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Sahoo K, Sundararajan V. Methods in DNA methylation array dataset analysis: A review. Comput Struct Biotechnol J 2024; 23:2304-2325. [PMID: 38845821 PMCID: PMC11153885 DOI: 10.1016/j.csbj.2024.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/25/2024] [Accepted: 05/08/2024] [Indexed: 06/09/2024] Open
Abstract
Understanding the intricate relationships between gene expression levels and epigenetic modifications in a genome is crucial to comprehending the pathogenic mechanisms of many diseases. With the advancement of DNA Methylome Profiling techniques, the emphasis on identifying Differentially Methylated Regions (DMRs/DMGs) has become crucial for biomarker discovery, offering new insights into the etiology of illnesses. This review surveys the current state of computational tools/algorithms for the analysis of microarray-based DNA methylation profiling datasets, focusing on key concepts underlying the diagnostic/prognostic CpG site extraction. It addresses methodological frameworks, algorithms, and pipelines employed by various authors, serving as a roadmap to address challenges and understand changing trends in the methodologies for analyzing array-based DNA methylation profiling datasets derived from diseased genomes. Additionally, it highlights the importance of integrating gene expression and methylation datasets for accurate biomarker identification, explores prognostic prediction models, and discusses molecular subtyping for disease classification. The review also emphasizes the contributions of machine learning, neural networks, and data mining to enhance diagnostic workflow development, thereby improving accuracy, precision, and robustness.
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Affiliation(s)
| | - Vino Sundararajan
- Correspondence to: Department of Bio Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632 014, Tamil Nadu, India.
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2
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Chun Y, Lee JH, Bunyavanich S. Epigenomic and epigenetic investigations of food allergy. Pediatr Allergy Immunol 2024; 35:e14065. [PMID: 38284919 PMCID: PMC10825314 DOI: 10.1111/pai.14065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 01/30/2024]
Abstract
As a potential link between genetic predisposition, environmental exposures, and food allergy outcomes, epigenetics has been a molecular variable of interest in ongoing efforts to understand food allergy mechanisms and outcomes. Here we review population-based investigations of epigenetic loci associated with food allergy, focusing on established clinical food allergy. We first provide an overview of epigenetic mechanisms that have been studied in cohorts with food allergy, predominantly DNA methylation but also microRNA. We then discuss investigations that have implemented epigenome-wide approaches aimed at genome-wide profiling and discovery. Such epigenome-wide studies have collectively identified differentially methylated and differentially regulated loci associated with T cell development, antigen presentation, reaction severity, and causal mediation in food allergy. We then discuss candidate-gene investigations that have honed in on Th1, Th2, T regulatory, and innate genes of a priori interest in food allergy. These studies have highlighted methylation changes in specific candidate genes as associated with T regulatory cell activity as well as differential methylation of Type 1 and Type 2 cytokine genes associated with various food allergies. Intriguingly, epigenetic loci associated with food allergy have also been explored as potential biomarkers for the clinical management of food allergy. We conclude by highlighting several priority directions for advancing population-based epigenomic and epigenetic understandings of food allergy.
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Affiliation(s)
- Yoojin Chun
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jo Hsuan Lee
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Supinda Bunyavanich
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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3
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Vigeland MD, Flåm ST, Vigeland MD, Espeland A, Zucknick M, Wigemyr M, Bråten LCH, Gjefsen E, Zwart JA, Storheim K, Pedersen LM, Selmer K, Lie BA, Gervin K, The Aim Study Group. Long-Term Use of Amoxicillin Is Associated with Changes in Gene Expression and DNA Methylation in Patients with Low Back Pain and Modic Changes. Antibiotics (Basel) 2023; 12:1217. [PMID: 37508313 PMCID: PMC10376514 DOI: 10.3390/antibiotics12071217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/09/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023] Open
Abstract
Long-term antibiotics are prescribed for a variety of medical conditions, recently including low back pain with Modic changes. The molecular impact of such treatment is unknown. We conducted longitudinal transcriptome and epigenome analyses in patients (n = 100) receiving amoxicillin treatment or placebo for 100 days in the Antibiotics in Modic Changes (AIM) study. Gene expression and DNA methylation were investigated at a genome-wide level at screening, after 100 days of treatment, and at one-year follow-up. We identified intra-individual longitudinal changes in gene expression and DNA methylation in patients receiving amoxicillin, while few changes were observed in patients receiving placebo. After 100 days of amoxicillin treatment, 28 genes were significantly differentially expressed, including the downregulation of 19 immunoglobulin genes. At one-year follow-up, the expression levels were still not completely restored. The significant changes in DNA methylation (n = 4548 CpGs) were mainly increased methylation levels between 100 days and one-year follow-up. Hence, the effects on gene expression occurred predominantly during treatment, while the effects on DNA methylation occurred after treatment. In conclusion, unrecognized side effects of long-term amoxicillin treatment were revealed, as alterations were observed in both gene expression and DNA methylation that lasted long after the end of treatment.
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Affiliation(s)
- Maria Dehli Vigeland
- Department of Research, Innovation and Education, Division of Clinical Neuroscience, Oslo University Hospital, 0450 Oslo, Norway
- Faculty of Medicine, University of Oslo, 0313 Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, 0450 Oslo, Norway
| | - Siri Tennebø Flåm
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, 0450 Oslo, Norway
| | - Magnus Dehli Vigeland
- Faculty of Medicine, University of Oslo, 0313 Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, 0450 Oslo, Norway
| | - Ansgar Espeland
- Department of Radiology, Haukeland University Hospital, 5021 Bergen, Norway
- Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway
| | - Manuela Zucknick
- Oslo Centre for Biostatistics and Epidemiology, University of Oslo, 0313 Oslo, Norway
| | - Monica Wigemyr
- Department of Research, Innovation and Education, Division of Clinical Neuroscience, Oslo University Hospital, 0450 Oslo, Norway
| | - Lars Christian Haugli Bråten
- Department of Research, Innovation and Education, Division of Clinical Neuroscience, Oslo University Hospital, 0450 Oslo, Norway
| | - Elisabeth Gjefsen
- Department of Research, Innovation and Education, Division of Clinical Neuroscience, Oslo University Hospital, 0450 Oslo, Norway
- Faculty of Medicine, University of Oslo, 0313 Oslo, Norway
| | - John-Anker Zwart
- Department of Research, Innovation and Education, Division of Clinical Neuroscience, Oslo University Hospital, 0450 Oslo, Norway
- Faculty of Medicine, University of Oslo, 0313 Oslo, Norway
| | - Kjersti Storheim
- Department of Research, Innovation and Education, Division of Clinical Neuroscience, Oslo University Hospital, 0450 Oslo, Norway
- Department of Physiotherapy, Oslo Metropolitan University, 0167 Oslo, Norway
| | - Linda Margareth Pedersen
- Department of Research, Innovation and Education, Division of Clinical Neuroscience, Oslo University Hospital, 0450 Oslo, Norway
- Department of Physiotherapy, Oslo Metropolitan University, 0167 Oslo, Norway
| | - Kaja Selmer
- Department of Research, Innovation and Education, Division of Clinical Neuroscience, Oslo University Hospital, 0450 Oslo, Norway
- Faculty of Medicine, University of Oslo, 0313 Oslo, Norway
- National Center for Epilepsy, Oslo University Hospital, 1337 Sandvika, Norway
| | - Benedicte Alexandra Lie
- Faculty of Medicine, University of Oslo, 0313 Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, 0450 Oslo, Norway
| | - Kristina Gervin
- Department of Research, Innovation and Education, Division of Clinical Neuroscience, Oslo University Hospital, 0450 Oslo, Norway
- Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, School of Pharmacy, University of Oslo, 0313 Oslo, Norway
| | - The Aim Study Group
- Department of Research, Innovation and Education, Division of Clinical Neuroscience, Oslo University Hospital, 0450 Oslo, Norway
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4
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Nannini DR, Zheng Y, Joyce BT, Kim K, Gao T, Wang J, Jacobs DR, Schreiner PJ, Yaffe K, Greenland P, Lloyd-Jones DM, Hou L. Genome-wide DNA methylation association study of recent and cumulative marijuana use in middle aged adults. Mol Psychiatry 2023; 28:2572-2582. [PMID: 37258616 PMCID: PMC10611566 DOI: 10.1038/s41380-023-02106-y] [Citation(s) in RCA: 4] [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] [Received: 11/03/2022] [Revised: 04/24/2023] [Accepted: 05/03/2023] [Indexed: 06/02/2023]
Abstract
Marijuana is a widely used psychoactive substance in the US and medical and recreational legalization has risen over the past decade. Despite the growing number of individuals using marijuana, studies investigating the association between epigenetic factors and recent and cumulative marijuana use remain limited. We therefore investigated the association between recent and cumulative marijuana use and DNA methylation levels. Participants from the Coronary Artery Risk Development in Young Adults Study with whole blood collected at examination years (Y) 15 and Y20 were randomly selected to undergo DNA methylation profiling at both timepoints using the Illumina MethylationEPIC BeadChip. Recent use of marijuana was queried at each examination and used to estimate cumulative marijuana use from Y0 to Y15 and Y20. At Y15 (n = 1023), we observed 22 and 31 methylation markers associated (FDR P ≤ 0.05) with recent and cumulative marijuana use and 132 and 16 methylation markers at Y20 (n = 883), respectively. We replicated 8 previously reported methylation markers associated with marijuana use. We further identified 640 cis-meQTLs and 198 DMRs associated with recent and cumulative use at Y15 and Y20. Differentially methylated genes were statistically overrepresented in pathways relating to cellular proliferation, hormone signaling, and infections as well as schizophrenia, bipolar disorder, and substance-related disorders. We identified numerous methylation markers, pathways, and diseases associated with recent and cumulative marijuana use in middle-aged adults, providing additional insight into the association between marijuana use and the epigenome. These results provide novel insights into the role marijuana has on the epigenome and related health conditions.
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Affiliation(s)
- Drew R Nannini
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
| | - Yinan Zheng
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Brian T Joyce
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Kyeezu Kim
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Tao Gao
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jun Wang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - David R Jacobs
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Pamela J Schreiner
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Kristine Yaffe
- University of California at San Francisco School of Medicine, San Francisco, CA, USA
| | - Philip Greenland
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Donald M Lloyd-Jones
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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5
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Chiapperino L, Paneni F. Why epigenetics is (not) a biosocial science and why that matters. Clin Epigenetics 2022; 14:144. [PMID: 36369214 PMCID: PMC9652908 DOI: 10.1186/s13148-022-01366-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 10/26/2022] [Indexed: 11/13/2022] Open
Abstract
Epigenetic modifications offer compelling evidence of the environmental etiology of complex diseases. Social and biographical conditions, as well as material exposures, all modulate our biology with consequences for risk predispositions and health conditions. Elucidating these complex biosocial loops is one of the main challenges animating epigenetics. Yet, research on the development of epigenetic biomarkers often pulls in a direction that departs from a view of biological determinants of health embedded in their social and material environment. Taking the example of the epigenetics of cardiovascular diseases, this paper illustrates how common understandings of epigenetic biomarkers strongly lean toward considering them as mere targets for molecular intervention, rather than as correlates of a complex biological and social patterning of disease. This reductionism about biosocial dynamics of disease, we argue, hampers the pursuit of the goals epigenetics has given itself (in cardiology and beyond). If epigenetic mechanisms point to the deep socio-environmental embeddedness of our health, we conclude, future designs and methods of this research may require an improved methodological consideration of a biosocial perspective.
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Affiliation(s)
- Luca Chiapperino
- grid.9851.50000 0001 2165 4204STS Lab, Institute of Social Sciences, Faculty of Social and Political Sciences, University of Lausanne, 1015 Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Quartier UNIL-Mouline, Institute of Social Sciences, Bâtiment Géopolis, Bureau 5556, 1015 Lausanne, Switzerland
| | - Francesco Paneni
- grid.412004.30000 0004 0478 9977University Heart Center, Department of Cardiology, University Hospital Zurich, Zurich, Switzerland ,grid.412004.30000 0004 0478 9977Center for Translational and Experimental Cardiology (CTEC), Department of Cardiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
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6
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Sprague AC, Niu L, Jandarov R, Zhang X, Zhang G, Chen A, Šarac J, Čoklo M, Missoni S, Rudan P, Langevin SM, Deka R. Stable methylation loci are associated with systolic blood pressure in a Croatian island population. Epigenomics 2022; 14:1343-1354. [PMID: 36453021 PMCID: PMC9816922 DOI: 10.2217/epi-2022-0279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/03/2022] [Indexed: 12/03/2022] Open
Abstract
Background: The objective was to identify stable and dynamic DNA methylation loci associated with cardiometabolic traits among an adult population from the Croatian island of Hvar. Materials & methods: An epigenome-wide association study was conducted using peripheral blood longitudinally collected at two time points 10 years apart via Infinium MethylationEPIC beadarray (n = 112). Stable and dynamic loci were identified using linear mixed models. Associations between cardiometabolic traits and loci were assessed using linear models. Results: 22 CpG loci were significantly associated with systolic blood pressure. Twenty were stable and two were dynamic. Conclusion: Multiple genes may be involved in the determination of systolic blood pressure level via stable epigenetic programming, potentially established earlier in life.
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Affiliation(s)
- Alexander C Sprague
- Division of Epidemiology, Department of Environmental & Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Liang Niu
- Division of Biostatistics & Bioinformatics, Department of Environmental & Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Roman Jandarov
- Division of Biostatistics & Bioinformatics, Department of Environmental & Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Xiang Zhang
- Division of Environmental Genetics & Molecular Toxicology, Department of Environmental & Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Ge Zhang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Aimin Chen
- Department of Biostatistics, Epidemiology & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jelena Šarac
- Institute for Anthropological Research, Zagreb, Croatia
| | - Miran Čoklo
- Institute for Anthropological Research, Zagreb, Croatia
| | - Sasa Missoni
- Institute for Anthropological Research, Zagreb, Croatia
| | - Pavao Rudan
- Anthropological Center & Scientific Council for Anthropological Research, Croatian Academy of Arts & Sciences, Zagreb, Croatia
| | - Scott M Langevin
- Division of Epidemiology, Department of Environmental & Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- University of Cincinnati Cancer Center, Cincinnati, OH 45267, USA
| | - Ranjan Deka
- Division of Epidemiology, Department of Environmental & Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
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7
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Li H, Xue YW, Quan Y, Zhang HY. Reducing Virus Infection Risk in Space Environments through Nutrient Supplementation. Genes (Basel) 2022; 13:genes13091536. [PMID: 36140704 PMCID: PMC9498414 DOI: 10.3390/genes13091536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/23/2022] [Accepted: 08/23/2022] [Indexed: 11/24/2022] Open
Abstract
Space exploration has brought many challenges to human physiology. In order to evaluate and reduce possible pathological reactions triggered by space environments, we conducted bioinformatics analyses on the methylation data of the Mars 520 mission and human transcriptome data in the experiment simulating gravity changes. The results suggest that gene expression levels and DNA methylation levels were changed under the conditions of isolation and gravity changes, and multiple viral infection-related pathways were found in the enrichment analysis results of changed genes including Epstein Barr virus (EBV) infection, Hepatitis B virus (HBV) infection, Herpes simplex virus (HSV) infection and Kaposi’s sarcoma-associated herpesvirus (KHSV) infection. In this study, we found that Epigallocatechin-3-gallate (EGCG) and vitamin D are helpful in reducing viral infection risk. In addition, the causal associations between nutrients and viral infections were calculated using Two sample Mendelian Randomization (2SMR) method, the results indicated that vitamin D can reduce EBV infection and HBV infection risk. In summary, our study suggests that space environments increase the risk of human viral infection, which may be reduced by supplementing EGCG and vitamin D. These results can be used to formulate medical plans for astronauts, which have practical application value for future space exploration.
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Affiliation(s)
| | | | - Yuan Quan
- Correspondence: ; Tel.: +86-18062425336
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8
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Komaki S, Ohmomo H, Hachiya T, Sutoh Y, Ono K, Furukawa R, Umekage S, Otsuka-Yamasaki Y, Minabe S, Takashima A, Tanno K, Sasaki M, Shimizu A. Evaluation of short-term epigenetic age fluctuation. Clin Epigenetics 2022; 14:76. [PMID: 35681206 PMCID: PMC9185970 DOI: 10.1186/s13148-022-01293-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/15/2022] [Indexed: 11/10/2022] Open
Abstract
Considerable effort has been spent on lowering and maintaining the epigenetic age. However, the extent to which epigenetic age fluctuates under normal conditions is poorly understood. Therefore, we analyzed methylation data from monocytes and peripheral blood mononuclear cells collected from two Japanese men. The ranges of the Pan-tissue, Skin and blood, and DNAm PhenoAge epigenetic age during 3 months were ≥ 5.62, ≥ 3.04, and ≥ 8.23 years, and the maximum daily changes were 5.21, 3.20, and 6.53 years, respectively. These fluctuations were not suppressed by correcting for cell-type composition. Although the underlying biological mechanism remains unclear, there was a nonnegligible degree of age fluctuation which should inform personalized clinical applications.
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Affiliation(s)
- Shohei Komaki
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Hideki Ohmomo
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Iwate, 028-3694, Japan.,Division of Biomedical Information Analysis, Institute for Biomedical Sciences, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan
| | - Tsuyoshi Hachiya
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Yoichi Sutoh
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Kanako Ono
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Ryohei Furukawa
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Iwate, 028-3694, Japan.,Department of Biology, Research and Education Center for Natural Sciences, Keio University, 4-1-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8521, Japan
| | - So Umekage
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Yayoi Otsuka-Yamasaki
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Shiori Minabe
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Akira Takashima
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Kozo Tanno
- Division of Clinical Research and Epidemiology, Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan.,Department of Hygiene and Preventive Medicine, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan
| | - Makoto Sasaki
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan.,Division of Ultrahigh Field MRI, Institute for Biomedical Sciences, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan
| | - Atsushi Shimizu
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1, Idaidori, Yahaba, Iwate, 028-3694, Japan. .,Division of Biomedical Information Analysis, Institute for Biomedical Sciences, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan.
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Ehrlich M. Risks and rewards of big-data in epigenomics research: an interview with Melanie Ehrlich. Epigenomics 2022; 14:351-358. [PMID: 35255735 DOI: 10.2217/epi-2022-0056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Melanie Ehrlich, PhD, is a professor in the Tulane Cancer Center, the Tulane Center for Medical Bioinformatics and Genomics and the Hayward Human Genetics Program at Tulane Medical School, New Orleans, LA. She obtained her PhD in molecular biology in 1971 from the State University of New York at Stony Brook and completed postdoctoral research at Albert Einstein College of Medicine in 1972. She has been working on various aspects of epigenetics, starting with DNA methylation, since 1973. Her group made many first findings about DNA methylation (see below). For example, in 1982 and 1983, in collaboration with Charles Gehrke at the University of Missouri, she was the first to report tissue-specific and cancer-specific differences in overall DNA methylation in humans. In 1985, Xian-Yang Zhang and Richard Wang in her lab discovered a class of human DNA sequences specifically hypomethylated in sperm. In 1998, her group was the first to describe extensive losses of DNA methylation in pericentromeric and centromeric DNA repeats in human cancer. Her lab's many publications on the prevalence of both DNA hypermethylation and hypomethylation in the same cancers brought needed balance to our understanding of the epigenetics of cancer and to its clinical implications [1]. Besides working on cancer epigenetics, her research group has helped elucidate cytogenetic and gene expression abnormalities in the immunodeficiency, centromeric and facial anomalies (ICF) syndrome, a rare recessive disease often caused by mutations in DNMT3B. Her group also studied the epigenetics and transcriptomics of facioscapulohumeral muscular dystrophy (FSHD), whose disease locus is a tandem 3.3-kb repeat at subtelomeric 4q (that happens to be hypomethylated in ICF DNA [2]). Her study of FSHD has taken her in the direction of muscle (skeletal muscle, heart and aorta) epigenetics [3-6]. Recently, she has led research that applies epigenetics much more rigorously than usual to the evaluation of genetic variants from genome-wide association studies (GWAS) of osteoporosis and obesity. In continued collaboration with Sriharsa Pradhan at New England Biolabs and Michelle Lacey at Tulane University, she has compared 5-hydroxymethylcytosine and 5-methylcytosine clustering in various human tissues [7] and is studying myoblast methylomes that they generated by a new high-resolution enzymatic technique (enzymatic methyl-seq).
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Affiliation(s)
- Melanie Ehrlich
- Tulane Cancer Center, Center for Medical Bioinformatics & Genomics, & Hayward Genetics Center, Tulane University, New Orleans, LA 70112, USA
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