UK CR. Prostate Cancer Statistics https://www.cancerresearchuk.org/health-professional/cancer-statistics/statistics-by-cancer-type/prostate-cancer.

Ahmad I, Mui E, Galbraith L, Patel R, Tan EH, Salji M, et al. Sleeping Beauty screen reveals Pparg activation in metastatic prostate cancer. Proc Natl Acad Sci. 2016;113:8290.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tibbo AJ, Hartley A, Vasan R, Shaw R, Galbraith L, Mui E, et al. MBTPS2 acts as a regulator of lipogenesis and cholesterol synthesis through SREBP signalling in prostate cancer. Br J Cancer. 2023;128:1991–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tang L, Nogales E, Ciferri C. Structure and function of SWI/SNF chromatin remodeling complexes and mechanistic implications for transcription. Prog Biophys Mol Biol. 2010;102:122–8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yegnasubramanian S, De Marzo AM, Nelson WG. Prostate cancer epigenetics: from basic mechanisms to clinical implications. Cold Spring Harb Perspect Med. 2019;1:9.

Flowers S, Nagl NG Jr., Beck GR Jr., Moran E. Antagonistic roles for BRM and BRG1 SWI/SNF complexes in differentiation. J Biol Chem. 2009;284:10067–75.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wu JN, Roberts CW. ARID1A mutations in cancer: another epigenetic tumor suppressor? Cancer Discov. 2013;3:35–43.

Article  CAS  PubMed  Google Scholar 

Wu RC, Wang TL, Shih Ie M. The emerging roles of ARID1A in tumor suppression. Cancer Biol Ther. 2014;15:655–64.

Article  PubMed  PubMed Central  Google Scholar 

Sen M, Wang X, Hamdan FH, Rapp J, Eggert J, Kosinsky RL, et al. ARID1A facilitates KRAS signaling-regulated enhancer activity in an AP1-dependent manner in colorectal cancer cells. Clin Epigenetics. 2019;11:92.

Article  PubMed  PubMed Central  Google Scholar 

Xu G, Chhangawala S, Cocco E, Razavi P, Cai Y, Otto JE, et al. ARID1A determines luminal identity and therapeutic response in estrogen-receptor-positive breast cancer. Nat Genet. 2020;52:198–207.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hiramatsu Y, Fukuda A, Ogawa S, Goto N, Ikuta K, Tsuda M, et al. Arid1a is essential for intestinal stem cells through Sox9 regulation. Proc Natl Acad Sci. 2019;116:1704–13.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wu C, Lyu J, Yang EJ, Liu Y, Zhang B, Shim JS. Targeting AURKA-CDC25C axis to induce synthetic lethality in ARID1A-deficient colorectal cancer cells. Nat Commun. 2018;9:3212.

Article  PubMed  PubMed Central  Google Scholar 

Shen J, Peng Y, Wei L, Zhang W, Yang L, Lan L, et al. ARID1A deficiency impairs the DNA damage checkpoint and sensitizes cells to PARP inhibitors. Cancer Discov. 2015;5:752–67.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Park Y, Chui MH, Suryo Rahmanto Y, Yu Z-C, Shamanna RA, Bellani MA, et al. Loss of ARID1A in Tumor Cells Renders Selective Vulnerability to Combined Ionizing Radiation and PARP Inhibitor Therapy. Clin Cancer Res. 2019;25:5584–94.

Jones S, Wang T-L, Shih I-M, Mao T-L, Nakayama K, Roden R, et al. Frequent mutations of chromatin remodeling gene <em>ARID1A</em> in ovarian clear cell carcinoma. Science 2010;330:228–31.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sandoval GJ, Pulice JL, Pakula H, Schenone M, Takeda DY, Pop M, et al. Binding of TMPRSS2-ERG to BAF chromatin remodeling complexes mediates prostate oncogenesis. Mol cell. 2018;71:554–66.e7.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dufour CR, Scholtes C, Yan M, Chen Y, Han L, Li T, et al. The mTOR chromatin-bound interactome in prostate cancer. Cell Rep. 2022;38:110534.

Article  CAS  PubMed  Google Scholar 

Wu X, Wu J, Huang J, Powell WC, Zhang J, Matusik RJ, et al. Generation of a prostate epithelial cell-specific Cre transgenic mouse model for tissue-specific gene ablation. Mech Dev. 2001;101:61–9.

Article  CAS  PubMed  Google Scholar 

Suzuki A, Yamaguchi MT, Ohteki T, Sasaki T, Kaisho T, Kimura Y, et al. T cell-specific loss of Pten leads to defects in central and peripheral tolerance. Immunity. 2001;14:523–34.

Article  CAS  PubMed  Google Scholar 

March HN, Rust AG, Wright NA, ten Hoeve J, de Ridder J, Eldridge M, et al. Insertional mutagenesis identifies multiple networks of cooperating genes driving intestinal tumorigenesis. Nat Genet. 2011;43:1202–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gao X, Tate P, Hu P, Tjian R, Skarnes WC, Wang Z. ES cell pluripotency and germ-layer formation require the SWI/SNF chromatin remodeling component BAF250a. Proc Natl Acad Sci USA. 2008;105:6656–61.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ahmad I, Patel R, Liu Y, Singh LB, Taketo MM, Wu XR, et al. Ras mutation cooperates with β-catenin activation to drive bladder tumourigenesis. Cell Death Dis. 2011;2:e124.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bioinformatics ASB FastQC. A quality control tool for high throughput sequence data Available from: https://www.bioinformatics.babraham.ac.uk/projects/fastqc.

Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34:i884–i90.

Article  PubMed  PubMed Central  Google Scholar 

Wingett SW, Andrews S. FastQ Screen: A tool for multi-genome mapping and quality control. F1000Res. 2018;7:1338.

Article  PubMed  PubMed Central  Google Scholar 

Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019;37:907–15.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078–9.

Article  PubMed  PubMed Central  Google Scholar 

Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30:923–30.

Article  CAS  PubMed  Google Scholar 

Team RC. R: A Language and Environment for Statistical Computing Available from: https://www.R-project.org/.

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, et al. Orchestrating high-throughput genomic analysis with Bioconductor. Nat Methods. 2015;12:115–21.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.

Article  PubMed  PubMed Central  Google Scholar 

Stephens M. False discovery rates: a new deal. Biostatistics. 2017;18:275–94.

PubMed  Google Scholar 

Cunningham F, Achuthan P, Akanni W, Allen J, Amode MR, Armean IM, et al. Ensembl 2019. Nucleic Acids Res. 2019;47:D745–d51.

Article  CAS  PubMed  Google Scholar 

Howe KL, Achuthan P, Allen J, Allen J, Alvarez-Jarreta J, Amode MR, et al. Ensembl 2021. Nucleic Acids Res. 2021;49:D884–d91.