{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T23:21:35Z","timestamp":1787008895995,"version":"build-2736575974"},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2023,11,13]],"date-time":"2023-11-13T00:00:00Z","timestamp":1699833600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Helsinki University Hospital Research Fund","award":["TYH2023338"],"award-info":[{"award-number":["TYH2023338"]}]},{"name":"Helsinki University Hospital Research Fund","award":["TYH2023312"],"award-info":[{"award-number":["TYH2023312"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,2,18]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Pathogenic germline variants in BRCA1-Associated Protein 1 (BAP1) cause BAP1 tumor predisposition syndrome (BAP1-TPDS). Carriers run especially a risk of uveal (UM) and cutaneous melanoma, malignant mesothelioma, and clear cell renal carcinoma. Approximately half of increasingly reported BAP1 variants lack accurate classification. Correct interpretation of pathogenicity can improve prognosis of the patients through tumor screening with better understanding of BAP1-TPDS.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We edited five rare BAP1 variants with differing functional characteristics identified from patients with UM in HAP1 cells using CRISPR-Cas9 and assayed their effect on cell adhesion\/spreading (at 4\u00a0h) and proliferation (at 48\u00a0h), measured as cell index (CI), using xCELLigence real-time analysis system.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>In BAP1 knockout HAP1 cultures, cell number was half of wild type (WT) cultures at 48\u00a0h (p\u2009=\u20090.00021), reaching confluence later, and CI was 78% reduced (p\u2009&amp;lt;\u20090.0001). BAP1-TPDS-associated null variants c.67+1G&amp;gt;T and c.1780_1781insT, and a likely pathogenic missense variant c.281A&amp;gt;G reduced adhesion (all p\u2009\u2264\u20090.015) and proliferation by 74%\u201383% (all p\u2009\u2264\u20090.032). Another likely pathogenic missense variant c.680G&amp;gt;A reduced both by at least 50% (all p\u2009\u2264\u20090.032), whereas cells edited with likely benign one c.1526C&amp;gt;T grew similarly to WT.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>BAP1 is essential for optimal fitness of HAP1 cells. Pathogenic and likely pathogenic BAP1 variants reduced cell fitness, reflected in adhesion\/spreading and proliferation properties. Further, moderate effects were quantifiable. Variant modelling in HAP1 with CRISPR-Cas9 enabled functional analysis of coding and non-coding region variants in an endogenous expression system.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/hmg\/ddad193","type":"journal-article","created":{"date-parts":[[2023,11,10]],"date-time":"2023-11-10T09:33:41Z","timestamp":1699608821000},"page":"426-434","source":"Crossref","is-referenced-by-count":5,"title":["Functional assay for assessment of pathogenicity of\n                    <i>BAP1<\/i>\n                    variants"],"prefix":"10.1093","volume":"33","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9257-9376","authenticated-orcid":false,"given":"Pauliina E","family":"Repo","sequence":"first","affiliation":[{"name":"Biomedicum Helsinki Eye Genetics Group, Folkh\u00e4lsan Research Center, , Haartmaninkatu 8, FI-00290, Helsinki , Finland"},{"name":"University of Helsinki and Helsinki University Hospital Ocular Oncology Service, Department of Ophthalmology, , Haartmaninkatu 4 C, PL220, FI-00029 HUS, Helsinki , Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael P","family":"Backlund","sequence":"additional","affiliation":[{"name":"Biomedicum Helsinki Eye Genetics Group, Folkh\u00e4lsan Research Center, , Haartmaninkatu 8, FI-00290, Helsinki , Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tero T","family":"Kivel\u00e4","sequence":"additional","affiliation":[{"name":"University of Helsinki and Helsinki University Hospital Ocular Oncology Service, Department of Ophthalmology, , Haartmaninkatu 4 C, PL220, FI-00029 HUS, Helsinki , Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9569-9146","authenticated-orcid":false,"given":"Joni A","family":"Turunen","sequence":"additional","affiliation":[{"name":"Biomedicum Helsinki Eye Genetics Group, Folkh\u00e4lsan Research Center, , Haartmaninkatu 8, FI-00290, Helsinki , Finland"},{"name":"University of Helsinki and Helsinki University Hospital Ophthalmic Genetics and Rare Eye Diseases Service, Department of Ophthalmology, , Haartmaninkatu 4 C, PL220, FI-00029 HUS, Helsinki , Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,11,13]]},"reference":[{"key":"2024022010043248400_ref1","doi-asserted-by":"crossref","first-page":"873","DOI":"10.1016\/j.jtho.2022.03.014","article-title":"Medical and surgical Care of Patients with mesothelioma and their relatives carrying germline BAP1 mutations","volume":"17","author":"Carbone","year":"2022","journal-title":"J Thorac Oncol"},{"key":"2024022010043248400_ref2","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1038\/s41568-020-0265-y","article-title":"Tumour predisposition and cancer syndromes as models to study gene-environment interactions","volume":"20","author":"Carbone","year":"2020","journal-title":"Nat Rev 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