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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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2
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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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3
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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: 10] [Impact Index Per Article: 5.0] [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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A Potential ceRNA Network for Neurological Damage in Preterm Infants. BIOMED RESEARCH INTERNATIONAL 2021; 2021:2628824. [PMID: 34471635 PMCID: PMC8405308 DOI: 10.1155/2021/2628824] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/05/2021] [Accepted: 08/03/2021] [Indexed: 12/13/2022]
Abstract
Objective This study is aimed at identifying key genes involved in neurological damage in preterm infants and at determining their potential circRNA-miRNA-mRNA regulatory mechanisms. Methods Differentially expressed miRNAs, mRNAs, and circRNAs were downloaded from the GEO database. GO and KEGG enrichment analyses were used to determine possible relevant functions of differentially expressed mRNAs. The TTRUST database was used to predict differential TF-mRNA regulatory relationships. Then, CircMIR, miRDB, TargetScan and miRTarBase were then used to map circRNA/miRNA-TF/mRNA interaction networks. Finally, GSEA enrichment analysis was performed on the core transcription factors. Results A total of 640 mRNAs, 139 circRNAs, and 206 differentially expressed miRNAs associated with neurological injury in preterm infants were obtained. Based on the findings of Cytoscape and PPI network analysis, the hsa_circ_0008439-hsa-mir-3665-STAT3-MMP3 regulatory axis was established. GSEA analysis revealed that suppressed expression levels of STAT3 were associated with upregulated oxidative phosphorylation pathways in the neurological injury group of preterm infants. Conclusions The circRNA-miRNA-TF-mRNA regulatory network of neurological injury in preterm infants can be used to elucidate on the pathogenesis of brain injury and help us with the early detection of brain injury in preterm infants.
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5
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Ball G, Seidlitz J, O’Muircheartaigh J, Dimitrova R, Fenchel D, Makropoulos A, Christiaens D, Schuh A, Passerat-Palmbach J, Hutter J, Cordero-Grande L, Hughes E, Price A, Hajnal JV, Rueckert D, Robinson EC, Edwards AD. Cortical morphology at birth reflects spatiotemporal patterns of gene expression in the fetal human brain. PLoS Biol 2020; 18:e3000976. [PMID: 33226978 PMCID: PMC7721147 DOI: 10.1371/journal.pbio.3000976] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 12/07/2020] [Accepted: 11/02/2020] [Indexed: 02/07/2023] Open
Abstract
Interruption to gestation through preterm birth can significantly impact cortical development and have long-lasting adverse effects on neurodevelopmental outcome. We compared cortical morphology captured by high-resolution, multimodal magnetic resonance imaging (MRI) in n = 292 healthy newborn infants (mean age at birth = 39.9 weeks) with regional patterns of gene expression in the fetal cortex across gestation (n = 156 samples from 16 brains, aged 12 to 37 postconceptional weeks [pcw]). We tested the hypothesis that noninvasive measures of cortical structure at birth mirror areal differences in cortical gene expression across gestation, and in a cohort of n = 64 preterm infants (mean age at birth = 32.0 weeks), we tested whether cortical alterations observed after preterm birth were associated with altered gene expression in specific developmental cell populations. Neonatal cortical structure was aligned to differential patterns of cell-specific gene expression in the fetal cortex. Principal component analysis (PCA) of 6 measures of cortical morphology and microstructure showed that cortical regions were ordered along a principal axis, with primary cortex clearly separated from heteromodal cortex. This axis was correlated with estimated tissue maturity, indexed by differential expression of genes expressed by progenitor cells and neurons, and engaged in stem cell differentiation, neuron migration, and forebrain development. Preterm birth was associated with altered regional MRI metrics and patterns of differential gene expression in glial cell populations. The spatial patterning of gene expression in the developing cortex was thus mirrored by regional variation in cortical morphology and microstructure at term, and this was disrupted by preterm birth. This work provides a framework to link molecular mechanisms to noninvasive measures of cortical development in early life and highlights novel pathways to injury in neonatal populations at increased risk of neurodevelopmental disorder. Interruption to gestation through preterm birth can significantly impact cortical development and have long-lasting adverse effects on neurodevelopmental outcome. A large neuroimaging study of newborn infants reveals how their cortical structure at birth is associated with patterns of gene expression in the fetal cortex and how this relationship is affected by preterm birth.
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Affiliation(s)
- Gareth Ball
- Developmental Imaging, Murdoch Children’s Research Institute, Melbourne, Australia
- Centre for the Developing Brain, Department of Perinatal Imaging & Health, King’s College London, United Kingdom
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
- * E-mail:
| | - Jakob Seidlitz
- Developmental Neurogenomics Unit, National Institute of Mental Health, Bethesda, United States of America
- Department of Psychiatry, University of Cambridge, United Kingdom
| | - Jonathan O’Muircheartaigh
- Centre for the Developing Brain, Department of Perinatal Imaging & Health, King’s College London, United Kingdom
| | - Ralica Dimitrova
- Centre for the Developing Brain, Department of Perinatal Imaging & Health, King’s College London, United Kingdom
| | - Daphna Fenchel
- Centre for the Developing Brain, Department of Perinatal Imaging & Health, King’s College London, United Kingdom
| | - Antonios Makropoulos
- Centre for the Developing Brain, Department of Perinatal Imaging & Health, King’s College London, United Kingdom
| | - Daan Christiaens
- Centre for the Developing Brain, Department of Perinatal Imaging & Health, King’s College London, United Kingdom
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Belgium
| | - Andreas Schuh
- Biomedical Image Analysis Group, Department of Computing, Imperial College London, United Kingdom
| | | | - Jana Hutter
- Centre for the Developing Brain, Department of Perinatal Imaging & Health, King’s College London, United Kingdom
| | - Lucilio Cordero-Grande
- Centre for the Developing Brain, Department of Perinatal Imaging & Health, King’s College London, United Kingdom
| | - Emer Hughes
- Centre for the Developing Brain, Department of Perinatal Imaging & Health, King’s College London, United Kingdom
| | - Anthony Price
- Centre for the Developing Brain, Department of Perinatal Imaging & Health, King’s College London, United Kingdom
| | - Jo V. Hajnal
- Centre for the Developing Brain, Department of Perinatal Imaging & Health, King’s College London, United Kingdom
| | - Daniel Rueckert
- Biomedical Image Analysis Group, Department of Computing, Imperial College London, United Kingdom
| | - Emma C. Robinson
- Centre for the Developing Brain, Department of Perinatal Imaging & Health, King’s College London, United Kingdom
| | - A David Edwards
- Centre for the Developing Brain, Department of Perinatal Imaging & Health, King’s College London, United Kingdom
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Costa D, Bonet N, Solé A, González de Aledo-Castillo JM, Sabidó E, Casals F, Rovira C, Nadal A, Marin JL, Cobo T, Castelo R. Genome-wide postnatal changes in immunity following fetal inflammatory response. FEBS J 2020; 288:2311-2331. [PMID: 33006196 PMCID: PMC8049052 DOI: 10.1111/febs.15578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/22/2020] [Accepted: 09/28/2020] [Indexed: 11/29/2022]
Abstract
The fetal inflammatory response (FIR) increases the risk of perinatal brain injury, particularly in extremely low gestational age newborns (ELGANs, < 28 weeks of gestation). One of the mechanisms contributing to such a risk is a postnatal intermittent or sustained systemic inflammation (ISSI) following FIR. The link between prenatal and postnatal systemic inflammation is supported by the presence of well‐established inflammatory biomarkers in the umbilical cord and peripheral blood. However, the extent of molecular changes contributing to this association is unknown. Using RNA sequencing and mass spectrometry proteomics, we profiled the transcriptome and proteome of archived neonatal dried blood spot (DBS) specimens from 21 ELGANs. Comparing FIR‐affected and unaffected ELGANs, we identified 782 gene and 27 protein expression changes of 50% magnitude or more, and an experiment‐wide significance level below 5% false discovery rate. These expression changes confirm the robust postnatal activation of the innate immune system in FIR‐affected ELGANs and reveal for the first time an impairment of their adaptive immunity. In turn, the altered pathways provide clues about the molecular mechanisms triggering ISSI after FIR, and the onset of perinatal brain injury. Databases EGAS00001003635 (EGA); PXD011626 (PRIDE).
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Affiliation(s)
- Daniel Costa
- Department of Pediatrics, Hospital de Figueres, Spain.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Núria Bonet
- Genomics Core Facility, Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Amanda Solé
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona, Spain.,Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | | | - Eduard Sabidó
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona, Spain.,Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Ferran Casals
- Genomics Core Facility, Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | | | - Alfons Nadal
- Department of Pathology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Spain
| | - Jose Luis Marin
- Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centre for Biomedical Research on Rare Diseases (CIBER-ER), University of Barcelona, Spain
| | - Teresa Cobo
- Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centre for Biomedical Research on Rare Diseases (CIBER-ER), University of Barcelona, Spain
| | - Robert Castelo
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Research Programme on Biomedical Informatics, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
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7
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Spada E, Calzari L, Corsaro L, Fazia T, Mencarelli M, Di Blasio AM, Bernardinelli L, Zangheri G, Vignali M, Gentilini D. Epigenome Wide Association and Stochastic Epigenetic Mutation Analysis on Cord Blood of Preterm Birth. Int J Mol Sci 2020; 21:ijms21145044. [PMID: 32708910 PMCID: PMC7403978 DOI: 10.3390/ijms21145044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 12/26/2022] Open
Abstract
Preterm birth (PTB) can be defined as the endpoint of a complex process that could be influenced by maternal and environmental factors. Epigenetics recently emerged as an interesting field of investigation since it represents an important mechanism of regulation. This study evaluates epigenetic impact of preterm birth on DNA methylation. Genome-wide DNAm was measured using the Illumina 450K array in cord blood samples obtained from 72 full term and 18 preterm newborns. Lymphocyte composition was calculated based on specific epigenetic markers that are present on the 450k array. Differential methylation analysis was performed both at site and region level; moreover, stochastic epigenetic mutations (SEMs) were also evaluated. The study showed significant differences in blood cell composition between the two groups. Moreover, after multiple testing correction, statistically significant differences in DNA methylation levels emerged between the two groups both at site and region levels. Results obtained were compared to those reported by previous EWAS, leading to a list of more consistent genes associated with PTB. Finally, the SEMs analysis revealed that the burden of SEMs resulted significantly higher in the preterm group. In conclusion, PTB resulted associated to specific epigenetic signatures that involve immune system. Moreover, SEMs analysis revealed an increased epigenetic drift at birth in the preterm group.
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Affiliation(s)
- Elena Spada
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy; (E.S.); (L.C.); (T.F.); (L.B.)
| | - Luciano Calzari
- Bioinformatics and Statistical Genomics Unit, Istituto Auxologico Italiano IRCCS, Cusano Milanino, 20095 Milano, Italy;
| | - Luigi Corsaro
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy; (E.S.); (L.C.); (T.F.); (L.B.)
| | - Teresa Fazia
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy; (E.S.); (L.C.); (T.F.); (L.B.)
| | - Monica Mencarelli
- Molecular Biology Laboratory, Istituto Auxologico Italiano IRCCS, Cusano Milanino, 20095 Milano, Italy; (M.M.); (A.M.D.B.)
| | - Anna Maria Di Blasio
- Molecular Biology Laboratory, Istituto Auxologico Italiano IRCCS, Cusano Milanino, 20095 Milano, Italy; (M.M.); (A.M.D.B.)
| | - Luisa Bernardinelli
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy; (E.S.); (L.C.); (T.F.); (L.B.)
| | - Giulia Zangheri
- Department of Biomedical Science for the Health, University of Milan, Macedonio Melloni Hospital, 20129 Milan, Italy; (G.Z.); (M.V.)
| | - Michele Vignali
- Department of Biomedical Science for the Health, University of Milan, Macedonio Melloni Hospital, 20129 Milan, Italy; (G.Z.); (M.V.)
| | - Davide Gentilini
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy; (E.S.); (L.C.); (T.F.); (L.B.)
- Bioinformatics and Statistical Genomics Unit, Istituto Auxologico Italiano IRCCS, Cusano Milanino, 20095 Milano, Italy;
- Correspondence: ; Tel.: +39-0382987541
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8
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Iacono D, Feltis GC. Impact of Apolipoprotein E gene polymorphism during normal and pathological conditions of the brain across the lifespan. Aging (Albany NY) 2020; 11:787-816. [PMID: 30677746 PMCID: PMC6366964 DOI: 10.18632/aging.101757] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 01/05/2019] [Indexed: 12/12/2022]
Abstract
The central nervous system (CNS) is the cellular substrate for the integration of complex, dynamic, constant, and simultaneous interactions among endogenous and exogenous stimuli across the entire human lifespan. Numerous studies on aging-related brain diseases show that some genes identified as risk factors for some of the most common neurodegenerative diseases - such as the allele 4 of APOE gene (APOE4) for Alzheimer's disease (AD) - have a much earlier neuro-anatomical and neuro-physiological impact. The impact of APOE polymorphism appears in fact to start as early as youth and early-adult life. Intriguingly, though, those same genes associated with aging-related brain diseases seem to influence different aspects of the brain functioning much earlier actually, that is, even from the neonatal periods and earlier. The APOE4, an allele classically associated with later-life neurodegenerative disorders as AD, seems in fact to exert a series of very early effects on phenomena of neuroplasticity and synaptogenesis that begin from the earliest periods of life such as the fetal ones.We reviewed some of the findings supporting the hypothesis that APOE polymorphism is an early modifier of various neurobiological aspects across the entire human lifespan - from the in-utero to the centenarian life - during both normal and pathological conditions of the brain.
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Affiliation(s)
- Diego Iacono
- Neuropathology Research, Biomedical Research Institute of New Jersey (BRInj), Cedar Knolls, NJ 07927, USA.,MidAtlantic Neonatology Associates (MANA), Morristown, NJ 07960, USA.,Atlantic Neuroscience Institute, Atlantic Health System (AHS), Overlook Medical Center, Summit, NJ 07901, USA
| | - Gloria C Feltis
- Neuropathology Research, Biomedical Research Institute of New Jersey (BRInj), Cedar Knolls, NJ 07927, USA
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Artificial Intelligence and the detection of pediatric concussion using epigenomic analysis. Brain Res 2019; 1726:146510. [PMID: 31628932 DOI: 10.1016/j.brainres.2019.146510] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 12/12/2022]
Abstract
Concussion, also referred to as mild traumatic brain injury (mTBI) is the most common type of traumatic brain injury. Currently concussion is an area ofintensescientific interest to better understand the biological mechanisms and for biomarker development. We evaluated whole genome-wide blood DNA cytosine ('CpG') methylation in 17 pediatric concussion isolated cases and 18 unaffected controls using Illumina Infinium MethylationEPIC assay. Pathway analysis was performed using Ingenuity Pathway Analysis to help elucidate the epigenetic and molecular mechanisms of the disorder. Area under the receiver operating characteristics (AUC) curves and FDR p-values were calculated for mTBI detection based on CpG methylation levels. Multiple Artificial Intelligence (AI) platforms including Deep Learning (DL), the newest form of AI, were used to predict concussion based on i) CpG methylation markers alone, and ii) combined epigenetic, clinical and demographic predictors. We found 449 CpG sites (473 genes), those were statistically significantly methylated in mTBI compared to controls. There were four CpGs with excellent individual accuracy (AUC ≥ 0.90-1.00) while 119 displayed good accuracy (AUC ≥ 0.80-0.89) for the prediction of mTBI. The CpG methylation changes ≥10% were observed in many CpG loci after concussion suggesting biological significance. Pathway analysis identified several biologically important neurological pathways that were perturbed including those associated with: impaired brain function, cognition, memory, neurotransmission, intellectual disability and behavioral change and associated disorders. The combination of epigenomic and clinical predictors were highly accurate for the detection of concusion using AI techniques. Using DL/AI, a combination of epigenomic and clinical markers had sensitivity and specificity ≧95% for prediction of mTBI. In this novel study, we identified significant methylation changes in multiple genes in response to mTBI. Gene pathways that were epigenetically dysregulated included several known to be involved in neurological function, thus giving biological plausibility to our findings.
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Liu C, Chen Y, Zhao D, Zhang J, Zhang Y. Association Between Funisitis and Childhood Intellectual Development: A Prospective Cohort Study. Front Neurol 2019; 10:612. [PMID: 31263446 PMCID: PMC6584799 DOI: 10.3389/fneur.2019.00612] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 05/24/2019] [Indexed: 01/13/2023] Open
Abstract
Background: Previous studies have suggested that prenatal inflammation could damage the immature brain of preterm infants. In this study, we aimed to investigate whether funisitis could affect childhood neurodevelopment. We hypothesized that childhood neurodevelopment would vary across groups with or without funisitis. Material sand Methods: Using data from the U.S. Collaborative Perinatal Project (1959–1976), 29,725 subjects with available intelligence quotient (IQ) were studied. Detailed placental examinations were conducted according to a standard protocol with quality control procedures. Multivariate logistic regression models were applied to evaluate the relationship between funisitis and IQ at age 4 or 7 years after adjusting for confounders. Results: Early preterm birth children with funisitis had a 3.0-fold (95% confidence interval 1.2, 7.3) risk of low full-scale IQ (<70) at age 4 years, which disappeared until age 7 years. Term birth children with funisitis had 1.9-fold (95% confidence interval 1.2, 3.0) risk of low performance IQ at age 7 years, but they did not have increased risk of low full-scale IQ. No difference in IQ score was found in late preterm birth children. Conclusion: Funisitis may injure the developmental brain of infants, leading to the relative low IQ in childhood at age 4, but the negative effect is only existed in performance IQ at age of 7.
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Affiliation(s)
- Chengbo Liu
- Department of Neonatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yan Chen
- Department of Neonatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Dongying Zhao
- Department of Neonatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jun Zhang
- Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yongjun Zhang
- Department of Neonatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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Inflammation-related epigenetic risk and child and adolescent mental health: A prospective study from pregnancy to middle adolescence. Dev Psychopathol 2018; 30:1145-1156. [PMID: 30068408 DOI: 10.1017/s0954579418000330] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In 785 mother-child (50% male) pairs from a longitudinal epidemiological birth cohort, we investigated associations between inflammation-related epigenetic polygenic risk scores (i-ePGS), environmental exposures, cognitive function, and child and adolescent internalizing and externalizing problems. We examined prenatal and postnatal effects. For externalizing problems, one prenatal effect was found: i-ePGS at birth associated with higher externalizing problems (ages 7-15) indirectly through lower cognitive function (age 7). For internalizing problems, we identified two effects. For a prenatal effect, i-ePGS at birth associated with higher internalizing symptoms via continuity in i-ePGS at age 7. For a postnatal effect, higher postnatal adversity exposure (birth through age 7) associated with higher internalizing problems (ages 7-15) via higher i-ePGS (age 7). Hence, externalizing problems were related mainly to prenatal effects involving lower cognitive function, whereas internalizing problems appeared related to both prenatal and postnatal effects. The present study supports a link between i-ePGS and child and adolescent mental health.
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Bennet L, Dhillon S, Lear CA, van den Heuij L, King V, Dean JM, Wassink G, Davidson JO, Gunn AJ. Chronic inflammation and impaired development of the preterm brain. J Reprod Immunol 2018; 125:45-55. [DOI: 10.1016/j.jri.2017.11.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 11/13/2017] [Accepted: 11/24/2017] [Indexed: 12/17/2022]
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Inflammatory molecules and neurotrophic factors as biomarkers of neuropsychomotor development in preterm neonates: A Systematic Review. Int J Dev Neurosci 2017; 65:29-37. [PMID: 29051031 DOI: 10.1016/j.ijdevneu.2017.10.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/13/2017] [Accepted: 10/15/2017] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVE To provide a systematic review investigating the role of inflammatory molecules and neurotrophic factors as biomarkers of neuropsychomotor development in preterm neonates. DATA SOURCE Databases including PubMed, BIREME, and Scopus were systematically searched. Observational studies, as well as transversal, and cohort studies using human subjects published from 1990 to September 2017 were eligible for inclusion. Two authors independently identified eligible studies and analyzed their characteristics, quality, and accuracy in depth. DATA SYNTHESIS 11 eligible studies clearly investigated the association between peripheral inflammation and motor and/or cognitive development in preterm infants. However, the selected populations differed in relation to the events associated with prematurity and the risk factors to abnormal motor and/or cognitive development. These studies measured circulating levels of cytokines, chemokines, adhesion molecules, acute phase proteins, and growth factors. The most commonly analyzed proteins were IL-1β, IL-6, TNF, CCL5/RANTES, CXCL8/IL-8, IGFBP-1, and VEGF. In seven of the eligible studies, plasma levels of IL-6 correlated with development delay. Two studies reported correlation between CXCL8/IL-8 plasma levels with cognitive and motor delay. In one study, higher levels of MCP-1/CCL2 were associated with better cognitive and motor outcome. CONCLUSION There is preliminary evidence indicating that circulating inflammatory molecules are associated with motor and cognitive development in preterm neonates, even considering different populations.
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