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Pereira QC, Fortunato IM, Oliveira FDS, Alvarez MC, dos Santos TW, Ribeiro ML. Polyphenolic Compounds: Orchestrating Intestinal Microbiota Harmony during Aging. Nutrients 2024; 16:1066. [PMID: 38613099 PMCID: PMC11013902 DOI: 10.3390/nu16071066] [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: 01/25/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
In the aging process, physiological decline occurs, posing a substantial threat to the physical and mental well-being of the elderly and contributing to the onset of age-related diseases. While traditional perspectives considered the maintenance of life as influenced by a myriad of factors, including environmental, genetic, epigenetic, and lifestyle elements such as exercise and diet, the pivotal role of symbiotic microorganisms had been understated. Presently, it is acknowledged that the intestinal microbiota plays a profound role in overall health by signaling to both the central and peripheral nervous systems, as well as other distant organs. Disruption in this bidirectional communication between bacteria and the host results in dysbiosis, fostering the development of various diseases, including neurological disorders, cardiovascular diseases, and cancer. This review aims to delve into the intricate biological mechanisms underpinning dysbiosis associated with aging and the clinical ramifications of such dysregulation. Furthermore, we aspire to explore bioactive compounds endowed with functional properties capable of modulating and restoring balance in this aging-related dysbiotic process through epigenetics alterations.
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Affiliation(s)
- Quélita Cristina Pereira
- Laboratory of Immunopharmacology and Molecular Biology, Sao Francisco University, Av. Sao Francisco de Assis, 218, Braganca Paulista 12916-900, SP, Brazil; (Q.C.P.); (I.M.F.); (F.d.S.O.); (M.C.A.); (T.W.d.S.)
| | - Isabela Monique Fortunato
- Laboratory of Immunopharmacology and Molecular Biology, Sao Francisco University, Av. Sao Francisco de Assis, 218, Braganca Paulista 12916-900, SP, Brazil; (Q.C.P.); (I.M.F.); (F.d.S.O.); (M.C.A.); (T.W.d.S.)
| | - Fabricio de Sousa Oliveira
- Laboratory of Immunopharmacology and Molecular Biology, Sao Francisco University, Av. Sao Francisco de Assis, 218, Braganca Paulista 12916-900, SP, Brazil; (Q.C.P.); (I.M.F.); (F.d.S.O.); (M.C.A.); (T.W.d.S.)
| | - Marisa Claudia Alvarez
- Laboratory of Immunopharmacology and Molecular Biology, Sao Francisco University, Av. Sao Francisco de Assis, 218, Braganca Paulista 12916-900, SP, Brazil; (Q.C.P.); (I.M.F.); (F.d.S.O.); (M.C.A.); (T.W.d.S.)
- Hematology and Transfusion Medicine Center, University of Campinas/Hemocentro, UNICAMP, Rua Carlos Chagas 480, Campinas 13083-878, SP, Brazil
| | - Tanila Wood dos Santos
- Laboratory of Immunopharmacology and Molecular Biology, Sao Francisco University, Av. Sao Francisco de Assis, 218, Braganca Paulista 12916-900, SP, Brazil; (Q.C.P.); (I.M.F.); (F.d.S.O.); (M.C.A.); (T.W.d.S.)
| | - Marcelo Lima Ribeiro
- Laboratory of Immunopharmacology and Molecular Biology, Sao Francisco University, Av. Sao Francisco de Assis, 218, Braganca Paulista 12916-900, SP, Brazil; (Q.C.P.); (I.M.F.); (F.d.S.O.); (M.C.A.); (T.W.d.S.)
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Yurkovich JT, Evans SJ, Rappaport N, Boore JL, Lovejoy JC, Price ND, Hood LE. The transition from genomics to phenomics in personalized population health. Nat Rev Genet 2024; 25:286-302. [PMID: 38093095 DOI: 10.1038/s41576-023-00674-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2023] [Indexed: 03/21/2024]
Abstract
Modern health care faces several serious challenges, including an ageing population and its inherent burden of chronic diseases, rising costs and marginal quality metrics. By assessing and optimizing the health trajectory of each individual using a data-driven personalized approach that reflects their genetics, behaviour and environment, we can start to address these challenges. This assessment includes longitudinal phenome measures, such as the blood proteome and metabolome, gut microbiome composition and function, and lifestyle and behaviour through wearables and questionnaires. Here, we review ongoing large-scale genomics and longitudinal phenomics efforts and the powerful insights they provide into wellness. We describe our vision for the transformation of the current health care from disease-oriented to data-driven, wellness-oriented and personalized population health.
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Affiliation(s)
- James T Yurkovich
- Phenome Health, Seattle, WA, USA
- Center for Phenomic Health, The Buck Institute for Research on Aging, Novato, CA, USA
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX, USA
| | - Simon J Evans
- Phenome Health, Seattle, WA, USA
- Center for Phenomic Health, The Buck Institute for Research on Aging, Novato, CA, USA
| | - Noa Rappaport
- Center for Phenomic Health, The Buck Institute for Research on Aging, Novato, CA, USA
- Institute for Systems Biology, Seattle, WA, USA
| | - Jeffrey L Boore
- Phenome Health, Seattle, WA, USA
- Center for Phenomic Health, The Buck Institute for Research on Aging, Novato, CA, USA
| | - Jennifer C Lovejoy
- Phenome Health, Seattle, WA, USA
- Center for Phenomic Health, The Buck Institute for Research on Aging, Novato, CA, USA
- Institute for Systems Biology, Seattle, WA, USA
| | - Nathan D Price
- Institute for Systems Biology, Seattle, WA, USA
- Thorne HealthTech, New York, NY, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Leroy E Hood
- Phenome Health, Seattle, WA, USA.
- Center for Phenomic Health, The Buck Institute for Research on Aging, Novato, CA, USA.
- Institute for Systems Biology, Seattle, WA, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA.
- Department of Immunology, University of Washington, Seattle, WA, USA.
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Stabile AM, Pistilli A, Mariangela R, Rende M, Bartolini D, Di Sante G. New Challenges for Anatomists in the Era of Omics. Diagnostics (Basel) 2023; 13:2963. [PMID: 37761332 PMCID: PMC10529314 DOI: 10.3390/diagnostics13182963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/08/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023] Open
Abstract
Anatomic studies have traditionally relied on macroscopic, microscopic, and histological techniques to investigate the structure of tissues and organs. Anatomic studies are essential in many fields, including medicine, biology, and veterinary science. Advances in technology, such as imaging techniques and molecular biology, continue to provide new insights into the anatomy of living organisms. Therefore, anatomy remains an active and important area in the scientific field. The consolidation in recent years of some omics technologies such as genomics, transcriptomics, proteomics, and metabolomics allows for a more complete and detailed understanding of the structure and function of cells, tissues, and organs. These have been joined more recently by "omics" such as radiomics, pathomics, and connectomics, supported by computer-assisted technologies such as neural networks, 3D bioprinting, and artificial intelligence. All these new tools, although some are still in the early stages of development, have the potential to strongly contribute to the macroscopic and microscopic characterization in medicine. For anatomists, it is time to hitch a ride and get on board omics technologies to sail to new frontiers and to explore novel scenarios in anatomy.
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Affiliation(s)
- Anna Maria Stabile
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
| | - Alessandra Pistilli
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
| | - Ruggirello Mariangela
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
| | - Mario Rende
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
| | - Desirée Bartolini
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
- Department of Pharmaceutical Sciences, University of Perugia, 06126 Perugia, Italy
| | - Gabriele Di Sante
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
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McMahon‑Cole H, Johnson A, Sadat Aghamiri S, Helikar T, Crawford LB. Modeling and Remodeling the Cell: How Digital Twins and HCMV Can Elucidate the Complex Interactions of Viral Latency, Epigenetic Regulation, and Immune Responses. CURRENT CLINICAL MICROBIOLOGY REPORTS 2023; 10:141-151. [PMID: 37901689 PMCID: PMC10601359 DOI: 10.1007/s40588-023-00201-w] [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] [Accepted: 07/12/2023] [Indexed: 10/31/2023]
Abstract
Purpose of Review Human cytomegalovirus (HCMV), while asymptomatic in most, causes significant complications during fetal development, following transplant or in immunosuppressed individuals. The host-virus interactions regulating viral latency and reactivation and viral control of the cellular environment (immune regulation, differentiation, epigenetics) are highly complex. Understanding these processes is essential to controlling infection and can be leveraged as a novel approach for understanding basic cell biology. Recent Findings Immune digital twins (IDTs) are digital simulations integrating knowledge of human immunology, physiology, and patient-specific clinical data to predict individualized immune responses and targeted treatments. Recent studies used IDTs to elucidate mechanisms of T cells, dendritic cells, and epigenetic control-all key to HCMV biology. Summary Here, we discuss how leveraging the unique biology of HCMV and IDTs will clarify immune response dynamics, host-virus interactions, and viral latency and reactivation and serve as a powerful IDT-validation platform for individualized and holistic health management.
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Affiliation(s)
- Hana McMahon‑Cole
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Alicia Johnson
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Sara Sadat Aghamiri
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Tomáš Helikar
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Lindsey B. Crawford
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Center for Virology, Lincoln, NE, USA
- Nebraska Center for Integrated Biomolecular Communication, Lincoln, NE, USA
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Ni W, Xue Q, Zhang S, Yang X, Wu S, He X, Xiao Y, Chang W, Wen Y, Huang Y, Wang YX, Chen D, Yang CX, Pan XF. High quality diet attenuated the positive association between polychlorinated biphenyls and premature mortality among middle-aged and older adults. ENVIRONMENTAL RESEARCH 2023; 231:116031. [PMID: 37156355 DOI: 10.1016/j.envres.2023.116031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/30/2023] [Accepted: 05/01/2023] [Indexed: 05/10/2023]
Abstract
OBJECTIVE Polychlorinated biphenyls (PCBs) have been reported to be a risk factor for premature death, while a high diet quality is thought to lower mortality risk. We aimed to examine whether PCBs were associated with higher all-cause and cause-specific mortality risk and whether such associations could be modified by the diet quality among US middle-aged and older adults. METHODS Included were 1259 participants aged 40 years or older from the 1999-2004 National Health and Nutrition Examination surveys. Exposure to PCBs was assessed in non-fasting serum samples, and mortality status was ascertained through December 31, 2019 using the public-use, linked mortality files. Diet quality was assessed using the Healthy Eating Index-2015 based on 24-h dietary recalls. Cox proportional hazard regression was applied to assess the associations of different PCB congener groups with mortality and the modifying effect by the diet quality. RESULTS During a median follow-up of 17.75 years, 419 deaths occurred, including 131 from cardiovascular disease (CVD) and 102 from cancer. Serum concentrations of dioxin-like PCBs and non-dioxin-like PCBs were significantly associated with all-cause mortality, with hazard ratios (HRs) of 1.84 (95% confidence interval [CI], 1.10, 2.99) and 1.82 (1.09, 3.03) for extreme-tertile comparisons. A significant interaction was noted between dioxin-like PCBs and diet quality (P for interaction: 0.012), with a substantially more pronounced association among participants with a low diet quality (HR, 3.47; 95% CI: 1.29, 9.32), compared to those with a high diet quality (HR, 0.98; 95% CI: 0.40, 2.43). A similar weaker association was observed for total PCBs in participants with a high diet quality (P for interaction: 0.032). However, effect modifications by diet quality were not noted for the associations between different PCB groups and CVD mortality. CONCLUSIONS While our findings need to be validated in other populations and mechanistic studies, they may suggest that a high quality diet could potentially attenuate the harmful effects of chronic PCB exposure.
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Affiliation(s)
- Weigui Ni
- Section of Epidemiology and Population Health, Ministry of Education Key Laboratory of Birth Defects and Related Diseases of Women and Children & National Medical Products Administration Key Laboratory for Technical Research on Drug Products in Vitro and in Vivo Correlation, West China Second University Hospital, Sichuan University; Shuangliu Institute of Women's and Children's Health, Shuangliu Maternal and Child Health Hospital, Chengdu, Sichuan, China; Department of Epidemiology and Biostatistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Qingping Xue
- Department of Epidemiology and Biostatistics, School of Public Health, Chengdu Medical College, Chengdu, Sichuan, China
| | - Shanshan Zhang
- Section of Epidemiology and Population Health, Ministry of Education Key Laboratory of Birth Defects and Related Diseases of Women and Children & National Medical Products Administration Key Laboratory for Technical Research on Drug Products in Vitro and in Vivo Correlation, West China Second University Hospital, Sichuan University; Shuangliu Institute of Women's and Children's Health, Shuangliu Maternal and Child Health Hospital, Chengdu, Sichuan, China; Department of Epidemiology and Biostatistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xue Yang
- Section of Epidemiology and Population Health, Ministry of Education Key Laboratory of Birth Defects and Related Diseases of Women and Children & National Medical Products Administration Key Laboratory for Technical Research on Drug Products in Vitro and in Vivo Correlation, West China Second University Hospital, Sichuan University; Shuangliu Institute of Women's and Children's Health, Shuangliu Maternal and Child Health Hospital, Chengdu, Sichuan, China; Department of Epidemiology and Biostatistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Shiyi Wu
- Section of Epidemiology and Population Health, Ministry of Education Key Laboratory of Birth Defects and Related Diseases of Women and Children & National Medical Products Administration Key Laboratory for Technical Research on Drug Products in Vitro and in Vivo Correlation, West China Second University Hospital, Sichuan University; Shuangliu Institute of Women's and Children's Health, Shuangliu Maternal and Child Health Hospital, Chengdu, Sichuan, China; Department of Epidemiology and Biostatistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xingcheng He
- Section of Epidemiology and Population Health, Ministry of Education Key Laboratory of Birth Defects and Related Diseases of Women and Children & National Medical Products Administration Key Laboratory for Technical Research on Drug Products in Vitro and in Vivo Correlation, West China Second University Hospital, Sichuan University; Shuangliu Institute of Women's and Children's Health, Shuangliu Maternal and Child Health Hospital, Chengdu, Sichuan, China
| | - Yan Xiao
- Section of Epidemiology and Population Health, Ministry of Education Key Laboratory of Birth Defects and Related Diseases of Women and Children & National Medical Products Administration Key Laboratory for Technical Research on Drug Products in Vitro and in Vivo Correlation, West China Second University Hospital, Sichuan University; Shuangliu Institute of Women's and Children's Health, Shuangliu Maternal and Child Health Hospital, Chengdu, Sichuan, China; Department of Epidemiology and Biostatistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wenling Chang
- Department of Epidemiology and Biostatistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ying Wen
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Yichao Huang
- Department of Toxicology, School of Public Health, Anhui Medical University, Hefei, China
| | - Yi-Xin Wang
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Da Chen
- School of Environment and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou, Guangdong, China
| | - Chun-Xia Yang
- Department of Epidemiology and Biostatistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China.
| | - Xiong-Fei Pan
- Section of Epidemiology and Population Health, Ministry of Education Key Laboratory of Birth Defects and Related Diseases of Women and Children & National Medical Products Administration Key Laboratory for Technical Research on Drug Products in Vitro and in Vivo Correlation, West China Second University Hospital, Sichuan University; Shuangliu Institute of Women's and Children's Health, Shuangliu Maternal and Child Health Hospital, Chengdu, Sichuan, China.
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Ramalhete L, Vigia E, Araújo R, Marques HP. Proteomics-Driven Biomarkers in Pancreatic Cancer. Proteomes 2023; 11:24. [PMID: 37606420 PMCID: PMC10443269 DOI: 10.3390/proteomes11030024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/28/2023] [Accepted: 08/03/2023] [Indexed: 08/23/2023] Open
Abstract
Pancreatic cancer is a devastating disease that has a grim prognosis, highlighting the need for improved screening, diagnosis, and treatment strategies. Currently, the sole biomarker for pancreatic ductal adenocarcinoma (PDAC) authorized by the U.S. Food and Drug Administration is CA 19-9, which proves to be the most beneficial in tracking treatment response rather than in early detection. In recent years, proteomics has emerged as a powerful tool for advancing our understanding of pancreatic cancer biology and identifying potential biomarkers and therapeutic targets. This review aims to offer a comprehensive survey of proteomics' current status in pancreatic cancer research, specifically accentuating its applications and its potential to drastically enhance screening, diagnosis, and treatment response. With respect to screening and diagnostic precision, proteomics carries the capacity to augment the sensitivity and specificity of extant screening and diagnostic methodologies. Nonetheless, more research is imperative for validating potential biomarkers and establishing standard procedures for sample preparation and data analysis. Furthermore, proteomics presents opportunities for unveiling new biomarkers and therapeutic targets, as well as fostering the development of personalized treatment strategies based on protein expression patterns associated with treatment response. In conclusion, proteomics holds great promise for advancing our understanding of pancreatic cancer biology and improving patient outcomes. It is essential to maintain momentum in investment and innovation in this arena to unearth more groundbreaking discoveries and transmute them into practical diagnostic and therapeutic strategies in the clinical context.
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Affiliation(s)
- Luís Ramalhete
- Blood and Transplantation Center of Lisbon—Instituto Português do Sangue e da Transplantação, Alameda das Linhas de Torres, n° 117, 1769-001 Lisbon, Portugal
- Nova Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
- iNOVA4Health—Advancing Precision Medicine, RG11: Reno-Vascular Diseases Group, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
| | - Emanuel Vigia
- Nova Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
- Centro Hospitalar de Lisboa Central, Department of Hepatobiliopancreatic and Transplantation, 1050-099 Lisbon, Portugal
| | - Rúben Araújo
- Nova Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
- CHRC—Comprehensive Health Research Centre, NOVA Medical School, 1150-199 Lisbon, Portugal
| | - Hugo Pinto Marques
- Nova Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
- Centro Hospitalar de Lisboa Central, Department of Hepatobiliopancreatic and Transplantation, 1050-099 Lisbon, Portugal
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Sulewska A, Pilz L, Manegold C, Ramlau R, Charkiewicz R, Niklinski J. A Systematic Review of Progress toward Unlocking the Power of Epigenetics in NSCLC: Latest Updates and Perspectives. Cells 2023; 12:cells12060905. [PMID: 36980246 PMCID: PMC10047383 DOI: 10.3390/cells12060905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/28/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
Epigenetic research has the potential to improve our understanding of the pathogenesis of cancer, specifically non-small-cell lung cancer, and support our efforts to personalize the management of the disease. Epigenetic alterations are expected to have relevance for early detection, diagnosis, outcome prediction, and tumor response to therapy. Additionally, epi-drugs as therapeutic modalities may lead to the recovery of genes delaying tumor growth, thus increasing survival rates, and may be effective against tumors without druggable mutations. Epigenetic changes involve DNA methylation, histone modifications, and the activity of non-coding RNAs, causing gene expression changes and their mutual interactions. This systematic review, based on 110 studies, gives a comprehensive overview of new perspectives on diagnostic (28 studies) and prognostic (25 studies) epigenetic biomarkers, as well as epigenetic treatment options (57 studies) for non-small-cell lung cancer. This paper outlines the crosstalk between epigenetic and genetic factors as well as elucidates clinical contexts including epigenetic treatments, such as dietary supplements and food additives, which serve as anti-carcinogenic compounds and regulators of cellular epigenetics and which are used to reduce toxicity. Furthermore, a future-oriented exploration of epigenetic studies in NSCLC is presented. The findings suggest that additional studies are necessary to comprehend the mechanisms of epigenetic changes and investigate biomarkers, response rates, and tailored combinations of treatments. In the future, epigenetics could have the potential to become an integral part of diagnostics, prognostics, and personalized treatment in NSCLC.
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Affiliation(s)
- Anetta Sulewska
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
- Correspondence: (A.S.); (J.N.)
| | - Lothar Pilz
- Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Christian Manegold
- Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Rodryg Ramlau
- Department of Oncology, Poznan University of Medical Sciences, 60-569 Poznan, Poland
| | - Radoslaw Charkiewicz
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Jacek Niklinski
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
- Correspondence: (A.S.); (J.N.)
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Ghosh AK, Shapiro MF, Abramson D. Closing the Knowledge Gap in the Long-Term Health Effects of Natural Disasters: A Research Agenda for Improving Environmental Justice in the Age of Climate Change. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:15365. [PMID: 36430084 PMCID: PMC9692460 DOI: 10.3390/ijerph192215365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/09/2022] [Accepted: 11/19/2022] [Indexed: 06/16/2023]
Abstract
Natural disasters continue to worsen in both number and intensity globally, but our understanding of their long-term consequences on individual and community health remains limited. As climate-focused researchers, we argue that a publicly funded research agenda that supports the comprehensive exploration of these risks, particularly among vulnerable groups, is urgently needed. This exploration must focus on the following three critical components of the research agenda to promote environmental justice in the age of climate change: (1) a commitment to long term surveillance and care to examine the health impacts of climate change over their life course; (2) an emphasis on interventions using implementation science frameworks; (3) the employment of a transdisciplinary approach to study, address, and intervene on structural disadvantage among vulnerable populations. Without doing so, we risk addressing these consequences in a reactive way at greater expense, limiting the opportunity to safeguard communities and vulnerable populations in the era of climate change.
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Affiliation(s)
- Arnab K. Ghosh
- Department of Medicine, Weill Cornell Medical College, Cornell University, Ithaca, NY 10065, USA
| | - Martin F. Shapiro
- Department of Medicine, Weill Cornell Medical College, Cornell University, Ithaca, NY 10065, USA
| | - David Abramson
- School of Global Public Health, New York University, 715/719 Broadway 12th Floor Room 1214, New York, NY 10003, USA
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Issah I, Arko-Mensah J, Rozek LS, Rentschler K, Agyekum TP, Dwumoh D, Batterman S, Robins TG, Fobil JN. Association between global DNA methylation (LINE-1) and occupational particulate matter exposure among informal electronic-waste recyclers in Ghana. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2022; 32:2406-2424. [PMID: 34404291 DOI: 10.1080/09603123.2021.1969007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Abstract
This study examined the associations between PM (2.5 and 10) and global DNA methylation among 100 e-waste workers and 51 non-e-waste workers serving as controls. Long interspersed nucleotide repetitive elements-1 (LINE-1) was measured by pyrosequencing. Personal PM2.5 and PM10 were measured over a 4-hour work-shift using real-time particulate monitors incorporated into a backpack . Linear regression models were used to assess the association between PM and LINE-1 DNA methylation. The concentrations of PM2.5 and PM10 were significantly higher among the e-waste workers than the controls (77.32 vs 34.88, p < 0.001 and 210.21 vs 121.92, p < 0.001, respectively). PM2.5 exposure was associated with increased LINE-1 CpG2 DNA methylation (β = 0.003; 95% CI; 0.001, 0.006; p = 0.022) but not with the average of all 4 CpG sites of LINE-1. In summary, high levels of PM2.5 exposure was associated with increased levels of global DNA methylation in a site-specific manner.
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Affiliation(s)
- Ibrahim Issah
- Department of Biological, Environmental and Occupational Health Sciences, University of Ghana, School of Public Health, Accra, Ghana
| | - John Arko-Mensah
- Department of Biological, Environmental and Occupational Health Sciences, University of Ghana, School of Public Health, Accra, Ghana
| | - Laura S Rozek
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Katie Rentschler
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Thomas P Agyekum
- Department of Biological, Environmental and Occupational Health Sciences, University of Ghana, School of Public Health, Accra, Ghana
| | - Duah Dwumoh
- Department of Biostatistics, University of Ghana School of Public Health, Legon, Ghana
| | - Stuart Batterman
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Thomas G Robins
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Julius N Fobil
- Department of Biological, Environmental and Occupational Health Sciences, University of Ghana, School of Public Health, Accra, Ghana
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Integrating epigenetics and metabolomics to advance treatments for pulmonary arterial hypertension. Biochem Pharmacol 2022; 204:115245. [PMID: 36096239 DOI: 10.1016/j.bcp.2022.115245] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/25/2022] [Accepted: 09/02/2022] [Indexed: 11/23/2022]
Abstract
Pulmonary arterial hypertension (PAH) is a devastating vascular disease with multiple etiologies. Emerging evidence supports a fundamental role for epigenetic machinery and metabolism in the initiation and progression of PAH. Here, we summarize emerging epigenetic mechanisms that have been identified as contributors to PAH evolution, specifically, DNA methylation, histone modifications, and microRNAs. Furthermore, the interplay between epigenetics with metabolism is explored while new crosstalk targets to be investigated in PAH are proposed that highlight multi-omics strategies including integrated epigenomics and metabolomics. Therapeutic opportunities and challenges associated with epigenetics and metabolomics in PAH are examined, highlighting the role that epigenetics and metabolomics have in facilitating early detection, personalized dietary plans, and advanced drug therapy for PAH.
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11
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Dupras C, Knoppers T, Palmour N, Beauchamp E, Liosi S, Siebert R, Berner AM, Beck S, Charest I, Joly Y. Researcher perspectives on ethics considerations in epigenetics: an international survey. Clin Epigenetics 2022; 14:110. [PMID: 36056446 PMCID: PMC9440515 DOI: 10.1186/s13148-022-01322-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 07/29/2022] [Indexed: 11/19/2022] Open
Abstract
Over the past decade, bioethicists, legal scholars and social scientists have started to investigate the potential implications of epigenetic research and technologies on medicine and society. There is growing literature discussing the most promising opportunities, as well as arising ethical, legal and social issues (ELSI). This paper explores the views of epigenetic researchers about some of these discussions. From January to March 2020, we conducted an online survey of 189 epigenetic researchers working in 31 countries. We questioned them about the scope of their field, opportunities in different areas of specialization, and ELSI in the conduct of research and knowledge translation. We also assessed their level of concern regarding four emerging non-medical applications of epigenetic testing—i.e., in life insurance, forensics, immigration and direct-to-consumer testing. Although there was strong agreement on DNA methylation, histone modifications, 3D structure of chromatin and nucleosomes being integral elements of the field, there was considerable disagreement on transcription factors, RNA interference, RNA splicing and prions. The most prevalent ELSI experienced or witnessed by respondents were in obtaining timely access to epigenetic data in existing databases, and in the communication of epigenetic findings by the media. They expressed high levels of concern regarding non-medical applications of epigenetics, echoing cautionary appraisals in the social sciences and humanities literature.
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Affiliation(s)
- Charles Dupras
- Centre of Genomics and Policy, McGill University, 740, Avenue Dr. Penfield, Suite 5200, Montreal, QC, H3A 0G1, Canada. .,School of Public Health, University of Montreal, 7101 Parc avenue, Montreal, QC, H3N 1X9, Canada.
| | - Terese Knoppers
- Centre of Genomics and Policy, McGill University, 740, Avenue Dr. Penfield, Suite 5200, Montreal, QC, H3A 0G1, Canada
| | - Nicole Palmour
- Centre of Genomics and Policy, McGill University, 740, Avenue Dr. Penfield, Suite 5200, Montreal, QC, H3A 0G1, Canada
| | - Elisabeth Beauchamp
- Centre of Genomics and Policy, McGill University, 740, Avenue Dr. Penfield, Suite 5200, Montreal, QC, H3A 0G1, Canada
| | - Stamatina Liosi
- Centre for Health Ethics and Law, University of Southampton, Building 4, Highfield, Southampton, SO17 1BJ, UK
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Alison May Berner
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 5PZ, UK
| | - Stephan Beck
- University College London (UCL) Cancer Institute, 72 Huntley Street, London, WC1E 6BT, UK
| | - Ian Charest
- Department of Psychology, Université de Montréal, 90, Avenue Vincent-d'Indy/Boulevard Édouard-Montpetit, Montréal, QC, H2V 2S9, Canada
| | - Yann Joly
- Centre of Genomics and Policy, McGill University, 740, Avenue Dr. Penfield, Suite 5200, Montreal, QC, H3A 0G1, Canada
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12
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Gorica E, Mohammed SA, Ambrosini S, Calderone V, Costantino S, Paneni F. Epi-Drugs in Heart Failure. Front Cardiovasc Med 2022; 9:923014. [PMID: 35911511 PMCID: PMC9326055 DOI: 10.3389/fcvm.2022.923014] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/17/2022] [Indexed: 11/13/2022] Open
Abstract
Unveiling the secrets of genome’s flexibility does not only foster new research in the field, but also gives rise to the exploration and development of novel epigenetic-based therapies as an approach to alleviate disease phenotypes. A better understanding of chromatin biology (DNA/histone complexes) and non-coding RNAs (ncRNAs) has enabled the development of epigenetic drugs able to modulate transcriptional programs implicated in cardiovascular diseases. This particularly applies to heart failure, where epigenetic networks have shown to underpin several pathological features, such as left ventricular hypertrophy, fibrosis, cardiomyocyte apoptosis and microvascular dysfunction. Targeting epigenetic signals might represent a promising approach, especially in patients with heart failure with preserved ejection fraction (HFpEF), where prognosis remains poor and breakthrough therapies have yet to be approved. In this setting, epigenetics can be employed for the development of customized therapeutic approaches thus paving the way for personalized medicine. Even though the beneficial effects of epi-drugs are gaining attention, the number of epigenetic compounds used in the clinical practice remains low suggesting that more selective epi-drugs are needed. From DNA-methylation changes to non-coding RNAs, we can establish brand-new regulations for drug targets with the aim of restoring healthy epigenomes and transcriptional programs in the failing heart. In the present review, we bring the timeline of epi-drug discovery and development, thus highlighting the emerging role of epigenetic therapies in heart failure.
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Affiliation(s)
- Era Gorica
- Center for Molecular Cardiology, University of Zürich, Schlieren, Switzerland.,Department of Pharmacy, University of Pisa, Pisa, Italy
| | - Shafeeq A Mohammed
- Center for Molecular Cardiology, University of Zürich, Schlieren, Switzerland
| | - Samuele Ambrosini
- Center for Molecular Cardiology, University of Zürich, Schlieren, Switzerland
| | | | - Sarah Costantino
- Center for Molecular Cardiology, University of Zürich, Schlieren, Switzerland.,Department of Cardiology, University Heart Center, Zurich, Switzerland
| | - Francesco Paneni
- Center for Molecular Cardiology, University of Zürich, Schlieren, Switzerland.,Department of Cardiology, University Heart Center, Zurich, Switzerland.,Department of Research and Education, University Hospital Zurich, Zurich, Switzerland
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13
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Zhou X, Chen H, Li J, Shi Y, Zhuang S, Liu N. The Role and Mechanism of Lysine Methyltransferase and Arginine Methyltransferase in Kidney Diseases. Front Pharmacol 2022; 13:885527. [PMID: 35559246 PMCID: PMC9086358 DOI: 10.3389/fphar.2022.885527] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/08/2022] [Indexed: 11/13/2022] Open
Abstract
Methylation can occur in both histones and non-histones. Key lysine and arginine methyltransferases under investigation for renal disease treatment include enhancer of zeste homolog 2 (EZH2), G9a, disruptor of telomeric silencing 1-like protein (DOT1L), and protein arginine methyltransferases (PRMT) 1 and 5. Recent studies have shown that methyltransferases expression and activity are also increased in several animal models of kidney injury, such as acute kidney injury(AKI), obstructive nephropathy, diabetic nephropathy and lupus nephritis. The inhibition of most methyltransferases can attenuate kidney injury, while the role of methyltransferase in different animal models remains controversial. In this article, we summarize the role and mechanism of lysine methyltransferase and arginine methyltransferase in various kidney diseases and highlight methyltransferase as a potential therapeutic target for kidney diseases.
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Affiliation(s)
- Xun Zhou
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Hui Chen
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jinqing Li
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yingfeng Shi
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shougang Zhuang
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Medicine, Rhode Island Hospital and Alpert Medical School, Brown University, Providence, RI, United States
| | - Na Liu
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
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14
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The existence of a nonclassical TCA cycle in the nucleus that wires the metabolic-epigenetic circuitry. Signal Transduct Target Ther 2021; 6:375. [PMID: 34728602 PMCID: PMC8563883 DOI: 10.1038/s41392-021-00774-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 09/12/2021] [Accepted: 09/15/2021] [Indexed: 12/12/2022] Open
Abstract
The scope and variety of the metabolic intermediates from the mitochondrial tricarboxylic acid (TCA) cycle that are engaged in epigenetic regulation of the chromatin function in the nucleus raise an outstanding question about how timely and precise supply/consumption of these metabolites is achieved in the nucleus. We report here the identification of a nonclassical TCA cycle in the nucleus (nTCA cycle). We found that all the TCA cycle-associated enzymes including citrate synthase (CS), aconitase 2 (ACO2), isocitrate dehydrogenase 3 (IDH3), oxoglutarate dehydrogenase (OGDH), succinyl-CoA synthetase (SCS), fumarate hydratase (FH), and malate dehydrogenase 2 (MDH2), except for succinate dehydrogenase (SDH), a component of electron transport chain for generating ATP, exist in the nucleus. We showed that these nuclear enzymes catalyze an incomplete TCA cycle similar to that found in cyanobacteria. We propose that the nTCA cycle is implemented mainly to generate/consume metabolic intermediates, not for energy production. We demonstrated that the nTCA cycle is intrinsically linked to chromatin dynamics and transcription regulation. Together, our study uncovers the existence of a nonclassical TCA cycle in the nucleus that links the metabolic pathway to epigenetic regulation.
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15
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Filipe AM, Lloyd S, Larivée A. Troubling Neurobiological Vulnerability: Psychiatric Risk and the Adverse Milieu in Environmental Epigenetics Research. FRONTIERS IN SOCIOLOGY 2021; 6:635986. [PMID: 33912612 PMCID: PMC8072338 DOI: 10.3389/fsoc.2021.635986] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/12/2021] [Indexed: 06/12/2023]
Abstract
In post-genomic science, the development of etiological models of neurobiological vulnerability to psychiatric risk has expanded exponentially in recent decades, particularly since the neuromolecular and biosocial turns in basic research. Among this research is that of McGill Group for Suicide Studies (MGSS) whose work centers on the identification of major risk factors and epigenetic traits that help to identify a specific profile of vulnerability to psychiatric conditions (e.g., depression) and predict high-risk behaviors (e.g., suicidality). Although the MGSS has attracted attention for its environmental epigenetic models of suicide risk over the years and the translation of findings from rodent studies into human populations, its overall agenda includes multiple research axes, ranging from retrospective studies to clinical and epidemiological research. Common to these research axes is a concern with the long-term effects of adverse experiences on maladaptive trajectories and negative mental health outcomes. As these findings converge with post-genomic understandings of health and also translate into new orientations in global public health, our article queries the ways in which neurobiological vulnerability is traced, measured, and profiled in environmental epigenetics and in the MGSS research. Inspired by the philosophy of Georges Canguilhem and by literature from the social studies of risk and critical public health, we explore how the epigenetic models of neurobiological vulnerability tie into a particular way of thinking about the normal, the pathological, and the milieu in terms of risk. Through this exploration, we examine how early life adversity (ELA) and neurobiological vulnerability are localized and materialized in those emerging models while also considering their broader conceptual and translational implications in the contexts of mental health and global public health interventions. In particular, we consider how narratives of maladaptive trajectories and vulnerable selves who are at risk of harm might stand in as a "new pathological" with healthy trajectories and resilient selves being potentially equated with a "new normal" way of living in the face of adversity. By troubling neurobiological vulnerability as a universal biosocial condition, we suggest that an ecosocial perspective may help us to think differently about the dynamics of mental health and distress in the adverse milieu.
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Affiliation(s)
- Angela Marques Filipe
- Department of Sociology and Centre for Research on Children & Families, McGill University, Montréal, QC, Canada
- Centre for Biomedicine, Self & Society, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephanie Lloyd
- Department of Anthropology, Université Laval, Québec, QC, Canada
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16
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Irvin MR, Jones AC, Claas SA, Arnett DK. DNA Methylation and Blood Pressure Phenotypes: A Review of the Literature. Am J Hypertens 2021; 34:267-273. [PMID: 33821945 DOI: 10.1093/ajh/hpab026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/23/2021] [Accepted: 01/27/2021] [Indexed: 12/20/2022] Open
Abstract
Genetic studies of DNA have been unable to explain a significant portion of the variance of the estimated heritability of blood pressure (BP). Epigenetic mechanisms, particularly DNA methylation, have helped explain additional biological processes linked to BP phenotypes and diseases. Candidate gene methylation studies and genome-wide methylation studies of BP have highlighted impactful cytosine-phosphate-guanine (CpG) markers across different ethnicities. Furthermore, many of these BP-related CpG sites are also linked to metabolism-related phenotypes. Integrating epigenome-wide association study data with other layers of molecular data such as genotype data (from single nucleotide polymorphism arrays or sequencing), other epigenetic data, and/or transcriptome data can provide additional information about the significance and complexity of these relationships. Recent data suggest that epigenetic changes can be consequences rather than causes of BP variation. Finally, these data can give insight into downstream effects of long-standing high BP (due to target organ damage (TOD)). The current review provides a literature overview of epigenetic modifications in BP and TOD. Recent studies strongly support the importance of epigenetic modifications, such as DNA methylation, in BP and TOD for relevant biological insights, reliable biomarkers, and possible future therapeutics.
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Affiliation(s)
- Marguerite R Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Alana C Jones
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Steven A Claas
- Department of Epidemiology, College of Public Health, University of Kentucky, Lexington, Kentucky, USA
| | - Donna K Arnett
- Department of Epidemiology, College of Public Health, University of Kentucky, Lexington, Kentucky, USA
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17
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Shantz E, Elliott SJ. From social determinants to social epigenetics: Health geographies of chronic disease. Health Place 2021; 69:102561. [PMID: 33761408 DOI: 10.1016/j.healthplace.2021.102561] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 01/25/2021] [Accepted: 03/09/2021] [Indexed: 01/11/2023]
Abstract
Social epigenetics explores relationships between social factors and health inequities embodied at the molecular level. Through modulating gene expression, epigenetic changes resulting from human-environment interactions may play a role in shaping health trajectories. This paper applies a health geography lens to explore the potential and support for conducting social epigenetic studies of chronic diseases with complex and dynamic etiologies. In so doing, we argue that social epigenetics presents a novel space for investigations of health and disease that is transdisciplinary and builds upon new understandings of bodies and place-based experiences. Given gender disparities in chronic diseases, we adopt a feminist perspective that cogitates the transactive relationships between gender and health/ill-health as mediated by biosocial processes at a variety of scales. Looking forward to the practical undertaking of social epigenetic studies, we assess existing theoretical and methodological support as well as insights to be gained. Reflecting upon the central tenets of health geography, we propose a unique positionality for health geographers to drive this field forward.
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Affiliation(s)
- Emily Shantz
- Department of Geography & Environmental Management, Faculty of Environment, University of Waterloo, 200 University Ave W, Waterloo, ON, N2L 3G1, Canada.
| | - Susan J Elliott
- Department of Geography & Environmental Management, Faculty of Environment, University of Waterloo, 200 University Ave W, Waterloo, ON, N2L 3G1, Canada
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18
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19
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Rugo HS, Jacobs I, Sharma S, Scappaticci F, Paul TA, Jensen-Pergakes K, Malouf GG. The Promise for Histone Methyltransferase Inhibitors for Epigenetic Therapy in Clinical Oncology: A Narrative Review. Adv Ther 2020; 37:3059-3082. [PMID: 32445185 PMCID: PMC7467409 DOI: 10.1007/s12325-020-01379-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Indexed: 12/21/2022]
Abstract
Epigenetic processes are essential for normal development and the maintenance of tissue-specific gene expression in mammals. Changes in gene expression and malignant cellular transformation can result from disruption of epigenetic mechanisms, and global disruption in the epigenetic landscape is a key feature of cancer. The study of epigenetics in cancer has revealed that human cancer cells harbor both genetic alterations and epigenetic abnormalities that interplay at all stages of cancer development. Unlike genetic mutations, epigenetic aberrations are potentially reversible through epigenetic therapy, providing a therapeutically relevant treatment option. Histone methyltransferase inhibitors are emerging as an epigenetic therapy approach with great promise in the field of clinical oncology. The recent accelerated approval of the enhancer of zeste homolog 2 (EZH2; also known as histone-lysine N-methyltransferase EZH2) inhibitor tazemetostat for metastatic or locally advanced epithelioid sarcoma marks the first approval of such a compound for the treatment of cancer. Many other histone methyltransferase inhibitors are currently in development, some of which are being tested in clinical studies. This review focuses on histone methyltransferase inhibitors, highlighting their potential in the treatment of cancer. We also discuss the role for such epigenetic drugs in overcoming epigenetically driven drug resistance mechanisms, and their value in combination with other therapeutic approaches such as immunotherapy.
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20
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Sherwood WB, Kothalawala DM, Kadalayil L, Ewart S, Zhang H, Karmaus W, Arshad SH, Holloway JW, Rezwan FI. Epigenome-Wide Association Study Reveals Duration of Breastfeeding Is Associated with Epigenetic Differences in Children. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E3569. [PMID: 32443666 PMCID: PMC7277240 DOI: 10.3390/ijerph17103569] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/15/2020] [Accepted: 05/17/2020] [Indexed: 12/21/2022]
Abstract
Several small studies have shown associations between breastfeeding and genome-wide DNA methylation (DNAm). We performed a comprehensive Epigenome-Wide Association Study (EWAS) to identify associations between breastfeeding and DNAm patterns in childhood. We analysed DNAm data from the Isle of Wight Birth Cohort at birth, 10, 18 and 26 years. The feeding method was categorized as breastfeeding duration >3 months and >6 months, and exclusive breastfeeding duration >3 months. EWASs using robust linear regression were performed to identify differentially methylated positions (DMPs) in breastfed and non-breastfed children at age 10 (false discovery rate of 5%). Differentially methylated regions (DMRs) were identified using comb-p. The persistence of significant associations was evaluated in neonates and individuals at 18 and 26 years. Two DMPs, in genes SNX25 and LINC00840, were significantly associated with breastfeeding duration >6 months at 10 years and was replicated for >3 months of exclusive breastfeeding. Additionally, a significant DMR spanning the gene FDFT1 was identified in 10-year-old children who were exposed to a breastfeeding duration >3 months. None of these signals persisted to 18 or 26 years. This study lends further support for a suggestive role of DNAm in the known benefits of breastfeeding on a child's future health.
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Affiliation(s)
- William B. Sherwood
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; (W.B.S.); (D.M.K.); (L.K.); (F.I.R.)
| | - Dilini M. Kothalawala
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; (W.B.S.); (D.M.K.); (L.K.); (F.I.R.)
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK;
| | - Latha Kadalayil
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; (W.B.S.); (D.M.K.); (L.K.); (F.I.R.)
| | - Susan Ewart
- College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA;
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, 236A Robison Hall, Memphis, TN 38152, USA; (H.Z.); (W.K.)
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, 236A Robison Hall, Memphis, TN 38152, USA; (H.Z.); (W.K.)
| | - S. Hasan Arshad
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK;
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
- The David Hide Asthma and Allergy Research Centre, St Mary’s Hospital, Isle of Wight PO30 5TG UK
| | - John W. Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; (W.B.S.); (D.M.K.); (L.K.); (F.I.R.)
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK;
| | - Faisal I. Rezwan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; (W.B.S.); (D.M.K.); (L.K.); (F.I.R.)
- School of Water, Energy and Environment, Cranfield University, Cranfield, Bedfordshire MK43 0AL, UK
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21
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D’Aquila P, Lynn Carelli L, De Rango F, Passarino G, Bellizzi D. Gut Microbiota as Important Mediator Between Diet and DNA Methylation and Histone Modifications in the Host. Nutrients 2020; 12:E597. [PMID: 32106534 PMCID: PMC7146473 DOI: 10.3390/nu12030597] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 02/21/2020] [Accepted: 02/21/2020] [Indexed: 12/14/2022] Open
Abstract
The human gut microbiota is a complex ecosystem consisting of trillions of microorganisms that inhabit symbiotically on and in the human intestine. They carry out, through the production of a series of metabolites, many important metabolic functions that complement the activity of mammalian enzymes and play an essential role in host digestion. Interindividual variability of microbiota structure, and consequently of the expression of its genes (microbiome), was largely ascribed to the nutritional regime. Diet influences microbiota composition and function with short- and long-term effects. In spite of the vast literature, molecular mechanisms underlying these effects still remain elusive. In this review, we summarized the current evidence on the role exerted by gut microbiota and, more specifically, by its metabolites in the establishment of the host epigenome. The interest in this topic stems from the fact that, by modulating DNA methylation and histone modifications, the gut microbiota does affect the cell activities of the hosting organism.
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Affiliation(s)
- Patrizia D’Aquila
- Department of Biology, Ecology and Earth Sciences (DIBEST), University of Calabria, 87036 Rende, Italy; (F.D.R.); (G.P.); (D.B.)
| | | | - Francesco De Rango
- Department of Biology, Ecology and Earth Sciences (DIBEST), University of Calabria, 87036 Rende, Italy; (F.D.R.); (G.P.); (D.B.)
| | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Sciences (DIBEST), University of Calabria, 87036 Rende, Italy; (F.D.R.); (G.P.); (D.B.)
| | - Dina Bellizzi
- Department of Biology, Ecology and Earth Sciences (DIBEST), University of Calabria, 87036 Rende, Italy; (F.D.R.); (G.P.); (D.B.)
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22
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Jeremias G, Gonçalves FJM, Pereira JL, Asselman J. Prospects for incorporation of epigenetic biomarkers in human health and environmental risk assessment of chemicals. Biol Rev Camb Philos Soc 2020; 95:822-846. [PMID: 32045110 DOI: 10.1111/brv.12589] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 01/28/2020] [Accepted: 01/30/2020] [Indexed: 12/18/2022]
Abstract
Epigenetic mechanisms have gained relevance in human health and environmental studies, due to their pivotal role in disease, gene × environment interactions and adaptation to environmental change and/or contamination. Epigenetic mechanisms are highly responsive to external stimuli and a wide range of chemicals has been shown to determine specific epigenetic patterns in several organisms. Furthermore, the mitotic/meiotic inheritance of such epigenetic marks as well as the resulting changes in gene expression and cell/organismal phenotypes has now been demonstrated. Therefore, epigenetic signatures are interesting candidates for linking environmental exposures to disease as well as informing on past exposures to stressors. Accordingly, epigenetic biomarkers could be useful tools in both prospective and retrospective risk assessment but epigenetic endpoints are currently not yet incorporated into risk assessments. Achieving a better understanding on this apparent impasse, as well as identifying routes to promote the application of epigenetic biomarkers within environmental risk assessment frameworks are the objectives of this review. We first compile evidence from human health studies supporting the use of epigenetic exposure-associated changes as reliable biomarkers of exposure. Then, specifically focusing on environmental science, we examine the potential and challenges of developing epigenetic biomarkers for environmental fields, and discuss useful organisms and appropriate sequencing techniques to foster their development in this context. Finally, we discuss the practical incorporation of epigenetic biomarkers in the environmental risk assessment of chemicals, highlighting critical data gaps and making key recommendations for future research within a regulatory context.
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Affiliation(s)
- Guilherme Jeremias
- Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal.,CESAM - Centre for Environmental and Marine Studies, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Fernando J M Gonçalves
- Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal.,CESAM - Centre for Environmental and Marine Studies, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Joana L Pereira
- Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal.,CESAM - Centre for Environmental and Marine Studies, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Jana Asselman
- Laboratory of Environmental Toxicology and Aquatic Ecology, Environmental Toxicology Unit - GhEnToxLab, Ghent University, 9000, Gent, Belgium
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23
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Hamamoto R, Komatsu M, Takasawa K, Asada K, Kaneko S. Epigenetics Analysis and Integrated Analysis of Multiomics Data, Including Epigenetic Data, Using Artificial Intelligence in the Era of Precision Medicine. Biomolecules 2019; 10:biom10010062. [PMID: 31905969 PMCID: PMC7023005 DOI: 10.3390/biom10010062] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 12/20/2019] [Accepted: 12/27/2019] [Indexed: 12/14/2022] Open
Abstract
To clarify the mechanisms of diseases, such as cancer, studies analyzing genetic mutations have been actively conducted for a long time, and a large number of achievements have already been reported. Indeed, genomic medicine is considered the core discipline of precision medicine, and currently, the clinical application of cutting-edge genomic medicine aimed at improving the prevention, diagnosis and treatment of a wide range of diseases is promoted. However, although the Human Genome Project was completed in 2003 and large-scale genetic analyses have since been accomplished worldwide with the development of next-generation sequencing (NGS), explaining the mechanism of disease onset only using genetic variation has been recognized as difficult. Meanwhile, the importance of epigenetics, which describes inheritance by mechanisms other than the genomic DNA sequence, has recently attracted attention, and, in particular, many studies have reported the involvement of epigenetic deregulation in human cancer. So far, given that genetic and epigenetic studies tend to be accomplished independently, physiological relationships between genetics and epigenetics in diseases remain almost unknown. Since this situation may be a disadvantage to developing precision medicine, the integrated understanding of genetic variation and epigenetic deregulation appears to be now critical. Importantly, the current progress of artificial intelligence (AI) technologies, such as machine learning and deep learning, is remarkable and enables multimodal analyses of big omics data. In this regard, it is important to develop a platform that can conduct multimodal analysis of medical big data using AI as this may accelerate the realization of precision medicine. In this review, we discuss the importance of genome-wide epigenetic and multiomics analyses using AI in the era of precision medicine.
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Affiliation(s)
- Ryuji Hamamoto
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (M.K.); (K.T.); (K.A.); (S.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
- Correspondence: ; Tel.: +81-3-3547-5271
| | - Masaaki Komatsu
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (M.K.); (K.T.); (K.A.); (S.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
| | - Ken Takasawa
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (M.K.); (K.T.); (K.A.); (S.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
| | - Ken Asada
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (M.K.); (K.T.); (K.A.); (S.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
| | - Syuzo Kaneko
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (M.K.); (K.T.); (K.A.); (S.K.)
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Abstract
Objectives: Firefighters have elevated cancer incidence and mortality rates. MicroRNAs play prominent roles in carcinogenesis, but have not been previously evaluated in firefighters. Methods: Blood from 52 incumbent and 45 new recruit nonsmoking firefighters was analyzed for microRNA expression, and the results adjusted for age, obesity, ethnicity, and multiple comparisons. Results: Nine microRNAs were identified with at least a 1.5-fold significant difference between groups. All six microRNAs with decreased expression in incumbent firefighters have been reported to have tumor suppressor activity or are associated with cancer survival, and two of the three microRNAs with increased expression in incumbent firefighters have activities consistent with cancer promotion, with the remaining microRNA associated with neurological disease. Conclusion: Incumbent firefighters showed differential microRNA expression compared with new recruits, providing potential mechanisms for increased cancer risk in firefighters.
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Bhargava A, Shukla A, Bunkar N, Shandilya R, Lodhi L, Kumari R, Gupta PK, Rahman A, Chaudhury K, Tiwari R, Goryacheva IY, Mishra PK. Exposure to ultrafine particulate matter induces NF-κβ mediated epigenetic modifications. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 252:39-50. [PMID: 31146237 DOI: 10.1016/j.envpol.2019.05.065] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/13/2019] [Accepted: 05/13/2019] [Indexed: 06/09/2023]
Abstract
Exposure to ultrafine particulate matter (PM0.1) is positively associated with the etiology of different acute and chronic disorders; however, the in-depth biological imprints that link these submicron particles with the disturbances in the epigenomic machinery are not well defined. Earlier, we showed that exposure to these particles causes significant disturbances in the mitochondrial machinery and triggers PI-3-kinase mediated DNA damage responses. In the present study, we aimed to further understand the epigenomic insights of the ultrafine PM exposure. The higher levels of intracellular reactive oxygen species and depleted Nrf-2 in ultrafine PM exposed cells reconfirmed its potential to induce oxidative stress. Importantly, the observed increase in the levels of NF-κβ and associated cytokines among exposed cells suggested the activation of NF-κβ mediated inflammatory loop which potentially serves as a platform for initiating epigenetic insinuations. This fact was strongly supported by the altered miRNA expression profile of the ultrafine PM exposed cells. These NF-κβ induced miRNA alterations were also found to be associated with other epigenetic targets as the exposed cells showed higher expression levels of DNA methyltransferases which positively corresponded with the global changes in DNA methylation levels. Upon further analysis, significant alterations in histone code were also reported in ultrafine PM exposed cells. Conclusively our results suggested that NF-κβ acts as an inflammatory switch that possesses the potential to induce genome-wide epigenetic modification upon ultrafine PM exposure.
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Affiliation(s)
- Arpit Bhargava
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Anushi Shukla
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Neha Bunkar
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Ruchita Shandilya
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Lalit Lodhi
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Roshani Kumari
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Pushpendra Kumar Gupta
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Akhlaqur Rahman
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Koel Chaudhury
- School of Medical Science & Technology, Indian Institute of Technology, Kharagpur, India
| | - Rajnarayan Tiwari
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Irina Yu Goryacheva
- Department of General and Inorganic Chemistry, Saratov State University, Saratov, Russia
| | - Pradyumna Kumar Mishra
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India.
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Hognon C, Gebus A, Barone G, Monari A. Human DNA Telomeres in Presence of Oxidative Lesions: The Crucial Role of Electrostatic Interactions on the Stability of Guanine Quadruplexes. Antioxidants (Basel) 2019; 8:antiox8090337. [PMID: 31443537 PMCID: PMC6770428 DOI: 10.3390/antiox8090337] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/14/2019] [Accepted: 08/20/2019] [Indexed: 01/23/2023] Open
Abstract
By using all atom molecular dynamics simulations, we studied the behavior of human DNA telomere sequences in guanine quadruplex (G4) conformation and in the presence of oxidative lesions, namely abasic sites. In particular, we evidenced that while removing one guanine base induces a significant alteration and destabilization of the involved leaflet, human telomere oligomers tend, in most cases, to maintain at least a partial quadruplex structure, eventually by replacing the empty site with undamaged guanines of different leaflets. This study shows that (i) the disruption of the quadruplex leaflets induces the release of at least one of the potassium cations embedded in the quadruplex channel and that (ii) the electrostatic interactions of the DNA sequence with the aforementioned cations are fundamental to the maintenance of the global quadruplex structure.
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Affiliation(s)
- Cecilia Hognon
- Université de Lorraine, CNRS, LPCT UMR 7019, F54000 Nancy, France.
| | - Adrien Gebus
- Université de Lorraine, CNRS, LPCT UMR 7019, F54000 Nancy, France
| | - Giampaolo Barone
- Department of Biological, Chenical and Pharmaceutical Sciences and Technologies, Università di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | - Antonio Monari
- Université de Lorraine, CNRS, LPCT UMR 7019, F54000 Nancy, France.
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Hognon C, Besancenot V, Gruez A, Grandemange S, Monari A. Cooperative Effects of Cytosine Methylation on DNA Structure and Dynamics. J Phys Chem B 2019; 123:7365-7371. [PMID: 31365827 DOI: 10.1021/acs.jpcb.9b05835] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The behavior of the structural parameters of DNA considering different levels of methylation in CpG islands is studied by means of full-atom molecular dynamics simulations and electronic circular dichroism, both in an artificial model system and in a gene promoter sequence. It is demonstrated that methylation although intrinsically brings quite local perturbations may, if its level is high enough, induce cooperative effects that strongly modify the DNA backbone torsional parameters altering the helicity as compared to the nonmethylated case. Because methylation of the CpG island is correlated with the regulation of gene expression, understanding the structural modifications induced in DNA is crucial to characterize all the fine equilibria into play in epigenetics phenomena.
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Affiliation(s)
- Cécilia Hognon
- Université de Lorraine and CNRS, UMR 7019 LPCT , F-54000 Nancy , France
| | | | - Arnaud Gruez
- Université de Lorraine and CNRS, UMR 7356 IMOPA , F-54000 Nancy , France
| | | | - Antonio Monari
- Université de Lorraine and CNRS, UMR 7019 LPCT , F-54000 Nancy , France
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Lozupone M, La Montagna M, D'Urso F, Daniele A, Greco A, Seripa D, Logroscino G, Bellomo A, Panza F. The Role of Biomarkers in Psychiatry. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1118:135-162. [PMID: 30747421 DOI: 10.1007/978-3-030-05542-4_7] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Psychiatric illnesses are cognitive and behavioral disorders of the brain. At present, psychiatric diagnosis is based on DSM-5 criteria. Even if endophenotype specificity for psychiatric disorders is discussed, it is difficult to study and identify psychiatric biomarkers to support diagnosis, prognosis, or clinical response to treatment. This chapter investigates the innovative biomarkers of psychiatric diseases for diagnosis and personalized treatment, in particular post-genomic data and proteomic analyses.
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Affiliation(s)
- Madia Lozupone
- Neurodegenerative Disease Unit, Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | - Maddalena La Montagna
- Psychiatric Unit, Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Francesca D'Urso
- Psychiatric Unit, Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Antonio Daniele
- Institute of Neurology, Catholic University of Sacred Heart, Rome, Italy.,Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Antonio Greco
- Geriatric Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, Foggia, Italy
| | - Davide Seripa
- Geriatric Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, Foggia, Italy
| | - Giancarlo Logroscino
- Neurodegenerative Disease Unit, Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari Aldo Moro, Bari, Italy.,Department of Clinical Research in Neurology, University of Bari Aldo Moro, Lecce, Italy
| | - Antonello Bellomo
- Psychiatric Unit, Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Francesco Panza
- Neurodegenerative Disease Unit, Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari Aldo Moro, Bari, Italy. .,Geriatric Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, Foggia, Italy. .,Department of Clinical Research in Neurology, University of Bari Aldo Moro, Lecce, Italy.
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Soza-Ried C, Bustamante E, Caglevic C, Rolfo C, Sirera R, Marsiglia H. Oncogenic role of arsenic exposure in lung cancer: A forgotten risk factor. Crit Rev Oncol Hematol 2019; 139:128-133. [PMID: 30878179 DOI: 10.1016/j.critrevonc.2019.01.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 01/11/2019] [Accepted: 01/17/2019] [Indexed: 12/14/2022] Open
Abstract
Several drinkable water sources worldwide have been highly contaminated with arsenic, which means that an estimated 160 million people have been exposed to this chemical agent. If we analyse exposure by region, we will find a high correlation between arsenic contamination and the incidence of lung cancer (among other malignancies). In order to determine what the risks of these exposures are, we need to understand how this chemical is processed in our body and how it is linked to cancer. In this article we reviewed how biotransformation of ingested arsenic may lead to cancer by modulating the activation of several essential signalling pathways such as EGFR, PI3K/AKT, RTK/Ras/PI3K, JNK/STAT3 and Nrf2-KEAP1; by producing epigenetics modifications and by disrupting normal expression of miRNAs. In order to design effective health policies, educational strategies, decontaminations plans and effective medical treatments are necessary to understand the impact of arsenic pollution and the relevance of the environment in our health.
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Affiliation(s)
- Cristian Soza-Ried
- Escuela de Bioquímica, Facultad de Ciencia, Universidad San Sebastián, Santiago, Chile; Fundación Oncoloop, Santiago, Chile
| | - Eva Bustamante
- Instituto Oncológico Fundación Arturo López, Santiago, Chile.
| | - Christian Caglevic
- Departamento Oncología Médica, Clínica Alemana, Santiago, Chile; Instituto Oncológico Fundación Arturo López, Santiago, Chile
| | - Christian Rolfo
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, USA
| | - Rafael Sirera
- Departamento de Biotecnología, Universitat Politenica de Valencia, España
| | - Hugo Marsiglia
- Instituto Oncológico Fundación Arturo López, Santiago, Chile
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Wu Y, Peterson KE, Sánchez BN, Dolinoy DC, Mercado-Garcia A, Téllez-Rojo MM, Goodrich JM. Association of blood leukocyte DNA methylation at LINE-1 and growth-related candidate genes with pubertal onset and progression. Epigenetics 2018; 13:1222-1233. [PMID: 30582410 PMCID: PMC6986794 DOI: 10.1080/15592294.2018.1556198] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 10/01/2018] [Accepted: 11/21/2018] [Indexed: 01/15/2023] Open
Abstract
Puberty is a developmentally plastic phase. Variations in pubertal tempo have implications for the risk of later adult diseases. Influences on pubertal tempo have been widely discussed, but the underlying biological mechanisms remain unclear. Epigenetic modifications are known to regulate development processes; they could play an important role in affecting pubertal outcomes. We conducted a population-based analysis to investigate the association of peripubertal blood DNA methylation at LINE-1 and growth-related candidate genes with pubertal onset and progression in healthy adolescents. The analytic sample included 114 males and 129 females aged 10 to 18 years. DNA methylation at growth-related candidate loci IGF2, H19, HSD11B2, as well as LINE-1 repetitive elements were quantified. Cox survival and ordinal regression models were used to examine sex- and locus-specific associations of epigenetic markers with pubertal development using physician-assessed Tanner stages and self-reported menarche, adjusted for covariates. Among boys, DNA methylation at H19 was associated with later pubarche. HSD11B2 methylation was associated with earlier onset of pubic hair and genitalia development and slower pubertal progression. IGF2 was associated with later onset of genital development. Among girls, LINE-1 methylation was associated with later onset of breast development. For each percent increase of methylation at H19, there was 5% increased odds in the earlier onset of breast development. DNA methylation of IGF2 was associated with earlier onset of pubic hair. DNA methylation at genes known to influence early-life growth may also influence pubertal outcomes.
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Affiliation(s)
- Yue Wu
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Karen E. Peterson
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Human Growth and Development, University of Michigan, Ann Arbor, MI, USA
| | - Brisa N. Sánchez
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Dana C. Dolinoy
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Human Growth and Development, University of Michigan, Ann Arbor, MI, USA
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Adriana Mercado-Garcia
- Center for Research on Nutrition and Health, National Institute of Public Health, Cuernavaca, Morelos, México
| | - Martha M. Téllez-Rojo
- Center for Research on Nutrition and Health, National Institute of Public Health, Cuernavaca, Morelos, México
| | - Jaclyn M. Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
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Pazos F, Garcia-Moreno A, Oliveros JC. Automatic detection of genomic regions with informative epigenetic patterns. BMC Genomics 2018; 19:847. [PMID: 30486775 PMCID: PMC6264639 DOI: 10.1186/s12864-018-5286-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 11/20/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Epigenetic phenomena are crucial for explaining the phenotypic plasticity seen in the cells of different tissues, developmental stages and diseases, all holding the same DNA sequence. As technology is allowing to retrieve epigenetic information in a genome-wide fashion, massive epigenomic datasets are being accumulated in public repositories. New approaches are required to mine those data to extract useful knowledge. We present here an automatic approach for detecting genomic regions with epigenetic variation patterns across samples related to a grouping of these samples, as a way of detecting regions functionally associated to the phenomenon behind the classification. RESULTS We show that the regions automatically detected by the method in the whole human genome associated to three different classifications of a set of epigenomes (cancer vs. healthy, brain vs. other organs, and fetal vs. adult tissues) are enriched in genes associated to these processes. CONCLUSIONS The method is fully automatic and can exhaustively scan the whole human genome at any resolution using large collections of epigenomes as input, although it also produces good results with small datasets. Consequently, it will be valuable for obtaining functional information from the incoming epigenomic information as it continues to accumulate.
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Affiliation(s)
- Florencio Pazos
- National Center for Biotechnology (CNB-CSIC), c/ Darwin, 3, 28049 Madrid, Spain
| | | | - Juan C. Oliveros
- National Center for Biotechnology (CNB-CSIC), c/ Darwin, 3, 28049 Madrid, Spain
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32
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Yau MYC, Xu L, Huang CL, Wong CM. Long Non-Coding RNAs in Obesity-Induced Cancer. Noncoding RNA 2018; 4:E19. [PMID: 30154386 PMCID: PMC6162378 DOI: 10.3390/ncrna4030019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 08/22/2018] [Accepted: 08/27/2018] [Indexed: 01/17/2023] Open
Abstract
Many mechanisms of obesity-induced cancers have been proposed. However, it remains unclear whether or not long non-coding RNAs (lncRNAs) play any role in obesity-induced cancers. In this article, we briefly discuss the generally accepted hypotheses explaining the mechanisms of obesity-induced cancers, summarize the latest evidence for the expression of a number of well-known cancer-associated lncRNAs in obese subjects, and propose the potential contribution of lncRNAs to obesity-induced cancers. We hope this review can serve as an inspiration to scientists to further explore the regulatory roles of lncRNAs in the development of obesity-induced cancers. Those findings will be fundamental in the development of effective therapeutics or interventions to combat this life-threatening adverse effect of obesity.
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Affiliation(s)
- Mabel Yin-Chun Yau
- School of Medical and Health Sciences, Tung Wah College, Hong Kong, China.
| | - Lu Xu
- Department of Medicine, The University of Hong Kong, Hong Kong, China.
| | - Chien-Ling Huang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China.
| | - Chi-Ming Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China.
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Liu J, Wang W, Zhu J, Li Y, Luo L, Huang Y, Zhang W. Di(2-ethylhexyl) phthalate (DEHP) influences follicular development in mice between the weaning period and maturity by interfering with ovarian development factors and microRNAs. ENVIRONMENTAL TOXICOLOGY 2018; 33:535-544. [PMID: 29385306 DOI: 10.1002/tox.22540] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/15/2018] [Accepted: 01/18/2018] [Indexed: 06/07/2023]
Abstract
Although studies have shown that di(2-ethylhexyl) phthalate (DEHP) can disrupt ovarian function, few reports have focused on follicular development in mice between the weaning period and maturity, especially with respect to microRNA (miRNA) expression. In this study, 21-day-old ICR mice were administered DEHP at doses of 0, 100, 400, and 1600 mg/(kg d) for 6 weeks by gavage. After DEHP administration, a significant decrease in the expression of follicle development-related factors (including c-kit, kitl, gdf9, and atm) was observed by quantitative real-time PCR (RT-PCR), but no significant difference in the proteins encoded by these genes was observed by Western blot. Bisulfite sequencing suggested that the total methylation percentages of promoter regions of these genes were not notably altered after DEHP exposure. However, RT-PCR revealed a significantly increased expression of ovarian miRNAs (let-7b, miR-17-5p miR-181a, and miR-151), which inhibit follicular granulosa cell proliferation. Overall, this study showed that DEHP administration from weaning to maturity could suppress the mRNA expression of follicular development factors, and this effect was not achieved through changes in the methylation of DNA in CpG islands of development factors. In addition, DEHP was shown to induce miRNAs to inhibit the proliferation of follicular granulosa cells and the anti-apoptosis function of KITL and GDF9 while increasing bax/bcl2 expression to further promote the apoptosis of granulosa cells.
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Affiliation(s)
- Jin Liu
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment factors and Cancer, Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, No. 1 Xuefu North Road, University Town, Fuzhou, 350122, China
| | - Wenxiang Wang
- Department of Health Inspection and Quarantine, School of Public Health, Fujian Medical University, No. 1 Xuefu North Road, University Town, Fuzhou, 350122, China
| | - Jianlin Zhu
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment factors and Cancer, Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, No. 1 Xuefu North Road, University Town, Fuzhou, 350122, China
| | - Yuchen Li
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment factors and Cancer, Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, No. 1 Xuefu North Road, University Town, Fuzhou, 350122, China
| | - Lingfeng Luo
- Fujian Provincial Key Laboratory of Environment factors and Cancer, Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, No. 1 Xuefu North Road, University Town, Fuzhou, 350122, China
| | - Yuanyuan Huang
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment factors and Cancer, Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, No. 1 Xuefu North Road, University Town, Fuzhou, 350122, China
| | - Wenchang Zhang
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment factors and Cancer, Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, No. 1 Xuefu North Road, University Town, Fuzhou, 350122, China
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Moraru A, de Almeida MM, Degryse JM. PALTEM: What Parameters Should Be Collected in Disaster Settings to Assess the Long-Term Outcomes of Famine? INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15050857. [PMID: 29693637 PMCID: PMC5981896 DOI: 10.3390/ijerph15050857] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/14/2018] [Accepted: 04/21/2018] [Indexed: 12/18/2022]
Abstract
Evidence suggests that nutritional status during fetal development and early life leaves an imprint on the genome, which leads to health outcomes not only on a person as an adult but also on his offspring. The purpose of this study is to bring forth an overview of the relevant parameters that need to be collected to assess the long-term and transgenerational health outcomes of famine. A literature search was conducted for the most pertinent articles on the epigenetic effects of famine. The results were compiled, synthesized and discussed with an expert in genetics for critical input and validation. Prenatal and early life exposure to famine was associated with metabolic, cardiovascular, respiratory, reproductive, neuropsychiatric and oncologic diseases. We propose a set of parameters to be collected in disaster settings to assess the long-term outcomes of famine: PALTEM (parameters to assess long-term effects of malnutrition).
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Affiliation(s)
- Alexandra Moraru
- Centre for Research on the Epidemiology of Disasters, Université Catholique de Louvain, Brussels 1200, Belgium.
| | - Maria Moitinho de Almeida
- Centre for Research on the Epidemiology of Disasters, Université Catholique de Louvain, Brussels 1200, Belgium.
| | - Jean-Marie Degryse
- Institute of Health and Society, Université Catholique de Louvain, Brussels 1200, Belgium.
- Department of Public Health and Primary Care, Katholieke Universiteit Leuven, Leuven 3000, Belgium.
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Dolley S. Big Data's Role in Precision Public Health. Front Public Health 2018; 6:68. [PMID: 29594091 PMCID: PMC5859342 DOI: 10.3389/fpubh.2018.00068] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 02/20/2018] [Indexed: 01/01/2023] Open
Abstract
Precision public health is an emerging practice to more granularly predict and understand public health risks and customize treatments for more specific and homogeneous subpopulations, often using new data, technologies, and methods. Big data is one element that has consistently helped to achieve these goals, through its ability to deliver to practitioners a volume and variety of structured or unstructured data not previously possible. Big data has enabled more widespread and specific research and trials of stratifying and segmenting populations at risk for a variety of health problems. Examples of success using big data are surveyed in surveillance and signal detection, predicting future risk, targeted interventions, and understanding disease. Using novel big data or big data approaches has risks that remain to be resolved. The continued growth in volume and variety of available data, decreased costs of data capture, and emerging computational methods mean big data success will likely be a required pillar of precision public health into the future. This review article aims to identify the precision public health use cases where big data has added value, identify classes of value that big data may bring, and outline the risks inherent in using big data in precision public health efforts.
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Budnik LT, Adam B, Albin M, Banelli B, Baur X, Belpoggi F, Bolognesi C, Broberg K, Gustavsson P, Göen T, Fischer A, Jarosinska D, Manservisi F, O’Kennedy R, Øvrevik J, Paunovic E, Ritz B, Scheepers PTJ, Schlünssen V, Schwarzenbach H, Schwarze PE, Sheils O, Sigsgaard T, Van Damme K, Casteleyn L. Diagnosis, monitoring and prevention of exposure-related non-communicable diseases in the living and working environment: DiMoPEx-project is designed to determine the impacts of environmental exposure on human health. J Occup Med Toxicol 2018; 13:6. [PMID: 29441119 PMCID: PMC5800006 DOI: 10.1186/s12995-018-0186-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 01/15/2018] [Indexed: 02/07/2023] Open
Abstract
The WHO has ranked environmental hazardous exposures in the living and working environment among the top risk factors for chronic disease mortality. Worldwide, about 40 million people die each year from noncommunicable diseases (NCDs) including cancer, diabetes, and chronic cardiovascular, neurological and lung diseases. The exposure to ambient pollution in the living and working environment is exacerbated by individual susceptibilities and lifestyle-driven factors to produce complex and complicated NCD etiologies. Research addressing the links between environmental exposure and disease prevalence is key for prevention of the pandemic increase in NCD morbidity and mortality. However, the long latency, the chronic course of some diseases and the necessity to address cumulative exposures over very long periods does mean that it is often difficult to identify causal environmental exposures. EU-funded COST Action DiMoPEx is developing new concepts for a better understanding of health-environment (including gene-environment) interactions in the etiology of NCDs. The overarching idea is to teach and train scientists and physicians to learn how to include efficient and valid exposure assessments in their research and in their clinical practice in current and future cooperative projects. DiMoPEx partners have identified some of the emerging research needs, which include the lack of evidence-based exposure data and the need for human-equivalent animal models mirroring human lifespan and low-dose cumulative exposures. Utilizing an interdisciplinary approach incorporating seven working groups, DiMoPEx will focus on aspects of air pollution with particulate matter including dust and fibers and on exposure to low doses of solvents and sensitizing agents. Biomarkers of early exposure and their associated effects as indicators of disease-derived information will be tested and standardized within individual projects. Risks arising from some NCDs, like pneumoconioses, cancers and allergies, are predictable and preventable. Consequently, preventative action could lead to decreasing disease morbidity and mortality for many of the NCDs that are of major public concern. DiMoPEx plans to catalyze and stimulate interaction of scientists with policy-makers in attacking these exposure-related diseases.
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Affiliation(s)
- Lygia Therese Budnik
- Division of Translational Toxicology and Immunology, Institute for Occupational and Maritime Medicine (ZfAM), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Balazs Adam
- Faculty of Public Health, Department of Preventive Medicine, University of Debrecen, Debrecen, Hungary
| | - Maria Albin
- Division of Occupational and Environmental Medicine, University of Lund, Lund, Sweden
- Karolinska Institutet, Institute of Environmental Medicine (IMM), Stockholm, Sweden
| | - Barbara Banelli
- Tumor Epigenetics Unit, Ospedale Policlinico San Martino, National Cancer Institute, IRCCS and University of Genoa, DISSAL, Genoa, Italy
| | - Xaver Baur
- European Society for Environmental and Occupational Medicine, Berlin, Germany
| | - Fiorella Belpoggi
- Cesare Maltoni Cancer Research Center, Ramazzini Institute, Bentivoglio, Bologna, Italy
| | - Claudia Bolognesi
- San Martino-IST Environmental Carcinogenesis Unit, IRCCS, Ospedale Policlinico San Martino, National Cancer Institute, Genoa, Italy
| | - Karin Broberg
- Karolinska Institutet, Institute of Environmental Medicine (IMM), Stockholm, Sweden
| | - Per Gustavsson
- Karolinska Institutet, Institute of Environmental Medicine (IMM), Stockholm, Sweden
| | - Thomas Göen
- Social and Environmental Medicine, Institute and Outpatient Clinic of Occupational, Friedrich-Alexander-University Erlangen-Nurnberg, Erlangen, Germany
| | - Axel Fischer
- Institute of Occupational Medicine, Charité Universitäts Medizin, Berlin, Germany
| | | | - Fabiana Manservisi
- Cesare Maltoni Cancer Research Center, Ramazzini Institute, Bentivoglio, Bologna, Italy
| | - Richard O’Kennedy
- Biomedical Diagnostics Institute, Dublin City University, Dublin, Ireland
| | | | | | - Beate Ritz
- Center for Occupational and Environmental Health, Fielding School of Public Health (FSPH), University of California Los Angeles (UCLA), Los Angeles, USA
| | - Paul T. J. Scheepers
- Radboud Institute for Health Sciences, Radboudumc (Radboud university medical center), Nijmegen, the Netherlands
| | - Vivi Schlünssen
- National Research Center for the Working Environment, Copenhagen, Denmark
- Department of Public Health, Section Environment, Occupation & Health & Danish Ramazzini Centre Aarhus, Aarhus University, Aarhus, Denmark
| | - Heidi Schwarzenbach
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | | | - Orla Sheils
- Department of Histopathology, Central Pathology Laboratory, St James’s Hospital, Trinity translational Medicine Institute, Dublin, Ireland
| | - Torben Sigsgaard
- Department of Public Health, Section Environment, Occupation & Health & Danish Ramazzini Centre Aarhus, Aarhus University, Aarhus, Denmark
| | - Karel Van Damme
- Center for Human Genetics, University of Leuven, Leuven, Belgium
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Arpón A, Milagro FI, Laja A, Segura V, de Pipaón MS, Riezu-Boj JI, Alfredo Martínez J. Methylation changes and pathways affected in preterm birth: a role for SLC6A3 in neurodevelopment. Epigenomics 2017; 10:91-103. [PMID: 29172706 DOI: 10.2217/epi-2017-0082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
AIM To analyze whether preterm newborns show differences in methylation patterns in comparison to full-term newborns in white blood cells. PATIENTS & METHODS Anthropometrical, biochemical features and methylation levels of preterm newborns (n = 24) and full-term newborns (n = 22) recruited in La Paz University Hospital (Spain) were assessed at 12 months of gestational age, whereas Bayley Scale of Infant Development was evaluated at 24/36 months. RESULTS From all the statistically significant CpGs, methylation levels of cg00997378 (SLC6A3 gene) showed the highest differences (p < 0.0001), being associated with prematurity risk factors. CONCLUSION SLC6A3 methylation, previously related to attention-deficit/hyperactivity disorder, neuronal function and behavior, might be a potential epigenetic biomarker with value in the early diagnosis and management of neurodevelopmental diseases in newborns.
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Affiliation(s)
- Ana Arpón
- Department of Nutrition, Food Sciences & Physiology, Universidad de Navarra, Irunlarrea 1, 31008 Pamplona, Spain.,Centre for Nutrition Research, Universidad de Navarra, Irunlarrea 1, 31008 Pamplona, Spain
| | - Fermín I Milagro
- Department of Nutrition, Food Sciences & Physiology, Universidad de Navarra, Irunlarrea 1, 31008 Pamplona, Spain.,Centre for Nutrition Research, Universidad de Navarra, Irunlarrea 1, 31008 Pamplona, Spain.,Spanish Biomedical Research Centre in Physiopathology of Obesity & Nutrition (CIBERobn), Institute of Health Carlos III, Madrid, Spain
| | - Ana Laja
- Department of Pharmaceutical & Health Sciences, Faculty of Pharmacy, CEU San Pablo University, Madrid, Spain
| | - Víctor Segura
- Unit of Bioinformatics, Centre for Applied Medical Research (CIMA), Universidad de Navarra, Pamplona, Spain
| | - Miguel Sáenz de Pipaón
- Neonatology Department, Hospital Universitario de la Paz, Madrid, Spain.,Instituto de Salud Carlos III, Red de Salud Materno Infantil y Desarrollo (SAMID), Madrid, Spain.,Department of Pediatrics, Universidad Autónoma de Madrid, Madrid, Spain
| | - José-Ignacio Riezu-Boj
- Department of Nutrition, Food Sciences & Physiology, Universidad de Navarra, Irunlarrea 1, 31008 Pamplona, Spain.,Centre for Nutrition Research, Universidad de Navarra, Irunlarrea 1, 31008 Pamplona, Spain.,Digestive disease and Nutrition group, Navarra Institute for Health Research (IdiSNa), Pamplona, Spain
| | - J Alfredo Martínez
- Department of Nutrition, Food Sciences & Physiology, Universidad de Navarra, Irunlarrea 1, 31008 Pamplona, Spain.,Centre for Nutrition Research, Universidad de Navarra, Irunlarrea 1, 31008 Pamplona, Spain.,Spanish Biomedical Research Centre in Physiopathology of Obesity & Nutrition (CIBERobn), Institute of Health Carlos III, Madrid, Spain.,Digestive disease and Nutrition group, Navarra Institute for Health Research (IdiSNa), Pamplona, Spain.,Madrid Institute of Advanced Studies (IMDEA), IMDEA Food, Madrid, Spain
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Lozupone M, Seripa D, Stella E, La Montagna M, Solfrizzi V, Quaranta N, Veneziani F, Cester A, Sardone R, Bonfiglio C, Giannelli G, Bisceglia P, Bringiotti R, Daniele A, Greco A, Bellomo A, Logroscino G, Panza F. Innovative biomarkers in psychiatric disorders: a major clinical challenge in psychiatry. Expert Rev Proteomics 2017; 14:809-824. [DOI: 10.1080/14789450.2017.1375857] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Madia Lozupone
- Neurodegenerative Disease Unit, Department of Basic Medicine, Neuroscience, and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | - Davide Seripa
- Geriatric Unit & Laboratory of Gerontology and Geriatrics, Department of Medical Sciences, IRCCS “Casa Sollievo della Sofferenza”, San Giovanni Rotondo, Foggia, Italy
| | - Eleonora Stella
- Psychiatric Unit, Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Maddalena La Montagna
- Psychiatric Unit, Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Vincenzo Solfrizzi
- Geriatric Medicine-Memory Unit and Rare Disease Centre, University of Bari Aldo Moro, Italy
| | | | - Federica Veneziani
- Psychiatric Unit, Department of Basic Medicine, Neuroscience and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | - Alberto Cester
- Department of Medicine Organization Geriatric Unit, CDCD, Dolo Hospital, Venezia, Italy
| | - Rodolfo Sardone
- Department of Epidemiology and Biostatistics, National Institute of Gastroenterology “Saverio de Bellis”, Research Hospital, Bari, Italy
| | - Caterina Bonfiglio
- Department of Epidemiology and Biostatistics, National Institute of Gastroenterology “Saverio de Bellis”, Research Hospital, Bari, Italy
| | - Gianluigi Giannelli
- Department of Epidemiology and Biostatistics, National Institute of Gastroenterology “Saverio de Bellis”, Research Hospital, Bari, Italy
| | - Paola Bisceglia
- Geriatric Unit & Laboratory of Gerontology and Geriatrics, Department of Medical Sciences, IRCCS “Casa Sollievo della Sofferenza”, San Giovanni Rotondo, Foggia, Italy
| | - Roberto Bringiotti
- Neurodegenerative Disease Unit, Department of Basic Medicine, Neuroscience, and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | - Antonio Daniele
- Institute of Neurology, Catholic University of Sacred Heart, Rome, Italy
| | - Antonio Greco
- Geriatric Unit & Laboratory of Gerontology and Geriatrics, Department of Medical Sciences, IRCCS “Casa Sollievo della Sofferenza”, San Giovanni Rotondo, Foggia, Italy
| | - Antonello Bellomo
- Psychiatric Unit, Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Giancarlo Logroscino
- Neurodegenerative Disease Unit, Department of Basic Medicine, Neuroscience, and Sense Organs, University of Bari Aldo Moro, Bari, Italy
- Department of Clinical Research in Neurology, University of Bari Aldo Moro, “Pia Fondazione Cardinale G. Panico”, Lecce, Italy
| | - Francesco Panza
- Neurodegenerative Disease Unit, Department of Basic Medicine, Neuroscience, and Sense Organs, University of Bari Aldo Moro, Bari, Italy
- Geriatric Unit & Laboratory of Gerontology and Geriatrics, Department of Medical Sciences, IRCCS “Casa Sollievo della Sofferenza”, San Giovanni Rotondo, Foggia, Italy
- Department of Clinical Research in Neurology, University of Bari Aldo Moro, “Pia Fondazione Cardinale G. Panico”, Lecce, Italy
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Makhathini KB, Abboussi O, Stein DJ, Mabandla MV, Daniels WM. Repetitive stress leads to impaired cognitive function that is associated with DNA hypomethylation, reduced BDNF and a dysregulated HPA axis. Int J Dev Neurosci 2017; 60:63-69. [DOI: 10.1016/j.ijdevneu.2017.04.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 03/13/2017] [Accepted: 04/11/2017] [Indexed: 11/28/2022] Open
Affiliation(s)
- Khayelihle B. Makhathini
- Department of Human PhysiologyCollege of Health Sciences, University of KwaZulu‐ NatalDurbanSouth Africa
| | - Oualid Abboussi
- Department of Human PhysiologyCollege of Health Sciences, University of KwaZulu‐ NatalDurbanSouth Africa
| | - Dan J. Stein
- Department of PsychiatryUniversity of Cape TownCape TownSouth Africa
| | - Musa V. Mabandla
- Department of Human PhysiologyCollege of Health Sciences, University of KwaZulu‐ NatalDurbanSouth Africa
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Goodman JI. Incorporation of an Epigenetic Evaluation into Safety Assessment: What we First Need to Know. CURRENT OPINION IN TOXICOLOGY 2017; 3:20-24. [PMID: 30740577 DOI: 10.1016/j.cotox.2017.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The rapidly evolving field of epigenetic regulation of gene expression is having an impact across the spectrum of biomedical research. Toxicologists have embraced this area as evidenced by their increasing focus on discerning potential epigenetic mechanisms underlying mechanisms by which chemical and physical agents might cause toxicity. It is not surprising that an interest in epigenetic mechanisms of toxicity would lead to a desire to incorporate an epigenetic component into safety assessment. However, premature movement in this direction carries the risk of imposing more confusion than light. This commentary provides an overview of epigenetics, with an emphasis on how the various epigenetic parameters are integrated, as a basis for understanding the complexity behind the desire to include epigenetic evaluations in safety evaluations. Basically, we have much more to learn before turning the goal into a reality. However, considerable progress has been made with regard to using epigenetic profiles as signatures of xenobiotic exposure.
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Affiliation(s)
- Jay I Goodman
- Michigan State University Department of Pharmacology and Toxicology East Lansing, Michigan 48824 USA
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41
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Barrett JR. Programming the Future: Epigenetics in the Context of DOHaD. ENVIRONMENTAL HEALTH PERSPECTIVES 2017; 125:A72. [PMID: 28362622 PMCID: PMC5382006 DOI: 10.1289/ehp.125-a72] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
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Hoffman JB, Petriello MC, Hennig B. Impact of nutrition on pollutant toxicity: an update with new insights into epigenetic regulation. REVIEWS ON ENVIRONMENTAL HEALTH 2017; 32:65-72. [PMID: 28076319 PMCID: PMC5489226 DOI: 10.1515/reveh-2016-0041] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/09/2016] [Indexed: 05/03/2023]
Abstract
Exposure to environmental pollutants is a global health problem and is associated with the development of many chronic diseases, including cardiovascular disease, diabetes and metabolic syndrome. There is a growing body of evidence that nutrition can both positively and negatively modulate the toxic effects of pollutant exposure. Diets high in proinflammatory fats, such as linoleic acid, can exacerbate pollutant toxicity, whereas diets rich in bioactive and anti-inflammatory food components, including omega-3 fatty acids and polyphenols, can attenuate toxicant-associated inflammation. Previously, researchers have elucidated direct mechanisms of nutritional modulation, including alteration of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling, but recently, increased focus has been given to the ways in which nutrition and pollutants affect epigenetics. Nutrition has been demonstrated to modulate epigenetic markers that have been linked either to increased disease risks or to protection against diseases. Overnutrition (i.e. obesity) and undernutrition (i.e. famine) have been observed to alter prenatal epigenetic tags that may increase the risk of offspring developing disease later in life. Conversely, bioactive food components, including curcumin, have been shown to alter epigenetic markers that suppress the activation of NF-κB, thus reducing inflammatory responses. Exposure to pollutants also alters epigenetic markers and may contribute to inflammation and disease. It has been demonstrated that pollutants, via epigenetic modulations, can increase the activation of NF-κB and upregulate microRNAs associated with inflammation, cardiac injury and oxidative damage. Importantly, recent evidence suggests that nutritional components, including epigallocatechin gallate (EGCG), can protect against pollutant-induced inflammation through epigenetic regulation of proinflammatory target genes of NF-κB. Further research is needed to better understand how nutrition can modulate pollutant toxicity through epigenetic regulation. Therefore, the objective of this review is to elucidate the current evidence linking epigenetic changes to pollutant-induced diseases and how this regulation may be modulated by nutrients allowing for the development of future personalized lifestyle interventions.
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Affiliation(s)
- Jessie B Hoffman
- Superfund Research Center, University of Kentucky, Lexington, KY 40536
- Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, KY 40536
| | - Michael C Petriello
- Superfund Research Center, University of Kentucky, Lexington, KY 40536
- Department of Animal and Food Sciences, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY 40536
| | - Bernhard Hennig
- Superfund Research Center, University of Kentucky, Lexington, KY 40536
- Department of Animal and Food Sciences, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY 40536
- Correspondence should be directed to: Bernhard Hennig, 900 S. Limestone Street, Superfund Research Center, University of Kentucky, Lexington, KY 40536, USA. Tel.: +1 859-218-1343; fax: +1 859-257-1811;
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Zhang J, Choudhury M. The plasticizer BBP selectively inhibits epigenetic regulator sirtuin during differentiation of C3H10T1/2 stem cell line. Toxicol In Vitro 2017; 39:75-83. [DOI: 10.1016/j.tiv.2016.11.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 11/29/2016] [Accepted: 11/30/2016] [Indexed: 01/04/2023]
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Montrose L, Ward TJ, Semmens EO, Cho YH, Brown B, Noonan CW. Dietary intake is associated with respiratory health outcomes and DNA methylation in children with asthma. Allergy Asthma Clin Immunol 2017; 13:12. [PMID: 28261276 PMCID: PMC5327515 DOI: 10.1186/s13223-017-0187-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 02/17/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Asthma is an increasingly common chronic disease among children, and data point toward a complex mechanism involving genetic, environmental and epigenetic factors. Epigenetic modifications such as DNA hypo- or hyper-methylation have been shown to occur in response to environmental exposures including dietary nutrients. METHODS Within the context of the asthma randomized trial of indoor wood smoke (ARTIS) study, we investigated relationships between diet, asthma health measures, and DNA methylation. Asthma health measures included a quality of life instrument, diurnal peak flow variability (dPFV) and forced expiratory volume in the first second (FEV1). Dietary intake was assessed with a food frequency questionnaire. Methylation levels of LINE-1 repetitive element and two promoter CpG sites for interferon gamma (IFNγ, -186 and -54) from buccal cell DNA were measured using pyrosequencing assays. RESULTS Data were collected on 32 children with asthma living in western Montana who were recruited to the ARTIS study. Selenium and several methyl donor dietary nutrients were positively associated with the asthma quality of life measure. Intake of methyl donating nutrients including folate was positively associated LINE-1 methylation and negatively associated with IFNγ CpG-186. Higher levels of LINE-1 methylation were associated with greater dPFV. CONCLUSION We identified several nutrients that were associated with improved quality of life measures among children with asthma. The IFNγ promoter CpG site -186 but not -54 was associated with the intake of selected dietary nutrients. However, in this small population of children with asthma, the IFNγ promoter CpG sites were not associated with respiratory health measures so it remains unclear through which epigenetic mechanism these nutrients are impacting the quality of life measure. These findings add to the evidence that dietary nutrients, particularly foods containing methyl donors, may be important for epigenetic regulation as it pertains to the control of asthma. Trial registration ClincialTrials.gov NCT00807183. Registered 10 December 2008.
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Affiliation(s)
- L Montrose
- School of Public Health, University of Michigan, 1420 Washington Heights, Ann Arbor, MI 48109 USA
| | - T J Ward
- Center for Environmental Health Sciences, University of Montana, 32 Campus Drive-159 Skaggs, Missoula, MT 59812 USA
| | - E O Semmens
- Center for Environmental Health Sciences, University of Montana, 32 Campus Drive-159 Skaggs, Missoula, MT 59812 USA
| | - Y H Cho
- Center for Environmental Health Sciences, University of Montana, 32 Campus Drive-159 Skaggs, Missoula, MT 59812 USA
| | - B Brown
- Department of Health and Human Performance, University of Montana, 32 Campus Drive, Missoula, MT 59812 USA
| | - C W Noonan
- Center for Environmental Health Sciences, University of Montana, 32 Campus Drive-159 Skaggs, Missoula, MT 59812 USA
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Ried J. Adam’s Apple and His Legacy: Ethical Perspectives on Epigenetics with an Excursion to the Field of Body Weight Regulation. Epigenetics 2017. [DOI: 10.1007/978-3-658-14460-9_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Holman DM, Buchanan ND. Opportunities During Early Life for Cancer Prevention: Highlights From a Series of Virtual Meetings With Experts. Pediatrics 2016; 138:S3-S14. [PMID: 27940972 PMCID: PMC5890502 DOI: 10.1542/peds.2015-4268c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/16/2016] [Indexed: 01/26/2023] Open
Abstract
Compelling evidence suggests that early life exposures can affect lifetime cancer risk. In 2014, the Centers for Disease Control and Prevention's (CDC's) Cancer Prevention Across the Lifespan Workgroup hosted a series of virtual meetings with select experts to discuss the state of the evidence linking factors during the prenatal period and early childhood to subsequent risk of both pediatric and adult cancers. In this article, we present the results from a qualitative analysis of the meeting transcripts and summarize themes that emerged from our discussions with meeting participants. Themes included the state of the evidence linking early life factors to cancer risk, research gaps and challenges, the level of evidence needed to support taking public health action, and the challenges of communicating complex, and sometimes conflicting, scientific findings to the public. Opportunities for collaboration among public health agencies and other stakeholders were identified during these discussions. Potential next steps for the CDC and its partners included advancing and building upon epidemiology and surveillance work, developing and using evidence from multiple sources to inform decision-making, disseminating and communicating research findings in a clear and effective way, and expanding collaborations with grantees and other partners. As the science on early life factors and cancer risk continues to evolve, there are opportunities for collaboration to translate science into actionable public health practice.
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Affiliation(s)
- Dawn M. Holman
- Division of Cancer Prevention and Control, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Natasha D. Buchanan
- Division of Cancer Prevention and Control, Centers for Disease Control and Prevention, Atlanta, Georgia
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Volz DC, Leet JK, Chen A, Stapleton H, Katiyar N, Kaundal R, Yu Y, Wang Y. Tris(1,3-dichloro-2-propyl)phosphate Induces Genome-Wide Hypomethylation within Early Zebrafish Embryos. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:10255-63. [PMID: 27574916 PMCID: PMC5080636 DOI: 10.1021/acs.est.6b03656] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Tris(1,3-dichloro-2-propyl)phosphate (TDCIPP) is a high-production volume organophosphate-based plasticizer and flame retardant widely used within the United States. Using zebrafish as a model, the objectives of this study were to determine whether (1) TDCIPP inhibits DNA methyltransferase (DNMT) within embryonic nuclear extracts; (2) uptake of TDCIPP from 0.75 h postfertilization (hpf, 2-cell) to 2 hpf (64-cell) or 6 hpf (shield stage) leads to impacts on the early embryonic DNA methylome; and (3) TDCIPP-induced impacts on cytosine methylation are localized to CpG islands within intergenic regions. Within this study, 5-azacytidine (5-azaC, a DNMT inhibitor) was used as a positive control. Although 5-azaC significantly inhibited zebrafish DNMT, TDCIPP did not affect DNMT activity in vitro at concentrations as high as 500 μM. However, rapid embryonic uptake of 5-azaC and TDCIPP from 0.75 to 2 hpf resulted in chemical- and chromosome-specific alterations in cytosine methylation at 2 hpf. Moreover, TDCIPP exposure predominantly resulted in hypomethylation of positions outside of CpG islands and within intragenic (exon) regions of the zebrafish genome. Overall, these findings provide the foundation for monitoring DNA methylation dynamics within zebrafish as well as identifying potential associations among TDCIPP exposure, adverse health outcomes, and DNA methylation status within human populations.
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Affiliation(s)
- David C. Volz
- Department
of Environmental Sciences, University of
California, Riverside, Riverside, California 92521, United States
- D. C. Volz. Phone: (951)
827-4450; Fax: (951) 827-3993; E-mail:
| | - Jessica K. Leet
- Department
of Environmental Health Sciences, University
of South Carolina, Columbia, South Carolina 29208, United States
| | - Albert Chen
- Division
of Environmental Sciences and Policy, Duke
University, Durham, North Carolina 27708, United States
| | - Heather
M. Stapleton
- Division
of Environmental Sciences and Policy, Duke
University, Durham, North Carolina 27708, United States
| | - Neerja Katiyar
- Bioinformatics
Facility, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California 92521, United States
| | - Rakesh Kaundal
- Bioinformatics
Facility, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California 92521, United States
| | - Yang Yu
- Department
of Chemistry, University of California,
Riverside, Riverside, California 92521, United States
| | - Yinsheng Wang
- Department
of Chemistry, University of California,
Riverside, Riverside, California 92521, United States
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Chatterjee O, Patil K, Sahu A, Gopalakrishnan L, Mol P, Advani J, Mukherjee S, Christopher R, Prasad TSK. An overview of the oxytocin-oxytocin receptor signaling network. J Cell Commun Signal 2016; 10:355-360. [PMID: 27624619 DOI: 10.1007/s12079-016-0353-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 09/06/2016] [Indexed: 12/17/2022] Open
Abstract
Oxytocin, a nine amino acid long neuropeptide hormone, is synthesized in the hypothalamus and stored and released from the neural lobe of the pituitary gland. Although commonly known for its central role in the regulation of parturition and lactation, oxytocin signaling also plays a key role in modulating social behavior, evoking contentment, initiating maternal behavior, inducing trust, generosity and bonding in humans and animals. Oxytocin signaling can prove to be of great importance in therapeutics and drug targeting because of its diverse range of actions. However, a well annotated map of oxytocin signaling pathway is currently lacking in the publicly available pathway resources. Therefore, we systematically curated the available signaling information of oxytocin from published literature and collated the data to develop a more complete map. We cataloged 66 molecules belonging to oxytocin signaling pathway, which included 9 protein-protein interactions, 39 post-translational modifications, 14 protein translocation events and 22 activation/inhibition events. Further, Oxytocin signaling network data is made freely available to academic fraternity by integrating this into NetPath ( http://www.netpath.org /), a freely available human signaling pathway resource developed previously by our group.
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Affiliation(s)
- Oishi Chatterjee
- International Technology Park, Institute of Bioinformatics, Bangalore, 560066, India
| | - Krutika Patil
- Molecular Endocrinology, National Institute for Research in Reproductive Health, Parel, Mumbai, 400012, India
| | - Apeksha Sahu
- International Technology Park, Institute of Bioinformatics, Bangalore, 560066, India
- Bioinformatics Centre, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | | | - Praseeda Mol
- International Technology Park, Institute of Bioinformatics, Bangalore, 560066, India
| | - Jayshree Advani
- International Technology Park, Institute of Bioinformatics, Bangalore, 560066, India
- Manipal University, Madhav Nagar, Manipal, 576 104, India
| | - Srabani Mukherjee
- Molecular Endocrinology, National Institute for Research in Reproductive Health, Parel, Mumbai, 400012, India
| | - Rita Christopher
- Department of Neurochemistry, National Institute of Mental Health and Neuro Sciences, Bangalore, 560029, India
| | - T S Keshava Prasad
- International Technology Park, Institute of Bioinformatics, Bangalore, 560066, India.
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, 575018, India.
- NIMHANS-IOB Proteomics and Bioinformatics Laboratory, National Institute of Mental Health and Neuro Sciences, Bangalore, 560029, India.
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Abstract
Exposure to environmental chemicals has adverse effects on the health and survival of humans. Emerging evidence supports the idea that exposure to endocrine-disrupting compounds (EDCs) can perturb an individual’s physiological set point and as a result increase his/her propensity toward several diseases. The purpose of this review is to provide an update on di-(2-ethylhexyl) phthalate, the primary plasticizer found in plastic medical devices used in neonatal intensive care units, its effects on the fetus and newborn, epidemiological studies, pharmacokinetics, toxicity and epigenetic implications. We searched the PubMed databases to identify relevant studies. Phthalates are known EDCs that primarily are used to improve the flexibility of polyvinyl chloride plastic products and are called plasticizers in lay terms. Neonates and infants are particularly vulnerable to the effects of phthalates, beginning with maternal exposure and placental transfer during gestation and during infancy following birth. In line with the developmental origins of adult disease, a focus on the effects of environmental chemicals in utero or early childhood on the genesis of adult diseases through epigenome modulation is timely and important. The epigenetic effects of phthalates have not been fully elucidated, but accumulating evidence suggests that they may be associated with adverse health effects, some of which may be heritable. Phthalate exposure during pregnancy and the perinatal period is particularly worrisome in health-care settings. Although the clinical significance of phthalate exposure has been difficult to assess with epidemiologic studies, the evidence that physiological changes occur due to exposure to phthalates is growing and points toward the need for more investigation at a molecular, specifically epigenetic level.
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Schiöth HB, Boström A, Murphy SK, Erhart W, Hampe J, Moylan C, Mwinyi J. A targeted analysis reveals relevant shifts in the methylation and transcription of genes responsible for bile acid homeostasis and drug metabolism in non-alcoholic fatty liver disease. BMC Genomics 2016; 17:462. [PMID: 27301979 PMCID: PMC4908840 DOI: 10.1186/s12864-016-2814-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 06/07/2016] [Indexed: 01/12/2023] Open
Abstract
Background Non-alcoholic fatty liver disease (NAFLD) is associated with a high risk for liver cirrhosis and cancer. Recent studies demonstrate that NAFLD significantly impacts on the genome wide methylation and expression reporting top hit genes to be associated with e.g. diabetes mellitus. In a targeted analysis we specifically investigate to what extent NAFLD is associated with methylation and transcriptional changes in gene networks responsible for drug metabolism (DM) and bile acid (BA) homeostasis, which may trigger liver and system toxic events. Methods We performed a systematic analysis of 73 genes responsible for BA homeostasis and DM based on liver derived methylation and expression data from three cohort studies including 103 NAFLD and 75 non-NAFLD patients. Using multiple linear regression models, we detected methylation differences in proximity to the transcriptional start site of these genes in two NAFLD cohorts and correlated the methylation of significantly changed CpG sites to transcriptional expression in a third cohort using robust multiple linear regression approaches. Results We detected 64 genes involved in BA homeostasis and DM to be significantly differentially methylated. In 26 of these genes, methylation significantly correlated with RNA expression, detecting i.e. genes such as CYP27A1, OSTɑ, and SLC27A5 (BA homeostasis), and SLCO2B1, SLC47A1, and several UGT and CYP genes (DM) to be NAFLD dependently modulated. Conclusions NAFLD is associated with significant shifts in the methylation of key genes responsible for BA and DM that are associated with transcriptional modulations. These findings have implications for BA composition, BA regulated metabolic pathways and for drug safety and efficacy. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2814-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Helgi B Schiöth
- Department of Neuroscience, Division of Functional Pharmacology, Uppsala University, Uppsala, Sweden
| | - Adrian Boström
- Department of Neuroscience, Division of Functional Pharmacology, Uppsala University, Uppsala, Sweden
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Wiebke Erhart
- Department of Internal Medicine I, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Jochen Hampe
- Medical Department I, University Hospital Dresden, Dresden, Germany
| | - Cynthia Moylan
- Department of Medicine, Duke University Medical Center, Durham, NC, USA.,Department of Medicine, Durham Veterans Affairs Medical Center, Durham, NC, USA
| | - Jessica Mwinyi
- Department of Neuroscience, Division of Functional Pharmacology, Uppsala University, Uppsala, Sweden.
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