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Carswell G, Chamberlin J, Bennett BD, Bushel PR, Chorley BN. Persistent gene expression and DNA methylation alterations linked to carcinogenic effects of dichloroacetic acid. Front Oncol 2024; 14:1389634. [PMID: 38764585 PMCID: PMC11099211 DOI: 10.3389/fonc.2024.1389634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 04/18/2024] [Indexed: 05/21/2024] Open
Abstract
Background Mechanistic understanding of transient exposures that lead to adverse health outcomes will enhance our ability to recognize biological signatures of disease. Here, we measured the transcriptomic and epigenomic alterations due to exposure to the metabolic reprogramming agent, dichloroacetic acid (DCA). Previously, we showed that exposure to DCA increased liver tumor incidence in B6C3F1 mice after continuous or early life exposures significantly over background level. Methods Using archived formalin-fixed liver samples, we utilized modern methodologies to measure gene expression and DNA methylation levels to link to previously generated phenotypic measures. Gene expression was measured by targeted RNA sequencing (TempO-seq 1500+ toxicity panel: 2754 total genes) in liver samples collected from 10-, 32-, 57-, and 78-week old mice exposed to deionized water (controls), 3.5 g/L DCA continuously in drinking water ("Direct" group), or DCA for 10-, 32-, or 57-weeks followed by deionized water until sample collection ("Stop" groups). Genome-scaled alterations in DNA methylation were measured by Reduced Representation Bisulfite Sequencing (RRBS) in 78-week liver samples for control, Direct, 10-week Stop DCA exposed mice. Results Transcriptomic changes were most robust with concurrent or adjacent timepoints after exposure was withdrawn. We observed a similar pattern with DNA methylation alterations where we noted attenuated differentially methylated regions (DMRs) in the 10-week Stop DCA exposure groups compared to the Direct group at 78-weeks. Gene pathway analysis indicated cellular effects linked to increased oxidative metabolism, a primary mechanism of action for DCA, closer to exposure windows especially early in life. Conversely, many gene signatures and pathways reversed patterns later in life and reflected more pro-tumorigenic patterns for both current and prior DCA exposures. DNA methylation patterns correlated to early gene pathway perturbations, such as cellular signaling, regulation and metabolism, suggesting persistence in the epigenome and possible regulatory effects. Conclusion Liver metabolic reprogramming effects of DCA interacted with normal age mechanisms, increasing tumor burden with both continuous and prior DCA exposure in the male B6C3F1 rodent model.
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Affiliation(s)
- Gleta Carswell
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States
| | - John Chamberlin
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States
- Oak Ridge Institute for Science and Education, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States
| | - Brian D. Bennett
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, United States
| | - Pierre R. Bushel
- Massive Genome Informatics Group, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, United States
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, United States
| | - Brian N. Chorley
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States
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Scher MS. Interdisciplinary fetal-neonatal neurology training applies neural exposome perspectives to neurology principles and practice. Front Neurol 2024; 14:1321674. [PMID: 38288328 PMCID: PMC10824035 DOI: 10.3389/fneur.2023.1321674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 12/07/2023] [Indexed: 01/31/2024] Open
Abstract
An interdisciplinary fetal-neonatal neurology (FNN) program over the first 1,000 days teaches perspectives of the neural exposome that are applicable across the life span. This curriculum strengthens neonatal neurocritical care, pediatric, and adult neurology training objectives. Teaching at maternal-pediatric hospital centers optimally merges reproductive, pregnancy, and pediatric approaches to healthcare. Phenotype-genotype expressions of health or disease pathways represent a dynamic neural exposome over developmental time. The science of uncertainty applied to FNN training re-enforces the importance of shared clinical decisions that minimize bias and reduce cognitive errors. Trainees select mentoring committee participants that will maximize their learning experiences. Standardized questions and oral presentations monitor educational progress. Master or doctoral defense preparation and competitive research funding can be goals for specific individuals. FNN principles applied to practice offer an understanding of gene-environment interactions that recognizes the effects of reproductive health on the maternal-placental-fetal triad, neonate, child, and adult. Pre-conception and prenatal adversities potentially diminish life-course brain health. Endogenous and exogenous toxic stressor interplay (TSI) alters the neural exposome through maladaptive developmental neuroplasticity. Developmental disorders and epilepsy are primarily expressed during the first 1,000 days. Communicable and noncommunicable illnesses continue to interact with the neural exposome to express diverse neurologic disorders across the lifespan, particularly during the critical/sensitive time periods of adolescence and reproductive senescence. Anomalous or destructive fetal neuropathologic lesions change clinical expressions across this developmental-aging continuum. An integrated understanding of reproductive, pregnancy, placental, neonatal, childhood, and adult exposome effects offers a life-course perspective of the neural exposome. Exosome research promises improved disease monitoring and drug delivery starting during pregnancy. Developmental origins of health and disease principles applied to FNN practice anticipate neurologic diagnoses with interventions that can benefit successive generations. Addressing health care disparities in the Global South and high-income country medical deserts require constructive dialogue among stakeholders to achieve medical equity. Population health policies require a brain capital strategy that reduces the global burden of neurologic diseases by applying FNN principles and practice. This integrative neurologic care approach will prolong survival with an improved quality of life for persons across the lifespan confronted with neurological disorders.
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Affiliation(s)
- Mark S. Scher
- Division of Pediatric Neurology, Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, OH, United States
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Bollati V, Biganzoli EM, Carugno M. What if … ? A new hypothesis to approach the relationship between environmental stimuli, biological features, and health. Heliyon 2023; 9:e22985. [PMID: 38058436 PMCID: PMC10696241 DOI: 10.1016/j.heliyon.2023.e22985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/24/2023] [Accepted: 11/23/2023] [Indexed: 12/08/2023] Open
Abstract
The "exposome" covers all disease determinants across a lifetime. Many exposome factors could induce epigenetic changes, especially in DNA methylation. Yet, the role of these modifications in disease development remains partly understood. Although the possible relationship among the exposome factors, epigenetic modifications, and health/disease has been investigated extensively, all previous studies start from the assumption that epigenetic changes are always detrimental to (or represent an adverse effect on) the health of the affected individual. We hereby propose a new approach to investigate these modifications, and their possible relation with human health, in the context of the exposome. Our hypothesis is based on the possibility that some environmentally-induced changes are plastic entities, responding physiologically to the environment to allow individual adaptation. Briefly, after evaluating the association between environmental exposure and the variation of a given biological parameter through regression models, we use the estimated regression function to predict values for each study subject. We then calculated the relative percent difference (PD) between the measured (i.e., observed) biological parameter and the predicted (i.e., expected) from the model. Notably, we have tested our hypothesis using two distinct models, specifically focusing on LINE-1 methylation and extracellular vesicles (EVs). We hypothesize that the greater the difference between the observed and the expected, the greater the inability of the subject to adapt to external stimuli.
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Affiliation(s)
- Valentina Bollati
- EPIGET - Epidemiology, Epigenetics and Toxicology Lab, Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan – Italy
- Epidemiology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan – Italy
| | - Elia Mario Biganzoli
- Department of Biomedical and Clinical Sciences (DIBIC), University of Milan, 20157 Milan, Italy
- Data Science Research Center (DSRC), University of Milan, 20157 Milan, Italy
| | - Michele Carugno
- EPIGET - Epidemiology, Epigenetics and Toxicology Lab, Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan – Italy
- Epidemiology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan – Italy
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Chauhan R, Archibong AE, Ramesh A. Imprinting and Reproductive Health: A Toxicological Perspective. Int J Mol Sci 2023; 24:16559. [PMID: 38068882 PMCID: PMC10706004 DOI: 10.3390/ijms242316559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/16/2023] [Accepted: 11/19/2023] [Indexed: 12/18/2023] Open
Abstract
This overview discusses the role of imprinting in the development of an organism, and how exposure to environmental chemicals during fetal development leads to the physiological and biochemical changes that can have adverse lifelong effects on the health of the offspring. There has been a recent upsurge in the use of chemical products in everyday life. These chemicals include industrial byproducts, pesticides, dietary supplements, and pharmaceutical products. They mimic the natural estrogens and bind to estradiol receptors. Consequently, they reduce the number of receptors available for ligand binding. This leads to a faulty signaling in the neuroendocrine system during the critical developmental process of 'imprinting'. Imprinting causes structural and organizational differentiation in male and female reproductive organs, sexual behavior, bone mineral density, and the metabolism of exogenous and endogenous chemical substances. Several studies conducted on animal models and epidemiological studies provide profound evidence that altered imprinting causes various developmental and reproductive abnormalities and other diseases in humans. Altered metabolism can be measured by various endpoints such as the profile of cytochrome P-450 enzymes (CYP450's), xenobiotic metabolite levels, and DNA adducts. The importance of imprinting in the potentiation or attenuation of toxic chemicals is discussed.
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Affiliation(s)
- Ritu Chauhan
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, TN 37208, USA;
| | - Anthony E. Archibong
- Department of Microbiology, Immunology and Physiology, Meharry Medical College, Nashville, TN 37208, USA;
| | - Aramandla Ramesh
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, TN 37208, USA;
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Tsalenchuk M, Gentleman SM, Marzi SJ. Linking environmental risk factors with epigenetic mechanisms in Parkinson's disease. NPJ Parkinsons Dis 2023; 9:123. [PMID: 37626097 PMCID: PMC10457362 DOI: 10.1038/s41531-023-00568-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Sporadic Parkinson's disease (PD) is a progressive neurodegenerative disease, with a complex risk structure thought to be influenced by interactions between genetic variants and environmental exposures, although the full aetiology is unknown. Environmental factors, including pesticides, have been reported to increase the risk of developing the disease. Growing evidence suggests epigenetic changes are key mechanisms by which these environmental factors act upon gene regulation, in disease-relevant cell types. We present a systematic review critically appraising and summarising the current body of evidence of the relationship between epigenetic mechanisms and environmental risk factors in PD to inform future research in this area. Epigenetic studies of relevant environmental risk factors in animal and cell models have yielded promising results, however, research in humans is just emerging. While published studies in humans are currently relatively limited, the importance of the field for the elucidation of molecular mechanisms of pathogenesis opens clear and promising avenues for the future of PD research. Carefully designed epidemiological studies carried out in PD patients hold great potential to uncover disease-relevant gene regulatory mechanisms. Therefore, to advance this burgeoning field, we recommend broadening the scope of investigations to include more environmental exposures, increasing sample sizes, focusing on disease-relevant cell types, and recruiting more diverse cohorts.
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Affiliation(s)
- Maria Tsalenchuk
- UK Dementia Research Institute, Imperial College London, London, UK
- Department of Brain Sciences, Imperial College London, London, UK
| | | | - Sarah J Marzi
- UK Dementia Research Institute, Imperial College London, London, UK.
- Department of Brain Sciences, Imperial College London, London, UK.
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Felsky D, Cannitelli A, Pipitone J. Whole Person Modeling: a transdisciplinary approach to mental health research. DISCOVER MENTAL HEALTH 2023; 3:16. [PMID: 37638348 PMCID: PMC10449734 DOI: 10.1007/s44192-023-00041-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 08/10/2023] [Indexed: 08/29/2023]
Abstract
The growing global burden of mental illness has prompted calls for innovative research strategies. Theoretical models of mental health include complex contributions of biological, psychosocial, experiential, and other environmental influences. Accordingly, neuropsychiatric research has self-organized into largely isolated disciplines working to decode each individual contribution. However, research directly modeling objective biological measurements in combination with cognitive, psychological, demographic, or other environmental measurements is only now beginning to proliferate. This review aims to (1) to describe the landscape of modern mental health research and current movement towards integrative study, (2) to provide a concrete framework for quantitative integrative research, which we call Whole Person Modeling, (3) to explore existing and emerging techniques and methods used in Whole Person Modeling, and (4) to discuss our observations about the scarcity, potential value, and untested aspects of highly transdisciplinary research in general. Whole Person Modeling studies have the potential to provide a better understanding of multilevel phenomena, deliver more accurate diagnostic and prognostic tests to aid in clinical decision making, and test long standing theoretical models of mental illness. Some current barriers to progress include challenges with interdisciplinary communication and collaboration, systemic cultural barriers to transdisciplinary career paths, technical challenges in model specification, bias, and data harmonization, and gaps in transdisciplinary educational programs. We hope to ease anxiety in the field surrounding the often mysterious and intimidating world of transdisciplinary, data-driven mental health research and provide a useful orientation for students or highly specialized researchers who are new to this area.
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Affiliation(s)
- Daniel Felsky
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, 250 College Street, Toronto, ON M5T 1R8 Canada
- Department of Psychiatry, Faculty of Medicine, University of Toronto, Toronto, ON Canada
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON Canada
- Rotman Research Institute, Baycrest Hospital, Toronto, ON Canada
- Faculty of Medicine, McMaster University, Hamilton, ON Canada
| | - Alyssa Cannitelli
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, 250 College Street, Toronto, ON M5T 1R8 Canada
- Faculty of Medicine, McMaster University, Hamilton, ON Canada
| | - Jon Pipitone
- Department of Psychiatry, Queen’s University, Kingston, ON Canada
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