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ABSTRACT SWI/SNF chromatin remodelers play critical roles in development and cancer. The causal links between SWI/SNF complex disassembly and carcinogenesis are obscured by redundancy

between paralogous components. Canonical BAF (cBAF)-specific paralogs ARID1A and ARID1B are synthetic lethal in some contexts, but simultaneous mutations in both ARID1s are prevalent in

cancer. To understand if and how cBAF abrogation causes cancer, we examined the physiological and biochemical consequences of ARID1A/ARID1B loss. In double-knockout liver and skin,

aggressive carcinogenesis followed dedifferentiation and hyperproliferation. In double-mutant endometrial cancer, add-back of either induced senescence. Biochemically, residual cBAF

subcomplexes resulting from loss of ARID1 scaffolding were unexpectedly found to disrupt a polybromo-containing BAF (pBAF) function. Of 69 mutations in the conserved scaffolding domains of

ARID1 proteins observed in human cancer, 37 caused complex disassembly, partially explaining their mutation spectra. ARID1-less, cBAF-less states promote carcinogenesis across tissues, and

suggest caution against paralog-directed therapies for ARID1-mutant cancer. Access through your institution Buy or subscribe This is a preview of subscription content, access via your

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institutional subscriptions * Read our FAQs * Contact customer support SIMILAR CONTENT BEING VIEWED BY OTHERS _ARID1A_ DEFICIENCY WEAKENS BRG1-RAD21 INTERACTION THAT JEOPARDIZES CHROMATIN

COMPACTNESS AND DRIVES LIVER CANCER CELL METASTASIS Article Open access 23 October 2021 GENOMIC PROFILING OF THE TRANSCRIPTION FACTOR ZFP148 AND ITS IMPACT ON THE P53 PATHWAY Article Open

access 25 August 2020 _ARID2_ DEFICIENCY PROMOTES TUMOR PROGRESSION AND IS ASSOCIATED WITH HIGHER SENSITIVITY TO CHEMOTHERAPY IN LUNG CANCER Article 19 March 2021 DATA AVAILABILITY All

sequencing data have been deposited in the Gene Expression Omnibus with the accession nos. GSE147664 for mRNA-seq and GSE140183 for ChIP–seq. Source data are provided with this paper. All

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626–630 (2010). Article  CAS  PubMed  PubMed Central  Google Scholar  Download references ACKNOWLEDGEMENTS We thank C. Kadoch, S. McBrayer, J. Wu, J. Xu, L. Banaszynski, X. Liu and S. Wang

for constructive comments on the manuscript; C. Lewis and J. Shelton for histopathology; Proteomics Core at UTSW (A. Lemoff) for MS; and the CRI Sequencing Core (J. Xu) for genomics. Funding

sources: NIH R03ES026397-01 (to T.W.), CPRIT RP150596 (to T.W.), CPRIT RP170267 (to H.Z.), NIH/NIDDK R01DK111588 (to H.Z.) and Stand Up To Cancer Innovative Research Grant (no.

SU2C-AACR-IRG 10-16 to H.Z.). AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * Children’s Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science

and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA Zixi Wang, Yuemeng Jia, Jen-Chieh Chuang, Xuxu Sun, Yu-Hsuan Lin, Cemre Celen, Lin Li, Fang Huang, Xin Liu 

& Hao Zhu * Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA Kenian Chen & Tao

Wang * Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA Diego H. Castrillon Authors * Zixi Wang View author publications You can also search for this

author inPubMed Google Scholar * Kenian Chen View author publications You can also search for this author inPubMed Google Scholar * Yuemeng Jia View author publications You can also search

for this author inPubMed Google Scholar * Jen-Chieh Chuang View author publications You can also search for this author inPubMed Google Scholar * Xuxu Sun View author publications You can

also search for this author inPubMed Google Scholar * Yu-Hsuan Lin View author publications You can also search for this author inPubMed Google Scholar * Cemre Celen View author publications

You can also search for this author inPubMed Google Scholar * Lin Li View author publications You can also search for this author inPubMed Google Scholar * Fang Huang View author

publications You can also search for this author inPubMed Google Scholar * Xin Liu View author publications You can also search for this author inPubMed Google Scholar * Diego H. Castrillon

View author publications You can also search for this author inPubMed Google Scholar * Tao Wang View author publications You can also search for this author inPubMed Google Scholar * Hao Zhu

View author publications You can also search for this author inPubMed Google Scholar CONTRIBUTIONS Z.W. and H.Z. conceived the project, performed the experiments and wrote the manuscript.

J-C.C., X.S., Z.W., L.L. and C.C. created and analyzed the mouse models. K.C., Y.J., X.S., F.H., X.L. and T.W. generated and analyzed genomic data. Y.-H.L. assisted with the histology

analysis. D.H.C edited the manuscript and provided assistance with disease models. CORRESPONDING AUTHOR Correspondence to Hao Zhu. ETHICS DECLARATIONS COMPETING INTERESTS At the time of

publication, H.Z. owned Ionis Pharmaceuticals stock worth less than $US10,000 and has active collaboration with Alnylam Pharmaceuticals and Twenty-Eight Seven Therapeutics. The remaining

authors declare no competing interests. ADDITIONAL INFORMATION PUBLISHER’S NOTE Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional

affiliations. EXTENDED DATA EXTENDED DATA FIG. 1 LOSS OF BOTH ARID1A AND ARID1B IN THE LIVER LEADS TO IMPAIRED LIVER FUNCTION. A Kaplan-Meier survival curve of WT and DKO mice within the

first month of life. B Body weight of WT and DKO mice at the age of 1 month (n = 12 and 8 mice). c-g. Liver function analysis using plasma (n = 6 and 5 mice for the _Arid1a__f/f_ group; 6

and 6 for the _Arid1b__f/f_ group; 8 and 8 for the _Arid1a__f/f__; Arid1b__f/f_ group). H Gross inspection of plasma from AKO, BKO and DKO and their corresponding WT mice. I IHC staining of

ARID1A and ARID1B on WT and DKO liver sections. J Western blot showing ARID1A and ARID1B protein levels in WT and DKO livers. K Quantification of Western blot data in J (n = 6 and 6 mice for

each group). Data are presented as mean ± s.d. (B-G,K). Statistical significance was determined by two-tailed unpaired Student’s t-tests with Welch’s correction (B-G, K). Source data

EXTENDED DATA FIG. 2 AAV MEDIATED DELETION OF ARID1A AND ARID1B IN THE LIVER LEADS TO ORGAN FAILURE. A Gross inspection of plasma from mice injected with AAV-GFP or AAV-Cre. B-F. Liver

function tests of _Arid1a__f/f__; Arid1b__f/f_ mice injected with AAV-GFP or AAV-Cre (n = 10 and 10 mice for AST; 9 and 10 for ALT; 9 and 11 for TBIL; 10 and 11 for ALKP; 9 and 11 for

Albumin. Data are presented as mean ± s.d. Statistical significance was determined by two-tailed unpaired Student’s t-tests with Welch’s correction). G Representative genome browser tracks

showing ARID1A binding to the promoter or enhancer regions of differentiation and Cytochrome P450 genes in liver. H IHC staining of EpCAM and CK-19 on AAV-Cre liver sections. Source data

EXTENDED DATA FIG. 3 CBAF SUBUNIT LEVELS SHOWED LIMITED TO NO DECREASE IN ARID1-LESS CELLS OR DKO LIVERS. A Western blot analysis of cBAF subunit levels in WT and ARID1-less H2.35 cells (n =

 3 and 3 independent clones). B Colony formation assay for control and ARID1-less H2.35 cells. 0.1 million H2.35 cells were seeded in each well of 6-well plate and cultured for 10 days in

the presence of Dox. C Western blot analysis of cBAF subunit levels in WT and DKO livers (n = 6 and 6 mice). Same batch of western blots/protein samples as in Extended Data Fig. 1j. D

Quantification of western blot data in c (Data are presented as mean ± s.d. Statistical significance was determined by two-tailed unpaired Student’s t-tests with Welch’s correction). Source

data EXTENDED DATA FIG. 4 CHIP-SEQ ANALYSIS OF SWI/SNF COMPLEXES BINDING TO GENOMIC DNA IN CONTROL AND ARID1-LESS H2.35 CELLS. A Expression of Ty1 tagged BRD9 and Brg1 in WT and ARID1-less

H2.35 cells. BRD9 expression was only examined using the Ty1 antibody due to the lack of a commercial anti-mouse BRD9 antibody. B Heatmap displaying ChIP-seq peaks of intact SWI/SNF

complexes in WT H2.35 cells. ARID1A, ARID1B, and BAF45d peaks were used to represent cBAF, ARID2 for pBAF, BRD9 for ncBAF, and Brg1 for all BAF complexes. 3000 bp upstream and downstream of

peak centers are shown in this figure (n = 2 independent ChIP experiments for each protein). C Venn diagram showing the shared and unique binding loci among three types of BAF complexes from

ChIP-seq data. D Comparison of BRD9 occupancies in control and ARID1-less cells. Heatmap and the corresponding averaged peak map and Venn diagram are shown (n = 2 and 2 independent ChIP

experiments). E Representative genome browser tracks showing that ncBAF binding was unaffected in ARID1-less cells (BRD9 peaks in ARID1-less cells). Source data EXTENDED DATA FIG. 5 MAPPING

OF DOMAINS, RESIDUES, AND MUTATIONS RESPONSIBLE FOR ARID1A’S SCAFFOLDING ROLE. A Multiple sequence alignment of ARID1A protein C-terminal regions from human, mouse, dog, bovine, rabbit,

chicken, clawed frog, and zebrafish showing two conserved ARID1 scaffolding domains (ASD1 and ASD2). B Secondary structure prediction of ARID1A using LCR-eXXXplorer server. Regions with a

score lower than 0.5 (shown as a cyan line for the IUPRED score and a red line for the ANCHOR score) are likely well-folded globular domains. C Alanine scans within ASD1 of ARID1A and IP

experiments to assess residues for cBAF subunit interactions. The indicated two residues were mutated to alanine in each construct. D IP experiments showing the influence of ARID1A missense

mutations within ASD2 on BAF subunit interactions. E Western blot showing the influence of ARID1A hotspot missense mutations on protein stability in H2.35 cells. F Western blot showing the

influence of ARID1A truncations on protein stability in H2.35 cells. Source data SUPPLEMENTARY INFORMATION REPORTING SUMMARY SUPPLEMENTARY TABLE Supplementary Tables 1 and 2. SOURCE DATA

SOURCE DATA FIG. 1 Statistical source data. SOURCE DATA FIG. 2 Unprocessed western blots. SOURCE DATA FIG. 3 Statistical source data. SOURCE DATA FIG. 5 Statistical source data. SOURCE DATA

FIG. 5 Unprocessed western blots. SOURCE DATA FIG. 6 Statistical source data. SOURCE DATA FIG. 6 Unprocessed western blots. SOURCE DATA FIG. 7 Statistical source data. SOURCE DATA FIG. 7

Unprocessed western blots. SOURCE DATA FIG. 8 Unprocessed western blots. SOURCE DATA EXTENDED DATA FIG. 1 Statistical source data. SOURCE DATA EXTENDED DATA FIG. 1 Unprocessed western blots.

SOURCE DATA EXTENDED DATA FIG. 2 Statistical source data. SOURCE DATA EXTENDED DATA FIG. 3 Statistical source data. SOURCE DATA EXTENDED DATA FIG. 3 Unprocessed western blots. SOURCE DATA

EXTENDED DATA FIG. 4 Unprocessed western blots. SOURCE DATA EXTENDED DATA FIG. 5 Unprocessed western blots. RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS

ARTICLE Wang, Z., Chen, K., Jia, Y. _et al._ Dual ARID1A/ARID1B loss leads to rapid carcinogenesis and disruptive redistribution of BAF complexes. _Nat Cancer_ 1, 909–922 (2020).

https://doi.org/10.1038/s43018-020-00109-0 Download citation * Received: 17 October 2019 * Accepted: 03 August 2020 * Published: 07 September 2020 * Issue Date: September 2020 * DOI:

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