ASXL3 bridges BRD4 to BAP1 complex and governs enhancer activity in small cell lung cancer

Abstract

Background: Small cell lung cancer (SCLC) is a more aggressive subtype of lung cancer that often results in rapid tumor growth, early metastasis, and acquired therapeutic resistance. Consequently, such phenotypical characteristics of SCLC set limitations on viable procedural options, making it difficult to develop both screenings and effective treatments. In this study, we examine a novel mechanistic insight in SCLC cells that could potentially provide a more sensitive therapeutic alternative for SCLC patients. Methods: Biochemistry studies, including size exclusion chromatography, mass spectrometry, and western blot analysis, were conducted to determine the protein-protein interaction between additional sex combs-like protein 3 (ASXL3) and bromodomain-containing protein 4 (BRD4). Genomic studies, including chromatin immunoprecipitation sequencing (ChIP-seq), RNA sequencing, and genome-wide analysis, were performed in both human and mouse SCLC cells to determine the dynamic relationship between BRD4/ASXL3/BAP1 epigenetic axis in chromatin binding and its effects on transcriptional activity. Results: We report a critical link between BAP1 complex and BRD4, which is bridged by the physical interaction between ASXL3 and BRD4 in an SCLC subtype (SCLC-A), which expresses a high level of ASCL1. We further showed that ASXL3 functions as an adaptor protein, which directly interacts with BRD4's extra-terminal (ET) domain via a novel BRD4 binding motif (BBM), and maintains chromatin occupancy of BRD4 to active enhancers. Genetic depletion of ASXL3 results in a genome-wide reduction of histone H3K27Ac levels and BRD4-dependent gene expression in SCLC. Pharmacologically induced inhibition with BET-specific chemical degrader (dBET6) selectively inhibits cell proliferation of a subtype of SCLC that is characterized with high expression of ASXL3. Conclusions: Collectively, this study provides a mechanistic insight into the oncogenic function of BRD4/ASXL3/ BAP1 epigenetic axis at active chromatin enhancers in SCLC-A subtype, as well as a potential new therapeutic option that could become more effective in treating SCLC patients with a biomarker of ASXL3-highly expressed SCLC cells.

RETRACTED ARTICLE: LncRNA PCAT6 regulates the progression of pituitary adenomas by regulating the miR-139-3p/BRD4 axis

“…Previous study confirmed that BRD4, whose effect was found up-regulated in PA, could regulate the growth of PA tumor in mice [ 30 , 31 ], and therefore, we chose BRD4 for further analysis in the current study. BRD4 has been widely reported to be involved in the development of various cancer types, including multiple myeloma [ 32 ], small cell lung cancer [ 33 ], and ovrican cancer [ 34 ]. The expression of BRD4 could notably affect multiple biological characteristics via different approaches.…”

Emerging multifaceted roles of BAP1 complexes in biological processes

“…These results from patients suggested a critical function of ASXL3 in neuronal development, differentiation, and function. Indeed, in our recent studies, we demonstrated that in comparison to ASXL1/2, ASXL3 is a more tissue-specific additional sex combs-like protein that is essential for BRD4-dependent enhancer activation in neuroendocrine cancer 16 .…”

“…Interestingly, different from ASXL1 and ASXL2, which are both expressed at a bulk level across most of the cell lines, the expression of ASXL3 is more tissue-specific and shown to be strongly enriched in neuroendocrine cell lines such as human small cell lung cancer cells (Fig. 1D ) 16 . This result suggests that there is a distinctive function in the chromatin localization among BAP1–ASXL1/ASXL2/ASXL3 complexes.…”

BAP1 constrains pervasive H2AK119ub1 to control the transcriptional potential of the genome

“…The most extensively characterised and evolutionary conserved of these DUBs is BAP1, which interacts with ASXL proteins to form the Polycomb Repressive Deubiquitinase complex (PR-DUB) (Scheuermann et al 2010; Wu et al 2015; Sahtoe et al 2016; Kloet et al 2016; Hauri et al 2016; Campagne et al 2019). Previous attempts to understand how BAP1 regulates gene expression and whether this relies on its H2AK119ub1 deubiquitylase activity have primarily focused on examining how the PR-DUB complex is targeted to gene promoters and distal regulatory elements, and how this regulates binding and/or activity of chromatin-modifying transcriptional co-activators (Li et al 2017b; Wang et al 2018; Campagne et al 2019; Kuznetsov et al 2019; Kolovos et al 2020; Szczepanski et al 2020). While this has revealed that BAP1 can remove H2AK119ub1 at specific loci, its primary site of action in the genome and the mechanisms by which it controls gene expression have appeared to be context-dependent and in some cases difficult to reconcile with the known roles of H2AK119ub1 in gene regulation.…”