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Milner JJ, Zadinsky JK, Shiao SPK. Nursing Informatics and Epigenetics: Methodological Considerations for Big Data Analysis. Comput Inform Nurs 2023; 41:369-376. [PMID: 36728378 PMCID: PMC10241417 DOI: 10.1097/cin.0000000000000992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Nursing informatics requires an understanding of patient-centered data and clinical workflow, and epigenetic research requires an understanding of data analysis. The purpose of this article is to document the methodology that nursing informatics specialists can use to conduct epigenetic research and subsequently strengthen patient-centered care. A pilot study of a secondary methylation data analysis using The Cancer Genome Atlas data from individuals with colon cancer is utilized to illustrate the methodology. The steps for conducting the study using public and free resources are discussed. These steps include finding a data source; downloading and analyzing differentially methylated regions; annotating differentially methylated region, gene ontology and function analysis; and reporting results. A model of epigenetic testing workflow is provided, as is a list of publicly available data and analysis sources that can be used to conduct epigenetic research.
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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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Satterlee JS, Chadwick LH, Tyson FL, McAllister K, Beaver J, Birnbaum L, Volkow ND, Wilder EL, Anderson JM, Roy AL. The NIH Common Fund/Roadmap Epigenomics Program: Successes of a comprehensive consortium. SCIENCE ADVANCES 2019; 5:eaaw6507. [PMID: 31501771 PMCID: PMC6719411 DOI: 10.1126/sciadv.aaw6507] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 06/07/2019] [Indexed: 05/12/2023]
Abstract
The NIH Roadmap Epigenomics Program was launched to deliver reference epigenomic data from human tissues and cells, develop tools and methods for analyzing the epigenome, discover novel epigenetic marks, develop methods to manipulate the epigenome, and determine epigenetic contributions to diverse human diseases. Here, we comment on the outcomes from this program: the scientific contributions made possible by a consortium approach and the challenges, benefits, and lessons learned from this group science effort.
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Affiliation(s)
- John S. Satterlee
- Division of Neuroscience and Behavior, National Institutes of Health (NIH), 6001 Executive Blvd., Bethesda, MD 20892, USA
- National Institute on Drug Abuse, NIH, 6001 Executive Blvd., Bethesda, MD 20892, USA
| | - Lisa H. Chadwick
- National Institute on Drug Abuse, NIH, 6001 Executive Blvd., Bethesda, MD 20892, USA
| | - Frederick L. Tyson
- National Institute of Environmental Health Sciences, NIH, 111 TW Alexander Dr., Durham, NC 27709, USA
| | - Kim McAllister
- National Institute of Environmental Health Sciences, NIH, 111 TW Alexander Dr., Durham, NC 27709, USA
| | - Jill Beaver
- Office of Strategic Coordination, Office of the Director, NIH, 6001 Executive Blvd., Bethesda, MD 20892, USA
- Division of Program Coordination, Planning, and Strategic Initiatives, Office of the Director, NIH, 1 Center Dr., Bethesda, MD 20892, USA
| | - Linda Birnbaum
- National Institute of Environmental Health Sciences, NIH, 111 TW Alexander Dr., Durham, NC 27709, USA
| | - Nora D. Volkow
- National Institute on Drug Abuse, NIH, 6001 Executive Blvd., Bethesda, MD 20892, USA
| | - Elizabeth L. Wilder
- Office of Strategic Coordination, Office of the Director, NIH, 6001 Executive Blvd., Bethesda, MD 20892, USA
- Division of Program Coordination, Planning, and Strategic Initiatives, Office of the Director, NIH, 1 Center Dr., Bethesda, MD 20892, USA
| | - James M. Anderson
- Division of Program Coordination, Planning, and Strategic Initiatives, Office of the Director, NIH, 1 Center Dr., Bethesda, MD 20892, USA
| | - Ananda L. Roy
- Office of Strategic Coordination, Office of the Director, NIH, 6001 Executive Blvd., Bethesda, MD 20892, USA
- Division of Program Coordination, Planning, and Strategic Initiatives, Office of the Director, NIH, 1 Center Dr., Bethesda, MD 20892, USA
- Corresponding author.
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Abstract
Self-sustained and synchronized to environmental stimuli, circadian clocks are under genetic and epigenetic regulation. Recent findings have greatly increased our understanding of epigenetic plasticity governed by circadian clock. Thus, the link between circadian clock and epigenetic machinery is reciprocal. Circadian clock can affect epigenetic features including genomic DNA methylation, noncoding RNA, mainly miRNA expression, and histone modifications resulted in their 24-h rhythms. Concomitantly, these epigenetic events can directly modulate cyclic system of transcription and translation of core circadian genes and indirectly clock output genes. Significant findings interlocking circadian clock, epigenetics, and cancer have been revealed, particularly in breast, colorectal, and blood cancers. Aberrant methylation of circadian gene promoter regions and miRNA expression affected circadian gene expression, together with 24-h expression oscillation pace have been frequently observed.
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Klein HU, Bennett DA, De Jager PL. The epigenome in Alzheimer's disease: current state and approaches for a new path to gene discovery and understanding disease mechanism. Acta Neuropathol 2016; 132:503-14. [PMID: 27573688 DOI: 10.1007/s00401-016-1612-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/14/2016] [Accepted: 08/24/2016] [Indexed: 02/07/2023]
Abstract
The advent of new technologies and analytic approaches is beginning to provide an unprecedented look at features of the human genome that affect RNA expression. These "epigenomic" features are found in a number of different forms: they include DNA methylation, covalent modifications of histone proteins and non-coding RNAs. Some of these features have now been implicated in Alzheimer's disease (AD). Here, we focus on recent studies that have identified robust observations relating to DNA methylation and chromatin in human brain tissue; these findings will ground the next generation of studies and provide a model for the design of such studies. Stemming from observations that compounds with histone deacetylase activity may be beneficial in AD, epigenome-wide studies in cortical samples from large numbers of human subjects have now shown that AD-associated epigenomic changes are reproducible, are not driven by genetic risk factors, and are widespread at specific locations in the genome. A fundamental question of whether such changes are causal remains to be demonstrated, but it is already clear that well-powered investigations of the human epigenome in the target organ of a neurodegenerative disease are feasible, are implicating new areas of the genome in the disease, and will be an important tool for future studies. We are now at an inflection point: as genome-wide association studies of genetic variants come to an end, a new generation of studies exploring the epigenome will provide an important new layer of information with which to enrich our understanding of AD pathogenesis and to possibly guide development of new therapeutic targets.
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Affiliation(s)
- Hans-Ulrich Klein
- Program in Translational Neuropsychiatric Genomics and Partners Multiple Sclerosis Center, Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, 77 Avenue Louis Pasteur, NRB 168, Boston, MA, 02115, USA
- Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Philip L De Jager
- Program in Translational Neuropsychiatric Genomics and Partners Multiple Sclerosis Center, Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, 77 Avenue Louis Pasteur, NRB 168, Boston, MA, 02115, USA.
- Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA.
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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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