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Franklin KA, Shields CE, Haynes KA. Beyond the marks: reader-effectors as drivers of epigenetics and chromatin engineering. Trends Biochem Sci 2022; 47:417-432. [PMID: 35427480 PMCID: PMC9074927 DOI: 10.1016/j.tibs.2022.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 02/27/2022] [Accepted: 03/01/2022] [Indexed: 10/18/2022]
Abstract
Chromatin is a system of proteins and DNA that regulates chromosome organization and gene expression in eukaryotes. Essential features that support these processes include biochemical marks on histones and DNA, 'writer' enzymes that generate or remove these marks and proteins that translate the marks into transcriptional regulation: reader-effectors. Here, we review recent studies that reveal how reader-effectors drive chromatin-mediated processes. Advances in proteomics and epigenomics have accelerated the discovery of chromatin marks and their correlation with gene states, outpacing our understanding of the corresponding reader-effectors. Therefore, we summarize the current state of knowledge and open questions about how reader-effectors impact cellular function and human disease and discuss how synthetic biology can deepen our knowledge of reader-effector activity.
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Affiliation(s)
- Kierra A Franklin
- Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA 30322, USA
| | - Cara E Shields
- Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA 30322, USA
| | - Karmella A Haynes
- Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA 30322, USA.
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2
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Wang H, Li J, He J, Liu Y, Feng W, Zhou H, Zhou M, Wei H, Lu Y, Peng W, Du F, Gong A, Xu M. Methyl-CpG-binding protein 2 drives the Furin/TGF-β1/Smad axis to promote epithelial-mesenchymal transition in pancreatic cancer cells. Oncogenesis 2020; 9:76. [PMID: 32848128 PMCID: PMC7450052 DOI: 10.1038/s41389-020-00258-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 06/30/2020] [Accepted: 07/15/2020] [Indexed: 11/23/2022] Open
Abstract
Methyl-CpG-binding protein 2 (MeCP2) has been characterized as an oncogene in several types of cancer. However, its precise role in pancreatic ductal adenocarcinoma (PDAC) remains unclear. Hence, this study aimed to evaluate the potential role of MeCP2 in pancreatic cancer progression. We found that MeCP2 was upregulated in pancreatic cancer tissues, enhanced migration, invasion, and proliferation in pancreatic cancer cells, and promoted tumorigenesis. Further evidence revealed that MeCP2 remarkably increased the mesenchymal markers vimentin, N-cadherin, and Snail, and downregulated the expression of the epithelial markers E-cadherin and ZO-1, indicating that MeCP2 promotes epithelial–mesenchymal transition (EMT). In addition, we found that MeCP2 upregulated the expression of Furin, activated TGF-β1, and increased the levels of p-Smad2/3. Importantly, we demonstrated that MeCP2, as a coactivator, enhanced Smad3 binding to the furin promoter to improve its transcription. Therefore, MeCP2/Smads drive the expression of Furin to activate TGF-β1, and in turn, phosphorylate Smad2/3, which forms a positive-feedback axis to promote EMT in pancreatic cancer cells.![]()
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Affiliation(s)
- Huizhi Wang
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, 438 Jiefang Road, Zhenjiang, 212000, China
| | - Jie Li
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, 438 Jiefang Road, Zhenjiang, 212000, China.,Department of Gastroenterology, The First People's Hospital of Jingzhou, 8 Aviation Road, Jingzhou, 434000, China
| | - Junbo He
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, 438 Jiefang Road, Zhenjiang, 212000, China
| | - Yawen Liu
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, 438 Jiefang Road, Zhenjiang, 212000, China
| | - Wen Feng
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, 438 Jiefang Road, Zhenjiang, 212000, China
| | - Hailang Zhou
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, 438 Jiefang Road, Zhenjiang, 212000, China
| | - Meng Zhou
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, 438 Jiefang Road, Zhenjiang, 212000, China
| | - Hong Wei
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, 438 Jiefang Road, Zhenjiang, 212000, China
| | - Ying Lu
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, 438 Jiefang Road, Zhenjiang, 212000, China
| | - Wanxin Peng
- Department of Cell Biology, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212000, China
| | - Fengyi Du
- Department of Cell Biology, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212000, China
| | - Aihua Gong
- Department of Cell Biology, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212000, China.
| | - Min Xu
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, 438 Jiefang Road, Zhenjiang, 212000, China.
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3
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Zhou Q, Guo J, Huang W, Yu X, Xu C, Long X. Linc-ROR promotes the progression of breast cancer and decreases the sensitivity to rapamycin through miR-194-3p targeting MECP2. Mol Oncol 2020; 14:2231-2250. [PMID: 32335998 PMCID: PMC7463371 DOI: 10.1002/1878-0261.12700] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/16/2020] [Accepted: 04/22/2020] [Indexed: 12/13/2022] Open
Abstract
linc‐ROR is reported to be a potential biomarker of breast cancer, but the detailed mechanism of linc‐ROR‐mediated breast cancer regulation has not been fully studied. We aimed to explore how linc‐ROR affects proliferation, metastasis, and drug sensitivity in breast cancer. Cell lines in which linc‐ROR was overexpressed or knocked down were constructed, and the cell proliferation, colony formation, cell migration, and invasion abilities of these lines were explored. A CCK‐8 assay was performed to determine the sensitivity of the breast cancer cells to rapamycin. Next‐generation sequencing was conducted to explore the detailed regulatory mechanism of linc‐ROR; differentially expressed RNAs in the linc‐ROR‐overexpressing cell line compared with the negative control were screened out, and their target genes were chosen to perform Gene Ontology analysis, Kyoto Encyclopedia of Genes and Genomes analysis, protein–protein interaction network analysis, and competing endogenous RNA (ceRNA) network analysis. The ceRNA mechanism of linc‐ROR for miR‐194‐3p, which targets MECP2, was determined through dual‐luciferase reporter assay, RT–qPCR, western blot, and rescue experiments. Finally, we found that linc‐ROR was upregulated in breast tumor tissues. linc‐ROR promoted the cell proliferation, colony formation, cell migration, and invasion of breast cancer and decreased the sensitivity of breast cancer cells to rapamycin. The overexpression of linc‐ROR triggered changes in the whole transcriptome of breast cancer cells, and a total of 85 lncRNAs, 414 microRNAs, 490 mRNAs, and 92 circRNAs were differentially expressed in the linc‐ROR‐overexpressing cell line compared with the negative control. Through a series of bioinformatic analyses, the ‘linc‐ROR/miR‐194‐3p/MECP2’ ceRNA regulatory axis was confirmed to be involved in the linc‐ROR‐mediated progression and drug sensitivity of breast cancer. In conclusion, linc‐ROR serves as an onco‐lncRNA in breast cancer and promotes the survival of breast cancer cells during rapamycin treatment by functioning as a ceRNA sponge for miR‐194‐3p, which targets MECP2.
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Affiliation(s)
- Qian Zhou
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, China
| | - Juan Guo
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, China
| | - Wenjie Huang
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, China
| | - Xiaosi Yu
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, China
| | - Chen Xu
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, China
| | - Xinghua Long
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, China
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Zeng Z, Li M, Chen J, Li Q, Ning Q, Zhao J, Xu Y, Xie J, Yu J. Reduced MBD2 expression enhances airway inflammation in bronchial epithelium in COPD. Int J Chron Obstruct Pulmon Dis 2018. [PMID: 29535511 PMCID: PMC5836663 DOI: 10.2147/copd.s148595] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Background Chronic obstructive pulmonary disease (COPD) is a common inflammatory lung disease characterized by inflammatory cells activation and production of inflammatory mediators. Methyl-CpG-binding domain protein 2 (MBD2) plays an important role in diverse immunological disorders by regulating immune cell functions, such as differentiation and mediator secretion. However, the role of MBD2 in COPD remains unknown. Methods MBD2 protein expression in lung tissues of patients with COPD and cigarette smoke (CS)-exposed mice were evaluated by Western blot and immunohistochemistry. The role of MBD2 in cigarette smoke extract (CSE)-induction of inflammatory mediator expression in the human bronchial epithelial (HBE) cell line was assessed by silencing MBD2 expression in vitro. The involvement of signaling pathways in mediation of inflammation was tested with signaling inhibitors. Results Compared with controls, MBD2 expression was distinctly reduced in the bronchial epithelium of both patients with COPD and CS-exposed mice. Moreover, MBD2 expression was decreased in HBE after CSE stimulation in vitro. Moreover, MBD2 knockdown enhanced interleukin (IL)-6 and IL-8 expression in HBE in the presence and absence of CSE treatment by the ERK signaling pathway. Conclusion MBD2 protein expression was reduced in the airway epithelium of COPD. In HBE, this reduced expression was associated with increased levels of IL-6 and IL-8 mediated by the ERK pathway. These results suggest that MBD2 could contribute to chronic airway inflammation in COPD.
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Affiliation(s)
- Zhilin Zeng
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease.,Department of Infectious Disease, Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Miao Li
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease
| | - Jinkun Chen
- Acadia Junior High School, Winnipeg, MB, Canada
| | - Qinghai Li
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease
| | - Qin Ning
- Department of Infectious Disease, Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Jianping Zhao
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease
| | - Yongjian Xu
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease
| | - Jungang Xie
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease
| | - Jun Yu
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
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5
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Ye M, Robson PJ, Eurich DT, Vena JE, Xu JY, Johnson JA. Cohort Profile: Alberta’s Tomorrow Project. Int J Epidemiol 2016; 46:1097-1098l. [DOI: 10.1093/ije/dyw256] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2016] [Indexed: 11/14/2022] Open
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Robertson DS, Prevost AT, Bowden J. Accounting for selection and correlation in the analysis of two-stage genome-wide association studies. Biostatistics 2016; 17:634-49. [PMID: 26993061 PMCID: PMC5031943 DOI: 10.1093/biostatistics/kxw012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 11/11/2015] [Accepted: 01/15/2016] [Indexed: 11/15/2022] Open
Abstract
The problem of selection bias has long been recognized in the analysis of two-stage trials, where promising candidates are selected in stage 1 for confirmatory analysis in stage 2. To efficiently correct for bias, uniformly minimum variance conditionally unbiased estimators (UMVCUEs) have been proposed for a wide variety of trial settings, but where the population parameter estimates are assumed to be independent. We relax this assumption and derive the UMVCUE in the multivariate normal setting with an arbitrary known covariance structure. One area of application is the estimation of odds ratios (ORs) when combining a genome-wide scan with a replication study. Our framework explicitly accounts for correlated single nucleotide polymorphisms, as might occur due to linkage disequilibrium. We illustrate our approach on the measurement of the association between 11 genetic variants and the risk of Crohn's disease, as reported in Parkes and others (2007. Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility. Nat. Gen. 39: (7), 830-832.), and show that the estimated ORs can vary substantially if both selection and correlation are taken into account.
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Affiliation(s)
- David S Robertson
- MRC Biostatistics Unit, IPH Forvie Site, Robinson Way, Cambridge CB2 0SR, UK
| | - A Toby Prevost
- Imperial College London, 1st Floor, Stadium House, 68 Wood Lane, London W12 7RH, UK
| | - Jack Bowden
- MRC Integrative Epidemiology Unit, University of Bristol, Oakfield House, Bristol BS8 2BN, UK and MRC Biostatistics Unit, IPH Forvie Site, Robinson Way, Cambridge CB2 0SR, UK
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7
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Kim I, Lee SH, Jeong J, Park JH, Yoo MA, Kim CM. Functional Profiling of Human MeCP2 by Automated Data Comparison Analysis and Computerized Expression Pathway Modeling. Healthc Inform Res 2016; 22:120-8. [PMID: 27200222 PMCID: PMC4871842 DOI: 10.4258/hir.2016.22.2.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/20/2015] [Accepted: 09/22/2015] [Indexed: 01/16/2023] Open
Abstract
OBJECTIVES Methyl-CpG binding protein 2 (MeCP2) is a ubiquitous epigenetic factor that represses gene expression by modifying chromatin. Mutations in the MeCP2 gene cause Rett syndrome, a progressive neurodevelopmental disorder. Recent studies also have shown that MeCP2 plays a role in carcinogenesis. Specifically, functional ablation of MeCP2 suppresses cell growth and leads to the proliferation of cancer cells. However, MeCP2's function in adult tissues remains poorly understood. We utilized a weight matrix-based comparison software to identify transcription factor binding site (TFBS) of MeCP2-regulated genes, which were recognized by cDNA microarray analysis. METHODS MeCP2 expression was silenced using annealed siRNA in HEK293 cells, and then a cDNA microarray analysis was performed. Functional analysis was carried out, and transcriptional levels in target genes regulated by MeCP2 were investigated. TFBS analysis was done within genes selected by the cDNA microarray analysis, using a weight matrix-based program and the TRANSFAC 6.0 database. RESULTS Among the differentially expressed genes with a change in expression greater than two-fold, 189 genes were up-regulated and 91 genes were down-regulated. Genes related to apoptosis and cell proliferation (JUN, FOSL2, CYR61, SKIL, ATF3, BMABI, BMPR2, RERE, and FALZ) were highly up-regulated. Genes with anti-apoptotic and anti-proliferative functions (HNRPA0, HIS1, and FOXC1) were down-regulated. Using TFBS analysis within putative promoters of novel candidate target genes of MeCP2, disease-related transcription factors were identified. CONCLUSIONS The present results provide insights into the new target genes regulated by MeCP2 under epigenetic control. This information will be valuable for further studies aimed at clarifying the pathogenesis of Rett syndrome and neoplastic diseases.
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Affiliation(s)
- Injoo Kim
- Department of Emergency Medical Technology, Dong-Eui Institute of Technology, Busan, Korea
| | - Shin Hae Lee
- Department of Biological Sciences, Inha University, Incheon, Korea
| | - Jinwoo Jeong
- Department of Emergency Medicine, Dong-A University College of Medicine, Busan, Korea
| | | | - Mi Ae Yoo
- Department of Molecular Biology, Pusan National University, Busan, Korea
| | - Cheol Min Kim
- Supercomputing Center, Pusan National University, Busan, Korea.; Research Center for Anti-Aging Technology Development, Pusan National University, Busan, Korea.; Department of Medical Informatics, Pusan National University School of Medicine, Yangsan, Korea
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8
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Du Q, Luu PL, Stirzaker C, Clark SJ. Methyl-CpG-binding domain proteins: readers of the epigenome. Epigenomics 2015; 7:1051-73. [DOI: 10.2217/epi.15.39] [Citation(s) in RCA: 265] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
How DNA methylation is interpreted and influences genome regulation remains largely unknown. Proteins of the methyl-CpG-binding domain (MBD) family are primary candidates for the readout of DNA methylation as they recruit chromatin remodelers, histone deacetylases and methylases to methylated DNA associated with gene repression. MBD protein binding requires both functional MBD domains and methyl-CpGs; however, some MBD proteins also bind unmethylated DNA and active regulatory regions via alternative regulatory domains or interaction with the nucleosome remodeling deacetylase (NuRD/Mi-2) complex members. Mutations within MBD domains occur in many diseases, including neurological disorders and cancers, leading to loss of MBD binding specificity to methylated sites and gene deregulation. Here, we summarize the current state of knowledge about MBD proteins and their role as readers of the epigenome.
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Affiliation(s)
- Qian Du
- Epigenetics Research Laboratory, Genomics & Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Phuc-Loi Luu
- Epigenetics Research Laboratory, Genomics & Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Clare Stirzaker
- Epigenetics Research Laboratory, Genomics & Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
- St Vincent's Clinical School, University of NSW, Darlinghurst, NSW 2010, Australia
| | - Susan J Clark
- Epigenetics Research Laboratory, Genomics & Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
- St Vincent's Clinical School, University of NSW, Darlinghurst, NSW 2010, Australia
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Sapkota Y. Germline DNA variations in breast cancer predisposition and prognosis: a systematic review of the literature. Cytogenet Genome Res 2014; 144:77-91. [PMID: 25401968 DOI: 10.1159/000369045] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2014] [Indexed: 11/19/2022] Open
Abstract
Breast cancer is the most common cancer and the second leading cause of death in women worldwide. The disease is caused by a combination of genetic, environmental, lifestyle, and reproductive risk factors. Linkage and family-based studies have identified many pathological germline mutations, which account for around 20% of the genetic risk of familial breast cancer. In recent years, single nucleotide polymorphism-based genetic association studies, especially genome-wide association studies (GWASs), have been very successful in uncovering low-penetrance common variants associated with breast cancer risk. These common variants alone may explain up to an additional 30% of the familial risk of breast cancer. With the advent of available genetic resources and growing collaborations among researchers across the globe, the much needed large sample size to capture variants with small effect sizes and low population frequencies is being addressed, and hence many more common variants are expected to be discovered in the coming days. Here, major GWASs conducted for breast cancer predisposition and prognosis until 2013 are summarized. Few studies investigating other forms of genetic variations contributing to breast cancer predisposition and disease outcomes are also discussed. Finally, the potential utility of the GWAS-identified variants in disease risk models and some future perspectives are presented.
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Affiliation(s)
- Yadav Sapkota
- The Neurogenetics Laboratory, Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Qld., Australia
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Liyanage VRB, Jarmasz JS, Murugeshan N, Del Bigio MR, Rastegar M, Davie JR. DNA modifications: function and applications in normal and disease States. BIOLOGY 2014; 3:670-723. [PMID: 25340699 PMCID: PMC4280507 DOI: 10.3390/biology3040670] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/22/2014] [Accepted: 09/24/2014] [Indexed: 12/12/2022]
Abstract
Epigenetics refers to a variety of processes that have heritable effects on gene expression programs without changes in DNA sequence. Key players in epigenetic control are chemical modifications to DNA, histone, and non-histone chromosomal proteins, which establish a complex regulatory network that controls genome function. Methylation of DNA at the fifth position of cytosine in CpG dinucleotides (5-methylcytosine, 5mC), which is carried out by DNA methyltransferases, is commonly associated with gene silencing. However, high resolution mapping of DNA methylation has revealed that 5mC is enriched in exonic nucleosomes and at intron-exon junctions, suggesting a role of DNA methylation in the relationship between elongation and RNA splicing. Recent studies have increased our knowledge of another modification of DNA, 5-hydroxymethylcytosine (5hmC), which is a product of the ten-eleven translocation (TET) proteins converting 5mC to 5hmC. In this review, we will highlight current studies on the role of 5mC and 5hmC in regulating gene expression (using some aspects of brain development as examples). Further the roles of these modifications in detection of pathological states (type 2 diabetes, Rett syndrome, fetal alcohol spectrum disorders and teratogen exposure) will be discussed.
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Affiliation(s)
- Vichithra R B Liyanage
- Department of Biochemistry and Medical Genetics, Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - Jessica S Jarmasz
- Department of Human Anatomy and Cell Science, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - Nanditha Murugeshan
- Department of Biochemistry and Medical Genetics, Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - Marc R Del Bigio
- Department of Human Anatomy and Cell Science, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - Mojgan Rastegar
- Department of Biochemistry and Medical Genetics, Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - James R Davie
- Department of Biochemistry and Medical Genetics, Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
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Abstract
Rett syndrome (RTT) is a severe and progressive neurological disorder, which mainly affects young females. Mutations of the methyl-CpG binding protein 2 (MECP2) gene are the most prevalent cause of classical RTT cases. MECP2 mutations or altered expression are also associated with a spectrum of neurodevelopmental disorders such as autism spectrum disorders with recent links to fetal alcohol spectrum disorders. Collectively, MeCP2 relation to these neurodevelopmental disorders highlights the importance of understanding the molecular mechanisms by which MeCP2 impacts brain development, mental conditions, and compromised brain function. Since MECP2 mutations were discovered to be the primary cause of RTT, a significant progress has been made in the MeCP2 research, with respect to the expression, function and regulation of MeCP2 in the brain and its contribution in RTT pathogenesis. To date, there have been intensive efforts in designing effective therapeutic strategies for RTT benefiting from mouse models and cells collected from RTT patients. Despite significant progress in MeCP2 research over the last few decades, there is still a knowledge gap between the in vitro and in vivo research findings and translating these findings into effective therapeutic interventions in human RTT patients. In this review, we will provide a synopsis of Rett syndrome as a severe neurological disorder and will discuss the role of MeCP2 in RTT pathophysiology.
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12
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Sapkota Y, Mackey JR, Lai R, Franco-Villalobos C, Lupichuk S, Robson PJ, Kopciuk K, Cass CE, Yasui Y, Damaraju S. Assessing SNP-SNP interactions among DNA repair, modification and metabolism related pathway genes in breast cancer susceptibility. PLoS One 2013; 8:e64896. [PMID: 23755158 PMCID: PMC3670937 DOI: 10.1371/journal.pone.0064896] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 04/19/2013] [Indexed: 01/23/2023] Open
Abstract
Genome-wide association studies (GWASs) have identified low-penetrance common variants (i.e., single nucleotide polymorphisms, SNPs) associated with breast cancer susceptibility. Although GWASs are primarily focused on single-locus effects, gene-gene interactions (i.e., epistasis) are also assumed to contribute to the genetic risks for complex diseases including breast cancer. While it has been hypothesized that moderately ranked (P value based) weak single-locus effects in GWASs could potentially harbor valuable information for evaluating epistasis, we lack systematic efforts to investigate SNPs showing consistent associations with weak statistical significance across independent discovery and replication stages. The objectives of this study were i) to select SNPs showing single-locus effects with weak statistical significance for breast cancer in a GWAS and/or candidate-gene studies; ii) to replicate these SNPs in an independent set of breast cancer cases and controls; and iii) to explore their potential SNP-SNP interactions contributing to breast cancer susceptibility. A total of 17 SNPs related to DNA repair, modification and metabolism pathway genes were selected since these pathways offer a priori knowledge for potential epistatic interactions and an overall role in breast carcinogenesis. The study design included predominantly Caucasian women (2,795 cases and 4,505 controls) from Alberta, Canada. We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs2297381; MLH1-rs1799977 and MDM2-rs769412) in logistic regression that conferred elevated risks for breast cancer (Pinteraction<7.3×10−3). Logic regression identified an interaction involving four SNPs (MBD2-rs4041245, MLH1-rs1799977, MDM2-rs769412, BRCA2-rs1799943) (Ppermutation = 2.4×10−3). SNPs involved in SNP-SNP interactions also showed single-locus effects with weak statistical significance, while BRCA2-rs1799943 showed stronger statistical significance (Pcorrelation/trend = 3.2×10−4) than the others. These single-locus effects were independent of body mass index. Our results provide a framework for evaluating SNPs showing statistically weak but reproducible single-locus effects for epistatic effects contributing to disease susceptibility.
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Affiliation(s)
- Yadav Sapkota
- Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - John R. Mackey
- Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Raymond Lai
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | | | - Sasha Lupichuk
- Department of Oncology, University of Calgary, Calgary, Alberta, Canada
- Tom Baker Cancer Centre, Alberta Health Services, Calgary, Alberta, Canada
| | - Paula J. Robson
- Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, Alberta, Canada
- Alberta Health Services – Cancer Care, Edmonton, Alberta, Canada
| | - Karen Kopciuk
- Department of Oncology, University of Calgary, Calgary, Alberta, Canada
- Department of Mathematics and Statistics, University of Calgary, Calgary, Alberta, Canada
| | - Carol E. Cass
- Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Yutaka Yasui
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Sambasivarao Damaraju
- Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- * E-mail:
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13
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Sapkota Y, Yasui Y, Lai R, Sridharan M, Robson PJ, Cass CE, Mackey JR, Damaraju S. Identification of a breast cancer susceptibility locus at 4q31.22 using a genome-wide association study paradigm. PLoS One 2013; 8:e62550. [PMID: 23717390 PMCID: PMC3661567 DOI: 10.1371/journal.pone.0062550] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 03/22/2013] [Indexed: 11/26/2022] Open
Abstract
More than 40 single nucleotide polymorphisms (SNPs) for breast cancer susceptibility were identified by genome-wide association studies (GWASs). However, additional SNPs likely contribute to breast cancer susceptibility and overall genetic risk, prompting this investigation for additional variants. Six putative breast cancer susceptibility SNPs identified in a two-stage GWAS that we reported earlier were replicated in a follow-up stage 3 study using an independent set of breast cancer cases and controls from Canada, with an overall cumulative sample size of 7,219 subjects across all three stages. The study design also encompassed the 11 variants from GWASs previously reported by various consortia between the years 2007–2009 to (i) enable comparisons of effect sizes, and (ii) identify putative prognostic variants across studies. All SNP associations reported with breast cancer were also adjusted for body mass index (BMI). We report a strong association with 4q31.22-rs1429142 (combined per allele odds ratio and 95% confidence interval = 1.28 [1.17–1.41] and Pcombined = 1.5×10−7), when adjusted for BMI. Ten of the 11 breast cancer susceptibility loci reported by consortia also showed associations in our predominantly Caucasian study population, and the associations were independent of BMI; four FGFR2 SNPs and TNRC9-rs3803662 were among the most notable associations. Since the original report by Garcia-Closas et al. 2008, this is the second study to confirm the association of 8q24.21-rs13281615 with breast cancer outcomes.
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Affiliation(s)
- Yadav Sapkota
- Cross Cancer Institute, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Yutaka Yasui
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Raymond Lai
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Malinee Sridharan
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Paula J. Robson
- Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, Alberta, Canada
- Alberta Health Services – Cancer Care, Edmonton, Alberta, Canada
| | - Carol E. Cass
- Cross Cancer Institute, Edmonton, Alberta, Canada
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - John R. Mackey
- Cross Cancer Institute, Edmonton, Alberta, Canada
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Sambasivarao Damaraju
- Cross Cancer Institute, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- * E-mail:
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Sapkota Y, Ghosh S, Lai R, Coe BP, Cass CE, Yasui Y, Mackey JR, Damaraju S. Germline DNA copy number aberrations identified as potential prognostic factors for breast cancer recurrence. PLoS One 2013; 8:e53850. [PMID: 23342018 PMCID: PMC3547038 DOI: 10.1371/journal.pone.0053850] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 12/05/2012] [Indexed: 11/30/2022] Open
Abstract
Breast cancer recurrence (BCR) is a common treatment outcome despite curative-intent primary treatment of non-metastatic breast cancer. Currently used prognostic and predictive factors utilize tumor-based markers, and are not optimal determinants of risk of BCR. Germline-based copy number aberrations (CNAs) have not been evaluated as determinants of predisposition to experience BCR. In this study, we accessed germline DNA from 369 female breast cancer subjects who received curative-intent primary treatment following diagnosis. Of these, 155 experienced BCR and 214 did not, after a median duration of follow up after breast cancer diagnosis of 6.35 years (range = 0.60–21.78) and 8.60 years (range = 3.08–13.57), respectively. Whole genome CNA genotyping was performed on the Affymetrix SNP array 6.0 platform. CNAs were identified using the SNP-Fast Adaptive States Segmentation Technique 2 algorithm implemented in Nexus Copy Number 6.0. Six samples were removed due to poor quality scores, leaving 363 samples for further analysis. We identified 18,561 CNAs with ≥1 kb as a predefined cut-off for observed aberrations. Univariate survival analyses (log-rank tests) identified seven CNAs (two copy number gains and five copy neutral-loss of heterozygosities, CN-LOHs) showing significant differences (P<2.01×10−5) in recurrence-free survival (RFS) probabilities with and without CNAs.We also observed three additional but distinct CN-LOHs showing significant differences in RFS probabilities (P<2.86×10−5) when analyses were restricted to stratified cases (luminal A, n = 208) only. After adjusting for tumor stage and grade in multivariate analyses (Cox proportional hazards models), all the CNAs remained strongly associated with the phenotype of BCR. Of these, we confirmed three CNAs at 17q11.2, 11q13.1 and 6q24.1 in representative samples using independent genotyping platforms. Our results suggest further investigations on the potential use of germline DNA variations as prognostic markers in cancer-associated phenotypes.
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Affiliation(s)
- Yadav Sapkota
- Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Sunita Ghosh
- Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Raymond Lai
- Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Bradley P. Coe
- Department of Genome Sciences, University of Washington, School of Medicine, Seattle, Washington, United States of America
| | - Carol E. Cass
- Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Yutaka Yasui
- Department of Public Health Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - John R. Mackey
- Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Sambasivarao Damaraju
- Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- * E-mail:
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Harbinder S, Lazzara CA, Klar AJ. Implication of the Strand-Specific Imprinting and Segregation Model: Integrating in utero Hormone Exposure, Stem Cell and Lateral Asymmetry Hypotheses in Breast Cancer Aetiology. HEREDITARY GENETICS : CURRENT RESEARCH 2013; 2013. [PMID: 34589269 PMCID: PMC8478350 DOI: 10.4172/2161-1041.s2-005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Known genetic mutations and familial hereditary factors account for less than 20–25% of breast cancer cases in women, therefore, most instances have been classified as sporadic cases of unknown aetiologies. Single nucleotide polymorphisms (SNPs) were considered as breast cancer risk factors, but numerous studies have failed to support this assertion. Recent evidence correlates aberrant epigenetic mechanisms in the development and metastatic progression of breast cancer, yet there has been limited progress made to identify the primary aetiology underlying sporadic cases of breast cancer. This has led some researchers to consider alternative hypotheses including in utero exposure to deleterious chemical agents during early development, the immortal strand and the strand-specific imprinting and selective chromatid segregation hypotheses. Here, we integrate prominent alternate models to help guide future research on this very important topic concerning human health.
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Affiliation(s)
- Singh Harbinder
- Department of Biological Sciences, Delaware State University, Dover, USA
| | - Carol A Lazzara
- Department of Biological Sciences, Delaware State University, Dover, USA
| | - Amar Js Klar
- Gene Regulation and Chromosome Biology Laboratory, Frederick National Laboratory for Cancer Research, National Institutes of Health, Frederick, USA
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