{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T16:44:30Z","timestamp":1790959470544,"version":"4.1.0"},"reference-count":87,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2020,10,15]],"date-time":"2020-10-15T00:00:00Z","timestamp":1602720000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000048","name":"American Cancer Society","doi-asserted-by":"publisher","award":["PF-17-163-02-DDC"],"award-info":[{"award-number":["PF-17-163-02-DDC"]}],"id":[{"id":"10.13039\/100000048","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000071","name":"National Institute of Child Health and Human Development","doi-asserted-by":"publisher","award":["HD099383-01"],"award-info":[{"award-number":["HD099383-01"]}],"id":[{"id":"10.13039\/100000071","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,12,18]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Although ARID1A mutations are a hallmark feature, mutations in other SWI\/SNF (SWItch\/Sucrose Non-Fermentable) chromatin remodeling subunits are also observed in endometrial neoplasms. Here, we interrogated the roles of Brahma\/SWI2-related gene 1 (BRG1, SMARCA4), the SWI\/SNF catalytic subunit, in the endometrial epithelium. BRG1 loss affects more than one-third of all active genes and highly overlaps with the ARID1A gene regulatory network. Chromatin immunoprecipitation studies revealed widespread subunit-specific differences in transcriptional regulation, as BRG1 promoter interactions are associated with gene activation, while ARID1A binding is associated with gene repression. However, we identified a physiologically relevant subset of BRG1 and ARID1A co-regulated epithelial identity genes. Mice were genetically engineered to inactivate BRG1 specifically in the endometrial epithelium. Endometrial glands were observed embedded in uterine myometrium, indicating adenomyosis-like phenotypes. Molecular similarities were observed between BRG1 and ARID1A mutant endometrial cells in vivo, including loss of epithelial cell adhesion and junction genes. Collectively, these studies illustrate overlapping contributions of multiple SWI\/SNF subunit mutations in the translocation of endometrium to distal sites, with loss of cell integrity being a common feature in SWI\/SNF mutant endometrial epithelia.<\/jats:p>","DOI":"10.1093\/hmg\/ddaa227","type":"journal-article","created":{"date-parts":[[2020,10,13]],"date-time":"2020-10-13T19:22:54Z","timestamp":1602616974000},"page":"3412-3430","source":"Crossref","is-referenced-by-count":19,"title":["SWI\/SNF inactivation in the endometrial epithelium leads to loss of epithelial integrity"],"prefix":"10.1093","volume":"29","author":[{"given":"Jake J","family":"Reske","sequence":"first","affiliation":[{"name":"Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mike R","family":"Wilson","sequence":"additional","affiliation":[{"name":"Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeanne","family":"Holladay","sequence":"additional","affiliation":[{"name":"Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marc","family":"Wegener","sequence":"additional","affiliation":[{"name":"Genomics Core Facility, Van Andel Research Institute, Grand Rapids, MI 49503, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marie","family":"Adams","sequence":"additional","affiliation":[{"name":"Genomics Core Facility, Van Andel Research Institute, Grand Rapids, MI 49503, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5775-2594","authenticated-orcid":false,"given":"Ronald L","family":"Chandler","sequence":"additional","affiliation":[{"name":"Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA"},{"name":"Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA"},{"name":"Department of Women\u2019s Health, Spectrum Health System, Grand Rapids, MI 49341, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,10,19]]},"reference":[{"key":"2020121910194126500_ref1","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.1500447","article-title":"Mammalian SWI\/SNF chromatin remodeling complexes and cancer: mechanistic insights gained from human genomics","volume":"1","author":"Kadoch","year":"2015","journal-title":"Sci. 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Genet."},{"key":"2020121910194126500_ref29","doi-asserted-by":"crossref","first-page":"D330","DOI":"10.1093\/nar\/gky1055","article-title":"The Gene Ontology Resource: 20 years and still GOing strong","volume":"47","author":"The Gene Ontology","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020121910194126500_ref30","doi-asserted-by":"crossref","first-page":"D100","DOI":"10.1093\/nar\/gky1128","article-title":"GTRD: a database on gene transcription regulation-2019 update","volume":"47","author":"Yevshin","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020121910194126500_ref31","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/s41576-018-0089-8","article-title":"Chromatin accessibility and the regulatory epigenome","volume":"20","author":"Klemm","year":"2019","journal-title":"Nat. Rev. Genet."},{"key":"2020121910194126500_ref32","doi-asserted-by":"crossref","DOI":"10.1093\/database\/bax028","article-title":"GeneHancer: genome-wide integration of enhancers and target genes in GeneCards","volume":"2017","author":"Fishilevich","year":"2017","journal-title":"Database (Oxford)"},{"key":"2020121910194126500_ref33","doi-asserted-by":"crossref","first-page":"2718","DOI":"10.1210\/en.2014-1265","article-title":"Lactoferrin-iCre: a new mouse line to study uterine epithelial gene function","volume":"155","author":"Daikoku","year":"2014","journal-title":"Endocrinology"},{"key":"2020121910194126500_ref34","doi-asserted-by":"crossref","first-page":"1937","DOI":"10.1084\/jem.20030714","article-title":"The role of Brg 1, a catalytic subunit of mammalian chromatin-remodeling complexes, in T cell development","volume":"198","author":"Gebuhr","year":"2003","journal-title":"J. Exp. Med."},{"key":"2020121910194126500_ref35","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1097\/GCO.0000000000000555","article-title":"A critical review of recent advances in the diagnosis, classification, and management of uterine adenomyosis","volume":"31","author":"Tan","year":"2019","journal-title":"Curr. Opin. Obstet. Gynecol."},{"key":"2020121910194126500_ref36","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-019-13708-y","article-title":"Uterine adenomyosis is an oligoclonal disorder associated with KRAS mutations","volume":"10","author":"Inoue","year":"2019","journal-title":"Nat. Commun."},{"key":"2020121910194126500_ref37","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1093\/humrep\/dez253","article-title":"A mouse model of endometriosis mimicking the natural spread of invasive endometrium","volume":"35","author":"Wilson","year":"2020","journal-title":"Hum. Reprod."},{"key":"2020121910194126500_ref38","volume-title":"Metastatic Cancer: Clinical and Biological Perspectives","author":"Jandial","year":"2013"},{"key":"2020121910194126500_ref39","doi-asserted-by":"crossref","first-page":"5094","DOI":"10.1210\/en.2009-0750","article-title":"Spatiotemporal coupling of focal extracellular matrix degradation and reconstruction in the menstrual human endometrium","volume":"150","author":"Gaide Chevronnay","year":"2009","journal-title":"Endocrinology"},{"key":"2020121910194126500_ref40","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1093\/molehr\/2.2.77","article-title":"The signals and molecular pathways involved in human menstruation, a unique process of tissue destruction and remodelling","volume":"2","author":"Tabibzadeh","year":"1996","journal-title":"Mol. Hum. Reprod."},{"key":"2020121910194126500_ref41","first-page":"1016","article-title":"Revisiting the hallmarks of cancer","volume":"7","author":"Fouad","year":"2017","journal-title":"Am. J. Cancer Res."},{"key":"2020121910194126500_ref42","first-page":"322","article-title":"Loss of the SWI\/SNF ATPase subunits BRM and BRG1 drives lung cancer development","volume":"3","author":"Marquez-Vilendrer","year":"2016","journal-title":"OncoTargets Ther."},{"key":"2020121910194126500_ref43","doi-asserted-by":"crossref","first-page":"5847","DOI":"10.1242\/jcs.01502","article-title":"Inducible changes in cell size and attachment area due to expression of a mutant SWI\/SNF chromatin remodeling enzyme","volume":"117","author":"Hill","year":"2004","journal-title":"J. Cell Sci."},{"key":"2020121910194126500_ref44","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1186\/1476-4598-9-280","article-title":"Modulation of extracellular matrix\/adhesion molecule expression by BRG1 is associated with increased melanoma invasiveness","volume":"9","author":"Saladi","year":"2010","journal-title":"Mol. Cancer"},{"key":"2020121910194126500_ref45","first-page":"881","article-title":"Progesterone inhibits human endometrial cancer cell growth and invasiveness: down-regulation of cellular adhesion molecules through progesterone B receptors","volume":"62","author":"Dai","year":"2002","journal-title":"Cancer Res."},{"key":"2020121910194126500_ref46","doi-asserted-by":"crossref","first-page":"3481","DOI":"10.1016\/j.bbamcr.2013.06.026","article-title":"Anoikis molecular pathways and its role in cancer progression","volume":"1833","author":"Paoli","year":"2013","journal-title":"Biochim. Biophys. Acta"},{"key":"2020121910194126500_ref47","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1038\/nrc3068","article-title":"SWI\/SNF nucleosome remodellers and cancer","volume":"11","author":"Wilson","year":"2011","journal-title":"Nat. Rev. Cancer"},{"key":"2020121910194126500_ref48","doi-asserted-by":"crossref","first-page":"968","DOI":"10.1097\/IGC.0000000000000454","article-title":"The risks for ovarian, endometrial, breast, colorectal, and other cancers in women with newly diagnosed endometriosis or adenomyosis: a population-based study","volume":"25","author":"Kok","year":"2015","journal-title":"Int. J. Gynecol. Cancer"},{"key":"2020121910194126500_ref49","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1016\/j.molcel.2018.06.040","article-title":"Binding of TMPRSS2-ERG to BAF chromatin remodeling complexes mediates prostate oncogenesis","volume":"71","author":"Sandoval","year":"2018","journal-title":"Mol. Cell"},{"key":"2020121910194126500_ref50","doi-asserted-by":"crossref","first-page":"1067","DOI":"10.1016\/j.molcel.2017.11.026","article-title":"AP-1 transcription factors and the BAF complex mediate signal-dependent enhancer selection","volume":"68","author":"Vierbuchen","year":"2017","journal-title":"Mol. Cell"},{"key":"2020121910194126500_ref51","doi-asserted-by":"crossref","first-page":"1059","DOI":"10.1016\/j.celrep.2014.02.038","article-title":"The hippo transducer TAZ interacts with the SWI\/SNF complex to regulate breast epithelial lineage commitment","volume":"6","author":"Skibinski","year":"2014","journal-title":"Cell Rep."},{"key":"2020121910194126500_ref52","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms14648","article-title":"The SWI\/SNF chromatin remodelling complex is required for maintenance of lineage specific enhancers","volume":"8","author":"Alver","year":"2017","journal-title":"Nat. Commun."},{"key":"2020121910194126500_ref53","doi-asserted-by":"crossref","first-page":"700","DOI":"10.1593\/neo.09406","article-title":"Aberrant methylation and reduced expression of LHX9 in malignant gliomas of childhood","volume":"11","author":"Vladimirova","year":"2009","journal-title":"Neoplasia"},{"key":"2020121910194126500_ref54","doi-asserted-by":"crossref","first-page":"909","DOI":"10.1038\/35002622","article-title":"The LIM homeobox gene Lhx9 is essential for mouse gonad formation","volume":"403","author":"Birk","year":"2000","journal-title":"Nature"},{"key":"2020121910194126500_ref55","article-title":"Annexin A2 acts as an adhesion molecule on the endometrial epithelium during implantation in mice","volume":"10","author":"Wang","year":"2015","journal-title":"PLoS One"},{"key":"2020121910194126500_ref56","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1016\/j.cell.2009.01.009","article-title":"Understanding the words of chromatin regulation","volume":"136","author":"Wu","year":"2009","journal-title":"Cell"},{"key":"2020121910194126500_ref57","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1042\/BJ20040524","article-title":"Two related ARID family proteins are alternative subunits of human SWI\/SNF complexes","volume":"383","author":"Wang","year":"2004","journal-title":"Biochem. J."},{"key":"2020121910194126500_ref58","doi-asserted-by":"crossref","first-page":"1662","DOI":"10.1101\/gad.1323805","article-title":"PBAF chromatin-remodeling complex requires a novel specificity subunit, BAF200, to regulate expression of selective interferon-responsive genes","volume":"19","author":"Yan","year":"2005","journal-title":"Genes Dev."},{"key":"2020121910194126500_ref59","author":"Reed","year":"2000"},{"key":"2020121910194126500_ref60","doi-asserted-by":"crossref","first-page":"351","DOI":"10.12717\/DR.2017.21.4.351","article-title":"A review of mechanisms of implantation","volume":"21","author":"Kim","year":"2017","journal-title":"Dev. Reprod."},{"key":"2020121910194126500_ref61","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1158\/2159-8290.CD-12-0095","article-title":"The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data","volume":"2","author":"Cerami","year":"2012","journal-title":"Cancer Discov."},{"key":"2020121910194126500_ref62","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet. J."},{"key":"2020121910194126500_ref63","author":"Andrews","year":"2010"},{"key":"2020121910194126500_ref64","doi-asserted-by":"crossref","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","article-title":"Multi QC: summarize analysis results for multiple tools and samples in a single report","volume":"32","author":"Ewels","year":"2016","journal-title":"Bioinformatics"},{"key":"2020121910194126500_ref65","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2020121910194126500_ref66","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"2020121910194126500_ref67","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1038\/nmeth.3885","article-title":"Data-driven hypothesis weighting increases detection power in genome-scale multiple testing","volume":"13","author":"Ignatiadis","year":"2016","journal-title":"Nat. Methods"},{"key":"2020121910194126500_ref68","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. 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Rep."},{"key":"2020121910194126500_ref72","doi-asserted-by":"crossref","first-page":"1813","DOI":"10.1101\/gr.136184.111","article-title":"ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia","volume":"22","author":"Landt","year":"2012","journal-title":"Genome Res."},{"key":"2020121910194126500_ref73","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"2020121910194126500_ref74","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","article-title":"Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities","volume":"38","author":"Heinz","year":"2010","journal-title":"Mol. 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Biotechnol."},{"key":"2020121910194126500_ref78","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"2020121910194126500_ref79","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1038\/ng0506-500","article-title":"Gene pattern 2. 0","volume":"38","author":"Reich","year":"2006","journal-title":"Nat. Genet."},{"key":"2020121910194126500_ref80","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"Cluster profiler: an R package for comparing biological themes among gene clusters","volume":"16","author":"Yu","year":"2012","journal-title":"OMICS"},{"key":"2020121910194126500_ref81","doi-asserted-by":"crossref","first-page":"2847","DOI":"10.1093\/bioinformatics\/btw313","article-title":"Complex heatmaps reveal patterns and correlations in multidimensional genomic data","volume":"32","author":"Gu","year":"2016","journal-title":"Bioinformatics"},{"key":"2020121910194126500_ref82","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1003118","article-title":"Software for computing and annotating genomic ranges","volume":"9","author":"Lawrence","year":"2013","journal-title":"PLoS Comput. 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