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Diagnostics of BAP1-Tumor Predisposition Syndrome by a Multitesting Approach: A Ten-Year-Long Experience. Diagnostics (Basel) 2022; 12:diagnostics12071710. [PMID: 35885614 PMCID: PMC9317020 DOI: 10.3390/diagnostics12071710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 11/17/2022] Open
Abstract
Germline mutations in the tumor suppressor gene BRCA1-associated protein-1 (BAP1) lead to BAP1 tumor predisposition syndrome (BAP1-TPDS), characterized by high susceptibility to several tumor types, chiefly melanoma, mesothelioma, renal cell carcinoma, and basal cell carcinoma. Here, we present the results of our ten-year experience in the molecular diagnosis of BAP1-TPDS, along with a clinical update and cascade genetic testing of previously reported BAP1-TPDS patients and their relatives. Specifically, we sequenced germline DNA samples from 101 individuals with suspected BAP1-TPDS and validated pathogenic variants (PVs) by assessing BAP1 somatic loss in matching tumor specimens. Overall, we identified seven patients (7/101, 6.9%) carrying six different germline BAP1 PVs, including one novel variant. Consistently, cascade testing revealed a total of seven BAP1 PV carriers. In addition, we explored the mutational burden of BAP1-TPDS tumors by targeted next-generation sequencing. Lastly, we found that certain tumors present in PV carriers retain a wild-type BAP1 allele, suggesting a sporadic origin of these tumors or a functional role of heterozygous BAP1 in neoplastic development. Altogether, our findings have important clinical implications for therapeutic response of BAP1-TPDS patients.
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Shao YF, DeBenedictis M, Yeaney G, Singh AD. Germ Line BAP1 Mutation in Patients with Uveal Melanoma and Renal Cell Carcinoma. Ocul Oncol Pathol 2021; 7:340-345. [PMID: 34722490 DOI: 10.1159/000516695] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 04/17/2021] [Indexed: 12/19/2022] Open
Abstract
Uveal melanoma (UM) and renal cell carcinoma (RCC) can occur sporadically and as a manifestation of BAP1 tumor predisposition syndrome. We aimed to understand the prevalence of germ line BAP1 pathogenic variants in patients with UM and RCC. We reviewed patients managed at Cleveland Clinic between November 2003 and November 2019 who were diagnosed with UM and RCC. Charts were reviewed for demographic and cancer-related characteristics. RCC samples were tested for BAP1 protein expression using immunohistochemical (IHC) staining, and testing for germ line BAP1 pathogenic variants was performed as part of routine clinical care. Thirteen patients were included in the study. The average age at diagnosis of UM was 61.3 years. Seven patients underwent fine-needle aspiration biopsy for prognostic testing of UM (low risk =5, high risk =2). Twelve patients were treated with plaque radiation therapy, and 3 patients developed metastatic disease requiring systemic therapy. The median time to diagnosis of RCC from time of diagnosis of UM was 0 months. RCC samples were available for 7 patients for BAP1 IHC staining (intact =6, loss =1). All patients underwent nephrectomy (total = 3, partial = 8, unknown =2), and 1 received systemic therapy for metastatic RCC. Six patients underwent germ line BAP1 genetic testing. Of these, 1 patient was heterozygous for a pathogenic variant of BAP1 gene: c.1781-1782delGG, p.Gly594Valfs*48. The overall prevalence of germ line BAP1 pathogenic variants in our study was high (1/6; 17%; 95% CI 0-46%). Patients with UM and RCC should be referred for genetic counseling to discuss genetic testing.
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Affiliation(s)
- Yusra F Shao
- Medicine Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | | | - Gabrielle Yeaney
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Arun D Singh
- Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio, USA
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Truderung OAH, Sagi JC, Semsei AF, Szalai C. Melanoma susceptibility: an update on genetic and epigenetic findings. INTERNATIONAL JOURNAL OF MOLECULAR EPIDEMIOLOGY AND GENETICS 2021; 12:71-89. [PMID: 34853632 PMCID: PMC8611230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
Malignant melanoma is one of the most highly ranked cancers in terms of years of life lost. Hereditary melanoma with its increased familial susceptibility is thought to affect up to 12% of all melanoma patients. In the past, only a few high-penetrance genes associated with familial melanoma, such as CDKN2A and CDK4, have been clinically tested. However, findings now indicate that melanoma is a cancer most likely to develop not only due to high-penetrance variants but also due to polygenic inheritance patterns, leaving no clear division between the hereditary and sporadic development of malignant melanoma. Various pathogenic low-penetrance variants were recently discovered through genome-wide association studies, and are now translated into polygenic risk scores. These can show superior sensitivity rates for the prediction of melanoma susceptibility and related mixed cancer syndromes than risk scores based on phenotypic traits of the patients, with odds ratios of up to 5.7 for patients in risk groups. In addition to describing genetic findings, we also review the first results of epigenetic research showing constitutional methylation changes that alter the susceptibility to cutaneous melanoma and its risk factors.
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Affiliation(s)
- Ole AH Truderung
- Department of Genetics, Cell- and Immunobiology, Semmelweis UniversityH-1089 Budapest, Hungary
| | - Judit C Sagi
- Department of Genetics, Cell- and Immunobiology, Semmelweis UniversityH-1089 Budapest, Hungary
| | - Agnes F Semsei
- Department of Genetics, Cell- and Immunobiology, Semmelweis UniversityH-1089 Budapest, Hungary
| | - Csaba Szalai
- Department of Genetics, Cell- and Immunobiology, Semmelweis UniversityH-1089 Budapest, Hungary
- Heim Pal Children’s HospitalH-1089 Budapest, Hungary
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Miller M, Schoenfield L, Abdel-Rahman M, Cebulla CM. Is Uveal Melanoma a Hormonally Sensitive Cancer? A Review of the Impact of Sex Hormones and Pregnancy on Uveal Melanoma. Ocul Oncol Pathol 2021; 7:239-250. [PMID: 34604195 PMCID: PMC8443925 DOI: 10.1159/000514650] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 01/21/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Despite a higher incidence and worse prognosis of uveal melanoma (UM) in men, there have been many case reports of pregnant patients with aggressive UM. This has led researchers to explore the influence of sex hormones and pregnancy on the development and progression of UM and hormones as potential therapeutic targets. SUMMARY A systematic literature review was conducted. More work is needed to elucidate the basis of sex differences in UM incidence and survival. The evaluation of germline BAP1 mutation would be beneficial in patients with UM presenting at a young age. Importantly, multiple studies reported no significant difference between the 5-year survival and 5-year metastasis-free survival rates between nonpregnant women with UM and pregnant women with UM. Multiple case-control studies disagree on how parity affects risk of UM. However, most studies agree that oral contraceptives and hormone replacement therapy have no effect on the incidence of UM. Current treatment strategies for pregnant patients with UM are discussed. Looking forward, this review reports recent research on targeted receptor-based chemotherapy, which is based on evidence of estrogen receptor (ER), estrogen-related receptor alpha (ERRα), and luteinizing hormone-releasing hormone (LHRH) receptor expression in UM. KEY MESSAGES Based on review of the literature, UM is not a contraindication to oral contraceptives, hormone replacement therapy, or pregnancy. Globe-sparing radiation can be used as a treatment option for pregnant patients. Due to the presence of ER on a subset of unselected UM, its potential for adjunctive targeted therapy with agents like tamoxifen should be explored. Lessons from cutaneous melanoma regarding tissue ratios of estrogen receptors (ERα:ERβ) should be applied to assess their therapeutic predictive value. In addition, ERRα-targeted therapeutics and LHRH analogs are worthy of further exploration in UM.
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Affiliation(s)
- Manisha Miller
- Havener Eye Institute, Department of Ophthalmology and Visual Sciences, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Lynn Schoenfield
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Mohamed Abdel-Rahman
- Havener Eye Institute, Department of Ophthalmology and Visual Sciences, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
- Division of Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Colleen M. Cebulla
- Havener Eye Institute, Department of Ophthalmology and Visual Sciences, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
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Singh N, Singh R, Bowen RC, Abdel-Rahman MH, Singh AD. Uveal Melanoma in BAP1 Tumor Predisposition Syndrome: Estimation of Risk. Am J Ophthalmol 2021; 224:172-177. [PMID: 33316260 DOI: 10.1016/j.ajo.2020.12.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 12/23/2022]
Abstract
PURPOSE To estimate point prevalence of uveal melanoma in the patients with germline BAP1 pathogenic variant. DESIGN Cohort study with risk assessment using Bayesian analysis. METHODS The point prevalence estimate was obtained by Bayes's rule of reverse conditional probabilities. The probability of uveal melanoma given that BAP1 mutation exists was derived from the prevalence of uveal melanoma, prevalence of germline BAP1 pathogenic variants, and the probability of germline BAP1 pathogenic variant given that uveal melanoma is present. Confidence intervals (CIs) for each variable were calculated as the mean of Bernoulli random variables and for the risk estimate, by the delta method. The age at diagnosis and the gender of the uveal melanoma patients with BAP1 germline pathogenic variants obtained from previous publications or from authors' unpublished cohort was compared with those in the Surveillance, Epidemiology, and End Results (SEER) database. RESULTS The point prevalence of uveal melanoma in patients with the germline BAP1 pathogenic variants in the US population was estimated to be 2.8% (95% CI, 0.88%-4.81%). In the SEER database, the median age at diagnosis of uveal melanomas was 63 (range 3-99 years) with a male-to-female ratio of 1.01:1. In comparison, uveal melanoma cases with BAP1 germline pathogenic variants from the US population (n = 27) had a median age at diagnosis of 50.5 years (range 16-71). CONCLUSIONS Quantification of the risk of developing uveal melanoma can enhance counseling regarding surveillance in patients with germline BAP1 pathogenic variant.
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Affiliation(s)
- Nakul Singh
- Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA
| | - Rahul Singh
- Department of Economics and Statistics and Data Science Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Randy Chris Bowen
- Department of Ophthalmic Oncology, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Mohamed H Abdel-Rahman
- Department of Ophthalmology and Visual Science, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA; Division of Human Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Arun D Singh
- Department of Ophthalmic Oncology, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio, USA.
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Repo P, Järvinen RS, Jäntti JE, Markkinen S, Täll M, Raivio V, Turunen JA, Kivelä TT. Population-based analysis of BAP1 germline variations in patients with uveal melanoma. Hum Mol Genet 2020; 28:2415-2426. [PMID: 31058963 DOI: 10.1093/hmg/ddz076] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/03/2019] [Accepted: 04/03/2019] [Indexed: 02/06/2023] Open
Abstract
Pathogenic germline variants in the BRCA1-associated protein 1 (BAP1) gene cause the BAP1 tumor predisposition syndrome (BAP1-TPDS) with increased risk of several cancers, the most frequent of which is uveal melanoma (UM). Pathogenicity of loss-of-function (LOF) BAP1 variants is clear, as opposed to that of missense and regulatory region variants. We sequenced the coding, promoter, untranslated region (UTR) and intronic regions of BAP1 and analyzed copy number variations (CNVs). In this nationwide study, the cohort comprised UM patients diagnosed between 2010 and 2017. These included 432 of 520 consecutive Finnish UM patients, 16 of whom were familial, and one additional patient from a Finnish-Swedish family. Twenty-one different rare variants were found: seven exonic, seven intronic, four 3' UTR and three promoter. We considered five variants likely to be pathogenic by effect on splicing, nuclear localization or deubiquitination activity. Intron 2 (c.67+1G>T) and exon 14 (c.1780_1781insT) LOF variants were presumed founder mutations, occurring in two and four families, respectively; both abolished nuclear localization in vitro. Intron 2, exons 5 (c.281A>G) and 9 (c.680G>A) missense variants markedly reduced deubiquitinating activity. A deep intronic 25 base pair deletion in intron 1 caused aberrant splicing in vitro. On the basis of functional studies and family cancer history, we classified four exon 13 missense variants as benign. No CNVs were found. The prevalence of pathogenic variants was 9/433 (2%) and 4/16 (25%) in Finnish UM families. Family cancer history and functional assays are indispensable when establishing the pathogenicity of BAP1 variants. Deep intronic variants can cause BAP1-TPDS.
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Affiliation(s)
- Pauliina Repo
- Folkhälsan Research Center, Biomedicum Helsinki, Haartmaninkatu, FI Helsinki, Finland.,Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu C, FI Helsinki, Finland
| | - Reetta-Stiina Järvinen
- Folkhälsan Research Center, Biomedicum Helsinki, Haartmaninkatu, FI Helsinki, Finland.,Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu C, FI Helsinki, Finland
| | - Johannes E Jäntti
- Folkhälsan Research Center, Biomedicum Helsinki, Haartmaninkatu, FI Helsinki, Finland
| | - Salla Markkinen
- Folkhälsan Research Center, Biomedicum Helsinki, Haartmaninkatu, FI Helsinki, Finland
| | - Martin Täll
- Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu C, FI Helsinki, Finland
| | - Virpi Raivio
- Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu C, FI Helsinki, Finland
| | - Joni A Turunen
- Folkhälsan Research Center, Biomedicum Helsinki, Haartmaninkatu, FI Helsinki, Finland.,Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu C, FI Helsinki, Finland
| | - Tero T Kivelä
- Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu C, FI Helsinki, Finland
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Abdel-Rahman MH, Sample KM, Pilarski R, Walsh T, Grosel T, Kinnamon D, Boru G, Massengill JB, Schoenfield L, Kelly B, Gordon D, Johansson P, DeBenedictis MJ, Singh A, Casadei S, Davidorf FH, White P, Stacey AW, Scarth J, Fewings E, Tischkowitz M, King MC, Hayward NK, Cebulla CM. Whole Exome Sequencing Identifies Candidate Genes Associated with Hereditary Predisposition to Uveal Melanoma. Ophthalmology 2019; 127:668-678. [PMID: 32081490 DOI: 10.1016/j.ophtha.2019.11.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/13/2019] [Accepted: 11/11/2019] [Indexed: 01/08/2023] Open
Abstract
PURPOSE To identify susceptibility genes associated with hereditary predisposition to uveal melanoma (UM) in patients with no detectable germline BAP1 alterations. DESIGN Retrospective case series from academic referral centers. PARTICIPANTS Cohort of 154 UM patients with high risk of hereditary cancer defined as patients with 1 or more of the following: (1) familial UM, (2) young age (<35 years) at diagnosis, (3) personal history of other primary cancers, and (4) family history of 2 or more primary cancers with no detectable mutation or deletion in BAP1 gene. METHODS Whole exome sequencing, a cancer gene panel, or both were carried out. Probands included 27 patients with familial UM, 1 patient with bilateral UM, 1 patient with congenital UM, and 125 UM patients with strong personal or family histories, or both, of cancer. Functional validation of variants was carried out by immunohistochemistry, reverse-transcriptase polymerase chain reaction, and genotyping. MAIN OUTCOME MEASURES Clinical characterization of UM patients with germline alterations in known cancer genes. RESULTS We identified actionable pathogenic variants in 8 known hereditary cancer predisposition genes (PALB2, MLH1, MSH6, CHEK2, SMARCE1, ATM, BRCA1, and CTNNA1) in 9 patients, including 3 of 27 patients (11%) with familial UM and 6 of 127 patients (4.7%) with a high risk for cancer. Two patients showed pathogenic variants in CHEK2 and PALB2, whereas variants in the other genes each occurred in 1 patient. Biallelic inactivation of PALB2 and MLH1 was observed in tumors from the respective patients. The frequencies of pathogenic variants in PALB2, MLH1, and SMARCE1 in UM patients were significantly higher than the observed frequencies in noncancer controls (PALB2: P = 0.02; odds ratio, 8.9; 95% confidence interval, 1.5-30.6; MLH1: P = 0.04; odds ratio, 25.4; 95% confidence interval, 1.2-143; SMARCE1: P = 0.001; odds ratio, 2047; 95% confidence interval, 52-4.5e15, respectively). CONCLUSIONS The study provided moderate evidence of gene and disease association of germline mutations in PALB2 and MLH1 with hereditary predisposition to UM. It also identified several other candidate susceptibility genes. The results suggest locus heterogeneity in predisposition to UM. Genetic testing for hereditary predisposition to cancer is warranted in UM patients with strong personal or family history of cancers, or both.
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Affiliation(s)
- Mohamed H Abdel-Rahman
- Department of Ophthalmology and Visual Science, Havener Eye Institute, The Ohio State University, Columbus, Ohio; Division of Human Genetics, Department of Internal Medicine, The Ohio State University, Columbus, Ohio.
| | - Klarke M Sample
- Department of Ophthalmology and Visual Science, Havener Eye Institute, The Ohio State University, Columbus, Ohio
| | - Robert Pilarski
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
| | - Tomas Walsh
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Timothy Grosel
- Department of Ophthalmology and Visual Science, Havener Eye Institute, The Ohio State University, Columbus, Ohio
| | - Daniel Kinnamon
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
| | - Getachew Boru
- Department of Ophthalmology and Visual Science, Havener Eye Institute, The Ohio State University, Columbus, Ohio
| | - James B Massengill
- Department of Ophthalmology and Visual Science, Havener Eye Institute, The Ohio State University, Columbus, Ohio
| | - Lynn Schoenfield
- Department of Pathology, The Ohio State University, Columbus, Ohio
| | - Ben Kelly
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - David Gordon
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - Peter Johansson
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Meghan J DeBenedictis
- Department of Ophthalmic Oncology, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio
| | - Arun Singh
- Department of Ophthalmic Oncology, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio
| | - Silvia Casadei
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Frederick H Davidorf
- Department of Ophthalmology and Visual Science, Havener Eye Institute, The Ohio State University, Columbus, Ohio
| | - Peter White
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - Andrew W Stacey
- Department of Ophthalmology, University of Washington, Seattle, Washington
| | - James Scarth
- Academic Laboratory of Medical Genetics and National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Ellie Fewings
- Academic Laboratory of Medical Genetics and National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Marc Tischkowitz
- Academic Laboratory of Medical Genetics and National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom; East Anglian Medical Genetics Service, Cambridge University Hospitals, Cambridge, United Kingdom
| | - Mary-Claire King
- Department of Genome Sciences, University of Washington, Seattle, Washington; Department of Medicine, University of Washington, Seattle, Washington
| | | | - Colleen M Cebulla
- Department of Ophthalmology and Visual Science, Havener Eye Institute, The Ohio State University, Columbus, Ohio
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