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Journal articles on the topic 'Epigenomics and epigenetics'
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1
Song, Pengtao, and Biaoru Li. "New Generation of Clinical Epigenetics Analysis and Diagnosis for Precision Medicine." Diagnostics 15, no. 12 (2025): 1539. https://doi.org/10.3390/diagnostics15121539.
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Following the application of epigenetic and epigenomics research into tumor diseases, cardiovascular disease, diabetes, hereditary diseases, and rare diseases, in vitro diagnostics (IVD) epigenetic and epigenomics are increasingly employed for those patients. Here, we review a clinical sampling of epigenetics and epigenomics from patients. We then present procedures, including the detection procedure of clinical epigenetic approaches from clinical samples, clinical epigenomic methods applied to those samples, the small cell number of epigenetics, and epigenomics. Finally, we present the current IVD of epigenetics and epigenomics used for clinical analysis and diagnosis, along with the development of approaches. To improve clinical study and diagnosis, we also introduce clinical research and clinical applications to develop a more comprehensive strategy to maximize the sensitivity and specificity of the epigenetics and epigenomics analysis and diagnosis.
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Bunnik, Eline M., Marjolein Timmers, and Ineke LLE Bolt. "Ethical Issues in Research and Development of Epigenome-wide Technologies." Epigenetics Insights 13 (January 2020): 251686572091325. http://dx.doi.org/10.1177/2516865720913253.
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To date, few scholarly discussions on ethical implications of epigenetics and epigenomics technologies have focused on the current phase of research and development, in which researchers are confronted with real and practical ethical dilemmas. In this article, a responsible research and innovation approach, using interviews and an expert meeting, is applied to a case of epigenomic test development for cervical cancer screening. This article provides an overview of ethical issues presently facing epigenomics researchers and test developers, and discusses 3 sets of issues in depth: (1) informed consent; (2) communication with donors and/or research participants, and (3) privacy and publication of data and research results. Although these issues are familiar to research ethics, some aspects are new and most require reinterpretation in the context of epigenomics technologies. With this article, we aim to start a discussion of the practical ethical issues rising in research and development of epigenomic technologies and to offer guidance for researchers working in the field of epigenetic and epigenomic technology.
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Leite, Michel Lopes, and Fabricio F. Costa. "Epigenomics, epigenetics, and cancer*." Revista Pan-Amazônica de Saúde 8, no. 4 (2017): 23–25. http://dx.doi.org/10.5123/s2176-62232017000400006.
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Jirtle, Randy L. "The science of hope: an interview with Randy Jirtle." Epigenomics 14, no. 6 (2022): 299–302. http://dx.doi.org/10.2217/epi-2022-0048.
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In this interview, Professor Randy L Jirtle speaks with Storm Johnson, Commissioning Editor for Epigenomics, on his work on genomic imprinting, environmental epigenomics and the fetal origins of disease susceptibility. Professor Randy Jirtle joined the Duke University Department of Radiology in 1977 and headed the Epigenetics and Imprinting Laboratory until 2012. He is now Professor of Epigenetics in the Department of Biological Sciences at North Carolina State University, Raleigh, NC, USA. Jirtle's research interests are in epigenetics, genomic imprinting and the fetal origins of disease susceptibility. He is known for his groundbreaking studies linking environmental exposures early in life to the development of adult diseases through changes in the epigenome and for determining the evolutionary origin of genomic imprinting in mammals. He has published over 200 peer-reviewed articles as well as the books Liver Regeneration and Carcinogenesis: Molecular and Cellular Mechanisms, Environmental Epigenomics in Health and Disease: Epigenetics and Disease Origins and Environmental Epigenomics in Health and Disease: Epigenetics and Complex Diseases. He was honored in 2006 with the Distinguished Achievement Award from the College of Engineering at the University of Wisconsin-Madison. In 2007, he was a featured scientist on the NOVA television program on epigenetics titled ‘Ghost in Your Genes’ and was nominated for Time Magazine's ‘Person of the Year’. He was the inaugural recipient of the Epigenetic Medicine Award in 2008 and received the STARS Lecture Award in Nutrition and Cancer from the National Cancer Institute in 2009. Jirtle was presented the Linus Pauling Award from the Institute of Functional Medicine in 2014. In 2017, ShortCutsTV produced the English documentary ‘Are You What Your Mother Ate? The Agouti Mouse Study’ based on his pioneering epigenetic research. He received the 2018 Northern Communities Health Foundation Visiting Professorship Award at the University of Adelaide, Australia. The Personalized Lifestyle Medicine Institute presented Jirtle with the Research and Innovation Leadership Award in 2019. Dr Jirtle was also given the Alexander Hollaender Award in 2019 at the 50th annual meeting of the Environmental Mutagenesis and Genomics Society.
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Majumder, Sanjoy, Rutupurna Das, Annapurna Sahoo, Kunja Bihari Satapathy, and Gagan Kumar Panigrahi. "Epigenetics, Epigenomics, and Personalized Medicine." Gene Expression 000, no. 000 (2024): 000. http://dx.doi.org/10.14218/ge.2024.00058.
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Peedicayil, J. "Beyond Genomics: Epigenetics and Epigenomics." Clinical Pharmacology & Therapeutics 84, no. 1 (2008): 25–26. http://dx.doi.org/10.1038/clpt.2008.26.
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Kim, Kyoung-Tae, Young-Seok Lee, and Inbo Han. "The Role of Epigenomics in Osteoporosis and Osteoporotic Vertebral Fracture." International Journal of Molecular Sciences 21, no. 24 (2020): 9455. http://dx.doi.org/10.3390/ijms21249455.
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Osteoporosis is a complex multifactorial condition of the musculoskeletal system. Osteoporosis and osteoporotic vertebral fracture (OVF) are associated with high medical costs and can lead to poor quality of life. Genetic factors are important in determining bone mass and structure, as well as any predisposition for bone degradation and OVF. However, genetic factors are not enough to explain osteoporosis development and OVF occurrence. Epigenetics describes a mechanism for controlling gene expression and cellular processes without altering DNA sequences. The main mechanisms in epigenetics are DNA methylation, histone modifications, and non-coding RNAs (ncRNAs). Recently, alterations in epigenetic mechanisms and their activity have been associated with osteoporosis and OVF. Here, we review emerging evidence that epigenetics contributes to the machinery that can alter DNA structure, gene expression, and cellular differentiation during physiological and pathological bone remodeling. A progressive understanding of normal bone metabolism and the role of epigenetic mechanisms in multifactorial osteopathy can help us better understand the etiology of the disease and convert this information into clinical practice. A deep understanding of these mechanisms will help in properly coordinating future individual treatments of osteoporosis and OVF.
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Mladenov, Velimir, Vasileios Fotopoulos, Eirini Kaiserli, et al. "Deciphering the Epigenetic Alphabet Involved in Transgenerational Stress Memory in Crops." International Journal of Molecular Sciences 22, no. 13 (2021): 7118. http://dx.doi.org/10.3390/ijms22137118.
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Although epigenetic modifications have been intensely investigated over the last decade due to their role in crop adaptation to rapid climate change, it is unclear which epigenetic changes are heritable and therefore transmitted to their progeny. The identification of epigenetic marks that are transmitted to the next generations is of primary importance for their use in breeding and for the development of new cultivars with a broad-spectrum of tolerance/resistance to abiotic and biotic stresses. In this review, we discuss general aspects of plant responses to environmental stresses and provide an overview of recent findings on the role of transgenerational epigenetic modifications in crops. In addition, we take the opportunity to describe the aims of EPI-CATCH, an international COST action consortium composed by researchers from 28 countries. The aim of this COST action launched in 2020 is: (1) to define standardized pipelines and methods used in the study of epigenetic mechanisms in plants, (2) update, share, and exchange findings in epigenetic responses to environmental stresses in plants, (3) develop new concepts and frontiers in plant epigenetics and epigenomics, (4) enhance dissemination, communication, and transfer of knowledge in plant epigenetics and epigenomics.
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Dar, Fayaz Ahmad, Naveed Ul Mushtaq, Seerat Saleem, Reiaz Ul Rehman, Tanvir Ul Hassan Dar, and Khalid Rehman Hakeem. "Role of Epigenetics in Modulating Phenotypic Plasticity against Abiotic Stresses in Plants." International Journal of Genomics 2022 (June 14, 2022): 1–13. http://dx.doi.org/10.1155/2022/1092894.
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Plants being sessile are always exposed to various environmental stresses, and to overcome these stresses, modifications at the epigenetic level can prove vital for their long-term survival. Epigenomics refers to the large-scale study of epigenetic marks on the genome, which include covalent modifications of histone tails (acetylation, methylation, phosphorylation, ubiquitination, and the small RNA machinery). Studies based on epigenetics have evolved over the years especially in understanding the mechanisms at transcriptional and posttranscriptional levels in plants against various environmental stimuli. Epigenomic changes in plants through induced methylation of specific genes that lead to changes in their expression can help to overcome various stress conditions. Recent studies suggested that epigenomics has a significant potential for crop improvement in plants. By the induction and modulation of various cellular processes like DNA methylation, histone modification, and biogenesis of noncoding RNAs, the plant genome can be activated which can help in achieving a quicker response against various plant stresses. Epigenetic modifications in plants allow them to adjust under varied environmental stresses by modulating their phenotypic plasticity and at the same time ensure the quality and yield of crops. The plasticity of the epigenome helps to adapt the plants during pre- and postdevelopmental processes. The variation in DNA methylation in different organisms exhibits variable phenotypic responses. The epigenetic changes also occur sequentially in the genome. Various studies indicated that environmentally stimulated epimutations produce variable responses especially in differentially methylated regions (DMR) that play a major role in the management of stress conditions in plants. Besides, it has been observed that environmental stresses cause specific changes in the epigenome that are closely associated with phenotypic modifications. However, the relationship between epigenetic modifications and phenotypic plasticity is still debatable. In this review, we will be discussing the role of various factors that allow epigenetic changes to modulate phenotypic plasticity against various abiotic stress in plants.
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Chen, Xiangsong, and Dao-Xiu Zhou. "Rice epigenomics and epigenetics: challenges and opportunities." Current Opinion in Plant Biology 16, no. 2 (2013): 164–69. http://dx.doi.org/10.1016/j.pbi.2013.03.004.
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Xanthopoulos, Charalampos, and Efterpi Kostareli. "Advances in Epigenetics and Epigenomics in Chronic Lymphocytic Leukemia." Current Genetic Medicine Reports 7, no. 4 (2019): 214–26. http://dx.doi.org/10.1007/s40142-019-00178-3.
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Abstract Purpose of Review The development and progression of chronic lymphocytic leukemia (CLL), a highly heterogenous B cell malignancy, are influenced by both genetic and environmental factors. Environmental factors, including pharmacological interventions, can affect the epigenetic landscape of CLL and thereby determine the CLL phenotype, clonal evolution, and clinical outcome. In this review, we critically present the latest advances in the field of CLL epigenomics/epigenetics in order to provide a systematic overview of to-date achievements and highlight the potential of epigenomics approaches in light of novel treatment therapies. Recent Findings Recent technological advances have enabled broad and precise mapping of the CLL epigenome. The identification of CLL-specific DNA methylation patterns has allowed for accurate CLL subtype definition, a better understanding of clonal origin and evolution, and the discovery of reliable biomarkers. More recently, studies have started to unravel the prognostic, predictive, and therapeutic potential of mapping chromatin dynamics and histone modifications in CLL. Finally, analysis of non-coding RNA expression has indicated their contribution to disease pathogenesis and helped to define prognostic subsets in CLL. Summary Overall, the potential of CLL epigenomics for predicting treatment response and resistance is mounting, especially with the advent of novel targeted CLL therapies.
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Płonka, Beata. "Nature or Nurture – Will Epigenomics Solve the Dilemma?" Studia Humana 5, no. 2 (2016): 13–36. http://dx.doi.org/10.1515/sh-2016-0007.
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AbstractThe concept of “nature and nurture” is used to distinguish between genetic and environmental influences on the formation of individual, mainly behavioral, traits. Different approaches that interpret nature and nurture as completely opposite or complementary aspects of human development have been discussed for decades. The paper addresses the most important points of nature vs nurture debate from the perspective of biological research, especially in the light of the recent findings in the field of epigenetics. The most important biological concepts, such as the trait, phenotype and genotype, as well as the evolution of other crucial notions are presented. Various attempts to find the main source of human variation are discussed - mainly the search for structural variants and the genome-wide association studies (GWAS). A new approach resulting from the discovery of “missing heritability”, as well as the current knowledge about the possible influence of epigenetic mechanisms on human traits are analyzed. Finally, the impact of epigenetic revolution on the society (public attitude, health policy, human rights etc.) is discussed.
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Hussey, Bethan, Martin R. Lindley, and Sarabjit Mastana. "Epigenetics and epigenomics: the future of nutritional interventions?" Future Science OA 3, no. 4 (2017): FSO237. http://dx.doi.org/10.4155/fsoa-2017-0088.
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Rosen, Evan D., Klaus H. Kaestner, Rama Natarajan, et al. "Epigenetics and Epigenomics: Implications for Diabetes and Obesity." Diabetes 67, no. 10 (2018): 1923–31. http://dx.doi.org/10.2337/db18-0537.
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Qureshi, Irfan A., and Mark F. Mehler. "Advances in Epigenetics and Epigenomics for Neurodegenerative Diseases." Current Neurology and Neuroscience Reports 11, no. 5 (2011): 464–73. http://dx.doi.org/10.1007/s11910-011-0210-2.
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Mathers, John C. "Session 2: Personalised nutrition Epigenomics: a basis for understanding individual differences?" Proceedings of the Nutrition Society 67, no. 4 (2008): 390–94. http://dx.doi.org/10.1017/s0029665108008744.
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Epigenetics encompasses changes to marks on the genome that are copied from one cell generation to the next, which may alter gene expression but which do not involve changes in the primary DNA sequence. These marks include DNA methylation (methylation of cytosines within CpG dinucleotides) and post-translational modifications (acetylation, methylation, phosphorylation and ubiquitination) of the histone tails protruding from nucleosome cores. The sum of genome-wide epigenetic patterns is known as the epigenome. It is hypothesised that altered epigenetic marking is a means through which evidence of environmental exposures (including nutritional status and dietary exposure) is received and recorded by the genome. At least some of these epigenetic marks are remembered through multiple cell generations and their effects may be revealed in altered gene expression and cell function. Altered epigenetic marking allows plasticity of phenotype in a fixed genotype. Despite their identical genotypes, monozygotic twins show increasing epigenetic diversity with age and with divergent lifestyles. Differences in epigenetic markings may explain some inter-individual variation in disease risk and in response to nutritional interventions.
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Laird, Peter W. "How epigenomics broke the mold: an interview with Peter W Laird." Epigenomics 14, no. 6 (2022): 303–8. http://dx.doi.org/10.2217/epi-2022-0066.
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In this interview, Professor Peter W Laird speaks with Storm Johnson, Commissioning Editor for Epigenomics, on his work to date in the field of cancer epigenetics. Dr Peter W Laird is a Professor at Van Andel Institute (VAI) in Grand Rapids, Michigan. He earned his B.S. and M.S., Cum Laude, from the University of Leiden, The Netherlands. He trained for his PhD with Dr Piet Borst, The Netherlands Cancer Institute, and as a postdoc with Dr Anton Berns, The Netherlands Cancer Institute, and with Dr Rudolf Jaenisch, at the Whitehead Institute for Biomedical Research in Cambridge, MA, USA. He joined the faculty at the University of Southern California in 1996, where he served as the Founding Director of the USC Epigenome Center and also as the Leader of the Epigenetics and Regulation Program of the Norris Comprehensive Cancer Center. In 2014, he relocated to VAI to join Dr Peter Jones in building an internationally acclaimed research center focused on Epigenetics. Dr Laird published the first demonstration of the causal role for DNA methylation in oncogenesis ( Cell, 1995) [ 1 ]. He served as the Principal Investigator for all DNA methylation data production for the Cancer Genome Atlas (TCGA) and led many TCGA analysis efforts. He has been awarded 10 patents related to DNA methylation technology by the United States Patent and Trademark Office, one of which is the basis for the first US FDA-approved blood-based DNA methylation assay for cancer (Epi proColon). His research findings include the report of a close link between DNA methylation and BRAF mutation in colorectal cancer ( Nature Genetics, 2006) [ 2 ], the discovery that embryonic stem cell polycomb repressor targets are predisposed to abnormal DNA methylation in cancer ( Nature Genetics, 2007) [ 3 ], the identification of a novel epigenetic subtype of glioma (G-CIMP), tightly associated with IDH1 mutation ( Cancer Cell, 2010) [ 4 ], and the connection between nuclear architecture, late replication, and domains of epigenetic instability ( Nature Genetics, 2011) [ 5 ], later showing a link with mitotic cell division, thus providing a mechanistic explanation for the loss of DNA methylation in aging and cancer first described four decades ago ( Nature Genetics, 2018) [ 6 ].
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Baccarelli, Andrea A., and José Ordovás. "Epigenetics of Early Cardiometabolic Disease: Mechanisms and Precision Medicine." Circulation Research 132, no. 12 (2023): 1648–62. http://dx.doi.org/10.1161/circresaha.123.322135.
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Epigenetics has transformed our understanding of the molecular basis of complex diseases, including cardiovascular and metabolic disorders. This review offers a comprehensive overview of the current state of knowledge on epigenetic processes implicated in cardiovascular and metabolic diseases, highlighting the potential of DNA methylation as a precision medicine biomarker and examining the impact of social determinants of health, gut bacterial epigenomics, noncoding RNA, and epitranscriptomics on disease development and progression. We discuss challenges and barriers to advancing cardiometabolic epigenetics research, along with the opportunities for novel preventive strategies, targeted therapies, and personalized medicine approaches that may arise from a better understanding of epigenetic processes. Emerging technologies, such as single-cell sequencing and epigenetic editing, hold the potential to further enhance our ability to dissect the complex interplay between genetic, environmental, and lifestyle factors. To translate research findings into clinical practice, interdisciplinary collaborations, technical and ethical considerations, and accessibility of resources and knowledge are crucial. Ultimately, the field of epigenetics has the potential to revolutionize the way we approach cardiovascular and metabolic diseases, paving the way for precision medicine and personalized health care, and improving the lives of millions of individuals worldwide affected by these conditions.
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Szyf, Moshe. "The epigenetics of early life adversity and trauma inheritance: an interview with Moshe Szyf." Epigenomics 14, no. 6 (2022): 309–14. http://dx.doi.org/10.2217/epi-2021-0483.
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In this interview, Professor Moshe Szyf speaks with Storm Johnson, Commissioning Editor for Epigenomics, on his work to date in the field of social epigenetics. Szyf received his PhD from the Hebrew University and did his postdoctoral fellowship in genetics at Harvard Medical School, joined the Department of Pharmacology and Therapeutics at McGill University in Montreal in 1989 and is a fellow of the Royal Society of Canada and the Academy of Health Sciences of Canada. He is the founding codirector of the Sackler Institute for Epigenetics and Psychobiology at McGill and is a Fellow of the Canadian Institute for Advanced Research Experience-Based Brain and Biological Development program. Szyf was the founder of the first pharma to develop epigenetic pharmacology, Methylgene Inc., and the journal Epigenetics. The Szyf lab proposed two decades ago that DNA methylation is a prime therapeutic target in cancer and other diseases and postulated and provided the first set of evidence that the social environment early in life can alter DNA methylation, launching the emerging field of social epigenetics.
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Kumar, Parvinder, Amrit Sudershan, Shikha Bharti, Javaid Hassan Sheikh, Showkat Ahmad Wani, and Hardeep Kumar. "Epigenetics in migraine: A review." IP Indian Journal of Neurosciences 9, no. 3 (2023): 122–31. http://dx.doi.org/10.18231/j.ijn.2023.026.
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Genetic diseases are not only caused by direct mutations in "genes," but also consequences of heritable change other than mutation referred to as epigenetics and the science called epigenomics. In the present study, we aimed to review epigenetics, where we covered a quick overview of epigenetics, diseases that are caused by epigenetic modification, epigenetic as risk factors linked with migraine a cause leads to the neurodegenerative condition, and most accepted mechanisms of epigenetics. A structured research article and review of the literature was searched in the electronic databases of Google Scholar, PubMed, Springer, and Elsevier until Nov 2022 using multiple keywords. Aberrant DNA methylation pattern including hypermethylation in genes such as SLC6A5, SLC2A9, and SLC38A4, , DOCK6, COMT, GIT2, ZNF234, SOCS1. EZH2, a DNMTs enzyme is generally associated with the downregulation of gene expression but in the case of microglial, it is responsible for the upregulation of various genes including TRAF3IP2, BCL2L11, ITGAM, DAB2, NLRP12, WNT3, ADAM10. Increased expression of miRNAs such as miR-34a-5p, miR-29c-5p, miR-382-5p, miR-155, miR-126, Let-7g, hsa-miR-34a-5p, hsa-miR-375. Migraine is not only caused by non-genetic factors/ environmental factors or by brain structural alterations or genetic variations but also by alteration in epigenetics and their interaction too with other elements.
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Baccarelli, Andrea. "ENVIRONMENTAL EPIGENETICS AND AGING." Innovation in Aging 3, Supplement_1 (2019): S735. http://dx.doi.org/10.1093/geroni/igz038.2696.
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Abstract The human epigenome is a flexible, environmental sensitive component of human biology that changes over time. Multiple studies have identified prospective changes in epigenetic marks that indicate that the epigenome ages as we grow older. These changes have been leveraged to create multiple indicators of age that may also predict mortality and age-related disease. There is ongoing research to determine the extent to which age-related epigenomics changes are inherent to cell biology and/or driven by lifestyle and environmental factors. In this presentation, I will review the current evidence derived from human aging studies and potential contributions to human health and disease. I will discuss the source of data, methodological challenges for large human studies, limitations and possible future directions.
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Hoque, Majedul, Kazi Emon, Kazi Emon Md Aktaruzzaman, Md Nahid Hasan, Arafath Jubayer, and Mohammad Sabbir Hossain. "A Mini Review on Cancer Epigenetics." Middle East Research Journal of Medical Sciences 3, no. 02 (2023): 28–38. http://dx.doi.org/10.36348/merjms.2023.v03i02.002.
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Cancer epigenetics is the study of epigenetic changes to cancer cells' DNA that don't involve a change in the nucleotide sequence but instead affect how the genetic code is expressed. The complicated disease of cancer is brought on by genetic and epigenetic changes in the regulation of cell division. Our knowledge of the molecular etiology of cancer has substantially advanced and also the discoveries in the fields of cancer genomics and epigenomics, which have improved our comprehension of the development and evolution of tumorigenic processes. The interaction between genetic and epigenetic mutations and their interaction with environmental factors, including our microbiome, that influences cellular metabolism and proliferation rates, must therefore be taken into account in any modern perspective on cancer research. Future genetic and epigenetic therapeutics as well as diagnostics and prognosis will all benefit from the integration and increased understanding of these processes. Here, we tried to give a general summary of the disrupted epigenetic processes in cancer and how they affect the beginning and development of the illness. In conclusion, we talked about how advanced experimental methods and computational tools, such as fresh methods for utilizing enormous data sets, could help us better understand and cure cancer.
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Roy, Suchismita, and Praveen Soni. "Unraveling the Epigenetic Landscape for Salt Tolerance in Plants." International Journal of Plant Biology 13, no. 4 (2022): 443–62. http://dx.doi.org/10.3390/ijpb13040036.
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In every organism, the expression of genes is regulated in response to the changes in the surrounding environment. The study of epigenetics in plants is essential in view of the improvement of agricultural productivity. Epigenetic modifications can enhance crops’ yield and stress tolerance without making any alteration within their genomic sequences. The routes of epigenetic modifications include processes such as methylation of DNA, modifications of histone proteins, chromatin remodeling, and non-coding RNA-mediated regulation of genes. Genome-wide epigenetic profiles, coined as the epigenome, of several plants have been identified in recent years. In the scope of this review, we are going to discuss progress made in the field of plant epigenomics under the limelight of stress tolerance, especially saline conditions.
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Alexander, Sheila A. "The Contributions of Nursing to Genetics, Epigenetics, Genomics, and Epigenomics." Biological Research For Nursing 17, no. 4 (2015): 362–63. http://dx.doi.org/10.1177/1099800415586250.
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Kato, Mitsuo, and Rama Natarajan. "Epigenetics and epigenomics in diabetic kidney disease and metabolic memory." Nature Reviews Nephrology 15, no. 6 (2019): 327–45. http://dx.doi.org/10.1038/s41581-019-0135-6.
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Li, Shanyi, Hsiao-Chen Dina Kuo, Ran Yin, et al. "Epigenetics/epigenomics of triterpenoids in cancer prevention and in health." Biochemical Pharmacology 175 (May 2020): 113890. http://dx.doi.org/10.1016/j.bcp.2020.113890.
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Augusto, Ronaldo de Carvalho, Aki Minoda, and Christoph Grunau. "A simple ATAC-seq protocol for population epigenetics." Wellcome Open Research 5 (June 9, 2020): 121. http://dx.doi.org/10.12688/wellcomeopenres.15552.1.
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We describe here a protocol for the generation of sequence-ready libraries for population epigenomics studies. The protocol is a streamlined version of the Assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) that provides a positive display of accessible, presumably euchromatic regions. The protocol is straightforward and can be used with small individuals such as daphnia and schistosome worms, and probably many other biological samples of comparable size, and it requires little molecular biology handling expertise.
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Ehrlich, Melanie. "Risks and rewards of big-data in epigenomics research: an interview with Melanie Ehrlich." Epigenomics 14, no. 6 (2022): 351–58. http://dx.doi.org/10.2217/epi-2022-0056.
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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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Pinel, Clémence. "When more data means better results: Abundance and scarcity in research collaborations in epigenetics." Social Science Information 59, no. 1 (2020): 35–58. http://dx.doi.org/10.1177/0539018419895456.
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Drawing upon ethnographic findings from an epigenetics research laboratory in the United Kingdom, this article explores practices of research collaborations in the field of epigenetics, and epigenomics research consortia in particular. I demonstrate that research consortia are key scientific infrastructures that enable the aggregation of masses of data deemed necessary for the production of results and the fostering of epistemic value. Building on Science and Technology Studies (STS) scholarship on value production, and the concept of asset, I show that the production of valuable research within epigenomics research consortia rests on the active organisation and management of abundance and scarcity. It involves shaping and standardising the masses of data gathered in consortia, while it also entails research teams enclosing their data within their laboratories’ walls. As they do so, research teams construct data into scarce and monopolised assets, which they can put to productive use in collaborative endeavours against a revenue. In addition to contributing empirical and critical insights into the ways epigenetics knowledge is formed and negotiated in specific research contexts, this article offers conceptual tools to examine and problematise knowledge production practices in data-intensive research more broadly. In particular, it points out that while contemporary big biology is marked by the generalised imperative to ‘share’ data and ‘open’ science, collaborative endeavours within research consortia are built around forms of exclusions.
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Biémont, C. "From genotype to phenotype. What do epigenetics and epigenomics tell us?" Heredity 105, no. 1 (2010): 1–3. http://dx.doi.org/10.1038/hdy.2010.66.
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Agarwal, Gaurav, Himabindu Kudapa, Abirami Ramalingam, et al. "Epigenetics and epigenomics: underlying mechanisms, relevance, and implications in crop improvement." Functional & Integrative Genomics 20, no. 6 (2020): 739–61. http://dx.doi.org/10.1007/s10142-020-00756-7.
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Augusto, Ronaldo de Carvalho, Oliver Rey, Céline Cosseau, et al. "A simple ATAC-seq protocol for population epigenetics." Wellcome Open Research 5 (January 7, 2021): 121. http://dx.doi.org/10.12688/wellcomeopenres.15552.2.
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We describe here a protocol for the generation of sequence-ready libraries for population epigenomics studies, and the analysis of alignment results. We show that the protocol can be used to monitor chromatin structure changes in populations when exposed to environmental cues. The protocol is a streamlined version of the Assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) that provides a positive display of accessible, presumably euchromatic regions. The protocol is straightforward and can be used with small individuals such as daphnia and schistosome worms, and probably many other biological samples of comparable size (~10,000 cells), and it requires little molecular biology handling expertise.
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Ramos, Paula S. "Epigenetics of scleroderma: Integrating genetic, ethnic, age, and environmental effects." Journal of Scleroderma and Related Disorders 4, no. 3 (2019): 238–50. http://dx.doi.org/10.1177/2397198319855872.
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Scleroderma or systemic sclerosis is thought to result from the interplay between environmental or non-genetic factors in a genetically susceptible individual. Epigenetic modifications are influenced by genetic variation and environmental exposures, and change with chronological age and between populations. Despite progress in identifying genetic, epigenetic, and environmental risk factors, the underlying mechanism of systemic sclerosis remains unclear. Since epigenetics provides the regulatory mechanism linking genetic and non-genetic factors to gene expression, understanding the role of epigenetic regulation in systemic sclerosis will elucidate how these factors interact to cause systemic sclerosis. Among the cell types under tight epigenetic control and susceptible to epigenetic dysregulation, immune cells are critically involved in early pathogenic events in the progression of fibrosis and systemic sclerosis. This review starts by summarizing the changes in DNA methylation, histone modification, and non-coding RNAs associated with systemic sclerosis. It then discusses the role of genetic, ethnic, age, and environmental effects on epigenetic regulation, with a focus on immune system dysregulation. Given the potential of epigenome editing technologies for cell reprogramming and as a therapeutic approach for durable gene regulation, this review concludes with a prospect on epigenetic editing. Although epigenomics in systemic sclerosis is in its infancy, future studies will help elucidate the regulatory mechanisms underpinning systemic sclerosis and inform the design of targeted epigenetic therapies to control its dysregulation.
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Pfeifer, Gerd P. "The ups and downs of DNA methylation: an interview with Gerd Pfeifer." Epigenomics 14, no. 6 (2022): 339–43. http://dx.doi.org/10.2217/epi-2021-0485.
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In this interview, Professor Gerd Pfeifer speaks with Storm Johnson, Commissioning Editor for Epigenomics, on his work to date in the field of DNA methylation. Dr Pfeifer received a PhD degree from the University of Frankfurt, Germany. After postdoctoral work, he became a faculty member at the Beckman Research Institute of the City of Hope (Duarte, CA) in 1991. He is currently a full professor at the Van Andel Institute in Grand Rapids, MI. Dr. Pfeifer has served on several NIH advisory committees and has published over 300 research papers. Dr Pfeifer's research interests are cancer etiology, molecular carcinogenesis and epigenetics. His expertise is in cellular and molecular biology. His lab currently works on epigenetic mechanisms of gene regulation in cancer and other diseases.
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Silva, Tiago C., Antonio Colaprico, Catharina Olsen, et al. "TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages." F1000Research 5 (June 29, 2016): 1542. http://dx.doi.org/10.12688/f1000research.8923.1.
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Biotechnological advances in sequencing have led to an explosion of publicly available data via large international consortia such as The Cancer Genome Atlas (TCGA), The Encyclopedia of DNA Elements (ENCODE), and The NIH Roadmap Epigenomics Mapping Consortium (Roadmap). These projects have provided unprecedented opportunities to interrogate the epigenome of cultured cancer cell lines as well as normal and tumor tissues with high genomic resolution. The bioconductor project offers more than 1,000 open-source software and statistical packages to analyze high-throughput genomic data. However, most packages are designed for specific data types (e.g. expression, epigenetics, genomics) and there is no comprehensive tool that provides a complete integrative analysis harnessing the resources and data provided by all three public projects. A need to create an integration of these different analyses was recently proposed. In this workflow, we provide a series of biologically focused integrative downstream analyses of different molecular data. We describe how to download, process and prepare TCGA data and by harnessing several key bioconductor packages, we describe how to extract biologically meaningful genomic and epigenomic data and by using Roadmap and ENCODE data, we provide a workplan to identify candidate biologically relevant functional epigenomic elements associated with cancer. To illustrate our workflow, we analyzed two types of brain tumors : low-grade glioma (LGG) versus high-grade glioma (glioblastoma multiform or GBM). This workflow introduces the following Bioconductor packages: AnnotationHub, ChIPSeeker, ComplexHeatmap, pathview, ELMER, GAIA, MINET, RTCGAtoolbox, TCGAbiolinks.
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Silva, Tiago C., Antonio Colaprico, Catharina Olsen, et al. "TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages." F1000Research 5 (December 28, 2016): 1542. http://dx.doi.org/10.12688/f1000research.8923.2.
Full textAbstract:
Biotechnological advances in sequencing have led to an explosion of publicly available data via large international consortia such as The Cancer Genome Atlas (TCGA), The Encyclopedia of DNA Elements (ENCODE), and The NIH Roadmap Epigenomics Mapping Consortium (Roadmap). These projects have provided unprecedented opportunities to interrogate the epigenome of cultured cancer cell lines as well as normal and tumor tissues with high genomic resolution. The Bioconductor project offers more than 1,000 open-source software and statistical packages to analyze high-throughput genomic data. However, most packages are designed for specific data types (e.g. expression, epigenetics, genomics) and there is no one comprehensive tool that provides a complete integrative analysis of the resources and data provided by all three public projects. A need to create an integration of these different analyses was recently proposed. In this workflow, we provide a series of biologically focused integrative analyses of different molecular data. We describe how to download, process and prepare TCGA data and by harnessing several key Bioconductor packages, we describe how to extract biologically meaningful genomic and epigenomic data. Using Roadmap and ENCODE data, we provide a work plan to identify biologically relevant functional epigenomic elements associated with cancer. To illustrate our workflow, we analyzed two types of brain tumors: low-grade glioma (LGG) versus high-grade glioma (glioblastoma multiform or GBM). This workflow introduces the following Bioconductor packages: AnnotationHub, ChIPSeeker, ComplexHeatmap, pathview, ELMER, GAIA, MINET, RTCGAToolbox, TCGAbiolinks.
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Šrut, Maja. "Environmental Epigenetics in Soil Ecosystems: Earthworms as Model Organisms." Toxics 10, no. 7 (2022): 406. http://dx.doi.org/10.3390/toxics10070406.
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One of the major emerging concerns within ecotoxicology is the effect of environmental pollutants on epigenetic changes, including DNA methylation, histone modifications, and non-coding RNAs. Epigenetic mechanisms regulate gene expression, meaning that the alterations of epigenetic marks can induce long-term physiological effects that can even be inherited across generations. Many invertebrate species have been used as models in environmental epigenetics, with a special focus on DNA methylation changes caused by environmental perturbations (e.g., pollution). Among soil organisms, earthworms are considered the most relevant sentinel organisms for anthropogenic stress assessment and are widely used as standard models in ecotoxicological testing of soil toxicity. In the last decade, several research groups have focused on assessing the impact of environmental stress on earthworm epigenetic mechanisms and tried to link these mechanisms to the physiological effects. The aim of this review is to give an overview and to critically examine the available literature covering this topic. The high level of earthworm genome methylation for an invertebrate species, responsiveness of epigenome to environmental stimuli, availability of molecular resources, and the possibility to study epigenetic inheritance make earthworms adequate models in environmental epigenomics. However, there are still many knowledge gaps that need to be filled in, before we can fully explore earthworms as models in this field. These include detailed characterization of the methylome using next-generation sequencing tools, exploration of multigenerational and transgenerational effects of pollutants, and information about other epigenetic mechanisms apart from DNA methylation. Moreover, the connection between epigenetic effects and phenotype has to be further explored.
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Lee, Daniel Y. "Cancer Epigenomics and Beyond: Advancing the Precision Oncology Paradigm." Journal of Immunotherapy and Precision Oncology 3, no. 4 (2020): 147–56. http://dx.doi.org/10.36401/jipo-20-18.
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ABSTRACT How cancers are characterized and treated has evolved over the past few decades. Major advances in genomics tools and techniques have revealed interlinked regulatory pathways of cancers with unprecedented detail. Early discoveries led to success with rationally targeted small molecules and more recently with immunomodulatory agents, setting the stage for precision oncology. However, drug resistance to every agent has thus far proven intractable, sending us back to fill the gaps in our rudimentary knowledge of tumor biology. Epigenetics is emerging as a fundamental process in every hallmark of cancer. Large-scale interrogation of the cancer epigenome continues to reveal new mechanisms of astounding complexity. In this review, I present selected experimental and clinical examples that have shaped our understanding of cancer at the molecular level. Translation of our collective erudition into revolutionary diagnostic and treatment strategies will advance the precision oncology paradigm.
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Kelsey, Karl. "Epigenetics, environment and epidemiology: an interview with Karl Kelsey." Epigenomics 14, no. 6 (2022): 323–26. http://dx.doi.org/10.2217/epi-2022-0008.
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In this interview, Professor Karl Kelsey speaks with Storm Johnson, Commissioning Editor for Epigenomics, on his work to date in the field of environmental epigenomics and epidemiology. Dr Karl Kelsey, MD, MOH is a Professor of Epidemiology and Pathology and Laboratory Medicine at Brown University. He is the Founding Director of the Center for Environmental Health and Technology and Head of the Environmental Health Section at the Department of Epidemiology. Dr Kelsey is interested in the application of laboratory-based biomarkers in environmental disease, with experience in chronic disease epidemiology and tumor biology. The goals of his work include a mechanistic understanding of individual susceptibility to exposure-related cancers. In addition, his laboratory is interested in tumor biology, investigating somatic alterations in tumor tissue from the patients who have developed exposure-related cancers. This work involves the use of an epidemiologic approach to characterize epigenetic and genetic alteration of genes in the causal pathway for malignancy. Active work includes several studies of individual susceptibility to cancer. Dr Kelsey's laboratory mainly investigates susceptibility to smoking-related lung cancer and studies multi-racial and ethnic populations. In addition, the laboratory is also involved with the study of inherited susceptibility to brain tumors and pancreatic cancer. Major case control studies that are ongoing in the laboratory include studies designed to understand inherited and acquired susceptibility in head and neck cancers. The laboratory is also involved in a case control study of asbestos-associated mesothelioma, arsenic exposure, cigarette smoking and bladder cancer. Considerable work is being devoted to understanding the mechanisms of action of both asbestos and arsenic including their ability to affect promoter methylation and gene silencing in carcinogenesis. Recent laboratory studies includes an interest in using newly developed DNA methylation biomarkers to probe immune profiles from archived blood. Dr Kelsey received his MD from the University of Minnesota and Masters of Occupational Health from Harvard University.
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Goodrich, Jaclyn. "Insights on exposure-induced disease susceptibility: an interview with Jaclyn Goodrich." Epigenomics 14, no. 6 (2022): 319–21. http://dx.doi.org/10.2217/epi-2022-0046.
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In this interview, Dr Jaclyn Goodrich speaks with Storm Johnson, Commissioning Editor for Epigenomics, on her work to date on environmental epigenetics and the impact of toxic exposures on susceptible populations. Jaclyn Goodrich is a research assistant professor of environmental health sciences at the University of Michigan School of Public Health (Ann Arbor, MI, USA). She obtained a doctorate in toxicology and completed postdoctoral training in environmental epigenomics at the University of Michigan. The overarching goal of her current research program is to identify environmental factors that modify the epigenome and increase risk for disease throughout the life course. She primarily conducts epidemiological studies to investigate the impact of toxic exposures on susceptible populations including children and occupationally exposed workers. She has coauthored more than 70 publications and is an active member of the Society of Toxicology and the Environmental Mutagenesis and Genomics Society.
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Figueroa, Maria Eugenia, John Greally, Ruud Delwel, and Ari M. Melnick. "Genome-Wide Epigenetics in Myeloid Leukemias." Blood 112, no. 11 (2008): sci—35—sci—35. http://dx.doi.org/10.1182/blood.v112.11.sci-35.sci-35.
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Abstract While the role of genetic alterations in cancer is well-recognized, epigenetic deregulation has only recently been identified as a hallmark of malignant transformation. The term “epigenetic” refers to a heritable regulation of gene expression that is not dependent on changes in the DNA sequence. These epigenetic modifications – including but not limited to DNA methylation and covalent modifications of histone tails – play a crucial role in determining chromatin structure and gene expression. Abnormal epigenetic regulation can lead to aberrant chromatin structure and deregulation of transcriptional activity. Epigenetic lesions can affect cancer-related genes, such as CDKN2B, CDKN2A, RB, and BRCA1, and it is not rare for epigenetic lesions to accompany genetic mutations of these and other genes, suggesting that epigenetic deregulation can form a part of the multi-step process of oncogenesis. An alteration in the distribution of DNA methylation has been demonstrated in AML as well as in other malignancies. Generally, intergenic DNA methylation is reported to decrease and promoter methylation to increase. Hypomethylation of DNA can lead to genomic instability and further increase the number of genetic lesions, while promoter hypermethylation has been associated with aberrant silencing of tumor suppressor genes. Altered levels of acetylation at specific histone residues were also shown to be associated with aberrant chromatin structure and gene deregulation in AML. Several oncogenic transcription factors and fusion proteins, such as PML-RARalpha, and AML1-ETO, can introduce aberrant epigenetic programming in myeloid cells through recruitment of epigenetic modifying enzymes to their target genes. However, the emerging field of epigenomic profiling has yielded evidence that epigenetic deregulation in AML is more profound and cannot always be linked to the presence of a given fusion protein. The mechanisms leading to genome-wide epigenetic deregulation still remain largely unidentified, although environmental factors and aging can contribute to this process. Current epigenetic profiling studies have revealed that DNA methylation or histone modification patterns can identify biologically distinct forms of AML that may not be readily identified through other methods. New data suggest that specific DNA methylation profiles may be associated with response to therapeutic agents, including epigenetic-targeted drugs. Numerous epigenetic candidate biomarkers have been recently described in both myeloid and lymphoid malignancies. Integrative analysis of DNA methylation, histone modifications, and gene expression may synergize to identify in far greater depth than single platform studies differences in gene regulation among leukemias. Overall, the emerging field of epigenomics provide a new opportunity to more accurately identify biological variation and therapeutically target acute myeloid leukemias.
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Abdelmoula, E., B. Abdelmoula, and N. Bouayed Abdelmoula. "Embodied cognition and urban design: Thoughts through epigenetic advances." European Psychiatry 67, S1 (2024): S626—S627. http://dx.doi.org/10.1192/j.eurpsy.2024.1299.
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IntroductionIn the history of urban planning, the cognitive trend has been a well-established entity since the work of the American urban planner during the mid-’90s; Kevin Lynch. However, for a long time, urban planning has been deprived of the contribution of scientific knowledge from cognitive neurosciences, with a lack of operational recommendations for urban projects.ObjectivesThis study aims to reveal the role of embodiment theories in the revolution of urban design and urban projects through emerging findings in epigenetics and post-genomic biology.MethodsWe conducted an exhaustive review of the scientific literature to establish the relationship between embodied cognition and urban design through advances in epigenetics as well as potential applications of such finding. Our inquiry was to find out whether there was a scientific way to measure and quantify the performance of urban spaces.ResultsOur review revealed that, epigenetics and epigenomics have provided new explanations and perspectives to certain debates on the theory of embodied cognition and that of enaction. Epigenetic marks constitute a bodily memory that enables cognition to emerge as a function of the level of adaptation to the environment. In fact, embodiment refers to thoughts, emotions and behaviors based on sensory experiences and bodily positions, while the enaction is a way of conceiving cognition that focuses on the way in which human organisms and minds organize themselves in interaction with the environment.ConclusionsCognition is the result of a level of adaptation to the environment determined by physiological parameters that confer possibilities of action depending on previous interactions with the environment. The regulation of epigenetic marks which are technically quantifiable is now recognized as the fundamental mechanism involved in the brain’s ability to create, dismantle or reorganize neural networks throughout life depending on various experiences including environmental ones.Disclosure of InterestNone Declared
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Lakshmi Priya R and Devi S. Nair. "Ayurvedic Personalized Healthcare: Integrating Genomics, Epigenomics and Traditional Wisdom." Journal of Ayurveda and Integrated Medical Sciences 9, no. 11 (2025): 192–97. https://doi.org/10.21760/jaims.9.11.27.
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In the evolving landscape of personalized medicine, integrating Ayurvedic principles with modern genomic science presents a transformative opportunity for healthcare. This paper explores the concept of Prakriti, the unique constitution of individuals as defined in Ayurveda, and its potential correlation with genetic profiles. By merging Ayurvedic insights with genomic and epigenomic research, we propose a framework for personalized healthcare that considers both genetic predispositions and lifestyle factors. The study outlines practical approaches, including the use of Single Nucleotide Polymorphism (SNP) analysis to identify genetic variations linked to specific Prakriti types, and the role of epigenetics in understanding how lifestyle choices influence gene expression. Additionally, we discuss the implementation of Genome-Wide Association Studies (GWAS) to identify biomarkers that can enhance disease prevention and treatment strategies tailored to individual needs. By fostering collaboration between Ayurvedic practitioners and genomic researchers, we aim to promote a holistic understanding of health that bridges ancient wisdom with contemporary science. Ultimately, this integration not only enriches personalized healthcare but also paves the way for innovative treatment solutions that honor both genetic diversity and traditional knowledge.
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Dudley, K. J., K. Revill, R. N. Clayton, and W. E. Farrell. "Pituitary tumours: all silent on the epigenetics front." Journal of Molecular Endocrinology 42, no. 6 (2009): 461–68. http://dx.doi.org/10.1677/jme-09-0009.
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Investigation of the epigenome of sporadic pituitary tumours is providing a more detailed understanding of aberrations that characterise this tumour type. Early studies, in this and other tumour types adopted candidate-gene approaches to characterise CpG island methylation as a mechanism responsible for or associated with gene silencing. However, more recently, investigators have adopted approaches that do not require a priori knowledge of the gene and transcript, as example differential display techniques, and also genome-wide, array-based approaches, to ‘uncover’ or ‘unmask’ silenced genes. Furthermore, through use of chromatin immunoprecipitation as a selective enrichment technique; we are now beginning to identify modifications that target the underlying histones themselves and that have roles in gene-silencing events. Collectively, these studies provided convincing evidence that change to the tumour epigenome are not simply epiphenomena but have functional consequences in the context of pituitary tumour evolution. Our ability to perform these types of studies has been and is increasingly reliant upon technological advances in the genomics and epigenomics arena. In this context, other more recent advances and developing technologies, and, in particular, next generation or flow cell re-sequencing techniques offer exciting opportunities for our future studies of this tumour type.
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Wu, Renyi, Lujing Wang, Ran Yin, et al. "Epigenetics/epigenomics and prevention by curcumin of early stages of inflammatory‐driven colon cancer." Molecular Carcinogenesis 59, no. 2 (2019): 227–36. http://dx.doi.org/10.1002/mc.23146.
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Karlsson, Oskar. "Epigenetics in the Anthropocene: an interview with Oskar Karlsson." Epigenomics 14, no. 6 (2022): 315–18. http://dx.doi.org/10.2217/epi-2022-0044.
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In this interview, Oskar Karlsson speaks with Storm Johnson, commissioning editor for Epigenomics, on his work to date in the field of toxicological origins of disease and gene–environment interactions. Oskar Karlsson, is an associate professor at the Science for Life Laboratory (SciLifeLab), Department of Environmental Science, Stockholm University, Sweden. Dr. Karlsson earned a PhD in toxicology at the Department of Pharmaceutical Bioscience, Uppsala University, and has also worked at Centre of Molecular Medicine, Karolinska Institute, as well as Harvard University School of Public Health. His research combines experimental model systems, computational and omics tools, and epidemiological studies to investigate the influence of environmental exposures on wildlife and human health, and underlying molecular mechanisms. In particular, his research focuses on developmental origins of health and disease with an emphasis on environmental exposures and epigenetic mechanisms. The projects concern the effects of exposures such as endocrine disrupting chemicals, flame retardants, pesticides, metals and particulate air pollution, as well as drugs, psycho-social stressors and ethnical disparities. Ongoing efforts include studies of paternal epigenetic inheritance in the ERC-funded project PATER.
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Shema, Efrat. "Abstract PR006: Single-molecule and single-cell epigenetics: Decoding the epigenome for cancer research and diagnostics." Cancer Research 82, no. 23_Supplement_2 (2022): PR006. http://dx.doi.org/10.1158/1538-7445.cancepi22-pr006.
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Abstract Genes and genomic elements are packaged by chromatin structures that regulate their activity. We developed a novel high-throughput single-molecule imaging technology to decode combinatorial modifications on millions of individual nucleosomes. We apply this technology to image nucleosomes and delineate their combinatorial epigenetic patterns, and how these patterns are deregulated in cancer. In addition, we adapt single-cell technologies based on CyTOF to profile the global levels of multiple histone modifications in single cells, thus revealing epigenetic heterogeneity in cancer. Our research focuses on pediatric gliomas harboring lysine to methionine substitution of residue 27 on histone H3 (K27M). We provide evidence for widespread effects of the H3-K27M oncohistone on multiple core epigenetic pathways, and highlight the capability of single-molecule and single-cell tools to reveal mechanisms of chromatin deregulation and heterogeneity in cancer. We also harness the single-molecule technology as a novel liquid biopsy approach, by comprehensively profiling combinatorial epigenetic marks of plasma-isolated nucleosomes. Applying this analysis to a cohort of plasma samples detect colorectal cancer at high accuracy and sensitivity, even at early stages. Finally, combining this proteomic analysis with single-molecule DNA sequencing reveals the tissue-of-origin of the tumor. Citation Format: Efrat Shema. Single-molecule and single-cell epigenetics: Decoding the epigenome for cancer research and diagnostics. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr PR006.
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Oliveira, Carolliny Texeira Neves, José Pedro Lima Marinho de Andrade, Lídian Sarah Rocha Vieira Sampaio, Marco Túlio Silva Jardim, and Kleber Alves Gomes. "TRANSTORNO DO ESPECTRO AUTISTA E SUA RELAÇÃO COM A EPIGENÉTICA: UMA REVISÃO DOS IMPACTOS NO DESENVOLVIMENTO INFANTIL." Revista ft 29, no. 143 (2025): 15–16. https://doi.org/10.69849/revistaft/ar10202502102015.
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Objective: To analyze how epigenetic mechanisms influence the development of Autism Spectrum Disorder (ASD) in childhood and analyze the implications of these influences for diagnosis and therapeutic approaches. Methods: An integrative literature review conducted in December 2024, using databases such as PubMed, SCIELO, and Acervo+ Index Base. The search utilized descriptors such as "Autism Spectrum Disorder”, “Autistic Disorder”, “Epigenomics”, “Multifactorial Inheritance” e “Developmental Disabilities", combined with the Boolean operator “AND”. Articles published between 2014 and 2024, with full text available in Portuguese, were included, while duplicated, incomplete, or out-of-period studies were excluded. Results: The final sample consisted of 9 articles, which indicated a significant relationship between prenatal, perinatal, and postnatal risk factors and the development of ASD. Key factors such as exposure to pesticides, prematurity, advanced parental age, and perinatal complications were highlighted. Epigenetic mechanisms such as DNA methylation and histone modifications were associated with changes in neurological development. Conclusion: Epigenetics plays a central role in understanding ASD by linking genetic and environmental factors to neurological development. Future studies are needed to further explore the mechanisms involved and promote personalized diagnostic and therapeutic interventions, contributing to the quality of life for affected children and their families.
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Al Jowf, Ghazi I., Clara Snijders, Bart P. F. Rutten, Laurence de Nijs, and Lars M. T. Eijssen. "The Molecular Biology of Susceptibility to Post-Traumatic Stress Disorder: Highlights of Epigenetics and Epigenomics." International Journal of Molecular Sciences 22, no. 19 (2021): 10743. http://dx.doi.org/10.3390/ijms221910743.
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Exposure to trauma is one of the most important and prevalent risk factors for mental and physical ill-health. Excessive or prolonged stress exposure increases the risk of a wide variety of mental and physical symptoms. However, people differ strikingly in their susceptibility to develop signs and symptoms of mental illness after traumatic stress. Post-traumatic stress disorder (PTSD) is a debilitating disorder affecting approximately 8% of the world’s population during their lifetime, and typically develops after exposure to a traumatic event. Despite that exposure to potentially traumatizing events occurs in a large proportion of the general population, about 80–90% of trauma-exposed individuals do not develop PTSD, suggesting an inter-individual difference in vulnerability to PTSD. While the biological mechanisms underlying this differential susceptibility are unknown, epigenetic changes have been proposed to underlie the relationship between exposure to traumatic stress and the susceptibility to develop PTSD. Epigenetic mechanisms refer to environmentally sensitive modifications to DNA and RNA molecules that regulate gene transcription without altering the genetic sequence itself. In this review, we provide an overview of various molecular biological, biochemical and physiological alterations in PTSD, focusing on changes at the genomic and epigenomic level. Finally, we will discuss how current knowledge may aid us in early detection and improved management of PTSD patients.
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Zotenko, Elena, Rachel Gittelman, Alan Selewa, et al. "Abstract 1955: Blood-based mapping of the personalized tumor epigenomic landscape." Cancer Research 85, no. 8_Supplement_1 (2025): 1955. https://doi.org/10.1158/1538-7445.am2025-1955.
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Abstract Background: Mapping the epigenetic landscape of tumors provides insights into regulatory and functional aspects beyond somatic mutations, offering valuable information that can influence clinical decisions and benefit the patient journey. Given the challenges of obtaining tissue biopsies, especially in the longitudinal monitoring or progression setting as tumors evolve due to selective pressure from treatment, the advantages of non-invasive liquid biopsies to characterize tumors through blood are highly beneficial. Here, we demonstrate that the epigenetic landscape of a patient’s tumor can be evaluated in plasma using an epigenetics circulating tumor DNA assay, providing a promising approach for non-invasive tumor profiling. Methods: We collected paired tumor and plasma samples from lung, breast and colorectal cancer patients, and applied an analytically validated next-generation sequencing epigenomics hybrid capture assay to measure DNA methylation across over 1.3 million CpG loci. A total of 44 patients (10 colorectal, 13 breast, 21 lung) with circulating tumor DNA (ctDNA) detected at a level of 0.5% or greater were included in the analysis. For each patient, we identified personalized tissue differentially methylated regions (DMRs) as the set of regions that were highly methylated in tissue but showed low methylation in an independent set of 197 cancer-free plasma samples. For each region from a personalized tissue DMR list, we computed the expected count in plasma as a function of tumor fraction and assay efficiency. Results: Across the 44 analyzed tissue samples, the median number of personalized tissue DMRs identified was 1, 133, with a range of 136 to 4, 220 and a standard deviation of 850. For paired tissue and plasma samples from the same patient the Spearman correlation between the expected and observed counts in plasma was high across all samples (Mean=0.687, SD=0.120). The correlation between expected and observed signals at personalized tissue DMRs was calculated for all possible plasma and tissue sample pairs, regardless of whether the samples were from the same patient. Notably, for 43 out of 44 plasma samples, the highest correlation between expected and observed plasma counts occurred with the plasma’s matched tissue sample (Mean difference=0.196, SD=0.096). Conclusions: These data demonstrate a strong concordance between a tumor tissue's unique epigenetic landscape and the epigenetic signal in plasma. Furthermore, the finding that each plasma sample correlated most with its paired tissue sample over other pairings indicates that the assay can reliably measure personalized tumor epigenetic features in plasma. This supports the use of an epigenetics-only ctDNA assay for monitoring patients and guiding treatment decisions. Citation Format: Elena Zotenko, Rachel Gittelman, Alan Selewa, Noam Vardi, Tam Banh, Gleb Martovetsky, Oscar Westesson, Emily Tsang, Sara Wienke, Drew Kennedy, Meromit Singer, Stefanie Mortimer, Darya Chudova. Blood-based mapping of the personalized tumor epigenomic landscape [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 1955.