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Choudhary P, Monasso GS, Karhunen V, Ronkainen J, Mancano G, Howe CG, Niu Z, Zeng X, Guan W, Dou J, Feinberg JI, Mordaunt C, Pesce G, Baïz N, Alfano R, Martens DS, Wang C, Isaevska E, Keikkala E, Mustaniemi S, Thio CHL, Fraszczyk E, Tobi EW, Starling AP, Cosin-Tomas M, Urquiza J, Röder S, Hoang TT, Page C, Jima DD, House JS, Maguire RL, Ott R, Pawlow X, Sirignano L, Zillich L, Malmberg A, Rauschert S, Melton P, Gong T, Karlsson R, Fore R, Perng W, Laubach ZM, Czamara D, Sharp G, Breton CV, Schisterman E, Yeung E, Mumford SL, Fallin MD, LaSalle JM, Schmidt RJ, Bakulski KM, Annesi-Maesano I, Heude B, Nawrot TS, Plusquin M, Ghantous A, Herceg Z, Nisticò L, Vafeiadi M, Kogevinas M, Vääräsmäki M, Kajantie E, Snieder H, Corpeleijn E, Steegers-Theunissen RPM, Yang IV, Dabelea D, Fossati S, Zenclussen AC, Herberth G, Magnus M, Håberg SE, London SJ, Munthe-Kaas MC, Murphy SK, Hoyo C, Ziegler AG, Hummel S, Witt SH, Streit F, Frank J, Räikkönen K, Lahti J, Huang RC, Almqvist C, Hivert MF, Jaddoe VWV, Järvelin MR, Kantomaa M, Felix JF, Sebert S. Maternal educational attainment in pregnancy and epigenome-wide DNA methylation changes in the offspring from birth until adolescence. Mol Psychiatry 2023:10.1038/s41380-023-02331-5. [PMID: 38052982 DOI: 10.1038/s41380-023-02331-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 11/07/2023] [Accepted: 11/15/2023] [Indexed: 12/07/2023]
Abstract
Maternal educational attainment (MEA) shapes offspring health through multiple potential pathways. Differential DNA methylation may provide a mechanistic understanding of these long-term associations. We aimed to quantify the associations of MEA with offspring DNA methylation levels at birth, in childhood and in adolescence. Using 37 studies from high-income countries, we performed meta-analysis of epigenome-wide association studies (EWAS) to quantify the associations of completed years of MEA at the time of pregnancy with offspring DNA methylation levels at birth (n = 9 881), in childhood (n = 2 017), and adolescence (n = 2 740), adjusting for relevant covariates. MEA was found to be associated with DNA methylation at 473 cytosine-phosphate-guanine sites at birth, one in childhood, and four in adolescence. We observed enrichment for findings from previous EWAS on maternal folate, vitamin-B12 concentrations, maternal smoking, and pre-pregnancy BMI. The associations were directionally consistent with MEA being inversely associated with behaviours including smoking and BMI. Our findings form a bridge between socio-economic factors and biology and highlight potential pathways underlying effects of maternal education. The results broaden our understanding of bio-social associations linked to differential DNA methylation in multiple early stages of life. The data generated also offers an important resource to help a more precise understanding of the social determinants of health.
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Affiliation(s)
- Priyanka Choudhary
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, 90014, Oulu, Finland.
| | - Giulietta S Monasso
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Ville Karhunen
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, 90014, Oulu, Finland
- Research Unit of Mathematical Sciences, Faculty of Science, University of Oulu, Oulu, Finland
| | - Justiina Ronkainen
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, 90014, Oulu, Finland
| | - Giulia Mancano
- Medical Research Council Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
- Bristol Medical School Population Health Sciences, University of Bristol, Bristol, UK
| | - Caitlin G Howe
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Zhongzheng Niu
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, 55455, USA
| | - John Dou
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jason I Feinberg
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MA, USA
| | - Charles Mordaunt
- Department of Medical Micriobiology and Immunology, University of California Davis, Davis, CA, USA
| | - Giancarlo Pesce
- Epidemiology of Allergic and Respiratory Diseases (EPAR) team, Faculté de Médecine Saint-Antoine, Institute Pierre Louis d'Epidemiologie et Sante Publique (IPLESP), Sorbonne Université and INSERM, Paris, France
- Paris-Saclay University, Paris-South University, UVSQ, Center for Research in Epidemiology and Population Health (CESP), INSERM, Villejuif, France
| | - Nour Baïz
- Institute Desbrest of Epidemiology and Public Health, University of Montpellier and INSERM, Montpellier, France
| | - Rossella Alfano
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Dries S Martens
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Congrong Wang
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Elena Isaevska
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin and CPO-Piemonte, Torino, Italy
| | - Elina Keikkala
- Department of Obstetrics and Gynaecology, Research Unit of Clinical Medicine, Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
- Finnish Institute for Health and Welfare, Population Health Unit, Public Health and Welfare, Helsinki and Oulu, Finland
| | - Sanna Mustaniemi
- Department of Obstetrics and Gynaecology, Research Unit of Clinical Medicine, Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
- Finnish Institute for Health and Welfare, Population Health Unit, Public Health and Welfare, Helsinki and Oulu, Finland
| | - Chris H L Thio
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Eliza Fraszczyk
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Elmar W Tobi
- Department of Obstetrics and Gynaecology, Division of Obstetrics and Prenatal Medicine, Erasmus MC, University Medical Center, 3000 CA, Rotterdam, the Netherlands
| | - Anne P Starling
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Marta Cosin-Tomas
- ISGlobal (Barcelona Institute for Global Health), Barcelona Biomedical Research Park (PRBB), Doctor Aiguader, 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Jose Urquiza
- ISGlobal (Barcelona Institute for Global Health), Barcelona Biomedical Research Park (PRBB), Doctor Aiguader, 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Stefan Röder
- Department for Environmental Immunology, Helmholtz Centre for Environmental Research, UFZ, Leipzig, Germany
| | - Thanh T Hoang
- Epidemiology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Christian Page
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Oslo Centre for Biostatistics and Epidemiology, Section for Research Support, Oslo University Hospital, Oslo, Norway
| | - Dereje D Jima
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27606, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27606, USA
| | - John S House
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27606, USA
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, Durham, NC, 27709, USA
| | - Rachel L Maguire
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, 27701, USA
| | - Raffael Ott
- Institute of Diabetes Research, Helmholtz Munich, German Research Center for Environmental Health, Munich, Germany
- Forschergruppe Diabetes eV, Neuherberg, Germany
| | - Xenia Pawlow
- Institute of Diabetes Research, Helmholtz Munich, German Research Center for Environmental Health, Munich, Germany
- Forschergruppe Diabetes eV, Neuherberg, Germany
| | - Lea Sirignano
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Lea Zillich
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Anni Malmberg
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | - Phillip Melton
- Menzies Institute of Medical Research, University of Tasmania, Hobart, TAS, Australia
- University of Western Australia, School of Population and Global Health, Perth, WA, Australia
| | - Tong Gong
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ruby Fore
- Division of Chronic Disease Research Across the Lifecourse (CoRAL), Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Wei Perng
- Department of Epidemiology and the Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Zachary M Laubach
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Darina Czamara
- Department Genes and Environment, Max Planck Institute for Psychiatry, Kraepelinstrasse 2+10, 80804, Munich, Germany
| | - Gemma Sharp
- Medical Research Council Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
- Bristol Medical School Population Health Sciences, University of Bristol, Bristol, UK
- School of Psychology, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Carrie V Breton
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Enrique Schisterman
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Edwina Yeung
- Epidemiology Branch, Division of Population Health Research, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20817, USA
| | - Sunni L Mumford
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Epidemiology Branch, Division of Population Health Research, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20817, USA
| | - M Daniele Fallin
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MA, USA
| | - Janine M LaSalle
- Department of Medical Micriobiology and Immunology, University of California Davis, Davis, CA, USA
| | - Rebecca J Schmidt
- Department of Public Health Sciences, School of Medicine, University of California Davis (UC Davis), Davis, CA, USA
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Isabella Annesi-Maesano
- Institute Desbrest of Epidemiology and Public Health, University of Montpellier and INSERM, Montpellier, France
| | - Barbara Heude
- Université de Paris Cité, Inserm, INRAE, Centre of Research in Epidemiology and StatisticS (CRESS), F-75004, Paris, France
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Michelle Plusquin
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Akram Ghantous
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France
| | - Zdenko Herceg
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France
| | - Lorenza Nisticò
- Centre for Behavioural Sciences and Mental Health, Istituto Superiore di Sanità, Viale Regina Elena, Rome, Italy
| | - Marina Vafeiadi
- Department of Social Medicine, School of Medicine, University of Crete, Heraklion, Crete, Greece
| | - Manolis Kogevinas
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Centro de Investigación Biomédicaen Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Marja Vääräsmäki
- Department of Obstetrics and Gynaecology, Research Unit of Clinical Medicine, Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
- Finnish Institute for Health and Welfare, Population Health Unit, Public Health and Welfare, Helsinki and Oulu, Finland
| | - Eero Kajantie
- Finnish Institute for Health and Welfare, Population Health Unit, Public Health and Welfare, Helsinki and Oulu, Finland
- Clinical Medicine Research Unit, Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Harold Snieder
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Eva Corpeleijn
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Regine P M Steegers-Theunissen
- Department of Obstetrics and Gynaecology, Division of Obstetrics and Prenatal Medicine, Erasmus MC, University Medical Center, 3000 CA, Rotterdam, the Netherlands
| | - Ivana V Yang
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Dana Dabelea
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Pediatrics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Serena Fossati
- ISGlobal (Barcelona Institute for Global Health), Barcelona Biomedical Research Park (PRBB), Doctor Aiguader, 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Ana C Zenclussen
- Department for Environmental Immunology, Helmholtz Centre for Environmental Research, UFZ, Leipzig, Germany
| | - Gunda Herberth
- Department for Environmental Immunology, Helmholtz Centre for Environmental Research, UFZ, Leipzig, Germany
| | - Maria Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Siri E Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Stephanie J London
- Epidemiology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Monica Cheng Munthe-Kaas
- Department of Pediatrics, Oncology and Hematology, Oslo University Hospital, Oslo, Norway
- Norwegian Institute of Public Health, Oslo, Norway
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, 27701, USA
| | - Cathrine Hoyo
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27606, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Anette-G Ziegler
- Institute of Diabetes Research, Helmholtz Munich, German Research Center for Environmental Health, Munich, Germany
- Forschergruppe Diabetes eV, Neuherberg, Germany
- Technical University Munich, School of Medicine, Forschergruppe Diabetes at Klinikum rechts der Isar, Munich, Germany
| | - Sandra Hummel
- Institute of Diabetes Research, Helmholtz Munich, German Research Center for Environmental Health, Munich, Germany
- Forschergruppe Diabetes eV, Neuherberg, Germany
- Technical University Munich, School of Medicine, Forschergruppe Diabetes at Klinikum rechts der Isar, Munich, Germany
| | - Stephanie H Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Center for Innovative Psychiatric and Psychotherapeutic Research, Biobank, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Fabian Streit
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Josef Frank
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Katri Räikkönen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jari Lahti
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Rae-Chi Huang
- Telethon Kids Institute, Perth, WA, Australia
- Edith Cowan University, School of Medicine and Health Sciences, Joondalup, WA, Australia
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Pediatric Allergy and Pulmonology Unit at Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Marie-France Hivert
- Division of Chronic Disease Research Across the Lifecourse (CoRAL), Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Marjo-Riitta Järvelin
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, 90014, Oulu, Finland
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, UK
| | - Marko Kantomaa
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, 90014, Oulu, Finland
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Sylvain Sebert
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, 90014, Oulu, Finland
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Mouat JS, Li S, Myint SS, Laufer BI, Lupo PJ, Schraw JM, Woodhouse JP, de Smith AJ, LaSalle JM. Epigenomic signature of major congenital heart defects in newborns with Down syndrome. Hum Genomics 2023; 17:92. [PMID: 37803336 PMCID: PMC10559462 DOI: 10.1186/s40246-023-00540-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 10/02/2023] [Indexed: 10/08/2023] Open
Abstract
BACKGROUND Congenital heart defects (CHDs) affect approximately half of individuals with Down syndrome (DS), but the molecular reasons for incomplete penetrance are unknown. Previous studies have largely focused on identifying genetic risk factors associated with CHDs in individuals with DS, but comprehensive studies of the contribution of epigenetic marks are lacking. We aimed to identify and characterize DNA methylation differences from newborn dried blood spots (NDBS) of DS individuals with major CHDs compared to DS individuals without CHDs. METHODS We used the Illumina EPIC array and whole-genome bisulfite sequencing (WGBS) to quantitate DNA methylation for 86 NDBS samples from the California Biobank Program: (1) 45 DS-CHD (27 female, 18 male) and (2) 41 DS non-CHD (27 female, 14 male). We analyzed global CpG methylation and identified differentially methylated regions (DMRs) in DS-CHD versus DS non-CHD comparisons (both sex-combined and sex-stratified) corrected for sex, age of blood collection, and cell-type proportions. CHD DMRs were analyzed for enrichment in CpG and genic contexts, chromatin states, and histone modifications by genomic coordinates and for gene ontology enrichment by gene mapping. DMRs were also tested in a replication dataset and compared to methylation levels in DS versus typical development (TD) WGBS NDBS samples. RESULTS We found global CpG hypomethylation in DS-CHD males compared to DS non-CHD males, which was attributable to elevated levels of nucleated red blood cells and not seen in females. At a regional level, we identified 58, 341, and 3938 CHD-associated DMRs in the Sex Combined, Females Only, and Males Only groups, respectively, and used machine learning algorithms to select 19 Males Only loci that could distinguish CHD from non-CHD. DMRs in all comparisons were enriched for gene exons, CpG islands, and bivalent chromatin and mapped to genes enriched for terms related to cardiac and immune functions. Lastly, a greater percentage of CHD-associated DMRs than background regions were differentially methylated in DS versus TD samples. CONCLUSIONS A sex-specific signature of DNA methylation was detected in NDBS of DS-CHD compared to DS non-CHD individuals. This supports the hypothesis that epigenetics can reflect the variability of phenotypes in DS, particularly CHDs.
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Affiliation(s)
- Julia S Mouat
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, University of California, Davis, CA, USA
| | - Shaobo Li
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Swe Swe Myint
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Benjamin I Laufer
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, University of California, Davis, CA, USA
| | - Philip J Lupo
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Jeremy M Schraw
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - John P Woodhouse
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Adam J de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, USA.
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA.
- Genome Center, University of California, Davis, CA, USA.
- MIND Institute, University of California, Davis, CA, USA.
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Sarode GV, Mazi TA, Neier K, Shibata NM, Jospin G, Harder NH, Caceres A, Heffern MC, Sharma AK, More SK, Dave M, Schroeder SM, Wang L, LaSalle JM, Lutsenko S, Medici V. The role of intestine in metabolic dysregulation in murine Wilson disease. Hepatol Commun 2023; 7:e0247. [PMID: 37695076 PMCID: PMC10497250 DOI: 10.1097/hc9.0000000000000247] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 06/24/2023] [Indexed: 09/12/2023] Open
Abstract
BACKGROUND The clinical manifestations of Wilson disease (WD) are related to copper accumulation in the liver and the brain, but little is known about other tissue involvement regarding metabolic changes in WD. In vitro studies suggested that the loss of intestinal ATP7B affects metabolic dysregulation in WD. We tested this hypothesis by evaluating the gut microbiota and lipidome in 2 mouse models of WD and by characterizing a new mouse model with a targeted deletion of Atp7b in the intestine. METHODS Cecal content 16S sequencing and untargeted hepatic and plasma lipidome analyses in the Jackson Laboratory toxic-milk and the Atp7b null global knockout mouse models of WD were profiled and integrated. Intestine-specific Atp7b knockout mice (Atp7bΔIEC) were generated and characterized using targeted lipidome analysis following a high-fat diet challenge. RESULTS Gut microbiota diversity was reduced in animal models of WD. Comparative prediction analysis revealed amino acid, carbohydrate, and lipid metabolism functions to be dysregulated in the WD gut microbial metagenome. Liver and plasma lipidomic profiles showed dysregulated triglyceride and diglyceride, phospholipid, and sphingolipid metabolism in WD models. However, Atp7bΔIEC mice did not show gut microbiome differences compared to wild type. When challenged with a high-fat diet, Atp7bΔIEC mice exhibited profound alterations to fatty acid desaturation and sphingolipid metabolism pathways as well as altered APOB48 distribution in intestinal epithelial cells. CONCLUSIONS Gut microbiome and lipidome underlie systemic metabolic manifestations in murine WD. Intestine-specific ATP7B deficiency affected both intestinal and systemic response to a high-fat challenge but not the microbiome profile, at least at early stages. WD is a systemic disease in which intestinal-specific ATP7B loss and diet influence the phenotype and the lipidome profile.
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Affiliation(s)
- Gaurav V. Sarode
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, UC Davis, Sacramento, California, USA
| | - Tagreed A. Mazi
- Department of Community Health Sciences - Clinical Nutrition, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Kari Neier
- Department of Medical Microbiology and Immunology, UC Davis School of Medicine, Genome Center, MIND Institute, Davis, California, USA
| | - Noreene M. Shibata
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, UC Davis, Sacramento, California, USA
| | | | - Nathaniel H.O. Harder
- Department of Chemistry, University of California Davis Genome Center, Davis, California, USA
| | - Amanda Caceres
- Department of Chemistry, University of California Davis Genome Center, Davis, California, USA
| | - Marie C. Heffern
- Department of Chemistry, University of California Davis Genome Center, Davis, California, USA
| | - Ashok K. Sharma
- Department of Gastroenterology, Inflammatory Bowel & Immunology Research Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Shyam K. More
- Cedars Sinai Medical Center, F. Widjaja Foundation Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Maneesh Dave
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, UC Davis, Sacramento, California, USA
| | - Shannon M. Schroeder
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, UC Davis, Sacramento, California, USA
| | - Li Wang
- Department of Physiology, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - Janine M. LaSalle
- Department of Medical Microbiology and Immunology, UC Davis School of Medicine, Genome Center, MIND Institute, Davis, California, USA
| | - Svetlana Lutsenko
- Department of Physiology, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - Valentina Medici
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, UC Davis, Sacramento, California, USA
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4
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Mouat JS, Li S, Myint SS, Laufer BI, Lupo PJ, Schraw JM, Woodhouse JP, de Smith AJ, LaSalle JM. Epigenomic signature of major congenital heart defects in newborns with Down syndrome. medRxiv 2023:2023.05.02.23289417. [PMID: 37205408 PMCID: PMC10187438 DOI: 10.1101/2023.05.02.23289417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Background Congenital heart defects (CHDs) affect approximately half of individuals with Down syndrome (DS) but the molecular reasons for incomplete penetrance are unknown. Previous studies have largely focused on identifying genetic risk factors associated with CHDs in individuals with DS, but comprehensive studies of the contribution of epigenetic marks are lacking. We aimed to identify and characterize DNA methylation differences from newborn dried blood spots (NDBS) of DS individuals with major CHDs compared to DS individuals without CHDs. Methods We used the Illumina EPIC array and whole-genome bisulfite sequencing (WGBS) to quantitate DNA methylation for 86 NDBS samples from the California Biobank Program: 1) 45 DS-CHD (27 female, 18 male) and 2) 41 DS non-CHD (27 female, 14 male). We analyzed global CpG methylation and identified differentially methylated regions (DMRs) in DS-CHD vs DS non-CHD comparisons (both sex-combined and sex-stratified) corrected for sex, age of blood collection, and cell type proportions. CHD DMRs were analyzed for enrichment in CpG and genic contexts, chromatin states, and histone modifications by genomic coordinates and for gene ontology enrichment by gene mapping. DMRs were also tested in a replication dataset and compared to methylation levels in DS vs typical development (TD) WGBS NDBS samples. Results We found global CpG hypomethylation in DS-CHD males compared to DS non-CHD males, which was attributable to elevated levels of nucleated red blood cells and not seen in females. At a regional level, we identified 58, 341, and 3,938 CHD-associated DMRs in the Sex Combined, Females Only, and Males Only groups, respectively, and used machine learning algorithms to select 19 Males Only loci that could distinguish CHD from non-CHD. DMRs in all comparisons were enriched for gene exons, CpG islands, and bivalent chromatin and mapped to genes enriched for terms related to cardiac and immune functions. Lastly, a greater percentage of CHD-associated DMRs than background regions were differentially methylated in DS vs TD samples. Conclusions A sex-specific signature of DNA methylation was detected in NDBS of DS-CHD compared to DS non-CHD individuals. This supports the hypothesis that epigenetics can reflect the variability of phenotypes in DS, particularly CHDs.
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Affiliation(s)
- Julia S Mouat
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA USA
- Genome Center, University of California, Davis, CA USA
- MIND Institute, University of California, Davis, CA USA
| | - Shaobo Li
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, CA USA
| | - Swe Swe Myint
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, CA USA
| | - Benjamin I Laufer
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA USA
- Genome Center, University of California, Davis, CA USA
- MIND Institute, University of California, Davis, CA USA
| | - Philip J Lupo
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - Jeremy M Schraw
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - John P Woodhouse
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - Adam J de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, CA USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA USA
- Genome Center, University of California, Davis, CA USA
- MIND Institute, University of California, Davis, CA USA
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5
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LaSalle JM. Epigenomic signatures reveal mechanistic clues and predictive markers for autism spectrum disorder. Mol Psychiatry 2023; 28:1890-1901. [PMID: 36650278 PMCID: PMC10560404 DOI: 10.1038/s41380-022-01917-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 01/18/2023]
Abstract
Autism spectrum disorder (ASD) comprises a heterogeneous group of neurodevelopmental outcomes in children with a commonality in deficits in social communication and language combined with repetitive behaviors and interests. The etiology of ASD is heterogeneous, as several hundred genes have been implicated as well as multiple in utero environmental exposures. Over the past two decades, epigenetic investigations, including DNA methylation, have emerged as a novel way to capture the complex interface of multivariate ASD etiologies. More recently, epigenome-wide association studies using human brain and surrogate accessible tissues have revealed some convergent genes that are epigenetically altered in ASD, many of which overlap with known genetic risk factors. Unlike transcriptomes, epigenomic signatures defined by DNA methylation from surrogate tissues such as placenta and cord blood can reflect past differences in fetal brain gene transcription, transcription factor binding, and chromatin. For example, the discovery of NHIP (neuronal hypoxia inducible, placenta associated) through an epigenome-wide association in placenta, identified a common genetic risk for ASD that was modified by prenatal vitamin use. While epigenomic signatures are distinct between different genetic syndromic causes of ASD, bivalent chromatin and some convergent gene pathways are consistently epigenetically altered in both syndromic and idiopathic ASD, as well as some environmental exposures. Together, these epigenomic signatures hold promising clues towards improved early prediction and prevention of ASD as well genes and gene pathways to target for pharmacological interventions. Future advancements in single cell and multi-omic technologies, machine learning, as well as non-invasive screening of epigenomic signatures during pregnancy or newborn periods are expected to continue to impact the translatability of the recent discoveries in epigenomics to precision public health.
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Affiliation(s)
- Janine M LaSalle
- Department of Medical Microbiology and Immunology, Perinatal Origins of Disparities Center, MIND Institute, Genome Center, Environmental Health Sciences Center, University of California Davis, Davis, CA, USA.
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6
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Phipps JE, Whipps MDM, D'Souza I, LaSalle JM, Simmons LA. Pregnant in a Pandemic: Mental Wellbeing and Associated Healthy Behaviors Among Pregnant People in California During COVID-19. Matern Child Health J 2023:10.1007/s10995-023-03657-w. [PMID: 37029891 PMCID: PMC10083068 DOI: 10.1007/s10995-023-03657-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2023] [Indexed: 04/09/2023]
Abstract
INTRODUCTION Pregnancy is a time of increased vulnerability to mental health disorders. Additionally, the COVID-19 pandemic has increased the incidence of depression and anxiety. Thus, we aimed to assess mental health and associated healthy behaviors of pregnant people in California during the pandemic in order to contextualize prenatal well-being during the first pandemic of the twenty-first century. METHODS We conducted an online cross-sectional study of 433 pregnant people from June 6 through July 29, 2020. We explored 3 hypotheses: (1) mental health would be worse during the pandemic than in general pregnant samples to date; (2) first-time pregnant people would have worse mental health; and (3) healthy behaviors would be positively related to mental health. RESULTS Many of our participants (22%) reported clinically significant depressive symptoms and 31% reported clinically significant anxiety symptoms. Multiparous pregnant people were more likely to express worries about their own health and wellbeing and the process of childbirth than were primiparous pregnant people. Additionally, as pregnancy advanced, sleep and nutrition worsened, while physical activity increased. Lastly, anxious-depressive symptomology was significantly predictive of participant sleep behaviors, nutrition, and physical activity during the past week. DISCUSSION Pregnant people had worse mental health during the pandemic, and this was associated with worse health-promoting behaviors. Given that the COVID-19 pandemic and associated risks are likely to persist due to low vaccination rates and the emergence of variants with high infection rates, care that promotes mental and physical well-being for the pregnant population should be a public health priority.
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Affiliation(s)
- Jennifer E Phipps
- Department of Human Ecology, Perinatal Origins of Disparities Center, University of California, Davis, 1 Shields Ave, Davis, CA, 95616, USA.
| | - Mackenzie D M Whipps
- Department of Human Ecology, Perinatal Origins of Disparities Center, University of California, Davis, 1 Shields Ave, Davis, CA, 95616, USA
| | - Indira D'Souza
- Department of Human Ecology, Perinatal Origins of Disparities Center, University of California, Davis, 1 Shields Ave, Davis, CA, 95616, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, Perinatal Origins of Disparities Center, University of California, Davis, 1 Shields Ave, Davis, CA, 95616, USA
| | - Leigh Ann Simmons
- Department of Human Ecology, Perinatal Origins of Disparities Center, University of California, Davis, 1 Shields Ave, Davis, CA, 95616, USA
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7
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Mouat JS, Li X, Neier K, Zhu Y, Mordaunt CE, La Merrill MA, Lehmler HJ, Jones MP, Lein PJ, Schmidt RJ, LaSalle JM. Networks of placental DNA methylation correlate with maternal serum PCB concentrations and child neurodevelopment. Environ Res 2023; 220:115227. [PMID: 36608759 PMCID: PMC10518186 DOI: 10.1016/j.envres.2023.115227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/21/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Gestational exposure to polychlorinated biphenyls (PCBs) has been associated with elevated risk for neurodevelopmental disorders. Placental epigenetics may serve as a potential mechanism of risk or marker of altered placental function. Prior studies have associated differential placental DNA methylation with maternal PCB exposure or with increased risk of autism spectrum disorder (ASD). However, sequencing-based placental methylomes have not previously been tested for simultaneous associations with maternal PCB levels and child neurodevelopmental outcomes. OBJECTIVES We aimed to identify placental DNA methylation patterns associated with maternal PCB levels and child neurodevelopmental outcomes in the high-risk ASD MARBLES cohort. METHODS We measured 209 PCB congeners in 104 maternal serum samples collected at delivery. We identified networks of DNA methylation from 147 placenta samples using the Comethyl R package, which performs weighted gene correlation network analysis for whole genome bisulfite sequencing data. We tested placental DNA methylation modules for association with maternal serum PCB levels, child neurodevelopment, and other participant traits. RESULTS PCBs 153 + 168, 170, 180 + 193, and 187 were detected in over 50% of maternal serum samples and were highly correlated with one another. Consistent with previous findings, maternal age was the strongest predictor of serum PCB levels, alongside year of sample collection, pre-pregnancy BMI, and polyunsaturated fatty acid levels. Twenty seven modules of placental DNA methylation were identified, including five which significantly correlated with one or more PCBs, and four which correlated with child neurodevelopment. Two modules associated with maternal PCB levels as well as child neurodevelopment, and mapped to CSMD1 and AUTS2, genes previously implicated in ASD and identified as differentially methylated regions in mouse brain and placenta following gestational PCB exposure. CONCLUSIONS Placental DNA co-methylation modules were associated with maternal PCBs and child neurodevelopment. Methylation of CSMD1 and AUTS2 could be markers of altered placental function and/or ASD risk following maternal PCB exposure.
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Affiliation(s)
- Julia S Mouat
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, USA; Perinatal Origins of Disparities Center, University of California, Davis, CA, USA; Genome Center, University of California, Davis, CA, USA; MIND Institute, University of California, Davis, CA, USA
| | - Xueshu Li
- Department of Occupational and Environmental Health, College of Public Health, University of Iowa, Iowa City, IA, USA
| | - Kari Neier
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, USA; Perinatal Origins of Disparities Center, University of California, Davis, CA, USA; Genome Center, University of California, Davis, CA, USA; MIND Institute, University of California, Davis, CA, USA
| | - Yihui Zhu
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, USA; Perinatal Origins of Disparities Center, University of California, Davis, CA, USA; Genome Center, University of California, Davis, CA, USA; MIND Institute, University of California, Davis, CA, USA
| | - Charles E Mordaunt
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, USA; Perinatal Origins of Disparities Center, University of California, Davis, CA, USA; Genome Center, University of California, Davis, CA, USA; MIND Institute, University of California, Davis, CA, USA
| | - Michele A La Merrill
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA; Department of Environmental Toxicology, University of California, Davis, CA, USA
| | - Hans-Joachim Lehmler
- Department of Occupational and Environmental Health, College of Public Health, University of Iowa, Iowa City, IA, USA
| | - Michael P Jones
- Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, IA, USA
| | - Pamela J Lein
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA; MIND Institute, University of California, Davis, CA, USA; Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Rebecca J Schmidt
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA; MIND Institute, University of California, Davis, CA, USA; Department of Public Health Sciences, School of Medicine, University of California, Davis, CA, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, USA; Perinatal Origins of Disparities Center, University of California, Davis, CA, USA; Genome Center, University of California, Davis, CA, USA; MIND Institute, University of California, Davis, CA, USA.
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8
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Sarode GV, Mazi TA, Neier K, Shibata NM, Jospin G, Harder NHO, Heffern MC, Sharma AK, More SK, Dave M, Schroeder SM, Wang L, LaSalle JM, Lutsenko S, Medici V. The role of intestine in metabolic dysregulation in murine Wilson disease. bioRxiv 2023:2023.01.13.524009. [PMID: 36711483 PMCID: PMC9882126 DOI: 10.1101/2023.01.13.524009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Background and aims Major clinical manifestations of Wilson disease (WD) are related to copper accumulation in the liver and the brain, and little is known about other tissues involvement in metabolic changes in WD. In vitro studies suggested that the loss of intestinal ATP7B could contribute to metabolic dysregulation in WD. We tested this hypothesis by evaluating gut microbiota and lipidome in two mouse models of WD and by characterizing a new mouse model with a targeted deletion of Atp7b in intestine. Methods Cecal content 16S sequencing and untargeted hepatic and plasma lipidome analyses in the Jackson Laboratory toxic-milk and the Atp7b null global knockout mouse models of WD were profiled and integrated. Intestine-specific Atp7b knockout mice ( Atp7b ΔIEC ) was generated using B6.Cg-Tg(Vil1-cre)997Gum/J mice and Atp7b Lox/Lox mice, and characterized using targeted lipidome analysis following a high-fat diet challenge. Results Gut microbiota diversity was reduced in animal models of WD. Comparative prediction analysis revealed amino acid, carbohydrate, and lipid metabolism functions to be dysregulated in the WD gut microbial metagenome. Liver and plasma lipidomic profiles showed dysregulated tri- and diglyceride, phospholipid, and sphingolipid metabolism in WD models. When challenged with a high-fat diet, Atp7b ΔIEC mice exhibited profound alterations to fatty acid desaturation and sphingolipid metabolism pathways as well as altered APOB48 distribution in intestinal epithelial cells. Conclusion Coordinated changes of gut microbiome and lipidome analyses underlie systemic metabolic manifestations in murine WD. Intestine-specific ATP7B deficiency affected both intestinal and systemic response to a high-fat challenge. WD is a systemic disease in which intestinal-specific ATP7B loss and diet influence phenotypic presentations.
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9
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Fernandez-Jimenez N, Fore R, Cilleros-Portet A, Lepeule J, Perron P, Kvist T, Tian FY, Lesseur C, Binder AM, Lozano M, Martorell-Marugán J, Loke YJ, Bakulski KM, Zhu Y, Forhan A, Sammallahti S, Everson TM, Chen J, Michels KB, Belmonte T, Carmona-Sáez P, Halliday J, Daniele Fallin M, LaSalle JM, Tost J, Czamara D, Fernández MF, Gómez-Martín A, Craig JM, Gonzalez-Alzaga B, Schmidt RJ, Dou JF, Muggli E, Lacasaña M, Vrijheid M, Marsit CJ, Karagas MR, Räikkönen K, Bouchard L, Heude B, Santa-Marina L, Bustamante M, Hivert MF, Bilbao JR. A meta-analysis of pre-pregnancy maternal body mass index and placental DNA methylation identifies 27 CpG sites with implications for mother-child health. Commun Biol 2022; 5:1313. [PMID: 36446949 PMCID: PMC9709064 DOI: 10.1038/s42003-022-04267-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/16/2022] [Indexed: 12/05/2022] Open
Abstract
Higher maternal pre-pregnancy body mass index (ppBMI) is associated with increased neonatal morbidity, as well as with pregnancy complications and metabolic outcomes in offspring later in life. The placenta is a key organ in fetal development and has been proposed to act as a mediator between the mother and different health outcomes in children. The overall aim of the present work is to investigate the association of ppBMI with epigenome-wide placental DNA methylation (DNAm) in 10 studies from the PACE consortium, amounting to 2631 mother-child pairs. We identify 27 CpG sites at which we observe placental DNAm variations of up to 2.0% per 10 ppBMI-unit. The CpGs that are differentially methylated in placenta do not overlap with CpGs identified in previous studies in cord blood DNAm related to ppBMI. Many of the identified CpGs are located in open sea regions, are often close to obesity-related genes such as GPX1 and LGR4 and altogether, are enriched in cancer and oxidative stress pathways. Our findings suggest that placental DNAm could be one of the mechanisms by which maternal obesity is associated with metabolic health outcomes in newborns and children, although further studies will be needed in order to corroborate these findings.
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Affiliation(s)
- Nora Fernandez-Jimenez
- grid.11480.3c0000000121671098Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country Spain
| | - Ruby Fore
- grid.38142.3c000000041936754XDepartment of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA USA
| | - Ariadna Cilleros-Portet
- grid.11480.3c0000000121671098Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country Spain
| | - Johanna Lepeule
- grid.418110.d0000 0004 0642 0153University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology Applied to Reproduction and Respiratory Health, IAB, Grenoble, France
| | - Patrice Perron
- grid.411172.00000 0001 0081 2808Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC Canada
| | - Tuomas Kvist
- grid.7737.40000 0004 0410 2071Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Fu-Ying Tian
- grid.189967.80000 0001 0941 6502Gangarosa Department of Environmental Health, Rollins School of Public Health at Emory University, Atlanta, GA USA
| | - Corina Lesseur
- grid.59734.3c0000 0001 0670 2351Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Alexandra M. Binder
- grid.410445.00000 0001 2188 0957Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI USA ,grid.19006.3e0000 0000 9632 6718Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA USA
| | - Manuel Lozano
- grid.5338.d0000 0001 2173 938XEpidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de València, Valencia, Spain ,grid.5338.d0000 0001 2173 938XPreventive Medicine and Public Health, Food Sciences, Toxicology and Forensic Medicine Department, Universitat de València, Valencia, Spain
| | - Jordi Martorell-Marugán
- grid.4489.10000000121678994Department of Statistics and Operations Research, University of Granada, Granada, Spain ,grid.4489.10000000121678994Bioinformatics Unit. GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Granada, Spain
| | - Yuk J. Loke
- grid.1058.c0000 0000 9442 535XMurdoch Children’s Research Institute, Parkville, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Paediatrics, University of Melbourne, Parkville, VIC Australia
| | - Kelly M. Bakulski
- grid.214458.e0000000086837370Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | - Yihui Zhu
- grid.27860.3b0000 0004 1936 9684Department of Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, CA USA
| | - Anne Forhan
- grid.508487.60000 0004 7885 7602Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, Paris, France
| | - Sara Sammallahti
- grid.5645.2000000040459992XDepartment of Child and Adolescent Psychiatry and Psychology, Erasmus MC Rotterdam, The Netherlands
| | - Todd M. Everson
- grid.189967.80000 0001 0941 6502Gangarosa Department of Environmental Health, Rollins School of Public Health at Emory University, Atlanta, GA USA ,grid.189967.80000 0001 0941 6502Department of Epidemiology, Rollins School of Public health at Emory University, Atlanta, GA USA
| | - Jia Chen
- grid.59734.3c0000 0001 0670 2351Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Karin B. Michels
- grid.19006.3e0000 0000 9632 6718Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA USA ,grid.5963.9Institute for Prevention and Cancer Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Thalia Belmonte
- grid.411342.10000 0004 1771 1175Health Research Institute of Asturias, ISPA and Biomedical Research and Innovation Institute of Cadiz (INiBICA), Research Unit, Puerta del Mar University Hospital, Cadiz, Spain
| | - Pedro Carmona-Sáez
- grid.4489.10000000121678994Department of Statistics and Operations Research, University of Granada, Granada, Spain ,grid.4489.10000000121678994Bioinformatics Unit. GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Granada, Spain
| | - Jane Halliday
- grid.1058.c0000 0000 9442 535XMurdoch Children’s Research Institute, Parkville, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Paediatrics, University of Melbourne, Parkville, VIC Australia
| | - M. Daniele Fallin
- grid.21107.350000 0001 2171 9311Wendy Klag Center for Autism and Developmental Disabilities, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD USA
| | - Janine M. LaSalle
- grid.27860.3b0000 0004 1936 9684Department of Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, CA USA
| | - Jorg Tost
- grid.418135.a0000 0004 0641 3404Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Darina Czamara
- grid.419548.50000 0000 9497 5095Max-Planck-Institute of Psychiatry, Department of Translational Research in Psychiatry, Munich, Germany
| | - Mariana F. Fernández
- grid.4489.10000000121678994University of Granada, Center for Biomedical Research (CIBM), Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain ,grid.466571.70000 0004 1756 6246CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Antonio Gómez-Martín
- grid.507088.2Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain ,grid.413740.50000 0001 2186 2871Andalusian School of Public Health (EASP), Granada, Spain
| | - Jeffrey M. Craig
- grid.1058.c0000 0000 9442 535XMurdoch Children’s Research Institute, Parkville, VIC Australia ,grid.1021.20000 0001 0526 7079Deakin University, IMPACT – the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, Australia
| | - Beatriz Gonzalez-Alzaga
- grid.507088.2Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain ,grid.413740.50000 0001 2186 2871Andalusian School of Public Health (EASP), Granada, Spain
| | - Rebecca J. Schmidt
- grid.27860.3b0000 0004 1936 9684Department of Public Health Sciences and the MIND Institute, University of California Davis School of Medicine, Davis, CA USA
| | - John F. Dou
- grid.214458.e0000000086837370Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | - Evelyne Muggli
- grid.1058.c0000 0000 9442 535XMurdoch Children’s Research Institute, Parkville, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Paediatrics, University of Melbourne, Parkville, VIC Australia
| | - Marina Lacasaña
- grid.507088.2Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain ,grid.466571.70000 0004 1756 6246CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain ,grid.413740.50000 0001 2186 2871Andalusian School of Public Health (EASP), Granada, Spain
| | - Martine Vrijheid
- grid.466571.70000 0004 1756 6246CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain ,grid.434607.20000 0004 1763 3517ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain ,grid.5612.00000 0001 2172 2676Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Carmen J. Marsit
- grid.189967.80000 0001 0941 6502Gangarosa Department of Environmental Health, Rollins School of Public Health at Emory University, Atlanta, GA USA ,grid.189967.80000 0001 0941 6502Department of Epidemiology, Rollins School of Public health at Emory University, Atlanta, GA USA
| | - Margaret R. Karagas
- grid.86715.3d0000 0000 9064 6198Department of Biochemistry and Functional Genomics, Universite de Sherbrooke, Sherbrooke, QC Canada
| | - Katri Räikkönen
- grid.7737.40000 0004 0410 2071Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Luigi Bouchard
- grid.86715.3d0000 0000 9064 6198Department of Biochemistry and Functional Genomics, Universite de Sherbrooke, Sherbrooke, QC Canada ,grid.459278.50000 0004 4910 4652Department of Laboratory Medicine, CIUSSS du Saguenay–Lac-St-Jean – Hôpital Universitaire de Chicoutimi, Chicoutimi, QC Canada
| | - Barbara Heude
- grid.508487.60000 0004 7885 7602Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, Paris, France
| | - Loreto Santa-Marina
- grid.466571.70000 0004 1756 6246CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain ,grid.432380.eBiodonostia, Epidemiology and Public Health Area, Environmental Epidemiology and Child Development Group, 20014 San Sebastian, Basque Country Spain ,Health Department of Basque Government, Sub-directorate of Public Health of Gipuzkoa, San Sebastian, Basque Country Spain
| | - Mariona Bustamante
- grid.466571.70000 0004 1756 6246CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain ,grid.434607.20000 0004 1763 3517ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain ,grid.5612.00000 0001 2172 2676Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marie-France Hivert
- grid.38142.3c000000041936754XDepartment of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA USA ,grid.411172.00000 0001 0081 2808Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC Canada ,grid.32224.350000 0004 0386 9924Diabetes Unit, Massachusetts General Hospital, Boston, MA USA
| | - Jose Ramon Bilbao
- grid.11480.3c0000000121671098Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country Spain ,grid.512890.7CIBER of diabetes and associated metabolic disorders (CIBERDEM), Madrid, Spain
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10
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Laufer BI, Hasegawa Y, Zhang Z, Hogrefe CE, Del Rosso LA, Haapanen L, Hwang H, Bauman MD, Van de Water J, Taha AY, Slupsky CM, Golub MS, Capitanio JP, VandeVoort CA, Walker CK, LaSalle JM. Multi-omic brain and behavioral correlates of cell-free fetal DNA methylation in macaque maternal obesity models. Nat Commun 2022; 13:5538. [PMID: 36130949 PMCID: PMC9492781 DOI: 10.1038/s41467-022-33162-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 09/06/2022] [Indexed: 11/28/2022] Open
Abstract
Maternal obesity during pregnancy is associated with neurodevelopmental disorder (NDD) risk. We utilized integrative multi-omics to examine maternal obesity effects on offspring neurodevelopment in rhesus macaques by comparison to lean controls and two interventions. Differentially methylated regions (DMRs) from longitudinal maternal blood-derived cell-free fetal DNA (cffDNA) significantly overlapped with DMRs from infant brain. The DMRs were enriched for neurodevelopmental functions, methylation-sensitive developmental transcription factor motifs, and human NDD DMRs identified from brain and placenta. Brain and cffDNA methylation levels from a large region overlapping mir-663 correlated with maternal obesity, metabolic and immune markers, and infant behavior. A DUX4 hippocampal co-methylation network correlated with maternal obesity, infant behavior, infant hippocampal lipidomic and metabolomic profiles, and maternal blood measurements of DUX4 cffDNA methylation, cytokines, and metabolites. We conclude that in this model, maternal obesity was associated with changes in the infant brain and behavior, and these differences were detectable in pregnancy through integrative analyses of cffDNA methylation with immune and metabolic factors.
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Affiliation(s)
- Benjamin I Laufer
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, 95616, USA
- UC Davis Genome Center, University of California, Davis, CA, 95616, USA
- MIND Institute, School of Medicine, University of California Davis, Sacramento, CA, 95817, USA
- Department of OMNI Bioinformatics, Genentech, Inc., South San Francisco, CA, 94080, USA
| | - Yu Hasegawa
- Department of Food Science and Technology, University of California Davis, Davis, CA, 95616, USA
| | - Zhichao Zhang
- Department of Food Science and Technology, University of California Davis, Davis, CA, 95616, USA
| | - Casey E Hogrefe
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
| | - Laura A Del Rosso
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
| | - Lori Haapanen
- MIND Institute, School of Medicine, University of California Davis, Sacramento, CA, 95817, USA
| | - Hyeyeon Hwang
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, 95616, USA
- UC Davis Genome Center, University of California, Davis, CA, 95616, USA
- MIND Institute, School of Medicine, University of California Davis, Sacramento, CA, 95817, USA
| | - Melissa D Bauman
- MIND Institute, School of Medicine, University of California Davis, Sacramento, CA, 95817, USA
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
- Department of Psychiatry and Behavioral Sciences, School of Medicine, University of California Davis, Davis, CA, 95616, USA
- Perinatal Origins of Disparities Center, University of California Davis, Davis, CA, 95616, USA
| | - Judy Van de Water
- Perinatal Origins of Disparities Center, University of California Davis, Davis, CA, 95616, USA
- Department of Internal Medicine, University of California Davis, Davis, CA, 95616, USA
| | - Ameer Y Taha
- Department of Food Science and Technology, University of California Davis, Davis, CA, 95616, USA
| | - Carolyn M Slupsky
- Department of Food Science and Technology, University of California Davis, Davis, CA, 95616, USA
- Perinatal Origins of Disparities Center, University of California Davis, Davis, CA, 95616, USA
- Department of Nutrition, University of California Davis, Davis, CA, 95616, USA
| | - Mari S Golub
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
| | - John P Capitanio
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
- Department of Psychology, University of California Davis, Davis, CA, 95616, USA
| | - Catherine A VandeVoort
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
- Department of Obstetrics and Gynecology, School of Medicine, University of California Davis, Davis, CA, 95616, USA
| | - Cheryl K Walker
- MIND Institute, School of Medicine, University of California Davis, Sacramento, CA, 95817, USA
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
- Perinatal Origins of Disparities Center, University of California Davis, Davis, CA, 95616, USA
- Department of Obstetrics and Gynecology, School of Medicine, University of California Davis, Davis, CA, 95616, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, 95616, USA.
- UC Davis Genome Center, University of California, Davis, CA, 95616, USA.
- MIND Institute, School of Medicine, University of California Davis, Sacramento, CA, 95817, USA.
- Perinatal Origins of Disparities Center, University of California Davis, Davis, CA, 95616, USA.
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11
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Maggio AG, Shu HT, Laufer BI, Bi C, Lai Y, LaSalle JM, Hu VW. Elevated exposures to persistent endocrine disrupting compounds impact the sperm methylome in regions associated with autism spectrum disorder. Front Genet 2022; 13:929471. [PMID: 36035158 PMCID: PMC9403863 DOI: 10.3389/fgene.2022.929471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Environmental exposures to endocrine disrupting compounds (EDCs) such as the organochlorines have been linked with various diseases including neurodevelopmental disorders. Autism spectrum disorder (ASD) is a highly complex neurodevelopmental disorder that is considered strongly genetic in origin due to its high heritability. However, the rapidly rising prevalence of ASD suggests that environmental factors may also influence risk for ASD. In the present study, whole genome bisulfite sequencing was used to identify genome-wide differentially methylated regions (DMRs) in a total of 52 sperm samples from a cohort of men from the Faroe Islands (Denmark) who were equally divided into high and low exposure groups based on their serum levels of the long-lived organochlorine 1,1-dichloro-2,2-bis(p-chlorophenyl)ethylene (DDE), a primary breakdown product of the now banned insecticide dichlorodiphenyltrichloroethane (DDT). Aside from being considered a genetic isolate, inhabitants of the Faroe Islands have a native diet that potentially exposes them to a wide range of seafood neurotoxicants in the form of persistent organic pollutants (POPs). The DMRs were mapped to the human genome using Bismark, a 3-letter aligner used for methyl-seq analyses. Gene ontology, functional, and pathway analyses of the DMR-associated genes showed significant enrichment for genes involved in neurological functions and neurodevelopmental processes frequently impacted by ASD. Notably, these genes also significantly overlap with autism risk genes as well as those previously identified in sperm from fathers of children with ASD in comparison to that of fathers of neurotypical children. These results collectively suggest a possible mechanism involving altered methylation of a significant number of neurologically relevant ASD risk genes for introducing epigenetic changes associated with environmental exposures into the sperm methylome. Such changes may provide the potential for transgenerational inheritance of ASD as well as other disorders.
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Affiliation(s)
- Angela G. Maggio
- Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - Henry T. Shu
- Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
- The Johns Hopkins University, School of Medicine, Baltimore, MD, United States
| | - Benjamin I. Laufer
- Genome Center, Perinatal Origins of Disparities Center, Environmental Health Sciences Center, Medical Microbiology and Immunology, MIND Institute, UC Davis School of Medicine, Davis, CA, United States
| | - Chongfeng Bi
- Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - Yinglei Lai
- Department of Statistics, The George Washington University, Washington, DC, United States
| | - Janine M. LaSalle
- Genome Center, Perinatal Origins of Disparities Center, Environmental Health Sciences Center, Medical Microbiology and Immunology, MIND Institute, UC Davis School of Medicine, Davis, CA, United States
| | - Valerie W. Hu
- Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
- *Correspondence: Valerie W. Hu,
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12
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Dou JF, Middleton LYM, Zhu Y, Benke KS, Feinberg JI, Croen LA, Hertz-Picciotto I, Newschaffer CJ, LaSalle JM, Fallin D, Schmidt RJ, Bakulski KM. Prenatal vitamin intake in first month of pregnancy and DNA methylation in cord blood and placenta in two prospective cohorts. Epigenetics Chromatin 2022; 15:28. [PMID: 35918756 PMCID: PMC9344645 DOI: 10.1186/s13072-022-00460-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/21/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Prenatal vitamin use is recommended before and during pregnancies for normal fetal development. Prenatal vitamins do not have a standard formulation, but many contain calcium, folic acid, iodine, iron, omega-3 fatty acids, zinc, and vitamins A, B6, B12, and D, and usually they contain higher concentrations of folic acid and iron than regular multivitamins in the US Nutrient levels can impact epigenetic factors such as DNA methylation, but relationships between maternal prenatal vitamin use and DNA methylation have been relatively understudied. We examined use of prenatal vitamins in the first month of pregnancy in relation to cord blood and placenta DNA methylation in two prospective pregnancy cohorts: the Early Autism Risk Longitudinal Investigation (EARLI) and Markers of Autism Risk Learning Early Signs (MARBLES) studies. RESULTS In placenta, prenatal vitamin intake was marginally associated with -0.52% (95% CI -1.04, 0.01) lower mean array-wide DNA methylation in EARLI, and associated with -0.60% (-1.08, -0.13) lower mean array-wide DNA methylation in MARBLES. There was little consistency in the associations between prenatal vitamin intake and single DNA methylation site effect estimates across cohorts and tissues, with only a few overlapping sites with correlated effect estimates. However, the single DNA methylation sites with p-value < 0.01 (EARLI cord nCpGs = 4068, EARLI placenta nCpGs = 3647, MARBLES cord nCpGs = 4068, MARBLES placenta nCpGs = 9563) were consistently enriched in neuronal developmental pathways. CONCLUSIONS Together, our findings suggest that prenatal vitamin intake in the first month of pregnancy may be related to lower placental global DNA methylation and related to DNA methylation in brain-related pathways in both placenta and cord blood.
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Affiliation(s)
- John F Dou
- Department of Epidemiology, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, USA
| | - Lauren Y M Middleton
- Department of Epidemiology, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, USA
| | - Yihui Zhu
- Department of Public Health Sciences and the M.I.N.D. Institute, School of Medicine, University of California, Davis, CA, USA
| | - Kelly S Benke
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Jason I Feinberg
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Lisa A Croen
- Kaiser Permanente Northern California, Oakland, CA, USA
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences and the M.I.N.D. Institute, School of Medicine, University of California, Davis, CA, USA
| | - Craig J Newschaffer
- College of Health and Human Development, Penn State University, State College, PA, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology and the M.I.N.D. Institute, School of Medicine, University of California, Davis, CA, USA
| | - Daniele Fallin
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Rebecca J Schmidt
- Department of Public Health Sciences and the M.I.N.D. Institute, School of Medicine, University of California, Davis, CA, USA
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, USA.
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13
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Abstract
The etiology of autism spectrum disorders (ASD) is complex, involving different combinations of genetic and environmental factors. My lab's approach has been to investigate DNA methylation as a tractable genome-wide modification at the interface of these complex interactions, reflecting past and future events in the molecular pathogenesis of ASD. Since X-linked genes were enriched in DNA methylation differences discovered from cord blood from newborns later diagnosed with ASD, this has prompted me to review and revisit the recent advancements in the field of X chromosome inactivation (XCI), particularly in humans and other primates. In this Perspective, I compare XCI mechanisms in different mammalian species, including the finding of the noncoding transcript XACT associated with X chromosome erosion in human pluripotent stem cells and recent findings from non-human primate post-implantation embryos. I focus on the experimentally challenging peri- and post-implantation stages of human development when the timing of XCI is prolonged and imprecise in humans. Collectively, this research has raised some important unanswered questions involving biased sex ratios in human births and the male bias in the incidence of ASD.
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Affiliation(s)
- Janine M LaSalle
- Department of Medical Microbiology and Immunology, Perinatal Origins of Disparities Center, MIND Institute, Genome Center, Environmental Health Sciences Center, University of California, Davis, Davis, CA, United States
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14
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Mordaunt CE, Mouat JS, Schmidt RJ, LaSalle JM. Comethyl: a network-based methylome approach to investigate the multivariate nature of health and disease. Brief Bioinform 2022; 23:bbab554. [PMID: 35037016 PMCID: PMC8921619 DOI: 10.1093/bib/bbab554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 11/15/2021] [Accepted: 12/04/2021] [Indexed: 11/14/2022] Open
Abstract
Health outcomes are frequently shaped by difficult to dissect inter-relationships between biological, behavioral, social and environmental factors. DNA methylation patterns reflect such multivariate intersections, providing a rich source of novel biomarkers and insight into disease etiologies. Recent advances in whole-genome bisulfite sequencing enable investigation of DNA methylation over all genomic CpGs, but existing bioinformatic approaches lack accessible system-level tools. Here, we develop the R package Comethyl, for weighted gene correlation network analysis of user-defined genomic regions that generates modules of comethylated regions, which are then tested for correlations with multivariate sample traits. First, regions are defined by CpG genomic location or regulatory annotation and filtered based on CpG count, sequencing depth and variability. Next, correlation networks are used to find modules of interconnected nodes using methylation values within the selected regions. Each module containing multiple comethylated regions is reduced in complexity to a single eigennode value, which is then tested for correlations with experimental metadata. Comethyl has the ability to cover the noncoding regulatory regions of the genome with high relevance to interpretation of genome-wide association studies and integration with other types of epigenomic data. We demonstrate the utility of Comethyl on a dataset of male cord blood samples from newborns later diagnosed with autism spectrum disorder (ASD) versus typical development. Comethyl successfully identified an ASD-associated module containing regions mapped to genes enriched for brain glial functions. Comethyl is expected to be useful in uncovering the multivariate nature of health disparities for a variety of common disorders. Comethyl is available at github.com/cemordaunt/comethyl with complete documentation and example analyses.
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Affiliation(s)
- Charles E Mordaunt
- Department of Medical Microbiology and Immunology, Genome Center, Perinatal Origins of Disparities Center, and MIND Institute, University of California, Davis, CA, USA
| | - Julia S Mouat
- Department of Medical Microbiology and Immunology, Genome Center, Perinatal Origins of Disparities Center, and MIND Institute, University of California, Davis, CA, USA
| | - Rebecca J Schmidt
- Department of Public Health Sciences, Perinatal Origins of Disparities Center, and MIND Institute, University of California, Davis, CA, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, Genome Center, Perinatal Origins of Disparities Center, and MIND Institute, University of California, Davis, CA, USA
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15
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Laufer BI, Neier K, Valenzuela AE, Yasui DH, Schmidt RJ, Lein PJ, LaSalle JM. Placenta and fetal brain share a neurodevelopmental disorder DNA methylation profile in a mouse model of prenatal PCB exposure. Cell Rep 2022; 38:110442. [PMID: 35235788 PMCID: PMC8941983 DOI: 10.1016/j.celrep.2022.110442] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/19/2021] [Accepted: 02/03/2022] [Indexed: 12/27/2022] Open
Abstract
Polychlorinated biphenyls (PCBs) are developmental neurotoxicants implicated as environmental risk factors for neurodevelopmental disorders (NDDs). Here, we report the effects of prenatal exposure to a human-relevant mixture of PCBs on the DNA methylation profiles of mouse placenta and fetal brain. Thousands of differentially methylated regions (DMRs) distinguish placenta and fetal brain from PCB-exposed mice from sex-matched vehicle controls. In both placenta and fetal brain, PCB-associated DMRs are enriched for functions related to neurodevelopment and cellular signaling and enriched within regions of bivalent chromatin. The placenta and brain PCB DMRs overlap significantly and map to a shared subset of genes enriched for Wnt signaling, Slit/Robo signaling, and genes differentially expressed in NDD models. The consensus PCB DMRs also significantly overlap with DMRs from human NDD brain and placenta. These results demonstrate that PCB-exposed placenta contains a subset of DMRs that overlap fetal brain DMRs relevant to an NDD.
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Affiliation(s)
- Benjamin I Laufer
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA; UC Davis Genome Center, University of California, Davis, Davis, CA 95616, USA; MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Kari Neier
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA; UC Davis Genome Center, University of California, Davis, Davis, CA 95616, USA; MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA; Perinatal Origins of Disparities Center, University of California, Davis, Davis, CA 95616, USA
| | - Anthony E Valenzuela
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Dag H Yasui
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA; UC Davis Genome Center, University of California, Davis, Davis, CA 95616, USA; MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Rebecca J Schmidt
- MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA; Perinatal Origins of Disparities Center, University of California, Davis, Davis, CA 95616, USA; Department of Public Health Sciences, School of Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Pamela J Lein
- MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA; Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA; UC Davis Genome Center, University of California, Davis, Davis, CA 95616, USA; MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA; Perinatal Origins of Disparities Center, University of California, Davis, Davis, CA 95616, USA.
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16
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Zhu Y, Gomez JA, Laufer BI, Mordaunt CE, Mouat JS, Soto DC, Dennis MY, Benke KS, Bakulski KM, Dou J, Marathe R, Jianu JM, Williams LA, Gutierrez Fugón OJ, Walker CK, Ozonoff S, Daniels J, Grosvenor LP, Volk HE, Feinberg JI, Fallin MD, Hertz-Picciotto I, Schmidt RJ, Yasui DH, LaSalle JM. Placental methylome reveals a 22q13.33 brain regulatory gene locus associated with autism. Genome Biol 2022; 23:46. [PMID: 35168652 PMCID: PMC8848662 DOI: 10.1186/s13059-022-02613-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 01/16/2022] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) involves complex genetics interacting with the perinatal environment, complicating the discovery of common genetic risk. The epigenetic layer of DNA methylation shows dynamic developmental changes and molecular memory of in utero experiences, particularly in placenta, a fetal tissue discarded at birth. However, current array-based methods to identify novel ASD risk genes lack coverage of the most structurally and epigenetically variable regions of the human genome. RESULTS We use whole genome bisulfite sequencing in placenta samples from prospective ASD studies to discover a previously uncharacterized ASD risk gene, LOC105373085, renamed NHIP. Out of 134 differentially methylated regions associated with ASD in placental samples, a cluster at 22q13.33 corresponds to a 118-kb hypomethylated block that replicates in two additional cohorts. Within this locus, NHIP is functionally characterized as a nuclear peptide-encoding transcript with high expression in brain, and increased expression following neuronal differentiation or hypoxia, but decreased expression in ASD placenta and brain. NHIP overexpression increases cellular proliferation and alters expression of genes regulating synapses and neurogenesis, overlapping significantly with known ASD risk genes and NHIP-associated genes in ASD brain. A common structural variant disrupting the proximity of NHIP to a fetal brain enhancer is associated with NHIP expression and methylation levels and ASD risk, demonstrating a common genetic influence. CONCLUSIONS Together, these results identify and initially characterize a novel environmentally responsive ASD risk gene relevant to brain development in a hitherto under-characterized region of the human genome.
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Affiliation(s)
- Yihui Zhu
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - J Antonio Gomez
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - Benjamin I Laufer
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - Charles E Mordaunt
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - Julia S Mouat
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - Daniela C Soto
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, CA, USA
| | - Megan Y Dennis
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, CA, USA
| | - Kelly S Benke
- Department of Public Health Sciences, University of California, Davis, CA, USA
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - John Dou
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Ria Marathe
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - Julia M Jianu
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - Logan A Williams
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - Orangel J Gutierrez Fugón
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - Cheryl K Walker
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
- Department of Obstetrics and Gynecology, University of California, Davis, CA, USA
| | - Sally Ozonoff
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
- Department of Psychiatry and Behavioral Sciences, Davis, CA, USA
| | - Jason Daniels
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Luke P Grosvenor
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Heather E Volk
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
- Wendy Klag Center for Autism and Developmental Disabilities, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Jason I Feinberg
- Wendy Klag Center for Autism and Developmental Disabilities, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - M Daniele Fallin
- Wendy Klag Center for Autism and Developmental Disabilities, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Irva Hertz-Picciotto
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
- Department of Public Health Sciences, University of California, Davis, CA, USA
| | - Rebecca J Schmidt
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
- Department of Public Health Sciences, University of California, Davis, CA, USA
| | - Dag H Yasui
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA.
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA.
- Genome Center, University of California, Davis, CA, USA.
- MIND Institute, School of Medicine, University of California, Davis, CA, USA.
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17
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Mouat JS, LaSalle JM. The Promise of DNA Methylation in Understanding Multigenerational Factors in Autism Spectrum Disorders. Front Genet 2022; 13:831221. [PMID: 35242170 PMCID: PMC8886225 DOI: 10.3389/fgene.2022.831221] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/28/2022] [Indexed: 12/14/2022] Open
Abstract
Autism spectrum disorder (ASD) is a group of neurodevelopmental disorders characterized by impairments in social reciprocity and communication, restrictive interests, and repetitive behaviors. Most cases of ASD arise from a confluence of genetic susceptibility and environmental risk factors, whose interactions can be studied through epigenetic mechanisms such as DNA methylation. While various parental factors are known to increase risk for ASD, several studies have indicated that grandparental and great-grandparental factors may also contribute. In animal studies, gestational exposure to certain environmental factors, such as insecticides, medications, and social stress, increases risk for altered behavioral phenotypes in multiple subsequent generations. Changes in DNA methylation, gene expression, and chromatin accessibility often accompany these altered behavioral phenotypes, with changes often appearing in genes that are important for neurodevelopment or have been previously implicated in ASD. One hypothesized mechanism for these phenotypic and methylation changes includes the transmission of DNA methylation marks at individual chromosomal loci from parent to offspring and beyond, called multigenerational epigenetic inheritance. Alternatively, intermediate metabolic phenotypes in the parental generation may confer risk from the original grandparental exposure to risk for ASD in grandchildren, mediated by DNA methylation. While hypothesized mechanisms require further research, the potential for multigenerational epigenetics assessments of ASD risk has implications for precision medicine as the field attempts to address the variable etiology and clinical signs of ASD by incorporating genetic, environmental, and lifestyle factors. In this review, we discuss the promise of multigenerational DNA methylation investigations in understanding the complex etiology of ASD.
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Affiliation(s)
- Julia S Mouat
- LaSalle Laboratory, Department of Medical Microbiology and Immunology, University of California, Davis, Davis, CA, United States
- Perinatal Origins of Disparities Center, University of California, Davis, Davis, CA, United States
- MIND Institute, School of Medicine, University of California, Davis, Davis, CA, United States
- Genome Center, University of California, Davis, Davis, CA, United States
| | - Janine M LaSalle
- LaSalle Laboratory, Department of Medical Microbiology and Immunology, University of California, Davis, Davis, CA, United States
- Perinatal Origins of Disparities Center, University of California, Davis, Davis, CA, United States
- MIND Institute, School of Medicine, University of California, Davis, Davis, CA, United States
- Genome Center, University of California, Davis, Davis, CA, United States
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18
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Abstract
Despite decades of investigation into the genetics of autism spectrum disorder (ASD), a current consensus in the field persists that ASD risk is too heterogeneous to be diagnosed by a single set of genetic variants. As such, ASD research has broadened to include assessment of other molecular biomarkers implicated in the condition that may be reflective of environmental exposures or gene by environment interactions. Epigenetic variance, and specifically differential DNA methylation, have emerged as areas of particularly high interest to ASD, as the epigenetic markers from specific chromatin loci collectively can reflect influences of multiple genetic and environmental factors and can also result in differential gene expression patterns. This review examines recent studies of the ASD epigenome, detailing common gene pathways found to be differentially methylated in people with ASD, and considers how these discoveries may inform our understanding of ASD etiology. We also consider future applications of epigenetics in ASD research and clinical practice, focusing on substratification, biomarker development, and experimental preclinical models of ASD that test causality. In combination with other -omics approaches, epigenomics allows an improved conceptualization of the multifactorial nature of ASD, and opens future lines of inquiry for both basic research and clinical practice.
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Affiliation(s)
- Logan A. Williams
- grid.27860.3b0000 0004 1936 9684Department of Medical Microbiology and Immunology, University of California Davis School of Medicine, Davis, CA USA ,grid.27860.3b0000 0004 1936 9684Perinatal Origins of Disparities Center, University of California Davis, Davis, CA USA ,grid.27860.3b0000 0004 1936 9684MIND Institute, University of California Davis, Davis, CA USA ,grid.27860.3b0000 0004 1936 9684Genome Center, University of California Davis, Davis, CA USA
| | - Janine M. LaSalle
- grid.27860.3b0000 0004 1936 9684Department of Medical Microbiology and Immunology, University of California Davis School of Medicine, Davis, CA USA ,grid.27860.3b0000 0004 1936 9684Perinatal Origins of Disparities Center, University of California Davis, Davis, CA USA ,grid.27860.3b0000 0004 1936 9684MIND Institute, University of California Davis, Davis, CA USA ,grid.27860.3b0000 0004 1936 9684Genome Center, University of California Davis, Davis, CA USA
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19
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Brown AP, Cai L, Laufer BI, Miller LA, LaSalle JM, Ji H. Long-term effects of wildfire smoke exposure during early life on the nasal epigenome in rhesus macaques. Environ Int 2022; 158:106993. [PMID: 34991254 PMCID: PMC8852822 DOI: 10.1016/j.envint.2021.106993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 05/17/2023]
Abstract
BACKGROUND Wildfire smoke is responsible for around 20% of all particulate emissions in the U.S. and affects millions of people worldwide. Children are especially vulnerable, as ambient air pollution exposure during early childhood is associated with reduced lung function. Most studies, however, have focused on the short-term impacts of wildfire smoke exposures. We aimed to identify long-term baseline epigenetic changes associated with early-life exposure to wildfire smoke. We collected nasal epithelium samples for whole genome bisulfite sequencing (WGBS) from two groups of adult female rhesus macaques: one group born just before the 2008 California wildfire season and exposed to wildfire smoke during early-life (n = 8), and the other group born in 2009 with no wildfire smoke exposure during early-life (n = 14). RNA-sequencing was also performed on a subset of these samples. RESULTS We identified 3370 differentially methylated regions (DMRs) (difference in methylation ≥ 5%, empirical p < 0.05) and 1 differentially expressed gene (FLOT2) (FDR < 0.05, fold of change ≥ 1.2). The DMRs were annotated to genes significantly enriched for synaptogenesis signaling, protein kinase A signaling, and a variety of immune processes, and some DMRs significantly correlated with gene expression differences. DMRs were also significantly enriched within regions of bivalent chromatin (top odds ratio = 1.46, q-value < 3 × 10-6) that often silence key developmental genes while keeping them poised for activation in pluripotent cells. CONCLUSIONS These data suggest that early-life exposure to wildfire smoke leads to long-term changes in the methylome over genes impacting the nervous and immune systems. Follow-up studies will be required to test whether these changes influence transcription following an immune/respiratory challenge.
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Affiliation(s)
- Anthony P Brown
- California National Primate Research Center, Davis, CA 95616, USA
| | - Lucy Cai
- California National Primate Research Center, Davis, CA 95616, USA
| | - Benjamin I Laufer
- Department of Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, CA 95616, USA
| | - Lisa A Miller
- California National Primate Research Center, Davis, CA 95616, USA; Department of Anatomy, Physiology and Cell biology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, CA 95616, USA
| | - Hong Ji
- California National Primate Research Center, Davis, CA 95616, USA; Department of Anatomy, Physiology and Cell biology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA.
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20
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Neier K, Grant TE, Palmer RL, Chappell D, Hakam SM, Yasui KM, Rolston M, Settles ML, Hunter SS, Madany A, Ashwood P, Durbin-Johnson B, LaSalle JM, Yasui DH. Sex disparate gut microbiome and metabolome perturbations precede disease progression in a mouse model of Rett syndrome. Commun Biol 2021; 4:1408. [PMID: 34916612 PMCID: PMC8677842 DOI: 10.1038/s42003-021-02915-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 11/11/2021] [Indexed: 12/24/2022] Open
Abstract
Rett syndrome (RTT) is a regressive neurodevelopmental disorder in girls, characterized by multisystem complications including gut dysbiosis and altered metabolism. While RTT is known to be caused by mutations in the X-linked gene MECP2, the intermediate molecular pathways of progressive disease phenotypes are unknown. Mecp2 deficient rodents used to model RTT pathophysiology in most prior studies have been male. Thus, we utilized a patient-relevant mouse model of RTT to longitudinally profile the gut microbiome and metabolome across disease progression in both sexes. Fecal metabolites were altered in Mecp2e1 mutant females before onset of neuromotor phenotypes and correlated with lipid deficiencies in brain, results not observed in males. Females also displayed altered gut microbial communities and an inflammatory profile that were more consistent with RTT patients than males. These findings identify new molecular pathways of RTT disease progression and demonstrate the relevance of further study in female Mecp2 animal models.
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Affiliation(s)
- Kari Neier
- UC Davis School of Medicine, Department of Medical Microbiology and Immunology, Genome Center, MIND Institute, Davis, CA, USA
| | - Tianna E Grant
- UC Davis School of Medicine, Department of Medical Microbiology and Immunology, Genome Center, MIND Institute, Davis, CA, USA
| | - Rebecca L Palmer
- UC Davis School of Medicine, Department of Medical Microbiology and Immunology, Genome Center, MIND Institute, Davis, CA, USA
| | - Demario Chappell
- UC Davis School of Medicine, Department of Medical Microbiology and Immunology, Genome Center, MIND Institute, Davis, CA, USA
| | - Sophia M Hakam
- UC Davis School of Medicine, Department of Medical Microbiology and Immunology, Genome Center, MIND Institute, Davis, CA, USA
| | | | - Matt Rolston
- UC Davis School of Medicine, Department of Medical Microbiology and Immunology, Genome Center, MIND Institute, Davis, CA, USA
| | | | | | - Abdullah Madany
- UC Davis School of Medicine, Department of Medical Microbiology and Immunology, Genome Center, MIND Institute, Davis, CA, USA
| | - Paul Ashwood
- UC Davis School of Medicine, Department of Medical Microbiology and Immunology, Genome Center, MIND Institute, Davis, CA, USA
| | - Blythe Durbin-Johnson
- UC Davis Genome Center, Davis, CA, USA
- UC Davis School of Medicine, Department of Public Health Sciences, Davis, CA, USA
| | - Janine M LaSalle
- UC Davis School of Medicine, Department of Medical Microbiology and Immunology, Genome Center, MIND Institute, Davis, CA, USA.
- UC Davis Genome Center, Davis, CA, USA.
| | - Dag H Yasui
- UC Davis School of Medicine, Department of Medical Microbiology and Immunology, Genome Center, MIND Institute, Davis, CA, USA
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21
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Breton CV, Landon R, Kahn LG, Enlow MB, Peterson AK, Bastain T, Braun J, Comstock SS, Duarte CS, Hipwell A, Ji H, LaSalle JM, Miller RL, Musci R, Posner J, Schmidt R, Suglia SF, Tung I, Weisenberger D, Zhu Y, Fry R. Exploring the evidence for epigenetic regulation of environmental influences on child health across generations. Commun Biol 2021; 4:769. [PMID: 34158610 PMCID: PMC8219763 DOI: 10.1038/s42003-021-02316-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 06/03/2021] [Indexed: 02/08/2023] Open
Abstract
Environmental exposures, psychosocial stressors and nutrition are all potentially important influences that may impact health outcomes directly or via interactions with the genome or epigenome over generations. While there have been clear successes in large-scale human genetic studies in recent decades, there is still a substantial amount of missing heritability to be elucidated for complex childhood disorders. Mounting evidence, primarily in animals, suggests environmental exposures may generate or perpetuate altered health outcomes across one or more generations. One putative mechanism for these environmental health effects is via altered epigenetic regulation. This review highlights the current epidemiologic literature and supporting animal studies that describe intergenerational and transgenerational health effects of environmental exposures. Both maternal and paternal exposures and transmission patterns are considered, with attention paid to the attendant ethical, legal and social implications.
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Affiliation(s)
- Carrie V Breton
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Remy Landon
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Linda G Kahn
- Department of Pediatrics, NYU Grossman School of Medicine, New York, NY, USA
| | - Michelle Bosquet Enlow
- Department of Psychiatry, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Alicia K Peterson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Theresa Bastain
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Joseph Braun
- Department of Epidemiology, Brown University School of Public Health, Providence, RI, USA
| | - Sarah S Comstock
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI, USA
| | - Cristiane S Duarte
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center and New York State Psychiatric Institute, New York, NY, USA
| | - Alison Hipwell
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hong Ji
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, California National Primate Research Center, University of California, Davis, Davis, CA, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, Davis, CA, USA
| | | | - Rashelle Musci
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jonathan Posner
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center and New York State Psychiatric Institute, New York, NY, USA
| | - Rebecca Schmidt
- Department of Public Health Sciences, UC Davis School of Medicine, Davis, CA, USA
| | | | - Irene Tung
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel Weisenberger
- Department of Biochemistry and Molecular Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yeyi Zhu
- Division of Research, Kaiser Permanente Northern California and Department of Epidemiology and Biostatistics, University of California, San Francisco, Oakland, CA, USA
| | - Rebecca Fry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, UNC Chapel Hill, Chapel Hill, NC, USA
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22
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Vogel Ciernia A, Laufer BI, Hwang H, Dunaway KW, Mordaunt CE, Coulson RL, Yasui DH, LaSalle JM. Epigenomic Convergence of Neural-Immune Risk Factors in Neurodevelopmental Disorder Cortex. Cereb Cortex 2021; 30:640-655. [PMID: 31240313 DOI: 10.1093/cercor/bhz115] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 12/11/2022] Open
Abstract
Neurodevelopmental disorders (NDDs) affect 7-14% of all children in developed countries and are one of the leading causes of lifelong disability. Epigenetic modifications are poised at the interface between genes and environment and are predicted to reveal insight into NDD etiology. Whole-genome bisulfite sequencing was used to examine DNA cytosine methylation in 49 human cortex samples from 3 different NDDs (autism spectrum disorder, Rett syndrome, and Dup15q syndrome) and matched controls. Integration of methylation changes across NDDs with relevant genomic and genetic datasets revealed differentially methylated regions (DMRs) unique to each type of NDD but with shared regulatory functions in neurons and microglia. NDD DMRs were enriched within promoter regions and for transcription factor binding sites with identified methylation sensitivity. DMRs from all 3 disorders were enriched for ontologies related to nervous system development and genes with disrupted expression in brain from neurodevelopmental or neuropsychiatric disorders. Genes associated with NDD DMRs showed expression patterns indicating an important role for altered microglial function during brain development. These findings demonstrate an NDD epigenomic signature in human cortex that will aid in defining therapeutic targets and early biomarkers at the interface of genetic and environmental NDD risk factors.
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Affiliation(s)
- A Vogel Ciernia
- Department of Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, CA 95616, USA
| | - B I Laufer
- Department of Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, CA 95616, USA
| | - H Hwang
- Department of Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, CA 95616, USA
| | - K W Dunaway
- Department of Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, CA 95616, USA
| | - C E Mordaunt
- Department of Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, CA 95616, USA
| | - R L Coulson
- Department of Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, CA 95616, USA
| | - D H Yasui
- Department of Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, CA 95616, USA
| | - J M LaSalle
- Department of Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, CA 95616, USA
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23
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Sarode GV, Neier K, Shibata NM, Shen Y, Goncharov DA, Goncharova EA, Mazi TA, Joshi N, Settles ML, LaSalle JM, Medici V. Wilson Disease: Intersecting DNA Methylation and Histone Acetylation Regulation of Gene Expression in a Mouse Model of Hepatic Copper Accumulation. Cell Mol Gastroenterol Hepatol 2021; 12:1457-1477. [PMID: 34098115 PMCID: PMC8487080 DOI: 10.1016/j.jcmgh.2021.05.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS The pathogenesis of Wilson disease (WD) involves hepatic and brain copper accumulation resulting from pathogenic variants affecting the ATP7B gene and downstream epigenetic and metabolic mechanisms. Prior methylome investigations in human WD liver and blood and in the Jackson Laboratory (Bar Harbor, ME) C3He-Atp7btx-j/J (tx-j) WD mouse model revealed an epigenetic signature of WD, including changes in histone deacetylase (HDAC) 5. We tested the hypothesis that histone acetylation is altered with respect to copper overload and aberrant DNA methylation in WD. METHODS We investigated class IIa HDAC4 and HDAC5 and H3K9/H3K27 histone acetylation in tx-j mouse livers compared with C3HeB/FeJ (C3H) control in response to 3 treatments: 60% kcal fat diet, D-penicillamine (copper chelator), and choline (methyl group donor). Experiments with copper-loaded hepatoma G2 cells were conducted to validate in vivo studies. RESULTS In 9-week tx-j mice, HDAC5 levels increased significantly after 8 days of a 60% kcal fat diet compared with chow. In 24-week tx-j mice, HDAC4/5 levels were reduced 5- to 10-fold compared with C3H, likely through mechanisms involving HDAC phosphorylation. HDAC4/5 levels were affected by disease progression and accompanied by increased acetylation. D-penicillamine and choline partially restored HDAC4/5 and H3K9ac/H3K27ac to C3H levels. Integrated RNA and chromatin immunoprecipitation sequencing analyses revealed genes regulating energy metabolism and cellular stress/development, which, in turn, were regulated by histone acetylation in tx-j mice compared with C3H mice, with Pparα and Pparγ among the most relevant targets. CONCLUSIONS These results suggest dietary modulation of class IIa HDAC4/5, and subsequent H3K9/H3K27 acetylation/deacetylation can regulate gene expression in key metabolic pathways in the pathogenesis of WD.
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Affiliation(s)
| | - Kari Neier
- Department of Medical Microbiology and Immunology, Genome Center, Davis, California
| | | | - Yuanjun Shen
- Division of Pulmonary, Critical Care and Sleep Medicine, Lung Center, Department of Internal Medicine, Davis, California
| | - Dmitry A. Goncharov
- Division of Pulmonary, Critical Care and Sleep Medicine, Lung Center, Department of Internal Medicine, Davis, California
| | - Elena A. Goncharova
- Division of Pulmonary, Critical Care and Sleep Medicine, Lung Center, Department of Internal Medicine, Davis, California
| | - Tagreed A. Mazi
- Department of Nutrition, Davis, California,Department of Community Health Sciences–Clinical Nutrition, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Nikhil Joshi
- Bioinformatics Core Facility, University of California–Davis, Davis, California
| | - Matthew L. Settles
- Bioinformatics Core Facility, University of California–Davis, Davis, California
| | - Janine M. LaSalle
- Department of Medical Microbiology and Immunology, Genome Center, Davis, California
| | - Valentina Medici
- Division of Gastroenterology and Hepatology, Davis, California,Correspondence Address correspondence to: Valentina Medici, MD, FAASLD, Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of California–Davis, 4150 V Street, Patient Support Services Building (PSSB) Suite 3500, Sacramento, California 95817. fax: (916) 734-7908.
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24
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Laufer BI, Gomez JA, Jianu JM, LaSalle JM. Stable DNMT3L overexpression in SH-SY5Y neurons recreates a facet of the genome-wide Down syndrome DNA methylation signature. Epigenetics Chromatin 2021; 14:13. [PMID: 33750431 PMCID: PMC7942011 DOI: 10.1186/s13072-021-00387-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/23/2021] [Indexed: 12/15/2022] Open
Abstract
Background Down syndrome (DS) is characterized by a genome-wide profile of differential DNA methylation that is skewed towards hypermethylation in most tissues, including brain, and includes pan-tissue differential methylation. The molecular mechanisms involve the overexpression of genes related to DNA methylation on chromosome 21. Here, we stably overexpressed the chromosome 21 gene DNA methyltransferase 3L (DNMT3L) in the human SH-SY5Y neuroblastoma cell line and assayed DNA methylation at over 26 million CpGs by whole genome bisulfite sequencing (WGBS) at three different developmental phases (undifferentiated, differentiating, and differentiated). Results DNMT3L overexpression resulted in global CpG and CpG island hypermethylation as well as thousands of differentially methylated regions (DMRs). The DNMT3L DMRs were skewed towards hypermethylation and mapped to genes involved in neurodevelopment, cellular signaling, and gene regulation. Consensus DNMT3L DMRs showed that cell lines clustered by genotype and then differentiation phase, demonstrating sets of common genes affected across neuronal differentiation. The hypermethylated DNMT3L DMRs from all pairwise comparisons were enriched for regions of bivalent chromatin marked by H3K4me3 as well as differentially methylated sites from previous DS studies of diverse tissues. In contrast, the hypomethylated DNMT3L DMRs from all pairwise comparisons displayed a tissue-specific profile enriched for regions of heterochromatin marked by H3K9me3 during embryonic development. Conclusions Taken together, these results support a mechanism whereby regions of bivalent chromatin that lose H3K4me3 during neuronal differentiation are targeted by excess DNMT3L and become hypermethylated. Overall, these findings demonstrate that DNMT3L overexpression during neurodevelopment recreates a facet of the genome-wide DS DNA methylation signature by targeting known genes and gene clusters that display pan-tissue differential methylation in DS. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00387-7.
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Affiliation(s)
- Benjamin I Laufer
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, 95616, USA.,Genome Center, University of California, Davis, CA, 95616, USA.,MIND Institute, University of California, Davis, CA, 95616, USA
| | - J Antonio Gomez
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, 95616, USA.,Genome Center, University of California, Davis, CA, 95616, USA.,MIND Institute, University of California, Davis, CA, 95616, USA
| | - Julia M Jianu
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, 95616, USA.,Genome Center, University of California, Davis, CA, 95616, USA.,MIND Institute, University of California, Davis, CA, 95616, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, 95616, USA. .,Genome Center, University of California, Davis, CA, 95616, USA. .,MIND Institute, University of California, Davis, CA, 95616, USA.
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25
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Abstract
Prader-Willi Syndrome (PWS) is a rare neurodevelopmental disorder that affects approximately 1 in 20,000 individuals worldwide. Symptom progression in PWS is classically characterized by two nutritional stages. Stage 1 is hypotonia characterized by poor muscle tone that leads to poor feeding behavior causing failure to thrive in early neonatal life. Stage 2 is followed by the development of extreme hyperphagia, also known as insatiable eating and fixation on food that often leads to obesity in early childhood. Other major features of PWS include obsessive-compulsive and hoarding behaviors, intellectual disability, and sleep abnormalities. PWS is genetic disorder mapping to imprinted 15q11.2-q13.3 locus, specifically at the paternally expressed SNORD116 locus of small nucleolar RNAs and noncoding host gene transcripts. SNORD116 is processed into several noncoding components and is hypothesized to orchestrate diurnal changes in metabolism through epigenetics, according to functional studies. Here, we review the current status of epigenetic mechanisms in PWS, with an emphasis on an emerging role for SNORD116 in circadian and sleep phenotypes. We also summarize current ongoing therapeutic strategies, as well as potential implications for more common human metabolic and psychiatric disorders.
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Affiliation(s)
| | - Janine M. LaSalle
- Department of Medical Microbiology and Immunology, Genome Center, MIND Institute, University of California, Davis, Davis, CA, United States
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26
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Zhu Y, Mordaunt CE, Durbin-Johnson BP, Caudill MA, Malysheva OV, Miller JW, Green R, James SJ, Melnyk SB, Fallin MD, Hertz-Picciotto I, Schmidt RJ, LaSalle JM. Expression Changes in Epigenetic Gene Pathways Associated With One-Carbon Nutritional Metabolites in Maternal Blood From Pregnancies Resulting in Autism and Non-Typical Neurodevelopment. Autism Res 2020; 14:11-28. [PMID: 33159718 PMCID: PMC7894157 DOI: 10.1002/aur.2428] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/16/2020] [Accepted: 10/21/2020] [Indexed: 12/15/2022]
Abstract
The prenatal period is a critical window for the development of autism spectrum disorder (ASD). The relationship between prenatal nutrients and gestational gene expression in mothers of children later diagnosed with ASD or non-typical development (Non-TD) is poorly understood. Maternal blood collected prospectively during pregnancy provides insights into the effects of nutrition, particularly one-carbon metabolites, on gene pathways and neurodevelopment. Genome-wide transcriptomes were measured with microarrays in 300 maternal blood samples in Markers of Autism Risk in Babies-Learning Early Signs. Sixteen different one-carbon metabolites, including folic acid, betaine, 5'-methyltretrahydrofolate (5-MeTHF), and dimethylglycine (DMG) were measured. Differential expression analysis and weighted gene correlation network analysis (WGCNA) were used to compare gene expression between children later diagnosed as typical development (TD), Non-TD and ASD, and to one-carbon metabolites. Using differential gene expression analysis, six transcripts (TGR-AS1, SQSTM1, HLA-C, and RFESD) were associated with child outcomes (ASD, Non-TD, and TD) with genome-wide significance. Genes nominally differentially expressed between ASD and TD significantly overlapped with seven high confidence ASD genes. WGCNA identified co-expressed gene modules significantly correlated with 5-MeTHF, folic acid, DMG, and betaine. A module enriched in DNA methylation functions showed a suggestive protective association with folic acid/5-MeTHF concentrations and ASD risk. Maternal plasma betaine and DMG concentrations were associated with a block of co-expressed genes enriched for adaptive immune, histone modification, and RNA processing functions. These results suggest that the prenatal maternal blood transcriptome is a sensitive indicator of gestational one-carbon metabolite status and changes relevant to children's later neurodevelopmental outcomes. LAY SUMMARY: Pregnancy is a time when maternal nutrition could interact with genetic risk for autism spectrum disorder. Blood samples collected during pregnancy from mothers who had a prior child with autism were examined for gene expression and nutrient metabolites, then compared to the diagnosis of the child at age three. Expression differences in gene pathways related to the immune system and gene regulation were observed for pregnancies of children with autism and non-typical neurodevelopment and were associated with maternal nutrients.
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Affiliation(s)
- Yihui Zhu
- Department of Medical Microbiology and Immunology, Genome Center, and Perinatal Origins of Disparities Center, University of California, Davis, California, USA.,MIND Institute, School of Medicine, University of California, Davis, California, USA
| | - Charles E Mordaunt
- Department of Medical Microbiology and Immunology, Genome Center, and Perinatal Origins of Disparities Center, University of California, Davis, California, USA.,MIND Institute, School of Medicine, University of California, Davis, California, USA
| | | | - Marie A Caudill
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Olga V Malysheva
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Joshua W Miller
- Department of Nutritional Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Ralph Green
- Department of Pathology and Laboratory Medicine, University of California Davis School of Medicine, Sacramento, California, USA
| | - S Jill James
- Department of Pediatrics, University of Arkansas for Medical Sciences, Arkansas Children's Research Institute, Little Rock, Arkansas, USA
| | - Stepan B Melnyk
- Department of Pediatrics, University of Arkansas for Medical Sciences, Arkansas Children's Research Institute, Little Rock, Arkansas, USA
| | - M Daniele Fallin
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Irva Hertz-Picciotto
- MIND Institute, School of Medicine, University of California, Davis, California, USA.,Department of Public Health Sciences, University of California, Davis, California, USA
| | - Rebecca J Schmidt
- MIND Institute, School of Medicine, University of California, Davis, California, USA.,Department of Public Health Sciences, University of California, Davis, California, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, Genome Center, and Perinatal Origins of Disparities Center, University of California, Davis, California, USA.,MIND Institute, School of Medicine, University of California, Davis, California, USA
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27
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Medici V, Sarode GV, Napoli E, Song GY, Shibata NM, Guimarães AO, Mordaunt CE, Kieffer DA, Mazi TA, Czlonkowska A, Litwin T, LaSalle JM, Giulivi C. mtDNA depletion-like syndrome in Wilson disease. Liver Int 2020; 40:2776-2787. [PMID: 32996699 PMCID: PMC8079140 DOI: 10.1111/liv.14646] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/13/2020] [Accepted: 08/14/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND AND AIMS Wilson disease (WD) is caused by mutations in the copper transporter ATP7B, with its main pathology attributed to copper-mediated oxidative damage. The limited therapeutic effect of copper chelators and the early occurrence of mitochondrial deficits, however, undermine the prevalence of this mechanism. METHODS We characterized mitochondrial DNA copy number and mutations as well as bioenergetic deficits in blood from patients with WD and in livers of tx-j mice, a mouse model of hepatic copper accumulation. In vitro experiments with hepatocytes treated with CuSO4 were conducted to validate in vivo studies. RESULTS Here, for the first time, we characterized the bioenergetic deficits in WD as consistent with a mitochondrial DNA depletion-like syndrome. This is evidenced by enriched DNA synthesis/replication pathways in serum metabolomics and decreased mitochondrial DNA copy number in blood of WD patients as well as decreased mitochondrial DNA copy number, increased citrate synthase activity, and selective Complex IV deficit in livers of the tx-j mouse model of WD. Tx-j mice treated with the copper chelator penicillamine, methyl donor choline or both ameliorated mitochondrial DNA damage but further decreased mitochondrial DNA copy number. Experiments with copper-loaded HepG2 cells validated the concept of a direct copper-mitochondrial DNA interaction. CONCLUSIONS This study underlines the relevance of targeting the copper-mitochondrial DNA pool in the treatment of WD separate from the established copper-induced oxidative stress-mediated damage.
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Affiliation(s)
- Valentina Medici
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, 4150 V Street, PSSB Suite 3500, University of California Davis, Sacramento, CA 95616,Correspondence: Authors share co-senior authorship, Valentina Medici, M.D., Professor, University of California Davis, Department of Internal Medicine, Division of Gastroenterology and Hepatology, 4150 V Street, PSSB Suite 3500, Sacramento, California 95817, ; Cecilia Giulivi, Ph.D., Professor, University of California Davis, Department of Molecular Biosciences, School of Veterinary Medicine, Medical Investigations of Neurodevelopmental Disorders (MIND) Institute, 1089 Veterinary Dr., 3017 Vet Med 3B, Davis, California 95616,
| | - Gaurav Vilas Sarode
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, 4150 V Street, PSSB Suite 3500, University of California Davis, Sacramento, CA 95616
| | - Eleonora Napoli
- Department of Molecular Biosciences, School of Veterinary Medicine, 1089 Veterinary Medicine Drive, University of California Davis, Davis, CA 95616
| | - Gyu-Young Song
- Department of Molecular Biosciences, School of Veterinary Medicine, 1089 Veterinary Medicine Drive, University of California Davis, Davis, CA 95616
| | - Noreene M. Shibata
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, 4150 V Street, PSSB Suite 3500, University of California Davis, Sacramento, CA 95616
| | - Andre Oliveira Guimarães
- Department of Molecular Biosciences, School of Veterinary Medicine, 1089 Veterinary Medicine Drive, University of California Davis, Davis, CA 95616,Laboratório de Ciências Físicas, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes RJ, Brazil
| | - Charles E. Mordaunt
- Department of Medical Microbiology and Immunology, Genome Center, University of California Davis, Davis, CA 95616,Medical Investigations of Neurodevelopmental Disorders (MIND) Institute, 2825 50 St, University of California Davis, Davis, CA 95817
| | - Dorothy A. Kieffer
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, 4150 V Street, PSSB Suite 3500, University of California Davis, Sacramento, CA 95616
| | - Tagreed A. Mazi
- Department of Nutrition, University of California Davis, Davis, CA 95616,Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Anna Czlonkowska
- Second Department of Neurology, Institute of Psychiatry and Neurology, Warsaw, Poland
| | - Tomasz Litwin
- Second Department of Neurology, Institute of Psychiatry and Neurology, Warsaw, Poland
| | - Janine M. LaSalle
- Department of Medical Microbiology and Immunology, Genome Center, University of California Davis, Davis, CA 95616,Medical Investigations of Neurodevelopmental Disorders (MIND) Institute, 2825 50 St, University of California Davis, Davis, CA 95817
| | - Cecilia Giulivi
- Department of Molecular Biosciences, School of Veterinary Medicine, 1089 Veterinary Medicine Drive, University of California Davis, Davis, CA 95616,Medical Investigations of Neurodevelopmental Disorders (MIND) Institute, 2825 50 St, University of California Davis, Davis, CA 95817,Correspondence: Authors share co-senior authorship, Valentina Medici, M.D., Professor, University of California Davis, Department of Internal Medicine, Division of Gastroenterology and Hepatology, 4150 V Street, PSSB Suite 3500, Sacramento, California 95817, ; Cecilia Giulivi, Ph.D., Professor, University of California Davis, Department of Molecular Biosciences, School of Veterinary Medicine, Medical Investigations of Neurodevelopmental Disorders (MIND) Institute, 1089 Veterinary Dr., 3017 Vet Med 3B, Davis, California 95616,
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28
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Mordaunt CE, Jianu JM, Laufer BI, Zhu Y, Hwang H, Dunaway KW, Bakulski KM, Feinberg JI, Volk HE, Lyall K, Croen LA, Newschaffer CJ, Ozonoff S, Hertz-Picciotto I, Fallin MD, Schmidt RJ, LaSalle JM. Cord blood DNA methylome in newborns later diagnosed with autism spectrum disorder reflects early dysregulation of neurodevelopmental and X-linked genes. Genome Med 2020; 12:88. [PMID: 33054850 PMCID: PMC7559201 DOI: 10.1186/s13073-020-00785-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/25/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a neurodevelopmental disorder with complex heritability and higher prevalence in males. The neonatal epigenome has the potential to reflect past interactions between genetic and environmental factors during early development and influence future health outcomes. METHODS We performed whole-genome bisulfite sequencing of 152 umbilical cord blood samples from the MARBLES and EARLI high-familial risk prospective cohorts to identify an epigenomic signature of ASD at birth. Samples were split into discovery and replication sets and stratified by sex, and their DNA methylation profiles were tested for differentially methylated regions (DMRs) between ASD and typically developing control cord blood samples. DMRs were mapped to genes and assessed for enrichment in gene function, tissue expression, chromosome location, and overlap with prior ASD studies. DMR coordinates were tested for enrichment in chromatin states and transcription factor binding motifs. Results were compared between discovery and replication sets and between males and females. RESULTS We identified DMRs stratified by sex that discriminated ASD from control cord blood samples in discovery and replication sets. At a region level, 7 DMRs in males and 31 DMRs in females replicated across two independent groups of subjects, while 537 DMR genes in males and 1762 DMR genes in females replicated by gene association. These DMR genes were significantly enriched for brain and embryonic expression, X chromosome location, and identification in prior epigenetic studies of ASD in post-mortem brain. In males and females, autosomal ASD DMRs were significantly enriched for promoter and bivalent chromatin states across most cell types, while sex differences were observed for X-linked ASD DMRs. Lastly, these DMRs identified in cord blood were significantly enriched for binding sites of methyl-sensitive transcription factors relevant to fetal brain development. CONCLUSIONS At birth, prior to the diagnosis of ASD, a distinct DNA methylation signature was detected in cord blood over regulatory regions and genes relevant to early fetal neurodevelopment. Differential cord methylation in ASD supports the developmental and sex-biased etiology of ASD and provides novel insights for early diagnosis and therapy.
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Affiliation(s)
- Charles E. Mordaunt
- Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California, Davis, CA USA
| | - Julia M. Jianu
- Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California, Davis, CA USA
| | - Benjamin I. Laufer
- Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California, Davis, CA USA
| | - Yihui Zhu
- Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California, Davis, CA USA
| | - Hyeyeon Hwang
- Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California, Davis, CA USA
| | - Keith W. Dunaway
- Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California, Davis, CA USA
| | - Kelly M. Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | - Jason I. Feinberg
- Wendy Klag Center for Autism and Developmental Disabilities, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD USA
| | - Heather E. Volk
- Wendy Klag Center for Autism and Developmental Disabilities, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD USA
| | - Kristen Lyall
- A. J. Drexel Autism Institute, Drexel University, Philadelphia, PA USA
| | - Lisa A. Croen
- Division of Research, Kaiser Permanente Northern California, Oakland, CA USA
| | - Craig J. Newschaffer
- Department of Biobehavioral Health, College of Health and Human Development, Pennsylvania State University, University Park, PA USA
| | - Sally Ozonoff
- Psychiatry and Behavioral Sciences and MIND Institute, University of California, Davis, CA USA
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences and MIND Institute, University of California, Davis, CA USA
| | - M. Daniele Fallin
- Wendy Klag Center for Autism and Developmental Disabilities, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD USA
| | - Rebecca J. Schmidt
- Department of Public Health Sciences and MIND Institute, University of California, Davis, CA USA
| | - Janine M. LaSalle
- Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California, Davis, CA USA
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29
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Laufer BI, Hwang H, Jianu JM, Mordaunt CE, Korf IF, Hertz-Picciotto I, LaSalle JM. Low-pass whole genome bisulfite sequencing of neonatal dried blood spots identifies a role for RUNX1 in Down syndrome DNA methylation profiles. Hum Mol Genet 2020; 29:3465-3476. [PMID: 33001180 PMCID: PMC7788293 DOI: 10.1093/hmg/ddaa218] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/16/2020] [Accepted: 09/25/2020] [Indexed: 12/17/2022] Open
Abstract
Neonatal dried blood spots (NDBS) are a widely banked sample source that enables retrospective investigation into early life molecular events. Here, we performed low-pass whole genome bisulfite sequencing (WGBS) of 86 NDBS DNA to examine early life Down syndrome (DS) DNA methylation profiles. DS represents an example of genetics shaping epigenetics, as multiple array-based studies have demonstrated that trisomy 21 is characterized by genome-wide alterations to DNA methylation. By assaying over 24 million CpG sites, thousands of genome-wide significant (q < 0.05) differentially methylated regions (DMRs) that distinguished DS from typical development and idiopathic developmental delay were identified. Machine learning feature selection refined these DMRs to 22 loci. The DS DMRs mapped to genes involved in neurodevelopment, metabolism, and transcriptional regulation. Based on comparisons with previous DS methylation studies and reference epigenomes, the hypermethylated DS DMRs were significantly (q < 0.05) enriched across tissues while the hypomethylated DS DMRs were significantly (q < 0.05) enriched for blood-specific chromatin states. A ~28 kb block of hypermethylation was observed on chromosome 21 in the RUNX1 locus, which encodes a hematopoietic transcription factor whose binding motif was the most significantly enriched (q < 0.05) overall and specifically within the hypomethylated DMRs. Finally, we also identified DMRs that distinguished DS NDBS based on the presence or absence of congenital heart disease (CHD). Together, these results not only demonstrate the utility of low-pass WGBS on NDBS samples for epigenome-wide association studies, but also provide new insights into the early life mechanisms of epigenomic dysregulation resulting from trisomy 21.
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Affiliation(s)
- Benjamin I Laufer
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA.,Genome Center, University of California, Davis, CA 95616, USA.,MIND Institute, University of California, Davis, CA 95616, USA
| | - Hyeyeon Hwang
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA.,Genome Center, University of California, Davis, CA 95616, USA.,MIND Institute, University of California, Davis, CA 95616, USA
| | - Julia M Jianu
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA.,Genome Center, University of California, Davis, CA 95616, USA.,MIND Institute, University of California, Davis, CA 95616, USA
| | - Charles E Mordaunt
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA.,Genome Center, University of California, Davis, CA 95616, USA.,MIND Institute, University of California, Davis, CA 95616, USA
| | - Ian F Korf
- Genome Center, University of California, Davis, CA 95616, USA.,Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Irva Hertz-Picciotto
- MIND Institute, University of California, Davis, CA 95616, USA.,Department of Public Health Sciences, School of Medicine, University of California, Davis, CA 95616, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA.,Genome Center, University of California, Davis, CA 95616, USA.,MIND Institute, University of California, Davis, CA 95616, USA
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30
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Yu P, Li J, Deng SP, Zhang F, Grozdanov PN, Chin EWM, Martin SD, Vergnes L, Islam MS, Sun D, LaSalle JM, McGee SL, Goh E, MacDonald CC, Jin P. Publisher Correction: Integrated analysis of a compendium of RNA-Seq datasets for splicing factors. Sci Data 2020; 7:267. [PMID: 32769981 PMCID: PMC7414123 DOI: 10.1038/s41597-020-00607-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Peng Yu
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China. .,Medical Big Data Center, Sichuan University, Chengdu, China.
| | - Jin Li
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX, 77030, USA
| | - Su-Ping Deng
- School of Electronic and Information Engineering, Suzhou University of Science and Technology, Suzhou, Jiangsu, 215009, China
| | - Feiran Zhang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Petar N Grozdanov
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, 79430, USA
| | - Eunice W M Chin
- Neuroscience Academic Clinical Programme, Duke-NUS Medical School, NA, Singapore
| | - Sheree D Martin
- Metabolic Reprogramming Laboratory, Metabolic Research Unit, School of Medicine and Centre for Molecular and Medical Research, Deakin University, Geelong, Victoria, Australia
| | - Laurent Vergnes
- Department of Human Genetics, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
| | - M Saharul Islam
- Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California Davis, Davis, CA, USA
| | - Deqiang Sun
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX, 77030, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California Davis, Davis, CA, USA
| | - Sean L McGee
- Metabolic Reprogramming Laboratory, Metabolic Research Unit, School of Medicine and Centre for Molecular and Medical Research, Deakin University, Geelong, Victoria, Australia
| | - Eyleen Goh
- Neuroscience Academic Clinical Programme, Duke-NUS Medical School, NA, Singapore
| | - Clinton C MacDonald
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, 79430, USA
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
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31
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Yu P, Li J, Deng SP, Zhang F, Grozdanov PN, Chin EWM, Martin SD, Vergnes L, Islam MS, Sun D, LaSalle JM, McGee SL, Goh E, MacDonald CC, Jin P. Integrated analysis of a compendium of RNA-Seq datasets for splicing factors. Sci Data 2020; 7:178. [PMID: 32546682 PMCID: PMC7297722 DOI: 10.1038/s41597-020-0514-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/13/2020] [Indexed: 02/05/2023] Open
Abstract
A vast amount of public RNA-sequencing datasets have been generated and used widely to study transcriptome mechanisms. These data offer precious opportunity for advancing biological research in transcriptome studies such as alternative splicing. We report the first large-scale integrated analysis of RNA-Seq data of splicing factors for systematically identifying key factors in diseases and biological processes. We analyzed 1,321 RNA-Seq libraries of various mouse tissues and cell lines, comprising more than 6.6 TB sequences from 75 independent studies that experimentally manipulated 56 splicing factors. Using these data, RNA splicing signatures and gene expression signatures were computed, and signature comparison analysis identified a list of key splicing factors in Rett syndrome and cold-induced thermogenesis. We show that cold-induced RNA-binding proteins rescue the neurite outgrowth defects in Rett syndrome using neuronal morphology analysis, and we also reveal that SRSF1 and PTBP1 are required for energy expenditure in adipocytes using metabolic flux analysis. Our study provides an integrated analysis for identifying key factors in diseases and biological processes and highlights the importance of public data resources for identifying hypotheses for experimental testing.
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Affiliation(s)
- Peng Yu
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China.
- Medical Big Data Center, Sichuan University, Chengdu, China.
| | - Jin Li
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX, 77030, USA
| | - Su-Ping Deng
- School of Electronic and Information Engineering, Suzhou University of Science and Technology, Suzhou, Jiangsu, 215009, China
| | - Feiran Zhang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Petar N Grozdanov
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, 79430, USA
| | - Eunice W M Chin
- Neuroscience Academic Clinical Programme, Duke-NUS Medical School, NA, Singapore
| | - Sheree D Martin
- Metabolic Reprogramming Laboratory, Metabolic Research Unit, School of Medicine and Centre for Molecular and Medical Research, Deakin University, Geelong, Victoria, Australia
| | - Laurent Vergnes
- Department of Human Genetics, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
| | - M Saharul Islam
- Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California Davis, Davis, CA, USA
| | - Deqiang Sun
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX, 77030, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California Davis, Davis, CA, USA
| | - Sean L McGee
- Metabolic Reprogramming Laboratory, Metabolic Research Unit, School of Medicine and Centre for Molecular and Medical Research, Deakin University, Geelong, Victoria, Australia
| | - Eyleen Goh
- Neuroscience Academic Clinical Programme, Duke-NUS Medical School, NA, Singapore
| | - Clinton C MacDonald
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, 79430, USA
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
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32
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Lopez SJ, Laufer BI, Beitnere U, Berg EL, Silverman JL, O'Geen H, Segal DJ, LaSalle JM. Imprinting effects of UBE3A loss on synaptic gene networks and Wnt signaling pathways. Hum Mol Genet 2020; 28:3842-3852. [PMID: 31625566 DOI: 10.1093/hmg/ddz221] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/21/2019] [Accepted: 09/04/2019] [Indexed: 12/13/2022] Open
Abstract
Ubiquitin E3 ligase 3A (UBE3A) encodes an E3 ubiquitin ligase whose loss from the maternal allele causes the neurodevelopmental disorder Angelman syndrome (AS). Previous studies of UBE3A function have not examined full Ube3a deletion in mouse, the complexity of imprinted gene networks in brain nor the molecular basis of systems-level cognitive dysfunctions in AS. We therefore utilized a systems biology approach to elucidate how UBE3A loss impacts the early postnatal brain in a novel CRISPR/Cas9-engineered rat Angelman model of a complete Ube3a deletion. Strand-specific transcriptome analysis of offspring from maternally or paternally inherited Ube3a deletions revealed the expected parental expression patterns of Ube3a sense and antisense transcripts by postnatal day 2 (P2) in hypothalamus and day 9 (P9) in cortex, compared to wild-type littermates. The dependency of genome-wide effects on parent-of-origin, Ube3a genotype and time (P2 and P9) was investigated through transcriptome (RNA sequencing of cortex and hypothalamus) and methylome (whole-genome bisulfite sequencing of hypothalamus). Weighted gene co-expression and co-methylation network analyses identified co-regulated networks in maternally inherited Ube3a deletion offspring enriched in postnatal developmental processes including Wnt signaling, synaptic regulation, neuronal and glial functions, epigenetic regulation, ubiquitin, circadian entrainment and splicing. Furthermore, we showed that loss of the paternal Ube3a antisense transcript resulted in both unique and overlapping dysregulated gene pathways with maternal loss, predominantly at the level of differential methylation. Together, these results provide a holistic examination of the molecular impacts of UBE3A loss in brain, supporting the existence of interactive epigenetic networks between maternal and paternal transcripts at the Ube3a locus.
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Affiliation(s)
- S Jesse Lopez
- Medical Immunology and Microbiology, University of California (UC) Davis School of Medicine, Davis, CA 95616, USA.,Genome Center, UC Davis, Davis, CA, USA.,Integrative Genetics and Genomics, UC Davis, Davis, CA 95616, USA.,Biochemistry and Molecular Medicine, UC Davis School of Medicine, Davis, CA 95616, USA.,Medical Investigation of Neurodevelopmental Disorders Institute, UC Davis Health, Sacramento, CA 95817, USA
| | - Benjamin I Laufer
- Medical Immunology and Microbiology, University of California (UC) Davis School of Medicine, Davis, CA 95616, USA.,Genome Center, UC Davis, Davis, CA, USA.,Medical Investigation of Neurodevelopmental Disorders Institute, UC Davis Health, Sacramento, CA 95817, USA
| | - Ulrika Beitnere
- Genome Center, UC Davis, Davis, CA, USA.,Biochemistry and Molecular Medicine, UC Davis School of Medicine, Davis, CA 95616, USA.,Medical Investigation of Neurodevelopmental Disorders Institute, UC Davis Health, Sacramento, CA 95817, USA
| | - Elizabeth L Berg
- Medical Investigation of Neurodevelopmental Disorders Institute, UC Davis Health, Sacramento, CA 95817, USA.,Psychiatry and Behavioral Sciences, UC Davis School of Medicine, Sacromento, CA 95817, USA
| | - Jill L Silverman
- Medical Investigation of Neurodevelopmental Disorders Institute, UC Davis Health, Sacramento, CA 95817, USA.,Psychiatry and Behavioral Sciences, UC Davis School of Medicine, Sacromento, CA 95817, USA
| | - Henriette O'Geen
- Genome Center, UC Davis, Davis, CA, USA.,Biochemistry and Molecular Medicine, UC Davis School of Medicine, Davis, CA 95616, USA.,Medical Investigation of Neurodevelopmental Disorders Institute, UC Davis Health, Sacramento, CA 95817, USA
| | - David J Segal
- Genome Center, UC Davis, Davis, CA, USA.,Integrative Genetics and Genomics, UC Davis, Davis, CA 95616, USA.,Biochemistry and Molecular Medicine, UC Davis School of Medicine, Davis, CA 95616, USA.,Medical Investigation of Neurodevelopmental Disorders Institute, UC Davis Health, Sacramento, CA 95817, USA
| | - Janine M LaSalle
- Medical Immunology and Microbiology, University of California (UC) Davis School of Medicine, Davis, CA 95616, USA.,Genome Center, UC Davis, Davis, CA, USA.,Integrative Genetics and Genomics, UC Davis, Davis, CA 95616, USA.,Medical Investigation of Neurodevelopmental Disorders Institute, UC Davis Health, Sacramento, CA 95817, USA
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33
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Casanova MF, Casanova EL, Frye RE, Baeza-Velasco C, LaSalle JM, Hagerman RJ, Scherer SW, Natowicz MR. Editorial: Secondary vs. Idiopathic Autism. Front Psychiatry 2020; 11:297. [PMID: 32346372 PMCID: PMC7171716 DOI: 10.3389/fpsyt.2020.00297] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/25/2020] [Indexed: 01/04/2023] Open
Affiliation(s)
- Manuel F Casanova
- School of Medicine Greenville, University of South Carolina, Greenville, SC, United States
| | - Emily L Casanova
- School of Medicine Greenville, University of South Carolina, Greenville, SC, United States
| | | | | | | | - Randi Jensen Hagerman
- Department of Pediatrics, UC Davis School of Medicine, Sacramento, CA, United States
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Adhikari A, Copping NA, Onaga B, Pride MC, Coulson RL, Yang M, Yasui DH, LaSalle JM, Silverman JL. Cognitive deficits in the Snord116 deletion mouse model for Prader-Willi syndrome. Neurobiol Learn Mem 2019; 165:106874. [PMID: 29800646 PMCID: PMC6520209 DOI: 10.1016/j.nlm.2018.05.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/24/2018] [Accepted: 05/16/2018] [Indexed: 01/12/2023]
Abstract
Prader-Willi syndrome (PWS) is an imprinted neurodevelopmental disease caused by a loss of paternal genes on chromosome 15q11-q13. It is characterized by cognitive impairments, developmental delay, sleep abnormalities, and hyperphagia often leading to obesity. Clinical research has shown that a lack of expression of SNORD116, a paternally expressed imprinted gene cluster that encodes multiple copies of a small nucleolar RNA (snoRNA) in both humans and mice, is most likely responsible for many PWS symptoms seen in humans. The majority of previous research using PWS preclinical models focused on characterization of the hyperphagic and metabolic phenotypes. However, a crucial understudied clinical phenotype is cognitive impairments and thus we investigated the learning and memory abilities using a model of PWS, with a heterozygous deletion in Snord116. We utilized the novel object recognition task, which doesn't require external motivation, or exhaustive swim training. Automated findings were further confirmed with manual scoring by a highly trained blinded investigator. We discovered deficits in Snord116+/- mutant mice in the novel object recognition, location memory and tone cue fear conditioning assays when compared to age-, sex- matched, littermate control Snord116+/+ mice. Further, we confirmed that despite physical neo-natal developmental delays, Snord116+/- mice had normal exploratory and motor abilities. These results show that the Snord116+/- deletion murine model is a valuable preclinical model for investigating learning and memory impairments in individuals with PWS without common confounding phenotypes.
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Affiliation(s)
- Anna Adhikari
- MIND Institute, University of California, Davis School of Medicine, Department of Psychiatry and Behavioral Sciences, Sacramento, CA, USA
| | - Nycole A Copping
- MIND Institute, University of California, Davis School of Medicine, Department of Psychiatry and Behavioral Sciences, Sacramento, CA, USA
| | - Beth Onaga
- MIND Institute, University of California, Davis School of Medicine, Department of Psychiatry and Behavioral Sciences, Sacramento, CA, USA
| | - Michael C Pride
- MIND Institute, University of California, Davis School of Medicine, Department of Psychiatry and Behavioral Sciences, Sacramento, CA, USA
| | - Rochelle L Coulson
- MIND Institute, Genome Center, UC Davis School of Medicine, Department of Medical Microbiology and Immunology, Davis, CA, USA
| | - Mu Yang
- Department of Psychiatry and Institute for Genomic Medicine, New York, NY, USA
| | - Dag H Yasui
- MIND Institute, Genome Center, UC Davis School of Medicine, Department of Medical Microbiology and Immunology, Davis, CA, USA
| | - Janine M LaSalle
- MIND Institute, Genome Center, UC Davis School of Medicine, Department of Medical Microbiology and Immunology, Davis, CA, USA
| | - Jill L Silverman
- MIND Institute, University of California, Davis School of Medicine, Department of Psychiatry and Behavioral Sciences, Sacramento, CA, USA.
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35
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Mordaunt CE, Park BY, Bakulski KM, Feinberg JI, Croen LA, Ladd-Acosta C, Newschaffer CJ, Volk HE, Ozonoff S, Hertz-Picciotto I, LaSalle JM, Schmidt RJ, Fallin MD. A meta-analysis of two high-risk prospective cohort studies reveals autism-specific transcriptional changes to chromatin, autoimmune, and environmental response genes in umbilical cord blood. Mol Autism 2019; 10:36. [PMID: 31673306 PMCID: PMC6814108 DOI: 10.1186/s13229-019-0287-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/08/2019] [Indexed: 12/17/2022] Open
Abstract
Background Autism spectrum disorder (ASD) is a neurodevelopmental disorder that affects more than 1% of children in the USA. ASD risk is thought to arise from both genetic and environmental factors, with the perinatal period as a critical window. Understanding early transcriptional changes in ASD would assist in clarifying disease pathogenesis and identifying biomarkers. However, little is known about umbilical cord blood gene expression profiles in babies later diagnosed with ASD compared to non-typically developing and non-ASD (Non-TD) or typically developing (TD) children. Methods Genome-wide transcript levels were measured by Affymetrix Human Gene 2.0 array in RNA from cord blood samples from both the Markers of Autism Risk in Babies-Learning Early Signs (MARBLES) and the Early Autism Risk Longitudinal Investigation (EARLI) high-risk pregnancy cohorts that enroll younger siblings of a child previously diagnosed with ASD. Younger siblings were diagnosed based on assessments at 36 months, and 59 ASD, 92 Non-TD, and 120 TD subjects were included. Using both differential expression analysis and weighted gene correlation network analysis, gene expression between ASD and TD, and between Non-TD and TD, was compared within each study and via meta-analysis. Results While cord blood gene expression differences comparing either ASD or Non-TD to TD did not reach genome-wide significance, 172 genes were nominally differentially expressed between ASD and TD cord blood (log2(fold change) > 0.1, p < 0.01). These genes were significantly enriched for functions in xenobiotic metabolism, chromatin regulation, and systemic lupus erythematosus (FDR q < 0.05). In contrast, 66 genes were nominally differentially expressed between Non-TD and TD, including 8 genes that were also differentially expressed in ASD. Gene coexpression modules were significantly correlated with demographic factors and cell type proportions. Limitations ASD-associated gene expression differences identified in this study are subtle, as cord blood is not the main affected tissue, it is composed of many cell types, and ASD is a heterogeneous disorder. Conclusions This is the first study to identify gene expression differences in cord blood specific to ASD through a meta-analysis across two prospective pregnancy cohorts. The enriched gene pathways support involvement of environmental, immune, and epigenetic mechanisms in ASD etiology.
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Affiliation(s)
- Charles E Mordaunt
- 1Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California, Davis, CA USA
| | - Bo Y Park
- 2Department of Public Health, California State University, Fullerton, CA USA
| | - Kelly M Bakulski
- 3Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | - Jason I Feinberg
- 4Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD USA
| | - Lisa A Croen
- 5Division of Research and Autism Research Program, Kaiser Permanente Northern California, Oakland, CA USA
| | | | - Craig J Newschaffer
- 6Department of Biobehavioral Health, College of Health and Human Development, Pennsylvania State University, University Park, PA USA
| | - Heather E Volk
- 4Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD USA
| | - Sally Ozonoff
- 7Psychiatry and Behavioral Sciences and MIND Institute, University of California, Davis, CA USA
| | - Irva Hertz-Picciotto
- 8Department of Public Health Sciences and MIND Institute, University of California, Davis, CA USA
| | - Janine M LaSalle
- 1Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California, Davis, CA USA
| | - Rebecca J Schmidt
- 8Department of Public Health Sciences and MIND Institute, University of California, Davis, CA USA
| | - M Daniele Fallin
- 4Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD USA
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36
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Zhu Y, Mordaunt CE, Yasui DH, Marathe R, Coulson RL, Dunaway KW, Jianu JM, Walker CK, Ozonoff S, Hertz-Picciotto I, Schmidt RJ, LaSalle JM. Placental DNA methylation levels at CYP2E1 and IRS2 are associated with child outcome in a prospective autism study. Hum Mol Genet 2019; 28:2659-2674. [PMID: 31009952 PMCID: PMC6687952 DOI: 10.1093/hmg/ddz084] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/25/2019] [Accepted: 04/15/2019] [Indexed: 12/20/2022] Open
Abstract
DNA methylation acts at the interface of genetic and environmental factors relevant for autism spectrum disorder (ASD). Placenta, normally discarded at birth, is a potentially rich source of DNA methylation patterns predictive of ASD in the child. Here, we performed whole methylome analyses of placentas from a prospective study MARBLES (Markers of Autism Risk in Babies-Learning Early Signs) of high-risk pregnancies. A total of 400 differentially methylated regions (DMRs) discriminated placentas stored from children later diagnosed with ASD compared to typically developing controls. These ASD DMRs were significantly enriched at promoters, mapped to 596 genes functionally enriched in neuronal development, and overlapped genetic ASD risk. ASD DMRs at CYP2E1 and IRS2 reached genome-wide significance, replicated by pyrosequencing and correlated with expression differences in brain. Methylation at CYP2E1 associated with both ASD diagnosis and genotype within the DMR. In contrast, methylation at IRS2 was unaffected by within DMR genotype but modified by preconceptional maternal prenatal vitamin use. This study therefore identified two potentially useful early epigenetic markers for ASD in placenta.
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Affiliation(s)
- Yihui Zhu
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, University of California, Davis, CA, USA
| | - Charles E Mordaunt
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, University of California, Davis, CA, USA
| | - Dag H Yasui
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, University of California, Davis, CA, USA
| | - Ria Marathe
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, University of California, Davis, CA, USA
| | - Rochelle L Coulson
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, University of California, Davis, CA, USA
| | - Keith W Dunaway
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, University of California, Davis, CA, USA
| | - Julia M Jianu
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, University of California, Davis, CA, USA
| | - Cheryl K Walker
- Department of Obstetrics & Gynecology, School of Medicine, MIND Institute, University of California, Davis, 95616, USA
| | - Sally Ozonoff
- MIND Institute, University of California, Davis, CA, USA
- Department of Psychiatry and Behavioral Sciences, School of Medicine, University of California, Davis, CA, USA
| | - Irva Hertz-Picciotto
- MIND Institute, University of California, Davis, CA, USA
- Department of Public Health Sciences, University of California, Davis, CA, USA
| | - Rebecca J Schmidt
- MIND Institute, University of California, Davis, CA, USA
- Department of Public Health Sciences, University of California, Davis, CA, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, University of California, Davis, CA, USA
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37
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Laufer BI, Hwang H, Vogel Ciernia A, Mordaunt CE, LaSalle JM. Whole genome bisulfite sequencing of Down syndrome brain reveals regional DNA hypermethylation and novel disorder insights. Epigenetics 2019; 14:672-684. [PMID: 31010359 PMCID: PMC6557615 DOI: 10.1080/15592294.2019.1609867] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/08/2019] [Accepted: 04/15/2019] [Indexed: 01/07/2023] Open
Abstract
Down Syndrome (DS) is the most common genetic cause of intellectual disability, in which an extra copy of human chromosome 21 (HSA21) affects regional DNA methylation profiles across the genome. Although DNA methylation has been previously examined at select regulatory regions across the genome in a variety of DS tissues and cells, differentially methylated regions (DMRs) have yet to be examined in an unbiased sequencing-based approach. Here, we present the first analysis of DMRs from whole genome bisulfite sequencing (WGBS) data of human DS and matched control brain, specifically frontal cortex. While no global differences in DNA methylation were observed, we identified 3,152 DS-DMRs across the entire genome, the majority of which were hypermethylated in DS. DS-DMRs were significantly enriched at CpG islands and de-enriched at specific gene body and regulatory regions. Functionally, the hypermethylated DS-DMRs were enriched for one-carbon metabolism, membrane transport, and glutamatergic synaptic signalling, while the hypomethylated DMRs were enriched for proline isomerization, glial immune response, and apoptosis. Furthermore, in a cross-tissue comparison to previous studies of DNA methylation from diverse DS tissues and reference epigenomes, hypermethylated DS-DMRs showed a strong cross-tissue concordance, while a more tissue-specific pattern was observed for the hypomethylated DS-DMRs. Overall, this approach highlights that low-coverage WGBS of clinical samples can identify epigenetic alterations to known biological pathways, which are potentially relevant to therapeutic treatments and include metabolic pathways. These results also provide new insights into the genome-wide effects of genetic alterations on DNA methylation profiles indicative of altered neurodevelopment and brain function.
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Affiliation(s)
- Benjamin I. Laufer
- Department of Medical Microbiology and Immunology, School of Medicine, Genome Center, MIND Institute, University of California, Davis, CA, USA
| | - Hyeyeon Hwang
- Department of Medical Microbiology and Immunology, School of Medicine, Genome Center, MIND Institute, University of California, Davis, CA, USA
| | - Annie Vogel Ciernia
- Department of Medical Microbiology and Immunology, School of Medicine, Genome Center, MIND Institute, University of California, Davis, CA, USA
| | - Charles E. Mordaunt
- Department of Medical Microbiology and Immunology, School of Medicine, Genome Center, MIND Institute, University of California, Davis, CA, USA
| | - Janine M. LaSalle
- Department of Medical Microbiology and Immunology, School of Medicine, Genome Center, MIND Institute, University of California, Davis, CA, USA
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Abstract
Wilson disease (WD) is a complex condition due to copper accumulation mainly in the liver and brain. The genetic base of WD is represented by pathogenic mutations of the copper-transporting gene ATP7B with consequent lack of copper excretion through the biliary tract. ATP7B is the only gene so far identified and known to be responsible for the development of the disease. Our understanding of the disease has been evolving as functional studies have associated specific disease-causing mutations with specific copper-transporter impairments. The most frequent variant in patients of European descent is the H1069Q missense mutation and it has been associated with protein misfolding, aberrant phosphorylation of the P-domain, and altered ATP binding orientation and affinity. Conversely, there is much less understanding of the relation between the genotype and the clinical manifestations of WD. WD is characterized by a highly varied and unpredictable presentation with different combined hepatic, neurological, and psychiatric symptoms. Several studies have attempted to correlate genotype and phenotype but the most recent evidences on larger populations failed to identify a relation between genotype and clinical presentations. Given that so far also modifier genes have not shown convincing association with WD, there is growing interest to identify epigenetic mechanisms of gene expression regulation as underlying the onset and progression of WD phenotype. Evidence from animal models indicated changes in methionine metabolism regulation with possible effects on DNA methylation. Mouse models of WD have indicated transcript level changes of genes related to DNA methylation in fetal and adult livers. And finally, evidence is accumulating regarding DNA methylation changes in patients with WD. It is unexplored how ATP7B genetic mutations combine with epigenetic changes to affect the phenotype. In conclusion, WD is a genetic disease with a complex regulation of its phenotype that includes molecular genetics and epigenetic mechanisms.
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Affiliation(s)
- Valentina Medici
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of California Davis, Sacramento, California, USA
| | - Janine M. LaSalle
- Department of Medical Microbiology and Immunology, University of California Davis, Sacramento, California, USA
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39
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Mordaunt CE, Kieffer DA, Shibata NM, Członkowska A, Litwin T, Weiss KH, Zhu Y, Bowlus CL, Sarkar S, Cooper S, Wan YJY, Ali MR, LaSalle JM, Medici V. Epigenomic signatures in liver and blood of Wilson disease patients include hypermethylation of liver-specific enhancers. Epigenetics Chromatin 2019; 12:10. [PMID: 30709419 PMCID: PMC6357467 DOI: 10.1186/s13072-019-0255-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/21/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Wilson disease (WD) is an autosomal recessive disease caused by mutations in ATP7B encoding a copper transporter. Consequent copper accumulation results in a variable WD clinical phenotype involving hepatic, neurologic, and psychiatric symptoms, without clear genotype-phenotype correlations. The goal of this study was to analyze alterations in DNA methylation at the whole-genome level in liver and blood from patients with WD to investigate epigenomic alterations associated with WD diagnosis and phenotype. We used whole-genome bisulfite sequencing (WGBS) to examine distinct cohorts of WD subjects to determine whether DNA methylation could differentiate patients from healthy subjects and subjects with other liver diseases and distinguish between different WD phenotypes. RESULTS WGBS analyses in liver identified 969 hypermethylated and 871 hypomethylated differentially methylated regions (DMRs) specifically identifying patients with WD, including 18 regions with genome-wide significance. WD-specific liver DMRs were associated with genes enriched for functions in folate and lipid metabolism and acute inflammatory response and could differentiate early from advanced fibrosis in WD patients. Functional annotation revealed that WD-hypermethylated liver DMRs were enriched in liver-specific enhancers, flanking active liver promoters, and binding sites of liver developmental transcription factors, including Hepatocyte Nuclear Factor 4 alpha (HNF4A), Retinoid X Receptor alpha (RXRA), Forkhead Box A1 (FOXA1), and FOXA2. DMRs associated with WD progression were also identified, including 15 with genome-wide significance. However, WD DMRs in liver were not related to large-scale changes in proportions of liver cell types. DMRs detected in blood differentiated WD patients from healthy and disease control subjects, and distinguished between patients with hepatic and neurologic WD manifestations. WD phenotype DMRs corresponded to genes enriched for functions in mental deterioration, abnormal B cell physiology, and as members of the polycomb repressive complex 1 (PRC1). 44 DMRs associated with WD phenotype tested in a small validation cohort had a predictive value of 0.9. CONCLUSIONS We identified a disease-mechanism relevant epigenomic signature of WD that reveals new insights into potential biomarkers and treatments for this complex monogenic disease.
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Affiliation(s)
- Charles E Mordaunt
- Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California Davis, Davis, CA, USA
| | - Dorothy A Kieffer
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of California Davis, Sacramento, CA, USA
| | - Noreene M Shibata
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of California Davis, Sacramento, CA, USA
| | - Anna Członkowska
- 2nd Department of Neurology, Institute of Psychiatry and Neurology, Warsaw, Poland
| | - Tomasz Litwin
- 2nd Department of Neurology, Institute of Psychiatry and Neurology, Warsaw, Poland
| | - Karl-Heinz Weiss
- Department of Internal Medicine IV, University Hospital Heidelberg, Heidelberg, Germany
| | - Yihui Zhu
- Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California Davis, Davis, CA, USA
| | - Christopher L Bowlus
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of California Davis, Sacramento, CA, USA
| | - Souvik Sarkar
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of California Davis, Sacramento, CA, USA
| | - Stewart Cooper
- California Pacific Medical Center, San Francisco, CA, USA
| | - Yu-Jui Yvonne Wan
- Department of Pathology and Laboratory Medicine, University of California Davis, Sacramento, CA, USA
| | - Mohamed R Ali
- Department of Surgery, University of California Davis, Sacramento, CA, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California Davis, Davis, CA, USA
| | - Valentina Medici
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of California Davis, Sacramento, CA, USA.
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40
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Lopez SJ, Segal DJ, LaSalle JM. UBE3A: An E3 Ubiquitin Ligase With Genome-Wide Impact in Neurodevelopmental Disease. Front Mol Neurosci 2019; 11:476. [PMID: 30686997 PMCID: PMC6338038 DOI: 10.3389/fnmol.2018.00476] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/05/2018] [Indexed: 12/11/2022] Open
Abstract
UBE3A is an E3 ubiquitin ligase encoded by an imprinted gene whose maternal deletion or duplication leads to distinct neurodevelopment disorders Angelman and Dup15q syndromes. Despite the known genetic basis of disease, how changes in copy number of a ubiquitin ligase gene can have widespread impact in early brain development is poorly understood. Previous studies have identified a wide array of UBE3A functions, interaction partners, and ubiquitin targets, but no central pathway fully explains its critical role in neurodevelopment. Here, we review recent UBE3A studies that have begun to investigate mechanistic, cellular pathways and the genome-wide impacts of alterations in UBE3A expression levels to gain broader insight into how UBE3A affects the developing brain. These studies have revealed that UBE3A is a multifunctional protein with important nuclear and cytoplasmic regulatory functions that impact proteasome function, Wnt signaling, circadian rhythms, imprinted gene networks, and chromatin. Synaptic functions of UBE3A interact with light exposures and mTOR signaling and are most critical in GABAergic neurons. Understanding the genome-wide influences of UBE3A will help uncover its role in early brain development and ultimately lead to identification of key therapeutic targets for UBE3A-related neurodevelopmental disorders.
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Affiliation(s)
- Simon Jesse Lopez
- Department of Medical Immunology and Microbiology, University of California, Davis, Davis, CA, United States.,Genome Center, University of California, Davis, Davis, CA, United States.,MIND Institute, University of California, Davis, Davis, CA, United States.,Integrative Genetics and Genomics, University of California, Davis, Davis, CA, United States
| | - David J Segal
- Genome Center, University of California, Davis, Davis, CA, United States.,MIND Institute, University of California, Davis, Davis, CA, United States.,Integrative Genetics and Genomics, University of California, Davis, Davis, CA, United States.,Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
| | - Janine M LaSalle
- Department of Medical Immunology and Microbiology, University of California, Davis, Davis, CA, United States.,Genome Center, University of California, Davis, Davis, CA, United States.,MIND Institute, University of California, Davis, Davis, CA, United States.,Integrative Genetics and Genomics, University of California, Davis, Davis, CA, United States
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41
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Vogel Ciernia A, Yasui DH, Pride MC, Durbin-Johnson B, Noronha AB, Chang A, Knotts TA, Rutkowsky JR, Ramsey JJ, Crawley JN, LaSalle JM. MeCP2 isoform e1 mutant mice recapitulate motor and metabolic phenotypes of Rett syndrome. Hum Mol Genet 2018; 27:4077-4093. [PMID: 30137367 PMCID: PMC6240741 DOI: 10.1093/hmg/ddy301] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/10/2018] [Accepted: 08/14/2018] [Indexed: 01/27/2023] Open
Abstract
Mutations in the X-linked gene MECP2 cause the majority of Rett syndrome (RTT) cases. Two differentially spliced isoforms of exons 1 and 2 (MeCP2-e1 and MeCP2-e2) contribute to the diverse functions of MeCP2, but only mutations in exon 1, not exon 2, are observed in RTT. We previously described an isoform-specific MeCP2-e1-deficient male mouse model of a human RTT mutation that lacks MeCP2-e1 while preserving expression of MeCP2-e2. However, RTT patients are heterozygous females that exhibit delayed and progressive symptom onset beginning in late infancy, including neurologic as well as metabolic, immune, respiratory and gastrointestinal phenotypes. Consequently, we conducted a longitudinal assessment of symptom development in MeCP2-e1 mutant females and males. A delayed and progressive onset of motor impairments was observed in both female and male MeCP2-e1 mutant mice, including hind limb clasping and motor deficits in gait and balance. Because these motor impairments were significantly impacted by age-dependent increases in body weight, we also investigated metabolic phenotypes at an early stage of disease progression. Both male and female MeCP2-e1 mutants exhibited significantly increased body fat compared to sex-matched wild-type littermates prior to weight differences. Mecp2e1-/y males exhibited significant metabolic phenotypes of hypoactivity, decreased energy expenditure, increased respiratory exchange ratio, but decreased food intake compared to wild-type. Untargeted analysis of lipid metabolites demonstrated a distinguishable profile in MeCP2-e1 female mutant liver characterized by increased triglycerides. Together, these results demonstrate that MeCP2-e1 mutation in mice of both sexes recapitulates early and progressive metabolic and motor phenotypes of human RTT.
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Affiliation(s)
- Annie Vogel Ciernia
- Department of Medical Microbiology and Immunology, UC Davis School of Medicine, University of California, Davis, CA, USA
- UC Davis Genome Center, University of California, Davis, CA, USA
- UC Davis MIND Institute, University of California, Davis, CA, USA
| | - Dag H Yasui
- Department of Medical Microbiology and Immunology, UC Davis School of Medicine, University of California, Davis, CA, USA
| | - Michael C Pride
- UC Davis MIND Institute, University of California, Davis, CA, USA
- Department of Psychiatry and Behavioral Sciences, UC Davis School of Medicine, University of California, Davis, CA, USA
| | - Blythe Durbin-Johnson
- Department of Public Health Sciences, UC Davis School of Medicine, University of California, Davis, CA, USA
| | - Adriana B Noronha
- Department of Medical Microbiology and Immunology, UC Davis School of Medicine, University of California, Davis, CA, USA
| | - Alene Chang
- Department of Medical Microbiology and Immunology, UC Davis School of Medicine, University of California, Davis, CA, USA
| | - Trina A Knotts
- Department of Molecular Biosciences, UC Davis School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Jennifer R Rutkowsky
- Department of Molecular Biosciences, UC Davis School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Jon J Ramsey
- Department of Molecular Biosciences, UC Davis School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Jacqueline N Crawley
- UC Davis MIND Institute, University of California, Davis, CA, USA
- Department of Psychiatry and Behavioral Sciences, UC Davis School of Medicine, University of California, Davis, CA, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, UC Davis School of Medicine, University of California, Davis, CA, USA
- UC Davis Genome Center, University of California, Davis, CA, USA
- UC Davis MIND Institute, University of California, Davis, CA, USA
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Coulson RL, Powell WT, Yasui DH, Dileep G, Resnick J, LaSalle JM. Prader-Willi locus Snord116 RNA processing requires an active endogenous allele and neuron-specific splicing by Rbfox3/NeuN. Hum Mol Genet 2018; 27:4051-4060. [PMID: 30124848 PMCID: PMC6240740 DOI: 10.1093/hmg/ddy296] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/10/2018] [Accepted: 07/03/2018] [Indexed: 12/18/2022] Open
Abstract
Prader-Willi syndrome (PWS), an imprinted neurodevelopmental disorder characterized by metabolic, sleep and neuropsychiatric features, is caused by the loss of paternal SNORD116, containing only non-coding RNAs (ncRNAs). The primary SNORD116 transcript is processed into small nucleolar RNAs (snoRNAs), which localize to nucleoli, and their spliced host gene 116HG, which is retained at its site of transcription. While functional complementation of the SNORD116 ncRNAs is a desirable goal for treating PWS, the mechanistic requirements of SNORD116 RNA processing are poorly understood. Here we developed and tested a novel transgenic mouse which ubiquitously expresses Snord116 on both a wild-type and a Snord116 paternal deletion (Snord116+/-) background. Interestingly, while the Snord116 transgene was ubiquitously expressed in multiple tissues, splicing of the transgene and production of snoRNAs was limited to brain tissues. Knockdown of Rbfox3, encoding neuron-specific splicing factor neuronal nuclei (NeuN) in Snord116+/--derived neurons, reduced splicing of the transgene in neurons. RNA fluorescence in situ hybridization for 116HG revealed a single significantly larger signal in transgenic mice, demonstrating colocalization of transgenic and endogenous 116HG RNAs. Similarly, significantly increased snoRNA levels were detected in transgenic neuronal nucleoli, indicating that transgenic Snord116 snoRNAs were effectively processed and localized. In contrast, neither transgenic 116HG nor snoRNAs were detectable in either non-neuronal tissues or Snord116+/- neurons. Together, these results demonstrate that exogenous expression and neuron-specific splicing of the Snord116 locus are insufficient to rescue the genetic deficiency of Snord116 paternal deletion. Elucidating the mechanisms regulating Snord116 processing and localization is essential to develop effective gene replacement therapies for PWS.
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Affiliation(s)
- Rochelle L Coulson
- Microbiology and Immunology, Genome Center, and MIND Institute, UC Davis School of Medicine, Davis, CA, USA
| | - Weston T Powell
- Microbiology and Immunology, Genome Center, and MIND Institute, UC Davis School of Medicine, Davis, CA, USA
| | - Dag H Yasui
- Microbiology and Immunology, Genome Center, and MIND Institute, UC Davis School of Medicine, Davis, CA, USA
| | - Gayathri Dileep
- Microbiology and Immunology, Genome Center, and MIND Institute, UC Davis School of Medicine, Davis, CA, USA
| | - James Resnick
- Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, FL, USA
| | - Janine M LaSalle
- Microbiology and Immunology, Genome Center, and MIND Institute, UC Davis School of Medicine, Davis, CA, USA
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Mordaunt CE, Shibata NM, Kieffer DA, Członkowska A, Litwin T, Weiss KH, Gotthardt DN, Olson K, Wei D, Cooper S, Wan YJY, Ali MR, LaSalle JM, Medici V. Epigenetic changes of the thioredoxin system in the tx-j mouse model and in patients with Wilson disease. Hum Mol Genet 2018; 27:3854-3869. [PMID: 30010856 PMCID: PMC6216211 DOI: 10.1093/hmg/ddy262] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 06/02/2018] [Accepted: 07/09/2018] [Indexed: 12/19/2022] Open
Abstract
Wilson disease (WD) is caused by mutations in the copper transporter ATP7B, leading to copper accumulation in the liver and brain. Excess copper inhibits S-adenosyl-L-homocysteine hydrolase, leading to variable WD phenotypes from widespread alterations in DNA methylation and gene expression. Previously, we demonstrated that maternal choline supplementation in the Jackson toxic milk (tx-j) mouse model of WD corrected higher thioredoxin 1 (TNX1) transcript levels in fetal liver. Here, we investigated the effect of maternal choline supplementation on genome-wide DNA methylation patterns in tx-j fetal liver by whole-genome bisulfite sequencing (WGBS). Tx-j Atp7b genotype-dependent differences in DNA methylation were corrected by choline for genes including, but not exclusive to, oxidative stress pathways. To examine phenotypic effects of postnatal choline supplementation, tx-j mice were randomized to one of six treatment groups: with or without maternal and/or continued choline supplementation, and with or without copper chelation with penicillamine (PCA) treatment. Hepatic transcript levels of TXN1 and peroxiredoxin 1 (Prdx1) were significantly higher in mice receiving maternal and continued choline with or without PCA treatment compared to untreated mice. A WGBS comparison of human WD liver and tx-j mouse liver demonstrated a significant overlap of differentially methylated genes associated with ATP7B deficiency. Further, eight genes in the thioredoxin (TXN) pathway were differentially methylated in human WD liver samples. In summary, Atp7b deficiency and choline supplementation have a genome-wide impact, including on TXN system-related genes, in tx-j mice. These findings could explain the variability of WD phenotype and suggest new complementary treatment options for WD.
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Affiliation(s)
- Charles E Mordaunt
- Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California, Davis, California, USA
| | - Noreene M Shibata
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of California, Davis, California, USA
| | - Dorothy A Kieffer
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of California, Davis, California, USA
| | - Anna Członkowska
- Second Department of Neurology, Institute of Psychiatry and Neurology, Warsaw, Poland
| | - Tomasz Litwin
- Second Department of Neurology, Institute of Psychiatry and Neurology, Warsaw, Poland
| | - Karl Heinz Weiss
- Department of Internal Medicine IV, University Hospital Heidelberg, Heidelberg, Germany
| | - Daniel N Gotthardt
- Department of Internal Medicine IV, University Hospital Heidelberg, Heidelberg, Germany
| | - Kristin Olson
- Department of Pathology, University of California, Davis, California, USA
| | - Dongguang Wei
- Department of Pathology, University of California, Davis, California, USA
| | - Stewart Cooper
- California Pacific Medical Center, San Francisco, California, USA
| | - Yu-Jui Yvonne Wan
- Department of Pathology, University of California, Davis, California, USA
| | - Mohamed R Ali
- Department of Surgery, University of California, Davis, California, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California, Davis, California, USA
| | - Valentina Medici
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of California, Davis, California, USA
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Hertz-Picciotto I, Schmidt RJ, Walker CK, Bennett DH, Oliver M, Shedd-Wise KM, LaSalle JM, Giulivi C, Puschner B, Thomas J, Roa DL, Pessah IN, Van de Water J, Tancredi DJ, Ozonoff S. A Prospective Study of Environmental Exposures and Early Biomarkers in Autism Spectrum Disorder: Design, Protocols, and Preliminary Data from the MARBLES Study. Environ Health Perspect 2018; 126:117004. [PMID: 30465702 PMCID: PMC6371714 DOI: 10.1289/ehp535] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 09/21/2018] [Accepted: 09/22/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND Until recently, environmental factors in autism spectrum disorder (ASD) were largely ignored. Over the last decade, altered risks from lifestyle, medical, chemical, and other factors have emerged through various study designs: whole population cohorts linked to diagnostic and/or exposure-related databases, large case-control studies, and smaller cohorts of children at elevated risk for ASD. OBJECTIVES This study aimed to introduce the MARBLES (Markers of Autism Risk in Babies-Learning Early Signs) prospective study and its goals, motivate the enhanced-risk cohort design, describe protocols and main exposures of interest, and present initial descriptive results for the study population. METHODS Families having one or more previous child with ASD were contacted before or during a pregnancy, and once the woman became pregnant, were invited to enroll. Data and biological samples were collected throughout pregnancy, at birth, and until the child's third birthday. Neurodevelopment was assessed longitudinally. The study began enrolling in 2006 and is ongoing. RESULTS As of 30 June 2018, 463 pregnant mothers have enrolled. Most mothers ([Formula: see text]) were thirty years of age or over, including 7.9% who are fourty years of age or over. The sample includes 22% Hispanic and another 25% nonHispanic Black, Asian, or multiracial participants; 24% were born outside the United States. Retention is high: 84% of participants whose pregnancies did not end in miscarriage completed the study or are still currently active. Among children evaluated at 36 months of age, 24% met criteria for ASD, and another 25% were assessed as nonASD nontypical development. CONCLUSION Few environmental studies of ASD prospectively obtain early-life exposure measurements. The MARBLES study fills this gap with extensive data and specimen collection beginning in pregnancy and has achieved excellent retention in an ethnically diverse study population. The 24% familial recurrence risk is consistent with recent reported risks observed in large samples of siblings of children diagnosed with ASD. https://doi.org/10.1289/EHP535.
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Affiliation(s)
- Irva Hertz-Picciotto
- Department of Public Health Sciences, School of Medicine, University of California Davis (UC Davis), Davis, California, USA
- UC Davis MIND (Medical Investigations of Neurodevelopmental Disorders) Institute, UC Davis, Davis, California, USA
| | - Rebecca J Schmidt
- Department of Public Health Sciences, School of Medicine, University of California Davis (UC Davis), Davis, California, USA
- UC Davis MIND (Medical Investigations of Neurodevelopmental Disorders) Institute, UC Davis, Davis, California, USA
| | - Cheryl K Walker
- UC Davis MIND (Medical Investigations of Neurodevelopmental Disorders) Institute, UC Davis, Davis, California, USA
- Department of Obstetrics & Gynecology, School of Medicine, UC Davis, Davis, California, USA
| | - Deborah H Bennett
- Department of Public Health Sciences, School of Medicine, University of California Davis (UC Davis), Davis, California, USA
| | - McKenzie Oliver
- Department of Public Health Sciences, School of Medicine, University of California Davis (UC Davis), Davis, California, USA
- UC Davis MIND (Medical Investigations of Neurodevelopmental Disorders) Institute, UC Davis, Davis, California, USA
| | - Kristine M Shedd-Wise
- Department of Public Health Sciences, School of Medicine, University of California Davis (UC Davis), Davis, California, USA
| | - Janine M LaSalle
- UC Davis MIND (Medical Investigations of Neurodevelopmental Disorders) Institute, UC Davis, Davis, California, USA
- Department of Molecular Biosciences, School of Veterinary Medicine, UC Davis, Davis, California, USA
| | - Cecilia Giulivi
- UC Davis MIND (Medical Investigations of Neurodevelopmental Disorders) Institute, UC Davis, Davis, California, USA
- Department of Medical Microbiology, School of Medicine, UC Davis, Davis, California, USA
| | - Birgit Puschner
- UC Davis MIND (Medical Investigations of Neurodevelopmental Disorders) Institute, UC Davis, Davis, California, USA
- Department of Medical Microbiology, School of Medicine, UC Davis, Davis, California, USA
| | - Jennifer Thomas
- Department of Public Health Sciences, School of Medicine, University of California Davis (UC Davis), Davis, California, USA
- UC Davis MIND (Medical Investigations of Neurodevelopmental Disorders) Institute, UC Davis, Davis, California, USA
| | - Dorcas L Roa
- UC Davis MIND (Medical Investigations of Neurodevelopmental Disorders) Institute, UC Davis, Davis, California, USA
| | - Isaac N Pessah
- UC Davis MIND (Medical Investigations of Neurodevelopmental Disorders) Institute, UC Davis, Davis, California, USA
- Department of Medical Microbiology, School of Medicine, UC Davis, Davis, California, USA
| | - Judy Van de Water
- UC Davis MIND (Medical Investigations of Neurodevelopmental Disorders) Institute, UC Davis, Davis, California, USA
- Department of Rheumatology and Allergy, School of Medicine, UC Davis, Davis, California, USA
| | - Daniel J Tancredi
- Department of Pediatrics, School of Medicine, UC Davis, Davis, California, USA
| | - Sally Ozonoff
- UC Davis MIND (Medical Investigations of Neurodevelopmental Disorders) Institute, UC Davis, Davis, California, USA
- Department of Psychiatry, School of Medicine, UC Davis, Davis, California, USA
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Vogel Ciernia A, Laufer BI, Dunaway KW, Mordaunt CE, Coulson RL, Totah TS, Stolzenberg DS, Frahm JC, Singh-Taylor A, Baram TZ, LaSalle JM, Yasui DH. Experience-dependent neuroplasticity of the developing hypothalamus: integrative epigenomic approaches. Epigenetics 2018; 13:318-330. [PMID: 29613827 DOI: 10.1080/15592294.2018.1451720] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Augmented maternal care during the first postnatal week promotes life-long stress resilience and improved memory compared with the outcome of routine rearing conditions. Recent evidence suggests that this programming commences with altered synaptic connectivity of stress sensitive hypothalamic neurons. However, the epigenomic basis of the long-lived consequences is not well understood. Here, we employed whole-genome bisulfite sequencing (WGBS), RNA-sequencing (RNA-seq), and a multiplex microRNA (miRNA) assay to examine the effects of augmented maternal care on DNA cytosine methylation, gene expression, and miRNA expression. A total of 9,439 differentially methylated regions (DMRs) associated with augmented maternal care were identified in male offspring hypothalamus, as well as a modest but significant decrease in global DNA methylation. Differentially methylated and expressed genes were enriched for functions in neurotransmission, neurodevelopment, protein synthesis, and oxidative phosphorylation, as well as known stress response genes. Twenty prioritized genes were identified as highly relevant to the stress resiliency phenotype. This combined unbiased approach enabled the discovery of novel genes and gene pathways that advance our understanding of the epigenomic mechanisms underlying the effects of maternal care on the developing brain.
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Affiliation(s)
- Annie Vogel Ciernia
- a Department of Medical Microbiology and Immunology , University of California , Davis , CA , USA
| | - Benjamin I Laufer
- a Department of Medical Microbiology and Immunology , University of California , Davis , CA , USA
| | - Keith W Dunaway
- a Department of Medical Microbiology and Immunology , University of California , Davis , CA , USA
| | - Charles E Mordaunt
- a Department of Medical Microbiology and Immunology , University of California , Davis , CA , USA
| | - Rochelle L Coulson
- a Department of Medical Microbiology and Immunology , University of California , Davis , CA , USA
| | - Theresa S Totah
- a Department of Medical Microbiology and Immunology , University of California , Davis , CA , USA
| | | | - Jaime C Frahm
- c Center for Comparative Medicine , University of California , Davis , CA , USA
| | - Akanksha Singh-Taylor
- d Department of Pediatrics and Anatomy/Neurobiology , University of California , Irvine , CA , USA
| | - Tallie Z Baram
- d Department of Pediatrics and Anatomy/Neurobiology , University of California , Irvine , CA , USA
| | - Janine M LaSalle
- a Department of Medical Microbiology and Immunology , University of California , Davis , CA , USA.,e UC Davis Genome Center , UC Davis , Davis , CA , USA.,f UC Davis MIND Institute , UC Davis , Davis , CA , USA
| | - Dag H Yasui
- a Department of Medical Microbiology and Immunology , University of California , Davis , CA , USA
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Dou J, Schmidt RJ, Benke KS, Newschaffer C, Hertz-Picciotto I, Croen LA, Iosif AM, LaSalle JM, Fallin MD, Bakulski KM. Cord blood buffy coat DNA methylation is comparable to whole cord blood methylation. Epigenetics 2018; 13:108-116. [PMID: 29451060 PMCID: PMC5836975 DOI: 10.1080/15592294.2017.1417710] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/29/2017] [Accepted: 12/08/2017] [Indexed: 12/12/2022] Open
Abstract
Cord blood DNA methylation is associated with numerous health outcomes and environmental exposures. Whole cord blood DNA reflects all nucleated blood cell types, while centrifuging whole blood separates red blood cells, generating a white blood cell buffy coat. Both sample types are used in DNA methylation studies. Cell types have unique methylation patterns and processing can impact cell distributions, which may influence comparability. We evaluated differences in cell composition and DNA methylation between cord blood buffy coat and whole cord blood samples. Cord blood DNA methylation was measured with the Infinium EPIC BeadChip (Illumina) in eight individuals, each contributing buffy coat and whole blood samples. We analyzed principal components (PC) of methylation, performed hierarchical clustering, and computed correlations of mean-centered methylation between pairs. We conducted moderated t-tests on single sites and estimated cell composition. DNA methylation PCs were associated with individual (PPC1 = 1.4 × 10-9; PPC2 = 2.9 × 10-5; PPC3 = 3.8 × 10-5; PPC4 = 4.2 × 10-6; PPC5 = 9.9 × 10-13, PPC6 = 1.3 × 10-11) and not with sample type (PPC1-6>0.7). Samples hierarchically clustered by individual. Pearson correlations of mean-centered methylation between paired samples ranged from r = 0.66 to r = 0.87. No individual site significantly differed between buffy coat and whole cord blood when adjusting for multiple comparisons (five sites had unadjusted P<10-5). Estimated cell type proportions did not differ by sample type (P = 0.46), and estimated proportions were highly correlated between paired samples (r = 0.99). Differences in methylation and cell composition between buffy coat and whole cord blood are much lower than inter-individual variation, demonstrating that both sample preparation types can be analytically combined and compared.
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Affiliation(s)
- John Dou
- Department of Epidemiology, School of Public Health, University of Michigan
| | - Rebecca J. Schmidt
- Department of Public Health Sciences, University of California Davis
- University of California Davis, MIND Institute
| | - Kelly S. Benke
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University
| | - Craig Newschaffer
- Department of Epidemiology and Biostatistics, Dornsife School of Public Health, Drexel University
- A.J. Drexel Autism Institute, Drexel University
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences, University of California Davis
- University of California Davis, MIND Institute
| | | | - Ana-Maria Iosif
- Department of Public Health Sciences, University of California Davis
- University of California Davis, MIND Institute
| | - Janine M. LaSalle
- University of California Davis, MIND Institute
- Department of Medical Microbiology and Immunology, Genome Center, University of California Davis
| | - M. Daniele Fallin
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins University
| | - Kelly M. Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan
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47
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Lopez SJ, Dunaway K, Islam MS, Mordaunt C, Vogel Ciernia A, Meguro-Horike M, Horike SI, Segal DJ, LaSalle JM. UBE3A-mediated regulation of imprinted genes and epigenome-wide marks in human neurons. Epigenetics 2017; 12:982-990. [PMID: 28925810 PMCID: PMC5788436 DOI: 10.1080/15592294.2017.1376151] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The dysregulation of genes in neurodevelopmental disorders that lead to social and cognitive phenotypes is a complex, multilayered process involving both genetics and epigenetics. Parent-of-origin effects of deletion and duplication of the 15q11-q13 locus leading to Angelman, Prader-Willi, and Dup15q syndromes are due to imprinted genes, including UBE3A, which is maternally expressed exclusively in neurons. UBE3A encodes a ubiquitin E3 ligase protein with multiple downstream targets, including RING1B, which in turn monoubiquitinates histone variant H2A.Z. To understand the impact of neuronal UBE3A levels on epigenome-wide marks of DNA methylation, histone variant H2A.Z positioning, active H3K4me3 promoter marks, and gene expression, we took a multi-layered genomics approach. We performed an siRNA knockdown of UBE3A in two human neuroblastoma cell lines, including parental SH-SY5Y and the SH(15M) model of Dup15q. Genes differentially methylated across cells with differing UBE3A levels were enriched for functions in gene regulation, DNA binding, and brain morphology. Importantly, we found that altering UBE3A levels had a profound epigenetic effect on the methylation levels of up to half of known imprinted genes. Genes with differential H2A.Z peaks in SH(15M) compared to SH-SY5Y were enriched for ubiquitin and protease functions and associated with autism, hypoactivity, and energy expenditure. Together, these results support a genome-wide epigenetic consequence of altered UBE3A levels in neurons and suggest that UBE3A regulates an imprinted gene network involving DNA methylation patterning and H2A.Z deposition.
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Affiliation(s)
- S Jesse Lopez
- a Medical Immunology and Microbiology , University of California , Davis , CA , USA.,b Genome Center , University of California , Davis , CA , USA.,c MIND Institute, University of California , Davis , CA , USA.,d Integrative Genetics and Genomics , University of California , Davis , CA , USA
| | - Keith Dunaway
- a Medical Immunology and Microbiology , University of California , Davis , CA , USA.,b Genome Center , University of California , Davis , CA , USA.,c MIND Institute, University of California , Davis , CA , USA.,d Integrative Genetics and Genomics , University of California , Davis , CA , USA
| | - M Saharul Islam
- a Medical Immunology and Microbiology , University of California , Davis , CA , USA.,b Genome Center , University of California , Davis , CA , USA.,c MIND Institute, University of California , Davis , CA , USA
| | - Charles Mordaunt
- a Medical Immunology and Microbiology , University of California , Davis , CA , USA.,b Genome Center , University of California , Davis , CA , USA.,c MIND Institute, University of California , Davis , CA , USA
| | - Annie Vogel Ciernia
- a Medical Immunology and Microbiology , University of California , Davis , CA , USA.,b Genome Center , University of California , Davis , CA , USA.,c MIND Institute, University of California , Davis , CA , USA
| | - Makiko Meguro-Horike
- f Advanced Science Research Center , Kanazawa University , 13-1 Takaramachi, Kanazawa , Ishikawa , Japan
| | - Shin-Ichi Horike
- f Advanced Science Research Center , Kanazawa University , 13-1 Takaramachi, Kanazawa , Ishikawa , Japan
| | - David J Segal
- b Genome Center , University of California , Davis , CA , USA.,c MIND Institute, University of California , Davis , CA , USA.,d Integrative Genetics and Genomics , University of California , Davis , CA , USA.,e Biochemistry and Molecular Medicine , University of California , Davis , CA , USA
| | - Janine M LaSalle
- a Medical Immunology and Microbiology , University of California , Davis , CA , USA.,b Genome Center , University of California , Davis , CA , USA.,c MIND Institute, University of California , Davis , CA , USA.,d Integrative Genetics and Genomics , University of California , Davis , CA , USA
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48
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Copping NA, Christian SGB, Ritter DJ, Islam MS, Buscher N, Zolkowska D, Pride MC, Berg EL, LaSalle JM, Ellegood J, Lerch JP, Reiter LT, Silverman JL, Dindot SV. Neuronal overexpression of Ube3a isoform 2 causes behavioral impairments and neuroanatomical pathology relevant to 15q11.2-q13.3 duplication syndrome. Hum Mol Genet 2017; 26:3995-4010. [PMID: 29016856 PMCID: PMC5886211 DOI: 10.1093/hmg/ddx289] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 06/21/2017] [Accepted: 07/10/2017] [Indexed: 01/07/2023] Open
Abstract
Maternally derived copy number gains of human chromosome 15q11.2-q13.3 (Dup15q syndrome or Dup15q) cause intellectual disability, epilepsy, developmental delay, hypotonia, speech impairments, and minor dysmorphic features. Dup15q syndrome is one of the most common and penetrant chromosomal abnormalities observed in individuals with autism spectrum disorder (ASD). Although ∼40 genes are located in the 15q11.2-q13.3 region, overexpression of the ubiquitin-protein E3A ligase (UBE3A) gene is thought to be the predominant molecular cause of the phenotypes observed in Dup15q syndrome. The UBE3A gene demonstrates maternal-specific expression in neurons and loss of maternal UBE3A causes Angelman syndrome, a neurodevelopmental disorder with some overlapping neurological features to Dup15q. To directly test the hypothesis that overexpression of UBE3A is an important underlying molecular cause of neurodevelopmental dysfunction, we developed and characterized a mouse overexpressing Ube3a isoform 2 in excitatory neurons. Ube3a isoform 2 is conserved between mouse and human and known to play key roles in neuronal function. Transgenic mice overexpressing Ube3a isoform 2 in excitatory forebrain neurons exhibited increased anxiety-like behaviors, learning impairments, and reduced seizure thresholds. However, these transgenic mice displayed normal social approach, social interactions, and repetitive motor stereotypies that are relevant to ASD. Reduced forebrain, hippocampus, striatum, amygdala, and cortical volume were also observed. Altogether, these findings show neuronal overexpression of Ube3a isoform 2 causes phenotypes translatable to neurodevelopmental disorders.
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Affiliation(s)
- Nycole A Copping
- MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA, USA
| | | | - Dylan J Ritter
- MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA, USA
- Texas A&M, College Station, TX, USA
| | - M Saharul Islam
- MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA, USA
| | - Nathalie Buscher
- MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA, USA
| | - Dorota Zolkowska
- MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA, USA
| | - Michael C Pride
- MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA, USA
| | - Elizabeth L Berg
- MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA, USA
| | - Janine M LaSalle
- MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA, USA
| | - Jacob Ellegood
- The Hospital for Sick Children, Mouse Imaging Centre, Toronto, ON, Canada
| | - Jason P Lerch
- The Hospital for Sick Children, Mouse Imaging Centre, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Lawrence T Reiter
- Departments of Neurology, Pediatrics and Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jill L Silverman
- MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA, USA
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49
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Vogel Ciernia A, Pride MC, Durbin-Johnson B, Noronha A, Chang A, Yasui DH, Crawley JN, LaSalle JM. Early motor phenotype detection in a female mouse model of Rett syndrome is improved by cross-fostering. Hum Mol Genet 2017; 26:1839-1854. [PMID: 28334953 PMCID: PMC6075042 DOI: 10.1093/hmg/ddx087] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 03/01/2017] [Accepted: 03/03/2017] [Indexed: 12/14/2022] Open
Abstract
Rett syndrome (RTT) is an X-linked neurodevelopmental disorder caused by mutations in the gene encoding methyl CpG binding protein 2 (MeCP2) that occur sporadically in 1:10,000 female births. RTT is characterized by a period of largely normal development followed by regression in language and motor skills at 6-18 months of age. Mecp2 mutant mice recapitulate many of the clinical features of RTT, but the majority of behavioral assessments have been conducted in male Mecp2 hemizygous null mice as offspring of heterozygous dams. Given that RTT patients are predominantly female, we conducted a systematic analysis of developmental milestones, sensory abilities, and motor deficits, following the longitudinal decline of function from early postnatal to adult ages in female Mecp2 heterozygotes of the conventional Bird line (Mecp2tm1.1bird-/+), as compared to their female wildtype littermate controls. Further, we assessed the impact of postnatal maternal environment on developmental milestones and behavioral phenotypes. Cross-fostering to CD1 dams accelerated several developmental milestones independent of genotype, and induced earlier onset of weight gain in adult female Mecp2tm1.1bird-/+ mice. Cross-fostering improved the sensitivity of a number of motor behaviors that resulted in observable deficits in Mecp2tm1.1bird-/+ mice at much earlier (6-7 weeks) ages than were previously reported (6-9 months). Our findings indicate that female Mecp2tm1.1bird-/+ mice recapitulate many of the motor aspects of RTT syndrome earlier than previously appreciated. In addition, rearing conditions may impact the phenotypic severity and improve the ability to detect genotype differences in female Mecp2 mutant mice.
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Affiliation(s)
| | | | | | - Adriana Noronha
- Medical Microbiology and Immunology
- Genome Center
- MIND Institute
| | - Alene Chang
- Medical Microbiology and Immunology
- Genome Center
- MIND Institute
| | - Dag H. Yasui
- Medical Microbiology and Immunology
- Genome Center
- MIND Institute
- Department of Psychiatry and Behavioral Sciences
| | | | - Janine M. LaSalle
- Medical Microbiology and Immunology
- Genome Center
- MIND Institute
- Department of Psychiatry and Behavioral Sciences
- Center for Children's Environmental Health, University of California, Davis, UC Davis, CA, USA
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50
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Breton CV, Marsit CJ, Faustman E, Nadeau K, Goodrich JM, Dolinoy DC, Herbstman J, Holland N, LaSalle JM, Schmidt R, Yousefi P, Perera F, Joubert BR, Wiemels J, Taylor M, Yang IV, Chen R, Hew KM, Freeland DMH, Miller R, Murphy SK. Small-Magnitude Effect Sizes in Epigenetic End Points are Important in Children's Environmental Health Studies: The Children's Environmental Health and Disease Prevention Research Center's Epigenetics Working Group. Environ Health Perspect 2017; 125:511-526. [PMID: 28362264 PMCID: PMC5382002 DOI: 10.1289/ehp595] [Citation(s) in RCA: 192] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 08/24/2016] [Accepted: 09/27/2016] [Indexed: 05/15/2023]
Abstract
BACKGROUND Characterization of the epigenome is a primary interest for children's environmental health researchers studying the environmental influences on human populations, particularly those studying the role of pregnancy and early-life exposures on later-in-life health outcomes. OBJECTIVES Our objective was to consider the state of the science in environmental epigenetics research and to focus on DNA methylation and the collective observations of many studies being conducted within the Children's Environmental Health and Disease Prevention Research Centers, as they relate to the Developmental Origins of Health and Disease (DOHaD) hypothesis. METHODS We address the current laboratory and statistical tools available for epigenetic analyses, discuss methods for validation and interpretation of findings, particularly when magnitudes of effect are small, question the functional relevance of findings, and discuss the future for environmental epigenetics research. DISCUSSION A common finding in environmental epigenetic studies is the small-magnitude epigenetic effect sizes that result from such exposures. Although it is reasonable and necessary that we question the relevance of such small effects, we present examples in which small effects persist and have been replicated across populations and across time. We encourage a critical discourse on the interpretation of such small changes and further research on their functional relevance for children's health. CONCLUSION The dynamic nature of the epigenome will require an emphasis on future longitudinal studies in which the epigenome is profiled over time, over changing environmental exposures, and over generations to better understand the multiple ways in which the epigenome may respond to environmental stimuli.
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Affiliation(s)
| | | | | | - Kari Nadeau
- Stanford University, Palo Alto, California, USA
- University of California, Berkeley, Berkeley, California, USA
| | | | | | | | - Nina Holland
- University of California, Berkeley, Berkeley, California, USA
| | | | | | - Paul Yousefi
- University of California, Berkeley, Berkeley, California, USA
| | | | - Bonnie R. Joubert
- National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina
| | - Joseph Wiemels
- University of California at San Francisco, San Francisco, California, USA
| | | | - Ivana V. Yang
- University of Colorado, Denver, Colorado, USA
- National Jewish Health, Denver, Colorado, USA
| | - Rui Chen
- Stanford University, Palo Alto, California, USA
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