key":"2025090403075024400_bib20","doi-asserted-by":"crossref","first-page":"1378","DOI":"10.1158\/2159-8290.CD-21-1168","article-title":"EGFR inhibition potentiates FGFR inhibitor therapy and overcomes resistance in FGFR2 fusion-positive cholangiocarcinoma","volume":"12","author":"Wu","year":"2022","journal-title":"Cancer Discov"},{"key":"2025090403075024400_bib21","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1158\/2159-8290.CD-15-1442","article-title":"Isocitrate dehydrogenase mutations confer dasatinib hypersensitivity and SRC dependence in intrahepatic cholangiocarcinoma","volume":"6","author":"Saha","year":"2016","journal-title":"Cancer Discov"},{"key":"2025090403075024400_bib22","doi-asserted-by":"crossref","first-page":"812","DOI":"10.1158\/2159-8290.CD-21-1077","article-title":"Mutant IDH inhibits IFN\u03b3-TET2 signaling to promote immunoevasion and tumor maintenance in cholangiocarcinoma","volume":"12","author":"Wu","year":"2022","journal-title":"Cancer Discov"},{"key":"2025090403075024400_bib23","doi-asserted-by":"crossref","first-page":"1747","DOI":"10.1158\/0008-5472.CAN-23-3298","article-title":"Whole-genome DNA methylation profiling of intrahepatic cholangiocarcinoma reveals prognostic subtypes with distinct biological drivers","volume":"84","author":"Liao","year":"2024","journal-title":"Cancer Res"},{"key":"2025090403075024400_bib24","doi-asserted-by":"crossref","first-page":"2412","DOI":"10.1158\/2159-8290.CD-23-0669","article-title":"MRTX1719 is an MTA-cooperative PRMT5 inhibitor that exhibits synthetic lethality in preclinical models and patients with MTAP-deleted cancer","volume":"13","author":"Engstrom","year":"2023","journal-title":"Cancer Discov"},{"key":"2025090403075024400_bib25","doi-asserted-by":"crossref","first-page":"199","DOI":"10.15698\/cst2020.08.228","article-title":"PRMT5 function and targeting in cancer","volume":"4","author":"Kim","year":"2020","journal-title":"Cell Stress"},{"key":"2025090403075024400_bib26","doi-asserted-by":"crossref","first-page":"2339","DOI":"10.1158\/2159-8290.CD-23-0383","article-title":"SHP2: a pleiotropic target at the interface of cancer and its microenvironment","volume":"13","author":"Sodir","year":"2023","journal-title":"Cancer Discov"},{"key":"2025090403075024400_bib27","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1016\/j.ccell.2021.12.006","article-title":"Proteogenomic characterization identifies clinically relevant subgroups of intrahepatic cholangiocarcinoma","volume":"40","author":"Dong","year":"2022","journal-title":"Cancer Cell"},{"key":"2025090403075024400_bib28","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1158\/1078-0432.CCR-23-1317","article-title":"Landscape of clinical resistance mechanisms to FGFR inhibitors in FGFR2-altered cholangiocarcinoma","volume":"30","author":"Wu","year":"2024","journal-title":"Clin Cancer Res"},{"key":"2025090403075024400_bib29","doi-asserted-by":"crossref","first-page":"102627","DOI":"10.1016\/j.ctrv.2023.102627","article-title":"Resistance mechanism to fibroblast growth factor receptor (FGFR) inhibitors in cholangiocarcinoma","volume":"121","author":"Lamarca","year":"2023","journal-title":"Cancer Treat Rev"},{"key":"2025090403075024400_bib30","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1038\/s43018-019-0018-6","article-title":"Discovering the anti-cancer potential of non-oncology drugs by systematic viability profiling","volume":"1","author":"Corsello","year":"2020","journal-title":"Nat Cancer"},{"key":"2025090403075024400_bib31","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1038\/nm.1922","article-title":"Regulation of endocytosis via the oxygen-sensing pathway","volume":"15","author":"Wang","year":"2009","journal-title":"Nat Med"},{"key":"2025090403075024400_bib32","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1038\/s41419-023-06201-4","article-title":"PTPN23 ubiquitination by WDR4 suppresses EGFR and c-MET degradation to define a lung cancer therapeutic target","volume":"14","author":"Singh","year":"2023","journal-title":"Cell Death Dis"},{"key":"2025090403075024400_bib33","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1038\/nature08779","article-title":"Systems survey of endocytosis by multiparametric image analysis","volume":"464","author":"Collinet","year":"2010","journal-title":"Nature"},{"key":"2025090403075024400_bib34","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1038\/s41575-023-00775-2","article-title":"Fetal liver development and implications for liver disease pathogenesis","volume":"20","author":"Lotto","year":"2023","journal-title":"Nat Rev Gastroenterol Hepatol"},{"key":"2025090403075024400_bib35","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.1016\/j.jhep.2018.01.005","article-title":"Development of the liver: insights into organ and tissue morphogenesis","volume":"68","author":"Ober","year":"2018","journal-title":"J Hepatol"},{"key":"2025090403075024400_bib36","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1128\/MCB.22.1.245-256.2002","article-title":"Formation of Tap\/NXT1 heterodimers activates Tap-dependent nuclear mRNA export by enhancing recruitment to nuclear pore complexes","volume":"22","author":"Wiegand","year":"2002","journal-title":"Mol Cell Biol"},{"key":"2025090403075024400_bib37","doi-asserted-by":"crossref","first-page":"2282","DOI":"10.1158\/2159-8290.CD-20-1213","article-title":"Selective modulation of a pan-essential protein as a therapeutic strategy in cancer","volume":"11","author":"Malone","year":"2021","journal-title":"Cancer Discov"},{"key":"2025090403075024400_bib38","doi-asserted-by":"crossref","first-page":"1363","DOI":"10.1101\/gr.240663.118","article-title":"Benchmark and integration of resources for the estimation of human transcription factor activities","volume":"29","author":"Garcia-Alonso","year":"2019","journal-title":"Genome Res"},{"key":"2025090403075024400_bib39","doi-asserted-by":"crossref","first-page":"932","DOI":"10.1016\/j.ccell.2019.04.007","article-title":"Genomic and transcriptomic profiling of combined hepatocellular and intrahepatic cholangiocarcinoma reveals distinct molecular subtypes","volume":"35","author":"Xue","year":"2019","journal-title":"Cancer Cell"},{"key":"2025090403075024400_bib40","doi-asserted-by":"crossref","first-page":"101394","DOI":"10.1016\/j.xcrm.2024.101394","article-title":"Lineage and ecology define liver tumor evolution in response to treatment","volume":"5","author":"Revsine","year":"2024","journal-title":"Cell Rep Med"},{"key":"2025090403075024400_bib41","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1038\/nrc1947","article-title":"Lineage dependency and lineage-survival oncogenes in human cancer","volume":"6","author":"Garraway","year":"2006","journal-title":"Nat Rev Cancer"},{"issue":"Suppl 1","key":"2025090403075024400_bib42","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1111\/liv.14093","article-title":"Anatomical, histomorphological and molecular classification of cholangiocarcinoma","volume":"39","author":"Kendall","year":"2019","journal-title":"Liver Int"},{"key":"2025090403075024400_bib43","doi-asserted-by":"crossref","first-page":"986","DOI":"10.1038\/modpathol.2017.22","article-title":"Dichotomy in intrahepatic cholangiocarcinomas based on histologic similarities to hilar cholangiocarcinomas","volume":"30","author":"Akita","year":"2017","journal-title":"Mod Pathol"},{"key":"2025090403075024400_bib44","doi-asserted-by":"crossref","first-page":"2091","DOI":"10.1002\/hep.30493","article-title":"Integrative analysis defines distinct prognostic subgroups of intrahepatic cholangiocarcinoma","volume":"69","author":"Goeppert","year":"2019","journal-title":"Hepatology"},{"key":"2025090403075024400_bib45","doi-asserted-by":"crossref","first-page":"359","DOI":"10.5858\/arpa.2022-0537-RA","article-title":"Cholangiocarcinoma: pathologic and molecular classification in the era of precision medicine","volume":"148","author":"Gopal","year":"2024","journal-title":"Arch Pathol Lab Med"},{"key":"2025090403075024400_bib46","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1002\/hep.32624","article-title":"Proteogenomic characterization of cholangiocarcinoma","volume":"77","author":"Deng","year":"2023","journal-title":"Hepatology"},{"key":"2025090403075024400_bib47","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1038\/s43018-023-00523-0","article-title":"SULT1A1-dependent sulfonation of alkylators is a lineage-dependent vulnerability of liver cancers","volume":"4","author":"Shi","year":"2023","journal-title":"Nat Cancer"},{"key":"2025090403075024400_bib48","doi-asserted-by":"crossref","first-page":"983","DOI":"10.1038\/nbt.3955","article-title":"Detection of dysregulated protein-association networks by high-throughput proteomics predicts cancer vulnerabilities","volume":"35","author":"Lapek","year":"2017","journal-title":"Nat Biotechnol"},{"key":"2025090403075024400_bib49","doi-asserted-by":"crossref","first-page":"1692","DOI":"10.1016\/j.celrep.2015.02.027","article-title":"YAP inhibition restores hepatocyte differentiation in advanced HCC, leading to tumor regression","volume":"10","author":"Fitamant","year":"2015","journal-title":"Cell Rep"},{"key":"2025090403075024400_bib50","first-page":"9","article-title":"YAP\/TAZ as master regulators in cancer: modulation, function and therapeutic approaches","volume":"4","author":"Piccolo","year":"2023","journal-title":"Nat Cancer"},{"key":"2025090403075024400_bib51","doi-asserted-by":"crossref","first-page":"975","DOI":"10.15252\/embr.201439951","article-title":"PARD3 induces TAZ activation and cell growth by promoting LATS1 and PP1 interaction","volume":"16","author":"Lv","year":"2015","journal-title":"EMBO Rep"},{"key":"2025090403075024400_bib52","doi-asserted-by":"crossref","first-page":"1431","DOI":"10.1083\/jcb.201612177","article-title":"Kindlin-2 regulates mesenchymal stem cell differentiation through control of YAP1\/TAZ","volume":"217","author":"Guo","year":"2018","journal-title":"J Cell Biol"},{"key":"2025090403075024400_bib53","doi-asserted-by":"crossref","first-page":"628","DOI":"10.1038\/nature13611","article-title":"Oncogene ablation-resistant pancreatic cancer cells depend on mitochondrial function","volume":"514","author":"Viale","year":"2014","journal-title":"Nature"},{"key":"2025090403075024400_bib54","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1016\/j.ccell.2019.12.006","article-title":"Treatment-induced tumor dormancy through YAP-mediated transcriptional reprogramming of the apoptotic pathway","volume":"37","author":"Kurppa","year":"2020","journal-title":"Cancer Cell"},{"key":"2025090403075024400_bib55","doi-asserted-by":"crossref","first-page":"625","DOI":"10.1038\/s41586-023-06676-3","article-title":"Disruption of sugar nucleotide clearance is a therapeutic vulnerability of cancer cells","volume":"623","author":"Doshi","year":"2023","journal-title":"Nature"},{"key":"2025090403075024400_bib56","doi-asserted-by":"crossref","first-page":"R512","DOI":"10.1016\/j.cub.2021.01.086","article-title":"WAVE regulatory complex","volume":"31","author":"Rottner","year":"2021","journal-title":"Curr Biol"},{"key":"2025090403075024400_bib57","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1038\/s41580-020-0255-7","article-title":"ERK signalling: a master regulator of cell behaviour, life and fate","volume":"21","author":"Lavoie","year":"2020","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2025090403075024400_bib58","doi-asserted-by":"crossref","first-page":"103892","DOI":"10.1016\/j.critrevonc.2022.103892","article-title":"Rare histotypes of epithelial biliary tract tumors: a literature review","volume":"181","author":"Sapuppo","year":"2023","journal-title":"Crit Rev Oncol Hematol"},{"key":"2025090403075024400_bib59","doi-asserted-by":"crossref","first-page":"621594","DOI":"10.3389\/fonc.2021.621594","article-title":"Treatment and survival patterns of primary adenosquamous carcinoma of the liver: a retrospective analysis","volume":"11","author":"Gou","year":"2021","journal-title":"Front Oncol"},{"key":"2025090403075024400_bib60","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1016\/j.ccell.2024.01.012","article-title":"Adeno-to-squamous transition drives resistance to KRAS inhibition in LKB1 mutant lung cancer","volume":"42","author":"Tong","year":"2024","journal-title":"Cancer Cell"},{"key":"2025090403075024400_bib61","doi-asserted-by":"crossref","first-page":"1060","DOI":"10.1016\/j.trecan.2022.08.005","article-title":"Mechanisms of PDAC subtype heterogeneity and therapy response","volume":"8","author":"Espinet","year":"2022","journal-title":"Trends Cancer"},{"key":"2025090403075024400_bib62","doi-asserted-by":"crossref","first-page":"479","DOI":"10.21873\/invivo.11798","article-title":"Anti-EGFR monoclonal antibodies in advanced biliary tract cancer: a systematic review and meta-analysis","volume":"34","author":"Rizzo","year":"2020","journal-title":"In Vivo"},{"key":"2025090403075024400_bib63","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1111\/his.13975","article-title":"The 2019 WHO classification of tumours of the digestive system","volume":"76","author":"Nagtegaal","year":"2020","journal-title":"Histopathology"},{"key":"2025090403075024400_bib64","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1136\/jcp-2024-209708","article-title":"Cholangiocarcinoma classification: current approach, relevance and challenges","volume":"78","author":"Goeppert","year":"2025","journal-title":"J Clin Pathol"},{"key":"2025090403075024400_bib65","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1038\/s41586-022-04984-8","article-title":"PI3K drives the de novo synthesis of coenzyme A from vitamin B5","volume":"608","author":"Dibble","year":"2022","journal-title":"Nature"},{"key":"2025090403075024400_bib66","doi-asserted-by":"crossref","first-page":"1870","DOI":"10.1038\/s42255-023-00915-7","article-title":"Vitamin B5 supports MYC oncogenic metabolism and tumor progression in breast cancer","volume":"5","author":"Kreuzaler","year":"2023","journal-title":"Nat Metab"},{"key":"2025090403075024400_bib67","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1038\/s41392-023-01649-4","article-title":"Nuclear transport proteins: structure, function, and disease relevance","volume":"8","author":"Yang","year":"2023","journal-title":"Signal Transduct Target Ther"},{"issue":"Suppl 4","key":"2025090403075024400_bib68","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1200\/JCO.2023.41.4_suppl.494","article-title":"Nanvuranlat, an L-type amino acid transporter (LAT1) inhibitor for patients with pretreated advanced refractory biliary tract cancer (BTC): primary endpoint results of a randomized, double-blind, placebo-controlled phase 2 study","volume":"41","author":"Furuse","year":"2023","journal-title":"J Clin Oncol"},{"key":"2025090403075024400_bib69","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1038\/s41572-022-00398-y","article-title":"Gallbladder cancer","volume":"8","author":"Roa","year":"2022","journal-title":"Nat Rev Dis Primers"},{"key":"2025090403075024400_bib70","doi-asserted-by":"crossref","first-page":"2012","DOI":"10.1158\/2159-8290.CD-23-0475","article-title":"RLY-4008, the first highly selective FGFR2 inhibitor with activity across FGFR2 alterations and resistance mutations","volume":"13","author":"Subbiah","year":"2023","journal-title":"Cancer Discov"},{"key":"2025090403075024400_bib71","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1016\/j.cels.2018.03.002","article-title":"Scalable open science approach for mutation calling of tumor exomes using multiple genomic pipelines","volume":"6","author":"Ellrott","year":"2018","journal-title":"Cell Syst"},{"key":"2025090403075024400_bib72","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/978-1-4939-3341-9_1","article-title":"Multiplexed quantitative proteomics for high-throughput comprehensive proteome comparisons of human cell lines","volume":"1394","author":"Edwards","year":"2016","journal-title":"Methods Mol Biol"},{"key":"2025090403075024400_bib73","doi-asserted-by":"crossref","first-page":"937","DOI":"10.1038\/nmeth.1714","article-title":"MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics","volume":"8","author":"Ting","year":"2011","journal-title":"Nat Methods"},{"key":"2025090403075024400_bib74","doi-asserted-by":"crossref","first-page":"7150","DOI":"10.1021\/ac502040v","article-title":"MultiNotch MS3 enables accurate, sensitive, and multiplexed detection of differential expression across cancer cell line proteomes","volume":"86","author":"McAlister","year":"2014","journal-title":"Anal Chem"},{"key":"2025090403075024400_bib75","doi-asserted-by":"crossref","first-page":"1241","DOI":"10.1021\/ac503934f","article-title":"Evaluating multiplexed quantitative phosphopeptide analysis on a hybrid quadrupole mass filter\/linear ion trap\/orbitrap mass spectrometer","volume":"87","author":"Erickson","year":"2015","journal-title":"Anal Chem"},{"key":"2025090403075024400_bib76","doi-asserted-by":"crossref","first-page":"976","DOI":"10.1016\/1044-0305(94)80016-2","article-title":"An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database","volume":"5","author":"Eng","year":"1994","journal-title":"J Am Soc Mass Spectrom"},{"key":"2025090403075024400_bib77","doi-asserted-by":"crossref","first-page":"1865","DOI":"10.1007\/s13361-015-1179-x","article-title":"A deeper look into Comet\u2013implementation and features","volume":"26","author":"Eng","year":"2015","journal-title":"J Am Soc Mass Spectrom"},{"key":"2025090403075024400_bib78","doi-asserted-by":"crossref","first-page":"1174","DOI":"10.1016\/j.cell.2010.12.001","article-title":"A tissue-specific atlas of mouse protein phosphorylation and expression","volume":"143","author":"Huttlin","year":"2010","journal-title":"Cell"},{"key":"2025090403075024400_bib79","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/nmeth1019","article-title":"Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry","volume":"4","author":"Elias","year":"2007","journal-title":"Nat Methods"},{"key":"2025090403075024400_bib80","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1016\/j.cell.2019.12.023","article-title":"Quantitative proteomics of the cancer cell line encyclopedia","volume":"180","author":"Nusinow","year":"2020","journal-title":"Cell"},{"key":"2025090403075024400_bib81","doi-asserted-by":"crossref","first-page":"3971","DOI":"10.1158\/0008-5472.CAN-21-0791","article-title":"Gene fusions create partner and collateral dependencies essential to cancer cell survival","volume":"81","author":"Gillani","year":"2021","journal-title":"Cancer Res"},{"key":"2025090403075024400_bib82","doi-asserted-by":"crossref","first-page":"660","DOI":"10.1016\/j.ccell.2023.03.007","article-title":"Generation and multi-dimensional profiling of a childhood cancer cell line atlas defines new therapeutic opportunities","volume":"41","author":"Sun","year":"2023","journal-title":"Cancer Cell"},{"key":"2025090403075024400_bib83","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J R Stat Soc Series B Stat Methodol"},{"key":"2025090403075024400_bib84","doi-asserted-by":"crossref","first-page":"R41","DOI":"10.1186\/gb-2011-12-4-r41","article-title":"GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers","volume":"12","author":"Mermel","year":"2011","journal-title":"Genome Biol"},{"key":"2025090403075024400_bib85","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1038\/ng0506-500","article-title":"GenePattern 2.0","volume":"38","author":"Reich","year":"2006","journal-title":"Nat Genet"},{"key":"2025090403075024400_bib86","doi-asserted-by":"crossref","first-page":"4415","DOI":"10.1093\/bioinformatics\/btac542","article-title":"DiNAMIC.Duo: detecting somatic DNA copy number differences without a normal reference","volume":"38","author":"Walter","year":"2022","journal-title":"Bioinformatics"},{"key":"2025090403075024400_bib87","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1038\/srep00336","article-title":"Consensus clustering in complex networks","volume":"2","author":"Lancichinetti","year":"2012","journal-title":"Sci Rep"},{"key":"2025090403075024400_bib88","doi-asserted-by":"crossref","first-page":"013142","DOI":"10.1063\/1.4790830","article-title":"Robust detection of dynamic community structure in networks","volume":"23","author":"Bassett","year":"2013","journal-title":"Chaos"},{"key":"2025090403075024400_bib89","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1007\/BF01908075","article-title":"Comparing partitions","volume":"2","author":"Hubert","year":"1985","journal-title":"J Classification"},{"key":"2025090403075024400_bib90","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1186\/s13059-021-02540-7","article-title":"Chronos: a cell population dynamics model of CRISPR experiments that improves inference of gene fitness effects","volume":"22","author":"Dempster","year":"2021","journal-title":"Genome Biol"},{"key":"2025090403075024400_bib91","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1038\/s41588-021-00819-w","article-title":"A first-generation pediatric cancer dependency map","volume":"53","author":"Dharia","year":"2021","journal-title":"Nat Genet"},{"key":"2025090403075024400_bib92","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1016\/j.cell.2017.07.005","article-title":"Project drive: a compendium of cancer dependencies and synthetic lethal relationships uncovered by large-scale, deep RNAi screening","volume":"170","author":"McDonald","year":"2017","journal-title":"Cell"},{"key":"2025090403075024400_bib93","doi-asserted-by":"crossref","first-page":"D1210","DOI":"10.1093\/nar\/gkad986","article-title":"COSMIC: a curated database of somatic variants and clinical data for cancer","volume":"52","author":"Sondka","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2025090403075024400_bib94","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1186\/1471-2105-12-323","article-title":"RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome","volume":"12","author":"Li","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2025090403075024400_bib95","doi-asserted-by":"crossref","first-page":"R29","DOI":"10.1186\/gb-2014-15-2-r29","article-title":"voom: precision weights unlock linear model analysis tools for RNA-seq read counts","volume":"15","author":"Law","year":"2014","journal-title":"Genome Biol"},{"key":"2025090403075024400_bib96","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1186\/1471-2105-14-128","article-title":"Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool","volume":"14","author":"Chen","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"2025090403075024400_bib97","doi-asserted-by":"crossref","first-page":"W90","DOI":"10.1093\/nar\/gkw377","article-title":"Enrichr: a comprehensive gene set enrichment analysis web server 2016 update","volume":"44","author":"Kuleshov","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2025090403075024400_bib98","doi-asserted-by":"crossref","first-page":"e90","DOI":"10.1002\/cpz1.90","article-title":"Gene set knowledge discovery with enrichr","volume":"1","author":"Xie","year":"2021","journal-title":"Curr Protoc"},{"key":"2025090403075024400_bib99","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1186\/s13059-023-03020-w","article-title":"Partial gene suppression improves identification of cancer vulnerabilities when CRISPR-Cas9 knockout is pan-lethal","volume":"24","author":"Krill-Burger","year":"2023","journal-title":"Genome Biol"},{"key":"2025090403075024400_bib100","doi-asserted-by":"crossref","first-page":"btac757","DOI":"10.1093\/bioinformatics\/btac757","article-title":"GSEApy: a comprehensive package for performing gene set enrichment analysis in Python","volume":"39","author":"Fang","year":"2023","journal-title":"Bioinformatics"},{"key":"2025090403075024400_bib101","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1093\/bioinformatics\/btr260","article-title":"Molecular signatures database (MSigDB) 3.0","volume":"27","author":"Liberzon","year":"2011","journal-title":"Bioinformatics"},{"key":"2025090403075024400_bib102","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/j.cels.2015.12.004","article-title":"The Molecular Signatures Database (MSigDB) hallmark gene set collection","volume":"1","author":"Liberzon","year":"2015","journal-title":"Cell Syst"}],"container-title":["Cancer Discovery"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/aacrjournals.org\/cancerdiscovery\/article-pdf\/doi\/10.1158\/2159-8290.CD-24-1383\/3604265\/cd-24-1383.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/aacrjournals.org\/cancerdiscovery\/article-pdf\/doi\/10.1158\/2159-8290.CD-24-1383\/3638632\/cd-24-1383.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/aacrjournals.org\/cancerdiscovery\/article-pdf\/15\/9\/1858\/3646633\/cd-24-1383.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/aacrjournals.org\/cancerdiscovery\/article-pdf\/15\/9\/1858\/3646633\/cd-24-1383.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,4]],"date-time":"2025-09-04T07:08:17Z","timestamp":1756969697000},"score":1,"resource":{"primary":{"URL":"https:\/\/aacrjournals.org\/cancerdiscovery\/article\/15\/9\/1858\/764365\/Generation-of-a-Biliary-Tract-Cancer-Cell-Line"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,12]]},"references-count":102,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2025,5,12]]},"published-print":{"date-parts":[[2025,9,4]]}},"URL":"https:\/\/doi.org\/10.1158\/2159-8290.cd-24-1383","relation":{"is-supplemented-by":[{"id-type":"doi","id":"10.1158\/2159-8290.30050661","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2159-8290.30050640","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2159-8290.30050670","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2159-8290.30050643","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2159-8290.30050676","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2159-8290.30050655","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2159-8290.30050652","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2159-8290.30050658","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2159-8290.30050667","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2159-8290.30050646","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2159-8290.30050649","asserted-by":"object"}],"has-preprint":[{"id-type":"doi","id":"10.1158\/2159-8290.c.8016663","asserted-by":"object"}]},"ISSN":["2159-8274","2159-8290"],"issn-type":[{"value":"2159-8274","type":"print"},{"value":"2159-8290","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,5,12]]}}}