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.


| INTRODUCTION
BRCA-1 associated protein 1 (BAP1) (MIM: 603089) is a tumor suppressor gene with variants that may present an increased risk of tumor development. 1,2[4] BAP1 pathogenic germline variants are reported to have a high penetrance rate in TPDS1, reaching up to 85% of affected individuals presenting with more than one of the aforementioned tumors. 3,4izabeth Casey West and Marco Chiappetta equally contributed to the manuscript (co-first authors).
Filippo Lococo and Luigi Boccuto equally contributed to the manuscript (co-last authors).
However, some BAP1 germline heterozygous missense variants have also been associated with a second condition: a neurodevelopmental disorder called Kury-Isidor syndrome (KURIS) (MIM: 619762), a rare syndromic form of intellectual disability and congenital developmental delay. 5This syndrome was only recently described and the actual incidence and clinical implications for patients and family management are still far from being established.
In this review, our objective is to examine the clinical and genetic characteristics of BAP1-TPDS1 and KURIS, suggest potential genotype-phenotype correlations, and investigate the impact of BAP1 germline alterations on clinical management and genetic counseling.

| BAP1 FUNCTION
The BRCA1-associated protein 1 (BAP1) tumor suppressor gene is located on chromosome 3p21.3and encodes a protein involved in multiple critical cellular functions, including cell proliferation and division, cell death, and DNA damage repair. 6The protein is a deubiquitinase enzyme (DUB) that regulates the ubiquitin-proteasome pathway, which play with these interactions due to its critical role in stabilizing Sp1 in the pathway toward inducing apoptosis. 8In addition to being a DUB for damaged DNA, BAP1 also plays an important role in the Polycomb repressive complex 2 (PRC2), which regulates the ubiquitination of Histone H2A lysine 119.Pathogenic BAP1 variants may lead to damage in chromatin structure by an excess of Histone H2A lysine 119 ubiquitination, which can negatively influence DNA transcription. 9For its centrality in life-sustaining processes, BAP1 genetic alterations are associated with severe conditions.Besides the aforementioned germline variants, BAP1 pathogenic variants are reported to occur somatically and are associated with various cancer types.Approximately 80% of the reported BAP1 variants were classified as somatic, but this percentage may be inflated due to germline variants being underscored based on tumor-only analyses. 10ss-of-function (LoF) BAP1 variants cause an increase in the activity of the ubiquitin-proteasome pathway, leading to the accumulation of damaged proteins, thereby contributing to cancer development.
Noticeably, not all BAP1 variants described so far are cancercausing.Table 1 includes BAP1 variants associated with TPDS1 as well as the ones causing a rare neurodevelopmental disorder, Kury-Isidor syndrome (KURIS).These variants were identified from the OMIM database 14 and the UCSC Genome Browser 15 due to the databases' extensive validation and evidence of the functional role of BAP1 variants.Of note, 106 unique germline BAP1 variants were identified from 181 families with significant cancer incidence in Walpole et al. 3 and 225 pathogenic variants have been identified in ClinVar. 16e trend emerging from the genetic findings reported so far indicates that the variants associated with a predisposition to cancer are null (splice site and truncated protein) while missense variants are associated with KURIS.Four missense variants from  As mentioned earlier, these variants elevate the risk of multiple cancer types, characterized by aggressiveness, rapid growth, and earlier onset compared to sporadic cases. 18The four main TPDS1-related cancers-uveal melanoma, malignant pleural mesothelioma, cutaneous melanoma, and renal cell carcinoma-exhibit significantly higher frequencies in individuals with germline BAP1 variants compared to the general population's lifetime risk.Uveal melanoma has the highest frequency at around 30%-34%, followed by mesothelioma (22%-25%), cutaneous melanoma (13%), and renal cell carcinoma (10%). 3,18Mice with germline BAP1 variants show increased susceptibility to environmental exposures, notably asbestos in malignant pleural mesothelioma. 19 familial cases of uveal melanoma, cutaneous melanoma, and malignant pleural mesothelioma, the detection of BAP1 pathogenic variants was reported in 25%, 0.7%, and 20%, respectively. 11,20,21In TPDS1 individuals, unique characteristics and disease progression may be observed.For instance, malignant pleural mesothelioma in TPDS1 patients has a median survival of 9-12 months, whereas those with mesothelioma and TPDS1 may surpass 60 months. 22,23TPDS1 individuals often receive an earlier diagnosis, approximately 10 years before the general population's average age of diagnosis. 23Managing TPDS1 families becomes intricate, requiring a balance between early diagnosis and treatment and the psychological implications of longterm surveillance.This paper aims to describe the clinical management of TPDS1 patients, focusing on malignant pleural mesothelioma.

| Kury-Isidor syndrome (KURIS)
Kury et al. 5 identified 11 individuals with a distinct neurodevelopmental disorder and heterozygous de novo BAP1 missense variants (see Table 1 and Figure 1).Intriguingly, none of the 11 subjects developed tumors of any type, although their ages ranged from 2 to 16 years at The site of the variants does not appear predictive of the associated phenotype, as all but one of the identified KURIS variants are in the peptidase-ubiquitin hydrolase domain (residues 5-233), similar to various TPDS1-associated variants (see Table 1 and Figure 1).The young age of the patients described limits definitive conclusions.Current treatment recommendations are per clinical guidelines for all potential cancer types associated with TPDS1, except uveal melanoma and malignant mesothelioma.BAP1 uveal melanoma is recommended to be treated like the aggressive class 2 tumors or monosomy three tumors, and malignant mesothelioma is recommended to be treated by a physician familiar with BAP1.The recommended prevention methods are similar to the general population for cutaneous melanomas.Uveal melanoma and malignant mesothelioma are recommended to avoid arc welding, asbestos exposure, and/or smoking. 24The risk of developing certain tumors-hepatocellular carcinoma, cholangiocarcinoma, and meningioma-has been proposed to be higher in carriers of BAP1 variants, but due to lack of validation, clinical management protocols should be considered depending on the detection of suggestive clinical traits or abnormal laboratory markers.

| Screening and surveillance of patients with BAP1-related malignant pleural mesothelioma
Individuals with TPDS1 and malignant pleural mesothelioma exhibit distinctive characteristics, setting them apart from those with sporadic mesothelioma.In summary, these patients are often younger, present more advanced disease, and have less or no asbestos exposure, yet demonstrate increased survival compared to sporadic cases. 25,26The presence of a BAP1 pathogenic variant can serve as a target for immunotherapy or targeted therapies, potentially improving survival rates. 11,27Due to these unique characteristics, specific screening criteria have been proposed to identify potential BAP1-TPDS1 patients (Table 2).
Recognizing patients with BAP1 variants is crucial not only for planning therapeutic strategies but also for the active surveillance of relatives and early detection of tumor-related conditions.Chau et al. 4 drawing from a population study in the Netherlands, suggested that two BAP1-TPDS1-associated tumors or the presence of one TPDS1-associated tumor in a first-or second-degree relative, coupled with a young age of tumor onset, strongly correlate with a genetic predisposition.This age criterion has been incorporated into the proposed RAI criteria for screening, 18 considering the onset of mesothelioma in patients under 50 years as indicative of a genetic predisposition.
Zauderer et al. 25 proposed similar screening criteria, detailing the type of tumor involved.TPDS1-suspected mesothelioma may manifest in patients with more than two relatives with a mesothelioma history, no known history of asbestos exposure, and an age below 50 years at diagnosis.If these criteria are met, BAP1 genetic analysis is considered appropriate.An essential aspect of screening exams is the combination of clinical and instrumental monitoring, as suggested by several studies, involving ophthalmologic and dermatologic evaluations, along with radiological follow-up using magnetic resonance or computed tomography for tumors in the brain, pleural cavity, or abdomen. 4,6,28 is crucial to note that the European guidelines on BAP1 surveillance, as outlined by Lalloo et al. 30 do not include MRI surveillance for mesothelioma due to a lack of evidence supporting its efficacy.These guidelines emphasize the importance of adhering to evidence-based practices in the diagnosis and surveillance of BAP1 tumor predisposition syndrome.
There is variability regarding the age and temporal interval of follow-up execution, particularly for uveal and skin evaluations, recommended to commence at 2 years. 6Conversely, screening for malignant pleural mesothelioma should begin between 30 and 40 years 6,28 and be conducted every 1-2 years.Determining the best diagnostic exam for early detection remains unclear, as blood markers are unreliable and CT scans may miss initial or small pleural nodules.
Therefore, magnetic resonance may be adopted in this setting, as previously reported. 28tient education and information are essential for cancer prevention, encouraging the avoidance of smoking and asbestos exposure and promoting awareness of cancer-related symptoms such as cough or dyspnea. 6However, executing any screening strategy can be highly stressful, requiring the involvement of different specialists.Psychological implications are particularly significant due to the long or life-long follow-up in young people or adolescents.Despite the age of incidence of suspected BAP1-TPDS1 mesothelioma being 50 years, surveillance for other tumors, such as melanoma, should begin at 16-18 years. 4,25Considering the potential for burnout and interruption of scheduled exams during a long-life follow-up, concerted efforts by public health institutions and patients are necessary to ensure the appropriate treatment for these individuals.
Surveillance appears to be associated with survival advantages and cost-effectiveness, as described by Walpole et al. 31 They reported an increased rate of cancers diagnosed at a late stage (62.8% vs. 10.7%) and a higher rate of BAP1-related deaths (50.2% vs. 35.4%) in the non-surveillance arm.Conversely, surveillance in patients with TPDS1 was linked to an increased survival of 4.9 years and an additional cost of US $6197.At the time of writing this manuscript, two clinical trials are underway to investigate the clinical history of TPDS1, aiming to identify the best surveillance strategy and assess effective cancer-specific survival rates in these patients.
The "Long-Term Follow-up of Mesothelioma Patients With Germline Mutations in BAP1 and Other Genes" trial (NCT03830229) 29 is responsible for the degradation of unnecessary or damaged proteins within the cell.It acts as a negative regulator in this pathway by removing ubiquitin, a tag that marks proteins for degradation from other proteins thereby stabilizing the proteins within the cell.The BAP1 protein resides in both the cytoplasm and nucleus of the cell, with different functions: it is involved in DNA repair mechanisms in the nucleus, while it regulates apoptosis in the cytoplasm.6BAP1 also plays a prominent role in regulating the tumor suppressor protein p53, which prevents the development of cancerous cells.PARP1 and 2 can induce the accumulation of BAP1 at sites of DNA damage where it then interacts with p53 to recruit DNA repair molecules such as BRCA-1, RAD51, and RPA.7 It has been shown that the C-terminal domain of p53 stabilizes Sp1, a transcription factor of Bax, directly regulating the Bax promoter.Bax is a protein that is upregulated and triggers the apoptotic cascade, effectively mitigating cancerous and damaged cell growth.BAP1 comes into

1
Graphical representation of pathogenic variants' distribution, type, and association in the BRCA1-associated protein 1 (BAP1) gene.KURIS, Kury-Isidor syndrome; TPDS1, tumor predisposition syndrome 1. the time of the study.All patients exhibited missense mutations causing a loss-of-function effect disrupting BAP1's deubiquitinase activity without affecting other protein functions.The associated erroneous histone ubiquitination in KURIS changed chromatin remodeling and downstream dysregulation in developmental genes.Given that KURIS has been described in only one study and in 11 young individuals, a longitudinal observational study on these 11 patients would be valuable to confirm whether these missense variants are associated with an increased oncogenic risk.

3 | RESULTS 3 . 1 |
Clinical management of patients with BAP1 germline variantsThe diagnosis of neurodevelopmental impairments in young subjects with KURIS may precede-and perhaps even suggest-the genetic test revealing the BAP1 variant.The lack of information on adult patients with KURIS hampers the design of specific surveillance or management protocols for this condition.Since it is not possible to rule out an increased oncogenic risk for subjects with KURIS-associated variants over their lifetime, the possibility of implementing a surveillance protocol should be discussed during the genetic counseling with the patient's family.For the BAP1 variants associated with TPDS1, instead, it is possible to exclude with significant confidence any risk to develop the neurodevelopmental, immune, digestive, or cardiac problems associated with KURIS, especially since most signs and symptoms are evident since the first years of life in subjects with KURIS.In fact, for individuals with TPDS1-associated BAP1 variants, the main concern is the increased risk of developing various types of cancer, particularly malignant pleural mesothelioma.Since TPDS1 is characterized by an autosomal dominant pattern of inheritance, individuals with germline BAP1 variants considered to cause this condition should receive genetic counseling even if they have not developed any tumor.The clinical presentation in individuals with TPDS1 may vary dramatically, and incomplete penetrance may occur in obligated carriers; moreover, a precise estimate of the risk of developing mesothelioma or other cancers is hampered by the lack of large studies on carriers of BAP1 germline variants.For these reasons, every individual with a variant causing a truncated BAP1 protein should be managed as a potential patient with TPDS1, even in the absence of signs and symptoms compatible with the clinical diagnosis of this condition.Genetic testing should be proposed for all first-degree relatives since they may be carriers of the same variant.Environmental factors, particularly asbestos, heavily influence the risk for malignant pleural mesothelioma: since it has been proved that a predisposing genetic profile may increase the chance of developing this aggressive cancer in the case of environmental asbestos exposure, BAP1 should be screened in individuals that might be exposed to this mineral.Interestingly, TPDS1 patients with mesotheliomas have a better prognosis than the ones with mesothelioma caused by asbestos alone. 11Nevertheless, they should follow a strict surveillance protocol based on periodic imaging (preferably MRI) and laboratory tests.The same protocol should be proposed to unaffected carriers of BAP1-TPDS1 variants as well, to diagnose the condition before the onset of any tumor and in consideration of the aggressive course of several types of cancers associated with TPDS1, like malignant pleural mesothelioma or uveal melanoma.
aims to study the natural history of patients and families with BAP1 germline variants and other DNA repair gene mutations, using non-invasive methods for early diagnosis.Similarly, findings emerging from a recent clinical trial propose photon-counting T A B L E 2 Proposed surveillance exams in TPDS1 (from literature and ongoing trials). of cell-free DNA every 2 years and yearly in individuals over 40, plus Uniportal VATS and laparoscopy every 3 years for individuals over 33 years old.32This trial aims to evaluate mesothelioma incidence and its natural history in terms of prognosis and therapy response, in association with the development and validation of screening using CT, cell-free DNA, and minimally invasive surgery.These two trials aim to provide robust information to improve the management of individuals with BAP1-TPDS1, especially in terms of early diagnosis and therapeutic strategies, while also assessing the possibility of prophylactic pleurectomy in high-risk patients.In summary, TPDS1 should be suspected in patients with a history of multiple and/or early onset BAP1-associated tumors, considering family history, before proceeding with a genetic test.Once the BAP1 germline variant is identified, surveillance should commence with the goal of achieving an early diagnosis, even though the appropriate types of exams and schedules still need to be defined.4| DISCUSSIONThe characterization of both germline and somatic BAP1 variants is integral to optimizing clinical management, follow-up protocols, and genetic counseling.Aligned with established guidelines such as the European guidelines by Lalloo et al.30 and the ESMO guidelines,33 comprehensive genetic testing is emphasized.Immediate genetic testing of germline DNA, preferably from blood specimens, is essential post-identification of BAP1 variants in cancerous cell DNA to minimize the risk of somatic mosaicism.The justification for these tests lies in confirming the same BAP1 variant in both tumor and non-tumor DNA, significantly impacting treatment approaches and overall prognosis.Furthermore, the identification of a germline BAP1 variant in individuals with TPDS1 warrants genetic counseling for the subject and relatives who may carry the same genetic alteration, sharing a similar risk of developing TPDS1-associated tumors.Recommending additional genetic studies is prudent to gather more information on both somatic and germline BAP1 variants, exploring potential genotypephenotype correlations with clinical characteristics like severity, age of onset, histological type, prognosis, and drug response.Conversely, detecting a germline BAP1 variant in a subject without TPDS1-associated tumors requires a different approach.Existing knowledge indicates that KURIS and TPDS1 are allelic and mutually exclusive conditions with clear genotype-phenotype correlations.Genetic counseling is advisable for healthy subjects with a germline BAP1 variant to determine its pathogenicity, association with KURIS (no documented increased risk for cancer development but possibly warranting surveillance protocols), or TPDS1 (increased risk of specific tumors, requiring specific surveillance protocols).Sharing information about the variant and associated risks with other family members should also be considered.This comprehensive approach to characterizing BAP1 variants, following established guidelines, contributes to enhanced clinical decision-making and effective genetic counseling for both affected individuals and their families.