BAP1 Tumor Predisposition Syndrome Research Articles

BRCA1-associated protein 1: Tumor predisposition syndrome and Kury-Isidor syndrome, from genotype-phenotype correlation to clinical management.

The BAP1 tumor suppressor gene encodes a deubiquitinase enzyme involved in several cellular activities, including DNA repair and apoptosis. Germline pathogenic variants in BAP1 have been associated with heritable conditions including BAP1 tumor predisposition syndrome 1 (BAP1-TPDS1) and a neurodevelopmental disorder known as Kury-Isidor syndrome (KURIS). Both these conditions are caused by monoallelic, dominant alterations of BAP1 but have never been reported in the same subject or family, suggesting a mutually exclusive genotype-phenotype correlation. This distinction is extremely important considering the early onset and aggressive nature of the types of cancer reported in individuals with TPDS1. Genetic counseling in subjects with germline BAP1 variants is fundamental to predicting the effect of the variant and the expected phenotype, assessing the potential risk of developing cancer for the tested subject and the family members who may carry the same variant and providing the multidisciplinary clinical team with the proper information to establish precise surveillance and management protocols.

Hereditary cancer syndromes with increased risk of renal cancer

Renal cancer (RC) is one of the three most common diseases in oncologic urology. Its accurate diagnosis and prognosis remain difficult and important problems. Some cases of RC are associated with hereditary cancer syndromes and are caused by germline mutations. This review describes monogenic forms of hereditary RC (von Hippel–Lindau syndrome, Birt–Hogg– Dubé syndrome, hereditary leiomyomatosis and renal cell cancer, hereditary papillary renal carcinoma, BAP1 tumor predisposition syndrome) and diseases with several candidate genes (SDH-mutated tumors, tuberous sclerosis complex). Additionally, the review discusses the increased risk of RC in patients with frequent hereditary cancer syndromes predisposing to the development of a wide range of tumor types: Lynch and Li-Fraumeni syndromes. RC in combination with other carcinomas can develop in patients carrying pathogenic mutations in the candidate genes of different hereditary cancer syndromes – multi-locus inherited neoplasia allele syndrome (MINAS) – which is especially important due to the growing role of high-throughput sequencing in practical oncologic genetics. Additionally, guidelines on modern laboratory genetic diagnostics and active surveillance are presented for each syndrome.

Functional assay for assessment of pathogenicity of BAP1 variants.

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. 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 4h) and proliferation (at 48h), measured as cell index (CI), using xCELLigence real-time analysis system. In BAP1 knockout HAP1 cultures, cell number was half of wild type (WT) cultures at 48h (p = 0.00021), reaching confluence later, and CI was 78% reduced (p < 0.0001). BAP1-TPDS-associated null variants c.67+1G>T and c.1780_1781insT, and a likely pathogenic missense variant c.281A>G reduced adhesion (all p ≤ 0.015) and proliferation by 74%-83% (all p ≤ 0.032). Another likely pathogenic missense variant c.680G>A reduced both by at least 50% (all p ≤ 0.032), whereas cells edited with likely benign one c.1526C>T grew similarly to WT. 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.

Loss of BAP1 Protein Expression by Immunohistochemistry in the Salivary Duct Carcinoma Component of an Intracapsular Carcinoma ex Pleomorphic Adenoma of the Parotid Gland.

BRCA1-associated protein 1 (BAP1) is a tumor suppressor gene that is altered in a variety of neoplasms as well as in BAP1 tumor predisposition syndrome. BAP1 alterations are associated with aggressive behavior in some malignancies and may have treatment implications in future. We present the first documented case of loss of BAP1 protein expression by immunohistochemistry in the salivary duct carcinoma (SDC) component of an intracapsular carcinoma ex pleomorphic adenoma (CXPA) in the context of molecular loss of function of BAP1 in the neoplasm. A woman of approximately 55years of age presented with a deep parotid lobe mass, which was resected and found to be CXPA. BAP1 immunohistochemistry and next-generation sequencing was performed to further characterize the neoplasm. The neoplasm showed loss of BAP1 protein expression in the SDC component but retention in the residual pleomorphic adenoma (PA). Next-generation sequencing confirmed a BAP1 loss of function alteration in the neoplasm. This is the first documented case report of BAP1 protein expression loss in the SDC component of a CXPA. Future studies are needed to investigate the relevance of BAP1 alterations in SDC and CXPA, which may have prognostic and treatment implications.

BAP1 Malignant Pleural Mesothelioma Mutations in Caenorhabditis elegans Reveal Synthetic Lethality between ubh-4/BAP1 and the Proteasome Subunit rpn-9/PSMD13.

The deubiquitinase BAP1 (BRCA1-associated protein 1) is associated with BAP1 tumor predisposition syndrome (TPDS). BAP1 is a tumor suppressor gene whose alterations in cancer are commonly caused by gene mutations leading to protein loss of function. By CRISPR-Cas, we have generated mutations in ubh-4, the BAP1 ortholog in Caenorhabditis elegans, to model the functional impact of BAP1 mutations. We have found that a mimicked BAP1 cancer missense mutation (UBH-4 A87D; BAP1 A95D) resembles the phenotypes of ubh-4 deletion mutants. Despite ubh-4 being ubiquitously expressed, the gene is not essential for viability and its deletion causes only mild phenotypes without affecting 20S proteasome levels. Such viability facilitated an RNAi screen for ubh-4 genetic interactors that identified rpn-9, the ortholog of human PSMD13, a gene encoding subunit of the regulatory particle of the 26S proteasome. ubh-4[A87D], similarly to ubh-4 deletion, cause a synthetic genetic interaction with rpn-9 inactivation affecting body size, lifespan, and the development of germ cells. Finally, we show how ubh-4 inactivation sensitizes animals to the chemotherapeutic agent Bortezomib, which is a proteasome inhibitor. Thus, we have established a model to study BAP1 cancer-related mutations in C. elegans, and our data points toward vulnerabilities that should be studied to explore therapeutic opportunities within the complexity of BAP1 tumors.

Difficult to Diagnose Cutaneous Melanoma in a Patient with BAP1 Tumor Predisposition Syndrome.

BRCA1-associated protein 1 (BAP1)-inactivated melanomas can occur sporadically or in germline contexts, particularly in recently recognized BAP1-tumor predisposition syndrome. Diagnosis represents a clinical and histopathological challenge, requiring comprehensive analysis of morphology and sometimes molecular analysis in addition to immunohistochemistry. We report a BAP1-inactivated cutaneous melanoma initially diagnosed as an atypical Spitz tumor on the auricle in a patient with BAP1-tumor predisposition syndrome. Immunohistochemistry, fluorescence in situ hybridization, and comparative genomic hybridization allowed diagnosis. Cutaneous BAP1-inactivated melanocytic tumors, previously classified as atypical Spitz Nevi, may have a dermal mitotic activity that can resemble melanoma and on the other hand, atypical Spitz tumors are sometimes difficult to differentiate from BAP1-inactivated melanoma. Specific criteria, requiring molecular diagnosis have been proposed in order to support melanoma diagnosis.

Mutational signature of extracranial meningioma metastases and their respective primary tumors

Extracranial metastases of intracranial meningiomas are rare. Little is known about the mutational pattern of these tumors and their metastatic seeding. Here, we retrospectively explored the molecular alterations of these metastatic lesions and their respective intracranial tumor manifestations.Histology and genome sequencing were performed in intracranial meningiomas and their extracranial metastatic lesions operated upon between 2002 and 2021. Next-generation DNA/RNA sequencing (NGS) and methylome analysis were performed to determine molecular alterations.We analyzed the tumors of five patients with clinically suspected metastases of a meningioma using methylome analysis and next generation panel sequencing of the primary tumors as well as the metastatic lesions. Metastases were found in the spinal cord and one in the lung. In four of these patients, molecular analyses confirmed metastatic disease, while the fifth patient was found to harbor two molecularly distinct meningiomas. On pathological assessment, the primary lesions ranged from CNS WHO grades 1 to 3 (integrated molecular-morphologic meningioma classification scores 2 to 6). Of the four true metastatic cases, three out of the four metastasizing tumors harbored alterations in the BAP1 gene, comprising a stop-mutation combined with copy-number loss (WHO grade 1), copy number loss (WHO grade 3) and a frameshift mutation (WHO grade 2). Furthermore, the latter was confirmed to harbor a BAP1 tumor predisposition syndrome. The fourth metastasizing tumor had copy-number losses in NF2 and PTEN. Only one of four showed CDKN2A homozygous deletion; none showed TERT promotor mutation.Our results molecularly confirm true metastatic disease in four meningioma patients. BAP1 gene alterations were the most frequent. Larger cohorts, most likely from multicenter studies are necessary to evaluate the role of BAP-1 alterations to further understand the metastatic spread in meningiomas. for metastatic spread and might indicate patients at risk for metastatic spread. Further explorations within larger cohorts are necessary to validate these findings which might influence the clinical management in the future.

Commentary: Case report: Mesothelioma and BAP1 tumor predisposition syndrome: implications for public health.

Commentary: Case report: Mesothelioma and BAP1 tumor predisposition syndrome: implications for public health.

BAP1-Inactivated Melanoma Arising From BAP1-Inactivated Melanocytic Tumor in a Patient With BAP1 Germline Mutation: A Case Report and Review of the Literature.

BAP1-inactivated melanocytic tumors represent a subset of epithelioid melanocytic neoplasms resulting from biallelic inactivation of the BAP1 gene and by a driver mutation that activate the MAP kinase pathway, most commonly BRAFV600E. They occur sporadically or, less common, in the setting of BAP1 tumor predisposition syndrome caused by a BAP1 germline mutation that predisposes to several malignancies including cutaneous and uveal melanoma. To date, only few cases of BAP1-inactivated melanomas have been reported. We present a case of a 35-year-old woman presented with a melanocytic lesion microscopically composed of 3 distinct melanocytic populations, suggesting a stepwise progression model to melanoma from a conventional nevus through a melanocytoma stage. This progression was also supported from a molecular viewpoint given BRAFV600E, BAP1, and TERT-p hot spot mutations detected by targeted mutational analysis. Four atypical melanocytic lesions were removed from the patient's back, and the same A BAP1 c.856A>T, p.(Lys286Ter) mutation was detected on either tumoral or normal tissue samples. To the best of our knowledge, this is the first case of BAP1-inactivated melanoma with a documented TERT-p hot spot mutation manifesting as the first presentation of BAP1 tumor predisposition syndrome.

S2334 Incidentally Diagnosed Triple Cancers Within 2 Years: A Novel Case of Rare Metachronous Cancers, Renal Cell Carcinoma, Cholangiocarcinoma, and Squamous Cell Carcinoma of the Gastroesophageal Junction

Introduction: The gastrointestinal (GI) tract is involved in many familial cancer syndromes usually involving the colon or stomach. We present a patient with 3 rare cancers that were detected within a span of 2 years in a single individual: clear cell renal cell carcinoma (ccRCC), cholangiocarcinoma (CCA), and esophageal squamous cell carcinoma (SCC); a combination not previously described in the literature Case Description/Methods: A 50-year-old male with a history of ccRCC, GERD, and CCA was admitted for evaluation of chronic abdominal pain during chemotherapy for CCA. Regarding his cancer history, ccRCC was incidentally diagnosed 18 months prior on a CT scan for diverticulitis. He underwent a left partial nephrectomy. Surveillance CT imaging 6 months after surgery revealed new incidental liver lesions. Biopsies confirmed metastatic CCA and he started chemotherapy. He noted a 15-year history of episodic abdominal pain and vomiting with no dysphagia or weight loss. Upper endoscopy 16 months prior was normal. He was a former smoker, drank alcohol a few times per month, used marijuana daily, and used cocaine rarely. His family history was significant for multiple cancers at a young age on his maternal side of unknown type. Physical exam showed diffuse abdominal tenderness, worse in the epigastrium without guarding. Labs showed mild anemia, normal BMP/LFTs, and negative H. pylori stool antigen. Upper endoscopy found nodularity adjacent to the esophagogastric junction (EGJ) with abnormal pit pattern under narrow band imaging (Figure). Biopsies confirmed invasive SCC. Staging endoscopic ultrasound showed T3N3 EGJ SCC. He was referred to oncology to discuss treatment options. Genetic testing was positive for BAP1 tumor predisposition syndrome (BAP1-TPDS) Discussion: A review of published literature did not yield a previous description of this combination of cancers in a single individual. BAP1-TPDS is an uncommon autosomal dominant syndrome caused by germline mutation in a tumor suppressor gene. Patients typically present with melanocytic tumors or malignant mesotheliomas but are at risk for RCC, hepatocellular carcinoma, meningioma and CCA. Literature has not revealed esophageal SCC to be associated. In addition to the incidental nature and timing of diagnosis of all 3 of these cancers within a short period of 2 years, the EGJ involvement is unusual. This case suggests atypical EGJ-SCC may be considered as part of the BAP1-TPDS tumor spectrum and warrant additional screening for at-risk individuals.Figure 1.: Left panel showing abnormal nodular mucosa adjacent to the gastro-esophageal junction under high-definition white light imaging. Right panel showing the same area under narrow band imaging.

Diagnostics of BAP1-Tumor Predisposition Syndrome by a Multitesting Approach: A Ten-Year-Long Experience.

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.

Germ Line BAP1 Mutation in Patients with Uveal Melanoma and Renal Cell Carcinoma

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.

16545 Atypical presentation of BAP1-deficient tumors and review of BAP1 tumor predisposition syndrome

BAP1-deficient tumors (BDTs) are skin-colored to reddish-brown papules which are highly prevalent in BAP1 tumor predisposition syndrome and present at a younger age on average than syndrome-associated malignancies. These melanocytic neoplasms have both characteristic clinical and histologic appearances, and demonstrate loss of BAP1 on immunohistochemical staining. Associated malignancies include uveal and cutaneous melanomas, renal cell carcinoma, and mesothelioma, among others. We present a case of 2 BDTs, one with unusual clinical presentation, found within 1 year on an adolescent with a family history significant for breast cancer, nonmelanoma skin cancer, and dysplastic nevi, prompting pending genetic testing.

MALIGNANT MESOTHELIOMA AND GERMLINE HETEROZYGOUS BAP1 MUTATION IN A YOUNG WOMAN PRESENTING WITH RECURRENT PLEURAL EFFUSIONS AND WORSENING PNEUMOTHORAX AFTER TALC PLEURODESIS

SESSION TITLE: Fellows Lung Cancer Posters SESSION TYPE: Fellow Case Report Posters PRESENTED ON: October 18-21, 2020 INTRODUCTION: Germline BAP1 mutations are associated with a pattern of hereditary malignancies, namely uveal and cutaneous melanoma, malignant mesothelioma (MM), and renal cell carcinoma. We present a rare case of a young woman who was diagnosed with malignant pleural and peritoneal mesothelioma. CASE PRESENTATION: A 23 year-old woman with no known medical conditions or exposure to asbestos was referred to medical oncology after completing a video-assisted thoracoscopic surgery (VATS) followed by talc pleurodesis for recurrent pleural effusions of unknown etiology. Initial pleural fluid studies showed total protein 4.5 g/dL and LDH 150 U/L. Pleural fluid contained clusters of atypical mesothelial cells surrounded by inflammation suggestive of reactive mesothelial hyperplasia. VATS found abnormal reticulated surfaces and a white plaque-like tissue at the apex. Pleural biopsies showed atypical mesothelial proliferation suspicious for MM in a background of reactive changes, but ultimately results were considered non-diagnostic. Due to inconclusive pathology we recommended further evaluation with diagnostic laparoscopy because her CT scans also showed small volume ascites and pelvic fluid. Studding was noted on peritoneum, bowel, pelvic tissues, and omentum, and biopsies showed markedly atypical proliferation of epithelioid cells forming glandular and tubulopapillary structures with disorganized growth and focal invasion into adjacent adipose tissue. Immunostains of tumor cells were consistent with mesothelial differentiation. BAP-1 immunohistochemistry showed loss of expression only in tumor cells. Collectively these features supported a diagnosis of MM of epithelioid type. Peripheral blood testing for BAP1 tumor predisposition syndrome (BAP1-TPDS) was positive for a heterozygous germline BAP1 mutation, c.2050 C>T, p.Gln684* (Pilarski et al. 2013, Haugh et al. 2017). Staging scans prior to chemotherapy showed interval development of a pneumothorax in the right lung months after her talc pleurodesis. She was treated with cisplatin, pemetrexed, and bevacizumab with subsequent improvement of her pneumothorax. DISCUSSION: Our case report showed the clinical features of a patient with MM from BAP1-TPDS. Loss of BAP1 expression can help distinguish MM from reactive mesothelial cells (Cigognetti et al. 2015). Progression of her disease after having a talc pleurodesis manifested radiographically as a worsening pneumothorax, and chemotherapy was able to reverse this process. CONCLUSIONS: Unexplained pleural effusions or pleural or peritoneal biopsies showing atypical mesothelial cells should have immunohistochemistry testing for loss of BAP1 expression to evaluate for MM. MM due to BAP1-TPDS is responsive chemotherapy. Young MM patients without risk factors for MM should have germline testing for BAP1-TPDS. Reference #1: Pilarski, Robert, et al. “Expanding the Clinical Phenotype of hereditaryBAP1cancer Predisposition Syndrome, Reporting Three New Cases.” Genes, Chromosomes and Cancer, vol. 53, no. 2, 15 Nov. 2013, pp. 177–182., doi:10.1002/gcc.22129. Reference #2: Haugh, Alexandra M., et al. “Genotypic and Phenotypic Features of BAP1 Cancer Syndrome.” JAMA Dermatology, vol. 153, no. 10, 9 Aug. 2017, p. 999-1006., doi:10.1001/jamadermatol.2017.2330. Reference #3: Cigognetti, Marta, et al. “BAP1 (BRCA1-Associated Protein 1) Is a Highly Specific Marker for Differentiating Mesothelioma from Reactive Mesothelial Proliferations.” Modern Pathology, vol. 28, no. 8, 29 May 2015, pp. 1043–1057., doi:10.1038/modpathol.2015.65. DISCLOSURES: Speaker/Speaker's Bureau relationship with Daiichi Sankyo/AstraZeneca Please note: $1-$1000 Added 03/18/2020 by Blakely Kute, source=Web Response, value=Honoraria No relevant relationships by Eric Luk, source=Web Response

Concurrent germline and somatic pathogenic BAP1 variants in a patient with metastatic bladder cancer

Germline pathogenic variants in the BRCA1-associated protein-1 (BAP1) gene cause the BAP1 tumor predisposition syndrome (TPDS). BAP1 TPDS is associated with an increased risk of uveal and cutaneous melanoma, mesothelioma, renal cell carcinoma, and several other cancer subtypes. Here, we report a germline nonsense BAP1 variant (c.850G>T, p.Glu284Ter) in a patient with bladder cancer and a strong family history of malignancy. Concurrently, we identified a somatic frameshift BAP1 variant, and as expected, immunostaining validated the loss of BAP1 protein in patient-derived tumor specimens. Together, these data provide strong evidence of pathogenicity in this case. With the addition of bladder cancer to the tumor types reported with germline BAP1 mutations, our understanding of the BAP1 TPDS continues to evolve, and may affect future screening and surveillance guidelines.

Families with BAP1-Tumor Predisposition Syndrome in The Netherlands: Path to Identification and a Proposal for Genetic Screening Guidelines.

Germline pathogenic variants in the BRCA1-associated protein-1 (BAP1) gene cause the BAP1-tumor predisposition syndrome (BAP1-TPDS, OMIM 614327). BAP1-TPDS is associated with an increased risk of developing uveal melanoma (UM), cutaneous melanoma (CM), malignant mesothelioma (MMe), renal cell carcinoma (RCC), meningioma, cholangiocarcinoma, multiple non-melanoma skin cancers, and BAP1-inactivated nevi. Because of this increased risk, it is important to identify patients with BAP1-TPDS. The associated tumors are treated by different medical disciplines, emphasizing the need for generally applicable guidelines for initiating genetic analysis. In this study, we describe the path to identification of BAP1-TPDS in 21 probands found in the Netherlands and the family history at the time of presentation. We report two cases of de novo BAP1 germline mutations (2/21, 9.5%). Findings of this study combined with previously published literature, led to a proposal of guidelines for genetic referral. We recommend genetic analysis in patients with ≥2 BAP1-TPDS-associated tumors in their medical history and/or family history. We also propose to test germline BAP1 in patients diagnosed with UM <40 years, CM <18 years, MMe <50 years, or RCC <46 years. Furthermore, other candidate susceptibility genes for tumor types associated with BAP1-TPDS are discussed, which can be included in gene panels when testing patients.

Population-based analysis of BAP1 germline variations in patients with uveal melanoma

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.

Commentary on BRCA1-Associated Protein-1 Tumor Predisposition Syndrome in a Patient With Numerous Basal Cell Carcinomas

Commentary on BRCA1-Associated Protein-1 Tumor Predisposition Syndrome in a Patient With Numerous Basal Cell Carcinomas

Comprehensive Study of the Clinical Phenotype of Germline BAP1 Variant-Carrying Families Worldwide.

The BRCA1-associated protein-1 (BAP1) tumor predisposition syndrome (BAP1-TPDS) is a hereditary tumor syndrome caused by germline pathogenic variants in BAP1 encoding a tumor suppressor associated with uveal melanoma, mesothelioma, cutaneous melanoma, renal cell carcinoma, and cutaneous BAP1-inactivated melanocytic tumors. However, the full spectrum of tumors associated with the syndrome is yet to be determined. Improved understanding of the BAP1-TPDS is crucial for appropriate clinical management of BAP1 germline variant carriers and their families, including genetic counseling and surveillance for new tumors. We collated germline variant status, tumor diagnoses, and information on BAP1 immunohistochemistry or loss of somatic heterozygosity on 106 published and 75 unpublished BAP1 germline variant-positive families worldwide to better characterize the genotypes and phenotypes associated with the BAP1-TPDS. Tumor spectrum and ages of onset were compared between missense and null variants. All statistical tests were two-sided. The 181 families carried 140 unique BAP1 germline variants. The collated data confirmed the core tumor spectrum associated with the BAP1-TPDS and showed that some families carrying missense variants can exhibit this phenotype. A variety of noncore BAP1-TPDS -associated tumors were found in families of variant carriers. Median ages of onset of core tumor types were lower in null than missense variant carriers for all tumors combined (P < .001), mesothelioma (P < .001), cutaneous melanoma (P < .001), and nonmelanoma skin cancer (P < .001). This analysis substantially increases the number of pathogenic BAP1 germline variants and refines the phenotype. It highlights the need for a curated registry of germline variant carriers for proper assessment of the clinical phenotype of the BAP1-TPDS and pathogenicity of new variants, thus guiding management of patients and informing areas requiring further research.

Comparison of Germline versus Somatic BAP1 Mutations for Risk of Metastasis in Uveal Melanoma

BackgroundGermline mutations in BAP1 have been associated with BAP1-Tumor Predisposition Syndrome (BAP1-TPDS), a predisposition to multiple tumors within a family that includes uveal melanoma (UM), cutaneous melanoma, malignant mesothelioma and renal cell carcinoma. Alternatively, somatic mutations in BAP1 in UM have been associated with high risk for metastasis. In this study, we compare the risk of metastasis in UM that carry germline versus somatic BAP1 mutations and mutation-negative tumors.MethodsDNA extracted from 142 UM and matched blood samples was sequenced using Sanger or next generation sequencing to identify BAP1 gene mutations.ResultsEleven of 142 UM (8%) carried germline BAP1 mutations, 43 (30%) had somatic mutations, and 88 (62%) were mutation-negative. All BAP1 mutations identified in blood samples were also present in the matched UM. There were 52 unique mutations in 54 tumors. All were pathogenic or likely pathogenic.A comparison of tumors carrying somatic vs. germline mutations, or no mutations, showed a higher frequency of metastasis in tumors carrying somatic mutations: 74% vs. 36%, P=0.03 and 74% vs. 26% P<0.001, respectively. Tumors with a somatic mutation compared to mutation-negative had an older age of diagnosis of (61.8 vs. 52.2 years, P=0.002), and shorter time to metastasis (16 vs. 26 months, P=0.04). Kaplan-Meier analysis further showed that tumors with somatic (vs. germline) mutations demonstrated a greater metastatic risk (P=0.03). Cox multivariate analysis showed in addition to chromosome-3 monosomy and larger tumor diameter, the presence of BAP1 somatic, but not germline mutations, was significantly associated with risk of metastasis(P=0.02).Personal or family history of BAP1-TPDS was available for 79 of the cases. All eight cases with germline mutations reported a history of BAP1-TPDS, which was significantly greater than what was observed in cases with somatic mutations (10 of 23, P=0.009) or mutation-negative cases (11 of 48, P<0.001).ConclusionsDefining germline vs. somatic nature of BAP1 mutations in UM can inform the individual about both the risk of metastasis, and the time to metastasis, which are critically important outcomes for the individual. This information can also change the cascade screening and surveillance of family members.