Therapeutic targeting of BAP1/ASXL3 sub-complex in ASCL1-dependent small cell lung cancer

Abstract

Small cell lung cancer (SCLC) is an aggressive disease, with patients diagnosed with either early-stage, limited stage, or extensive stage of SCLC tumor progression. Discovering and targeting the functional biomarkers for SCLC will be crucial in understanding the molecular basis underlying SCLC tumorigenesis to better assist in improving clinical treatment. Emerging studies have demonstrated that dysregulations in BAP1 histone H2A deubiquitinase complex are collectively associated with pathogenesis in human SCLC. Here, we investigated the function of the oncogenic BAP1/ASXL3/BRD4 epigenetic axis in SCLC by developing a next-generation BAP1 inhibitor, iBAP-II, and focusing on the epigenetic balance established between BAP1 and non-canonical PRC1 complexes in regulating SCLC-specific transcriptional programming. We further demonstrated that pharmacologic inhibition of BAP1’s catalytic activity disrupted BAP1/ASXL3/BRD4 epigenetic axis by inducing protein degradation of the ASXL3 scaffold protein, which bridges BRD4 and BAP1 at active enhancers. Furthermore, treatment of iBAP-II represses neuroendocrine lineage-specific ASCL1/MYCL/E2F signaling in SCLC cell lines, and dramatically inhibits SCLC cell viability and tumor growth in vivo. In summary, this study has provided mechanistic insight into the oncogenic function of BAP1 in SCLC and highlighted the potential of targeting BAP1’s activity as a novel SCLC therapy.

MBD5 and MBD6 stabilize the BAP1 complex and promote BAP1-dependent cancer

“…Our recent studies have uncovered an essential oncogenic function of BAP1 in human small cell lung cancer (SCLC) [18]. Depletion of BAP1 or treatment with BAP1-specific inhibitors could significantly reduce SCLC tumor growth in vitro and in vivo [18]. In our current studies, we found that the expression of MBD6 is consistently higher than MBD5 across 51 SCLC cell lines, and functions as the predominant form in the BAP1 complex.…”

“…Emerging studies have revealed that the dysregulation or mutations within the BAP1 complex were demonstrated to be critical for tumorigenesis. Our recent studies have uncovered an essential oncogenic function of BAP1 in human small cell lung cancer (SCLC) [18]. Depletion of BAP1 or treatment with BAP1-specific inhibitors could significantly reduce SCLC tumor growth in vitro and in vivo [18].…”

“…Emerging studies from other groups as well as our own have revealed a critical oncogenic role of BAP1 in multiple human cancers, including breast cancer [19], leukemia [16,29,31], and small cell lung cancer (SCLC) [15,32]. We have recently shown that depletion of BAP1 by CRISPR or treatment with BAP1 inhibitors could reduce SCLC tumor growth in vitro and in vivo [18]. To study the impact of MBD5 and MBD6 on BAP1's function in SCLC pathogenesis, we depleted MBD5 or MBD6 with two distinct CRISPR sgRNAs in three different human SCLC cell lines.…”

“…Designed sgRNAs were cloned into lentiCRISPR v2 (Addgene, 52961) vector. Lentiviral-mediated CRISPR/Cas9 knockout was described previously [18]. For RNA interference in Drosophila cells, the S2 cells are maintained at 2×10 6 cells/ml in serum-free SFX medium (containing 1% penicillin/streptomycin) prior to RNAi treatment.…”

“…In SCLC cells, the lineage-specific scaffold subunit ASXL3 directly links BRD4 to BAP1 at active enhancers and drives oncogenic gene expression [17]. Genetic depletion of BAP1 or inhibition of BAP1 activity by small molecule inhibitors [18] could dramatically reduce the tumor growth of BAP1-dependent cancer, such as ASXL1-mutant leukemia [19], breast cancer [19], and SCLC [18].…”