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Eaves LA, Harrington CE, Fry RC. Epigenetic Responses to Nonchemical Stressors: Potential Molecular Links to Perinatal Health Outcomes. Curr Environ Health Rep 2024; 11:145-157. [PMID: 38580766 DOI: 10.1007/s40572-024-00435-w] [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] [Accepted: 02/06/2024] [Indexed: 04/07/2024]
Abstract
PURPOSE OF REVIEW We summarize the recent literature investigating exposure to four nonchemical stressors (financial stress, racism, psychosocial stress, and trauma) and DNA methylation, miRNA expression, and mRNA expression. We also highlight the relationships between these epigenetic changes and six critical perinatal outcomes (preterm birth, low birth weight, preeclampsia, gestational diabetes, childhood allergic disease, and childhood neurocognition). RECENT FINDINGS Multiple studies have found financial stress, psychosocial stress, and trauma to be associated with DNA methylation and/or miRNA and mRNA expression. Fewer studies have investigated the effects of racism. The majority of studies assessed epigenetic or genomic changes in maternal blood, cord blood, or placenta. Several studies included multi-OMIC assessments in which DNA methylation and/or miRNA expression were associated with gene expression. There is strong evidence for the role of epigenetics in driving the health outcomes considered. A total of 22 biomarkers, including numerous HPA axis genes, were identified to be epigenetically altered by both stressors and outcomes. Epigenetic changes related to inflammation, the immune and endocrine systems, and cell growth and survival were highlighted across numerous studies. Maternal exposure to nonchemical stressors is associated with epigenetic and/or genomic changes in a tissue-specific manner among inflammatory, immune, endocrine, and cell growth-related pathways, which may act as mediating pathways to perinatal health outcomes. Future research can test the mediating role of the specific biomarkers identified as linked with both stressors and outcomes. Understanding underlying epigenetic mechanisms altered by nonchemical stressors can provide a better understanding of how chemical and nonchemical exposures interact.
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Affiliation(s)
- Lauren A Eaves
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Cailee E Harrington
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Rebecca C Fry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA.
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA.
- Curriculum in Toxicology and Environmental Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, USA.
- Department of Pediatrics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA.
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Shorey-Kendrick LE, Davis B, Gao L, Park B, Vu A, Morris CD, Breton CV, Fry R, Garcia E, Schmidt RJ, O’Shea TM, Tepper RS, McEvoy CT, Spindel ER. Development and Validation of a Novel Placental DNA Methylation Biomarker of Maternal Smoking during Pregnancy in the ECHO Program. ENVIRONMENTAL HEALTH PERSPECTIVES 2024; 132:67005. [PMID: 38885141 PMCID: PMC11218700 DOI: 10.1289/ehp13838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 02/27/2024] [Accepted: 05/22/2024] [Indexed: 06/20/2024]
Abstract
BACKGROUND Maternal cigarette smoking during pregnancy (MSDP) is associated with numerous adverse health outcomes in infants and children with potential lifelong consequences. Negative effects of MSDP on placental DNA methylation (DNAm), placental structure, and function are well established. OBJECTIVE Our aim was to develop biomarkers of MSDP using DNAm measured in placentas (N = 96 ), collected as part of the Vitamin C to Decrease the Effects of Smoking in Pregnancy on Infant Lung Function double-blind, placebo-controlled randomized clinical trial conducted between 2012 and 2016. We also aimed to develop a digital polymerase chain reaction (PCR) assay for the top ranking cytosine-guanine dinucleotide (CpG) so that large numbers of samples can be screened for exposure at low cost. METHODS We compared the ability of four machine learning methods [logistic least absolute shrinkage and selection operator (LASSO) regression, logistic elastic net regression, random forest, and gradient boosting machine] to classify MSDP based on placental DNAm signatures. We developed separate models using the complete EPIC array dataset and on the subset of probes also found on the 450K array so that models exist for both platforms. For comparison, we developed a model using CpGs previously associated with MSDP in placenta. For each final model, we used model coefficients and normalized beta values to calculate placental smoking index (PSI) scores for each sample. Final models were validated in two external datasets: the Extremely Low Gestational Age Newborn observational study, N = 426 ; and the Rhode Island Children's Health Study, N = 237 . RESULTS Logistic LASSO regression demonstrated the highest performance in cross-validation testing with the lowest number of input CpGs. Accuracy was greatest in external datasets when using models developed for the same platform. PSI scores in smokers only (n = 72 ) were moderately correlated with maternal plasma cotinine levels. One CpG (cg27402634), with the largest coefficient in two models, was measured accurately by digital PCR compared with measurement by EPIC array (R 2 = 0.98 ). DISCUSSION To our knowledge, we have developed the first placental DNAm-based biomarkers of MSDP with broad utility to studies of prenatal disease origins. https://doi.org/10.1289/EHP13838.
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Affiliation(s)
- Lyndsey E. Shorey-Kendrick
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Brett Davis
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Lina Gao
- Biostatistics Shared Resources, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
- Bioinformatics & Biostatistics Core, Oregon National Primate Research Center, Oregon Health & Science University, Portland, Oregon, USA
| | - Byung Park
- Biostatistics Shared Resources, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
- Bioinformatics & Biostatistics Core, Oregon National Primate Research Center, Oregon Health & Science University, Portland, Oregon, USA
- Oregon Health & Science University–Portland State University School of Public Health, Portland, Oregon, USA
| | - Annette Vu
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon, USA
| | - Cynthia D. Morris
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon, USA
- Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Carrie V. Breton
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA
| | - Rebecca Fry
- Department of Environmental Sciences and Engineering, UNC Gillings School of Public Health, Chapel Hill, North Carolina, USA
| | - Erika Garcia
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA
| | - Rebecca J. Schmidt
- Department of Public Health Sciences, School of Medicine, University of California, Davis, Davis, California, USA
- MIND Institute, School of Medicine, University of California Davis, Davis, California, USA
| | - T. Michael O’Shea
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Robert S. Tepper
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Cindy T. McEvoy
- Department of Pediatrics, Oregon Health & Science University, Portland, Oregon, USA
| | - Eliot R. Spindel
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
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Heyob KM, Khuhro Z, Khan AQ, Brown D, Tipple TE, Rogers LK. Effects of DNA methylase inhibitors in a murine model of severe BPD. Respir Physiol Neurobiol 2023; 313:104060. [PMID: 37031925 DOI: 10.1016/j.resp.2023.104060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/21/2023] [Accepted: 04/06/2023] [Indexed: 04/11/2023]
Abstract
DNA methylation is necessary for developmental gene regulation, but adverse environments result in aberrant methylation and gene silencing. The current pilot study tested the hypothesis that treatment with DNA methylation inhibitors (decitabine; RG108) would improve alveolarization in a newborn murine model of severe bronchopulmonary dysplasia. Newborn mice exposed to maternal inflammation (LPS) and neonatal hyperoxia (85% O2) were treated with decitabine (p3, 0.1 mg/kg; p2, 4, 6, 0.1 mg/kg; or p2, 4, 6, 0.15 mg/kg) or RG108 (p3, 0.0013 mg/kg) delivered intranasally. Modest improvements in alveolarization were observed with decitabine, but no differences were observed with RG108. Attenuated phospho-SMAD2/3 levels and greater surfactant protein C protein levels compared to vehicle were observed with some tested doses. No detrimental side effects were observed with the doses used in this study. In summary, our pilot investigations identified a safe dose for intranasal administration of both methylation inhibitors and provides a foundation for further studies into methylation inhibitors in the context of neonatal lung injury.
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Affiliation(s)
- Kathryn M Heyob
- Center for Perinatal Research, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Zahra Khuhro
- Center for Perinatal Research, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Aiman Q Khan
- Center for Perinatal Research, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Dorian Brown
- Center for Perinatal Research, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Trent E Tipple
- Section of Neonatal-Perinatal Medicine, Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Lynette K Rogers
- Center for Perinatal Research, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University, Columbus, OH, USA.
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Freedman AN, Clark J, Eaves LA, Roell K, Oran A, Koval L, Rager J, Santos HP, Kuban K, Joseph RM, Frazier J, Marsit CJ, Burt AA, O’Shea TM, Fry RC. A multi-omic approach identifies an autism spectrum disorder (ASD) regulatory complex of functional epimutations in placentas from children born preterm. Autism Res 2023; 16:918-934. [PMID: 36938998 PMCID: PMC10192070 DOI: 10.1002/aur.2915] [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: 09/16/2022] [Accepted: 02/25/2023] [Indexed: 03/21/2023]
Abstract
Children born preterm are at heightened risk of neurodevelopmental impairments, including Autism Spectrum Disorder (ASD). The placenta is a key regulator of neurodevelopmental processes, though the precise underlying molecular mechanisms remain unclear. Here, we employed a multi-omic approach to identify placental transcriptomic and epigenetic modifications related to ASD diagnosis at age 10, among children born preterm. Working with the extremely low gestational age (ELGAN) cohort, we hypothesized that a pro-inflammatory placental environment would be predictive of ASD diagnosis at age 10. Placental messenger RNA (mRNA) expression, CpG methylation, and microRNA (miRNA) expression were compared among 368 ELGANs (28 children diagnosed with ASD and 340 children without ASD). A total of 111 genes displayed expression levels in the placenta that were associated with ASD. Within these ASD-associated genes is an ASD regulatory complex comprising key genes that predicted ASD case status. Genes with expression that predicted ASD case status included Ewing Sarcoma Breakpoint Region 1 (EWSR1) (OR: 6.57 (95% CI: 2.34, 23.58)) and Bromodomain Adjacent To Zinc Finger Domain 2A (BAZ2A) (OR: 0.12 (95% CI: 0.03, 0.35)). Moreover, of the 111 ASD-associated genes, nine (8.1%) displayed associations with CpG methylation levels, while 14 (12.6%) displayed associations with miRNA expression levels. Among these, LRR Binding FLII Interacting Protein 1 (LRRFIP1) was identified as being under the control of both CpG methylation and miRNAs, displaying an OR of 0.42 (95% CI: 0.17, 0.95). This gene, as well as others identified as having functional epimutations, plays a critical role in immune system regulation and inflammatory response. In summary, a multi-omic approach was used to identify functional epimutations in the placenta that are associated with the development of ASD in children born preterm, highlighting future avenues for intervention.
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Affiliation(s)
- Anastasia N. Freedman
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jeliyah Clark
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
- Institute for Environmental Health Solutions, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Lauren A. Eaves
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
- Institute for Environmental Health Solutions, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Kyle Roell
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
- Institute for Environmental Health Solutions, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Ali Oran
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
- Institute for Environmental Health Solutions, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Lauren Koval
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
- Institute for Environmental Health Solutions, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Julia Rager
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
- Institute for Environmental Health Solutions, University of North Carolina, Chapel Hill, North Carolina, USA
- Curriculum in Toxicology and Environmental Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Hudson P Santos
- Institute for Environmental Health Solutions, University of North Carolina, Chapel Hill, North Carolina, USA
- School of Nursing and Health Studies, University of Miami, Coral Gables, FL, USA
| | - Karl Kuban
- Department of Pediatrics, Division of Child Neurology, Boston Medical Center, Boston, Massachusetts, USA
| | - Robert M. Joseph
- Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Jean Frazier
- Eunice Kennedy Shriver Center, Department of Psychiatry, University of Massachusetts Medical School/University of Massachusetts Memorial Health Care, Worcester, MA, USA
| | - Carmen J. Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, United States of America
| | - Amber A. Burt
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, United States of America
| | - T. Michael O’Shea
- Department of Pediatrics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Rebecca C. Fry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
- Institute for Environmental Health Solutions, University of North Carolina, Chapel Hill, North Carolina, USA
- Curriculum in Toxicology and Environmental Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
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O'Shea TM, McGrath M, Aschner JL, Lester B, Santos HP, Marsit C, Stroustrup A, Emmanuel C, Hudak M, McGowan E, Patel S, Fry RC. Environmental influences on child health outcomes: cohorts of individuals born very preterm. Pediatr Res 2023; 93:1161-1176. [PMID: 35948605 PMCID: PMC9363858 DOI: 10.1038/s41390-022-02230-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/27/2022] [Accepted: 07/19/2022] [Indexed: 12/05/2022]
Abstract
The National Institutes of Health's Environmental influences on Child Health Outcomes (ECHO) Program was designed to address solution-oriented research questions about the links between children's early life environment and their risks of pre-, peri-, and post-natal complications, asthma, obesity, neurodevelopmental disorders, and positive health. Children born very preterm are at increased risk for many of the outcomes on which ECHO focuses, but the contributions of environmental factors to this risk are not well characterized. Three ECHO cohorts consist almost exclusively of individuals born very preterm. Data provided to ECHO from cohorts can be used to address hypotheses about (1) differential risks of chronic health and developmental conditions between individuals born very preterm and those born at term; (2) health disparities across social determinants of health; and (3) mechanisms linking early-life exposures and later-life outcomes among individuals born very preterm. IMPACT: The National Institutes of Health's Environmental Influences on Child Health Outcomes Program is conducting solution-oriented research on the links between children's environment and health. Three ECHO cohorts comprise study participants born very preterm; these cohorts have enrolled, to date, 1751 individuals born in 14 states in the U.S. in between April 2002 and March 2020. Extensive data are available on early-life environmental exposures and child outcomes related to neurodevelopment, asthma, obesity, and positive health. Data from ECHO preterm cohorts can be used to address questions about the combined effects of preterm birth and environmental exposures on child health outcomes.
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Affiliation(s)
- T Michael O'Shea
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC, USA.
| | - Monica McGrath
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Judy L Aschner
- Department of Pediatrics, Joseph M. Sanzari Children's Hospital at Hackensack University Medical Center, Hackensack, NJ, USA
- Department of Pediatrics, Hackensack Meridian School of Medicine, Nutley, NJ, USA
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Barry Lester
- Department of Pediatrics, Women & Infants Hospital, Brown University, Providence, RI, USA
- Brown Center for the Study of Children at Risk, Warren Alpert Medical School of Brown University, Women & Infants Hospital, Providence, RI, USA
- Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Hudson P Santos
- Biobehavioral Laboratory, School of Nursing, The University of North Carolina, Chapel Hill, NC, USA
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina, Chapel Hill, NC, USA
| | - Carmen Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Annemarie Stroustrup
- Departments of Pediatrics and Occupational Medicine, Epidemiology and Prevention, Zucker School of Medicine at Hofstra, Northwell Health, Cohen Children's Medical Center, New Hyde Park, NY, USA
| | - Crisma Emmanuel
- Biobehavioral Laboratory, School of Nursing, The University of North Carolina, Chapel Hill, NC, USA
| | - Mark Hudak
- Department of Pediatrics, University of Florida College of Medicine - Jacksonville, Jacksonville, FL, USA
| | - Elisabeth McGowan
- Women & Infants Hospital, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Simran Patel
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Rebecca C Fry
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina, Chapel Hill, NC, USA
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina, Chapel Hill, NC, USA
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6
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Eaves LA, Enggasser AE, Camerota M, Gogcu S, Gower WA, Hartwell H, Jackson WM, Jensen E, Joseph RM, Marsit CJ, Roell K, Santos HP, Shenberger JS, Smeester L, Yanni D, Kuban KCK, O'Shea TM, Fry RC. CpG methylation patterns in placenta and neonatal blood are differentially associated with neonatal inflammation. Pediatr Res 2023; 93:1072-1084. [PMID: 35764815 PMCID: PMC10289042 DOI: 10.1038/s41390-022-02150-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 05/09/2022] [Accepted: 05/26/2022] [Indexed: 12/29/2022]
Abstract
BACKGROUND Infants born extremely premature are at increased risk for health complications later in life for which neonatal inflammation may be a contributing biological driver. Placental CpG methylation provides mechanistic information regarding the relationship between prenatal epigenetic programming, prematurity, neonatal inflammation, and later-in-life health. METHODS We contrasted CpG methylation in the placenta and neonatal blood spots in relation to neonatal inflammation in the Extremely Low Gestational Age Newborn (ELGAN) cohort. Neonatal inflammation status was based on the expression of six inflammation-related proteins, assessed as (1) day-one inflammation (DOI) or (2) intermittent or sustained systemic inflammation (ISSI, inflammation on ≥2 days in the first 2 postnatal weeks). Epigenome-wide CpG methylation was assessed in 354 placental samples and 318 neonatal blood samples. RESULTS Placental CpG methylation displayed the strongest association with ISSI (48 CpG sites) but was not associated with DOI. This was in contrast to CpG methylation in blood spots, which was associated with DOI (111 CpG sites) and not with ISSI (one CpG site). CONCLUSIONS Placental CpG methylation was strongly associated with ISSI, a measure of inflammation previously linked to later-in-life cognitive impairment, while day-one neonatal blood methylation was associated with DOI. IMPACT Neonatal inflammation increases the risk of adverse later-life outcomes, especially in infants born extremely preterm. CpG methylation in the placenta and neonatal blood spots were evaluated in relation to neonatal inflammation assessed via circulating proteins as either (i) day-one inflammation (DOI) or (ii) intermittent or sustained systemic inflammation (ISSI, inflammation on ≥2 days in the first 2 weeks). Tissue specificity was observed in epigenetic-inflammatory relationships: placental CpG methylation was associated with ISSI, neonatal blood CpG methylation was associated with DOI. Supporting the placental origins of disease framework, placental epigenetic patterns are associated with a propensity for ISSI in neonates.
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Affiliation(s)
- Lauren A Eaves
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Adam E Enggasser
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Marie Camerota
- Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, RI, USA
| | - Semsa Gogcu
- Division of Neonatology, Department of Pediatrics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - William A Gower
- Department of Pediatrics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Hadley Hartwell
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wesley M Jackson
- Department of Pediatrics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Elizabeth Jensen
- Department of Epidemiology and Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Robert M Joseph
- Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, MA, USA
| | - Carmen J Marsit
- Gangarosa Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Kyle Roell
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hudson P Santos
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- School of Nursing & Health Studies, University of Miami, Miami, FL, USA
| | - Jeffrey S Shenberger
- Division of Neonatology, Department of Pediatrics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Lisa Smeester
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Diana Yanni
- Department of Neonatology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Karl C K Kuban
- Division of Pediatric Neurology, Department of Pediatrics, School of Medicine, Boston University Medical Center, Boston, MA, USA
| | - T Michael O'Shea
- Department of Pediatrics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Rebecca C Fry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Zhou G, Fichorova RN, Holzman C, Chen B, Chang C, Kasten EP, Hoffmann HM. Placental circadian lincRNAs and spontaneous preterm birth. Front Genet 2023; 13:1051396. [PMID: 36712876 PMCID: PMC9874002 DOI: 10.3389/fgene.2022.1051396] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/28/2022] [Indexed: 01/12/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have a much higher cell- and/or tissue-specificity compared to mRNAs in most cases, making them excellent candidates for therapeutic applications to reduce off-target effects. Placental long non-coding RNAs have been investigated in the pathogenesis of preeclampsia (often causing preterm birth (PTB)), but less is known about their role in preterm birth. Preterm birth occurs in 11% of pregnancies and is the most common cause of death among infants in the world. We recently identified that genes that drive circadian rhythms in cells, termed molecular clock genes, are deregulated in maternal blood of women with spontaneous PTB (sPTB) and in the placenta of women with preeclampsia. Next, we focused on circadian genes-correlated long intergenic non-coding RNAs (lincRNAs, making up most of the long non-coding RNAs), designated as circadian lincRNAs, associated with sPTB. We compared the co-altered circadian transcripts-correlated lincRNAs expressed in placentas of sPTB and term births using two published independent RNAseq datasets (GSE73712 and GSE174415). Nine core clock genes were up- or downregulated in sPTB versus term birth, where the RORA transcript was the only gene downregulated in sPTB across both independent datasets. We found that five circadian lincRNAs (LINC00893, LINC00265, LINC01089, LINC00482, and LINC00649) were decreased in sPTB vs term births across both datasets (p ≤ .0222, FDR≤.1973) and were negatively correlated with the dataset-specific clock genes-based risk scores (correlation coefficient r = -.65 ∼ -.43, p ≤ .0365, FDR≤.0601). Gene set variation analysis revealed that 65 pathways were significantly enriched by these same five differentially expressed lincRNAs, of which over 85% of the pathways could be linked to immune/inflammation/oxidative stress and cell cycle/apoptosis/autophagy/cellular senescence. These findings may improve our understanding of the pathogenesis of spontaneous preterm birth and provide novel insights into the development of potentially more effective and specific therapeutic targets against sPTB.
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Affiliation(s)
- Guoli Zhou
- Clinical and Translational Sciences Institute, Michigan State University, East Lansing, MI, United States,*Correspondence: Guoli Zhou, ; Hanne M. Hoffmann,
| | - Raina N. Fichorova
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Claudia Holzman
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, United States
| | - Bin Chen
- Department of Pediatrics and Human Development, Michigan State University, East Lansing, MI, United States
| | - Chi Chang
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, United States
| | - Eric P. Kasten
- Clinical and Translational Sciences Institute, Michigan State University, East Lansing, MI, United States,Department of Radiology, Michigan State University, East Lansing, MI, United States
| | - Hanne M. Hoffmann
- Department of Animal Science, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, United States,*Correspondence: Guoli Zhou, ; Hanne M. Hoffmann,
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Carrasco-Wong I, González-Ortiz M, Araujo GG, Lima VV, Giachini FR, Stojanova J, Moller A, Martín SS, Escudero P, Damiano AE, Sosa-Macias M, Galaviz-Hernandez C, Teran E, Escudero C. The Placental Function Beyond Pregnancy: Insights from Latin America. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1428:287-307. [PMID: 37466779 DOI: 10.1007/978-3-031-32554-0_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Currently, more than 100,000 papers had been published studying the placenta in both physiological and pathological contexts. However, relevant health conditions affecting placental function, mostly found in low-income countries, should be evaluated deeper. This review will raise some - of what we think necessary - points of discussion regarding challenging topics not fully understood, including the paternal versus maternal contribution on placental genes imprinting, placenta-brain communication, and some environmental conditions affecting the placenta. The discussions are parts of an international effort to fulfil some gaps observed in this area, and Latin-American research groups currently evaluate that.
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Affiliation(s)
- Ivo Carrasco-Wong
- Cellular Signaling and Differentiation Laboratory (CSDL), School of Medical Technology, Medicine and Science Faculty, Universidad San Sebastián, Santiago, Chile
| | - Marcelo González-Ortiz
- Laboratorio de Investigación Materno-Fetal (LIMaF), Departamento de Obstetricia y Ginecología, Facultad de Medicina, Universidad de Concepción, Concepción, Chile
- Group of Research and Innovation in Vascular Health (GRIVAS Health), Chillan, Chile
| | - Gabriel Gomes Araujo
- Laboratory of Vascular Biology, Institute of Health Sciences and Health, Universidade Federal de Mato Grosso, Barra do Garcas, Brazil
| | - Victor V Lima
- Laboratory of Vascular Biology, Institute of Health Sciences and Health, Universidade Federal de Mato Grosso, Barra do Garcas, Brazil
| | - Fernanda R Giachini
- Laboratory of Vascular Biology, Institute of Health Sciences and Health, Universidade Federal de Mato Grosso, Barra do Garcas, Brazil
| | - Jana Stojanova
- Interdisciplinary Centre for Health Studies (CIESAL), Universidad de Valparaíso, Viña del Mar, Chile
| | - Alejandra Moller
- Escuela de Tecnología Médica, Facultad de Medicina, Universidad de Valparaíso, Viña del Mar, Chile
| | - Sebastián San Martín
- Group of Research and Innovation in Vascular Health (GRIVAS Health), Chillan, Chile
- Biomedical Research Centre, School of Medicine, Universidad de Valparaíso, Viña del Mar, Chile
| | - Pablo Escudero
- Faculty of Medicine, Universidad San Sebastian, Sede Concepcion, Chile
| | - Alicia E Damiano
- Laboratorio de Biología de la Reproducción, Instituto de Fisiología y Biofísica Bernardo Houssay (IFIBIO)- CONICET- Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
- Cátedra de Biología Celular y Molecular, Departamento de Ciencias Biológicas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Martha Sosa-Macias
- Genomics Academia, Instituto Politécnico Nacional-CIIDIR Durango, Durango, Mexico
| | | | - Enrique Teran
- Colegio de Ciencias de la Salud, Universidad San Francisco de Quito, Quito, Ecuador
| | - Carlos Escudero
- Group of Research and Innovation in Vascular Health (GRIVAS Health), Chillan, Chile.
- Vascular Physiology Laboratory, Basic Sciences Department, Faculty of Sciences, Universidad del Bio-Bio, Chillan, Chile.
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9
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Durbagula S, Korlimarla A, Ravikumar G, Valiya Parambath S, Kaku SM, Visweswariah AM. Prenatal epigenetic factors are predisposing for neurodevelopmental disorders—Considering placenta as a model. Birth Defects Res 2022; 114:1324-1342. [DOI: 10.1002/bdr2.2119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 09/29/2022] [Accepted: 10/03/2022] [Indexed: 11/16/2022]
Affiliation(s)
- Srividhya Durbagula
- St. John's Medical College Bangalore India
- St. John's Research Institute Bangalore India
| | - Aruna Korlimarla
- St. John's Research Institute Bangalore India
- Department of Research Sri Shankara Cancer Hospital and Research Center Bangalore India
| | | | - Snijesh Valiya Parambath
- St. John's Medical College Bangalore India
- Department of Molecular Medicine St. John's Research Institute Bangalore India
| | - Sowmyashree Mayur Kaku
- St. John's Medical College Bangalore India
- Centre for Advanced Research and Excellence in Autism and Developmental Disorders (CARE ADD) St. John's Research Institute Bangalore India
| | - Ashok Mysore Visweswariah
- St. John's Medical College Bangalore India
- Centre for Advanced Research and Excellence in Autism and Developmental Disorders (CARE ADD) St. John's Research Institute Bangalore India
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10
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Marable CA, Roell K, Kuban K, O’Shea TM, Fry RC. Placental transcriptional signatures associated with cerebral white matter damage in the neonate. Front Neurosci 2022; 16:1017953. [PMID: 36389237 PMCID: PMC9650394 DOI: 10.3389/fnins.2022.1017953] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/04/2022] [Indexed: 09/10/2023] Open
Abstract
Cerebral white matter is the most common anatomic location of neonatal brain injury in preterm newborns. Factors that predispose preterm newborns to white matter damage are understudied. In relation to studies of the placenta-brain-axis, dysregulated placental gene expression may play a role in preterm brain damage given its implication in programming early life origins of disease, including neurological disorders. There is a critical need to investigate the relationships between the placental transcriptome and white matter damage in the neonate. In a cohort of extremely low gestational age newborns (ELGANs), we aimed to investigate the relationship between the placental transcriptome and white matter damage as assessed by neonatal cranial ultrasound studies (echolucency and/or ventriculomegaly). We hypothesized that genes involved in inflammatory processes would be more highly expressed in placentas of ELGANs who developed ultrasound-defined indicators of white matter damage. Relative to either form of white matter damage, 659 placental genes displayed altered transcriptional profiles. Of these white matter damage-associated genes, largely distinct patterns of gene expression were observed in the study (n = 415/659 genes). Specifically, 381 genes were unique to echolucency and 34 genes were unique to ventriculomegaly. Pathways involved in hormone disruption and metabolism were identified among the unique echolucency or ventriculomegaly genes. Interestingly, a common set of 244 genes or 37% of all genes was similarly dysregulated in the placenta relative to both echolucency and ventriculomegaly. For this common set of white matter damage-related genes, pathways involved in inflammation, immune response and apoptosis, were enriched. Among the white matter damage-associated genes are genes known to be involved in Autism Spectrum Disorder (ASD) and endocrine system disorders. These data highlight differential mRNA expression patterning in the placenta and provide insight into potential etiologic factors that may predispose preterm newborns to white matter damage. Future studies will build upon this work to include functional measures of neurodevelopment as well as measures of brain volume later in life.
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Affiliation(s)
- Carmen Amelia Marable
- School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Kyle Roell
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Institute for Environmental Health Solutions, Gilling School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Karl Kuban
- Division of Pediatric Neurology, Department of Pediatrics, Boston University Medical Center, Boston, MA, United States
| | - T. Michael O’Shea
- Department of Pediatrics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Rebecca C. Fry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Institute for Environmental Health Solutions, Gilling School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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11
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Freedman AN, Eaves LA, Rager JE, Gavino-Lopez N, Smeester L, Bangma J, Santos HP, Joseph RM, Kuban KC, O'Shea TM, Fry RC. The placenta epigenome-brain axis: placental epigenomic and transcriptomic responses that preprogram cognitive impairment. Epigenomics 2022; 14:897-911. [PMID: 36073148 PMCID: PMC9475498 DOI: 10.2217/epi-2022-0061] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Aim: The placenta-brain axis reflects a developmental linkage where disrupted placental function is associated with impaired neurodevelopment later in life. Placental gene expression and the expression of epigenetic modifiers such as miRNAs may be tied to these impairments and are understudied. Materials & methods: The expression levels of mRNAs (n = 37,268) and their targeting miRNAs (n = 2083) were assessed within placentas collected from the ELGAN study cohort (n = 386). The ELGAN adolescents were assessed for neurocognitive function at age 10 and the association with placental mRNA/miRNAs was determined. Results: Placental mRNAs related to inflammatory and apoptotic processes are under miRNA control and associated with cognitive impairment at age 10. Conclusion: Findings highlight key placenta epigenome-brain relationships that support the developmental origins of health and disease hypothesis.
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Affiliation(s)
- Anastasia N Freedman
- Department of Environmental Sciences & Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Lauren A Eaves
- Department of Environmental Sciences & Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA.,Institute for Environmental Health Solutions, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Julia E Rager
- Department of Environmental Sciences & Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA.,Curriculum in Toxicology & Environmental Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA.,Institute for Environmental Health Solutions, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Noemi Gavino-Lopez
- Department of Environmental Sciences & Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Lisa Smeester
- Department of Environmental Sciences & Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA.,Institute for Environmental Health Solutions, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jacqueline Bangma
- Department of Environmental Sciences & Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA.,Institute for Environmental Health Solutions, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Hudson P Santos
- Institute for Environmental Health Solutions, University of North Carolina, Chapel Hill, NC 27599, USA.,School of Nursing and Health Studies, University of Miami, Coral Gables, FL 33124, USA
| | - Robert M Joseph
- Department of Anatomy & Neurobiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Karl Ck Kuban
- Department of Pediatrics, Division of Child Neurology, Boston Medical Center, Boston, MA 02118, USA
| | - Thomas Michael O'Shea
- Department of Pediatrics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Rebecca C Fry
- Department of Environmental Sciences & Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA.,Curriculum in Toxicology & Environmental Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA.,Institute for Environmental Health Solutions, University of North Carolina, Chapel Hill, NC 27599, USA
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12
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Andrews SV, Yang IJ, Froehlich K, Oskotsky T, Sirota M. Large-scale placenta DNA methylation integrated analysis reveals fetal sex-specific differentially methylated CpG sites and regions. Sci Rep 2022; 12:9396. [PMID: 35672357 PMCID: PMC9174475 DOI: 10.1038/s41598-022-13544-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 05/17/2022] [Indexed: 11/14/2022] Open
Abstract
Although male–female differences in placental structure and function have been observed, little is understood about their molecular underpinnings. Here, we present a mega-analysis of 14 publicly available placenta DNA methylation (DNAm) microarray datasets to identify individual CpGs and regions associated with fetal sex. In the discovery dataset of placentas from full term pregnancies (N = 532 samples), 5212 CpGs met genome-wide significance (p < 1E−8) and were enriched in pathways such as keratinization (FDR p-value = 7.37E−14), chemokine activity (FDR p-value = 1.56E−2), and eosinophil migration (FDR p-value = 1.83E−2). Nine differentially methylated regions were identified (fwerArea < 0.1) including a region in the promoter of ZNF300 that showed consistent differential DNAm in samples from earlier timepoints in pregnancy and appeared to be driven predominately by effects in the trophoblast cell type. We describe the largest study of fetal sex differences in placenta DNAm performed to date, revealing genes and pathways characterizing sex-specific placenta function and health outcomes later in life.
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Affiliation(s)
- Shan V Andrews
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA
| | - Irene J Yang
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA.,Dougherty Valley High School, San Ramon, CA, USA
| | - Karolin Froehlich
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA
| | - Tomiko Oskotsky
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA. .,Department of Pediatrics, UCSF, San Francisco, CA, USA.
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA. .,Department of Pediatrics, UCSF, San Francisco, CA, USA.
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13
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Bangma JT, Hartwell H, Santos HP, O'Shea TM, Fry RC. Placental programming, perinatal inflammation, and neurodevelopment impairment among those born extremely preterm. Pediatr Res 2021; 89:326-335. [PMID: 33184498 PMCID: PMC7658618 DOI: 10.1038/s41390-020-01236-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 09/02/2020] [Accepted: 10/08/2020] [Indexed: 01/30/2023]
Abstract
Individuals born extremely preterm are at significant risk for impaired neurodevelopment. After discharge from the neonatal intensive care, associations between the child's well-being and factors in the home and social environment become increasingly apparent. Mothers' prenatal health and socioeconomic status are associated with neurodevelopmental outcomes, and emotional and behavioral problems. Research on early life risk factors and on mechanisms underlying inter-individual differences in neurodevelopment later in life can inform the design of personalized approaches to prevention. Here, we review early life predictors of inter-individual differences in later life neurodevelopment among those born extremely preterm. Among biological mechanisms that mediate relationships between early life predictors and later neurodevelopmental outcomes, we highlight evidence for disrupted placental processes and regulated at least in part via epigenetic mechanisms, as well as perinatal inflammation. In relation to these mechanisms, we focus on four prenatal antecedents of impaired neurodevelopment, namely, (1) fetal growth restriction, (2) maternal obesity, (3) placental microorganisms, and (4) socioeconomic adversity. In the future, this knowledge may inform efforts to detect and prevent adverse outcomes in infants born extremely preterm. IMPACT: This review highlights early life risk factors and mechanisms underlying inter-individual differences in neurodevelopment later in life. The review emphasizes research on early life risk factors (fetal growth restriction, maternal obesity, placental microorganisms, and socioeconomic adversity) and on mechanisms (disrupted placental processes and perinatal inflammation) underlying inter-individual differences in neurodevelopment later in life. The findings highlighted here may inform efforts to detect and prevent adverse outcomes in infants born extremely preterm.
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Affiliation(s)
- Jacqueline T Bangma
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hadley Hartwell
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hudson P Santos
- Biobehavioral Laboratory, School of Nursing, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - T Michael O'Shea
- Department of Pediatrics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rebecca C Fry
- Biobehavioral Laboratory, School of Nursing, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Toxicology and Environmental Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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14
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Collier ARY, Ledyard R, Montoya-Williams D, Qiu M, Dereix AE, Farrokhi MR, Hacker MR, Burris HH. Racial and ethnic representation in epigenomic studies of preterm birth: a systematic review. Epigenomics 2020; 13:1735-1746. [PMID: 33264049 DOI: 10.2217/epi-2020-0007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Aim: We conducted a systematic review evaluating race/ethnicity representation in DNA methylomic studies of preterm birth. Data sources: PubMed, EMBASE, CINHAL, Scopus and relevant citations from 1 January 2000 to 30 June 2019. Study appraisal & synthesis methods: Two authors independently identified abstracts comparing DNA methylomic differences between term and preterm births that included race/ethnicity data. Results: 16 studies were included. Black and non-Hispanic Black deliveries were well represented (28%). However, large studies originating from more than 95% White populations were excluded due to unreported race/ethnicity data. Most studies were cross-sectional, allowing for reverse causation. Most studies were also racially/ethnically homogeneous, preventing direct comparison of DNA methylomic differences across race/ethnicities. Conclusion: In DNA methylomic studies, Black women and infants were well represented. However, the literature has limitations and precludes drawing definitive conclusions.
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Affiliation(s)
- Ai-Ris Y Collier
- Department of Obstetrics & Gynecology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA.,Department of Obstetrics, Gynecology, & Reproductive Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Rachel Ledyard
- Division of Neonatology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Diana Montoya-Williams
- Division of Neonatology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Maylene Qiu
- Biomedical Library, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alexandra E Dereix
- Division of Neonatology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Loyola University Chicago Stritch School of Medicine, Maywood, IL 60153, USA
| | - Minou Raschid Farrokhi
- Department of Obstetrics & Gynecology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA.,Colby College, Waterville, ME 04901, USA
| | - Michele R Hacker
- Department of Obstetrics & Gynecology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA.,Department of Obstetrics, Gynecology, & Reproductive Biology, Harvard Medical School, Boston, MA 02115, USA.,Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA 02115, USA
| | - Heather H Burris
- Division of Neonatology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
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15
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Shanthikumar S, Neeland MR, Maksimovic J, Ranganathan SC, Saffery R. DNA methylation biomarkers of future health outcomes in children. Mol Cell Pediatr 2020; 7:7. [PMID: 32642955 PMCID: PMC7343681 DOI: 10.1186/s40348-020-00099-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/25/2020] [Indexed: 11/10/2022] Open
Abstract
Biomarkers which predict future health outcomes are key to the goals of precision health. Such biomarkers do not have to be involved in the causal pathway of a disease, and their performance is best assessed using statistical tests of clinical performance and evaluation of net health impact. DNA methylation is the most commonly studied epigenetic process and represents a potential biomarker of future health outcomes. We review 25 studies in non-oncological paediatric conditions where DNA methylation biomarkers of future health outcomes are assessed. Whilst a number of positive findings have been described, the body of evidence is severely limited by issues with outcome measures, tissue-specific samples, accounting for sample cell type heterogeneity, lack of appropriate statistical testing, small effect sizes, limited validation, and no assessment of net health impact. Future studies should concentrate on careful study design to overcome these issues, and integration of DNA methylation data with other 'omic', clinical, and environmental data to generate the most clinically useful biomarkers of paediatric disease.
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Affiliation(s)
- Shivanthan Shanthikumar
- Respiratory and Sleep Medicine, Royal Children's Hospital, Flemington Road, Parkville, Melbourne, Victoria, 3052, Australia. .,Respiratory Diseases, Murdoch Children's Research Institute, Melbourne, Australia. .,Department of Paediatrics, The University of Melbourne, Melbourne, Australia.
| | - Melanie R Neeland
- Department of Paediatrics, The University of Melbourne, Melbourne, Australia.,Epigenetics, Murdoch Children's Research Institute, Melbourne, Australia
| | - Jovana Maksimovic
- Respiratory Diseases, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Australia.,Computational Biology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Sarath C Ranganathan
- Respiratory and Sleep Medicine, Royal Children's Hospital, Flemington Road, Parkville, Melbourne, Victoria, 3052, Australia.,Respiratory Diseases, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | - Richard Saffery
- Department of Paediatrics, The University of Melbourne, Melbourne, Australia.,Epigenetics, Murdoch Children's Research Institute, Melbourne, Australia
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16
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Oldenburg KS, O’Shea TM, Fry RC. Genetic and epigenetic factors and early life inflammation as predictors of neurodevelopmental outcomes. Semin Fetal Neonatal Med 2020; 25:101115. [PMID: 32444251 PMCID: PMC7363586 DOI: 10.1016/j.siny.2020.101115] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Among individuals born very preterm, perinatal inflammation, particularly if sustained or recurring, is highly likely to contribute to adverse neurodevelopmental outcomes, including cerebral white matter damage, cerebral palsy, cognitive impairment, attention-deficit/hyperactivity disorder, and autism spectrum disorder. Antecedents and correlates of perinatal inflammation include socioeconomic disadvantage, maternal obesity, maternal infections, fetal growth restriction, neonatal sepsis, necrotizing enterocolitis, and prolonged mechanical ventilation. Genetic factors can modify susceptibility to perinatal inflammation and to neurodevelopmental disorders. Preliminary evidence supports a role of epigenetic markers as potential mediators of the presumed effects of preterm birth and/or its consequences on neurodevelopment later in life. Further study is needed of factors such as sex, psychosocial stressors, and environmental exposures that could modify the relationship of early life inflammation to later neurodevelopmental impairments. Also needed are pharmacological and non-pharmacological interventions to attenuate inflammation towards the goal of improving the neurodevelopment of individuals born very preterm.
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Affiliation(s)
- Kirsi S. Oldenburg
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill
| | - T. Michael O’Shea
- Department of Pediatrics (Neonatology), University of North Carolina School of Medicine
| | - Rebecca C. Fry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill
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17
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Denomme MM, Parks JC, McCallie BR, McCubbin NI, Schoolcraft WB, Katz-Jaffe MG. Advanced paternal age directly impacts mouse embryonic placental imprinting. PLoS One 2020; 15:e0229904. [PMID: 32142542 PMCID: PMC7059926 DOI: 10.1371/journal.pone.0229904] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 02/17/2020] [Indexed: 11/18/2022] Open
Abstract
The placental epigenome plays a critical role in regulating mammalian growth and development. Alterations to placental methylation, often observed at imprinted genes, can lead to adverse pregnancy complications such as intrauterine growth restriction and preterm birth. Similar associations have been observed in offspring derived from advanced paternal age fathers. As parental age at time of conception continues to rise, the impact of advanced paternal age on these reproductive outcomes is a growing concern, but limited information is available on the molecular mechanisms affected in utero. This longitudinal murine research study thus investigated the impact of paternal aging on genomic imprinting in viable F1 embryonic portions of the placentas derived from the same paternal males when they were young (4-6 months) and when they aged (11-15 months). The use of a controlled outbred mouse model enabled analysis of offspring throughout the natural lifetime of the same paternal males and excluded confounding factors like female age or infertility. Firstly, paternal age significantly impacted embryonic placental weight, fetal weight and length. Targeted bisulfite sequencing was utilized to examine imprinted methylation at the Kcnq1ot1 imprinting control region, with significant hypermethylation observed upon natural paternal aging. Quantitative real-time PCR assessed imprinted gene expression levels at various imprinting clusters, resulting in transcript level alterations attributable to advanced paternal age. In summary, our results demonstrate a paternal age effect with dysregulation at numerous imprinted loci, providing a mechanism for future adverse placental and offspring health conditions.
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Affiliation(s)
| | - Jason C. Parks
- Fertility Labs of Colorado, Lone Tree, CO, United States of America
| | | | | | | | - Mandy G. Katz-Jaffe
- Fertility Labs of Colorado, Lone Tree, CO, United States of America
- Colorado Center for Reproductive Medicine, Lone Tree, CO, United States of America
- * E-mail:
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18
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Scarpato R, Testi S, Colosimo V, Garcia Crespo C, Micheli C, Azzarà A, Tozzi MG, Ghirri P. Role of oxidative stress, genome damage and DNA methylation as determinants of pathological conditions in the newborn: an overview from conception to early neonatal stage. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 783:108295. [DOI: 10.1016/j.mrrev.2019.108295] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 11/25/2019] [Accepted: 12/24/2019] [Indexed: 12/15/2022]
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19
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Bulka CM, Dammann O, Santos HP, VanderVeen DK, Smeester L, Fichorova R, O'Shea TM, Fry RC. Placental CpG Methylation of Inflammation, Angiogenic, and Neurotrophic Genes and Retinopathy of Prematurity. Invest Ophthalmol Vis Sci 2019; 60:2888-2894. [PMID: 31266060 PMCID: PMC6607927 DOI: 10.1167/iovs.18-26466] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Purpose Extremely preterm infants are at increased risk for retinopathy of prematurity (ROP). We previously identified several inflammatory proteins that were expressed early in life and are associated with an increased risk of ROP and several angiogenic and neurotrophic growth factors in the neonatal systemic circulation that are associated with a lower risk of ROP. In this paper, we report the results of a set of analyses designed to test the hypothesis that placental CpG methylation levels of 12 inflammation-, angiogenic-, and neurotrophic-associated genes predict the occurrence of prethreshold ROP in extremely preterm newborns. Methods We used placental CpG methylation data from 395 newborns from the Extremely Low Gestational Age Newborns study. Results Multivariable regression models revealed that placental DNA methylation of 16 CpG sites representing 8 genes were associated with prethreshold ROP. Specifically, CpG methylation in the serum amyloid A SAA1 and SAA2, brain-derived neurotrophic factor (BDNF), myeloperoxidase (MPO), C-reactive protein (CRP), angiopoietin 1 (ANGPT1), and tumor necrosis factor receptor superfamily member 1B (TNFRSF1B) genes was associated with a lower risk of prethreshold ROP. Conversely, CpG methylation at three probes within tumor necrosis factor receptor superfamily member 1A (TNFRSF1A) and in two alternative probes within the BDNF and ANGPT1 genes was associated with an increased risk of ROP. Conclusions CpG methylation may be a useful marker for improving ROP prediction, opening the opportunity for early intervention to lessen disease severity.
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Affiliation(s)
- Catherine M Bulka
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States
| | - Olaf Dammann
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, Massachusetts, United States.,Perinatal Neuroepidemiology Unit, Department of Gynecology and Obstetrics, Hannover Medical School, Hannover, Germany
| | - Hudson P Santos
- School of Nursing, University of North Carolina, Chapel Hill, North Carolina, United States
| | - Deborah K VanderVeen
- Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts, United States
| | - Lisa Smeester
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States.,Institute for Environmental Health Solutions, Gilling School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States
| | - Raina Fichorova
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham And Women's Hospital, Boston, Massachusetts, United States
| | - T Michael O'Shea
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina, United States
| | - Rebecca C Fry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States.,Institute for Environmental Health Solutions, Gilling School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States.,Curriculum in Toxicology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States
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20
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Human placental methylome in the interplay of adverse placental health, environmental exposure, and pregnancy outcome. PLoS Genet 2019; 15:e1008236. [PMID: 31369552 PMCID: PMC6675049 DOI: 10.1371/journal.pgen.1008236] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The placenta is the interface between maternal and fetal circulations, integrating maternal and fetal signals to selectively regulate nutrient, gas, and waste exchange, as well as secrete hormones. In turn, the placenta helps create the in utero environment and control fetal growth and development. The unique epigenetic profile of the human placenta likely reflects its early developmental separation from the fetus proper and its role in mediating maternal–fetal exchange that leaves it open to a range of exogenous exposures in the maternal circulation. In this review, we cover recent advances in DNA methylation in the context of placental function and development, as well as the interaction between the pregnancy and the environment.
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21
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Microorganisms in the Placenta: Links to Early-Life Inflammation and Neurodevelopment in Children. Clin Microbiol Rev 2019; 32:32/3/e00103-18. [PMID: 31043389 DOI: 10.1128/cmr.00103-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Prenatal exposure to various stressors can influence both early and later life childhood health. Microbial infection of the intrauterine environment, specifically within the placenta, has been associated with deleterious birth outcomes, such as preterm birth, as well as adverse neurological outcomes later in life. The relationships among microorganisms in the placenta, placental function, and fetal development are not well understood. Microorganisms have been associated with perinatal inflammatory responses that have the potential for disrupting fetal brain development. Microbial presence has also been associated with epigenetic modifications in the placenta, as well other tissues. Here we review research detailing the presence of microorganisms in the placenta and associations among such microorganisms, placental DNA methylation, perinatal inflammation, and neurodevelopmental outcomes.
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22
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Epigenome-wide Analysis Identifies Genes and Pathways Linked to Neurobehavioral Variation in Preterm Infants. Sci Rep 2019; 9:6322. [PMID: 31004082 PMCID: PMC6474865 DOI: 10.1038/s41598-019-42654-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 04/03/2019] [Indexed: 02/07/2023] Open
Abstract
Neonatal molecular biomarkers of neurobehavioral responses (measures of brain-behavior relationships), when combined with neurobehavioral performance measures, could lead to better predictions of long-term developmental outcomes. To this end, we examined whether variability in buccal cell DNA methylation (DNAm) associated with neurobehavioral profiles in a cohort of infants born less than 30 weeks postmenstrual age (PMA) and participating in the Neonatal Neurobehavior and Outcomes in Very Preterm Infants (NOVI) Study (N = 536). We tested whether epigenetic age, age acceleration, or DNAm levels at individual loci differed between infants based on their NICU Network Neurobehavioral Scale (NNNS) profile classifications. We adjusted for recruitment site, infant sex, PMA, and tissue heterogeneity. Infants with an optimally well-regulated NNNS profile had older epigenetic age compared to other NOVI infants (β1 = 0.201, p-value = 0.026), but no significant difference in age acceleration. In contrast, infants with an atypical NNNS profile had differential methylation at 29 CpG sites (FDR < 10%). Some of the genes annotated to these CpGs included PLA2G4E, TRIM9, GRIK3, and MACROD2, which have previously been associated with neurological structure and function, or with neurobehavioral disorders. These findings contribute to the existing evidence that neonatal epigenetic variations may be informative for infant neurobehavior.
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23
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Naruse K, Tsunemi T, Kawahara N, Kobayashi H. Preliminary evidence of a paternal-maternal genetic conflict on the placenta: Link between imprinting disorder and multi-generational hypertensive disorders. Placenta 2019; 84:69-73. [PMID: 30846225 DOI: 10.1016/j.placenta.2019.02.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/21/2019] [Accepted: 02/19/2019] [Indexed: 01/07/2023]
Abstract
There has been great research progress on hypertensive disorders in pregnancy (HDP) in the last few decades. Failure of placentation, especially a lack of uterine spiral artery remodeling, is the main pathological finding of HDP. Currently, members of the vascular endothelial growth factor family are used as markers for the early prediction of onset of HDP. Epidemiologic research has also shown that HDP can have effects on the next generation infants, representing a Development Origins of Health and Disease-related disease. However, the precise pathogenic mechanism and the effect of HDP on the offspring remain unclear. The group of strong pro-inflammatory molecules known as "danger signals" have been shown to be released from the placental trophoblast surface and increase in the maternal circulation in HDP, which are then possibly transported into the fetal circulation. These signals, including fatty acids or adipocytokines, may alter the offspring's health in later life. Moreover, a hypoxic condition alters placental methylation, and the change may be passed onto the fetus. Although the genetic origin of the disease is still unknown, a hypothesis has been put forward that a paternal-maternal genetic conflict, mainly at imprinting lesion sites, may be a key factor for disease initiation. In particular, an imbalance in paternal and maternal factors may impede proper placentation, trophoblast invasion, decidualization or immune moderation so as to achieve better nutrition for the fetus (paternal) versus ensuring safe delivery and further pregnancy (maternal). Here, we review this research progress on HDP and focus on this novel genetic conflict concept, which is expected to provide new insight into the cause, pathophysiology, and multi-generational effects of HDP.
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Affiliation(s)
- Katsuhiko Naruse
- Department of Obstetrics and Gynecology, Nara Medical University, Japan; St.Barnabas' Hospital, Osaka, Japan.
| | - Taihei Tsunemi
- Department of Obstetrics and Gynecology, Nara Medical University, Japan
| | - Naoki Kawahara
- Department of Obstetrics and Gynecology, Nara Medical University, Japan
| | - Hiroshi Kobayashi
- Department of Obstetrics and Gynecology, Nara Medical University, Japan
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24
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Hawkins LJ, Al-Attar R, Storey KB. Transcriptional regulation of metabolism in disease: From transcription factors to epigenetics. PeerJ 2018; 6:e5062. [PMID: 29922517 PMCID: PMC6005171 DOI: 10.7717/peerj.5062] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/04/2018] [Indexed: 12/13/2022] Open
Abstract
Every cell in an individual has largely the same genomic sequence and yet cells in different tissues can present widely different phenotypes. This variation arises because each cell expresses a specific subset of genomic instructions. Control over which instructions, or genes, are expressed is largely controlled by transcriptional regulatory pathways. Each cell must assimilate a huge amount of environmental input, and thus it is of no surprise that transcription is regulated by many intertwining mechanisms. This large regulatory landscape means there are ample possibilities for problems to arise, which in a medical context means the development of disease states. Metabolism within the cell, and more broadly, affects and is affected by transcriptional regulation. Metabolism can therefore contribute to improper transcriptional programming, or pathogenic metabolism can be the result of transcriptional dysregulation. Here, we discuss the established and emerging mechanisms for controling transcription and how they affect metabolism in the context of pathogenesis. Cis- and trans-regulatory elements, microRNA and epigenetic mechanisms such as DNA and histone methylation, all have input into what genes are transcribed. Each has also been implicated in diseases such as metabolic syndrome, various forms of diabetes, and cancer. In this review, we discuss the current understanding of these areas and highlight some natural models that may inspire future therapeutics.
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Affiliation(s)
- Liam J Hawkins
- Institute of Biochemistry, Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Rasha Al-Attar
- Institute of Biochemistry, Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Kenneth B Storey
- Institute of Biochemistry, Department of Biology, Carleton University, Ottawa, ON, Canada
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