ARID1B is a specific vulnerability in ARID1A-mutant cancers

Abstract

Recent studies have revealed that ARID1A, encoding AT-rich interactive domain 1A (SWI-like), is frequently mutated across a variety of human cancers and also has bona fide tumor suppressor properties. Consequently, identification of vulnerabilities conferred by ARID1A mutation would have major relevance for human cancer. Here, using a broad screening approach, we identify ARID1B, an ARID1A homolog whose gene product is mutually exclusive with ARID1A in SWI/SNF complexes, as the number 1 gene preferentially required for the survival of ARID1A-mutant cancer cell lines. We show that loss of ARID1B in ARID1A-deficient backgrounds destabilizes SWI/SNF and impairs proliferation in both cancer cells and primary cells. We also find that ARID1A and ARID1B are frequently co-mutated in cancer but that ARID1A-deficient cancers retain at least one functional ARID1B allele. These results suggest that loss of ARID1A and ARID1B alleles cooperatively promotes cancer formation but also results in a unique functional dependence. The results further identify ARID1B as a potential therapeutic target for ARID1A-mutant cancers.

Figure 1. ARID1B is a specific vulnerability in ARID1A-mutant cancer cell lines

(a) Rank list of vulnerabilities identified by screen of Achilles platform cell lines. ARID1B is the #1 gene preferentially essential for the growth of ARID1A-mutant cancer cell lines as compared to wildtype cancer cell lines. (b) Effects of ARID1B shRNAs across cell lines in the Achilles screen. Negative values indicate growth inhibition while positive values reflect growth enhancement. In the top panel, cell lines with any identified ARID1A mutation compared to the reference genome are indicated in red. In the bottom panel, only those cell lines with clear inactivating mutations in ARID1A are shown in red. (c) Immunoblots showing the results of two independent shRNAs targeting ARID1B in ES-2 and 293T (ARID1A-wildtype lines) and in OVISE, and TOV21G (ARID1A-mutant lines). (d) Proliferation of wildtype (ES-2 and 293T) and ARID1A-mutant (OVISE and TOV21G) cell lines in response to two independent ARID1B shRNAs. * p<0.0002 **p<4×10⁻⁸ #p>0.05 ##p<0.05 Data are expressed as mean ± S.D. (e) Colony formation in response to ARID1B knockdown in wildtype and ARID1A-mutant cell lines.

Figure 2. ARID1B is required for the maintenance of an intact SWI/SNF complex in ARID1A-mutant cancer cell lines and primary cells

(a) Immunoprecipitation of the SWI/SNF complex by SMARCC1 from the nuclear extract of ES-2, OVISE, and TOV21G cells upon treatment with control shRNA or two independent ARID1B shRNAs. (b) Sucrose sedimentation (20−50%) assay of SWI/SNF complex from ARID1A-mutant TOV21G cells treated with either control shRNA (top half) or ARID1B shRNA (bottom half). (c) Immunoprecipitation of the SWI/SNF complex by Smarcc1 from the nuclear extract of MEFs with indicated treatment. (d) Sucrose sedimentation (20−50%) assay of the SWI/SNF complex from the nuclear extract of MEFs with indicated treatment: control shRNA treated MEFs (top half) or Arid1a knockout (KO) and Arid1b knockdown (KD) MEFs (bottom half) (e) Model: Inactivating mutations in ARID1A promote oncogenic transformation but also create specific dependency on ARID1B. Inhibition of ARID1B in ARID1A-mutant cells destabilizes the SWI/SNF complex and results in impaired cell growth.