{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,14]],"date-time":"2026-03-14T22:15:07Z","timestamp":1773526507821,"version":"3.50.1"},"reference-count":80,"publisher":"MDPI AG","issue":"14","license":[{"start":{"date-parts":[[2023,7,15]],"date-time":"2023-07-15T00:00:00Z","timestamp":1689379200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R01CA205632"],"award-info":[{"award-number":["R01CA205632"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R21CA226542"],"award-info":[{"award-number":["R21CA226542"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["T32CA009686"],"award-info":[{"award-number":["T32CA009686"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["F30CA250307"],"award-info":[{"award-number":["F30CA250307"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Mutations in the gene ankyrin repeat domain containing 11 (ANKRD11\/ANCO1) play a role in neurodegenerative disorders, and its loss of heterozygosity and low expression are seen in some cancers. Here, we show that low ANCO1 mRNA and protein expression levels are prognostic markers for poor clinical outcomes in breast cancer and that loss of nuclear ANCO1 protein expression predicts lower overall survival of patients with triple-negative breast cancer (TNBC). Knockdown of ANCO1 in early-stage TNBC cells led to aneuploidy, cellular senescence, and enhanced invasion in a 3D matrix. The presence of a subpopulation of ANCO1-depleted cells enabled invasion of the overall cell population in vitro and they converted more rapidly to invasive lesions in a xenograft mouse model. In ANCO1-depleted cells, ChIP-seq analysis showed a global increase in H3K27Ac signals that were enriched for AP-1, TEAD, STAT3, and NF\u03baB motifs. ANCO1-regulated H3K27Ac peaks had a significantly higher overlap with known breast cancer enhancers compared to ANCO1-independent ones. H3K27Ac engagement was associated with transcriptional activation of genes in the PI3K-AKT, epithelial\u2013mesenchymal transition (EMT), and senescence pathways. In conclusion, ANCO1 has hallmarks of a tumor suppressor whose loss of expression activates breast-cancer-specific enhancers and oncogenic pathways that can accelerate the early-stage progression of breast cancer.<\/jats:p>","DOI":"10.3390\/ijms241411505","type":"journal-article","created":{"date-parts":[[2023,7,17]],"date-time":"2023-07-17T00:35:04Z","timestamp":1689554104000},"page":"11505","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Loss of ANCO1 Expression Regulates Chromatin Accessibility and Drives Progression of Early-Stage Triple-Negative Breast Cancer"],"prefix":"10.3390","volume":"24","author":[{"given":"Meng","family":"Yuan","sequence":"first","affiliation":[{"name":"Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Megan E.","family":"Barefoot","sequence":"additional","affiliation":[{"name":"Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kendell","family":"Peterson","sequence":"additional","affiliation":[{"name":"Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Moray J.","family":"Campbell","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7442-8411","authenticated-orcid":false,"given":"Jan K.","family":"Blancato","sequence":"additional","affiliation":[{"name":"Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-8280-6413","authenticated-orcid":false,"given":"Manjing","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Bioinformatics and Biomathematics, Georgetown University, Washington, DC 20057, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3991-2766","authenticated-orcid":false,"given":"Marcel O.","family":"Schmidt","sequence":"additional","affiliation":[{"name":"Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8581-6222","authenticated-orcid":false,"given":"Amber J.","family":"Kiliti","sequence":"additional","affiliation":[{"name":"Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6173-9082","authenticated-orcid":false,"given":"Hong-Bin","family":"Fang","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Bioinformatics and Biomathematics, Georgetown University, Washington, DC 20057, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0570-4950","authenticated-orcid":false,"given":"Anton","family":"Wellstein","sequence":"additional","affiliation":[{"name":"Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6585-8612","authenticated-orcid":false,"given":"Anna T.","family":"Riegel","sequence":"additional","affiliation":[{"name":"Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5344-3575","authenticated-orcid":false,"given":"Ghada M.","family":"Sharif","sequence":"additional","affiliation":[{"name":"Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2023,7,15]]},"reference":[{"key":"ref_1","unstructured":"American Cancer Society (2023, April 27). Triple-Negative Breast Cancer. Available online: https:\/\/www.cancer.org\/cancer\/breast-cancer\/about\/types-of-breast-cancer\/triple-negative.html."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1016\/j.ajhg.2011.06.007","article-title":"Mutations in ANKRD11 cause KBG syndrome, characterized by intellectual disability, skeletal malformations, and macrodontia","volume":"89","author":"Sirmaci","year":"2011","journal-title":"Am. J. Hum. Genet."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"649","DOI":"10.1038\/s41576-018-0031-0","article-title":"Diagnosis and management of Cornelia de Lange syndrome: First international consensus statement","volume":"19","author":"Kline","year":"2018","journal-title":"Nat. Rev. Genet."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1006\/geno.2002.6828","article-title":"Sequencing, transcript identification, and quantitative gene expression profiling in the breast cancer loss of heterozygosity region 16q24.3 reveal three potential tumor-suppressor genes","volume":"80","author":"Powell","year":"2002","journal-title":"Genomics"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"748","DOI":"10.1086\/378522","article-title":"Pooled analysis of loss of heterozygosity in breast cancer: A genome scan provides comparative evidence for multiple tumor suppressors and identifies novel candidate regions","volume":"73","author":"Miller","year":"2003","journal-title":"Am. J. Hum. Genet."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"e48741","DOI":"10.15252\/embr.201948741","article-title":"Loss of ANCO1 repression at AIB1\/YAP targets drives breast cancer progression","volume":"21","author":"Kushner","year":"2020","journal-title":"EMBO Rep."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Jiang, G., Zhang, S., Yazdanparast, A., Li, M., Pawar, A.V., Liu, Y., Inavolu, S.M., and Cheng, L. (2016). Comprehensive comparison of molecular portraits between cell lines and tumors in breast cancer. BMC Genom., 17.","DOI":"10.1186\/s12864-016-2911-z"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"3300","DOI":"10.1016\/j.ejca.2012.03.023","article-title":"Specific-site methylation of tumour suppressor ANKRD11 in breast cancer","volume":"48","author":"Lim","year":"2012","journal-title":"Eur. J. Cancer"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"5238","DOI":"10.1038\/s41467-021-25467-w","article-title":"Single allele loss-of-function mutations select and sculpt conditional cooperative networks in breast cancer","volume":"12","author":"Schachter","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1016\/j.devcel.2014.11.031","article-title":"Ankrd11 is a chromatin regulator involved in autism that is essential for neural development","volume":"32","author":"Gallagher","year":"2015","journal-title":"Dev. Cell"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"33799","DOI":"10.1074\/jbc.M403997200","article-title":"Identification of a novel family of ankyrin repeats containing cofactors for p160 nuclear receptor coactivators","volume":"279","author":"Zhang","year":"2004","journal-title":"J. Biol. Chem."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1042\/BJ20071484","article-title":"Ankyrin repeats-containing cofactors interact with ADA3 and modulate its co-activator function","volume":"413","author":"Li","year":"2008","journal-title":"Biochem. J."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"846","DOI":"10.1210\/me.2013-1379","article-title":"Regulation of HER2 oncogene transcription by a multifunctional coactivator\/corepressor complex","volume":"28","author":"Garee","year":"2014","journal-title":"Mol. Endocrinol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"3541","DOI":"10.1242\/jcs.026351","article-title":"Identification of ANKRD11 as a p53 coactivator","volume":"121","author":"Neilsen","year":"2008","journal-title":"J. Cell Sci."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1319","DOI":"10.1038\/nm.4405","article-title":"Chromosome 1q21.3 amplification is a trackable biomarker and actionable target for breast cancer recurrence","volume":"23","author":"Goh","year":"2017","journal-title":"Nat. Med."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Cancer Genome Atlas Network (2012). Comprehensive molecular portraits of human breast tumours. Nature, 490, 61\u201370.","DOI":"10.1038\/nature11412"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1038\/nature10983","article-title":"The genomic and transcriptomic architecture of 2000 breast tumours reveals novel subgroups","volume":"486","author":"Curtis","year":"2012","journal-title":"Nature"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1007\/s10549-019-05485-5","article-title":"The orphan nuclear receptor estrogen-related receptor beta (ERR\u03b2) in triple-negative breast cancer","volume":"179","author":"Fernandez","year":"2020","journal-title":"Breast Cancer Res. Treat."},{"key":"ref_19","first-page":"6075","article-title":"Isolation and characterization of a spontaneously immortalized human breast epithelial cell line, MCF-10","volume":"50","author":"Soule","year":"1990","journal-title":"Cancer Res."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1093\/jnci\/92.14.1185a","article-title":"MCF10DCIS.com xenograft model of human comedo ductal carcinoma in situ","volume":"92","author":"Miller","year":"2000","journal-title":"JNCI J. Natl. Cancer Inst."},{"key":"ref_21","first-page":"215","article-title":"Reproducibility of LSI HER-2\/neu SpectrumOrange and CEP 17 SpectrumGreen Dual Color deoxyribonucleic acid probe kit. For enumeration of gene amplification in paraffin-embedded specimens: A multicenter clinical validation study","volume":"28","author":"Masood","year":"1998","journal-title":"Ann. Clin. Lab. Sci."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1111\/febs.15570","article-title":"A guide to assessing cellular senescence in vitro and in vivo","volume":"288","author":"Baker","year":"2021","journal-title":"FEBS J."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"9363","DOI":"10.1073\/pnas.92.20.9363","article-title":"A biomarker that identifies senescent human cells in culture and in aging skin in vivo","volume":"92","author":"Dimri","year":"1995","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1016\/S1046-2023(03)00032-X","article-title":"Morphogenesis and oncogenesis of MCF-10A mammary epithelial acini grown in three-dimensional basement membrane cultures","volume":"30","author":"Debnath","year":"2003","journal-title":"Methods"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1038\/nrm859","article-title":"Building epithelial architecture: Insights from three-dimensional culture models","volume":"3","author":"Zegers","year":"2002","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1111","DOI":"10.1093\/jnci\/50.5.1111","article-title":"On the origin and progression of ductal carcinoma in the human breast","volume":"50","author":"Wellings","year":"1973","journal-title":"J. Natl. Cancer Inst."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"26813","DOI":"10.1074\/jbc.M110.216200","article-title":"Role of the nuclear receptor coactivator AIB1-\u03944 splice variant in the control of gene transcription","volume":"286","author":"Chien","year":"2011","journal-title":"J. Biol. Chem."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"4230","DOI":"10.1158\/0008-5472.CAN-20-3625","article-title":"An AIB1 isoform alters enhancer access and enables progression of early-stage triple-negative breast cancer","volume":"81","author":"Sharif","year":"2021","journal-title":"Cancer Res."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1016\/j.ccr.2008.03.007","article-title":"Regulation of in situ to invasive breast carcinoma transition","volume":"13","author":"Hu","year":"2008","journal-title":"Cancer Cell"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"3033","DOI":"10.1038\/onc.2013.263","article-title":"The nuclear coactivator Amplified in Breast Cancer 1 maintains tumor initiating cells during development of Ductal Carcinoma In Situ","volume":"33","author":"Ory","year":"2014","journal-title":"Oncogene"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"21931","DOI":"10.1073\/pnas.1016071107","article-title":"Histone H3K27ac separates active from poised enhancers and predicts developmental state","volume":"107","author":"Creyghton","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1469","DOI":"10.1038\/s41591-018-0091-x","article-title":"Enhancer mapping uncovers phenotypic heterogeneity and evolution in patients with luminal breast cancer","volume":"24","author":"Patten","year":"2018","journal-title":"Nat. Med."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1472","DOI":"10.1101\/gad.995802","article-title":"Mammalian cell size is controlled by mTOR and its downstream targets S6K1 and 4EBP1\/eIF4E","volume":"16","author":"Fingar","year":"2002","journal-title":"Gene. Dev."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1080\/19336918.2015.1016686","article-title":"A new role for the PI3K\/Akt signaling pathway in the epithelial-mesenchymal transition","volume":"9","author":"Xu","year":"2015","journal-title":"Cell Adhes. Migr."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"2390","DOI":"10.1038\/sj.onc.1204383","article-title":"AP-1 in cell proliferation and survival","volume":"20","author":"Shaulian","year":"2001","journal-title":"Oncogene"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/sj.onc.1209759","article-title":"Transcription factors control invasion: AP-1 the first among equals","volume":"26","author":"Ozanne","year":"2007","journal-title":"Oncogene"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"862","DOI":"10.1016\/j.tibs.2017.09.003","article-title":"Regulation of the Hippo pathway transcription factor TEAD","volume":"42","author":"Lin","year":"2017","journal-title":"Trends Biochem. Sci."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"E2441","DOI":"10.1073\/pnas.1212021109","article-title":"The Hippo pathway target, YAP, promotes metastasis through its TEAD-interaction domain","volume":"109","author":"Lamar","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1016\/j.trecan.2019.02.010","article-title":"YAP\/TAZ signaling and resistance to cancer therapy","volume":"5","author":"Nguyen","year":"2019","journal-title":"Trends Cancer"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1218","DOI":"10.1038\/ncb3216","article-title":"Genome-wide association between YAP\/TAZ\/TEAD and AP-1 at enhancers drives oncogenic growth","volume":"17","author":"Zanconato","year":"2015","journal-title":"Nat. Cell Biol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"798","DOI":"10.1038\/nrc2734","article-title":"STATs in cancer inflammation and immunity: A leading role for STAT3","volume":"9","author":"Yu","year":"2009","journal-title":"Nat. Rev. Cancer"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1038\/nri.2017.142","article-title":"NF-\u03baB, inflammation, immunity and cancer: Coming of age","volume":"18","author":"Taniguchi","year":"2018","journal-title":"Nat. Rev. Immunol."},{"key":"ref_43","first-page":"S44-1","article-title":"Tissue factor promotes oncogenic senescence signaling and radiation resistance in glioblastoma","volume":"10","author":"Jeon","year":"2022","journal-title":"Brain Tumor Res. Treat."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"R77","DOI":"10.1530\/JME-20-0176","article-title":"Malic enzyme 1 (ME1) in the biology of cancer: It is not just intermediary metabolism","volume":"65","author":"Simmen","year":"2020","journal-title":"J. Mol. Endocrinol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1038\/nature11776","article-title":"Reciprocal regulation of p53 and malic enzymes modulates metabolism and senescence","volume":"493","author":"Jiang","year":"2013","journal-title":"Nature"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"25742","DOI":"10.18632\/oncotarget.8264","article-title":"Sciellin mediates mesenchymal-to-epithelial transition in colorectal cancer hepatic metastasis","volume":"7","author":"Chou","year":"2016","journal-title":"Oncotarget"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"4990","DOI":"10.1038\/onc.2016.29","article-title":"Topoisomerase II\u03b1 mediates TCF-dependent epithelial\u2013mesenchymal transition in colon cancer","volume":"35","author":"Zhou","year":"2016","journal-title":"Oncogene"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"2148","DOI":"10.1038\/jid.2012.78","article-title":"Heparin-binding EGF-like growth factor promotes epithelial-mesenchymal transition in human keratinocytes","volume":"132","author":"Stoll","year":"2012","journal-title":"J. Investig. Dermatol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"11011","DOI":"10.1093\/nar\/gku814","article-title":"Transcriptional complexity and roles of Fra-1\/AP-1 at the uPA\/Plau locus in aggressive breast cancer","volume":"42","author":"Tolza","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"1637","DOI":"10.1016\/j.ajpath.2019.03.012","article-title":"Silencing of LAMC2 reverses epithelial-mesenchymal transition and inhibits angiogenesis in cholangiocarcinoma via inactivation of the epidermal growth factor receptor signaling pathway","volume":"189","author":"Pei","year":"2019","journal-title":"Am. J. Pathol."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1016\/j.cell.2011.02.013","article-title":"Hallmarks of cancer: The next generation","volume":"144","author":"Hanahan","year":"2011","journal-title":"Cell"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"1347","DOI":"10.1016\/j.cell.2018.08.027","article-title":"The multifaceted role of chromosomal instability in cancer and its microenvironment","volume":"174","author":"Bakhoum","year":"2018","journal-title":"Cell"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"2440","DOI":"10.1016\/j.devcel.2021.07.006","article-title":"Gene copy-number changes and chromosomal instability induced by aneuploidy confer resistance to chemotherapy","volume":"56","author":"Ippolito","year":"2021","journal-title":"Dev. Cell"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"2828","DOI":"10.1080\/15384101.2019.1658476","article-title":"The expanding phenotypes of cohesinopathies: One ring to rule them all!","volume":"18","author":"Vliet","year":"2019","journal-title":"Cell Cycle"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1111\/cge.12564","article-title":"Broadening of cohesinopathies: Exome sequencing identifies mutations in ANKRD11 in two patients with Cornelia de Lange-overlapping phenotype","volume":"89","author":"Parenti","year":"2016","journal-title":"Clin. Genet."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1007\/s00439-014-1509-2","article-title":"Characterization of ANKRD11 mutations in humans and mice related to KBG syndrome","volume":"134","author":"Walz","year":"2015","journal-title":"Hum. Genet."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"2836","DOI":"10.1038\/onc.2011.456","article-title":"Mutant p53 drives multinucleation and invasion through a process that is suppressed by ANKRD11","volume":"31","author":"Noll","year":"2012","journal-title":"Oncogene"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"973","DOI":"10.1038\/ncb1909","article-title":"Persistent DNA damage signalling triggers senescence-associated inflammatory cytokine secretion","volume":"11","author":"Rodier","year":"2009","journal-title":"Nat. Cell Biol."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.1038\/ncb3195","article-title":"MTOR regulates the pro-tumorigenic senescence-associated secretory phenotype by promoting IL1A translation","volume":"17","author":"Laberge","year":"2015","journal-title":"Nat. Cell Biol."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1038\/nrc.2016.62","article-title":"The role of enhancers in cancer","volume":"16","author":"Sur","year":"2016","journal-title":"Nat. Rev. Cancer"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"1322","DOI":"10.1038\/ncb2615","article-title":"YAP mediates crosstalk between the Hippo and PI(3)K\u2013TOR pathways by suppressing PTEN via miR-29","volume":"14","author":"Tumaneng","year":"2012","journal-title":"Nat. Cell Biol."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1210\/me.2004-0106","article-title":"Overexpression of an N-terminally truncated isoform of the nuclear receptor coactivator amplified in breast cancer 1 leads to altered proliferation of mammary epithelial cells in transgenic mice","volume":"19","author":"Tilli","year":"2005","journal-title":"Mol. Endocrinol."},{"key":"ref_63","unstructured":"Kassambara, A., Kosinski, M., and Biecek, P. (2023, July 09). Survminer: Drawing Survival Curves Using \u2018ggplot2\u2019. R Package Version 0.4.9. Available online: https:\/\/cran.r-project.org\/web\/packages\/survminer\/index.html."},{"key":"ref_64","unstructured":"Wickham, H., Fran\u00e7ois, R., Henry, L., M\u00fcller, K., and Vaughan, D. (2023, July 09). dplyr: A Grammar of Data Manipulation. Available online: https:\/\/dplyr.tidyverse.org."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"2934","DOI":"10.1073\/pnas.83.9.2934","article-title":"Cytogenetic analysis using quantitative, high-sensitivity, fluorescence hybridization","volume":"83","author":"Pinkel","year":"1986","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Lin, Y.-N., Nasir, A., Camacho, S., Berry, D.L., Schmidt, M.O., Pearson, G.W., Riegel, A.T., and Wellstein, A. (2020). Monitoring cancer cell invasion and T-Cell cytotoxicity in 3D culture. J. Vis. Exp., e61392.","DOI":"10.3791\/61392-v"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: A Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"4288","DOI":"10.1093\/nar\/gks042","article-title":"Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation","volume":"40","author":"McCarthy","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref_69","first-page":"1438","article-title":"From reads to genes to pathways: Differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline","volume":"5","author":"Chen","year":"2016","journal-title":"F1000research"},{"key":"ref_70","unstructured":"Ploner, A. (2023, July 09). heatplus: Heatmaps with Row and\/or Column Covariates and Colored Clusters. R Package Version 3.6.0. Available online: https:\/\/github.com\/alexploner\/Heatplus."},{"key":"ref_71","doi-asserted-by":"crossref","unstructured":"Wickham, H. (2016). ggplot2: Elegant Graphics for Data Analysis, Springer. Available online: https:\/\/ggplot2.tidyverse.org.","DOI":"10.1007\/978-3-319-24277-4"},{"key":"ref_72","unstructured":"Slowikowski, K. (2023, July 09). ggrepel: Automatically Position Non-Overlapping Text Labels with \u2018ggplot2\u2019. R Package Version 0.9.2. Available online: https:\/\/github.com\/slowkow\/ggrepel."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1101\/gr.229102","article-title":"The human genome browser at UCSC","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"e95","DOI":"10.1093\/nar\/gku351","article-title":"De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: Controlling error rates correctly","volume":"42","author":"Lun","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"e45","DOI":"10.1093\/nar\/gkv1191","article-title":"csaw: A Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows","volume":"44","author":"Lun","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_76","doi-asserted-by":"crossref","unstructured":"Zhu, L.J., Gazin, C., Lawson, N.D., Pag\u00e8s, H., Lin, S.M., Lapointe, D.S., and Green, M.R. (2010). ChIPpeakAnno: A Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinform., 11.","DOI":"10.1186\/1471-2105-11-237"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1007\/978-1-62703-607-8_8","article-title":"Integrative analysis of ChIP-chip and ChIP-seq dataset","volume":"1067","author":"Zhu","year":"2013","journal-title":"Methods Mol. Biol."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"R137","DOI":"10.1186\/gb-2008-9-9-r137","article-title":"Model-based analysis of ChIP-Seq (MACS)","volume":"9","author":"Zhang","year":"2008","journal-title":"Genome Biol."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"W160","DOI":"10.1093\/nar\/gkw257","article-title":"deepTools2: A next generation web server for deep-sequencing data analysis","volume":"44","author":"Ryan","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_80","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. Cell"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/24\/14\/11505\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T20:12:44Z","timestamp":1760127164000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/24\/14\/11505"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,7,15]]},"references-count":80,"journal-issue":{"issue":"14","published-online":{"date-parts":[[2023,7]]}},"alternative-id":["ijms241411505"],"URL":"https:\/\/doi.org\/10.3390\/ijms241411505","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,7,15]]}}}