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Hernandez A, Delgado-González E, Varman Durairaj R, Reyes-Haro D, Martínez-Torres A, Espinosa F. Striatal Synaptic Changes and Behavior in Adult mouse Upon Prenatal Exposure to Valproic Acid. Brain Res 2023:148461. [PMID: 37308047 DOI: 10.1016/j.brainres.2023.148461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/14/2023]
Abstract
Autism spectrum disorders (ASD) are a group of neurodevelopmental disorders characterized by persistent deficits in social communication and social interaction. Altered synaptogenesis and aberrant connectivity responsible for social behavior and communication have been reported in autism pathogenesis. Autism has a strong genetic and heritable component; however, environmental factors including toxins, pesticides, infection and in utero exposure to drugs such as VPA have also been implicated in ASD. Administration of VPA during pregnancy has been used as a rodent model to study pathophysiological mechanisms involved in ASD, and in this study, we used the mouse model of prenatal exposure to VPA to assess the effects on striatal and dorsal hippocampus function in adult mice. Alterations in repetitive behaviors and shift habits were observed in mice prenatally exposed to VPA. In particular, such mice presented a better performance in learned motor skills and cognitive deficits in Y-maze learning frequently associated with striatal and hippocampal function. These behavioral changes were associated with a decreased level of proteins involved in the formation and maintenance of excitatory synapses, such as Nlgn-1 and PSD-95. In conclusion, motor skill abilities, repetitive behaviors, and impaired flexibility to shift habits are associated with reduced striatal excitatory synaptic function in the adult mouse prenatally exposed to VPA.
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Affiliation(s)
- Adan Hernandez
- Departamento de Neurobiología Celular y Molecular, Laboratorio de Neurobiología Molecular y Celular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla, 76230 Santiago de Querétaro, Querétaro, México.
| | - Evangelina Delgado-González
- Departamento de Neurobiología Celular y Molecular, Laboratorio de Neurobiología Molecular y Celular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla, 76230 Santiago de Querétaro, Querétaro, México
| | - Ragu Varman Durairaj
- Departamento de Neurobiología Celular y Molecular, Laboratorio de Neurobiología Molecular y Celular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla, 76230 Santiago de Querétaro, Querétaro, México; Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Daniel Reyes-Haro
- Departamento de Neurobiología Celular y Molecular, Laboratorio de Neurobiología Molecular y Celular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla, 76230 Santiago de Querétaro, Querétaro, México
| | - Ataúlfo Martínez-Torres
- Departamento de Neurobiología Celular y Molecular, Laboratorio de Neurobiología Molecular y Celular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla, 76230 Santiago de Querétaro, Querétaro, México
| | - Felipe Espinosa
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390
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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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3
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Chen WX, Liu B, Zhou L, Xiong X, Fu J, Huang ZF, Tan T, Tang M, Wang J, Tang YP. De novo mutations within metabolism networks of amino acid/protein/energy in Chinese autistic children with intellectual disability. Hum Genomics 2022; 16:52. [PMID: 36320054 PMCID: PMC9623983 DOI: 10.1186/s40246-022-00427-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/19/2022] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) is often accompanied by intellectual disability (ID). Despite extensive studies, however, the genetic basis for this comorbidity is still not clear. In this study, we tried to develop an analyzing pipeline for de novo mutations and possible pathways related to ID phenotype in ASD. Whole-exome sequencing (WES) was performed to screen de novo mutations and candidate genes in 79 ASD children together with their parents (trios). The de novo altering genes and relative pathways which were associated with ID phenotype were analyzed. The connection nodes (genes) of above pathways were selected, and the diagnostic value of these selected genes for ID phenotype in the study population was also evaluated. RESULTS We identified 89 de novo mutant genes, of which 34 genes were previously reported to be associated with ASD, including double hits in the EGF repeats of NOTCH1 gene (p.V999M and p.S1027L). Interestingly, of these 34 genes, 22 may directly affect intelligence quotient (IQ). Further analyses revealed that these IQ-related genes were enriched in protein synthesis, energy metabolism, and amino acid metabolism, and at least 9 genes (CACNA1A, ALG9, PALM2, MGAT4A, PCK2, PLEKHA1, PSME3, ADI1, and TLE3) were involved in all these three pathways. Seven patients who harbored these gene mutations showed a high prevalence of a low IQ score (< 70), a non-verbal language, and an early diagnostic age (< 4 years). Furthermore, our panel of these 9 genes reached a 10.2% diagnostic rate (5/49) in early diagnostic patients with a low IQ score and also reached a 10% diagnostic yield in those with both a low IQ score and non-verbal language (4/40). CONCLUSION We found some new genetic disposition for ASD accompanied with intellectual disability in this study. Our results may be helpful for etiologic research and early diagnoses of intellectual disability in ASD. Larger population studies and further mechanism studies are warranted.
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Affiliation(s)
- Wen-Xiong Chen
- grid.410737.60000 0000 8653 1072The Assessment and Intervention Center for Autistic Children, Department of Neurology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 Guangdong China
| | - Bin Liu
- grid.410737.60000 0000 8653 1072Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 China ,grid.258164.c0000 0004 1790 3548Department of Biobank, Shenzhen Baoan Women’s and Children’s Hospital, Jinan University, Shenzhen, 518102 Guangdong China
| | - Lijie Zhou
- grid.412719.8Department of Pediatric Rehabilitation, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Xiaoli Xiong
- grid.410737.60000 0000 8653 1072Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 China
| | - Jie Fu
- grid.410737.60000 0000 8653 1072Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 China
| | - Zhi-Fang Huang
- grid.410737.60000 0000 8653 1072The Assessment and Intervention Center for Autistic Children, Department of Neurology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 Guangdong China
| | - Ting Tan
- grid.410737.60000 0000 8653 1072Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 China
| | - Mingxi Tang
- grid.488387.8Department of Pathology, Affiliated Hospital of Southwest Medical University, Luzhou, 646000 Sichuan China
| | - Jun Wang
- grid.412719.8Department of Pediatric Rehabilitation, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Ya-Ping Tang
- grid.410737.60000 0000 8653 1072Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 China ,grid.412719.8Department of Pediatric Rehabilitation, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China ,grid.12981.330000 0001 2360 039XGuangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080 Guangdong China
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4
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Zhang C, Yan L, Qiao J. Effect of advanced parental age on pregnancy outcome and offspring health. J Assist Reprod Genet 2022; 39:1969-1986. [PMID: 35925538 PMCID: PMC9474958 DOI: 10.1007/s10815-022-02533-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/24/2021] [Indexed: 10/16/2022] Open
Abstract
PURPOSE Fertility at advanced age has become increasingly common, but the aging of parents may adversely affect the maturation of gametes and the development of embryos, and therefore the effects of aging are likely to be transmitted to the next generation. This article reviewed the studies in this field in recent years. METHODS We searched the relevant literature in recent years with the keywords of "advanced maternal/paternal age" combined with "adverse pregnancy outcome" or "birth defect" in the PubMed database and classified the effects of parental advanced age on pregnancy outcomes and birth defects. Related studies on the effect of advanced age on birth defects were classified as chromosomal abnormalities, neurological and psychiatric disorders, and other systemic diseases. The effect of assisted reproduction technology (ART) on fertility in advanced age was also discussed. RESULTS Differences in the definition of the range of advanced age and other confounding factors among studies were excluded, most studies believed that advanced parental age would affect pregnancy outcomes and birth defects in offspring. CONCLUSION To some extent, advanced parental age caused adverse pregnancy outcomes and birth defects. The occurrence of these results was related to the molecular genetic changes caused by aging, such as gene mutations, epigenetic variations, etc. Any etiology of adverse pregnancy outcomes and birth defects related to aging might be more than one. The detrimental effect of advanced age can be corrected to some extent by ART.
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Affiliation(s)
- Cong Zhang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North garden road, Haidian district, Beijing, 100191, People's Republic of China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
- Research Units of Comprehensive Diagnosis and Treatment of Oocyte Maturation Arrest (Chinese Academy of Medical Sciences), Beijing, 100191, China
- Savid Medical College (University of Chinese Academy of Sciences), Beijing, 100049, China
| | - Liying Yan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North garden road, Haidian district, Beijing, 100191, People's Republic of China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
- Research Units of Comprehensive Diagnosis and Treatment of Oocyte Maturation Arrest (Chinese Academy of Medical Sciences), Beijing, 100191, China
| | - Jie Qiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North garden road, Haidian district, Beijing, 100191, People's Republic of China.
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China.
- Research Units of Comprehensive Diagnosis and Treatment of Oocyte Maturation Arrest (Chinese Academy of Medical Sciences), Beijing, 100191, China.
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5
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Takayama K, Tobori S, Andoh C, Kakae M, Hagiwara M, Nagayasu K, Shirakawa H, Ago Y, Kaneko S. Autism Spectrum Disorder Model Mice Induced by Prenatal Exposure to Valproic Acid Exhibit Enhanced Empathy-Like Behavior <i>via</i> Oxytocinergic Signaling. Biol Pharm Bull 2022; 45:1124-1132. [DOI: 10.1248/bpb.b22-00200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Kaito Takayama
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Shota Tobori
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Chihiro Andoh
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Masashi Kakae
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Masako Hagiwara
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Kazuki Nagayasu
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Hisashi Shirakawa
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Yukio Ago
- Department of Cellular and Molecular Pharmacology, Graduate School of Biomedical and Health Sciences, Hiroshima University
| | - Shuji Kaneko
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University
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6
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The Role of Genetics, Epigenetics, and the Environment in ASD: A Mini Review. EPIGENOMES 2022; 6:epigenomes6020015. [PMID: 35735472 PMCID: PMC9222497 DOI: 10.3390/epigenomes6020015] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/12/2022] [Accepted: 06/16/2022] [Indexed: 01/21/2023] Open
Abstract
According to recent findings, variances in autism spectrum disorder (ASD) risk factors might be determined by several factors, including molecular genetic variants. Accumulated evidence has also revealed the important role of biological and chemical pathways in ASD aetiology. In this paper, we assess several reviews with regard to their quality of evidence and provide a brief outline of the presumed mechanisms of the genetic, epigenetic, and environmental risk factors of ASD. We also review some of the critical literature, which supports the basis of each factor in the underlying and specific risk patterns of ASD. Finally, we consider some of the implications of recent research regarding potential molecular targets for future investigations.
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7
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Epigenome-Wide Analysis Reveals DNA Methylation Alteration in ZFP57 and Its Target RASGFR2 in a Mexican Population Cohort with Autism. CHILDREN (BASEL, SWITZERLAND) 2022; 9:children9040462. [PMID: 35455506 PMCID: PMC9025761 DOI: 10.3390/children9040462] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/18/2022] [Accepted: 03/20/2022] [Indexed: 12/17/2022]
Abstract
Autism Spectrum Disorders (ASD) comprise a group of heterogeneous and complex neurodevelopmental disorders. Genetic and environmental factors contribute to ASD etiology. DNA methylation is particularly relevant for ASD due to its mediating role in the complex interaction between genotype and environment and has been implicated in ASD pathophysiology. The lack of diversity in DNA methylation studies in ASD individuals is remarkable. Since genetic and environmental factors are likely to vary across populations, the study of underrepresented populations is necessary to understand the molecular alterations involved in ASD and the risk factors underlying these changes. This study explored genome-wide differences in DNA methylation patterns in buccal epithelium cells between Mexican ASD patients (n = 27) and age-matched typically developing (TD: n = 15) children. DNA methylation profiles were evaluated with the Illumina 450k array. We evaluated the interaction between sex and ASD and found a differentially methylated region (DMR) over the 5′UTR region of ZFP57 and one of its targets, RASGRF2. These results match previous findings in brain tissue, which may indicate that ZFP57 could be used as a proxy for DNA methylation in different tissues. This is the first study performed in a Mexican, and subsequently, Latin American, population that evaluates DNA methylation in ASD patients.
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8
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Almandil NB, AlSulaiman A, Aldakeel SA, Alkuroud DN, Aljofi HE, Alzahrani S, Al-mana A, Alfuraih AA, Alabdali M, Alkhamis FA, AbdulAzeez S, Borgio JF. Integration of Transcriptome and Exome Genotyping Identifies Significant Variants with Autism Spectrum Disorder. Pharmaceuticals (Basel) 2022; 15:ph15020158. [PMID: 35215271 PMCID: PMC8880056 DOI: 10.3390/ph15020158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/16/2022] [Accepted: 01/25/2022] [Indexed: 02/06/2023] Open
Abstract
Autism is a complex disease with genetic predisposition factors. Real factors for treatment and early diagnosis are yet to be defined. This study integrated transcriptome and exome genotyping for identifying functional variants associated with autism spectrum disorder and their impact on gene expression to find significant variations. More than 1800 patients were screened, and 70 (47 male/23 female) with an average age of 7.56 ± 3.68 years fulfilled the DSM-5 criteria for autism. Analysis revealed 682 SNPs of 589 genes significantly (p < 0.001) associated with autism among the putative functional exonic variants (n = 243,345) studied. Olfactory receptor genes on chromosome 6 were significant after Bonferroni correction (α = 0.05/243345 = 2.05 × 10−7) with a high degree of linkage disequilibrium on 6p22.1 (p = 6.71 × 10−9). The differentially expressed gene analysis of autistic patients compared to controls in whole RNA sequencing identified significantly upregulated (foldchange ≥ 0.8 and p-value ≤ 0.05; n = 125) and downregulated (foldchange ≤ −0.8 and p-value ≤ 0.05; n = 117) genes. The integration of significantly up- and downregulated genes and genes of significant SNPs identified regulatory variants (rs6657480, rs3130780, and rs1940475) associated with the up- (ITGB3BP) and downregulation (DDR1 and MMP8) of genes in autism spectrum disorder in people of Arab ancestries. The significant variants could be a biomarker of interest for identifying early autism among Arabs and helping to characterize the genes involved in the susceptibility mechanisms for autistic subjects.
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Affiliation(s)
- Noor B. Almandil
- Department of Clinical Pharmacy Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
| | - Abdulla AlSulaiman
- Department of Neurology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (A.A.); (M.A.); (F.A.A.)
| | - Sumayh A. Aldakeel
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (S.A.A.); (D.N.A.); (A.A.A.); (S.A.)
| | - Deem N. Alkuroud
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (S.A.A.); (D.N.A.); (A.A.A.); (S.A.)
| | - Halah Egal Aljofi
- Environmental Health Research Area, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
| | - Safah Alzahrani
- Department of Mental Health, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (S.A.); (A.A.-m.)
- King Fahad Hospital of the University, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia
| | - Aishah Al-mana
- Department of Mental Health, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (S.A.); (A.A.-m.)
- King Fahad Hospital of the University, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia
| | - Asma A. Alfuraih
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (S.A.A.); (D.N.A.); (A.A.A.); (S.A.)
| | - Majed Alabdali
- Department of Neurology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (A.A.); (M.A.); (F.A.A.)
| | - Fahd A. Alkhamis
- Department of Neurology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (A.A.); (M.A.); (F.A.A.)
| | - Sayed AbdulAzeez
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (S.A.A.); (D.N.A.); (A.A.A.); (S.A.)
| | - J. Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (S.A.A.); (D.N.A.); (A.A.A.); (S.A.)
- Correspondence: ; Tel.: +966-13-3330864
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Marí-Bauset S, Peraita-Costa I, Donat-Vargas C, Llopis-González A, Marí-Sanchis A, Llopis-Morales J, Morales Suárez-Varela M. Systematic review of prenatal exposure to endocrine disrupting chemicals and autism spectrum disorder in offspring. AUTISM : THE INTERNATIONAL JOURNAL OF RESEARCH AND PRACTICE 2022; 26:6-32. [PMID: 34412519 DOI: 10.1177/13623613211039950] [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: 11/17/2022]
Abstract
LAY ABSTRACT Autism spectrum disorders comprise a complex group with many subtypes of behaviorally defined neurodevelopmental abnormalities in two core areas: deficits in social communication and fixated, restricted, repetitive, or stereotyped behaviors and interests each with potential unique risk factors and characteristics. The underlying mechanisms and the possible causes of autism spectrum disorder remain elusive and while increased prevalence is undoubtable, it is unclear if it is a reflection of diagnostic improvement or emerging risk factors such as endocrine disrupting chemicals. Epidemiological studies, which are used to study the relation between endocrine disrupting chemicals and autism spectrum disorder, can have inherent methodological challenges that limit the quality and strength of their findings. The objective of this work is to systematically review the treatment of these challenges and assess the quality and strength of the findings in the currently available literature. The overall quality and strength were "moderate" and "limited," respectively. Risk of bias due to the exclusion of potential confounding factors and the lack of accuracy of exposure assessment methods were the most prevalent. The omnipresence of endocrine disrupting chemicals and the biological plausibility of the association between prenatal exposure and later development of autism spectrum disorder highlight the need to carry out well-designed epidemiological studies that overcome the methodological challenges observed in the currently available literature in order to be able to inform public policy to prevent exposure to these potentially harmful chemicals and aid in the establishment of predictor variables to facilitate early diagnosis of autism spectrum disorder and improve long-term outcomes.
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Affiliation(s)
- Salvador Marí-Bauset
- Unit of Public Health and Environmental Care, Department of Preventive Medicine and Public Health, Food Sciences, Toxicology and Forensic Medicine, University of Valencia, Spain
| | - Isabel Peraita-Costa
- Unit of Public Health and Environmental Care, Department of Preventive Medicine and Public Health, Food Sciences, Toxicology and Forensic Medicine, University of Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Institute of Health Carlos III, Spain
| | | | - Agustín Llopis-González
- Unit of Public Health and Environmental Care, Department of Preventive Medicine and Public Health, Food Sciences, Toxicology and Forensic Medicine, University of Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Institute of Health Carlos III, Spain
| | | | - Juan Llopis-Morales
- Unit of Public Health and Environmental Care, Department of Preventive Medicine and Public Health, Food Sciences, Toxicology and Forensic Medicine, University of Valencia, Spain
| | - María Morales Suárez-Varela
- Unit of Public Health and Environmental Care, Department of Preventive Medicine and Public Health, Food Sciences, Toxicology and Forensic Medicine, University of Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Institute of Health Carlos III, Spain
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10
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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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Lussier AA, Bodnar TS, Moksa M, Hirst M, Kobor MS, Weinberg J. Prenatal Adversity Alters the Epigenetic Profile of the Prefrontal Cortex: Sexually Dimorphic Effects of Prenatal Alcohol Exposure and Food-Related Stress. Genes (Basel) 2021; 12:genes12111773. [PMID: 34828381 PMCID: PMC8622940 DOI: 10.3390/genes12111773] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/28/2021] [Accepted: 11/06/2021] [Indexed: 01/02/2023] Open
Abstract
Prenatal adversity or stress can have long-term consequences on developmental trajectories and health outcomes. Although the biological mechanisms underlying these effects are poorly understood, epigenetic modifications, such as DNA methylation, have the potential to link early-life environments to alterations in physiological systems, with long-term functional implications. We investigated the consequences of two prenatal insults, prenatal alcohol exposure (PAE) and food-related stress, on DNA methylation profiles of the rat brain during early development. As these insults can have sex-specific effects on biological outcomes, we analyzed epigenome-wide DNA methylation patterns in prefrontal cortex, a key brain region involved in cognition, executive function, and behavior, of both males and females. We found sex-dependent and sex-concordant influences of these insults on epigenetic patterns. These alterations occurred in genes and pathways related to brain development and immune function, suggesting that PAE and food-related stress may reprogram neurobiological/physiological systems partly through central epigenetic changes, and may do so in a sex-dependent manner. Such epigenetic changes may reflect the sex-specific effects of prenatal insults on long-term functional and health outcomes and have important implications for understanding possible mechanisms underlying fetal alcohol spectrum disorder and other neurodevelopmental disorders.
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Affiliation(s)
- Alexandre A. Lussier
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Correspondence: (A.A.L.); (J.W.)
| | - Tamara S. Bodnar
- Department of Cellular and Physiological Sciences, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada;
| | - Michelle Moksa
- Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (M.M.); (M.H.)
| | - Martin Hirst
- Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (M.M.); (M.H.)
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Michael S. Kobor
- BC Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada;
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC V5Z 4H4, Canada
- Program in Child and Brain Development, CIFAR, MaRS Centre, West Tower, 661 University Ave., Suite 505, Toronto, ON M5G 1M1, Canada
| | - Joanne Weinberg
- Department of Cellular and Physiological Sciences, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada;
- Correspondence: (A.A.L.); (J.W.)
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Pathogenic DNM1L Variant (1085G>A) Linked to Infantile Progressive Neurological Disorder: Evidence of Maternal Transmission by Germline Mosaicism and Influence of a Contemporary in cis Variant (1535T>C). Genes (Basel) 2021; 12:genes12091295. [PMID: 34573276 PMCID: PMC8467311 DOI: 10.3390/genes12091295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/13/2021] [Accepted: 08/19/2021] [Indexed: 01/23/2023] Open
Abstract
Mitochondria are dynamic organelles undergoing continuous fusion and fission with Drp1, encoded by the DNM1L gene, required for mitochondrial fragmentation. DNM1L dominant pathogenic variants lead to progressive neurological disorders with early exitus. Herein we report on the case of a boy affected by epileptic encephalopathy carrying two heterozygous variants (in cis) of the DNM1L gene: a pathogenic variant (PV) c.1085G>A (p.Gly362Asp) accompanied with a variant of unknown significance (VUS) c.1535T>C (p.Ile512Thr). Amplicon sequencing of the mother’s DNA revealed the presence of the PV and VUS in 5% of cells, with the remaining cells presenting only VUS. Functional investigations performed on the patient and his mother’s cells unveiled altered mitochondrial respiratory chain activities, network architecture and Ca2+ homeostasis as compared with healthy unrelated subjects’ samples. Modelling Drp1 harbouring the two variants, separately or in combination, resulted in structural changes as compared with Wt protein. Considering the clinical history of the mother, PV transmission by a maternal germline mosaicism mechanism is proposed. Altered Drp1 function leads to changes in the mitochondrial structure and bioenergetics as well as in Ca2+ homeostasis. The novel VUS might be a modifier that synergistically worsens the phenotype when associated with the PV.
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Bam S, Buchanan E, Mahony C, O'Ryan C. DNA Methylation of PGC-1α Is Associated With Elevated mtDNA Copy Number and Altered Urinary Metabolites in Autism Spectrum Disorder. Front Cell Dev Biol 2021; 9:696428. [PMID: 34381777 PMCID: PMC8352569 DOI: 10.3389/fcell.2021.696428] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/05/2021] [Indexed: 12/12/2022] Open
Abstract
Autism spectrum disorder (ASD) is a complex disorder that is underpinned by numerous dysregulated biological pathways, including pathways that affect mitochondrial function. Epigenetic mechanisms contribute to this dysregulation and DNA methylation is an important factor in the etiology of ASD. We measured DNA methylation of peroxisome proliferator-activated receptor-gamma coactivator-1 alpha (PGC-1α), as well as five genes involved in regulating mitochondrial homeostasis to examine mitochondrial dysfunction in an ASD cohort of South African children. Using targeted Next Generation bisulfite sequencing, we found differential methylation (p < 0.05) at six key genes converging on mitochondrial biogenesis, fission and fusion in ASD, namely PGC-1α, STOML2, MFN2, FIS1, OPA1, and GABPA. PGC-1α, the transcriptional regulator of biogenesis, was significantly hypermethylated at eight CpG sites in the gene promoter, one of which contained a putative binding site for CAMP response binding element 1 (CREB1) (p = 1 × 10–6). Mitochondrial DNA (mtDNA) copy number, a marker of mitochondrial function, was elevated (p = 0.002) in ASD compared to controls and correlated significantly with DNA methylation at the PGC-1α promoter and there was a positive correlation between methylation at PGC-1α CpG#1 and mtDNA copy number (Spearman’s r = 0.2, n = 49, p = 0.04) in ASD. Furthermore, DNA methylation at PGC-1α CpG#1 and mtDNA copy number correlated significantly (p < 0.05) with levels of urinary organic acids associated with mitochondrial dysfunction, oxidative stress, and neuroendocrinology. Our data show differential methylation in ASD at six key genes converging on PGC-1α-dependent regulation of mitochondrial biogenesis and function. We demonstrate that methylation at the PGC-1α promoter is associated with elevated mtDNA copy number and metabolomic evidence of mitochondrial dysfunction in ASD. This highlights an unexplored role for DNA methylation in regulating specific pathways involved in mitochondrial biogenesis, fission and fusion contributing to mitochondrial dysfunction in ASD.
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Affiliation(s)
- Sophia Bam
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Erin Buchanan
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Caitlyn Mahony
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Colleen O'Ryan
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
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14
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Chaudhury S. Epigenetic regulation in Autism spectrum disorder. AIMS GENETICS 2021. [DOI: 10.3934/genet.2016.4.292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
AbstractAutism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by an impaired social communication skill and often results in repetitive, stereotyped behavior which is observed in children during the first few years of life. Other characteristic of this disorder includes language disabilities, difficulties in sensory integration, lack of reciprocal interactions and in some cases, cognitive delays. One percentage of the general population is affected by ASD and is four times more common in boys than girls. There are hundreds of genes, which has been identified to be associated with ASD etiology. However it remains difficult to comprehend our understanding in defining the genetic architecture necessary for complete exposition of its pathophysiology. Seeing the complexity of the disease, it is important to adopt a multidisciplinary approach which should not only focus on the “genetics” of autism but also on epigenetics, transcriptomics, immune system disruption and environmental factors that could all impact the pathogenesis of the disease. As environmental factors also play a key role in regulating the trigger of ASD, the role of chromatin remodeling and DNA methylation has started to emerge. Such epigenetic modifications directly link molecular regulatory pathways and environmental factors, which might be able to explain some aspects of complex disorders like ASD. The present review will focus on the role of epigenetic regulation in defining the underlying cause for ASD.
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Affiliation(s)
- Sraboni Chaudhury
- Molecular and Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI-48109, USA
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15
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Martinez-Pinteño A, Rodriguez N, Blázquez A, Plana MT, Varela E, Gassó P, Lafuente A, Lazaro L, Mas S. DNA Methylation of Fluoxetine Response in Child and Adolescence: Preliminary Results. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2021; 14:459-467. [PMID: 33907441 PMCID: PMC8064712 DOI: 10.2147/pgpm.s289480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/29/2020] [Indexed: 12/28/2022]
Abstract
Purpose The search for predictors of antidepressant response is gaining increasing attention, with epigenetic markers attracting a great deal of interest. We performed a genome-wide study assessing baseline differences in DNA methylation between Responders and Non-Responders. Patients and Methods Twenty-two children and adolescents, receiving fluoxetine treatment for the first time, were classified as Responders or Non-Responders according to CGI-I score after 8 weeks of fluoxetine treatment. Genome-wide DNA methylation was profiled using the Illumina Infinium MethylationEPIC BeadChip Kit and analyzed using the Chip Analysis Methylation Pipeline (ChAMP). Results We identified 21 CpG sites significantly (FDR<0.05) associated with fluoxetine response that showed meaningful differences (Δβ> ±0.2) in methylation level between Responders and Non-Responders. Two genes, RHOJ (Ras Homolog Family Member J) and OR2L13 (Olfactory Receptor family 2 subfamily L member 13), presented more than one significant CpG sites. Conclusion Our findings provide new insights into the molecular mechanisms underlying the complex phenotype of antidepressant response, indicating that methylation at specific genes could be a promising biomarker that needs further replication in large cohorts.
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Affiliation(s)
- Albert Martinez-Pinteño
- Department of Basic Clinal Practice, Pharmacology Unit, University of Barcelona, Barcelona, Spain
| | - Natalia Rodriguez
- Department of Basic Clinal Practice, Pharmacology Unit, University of Barcelona, Barcelona, Spain
| | - Ana Blázquez
- Department of Child and Adolescent Psychiatry and Psychology, Institute of Neurosciences, Hospital Clinic de Barcelona, Barcelona, Spain
| | - Maria Teresa Plana
- Department of Child and Adolescent Psychiatry and Psychology, Institute of Neurosciences, Hospital Clinic de Barcelona, Barcelona, Spain
| | - Eva Varela
- Department of Child and Adolescent Psychiatry and Psychology, Institute of Neurosciences, Hospital Clinic de Barcelona, Barcelona, Spain
| | - Patricia Gassó
- Department of Basic Clinal Practice, Pharmacology Unit, University of Barcelona, Barcelona, Spain.,Clinical and Experimental Neuroscience Area, The August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Amalia Lafuente
- Department of Basic Clinal Practice, Pharmacology Unit, University of Barcelona, Barcelona, Spain.,Clinical and Experimental Neuroscience Area, The August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,G04 Group, Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Carlos III Health Institute, Madrid, Spain
| | - Luisa Lazaro
- Department of Child and Adolescent Psychiatry and Psychology, Institute of Neurosciences, Hospital Clinic de Barcelona, Barcelona, Spain.,Clinical and Experimental Neuroscience Area, The August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,G04 Group, Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Carlos III Health Institute, Madrid, Spain.,Department of Medicine, University of Barcelona, Barcelona, Spain
| | - Sergi Mas
- Department of Basic Clinal Practice, Pharmacology Unit, University of Barcelona, Barcelona, Spain.,Clinical and Experimental Neuroscience Area, The August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,G04 Group, Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Carlos III Health Institute, Madrid, Spain
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16
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DNA methylation in children with prenatal methamphetamine exposure and environmental adversity. Pediatr Res 2021; 89:1152-1156. [PMID: 32663835 PMCID: PMC7855315 DOI: 10.1038/s41390-020-1058-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 06/01/2020] [Accepted: 06/25/2020] [Indexed: 11/09/2022]
Abstract
BACKGROUND Methamphetamine (MA) use during pregnancy is a significant public health concern in the United States and affects long-term brain and behavioral development in children. We hypothesized that prenatal MA exposure would be related to greater DNA methylation of HSD11B2 and postnatal environmental stress. METHODS The Infant Development, Environment, and Lifestyle Study (IDEAL), a longitudinal study of prenatal MA exposure enrolled mother-infant dyads in California, Hawaii, Iowa, and Oklahoma. Prenatal exposure was defined by maternal self-report and/or meconium toxicology screening. At ages 10-11 years, 100 children were assessed for drug exposure and DNA methylation of HSD11B2. Hierarchical linear models were used to determine the association between prenatal MA exposure and methylation of HSD11B2 at four CpG sites. RESULTS Prenatal MA exposure (1.4% vs 0.31%, P < 0.01) and early childhood adversity (3.0 vs 2.0, P < 0.01) were associated with greater DNA methylation of HSD11B2 at the CpG2 site. The statistically significant effects of early childhood adversity (B = 0.11, P < 0.01) and prenatal MA exposure (B = 0.32, P = 0.03) on DNA methylation remained after adjusting for covariates. CONCLUSIONS Prenatal MA exposure is related to postnatal childhood adversity and epigenetic alterations in HSD11B2, an important gene along the stress response pathway suggesting prenatal and postnatal programming effects. IMPACT Prenatal methamphetamine exposure has been associated with developmental issues in newborns, yet little is known about the stress pathophysiology of methamphetamine on neurobehavior. This is the first evidence that prenatal methamphetamine exposure acts as a stressor, confirming the third pathophysiology of methamphetamine exposure.
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Kato Y, Kuwabara H, Okada T, Munesue T, Benner S, Kuroda M, Kojima M, Yassin W, Eriguchi Y, Kameno Y, Murayama C, Nishimura T, Tsuchiya K, Kasai K, Ozaki N, Kosaka H, Yamasue H. Oxytocin-induced increase in N,N-dimethylglycine and time course of changes in oxytocin efficacy for autism social core symptoms. Mol Autism 2021; 12:15. [PMID: 33622389 PMCID: PMC7903697 DOI: 10.1186/s13229-021-00423-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 02/12/2021] [Indexed: 11/12/2022] Open
Abstract
Background Oxytocin is expected as a novel therapeutic agent for autism spectrum disorder (ASD) core symptoms. However, previous results on the efficacy of repeated administrations of oxytocin are controversial. Recently, we reported time-course changes in the efficacy of the neuropeptide underlying the controversial effects of repeated administration; however, the underlying mechanisms remained unknown. Methods The current study explored metabolites representing the molecular mechanisms of oxytocin’s efficacy using high-throughput metabolomics analysis on plasma collected before and after 6-week repeated intranasal administration of oxytocin (48 IU/day) or placebo in adult males with ASD (N = 106) who participated in a multi-center, parallel-group, double-blind, placebo-controlled, randomized controlled trial. Results Among the 35 metabolites measured, a significant increase in N,N-dimethylglycine was detected in the subjects administered oxytocin compared with those given placebo at a medium effect size (false discovery rate (FDR) corrected P = 0.043, d = 0.74, N = 83). Furthermore, subgroup analyses of the participants displaying a prominent time-course change in oxytocin efficacy revealed a significant effect of oxytocin on N,N-dimethylglycine levels with a large effect size (PFDR = 0.004, d = 1.13, N = 60). The increase in N,N-dimethylglycine was significantly correlated with oxytocin-induced clinical changes, assessed as changes in quantifiable characteristics of autistic facial expression, including both of improvements between baseline and 2 weeks (PFDR = 0.006, r = − 0.485, N = 43) and deteriorations between 2 and 4 weeks (PFDR = 0.032, r = 0.415, N = 37). Limitations The metabolites changes caused by oxytocin administration were quantified using peripheral blood and therefore may not directly reflect central nervous system changes. Conclusion Our findings demonstrate an association of N,N-dimethylglycine upregulation with the time-course change in the efficacy of oxytocin on autistic social deficits. Furthermore, the current findings support the involvement of the N-methyl-D-aspartate receptor and neural plasticity to the time-course change in oxytocin’s efficacy. Trial registration: A multi-center, parallel-group, placebo-controlled, double-blind, confirmatory trial of intranasal oxytocin in participants with autism spectrum disorders (the date registered: 30 October 2014; UMIN Clinical Trials Registry: https://upload.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000017703) (UMIN000015264).
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Affiliation(s)
- Yasuhiko Kato
- Department of Psychiatry, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashiku, Hamamatsu City, 431-3192, Japan
| | - Hitoshi Kuwabara
- Department of Psychiatry, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashiku, Hamamatsu City, 431-3192, Japan
| | - Takashi Okada
- Department of Psychiatry, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Toshio Munesue
- Research Center for Child Mental Development, Kanazawa University, 13-1 Takara-machi, Kanazawa, 920-8640, Japan
| | - Seico Benner
- Department of Psychiatry, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashiku, Hamamatsu City, 431-3192, Japan
| | - Miho Kuroda
- Department of Child Neuropsychiatry, School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Masaki Kojima
- Department of Child Neuropsychiatry, School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Walid Yassin
- Department of Child Neuropsychiatry, School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Yosuke Eriguchi
- Department of Child Neuropsychiatry, School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Yosuke Kameno
- Department of Psychiatry, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashiku, Hamamatsu City, 431-3192, Japan
| | - Chihiro Murayama
- Department of Psychiatry, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashiku, Hamamatsu City, 431-3192, Japan
| | - Tomoko Nishimura
- United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Osaka/Kanazawa/Hamamatsu/Chiba/Fukui, Japan
| | - Kenji Tsuchiya
- United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Osaka/Kanazawa/Hamamatsu/Chiba/Fukui, Japan
| | - Kiyoto Kasai
- Department of Neuropsychiatry, School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Norio Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Hirotaka Kosaka
- Department of Neuropsychiatry, Faculty of Medical Sciences, University of Fukui, Eiheiji, Fukui, 910-1193, Japan
| | - Hidenori Yamasue
- Department of Psychiatry, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashiku, Hamamatsu City, 431-3192, Japan. .,United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Osaka/Kanazawa/Hamamatsu/Chiba/Fukui, Japan.
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Kling T, Wenger A, Carén H. DNA methylation-based age estimation in pediatric healthy tissues and brain tumors. Aging (Albany NY) 2020; 12:21037-21056. [PMID: 33168783 PMCID: PMC7695434 DOI: 10.18632/aging.202145] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/03/2020] [Indexed: 12/20/2022]
Abstract
Several DNA methylation clocks have been developed to reflect chronological age of human tissues, but most clocks have been trained on adult samples. The rapid methylome changes in children and the role of epigenetics in pediatric tumors calls for tools accurately estimating methylation age in children. We aimed to evaluate seven methylation clocks in multiple tissues from healthy children to inform future studies on the optimal clock for pediatric cohorts, and analyzed the methylation age in brain tumors. We found that clocks trained on pediatric samples were the best in all tested tissues, highlighting the need for dedicated clocks. For blood samples, the Skin and blood clock had the best correlation with chronological age, while PedBE was the most accurate for saliva and buccal samples, and Horvath for brain tissue. Horvath methylation age was accelerated in pediatric brain tumors and the acceleration was subtype-specific for atypical teratoid rhabdoid tumor (ATRT), ependymoma, medulloblastoma and glioma. The subtypes with the highest acceleration corresponded to the worst prognostic categories in ATRT, ependymoma and glioma, whereas the relationship was reversed in medulloblastoma. This suggests that methylation age has potential as a prognostic biomarker in pediatric brain tumors and should be further explored.
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Affiliation(s)
- Teresia Kling
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Wenger
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Helena Carén
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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19
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Everson TM, O'Shea TM, Burt A, Hermetz K, Carter BS, Helderman J, Hofheimer JA, McGowan EC, Neal CR, Pastyrnak SL, Smith LM, Soliman A, DellaGrotta SA, Dansereau LM, Padbury JF, Lester BM, Marsit CJ. Serious neonatal morbidities are associated with differences in DNA methylation among very preterm infants. Clin Epigenetics 2020; 12:151. [PMID: 33076993 PMCID: PMC7574188 DOI: 10.1186/s13148-020-00942-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 09/28/2020] [Indexed: 12/22/2022] Open
Abstract
Background Infants born very preterm are more likely to experience neonatal morbidities compared to their term peers. Variations in DNA methylation (DNAm) associated with these morbidities may yield novel information about the processes impacted by these morbidities. Methods This study included 532 infants born < 30 weeks gestation, participating in the Neonatal Neurobehavior and Outcomes in Very Preterm Infants study. We used a neonatal morbidity risk score, which was an additive index of the number of morbidities experienced during the NICU stay, including bronchopulmonary dysplasia (BPD), severe brain injury, serious neonatal infections, and severe retinopathy of prematurity. DNA was collected from buccal cells at discharge from the NICU, and DNAm was measured using the Illumina MethylationEPIC. We tested for differential methylation in association with the neonatal morbidity risk score then tested for differentially methylated regions (DMRs) and overrepresentation of biological pathways. Results We identified ten differentially methylated CpGs (α Bonferroni-adjusted for 706,278 tests) that were associated with increasing neonatal morbidity risk scores at three intergenic regions and at HPS4, SRRD, FGFR1OP, TNS3, TMEM266, LRRC3B, ZNF780A, and TENM2. These mostly followed dose–response patterns, for 8 CpGs increasing DNAm associated with increased numbers of morbidities, while for 2 CpGs the risk score was associated with decreasing DNAm. BPD was the most substantial contributor to differential methylation. We also identified seven potential DMRs and over-representation of genes involved in Wnt signaling; however, these results were not significant after Bonferroni adjustment for multiple testing. Conclusions Neonatal DNAm, within genes involved in fibroblast growth factor activities, cellular invasion and migration, and neuronal signaling and development, are sensitive to the neonatal health complications of prematurity. We hypothesize that these epigenetic features may be representative of an integrated marker of neonatal health and development and are promising candidates to integrate with clinical information for studying developmental impairments in childhood.
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Affiliation(s)
- Todd M Everson
- Gangarosa Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, USA.
| | - T Michael O'Shea
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Amber Burt
- Gangarosa Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Karen Hermetz
- Gangarosa Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Brian S Carter
- Department of Pediatrics-Neonatology, Children's Mercy Hospital, Kansas City, MO, USA
| | - Jennifer Helderman
- Department of Pediatrics, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Julie A Hofheimer
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Elisabeth C McGowan
- Department of Pediatrics, Brown Alpert Medical School and Women and Infants Hospital, Providence, RI, USA
| | - Charles R Neal
- Department of Pediatrics, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, USA
| | - Steven L Pastyrnak
- Department of Pediatrics, Spectrum Health-Helen Devos Hospital, Grand Rapids, MI, USA
| | - Lynne M Smith
- Department of Pediatrics, Lundquist Institute At Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Antoine Soliman
- Department of Pediatrics, Miller Children's and Women's Hospital Long Beach, Long Beach, CA, USA
| | - Sheri A DellaGrotta
- Brown Center for the Study of Children at Risk, Brown Alpert Medical School and Women and Infants Hospital, Providence, RI, USA
| | - Lynne M Dansereau
- Brown Center for the Study of Children at Risk, Brown Alpert Medical School and Women and Infants Hospital, Providence, RI, USA
| | - James F Padbury
- Department of Pediatrics, Brown Alpert Medical School and Women and Infants Hospital, Providence, RI, USA
| | - Barry M Lester
- Department of Pediatrics, Brown Alpert Medical School and Women and Infants Hospital, Providence, RI, USA.,Brown Center for the Study of Children at Risk, Brown Alpert Medical School and Women and Infants Hospital, Providence, RI, USA.,Department of Psychiatry and Human Behavior, Brown Alpert Medical School, Providence, RI, USA
| | - Carmen J Marsit
- Gangarosa Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, USA
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20
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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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21
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McEwen LM, O'Donnell KJ, McGill MG, Edgar RD, Jones MJ, MacIsaac JL, Lin DTS, Ramadori K, Morin A, Gladish N, Garg E, Unternaehrer E, Pokhvisneva I, Karnani N, Kee MZL, Klengel T, Adler NE, Barr RG, Letourneau N, Giesbrecht GF, Reynolds JN, Czamara D, Armstrong JM, Essex MJ, de Weerth C, Beijers R, Tollenaar MS, Bradley B, Jovanovic T, Ressler KJ, Steiner M, Entringer S, Wadhwa PD, Buss C, Bush NR, Binder EB, Boyce WT, Meaney MJ, Horvath S, Kobor MS. The PedBE clock accurately estimates DNA methylation age in pediatric buccal cells. Proc Natl Acad Sci U S A 2020; 117:23329-23335. [PMID: 31611402 PMCID: PMC7519312 DOI: 10.1073/pnas.1820843116] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The development of biological markers of aging has primarily focused on adult samples. Epigenetic clocks are a promising tool for measuring biological age that show impressive accuracy across most tissues and age ranges. In adults, deviations from the DNA methylation (DNAm) age prediction are correlated with several age-related phenotypes, such as mortality and frailty. In children, however, fewer such associations have been made, possibly because DNAm changes are more dynamic in pediatric populations as compared to adults. To address this gap, we aimed to develop a highly accurate, noninvasive, biological measure of age specific to pediatric samples using buccal epithelial cell DNAm. We gathered 1,721 genome-wide DNAm profiles from 11 different cohorts of typically developing individuals aged 0 to 20 y old. Elastic net penalized regression was used to select 94 CpG sites from a training dataset (n = 1,032), with performance assessed in a separate test dataset (n = 689). DNAm at these 94 CpG sites was highly predictive of age in the test cohort (median absolute error = 0.35 y). The Pediatric-Buccal-Epigenetic (PedBE) clock was characterized in additional cohorts, showcasing the accuracy in longitudinal data, the performance in nonbuccal tissues and adult age ranges, and the association with obstetric outcomes. The PedBE tool for measuring biological age in children might help in understanding the environmental and contextual factors that shape the DNA methylome during child development, and how it, in turn, might relate to child health and disease.
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Affiliation(s)
- Lisa M McEwen
- Department of Medical Genetics, University of British Columbia-BC Children's Hospital Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - Kieran J O'Donnell
- Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada H4H 1R3
- Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR) Institute, Toronto, ON, Canada M5G 1M1
| | - Megan G McGill
- Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada H4H 1R3
| | - Rachel D Edgar
- Department of Medical Genetics, University of British Columbia-BC Children's Hospital Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - Meaghan J Jones
- Department of Medical Genetics, University of British Columbia-BC Children's Hospital Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - Julia L MacIsaac
- Department of Medical Genetics, University of British Columbia-BC Children's Hospital Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - David Tse Shen Lin
- Department of Medical Genetics, University of British Columbia-BC Children's Hospital Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - Katia Ramadori
- Department of Medical Genetics, University of British Columbia-BC Children's Hospital Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - Alexander Morin
- Department of Medical Genetics, University of British Columbia-BC Children's Hospital Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - Nicole Gladish
- Department of Medical Genetics, University of British Columbia-BC Children's Hospital Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - Elika Garg
- Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada H4H 1R3
| | - Eva Unternaehrer
- Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada H4H 1R3
| | - Irina Pokhvisneva
- Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada H4H 1R3
| | - Neerja Karnani
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR); Singapore 117609
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596
| | - Michelle Z L Kee
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR); Singapore 117609
| | - Torsten Klengel
- Department of Psychiatry, Harvard Medical School-McLean Hospital, Belmont, MA 02478
| | - Nancy E Adler
- Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR) Institute, Toronto, ON, Canada M5G 1M1
- Department of Psychiatry, University of California, San Francisco, CA 94143
- Department of Pediatrics, University of California, San Francisco, CA 94143
| | - Ronald G Barr
- Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR) Institute, Toronto, ON, Canada M5G 1M1
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Nicole Letourneau
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada T2N 4N1
- Faculty of Nursing, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Gerald F Giesbrecht
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada T2N 4N1
- Department of Paediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - James N Reynolds
- Department of Biomedical and Molecular Sciences, School of Medicine, Queen's University, Kingston, ON, Canada K7L 3N6
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Jeffrey M Armstrong
- Department of Psychiatry, University of Wisconsin-Madison, Madison, WI 53706
| | - Marilyn J Essex
- Department of Psychiatry, University of Wisconsin-Madison, Madison, WI 53706
| | - Carolina de Weerth
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 HR, Nijmegen, The Netherlands
| | - Roseriet Beijers
- Behavioural Science Institute, Radboud University, 6525 HR, Nijmegen, The Netherlands
| | - Marieke S Tollenaar
- Leiden Institute for Brain and Cognition, Institute of Psychology, Leiden University, 2300 RB, Leiden, The Netherlands
| | - Bekh Bradley
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30322
| | - Tanja Jovanovic
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30322
| | - Kerry J Ressler
- Department of Psychiatry, Harvard Medical School-McLean Hospital, Belmont, MA 02478
| | - Meir Steiner
- Department of Psychiatry and Behavioural Neurosciences, St. Joseph's Healthcare Hamilton, McMaster University, Hamilton, ON, Canada L8S 4L8
| | - Sonja Entringer
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Institute of Medical Psychology, 10117 Berlin, Germany
- Development, Health, and Disease Research Program, University of California, Irvine, CA 92617
| | - Pathik D Wadhwa
- Development, Health, and Disease Research Program, University of California, Irvine, CA 92617
- Department of Psychiatry and Human Behavior, School of Medicine, University of California, Irvine, CA, 92617
- Department of Obstetrics and Gynecology, School of Medicine, University of California, Irvine, CA, 92617
- Department of Epidemiology, School of Medicine, University of California, Irvine, CA, 92617
| | - Claudia Buss
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Institute of Medical Psychology, 10117 Berlin, Germany
| | - Nicole R Bush
- Department of Psychiatry, University of California, San Francisco, CA 94143
| | - Elisabeth B Binder
- Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR) Institute, Toronto, ON, Canada M5G 1M1
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30322
| | - W Thomas Boyce
- Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR) Institute, Toronto, ON, Canada M5G 1M1
- Department of Psychiatry, University of California, San Francisco, CA 94143
- Department of Pediatrics, University of California, San Francisco, CA 94143
| | - Michael J Meaney
- Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada H4H 1R3
- Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR) Institute, Toronto, ON, Canada M5G 1M1
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR); Singapore 117609
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095;
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA 90095
| | - Michael S Kobor
- Department of Medical Genetics, University of British Columbia-BC Children's Hospital Research Institute, Vancouver, BC, Canada V5Z 4H4;
- Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR) Institute, Toronto, ON, Canada M5G 1M1
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22
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Lee EC, Hu VW. Phenotypic Subtyping and Re-Analysis of Existing Methylation Data from Autistic Probands in Simplex Families Reveal ASD Subtype-Associated Differentially Methylated Genes and Biological Functions. Int J Mol Sci 2020; 21:E6877. [PMID: 32961747 PMCID: PMC7555936 DOI: 10.3390/ijms21186877] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 12/27/2022] Open
Abstract
Autism spectrum disorder (ASD) describes a group of neurodevelopmental disorders with core deficits in social communication and manifestation of restricted, repetitive, and stereotyped behaviors. Despite the core symptomatology, ASD is extremely heterogeneous with respect to the severity of symptoms and behaviors. This heterogeneity presents an inherent challenge to all large-scale genome-wide omics analyses. In the present study, we address this heterogeneity by stratifying ASD probands from simplex families according to the severity of behavioral scores on the Autism Diagnostic Interview-Revised diagnostic instrument, followed by re-analysis of existing DNA methylation data from individuals in three ASD subphenotypes in comparison to that of their respective unaffected siblings. We demonstrate that subphenotyping of cases enables the identification of over 1.6 times the number of statistically significant differentially methylated regions (DMR) and DMR-associated genes (DAGs) between cases and controls, compared to that identified when all cases are combined. Our analyses also reveal ASD-related neurological functions and comorbidities that are enriched among DAGs in each phenotypic subgroup but not in the combined case group. Moreover, relational gene networks constructed with the DAGs reveal signaling pathways associated with specific functions and comorbidities. In addition, a network comprised of DAGs shared among all ASD subgroups and the combined case group is enriched in genes involved in inflammatory responses, suggesting that neuroinflammation may be a common theme underlying core features of ASD. These findings demonstrate the value of phenotype definition in methylomic analyses of ASD and may aid in the development of subtype-directed diagnostics and therapeutics.
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Affiliation(s)
| | - Valerie W. Hu
- Department of Biochemistry and Molecular Medicine, The George Washington University, School of Medicine and Health Sciences, Washington, DC 20037, USA;
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23
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Stathopoulos S, Gaujoux R, Lindeque Z, Mahony C, Van Der Colff R, Van Der Westhuizen F, O'Ryan C. DNA Methylation Associated with Mitochondrial Dysfunction in a South African Autism Spectrum Disorder Cohort. Autism Res 2020; 13:1079-1093. [PMID: 32490597 PMCID: PMC7496548 DOI: 10.1002/aur.2310] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 01/24/2020] [Accepted: 04/20/2020] [Indexed: 02/06/2023]
Abstract
Autism spectrum disorder (ASD) is characterized by phenotypic heterogeneity and a complex genetic architecture which includes distinctive epigenetic patterns. We report differential DNA methylation patterns associated with ASD in South African children. An exploratory whole‐epigenome methylation screen using the Illumina 450 K MethylationArray identified differentially methylated CpG sites between ASD and controls that mapped to 898 genes (P ≤ 0.05) which were enriched for nine canonical pathways converging on mitochondrial metabolism and protein ubiquitination. Targeted Next Generation Bisulfite Sequencing of 27 genes confirmed differential methylation between ASD and control in our cohort. DNA pyrosequencing of two of these genes, the mitochondrial enzyme Propionyl‐CoA Carboxylase subunit Beta (PCCB) and Protocadherin Alpha 12 (PCDHA12), revealed a wide range of methylation levels (9–49% and 0–54%, respectively) in both ASD and controls. Three CpG loci were differentially methylated in PCCB (P ≤ 0.05), while PCDHA12, previously linked to ASD, had two significantly different CpG sites (P ≤ 0.001) between ASD and control. Differentially methylated CpGs were hypomethylated in ASD. Metabolomic analysis of urinary organic acids revealed that three metabolites, 3‐hydroxy‐3‐methylglutaric acid (P = 0.008), 3‐methyglutaconic acid (P = 0.018), and ethylmalonic acid (P = 0.043) were significantly elevated in individuals with ASD. These metabolites are directly linked to mitochondrial respiratory chain disorders, with a putative link to PCCB, consistent with impaired mitochondrial function. Our data support an association between DNA methylation and mitochondrial dysfunction in the etiology of ASD. Autism Res 2020, 13: 1079‐1093. © 2020 The Authors. Autism Research published by International Society for Autism Research published by Wiley Periodicals, Inc. Lay Summary Epigenetic changes are chemical modifications of DNA which can change gene function. DNA methylation, a type of epigenetic modification, is linked to autism. We examined DNA methylation in South African children with autism and identified mitochondrial genes associated with autism. Mitochondria are power‐suppliers in cells and mitochondrial genes are essential to metabolism and energy production, which are important for brain cells during development. Our findings suggest that some individuals with ASD also have mitochondrial dysfunction.
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Affiliation(s)
- Sofia Stathopoulos
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | | | - Zander Lindeque
- Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Caitlyn Mahony
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Rachelle Van Der Colff
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | | | - Colleen O'Ryan
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
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24
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Abdelzaher LA, Hussein OA, Ashry IEM. The Novel Potential Therapeutic Utility of Montelukast in Alleviating Autistic Behavior Induced by Early Postnatal Administration of Thimerosal in Mice. Cell Mol Neurobiol 2020; 41:129-150. [PMID: 32303879 DOI: 10.1007/s10571-020-00841-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 04/01/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND AND AIM: Thimerosal (THIM) is a mercury-containing preservative widely used in many biological and medical products including many vaccines. It has been accused of being a possible etiological factor for some neurodevelopmental disorders such as autistic spectrum disorders (ASDs). In our study, the potential therapeutic effect of montelukast, a leukotriene receptor antagonist used to treat seasonal allergies and asthma, on THIM mice model (ASDs model) was examined. METHODOLOGY Newborn mice were randomly distributed into three groups: (Group 1) Control (Cont.) group received saline injections. (Group 2) THIM-treated (THIM) group received THIM intramuscular (IM) at a dose of 3000 μg Hg/kg on postnatal days 7, 9, 11, and 15. (Group 3) Montelukast-treated (Monte) group received THIM followed by montelukast sodium (10 mg/kg/day) intraperitoneal (IP) for 3 weeks. Mice were evaluated for growth development, social interactions, anxiety, locomotor activity, and cognitive function. Brain histopathology, alpha 7 nicotinic acetylcholine receptors (α7nAChRs), nuclear factor kappa B p65 (NF-κB p65), apoptotic factor (Bax), and brain injury markers were evaluated as well. RESULTS THIIM significantly impaired social activity and growth development. Montelukast mitigated THIM-induced social deficit probably through α7nAChRs upregulation, NF-κB p65, Bax, and brain injury markers downregulation, thus suppressing THIM-induced neuronal toxicity and inflammation. CONCLUSION Neonatal exposure to THIM can induce growth retardation and abnormal social interactions similar to those observed in ASDs. Some of these abnormalities could be ameliorated by montelukast via upregulation of α7nAChRs that inhibited NF-κB activation and significant suppression of neuronal injury and the associated apoptosis.
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Affiliation(s)
- Lobna A Abdelzaher
- Department of Pharmacology, Faculty of Medicine, Assiut University, Assiut, Egypt.
| | - Ola A Hussein
- Department of Histology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - I E M Ashry
- Department of Pharmacology, Faculty of Medicine, Assiut University, Assiut, Egypt
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25
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Ganesan H, Balasubramanian V, Iyer M, Venugopal A, Subramaniam MD, Cho SG, Vellingiri B. mTOR signalling pathway - A root cause for idiopathic autism? BMB Rep 2020. [PMID: 31186084 PMCID: PMC6675248 DOI: 10.5483/bmbrep.2019.52.7.137] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental monogenic disorder with a strong genetic influence. Idiopathic autism could be defined as a type of autism that does not have a specific causative agent. Among signalling cascades, mTOR signalling pathway plays a pivotal role not only in cell cycle, but also in protein synthesis and regulation of brain homeostasis in ASD patients. The present review highlights, underlying mechanism of mTOR and its role in altered signalling cascades as a triggering factor in the onset of idiopathic autism. Further, this review discusses how distorted mTOR signalling pathway stimulates truncated translation in neuronal cells and leads to downregulation of protein synthesis at dendritic spines of the brain. This review concludes by suggesting downstream regulators such as p70S6K, eIF4B, eIF4E of mTOR signalling pathway as promising therapeutic targets for idiopathic autistic individuals. [BMB Reports 2019; 52(7): 424-433].
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Affiliation(s)
- Harsha Ganesan
- Human Molecular Cytogenetics and Stem Cell Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore 641046, Tamil Nadu, India
| | - Venkatesh Balasubramanian
- Human Molecular Cytogenetics and Stem Cell Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore 641046, Tamil Nadu, India
| | - Mahalaxmi Iyer
- Department of Zoology, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore 641043, Tamil Nadu, India
| | - Anila Venugopal
- Human Molecular Cytogenetics and Stem Cell Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore 641046, Tamil Nadu, India
| | - Mohana Devi Subramaniam
- Department of Genetics and Molecular Biology, Vision Research Foundation, Sankara Nethralaya, Chennai 600006, Tamil Nadu, India
| | - Ssang-Goo Cho
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Korea
| | - Balachandar Vellingiri
- Human Molecular Cytogenetics and Stem Cell Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore 641046, Tamil Nadu, India
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26
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New Horizons for Molecular Genetics Diagnostic and Research in Autism Spectrum Disorder. ADVANCES IN NEUROBIOLOGY 2020; 24:43-81. [PMID: 32006356 DOI: 10.1007/978-3-030-30402-7_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Autism spectrum disorder (ASD) is a highly heritable, heterogeneous, and complex pervasive neurodevelopmental disorder (PND) characterized by distinctive abnormalities of human cognitive functions, social interaction, and speech development.Nowadays, several genetic changes including chromosome abnormalities, genetic variations, transcriptional epigenetics, and noncoding RNA have been identified in ASD. However, the association between these genetic modifications and ASDs has not been confirmed yet.The aim of this review is to summarize the key findings in ASD from genetic viewpoint that have been identified from the last few decades of genetic and molecular research.
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27
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Hong SJ, Valk SL, Di Martino A, Milham MP, Bernhardt BC. Multidimensional Neuroanatomical Subtyping of Autism Spectrum Disorder. Cereb Cortex 2019; 28:3578-3588. [PMID: 28968847 DOI: 10.1093/cercor/bhx229] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 08/23/2017] [Indexed: 12/15/2022] Open
Abstract
Autism spectrum disorder (ASD) is a group of neurodevelopmental disorders with multiple biological etiologies and highly variable symptoms. Using a novel analytical framework that integrates cortex-wide MRI markers of vertical (i.e., thickness, tissue contrast) and horizontal (i.e., surface area, geodesic distance) cortical organization, we could show that a large multi-centric cohort of individuals with ASD falls into 3 distinctive anatomical subtypes (ASD-I: cortical thickening, increased surface area, tissue blurring; ASD-II: cortical thinning, decreased distance; ASD-III: increased distance). Bootstrap analysis indicated a high consistency of these biotypes across thousands of simulations, while analysis of behavioral phenotypes and resting-state fMRI showed differential symptom load (i.e., Autism Diagnostic Observation Schedule; ADOS) and instrinsic connectivity anomalies in communication and social-cognition networks. Notably, subtyping improved supervised learning approaches predicting ADOS score in single subjects, with significantly increased performance compared to a subtype-blind approach. The existence of different subtypes may reconcile previous results so far not converging on a consistent pattern of anatomical anomalies in autism, and possibly relate the presence of diverging corticogenic and maturational anomalies. The high accuracy for symptom severity prediction indicates benefits of MRI biotyping for personalized diagnostics and may guide the development of targeted therapeutic strategies.
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Affiliation(s)
- Seok-Jun Hong
- Multimodal Imaging and Connectome Analysis Laboratory, Montreal Neurological Institute and Hospital, McGill University, 3801 University Street, Montreal, QC, Canada
| | - Sofie L Valk
- Department of Social Neuroscience, Max Planck Institute for Human Cognitive and Brain Sciences, Stephanstrasse 1a, Leipzig, Germany
| | - Adriana Di Martino
- Department of Child and Adolescent Psychiatry, Child Study Center at NYU Langone Health, 1 Park Avenue, New York, NY, USA
| | - Michael P Milham
- Center for the Developing Brain, Child Mind Institute, 445 Park Avenue, New York, NY, USA.,Center for Biomedical Imaging and Neuromodulation, Nathan Kline Institute, 140 Old Orangeburg Rd, Orangeburg, New York, NY, USA
| | - Boris C Bernhardt
- Multimodal Imaging and Connectome Analysis Laboratory, Montreal Neurological Institute and Hospital, McGill University, 3801 University Street, Montreal, QC, Canada
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28
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Kimura R, Nakata M, Funabiki Y, Suzuki S, Awaya T, Murai T, Hagiwara M. An epigenetic biomarker for adult high-functioning autism spectrum disorder. Sci Rep 2019; 9:13662. [PMID: 31541176 PMCID: PMC6754433 DOI: 10.1038/s41598-019-50250-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 09/09/2019] [Indexed: 12/22/2022] Open
Abstract
Increasing evidence suggests that epigenetic mechanisms play a role in the etiology of autism spectrum disorder (ASD). To date, several studies have attempted to identify epigenetic biomarkers for ASD. However, reliable markers remain to be established and most of these studies have focused on pediatric patients with ASD. In this study, we sought to find an epigenetic DNA methylation biomarker from peripheral blood for adult patients with high-functioning ASD. DNA methylation profiles were analyzed using the Illumina 450 K methylation array. To identify robust candidate markers, we employed two types of machine-learning algorithms for marker selection. We identified a potential marker (cg20793532) for which is the AUC value was 0.79. Notably, cg20793532 was annotated to the PPP2R2C gene, which was hypermethylated and down-regulated in blood from ASD patients compared to that in the controls. Although requiring careful interpretation, this pilot study seems to provide a potential blood biomarker for identifying individuals with high-functioning ASD.
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Affiliation(s)
- Ryo Kimura
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan.
| | - Masatoshi Nakata
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Yasuko Funabiki
- Department of Cognitive and Behavioral Science, Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, 606-8501, Japan.,Department of Psychiatry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Shiho Suzuki
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Tomonari Awaya
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Toshiya Murai
- Department of Psychiatry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan.
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Siu MT, Butcher DT, Turinsky AL, Cytrynbaum C, Stavropoulos DJ, Walker S, Caluseriu O, Carter M, Lou Y, Nicolson R, Georgiades S, Szatmari P, Anagnostou E, Scherer SW, Choufani S, Brudno M, Weksberg R. Functional DNA methylation signatures for autism spectrum disorder genomic risk loci: 16p11.2 deletions and CHD8 variants. Clin Epigenetics 2019; 11:103. [PMID: 31311581 PMCID: PMC6636171 DOI: 10.1186/s13148-019-0684-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 05/15/2019] [Indexed: 12/19/2022] Open
Abstract
Background Autism spectrum disorder (ASD) is a common and etiologically heterogeneous neurodevelopmental disorder. Although many genetic causes have been identified (> 200 ASD-risk genes), no single gene variant accounts for > 1% of all ASD cases. A role for epigenetic mechanisms in ASD etiology is supported by the fact that many ASD-risk genes function as epigenetic regulators and evidence that epigenetic dysregulation can interrupt normal brain development. Gene-specific DNAm profiles have been shown to assist in the interpretation of variants of unknown significance. Therefore, we investigated the epigenome in patients with ASD or two of the most common genomic variants conferring increased risk for ASD. Genome-wide DNA methylation (DNAm) was assessed using the Illumina Infinium HumanMethylation450 and MethylationEPIC arrays in blood from individuals with ASD of heterogeneous, undefined etiology (n = 52), and individuals with 16p11.2 deletions (16p11.2del, n = 9) or pathogenic variants in the chromatin modifier CHD8 (CHD8+/−, n = 7). Results DNAm patterns did not clearly distinguish heterogeneous ASD cases from controls. However, the homogeneous genetically-defined 16p11.2del and CHD8+/− subgroups each exhibited unique DNAm signatures that distinguished 16p11.2del or CHD8+/− individuals from each other and from heterogeneous ASD and control groups with high sensitivity and specificity. These signatures also classified additional 16p11.2del (n = 9) and CHD8 (n = 13) variants as pathogenic or benign. Our findings that DNAm alterations in each signature target unique genes in relevant biological pathways including neural development support their functional relevance. Furthermore, genes identified in our CHD8+/− DNAm signature in blood overlapped differentially expressed genes in CHD8+/− human-induced pluripotent cell-derived neurons and cerebral organoids from independent studies. Conclusions DNAm signatures can provide clinical utility complementary to next-generation sequencing in the interpretation of variants of unknown significance. Our study constitutes a novel approach for ASD risk-associated molecular classification that elucidates the vital cross-talk between genetics and epigenetics in the etiology of ASD. Electronic supplementary material The online version of this article (10.1186/s13148-019-0684-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- M T Siu
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - D T Butcher
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - A L Turinsky
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - C Cytrynbaum
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, 555 University Ave, Toronto, Ontario, M5G 1X8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - D J Stavropoulos
- Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - S Walker
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - O Caluseriu
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - M Carter
- Department of Genetics, The Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Y Lou
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - R Nicolson
- Department of Psychiatry, University of Western Ontario, London, Ontario, Canada
| | - S Georgiades
- Department of Psychiatry and Behavioural Neurosciences, Offord Centre for Child Studies, McMaster University, Hamilton, Ontario, Canada
| | - P Szatmari
- Child and Youth Mental Health Collaborative, Centre for Addiction and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - E Anagnostou
- Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - S W Scherer
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - S Choufani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - M Brudno
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - R Weksberg
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada. .,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, 555 University Ave, Toronto, Ontario, M5G 1X8, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. .,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada. .,Institute of Medical Science, School of Graduate Studies, University of Toronto, Toronto, Ontario, Canada.
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30
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Wani AL, Shadab GHA. Brain, behavior and the journey towards neuroepigenetic therapeutics. Epigenomics 2019; 11:969-981. [PMID: 31144515 DOI: 10.2217/epi-2018-0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Epigenetics has brought about a major shift in our understanding of biological mechanisms and their associated health effects. Strong epigenetic components have been found to be involved in the progression of many diseases. In several human diseases, including debilitating psychiatric disorders, altered epigenetic status has been found as one of the main causes. With continuous progress on drug development, researchers are enthusiastic toward epigenetic therapeutics which could possibly reverse epigenetic modifications. In this article certain developments in epigenetic therapeutics are highlighted, the indiscriminate use of which could also be associated with potential risk. These risks may partly be due to our limited knowledge on genes and the mechanisms underlying epigenetic involvement in different diseases. Epigenetic changes are fundamentally important for a large number of bodily functions; nonspecific usage of therapeutics could be potentially harmful therefore there is a need to harness epigenetics positively.
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Affiliation(s)
- Ab Latif Wani
- Cytogenetics & Molecular Toxicology Laboratory, Section of Genetics, Department of Zoology, Aligarh Muslim University, Aligarh, Uttar Pradesh, 202002, India
| | - Gg Hammad Ahmad Shadab
- Cytogenetics & Molecular Toxicology Laboratory, Section of Genetics, Department of Zoology, Aligarh Muslim University, Aligarh, Uttar Pradesh, 202002, India
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31
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Mansell G, Gorrie-Stone TJ, Bao Y, Kumari M, Schalkwyk LS, Mill J, Hannon E. Guidance for DNA methylation studies: statistical insights from the Illumina EPIC array. BMC Genomics 2019; 20:366. [PMID: 31088362 PMCID: PMC6518823 DOI: 10.1186/s12864-019-5761-7] [Citation(s) in RCA: 159] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 05/02/2019] [Indexed: 12/12/2022] Open
Abstract
Background There has been a steady increase in the number of studies aiming to identify DNA methylation differences associated with complex phenotypes. Many of the challenges of epigenetic epidemiology regarding study design and interpretation have been discussed in detail, however there are analytical concerns that are outstanding and require further exploration. In this study we seek to address three analytical issues. First, we quantify the multiple testing burden and propose a standard statistical significance threshold for identifying DNA methylation sites that are associated with an outcome. Second, we establish whether linear regression, the chosen statistical tool for the majority of studies, is appropriate and whether it is biased by the underlying distribution of DNA methylation data. Finally, we assess the sample size required for adequately powered DNA methylation association studies. Results We quantified DNA methylation in the Understanding Society cohort (n = 1175), a large population based study, using the Illumina EPIC array to assess the statistical properties of DNA methylation association analyses. By simulating null DNA methylation studies, we generated the distribution of p-values expected by chance and calculated the 5% family-wise error for EPIC array studies to be 9 × 10− 8. Next, we tested whether the assumptions of linear regression are violated by DNA methylation data and found that the majority of sites do not satisfy the assumption of normal residuals. Nevertheless, we found no evidence that this bias influences analyses by increasing the likelihood of affected sites to be false positives. Finally, we performed power calculations for EPIC based DNA methylation studies, demonstrating that existing studies with data on ~ 1000 samples are adequately powered to detect small differences at the majority of sites. Conclusion We propose that a significance threshold of P < 9 × 10− 8 adequately controls the false positive rate for EPIC array DNA methylation studies. Moreover, our results indicate that linear regression is a valid statistical methodology for DNA methylation studies, despite the fact that the data do not always satisfy the assumptions of this test. These findings have implications for epidemiological-based studies of DNA methylation and provide a framework for the interpretation of findings from current and future studies. Electronic supplementary material The online version of this article (10.1186/s12864-019-5761-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Georgina Mansell
- University of Exeter Medical School, University of Exeter, RD&E Hospital, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Tyler J Gorrie-Stone
- School of Biological Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK
| | - Yanchun Bao
- Institute for Social and Economic Research, University of Essex, Colchester, Essex, CO3 3LG, UK
| | - Meena Kumari
- Institute for Social and Economic Research, University of Essex, Colchester, Essex, CO3 3LG, UK
| | - Leonard S Schalkwyk
- School of Biological Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, RD&E Hospital, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, RD&E Hospital, Barrack Road, Exeter, Devon, EX2 5DW, UK.
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Epigenome-wide Analysis Identifies Genes and Pathways Linked to Neurobehavioral Variation in Preterm Infants. Sci Rep 2019; 9:6322. [PMID: 31004082 PMCID: PMC6474865 DOI: 10.1038/s41598-019-42654-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 04/03/2019] [Indexed: 02/07/2023] Open
Abstract
Neonatal molecular biomarkers of neurobehavioral responses (measures of brain-behavior relationships), when combined with neurobehavioral performance measures, could lead to better predictions of long-term developmental outcomes. To this end, we examined whether variability in buccal cell DNA methylation (DNAm) associated with neurobehavioral profiles in a cohort of infants born less than 30 weeks postmenstrual age (PMA) and participating in the Neonatal Neurobehavior and Outcomes in Very Preterm Infants (NOVI) Study (N = 536). We tested whether epigenetic age, age acceleration, or DNAm levels at individual loci differed between infants based on their NICU Network Neurobehavioral Scale (NNNS) profile classifications. We adjusted for recruitment site, infant sex, PMA, and tissue heterogeneity. Infants with an optimally well-regulated NNNS profile had older epigenetic age compared to other NOVI infants (β1 = 0.201, p-value = 0.026), but no significant difference in age acceleration. In contrast, infants with an atypical NNNS profile had differential methylation at 29 CpG sites (FDR < 10%). Some of the genes annotated to these CpGs included PLA2G4E, TRIM9, GRIK3, and MACROD2, which have previously been associated with neurological structure and function, or with neurobehavioral disorders. These findings contribute to the existing evidence that neonatal epigenetic variations may be informative for infant neurobehavior.
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Turinsky AL, Butcher DT, Choufani S, Weksberg R, Brudno M. Don't brush off buccal data heterogeneity. Epigenetics 2019; 14:109-117. [PMID: 30821575 DOI: 10.1080/15592294.2019.1581592] [Citation(s) in RCA: 5] [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
Buccal epithelial cells are among the most clinically accessible tissues and are increasingly being used to identify epigenetic disease patterns. However, substantial variation in buccal DNA methylation patterns indicates heterogeneity of cell types within and between samples, raising questions of data quality. We systematically estimated cell-type composition for a large collection of buccal and saliva samples from 11 published studies of DNA methylation. In these we identified numerous cases of buccal samples with questionable purity, which may be affected by sampling from individuals with neurodevelopmental disorders, and by the brushes used for sample collection. Further challenges are involved in comparisons with tissues such as saliva, in which buccal component varies widely. We propose a reference-based method of correcting for buccal purity that reduces unwanted variation while preserving cross-tissue differences. Our work demonstrates the wide variation of buccal quality in epigenetic studies and suggests a possible approach to overcome this issue.
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Affiliation(s)
- Andrei L Turinsky
- a Program in Genetics and Genome Biology , The Hospital for Sick Children , Toronto , Ontario , Canada.,b Centre for Computational Medicine , The Hospital for Sick Children , Toronto , Ontario , Canada
| | - Darci T Butcher
- c Department of Pathology and Molecular Medicine , McMaster University , Hamilton , Ontario , Canada
| | - Sanaa Choufani
- a Program in Genetics and Genome Biology , The Hospital for Sick Children , Toronto , Ontario , Canada
| | - Rosanna Weksberg
- a Program in Genetics and Genome Biology , The Hospital for Sick Children , Toronto , Ontario , Canada.,d Division of Clinical and Metabolic Genetics , The Hospital for Sick Children , Toronto , Ontario , Canada.,e Department of Molecular Genetics , University of Toronto , Toronto , Ontario , Canada.,f Department of Pediatrics , University of Toronto , Toronto , Ontario , Canada.,g Institute of Medical Sciences, School of Graduate Studies , University of Toronto , Toronto , Ontario , Canada
| | - Michael Brudno
- a Program in Genetics and Genome Biology , The Hospital for Sick Children , Toronto , Ontario , Canada.,b Centre for Computational Medicine , The Hospital for Sick Children , Toronto , Ontario , Canada.,h Department of Computer Science , University of Toronto , Toronto , Ontario , Canada
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34
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Wiśniowiecka-Kowalnik B, Nowakowska BA. Genetics and epigenetics of autism spectrum disorder-current evidence in the field. J Appl Genet 2019; 60:37-47. [PMID: 30627967 PMCID: PMC6373410 DOI: 10.1007/s13353-018-00480-w] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 12/14/2018] [Accepted: 12/18/2018] [Indexed: 12/26/2022]
Abstract
Autism spectrum disorders (ASD) is a heterogenous group of neurodevelopmental disorders characterized by problems in social interaction and communication as well as the presence of repetitive and stereotyped behavior. It is estimated that the prevalence of ASD is 1–2% in the general population with the average male to female ratio 4–5:1. Although the causes of ASD remain largely unknown, the studies have shown that both genetic and environmental factors play an important role in the etiology of these disorders. Array comparative genomic hybridization and whole exome/genome sequencing studies identified common and rare copy number or single nucleotide variants in genes encoding proteins involved in brain development, which play an important role in neuron and synapse formation and function. The genetic etiology is recognized in ~ 25–35% of patients with ASD. In this article, we review the current state of knowledge about the genetic etiology of ASD and also propose a diagnostic algorithm for patients.
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35
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Integration of DNA methylation patterns and genetic variation in human pediatric tissues help inform EWAS design and interpretation. Epigenetics Chromatin 2019; 12:1. [PMID: 30602389 PMCID: PMC6314079 DOI: 10.1186/s13072-018-0245-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/18/2018] [Indexed: 02/06/2023] Open
Abstract
Background The widespread use of accessible peripheral tissues for epigenetic analyses has prompted increasing interest in the study of tissue-specific DNA methylation (DNAm) variation in human populations. To date, characterizations of inter-individual DNAm variability and DNAm concordance across tissues have been largely performed in adult tissues and therefore are limited in their relevance to DNAm profiles from pediatric samples. Given that DNAm patterns in early life undergo rapid changes and have been linked to a wide range of health outcomes and environmental exposures, direct investigations of tissue-specific DNAm variation in pediatric samples may help inform the design and interpretation of DNAm analyses from early life cohorts. In this study, we present a systematic comparison of genome-wide DNAm patterns between matched pediatric buccal epithelial cells (BECs) and peripheral blood mononuclear cells (PBMCs), two of the most widely used peripheral tissues in human epigenetic studies. Specifically, we assessed DNAm variability, cross-tissue DNAm concordance and genetic determinants of DNAm across two independent early life cohorts encompassing different ages. Results BECs had greater inter-individual DNAm variability compared to PBMCs and highly the variable CpGs are more likely to be positively correlated between the matched tissues compared to less variable CpGs. These sites were enriched for CpGs under genetic influence, suggesting that a substantial proportion of DNAm covariation between tissues can be attributed to genetic variation. Finally, we demonstrated the relevance of our findings to human epigenetic studies by categorizing CpGs from published DNAm association studies of pediatric BECs and peripheral blood. Conclusions Taken together, our results highlight a number of important considerations and practical implications in the design and interpretation of EWAS analyses performed in pediatric peripheral tissues. Electronic supplementary material The online version of this article (10.1186/s13072-018-0245-6) contains supplementary material, which is available to authorized users.
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Lussier AA, Bodnar TS, Mingay M, Morin AM, Hirst M, Kobor MS, Weinberg J. Prenatal Alcohol Exposure: Profiling Developmental DNA Methylation Patterns in Central and Peripheral Tissues. Front Genet 2018; 9:610. [PMID: 30568673 PMCID: PMC6290329 DOI: 10.3389/fgene.2018.00610] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/19/2018] [Indexed: 12/17/2022] Open
Abstract
Background: Prenatal alcohol exposure (PAE) can alter the development of neurobiological systems, leading to lasting neuroendocrine, neuroimmune, and neurobehavioral deficits. Although the etiology of this reprogramming remains unknown, emerging evidence suggests DNA methylation as a potential mediator and biomarker for the effects of PAE due to its responsiveness to environmental cues and relative stability over time. Here, we utilized a rat model of PAE to examine the DNA methylation profiles of rat hypothalami and leukocytes at four time points during early development to assess the genome-wide impact of PAE on the epigenome and identify potential biomarkers of PAE. Our model of PAE resulted in blood alcohol levels of ~80-150 mg/dl throughout the equivalent of the first two trimesters of human pregnancy. Hypothalami were analyzed on postnatal days (P) 1, 8, 15, 22 and leukocytes at P22 to compare central and peripheral markers. Genome-wide DNA methylation analysis was performed by methylated DNA immunoprecipitation followed by next-generation sequencing. Results: PAE resulted in lasting changes to DNA methylation profiles across all four ages, with 118 differentially methylated regions (DMRs) displaying persistent alterations across the developmental period at a false-discovery rate (FDR) < 0.05. In addition, 299 DMRs showed the same direction of change in the hypothalamus and leukocytes of P22 pups at an FDR < 0.05, with some genes overlapping with the developmental profile findings. The majority of these DMRs were located in intergenic regions, which contained several computationally-predicted transcription factor binding sites. Differentially methylated genes were generally involved in immune function, epigenetic remodeling, metabolism, and hormonal signaling, as determined by gene ontology analyses. Conclusions: Persistent DNA methylation changes in the hypothalamus may be associated with the long-term physiological and neurobehavioral alterations in observed in PAE. Furthermore, correlations between epigenetic alterations in peripheral tissues and those in the brain will provide a foundation for the development of biomarkers of fetal alcohol spectrum disorder (FASD). Finally, findings from studies of PAE provide important insight into the etiology of neurodevelopmental and mental health disorders, as they share numerous phenotypes and comorbidities.
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Affiliation(s)
- Alexandre A Lussier
- Department of Cellular & Physiological Sciences, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada.,Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Tamara S Bodnar
- Department of Cellular & Physiological Sciences, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Matthew Mingay
- Department of Microbiology and Immunology, Michael Smith Laboratories Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada
| | - Alexandre M Morin
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Martin Hirst
- Department of Microbiology and Immunology, Michael Smith Laboratories Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency Research Centre, BC Cancer Agency, Vancouver, BC, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada.,Human Early Learning Partnership, University of British Columbia, Vancouver, BC, Canada
| | - Joanne Weinberg
- Department of Cellular & Physiological Sciences, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
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Abstract
Prenatal adversity shapes child neurodevelopment and risk for later mental health problems. The quality of the early care environment can buffer some of the negative effects of prenatal adversity on child development. Retrospective studies, in adult samples, highlight epigenetic modifications as sentinel markers of the quality of the early care environment; however, comparable data from pediatric cohorts are lacking. Participants were drawn from the Maternal Adversity Vulnerability and Neurodevelopment (MAVAN) study, a longitudinal cohort with measures of infant attachment, infant development, and child mental health. Children provided buccal epithelial samples (mean age = 6.99, SD = 1.33 years, n = 226), which were used for analyses of genome-wide DNA methylation and genetic variation. We used a series of linear models to describe the association between infant attachment and (a) measures of child outcome and (b) DNA methylation across the genome. Paired genetic data was used to determine the genetic contribution to DNA methylation at attachment-associated sites. Infant attachment style was associated with infant cognitive development (Mental Development Index) and behavior (Behavior Rating Scale) assessed with the Bayley Scales of Infant Development at 36 months. Infant attachment style moderated the effects of prenatal adversity on Behavior Rating Scale scores at 36 months. Infant attachment was also significantly associated with a principal component that accounted for 11.9% of the variation in genome-wide DNA methylation. These effects were most apparent when comparing children with a secure versus a disorganized attachment style and most pronounced in females. The availability of paired genetic data revealed that DNA methylation at approximately half of all infant attachment-associated sites was best explained by considering both infant attachment and child genetic variation. This study provides further evidence that infant attachment can buffer some of the negative effects of early adversity on measures of infant behavior. We also highlight the interplay between infant attachment and child genotype in shaping variation in DNA methylation. Such findings provide preliminary evidence for a molecular signature of infant attachment and may help inform attachment-focused early intervention programs.
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Bush NR, Edgar RD, Park M, MacIsaac JL, McEwen LM, Adler NE, Essex MJ, Kobor MS, Boyce WT. The biological embedding of early-life socioeconomic status and family adversity in children's genome-wide DNA methylation. Epigenomics 2018; 10:1445-1461. [PMID: 30351206 PMCID: PMC6462839 DOI: 10.2217/epi-2018-0042] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Aim: To examine variation in child DNA methylation to assess its potential as a pathway for effects of childhood social adversity on health across the life course. Materials & methods: In a diverse, prospective community sample of 178 kindergarten children, associations between three types of social experience and DNA methylation within buccal epithelial cells later in childhood were examined. Results: Family income, parental education and family psychosocial adversity each associated with increased or decreased DNA methylation (488, 354 and 102 sites, respectively) within a unique set of genomic CpG sites. Gene ontology analyses pointed to genes serving immune and developmental regulation functions. Conclusion: Findings provided support for DNA methylation as a biomarker linking early-life social experiences with later life health in humans.
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Affiliation(s)
- Nicole R Bush
- Department of Psychiatry, Center for Health & Community, Weill Neuroscience Institute, University of California, San Francisco, 3333 California Street, Suite 465, San Francisco, CA 94118, USA.,Department of Pediatrics, Division of Developmental Medicine, University of California, San Francisco, 550 16th Street, San Francisco, CA 94158, USA
| | - Rachel D Edgar
- Department of Medical Genetics, BC Children's Hospital, Centre for Molecular Medicine & Therapeutics, University of British Columbia, 950 West 28th Ave., Vancouver, BC V5Z 4H4, Canada
| | - Mina Park
- School of Population & Public Health, BC Children's Hospital, University of British Columbia, 4480 Oak St, Vancouver, BC V6H 3N1, Canada
| | - Julia L MacIsaac
- Department of Medical Genetics, BC Children's Hospital, Centre for Molecular Medicine & Therapeutics, University of British Columbia, 950 West 28th Ave., Vancouver, BC V5Z 4H4, Canada
| | - Lisa M McEwen
- Department of Medical Genetics, BC Children's Hospital, Centre for Molecular Medicine & Therapeutics, University of British Columbia, 950 West 28th Ave., Vancouver, BC V5Z 4H4, Canada
| | - Nancy E Adler
- Department of Psychiatry, Center for Health & Community, Weill Neuroscience Institute, University of California, San Francisco, 3333 California Street, Suite 465, San Francisco, CA 94118, USA
| | - Marilyn J Essex
- Department of Psychiatry, University of Wisconsin, Madison,16330 Ellendale Road, Dallas, OR 97338, USA
| | - Michael S Kobor
- Department of Medical Genetics, BC Children's Hospital, Centre for Molecular Medicine & Therapeutics, University of British Columbia, 950 West 28th Ave., Vancouver, BC V5Z 4H4, Canada
| | - W Thomas Boyce
- Department of Psychiatry, Center for Health & Community, Weill Neuroscience Institute, University of California, San Francisco, 3333 California Street, Suite 465, San Francisco, CA 94118, USA.,Department of Pediatrics, Division of Developmental Medicine, University of California, San Francisco, 550 16th Street, San Francisco, CA 94158, USA
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Andrews SV, Sheppard B, Windham GC, Schieve LA, Schendel DE, Croen LA, Chopra P, Alisch RS, Newschaffer CJ, Warren ST, Feinberg AP, Fallin MD, Ladd-Acosta C. Case-control meta-analysis of blood DNA methylation and autism spectrum disorder. Mol Autism 2018; 9:40. [PMID: 29988321 PMCID: PMC6022498 DOI: 10.1186/s13229-018-0224-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/21/2018] [Indexed: 11/10/2022] Open
Abstract
Background Several reports have suggested a role for epigenetic mechanisms in ASD etiology. Epigenome-wide association studies (EWAS) in autism spectrum disorder (ASD) may shed light on particular biological mechanisms. However, studies of ASD cases versus controls have been limited by post-mortem timing and severely small sample sizes. Reports from in-life sampling of blood or saliva have also been very limited in sample size and/or genomic coverage. We present the largest case-control EWAS for ASD to date, combining data from population-based case-control and case-sibling pair studies. Methods DNA from 968 blood samples from children in the Study to Explore Early Development (SEED 1) was used to generate epigenome-wide array DNA methylation (DNAm) data at 485,512 CpG sites for 453 cases and 515 controls, using the Illumina 450K Beadchip. The Simons Simplex Collection (SSC) provided 450K array DNAm data on an additional 343 cases and their unaffected siblings. We performed EWAS meta-analysis across results from the two data sets, with adjustment for sex and surrogate variables that reflect major sources of biological variation and technical confounding such as cell type, batch, and ancestry. We compared top EWAS results to those from a previous brain-based analysis. We also tested for enrichment of ASD EWAS CpGs for being targets of meQTL associations using available SNP genotype data in the SEED sample. Findings In this meta-analysis of blood-based DNA from 796 cases and 858 controls, no single CpG met a Bonferroni discovery threshold of p < 1.12 × 10− 7. Seven CpGs showed differences at p < 1 × 10− 5 and 48 at 1 × 10− 4. Of the top 7, 5 showed brain-based ASD associations as well, often with larger effect sizes, and the top 48 overall showed modest concordance (r = 0.31) in direction of effect with cerebellum samples. Finally, we observed suggestive evidence for enrichment of CpG sites controlled by SNPs (meQTL targets) among the EWAS CpG hits, which was consistent across EWAS and meQTL discovery p value thresholds. Conclusions No single CpG site showed a large enough DNAm difference between cases and controls to achieve epigenome-wide significance in this sample size. However, our results suggest the potential to observe disease associations from blood-based samples. Among the seven sites achieving suggestive statistical significance, we observed consistent, and stronger, effects at the same sites among brain samples. Discovery-oriented EWAS for ASD using blood samples will likely need even larger samples and unified genetic data to further understand DNAm differences in ASD. Electronic supplementary material The online version of this article (10.1186/s13229-018-0224-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shan V Andrews
- 1Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD 21205 USA.,2Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, W6509, Baltimore, MD 21205 USA
| | - Brooke Sheppard
- 1Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD 21205 USA.,2Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, W6509, Baltimore, MD 21205 USA
| | - Gayle C Windham
- 3California Department of Public Health, Environmental Health Investigations Branch, 850 Marina Bay Parkway, Richmond, CA 94804 USA
| | - Laura A Schieve
- 4National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, MS E-86, 1600 Clifton Road, Atlanta, GA 30333 USA
| | - Diana E Schendel
- 5Deparment of Public Health, Section of Epidemiology, Aarhus University, Aarhus, Denmark.,6Department of Economics and Business, National Centre for Register-based Research, Aarhus University, Aarhus, Denmark.,7Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Lisa A Croen
- 8Kaiser Permanente Division of Research, 2000 Broadway, Oakland, CA 94612 USA
| | - Pankaj Chopra
- 9Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322 USA
| | - Reid S Alisch
- 10Department of Psychiatry, University of Wisconsin-Madison, 6001 Research Park Blvd, Madison, WI 53719 USA
| | - Craig J Newschaffer
- 11Department of Epidemiology and Biostatistics, Drexel University School of Public Health, 3215 Market Street, Philadelphia, PA 19104 USA.,A.J. Drexel Autism Institute, 3020 Market Street Suite 560, Philadelphia, PA 19104 USA
| | - Stephen T Warren
- 9Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322 USA.,13Department of Biochemistry, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322 USA.,14Department of Pediatrics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322 USA
| | - Andrew P Feinberg
- 15Center for Epigenetics, Johns Hopkins School of Medicine, 855 N. Wolfe Street, Baltimore, MD 21205 USA.,16Department of Medicine, Johns Hopkins School of Medicine, 855 N. Wolfe Street, Baltimore, MD 21205 USA
| | - M Daniele Fallin
- 2Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, W6509, Baltimore, MD 21205 USA.,15Center for Epigenetics, Johns Hopkins School of Medicine, 855 N. Wolfe Street, Baltimore, MD 21205 USA.,17Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, 624 N. Broadway, HH850, Baltimore, MD 21205 USA
| | - Christine Ladd-Acosta
- 1Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD 21205 USA.,2Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, W6509, Baltimore, MD 21205 USA
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Kong Y, Berko ER, Marcketta A, Maqbool SB, Simões-Pires CA, Kronn DF, Ye KQ, Suzuki M, Auton A, Greally JM. Detecting, quantifying, and discriminating the mechanism of mosaic chromosomal aneuploidies using MAD-seq. Genome Res 2018; 28:1039-1052. [PMID: 29773658 PMCID: PMC6028128 DOI: 10.1101/gr.226282.117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 04/04/2018] [Indexed: 01/23/2023]
Abstract
Current approaches to detect and characterize mosaic chromosomal aneuploidy are limited by sensitivity, efficiency, cost, or the need to culture cells. We describe the mosaic aneuploidy detection by massively parallel sequencing (MAD-seq) capture assay and the MADSEQ analytical approach that allow low (<10%) levels of mosaicism for chromosomal aneuploidy or regional loss of heterozygosity to be detected, assigned to a meiotic or mitotic origin, and quantified as a proportion of the cells in the sample. We show results from a multi-ethnic MAD-seq (meMAD-seq) capture design that works equally well in populations of diverse racial and ethnic origins and how the MADSEQ analytical approach can be applied to exome or whole-genome sequencing data, revealing previously unrecognized aneuploidy or copy number neutral loss of heterozygosity in samples studied by the 1000 Genomes Project, cell lines from public repositories, and one of the Illumina Platinum Genomes samples. We have made the meMAD-seq capture design and MADSEQ analytical software open for unrestricted use, with the goal that they can be applied in clinical samples to allow new insights into the unrecognized prevalence of mosaic chromosomal aneuploidy in humans and its phenotypic associations.
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Affiliation(s)
- Yu Kong
- Department of Genetics and Center for Epigenomics, Albert Einstein College of Medicine, New York, New York 10461, USA
| | - Esther R Berko
- Department of Genetics and Center for Epigenomics, Albert Einstein College of Medicine, New York, New York 10461, USA
| | - Anthony Marcketta
- Department of Genetics and Center for Epigenomics, Albert Einstein College of Medicine, New York, New York 10461, USA
| | - Shahina B Maqbool
- Department of Genetics and Center for Epigenomics, Albert Einstein College of Medicine, New York, New York 10461, USA
| | - Claudia A Simões-Pires
- Department of Genetics and Center for Epigenomics, Albert Einstein College of Medicine, New York, New York 10461, USA
| | - David F Kronn
- Department of Pediatrics, New York Medical College, Valhalla, New York 10595, USA
| | - Kenny Q Ye
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, New York, New York 10461, USA
| | - Masako Suzuki
- Department of Genetics and Center for Epigenomics, Albert Einstein College of Medicine, New York, New York 10461, USA
| | - Adam Auton
- Department of Genetics and Center for Epigenomics, Albert Einstein College of Medicine, New York, New York 10461, USA
| | - John M Greally
- Department of Genetics and Center for Epigenomics, Albert Einstein College of Medicine, New York, New York 10461, USA
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41
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Moosa A, Shu H, Sarachana T, Hu VW. Are endocrine disrupting compounds environmental risk factors for autism spectrum disorder? Horm Behav 2018; 101:13-21. [PMID: 29042182 PMCID: PMC5913002 DOI: 10.1016/j.yhbeh.2017.10.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 09/25/2017] [Accepted: 10/10/2017] [Indexed: 11/30/2022]
Abstract
Recent research on the etiology of autism spectrum disorder (ASD) has shifted in part from a singular focus on genetic causes to the involvement of environmental factors and their gene interactions. This shift in focus is a result of the rapidly increasing prevalence of ASD coupled with the incomplete penetrance of this disorder in monozygotic twins. One such area of environmentally focused research is the association of exposures to endocrine disrupting compounds (EDCs) with elevated risk for ASD. EDCs are exogenous chemicals that can alter endogenous hormone activity and homeostasis, thus potentially disrupting the action of sex and other natural hormones at all stages of human development. Inasmuch as sex hormones play a fundamental role in brain development and sexual differentiation, exposure to EDCs in utero during critical stages of development can have lasting neurological and other physiological influences on the developing fetus and, ultimately, the child as well as adult. This review will focus on the possible contributions of EDCs to autism risk and pathogenesis by first discussing the influence of endogenous sex hormones on the autistic phenotype, followed by a review of documented human exposures to EDCs and associations with behaviors relevant to ASD. Mechanistic links between EDC exposures and aberrant neurodevelopment and behaviors are then considered, with emphasis on EDC-induced transcriptional profiles derived from animal and cellular studies. Finally, this review will discuss possible mechanisms through which EDC exposure can lead to persistent changes in gene expression and phenotype, which may in turn contribute to transgenerational inheritance of ASD.
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Affiliation(s)
- Amer Moosa
- Dept. of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Sciences, 2300 Eye St., NW, Washington, DC 20037, United States.
| | - Henry Shu
- Dept. of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Sciences, 2300 Eye St., NW, Washington, DC 20037, United States.
| | - Tewarit Sarachana
- Department of Clinical Chemistry, Medical Technology Branch, Faculty of Allied Health Sciences, Chulalongkorn University, 154 Rama I Rd., Wangmai, Pathumwan, Bangkok 10330, Thailand.
| | - Valerie W Hu
- Dept. of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Sciences, 2300 Eye St., NW, Washington, DC 20037, United States.
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42
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Liu C, Jiao C, Wang K, Yuan N. DNA Methylation and Psychiatric Disorders. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 157:175-232. [PMID: 29933950 DOI: 10.1016/bs.pmbts.2018.01.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
DNA methylation has been an important area of research in the study of molecular mechanism to psychiatric disorders. Recent evidence has suggested that abnormalities in global methylation, methylation of genes, and pathways could play a role in the etiology of many forms of mental illness. In this article, we review the mechanisms of DNA methylation, including the genetic and environmental factors affecting methylation changes. We report and discuss major findings regarding DNA methylation in psychiatric patients, both within the context of global methylation studies and gene-specific methylation studies. Finally, we discuss issues surrounding data quality improvement, the limitations of current methylation analysis methods, and the possibility of using DNA methylation-based treatment for psychiatric disorders in the future.
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Affiliation(s)
- Chunyu Liu
- University of Illinois, Chicago, IL, United States; School of Life Science, Central South University, Changsha, China.
| | - Chuan Jiao
- School of Life Science, Central South University, Changsha, China
| | - Kangli Wang
- School of Life Science, Central South University, Changsha, China
| | - Ning Yuan
- Hunan Brain Hospital, Changsha, China
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43
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Cataldo I, Azhari A, Esposito G. A Review of Oxytocin and Arginine-Vasopressin Receptors and Their Modulation of Autism Spectrum Disorder. Front Mol Neurosci 2018; 11:27. [PMID: 29487501 PMCID: PMC5816822 DOI: 10.3389/fnmol.2018.00027] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 01/18/2018] [Indexed: 12/24/2022] Open
Abstract
Oxytocin (OXT) and arginine-vasopressin (AVP) play a key regulatory part in social and affiliative behaviors; two aspects highly compromised in Autism Spectrum Disorder (ASD). Furthermore, variants in the adjacent oxytocin-vasopressin gene regions have been found to be associated with ASD diagnosis and endophenotypes. This review focuses mainly on common OXTr single nucleotide polymorphisms (SNPs), AVPR1a microsatellites and AVPR1b polymorphisms in relation to the development of autism. Although these genes did not surface in genome-wide association studies, evidence supports the hypothesis that these receptors and their polymorphisms are widely involved in the regulation of social behavior, and in modulating neural and physiological pathways contributing to the etiology of ASD. With a specific focus on variants considered to be among the most prevalent in the development of ASD, these issues will be discussed in-depth and suggestions to approach inconsistencies in the present literature will be provided. Translational implications and future directions are deliberated from a short-term and a forward-looking perspective. While the scientific community has made significant progress in enhancing our understanding of ASD, more research is required for the ontology of this disorder to be fully elucidated. By supplementing information related to genetics, highlighting the differences across male and female sexes, this review provides a wider view of the current state of knowledge of OXTr and AVPr mechanisms of functioning, eventually addressing future research in the identification of further risk factors, to build new strategies for early interventions.
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Affiliation(s)
- Ilaria Cataldo
- Department of Psychology and Cognitive Science, University of Trento, Rovereto, Italy.,Mobile and Social Computing Lab, Fondazione Bruno Kessler, Trento, Italy
| | - Atiqah Azhari
- Division of Psychology, School of Social Sciences, Nanyang Technological University, Singapore, Singapore
| | - Gianluca Esposito
- Department of Psychology and Cognitive Science, University of Trento, Rovereto, Italy.,Division of Psychology, School of Social Sciences, Nanyang Technological University, Singapore, Singapore
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44
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Lussier AA, Morin AM, MacIsaac JL, Salmon J, Weinberg J, Reynolds JN, Pavlidis P, Chudley AE, Kobor MS. DNA methylation as a predictor of fetal alcohol spectrum disorder. Clin Epigenetics 2018; 10:5. [PMID: 29344313 PMCID: PMC5767049 DOI: 10.1186/s13148-018-0439-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 01/04/2018] [Indexed: 12/22/2022] Open
Abstract
Background Fetal alcohol spectrum disorder (FASD) is a developmental disorder that manifests through a range of cognitive, adaptive, physiological, and neurobiological deficits resulting from prenatal alcohol exposure. Although the North American prevalence is currently estimated at 2-5%, FASD has proven difficult to identify in the absence of the overt physical features characteristic of fetal alcohol syndrome. As interventions may have the greatest impact at an early age, accurate biomarkers are needed to identify children at risk for FASD. Building on our previous work identifying distinct DNA methylation patterns in children and adolescents with FASD, we have attempted to validate these associations in a different clinical cohort and to use our DNA methylation signature to develop a possible epigenetic predictor of FASD. Methods Genome-wide DNA methylation patterns were analyzed using the Illumina HumanMethylation450 array in the buccal epithelial cells of a cohort of 48 individuals aged 3.5-18 (24 FASD cases, 24 controls). The DNA methylation predictor of FASD was built using a stochastic gradient boosting model on our previously published dataset FASD cases and controls (GSE80261). The predictor was tested on the current dataset and an independent dataset of 48 autism spectrum disorder cases and 48 controls (GSE50759). Results We validated findings from our previous study that identified a DNA methylation signature of FASD, replicating the altered DNA methylation levels of 161/648 CpGs in this independent cohort, which may represent a robust signature of FASD in the epigenome. We also generated a predictive model of FASD using machine learning in a subset of our previously published cohort of 179 samples (83 FASD cases, 96 controls), which was tested in this novel cohort of 48 samples and resulted in a moderately accurate predictor of FASD status. Upon testing the algorithm in an independent cohort of individuals with autism spectrum disorder, we did not detect any bias towards autism, sex, age, or ethnicity. Conclusion These findings further support the association of FASD with distinct DNA methylation patterns, while providing a possible entry point towards the development of epigenetic biomarkers of FASD.
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Affiliation(s)
- Alexandre A. Lussier
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, British Columbia Canada
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia Canada
| | - Alexander M. Morin
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, British Columbia Canada
| | - Julia L. MacIsaac
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, British Columbia Canada
| | - Jenny Salmon
- Department of Pediatrics and Child Health, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba Canada
- Department of Biochemistry and Medical Genetics, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba Canada
| | - Joanne Weinberg
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia Canada
| | - James N. Reynolds
- Department of Biomedical and Molecular Sciences, Centre for Neuroscience Studies, Queen’s University, Kingston, Ontario Canada
| | - Paul Pavlidis
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columnbia Canada
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia Canada
| | - Albert E. Chudley
- Department of Pediatrics and Child Health, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba Canada
- Department of Biochemistry and Medical Genetics, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba Canada
| | - Michael S. Kobor
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, British Columbia Canada
- Human Early Learning Partnership, University of British Columbia, Vancouver, British Columbia Canada
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Forsberg SL, Ilieva M, Maria Michel T. Epigenetics and cerebral organoids: promising directions in autism spectrum disorders. Transl Psychiatry 2018; 8:14. [PMID: 29317608 PMCID: PMC5802583 DOI: 10.1038/s41398-017-0062-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 10/26/2017] [Indexed: 01/04/2023] Open
Abstract
Autism spectrum disorders (ASD) affect 1 in 68 children in the US according to the Centers for Disease Control and Prevention (CDC). It is characterized by impairments in social interactions and communication, restrictive and repetitive patterns of behaviors, and interests. Owing to disease complexity, only a limited number of treatment options are available mainly for children that alleviate but do not cure the debilitating symptoms. Studies confirm a genetic link, but environmental factors, such as medications, toxins, and maternal infection during pregnancy, as well as birth complications also play a role. Some studies indicate a set of candidate genes with different DNA methylation profiles in ASD compared to healthy individuals. Thus epigenetic alterations could help bridging the gene-environment gap in deciphering the underlying neurobiology of autism. However, epigenome-wide association studies (EWAS) have mainly included a very limited number of postmortem brain samples. Hence, cellular models mimicking brain development in vitro will be of great importance to study the critical epigenetic alterations and when they might happen. This review will give an overview of the state of the art concerning knowledge on epigenetic changes in autism and how new, cutting edge expertise based on three-dimensional (3D) stem cell technology models (brain organoids) can contribute in elucidating the multiple aspects of disease mechanisms.
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Affiliation(s)
- Sheena Louise Forsberg
- Department of Psychiatry, Institute for Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Mirolyuba Ilieva
- Department of Psychiatry, Institute for Clinical Research, University of Southern Denmark, Odense, Denmark.
| | - Tanja Maria Michel
- Department of Psychiatry, Institute for Clinical Research, University of Southern Denmark, Odense, Denmark
- Department of Psychiatry, Psychiatry in the region of Southern Denmark, Odense, Denmark
- Odense Center for Applied Neuroscience BRIDGE, University of Southern Denmark, Psychiatry in the Region of Southern Denmark, Odense University Hospital, Odense, Denmark
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46
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Nicolini C, Fahnestock M. The valproic acid-induced rodent model of autism. Exp Neurol 2018; 299:217-227. [DOI: 10.1016/j.expneurol.2017.04.017] [Citation(s) in RCA: 235] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 04/26/2017] [Accepted: 04/28/2017] [Indexed: 01/12/2023]
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47
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Qureshi IA, Mehler MF. Epigenetic mechanisms underlying nervous system diseases. HANDBOOK OF CLINICAL NEUROLOGY 2018; 147:43-58. [PMID: 29325627 DOI: 10.1016/b978-0-444-63233-3.00005-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Epigenetic mechanisms act as control systems for modulating genomic structure and activity in response to evolving profiles of cell-extrinsic, cell-cell, and cell-intrinsic signals. These dynamic processes are responsible for mediating cell- and tissue-specific gene expression and function and gene-gene and gene-environmental interactions. The major epigenetic mechanisms include DNA methylation and hydroxymethylation; histone protein posttranslational modifications, nucleosome remodeling/repositioning, and higher-order chromatin reorganization; noncoding RNA regulation; and RNA editing. These mechanisms are intimately involved in executing fundamental genomic programs, including gene transcription, posttranscriptional RNA processing and transport, translation, X-chromosome inactivation, genomic imprinting, retrotransposon regulation, DNA replication, and DNA repair and the maintenance of genomic stability. For the nervous system, epigenetics offers a novel and robust framework for explaining how brain development and aging occur, neural cellular diversity is generated, synaptic and neural network connectivity and plasticity are mediated, and complex cognitive and behavioral phenotypes are inherited transgenerationally. Epigenetic factors and processes are, not surprisingly, implicated in nervous system disease pathophysiology through several emerging paradigms - mutations and genetic variation in genes encoding epigenetic factors; impairments in epigenetic factor expression, localization, and function; epigenetic mechanisms modulating disease-associated factors and pathways; and the presence of deregulated epigenetic profiles in central and peripheral tissues.
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Affiliation(s)
- Irfan A Qureshi
- Roslyn and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine; Institute for Brain Disorders and Neural Regeneration; Departments of Neurology, Neuroscience, Psychiatry and Behavioral Sciences and Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Mark F Mehler
- Roslyn and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine; Institute for Brain Disorders and Neural Regeneration; Departments of Neurology, Neuroscience, Psychiatry and Behavioral Sciences; Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities; Einstein Cancer Center; Ruth L. and David S. Gottesman Stem Cell Institute; and Center for Epigenomics and Institute for Aging Research, Albert Einstein College of Medicine, Bronx, NY, United States.
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48
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Andrews SV, Ellis SE, Bakulski KM, Sheppard B, Croen LA, Hertz-Picciotto I, Newschaffer CJ, Feinberg AP, Arking DE, Ladd-Acosta C, Fallin MD. Cross-tissue integration of genetic and epigenetic data offers insight into autism spectrum disorder. Nat Commun 2017; 8:1011. [PMID: 29066808 PMCID: PMC5654961 DOI: 10.1038/s41467-017-00868-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 07/28/2017] [Indexed: 01/07/2023] Open
Abstract
Integration of emerging epigenetic information with autism spectrum disorder (ASD) genetic results may elucidate functional insights not possible via either type of information in isolation. Here we use the genotype and DNA methylation (DNAm) data from cord blood and peripheral blood to identify SNPs associated with DNA methylation (meQTL lists). Additionally, we use publicly available fetal brain and lung meQTL lists to assess enrichment of ASD GWAS results for tissue-specific meQTLs. ASD-associated SNPs are enriched for fetal brain (OR = 3.55; P < 0.001) and peripheral blood meQTLs (OR = 1.58; P < 0.001). The CpG targets of ASD meQTLs across cord, blood, and brain tissues are enriched for immune-related pathways, consistent with other expression and DNAm results in ASD, and reveal pathways not implicated by genetic findings. This joint analysis of genotype and DNAm demonstrates the potential of both brain and blood-based DNAm for insights into ASD and psychiatric phenotypes more broadly. “There have been a number of recent epigenetic studies on autism spectrum disorder. Here, the authors integrate genetic and epigenetic data from cord and peripheral blood and also from brain tissues to show the potential of blood-based epigenetic data to provide insights into psychiatric disorders.”
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Affiliation(s)
- Shan V Andrews
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615N. Wolfe St, Baltimore, MD, 21205, USA.,Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD, 21205, USA
| | - Shannon E Ellis
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, 733 N. Broadway, Baltimore, MD, 21205, USA
| | - Kelly M Bakulski
- Department of Epidemiology, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Brooke Sheppard
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615N. Wolfe St, Baltimore, MD, 21205, USA.,Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD, 21205, USA
| | - Lisa A Croen
- Division of Research, Kaiser Permanente Northern California, 2000 Broadway, Oakland, CA, 94612, USA
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences, School of Medicine, University of California Davis, 4610 X St, Sacramento, CA, 95817, USA.,MIND Institute, University of California Davis, 2825 50th St, Sacramento, CA, 95817, USA
| | - Craig J Newschaffer
- AJ Drexel Autism Institute, Drexel University, 3020 Market St #560, Philadelphia, PA, 19104, USA.,Department of Epidemiology and Biostatistics, Drexel University Dornsife School of Public Health, 3125 Market St, Philadelphia, PA, 19104, USA
| | - Andrew P Feinberg
- Center for Epigenetics, Institute for Basic Biomedical Sciences, Johns Hopkins School of Medicine, 733 N. Broadway, Baltimore, MD, 21205, USA.,Department of Medicine, Johns Hopkins School of Medicine, 733 N. Broadway, Baltimore, MD, 21205, USA
| | - Dan E Arking
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD, 21205, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, 733 N. Broadway, Baltimore, MD, 21205, USA
| | - Christine Ladd-Acosta
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615N. Wolfe St, Baltimore, MD, 21205, USA. .,Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD, 21205, USA. .,Center for Epigenetics, Institute for Basic Biomedical Sciences, Johns Hopkins School of Medicine, 733 N. Broadway, Baltimore, MD, 21205, USA.
| | - M Daniele Fallin
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD, 21205, USA. .,Center for Epigenetics, Institute for Basic Biomedical Sciences, Johns Hopkins School of Medicine, 733 N. Broadway, Baltimore, MD, 21205, USA. .,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, 624 N. Broadway, Baltimore, MD, 21205, USA.
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Siu MT, Weksberg R. Epigenetics of Autism Spectrum Disorder. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 978:63-90. [PMID: 28523541 DOI: 10.1007/978-3-319-53889-1_4] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Autism spectrum disorder (ASD), one of the most common childhood neurodevelopmental disorders (NDDs), is diagnosed in 1 of every 68 children. ASD is incredibly heterogeneous both clinically and aetiologically. The etiopathogenesis of ASD is known to be complex, including genetic, environmental and epigenetic factors. Normal epigenetic marks modifiable by both genetics and environmental exposures can result in epigenetic alterations that disrupt the regulation of gene expression, negatively impacting biological pathways important for brain development. In this chapter we aim to summarize some of the important literature that supports a role for epigenetics in the underlying molecular mechanism of ASD. We provide evidence from work in genetics, from environmental exposures and finally from more recent studies aimed at directly determining ASD-specific epigenetic patterns, focusing mainly on DNA methylation (DNAm). Finally, we briefly discuss some of the implications of current research on potential epigenetic targets for therapeutics and novel avenues for future work.
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Affiliation(s)
- Michelle T Siu
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1X8, Canada
| | - Rosanna Weksberg
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1X8, Canada. .,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1X8, Canada. .,Department of Paediatrics, University of Toronto, Toronto, ON, M5S 1A1, Canada. .,Institute of Medical Science, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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Gene-wide Association Study Reveals RNF122 Ubiquitin Ligase as a Novel Susceptibility Gene for Attention Deficit Hyperactivity Disorder. Sci Rep 2017; 7:5407. [PMID: 28710364 PMCID: PMC5511183 DOI: 10.1038/s41598-017-05514-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/31/2017] [Indexed: 01/07/2023] Open
Abstract
Attention Deficit Hyperactivity Disorder (ADHD) is a common childhood-onset neurodevelopmental condition characterized by pervasive impairment of attention, hyperactivity, and/or impulsivity that can persist into adulthood. The aetiology of ADHD is complex and multifactorial and, despite the wealth of evidence for its high heritability, genetic studies have provided modest evidence for the involvement of specific genes and have failed to identify consistent and replicable results. Due to the lack of robust findings, we performed gene-wide and pathway enrichment analyses using pre-existing GWAS data from 607 persistent ADHD subjects and 584 controls, produced by our group. Subsequently, expression profiles of genes surpassing a follow-up threshold of P-value < 1e-03 in the gene-wide analyses were tested in peripheral blood mononucleated cells (PBMCs) of 45 medication-naive adults with ADHD and 39 healthy unrelated controls. We found preliminary evidence for genetic association between RNF122 and ADHD and for its overexpression in adults with ADHD. RNF122 encodes for an E3 ubiquitin ligase involved in the proteasome-mediated processing, trafficking, and degradation of proteins that acts as an essential mediator of the substrate specificity of ubiquitin ligation. Thus, our findings support previous data that place the ubiquitin-proteasome system as a promising candidate for its involvement in the aetiology of ADHD.
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