ARID1A facilitates KRAS signaling-regulated enhancer activity in an AP1-dependent manner in colorectal cancer cells
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BACKGROUND: ARID1A (AT-rich interactive domain-containing protein 1A) is a subunit of the BAF chromatin remodeling complex and plays roles in transcriptional regulation and DNA damage response. Mutations in ARID1A that lead to inactivation or loss of expression are frequent and widespread across many cancer types including colorectal cancer (CRC). A tumor suppressor role of ARID1A has been established in a number of tumor types including CRC where the genetic inactivation of Arid1a alone led to the formation of invasive colorectal adenocarcinomas in mice. Mechanistically, ARID1A has been described to largely function through the regulation of enhancer activity. METHODS: To mimic ARID1A-deficient colorectal cancer, we used CRISPR/Cas9-mediated gene editing to inactivate the ARID1A gene in established colorectal cancer cell lines. We integrated gene expression analyses with genome-wide ARID1A occupancy and epigenomic mapping data to decipher ARID1A-dependent transcriptional regulatory mechanisms. RESULTS: Interestingly, we found that CRC cell lines harboring KRAS mutations are critically dependent on ARID1A function. In the absence of ARID1A, proliferation of these cell lines is severely impaired, suggesting an essential role for ARID1A in this context. Mechanistically, we showed that ARID1A acts as a co-factor at enhancers occupied by AP1 transcription factors acting downstream of the MEK/ERK pathway. Consistently, loss of ARID1A led to a disruption of KRAS/AP1-dependent enhancer activity, accompanied by a downregulation of expression of the associated target genes. CONCLUSIONS: We identify a previously unknown context-dependent tumor-supporting function of ARID1A in CRC downstream of KRAS signaling. Upon the loss of ARID1A in KRAS-mutated cells, enhancers that are co-occupied by ARID1A and the AP1 transcription factors become inactive, thereby leading to decreased target gene expression. Thus, targeting of the BAF complex in KRAS-mutated CRC may offer a unique, previously unknown, context-dependent therapeutic option in CRC.
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In KRAS-mutated colon cancer, a similar tumor-supporting role of ARID1A was required for MEK/ERK signaling.
“In KRAS-mutated colon cancer, a similar tumor-supporting role of ARID1A was required for MEK/ERK signaling66.”
From Impact of KRAS mutations and co-mutations on clinical outcomes in pancreatic ductal adenocarcinoma (2024) · cites this paper as [66]
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The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041 · see citing works
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607 · see citing works
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400 · see citing works
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625 · see citing works
Model-based Analysis of ChIP-Seq (MACS)
Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386 · see citing works
Cerami, E., Gao, J., Dogrusoz, U., Gross, B. E., Sumer, S. O., Aksoy, B. A., Jacobsen, A., Byrne, C. J., Heuer, M. L., Larsson, E., et al. (2012) · Cancer Discovery · doi:10.1158/2159-8290.cd-12-0095 · Cited by 17,455 · see citing works
Robinson, J. T., Thorvaldsdóttir, H., Winckler, W., Guttman, M., Lander, E. S., Getz, G., & Mesirov, J. P. (2011) · Nature Biotechnology · doi:10.1038/nbt.1754 · Cited by 15,390 · see citing works
Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal
Gao, J., Aksoy, B. A., Dogrusoz, U., Dresdner, G., Gross, B., Sumer, S. O., Sun, Y., Jacobsen, A., Sinha, R., Larsson, E., et al. (2013) · Science Signaling · doi:10.1126/scisignal.2004088 · Cited by 15,160 · see citing works
Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y. C., Laslo, P., Cheng, J. X., Murre, C., Singh, H., & Glass, C. K. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.05.004 · Cited by 13,382 · see citing works
A genetic model for colorectal tumorigenesis
Fearon, E. R., & Vogelstein, B. (1990) · Cell · doi:10.1016/0092-8674(90)90186-i · Cited by 12,132 · see citing works
Trapnell, C., Roberts, A., Goff, L. A., Pertea, G. M., Kim, D., Kelley, D. R., Pimentel, H., Salzberg, S. L., Rinn, J. L., & Pachter, L. S. (2012) · Nature Protocols · doi:10.1038/nprot.2012.016 · Cited by 11,930 · see citing works
Genome engineering using the CRISPR-Cas9 system
Ran, F. A., Hsu, P. D., Wright, J., Agarwala, V., Scott, D. A., & Zhang, F. (2013) · Nature Protocols · doi:10.1038/nprot.2013.143 · Cited by 11,133 · see citing works
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update
Kuleshov, M. V., Jones, M. R., Rouillard, A. D., Fernandez, N. F., Duan, Q., Wang, Z., Koplev, S., Jenkins, S. L., Jagodnik, K. M., Lachmann, A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw377 · Cited by 10,799 · see citing works
Mootha, V. K., Lindgren, C. M., Eriksson, K.-F., Subramanian, A., Sihag, S., Lehar, J., Puigserver, P., Carlsson, E., Ridderstråle, M., Laurila, E., et al. (2003) · Nature Genetics · doi:10.1038/ng1180 · Cited by 10,197 · see citing works
deepTools2: a next generation web server for deep-sequencing data analysis
Ramírez, F., Ryan, D. P., Grüning, B., Bhardwaj, V., Kilpert, F., Richter, A. S., Heyne, S., Dündar, F., & Manke, T. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw257 · Cited by 8,096 · see citing works
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool
Chen, E. Y., Tan, C. M., Kou, Y., Duan, Q., Wang, Z., Meirelles, G. V., Clark, N. R., & Ma’ayan, A. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-128 · Cited by 7,814 · see citing works
GREAT improves functional interpretation of cis-regulatory regions
McLean, C. Y., Bristor, D., Hiller, M., Clarke, S. L., Schaar, B. T., Lowe, C. B., Wenger, A. M., & Bejerano, G. (2010) · Nature Biotechnology · doi:10.1038/nbt.1630 · Cited by 4,502 · see citing works
Cohesin Loss Eliminates All Loop Domains
Rao, S. S. P., Huang, S.-C., Glenn St Hilaire, B., Engreitz, J. M., Perez, E. M., Kieffer-Kwon, K.-R., Sanborn, A. L., Johnstone, S. E., Bascom, G. D., Bochkov, I. D., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.026 · Cited by 1,883 · see citing works
<i>ARID1A</i> Mutations in Endometriosis-Associated Ovarian Carcinomas
Wiegand, K. C., Shah, S. P., Al-Agha, O. M., Zhao, Y., Tse, K., Zeng, T., Senz, J., McConechy, M. K., Anglesio, M. S., Kalloger, S. E., et al. (2010) · New England Journal of Medicine · doi:10.1056/nejmoa1008433 · Cited by 1,712 · see citing works
Whitmarsh, A. J., & Davis, R. J. (1996) · Journal of Molecular Medicine · doi:10.1007/s001090050063 · Cited by 1,543 · see citing works
Rouillard, A. D., Gundersen, G. W., Fernandez, N. F., Wang, Z., Monteiro, C. D., McDermott, M. G., & Ma’ayan, A. (2016) · Database · doi:10.1093/database/baw100 · Cited by 1,515 · see citing works
Ras oncogenes: split personalities
Karnoub, A. E., & Weinberg, R. A. (2008) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2438 · Cited by 1,467 · see citing works
Kadoch, C., Hargreaves, D. C., Hodges, H. C., Elias, L., Ho, L., Ranish, J. A., & Crabtree, G. R. (2013) · Nature Genetics · doi:10.1038/ng.2628 · Cited by 1,444 · see citing works
The selection and function of cell type-specific enhancers
Heinz, S., Romanoski, C. E., Benner, C., & Glass, C. K. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3949 · Cited by 1,010 · see citing works
High-resolution TADs reveal DNA sequences underlying genome organization in flies
Ramírez, F., Bhardwaj, V., Arrigoni, L., Lam, K. C., Grüning, B. A., Villaveces, J. M., Habermann, B. H., Akhtar, A., & Manke, T. (2018) · Nature Communications · doi:10.1038/s41467-017-02525-w · Cited by 974 · see citing works
Nucleosome disruption and enhancement of activator binding by a human SW1/SNF complex
Kwon, H., Imbalzano, A. N., Khavari, P. A., Kingston, R. E., & Green, M. R. (1994) · Nature · doi:10.1038/370477a0 · Cited by 780 · see citing works
Synthetic lethality by targeting EZH2 methyltransferase activity in ARID1A-mutated cancers
Bitler, B. G., Aird, K. M., Гарипов, А. Р., Li, H., Amatangelo, M. D., Kossenkov, A. V., Schultz, D., Liu, Q., Shih, I., Conejo-Garcia, J. R., et al. (2015) · Nature Medicine · doi:10.1038/nm.3799 · Cited by 683 · see citing works
Reconstitution of a Core Chromatin Remodeling Complex from SWI/SNF Subunits
Phelan, M. L., Sif, S., Narlikar, G. J., & Kingston, R. E. (1999) · Molecular Cell · doi:10.1016/s1097-2765(00)80315-9 · Cited by 629 · see citing works
Facilitated binding of TATA-binding protein to nucleosomal DNA
Imbalzano, A. N., Kwon, H., Green, M. R., & Kingston, R. E. (1994) · Nature · doi:10.1038/370481a0 · Cited by 591 · see citing works
The Spectrum of SWI/SNF Mutations, Ubiquitous in Human Cancers
Shain, A. H., & Pollack, J. R. (2013) · PLoS ONE · doi:10.1371/journal.pone.0055119 · Cited by 578 · see citing works
ARID1A Deficiency Impairs the DNA Damage Checkpoint and Sensitizes Cells to PARP Inhibitors
Shen, J., Peng, Y., Wei, L., Zhang, W., Yang, L., Lan, L., Kapoor, P., Ju, Z., Mo, Q., Shih, I.-M., et al. (2015) · Cancer Discovery · doi:10.1158/2159-8290.cd-14-0849 · Cited by 522 · see citing works
AP-1 Transcription Factors and the BAF Complex Mediate Signal-Dependent Enhancer Selection
Vierbuchen, T., Ling, E., Cowley, C. J., Couch, C. H., Wang, X., Harmin, D. A., Roberts, C. W. M., & Greenberg, M. E. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.11.026 · Cited by 455 · see citing works
Self-citationGuan, B., Wang, T., & Shih, I. (2011) · Cancer Research · doi:10.1158/0008-5472.can-11-1562 · Cited by 445 · see citing works
Ho, L., Jothi, R., Ronan, J. L., Cui, K., Zhao, K., & Crabtree, G. R. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0812888106 · Cited by 427 · see citing works
The SWI/SNF chromatin remodelling complex is required for maintenance of lineage specific enhancers
Alver, B. H., Kim, K. H., Lu, P., Wang, X., Manchester, H. E., Wang, W., Haswell, J. R., Park, P. J., & Roberts, C. W. M. (2017) · Nature Communications · doi:10.1038/ncomms14648 · Cited by 427 · see citing works
Self-citationMichel, B. C., D’Avino, A. R., Cassel, S. H., Mashtalir, N., McKenzie, Z. M., McBride, M. J., Valencia, A. M., Zhou, Q., Bocker, M., Soares, L. M. M., et al. (2018) · Nature Cell Biology · doi:10.1038/s41556-018-0221-1 · Cited by 423 · see citing works
(2014) · Choice Reviews Online · doi:10.5860/choice.51-6210 · Cited by 381 · see citing works
Olig2 Targets Chromatin Remodelers to Enhancers to Initiate Oligodendrocyte Differentiation
Yu, Y., Chen, Y., Kim, B., Wang, H., Zhao, C., He, X., Liu, L., Liu, W., Wu, L. M. N., Mao, M., et al. (2013) · Cell · doi:10.1016/j.cell.2012.12.006 · Cited by 375 · see citing works
SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation
Wang, X., Lee, R. S., Alver, B., Haswell, J. R., Wang, S., Mieczkowski, J., Drier, Y., Gillespie, S. M., Archer, T. C., Wu, J. N., et al. (2016) · Nature Genetics · doi:10.1038/ng.3746 · Cited by 370 · see citing works
Self-citationDistinct Properties of Cell-Type-Specific and Shared Transcription Factor Binding Sites
Gertz, J., Savic, D., Varley, K. E., Partridge, E. C., Safi, A., Jain, P., Cooper, G. M., Reddy, T. E., Crawford, G. E., & Myers, R. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.08.037 · Cited by 363 · see citing works
ARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice
Mathur, R., Alver, B., Roman, A. K. S., Wilson, B. G., Wang, X., Agoston, A. T., Park, P. J., Shivdasani, R. A., & Roberts, C. W. M. (2016) · Nature Genetics · doi:10.1038/ng.3744 · Cited by 356 · see citing works
Self-citationGao, X., Tate, P. H., Hu, P., Tjian, R., Skarnes, W. C., & Wang, Z. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0801802105 · Cited by 336 · see citing works
Chandler, R. L., Damrauer, J. S., Raab, J. R., Schisler, J. C., Wilkerson, M. D., Didion, J. P., Starmer, J., Serber, D., Yee, D., Xiong, J., et al. (2015) · Nature Communications · doi:10.1038/ncomms7118 · Cited by 320 · see citing works
A Specificity and Targeting Subunit of a Human SWI/SNF Family-Related Chromatin-Remodeling Complex
Nie, Z., Xue, Y., Yang, D., Zhou, S., Deroo, B. J., Archer, T., & Wang, W. (2000) · Molecular and Cellular Biology · doi:10.1128/mcb.20.23.8879-8888.2000 · Cited by 298 · see citing works
Somatic mutations in the chromatin remodeling gene ARID1A occur in several tumor types
Jones, S., Li, M., Parsons, D. W., Zhang, X., Wesseling, J., Kristel, P., Schmidt, M. K., Markowitz, S. D., Yan, H., Bigner, D. D., et al. (2011) · Human Mutation · doi:10.1002/humu.21633 · Cited by 277 · see citing works
Isobe, T., Okuyama, T., Toyoda, H., Komurasaki, T., Uchida, D., Takayama, Y., & Hanada, K. (1995) · Journal of Biological Chemistry · doi:10.1074/jbc.270.13.7495 · Cited by 269 · see citing works
Regulation of gene transcription by mitogen-activated protein kinase signaling pathways
Whitmarsh, A. J. (2006) · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research · doi:10.1016/j.bbamcr.2006.11.011 · Cited by 259 · see citing works
Reciprocal regulation of CD4/CD8 expression by SWI/SNF-like BAF complexes
Chi, T. H., Wan, M., Zhao, K., Taniuchi, I., Chen, L., Littman, D. R., & Crabtree, G. R. (2002) · Nature · doi:10.1038/nature00876 · Cited by 249 · see citing works
ARID1A-mutated ovarian cancers depend on HDAC6 activity
Bitler, B. G., Wu, S., Park, P. H., Hai, Y., Aird, K. M., Wang, Y., Zhai, Y., Kossenkov, A. V., Vara-Ailor, A., Rauscher, F. J., et al. (2017) · Nature Cell Biology · doi:10.1038/ncb3582 · Cited by 232 · see citing works
Chèneby, J., Gheorghe, M., Artufel, M., Mathelier, A., & Ballester, B. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1092 · Cited by 232 · see citing works
Zirkel, A., Nikolic, M., Sofiadis, K., Mallm, J.-P., Brackley, C. A., Gothe, H., Drechsel, O., Becker, C., Altmüller, J., Josipovic, N., et al. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.03.030 · Cited by 226 · see citing works
Self-citationChromatin accessibility underlies synthetic lethality of SWI/SNF subunits in ARID1A-mutant cancers
Kelso, T. W. R., Porter, D. K., Amaral, M. L., Shokhirev, M. N., Benner, C. W., & Hargreaves, D. C. (2017) · eLife · doi:10.7554/elife.30506 · Cited by 191 · see citing works
Hu, G., Schones, D. E., Cui, K., Ybarra, R., Northrup, D., Tang, Q., Gattinoni, L., Restifo, N. P., Huang, S., & Zhao, K. (2011) · Genome Research · doi:10.1101/gr.121145.111 · Cited by 186 · see citing works
Positively selected enhancer elements endow osteosarcoma cells with metastatic competence
Morrow, J. J., Bayles, I., Funnell, A. P. W., Miller, T. E., Saiakhova, A., Lizardo, M. M., Bartels, C. F., Kapteijn, M. Y., Hung, S., Mendoza, A., et al. (2018) · Nature Medicine · doi:10.1038/nm.4475 · Cited by 161 · see citing works
Loss of ARID1A expression sensitizes cancer cells to PI3K- and AKT-inhibition
Samartzis, E. P., Gutsche, K., Dedes, K. J., Fink, D. A., Stucki, M., & Imesch, P. (2014) · Oncotarget · doi:10.18632/oncotarget.2092 · Cited by 146 · see citing works
Chu, T., Rice, E. J., Booth, G. T., Salamanca, H. H., Wang, Z., Core, L. J., Longo, S. L., Corona, R. J., Chin, L. S., Lis, J. T., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0244-3 · Cited by 129 · see citing works
Genome-Wide Transcriptional Regulation Mediated by Biochemically Distinct SWI/SNF Complexes
Raab, J. R., Resnick, S. J., & Magnuson, T. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005748 · Cited by 125 · see citing works
The Tumor Suppressor ARID1A Controls Global Transcription via Pausing of RNA Polymerase II
Trizzino, M., Barbieri, E., Petracovici, A., Wu, S., Welsh, S. A., Owens, T. A., Licciulli, S., Zhang, R., & Gardini, A. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.05.097 · Cited by 97 · see citing works
Lowery, W. J., Schildkraut, J. M., Akushevich, L., Bentley, R. C., Marks, J. R., Huntsman, D. D., & Berchuck, A. (2011) · International Journal of Gynecological Cancer · doi:10.1097/igc.0b013e318231f140 · Cited by 96 · see citing works
Shema, E., Nikolov, M., Haj‐Yahya, M., Siman, P., Allemand, E., Yamaguchi, Y., Muchardt, C., Urlaub, H., Brik, A., Oren, M., et al. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.07.014 · Cited by 93 · see citing works
Expression of p270 (ARID1A), a component of human SWI/SNF complexes, in human tumors
Wang, X., Nagl, N. G., Flowers, S. J., Zweitzig, D. R., Dallas, P. B., & Morán, E. (2004) · International Journal of Cancer · doi:10.1002/ijc.20450 · Cited by 93 · see citing works
Self-citationThe SWI/SNF chromatin‐remodeling complex subunit SNF5 is essential for hepatocyte differentiation
Gresh, L., Bourachot, B., Reimann, A., Guigas, B., Fiette, L., Garbay, S., Muchardt, C., Hue, L., Pontoglio, M., Yaniv, M., et al. (2005) · The EMBO Journal · doi:10.1038/sj.emboj.7600802 · Cited by 90 · see citing works
p300/CREB Binding Protein-Related Protein p270 Is a Component of Mammalian SWI/SNF Complexes
Dallas, P. B., Cheney, I. W., Liao, D.-W., Bowrin, V., Byam, W., Pacchione, S. J., Kobayashi, R., Yaciuk, P., & Morán, E. (1998) · Molecular and Cellular Biology · doi:10.1128/mcb.18.6.3596 · Cited by 88 · see citing works
Genomic and functional evidence for an ARID1A tumor suppressor role
Huang, J., Zhao, Y., Li, Y., Fletcher, J. A., & Xiao, S. (2007) · Genes Chromosomes and Cancer · doi:10.1002/gcc.20459 · Cited by 79 · see citing works
TCR-dependent transformation of mature memory phenotype T cells in mice.
Wang, X., Werneck, M. B. F., Wilson, B., Kim, H.-J., Kluk, M., Thom, C. S., Wischhusen, J., Evans, J. A., Jesneck, J., Nguyen, P., et al. (2011) · Journal of Clinical Investigation · doi:10.1172/jci37210 · Cited by 72 · see citing works
Self-citationKuramochi, H., Nakajima, G., Kaneko, Y., Nakamura, A., Inoue, Y., Yamamoto, M., & Hayashi, K. (2012) · BMC Cancer · doi:10.1186/1471-2407-12-88 · Cited by 62 · see citing works
Tian, B., Zhao, Y., Kalita, M. K., Edeh, C. B., Paessler, S., Casola, A., Teng, M. N., Garofalo, R. P., & Brasier, A. R. (2013) · Journal of Virology · doi:10.1128/jvi.03399-12 · Cited by 61 · see citing works
Zhai, Y., Kuick, R. D., Tipton, C. B., WU, R. T., Sessine, M. S., Wang, Z., Baker, S. J., Fearon, E. R., & Cho, K. R. (2015) · The Journal of Pathology · doi:10.1002/path.4599 · Cited by 56 · see citing works
Lakshminarasimhan, R., Andreu‐Vieyra, C., Lawrenson, K., Duymich, C. E., Gayther, S. A., Liang, G., & Jones, P. A. (2017) · Cancer Letters · doi:10.1016/j.canlet.2017.04.040 · Cited by 54 · see citing works
Arid1a restrains Kras-dependent changes in acinar cell identity
Livshits, G., Alonso-Curbelo, D., Morris, J. P., Koche, R., Saborowski, M., Wilkinson, J. E., & Lowe, S. W. (2018) · eLife · doi:10.7554/elife.35216 · Cited by 48 · see citing works
Kwan, S.-Y., Cheng, X., Tsang, Y. T. M., Choi, J.-S., Kwan, S., Izaguirre, D. I., Kwan, H. S., Gershenson, D. M., & Wong, K. (2016) · Oncotarget · doi:10.18632/oncotarget.10921 · Cited by 44 · see citing works
Holik, A. Z., Young, M. A., Krzystyniak, J., Williams, G. T., METZGER, D., Shorning, B. Y., & Clarke, A. R. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004453 · Cited by 43 · see citing works
Sugiyama, M., Oki, E., Nakaji, Y., Tsutsumi, S., Ono, N., Nakanishi, R., Sugiyama, M., Nakashima, Y., Sonoda, H., Ohgaki, K., et al. (2016) · Cancer Science · doi:10.1111/cas.13075 · Cited by 38 · see citing works
Abstract LB-096: SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation
Wang, X., Lee, R., Alver, B., Haswell, J. R., Wang, S., Troisi, E. C., Bernstein, B., Park, P. J., & Roberts, C. W. M. (2017) · Cancer Research · doi:10.1158/1538-7445.am2017-lb-096 · Cited by 4 · see citing works
Self-citationMathur, R., Alver, B., Roman, A. K. S., Wilson, B. G., Wang, X., Agoston, A. T., Park, P. J., Shivdasani, R. A., & Roberts, C. W. M. (2017) · Cancer Research · doi:10.1158/1538-7445.am2017-lb-286 · Cited by 2 · see citing works
Self-citationSun, X., Wang, S. C., Zhang, S., & Zhu, H. (2018) · Cancer Research · doi:10.1158/1538-7445.mousemodels17-a52 · Cited by 2 · see citing works
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Yousef, A., Yousef, M., Chowdhury, S., Abdilleh, K., Knafl, M., Edelkamp, P., Alfaro-Munoz, K., Chacko, R., Peterson, J., Smaglo, B. G., et al. (2024) · npj Precision Oncology · doi:10.1038/s41698-024-00505-0 · Cited by 93 · see citing works
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The mechanisms of action of chromatin remodelers and implications in development and disease
Sahu, R. K., Singh, S., & Tomar, R. S. (2020) · Biochemical Pharmacology · doi:10.1016/j.bcp.2020.114200 · Cited by 50 · see citing works
Lin, C.-C., Kuo, I., Wu, L., Kuan, W.-H., Liao, S., Jen, J., Yang, Y.-E., Tang, C., Chen, Y., & Wang, Y. (2020) · Theranostics · doi:10.7150/thno.47491 · Cited by 42 · see citing works
Hu, B., Lin, J., Yang, X., & Sang, X. (2020) · Cell Proliferation · doi:10.1111/cpr.12791 · Cited by 40 · see citing works
Wu, K., Rodrigues, L., Post, G. S., Harvey, G., White, M. E., Miller, A., Lambert, L., Lewis, B., Lopes, C., & Zou, J. (2023) · npj Precision Oncology · doi:10.1038/s41698-023-00346-3 · Cited by 39 · see citing works
Bhattacharya, A., Fushimi, A., Yamashita, N., Hagiwara, M., Morimoto, Y., Rajabi, H., Long, M. D., Abdulla, M., Ahmad, R., Street, K., et al. (2022) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-21-0672 · Cited by 37 · see citing works
ARID1A mutations in cancer development: mechanism and therapy
Zhang, X., Zhang, Y., Zhao, J., Wu, Y., Zhang, N., & Shen, W. (2023) · Carcinogenesis · doi:10.1093/carcin/bgad011 · Cited by 36 · see citing works
Xu, C., Huang, K. K., Law, J. H., Chua, J. S., Sheng, T., Flores, N. M., Pizzi, M. P., Okabe, A., Tan, A. L. K., Zhu, F., et al. (2023) · Gut · doi:10.1136/gutjnl-2022-328332 · Cited by 34 · see citing works
Kim, Y. R., Joo, J., Lee, H. J., Kim, C., Park, J.-C., Yu, Y. S., Kim, C. R., Lee, D. H., Cha, J., Kwon, H., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-51050-0 · Cited by 33 · see citing works
STAT3 is a biologically relevant therapeutic target in H3K27M-mutant diffuse midline glioma
Zhang, L., Nesvick, C. L., Day, C. A., Choi, J., Lu, V. M., Peterson, T. E., Power, E. A., Anderson, J. B., Hamdan, F. H., Decker, P. A., et al. (2022) · Neuro-Oncology · doi:10.1093/neuonc/noac093 · Cited by 33 · see citing works
Self-citationDarbandi, S. F., An, J., Lim, K. J., Page, N. F., Liang, L., Young, D. M., Ypsilanti, A. R., State, M. W., Nord, A. S., Sanders, S., et al. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.114329 · Cited by 32 · see citing works
Roles of ARID1A variations in colorectal cancer: a collaborative review
Zhao, S., Wu, W., Jiang, Z., Tang, F., Ding, L., Xu, W., & Ruan, L. (2022) · Molecular Medicine · doi:10.1186/s10020-022-00469-6 · Cited by 28 · see citing works
Diagnostic significance and prognostic role of the ARID1A gene in cancer outcomes (Review)
Pavlidou, E., & Balis, V. (2020) · World Academy of Sciences Journal · doi:10.3892/wasj.2020.37 · Cited by 26 · see citing works
Angelico, G., Attanasio, G., Colarossi, L., Colarossi, C., Montalbano, M., Aiello, E., Vendra, F. D., Mare, M., Orsi, N. M., & Memeo, L. (2024) · Cancers · doi:10.3390/cancers16112062 · Cited by 25 · see citing works
Tomasini, P. P., Guecheva, T. N., Leguisamo, N. M., Péricart, S., Brunac, A., Hoffmann, J., & Saffi, J. (2021) · Cancers · doi:10.3390/cancers13133130 · Cited by 24 · see citing works
Bhattacharya, A., Fushimi, A., Wang, K., Yamashita, N., Morimoto, Y., Ishikawa, S., Daimon, T., Liu, T., Liu, S., Long, M. D., et al. (2023) · Communications Biology · doi:10.1038/s42003-023-05395-9 · Cited by 24 · see citing works
Odnokoz, O., Wavelet-Vermuse, C., Hophan, S. L., Bulun, S. E., & Wan, Y. (2021) · Epigenomics · doi:10.2217/epi-2020-0414 · Cited by 21 · see citing works
Liu, S., Cao, W., Niu, Y., Luo, J., Zhao, Y., Hu, Z., & Zong, C. C. (2021) · eLife · doi:10.7554/elife.64204 · Cited by 21 · see citing works
Paradoxical Role of AT-rich Interactive Domain 1A in Restraining Pancreatic Carcinogenesis
Ferri-Borgogno, S., Barui, S., McGee, A. M., Griffiths, T., Singh, P. K., Piett, C. G., Ghosh, B., Bhattacharyya, S., Singhi, A., Pradhan, K., et al. (2020) · Cancers · doi:10.3390/cancers12092695 · Cited by 22 · see citing works
PDP1 promotes KRAS mutant colorectal cancer progression by serving as a scaffold for BRAF and MEK1
Yuan, M., Zhang, C., Chen, S., Ye, S., Liu, H., Ke, H., Huang, J., Liang, G., Yu, R., Hu, T., et al. (2024) · Cancer Letters · doi:10.1016/j.canlet.2024.217007 · Cited by 22 · see citing works
TP53-Status-Dependent Oncogenic EZH2 Activity in Pancreatic Cancer
Versemann, L., Patil, S., Steuber, B., Zhang, Z., Kopp, W., Krawczyk, H. E., Kaulfuß, S., Wollnik, B., Ströbel, P., Neeße, A., et al. (2022) · Cancers · doi:10.3390/cancers14143451 · Cited by 19 · see citing works
Self-citationCharacterization of G-quadruplex formation in the ARID1A promoter
Yan, T., Zhao, B., Wu, Q., Wang, W., Shi, J., Li, D., Stovall, D. B., & Sui, G. (2020) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2020.01.210 · Cited by 16 · see citing works
Hamdan, F. H., Abdelrahman, A. M., Kutschat, A. P., Wang, X., Ekstrom, T. L., Jalan‐Sakrikar, N., Wippel, C. W., Taheri, N., Tamon, L., Kopp, W., et al. (2023) · Gut · doi:10.1136/gutjnl-2022-328154 · Cited by 15 · see citing works
Self-citationRemodeling of the ARID1A tumor suppressor
Luo, Q., Wu, X., & Liu, Z. (2020) · Cancer Letters · doi:10.1016/j.canlet.2020.07.026 · Cited by 14 · see citing works
Hu, H., Chen, Z., Ji, L., Wang, Y., Yang, M., Lai, R., Zhong, Y., Zhang, X., & Wang, L. (2020) · Cancer Letters · doi:10.1016/j.canlet.2020.08.034 · Cited by 13 · see citing works
ARID1A and Its Impact Across the Hallmarks of Cancer
Kearns, B., McKell, A., Steveson, I., Worley, P., Barton, B., Bennett, J., Anderson, D., Harris, J., Christensen, J., & Barrott, J. J. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26104644 · Cited by 10 · see citing works
Yunos, R. I. M., Mutalib, N. A., Tieng, F. Y. F., Abu, N., & Jamal, R. (2020) · Biomolecules · doi:10.3390/biom10030476 · Cited by 10 · see citing works
PHF13 epigenetically activates TGFβ driven epithelial to mesenchymal transition
Sun, Y., Li, D., Liu, H., Huang, Y., Meng, F., Tang, J., Li, Z., & Xie, W. (2022) · Cell Death and Disease · doi:10.1038/s41419-022-04940-4 · Cited by 10 · see citing works
Zhang, Z., Wang, X., Hamdan, F. H., Likhobabina, A., Patil, S., Aperdannier, L., Sen, M., Traub, J., Neeße, A., Fischer, A., et al. (2023) · Cellular and Molecular Gastroenterology and Hepatology · doi:10.1016/j.jcmgh.2023.01.015 · Cited by 9 · see citing works
Self-citationPrognostic utility of TME-associated genes in pancreatic cancer
Nie, Y., Xu, L., Bai, Z., Liu, Y., Wang, S., Zeng, Q., Gao, X., Xia, X., & Chang, D. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2023.1218774 · Cited by 8 · see citing works
Li, P., Meng, Q., Xue, Y., Teng, Z., Chen, H., Zhang, J., Xu, Y., Wang, S., Yu, R., Ou, Q., et al. (2022) · Frontiers in Oncology · doi:10.3389/fonc.2022.1000146 · Cited by 8 · see citing works
Advances in the study of the role of high-frequency mutant subunits of the SWI/SNF complex in tumors
Zhao, J., Zhu, J., Tang, Y., Zheng, K., & Li, Z. (2024) · Frontiers in Oncology · doi:10.3389/fonc.2024.1463892 · Cited by 7 · see citing works
Revealing ARID1A Function in Gastric Cancer from the Bottom Up
Zafra, M. P., & Dow, L. E. (2021) · Cancer Discovery · doi:10.1158/2159-8290.cd-21-0271 · Cited by 7 · see citing works
Hartley, A., Galbraith, L. C. A., Shaw, R., Tibbo, A. J., Veeratterapillay, R., Wilson, L., Heer, R., Blyth, K., Leung, H. Y., & Ahmad, I. (2025) · British Journal of Cancer · doi:10.1038/s41416-025-02944-3 · Cited by 6 · see citing works
Evidence of histone modification affecting ARID1A expression in colorectal cancer cell lines.
Erfani, M., Zamani, M., & Mokarram, P. (2022) · Gastroenterology and hepatology from bed to bench. · Cited by 6 · see citing works
Opening and changing: mammalian SWI/SNF complexes in organ development and carcinogenesis
Sailik, F. A., Emerald, B. S., & Ansari, S. A. (2024) · Open Biology · doi:10.1098/rsob.240039 · Cited by 6 · see citing works
ARID1A Deficiency Regulates Anti-Tumor Immune Response in Esophageal Adenocarcinoma
Zhang, L., Zheng, Y., Chien, W., Ziman, B., Billet, S., Koeffler, H. P., Lin, D., & Bhowmick, N. A. (2023) · Cancers · doi:10.3390/cancers15225377 · Cited by 5 · see citing works
Villanueva, J., Kwong, L. N., Han, T., Martinez, S. A., Shanahan, M. T., Kanke, M., Dow, L. E., Danko, C. G., & Sethupathy, P. (2022) · BMC Genomics · doi:10.1186/s12864-022-09018-1 · Cited by 5 · see citing works
Genome-Wide CRISPR Screen Identifies KEAP1 Perturbation as a Vulnerability of ARID1A-Deficient Cells
Fournier, L.-A., Kalantari, F., Wells, J. P., Lee, J. S., Trigo‐Gonzalez, G., Moksa, M., Smith, T., White, J., Shanks, A., Wang, S., et al. (2024) · Cancers · doi:10.3390/cancers16172949 · Cited by 4 · see citing works
Chromatin remodeling complexes: architects influencing breast cancer progression
Giovani, O., Eckersley, G. S., Jones, H. R., & Nagarajan, S. (2025) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2025.1690350 · Cited by 3 · see citing works
Nesvick, C. L., Zhang, L., Yan, Y., Wixom, A. Q., Hamdan, F. H., Ge, J., Anderson, J. B., Gaspar‐Maia, A., Johnsen, S. A., & Daniels, D. J. (2025) · Neuro-Oncology · doi:10.1093/neuonc/noaf081 · Cited by 4 · see citing works
Self-citationEvaluating the ‘ARID’ landscape of SWI/SNF complexes with relevance to cancer
Hore, P., Sarkar, S., & Bashyam, M. D. (2025) · Gene · doi:10.1016/j.gene.2025.149664 · Cited by 2 · see citing works
The role of SWI/SNF complexes in digestive system neoplasms
Liang, H., Zheng, X., Zhang, X., Zhang, Y., & Zheng, J. (2024) · Medical Oncology · doi:10.1007/s12032-024-02343-3 · Cited by 2 · see citing works
ARID1A: Multiple functions in human pregnancy
Zhu, C., Zhu, B., Xu, S., Li, L., Song, Y., & Tang, C. (2025) · Journal of Reproductive Immunology · doi:10.1016/j.jri.2025.104448 · Cited by 2 · see citing works
Chen, S.-T. (2025) · New medicine. · doi:10.61958/nmeb9298 · Cited by 2 · see citing works
Critical Differential Expression Assessment for Individual Bulk RNA-Seq ProjectsPreprint
Warden, C., & Wu, X. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.10.579728 · Cited by 2 · see citing works
Diet-induced chromatin states influence intestinal stem cell memoryPreprint
Saiz, D. R., Millan, Y. B., McDermott, T. H., Cerna, G., Sankar, S., Farnsworth, F., Uher, E., Lahiri, G., Lintecum, K., Mullen, K. F., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.19.706894 · Cited by 2 · see citing works
MDM2 binds and suppresses RNA polymerase III to restrain the innate immune response to cytosolic DNA
Weber, S., Manzini, V., Dietrich, H., Schotte, H., Moshkovskii, S. A., Hackert, P., Duman, E. T., Vu, N. Q., Prokakis, E., Salinas, G., et al. (2026) · Cell Death and Differentiation · doi:10.1038/s41418-026-01834-2 · Cited by 1 · see citing works
Autism-associated transcriptional regulators target shared loci proximal to brain-expressed genesPreprint
Darbandi, S. F., An, J., Lim, K. J., Page, N. F., Liang, L., Ypsilanti, A. R., Markenscoff-Papadimitriou, E., State, M. W., Nord, A. S., Sanders, S., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.10.17.512583 · Cited by 1 · see citing works
High-resolution topographic mapping of Phobos by the HRSC on MARS-EXPRESS
Giese, B., Oberst, J., & Neukum, G. (2005) · elib (German Aerospace Center)
Villanueva, J., Kwong, L. N., Han, T., Martinez, S. A., Shanahan, M. T., Kanke, M., Dow, L. E., Danko, C. G., & Sethupathy, P. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.12.13.472432
Gerber, S. (2020) · doi:10.53846/goediss-8184
Fos/AP-1 as an Exemplar for the Study of Neuronal Activity-Dependent Gene Regulation
Griffith, E. C., & Greenberg, M. E. (2024) · Springer eBooks · doi:10.1007/978-3-031-68550-7_1
Interclonal cooperation and suppression shape early Ras-driven tumour growthPreprint
Teles-Reis, J., Dillard, C., Antunes, M. G., Jain, A., Ruiz-Duran, P., Deng, M., Liu, D., Gaudin, C., Nakken, S., Singh, A., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.19.706761
Étude des éléments cis-régulateurs à différentes échelles : approches fondamentales à appliquer
Hammal, F. (2023) · theses.fr (ABES) · doi:10.70675/90dfd1eczcfebz4ccfz9115z46efa92c2877
ARID1A regulates colorectal cancer metastasis through the AKT/mTOR/p70S6K pathway
Zhang, Y., Duan, X., Hou, H., Wang, G., Lin, Q., Li, Y., Lan, H., Huo, X., Yang, F., Fu, G., et al. (2026) · Translational Oncology · doi:10.1016/j.tranon.2026.102928
- Authors
- Sen, M., Wang, X., Hamdan, F. H., Rapp, J., Eggert, J., Kosinsky, R. L., Wegwitz, F., Kutschat, A. P., Younesi, F. S., Gaedcke, J., Grade, M., Hessmann, E., Papantonis, A., Strӧbel, P., & Johnsen, S. A.
- Affiliations
- Universitätsmedizin Göttingen (DE)
- Mayo Clinic (US)
- Corresponding author
- Johnsen, Steven A.
- ORCID
- Venue
- Clinical Epigenetics
- Published
- 2019-06-19
- Volume
- 11
- Issue
- 1
- Pages
- 92-92
- ISSN
- 1868-7075 (ISSN-L)
- 1868-7083
- PMC
- PMC6585056
- OpenAlex
- W2949636912
- Cited by
- 61
- References
- 76
- Citations by year
- 2026: 4 · 2025: 7 · 2024: 11 · 2023: 10 · 2022: 9 · 2021: 9 · 2020: 10
- FWCI
- 2.32
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Clinical Epigenetics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- GoeScholar The Publication Server of the Georg-August-Universität Göttingen (Georg-August-Universität Göttingen) (submittedVersion, cc-by)
- Funders
- Deutsche Forschungsgemeinschaft (GSC 226)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- ARID1A, colorectal cancer, KRAS signaling, enhancer activity, AP-1 transcription factor, BAF chromatin remodeling complex, MEK/ERK signaling, transcriptional regulation, tumor suppressor, cell proliferation, CRISPR/Cas9 genome editing, therapeutic target
- MeSH terms
- Gene Editing, DNA-Binding Proteins, Enhancer Elements, Genetic, Humans, Mutation, Transcription Factors, Colorectal Neoplasms, Signal Transduction, Gene Expression Regulation, Neoplastic, Proto-Oncogene Proteins p21(ras), Transcription Factor AP-1, HT29 Cells, DNA Methylation, MAP Kinase Signaling System, HCT116 Cells, Cell Proliferation, Genome-Wide Association Study, CRISPR-Cas Systems
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