Biological Mechanisms and Clinical Significance of BAP1 Mutations in Human Cancer

Abstract

Among more than 200 BAP1-mutant families affected by the "BAP1 cancer syndrome," nearly all individuals inheriting a BAP1 mutant allele developed one or more malignancies during their lifetime, mostly uveal and cutaneous melanoma, mesothelioma, and clear-cell renal cell carcinoma. These cancer types are also those that, when they occur sporadically, are more likely to carry somatic biallelic BAP1 mutations. Mechanistic studies revealed that the tumor suppressor function of BAP1 is linked to its dual activity in the nucleus, where it is implicated in a variety of processes including DNA repair and transcription, and in the cytoplasm, where it regulates cell death and mitochondrial metabolism. BAP1 activity in tumor suppression is cell type- and context-dependent. BAP1 has emerged as a critical tumor suppressor across multiple cancer types, predisposing to tumor development when mutated in the germline as well as somatically. Moreover, BAP1 has emerged as a key regulator of gene-environment interaction.This article is highlighted in the In This Issue feature, p. 1079.

Figure 1.

BAP1 nuclear and cytoplasmic physiologic activities. BAP1 nuclear activities (top). BAP1 stabilizes and recruits INO80 to replication forks, via the interaction with H2A-Ub, for efficient replication fork progression and DNA replication, thereby ensuring genome stability (21, 22). Nuclear BAP1 regulates gene expression through effects on a number of epigenetic modifications and interaction with transcription factors. The interaction of BAP1–ASXL1 with HCF1–FOXK1 allows deubiquitylation and thereby stabilization of OGT, HCF1, and potentially other unknown targets to regulate transcription. The BAP1–ASXL1–HCF1–OGT complex localizes on numerous gene-regulatory elements, possibly through factors such as FOXK1, and functions as either a gene-specific activator or repressor complex on distinct genes (–30). BAP1 suppresses tumor development by repressing SLC7A11 expression through regulation of H2A-Ub levels on the SLC7A11 promoter and inducing ferroptosis. SLC7A11 imports extracellular cystine, which is subsequently converted to cysteine in cells; cysteine is a rate-limiting precursor for glutathione (GSH) biosynthesis; GSH is used as a cofactor by glutathione peroxidase 4 to reduce lipid reactive oxygen species (ROS) to lipid alcohols; overproduction of lipid ROS in cells results in ferroptosis (34). By binding BARD1 (2), BAP1 participates in the double-strand DNA break repair process (31, 32). This RAD51-dependent DNA repair pathway is highly regulated and includes many proteins that, in addition to BARD1, may also be substrates for BAP1-mediated ubiquitin hydrolysis. Exposure to DNA-damaging agents, such as asbestos, UV light, and ionizing radiation, induces DNA damage that is rapidly repaired with the help of nuclear BAP1. BAP1 cytoplasmic activities (bottom). The integrity of the IP3R3 ER channels requires the presence of normal amounts of BAP1 that remove ubiquitin from IP3R3. The balance between ubiquitylation mediated by FBXL2 (150) and deubiquitylation mediated by BAP1 (4) maintains a proper amount of IP3R3 required for Ca²⁺ transfer from the ER to the mitochondria. Mitochondria need Ca²⁺ for oxidative phosphorylation; however, higher than physiologic Ca²⁺ concentrations in the mitochondria cause apoptosis, a mechanism used to eliminate cells that accumulate extensive DNA damage that cannot be repaired. This mechanism prevents cells with DNA damage from propagating, thus preventing cancer development (4). MCU, mitochondrial calcium uniporter.

Figure 2.

Cancer types and age of onset of tumors presenting in BAP1^+/− carriers. A, Occurrence of cancer types expressed as percentage. Data were collected from 45 articles published up to September 30, 2019 (, , , , –, , , , , –, , , –177), for a total of 350 BAP1^+/− carriers (all ages); of them, 295 (84.3%) developed cancer, for a total of 442 different cancers (as several of them developed more than one cancer). Note that to avoid the risk of including nonpathogenic BAP1 variants, we used very stringent criteria to select these patients: Only germline BAP1 mutation carriers with a family history of BAP1-core cancers were included. Specifically, the cohort shown in this figure includes cases from 140 published families. Core cancers of the BAP1 cancer syndrome are indicated in bold. CM, cutaneous melanoma; MM, malignant mesothelioma all sites; Pl, pleural malignant mesothelioma; Pt, peritoneal malignant mesothelioma; u, malignant mesothelioma, site not specified; UVM, uveal melanoma; C, carcinoma. B, The percentage of BAP1^+/− carriers of all ages with one or multiple cancers. The average age of diagnosis of the first cancer, and relative range in years, are shown in parentheses. Individuals in the group “Cancer-free individuals” are 50 years of age or younger, and thus have not reached the age when cancer has occurred in most BAP1^+/−-mutant carriers. N, number of individuals; n, number of individuals whose age at diagnosis was known. Example: 7.4% of patients developed 3 different cancers (total of 26 patients). The age of onset of tumors was known for only 22 of 26 of them; the median age of first tumor onset was 48.5 years; the range of first tumor development was between 34 and 72 years old.

Figure 3.

BAP1 mutations in uveal melanoma (UVM). A, Uveal melanomas arise in the iris, ciliary body, and choroid of the uveal tract of the eye. Their metastatic potential is determined by mutually exclusive “BSE” progression mutations in BAP1, SF3B1 (and rarely in other splicing factors), and EIF1AX. Inactivating mutations in BAP1, when coupled with the loss of the other copy of chromosome 3, result in high metastatic risk associated with the class 2 gene-expression profile. Hemizygous mutations in SF3B1 (or rarely in other splicing factors) retain the class 1 gene expression profile and are associated with intermediate metastatic risk. Hemizygous mutations in the translation initiation factor EIF1AX also retain the class 1 gene expression profile and are associated with low metastatic risk. Uveal melanomas without BSE mutations have a prognosis similar to those with EIF1AX mutations. This figure represents a synopsis of published data (68, 101, 178). B, Recent work indicates that BAP1 regulates the switch from progenitor to differentiated cell types in vertebrate development, not only through effects on H2A ubiquitination but perhaps more importantly by repressing HDACs and allowing acetylation of H3K27 to activate genes involved in differentiation in neural crest and other lineages. Loss of BAP1 abrogates this differentiation switch in development that parallels phenotypic and transcriptomic alterations observed in association with BAP1 mutation in uveal melanoma (114).

Figure 4.

BAP1 and PBRM1 establish the foundation for a molecular genetic classification of renal cancer with prognostic implications. ccRCC can be classified into 4 subtypes according to BAP1 and PBRM1 status, and these subtypes are associated with differential kidney cancer–specific survival in patients (20, 98). Targeted disruption of Vhl and either Pbrm1 or Bap1 genes in the mouse kidney induces ccRCC of low and high grade, respectively, similar to human tumors (117). The pie chart shows the inactivation of PBRM1, as shown by loss of protein expression, in 55% of cases. By measuring protein expression, we are able to integrate both mutational and epigenetic mechanisms of gene inactivation.

Figure 5.

BAP1 immunostaining in mesothelioma. Wild-type BAP1. Epithelioid (A) and biphasic (B) mesotheliomas with wild-type BAP1 found in about 30% of cases show both nuclear and cytoplasmic BAP1 staining, as observed in nearby benign reactive cells. Nuclear and cytoplasmic staining in these cases is strong evidence of wild-type BAP1 but is not helpful in the differential diagnosis. C and D, Mutated BAP1. Negative nuclear and cytoplasmic BAP1 staining is found in about two thirds of the mutated cases, and it is associated with positive staining in nearby stromal and inflammatory cells. This is strong evidence of malignancy and supports the diagnosis of mesothelioma over other cancer types that can metastasize to the pleura/peritoneum. This IHC pattern is seen mostly in tumors carrying truncating mutations resulting in large BAP1 deletions. C, Epithelioid mesothelioma; only the epithelioid mesothelioma cells lost BAP1 staining. D, The presence of spindle tumor cells (BAP1-negative) supports the diagnosis of biphasic mesothelioma. W, representative BAP1 truncating mutation found in the W family. E and F, Mutated BAP1. Negative nuclear staining but positive cytoplasmic BAP1 staining is found in about one third of the mutated cases together with positive nuclear and cytoplasmic staining in nearby stromal and inflammatory cells. As for C and D, this is also strong evidence of malignancy and supports the diagnosis of mesothelioma over other cancer types that can metastasize to the pleura/peritoneum. This IHC pattern is seen mostly in tumors carrying truncating mutations resulting in small BAP1 deletions. E, Epithelioid mesothelioma; only the epithelioid mesothelioma cells lost BAP1 nuclear staining. F, The presence of spindle tumor cells with negative nuclear BAP1 staining supports the diagnosis of biphasic mesothelioma. Note that BAP1 is retained in the nuclei of background reactive benign mesothelial spindle cells; the latter have a slightly smaller size and bland nuclear features. L, representative BAP1 truncating mutation found in the L family.

Figure 6.

Survival analysis of individuals with sporadic mesothelioma or familial mesothelioma by BAP1 mutation status. Kaplan–Meier survival probability versus years with number at risk. Survival data combine results from references: (54, 67, 99). Blue, familial BAP1^WT mesothelioma (median survival, 8 years; 10-year survival, 42.0%); red: familial BAP1^+/− mesothelioma (median survival, 5 years; 10-year survival, 14.1%); green: SEER, stage I (median survival, 11 months; 10-year survival, 9.2%); brown: SEER, all stages (median survival, 8 months; 10-year survival, 3.3%). Rows below the graph indicate the number of patients at risk in each cohort per year. BAP1^+/−, heterozygous BAP1-inactivating mutations; BAP1^WT, wild-type BAP1; MM, malignant mesothelioma.