An overview of BAP1 biological functions and current therapeutics

Abstract

BRCA1-associated protein 1 (BAP1) is a tumor suppressor gene that was first identified in 1998. Germline loss-of-function variants in BAP1 are associated with a tumor predisposition syndrome with at least four cancers: uveal melanoma (UM), malignant mesothelioma (MMe), renal cell carcinoma (RCC), and cutaneous melanoma (CM). Furthermore, somatic BAP1 mutations are important drivers for several cancers most notably UM, MMe, RCC, intrahepatic cholangiocarcinoma (ICC) and hepatocellular carcinoma (HCC). Emerging evidence substantiates the fundamental role of BAP1 in suppressing cancer initiation and progression by tuning DNA damage repair, apoptosis, ferroptosis, immune response, Warburg phenomenon, and metastasis. Multiple treatment strategies such as poly (ADP-ribose) polymerase (PARP) inhibitors, EZH2 inhibitors, alkylating agents, and immunotherapy have been used as potential therapies for BAP1-mutated tumors. Although these agents showed promising results in BAP1-mutated tumors in preclinical studies, the results of most clinical trials are still dismal. The objectives of this review are to summarize the current state of knowledge regarding the biological functions of BAP1, the implications of these functions in tumorigenesis, and the current progress in BAP1-targeted therapy.

Keywords: Alkylating agent; BRCA1-associated protein 1 (BAP1); EZH2 inhibitors; HDAC inhibitors; Immunotherapy; PARP inhibitors; Therapeutics.

Figure 1.. Schematic diagram illustrating the molecular structure of BAP1 protein.

BAP1 is composed of 729 amino acid (AA) and contains multiple domains that interact with several target proteins. The catalytic ubiquitin C-terminal hydrolase (UCH) domain of BAP1 is located at the N-terminal region and comprises 250 AA (1 – 250 AA). BAP1 contains two nuclear localization signals (NLS) located at 656 – 661 and 717 – 722 AA. Other domains of BAP1 include BARD1-binding region (182–365); HCF1-binding motif (HBM) (365–385); FOXK1/K2-binding region (477–526); BRCA1-binding region (596–721); C-terminal-binding domain (CTD) and ASXL1/2-binding domain (635–693); Ying Yang 1 (YY1)-binding domain (642–686).

Figure 2.. BAP1 regulates DNA damage repair, apoptosis, and ferroptosis.

BRCA1-associated protein 1 (BAP1) regulates DNA double strand breaks (DSBs) through the interaction with homologous recombination (HR) proteins including RAD51, breast cancer gene 1 (BRCA1), and BRCA1 associated ring domain 1 (BARD1) as well as poly (ADP) ribose polymerase (PARP) and the recruitment of these proteins to the sites of DNA damage. BAP1 also regulates single strand breaks (SSBs) via nucleotide excision repair (NER). PARP interacts with BAP1 and induces PARylation of BAP1, which in turn, stabilizes BAP1 by preventing BAP1 ubiquitylation by E3 ubiquitin ligase. BAP1-PARP complex is then recruited to the sites of SSB to regulate NER. BAP1 triggers ferroptosis through repressing the transcription of solute carrier family 7-member 11 (SLC7A11) gene that encodes for SLC7A11 transporter. SLC7A11 mediates the influx of cystine which is further converted into cysteine and reduced glutathione (GSH). GSH inhibits the formation of lipid peroxides and thus suppressing ferroptosis. By inhibiting SLC7A11 transcription, BAP1 inhibits the formation of GSH and consequently stimulates the production of lipid peroxides to induce ferroptosis. BAP1 regulates apoptosis by deubiquitiylation and stabilization of inositol 1,4,5-trisphosphate receptor, type 3 (IP3R3). IP3R3 mediates Ca²⁺ outflux from endoplasmic reticulum (ER) resulting in increased cytosolic Ca²⁺ concentrations. The increased Ca²⁺ enters the mitochondria and promotes mitochondrial stress, ultimately leading to the release of cytochrome C and apoptosis induction. BAP1 also interacts with 14–3-3 proteins to stimulate the release of proapoptotic proteins, BCL2-associated X protein (BAX) and BCL-2 antagonist killer (BAK). Furthermore, BAP1 promotes apoptosis through inhibiting the release of B-cell lymphoma 2 (BCL-2) protein, resulting in blocking the inhibitory effect of BCL-2 on the release of proapoptotic proteins.

Figure 3.. BAP1 loss is associated with distinct immunological phenotype.

Tumors with loss or inactivating mutations in BAP1 show upregulated expression of tumor secreted protein 1 (PROS1). PROS1 is a ligand of macrophage receptor tyrosine kinase family (MERTK) and activation of this receptor results in suppression of proinflammatory macrophage 1 (M1) polarization and activation of anti-inflammatory macrophages 2 (M2) polarization. The polarized M2 macrophages secret cytokines that suppress immune response. BAP1 negative tumors are associated with infiltration of regulatory T cells (Tregs) that express high amounts of c-c chemokine receptor type 5 (CCR5), human leukocyte antigen – DR isotype (HLA-DR), and cluster of differentiation 28 and 38 (CD28/CD38). Activation of Tregs leads to inhibition of cytolytic T cells and immune response. Tumor microenvironment of BAP1-negative tumors is infiltrated with high amounts of lymphocyte activation gene 3 (LAG3), a critical immune checkpoint receptor, leading to suppression of cytolytic T cells and immune response.

Figure 4.. Schematic diagram illustrating the current hypotheses regarding how BAP1 loss and/or mutations impact different therapeutic strategies.

Poly (ADP) ribose polymerase (PARP) repairs single strand break (SSB) by base excision repair (BER). In the presence of PARP inhibitors, failure to repair SSBs can result in double-strand breaks (DSBs) which in normal cells are repaired by homologous recombination (HR) leading to cell survival. Loss of BAP1 is hypothesized to impair HR repair rendering those tumors more vulnerable to the synthetic lethality induced by PARP inhibitors. BAP1 loss and/or inactivating mutations result in upregulation of EZH2 (enhancer of the zeste 2 polycomb repressive complex 2 subunit), histone deacetylase (HDAC), programmed cell death protein 1 (PD-1), programmed death-ligand 1 (PD-L1), lymphocyte activation gene 3 (LAG3), and C-C chemokine receptor type 5 (CCR5). Thus, EZH2, HDAC, and immune checkpoint inhibitors can be used as potential therapeutic targets in BAP1-mutated tumors.

Figure 5.. Proposed diagram showing how BAP1 loss contributes to carcinogenesis.

(A) At the beginning, a single germline or somatic mutation hits only one copy of BAP1 gene. Later, the wildtype copy of BAP1 gene is subjected to a second hit deletion resulting in total loss of BAP1 function. (B) BAP1 regulates tumorigenesis at two stages, initiation, and progression. At the first stage, loss or inactivating mutations of BAP1 impairs the ability of BAP1 to repair DNA damage and to induce apoptosis resulting in accumulation of genetic mutations, genomic instability, and initiation of cancer. At the second level, BAP1 regulates tumor progression and metastasis; BAP1 loss of function results in activation of Warburg effect and suppression of apoptosis, ferroptosis, and immune response. These integrated effects ultimately promote tumor growth and favor tumor metastasis.