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A compendium of Amplification-Related Gain Of Sensitivity genes in human cancer
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Cancer precision medicine. Dana Farber Canc Inst, Dept Med Oncol, Boston, MA 02215 USA.;Dana Farber Canc Inst, Ctr Neurooncol, Boston, MA 02215 USA.;Dana Farber Canc Inst, Dept Canc Biol, Boston, MA 02215 USA.;Harvard Med Sch, Boston, MA 02115 USA.;Broad Inst Harvard & MIT, Cambridge, MA 02142 USA..ORCID iD: 0000-0002-2983-4020
Netherlands Canc Inst, Oncode Inst, Div Cell Biol, Amsterdam, Netherlands.;Univ Med Ctr Groningen UMCG, European Res Inst Biol Ageing ERIBA, Groningen, Netherlands.;Helmholtz Munich, Inst Computat Biol, Neuherberg, Germany.;Med Univ Innsbruck, Inst Bioinformat, Innsbruck, Austria..ORCID iD: 0000-0002-6862-5221
Dana Farber Canc Inst, Dept Med Oncol, Boston, MA 02215 USA.;Dana Farber Canc Inst, Ctr Neurooncol, Boston, MA 02215 USA.;Dana Farber Canc Inst, Dept Canc Biol, Boston, MA 02215 USA.;Broad Inst Harvard & MIT, Cambridge, MA 02142 USA..ORCID iD: 0009-0001-9967-1538
Univ Med Ctr Groningen UMCG, European Res Inst Biol Ageing ERIBA, Groningen, Netherlands..
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2025 (English)In: Nature Communications, E-ISSN 2041-1723, Vol. 16, no 1, article id 1077Article in journal (Refereed) Published
Abstract [en]

While the effect of amplification-induced oncogene expression in cancer is known, the impact of copy-number gains on "bystander" genes is less understood. We create a comprehensive map of dosage compensation in cancer by integrating expression and copy number profiles from over 8000 tumors in The Cancer Genome Atlas and cell lines from the Cancer Cell Line Encyclopedia. Additionally, we analyze 17 cancer open reading frame screens to identify genes toxic to cancer cells when overexpressed. Combining these approaches, we propose a class of 'Amplification-Related Gain Of Sensitivity' (ARGOS) genes located in commonly amplified regions, yet expressed at lower levels than expected by their copy number, and toxic when overexpressed. We validate RBM14 as an ARGOS gene in lung and breast cancer cells, and suggest a toxicity mechanism involving altered DNA damage response and STING signaling. We additionally observe increased patient survival in a radiation-treated cancer cohort with RBM14 amplification.

Place, publisher, year, edition, pages
Springer Nature, 2025. Vol. 16, no 1, article id 1077
National Category
Cancer and Oncology Medical Genetics and Genomics
Identifiers
URN: urn:nbn:se:uu:diva-550677DOI: 10.1038/s41467-025-56301-2ISI: 001408553700011PubMedID: 39870664Scopus ID: 2-s2.0-85217190281OAI: oai:DiVA.org:uu-550677DiVA, id: diva2:1940378
Funder
Swedish Research Council, 2022-01539EU, European Research Council, 945674Available from: 2025-02-26 Created: 2025-02-26 Last updated: 2025-04-25Bibliographically approved

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