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Roberts SA, Brown AJ, Wyrick JJ. Recurrent Noncoding Mutations in Skin Cancers: UV Damage Susceptibility or Repair Inhibition as Primary Driver? Bioessays 2019; 41:e1800152. [PMID: 30801747 PMCID: PMC6571124 DOI: 10.1002/bies.201800152] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 12/05/2018] [Indexed: 12/14/2022]
Abstract
Somatic mutations arising in human skin cancers are heterogeneously distributed across the genome, meaning that certain genomic regions (e.g., heterochromatin or transcription factor binding sites) have much higher mutation densities than others. Regional variations in mutation rates are typically not a consequence of selection, as the vast majority of somatic mutations in skin cancers are passenger mutations that do not promote cell growth or transformation. Instead, variations in DNA repair activity, due to chromatin organization and transcription factor binding, have been proposed to be a primary driver of mutational heterogeneity in melanoma. However, as discussed in this review here, recent studies indicate that chromatin organization and transcription factor binding also significantly modulate the rate at which UV lesions form in DNA. The authors propose that local variations in lesion susceptibility may be an important driver of mutational hotspots in melanoma and other skin cancers, particularly at binding sites for ETS transcription factors.
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Affiliation(s)
- Steven A. Roberts
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164
| | - Alexander J. Brown
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164
| | - John J. Wyrick
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164
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Liu Y, Jin X, Li Y, Ruan Y, Lu Y, Yang M, Lin D, Song P, Guo Y, Zhao S, Dong B, Xie Y, Dang Q, Quan C. DNA methylation of claudin-6 promotes breast cancer cell migration and invasion by recruiting MeCP2 and deacetylating H3Ac and H4Ac. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2016; 35:120. [PMID: 27461117 PMCID: PMC4962420 DOI: 10.1186/s13046-016-0396-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/13/2016] [Indexed: 11/30/2022]
Abstract
Background Claudin-6 (CLDN6), a member of claudin transmembrane protein family, has recently been reported to be undetectable or at low levels in human breast cancer cell lines and tissues and plays a role in suppression of migration and invasion in breast cancer cells. In addition, it is reported that CLDN6 expression is regulated by DNA methylation in various human cancers and cell lines. However, it is unclear how DNA methylation regulates CLDN6 expression. Here we show the mechanism by which DNA methylation regulates CLDN6 expression in human breast cancer cell line MCF-7. Methods RT-PCR, Western blot and immunofluorescent staining were utilized to investigate CLDN6 expression in breast cancer tissues and MCF-7 cells. Methylation-Specific PCR (MSP) was applied to determine DNA methylation status in CLDN6 gene promoter region. Wound-healing assay and invasion assay were utilized to test mobility of MCF-7 cells treated with 5-aza-dC (DNA methyltransferase inhibitor). MeCP2 binding, H3Ac and H4Ac in CLDN6 promoter region were analyzed by ChIP assay. Nuclease accessibility assay was performed for analysis of the chromatin conformation of CLDN6 gene. To study the role of CLDN6 in malignant progression, we used RNAi to knockdown CLDN6 expression in MCF-7 cells treated with 5-aza-dC, and examined the mobility of MCF-7 cells by wound-healing assay and invasion assay. Results 5-aza-dC and TSA (histone deacetylase inhibitor) application induced CLDN6 expression in MCF-7 cells respectively and synergistically. 5-aza-dC treatment induced CLDN6 demethylation, inhibited MeCP2 binding to CLDN6 promoter and increased H3Ac and H4Ac in the promoter. In addition, TSA increased H4Ac, not H3Ac in the promoter. The chromatin structure of CLDN6 gene became looser than the control group after treating with 5-aza-dC in MCF-7 cells. 5-aza-dC up-regulated CLDN6 expression and suppressed migration and invasion in MCF-7 cells, whereas CLDN6 silence restored tumor malignance in MCF-7 cells. Conclusions DNA methylation down-regulates CLDN6 expression through MeCP2 binding to the CLDN6 promoter, deacetylating H3 and H4, and altering chromatin structure, consequently promoting migratory and invasive phenotype in MCF-7 cells.
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Affiliation(s)
- Yafang Liu
- The Key Laboratory of Pathology, Ministry of Education, College of Basic Medical Science, Jilin University, 126 Xinmin Street, Changchun, Jilin, 130021, China.,Department of Pathology, the First Affiliated Hospital of Jilin University, 126 Xinmin Street, Changchun, Jilin, 130021, China
| | - Xiangshu Jin
- The Key Laboratory of Pathology, Ministry of Education, College of Basic Medical Science, Jilin University, 126 Xinmin Street, Changchun, Jilin, 130021, China
| | - Yanru Li
- The Key Laboratory of Pathology, Ministry of Education, College of Basic Medical Science, Jilin University, 126 Xinmin Street, Changchun, Jilin, 130021, China
| | - Yang Ruan
- The Key Laboratory of Pathology, Ministry of Education, College of Basic Medical Science, Jilin University, 126 Xinmin Street, Changchun, Jilin, 130021, China
| | - Yan Lu
- The Key Laboratory of Pathology, Ministry of Education, College of Basic Medical Science, Jilin University, 126 Xinmin Street, Changchun, Jilin, 130021, China
| | - Minlan Yang
- The Key Laboratory of Pathology, Ministry of Education, College of Basic Medical Science, Jilin University, 126 Xinmin Street, Changchun, Jilin, 130021, China
| | - Dongjing Lin
- The Key Laboratory of Pathology, Ministry of Education, College of Basic Medical Science, Jilin University, 126 Xinmin Street, Changchun, Jilin, 130021, China
| | - Peiye Song
- The Key Laboratory of Pathology, Ministry of Education, College of Basic Medical Science, Jilin University, 126 Xinmin Street, Changchun, Jilin, 130021, China
| | - Yantong Guo
- The Key Laboratory of Pathology, Ministry of Education, College of Basic Medical Science, Jilin University, 126 Xinmin Street, Changchun, Jilin, 130021, China
| | - Shuai Zhao
- The Key Laboratory of Pathology, Ministry of Education, College of Basic Medical Science, Jilin University, 126 Xinmin Street, Changchun, Jilin, 130021, China
| | - Bing Dong
- The Key Laboratory of Pathology, Ministry of Education, College of Basic Medical Science, Jilin University, 126 Xinmin Street, Changchun, Jilin, 130021, China
| | - Yinping Xie
- The Key Laboratory of Pathology, Ministry of Education, College of Basic Medical Science, Jilin University, 126 Xinmin Street, Changchun, Jilin, 130021, China
| | - Qihua Dang
- The Key Laboratory of Pathology, Ministry of Education, College of Basic Medical Science, Jilin University, 126 Xinmin Street, Changchun, Jilin, 130021, China
| | - Chengshi Quan
- The Key Laboratory of Pathology, Ministry of Education, College of Basic Medical Science, Jilin University, 126 Xinmin Street, Changchun, Jilin, 130021, China.
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Cadet J, Mouret S, Ravanat JL, Douki T. Photoinduced damage to cellular DNA: direct and photosensitized reactions. Photochem Photobiol 2012; 88:1048-65. [PMID: 22780837 DOI: 10.1111/j.1751-1097.2012.01200.x] [Citation(s) in RCA: 204] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The survey focuses on recent aspects of photochemical reactions to cellular DNA that are implicated through the predominant formation of mostly bipyrimidine photoproducts in deleterious effects of human exposure to sunlight. Recent developments in analytical methods have allowed accurate and quantitative measurements of the main DNA photoproducts in cells and human skin. Highly mutagenic CC and CT bipyrimidine photoproducts, including cyclobutane pyrimidine dimers and pyrimidine (6-4) pyrimidone photoproducts (6-4PPs) are generated in low yields with respect to TT and TC photoproducts. Another striking finding deals with the formation of Dewar valence isomers, the third class of bipyrimidine photoproducts that is accounted for by UVA-mediated isomerization of initially UVB generated 6-4PPs. Cyclobutadithymine (T<>T) has been unambiguously shown to be involved in the genotoxicity of UVA radiation. Thus, T<>T is formed in UVA-irradiated cellular DNA according to a direct excitation mechanism with a higher efficiency than oxidatively generated DNA damage that arises mostly through the Type II photosensitization mechanism. C<>C and C<>T are repaired at rates intermediate between those of T<>T and 6-4TT. Evidence has been also provided for the occurrence of photosensitized reactions mediated by exogenous agents that act either in an independent way or through photodynamic effects.
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Affiliation(s)
- Jean Cadet
- Laboratoire Lésions des Acides Nucléiques, SCIB-UMR-E n°3, CEA/UJF, Institut Nanosciences et Cryogénie, CEA/Grenoble, Grenoble Cedex, France
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Song Q, Sherrer SM, Suo Z, Taylor JS. Preparation of site-specific T=mCG cis-syn cyclobutane dimer-containing template and its error-free bypass by yeast and human polymerase η. J Biol Chem 2012; 287:8021-8. [PMID: 22262850 DOI: 10.1074/jbc.m111.333591] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
C-to-T mutations are a hallmark of UV light and, in humans, occur preferentially at methylated Py(m)CG sites, which are also sites of preferential cyclobutane pyrimidine dimer (CPD) formation. In response, cells have evolved DNA damage bypass polymerases, of which polymerase η (pol η) appears to be specifically adapted to synthesize past cis-syn CPDs. Although T=T CPDs are stable, CPDs containing C or 5-methylcytosine ((m)C) are not and spontaneously deaminate to U or T at pH 7 and 37 °C over a period of hours or days, making their preparation and study difficult. Furthermore, there is evidence to suggest that, depending on solvent polarity, a C or an (m)C in a CPD can adopt three tautomeric forms, one of which could code as T. Although many in vitro studies have established that synthesis past T or U in a CPD by pol η occurs in a highly error-free manner, the only in vitro evidence that synthesis past C or (m)C in a CPD also occurs in an error-free manner is for an (m)C in the 5'-position of an (m)C=T CPD. Herein, we describe the preparation and characterization of an oligodeoxynucleotide containing a CPD of a T(m)CG site, one of the major sites of C methylation and C-to-T mutations found in the p53 gene of basal and squamous cell cancers. We also demonstrate that both yeast and human pol η synthesize past the 3'-(m)C CPD in a >99% error-free manner, consistent with the highly water-exposed nature of the active site.
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Affiliation(s)
- Qian Song
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, USA
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Song Q, Cannistraro VJ, Taylor JS. Rotational position of a 5-methylcytosine-containing cyclobutane pyrimidine dimer in a nucleosome greatly affects its deamination rate. J Biol Chem 2010; 286:6329-35. [PMID: 21160086 DOI: 10.1074/jbc.m110.183178] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
C to T mutation hotspots in skin cancers occur primarily at methylated CpG sites that coincide with sites of UV-induced cyclobutane pyrimidine dimer (CPD) formation. These mutations are proposed to arise from the insertion of A by DNA polymerase η opposite the T that results from deamination of the methylC ((m)C) within the CPD. Although the frequency of CPD formation and repair is modestly modulated by its rotational position within a nucleosome, the effect of position on the rate of (m)C deamination in a CPD has not been previously studied. We now report that deamination of a T(m)C CPD whose sugar phosphate backbone is positioned against the histone core surface decreases by a factor of 4.7, whereas that of a T(m)C CPD positioned away from the surface increases by a factor of 8.9 when compared with unbound DNA. Because the (m)Cs undergoing deamination are in similar steric environments, the difference in rate appears to be a consequence of a difference in the flexibility and compression of the two sites due to DNA bending. Considering that formation of the CPD positioned away from the surface is also enhanced by a factor of two, a T(m)CG site in this position might be expected to have up to an 84-fold higher probability of resulting in a UV-induced (m)C to T mutation than one positioned against the surface. These results indicate that rotational position may play an important role in the formation of UV-induced C to T mutation hotspots, as well as in the mutagenic mechanism of other DNA lesions.
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Affiliation(s)
- Qian Song
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, USA
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