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ARID1A and the BAF complex are determinants of breast cancer treatment response [CRISPR gRNA-seq]

ABSTRACT: Global CRISPR screens provide an unparalleled, longer-term experimental approach for the identification of essential genes in drug resistance. We used an ~18,000 gene deletion screen to discover ARID1A and other BAF complex components as the most critical factors required for response to two classes of Estrogen Receptor (ER) antagonists, namely ER degraders and Selective Estrogen Receptor Modulators (SERMs). Unexpectedly, ARID1A was also the top candidate for response to the BET inhibitor JQ1, but in the opposite direction, where loss of ARID1A sensitised breast cancer cells to BET inhibition. We show that ARIDA binds chromatin at ER cis-regulatory elements and can physically associate with ER in model systems and primary tumour samples. ARID1A binding to ER enhancer elements, can occur in the absence of ER, suggesting that its repressive activity occurs in an enhancer-specific, but ER-independent manner. Specific targeting of ARID1A validated the CRISPR screen and shows that depletion of BAF activity, does not result in redundancy from P-BAF, the other ATP-dependent chromatin remodelling complex, but instead results in loss of HDAC1 binding, increased Histone 4 lysine acetylation and subsequent BRD4-driven growth. ARID1A and the BAF complex therefore function as a critical mechanism of antiestrogen activity and mutation or depletion in BAF activity drives a BRD4-mediated proliferative program that is refractory to ER targeted agents. Since ARID1A is mutated in a subset of treatment-resistant disease, these findings provide mechanistic insight and treatment strategies for patients, based on BAF complex fidelity status.

ORGANISM(S): Homo sapiens

PROVIDER: GSE123283 | GEO | 2019/10/30

REPOSITORIES: GEO

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Project description:Following the discovery of BRD4 as a non-oncogene addiction target in acute myeloid leukemia (AML), BET inhibitors are being explored as promising therapeutic avenue in numerous cancers. While clinical trials have reported single-agent activity in advanced hematologic malignancies, mechanisms determining the response to BET inhibition remain poorly understood. To identify factors involved in primary and acquired BET resistance in leukemia, we performed a chromatin-focused shRNAmir screen in a sensitive MLL/AF9; NrasG12D‑driven AML model, and investigated dynamic transcriptional profiles in sensitive and resistant murine and human leukemias. Our screen reveals that suppression of the PRC2 complex, contrary to effects in other contexts, promotes BET resistance in AML. PRC2 suppression does not directly affect the regulation of Brd4-dependent transcripts, but facilitates the remodeling of regulatory pathways that restore the transcription of key targets such as Myc. Similarly, while BET inhibition triggers acute MYC repression in human leukemias regardless of their sensitivity, resistant leukemias are uniformly characterized by their ability to rapidly restore MYC transcription. This process involves the activation and recruitment of WNT signaling components, which compensate for the loss of BRD4 and drive resistance in various cancer models. Dynamic ChIP- and STARR-seq enhancer profiles reveal that BET-resistant states are characterized by remodeled regulatory landscapes, involving the activation of a focal MYC enhancer that recruits WNT machinery in response to BET inhibition. Together, our results identify and validate WNT signaling as a driver and candidate biomarker of primary and acquired BET resistance in leukemia, and implicate the rewiring of transcriptional programs as an important mechanism promoting resistance to BET inhibitors and, potentially, other chromatin-targeted therapies. RNA-Seq of DMSO- or JQ1-treated cancer cell lines; ChIP-seq for H3K36me3 and H3K27me3 in a leukemia cell line treated either with DMSO or JQ1, ChIP-seq for H3K27ac in resistant and sensitive mouse and human leukemia. Functional enhancer mapping (STARR-seq) in K-562 treated either with DMSO or JQ1.

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ARID1A and the BAF complex are determinants of breast cancer treatment response [CRISPR gRNA-seq]

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