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Article: Disruption of a -35 kb Enhancer Impairs CTCF Binding and MLH1 Expression in Colorectal Cells

TitleDisruption of a -35 kb Enhancer Impairs CTCF Binding and MLH1 Expression in Colorectal Cells
Authors
Issue Date2018
PublisherAmerican Association for Cancer Research. The Journal's web site is located at http://clincancerres.aacrjournals.org/
Citation
Clinical Cancer Research, 2018, v. 24 n. 18, p. 4602-4611 How to Cite?
AbstractPurpose:MLH1 is a major tumor suppressor gene involved in the pathogenesis of Lynch syndrome and various sporadic cancers. Despite their potential pathogenic importance, genomic regions capable of regulating MLH1 expression over long distances have yet to be identified.Experimental Design: Here, we use chromosome conformation capture (3C) to screen a 650-kb region flanking the MLH1 locus to identify interactions between the MLH1 promoter and distal regions in MLH1-expressing and nonexpressing cells. Putative enhancers were functionally validated using luciferase reporter assays, chromatin immunoprecipitation, and CRISPR-Cas9-mediated deletion of endogenous regions. To evaluate whether germline variants in the enhancer might contribute to impaired MLH1 expression in patients with suspected Lynch syndrome, we also screened germline DNA from a cohort of 74 patients with no known coding mutations or epimutations at the MLH1 promoter.Results: A 1.8-kb DNA fragment, 35 kb upstream of the MLH1 transcription start site enhances MLH1 gene expression in colorectal cells. The enhancer was bound by CTCF and CRISPR-Cas9-mediated deletion of a core binding region impairs endogenous MLH1 expression. A total of 5.4% of suspected Lynch syndrome patients have a rare single-nucleotide variant (G > A; rs143969848; 2.5% in gnomAD European, non-Finnish) within a highly conserved CTCF-binding motif, which disrupts enhancer activity in SW620 colorectal carcinoma cells.Conclusions: A CTCF-bound region within the MLH1-35 enhancer regulates MLH1 expression in colorectal cells and is worthy of scrutiny in future genetic screening strategies for suspected Lynch syndrome associated with loss of MLH1 expression. Clin Cancer Res; 24(18); 4602-11. (c)2018 AACR.
Persistent Identifierhttp://hdl.handle.net/10722/267377
ISSN
2023 Impact Factor: 10.0
2023 SCImago Journal Rankings: 4.623
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorLiu, Q-
dc.contributor.authorThoms, JAI-
dc.contributor.authorNunez, AC-
dc.contributor.authorHuang, Y-
dc.contributor.authorKnezevic, K-
dc.contributor.authorPackham, D-
dc.contributor.authorPoulos, RC-
dc.contributor.authorWilliams, R-
dc.contributor.authorBeck, D-
dc.contributor.authorHawkins, NJ-
dc.contributor.authorWard, RL-
dc.contributor.authorWong, WHJ-
dc.contributor.authorHesson, LB-
dc.contributor.authorSloane, MA-
dc.contributor.authorPimanda, JE-
dc.date.accessioned2019-02-18T09:00:46Z-
dc.date.available2019-02-18T09:00:46Z-
dc.date.issued2018-
dc.identifier.citationClinical Cancer Research, 2018, v. 24 n. 18, p. 4602-4611-
dc.identifier.issn1078-0432-
dc.identifier.urihttp://hdl.handle.net/10722/267377-
dc.description.abstractPurpose:MLH1 is a major tumor suppressor gene involved in the pathogenesis of Lynch syndrome and various sporadic cancers. Despite their potential pathogenic importance, genomic regions capable of regulating MLH1 expression over long distances have yet to be identified.Experimental Design: Here, we use chromosome conformation capture (3C) to screen a 650-kb region flanking the MLH1 locus to identify interactions between the MLH1 promoter and distal regions in MLH1-expressing and nonexpressing cells. Putative enhancers were functionally validated using luciferase reporter assays, chromatin immunoprecipitation, and CRISPR-Cas9-mediated deletion of endogenous regions. To evaluate whether germline variants in the enhancer might contribute to impaired MLH1 expression in patients with suspected Lynch syndrome, we also screened germline DNA from a cohort of 74 patients with no known coding mutations or epimutations at the MLH1 promoter.Results: A 1.8-kb DNA fragment, 35 kb upstream of the MLH1 transcription start site enhances MLH1 gene expression in colorectal cells. The enhancer was bound by CTCF and CRISPR-Cas9-mediated deletion of a core binding region impairs endogenous MLH1 expression. A total of 5.4% of suspected Lynch syndrome patients have a rare single-nucleotide variant (G > A; rs143969848; 2.5% in gnomAD European, non-Finnish) within a highly conserved CTCF-binding motif, which disrupts enhancer activity in SW620 colorectal carcinoma cells.Conclusions: A CTCF-bound region within the MLH1-35 enhancer regulates MLH1 expression in colorectal cells and is worthy of scrutiny in future genetic screening strategies for suspected Lynch syndrome associated with loss of MLH1 expression. Clin Cancer Res; 24(18); 4602-11. (c)2018 AACR.-
dc.languageeng-
dc.publisherAmerican Association for Cancer Research. The Journal's web site is located at http://clincancerres.aacrjournals.org/-
dc.relation.ispartofClinical Cancer Research-
dc.titleDisruption of a -35 kb Enhancer Impairs CTCF Binding and MLH1 Expression in Colorectal Cells-
dc.typeArticle-
dc.identifier.emailWong, WHJ: jwhwong@hku.hk-
dc.identifier.authorityWong, WHJ=rp02363-
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1158/1078-0432.CCR-17-3678-
dc.identifier.scopuseid_2-s2.0-85053183071-
dc.identifier.hkuros296869-
dc.identifier.volume24-
dc.identifier.issue18-
dc.identifier.spage4602-
dc.identifier.epage4611-
dc.identifier.isiWOS:000444768200027-
dc.publisher.placeUnited States-
dc.identifier.issnl1078-0432-

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