Clinical Description
BAP1 tumor predisposition syndrome (BAP1-TPDS) is associated with increased risk for a number of cancers and a specific skin lesion, BAP1-inactivated melanocytic tumor (BIMT; formerly called atypical Spitz tumor). Affected individuals can have more than one type of primary cancer [Abdel-Rahman et al 2011, Testa et al 2011, Wiesner et al 2011, Popova et al 2013, Walpole et al 2018].
Because of the limited number of families reported to date and ascertainment bias of groups focusing on uveal melanoma, malignant mesothelioma, and cutaneous melanoma, the penetrance and frequencies of the various BAP1-associated tumors are yet to be determined. In an attempt to adjust for ascertainment bias, Walpole et al [2018] (as noted below) compared the prevalence of each component tumor in probands with BAP1-TPDS to the prevalence in relatives known to also have a BAP1 pathogenic variant. It has been well established, however, that the following tumor types are associated with BAP1-TPDS.
BAP1-inactivated melanocytic tumor (BIMT; formerly called atypical Spitz tumor). The natural history of these lesions is not clearly known. It appears that individuals with BAP1-TPDS typically have multiple lesions [Haugh et al 2017]. BIMT are skin colored to reddish brown, averaging 5 mm in diameter; the histologic findings are between those of a Spitz nevus and a melanoma. Both copies of BAP1 are inactivated, leading to loss of staining for the BAP1 protein on immunohistochemistry; in addition, BIMT usually have somatic BRAF pathogenic variant p.Val600Glu.
Uveal melanoma (UM) is the cancer most commonly reported in persons with BAP1-TPDS (36% of probands and 16% of relatives reported with BAP1-TPDS have UM), and it is the cancer with the earliest reported age of diagnosis (age 16 years) [Walpole et al 2018]. Median age of onset of UM in persons with BAP1-TPDS is 53 years, which is younger than the onset of UM in the general population (62 years). The tumors are generally more aggressive class 2 (i.e., high metastatic risk) tumors with reduced survival [Njauw et al 2012, Rai et al 2016]. In one study, mean length of survival in persons whose UM lacked BAP1 expression was 4.74 years compared to 9.97 years in persons whose tumors expressed BAP1 [Kalirai et al 2014].
Malignant mesothelioma (MMe) is the second most frequent cancer (25% of probands and 19% of relatives) identified in individuals with BAP1-TPDS [Walpole et al 2018]. Several studies have shown that the median age of onset of MMe in individuals with BAP1-TPDS was significantly earlier (55 to 58 years) than that of sporadic MMe (68-72 years) [Baumann et al 2015, Ohar et al 2016, Walpole et al 2018]. In the general population, pleural MMe accounts for about 80% and peritoneal MMe constitutes most of the remaining MMe. However, in individuals with BAP1-TPDS the ratio of peritoneal to pleural involvement is significantly higher [Carbone et al 2015, Cheung et al 2015, Ohar et al 2016, Walpole et al 2018]. In BAP1-TPDS the majority of peritoneal MMe occurs in women, in contrast to the general population, in which men are more likely to have this tumor type [Walpole et al 2018].
In contrast to survival in persons with BAP1-related cutaneous melanoma, UM, or renal cell carcinoma, survival in persons with BAP1-related MMe may be significantly longer, especially in those with pleural mesothelioma [Baumann et al 2015, Pastorino et al 2018, Wang et al 2018, Hassan et al 2019].
Growing evidence suggests that BAP1 pathogenic variants interact with environmental asbestos exposure to increase the risk for MMe [Xu et al 2014, Kadariya et al 2016].
Cutaneous melanoma (CM). First reported in association with BAP1-TPDS in 2011, CM is now known to be the third most common cancer in BAP1-TPDS, occurring in 13% of affected individuals [Wiesner et al 2011]. Interestingly, Walpole et al [2018] found CM in 45% of probands but in no relatives affected with BAP1-TPDS [Walpole et al 2018]. Multiple primary cutaneous melanomas are common. The median age of onset of CM in individuals with BAP1-TPDS is earlier than in the general population (39 vs 58 years). While it is possible that BAP1-related CM is more aggressive than CM in the general population, the data are currently inconsistent [Gupta et al 2015, Kumar et al 2015, Rai et al 2016, Liu-Smith & Lu 2020].
Renal cell carcinoma (RCC). Heterozygous BAP1 germline pathogenic variants are specifically associated with an increased risk for RCC, in particular those with clear cell morphology [Haas & Nathanson 2014]. Walpole et al [2018] found RCC in 10% of probands and relatives with BAP1-TPDS, although the specific histology was not always known and additional morphologies including papillary and chromophobe cell tumors were also observed. Median age of RCC diagnosis appears to be younger in persons with BAP1-TPDS than in the general population (47-50 vs 64 years), and length of survival is decreased in persons with BAP1-related RCC [Rai et al 2016]. Histology of these tumors is distinct from tumors not associated with pathogenic variants in BAP1, with higher grade at diagnosis and lack of somatic PBRM1 pathogenic variants (which are common in RCC not associated with pathogenic variants in BAP1) [Peña-Llopis et al 2012].
Basal cell carcinoma
(BCC) has recently been confirmed as a tumor in the BAP1-TPDS spectrum [de la Fouchardière et al 2015b, Mochel et al 2015, Wadt et al 2015]. Multiple primary basal cell carcinomas are common. Walpole et al [2018] found that the median age of diagnosis for non-melanoma skin cancer (primarily BCC) was 44 years.
Meningioma, particularly a high-grade rhabdoid subtype, has been suggested to be associated with BAP1-TPDS [Abdel-Rahman et al 2011, Cheung et al 2015, de la Fouchardière et al 2015a, Wadt et al 2015, Shankar et al 2017]. This is further supported by identification of this tumor in 8.5% of probands with BAP1-TPDS and 2.2% of relatives with the BAP1 pathogenic variant.
Cholangiocarcinoma has also been suggested to be part of BAP1-TPDS [Njauw et al 2012, Pilarski et al 2014, Wadt et al 2015]. Walpole et al [2018] found this cancer in 1.4% of probands with BAP1-TPDS but in none of the relatives.
Hepatocellular carcinoma (HCC). Germline BAP1 pathogenic variants have been observed in 0.5% of unselected individuals with HCC [Huang et al 2018]. Walpole et al [2018] identified HCC in 0.7% of probands with BAP1-TPDS and 1.6% of relatives with the BAP1 pathogenic variant.
Other cancers with some evidence (although inconsistent) supporting inclusion in the BAP1-TPDS spectrum are the following (in alphabetic order):
Breast cancer [
Testa et al 2011,
Njauw at al 2012,
Popova et al 2013,
Abdel-Rahman et al 2016]. Although breast cancer has been reported in individuals with germline pathogenic variants in
BAP1, in one individual biallelic inactivation was not observed in the tumor tissue. In addition, no
BAP1 pathogenic variants were detected in any of the 1,078 breast cancers included in The Cancer Genome Atlas (TCGA) project, suggesting that breast cancer is likely not part of the phenotype.
Urinary bladder carcinoma. One individual was reported with a
BAP1 germline pathogenic variant and evidence of biallelic inactivation in the tumor [
Tesch et al 2020].
Prevalence
The prevalence of BAP1-TPDS is unknown. Based on data from the Genome Aggregation Database (gnomAD), the carrier frequency is 1:26,837 in the general population. In the cancer cohort from the TCGA, the frequency was 8:10,389 (1:1,299).
The prevalence of BAP1-TPDS ranges from 1%-2% in persons with UM,1%-3% in persons with MMe [Huang et al 2018, Panou et al 2018], 1%-1.5% in those with RCC [Carlo et al 2018, Wu et al 2019], and 0.5% in persons with HCC. Several large studies showed that BAP1-TPDS is rare in those with CM (0.1%) [Aoude et al 2015, O'Shea et al 2017]. The prevalence of BAP1-TPDS in persons with other cancers is unknown.
UM. The prevalence of germline BAP1 pathogenic variants in unselected individuals with UM is 1%-2% [Aoude et al 2013a, Gupta et al 2015, Repo et al 2019]; in contrast, the frequency is 20%-30% in persons with UM who have a family history of UM [Turunen et al 2016, Rai et al 2017].
MMe. Germline BAP1 pathogenic variants have been identified in 1%-3% of simplex cases and 6%-7.7% (9:153) of individuals with familial MMe [Betti et al 2015, Ohar et al 2016, Betti et al 2018].
CM. Germline BAP1 pathogenic variants were observed rarely in two large studies of sporadic CM with a prevalence of 3:1,197 (0.25%) and 0:1109 [Aoude et al 2015, O'Shea et al 2017]. Also, germline BAP1 pathogenic variants are rare in familial CM (0%-0.7%), particularly in those with no other cancers observed in the family [Njauw et al 2012, Boru et al 2019, Potjer et al 2019].