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Mouat JS, Krigbaum NY, Hakam S, Thrall E, Mellis J, Yasui DH, Cirillo PM, Ludena Y, Schmidt RJ, La Merrill MA, Hertz-Picciotto I, Cohn BA, LaSalle JM. Females with autism spectrum disorders show stronger DNA methylation signatures than males in perinatal tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.11.603098. [PMID: 39026708 PMCID: PMC11257592 DOI: 10.1101/2024.07.11.603098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Autism spectrum disorder (ASD) comprises a group of neurodevelopmental conditions currently diagnosed by behavioral assessment in childhood, with reported underdiagnosis in females. Though diagnosis in early life is linked to improved outcomes, we currently lack objective screening tools for newborns. To address this gap, we sought to identify a sex-specific DNA methylation signature for ASD using perinatal tissues that reflect dysregulation in the brain. DNA methylation was assayed from ASD and typically developing (TD) newborn blood, umbilical cord blood, placenta, and post-mortem cortex samples using whole genome bisulfite sequencing (WGBS) in a total of 511 samples. We found that methylation levels of differentially methylated regions (DMRs) differentiated samples by ASD diagnosis in females more than males across the perinatal tissues. We tested three theories for ASD sex differences in newborn blood, finding epigenetic support for an X chromosome-related female protective effect, as well as a high replication rate of DMRs (48.1%) in females across two independent cohorts. In our pan-tissue analysis, three genes (X-linked BCOR, GALNT9, OPCML) mapped to ASD DMRs replicated in all four female tissues. ASD DMRs from all tissues were enriched for neuro-related processes (females) and SFARI ASD-risk genes (females and males). Overall, we found a highly replicated methylation signature of ASD in females across perinatal tissues that reflected dysregulation in the brain and involvement of X chromosome epigenetics. This comparative study of perinatal tissues shows the promise of newborn blood DNA methylation biomarkers for early detection of females at risk for ASD and emphasizes the importance of sex-stratification in ASD studies.
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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
| | - Nickilou Y Krigbaum
- Child Health and Development Studies, Public Health Institute, Berkeley, CA USA
| | - Sophia Hakam
- 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
| | - Emily Thrall
- 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
| | - Julia Mellis
- 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
| | - Dag H Yasui
- 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
| | - Piera M Cirillo
- Child Health and Development Studies, Public Health Institute, Berkeley, CA USA
| | - Yunin Ludena
- MIND Institute, 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, University of California, Davis, CA USA
- Department of Public Health Sciences, University of California, Davis, CA USA
| | - Michele A La Merrill
- Perinatal Origins of Disparities Center, University of California, Davis, CA USA
- Genome Center, University of California, Davis, CA USA
- Department of Environmental Toxicology, University of California, Davis, CA USA
- Environmental Health Sciences Center, University of California, Davis, CA USA
| | - Irva Hertz-Picciotto
- Perinatal Origins of Disparities Center, University of California, Davis, CA USA
- MIND Institute, University of California, Davis, CA USA
- Department of Public Health Sciences, University of California, Davis, CA USA
- Environmental Health Sciences Center, University of California, Davis, CA USA
| | - Barbara A Cohn
- Child Health and Development Studies, Public Health Institute, Berkeley, 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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Kaplan ZB, Pearce EN, Lee SY, Shin HM, Schmidt RJ. Maternal Thyroid Dysfunction During Pregnancy as an Etiologic Factor in Autism Spectrum Disorder: Challenges and Opportunities for Research. Thyroid 2024; 34:144-157. [PMID: 38149625 PMCID: PMC10884547 DOI: 10.1089/thy.2023.0391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
Background: Autism spectrum disorder (ASD) is a neurodevelopmental condition with unknown etiology. Both genetic and environmental factors have been associated with ASD. Environmental exposures during the prenatal period may play an important role in ASD development. This narrative review critically examines the evidence for a relationship between maternal thyroid dysfunction during pregnancy and ASD in the child. Summary: Studies that assessed the associations of hypothyroidism, hyperthyroidism, hypothyroxinemia, thyroid hormone concentrations, or autoimmune thyroid disease with ASD outcomes were included. Most research focused on the relationship between hypothyroidism and ASD. Multiple population-based studies found that maternal hypothyroidism was associated with higher likelihood of an ASD diagnosis in offspring. Associations with other forms of maternal thyroid dysfunction were less consistent. Findings may have been affected by misclassification bias, survival bias, or publication bias. Studies using medical records may have misclassified subclinical thyroid dysfunction as euthyroidism. Two studies that assessed children at early ages may have misclassified those with ASD as typically developing. Most studies adjusted for maternal body mass index (BMI) and/or mental illness, but not interpregnancy interval or pesticide exposure, all factors associated with fetal survival and ASD. Most studies reported a combination of null and statistically significant findings, although publication bias is still possible. Conclusions: Overall, evidence supported a positive association between maternal thyroid dysfunction during pregnancy and ASD outcomes in the child, especially for hypothyroidism. Future studies could reduce misclassification bias by using laboratory measures instead of medical records to ascertain thyroid dysfunction and evaluating children for ASD at an age when it can be reliably detected. Survival bias could be further mitigated by adjusting models for more factors associated with fetal survival and ASD. Additional research is needed to comprehensively understand the roles of maternal levothyroxine treatment, iodine deficiency, or exposure to thyroid-disrupting compounds in the relationship between maternal thyroid dysfunction and child ASD outcomes.
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Affiliation(s)
- Zoe B Kaplan
- Department of Public Health Sciences, School of Medicine, University of California, Davis, Davis, California, USA
| | - Elizabeth N Pearce
- Department of Medicine, Section of Endocrinology, Diabetes, Nutrition, and Weight Management, Boston University Chobanian & Avesidian School of Medicine, Boston, Massachusetts, USA
| | - Sun Y Lee
- Department of Medicine, Section of Endocrinology, Diabetes, Nutrition, and Weight Management, Boston University Chobanian & Avesidian School of Medicine, Boston, Massachusetts, USA
| | - Hyeong-Moo Shin
- Department of Environmental Science, Baylor University, Waco, Texas, USA
| | - Rebecca J Schmidt
- Department of Public Health Sciences, School of Medicine, University of California, Davis, Davis, California, USA
- The MIND Institute, School of Medicine, University of California, Davis, Sacramento, California, USA
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Noort RJ, Zhu H, Flemmer RT, Moore CS, Belbin TJ, Esseltine JL. Apically localized PANX1 impacts neuroepithelial expansion in human cerebral organoids. Cell Death Discov 2024; 10:22. [PMID: 38212304 PMCID: PMC10784521 DOI: 10.1038/s41420-023-01774-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/01/2023] [Accepted: 12/11/2023] [Indexed: 01/13/2024] Open
Abstract
Dysfunctional paracrine signaling through Pannexin 1 (PANX1) channels is linked to several adult neurological pathologies and emerging evidence suggests that PANX1 plays an important role in human brain development. It remains unclear how early PANX1 influences brain development, or how loss of PANX1 alters the developing human brain. Using a cerebral organoid model of early human brain development, we find that PANX1 is expressed at all stages of organoid development from neural induction through to neuroepithelial expansion and maturation. Interestingly, PANX1 cellular distribution and subcellular localization changes dramatically throughout cerebral organoid development. During neural induction, PANX1 becomes concentrated at the apical membrane domain of neural rosettes where it co-localizes with several apical membrane adhesion molecules. During neuroepithelial expansion, PANX1-/- organoids are significantly smaller than control and exhibit significant gene expression changes related to cell adhesion, WNT signaling and non-coding RNAs. As cerebral organoids mature, PANX1 expression is significantly upregulated and is primarily localized to neuronal populations outside of the ventricular-like zones. Ultimately, PANX1 protein can be detected in all layers of a 21-22 post conception week human fetal cerebral cortex. Together, these results show that PANX1 is dynamically expressed by numerous cell types throughout embryonic and early fetal stages of human corticogenesis and loss of PANX1 compromises neuroepithelial expansion due to dysregulation of cell-cell and cell-matrix adhesion, perturbed intracellular signaling, and changes to gene regulation.
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Affiliation(s)
- Rebecca J Noort
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, A1B 3V6, NL, Canada
| | - Hanrui Zhu
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, A1B 3V6, NL, Canada
| | - Robert T Flemmer
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, A1B 3V6, NL, Canada
| | - Craig S Moore
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, A1B 3V6, NL, Canada
| | - Thomas J Belbin
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, A1B 3V6, NL, Canada
- Discipline of Oncology, Faculty of sp. Medicine, Memorial University of Newfoundland, St. John's, A1B 3V6, NL, Canada
| | - Jessica L Esseltine
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, A1B 3V6, NL, Canada.
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Bečeheli I, Horvatiček M, Perić M, Nikolić B, Holuka C, Klasić M, Ivanišević M, Starčević M, Desoye G, Hranilović D, Turner JD, Štefulj J. Methylation of serotonin regulating genes in cord blood cells: association with maternal metabolic parameters and correlation with methylation in peripheral blood cells during childhood and adolescence. Clin Epigenetics 2024; 16:4. [PMID: 38172913 PMCID: PMC10765867 DOI: 10.1186/s13148-023-01610-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Serotonin (5-hydroxytryptamine, 5-HT) signaling is involved in neurodevelopment, mood regulation, energy metabolism, and other physiological processes. DNA methylation plays a significant role in modulating the expression of genes responsible for maintaining 5-HT balance, such as 5-HT transporter (SLC6A4), monoamine oxidase A (MAOA), and 5-HT receptor type 2A (HTR2A). Maternal metabolic health can influence long-term outcomes in offspring, with DNA methylation mediating these effects. We investigated associations between maternal metabolic parameters-pre-pregnancy body mass index (pBMI), gestational weight gain (GWG), and glucose tolerance status (GTS), i.e., gestational diabetes mellitus (GDM) versus normal glucose tolerance (NGT)-and cord blood methylation of SLC6A4, MAOA, and HTR2A in participants from our PlaNS birth cohort. CpG sites (15, 9, and 2 in each gene, respectively) were selected based on literature and in silico data. Methylation levels were quantified by bisulfite pyrosequencing. We also examined the stability of methylation patterns in these genes in circulating blood cells from birth to adolescence using longitudinal DNA methylation data from the ARIES database. RESULTS None of the 203 PlaNS mothers included in this study had preexisting diabetes, 99 were diagnosed with GDM, and 104 had NGT; all neonates were born at full term by planned Cesarean section. Methylation at most CpG sites differed between male and female newborns. SLC6A4 methylation correlated inversely with maternal pBMI and GWG, while methylation at HTR2A site -1665 correlated positively with GWG. None of the maternal metabolic parameters statistically associated with MAOA methylation. DNA methylation data in cord blood and peripheral blood at ages 7 and 15 years were available for 808 participants from the ARIES database; 4 CpG sites (2 in SLC6A4 and 2 in HTR2A) overlapped between the PlaNS and ARIES cohorts. A positive correlation between methylation levels in cord blood and peripheral blood at 7 and 15 years of age was observed for both SLC6A4 and HTR2A CpG sites. CONCLUSIONS Methylation of 5-HT regulating genes in cord blood cells is influenced by neonatal sex, with maternal metabolism playing an additional role. Inter-individual variations present in circulating blood cells at birth are still pronounced in childhood and adolescence.
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Affiliation(s)
- Ivona Bečeheli
- Division of Molecular Biology, Ruđer Bošković Institute, 10000, Zagreb, Croatia
| | - Marina Horvatiček
- Division of Molecular Biology, Ruđer Bošković Institute, 10000, Zagreb, Croatia
| | - Maja Perić
- Division of Molecular Biology, Ruđer Bošković Institute, 10000, Zagreb, Croatia
| | - Barbara Nikolić
- Department of Biology, Faculty of Science, University of Zagreb, 10000, Zagreb, Croatia
| | - Cyrielle Holuka
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354, Esch-sur-Alzette, Luxembourg
- Faculty of Science, University of Luxembourg, 4365, Belval, Luxembourg
| | - Marija Klasić
- Department of Biology, Faculty of Science, University of Zagreb, 10000, Zagreb, Croatia
| | - Marina Ivanišević
- Department of Obstetrics and Gynecology, University Hospital Centre Zagreb, 10000, Zagreb, Croatia
| | - Mirta Starčević
- Department of Neonatology, University Hospital Centre Zagreb, 10000, Zagreb, Croatia
| | - Gernot Desoye
- Department of Obstetrics and Gynecology, Medical University of Graz, 8036, Graz, Austria
| | - Dubravka Hranilović
- Department of Biology, Faculty of Science, University of Zagreb, 10000, Zagreb, Croatia
| | - Jonathan D Turner
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354, Esch-sur-Alzette, Luxembourg
| | - Jasminka Štefulj
- Division of Molecular Biology, Ruđer Bošković Institute, 10000, Zagreb, Croatia.
- University Department of Psychology, Catholic University of Croatia, 10000, Zagreb, Croatia.
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Alberca CD, Papale LA, Madrid A, Alisch RS. Hippocampal and peripheral blood DNA methylation signatures correlate at the gene and pathway level in a mouse model of autism. Hum Mol Genet 2023; 32:3312-3322. [PMID: 37658766 DOI: 10.1093/hmg/ddad137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/02/2023] [Accepted: 08/21/2023] [Indexed: 09/05/2023] Open
Abstract
Autism spectrum disorders (ASD) are polygenic multifactorial disorders influenced by environmental factors. ASD-related differential DNA methylation has been found in human peripheral tissues, such as placenta, paternal sperm, buccal epithelium, and blood. However, these data lack direct comparison of DNA methylation levels with brain tissue from the same individual to determine the extent that peripheral tissues are surrogates for behavior-related disorders. Here, whole genome methylation profiling at all the possible sites throughout the mouse genome (>25 million) from both brain and blood tissues revealed novel insights into the systemic contributions of DNA methylation to ASD. Sixty-six differentially methylated regions (DMRs) share the same genomic coordinates in these two tissues, many of which are linked to risk genes for neurodevelopmental disorders and intellectual disabilities (e.g. Prkch, Ptn, Hcfc1, Mid1, and Nfia). Gene ontological pathways revealed a significant number of common terms between brain and blood (N = 65 terms), and nearly half (30/65) were associated with brain/neuronal development. Furthermore, seven DMR-associated genes among these terms contain methyl-sensitive transcription factor sequence motifs within the DMRs of both tissues; four of them (Cux2, Kcnip2, Fgf13, and Mrtfa) contain the same methyl-sensitive transcription factor binding sequence motifs (HES1/2/5, TBX2 and TFAP2C), suggesting DNA methylation influences the binding of common transcription factors required for gene expression. Together, these findings suggest that peripheral blood is a good surrogate tissue for brain and support that DNA methylation contributes to altered gene regulation in the pathogenesis of ASD.
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Affiliation(s)
- Carolina D Alberca
- Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, 600 Highland Avenue, Madison, WI 53705, United States
| | - Ligia A Papale
- Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, 600 Highland Avenue, Madison, WI 53705, United States
| | - Andy Madrid
- Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, 600 Highland Avenue, Madison, WI 53705, United States
| | - Reid S Alisch
- Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, 600 Highland Avenue, Madison, WI 53705, United States
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McCanlies EC, Gu JK, Kashon M, Yucesoy B, Ma CC, Sanderson WT, Kim K, Ludeña-Rodriguez YJ, Hertz-Picciotto I. Parental occupational exposure to solvents and autism spectrum disorder: An exploratory look at gene-environment interactions. ENVIRONMENTAL RESEARCH 2023; 228:115769. [PMID: 37004853 PMCID: PMC10273405 DOI: 10.1016/j.envres.2023.115769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 05/16/2023]
Affiliation(s)
- Erin C McCanlies
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV, 26505, USA.
| | - Ja Kook Gu
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV, 26505, USA
| | - Michael Kashon
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV, 26505, USA
| | - Berran Yucesoy
- Former Affiliate of Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV, 26505, USA
| | - Claudia C Ma
- Former Affiliate of Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV, 26505, USA
| | | | - Kyoungmi Kim
- Department of Public Health Sciences, University of California, Davis, CA, 95616, USA
| | | | - Irva Hertz-Picciotto
- Department of Public Health Sciences, University of California, Davis, CA, 95616, USA
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Wang T, Liu L, Fan T, Xia K, Sun Z. Shared and divergent contribution of vitamin A and oxytocin to the aetiology of autism spectrum disorder. Comput Struct Biotechnol J 2023; 21:3109-3123. [PMID: 38213898 PMCID: PMC10782014 DOI: 10.1016/j.csbj.2023.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/15/2023] [Accepted: 05/15/2023] [Indexed: 01/13/2024] Open
Abstract
Rare genetic variations contribute to the heterogeneity of autism spectrum disorder (ASD) and the responses to various interventions for ASD probands. However, the associated molecular underpinnings remain unclear. Herein, we estimated the association between rare genetic variations in 410 vitamin A (VA)-related genes (VARGs) and ASD aetiology using publicly available de novo mutations (DNMs), rare inherited variants, and copy number variations (CNVs) from about 50,000 ASD probands and 20,000 normal controls (discovery and validation cohorts). Additionally, given the functional relevance of VA and oxytocin, we systematically compared the similarities and differences between VA and oxytocin with respect to ASD aetiology and evaluated their potential for clinical applications. Functional DNMs and pathogenic CNVs in VARGs contributed to ASD pathogenesis in the discovery and validation cohorts. Additionally, 324 potential VA-related biomarkers were identified, 243 of which were shared with previously identified oxytocin-related biomarkers, while 81 were unique VA biomarkers. Moreover, multivariable logistic regression analysis revealed that both VA- and oxytocin-related biomarkers were able to predict ASD aetiology for individuals carrying functional DNM in corresponding biomarkers with an average precision of 0.94. As well as, convergent and divergent functions were also identified between VA- and oxytocin-related biomarkers. The findings of this study provide a basis for future studies aimed at understanding the pathophysiological mechanisms underlying ASD while also defining a set of potential molecular biomarkers for adjuvant diagnosis and intervention in ASD.
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Affiliation(s)
- Tao Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Kaifu District, Changsha, Hunan 410078, China
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Liqiu Liu
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Tianda Fan
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Kaifu District, Changsha, Hunan 410078, China
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Kun Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Kaifu District, Changsha, Hunan 410078, China
- CAS Center for Excellence in Brain Science and Intelligences Technology (CEBSIT), Shanghai 200031, China
- Hengyang Medical School, University of South China, Hengyang, Hunan 410078, China
| | - Zhongsheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Chinese Academy of Sciences, Beijing 100101, China
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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] [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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9
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Hu J, Xu X, Li J, Jiang Y, Hong X, Rexrode KM, Wang G, Hu FB, Zhang H, Karmaus WJ, Wang X, Liang L. Sex differences in the intergenerational link between maternal and neonatal whole blood DNA methylation: a genome-wide analysis in 2 birth cohorts. Clin Epigenetics 2023; 15:51. [PMID: 36966332 PMCID: PMC10040137 DOI: 10.1186/s13148-023-01442-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 02/06/2023] [Indexed: 03/27/2023] Open
Abstract
BACKGROUND The mother-child inheritance of DNA methylation (DNAm) variations could contribute to the inheritance of disease susceptibility across generations. However, no study has investigated patterns of mother-child associations in DNAm at the genome-wide scale. It remains unknown whether there are sex differences in mother-child DNAm associations. RESULTS Using genome-wide DNAm profiling data (721,331 DNAm sites, including 704,552 on autosomes and 16,779 on the X chromosome) of 396 mother-newborn pairs (54.5% male) from the Boston Birth Cohort, we found significant sex differences in mother-newborn correlations in genome-wide DNAm patterns (Spearman's rho = 0.91-0.98; p = 4.0 × 10-8), with female newborns having stronger correlations. Sex differences in correlations were attenuated but remained significant after excluding X-chromosomal DNAm sites (Spearman's rho = 0.91-0.98; p = 0.035). Moreover, 89,267 DNAm sites (12.4% of all analyzed, including 88,051 [12.5% of analyzed] autosomal and 1,216 [7.2% of analyzed] X-chromosomal sites) showed significant mother-newborn associations in methylation levels, and the top autosomal DNAm sites had high heritability than the genome-wide background (e.g., the top 100 autosomal DNAm sites had a medium h2 of 0.92). Additionally, significant interactions between newborn sex and methylation levels were observed for 11 X-chromosomal and 4 autosomal DNAm sites that were mapped to genes that have been associated with sex-specific disease/traits or early development (e.g., EFHC2, NXY, ADCYAP1R1, and BMP4). Finally, 18,769 DNAm sites (14,482 [77.2%] on the X chromosome) showed mother-newborn differences in methylation levels that were significantly associated with newborn sex, and the top autosomal DNAm sites had relatively small heritability (e.g., the top 100 autosomal DNAm sites had a medium h2 of 0.23). These DNAm sites were mapped to 2,532 autosomal genes and 978 X-chromosomal genes with significant enrichment in pathways involved in neurodegenerative and psychological diseases, development, neurophysiological process, immune response, and sex-specific cancers. Replication analysis in the Isle of Wight birth cohort yielded consistent results. CONCLUSION In two independent birth cohorts, we demonstrated strong mother-newborn correlations in whole blood DNAm on both autosomes and ChrX, and such correlations vary substantially by sex. Future studies are needed to examine to what extent our findings contribute to developmental origins of pediatric and adult diseases with well-observed sex differences.
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Affiliation(s)
- Jie Hu
- Division of Women's Health, Department of Medicine, Bigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA
| | - Xin Xu
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA
| | - Jun Li
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yu Jiang
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Xiumei Hong
- Center On the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Kathryn M Rexrode
- Division of Women's Health, Department of Medicine, Bigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Guoying Wang
- Center On the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Frank B Hu
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Wilfried J Karmaus
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Xiaobin Wang
- Center On the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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10
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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. ENVIRONMENTAL RESEARCH 2023; 220:115227. [PMID: 36608759 PMCID: PMC10518186 DOI: 10.1016/j.envres.2023.115227] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [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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11
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Feil D, Abrishamcar S, Christensen GM, Vanker A, Koen N, Kilanowski A, Hoffman N, Wedderburn CJ, Donald KA, Kobor MS, Zar HJ, Stein DJ, Hüls A. DNA methylation as a potential mediator of the association between indoor air pollution and neurodevelopmental delay in a South African birth cohort. Clin Epigenetics 2023; 15:31. [PMID: 36855151 PMCID: PMC9972733 DOI: 10.1186/s13148-023-01444-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 02/08/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Exposure to indoor air pollution during pregnancy has been linked to neurodevelopmental delay in toddlers. Epigenetic modification, particularly DNA methylation (DNAm), may explain this link. In this study, we employed three high-dimensional mediation analysis methods (HIMA, DACT, and gHMA) followed by causal mediation analysis to identify differentially methylated CpG sites and genes that mediate the association between indoor air pollution and neurodevelopmental delay. Analyses were performed using data from 142 mother to child pairs from a South African birth cohort, the Drakenstein Child Health Study. DNAm from cord blood was measured using the Infinium MethylationEPIC and HumanMethylation450 arrays. Neurodevelopment was assessed at age 2 years using the Bayley Scores of Infant and Toddler Development, 3rd edition across four domains (cognitive development, general adaptive behavior, language, and motor function). Particulate matter with an aerodynamic diameter of 10 μm or less (PM10) was measured inside participants' homes during the second trimester of pregnancy. RESULTS A total of 29 CpG sites and 4 genes (GOPC, RP11-74K11.1, DYRK1A, RNMT) were identified as significant mediators of the association between PM10 and cognitive neurodevelopment. The estimated proportion mediated (95%-confidence interval) ranged from 0.29 [0.01, 0.86] for cg00694520 to 0.54 [0.11, 1.56] for cg05023582. CONCLUSIONS Our findings suggest that DNAm may mediate the association between prenatal PM10 exposure and cognitive neurodevelopment. DYRK1A and several genes that our CpG sites mapped to, including CNKSR1, IPO13, IFNGR1, LONP2, and CDH1, are associated with biological pathways implicated in cognitive neurodevelopment and three of our identified CpG sites (cg23560546 [DAPL1], cg22572779 [C6orf218], cg15000966 [NT5C]) have been previously associated with fetal brain development. These findings are novel and add to the limited literature investigating the relationship between indoor air pollution, DNAm, and neurodevelopment, particularly in low- and middle-income country settings and non-white populations.
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Affiliation(s)
- Dakotah Feil
- Department of Epidemiology, Rollins School of Public Health, Emory University, 1518 Clifton Road, Atlanta, GA, 30322, USA
| | - Sarina Abrishamcar
- Department of Epidemiology, Rollins School of Public Health, Emory University, 1518 Clifton Road, Atlanta, GA, 30322, USA
| | - Grace M Christensen
- Department of Epidemiology, Rollins School of Public Health, Emory University, 1518 Clifton Road, Atlanta, GA, 30322, USA
| | - Aneesa Vanker
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, SA and SA-MRC Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Nastassja Koen
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
- South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, University of Cape Town, Cape Town, South Africa
| | - Anna Kilanowski
- Department of Epidemiology, Rollins School of Public Health, Emory University, 1518 Clifton Road, Atlanta, GA, 30322, USA
- German Research Center for Environmental Health, Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
- Institute for Medical Information Processing, Biometry, and Epidemiology, Pettenkofer School of Public Health, LMU Munich, Munich, Germany
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, University of Munich Medical Center, Munich, Germany
| | - Nadia Hoffman
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - Catherine J Wedderburn
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, SA and SA-MRC Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK
| | - Kirsten A Donald
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, SA and SA-MRC Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Michael S Kobor
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC, Canada
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, SA and SA-MRC Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Dan J Stein
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
- South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, University of Cape Town, Cape Town, South Africa
| | - Anke Hüls
- Department of Epidemiology, Rollins School of Public Health, Emory University, 1518 Clifton Road, Atlanta, GA, 30322, USA.
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
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12
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Pu Y, An J, Mo X. Liquid Biopsy in Adverse Neurodevelopment of Children: Problems and Prospects. Methods Mol Biol 2023; 2695:337-349. [PMID: 37450130 DOI: 10.1007/978-1-0716-3346-5_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Neurodevelopmental disorders in children have an important impact on the quality of life in the whole life cycle. Severe neurodevelopmental disorders will become a serious social and family burden and an important social and economic problem. The early and middle childhood is the critical period of children's neurodevelopment. Early diagnosis of neurological disorders plays an important role in guiding children's neurological development. Existing monitoring tools lack prenatal and even early assessment of children's neurodevelopment, so reliable biomarkers are conducive to personalized care at an earlier stage. In this review, we will discuss different methods of neurodevelopmental monitoring at different times and the role and evaluation of liquid biopsy in neurodevelopmental monitoring.
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Affiliation(s)
- Yiwei Pu
- Department of Cardiothoracic Surgery, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Jia An
- Department of Cardiothoracic Surgery, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Xuming Mo
- Department of Cardiothoracic Surgery, Children's Hospital of Nanjing Medical University, Nanjing, China.
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13
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Anna S, Magdalena J. Editorial: Epigenomic contributions to autism spectrum disorders. Front Neurosci 2023; 17:1177378. [PMID: 37144095 PMCID: PMC10151758 DOI: 10.3389/fnins.2023.1177378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/27/2023] [Indexed: 05/06/2023] Open
Affiliation(s)
- Starnawska Anna
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, CGPM, and Center for Integrative Sequencing, iSEQ, Aarhus, Denmark
- *Correspondence: Starnawska Anna
| | - Janecka Magdalena
- Seaver Autism Center, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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14
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Manoj G, Anjali K, Presannan A, Melethadathil N, Suravajhala R, Suravajhala P. Epigenetics, genomics imprinting and non-coding RNAs. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 197:93-104. [PMID: 37019598 DOI: 10.1016/bs.pmbts.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Epigenetic traits are heritable phenotypes caused by alterations in chromosomes rather than DNA sequences. The actual epigenetic expression of the somatic cells of a species is identical, however, they may show distinct subtleties in various cell types in which they may be affected. Several recent studies demonstrated that the epigenetic system plays a very important role in regulating all biological natural processes in the body from birth to death. We outline the essential elements of epigenetics, genomic imprinting, and non-coding RNAs in this mini-review.
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Affiliation(s)
- Gautham Manoj
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Krishna Anjali
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Anandhu Presannan
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | | | - Renuka Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India.
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15
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Liao Q, Tang P, Pan D, Song Y, Lei L, Liang J, Liu B, Lin M, Huang H, Mo M, Huang C, Wei M, Liu S, Huang D, Qiu X. Association of serum per- and polyfluoroalkyl substances and gestational anemia during different trimesters in Zhuang ethnic pregnancy women of Guangxi, China. CHEMOSPHERE 2022; 309:136798. [PMID: 36220436 DOI: 10.1016/j.chemosphere.2022.136798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Gestational anemia is a complication of pregnancy, and a low level of hemoglobin (Hb) has been linked to adverse pregnancy outcomes. Previous studies reported that PFASs were more strongly associated with Hb than red blood cells, indicating that Hb is more susceptible to the effect of PFASs. However, the evidences regarding the effects of per- and polyfluoroalkyl substances (PFASs) on gestational anemia are currently limited. Therefore, it is important to explore the effects of PFASs on anemia in Chinese pregnant women. METHODS A total of 821 pregnant women were recruited between June 2015 and April 2019 in the Guangxi Zhuang Birth Cohort. The concentrations of PFASs were assessed in maternal serum before 12 gestational weeks. To determine both individual and combined associations of PFASs exposure with anemia in the three stages of pregnancy, binary logistic regression, Bayesian kernel machine regression (BKMR), and weighted quantile sum (WQS) regression models were employed. RESULTS In single-pollutant analysis, maternal exposure to perfluorododecanoic acid (PFDoA) and perfluoroheptanoic acid (PFHpA) were associated with anemia in the first trimester, exposure to PFHpA and perfluorobutanesulfonic acid (PFBS) were associated with anemia in the second trimester, and exposure to perfluorodecanoic acid (PFDA) and perfluorononanoic acid (PFNA) were associated with anemia in the third trimester. Notably, perfluoroundecanoic acid (PFUnA) had a nonlinear association with anemia in the third trimester. In multiple-pollutant analysis, a positive association of PFDoA with anemia in the first trimester and a negative association of PFBS with anemia in the second trimester were confirmed by BKMR. Exposure to PFASs mixture was not associated with anemia in all three trimesters. In WQS, there was a significantly negative association between the PFAS mixture and anemia in the second trimester. CONCLUSION Maternal exposure to PFASs is associated with gestational anemia in different trimesters.
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Affiliation(s)
- Qian Liao
- Department of Epidemiology and Health Statistics, School of Public Health, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Peng Tang
- Department of Epidemiology and Health Statistics, School of Public Health, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Dongxiang Pan
- Department of Epidemiology and Health Statistics, School of Public Health, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Yanye Song
- The Third Affiliated Hospital of Guangxi Medical University, Nanning, 530031, Guangxi, China
| | - Lei Lei
- Department of Epidemiology and Health Statistics, School of Public Health, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Jun Liang
- Department of Epidemiology and Health Statistics, School of Public Health, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Bihu Liu
- Department of Epidemiology and Health Statistics, School of Public Health, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Mengrui Lin
- Department of Sanitary Chemistry, School of Public Health, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Huishen Huang
- Department of Epidemiology and Health Statistics, School of Public Health, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Meile Mo
- Department of Epidemiology and Health Statistics, School of Public Health, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Chengtuo Huang
- Department of Physical Examination, Guangxi Tiandong Hospital of Traditional Chinese Medicine, Tiandong, 531500, Guangxi, China
| | - Ming Wei
- Department of Obstetrics and Gynecology, Child Hygiene, Maternal and Child Health Care Hospital of Tianyang District, Baise City, 542899, Guangxi, China
| | - Shun Liu
- Department of Maternal, Child and Adolescent Health, School of Public Health, Guangxi Medical University, Nanning, 530021, Guangxi, China.
| | - Dongping Huang
- Department of Sanitary Chemistry, School of Public Health, Guangxi Medical University, Nanning, 530021, Guangxi, China.
| | - Xiaoqiang Qiu
- Department of Epidemiology and Health Statistics, School of Public Health, Guangxi Medical University, Nanning, 530021, Guangxi, China.
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16
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Hüls A, Wedderburn CJ, Groenewold NA, Gladish N, Jones MJ, Koen N, MacIsaac JL, Lin DTS, Ramadori KE, Epstein MP, Donald KA, Kobor MS, Zar HJ, Stein DJ. Newborn differential DNA methylation and subcortical brain volumes as early signs of severe neurodevelopmental delay in a South African Birth Cohort Study. World J Biol Psychiatry 2022; 23:601-612. [PMID: 34895032 PMCID: PMC9273810 DOI: 10.1080/15622975.2021.2016955] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 01/25/2023]
Abstract
OBJECTIVES Early detection of neurodevelopmental delay is crucial for intervention and treatment strategies. We analysed associations between newborn DNA methylation (DNAm), neonatal magnetic resonance imaging (MRI) neuroimaging data, and neurodevelopment. METHODS Neurodevelopment was assessed in 161 children from the South African Drakenstein Child Health Study at 2 years of age using the Bayley Scales of Infant and Toddler Development III. We performed an epigenome-wide association study of neurodevelopmental delay using DNAm from cord blood. Subsequently, we analysed if associations between DNAm and neurodevelopmental delay were mediated by altered neonatal brain volumes (subset of 51 children). RESULTS Differential DNAm at SPTBN4 (cg26971411, Δbeta = -0.024, p-value = 3.28 × 10-08), and two intergenic regions (chromosome 11: cg00490349, Δbeta = -0.036, p-value = 3.02 × 10-08; chromosome 17: cg15660740, Δbeta = -0.078, p-value = 6.49 × 10-08) were significantly associated with severe neurodevelopmental delay. While these associations were not mediated by neonatal brain volume, neonatal caudate volumes were independently associated with neurodevelopmental delay, particularly in language (Δcaudate volume = 165.30 mm3, p = 0.0443) and motor (Δcaudate volume = 365.36 mm3, p-value = 0.0082) domains. CONCLUSIONS Differential DNAm from cord blood and increased neonatal caudate volumes were independently associated with severe neurodevelopmental delay at 2 years of age. These findings suggest that neurobiological signals for severe developmental delay may be detectable in very early life.
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Affiliation(s)
- Anke Hüls
- Department of Epidemiology and Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Catherine J Wedderburn
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Nynke A Groenewold
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
- South African Medical Research Council (SAMRC) Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Nicole Gladish
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
- BC Children's Hospital Research Institute, Vancouver, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, Canada
| | - Meaghan J Jones
- Department of Biochemistry and Medical Genetics, University of Manitoba, and Children's Hospital Research Institute of Manitoba, Winnipeg, Canada
| | - Nastassja Koen
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
- South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, University of Cape Town, Cape Town, South Africa
| | - Julia L MacIsaac
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
- BC Children's Hospital Research Institute, Vancouver, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, Canada
| | - David T S Lin
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
- BC Children's Hospital Research Institute, Vancouver, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, Canada
| | - Katia E Ramadori
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
- BC Children's Hospital Research Institute, Vancouver, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, Canada
| | - Michael P Epstein
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Kirsten A Donald
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Michael S Kobor
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
- BC Children's Hospital Research Institute, Vancouver, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, Canada
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa
- South African Medical Research Council (SAMRC) Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Dan J Stein
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
- South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, University of Cape Town, Cape Town, South Africa
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17
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Christensen GM, Rowcliffe C, Chen J, Vanker A, Koen N, Jones MJ, Gladish N, Hoffman N, Donald KA, Wedderburn CJ, Kobor MS, Zar HJ, Stein DJ, Hüls A. In-utero exposure to indoor air pollution or tobacco smoke and cognitive development in a South African birth cohort study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 834:155394. [PMID: 35460774 PMCID: PMC9177804 DOI: 10.1016/j.scitotenv.2022.155394] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/15/2022] [Accepted: 04/15/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND AND AIMS There is increasing evidence indicating that air pollution exposure is associated with neuronal damage. Since pregnancy is a critical window of vulnerability, air pollution exposure during this period could have adverse effects on neurodevelopment. This study aims 1) to analyze associations of prenatal exposure to indoor air pollution (particulate matter with diameters ≤10 μm, PM10) and tobacco smoke with neurodevelopment and 2) to determine whether these associations are mediated by deviations of epigenetic gestational age from chronological gestational age (ΔGA). METHODS Data of 734 children from the South African Drakenstein Child Health Study were analyzed. Prenatal PM10 exposure was measured using devices placed in the families' homes. Maternal smoking during pregnancy was determined by maternal urine cotinine measures. The Bayley Scales of Infant and Toddler Development III (BSID-III) was used to measure cognition, language and motor development and adaptive behavior at two years of age. Linear regression models adjusted for maternal age, gestational age, sex of child, ancestry, birth weight/length, and socioeconomic status were used to explore associations between air pollutants and BSID-III scores. A mediation analysis was conducted to analyze if these associations were mediated by ΔGA using DNA methylation measurements from cord blood. RESULTS An increase of one interquartile range in natural-log transformed PM10 (lnPM10; 1.58 μg/m3) was significantly associated with lower composite scores in cognition, language, and adaptive behavior sub-scores (composite score β-estimate [95%-confidence interval]: -0.950 [-1.821, -0.120]). Maternal smoking was significantly associated with lower adaptive behavior scores (-3.386 [-5.632, -1.139]). Associations were not significantly mediated by ΔGA (e.g., for PM10 and cognition, proportion mediated [p-value]: 4% [0.52]). CONCLUSION We found an association of prenatal exposure to indoor air pollution (PM10) and tobacco smoke on neurodevelopment at two years of age, particularly cognition, language, and adaptive behavior. Further research is needed to understand underlying biological mediators.
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Affiliation(s)
- Grace M Christensen
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Claire Rowcliffe
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Junyu Chen
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Aneesa Vanker
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, South Africa
| | - Nastassja Koen
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa; Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa; South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, University of Cape Town, Cape Town, South Africa
| | - Meaghan J Jones
- Department of Biochemistry and Medical Genetics, University of Manitoba, Children's Hospital Research, Institute of Manitoba, Winnipeg, Canada
| | - Nicole Gladish
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; BC Children's Hospital Research Institute, Vancouver, BC, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, BC, Canada
| | - Nadia Hoffman
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa; Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - Kirsten A Donald
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, South Africa; Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Catherine J Wedderburn
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, South Africa; Neuroscience Institute, University of Cape Town, Cape Town, South Africa; Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - Michael S Kobor
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; BC Children's Hospital Research Institute, Vancouver, BC, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, BC, Canada
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, South Africa; South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, University of Cape Town, Cape Town, South Africa
| | - Dan J Stein
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa; Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa; South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, University of Cape Town, Cape Town, South Africa
| | - Anke Hüls
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA; Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, USA.
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18
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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] [Abstract] [Key Words] [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
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19
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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: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [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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20
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Kallak TK, Fransson E, Bränn E, Berglund H, Lager S, Comasco E, Lyle R, Skalkidou A. Maternal prenatal depressive symptoms and toddler behavior: an umbilical cord blood epigenome-wide association study. Transl Psychiatry 2022; 12:186. [PMID: 35513368 PMCID: PMC9072531 DOI: 10.1038/s41398-022-01954-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 11/09/2022] Open
Abstract
Children of mothers with prenatal depressive symptoms (PND) have a higher risk of behavioral problems; fetal programming through DNA methylation is a possible underlying mechanism. This study investigated DNA methylation in cord blood to identify possible "at birth" signatures that may indicate susceptibility to behavioral problems at 18 months of age. Cord blood was collected from 256 children of mothers who had self-reported on symptoms of depression during pregnancy and the behavior of their child at 18 months of age. Whole genome DNA methylation was assessed using Illumina MethylationEPIC assay. The mother and child pairs were categorized into four groups, based on both self-reported depressive symptoms, PND or Healthy control (HC), and scores from the Child Behavior checklist (high or low for internalizing, externalizing, and total scores). Adjustments were made for batch effects, cell-type, and clinical covariates. Differentially methylated sites were identified using Kruskal-Wallis test, and Benjamini-Hochberg adjusted p values < 0.05 were considered significant. The analysis was also stratified by sex of the child. Among boys, we observed higher and correlated DNA methylation of one CpG-site in the promoter region of TPP1 in the HC group, with high externalizing scores compared to HC with low externalizing scores. Boys in the PND group showed lower DNA methylation in NUDT15 among those with high, compared to low, internalizing scores; the DNA methylation levels of CpGs in this gene were positively correlated with the CBCL scores. Hence, the differentially methylated CpG sites could be of interest for resilience, regardless of maternal mental health during pregnancy. The findings are in a relatively healthy study cohort, thus limiting the possibility of detecting strong effects associated with behavioral difficulties. This is the first investigation of cord blood DNA methylation signs of fetal programming of PND on child behavior at 18 months of age and thus calls for independent replications.
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Affiliation(s)
| | - Emma Fransson
- grid.8993.b0000 0004 1936 9457Department of Women’s and Children’s Health, Uppsala University, Uppsala, Sweden
| | - Emma Bränn
- grid.8993.b0000 0004 1936 9457Department of Women’s and Children’s Health, Uppsala University, Uppsala, Sweden
| | - Hanna Berglund
- grid.8993.b0000 0004 1936 9457Department of Women’s and Children’s Health, Uppsala University, Uppsala, Sweden
| | - Susanne Lager
- grid.8993.b0000 0004 1936 9457Department of Women’s and Children’s Health, Uppsala University, Uppsala, Sweden
| | - Erika Comasco
- grid.8993.b0000 0004 1936 9457Department of Women’s and Children’s Health, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Robert Lyle
- Department of Medical Genetics and Norwegian Sequencing Centre (NSC), Oslo University Hospital, Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Alkistis Skalkidou
- grid.8993.b0000 0004 1936 9457Department of Women’s and Children’s Health, Uppsala University, Uppsala, Sweden
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21
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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] [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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22
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LaSalle JM. X Chromosome Inactivation Timing is Not e XACT: Implications for Autism Spectrum Disorders. Front Genet 2022; 13:864848. [PMID: 35356429 PMCID: PMC8959653 DOI: 10.3389/fgene.2022.864848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
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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23
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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] [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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24
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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] [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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25
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Williams LA, LaSalle JM. Future Prospects for Epigenetics in Autism Spectrum Disorder. Mol Diagn Ther 2022; 26:569-579. [PMID: 35962910 PMCID: PMC9626414 DOI: 10.1007/s40291-022-00608-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2022] [Indexed: 12/30/2022]
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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26
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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. ENVIRONMENT INTERNATIONAL 2022; 158:106993. [PMID: 34991254 PMCID: PMC8852822 DOI: 10.1016/j.envint.2021.106993] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [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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27
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Erbescu A, Papuc SM, Budisteanu M, Arghir A, Neagu M. Re-emerging concepts of immune dysregulation in autism spectrum disorders. Front Psychiatry 2022; 13:1006612. [PMID: 36339838 PMCID: PMC9626859 DOI: 10.3389/fpsyt.2022.1006612] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by communication and social interaction deficits, and by restricted interests and stereotyped, repetitive behavior patterns. ASD has a strong genetic component and a complex architecture characterized by the interplay of rare and common genetic variants. Recently, increasing evidence suggest a significant contribution of immune system dysregulation in ASD. The present paper reviews the latest updates regarding the altered immune landscape of this complex disorder highlighting areas with potential for biomarkers discovery as well as personalization of therapeutic approaches. Cross-talk between the central nervous system and immune system has long been envisaged and recent evidence brings insights into the pathways connecting the brain to the immune system. Disturbance of cytokine levels plays an important role in the establishment of a neuroinflammatory milieu in ASD. Several other immune molecules involved in antigen presentation and inflammatory cellular phenotypes are also at play in ASD. Maternal immune activation, the presence of brain-reactive antibodies and autoimmunity are other potential prenatal and postnatal contributors to ASD pathophysiology. The molecular players involved in oxidative-stress response and mitochondrial system function, are discussed as contributors to the pro-inflammatory pattern. The gastrointestinal inflammation pathways proposed to play a role in ASD are also discussed. Moreover, the body of evidence regarding some of the genetic factors linked to the immune system dysregulation is reviewed and discussed. Last, but not least, the epigenetic traits and their interactions with the immune system are reviewed as an expanding field in ASD research. Understanding the immune-mediated pathways that influence brain development and function, metabolism, and intestinal homeostasis, may lead to the identification of robust diagnostic or predictive biomarkers for ASD individuals. Thus, novel therapeutic approaches could be developed, ultimately aiming to improve their quality of life.
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Affiliation(s)
- Alina Erbescu
- Victor Babes National Institute of Pathology, Bucharest, Romania.,Faculty of Biology, Doctoral School, University of Bucharest, Bucharest, Romania
| | | | - Magdalena Budisteanu
- Victor Babes National Institute of Pathology, Bucharest, Romania.,Prof. Dr. Alex. Obregia Clinical Hospital of Psychiatry, Bucharest, Romania.,Faculty of Medicine, Titu Maiorescu University, Bucharest, Romania
| | - Aurora Arghir
- Victor Babes National Institute of Pathology, Bucharest, Romania
| | - Monica Neagu
- Victor Babes National Institute of Pathology, Bucharest, Romania.,Faculty of Biology, Doctoral School, University of Bucharest, Bucharest, Romania.,Colentina Clinical Hospital, Bucharest, Romania
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28
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Bakulski KM, Dou JF, Feinberg JI, Aung MT, Ladd-Acosta C, Volk HE, Newschaffer CJ, Croen LA, Hertz-Picciotto I, Levy SE, Landa R, Feinberg AP, Fallin MD. Autism-Associated DNA Methylation at Birth From Multiple Tissues Is Enriched for Autism Genes in the Early Autism Risk Longitudinal Investigation. Front Mol Neurosci 2021; 14:775390. [PMID: 34899183 PMCID: PMC8655859 DOI: 10.3389/fnmol.2021.775390] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/28/2021] [Indexed: 12/30/2022] Open
Abstract
Background: Pregnancy measures of DNA methylation, an epigenetic mark, may be associated with autism spectrum disorder (ASD) development in children. Few ASD studies have considered prospective designs with DNA methylation measured in multiple tissues and tested overlap with ASD genetic risk loci. Objectives: To estimate associations between DNA methylation in maternal blood, cord blood, and placenta and later diagnosis of ASD, and to evaluate enrichment of ASD-associated DNA methylation for known ASD-associated genes. Methods: In the Early Autism Risk Longitudinal Investigation (EARLI), an ASD-enriched risk birth cohort, genome-scale maternal blood (early n = 140 and late n = 75 pregnancy), infant cord blood (n = 133), and placenta (maternal n = 106 and fetal n = 107 compartments) DNA methylation was assessed on the Illumina 450k HumanMethylation array and compared to ASD diagnosis at 36 months of age. Differences in site-specific and global methylation were tested with ASD, as well as enrichment of single site associations for ASD risk genes (n = 881) from the Simons Foundation Autism Research Initiative (SFARI) database. Results: No individual DNA methylation site was associated with ASD at genome-wide significance, however, individual DNA methylation sites nominally associated with ASD (P < 0.05) in each tissue were highly enriched for SFARI genes (cord blood P = 7.9 × 10-29, maternal blood early pregnancy P = 6.1 × 10-27, maternal blood late pregnancy P = 2.8 × 10-16, maternal placenta P = 5.6 × 10-15, fetal placenta P = 1.3 × 10-20). DNA methylation sites nominally associated with ASD across all five tissues overlapped at 144 (29.5%) SFARI genes. Conclusion: DNA methylation sites nominally associated with later ASD diagnosis in multiple tissues were enriched for ASD risk genes. Our multi-tissue study demonstrates the utility of examining DNA methylation prior to ASD diagnosis.
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Affiliation(s)
- Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - John F Dou
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Jason I Feinberg
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States.,Wendy Klag Center for Autism and Developmental Disabilities, Baltimore, MD, United States.,Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Max T Aung
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Christine Ladd-Acosta
- Wendy Klag Center for Autism and Developmental Disabilities, Baltimore, MD, United States.,Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Heather E Volk
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States.,Wendy Klag Center for Autism and Developmental Disabilities, Baltimore, MD, United States
| | - Craig J Newschaffer
- College of Health and Human Development, Penn State University, State College, PA, United States
| | - Lisa A Croen
- Kaiser Permanente Division of Research, Oakland, CA, United States
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences, School of Medicine, University of California, Davis, Davis, CA, United States.,MIND Institute, University of California, Davis, Davis, CA, United States
| | - Susan E Levy
- Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Rebecca Landa
- Kennedy Krieger Institute Center for Autism and Related Disorders, Baltimore, MD, United States
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD, United States.,Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, United States.,Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Margaret D Fallin
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States.,Wendy Klag Center for Autism and Developmental Disabilities, Baltimore, MD, United States.,Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD, United States
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29
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Coppedè F. The diagnostic potential of the epigenome in autism spectrum disorders. Epigenomics 2021; 13:1587-1590. [PMID: 34617447 DOI: 10.2217/epi-2021-0338] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Tweetable abstract The diagnostic application of genome-wide methylation signatures is increasing in various syndromic forms of autism, but further studies are warranted to clarify whether epigenetic biomarkers can be of diagnostic utility in idiopathic ASD.
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Affiliation(s)
- Fabio Coppedè
- Department of Translational Research & of New Surgical & Medical Technologies, University of Pisa, Via Roma 55, Pisa, 56126, Italy
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30
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Mahony C, O’Ryan C. Convergent Canonical Pathways in Autism Spectrum Disorder from Proteomic, Transcriptomic and DNA Methylation Data. Int J Mol Sci 2021; 22:ijms221910757. [PMID: 34639097 PMCID: PMC8509728 DOI: 10.3390/ijms221910757] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/27/2021] [Accepted: 10/01/2021] [Indexed: 12/20/2022] Open
Abstract
Autism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder with extensive genetic and aetiological heterogeneity. While the underlying molecular mechanisms involved remain unclear, significant progress has been facilitated by recent advances in high-throughput transcriptomic, epigenomic and proteomic technologies. Here, we review recently published ASD proteomic data and compare proteomic functional enrichment signatures with those of transcriptomic and epigenomic data. We identify canonical pathways that are consistently implicated in ASD molecular data and find an enrichment of pathways involved in mitochondrial metabolism and neurogenesis. We identify a subset of differentially expressed proteins that are supported by ASD transcriptomic and DNA methylation data. Furthermore, these differentially expressed proteins are enriched for disease phenotype pathways associated with ASD aetiology. These proteins converge on protein–protein interaction networks that regulate cell proliferation and differentiation, metabolism, and inflammation, which demonstrates a link between canonical pathways, biological processes and the ASD phenotype. This review highlights how proteomics can uncover potential molecular mechanisms to explain a link between mitochondrial dysfunction and neurodevelopmental pathology.
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31
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Wei S, Tao J, Xu J, Chen X, Wang Z, Zhang N, Zuo L, Jia Z, Chen H, Sun H, Yan Y, Zhang M, Lv H, Kong F, Duan L, Ma Y, Liao M, Xu L, Feng R, Liu G, Project TEWAS, Jiang Y. Ten Years of EWAS. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2100727. [PMID: 34382344 PMCID: PMC8529436 DOI: 10.1002/advs.202100727] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/11/2021] [Indexed: 06/13/2023]
Abstract
Epigenome-wide association study (EWAS) has been applied to analyze DNA methylation variation in complex diseases for a decade, and epigenome as a research target has gradually become a hot topic of current studies. The DNA methylation microarrays, next-generation, and third-generation sequencing technologies have prepared a high-quality platform for EWAS. Here, the progress of EWAS research is reviewed, its contributions to clinical applications, and mainly describe the achievements of four typical diseases. Finally, the challenges encountered by EWAS and make bold predictions for its future development are presented.
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Affiliation(s)
- Siyu Wei
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Junxian Tao
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Jing Xu
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Xingyu Chen
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Zhaoyang Wang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Nan Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Lijiao Zuo
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Zhe Jia
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Haiyan Chen
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Hongmei Sun
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Yubo Yan
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Mingming Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Hongchao Lv
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Fanwu Kong
- The EWAS ProjectHarbinChina
- Department of NephrologyThe Second Affiliated HospitalHarbin Medical UniversityHarbin150001China
| | - Lian Duan
- The EWAS ProjectHarbinChina
- The First Affiliated Hospital of Wenzhou Medical UniversityWenzhou325000China
| | - Ye Ma
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Mingzhi Liao
- The EWAS ProjectHarbinChina
- College of Life SciencesNorthwest A&F UniversityYanglingShanxi712100China
| | - Liangde Xu
- The EWAS ProjectHarbinChina
- School of Biomedical EngineeringWenzhou Medical UniversityWenzhou325035China
| | - Rennan Feng
- The EWAS ProjectHarbinChina
- Department of Nutrition and Food HygienePublic Health CollegeHarbin Medical UniversityHarbin150081China
| | - Guiyou Liu
- The EWAS ProjectHarbinChina
- Beijing Institute for Brain DisordersCapital Medical UniversityBeijing100069China
| | | | - Yongshuai Jiang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
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32
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Abdolmaleky HM, Zhou JR, Thiagalingam S. Cataloging recent advances in epigenetic alterations in major mental disorders and autism. Epigenomics 2021; 13:1231-1245. [PMID: 34318684 PMCID: PMC8738978 DOI: 10.2217/epi-2021-0074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/12/2021] [Indexed: 11/21/2022] Open
Abstract
During the last two decades, diverse epigenetic modifications including DNA methylation, histone modifications, RNA editing and miRNA dysregulation have been associated with psychiatric disorders. A few years ago, in a review we outlined the most common epigenetic alterations in major psychiatric disorders (e.g., aberrant DNA methylation of DTNBP1, HTR2A, RELN, MB-COMT and PPP3CC, and increased expression of miR-34a and miR-181b). Recent follow-up studies have uncovered other DNA methylation aberrations affecting several genes in mental disorders, in addition to dysregulation of many miRNAs. Here, we provide an update on new epigenetic findings and highlight potential origin of the diversity and inconsistencies, focusing on drug effects, tissue/cell specificity of epigenetic landscape and discuss shortcomings of the current diagnostic criteria in mental disorders.
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Affiliation(s)
- Hamid Mostafavi Abdolmaleky
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, 02118 MA, USA
- Department of Surgery, Nutrition/Metabolism Laboratory, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, 02215 MA, USA
| | - Jin-Rong Zhou
- Department of Surgery, Nutrition/Metabolism Laboratory, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, 02215 MA, USA
| | - Sam Thiagalingam
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, 02118 MA, USA
- Genetics & Genomics Graduate Program, Boston University School of Medicine, Boston, 02118 MA, USA
- Department of Pathology & Laboratory Medicine, Boston University School of Medicine, Boston, 02218 MA, USA
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33
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Campbell KA, Hickman R, Fallin MD, Bakulski KM. Prenatal exposure to metals and autism spectrum disorder: Current status and future directions. CURRENT OPINION IN TOXICOLOGY 2021; 26:39-48. [PMID: 39119269 PMCID: PMC11309009 DOI: 10.1016/j.cotox.2021.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental disorder with genetic and environmental contributors to etiology. Many metals have the potential to be neurotoxic and their exposures are widespread. The field of metals exposure and ASD research is emerging, and in this review article we assess the current state of the literature, with emphasis on the previous two years. Epidemiology studies are discussed with respect to exposure timing, exposure matrix, and outcome assessment. Toxicology studies are described for exposure dosing and timing, as well as behavioral and molecular outcomes. Further epidemiological and toxicological investigations can identify the timing and importance of metals as ASD risk factors and uncover biological mechanisms for risk mitigation and therapeutic strategies.
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Affiliation(s)
- Kyle A. Campbell
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Ruby Hickman
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - M. Daniele Fallin
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Kelly M. Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
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34
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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] [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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35
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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] [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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