{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T01:45:37Z","timestamp":1760060737299,"version":"build-2065373602"},"reference-count":59,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2025,9,25]],"date-time":"2025-09-25T00:00:00Z","timestamp":1758758400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Young Talents Program of Sun Yat-sen University Cancer Center","award":["YTP-SYSUCC-0029","32370698"],"award-info":[{"award-number":["YTP-SYSUCC-0029","32370698"]}]},{"DOI":"10.13039\/501100001809","name":"Natural Science Foundation of China","doi-asserted-by":"publisher","award":["YTP-SYSUCC-0029","32370698"],"award-info":[{"award-number":["YTP-SYSUCC-0029","32370698"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biology"],"abstract":"<jats:p>Phase separation is one of the mechanisms critical for protein function, and its aberrances are associated with cancer development. However, mutations that affect protein phase separation and cancer development have not been systematically identified and analyzed. In this study, we systematically identified the mutations affecting protein liquid\u2013liquid phase separation in multiple cancers. We calculated the phase separation scores alterations for over 1,200,000 mutations across 16 cancer types using the TCGA dataset. We then performed pathway enrichment, kinase, TF enrichment, and survival analysis to identify related biological processes and clinical implications. Nearly 10% of the mutations were defined to affect phase separation in pan-cancer. These mutations occupied a consistent percentage in each cancer type. Extremely influencing mutations accumulate on stomach adenocarcinoma (STAD), uterine corpus endometrial carcinoma (UCEC), and skin cutaneous melanoma (SKCM). Moreover, proteins carrying these mutations are enriched in cancer-related pathways, including TGF-beta signaling pathways and polycomb repressive complex. Phase separation of these proteins would be regulated by kinases, including CDK1, CDK2, and EGFR, and transcription factors, including ZNF407, ZNF318, and MGA proteins, to play functions in cancer. Protein\u2013Protein Interaction Network revealed that these phase separation proteins are highly interconnected. Finally, patients carrying mutations that positively affect the protein phase separation are associated with poor prognosis in skin cutaneous melanoma (SKCM) and lung squamous cell carcinoma (LUSC), which could be partially explained by the pathogenicity of these mutations. The study provided a pan-cancer landscape for depicting the association of phase separation and cancer mutations, which would be a rich data resource for understanding the association of cancer mutations and phase separation.<\/jats:p>","DOI":"10.3390\/biology14101320","type":"journal-article","created":{"date-parts":[[2025,9,25]],"date-time":"2025-09-25T07:46:49Z","timestamp":1758786409000},"page":"1320","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Pan-Cancer Analysis of Mutations Affecting Protein Liquid\u2013Liquid Phase Separation Revealing Clinical Implications"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0009-0005-1965-0059","authenticated-orcid":false,"given":"Xiaoping","family":"Cen","sequence":"first","affiliation":[{"name":"State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China"},{"name":"Digital Health Center, Berlin Institute of Health (BIH), Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin, 10178 Berlin, Germany"},{"name":"College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-5549-6170","authenticated-orcid":false,"given":"Lulu","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kai","family":"Yu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0858-3410","authenticated-orcid":false,"given":"Huanming","family":"Yang","sequence":"additional","affiliation":[{"name":"College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China"},{"name":"HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), Zhejiang Cancer Hospital, Hangzhou 310022, China"},{"name":"BGI, Shenzhen 518083, China"},{"name":"James D. Watson Institute of Genome Sciences, Hangzhou 310029, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roland","family":"Eils","sequence":"additional","affiliation":[{"name":"Digital Health Center, Berlin Institute of Health (BIH), Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin, 10178 Berlin, Germany"},{"name":"Intelligent Medicine Institute, Fudan University, Shanghai 200032, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Dong","sequence":"additional","affiliation":[{"name":"HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), Zhejiang Cancer Hospital, Hangzhou 310022, China"},{"name":"Clin Lab, BGI Genomics, Beijing 100000, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huan","family":"Lin","sequence":"additional","affiliation":[{"name":"The Affiliated TCM Hospital of Guangzhou Medical University, Guangzhou 510020, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9698-0610","authenticated-orcid":false,"given":"Zexian","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,9,25]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1016\/j.tcb.2018.02.004","article-title":"Protein Phase Separation: A New Phase in Cell Biology","volume":"28","author":"Boeynaems","year":"2018","journal-title":"Trends Cell Biol."},{"key":"ref_2","first-page":"649","article-title":"Kinase regulation by liquid\u2013liquid phase separation","volume":"33","author":"Andersen","year":"2022","journal-title":"Trends Cell Biol."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Wang, B., Zhang, L., Dai, T., Qin, Z., Lu, H., Zhang, L., and Zhou, F. 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