Citation: Cole, Y.C.; Zhang, Y.-Z.; Gallo, B.; Januszewski, A.P.; Nastase, A.; Essex, D.J.; Thaung, C.M.H.; Cohen, V.M.L.; Sagoo, M.S.; Bowcock, A.M. Correlation between BAP1 Localization, Driver Mutations, and Patient Survival in Uveal Melanoma. Cancers 2022, 14, 4105. https:// doi.org/10.3390/cancers14174105 Academic Editors: Alfonso Baldi and Ulrich Pfeffer Received: 25 July 2022 Accepted: 13 August 2022 Published: 25 August 2022 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). cancers Article Correlation between BAP1 Localization, Driver Mutations, and Patient Survival in Uveal Melanoma Yasemin C. Cole 1 , Yu-Zhi Zhang 1,2 , Beatrice Gallo 3 , Adam P. Januszewski 1 , Anca Nastase 1 , David J. Essex 3 , Caroline M. H. Thaung 4,5 , Victoria M. L. Cohen 3,4 , Mandeep S. Sagoo 3,4 and Anne M. Bowcock 1,6, * 1 National Heart and Lung Institute, Imperial College London, London SW3 6LR, UK 2 Department of Histopathology, Royal Brompton and Harefield NHS Foundation Trust, London SW3 6NP, UK 3 Ocular Oncology Service, Moorfields Eye Hospital & St. Bartholomew’s Hospital, London EC1V 2PD, UK 4 Moorfields Eye Hospital, London EC1V 2PD, UK 5 Department of Eye Pathology, UCL Institute of Ophthalmology, London EC1V 9EL, UK 6 Departments of Oncological Sciences, Dermatology and Genetics & Genome Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA * Correspondence: anne.bowcock@mssm.edu; Tel.: +1-212-659-8256 Simple Summary: 100 uveal melanomas from the UK were analyzed for molecular biomarkers, including alterations of chromosomes 3 and 8, cellular localization of BAP1, and genes known to be mutated in uveal melanoma. Consistent with earlier studies, loss of nuclear BAP1 (nBAP1) predicted shorter overall survival. Tumors with BAP1 loss of function mutations frequently exhibited heterogeneous BAP1 staining, and tumors with ≥25% loss of nBAP1 were a more reliable prognosistic indicator than chromosome 3 loss (LOH3) or chromosome 8q gain. Regardless of mutation class, most BAP1 mutations led to loss of nBAP1 and aberrant expression of cBAP1. Abstract: Uveal melanoma (UM) is an uncommon but highly aggressive ocular malignancy. Poor overall survival is associated with deleterious BAP1 alterations, which frequently occur with mono- somy 3 (LOH3) and a characteristic gene expression profile. Tumor DNA from a cohort of 100 UM patients from Moorfields Biobank (UK) that had undergone enucleation were sequenced for known UM driver genes (BAP1, SF3B1, EIF1AX, GNAQ, and GNA11). Immunohistochemical staining of BAP1 and interphase FISH for chromosomes 3 and 8 was performed, and cellular localization of BAP1 was correlated with BAP1 mutations. Wildtype (WT) BAP1 staining was characterized by nBAP1 expression with <10% cytoplasmic BAP1 (cBAP1). Tumors exhibited heterogeneity with respect to BAP1 staining with different percentages of nBAP1 loss: ≥25% loss of nuclear BAP1 (nBAP1) was superior to chr8q and LOH3 as a prognostic indicator. Of the successfully sequenced UMs, 38% harbored oncogenic mutations in GNA11 and 48% harbored mutations in GNAQ at residues 209 or 183. Of the secondary drivers, 39% of mutations were in BAP1, 11% were in EIF1AX, and 20% were in the SF3B1 R625 hotspot. Most tumors with SF3B1 or EIF1AX mutations retained nuclear BAP1 (nBAP1). The majority of tumor samples with likely pathogenic BAP1 mutations, regardless of mutation class, displayed ≥25% loss of nBAP1. This included all tumors with truncating mutations and 80% of tumors with missense mutations. In addition, 60% of tumors with truncating mutations and 82% of tumors with missense mutations expressed >10% cBAP1. Keywords: uveal melanoma; biomarkers; survival; metastasis; BAP1; SF3B1; EIF1AX; monosomy 3; immunohistochemistry; nonsense-mediated decay 1. Introduction Approximately 7000 individuals worldwide per year are diagnosed with uveal melanoma (UM) [1], accounting for 3.7% of all melanomas [1,2]. Although a relatively rare malignancy, UM is associated with significant morbidity, including, but not limited to, the loss of sight and ultimately the eye in advanced stages. UM arises from melanocytes of the uveal Cancers 2022, 14, 4105. https://doi.org/10.3390/cancers14174105 https://www.mdpi.com/journal/cancers