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Fritsche K, Boccellato F, Schlaermann P, Koeppel M, Denecke C, Link A, Malfertheiner P, Gut I, Meyer TF, Berger H. DNA methylation in human gastric epithelial cells defines regional identity without restricting lineage plasticity. Clin Epigenetics 2022; 14:193. [PMID: 36585699 PMCID: PMC9801550 DOI: 10.1186/s13148-022-01406-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 12/13/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Epigenetic modifications in mammalian DNA are commonly manifested by DNA methylation. In the stomach, altered DNA methylation patterns have been observed following chronic Helicobacter pylori infections and in gastric cancer. In the context of epigenetic regulation, the regional nature of the stomach has been rarely considered in detail. RESULTS Here, we establish gastric mucosa derived primary cell cultures as a reliable source of native human epithelium. We describe the DNA methylation landscape across the phenotypically different regions of the healthy human stomach, i.e., antrum, corpus, fundus together with the corresponding transcriptomes. We show that stable regional DNA methylation differences translate to a limited extent into regulation of the transcriptomic phenotype, indicating a largely permissive epigenetic regulation. We identify a small number of transcription factors with novel region-specific activity and likely epigenetic impact in the stomach, including GATA4, IRX5, IRX2, PDX1 and CDX2. Detailed analysis of the Wnt pathway reveals differential regulation along the craniocaudal axis, which involves non-canonical Wnt signaling in determining cell fate in the proximal stomach. By extending our analysis to pre-neoplastic lesions and gastric cancers, we conclude that epigenetic dysregulation characterizes intestinal metaplasia as a founding basis for functional changes in gastric cancer. We present insights into the dynamics of DNA methylation across anatomical regions of the healthy stomach and patterns of its change in disease. Finally, our study provides a well-defined resource of regional stomach transcription and epigenetics.
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Affiliation(s)
- Kristin Fritsche
- grid.418159.00000 0004 0491 2699Department of Molecular Biology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117 Berlin, Germany
| | - Francesco Boccellato
- grid.418159.00000 0004 0491 2699Department of Molecular Biology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117 Berlin, Germany ,grid.4991.50000 0004 1936 8948Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Philipp Schlaermann
- grid.418159.00000 0004 0491 2699Department of Molecular Biology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117 Berlin, Germany
| | - Max Koeppel
- grid.418159.00000 0004 0491 2699Department of Molecular Biology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117 Berlin, Germany
| | - Christian Denecke
- grid.6363.00000 0001 2218 4662Center for Bariatric and Metabolic Surgery, Center of Innovative Surgery (ZIC), Department of Surgery, Campus Virchow Klinikum and Campus Mitte, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Alexander Link
- grid.5807.a0000 0001 1018 4307Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-Von-Guericke University Hospital, Magdeburg, Germany
| | - Peter Malfertheiner
- grid.5807.a0000 0001 1018 4307Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-Von-Guericke University Hospital, Magdeburg, Germany
| | - Ivo Gut
- grid.452341.50000 0004 8340 2354Centro Nacional de Análisis Genómico (CNAG-CRG), Barcelona, Spain
| | - Thomas F. Meyer
- grid.418159.00000 0004 0491 2699Department of Molecular Biology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117 Berlin, Germany ,grid.412468.d0000 0004 0646 2097Laboratory of Infection Oncology, Institute of Clinical Molecular Biology, Christian Albrecht University of Kiel and University Hospital Schleswig-Holstein – Campus Kiel, Rosalind-Franklin-Straße 12, 24105 Kiel, Germany
| | - Hilmar Berger
- grid.418159.00000 0004 0491 2699Department of Molecular Biology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117 Berlin, Germany ,grid.412468.d0000 0004 0646 2097Laboratory of Infection Oncology, Institute of Clinical Molecular Biology, Christian Albrecht University of Kiel and University Hospital Schleswig-Holstein – Campus Kiel, Rosalind-Franklin-Straße 12, 24105 Kiel, Germany
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2
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Liu C, Wang Z, Hui Q, Goldberg J, Smith NL, Shah AJ, Murrah N, Shallenberger L, Diggers E, Bremner JD, Sun YV, Vaccarino V. Association between depression and epigenetic age acceleration: A co-twin control study. Depress Anxiety 2022; 39:741-750. [PMID: 35758529 PMCID: PMC9729366 DOI: 10.1002/da.23279] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 05/26/2022] [Accepted: 06/18/2022] [Indexed: 01/27/2023] Open
Abstract
INTRODUCTION Prior studies have shown inconsistent findings of an association between depression and epigenetic aging. DNA methylation (DNAm) age acceleration can measure biological aging. We adopted a robust co-twin control study design to examine whether depression is associated with DNAm age acceleration after accounting for the potential confounding influences of genetics and family environment. METHODS We analyzed data on a sub-cohort of the Vietnam Era Twin Registry. A total of 291 twins participated at baseline and 177 at follow-up visit after a mean of 11.7 years, with 111 participants having DNA samples for both time points. Depression was measured using the Beck Depression Inventory II (BDI-II). Six measures of DNAm age acceleration were computed at each time point, including Horvath's DNAm age acceleration (HorvathAA), intrinsic epigenetic age acceleration (IEAA), Hannum's DNAm age acceleration (HannumAA), extrinsic epigenetic age acceleration (EEAA), GrimAge acceleration (GrimAA), and PhenoAge acceleration (PhenoAA). Mixed-effects modeling was used to assess the within-pair association between depression and DNAm age acceleration. RESULTS At baseline, a 10-unit higher BDI-II total score was associated with HannumAA (0.73 years, 95% confidence interval [CI] 0.13-1.33, p = .019) and EEAA (0.94 years, 95% CI 0.22-1.66, p = .012). At follow-up, 10-unit higher BDI-II score was associated with PhenoAA (1.32 years, 95% CI 0.18-2.47, p = .027). CONCLUSION We identified that depression is associated with higher levels of DNAm age acceleration. Further investigation is warranted to better understand the underlying mechanisms for the potential causal relationship between depression and accelerated aging.
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Affiliation(s)
- Chang Liu
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE, Atlanta, GA
| | - Zeyuan Wang
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE, Atlanta, GA
| | - Qin Hui
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE, Atlanta, GA
| | - Jack Goldberg
- Vietnam Era Twin Registry, Seattle Epidemiologic Research and Information Center, Cooperative Studies Program, Office of Research and Development, Department of Veterans Affairs, Seattle, WA, USA
| | - Nicholas L. Smith
- Vietnam Era Twin Registry, Seattle Epidemiologic Research and Information Center, Cooperative Studies Program, Office of Research and Development, Department of Veterans Affairs, Seattle, WA, USA
| | - Amit J. Shah
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE, Atlanta, GA
- Department of Medicine, Division of Cardiology, Emory University School of Medicine, Atlanta, GA
- Atlanta VA Health Care System, 1670 Clairmont Road, Decatur, GA 30033, USA
| | - Nancy Murrah
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE, Atlanta, GA
| | - Lucy Shallenberger
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE, Atlanta, GA
| | - Emily Diggers
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE, Atlanta, GA
| | - J. Douglas Bremner
- Atlanta VA Health Care System, 1670 Clairmont Road, Decatur, GA 30033, USA
- Departments of Psychiatry and Behavioral Sciences and Radiology and Imaging Sciences, Emory University School of Medicine, Atlanta, GA
| | - Yan V. Sun
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE, Atlanta, GA
- Atlanta VA Health Care System, 1670 Clairmont Road, Decatur, GA 30033, USA
| | - Viola Vaccarino
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE, Atlanta, GA
- Department of Medicine, Division of Cardiology, Emory University School of Medicine, Atlanta, GA
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3
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Donohue LK, Guo MG, Zhao Y, Jung N, Bussat RT, Kim DS, Neela PH, Kellman LN, Garcia OS, Meyers RM, Altman RB, Khavari PA. A cis-regulatory lexicon of DNA motif combinations mediating cell-type-specific gene regulation. CELL GENOMICS 2022; 2:100191. [PMID: 36742369 PMCID: PMC9894309 DOI: 10.1016/j.xgen.2022.100191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Gene expression is controlled by transcription factors (TFs) that bind cognate DNA motif sequences in cis-regulatory elements (CREs). The combinations of DNA motifs acting within homeostasis and disease, however, are unclear. Gene expression, chromatin accessibility, TF footprinting, and H3K27ac-dependent DNA looping data were generated and a random-forest-based model was applied to identify 7,531 cell-type-specific cis-regulatory modules (CRMs) across 15 diploid human cell types. A co-enrichment framework within CRMs nominated 838 cell-type-specific, recurrent heterotypic DNA motif combinations (DMCs), which were functionally validated using massively parallel reporter assays. Cancer cells engaged DMCs linked to neoplasia-enabling processes operative in normal cells while also activating new DMCs only seen in the neoplastic state. This integrative approach identifies cell-type-specific cis-regulatory combinatorial DNA motifs in diverse normal and diseased human cells and represents a general framework for deciphering cis-regulatory sequence logic in gene regulation.
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Affiliation(s)
- Laura K.H. Donohue
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA,Synthego, Redwood City, CA, USA,These authors contributed equally
| | - Margaret G. Guo
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA,Stanford Program in Biomedical Informatics, Stanford University, Stanford, CA, USA,These authors contributed equally
| | - Yang Zhao
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA,Synthego, Redwood City, CA, USA
| | - Namyoung Jung
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA,Department of Life Science, Pohang University of Science and Technology, Pohang, Korea
| | - Rose T. Bussat
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA,23andMe, Inc., Sunnyvale, CA, USA
| | - Daniel S. Kim
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA,Stanford Program in Biomedical Informatics, Stanford University, Stanford, CA, USA
| | - Poornima H. Neela
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA,Fauna Bio, Emeryville, CA, USA
| | - Laura N. Kellman
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA,Stanford Program in Cancer Biology, Stanford University, Stanford, CA, USA
| | - Omar S. Garcia
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Robin M. Meyers
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Russ B. Altman
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA,Stanford Program in Biomedical Informatics, Stanford University, Stanford, CA, USA,Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Paul A. Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA,Stanford Program in Cancer Biology, Stanford University, Stanford, CA, USA,Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA,Lead contact,Correspondence:
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4
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Lim IY, Lin X, Teh AL, Wu Y, Chen L, He M, Chan SY, MacIsaac JL, Chan JKY, Tan KH, Chong MFF, Kobor MS, Godfrey KM, Meaney MJ, Lee YS, Eriksson JG, Gluckman PD, Chong YS, Karnani N. Dichotomy in the Impact of Elevated Maternal Glucose Levels on Neonatal Epigenome. J Clin Endocrinol Metab 2022; 107:e1277-e1292. [PMID: 34633450 PMCID: PMC8852163 DOI: 10.1210/clinem/dgab710] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Indexed: 01/22/2023]
Abstract
CONTEXT Antenatal hyperglycemia is associated with increased risk of future adverse health outcomes in both mother and child. Variations in offspring's epigenome can reflect the impact and response to in utero glycemic exposure, and may have different consequences for the child. OBJECTIVE We examined possible differences in associations of basal glucose status and glucose handling during pregnancy with both clinical covariates and offspring cord tissue DNA methylation. RESEARCH DESIGN AND METHODS This study included 830 mother-offspring dyads from the Growing Up in Singapore Towards Healthy Outcomes cohort. The fetal epigenome of umbilical cord tissue was profiled using Illumina HumanMethylation450 arrays. Associations of maternal mid-pregnancy fasting (fasting plasma glucose [FPG]) and 2-hour plasma glucose (2hPG) after a 75-g oral glucose challenge with both maternal clinical phenotypes and offspring epigenome at delivery were investigated separately. RESULTS Maternal age, prepregnancy body mass index, and blood pressure measures were associated with both FPG and 2hPG, whereas Chinese ethnicity (P = 1.9 × 10-4), maternal height (P = 1.1 × 10-4), pregnancy weight gain (P = 2.2 × 10-3), prepregnancy alcohol consumption (P = 4.6 × 10-4), and tobacco exposure (P = 1.9 × 10-3) showed significantly opposite associations between the 2 glucose measures. Most importantly, we observed a dichotomy in the effects of these glycemic indices on the offspring epigenome. Offspring born to mothers with elevated 2hPG showed global hypomethylation. CpGs most associated with the 2 measures also reflected differences in gene ontologies and had different associations with offspring birthweight. CONCLUSIONS Our findings suggest that 2 traditionally used glycemic indices for diagnosing gestational diabetes may reflect distinctive pathophysiologies in pregnancy, and have differential impacts on the offspring's DNA methylome.
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Affiliation(s)
- Ives Yubin Lim
- Singapore Institute for Clinical Sciences (SICS), A*STAR, 117609, Singapore
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 119228, Singapore
- Bioinformatics Institute (BII), A*STAR, 138671, Singapore
| | - Xinyi Lin
- Singapore Institute for Clinical Sciences (SICS), A*STAR, 117609, Singapore
- Centre for Quantitative Medicine, Duke-National University of Singapore (NUS) Medical School, 169857, Singapore
- Singapore Clinical Research Institute, 138669, Singapore
| | - Ai Ling Teh
- Singapore Institute for Clinical Sciences (SICS), A*STAR, 117609, Singapore
| | - Yonghui Wu
- Singapore Institute for Clinical Sciences (SICS), A*STAR, 117609, Singapore
| | - Li Chen
- Singapore Institute for Clinical Sciences (SICS), A*STAR, 117609, Singapore
| | - Menglan He
- Duke-NUS Medical School, 169857, Singapore
| | - Shiao-Yng Chan
- Singapore Institute for Clinical Sciences (SICS), A*STAR, 117609, Singapore
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 119228, Singapore
| | - Julia L MacIsaac
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Jerry K Y Chan
- KK Women’s and Children’s Hospital, 229899, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore (NUS), Singapore
| | - Kok Hian Tan
- KK Women’s and Children’s Hospital, 229899, Singapore
| | - Mary Foong Fong Chong
- Singapore Institute for Clinical Sciences (SICS), A*STAR, 117609, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore (NUS), Singapore
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Keith M Godfrey
- MRC Lifecourse Epidemiology Unit and NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, SO16 6YD, UK
| | - Michael J Meaney
- Singapore Institute for Clinical Sciences (SICS), A*STAR, 117609, Singapore
- Douglas Mental Health University Institute, McGill University, Montréal, Canada
| | - Yung Seng Lee
- Singapore Institute for Clinical Sciences (SICS), A*STAR, 117609, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, NUS, 119228, Singapore
- Division of Paediatric Endocrinology and Diabetes, Khoo Teck Puat-National University Children’s Medical Institute, National University Hospital, Singapore
| | - Johan G Eriksson
- Singapore Institute for Clinical Sciences (SICS), A*STAR, 117609, Singapore
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 119228, Singapore
- Department of General Practice and Primary Health Care, University of Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Peter D Gluckman
- Singapore Institute for Clinical Sciences (SICS), A*STAR, 117609, Singapore
- Centre for Human Evolution, Adaptation and Disease, Liggins Institute, University of Auckland, Auckland, 1142, New Zealand
| | - Yap Seng Chong
- Singapore Institute for Clinical Sciences (SICS), A*STAR, 117609, Singapore
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 119228, Singapore
| | - Neerja Karnani
- Singapore Institute for Clinical Sciences (SICS), A*STAR, 117609, Singapore
- Bioinformatics Institute (BII), A*STAR, 138671, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, NUS, 117596, Singapore
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5
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Wang Z, Hui Q, Goldberg J, Smith N, Kaseer B, Murrah N, Levantsevych OM, Shallenberger L, Diggers E, Bremner JD, Vaccarino V, Sun YV. Association Between Posttraumatic Stress Disorder and Epigenetic Age Acceleration in a Sample of Twins. Psychosom Med 2022; 84:151-158. [PMID: 34629427 PMCID: PMC8831461 DOI: 10.1097/psy.0000000000001028] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
OBJECTIVE Posttraumatic stress disorder (PTSD) has been related to accelerated biological aging processes, but objective evidence for this association is limited. DNA methylation (DNAm) age acceleration is a novel measure of biological aging that may help clarify if PTSD is related to biological aging processes. We aim to examine whether PTSD is associated with biological aging using a comprehensive set of DNAm age acceleration markers and to what extent the unshared environment contributes to the association. METHODS Using a cross-sectional co-twin control study design, we investigated the association of the clinical diagnosis and symptom severity of PTSD with six measurements of DNAm age acceleration based on epigenome-wide data derived from peripheral blood lymphocytes of 296 male twins from the Vietnam Era Twin Registry. RESULTS Twins with current PTSD had significantly advanced DNAm age acceleration compared with twins without PTSD for five of six measures of DNAm age acceleration. Across almost all measures of DNAm age acceleration, twins with current PTSD were "epigenetically older" than their twin brothers without PTSD: estimated differences ranged between 1.6 (95% confidence interval = 0.0-3.1) and 2.7 (95% confidence interval = 0.5-4.8) biological age year-equivalents. A higher Clinician-Administered PTSD Scale score was also associated with a higher within-pair DNAm age acceleration. Results remained consistent after adjustment for behavioral and cardiovascular risk factors. CONCLUSIONS PTSD is associated with epigenetic age acceleration, primarily through unshared environmental mechanisms as opposed to genetic or familial factors. These results suggest that PTSD is related to systemic processes relevant to biological aging.
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Affiliation(s)
- Zeyuan Wang
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE, Atlanta, GA
| | - Qin Hui
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE, Atlanta, GA
| | - Jack Goldberg
- Vietnam Era Twin Registry, Seattle Epidemiologic Research and Information Center, US Department of Veterans Affairs, Seattle, WA
| | - Nicholas Smith
- Vietnam Era Twin Registry, Seattle Epidemiologic Research and Information Center, US Department of Veterans Affairs, Seattle, WA
| | - Belal Kaseer
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE, Atlanta, GA
| | - Nancy Murrah
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE, Atlanta, GA
| | - Oleksiy M. Levantsevych
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE, Atlanta, GA
| | - Lucy Shallenberger
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE, Atlanta, GA
| | - Emily Diggers
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE, Atlanta, GA
| | - J. Douglas Bremner
- Departments of Psychiatry and Behavioral Sciences and Radiology and Imaging Sciences, Emory University School of Medicine, Atlanta, GA
- Atlanta VA Health Care System, 1670 Clairmont Road, Decatur, GA 30033, USA
| | - Viola Vaccarino
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE, Atlanta, GA
| | - Yan V. Sun
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE, Atlanta, GA
- Atlanta VA Health Care System, 1670 Clairmont Road, Decatur, GA 30033, USA
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García-García L, Fernández-Tabanera E, Cervera ST, Melero-Fernández de Mera RM, Josa S, González-González L, Rodríguez-Martín C, Grünewald TGP, Alonso J. The Transcription Factor FEZF1, a Direct Target of EWSR1-FLI1 in Ewing Sarcoma Cells, Regulates the Expression of Neural-Specific Genes. Cancers (Basel) 2021; 13:5668. [PMID: 34830820 PMCID: PMC8616448 DOI: 10.3390/cancers13225668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 11/16/2022] Open
Abstract
Ewing sarcoma is a rare pediatric tumor characterized by chromosomal translocations that give rise to aberrant chimeric transcription factors (e.g., EWSR1-FLI1). EWSR1-FLI1 promotes a specific cellular transcriptional program. Therefore, the study of EWSR1-FLI1 target genes is important to identify critical pathways involved in Ewing sarcoma tumorigenesis. In this work, we focused on the transcription factors regulated by EWSR1-FLI1 in Ewing sarcoma. Transcriptomic analysis of the Ewing sarcoma cell line A673 indicated that one of the genes more strongly upregulated by EWSR1-FLI1 was FEZF1 (FEZ family zinc finger protein 1), a transcriptional repressor involved in neural cell identity. The functional characterization of FEZF1 was performed in three Ewing sarcoma cell lines (A673, SK-N-MC, SK-ES-1) through an shRNA-directed silencing approach. FEZF1 knockdown inhibited clonogenicity and cell proliferation. Finally, the analysis of the FEZF1-dependent expression profile in A673 cells showed several neural genes regulated by FEZF1 and concomitantly regulated by EWSR1-FLI1. In summary, FEZF1 is transcriptionally regulated by EWSR1-FLI1 in Ewing sarcoma cells and is involved in the regulation of neural-specific genes, which could explain the neural-like phenotype observed in several Ewing sarcoma tumors and cell lines.
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Affiliation(s)
- Laura García-García
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (L.G.-G.); (E.F.-T.); (S.T.C.); (R.M.M.-F.d.M.); (S.J.); (L.G.-G.); (C.R.-M.)
| | - Enrique Fernández-Tabanera
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (L.G.-G.); (E.F.-T.); (S.T.C.); (R.M.M.-F.d.M.); (S.J.); (L.G.-G.); (C.R.-M.)
- Centro de Investigación, Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Saint T. Cervera
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (L.G.-G.); (E.F.-T.); (S.T.C.); (R.M.M.-F.d.M.); (S.J.); (L.G.-G.); (C.R.-M.)
- Centro de Investigación, Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Raquel M. Melero-Fernández de Mera
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (L.G.-G.); (E.F.-T.); (S.T.C.); (R.M.M.-F.d.M.); (S.J.); (L.G.-G.); (C.R.-M.)
- Centro de Investigación, Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Santiago Josa
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (L.G.-G.); (E.F.-T.); (S.T.C.); (R.M.M.-F.d.M.); (S.J.); (L.G.-G.); (C.R.-M.)
| | - Laura González-González
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (L.G.-G.); (E.F.-T.); (S.T.C.); (R.M.M.-F.d.M.); (S.J.); (L.G.-G.); (C.R.-M.)
| | - Carlos Rodríguez-Martín
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (L.G.-G.); (E.F.-T.); (S.T.C.); (R.M.M.-F.d.M.); (S.J.); (L.G.-G.); (C.R.-M.)
- Centro de Investigación, Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Thomas G. P. Grünewald
- Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany;
- Hopp-Children’s Cancer Center (KiTZ), 69120 Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Javier Alonso
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (L.G.-G.); (E.F.-T.); (S.T.C.); (R.M.M.-F.d.M.); (S.J.); (L.G.-G.); (C.R.-M.)
- Centro de Investigación, Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III, 28029 Madrid, Spain
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7
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Wu D, Li Y, Ren Q, Pei S, Wang L, Yang L, Chong Y, Sun S, Hao J, Feng F. TANC1 methylation as a novel biomarker for the diagnosis of patients with anti-tuberculosis drug-induced liver injury. Sci Rep 2021; 11:17423. [PMID: 34465797 PMCID: PMC8408132 DOI: 10.1038/s41598-021-96869-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 08/11/2021] [Indexed: 01/02/2023] Open
Abstract
We aimed to elucidate the differences in genomic methylation patterns between ADLI and non-ADLI patients to identify DNA methylation-based biomarkers. Genome-wide DNA methylation patterns were obtained using Infinium MethylationEPIC (EPIC) BeadChip array to analyze 14 peripheral blood samples (7 ADLI cases, 7 non-ADLI controls). Changes in the mRNA and DNA methylation in the target genes of another 120 peripheral blood samples (60 ADLI cases, 60 non-ADLI controls) were analyzed by real-time polymerase chain reaction and pyrosequencing, respectively. A total of 308 hypermethylated CpG sites and 498 hypomethylated CpG sites were identified. Significantly, hypermethylated CpG sites cg06961147 and cg24666046 in TANC1 associated with ADLI was identified by genome-wide DNA methylation profiling. The mRNA expression of TANC1 was lower in the cases compared to the controls. Pyrosequencing validated these two differentially methylated loci, which was consistent with the results from the EPIC BeadChip array. Receiver operating characteristic analysis indicated that the area under the curve of TANC1 (cg06961147, cg24666046, and their combinations) was 0.812, 0.842, and 0.857, respectively. These results indicate that patients with ADLI have different genomic methylation patterns than patients without ADLI. The hypermethylated differentially methylated site cg06961147 combined with cg24666046 in TANC1 provides evidence for the diagnosis of ADLI.
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Affiliation(s)
- Dongxue Wu
- School of Public Health, North China University of Science and Technology, Tangshan, 063210, China
| | - Yuhong Li
- School of Public Health, North China University of Science and Technology, Tangshan, 063210, China
| | - Qi Ren
- School of Public Health, North China University of Science and Technology, Tangshan, 063210, China
| | - Shengfei Pei
- School of Public Health, North China University of Science and Technology, Tangshan, 063210, China
| | - Lin Wang
- School of Public Health, North China University of Science and Technology, Tangshan, 063210, China
| | - Luming Yang
- School of Public Health, North China University of Science and Technology, Tangshan, 063210, China
| | - Yingzhi Chong
- School of Public Health, North China University of Science and Technology, Tangshan, 063210, China
| | - Shufeng Sun
- College of Nursing and Rehabilitation, North China University of Science and Technology, Tangshan, 063210, China
| | - Jinqi Hao
- School of Public Health, North China University of Science and Technology, Tangshan, 063210, China.,School of Public Health, Baotou Medical College, Inner Mongolia University of Science and Technology, Baotou City, 014040, Inner Mongolia, China
| | - Fumin Feng
- School of Public Health, North China University of Science and Technology, Tangshan, 063210, China. .,School of Life Science, North China University of Science and Technology, Tangshan, 063210, China.
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8
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Li M, Sun X, Yao H, Chen W, Zhang F, Gao S, Zou X, Chen J, Qiu S, Wei H, Hu Z, Chen W. Genomic methylation variations predict the susceptibility of six chemotherapy related adverse effects and cancer development for Chinese colorectal cancer patients. Toxicol Appl Pharmacol 2021; 427:115657. [PMID: 34332992 DOI: 10.1016/j.taap.2021.115657] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/08/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) remains a major concern with high morbidity and mortality worldwide. Despite the positive influence of chemotherapy on the decline in CRC mortality, the negative influence of chemotherapy-related adverse effects (CRAEs) caused by capecitabine (Cap) remains a challenging problem. DNA methylation alteration plays a pivotal role in gene expression regulation. Here, we aimed to screen reliable and novel biomarkers for CRC diagnosis and CRAE prediction using the advanced Illumina Infinium MethylationEPIC (850 K) BeadChip. Paired tumor and normal tissues from 21 Chinese CRC patients who received Cap-based adjuvant chemotherapy were analyzed. CRC-related methylation was characterized by hypermethylated promoter islands and hypomethylated intragenic openseas; CRAE-related methylation was characterized by hyper- (or hypo-) methylated intragenic (or intergenic) regions. Based on three types of methylation profiles (differentially methylated probes, differentially methylated regions, and gene-function-differentially methylated regions), pathway enrichment analyses revealed that CRC-related genes were significantly enriched in the neuronal system, metabolism of RNA, and extracellular matrix organization; CRAE-related genes were abundantly enriched in pathways controlling regeneration functions and immune response. Finally, based on genes within the mostly related pathways and LASSO logistic regression selection, the integrated-methylation-marker systems developed here demonstrated high discriminative accuracy in both CRC diagnosis (AUROC = 1) and CRAE prediction (AUROC = 0.817-1). In conclusion, we conducted a comprehensive DNA methylation analysis of CRC patients with chemotherapy, which provided new insights into the formation of CRC and CRAEs. Most importantly, our findings identified potentially CRAE-related metabolic pathways and markers, providing a valuable reference for personalized medicine promising better safety. Trail registration:ClinicalTrials.gov,NCT03030508, Registered 25 January 2017,https://www.clinicaltrials.gov/ct2/show/NCT03030508?term=NCT03030508&draw=2&rank=1.
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Affiliation(s)
- Mingming Li
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Xiaomeng Sun
- Research Institute, GloriousMed Clinical Laboratory Co., Ltd., Shanghai 201318, China
| | - Houshan Yao
- Department of General Surgery, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Wei Chen
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Feng Zhang
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Shouhong Gao
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Xun Zou
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Jiani Chen
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Shi Qiu
- Traditional Chinese Medicine Resource and Technology Center, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Hua Wei
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China; Department of Pharmacy, 905th Hospital of PLA Navy, Naval Medical University, Shanghai 200052, China.
| | - Zhiqian Hu
- Department of General Surgery, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China; Department of Gastrointestinal Surgery, Tongji Hospital, Medical College of Tongji University, Shanghai 200065, China.
| | - Wansheng Chen
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China; Traditional Chinese Medicine Resource and Technology Center, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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9
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Fan K, Moore JE, Zhang XO, Weng Z. Genetic and epigenetic features of promoters with ubiquitous chromatin accessibility support ubiquitous transcription of cell-essential genes. Nucleic Acids Res 2021; 49:5705-5725. [PMID: 33978759 PMCID: PMC8191798 DOI: 10.1093/nar/gkab345] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 03/19/2021] [Accepted: 05/01/2021] [Indexed: 12/04/2022] Open
Abstract
Gene expression is controlled by regulatory elements within accessible chromatin. Although most regulatory elements are cell type-specific, a subset is accessible in nearly all the 517 human and 94 mouse cell and tissue types assayed by the ENCODE consortium. We systematically analyzed 9000 human and 8000 mouse ubiquitously-accessible candidate cis-regulatory elements (cCREs) with promoter-like signatures (PLSs) from ENCODE, which we denote ubi-PLSs. These are more CpG-rich than non-ubi-PLSs and correspond to genes with ubiquitously high transcription, including a majority of cell-essential genes. ubi-PLSs are enriched with motifs of ubiquitously-expressed transcription factors and preferentially bound by transcriptional cofactors regulating ubiquitously-expressed genes. They are highly conserved between human and mouse at the synteny level but exhibit frequent turnover of motif sites; accordingly, ubi-PLSs show increased variation at their centers compared with flanking regions among the ∼186 thousand human genomes sequenced by the TOPMed project. Finally, ubi-PLSs are enriched in genes implicated in Mendelian diseases, especially diseases broadly impacting most cell types, such as deficiencies in mitochondrial functions. Thus, a set of roughly 9000 mammalian promoters are actively maintained in an accessible state across cell types by a distinct set of transcription factors and cofactors to ensure the transcriptional programs of cell-essential genes.
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Affiliation(s)
- Kaili Fan
- Program in Bioinformatics and Integrative Biology, UMass Medical School, Worcester, MA, USA
| | - Jill E Moore
- Program in Bioinformatics and Integrative Biology, UMass Medical School, Worcester, MA, USA
| | - Xiao-ou Zhang
- Program in Bioinformatics and Integrative Biology, UMass Medical School, Worcester, MA, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, UMass Medical School, Worcester, MA, USA
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10
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Landmesser U, Poller W, Tsimikas S, Most P, Paneni F, Lüscher TF. From traditional pharmacological towards nucleic acid-based therapies for cardiovascular diseases. Eur Heart J 2021; 41:3884-3899. [PMID: 32350510 DOI: 10.1093/eurheartj/ehaa229] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/17/2020] [Accepted: 03/12/2020] [Indexed: 02/06/2023] Open
Abstract
Nucleic acid-based therapeutics are currently developed at large scale for prevention and management of cardiovascular diseases (CVDs), since: (i) genetic studies have highlighted novel therapeutic targets suggested to be causal for CVD; (ii) there is a substantial recent progress in delivery, efficacy, and safety of nucleic acid-based therapies; (iii) they enable effective modulation of therapeutic targets that cannot be sufficiently or optimally addressed using traditional small molecule drugs or antibodies. Nucleic acid-based therapeutics include (i) RNA-targeted therapeutics for gene silencing; (ii) microRNA-modulating and epigenetic therapies; (iii) gene therapies; and (iv) genome-editing approaches (e.g. CRISPR-Cas-based): (i) RNA-targeted therapeutics: several large-scale clinical development programmes, using antisense oligonucleotides (ASO) or short interfering RNA (siRNA) therapeutics for prevention and management of CVD have been initiated. These include ASO and/or siRNA molecules to lower apolipoprotein (a) [apo(a)], proprotein convertase subtilisin/kexin type 9 (PCSK9), apoCIII, ANGPTL3, or transthyretin (TTR) for prevention and treatment of patients with atherosclerotic CVD or TTR amyloidosis. (ii) MicroRNA-modulating and epigenetic therapies: novel potential therapeutic targets are continually arising from human non-coding genome and epigenetic research. First microRNA-based therapeutics or therapies targeting epigenetic regulatory pathways are in clinical studies. (iii) Gene therapies: EMA/FDA have approved gene therapies for non-cardiac monogenic diseases and LDL receptor gene therapy is currently being examined in patients with homozygous hypercholesterolaemia. In experimental studies, gene therapy has significantly improved cardiac function in heart failure animal models. (iv) Genome editing approaches: these technologies, such as using CRISPR-Cas, have proven powerful in stem cells, however, important challenges are remaining, e.g. low rates of homology-directed repair in somatic cells such as cardiomyocytes. In summary, RNA-targeted therapies (e.g. apo(a)-ASO and PCSK9-siRNA) are now in large-scale clinical outcome trials and will most likely become a novel effective and safe therapeutic option for CVD in the near future. MicroRNA-modulating, epigenetic, and gene therapies are tested in early clinical studies for CVD. CRISPR-Cas-mediated genome editing is highly effective in stem cells, but major challenges are remaining in somatic cells, however, this field is rapidly advancing.
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Affiliation(s)
- Ulf Landmesser
- Department of Cardiology, Campus Benjamin Franklin, CC11 (Cardiovascular Medicine), Charite-Universitätsmedizin Berlin, Hindenburgdamm 30, 12203 Berlin, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany.,Berlin Institute of Health, Anna-Louisa-Karsch-Strasse 2, 10178 Berlin, Germany
| | - Wolfgang Poller
- Department of Cardiology, Campus Benjamin Franklin, CC11 (Cardiovascular Medicine), Charite-Universitätsmedizin Berlin, Hindenburgdamm 30, 12203 Berlin, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | - Sotirios Tsimikas
- Division of Cardiovascular Medicine, Sulpizio Cardiovascular Center, University of California San Diego, 9500 Gilman Drive, BSB 1080, La Jolla, CA 92093-0682, USA
| | - Patrick Most
- German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, University of Heidelberg, Heidelberg, Germany.,Center for Translational Medicine, Jefferson Medical College, 1020 Locust Street, Philadelphia, PA 19107, USA.,Molecular and Translational Cardiology, Department of Medicine III, Heidelberg University Hospital, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany
| | - Francesco Paneni
- Center for Molecular Cardiology, University of Zürich, Wagistrasse 12, 8952 Schlieren, Switzerland.,Department of Cardiology, University Heart Center, University Hospital Zurich, Rämistrasse 100, 8091 Zurich, Switzerland.,Department of Research and Education, University Hospital Zurich, Rämistrasse 100, MOU2, 8091 Zurich, Switzerland
| | - Thomas F Lüscher
- Center for Molecular Cardiology, University of Zürich, Wagistrasse 12, 8952 Schlieren, Switzerland.,Research, Education and Development, Royal Brompton and Harefield Hospital Trust and Imperial College London, National Heart and Lung Institute, Guy Scadding Building, Dovehouse Street, London SW3 6LY, UK
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11
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Eales JM, Jiang X, Xu X, Saluja S, Akbarov A, Cano-Gamez E, McNulty MT, Finan C, Guo H, Wystrychowski W, Szulinska M, Thomas HB, Pramanik S, Chopade S, Prestes PR, Wise I, Evangelou E, Salehi M, Shakanti Y, Ekholm M, Denniff M, Nazgiewicz A, Eichinger F, Godfrey B, Antczak A, Glyda M, Król R, Eyre S, Brown J, Berzuini C, Bowes J, Caulfield M, Zukowska-Szczechowska E, Zywiec J, Bogdanski P, Kretzler M, Woolf AS, Talavera D, Keavney B, Maffia P, Guzik TJ, O'Keefe RT, Trynka G, Samani NJ, Hingorani A, Sampson MG, Morris AP, Charchar FJ, Tomaszewski M. Uncovering genetic mechanisms of hypertension through multi-omic analysis of the kidney. Nat Genet 2021; 53:630-637. [PMID: 33958779 DOI: 10.1038/s41588-021-00835-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/04/2021] [Indexed: 02/02/2023]
Abstract
The kidney is an organ of key relevance to blood pressure (BP) regulation, hypertension and antihypertensive treatment. However, genetically mediated renal mechanisms underlying susceptibility to hypertension remain poorly understood. We integrated genotype, gene expression, alternative splicing and DNA methylation profiles of up to 430 human kidneys to characterize the effects of BP index variants from genome-wide association studies (GWASs) on renal transcriptome and epigenome. We uncovered kidney targets for 479 (58.3%) BP-GWAS variants and paired 49 BP-GWAS kidney genes with 210 licensed drugs. Our colocalization and Mendelian randomization analyses identified 179 unique kidney genes with evidence of putatively causal effects on BP. Through Mendelian randomization, we also uncovered effects of BP on renal outcomes commonly affecting patients with hypertension. Collectively, our studies identified genetic variants, kidney genes, molecular mechanisms and biological pathways of key relevance to the genetic regulation of BP and inherited susceptibility to hypertension.
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Affiliation(s)
- James M Eales
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Xiao Jiang
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Xiaoguang Xu
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Sushant Saluja
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Artur Akbarov
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Eddie Cano-Gamez
- Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Michelle T McNulty
- Division of Nephrology, Boston Children's Hospital, Boston, MA, USA.,The Broad Institute, Cambridge, MA, USA
| | - Christopher Finan
- Institute of Cardiovascular Science, University College London, London, UK
| | - Hui Guo
- Centre for Biostatistics, School of Health Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Wojciech Wystrychowski
- Department of General, Vascular and Transplant Surgery, Medical University of Silesia, Katowice, Poland
| | - Monika Szulinska
- Department of Obesity, Metabolic Disorders Treatment and Clinical Dietetics, Karol Marcinkowski University of Medical Sciences, Poznan, Poland
| | - Huw B Thomas
- Division of Evolution and Genomic Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Sanjeev Pramanik
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK.,East Lancashire Hospitals NHS Trust, Blackburn, UK
| | - Sandesh Chopade
- Institute of Cardiovascular Science, University College London, London, UK
| | - Priscilla R Prestes
- Health Innovation and Transformation Centre, School of Science, Psychology and Sport, Federation University Australia, Ballarat, Victoria, Australia
| | - Ingrid Wise
- Australian Institute of Tropical Health & Medicine, James Cook University, Cairns, Queensland, Australia
| | - Evangelos Evangelou
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK.,Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
| | - Mahan Salehi
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Yusif Shakanti
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Mikael Ekholm
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK.,Department of Clinical Sciences, Danderyd Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Matthew Denniff
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Alicja Nazgiewicz
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Felix Eichinger
- Department of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Bradley Godfrey
- Department of Urology and Uro-oncology, Karol Marcinkowski University of Medical Sciences, Poznan, Poland
| | - Andrzej Antczak
- Department of Urology and Uro-oncology, Karol Marcinkowski University of Medical Sciences, Poznan, Poland
| | - Maciej Glyda
- Department of Transplantology and General Surgery Poznan, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Robert Król
- Department of General, Vascular and Transplant Surgery, Medical University of Silesia, Katowice, Poland
| | - Stephen Eyre
- Division of Musculoskeletal and Dermatological Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Jason Brown
- Division of Research and Innovation, Manchester University NHS Foundation Trust, Manchester, UK
| | - Carlo Berzuini
- Centre for Biostatistics, School of Health Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - John Bowes
- Division of Musculoskeletal and Dermatological Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Mark Caulfield
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.,National Institute for Health Research, Barts Cardiovascular Biomedical Research Centre, Queen Mary University of London, London, UK
| | | | - Joanna Zywiec
- Department of Internal Medicine, Diabetology and Nephrology, Zabrze, Medical University of Silesia, Katowice, Poland
| | - Pawel Bogdanski
- Department of Obesity, Metabolic Disorders Treatment and Clinical Dietetics, Karol Marcinkowski University of Medical Sciences, Poznan, Poland
| | | | - Adrian S Woolf
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.,Royal Manchester Children's Hospital and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - David Talavera
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Bernard Keavney
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK.,Division of Cardiology and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Pasquale Maffia
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.,Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.,Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Tomasz J Guzik
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.,Department of Internal and Agricultural Medicine, Jagiellonian University College of Medicine, Kraków, Poland
| | - Raymond T O'Keefe
- Division of Evolution and Genomic Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Gosia Trynka
- Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK.,Open Targets, Wellcome Genome Campus, Cambridge, UK
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK.,National Institute for Health Research, Leicester Biomedical Research Centre, Leicester, UK
| | - Aroon Hingorani
- Institute of Cardiovascular Science, University College London, London, UK
| | - Matthew G Sampson
- Division of Nephrology, Boston Children's Hospital, Boston, MA, USA.,The Broad Institute, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Andrew P Morris
- Division of Musculoskeletal and Dermatological Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK.,Department of Biostatistics, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Fadi J Charchar
- Health Innovation and Transformation Centre, School of Science, Psychology and Sport, Federation University Australia, Ballarat, Victoria, Australia.,Department of Cardiovascular Sciences, University of Leicester, Leicester, UK.,Department of Physiology, University of Melbourne, Parkville, Victoria, Australia
| | - Maciej Tomaszewski
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK. .,Manchester Heart Centre and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK.
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12
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Cho YD, Kim WJ, Ryoo HM, Kim HG, Kim KH, Ku Y, Seol YJ. Current advances of epigenetics in periodontology from ENCODE project: a review and future perspectives. Clin Epigenetics 2021; 13:92. [PMID: 33902683 PMCID: PMC8077755 DOI: 10.1186/s13148-021-01074-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 04/12/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The Encyclopedia of DNA Elements (ENCODE) project has advanced our knowledge of the functional elements in the genome and epigenome. The aim of this article was to provide the comprehension about current research trends from ENCODE project and establish the link between epigenetics and periodontal diseases based on epigenome studies and seek the future direction. MAIN BODY Global epigenome research projects have emphasized the importance of epigenetic research for understanding human health and disease, and current international consortia show an improved interest in the importance of oral health with systemic health. The epigenetic studies in dental field have been mainly conducted in periodontology and have focused on DNA methylation analysis. Advances in sequencing technology have broadened the target for epigenetic studies from specific genes to genome-wide analyses. CONCLUSIONS In line with global research trends, further extended and advanced epigenetic studies would provide crucial information for the realization of comprehensive dental medicine and expand the scope of ongoing large-scale research projects.
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Affiliation(s)
- Young-Dan Cho
- Department of Periodontology, School of Dentistry and Dental Research Institute, Seoul National University and Seoul National University Dental Hospital, Yeongeon-dong, Jongno-gu, Seoul, 03080, Korea
| | - Woo-Jin Kim
- Department of Molecular Genetics, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, Korea
| | - Hyun-Mo Ryoo
- Department of Molecular Genetics, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, Korea
| | - Hong-Gee Kim
- Biomedical Knowledge Engineering Laboratory, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, Korea
| | - Kyoung-Hwa Kim
- Department of Periodontology, School of Dentistry and Dental Research Institute, Seoul National University and Seoul National University Dental Hospital, Yeongeon-dong, Jongno-gu, Seoul, 03080, Korea
| | - Young Ku
- Department of Periodontology, School of Dentistry and Dental Research Institute, Seoul National University and Seoul National University Dental Hospital, Yeongeon-dong, Jongno-gu, Seoul, 03080, Korea
| | - Yang-Jo Seol
- Department of Periodontology, School of Dentistry and Dental Research Institute, Seoul National University and Seoul National University Dental Hospital, Yeongeon-dong, Jongno-gu, Seoul, 03080, Korea.
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13
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The Role of H3K4 Trimethylation in CpG Islands Hypermethylation in Cancer. Biomolecules 2021; 11:biom11020143. [PMID: 33499170 PMCID: PMC7912453 DOI: 10.3390/biom11020143] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/30/2020] [Accepted: 01/15/2021] [Indexed: 01/01/2023] Open
Abstract
CpG methylation in transposons, exons, introns and intergenic regions is important for long-term silencing, silencing of parasitic sequences and alternative promoters, regulating imprinted gene expression and determining X chromosome inactivation. Promoter CpG islands, although rich in CpG dinucleotides, are unmethylated and remain so during all phases of mammalian embryogenesis and development, except in specific cases. The biological mechanisms that contribute to the maintenance of the unmethylated state of CpG islands remain elusive, but the modification of established DNA methylation patterns is a common feature in all types of tumors and is considered as an event that intrinsically, or in association with genetic lesions, feeds carcinogenesis. In this review, we focus on the latest results describing the role that the levels of H3K4 trimethylation may have in determining the aberrant hypermethylation of CpG islands in tumors.
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14
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Chitpin JG, Awdeh A, Perkins TJ. RECAP reveals the true statistical significance of ChIP-seq peak calls. Bioinformatics 2020; 35:3592-3598. [PMID: 30824903 PMCID: PMC6761936 DOI: 10.1093/bioinformatics/btz150] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 01/18/2019] [Accepted: 02/27/2019] [Indexed: 12/29/2022] Open
Abstract
Motivation Chromatin Immunopreciptation (ChIP)-seq is used extensively to identify sites of transcription factor binding or regions of epigenetic modifications to the genome. A key step in ChIP-seq analysis is peak calling, where genomic regions enriched for ChIP versus control reads are identified. Many programs have been designed to solve this task, but nearly all fall into the statistical trap of using the data twice—once to determine candidate enriched regions, and again to assess enrichment by classical statistical hypothesis testing. This double use of the data invalidates the statistical significance assigned to enriched regions, thus the true significance or reliability of peak calls remains unknown. Results Using simulated and real ChIP-seq data, we show that three well-known peak callers, MACS, SICER and diffReps, output biased P-values and false discovery rate estimates that can be many orders of magnitude too optimistic. We propose a wrapper algorithm, RECAP, that uses resampling of ChIP-seq and control data to estimate a monotone transform correcting for biases built into peak calling algorithms. When applied to null hypothesis data, where there is no enrichment between ChIP-seq and control, P-values recalibrated by RECAP are approximately uniformly distributed. On data where there is genuine enrichment, RECAP P-values give a better estimate of the true statistical significance of candidate peaks and better false discovery rate estimates, which correlate better with empirical reproducibility. RECAP is a powerful new tool for assessing the true statistical significance of ChIP-seq peak calls. Availability and implementation The RECAP software is available through www.perkinslab.ca or on github at https://github.com/theodorejperkins/RECAP. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Justin G Chitpin
- Translational and Molecular Medicine Program, University of Ottawa, Ottawa, ON K1H8M5, Canada.,Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada
| | - Aseel Awdeh
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada.,School of Electrical Engineering and Computer Science, University of Ottawa, Ottawa, ON K1N6N5, Canada
| | - Theodore J Perkins
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada.,School of Electrical Engineering and Computer Science, University of Ottawa, Ottawa, ON K1N6N5, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H8M5, Canada
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15
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Joshi R, Castro De Moura M, Piñeyro D, Alvarez-Errico D, Arribas C, Esteller M. The DNA methylation landscape of human cancer organoids available at the American type culture collection. Epigenetics 2020; 15:1167-1177. [PMID: 32396494 PMCID: PMC7595613 DOI: 10.1080/15592294.2020.1762398] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
One caveat in cancer research is the dependence of certain experimental systems that might not really reflect the properties of the primary tumours. The recent irruption of 3D cultured cells termed organoids could render a better representation of the original tumour sample. However, every laboratory has its own protocol and tissue-provider to establish these cancer models, preventing further dissemination and validation of the obtained data. To address this problem, the Human Cancer Models Initiative (HCMI) has selected the American Type Culture Collection (ATCC) to make available organoid models to the scientific community. In this regard, no epigenetic information is available for these samples and, overall, the DNA methylation profiles of human cancer organoids are largely unknown. Herein, we provide the DNA methylation landscape of 25 human cancer organoids available at the ATCC using a microarray that interrogates more than 850,000 CpG sites. We observed that the studied organoids retain the epigenetic setting of their original primary cancer type; that exhibit a DNA methylation landscape characteristic of transformed tissues excluding an overgrowth of normal-matched cells; and that are closer to the DNA methylation profiles of the corresponding primary tumours than to established 2D cell lines. Most importantly, the obtained DNA methylation results are freely available to everyone for further data mining. Thus, our findings support from the epigenetic standpoint that the ATCC human cancer organoids recapitulate many of the features of the disorder in the patient and are excellent tools to be shared among investigators for further tumour biology research.
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Affiliation(s)
- Ricky Joshi
- Josep Carreras Leukaemia Research Institute (IJC), Badalona , Barcelona, Spain
| | | | - David Piñeyro
- Josep Carreras Leukaemia Research Institute (IJC), Badalona , Barcelona, Spain
| | | | - Carles Arribas
- Josep Carreras Leukaemia Research Institute (IJC), Badalona , Barcelona, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona , Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA) , Barcelona, Spain.,Centro de Investigacion Biomedica en Red Cancer (CIBERONC) , Madrid, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB) , Barcelona, Spain
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16
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Mona B, Villarreal J, Savage TK, Kollipara RK, Boisvert BE, Johnson JE. Positive autofeedback regulation of Ptf1a transcription generates the levels of PTF1A required to generate itch circuit neurons. Genes Dev 2020; 34:621-636. [PMID: 32241803 PMCID: PMC7197352 DOI: 10.1101/gad.332577.119] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 03/13/2020] [Indexed: 11/24/2022]
Abstract
In this study, Mona et al. set out to investigate the role of Ptf1a in specifying a subset of dorsal spinal cord inhibitory neurons in mice in vivo. The authors used CRISPR to target multiple noncoding sequences with putative cis-regulatory activity controlling Ptf1a and demonstrate a requirement for positive transcriptional autoregulatory feedback to attain the levels of PTF1A necessary for generating correctly balanced neuronal circuits. Peripheral somatosensory input is modulated in the dorsal spinal cord by a network of excitatory and inhibitory interneurons. PTF1A is a transcription factor essential in dorsal neural tube progenitors for specification of these inhibitory neurons. Thus, mechanisms regulating Ptf1a expression are key for generating neuronal circuits underlying somatosensory behaviors. Mutations targeted to distinct cis-regulatory elements for Ptf1a in mice, tested the in vivo contribution of each element individually and in combination. Mutations in an autoregulatory enhancer resulted in reduced levels of PTF1A, and reduced numbers of specific dorsal spinal cord inhibitory neurons, particularly those expressing Pdyn and Gal. Although these mutants survive postnatally, at ∼3–5 wk they elicit a severe scratching phenotype. Behaviorally, the mutants have increased sensitivity to itch, but acute sensitivity to other sensory stimuli such as mechanical or thermal pain is unaffected. We demonstrate a requirement for positive transcriptional autoregulatory feedback to attain the level of the neuronal specification factor PTF1A necessary for generating correctly balanced neuronal circuits.
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Affiliation(s)
- Bishakha Mona
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Juan Villarreal
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Trisha K Savage
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Rahul K Kollipara
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Brooke E Boisvert
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jane E Johnson
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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17
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Cruz Díaz LA, Gutiérrez Ortega A, Chávez Álvarez RDC, Velarde Félix JS, Prado Montes de Oca E. Regulatory SNP rs5743417 impairs constitutive expression of human β-defensin 1 and has high frequency in Africans and Afro-Americans. Int J Immunogenet 2020; 47:332-341. [PMID: 31994826 DOI: 10.1111/iji.12475] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/26/2019] [Accepted: 01/02/2020] [Indexed: 01/01/2023]
Abstract
The prediction of regulatory single nucleotide polymorphisms (rSNPs) in proximal promoters of disease-related genes could be a useful tool for personalized medicine in both patient stratification and customized therapy. Using our previously reported method of rSNPs prediction (currently a software called SNPClinic v.1.0) as well as with PredictSNP tool, we performed in silico prediction of regulatory SNPs in the antimicrobial peptide human β-defensin 1 gene in three human cell lines from 1,000 Genomes Project (1kGP), namely A549 (epithelial cell line), HL-60 (neutrophils) and TH 1 (lymphocytes). These predictions were run in a proximal pseudo-promoter comprising all common alleles on each polymorphic site according to the 1,000 Genomes Project data (1kGP: ALL). Plasmid vectors containing either the major or the minor allele of a putative rSNP rs5743417 (categorized as regulatory by SNPClinic and confirmed by PredictSNP) and a non-rSNP negative control were transfected to lung A549 human epithelial cell line. We assessed functionality of rSNPs by qPCR using the Pfaffl method. In A549 cells, minor allele of the SNP rs5743417 G→A showed a significant reduction in gene expression, diminishing DEFB1 transcription by 33% when compared with the G major allele (p-value = .03). SNP rs5743417 minor allele has high frequency in Gambians (8%, 1kGP population: GWD) and Afro-Americans (3.3%, 1kGP population: ASW). This SNP alters three transcription factors binding sites (TFBSs) comprising SREBP2 (sterols and haematopoietic pathways), CREB1 (cAMP, insulin and TNF pathways) and JUND (apoptosis, senescence and stress pathways) in the proximal promoter of DEFB1. Further in silico analysis reveals that this SNP also overlaps with GS1-24F4.2, a lincRNA gene complementary to the X Kell blood group related 5 (XKR5) mRNA. The potential clinical impact of the altered constitutive expression of DEFB1 caused by rSNP rs5743417 in DEFB1-associated diseases as tuberculosis, COPD, asthma, cystic fibrosis and cancer in African and Afro-American populations deserves further research.
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Affiliation(s)
- Luis Antonio Cruz Díaz
- Interinstitutional Posgrade in Science and Technology (PICYT), Research Center of Technology and Design Assistance of Jalisco State, (CIATEJ A.C.), Guadalajara, Mexico.,Laboratory of Regulatory SNPs, Personalized Medicine National Laboratory (LAMPER), Pharmaceutical and Medical Biotechnology, Central Unit, CIATEJ A.C., National Council of Science and Technology (CONACYT), Guadalajara, Mexico
| | - Abel Gutiérrez Ortega
- Laboratory of Regulatory SNPs, Personalized Medicine National Laboratory (LAMPER), Pharmaceutical and Medical Biotechnology, Central Unit, CIATEJ A.C., National Council of Science and Technology (CONACYT), Guadalajara, Mexico
| | - Rocío Del Carmen Chávez Álvarez
- Laboratory of Regulatory SNPs, Personalized Medicine National Laboratory (LAMPER), Pharmaceutical and Medical Biotechnology, Central Unit, CIATEJ A.C., National Council of Science and Technology (CONACYT), Guadalajara, Mexico
| | - Jesús Salvador Velarde Félix
- Faculty of Chemical and Biological Sciences, Autonomous University of Sinaloa, Culiacan, Mexico.,Faculty of Biology, Autonomous University of Sinaloa, Culiacan, Mexico.,Genomic Medicine Center, Dr. Bernardo J. Gastélum Primary Care Hospital, Sinaloa Health Ministry, Culiacan, Mexico
| | - Ernesto Prado Montes de Oca
- Laboratory of Regulatory SNPs, Personalized Medicine National Laboratory (LAMPER), Pharmaceutical and Medical Biotechnology, Central Unit, CIATEJ A.C., National Council of Science and Technology (CONACYT), Guadalajara, Mexico.,Laboratory of Pharmacogenomics and Preventive Medicine, Personalized Medicine National Laboratory (LAMPER), Pharmaceutical and Medical Biotechnology, Central Unit, CIATEJ A.C., CONACYT, Guadalajara, Mexico.,Scripps Research Translational Institute, La Jolla, CA, USA.,Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA, USA
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18
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Mallik S, Odom GJ, Gao Z, Gomez L, Chen X, Wang L. An evaluation of supervised methods for identifying differentially methylated regions in Illumina methylation arrays. Brief Bioinform 2019; 20:2224-2235. [PMID: 30239597 PMCID: PMC6954393 DOI: 10.1093/bib/bby085] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/24/2018] [Accepted: 08/16/2018] [Indexed: 01/19/2023] Open
Abstract
Epigenome-wide association studies (EWASs) have become increasingly popular for studying DNA methylation (DNAm) variations in complex diseases. The Illumina methylation arrays provide an economical, high-throughput and comprehensive platform for measuring methylation status in EWASs. A number of software tools have been developed for identifying disease-associated differentially methylated regions (DMRs) in the epigenome. However, in practice, we found these tools typically had multiple parameter settings that needed to be specified and the performance of the software tools under different parameters was often unclear. To help users better understand and choose optimal parameter settings when using DNAm analysis tools, we conducted a comprehensive evaluation of 4 popular DMR analysis tools under 60 different parameter settings. In addition to evaluating power, precision, area under precision-recall curve, Matthews correlation coefficient, F1 score and type I error rate, we also compared several additional characteristics of the analysis results, including the size of the DMRs, overlap between the methods and execution time. The results showed that none of the software tools performed best under their default parameter settings, and power varied widely when parameters were changed. Overall, the precision of these software tools were good. In contrast, all methods lacked power when effect size was consistent but small. Across all simulation scenarios, comb-p consistently had the best sensitivity as well as good control of false-positive rate.
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Affiliation(s)
- Saurav Mallik
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, USA
- Joint First Authors
| | - Gabriel J Odom
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, USA
- Joint First Authors
| | - Zhen Gao
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Lissette Gomez
- Dr. John T. Macdonald Foundation, Department of Human Genetics, and John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Xi Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
- Dr. John T. Macdonald Foundation, Department of Human Genetics, and John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
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19
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Park CS, De T, Xu Y, Zhong Y, Smithberger E, Alarcon C, Gamazon ER, Perera MA. Hepatocyte gene expression and DNA methylation as ancestry-dependent mechanisms in African Americans. NPJ Genom Med 2019; 4:29. [PMID: 31798965 PMCID: PMC6877651 DOI: 10.1038/s41525-019-0102-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 09/27/2019] [Indexed: 12/13/2022] Open
Abstract
African Americans (AAs) are an admixed population with widely varying proportion of West African ancestry (WAA). Here we report the correlation of WAA to gene expression and DNA methylation in AA-derived hepatocytes, a cell type important in disease and drug response. We perform mediation analysis to test whether methylation is a mediator of the effect of ancestry on expression. GTEx samples and a second cohort are used as validation. One hundred and thirty-one genes are associated with WAA (FDR < 0.10), 28 of which replicate and represent 220 GWAS phenotypes. Among PharmGKB pharmacogenes, VDR, PTGIS, ALDH1A1, CYP2C19, and P2RY1 nominally associate with WAA (p < 0.05). We find 1037 WAA-associated, differentially methylated regions (FDR < 0.05), with hypomethylated genes enriched in drug-response pathways. In conclusion, WAA contributes to variability in hepatocyte expression and DNA methylation with identified genes previously implicated for diseases disproportionately affecting AAs, including cardiovascular (PTGIS, PLAT) and renal (APOL1) disease, and drug response (CYP2C19).
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Affiliation(s)
- C. S. Park
- Department of Pharmacology, Center for Pharmacogenomics, Feinberg School of Medicine, Northwestern University, Chicago, IL USA
| | - T. De
- Department of Pharmacology, Center for Pharmacogenomics, Feinberg School of Medicine, Northwestern University, Chicago, IL USA
| | - Y. Xu
- Department of Pharmacology, Center for Pharmacogenomics, Feinberg School of Medicine, Northwestern University, Chicago, IL USA
- Center for Translational Data Science, University of Chicago, Chicago, IL USA
| | - Y. Zhong
- Department of Pharmacology, Center for Pharmacogenomics, Feinberg School of Medicine, Northwestern University, Chicago, IL USA
| | - E. Smithberger
- Department of Pharmacology, Center for Pharmacogenomics, Feinberg School of Medicine, Northwestern University, Chicago, IL USA
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC USA
| | - C. Alarcon
- Department of Pharmacology, Center for Pharmacogenomics, Feinberg School of Medicine, Northwestern University, Chicago, IL USA
| | - E. R. Gamazon
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Vanderbilt University School of Medicine, Nashville, TN USA
- Data Science Institute, Vanderbilt University, Nashville, TN USA
- Clare Hall, University of Cambridge, Cambridge, UK
| | - M. A. Perera
- Department of Pharmacology, Center for Pharmacogenomics, Feinberg School of Medicine, Northwestern University, Chicago, IL USA
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20
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Nikitin D, Kolosov N, Murzina A, Pats K, Zamyatin A, Tkachev V, Sorokin M, Kopylov P, Buzdin A. Retroelement-Linked H3K4me1 Histone Tags Uncover Regulatory Evolution Trends of Gene Enhancers and Feature Quickly Evolving Molecular Processes in Human Physiology. Cells 2019; 8:cells8101219. [PMID: 31597351 PMCID: PMC6830109 DOI: 10.3390/cells8101219] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/25/2019] [Accepted: 10/01/2019] [Indexed: 12/20/2022] Open
Abstract
Background: Retroelements (REs) are mobile genetic elements comprising ~40% of human DNA. They can reshape expression patterns of nearby genes by providing various regulatory sequences. The proportion of regulatory sequences held by REs can serve a measure of regulatory evolution rate of the respective genes and molecular pathways. Methods: We calculated RE-linked enrichment scores for individual genes and molecular pathways based on ENCODE project epigenome data for enhancer-specific histone modification H3K4me1 in five human cell lines. We identified consensus groups of molecular processes that are enriched and deficient in RE-linked H3K4me1 regulation. Results: We calculated H3K4me1 RE-linked enrichment scores for 24,070 human genes and 3095 molecular pathways. We ranked genes and pathways and identified those statistically significantly enriched and deficient in H3K4me1 RE-linked regulation. Conclusion: Non-coding RNA genes were statistically significantly enriched by RE-linked H3K4me1 regulatory modules, thus suggesting their high regulatory evolution rate. The processes of gene silencing by small RNAs, DNA metabolism/chromatin structure, sensory perception/neurotransmission and lipids metabolism showed signs of the fastest regulatory evolution, while the slowest processes were connected with immunity, protein ubiquitination/degradation, cell adhesion, migration and interaction, metals metabolism/ion transport, cell death, intracellular signaling pathways.
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Affiliation(s)
- Daniil Nikitin
- Group for genomic analysis of cell signaling systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia.
- Omicsway Corp., Walnut, CA 91789, USA.
| | | | | | - Karina Pats
- ITMO University, 195251 Saint-Petersburg, Russia.
| | | | | | - Maxim Sorokin
- Omicsway Corp., Walnut, CA 91789, USA.
- Institute of Personalized Medicine, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia.
| | - Philippe Kopylov
- Institute of Personalized Medicine, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia.
| | - Anton Buzdin
- Group for genomic analysis of cell signaling systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia.
- Omicsway Corp., Walnut, CA 91789, USA.
- Institute of Personalized Medicine, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia.
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21
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Alsaleh H, Haddrill PR. Identifying blood-specific age-related DNA methylation markers on the Illumina MethylationEPIC® BeadChip. Forensic Sci Int 2019; 303:109944. [PMID: 31546163 DOI: 10.1016/j.forsciint.2019.109944] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 08/14/2019] [Accepted: 09/01/2019] [Indexed: 01/02/2023]
Abstract
The past decade has seen rapid development in DNA methylation (DNAm) microarrays, including the Illumina HumanMethylation27 and HumanMethylation450 (450K) chips, which have played an essential role in identifying and evaluating age-related (AR) DNAm markers in different tissues. Recently, a new array, the Illumina MethylationEPIC (EPIC) was introduced, with nearly double the number of probes as the 450K (∼850,000 probes). In this study, we test these newly added probes for age association using a large cohort of 754 DNAm profiles from blood samples assayed on the EPIC BeadChip, for individuals aged 0-88 years old. 52 AR CpG sites (Spearman's abs(rho) >0.6 and P-value <10-83) were identified, 21 of which were novel sites and mapped to 18 genes, nine of which (LHFPL4, SLC12A8, EGFEM1P, GPR158, TAL1, KIAA1755, LOC730668, DUSP16, and FAM65C) have never previously been reported to be associated with age. The data were subsequently split into a 527-sample training set and a 227-sample testing set to build and validate two age prediction models using elastic net regression and multivariate regression. Elastic net regression selected 425 CpG markers with a mean absolute deviation (MAD) of 2.6 years based on the testing set. To build a multivariate linear regression model, AR CpG sites with R2 > 0.5 at FDR < 0.05 were input into stepwise regression to select the best subset for age prediction. The resulting six CpG markers were linearly modelled with age and explained 81% of age-correlated variation in DNAm levels. Age estimation accuracy using bootstrap analysis was 4.5 years, with 95% confidence intervals of 4.56 to 4.57 years based on the testing set. These results suggest that EPIC BeadChip probes for age estimation fall within the range of probes found on the previous Illumina HumanMethylation platforms in terms of their age-prediction ability.
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Affiliation(s)
- Hussain Alsaleh
- Centre for Forensic Science, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, Scotland, UK; General Department for Forensic Evidence, State of Kuwait Ministry of Interior, Kuwait.
| | - Penelope R Haddrill
- Centre for Forensic Science, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, Scotland, UK
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22
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Dhaliwal A, Pelka S, Gray DS, Moghe PV. Engineering Lineage Potency and Plasticity of Stem Cells using Epigenetic Molecules. Sci Rep 2018; 8:16289. [PMID: 30389989 PMCID: PMC6215020 DOI: 10.1038/s41598-018-34511-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 10/11/2018] [Indexed: 12/17/2022] Open
Abstract
Stem cells are considered as a multipotent regenerative source for diseased and dysfunctional tissues. Despite the promise of stem cells, the inherent capacity of stem cells to convert to tissue-specific lineages can present a major challenge to the use of stem cells for regenerative medicine. We hypothesized that epigenetic regulating molecules can modulate the stem cell’s developmental program, and thus potentially overcome the limited lineage differentiation that human stem cells exhibit based on the source and processing of stem cells. In this study, we screened a library of 84 small molecule pharmacological agents indicated in nucleosomal modification and identified a sub-set of specific molecules that influenced osteogenesis in human mesenchymal stem cells (hMSCs) while maintaining cell viability in-vitro. Pre-treatment with five candidate hits, Gemcitabine, Decitabine, I-CBP112, Chidamide, and SIRT1/2 inhibitor IV, maximally enhanced osteogenesis in-vitro. In contrast, five distinct molecules, 4-Iodo-SAHA, Scriptaid, AGK2, CI-amidine and Delphidine Chloride maximally inhibited osteogenesis. We then tested the role of these molecules on hMSCs derived from aged human donors and report that small epigenetic molecules, namely Gemcitabine and Chidamide, can significantly promote osteogenic differentiation by 5.9- and 2.3-fold, respectively. Taken together, this study demonstrates new applications of identified small molecule drugs for sensitively regulating the lineage plasticity fates of bone-marrow derived mesenchymal stem cells through modulating the epigenetic profile of the cells.
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Affiliation(s)
- Anandika Dhaliwal
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States
| | - Sandra Pelka
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States
| | - David S Gray
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States
| | - Prabhas V Moghe
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States. .,Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, NJ, United States.
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23
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Methylome of human skeletal muscle after acute & chronic resistance exercise training, detraining & retraining. Sci Data 2018; 5:180213. [PMID: 30375987 PMCID: PMC6207066 DOI: 10.1038/sdata.2018.213] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/22/2018] [Indexed: 01/08/2023] Open
Abstract
DNA methylation is an important epigenetic modification that can regulate gene expression following environmental encounters without changes to the genetic code. Using Infinium MethylationEPIC BeadChip Arrays (850,000 CpG sites) we analysed for the first time, DNA isolated from untrained human skeletal muscle biopsies (vastus lateralis) at baseline (rest) and immediately following an acute (single) bout of resistance exercise. In the same participants, we also analysed the methylome following a period of muscle growth (hypertrophy) evoked via chronic (repeated bouts-3 sessions/wk) resistance exercise (RE) (training) over 7-weeks, followed by complete exercise cessation for 7-weeks returning muscle back to baseline levels (detraining), and finally followed by a subsequent 7-week period of RE-induced hypertrophy (retraining). These valuable methylome data sets described in the present manuscript and deposited in an open-access repository can now be shared and re-used to enable the identification of epigenetically regulated genes/networks that are modified after acute anabolic stimuli and hypertrophy, and further investigate the phenomenon of epigenetic memory in skeletal muscle.
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24
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Zhang Q, Marioni RE, Robinson MR, Higham J, Sproul D, Wray NR, Deary IJ, McRae AF, Visscher PM. Genotype effects contribute to variation in longitudinal methylome patterns in older people. Genome Med 2018; 10:75. [PMID: 30348214 PMCID: PMC6198530 DOI: 10.1186/s13073-018-0585-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 09/27/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND DNA methylation levels change along with age, but few studies have examined the variation in the rate of such changes between individuals. METHODS We performed a longitudinal analysis to quantify the variation in the rate of change of DNA methylation between individuals using whole blood DNA methylation array profiles collected at 2-4 time points (N = 2894) in 954 individuals (67-90 years). RESULTS After stringent quality control, we identified 1507 DNA methylation CpG sites (rsCpGs) with statistically significant variation in the rate of change (random slope) of DNA methylation among individuals in a mixed linear model analysis. Genes in the vicinity of these rsCpGs were found to be enriched in Homeobox transcription factors and the Wnt signalling pathway, both of which are related to ageing processes. Furthermore, we investigated the SNP effect on the random slope. We found that 4 out of 1507 rsCpGs had one significant (P < 5 × 10-8/1507) SNP effect and 343 rsCpGs had at least one SNP effect (436 SNP-probe pairs) reaching genome-wide significance (P < 5 × 10-8). Ninety-five percent of the significant (P < 5 × 10-8) SNPs are on different chromosomes from their corresponding probes. CONCLUSIONS We identified CpG sites that have variability in the rate of change of DNA methylation between individuals, and our results suggest a genetic basis of this variation. Genes around these CpG sites have been reported to be involved in the ageing process.
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Affiliation(s)
- Qian Zhang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Riccardo E Marioni
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Matthew R Robinson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jon Higham
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Duncan Sproul
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Edinburgh Cancer Research Centre, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- The Queensland Brain Institute, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- The Queensland Brain Institute, The University of Queensland, St Lucia, QLD, 4072, Australia
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25
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van Dongen J, Ehli EA, Jansen R, van Beijsterveldt CEM, Willemsen G, Hottenga JJ, Kallsen NA, Peyton SA, Breeze CE, Kluft C, Heijmans BT, Bartels M, Davies GE, Boomsma DI. Genome-wide analysis of DNA methylation in buccal cells: a study of monozygotic twins and mQTLs. Epigenetics Chromatin 2018; 11:54. [PMID: 30253792 PMCID: PMC6156977 DOI: 10.1186/s13072-018-0225-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 09/17/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND DNA methylation arrays are widely used in epigenome-wide association studies and methylation quantitative trait locus (mQTL) studies. Here, we performed the first genome-wide analysis of monozygotic (MZ) twin correlations and mQTLs on data obtained with the Illumina MethylationEPIC BeadChip (EPIC array) and compared the performance of the EPIC array to the Illumina HumanMethylation450 BeadChip (HM450 array) for buccal-derived DNA. RESULTS Good-quality EPIC data were obtained for 102 buccal-derived DNA samples from 49 MZ twin pairs (mean age = 7.5 years, range = 1-10). Differences between MZ twins in the cellular content of buccal swabs were a major driver for differences in their DNA methylation profiles, highlighting the importance to adjust for cellular composition in DNA methylation studies of buccal-derived DNA. After adjusting for cellular composition, the genome-wide mean correlation (r) between MZ twins was 0.21 for the EPIC array, and cis mQTL analysis in 84 twins identified 1,296,323 significant associations (FDR 5%), encompassing 33,749 methylation sites and 616,029 genetic variants. MZ twin correlations were slightly larger (p < 2.2 × 10-16) for novel EPIC probes (N = 383,066, mean r = 0.22) compared to probes that are also present on HM450 (N = 406,822, mean r = 0.20). In line with this observation, a larger percentage of novel EPIC probes was associated with genetic variants (novel EPIC probes with significant mQTL 4.7%, HM450 probes with mQTL 3.9%, p < 2.2 × 10-16). Methylation sites with a large MZ correlation and sites associated with mQTLs were most strongly enriched in epithelial cell DNase I hypersensitive sites (DHSs), enhancers, and histone mark H3K4me3. CONCLUSIONS We conclude that the contribution of familial factors to individual differences in DNA methylation and the effect of mQTLs are larger for novel EPIC probes, especially those within regulatory elements connected to active regions specific to the investigated tissue.
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Affiliation(s)
- Jenny van Dongen
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Van Der Boechorststraat 1, 1081BT Amsterdam, The Netherlands
| | - Erik A. Ehli
- Avera Institute for Human Genetics, 3720 W. 69th Street, Sioux Falls, SD 57108 USA
| | - Rick Jansen
- Department of Psychiatry, VU University Medical Center, Oldenaller 1, 1081 HJ Amsterdam, The Netherlands
| | - Catharina E. M. van Beijsterveldt
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Van Der Boechorststraat 1, 1081BT Amsterdam, The Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Van Der Boechorststraat 1, 1081BT Amsterdam, The Netherlands
| | - Jouke J. Hottenga
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Van Der Boechorststraat 1, 1081BT Amsterdam, The Netherlands
| | - Noah A. Kallsen
- Avera Institute for Human Genetics, 3720 W. 69th Street, Sioux Falls, SD 57108 USA
| | - Shanna A. Peyton
- Avera Institute for Human Genetics, 3720 W. 69th Street, Sioux Falls, SD 57108 USA
| | - Charles E. Breeze
- Altius Institute for Biomedical Sciences, 2211 Elliott Ave, Seattle, WA 98121 USA
| | - Cornelis Kluft
- Good Biomarker Sciences, Zernikedreef 8, 2333 CL Leiden, The Netherlands
| | - Bastiaan T. Heijmans
- Molecular Epidemiology Section, Leiden University Medical Center, Postal Zone S-05-P, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Meike Bartels
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Van Der Boechorststraat 1, 1081BT Amsterdam, The Netherlands
| | - Gareth E. Davies
- Avera Institute for Human Genetics, 3720 W. 69th Street, Sioux Falls, SD 57108 USA
| | - Dorret I. Boomsma
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Van Der Boechorststraat 1, 1081BT Amsterdam, The Netherlands
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26
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Gallardo-Gómez M, Moran S, Páez de la Cadena M, Martínez-Zorzano VS, Rodríguez-Berrocal FJ, Rodríguez-Girondo M, Esteller M, Cubiella J, Bujanda L, Castells A, Balaguer F, Jover R, De Chiara L. A new approach to epigenome-wide discovery of non-invasive methylation biomarkers for colorectal cancer screening in circulating cell-free DNA using pooled samples. Clin Epigenetics 2018; 10:53. [PMID: 29686738 PMCID: PMC5902929 DOI: 10.1186/s13148-018-0487-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/02/2018] [Indexed: 12/16/2022] Open
Abstract
Background Colorectal cancer is the fourth cause of cancer-related deaths worldwide, though detection at early stages associates with good prognosis. Thus, there is a clear demand for novel non-invasive tests for the early detection of colorectal cancer and premalignant advanced adenomas, to be used in population-wide screening programs. Aberrant DNA methylation detected in liquid biopsies, such as serum circulating cell-free DNA (cfDNA), is a promising source of non-invasive biomarkers. This study aimed to assess the feasibility of using cfDNA pooled samples to identify potential serum methylation biomarkers for the detection of advanced colorectal neoplasia (colorectal cancer or advanced adenomas) using microarray-based technology. Results cfDNA was extracted from serum samples from 20 individuals with no colorectal findings, 20 patients with advanced adenomas, and 20 patients with colorectal cancer (stages I and II). Two pooled samples were prepared for each pathological group using equal amounts of cfDNA from 10 individuals, sex-, age-, and recruitment hospital-matched. We measured the methylation levels of 866,836 CpG positions across the genome using the MethylationEPIC array. Pooled serum cfDNA methylation data meets the quality requirements. The proportion of detected CpG in all pools (> 99% with detection p value < 0.01) exceeded Illumina Infinium methylation data quality metrics of the number of sites detected. The differential methylation analysis revealed 1384 CpG sites (5% false discovery rate) with at least 10% difference in the methylation level between no colorectal findings controls and advanced neoplasia, the majority of which were hypomethylated. Unsupervised clustering showed that cfDNA methylation patterns can distinguish advanced neoplasia from healthy controls, as well as separate tumor tissue from healthy mucosa in an independent dataset. We also observed that advanced adenomas and stage I/II colorectal cancer methylation profiles, grouped as advanced neoplasia, are largely homogenous and clustered close together. Conclusions This preliminary study shows the viability of microarray-based methylation biomarker discovery using pooled serum cfDNA samples as an alternative approach to tissue specimens. Our strategy sets an open door for deciphering new non-invasive biomarkers not only for colorectal cancer detection, but also for other types of cancers.
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Affiliation(s)
- María Gallardo-Gómez
- 1Department of Biochemistry, Genetics and Immunology, Centro Singular de Investigación de Galicia (CINBIO), University of Vigo, Campus As Lagoas-Marcosende s/n, 36310 Vigo, Spain
| | - Sebastian Moran
- 2Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - María Páez de la Cadena
- 1Department of Biochemistry, Genetics and Immunology, Centro Singular de Investigación de Galicia (CINBIO), University of Vigo, Campus As Lagoas-Marcosende s/n, 36310 Vigo, Spain
| | - Vicenta Soledad Martínez-Zorzano
- 1Department of Biochemistry, Genetics and Immunology, Centro Singular de Investigación de Galicia (CINBIO), University of Vigo, Campus As Lagoas-Marcosende s/n, 36310 Vigo, Spain
| | - Francisco Javier Rodríguez-Berrocal
- 1Department of Biochemistry, Genetics and Immunology, Centro Singular de Investigación de Galicia (CINBIO), University of Vigo, Campus As Lagoas-Marcosende s/n, 36310 Vigo, Spain
| | - Mar Rodríguez-Girondo
- 3Department of Medical Statistics and Bioinformatics, Leiden University Medical Centre, Leiden, The Netherlands.,4SiDOR Research Group and Centro de Investigaciones Biomédicas (CINBIO), Faculty of Economics and Business Administration, University of Vigo, Vigo, Spain
| | - Manel Esteller
- 2Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Joaquín Cubiella
- 5Department of Gastroenterology, Complexo Hospitalario Universitario de Ourense, Instituto de Investigación Biomédica Galicia Sur, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Ourense, Spain
| | - Luis Bujanda
- 6Department of Gastroenterology, Instituto Biodonostia, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Universidad del País Vasco (UPV/EHU), San Sebastián, Spain
| | - Antoni Castells
- 7Gastroenterology Department, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain
| | - Francesc Balaguer
- 7Gastroenterology Department, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain
| | - Rodrigo Jover
- 8Department of Gastroenterology, Hospital General Universitario de Alicante, Alicante, Spain
| | - Loretta De Chiara
- 1Department of Biochemistry, Genetics and Immunology, Centro Singular de Investigación de Galicia (CINBIO), University of Vigo, Campus As Lagoas-Marcosende s/n, 36310 Vigo, Spain
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27
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Lin X, Teh AL, Chen L, Lim IY, Tan PF, MacIsaac JL, Morin AM, Yap F, Tan KH, Saw SM, Lee YS, Holbrook JD, Godfrey KM, Meaney MJ, Kobor MS, Chong YS, Gluckman PD, Karnani N. Choice of surrogate tissue influences neonatal EWAS findings. BMC Med 2017; 15:211. [PMID: 29202839 PMCID: PMC5715509 DOI: 10.1186/s12916-017-0970-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 10/31/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Epigenomes are tissue specific and thus the choice of surrogate tissue can play a critical role in interpreting neonatal epigenome-wide association studies (EWAS) and in their extrapolation to target tissue. To develop a better understanding of the link between tissue specificity and neonatal EWAS, and the contributions of genotype and prenatal factors, we compared genome-wide DNA methylation of cord tissue and cord blood, two of the most accessible surrogate tissues at birth. METHODS In 295 neonates, DNA methylation was profiled using Infinium HumanMethylation450 beadchip arrays. Sites of inter-individual variability in DNA methylation were mapped and compared across the two surrogate tissues at birth, i.e., cord tissue and cord blood. To ascertain the similarity to target tissues, DNA methylation profiles of surrogate tissues were compared to 25 primary tissues/cell types mapped under the Epigenome Roadmap project. Tissue-specific influences of genotype on the variable CpGs were also analyzed. Finally, to interrogate the impact of the in utero environment, EWAS on 45 prenatal factors were performed and compared across the surrogate tissues. RESULTS Neonatal EWAS results were tissue specific. In comparison to cord blood, cord tissue showed higher inter-individual variability in the epigenome, with a lower proportion of CpGs influenced by genotype. Both neonatal tissues were good surrogates for target tissues of mesodermal origin. They also showed distinct phenotypic associations, with effect sizes of the overlapping CpGs being in the same order of magnitude. CONCLUSIONS The inter-relationship between genetics, prenatal factors and epigenetics is tissue specific, and requires careful consideration in designing and interpreting future neonatal EWAS. TRIAL REGISTRATION This birth cohort is a prospective observational study, designed to study the developmental origins of health and disease, and was retrospectively registered on 1 July 2010 under the identifier NCT01174875 .
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Affiliation(s)
- Xinyi Lin
- Singapore Institute for Clinical Sciences, A*STAR, Singapore, 117609, Singapore.,Duke NUS Medical School, Singapore, 169857, Singapore
| | - Ai Ling Teh
- Singapore Institute for Clinical Sciences, A*STAR, Singapore, 117609, Singapore
| | - Li Chen
- Singapore Institute for Clinical Sciences, A*STAR, Singapore, 117609, Singapore
| | - Ives Yubin Lim
- Singapore Institute for Clinical Sciences, A*STAR, Singapore, 117609, Singapore
| | - Pei Fang Tan
- Singapore Institute for Clinical Sciences, A*STAR, Singapore, 117609, Singapore
| | - Julia L MacIsaac
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Alexander M Morin
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Fabian Yap
- KK Women's and Children's Hospital, Singapore, 229899, Singapore
| | - Kok Hian Tan
- KK Women's and Children's Hospital, Singapore, 229899, Singapore
| | - Seang Mei Saw
- Duke NUS Medical School, Singapore, 169857, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, 117597, Singapore.,Singapore Eye Research Institute, Singapore, 169856, Singapore
| | - Yung Seng Lee
- Singapore Institute for Clinical Sciences, A*STAR, Singapore, 117609, Singapore.,Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore.,Division of Paediatric Endocrinology and Diabetes, Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, 119228, Singapore
| | - Joanna D Holbrook
- Singapore Institute for Clinical Sciences, A*STAR, Singapore, 117609, Singapore.,NIHR Biomedical Research Centre, University of Southampton, Southampton, SO16 6YD, UK
| | - Keith M Godfrey
- MRC Lifecourse Epidemiology Unit and NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, SO16 6YD, UK
| | - Michael J Meaney
- Singapore Institute for Clinical Sciences, A*STAR, Singapore, 117609, Singapore.,Ludmer Centre for Neuroinformatics and Mental Health, Douglas University Mental Health Institute, McGill University, Montreal, Quebec, H4H 1R3, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Yap Seng Chong
- Singapore Institute for Clinical Sciences, A*STAR, Singapore, 117609, Singapore.,Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Peter D Gluckman
- Singapore Institute for Clinical Sciences, A*STAR, Singapore, 117609, Singapore.,Centre for Human Evolution, Adaptation and Disease, Liggins Institute, University of Auckland, Auckland, 1142, New Zealand
| | - Neerja Karnani
- Singapore Institute for Clinical Sciences, A*STAR, Singapore, 117609, Singapore. .,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore.
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28
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Eckstein M, Rea M, Fondufe-Mittendorf YN. Transient and permanent changes in DNA methylation patterns in inorganic arsenic-mediated epithelial-to-mesenchymal transition. Toxicol Appl Pharmacol 2017; 331:6-17. [PMID: 28336213 PMCID: PMC5747965 DOI: 10.1016/j.taap.2017.03.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 03/16/2017] [Indexed: 12/12/2022]
Abstract
Chronic low dose inorganic arsenic exposure causes cells to take on an epithelial-to-mesenchymal phenotype, which is a crucial process in carcinogenesis. Inorganic arsenic is not a mutagen and thus epigenetic alterations have been implicated in this process. Indeed, during the epithelial-to-mesenchymal transition, morphologic changes to cells correlate with changes in chromatin structure and gene expression, ultimately driving this process. However, studies on the effects of inorganic arsenic exposure/withdrawal on the epithelial-to-mesenchymal transition and the impact of epigenetic alterations in this process are limited. In this study we used high-resolution microarray analysis to measure the changes in DNA methylation in cells undergoing inorganic arsenic-induced epithelial-to-mesenchymal transition, and on the reversal of this process, after removal of the inorganic arsenic exposure. We found that cells exposed to chronic, low-dose inorganic arsenic exposure showed 30,530 sites were differentially methylated, and with inorganic arsenic withdrawal several differential methylated sites were reversed, albeit not completely. Furthermore, these changes in DNA methylation mainly correlated with changes in gene expression at most sites tested but not at all. This study suggests that DNA methylation changes on gene expression are not clear-cut and provide a platform to begin to uncover the relationship between DNA methylation and gene expression, specifically within the context of inorganic arsenic treatment.
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Affiliation(s)
- Meredith Eckstein
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Matthew Rea
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
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29
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Epigenome Aberrations: Emerging Driving Factors of the Clear Cell Renal Cell Carcinoma. Int J Mol Sci 2017; 18:ijms18081774. [PMID: 28812986 PMCID: PMC5578163 DOI: 10.3390/ijms18081774] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 07/29/2017] [Accepted: 08/12/2017] [Indexed: 12/13/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC), the most common form of Kidney cancer, is characterized by frequent mutations of the von Hippel-Lindau (VHL) tumor suppressor gene in ~85% of sporadic cases. Loss of pVHL function affects multiple cellular processes, among which the activation of hypoxia inducible factor (HIF) pathway is the best-known function. Constitutive activation of HIF signaling in turn activates hundreds of genes involved in numerous oncogenic pathways, which contribute to the development or progression of ccRCC. Although VHL mutations are considered as drivers of ccRCC, they are not sufficient to cause the disease. Recent genome-wide sequencing studies of ccRCC have revealed that mutations of genes coding for epigenome modifiers and chromatin remodelers, including PBRM1, SETD2 and BAP1, are the most common somatic genetic abnormalities after VHL mutations in these tumors. Moreover, recent research has shed light on the extent of abnormal epigenome alterations in ccRCC tumors, including aberrant DNA methylation patterns, abnormal histone modifications and deregulated expression of non-coding RNAs. In this review, we discuss the epigenetic modifiers that are commonly mutated in ccRCC, and our growing knowledge of the cellular processes that are impacted by them. Furthermore, we explore new avenues for developing therapeutic approaches based on our knowledge of epigenome aberrations of ccRCC.
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30
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Kim M, Costello J. DNA methylation: an epigenetic mark of cellular memory. Exp Mol Med 2017; 49:e322. [PMID: 28450738 PMCID: PMC6130213 DOI: 10.1038/emm.2017.10] [Citation(s) in RCA: 236] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 12/14/2016] [Indexed: 02/07/2023] Open
Abstract
DNA methylation is a stable epigenetic mark that can be inherited through multiple cell divisions. During development and cell differentiation, DNA methylation is dynamic, but some DNA methylation patterns may be retained as a form of epigenetic memory. DNA methylation profiles can be useful for the lineage classification and quality control of stem cells such as embryonic stem cells, induced pluripotent cells and mesenchymal stem cells. During cancer initiation and progression, genome-wide and gene-specific DNA methylation changes occur as a consequence of mutated or deregulated chromatin regulators. Early aberrant DNA methylation states occurring during transformation appear to be retained during tumor evolution. Similarly, DNA methylation differences among different regions of a tumor reflect the history of cancer cells and their response to the tumor microenvironment. Therefore, DNA methylation can be a useful molecular marker for cancer diagnosis and drug treatment.
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Affiliation(s)
- Mirang Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea.,Department of Functional Genomics, University of Science and Technology, Daejeon, Korea
| | - Joseph Costello
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
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31
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SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata. PLoS One 2017; 12:e0175310. [PMID: 28403240 PMCID: PMC5389787 DOI: 10.1371/journal.pone.0175310] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 03/23/2017] [Indexed: 12/16/2022] Open
Abstract
The Encyclopedia of DNA elements (ENCODE) project is an ongoing collaborative effort to create a comprehensive catalog of functional elements initiated shortly after the completion of the Human Genome Project. The current database exceeds 6500 experiments across more than 450 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the H. sapiens and M. musculus genomes. All ENCODE experimental data, metadata, and associated computational analyses are submitted to the ENCODE Data Coordination Center (DCC) for validation, tracking, storage, unified processing, and distribution to community resources and the scientific community. As the volume of data increases, the identification and organization of experimental details becomes increasingly intricate and demands careful curation. The ENCODE DCC has created a general purpose software system, known as SnoVault, that supports metadata and file submission, a database used for metadata storage, web pages for displaying the metadata and a robust API for querying the metadata. The software is fully open-source, code and installation instructions can be found at: http://github.com/ENCODE-DCC/snovault/ (for the generic database) and http://github.com/ENCODE-DCC/encoded/ to store genomic data in the manner of ENCODE. The core database engine, SnoVault (which is completely independent of ENCODE, genomic data, or bioinformatic data) has been released as a separate Python package.
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32
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Collings CK, Anderson JN. Links between DNA methylation and nucleosome occupancy in the human genome. Epigenetics Chromatin 2017; 10:18. [PMID: 28413449 PMCID: PMC5387343 DOI: 10.1186/s13072-017-0125-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/03/2017] [Indexed: 12/20/2022] Open
Abstract
Background DNA methylation is an epigenetic modification that is enriched in heterochromatin but depleted at active promoters and enhancers. However, the debate on whether or not DNA methylation is a reliable indicator of high nucleosome occupancy has not been settled. For example, the methylation levels of DNA flanking CTCF sites are higher in linker DNA than in nucleosomal DNA, while other studies have shown that the nucleosome core is the preferred site of methylation. In this study, we make progress toward understanding these conflicting phenomena by implementing a bioinformatics approach that combines MNase-seq and NOMe-seq data and by comprehensively profiling DNA methylation and nucleosome occupancy throughout the human genome. Results The results demonstrated that increasing methylated CpG density is correlated with nucleosome occupancy in the total genome and within nearly all subgenomic regions. Features with elevated methylated CpG density such as exons, SINE-Alu sequences, H3K36-trimethylated peaks, and methylated CpG islands are among the highest nucleosome occupied elements in the genome, while some of the lowest occupancies are displayed by unmethylated CpG islands and unmethylated transcription factor binding sites. Additionally, outside of CpG islands, the density of CpGs within nucleosomes was shown to be important for the nucleosomal location of DNA methylation with low CpG frequencies favoring linker methylation and high CpG frequencies favoring core particle methylation. Prominent exceptions to the correlations between methylated CpG density and nucleosome occupancy include CpG islands marked by H3K27me3 and CpG-poor heterochromatin marked by H3K9me3, and these modifications, along with DNA methylation, distinguish the major silencing mechanisms of the human epigenome. Conclusions Thus, the relationship between DNA methylation and nucleosome occupancy is influenced by the density of methylated CpG dinucleotides and by other epigenomic components in chromatin. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0125-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Clayton K Collings
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 E. Superior Street, Chicago, IL 60611 USA
| | - John N Anderson
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907 USA
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33
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Volkov P, Bacos K, Ofori JK, Esguerra JLS, Eliasson L, Rönn T, Ling C. Whole-Genome Bisulfite Sequencing of Human Pancreatic Islets Reveals Novel Differentially Methylated Regions in Type 2 Diabetes Pathogenesis. Diabetes 2017; 66:1074-1085. [PMID: 28052964 DOI: 10.2337/db16-0996] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 12/28/2016] [Indexed: 11/13/2022]
Abstract
Current knowledge about the role of epigenetics in type 2 diabetes (T2D) remains limited. Only a few studies have investigated DNA methylation of selected candidate genes or a very small fraction of genomic CpG sites in human pancreatic islets, the tissue of primary pathogenic importance for diabetes. Our aim was to characterize the whole-genome DNA methylation landscape in human pancreatic islets, to identify differentially methylated regions (DMRs) in diabetic islets, and to investigate the function of DMRs in islet biology. Here, we performed whole-genome bisulfite sequencing, which is a comprehensive and unbiased method to study DNA methylation throughout the genome at a single nucleotide resolution, in pancreatic islets from donors with T2D and control subjects without diabetes. We identified 25,820 DMRs in islets from individuals with T2D. These DMRs cover loci with known islet function, e.g., PDX1, TCF7L2, and ADCY5 Importantly, binding sites previously identified by ChIP-seq for islet-specific transcription factors, enhancer regions, and different histone marks were enriched in the T2D-associated DMRs. We also identified 457 genes, including NR4A3, PARK2, PID1, SLC2A2, and SOCS2, that had both DMRs and significant expression changes in T2D islets. To mimic the situation in T2D islets, candidate genes were overexpressed or silenced in cultured β-cells. This resulted in impaired insulin secretion, thereby connecting differential methylation to islet dysfunction. We further explored the islet methylome and found a strong link between methylation levels and histone marks. Additionally, DNA methylation in different genomic regions and of different transcript types (i.e., protein coding, noncoding, and pseudogenes) was associated with islet expression levels. Our study provides a comprehensive picture of the islet DNA methylome in individuals with and without diabetes and highlights the importance of epigenetic dysregulation in pancreatic islets and T2D pathogenesis.
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Affiliation(s)
- Petr Volkov
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Karl Bacos
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Jones K Ofori
- Islet Cell Exocytosis Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Jonathan Lou S Esguerra
- Islet Cell Exocytosis Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Lena Eliasson
- Islet Cell Exocytosis Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Tina Rönn
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
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34
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Wanner N, Bechtel-Walz W. Epigenetics of kidney disease. Cell Tissue Res 2017; 369:75-92. [PMID: 28286899 DOI: 10.1007/s00441-017-2588-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 02/15/2017] [Indexed: 02/06/2023]
Abstract
DNA methylation and histone modifications determine renal programming and the development and progression of renal disease. The identification of the way in which the renal cell epigenome is altered by environmental modifiers driving the onset and progression of renal diseases has extended our understanding of the pathophysiology of kidney disease progression. In this review, we focus on current knowledge concerning the implications of epigenetic modifications during renal disease from early development to chronic kidney disease progression including renal fibrosis, diabetic nephropathy and the translational potential of identifying new biomarkers and treatments for the prevention and therapy of chronic kidney disease and end-stage kidney disease.
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Affiliation(s)
- Nicola Wanner
- Department of Medicine IV, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,Center for Systems Biology (ZBSA), Albert-Ludwigs-University, Freiburg, Germany. .,Renal Division, University Hospital Freiburg, Breisacher Strasse 66, 79106, Freiburg, Germany.
| | - Wibke Bechtel-Walz
- Department of Medicine IV, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,Renal Division, University Hospital Freiburg, Breisacher Strasse 66, 79106, Freiburg, Germany.
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35
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Te Pas MFW, Madsen O, Calus MPL, Smits MA. The Importance of Endophenotypes to Evaluate the Relationship between Genotype and External Phenotype. Int J Mol Sci 2017; 18:E472. [PMID: 28241430 PMCID: PMC5344004 DOI: 10.3390/ijms18020472] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 02/02/2017] [Accepted: 02/13/2017] [Indexed: 02/06/2023] Open
Abstract
With the exception of a few Mendelian traits, almost all phenotypes (traits) in livestock science are quantitative or complex traits regulated by the expression of many genes. For most of the complex traits, differential expression of genes, rather than genomic variation in the gene coding sequences, is associated with the genotype of a trait. The expression profiles of the animal's transcriptome, proteome and metabolome represent endophenotypes that influence/regulate the externally-observed phenotype. These expression profiles are generated by interactions between the animal's genome and its environment that range from the cellular, up to the husbandry environment. Thus, understanding complex traits requires knowledge about not only genomic variation, but also environmental effects that affect genome expression. Gene products act together in physiological pathways and interaction networks (of pathways). Due to the lack of annotation of the functional genome and ontologies of genes, our knowledge about the various biological systems that contribute to the development of external phenotypes is sparse. Furthermore, interaction with the animals' microbiome, especially in the gut, greatly influences the external phenotype. We conclude that a detailed understanding of complex traits requires not only understanding of variation in the genome, but also its expression at all functional levels.
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Affiliation(s)
- Marinus F W Te Pas
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, 6700AH Wageningen, The Netherlands.
| | - Ole Madsen
- Animal Breeding and Genomics, Wageningen University, 6700AH Wageningen, The Netherlands.
| | - Mario P L Calus
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, 6700AH Wageningen, The Netherlands.
| | - Mari A Smits
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, 6700AH Wageningen, The Netherlands.
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Abstract
The majority of kidney cancers are associated with mutations in the von Hippel-Lindau gene and a small proportion are associated with infrequent mutations in other well characterized tumour-suppressor genes. In the past 15 years, efforts to uncover other key genes involved in renal cancer have identified many genes that are dysregulated or silenced via epigenetic mechanisms, mainly through methylation of promoter CpG islands or dysregulation of specific microRNAs. In addition, the advent of next-generation sequencing has led to the identification of several novel genes that are mutated in renal cancer, such as PBRM1, BAP1 and SETD2, which are all involved in histone modification and nucleosome and chromatin remodelling. In this Review, we discuss how altered DNA methylation, microRNA dysregulation and mutations in histone-modifying enzymes disrupt cellular pathways in renal cancers.
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Affiliation(s)
- Mark R Morris
- Brain Tumour Research Centre, Wolverhampton School of Sciences, University of Wolverhampton, Wulfruna Street, Wolverhampton WV1 1LY, UK
| | - Farida Latif
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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Abstract
The enabling technologies of synthetic biology are opening up new opportunities for engineering and enhancement of mammalian cells. This will stimulate diverse applications in many life science sectors such as regenerative medicine, development of biosensing cell lines, therapeutic protein production, and generation of new synthetic genetic regulatory circuits. Harnessing the full potential of these new engineering-based approaches requires the design and assembly of large DNA constructs-potentially up to chromosome scale-and the effective delivery of these large DNA payloads to the host cell. Random integration of large transgenes, encoding therapeutic proteins or genetic circuits into host chromosomes, has several drawbacks such as risks of insertional mutagenesis, lack of control over transgene copy-number and position-specific effects; these can compromise the intended functioning of genetic circuits. The development of a system orthogonal to the endogenous genome is therefore beneficial. Mammalian artificial chromosomes (MACs) are functional, add-on chromosomal elements, which behave as normal chromosomes-being replicating and portioned to daughter cells at each cell division. They are deployed as useful gene expression vectors as they remain independent from the host genome. MACs are maintained as a single-copy and can accommodate multiple gene expression cassettes of, in theory, unlimited DNA size (MACs up to 10 megabases have been constructed). MACs therefore enabled control over ectopic gene expression and represent an excellent platform to rapidly prototype and characterize novel synthetic gene circuits without recourse to engineering the host genome. This review describes the obstacles synthetic biologists face when working with mammalian systems and how the development of improved MACs can overcome these-particularly given the spectacular advances in DNA synthesis and assembly that are fuelling this research area.
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Affiliation(s)
- Andrea Martella
- School of Biological Sciences, The University of Edinburgh , The King's Buildings, Edinburgh EH9 3BF, U.K
| | - Steven M Pollard
- MRC Centre for Regenerative Medicine, The University of Edinburgh , Edinburgh bioQuarter, 5 Little France Drive, Edinburgh, EH16 4UU, U.K
| | - Junbiao Dai
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Yizhi Cai
- School of Biological Sciences, The University of Edinburgh , The King's Buildings, Edinburgh EH9 3BF, U.K
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Pidsley R, Zotenko E, Peters TJ, Lawrence MG, Risbridger GP, Molloy P, Van Djik S, Muhlhausler B, Stirzaker C, Clark SJ. Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling. Genome Biol 2016; 17:208. [PMID: 27717381 PMCID: PMC5055731 DOI: 10.1186/s13059-016-1066-1] [Citation(s) in RCA: 760] [Impact Index Per Article: 95.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 09/19/2016] [Indexed: 02/06/2023] Open
Abstract
Background In recent years the Illumina HumanMethylation450 (HM450) BeadChip has provided a user-friendly platform to profile DNA methylation in human samples. However, HM450 lacked coverage of distal regulatory elements. Illumina have now released the MethylationEPIC (EPIC) BeadChip, with new content specifically designed to target these regions. We have used HM450 and whole-genome bisulphite sequencing (WGBS) to perform a critical evaluation of the new EPIC array platform. Results EPIC covers over 850,000 CpG sites, including >90 % of the CpGs from the HM450 and an additional 413,743 CpGs. Even though the additional probes improve the coverage of regulatory elements, including 58 % of FANTOM5 enhancers, only 7 % distal and 27 % proximal ENCODE regulatory elements are represented. Detailed comparisons of regulatory elements from EPIC and WGBS show that a single EPIC probe is not always informative for those distal regulatory elements showing variable methylation across the region. However, overall data from the EPIC array at single loci are highly reproducible across technical and biological replicates and demonstrate high correlation with HM450 and WGBS data. We show that the HM450 and EPIC arrays distinguish differentially methylated probes, but the absolute agreement depends on the threshold set for each platform. Finally, we provide an annotated list of probes whose signal could be affected by cross-hybridisation or underlying genetic variation. Conclusion The EPIC array is a significant improvement over the HM450 array, with increased genome coverage of regulatory regions and high reproducibility and reliability, providing a valuable tool for high-throughput human methylome analyses from diverse clinical samples. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1066-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ruth Pidsley
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, 2010, NSW, Australia.,St Vincent's Clinical School, University of NSW, Sydney, 2010, NSW, Australia
| | - Elena Zotenko
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, 2010, NSW, Australia.,St Vincent's Clinical School, University of NSW, Sydney, 2010, NSW, Australia
| | - Timothy J Peters
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, 2010, NSW, Australia
| | - Mitchell G Lawrence
- Prostate Research Group, Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash Partners Comprehensive Cancer Consortium, Monash University, Clayton, Melbourne, VIC, 3800, Australia
| | - Gail P Risbridger
- Prostate Research Group, Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash Partners Comprehensive Cancer Consortium, Monash University, Clayton, Melbourne, VIC, 3800, Australia
| | - Peter Molloy
- CSIRO, Health and Biosecurity, PO Box 52, North Ryde, NSW, 1670, Australia
| | - Susan Van Djik
- CSIRO, Health and Biosecurity, PO Box 52, North Ryde, NSW, 1670, Australia
| | - Beverly Muhlhausler
- FOODplus Research Centre, Department of Food and Wine Science, School of Agriculture Food and Wine, Waite Campus, The University of Adelaide, Adelaide, SA, Australia.,Child Nutrition Research Centre, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Clare Stirzaker
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, 2010, NSW, Australia.,St Vincent's Clinical School, University of NSW, Sydney, 2010, NSW, Australia
| | - Susan J Clark
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, 2010, NSW, Australia. .,St Vincent's Clinical School, University of NSW, Sydney, 2010, NSW, Australia.
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Mazina MY, Nikolenko JV, Fursova NA, Nedil'ko PN, Krasnov AN, Vorobyeva NE. Early-late genes of the ecdysone cascade as models for transcriptional studies. Cell Cycle 2016; 14:3593-601. [PMID: 26506480 DOI: 10.1080/15384101.2015.1100772] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
The DHR3 and Hr4 early-late genes of the ecdysone cascade are described as models for transcriptional studies in Drosophila cells. In a set of experiments, it became clear that these genes are a convenient and versatile system for research into the physiological conditions upon 20-hydroxyecdysone induction. DHR3 and Hr4 gene transcription is characterized by fast activation kinetics, which enables transcriptional studies without the influence of indirect effects. A limited number of activated genes (only 73 genes are induced one hour after treatment) promote the selectivity of transcriptional studies via 20-hydroxyecdysone induction. DHR3 and Hr4 gene expression is dose dependent, is completely controlled by the hormone titer and decreases within hours of 20-hydroxyecdysone withdrawal. The DHR3 and Hr4 gene promoters become functional within 20 minutes after induction, which makes them useful tools for investigation if the early activation process. Their transcription is controlled by the RNA polymerase II pausing mechanism, which is widespread in the genome of Drosophila melanogaster but is still underinvestigated. Uniform expression activation of the DHR3 and Hr4 genes in a cell population was confirmed at both the RNA and protein levels. Homogeneity of the transcription response makes DHR3/Hr4 system valuable for investigation of the protein dynamics during transcription induction.
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Affiliation(s)
- Marina Yu Mazina
- a Department of Transcription Regulation and Chromatin Dynamic ; Institute of Gene Biology , Russian Academy of Sciences ; Moscow , Russia
| | - Julia V Nikolenko
- a Department of Transcription Regulation and Chromatin Dynamic ; Institute of Gene Biology , Russian Academy of Sciences ; Moscow , Russia
| | - Nadezda A Fursova
- a Department of Transcription Regulation and Chromatin Dynamic ; Institute of Gene Biology , Russian Academy of Sciences ; Moscow , Russia
| | - Petr N Nedil'ko
- a Department of Transcription Regulation and Chromatin Dynamic ; Institute of Gene Biology , Russian Academy of Sciences ; Moscow , Russia
| | - Aleksey N Krasnov
- a Department of Transcription Regulation and Chromatin Dynamic ; Institute of Gene Biology , Russian Academy of Sciences ; Moscow , Russia
| | - Nadezhda E Vorobyeva
- a Department of Transcription Regulation and Chromatin Dynamic ; Institute of Gene Biology , Russian Academy of Sciences ; Moscow , Russia
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41
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Characterization of new RNA polymerase III and RNA polymerase II transcriptional promoters in the Bovine Leukemia Virus genome. Sci Rep 2016; 6:31125. [PMID: 27545598 PMCID: PMC4992882 DOI: 10.1038/srep31125] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/11/2016] [Indexed: 12/23/2022] Open
Abstract
Bovine leukemia virus latency is a viral strategy used to escape from the host immune system and contribute to tumor development. However, a highly expressed BLV micro-RNA cluster has been reported, suggesting that the BLV silencing is not complete. Here, we demonstrate the in vivo recruitment of RNA polymerase III to the BLV miRNA cluster both in BLV-latently infected cell lines and in ovine BLV-infected primary cells, through a canonical type 2 RNAPIII promoter. Moreover, by RPC6-knockdown, we showed a direct functional link between RNAPIII transcription and BLV miRNAs expression. Furthermore, both the tumor- and the quiescent-related isoforms of RPC7 subunits were recruited to the miRNA cluster. We showed that the BLV miRNA cluster was enriched in positive epigenetic marks. Interestingly, we demonstrated the in vivo recruitment of RNAPII at the 3′LTR/host genomic junction, associated with positive epigenetic marks. Functionally, we showed that the BLV LTR exhibited a strong antisense promoter activity and identified cis-acting elements of an RNAPII-dependent promoter. Finally, we provided evidence for an in vivo collision between RNAPIII and RNAPII convergent transcriptions. Our results provide new insights into alternative ways used by BLV to counteract silencing of the viral 5′LTR promoter.
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42
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Razzouk S. Regulatory elements and genetic variations in periodontal diseases. Arch Oral Biol 2016; 72:106-115. [PMID: 27569042 DOI: 10.1016/j.archoralbio.2016.08.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 08/11/2016] [Accepted: 08/16/2016] [Indexed: 01/01/2023]
Abstract
OBJECTIVE Current evidence suggests that many GWAS and IL1 SNPs are associated with periodontal diseases but their functional role remains ambiguous. Therefore, it is imperative to elucidate the molecular pathways through which these SNPs might act on the development of the disease. The purpose of this review was to highlight the regulatory elements of noncoding regions of the genome and provide insights on the functional role of periodontitis-associated GWAS and IL1 SNPs. DESIGN A search was performed using ENCODE data available on different browsers. RESULTS GWAS and IL1 SNPs overlap DNase I hypersensitivity sites, histone modifications and transcription binding sites. Some of these noncoding variants influenced the transcription activity of inflammatory genes. CONCLUSION SNPs associated with periodontal diseases may contribute to the development of the disorder through their functional roles. Unraveling the character of genetic components might explain the diversity of clinical phenotypes among population groups as well as disease susceptibility.
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Affiliation(s)
- Sleiman Razzouk
- Adjunct faculty, Department of Periodontology and Implant Dentistry, New York University College of Dentistry, New York, United States; Private Practice, Beirut, Lebanon.
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43
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Teruel M, Alarcón-Riquelme ME. The genetic basis of systemic lupus erythematosus: What are the risk factors and what have we learned. J Autoimmun 2016; 74:161-175. [PMID: 27522116 DOI: 10.1016/j.jaut.2016.08.001] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 08/02/2016] [Indexed: 12/19/2022]
Abstract
The genome-wide association study is a free-hypothesis approach based on screening of thousands or even millions of genetic variants distributed throughout the whole human genome in relation to a phenotype. The relevant role of the genome-wide association studies in the last decade is undisputed because it has permitted to elucidate multiple risk genetic factors associated with the susceptibility to several human complex diseases. Regarding systemic lupus erythematosus (SLE) this approach has allowed to identify more than 60 risk loci for SLE susceptibility across populations to date, increasing our understanding on the pathogenesis of this disease. We present the latest findings in the genetic of SLE across populations using genome-wide approaches. These studies revealed that most of the genetic risk is shared across borders and ethnicities. Finally, we focus on describing the most important risk loci for SLE attempting to cover the genetic findings in relation to functional polymorphisms, such as missense single nucleotide polymorphisms (SNPs) or regulatory variants involved in the development of the disease. The functional studies try to identify the causality of some GWAS-associated variants, many of which fall in non-coding regions of the genome, suggesting a regulatory role. Many loci show an environmental interaction, another aspect revealed by the studies of epigenetic modifications and those associated with genetic variants. Finally, new-generation sequencing technologies can open other paths in the research on SLE genetics, the role of rare variants and the detailed identification of causal regulatory variation. The clinical relevance of the genetic factors will be shown when we are able to use them or in combination with other molecular measurements to re-classify a heterogeneous disease such as SLE.
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Affiliation(s)
- Maria Teruel
- Center for Genomics and Oncological Research, GENYO, Pfizer/University of Granada/Andalusian Government, PTS, Granada, 18016, Spain.
| | - Marta E Alarcón-Riquelme
- Center for Genomics and Oncological Research, GENYO, Pfizer/University of Granada/Andalusian Government, PTS, Granada, 18016, Spain; Institute of Environmental Medicine, Karolinska Institute, Stockholm, 171 67, Sweden.
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Verma M. Genome-wide association studies and epigenome-wide association studies go together in cancer control. Future Oncol 2016; 12:1645-64. [PMID: 27079684 PMCID: PMC5551540 DOI: 10.2217/fon-2015-0035] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/22/2016] [Indexed: 02/07/2023] Open
Abstract
Completion of the human genome a decade ago laid the foundation for: using genetic information in assessing risk to identify individuals and populations that are likely to develop cancer, and designing treatments based on a person's genetic profiling (precision medicine). Genome-wide association studies (GWAS) completed during the past few years have identified risk-associated single nucleotide polymorphisms that can be used as screening tools in epidemiologic studies of a variety of tumor types. This led to the conduct of epigenome-wide association studies (EWAS). This article discusses the current status, challenges and research opportunities in GWAS and EWAS. Information gained from GWAS and EWAS has potential applications in cancer control and treatment.
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Affiliation(s)
- Mukesh Verma
- Methods & Technologies Branch, Epidemiology & Genomics Research Program, Division of Cancer Control & Population Sciences, National Cancer Institute (NCI), NIH, 9609 Medical Center Drive, Suite 4E102, Rockville, MD 20850, USA
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45
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Banijamali M, Rabbani-Chadegani A, Shahhoseini M. Lithium attenuates lead induced toxicity on mouse non-adherent bone marrow cells. J Trace Elem Med Biol 2016; 36:7-15. [PMID: 27259346 DOI: 10.1016/j.jtemb.2016.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 03/08/2016] [Accepted: 03/17/2016] [Indexed: 01/05/2023]
Abstract
Lead is a poisonous heavy metal that occurs in all parts of environment and causes serious health problems in humans. The aim of the present study was to investigate the possible protective effect of lithium against lead nitrate induced toxicity in non-adherent bone marrow stem cells. Trypan blue and MTT assays represented that exposure of the cells to different concentrations of lead nitrate decreased viability in a dose dependent manner, whereas, pretreatment of the cells with lithium protected the cells against lead toxicity. Lead reduced the number and differentiation status of bone marrow-derived precursors when cultured in the presence of colony stimulating factor (CSF), while the effect was attenuated by lithium. The cells treated with lead nitrate exhibited cell shrinkage, DNA fragmentation, anion superoxide production, but lithium prevented lead action. Moreover, apoptotic indexes such as PARP cleavage and release of HMGB1 induced by lead, were protected by lithium, suggesting anti-apoptotic effect of lithium. Immunoblot analysis of histone H3K9 acetylation indicated that lithium overcame lead effect on acetylation. In conclusion, lithium efficiently reduces lead toxicity suggesting new insight into lithium action which may contribute to increased cell survival. It also provides a potentially new therapeutic strategy for lithium and a cost-effective approach to minimize destructive effects of lead on bone marrow stem cells.
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Affiliation(s)
- Mahsan Banijamali
- Department of Biochemistry, Institute Of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Azra Rabbani-Chadegani
- Department of Biochemistry, Institute Of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
| | - Maryam Shahhoseini
- Department of Genetics, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
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46
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Dechamethakun S, Muramatsu M. Long noncoding RNA variations in cardiometabolic diseases. J Hum Genet 2016; 62:97-104. [PMID: 27305986 DOI: 10.1038/jhg.2016.70] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 04/27/2016] [Accepted: 05/06/2016] [Indexed: 12/18/2022]
Abstract
Cardiometabolic diseases are characterized as a combination of multiple risk factors for cardiovascular disease (CVD) and metabolic diseases including diabetes mellitus, dyslipidemia, hypertension and abdominal obesity. This cluster of abnormalities individually and interdependently leads to atherosclerosis and CVD morbidity and mortality. In the past decade, genome-wide association studies (GWASs) have identified a series of cardiometabolic disease-associated variants that can collectively explain a small proportion of the variability. Intriguingly, the susceptibility variants imputed from GWASs usually do not reside in the coding regions, suggesting a crucial role of the noncoding elements of the genome. In recent years, emerging evidence suggests that noncoding RNA (ncRNA) is functional for physiology and pathophysiology of human diseases. These include microRNAs and long noncoding RNAs (lncRNAs) that are now implicated in human diseases. The ncRNAs can interact with each other and with proteins, to interfere gene expressions, leading to the development of many human disorders. Although evidence suggests the functional role of lncRNAs in cardiometabolic traits, the molecular mechanisms of gene regulation underlying cardiometabolic diseases remain to be better defined. Here, we summarize the recent discoveries of lncRNA variations in the context of cardiometabolic diseases.
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Affiliation(s)
- Sariya Dechamethakun
- Department of Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masaaki Muramatsu
- Department of Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
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47
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Leenen FAD, Vernocchi S, Hunewald OE, Schmitz S, Molitor AM, Muller CP, Turner JD. Where does transcription start? 5'-RACE adapted to next-generation sequencing. Nucleic Acids Res 2016; 44:2628-45. [PMID: 26615195 PMCID: PMC4824077 DOI: 10.1093/nar/gkv1328] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 11/11/2015] [Accepted: 11/13/2015] [Indexed: 01/27/2023] Open
Abstract
The variability and complexity of the transcription initiation process was examined by adapting RNA ligase-mediated rapid amplification of 5' cDNA ends (5'-RACE) to Next-Generation Sequencing (NGS). We oligo-labelled 5'-m(7)G-capped mRNA from two genes, the simple mono-exonic Beta-2-Adrenoceptor (ADRB2R)and the complex multi-exonic Glucocorticoid Receptor (GR, NR3C1), and detected a variability in TSS location that has received little attention up to now. Transcription was not initiated at a fixed TSS, but from loci of 4 to 10 adjacent nucleotides. Individual TSSs had frequencies from <0.001% to 38.5% of the total gene-specific 5' m(7)G-capped transcripts. ADRB2R used a single locus consisting of 4 adjacent TSSs. Unstimulated, the GR used a total of 358 TSSs distributed throughout 38 loci, that were principally in the 5' UTRs and were spliced using established donor and acceptor sites. Complete demethylation of the epigenetically sensitive GR promoter with 5-azacytidine induced one new locus and 127 TSSs, 12 of which were unique. We induced GR transcription with dexamethasone and Interferon-γ, adding one new locus and 185 additional TSSs distributed throughout the promoter region. In-vitro the TSS microvariability regulated mRNA translation efficiency and the relative abundance of the different GRN-terminal protein isoform levels.
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Affiliation(s)
- Fleur A D Leenen
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-Sur-Alzette L-4354, Grand-Duchy of Luxembourg Department of Immunology, Research Institute of Psychobiology, University of Trier, Trier D-54290, Germany
| | - Sara Vernocchi
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-Sur-Alzette L-4354, Grand-Duchy of Luxembourg Department of Immunology, Research Institute of Psychobiology, University of Trier, Trier D-54290, Germany
| | - Oliver E Hunewald
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-Sur-Alzette L-4354, Grand-Duchy of Luxembourg
| | - Stephanie Schmitz
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-Sur-Alzette L-4354, Grand-Duchy of Luxembourg
| | - Anne M Molitor
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-Sur-Alzette L-4354, Grand-Duchy of Luxembourg
| | - Claude P Muller
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-Sur-Alzette L-4354, Grand-Duchy of Luxembourg Department of Immunology, Research Institute of Psychobiology, University of Trier, Trier D-54290, Germany
| | - Jonathan D Turner
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-Sur-Alzette L-4354, Grand-Duchy of Luxembourg
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48
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Das M, Sha J, Hidalgo B, Aslibekyan S, Do AN, Zhi D, Sun D, Zhang T, Li S, Chen W, Srinivasan SR, Tiwari HK, Absher D, Ordovas JM, Berenson GS, Arnett DK, Irvin MR. Association of DNA Methylation at CPT1A Locus with Metabolic Syndrome in the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) Study. PLoS One 2016; 11:e0145789. [PMID: 26808626 PMCID: PMC4726462 DOI: 10.1371/journal.pone.0145789] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 12/08/2015] [Indexed: 12/22/2022] Open
Abstract
In this study, we conducted an epigenome-wide association study of metabolic syndrome (MetS) among 846 participants of European descent in the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN). DNA was isolated from CD4+ T cells and methylation at ~470,000 cytosine-phosphate-guanine dinucleotide (CpG) pairs was assayed using the Illumina Infinium HumanMethylation450 BeadChip. We modeled the percentage methylation at individual CpGs as a function of MetS using linear mixed models. A Bonferroni-corrected P-value of 1.1 x 10−7 was considered significant. Methylation at two CpG sites in CPT1A on chromosome 11 was significantly associated with MetS (P for cg00574958 = 2.6x10-14 and P for cg17058475 = 1.2x10-9). Significant associations were replicated in both European and African ancestry participants of the Bogalusa Heart Study. Our findings suggest that methylation in CPT1A is a promising epigenetic marker for MetS risk which could become useful as a treatment target in the future.
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Affiliation(s)
- Mithun Das
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Jin Sha
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Bertha Hidalgo
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Stella Aslibekyan
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Anh N. Do
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Degui Zhi
- Department of Biostatistics, Section on Statistical Genetics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Dianjianyi Sun
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States of America
| | - Tao Zhang
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States of America
| | - Shengxu Li
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States of America
| | - Wei Chen
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States of America
| | - Sathanur R. Srinivasan
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States of America
| | - Hemant K. Tiwari
- Department of Biostatistics, Section on Statistical Genetics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Devin Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Jose M. Ordovas
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, United States of America
- IMDEA Food, Madrid, Spain
| | - Gerald S. Berenson
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States of America
| | - Donna K. Arnett
- Dean’s Office, College of Public Health, University of Kentucky, Lexington, KY, United States of America
| | - Marguerite R. Irvin
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, United States of America
- * E-mail:
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He F, Li Y, Tang YH, Ma J, Zhu H. Identifying micro-inversions using high-throughput sequencing reads. BMC Genomics 2016; 17 Suppl 1:4. [PMID: 26818118 PMCID: PMC4895285 DOI: 10.1186/s12864-015-2305-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The identification of inversions of DNA segments shorter than read length (e.g., 100 bp), defined as micro-inversions (MIs), remains challenging for next-generation sequencing reads. It is acknowledged that MIs are important genomic variation and may play roles in causing genetic disease. However, current alignment methods are generally insensitive to detect MIs. Here we develop a novel tool, MID (Micro-Inversion Detector), to identify MIs in human genomes using next-generation sequencing reads. RESULTS The algorithm of MID is designed based on a dynamic programming path-finding approach. What makes MID different from other variant detection tools is that MID can handle small MIs and multiple breakpoints within an unmapped read. Moreover, MID improves reliability in low coverage data by integrating multiple samples. Our evaluation demonstrated that MID outperforms Gustaf, which can currently detect inversions from 30 bp to 500 bp. CONCLUSIONS To our knowledge, MID is the first method that can efficiently and reliably identify MIs from unmapped short next-generation sequencing reads. MID is reliable on low coverage data, which is suitable for large-scale projects such as the 1000 Genomes Project (1KGP). MID identified previously unknown MIs from the 1KGP that overlap with genes and regulatory elements in the human genome. We also identified MIs in cancer cell lines from Cancer Cell Line Encyclopedia (CCLE). Therefore our tool is expected to be useful to improve the study of MIs as a type of genetic variant in the human genome. The source code can be downloaded from: http://cqb.pku.edu.cn/ZhuLab/MID .
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Affiliation(s)
- Feifei He
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, and Center for Quantitative Biology, Peking University, Beijing, 100871, China.
| | - Yang Li
- Department of Bioengineering, University of Illinois, Urbana, IL, 61801, USA.
| | - Yu-Hang Tang
- Division of Applied Mathematics, Brown University, Providence, RI, 02912, USA.
| | - Jian Ma
- Department of Bioengineering, University of Illinois, Urbana, IL, 61801, USA. .,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA.
| | - Huaiqiu Zhu
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, and Center for Quantitative Biology, Peking University, Beijing, 100871, China.
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Moran S, Arribas C, Esteller M. Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences. Epigenomics 2015; 8:389-99. [PMID: 26673039 PMCID: PMC4864062 DOI: 10.2217/epi.15.114] [Citation(s) in RCA: 446] [Impact Index Per Article: 49.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Aim: DNA methylation is the best known epigenetic mark. Cancer and other pathologies show an altered DNA methylome. However, delivering complete DNA methylation maps is compromised by the price and labor-intensive interpretation of single nucleotide methods. Material & methods: Following the success of the HumanMethylation450 BeadChip (Infinium) methylation microarray (450K), we report the technical and biological validation of the newly developed MethylationEPIC BeadChip (Infinium) microarray that covers over 850,000 CpG methylation sites (850K). The 850K microarray contains >90% of the 450K sites, but adds 333,265 CpGs located in enhancer regions identified by the ENCODE and FANTOM5 projects. Results & conclusion: The 850K array demonstrates high reproducibility at the 450K CpG sites, is consistent among technical replicates, is reliable in the matched study of fresh frozen versus formalin-fixed paraffin-embeded samples and is also useful for 5-hydroxymethylcytosine. These results highlight the value of the MethylationEPIC BeadChip as a useful tool for the analysis of the DNA methylation profile of the human genome.
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Affiliation(s)
- Sebastian Moran
- Cancer Epigenetics & Biology Program (PEBC), 08908 L'Hospitalet, Barcelona, Catalonia, Spain
| | - Carles Arribas
- Cancer Epigenetics & Biology Program (PEBC), 08908 L'Hospitalet, Barcelona, Catalonia, Spain
| | - Manel Esteller
- Cancer Epigenetics & Biology Program (PEBC), 08908 L'Hospitalet, Barcelona, Catalonia, Spain.,Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
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