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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] [What about the content of this article? (0)] [Affiliation(s)] [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 Results Transcriptomic changes were most robust with concurrent or adjacent timepoints after exposure was withdrawn.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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Labaut L, Lage-Castellanos A, Rodrigo MJ, Herrero-Roldán S, Mitchell C, Fisher J, León I. Mother adversity and co-residence time impact mother-child similarity in genome-wide and gene-specific methylation profiles. Clin Epigenetics 2024; 16:44. [PMID: 38509601 PMCID: PMC10953278 DOI: 10.1186/s13148-024-01655-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/08/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND The effects of adverse life events on physical and psychological health, with DNA methylation (DNAm) as a critical underlying mechanism, have been extensively studied. However, the epigenetic resemblance between mother and child in the context of neglectful caregiving, and whether it may be shaped by the emotional impact of maternal stressful events and the duration of co-residence (indexed by child age), remains unknown. The present study examined mother-child similarity in methylation profiles, considering the potential effect of mother adversity, mother empathy, neglect-control group, child age (an index of years of mother-child co-residence), and mother age. Using Illumina Epic arrays, we quantified DNAm in 115 mother-child saliva samples. We obtained a methylation similarity index by computing correlation coefficients between methylation profiles within dyads, for the entire epigenome, and five specific genes related to stress and empathy: NR3C1, FKPB5, OXTR, SCL6A4, and BDNF. RESULTS The methylation profiles of the mother-child familial pairs significantly correlated as compared to mother-child random pairs for the entire epigenome and NR3C1, FKBP5, OXTR and BDNF genes. Next, multiple linear regression models observed associations of mother adversity, child age, and neglect-control group on mother-child methylation similarity, only significant in mother-child familial pairs, after correcting for multiple comparisons. Higher mother adversity was associated with lower mother-child methylation similarity for the epigenome-wide analysis, for the BDNF gene, and in the neglect-control group for the OXTR gene. In turn, being an older child (longer co-residence) was associated with higher mother-child methylation similarity. CONCLUSIONS Mother adversity and co-residence time are modulating factors in the intergenerational methylation process that offer a window into development-dependent adaptations that can be affected by both hereditary and environmental factors, significantly observed only in biological dyads. A twofold implication for child well-being emerges, one is positive in that children of mothers exposed to life adversity or neglect did not necessarily inherit their methylation patterns. The other is concerning due to the influence of time spent living together, which affects similarity with the mother and potentially increases the risk of inheriting an epigenetic profile associated with future dysfunctional parenting patterns. This underscores the importance of the 'the earlier, the better' recommendation by the Child Protection System, which is not always followed.
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Affiliation(s)
- Lucía Labaut
- Instituto Universitario de Neurociencia, Campus de Guajara, Universidad de La Laguna, 38201, La Laguna, Tenerife, Spain
| | - Agustín Lage-Castellanos
- Department of NeuroInformatics, Cuban Center for Neuroscience, Havana, Cuba
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - María José Rodrigo
- Instituto Universitario de Neurociencia, Campus de Guajara, Universidad de La Laguna, 38201, La Laguna, Tenerife, Spain
- Facultad de Psicología, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Silvia Herrero-Roldán
- Instituto Universitario de Neurociencia, Campus de Guajara, Universidad de La Laguna, 38201, La Laguna, Tenerife, Spain
- Facultad de Ciencias Sociales Aplicadas y de la Comunicación, UNIE Universidad, Madrid, Spain
| | - Colter Mitchell
- Institute for Social Research, University of Michigan, Ann Abor, MI, USA
| | - Jonah Fisher
- Institute for Social Research, University of Michigan, Ann Abor, MI, USA
| | - Inmaculada León
- Instituto Universitario de Neurociencia, Campus de Guajara, Universidad de La Laguna, 38201, La Laguna, Tenerife, Spain.
- Facultad de Psicología, Universidad de La Laguna, San Cristóbal de La Laguna, Spain.
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Chou HH, Chen CC, Tsai CF, Kuo PL, Chiou YY. Associations between maternal chronic diseases and congenital anomalies of the kidney and urinary tract in offspring: a population-based cohort study. Clin Kidney J 2023; 16:2652-2660. [PMID: 38046024 PMCID: PMC10689185 DOI: 10.1093/ckj/sfad217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Indexed: 12/05/2023] Open
Abstract
Background The relationship between maternal chronic diseases and congenital anomalies of the kidneys and urinary tract (CAKUT) in offspring still needs elucidation. This study aimed to comprehensively evaluate the associations between maternal chronic disease and CAKUT in their offspring. Methods Data of mothers and children were extracted from the Taiwan Maternal and Child Health Database and National Health Insurance Research Database. The concept of developmental origins of health and disease (DOHaD) was used to select maternal chronic diseases. Results The study cohort included 1 196 175 mothers and 1 628 706 offspring. Analysis showed that maternal chronic diseases, especially type 1 diabetes, type 2 diabetes, gestational diabetes, connective tissue disorders and CAKUT were highly associated with CAKUT in the offspring. Higher maternal age, abnormal birthweight (>3500 g or <2500 g), gestational age <36 weeks and birth order <2 were all associated with a higher risk of CAKUT. Maternal chronic hypertension and taking angiotensin-related drugs increased the odds ratios of obstructive kidney disease in the offspring. Offspring tended to have the same type of CAKUT as their mothers. Conclusion Maternal chronic diseases, older maternal age and abnormal birthweight are risk factors for CAKUT. Also, a percentage of patients with CAKUT were not full-term newborns. Results support prenatal counselling and health management of pregnant women with chronic diseases and extra care for infants with a high risk of anomalies. It is strongly recommended that prevention of CAKUT in offspring should start with care of the mothers' prenatal chronic diseases.
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Affiliation(s)
- Hsin-Hsu Chou
- Department of Pediatrics, Ditmanson Medical Foundation Chiayi Christian Hospital, Chia-Yi City, Taiwan
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung City, Taiwan
| | - Chih-Chia Chen
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan City, Taiwan
- Department of Pediatrics, Division of Pediatric Nephrology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan City, Taiwan
| | - Ching-Fang Tsai
- Department of Medical Research, Clinical Data Center, Ditmanson Medical Foundation Chiayi Christian Hospital, Chia-Yi City, Taiwan
| | - Pao-Lin Kuo
- Department of Obstetrics and Gynecology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan City, Taiwan
| | - Yuan-Yow Chiou
- Department of Pediatrics, Division of Pediatric Nephrology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan City, Taiwan
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Cardenas A, Fadadu R, Bunyavanich S. Climate change and epigenetic biomarkers in allergic and airway diseases. J Allergy Clin Immunol 2023; 152:1060-1072. [PMID: 37741554 PMCID: PMC10843253 DOI: 10.1016/j.jaci.2023.09.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/18/2023] [Accepted: 09/18/2023] [Indexed: 09/25/2023]
Abstract
Human epigenetic variation is associated with both environmental exposures and allergic diseases and can potentially serve as a biomarker connecting climate change with allergy and airway diseases. In this narrative review, we summarize recent human epigenetic studies examining exposure to temperature, precipitation, extreme weather events, and malnutrition to discuss findings as they relate to allergic and airway diseases. Temperature has been the most widely studied exposure, with the studies implicating both short-term and long-term exposures with epigenetic alterations and epigenetic aging. Few studies have examined natural disasters or extreme weather events. The studies available have reported differential DNA methylation of multiple genes and pathways, some of which were previously associated with asthma or allergy. Few studies have integrated climate-related events, epigenetic biomarkers, and allergic disease together. Prospective longitudinal studies are needed along with the collection of target tissues beyond blood samples, such as nasal and skin cells. Finally, global collaboration to increase diverse representation of study participants, particularly those most affected by climate injustice, as well as strengthen replication, validation, and harmonization of measurements will be needed to elucidate the impacts of climate change on the human epigenome.
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Affiliation(s)
- Andres Cardenas
- Department of Epidemiology and Population Health, Stanford University, Stanford, Calif.
| | - Raj Fadadu
- School of Medicine, University of California, San Francisco, Calif
| | - Supinda Bunyavanich
- Division of Allergy and Immunology, Department of Pediatrics, and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
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Cardenas A, Fadadu RP, Koppelman GH. Epigenome-wide association studies of allergic disease and the environment. J Allergy Clin Immunol 2023; 152:582-590. [PMID: 37295475 PMCID: PMC10564109 DOI: 10.1016/j.jaci.2023.05.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/04/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023]
Abstract
The epigenome is at the intersection of the environment, genotype, and cellular response. DNA methylation of cytosine nucleotides, the most studied epigenetic modification, has been systematically evaluated in human studies by using untargeted epigenome-wide association studies (EWASs) and shown to be both sensitive to environmental exposures and associated with allergic diseases. In this narrative review, we summarize findings from key EWASs previously conducted on this topic; interpret results from recent studies; and discuss the strengths, challenges, and opportunities regarding epigenetics research on the environment-allergy relationship. The majority of these EWASs have systematically investigated select environmental exposures during the prenatal and early childhood periods and allergy-associated epigenetic changes in leukocyte-isolated DNA and more recently in nasal cells. Overall, many studies have found consistent DNA methylation associations across cohorts for certain exposures, such as smoking (eg, aryl hydrocarbon receptor repressor gene [AHRR] gene), and allergic diseases (eg, EPX gene). We recommend the integration of both environmental exposures and allergy or asthma within long-term prospective designs to strengthen causality as well as biomarker development. Future studies should collect paired target tissues to examine compartment-specific epigenetic responses, incorporate genetic influences in DNA methylation (methylation quantitative trait locus), replicate findings across diverse populations, and carefully interpret epigenetic signatures from bulk, target tissue or isolated cells.
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Affiliation(s)
- Andres Cardenas
- Department of Epidemiology and Population Health, Stanford School of Medicine, Stanford University, Stanford, Calif
| | - Raj P Fadadu
- School of Medicine, University of California, San Francisco, Calif
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, Groningen, The Netherlands; Groningen Research Institute of Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
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6
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Ma H, Wang X, Liang Z, Li X, Heianza Y, He J, Chen W, Bazzano L, Qi L. BMI change during childhood, DNA methylation change at TXNIP, and glucose change during midlife. Obesity (Silver Spring) 2023; 31:2150-2158. [PMID: 37415079 PMCID: PMC10524171 DOI: 10.1002/oby.23806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/28/2023] [Accepted: 04/29/2023] [Indexed: 07/08/2023]
Abstract
OBJECTIVE This study investigated whether changes in DNA methylation (DNAm) at TXNIP are associated with glycemic changes and whether such an association differs with early-life adiposity changes. METHODS A total of 594 Bogalusa Heart Study participants who had blood DNAm measurements at two time points in midlife were included. Of them, 353 participants had at least four BMI measurements during childhood and adolescence. The incremental area under the curve was calculated as a measure of long-term trends of BMI during childhood and adolescence. RESULTS Increase in DNAm at TXNIP was significantly associated with decrease in fasting plasma glucose (FPG) independent of covariates (p < 0.001). The study found that the strength of this relationship was significantly modified by a trend of increasing BMI during childhood and adolescence (p-interaction = 0.003). Each 1% increase in DNAm at TXNIP was associated with a 2.90- (0.77) mg/dL decrease in FPG among participants with the highest tertile of BMI incremental area under the curve and a 0.96- (0.38) mg/dL decrease among those with the middle tertile, whereas no association was observed among participants with the lowest tertile. CONCLUSIONS These results indicate that changes in blood DNAm at TXNIP are significantly associated with changes in FPG in midlife, and this association was modified by BMI trends during childhood and adolescence.
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Affiliation(s)
- Hao Ma
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Xuan Wang
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Zhaoxia Liang
- Obstetrical Department, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiang Li
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Yoriko Heianza
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Jiang He
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Wei Chen
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Lydia Bazzano
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Lu Qi
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
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Hagenbeek FA, Hirzinger JS, Breunig S, Bruins S, Kuznetsov DV, Schut K, Odintsova VV, Boomsma DI. Maximizing the value of twin studies in health and behaviour. Nat Hum Behav 2023:10.1038/s41562-023-01609-6. [PMID: 37188734 DOI: 10.1038/s41562-023-01609-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/19/2023] [Indexed: 05/17/2023]
Abstract
In the classical twin design, researchers compare trait resemblance in cohorts of identical and non-identical twins to understand how genetic and environmental factors correlate with resemblance in behaviour and other phenotypes. The twin design is also a valuable tool for studying causality, intergenerational transmission, and gene-environment correlation and interaction. Here we review recent developments in twin studies, recent results from twin studies of new phenotypes and recent insights into twinning. We ask whether the results of existing twin studies are representative of the general population and of global diversity, and we conclude that stronger efforts to increase representativeness are needed. We provide an updated overview of twin concordance and discordance for major diseases and mental disorders, which conveys a crucial message: genetic influences are not as deterministic as many believe. This has important implications for public understanding of genetic risk prediction tools, as the accuracy of genetic predictions can never exceed identical twin concordance rates.
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Affiliation(s)
- Fiona A Hagenbeek
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands.
| | - Jana S Hirzinger
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Sophie Breunig
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Department of Psychology & Neuroscience, University of Colorado Boulder, Boulder, CO, USA
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
| | - Susanne Bruins
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Dmitry V Kuznetsov
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Faculty of Sociology, Bielefeld University, Bielefeld, Germany
| | - Kirsten Schut
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Nightingale Health Plc, Helsinki, Finland
| | - Veronika V Odintsova
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, the Netherlands
- Department of Psychiatry, University Medical Center of Groningen, University of Groningen, Groningen, the Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands.
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, the Netherlands.
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8
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LaSalle JM. Epigenomic signatures reveal mechanistic clues and predictive markers for autism spectrum disorder. Mol Psychiatry 2023; 28:1890-1901. [PMID: 36650278 PMCID: PMC10560404 DOI: 10.1038/s41380-022-01917-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 01/18/2023]
Abstract
Autism spectrum disorder (ASD) comprises a heterogeneous group of neurodevelopmental outcomes in children with a commonality in deficits in social communication and language combined with repetitive behaviors and interests. The etiology of ASD is heterogeneous, as several hundred genes have been implicated as well as multiple in utero environmental exposures. Over the past two decades, epigenetic investigations, including DNA methylation, have emerged as a novel way to capture the complex interface of multivariate ASD etiologies. More recently, epigenome-wide association studies using human brain and surrogate accessible tissues have revealed some convergent genes that are epigenetically altered in ASD, many of which overlap with known genetic risk factors. Unlike transcriptomes, epigenomic signatures defined by DNA methylation from surrogate tissues such as placenta and cord blood can reflect past differences in fetal brain gene transcription, transcription factor binding, and chromatin. For example, the discovery of NHIP (neuronal hypoxia inducible, placenta associated) through an epigenome-wide association in placenta, identified a common genetic risk for ASD that was modified by prenatal vitamin use. While epigenomic signatures are distinct between different genetic syndromic causes of ASD, bivalent chromatin and some convergent gene pathways are consistently epigenetically altered in both syndromic and idiopathic ASD, as well as some environmental exposures. Together, these epigenomic signatures hold promising clues towards improved early prediction and prevention of ASD as well genes and gene pathways to target for pharmacological interventions. Future advancements in single cell and multi-omic technologies, machine learning, as well as non-invasive screening of epigenomic signatures during pregnancy or newborn periods are expected to continue to impact the translatability of the recent discoveries in epigenomics to precision public health.
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Affiliation(s)
- Janine M LaSalle
- Department of Medical Microbiology and Immunology, Perinatal Origins of Disparities Center, MIND Institute, Genome Center, Environmental Health Sciences Center, University of California Davis, Davis, CA, USA.
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Lu AKM, Hsieh S, Yang CT, Wang XY, Lin SH. DNA methylation signature of psychological resilience in young adults: Constructing a methylation risk score using a machine learning method. Front Genet 2023; 13:1046700. [PMID: 36712885 PMCID: PMC9877348 DOI: 10.3389/fgene.2022.1046700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/29/2022] [Indexed: 01/15/2023] Open
Abstract
Resilience is a process associated with the ability to recover from stress and adversity. We aimed to explore the resilience-associated DNA methylation signatures and evaluate the abilities of methylation risk scores to discriminate low resilience (LR) individuals. The study recruited 78 young adults and used Connor-Davidson Resilience Scale (CD-RISC) to divide them into low and high resilience groups. We randomly allocated all participants of two groups to the discovery and validation sets. We used the blood DNA of the subjects to conduct a genome-wide methylation scan and identify the significant methylation differences of CpG Sites in the discovery set. Moreover, the classification accuracy of the DNA methylation probes was confirmed in the validation set by real-time quantitative methylation-specific polymerase chain reaction. In the genome-wide methylation profiling between LR and HR individuals, seventeen significantly differentially methylated probes were detected. In the validation set, nine DNA methylation signatures within gene coding regions were selected for verification. Finally, three methylation probes [cg18565204 (AARS), cg17682313 (FBXW7), and cg07167608 (LINC01107)] were included in the final model of the methylation risk score for LR versus HR. These methylation risk score models of low resilience demonstrated satisfactory discrimination by logistic regression and support vector machine, with an AUC of 0.81 and 0.93, accuracy of 72.3% and 87.1%, sensitivity of 75%, and 87.5%, and specificity of 70% and 80%. Our findings suggest that methylation signatures can be utilized to identify individuals with LR and establish risk score models that may contribute to the field of psychology.
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Affiliation(s)
- Andrew Ke-Ming Lu
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shulan Hsieh
- Department of Psychology, College of Social Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Cheng-Ta Yang
- Department of Psychology, College of Social Sciences, National Cheng Kung University, Tainan, Taiwan,Graduate Institute of Mind, Brain, and Consciousness, Taipei Medical University, Taipei, Taiwan
| | - Xin-Yu Wang
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Sheng-Hsiang Lin
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan,Department of Public Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan,Biostatistics Consulting Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan,*Correspondence: Sheng-Hsiang Lin,
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Hart DA. One of the Primary Functions of Tissue-Resident Pluripotent Pericytes Cells May Be to Regulate Normal Organ Growth and Maturation: Implications for Attempts to Repair Tissues Later in Life. Int J Mol Sci 2022; 23:5496. [PMID: 35628309 PMCID: PMC9146368 DOI: 10.3390/ijms23105496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 12/04/2022] Open
Abstract
Adult mesenchymal stem cells were reported more than 30 years ago. Since then, their potential to repair and regenerate damaged or diseased tissues has been studied intensively in both preclinical models and human trials. Most of the need for such tissue repair/regeneration is in older populations, so much of the effort has been performed with autologous cells in older patients. However, success has been difficult to achieve. In the literature, it has been noted that such progenitor cells from younger individuals often behave with more vigorous activity and are functionally enhanced compared to those from older individuals or animals. In addition, cells with the characteristics of mesenchymal stem cells or pluripotent mesenchymal regulatory cells exist in nearly all tissues and organs as pericytes since fetal life. Such evidence raises the possibility that one of the primary roles of these organ-specific cells is to regulate organ growth and maturation, and then subsequently play a role in the maintenance of organ integrity. This review will discuss the evidence to support this concept and the implications of such a concept regarding the use of these progenitor cells for the repair and regeneration of tissues damaged by injury or disease later in life. For the latter, it may be necessary to return the organ-specific progenitor cells to the functional state that contributed to their effectiveness during growth and maturation rather than attempting to use them after alterations imposed during the aging process have been established and their function compromised.
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