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Genome-Wide DNA Methylation Analysis Reveals Epigenetic Pattern of SH2B1 in Chinese Monozygotic Twins Discordant for Autism Spectrum Disorder

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Genome-Wide DNA Methylation Analysis Reveals Epigenetic Pattern of SH2B1 in Chinese Monozygotic Twins Discordant for Autism Spectrum Disorder fnins-13-00712 July 15, 2019 Time: 15:26 # 1 ORIGINAL RESEARCH published: 17 July 2019 doi: 10.3389/fnins.2019.00712 Genome-Wide DNA Methylation Analysis Reveals Epigenetic Pattern of SH2B1 in Chinese Monozygotic Twins Discordant for Autism Spectrum Disorder Shuang Liang1, Zhenzhi Li2, Yihan Wang3, Xiaodan Li1, Xiaolei Yang1, Xiaolei Zhan1, Yan Huang1, Zhaomin Gao1, Min Zhang3, Caihong Sun1, Yan Zhang3* and Lijie Wu1* 1 Department of Child and Adolescent Health, School of Public Health, Harbin Medical University, Harbin, China, 2 Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, United States, 3 College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder. Aberrant Edited by: DNA methylation has been observed in ASD but the mechanisms remain largely Leonard C. Schalkwyk, unknown. Here, we employed discordant monozygotic twins to investigate the University of Essex, United Kingdom contribution of DNA methylation to ASD etiology. Genome-wide DNA methylation Reviewed by: analysis was performed using samples obtained from five pairs of ASD-discordant Claus Jürgen Scholz, Labor Dr. Wisplinghoff, Germany monozygotic twins, which revealed a total of 2,397 differentially methylated genes. Emma Louise Dempster, Further, such gene list was annotated with Kyoto Encyclopedia of Genes and Genomes University of Exeter, United Kingdom and demonstrated predominant activation of neurotrophin signaling pathway in ASD- *Correspondence: Lijie Wu discordant monozygotic twins. The methylation of SH2B1 gene was further confirmed [email protected] in the ASD-discordant, ASD-concordant monozygotic twins, and a set of 30 pairs of Yan Zhang sporadic case-control by bisulfite-pyrosequencing. The results showed that there was [email protected] a greater DNA methylation difference in ASD-discordant monozygotic twins than ASD- Specialty section: concordant monozygotic twins. Further, verification of the Chr.16:28856743 of SH2B1 This article was submitted to Neurogenomics, showed significant differences in DNA methylation between case and control. These a section of the journal results suggest abnormal methylation of SH2B1 is associated with ASD etiology. Our Frontiers in Neuroscience data suggest that it might be worthwhile to further explore the functions of SH2B1 and Received: 01 November 2018 related genes of neurotrophin signaling pathway in ASD. Accepted: 24 June 2019 Published: 17 July 2019 Keywords: autism spectrum disorder, monozygotic twins, discordant, DNA methylation, SH2B1 Citation: Liang S, Li Z, Wang Y, Li X, Yang X, Zhan X, Huang Y, Gao Z, INTRODUCTION Zhang M, Sun C, Zhang Y and Wu L (2019) Genome-Wide DNA Autism spectrum disorder (ASD) is a group of serious neurodevelopmental disorders defined in an Methylation Analysis Reveals individual by deficits in social interaction and communication, accompanied by restricted interests Epigenetic Pattern of SH2B1 in Chinese Monozygotic Twins and stereotypical repetitive behaviors. ASD affects 1–2% of children and confers severe lifelong Discordant for Autism Spectrum disability, thus ASD has become a growing clinical and public health problem worldwide (Kim Disorder. Front. Neurosci. 13:712. et al., 2011; Elsabbagh et al., 2012; Hill et al., 2015). Traditionally, the etiology for ASD mainly doi: 10.3389/fnins.2019.00712 attributed to different genetic variants such as de novo mutations, copy number variations (CNV), Frontiers in Neuroscience| www.frontiersin.org 1 July 2019| Volume 13| Article 712 fnins-13-00712 July 15, 2019 Time: 15:26 # 2 Liang et al. Epigenome Changes in ASD Twins and single-nucleotide polymorphisms (SNP) (State and Levitt, of ASD-concordant MZ twins and 30 pairs of sporadic patients 2011; Neale et al., 2012). Although focuses on research efforts with aged-, sex-matched controls were invited to participate. have grown in intensity during the past decade and due to More than two experienced psychiatrists independently issued the highly clinical and etiological heterogeneous nature of ASD diagnoses according to the criteria of international ASD, no findings of biological or clinical markers have been Diagnostic and Statistical Manual of Mental Disorders, 5th Ed definitively identified. This shows that additional epigenetic (DSM-5). All probands were also administered by the Autism or environmental factors are an underlying cause for the Diagnostic Observation Schedule-generic (ADOS) (Lord et al., susceptibility to ASD. A more recent twin study further suggested 2000), and were all found to meet the criteria for autism. that an environmental contribution might be a potentially The ADOS, a semi-structured observational instrument, is substantial role for ASD etiology (Hallmayer et al., 2011; Schendel made up for four modules to assess social and communicative et al., 2014). A large survey of over 14,000 children with ASD in abilities in individuals suspected of having ASD, in which two Sweden revealed that heritable factors were found to contribute different cut-points that depend on symptom severity result to about half of ASD risk and the other half were contributed in a diagnosis of (i) ASD (milder variant) or (ii) autism (more from undetected genetic factors, environmental effects and/or severe variant). Cases with Rett syndrome, tuberous sclerosis, stochastic effects. fragile-X syndrome, and any other neurological conditions The epigenetic mechanisms allow stable regulation of gene suspected to be associated with autism, were excluded by expression without altering the DNA sequence that is optimally clinical examination and molecular genetic tests of the FMR1 positioned between the genome and the environment (Vogel gene (Khaniani et al., 2008). The standard biosecurity and Ciernia and LaSalle, 2016). Environmentally driven changes institutional safety procedures for the blood collection have have also propelled the development of neuropsychiatric been carried out. This study was performed in accordance diseases via the alteration of epigenetic profiles, including with the recommendations of Institutional Research Board of classic ASD (Schanen, 2006; Grafodatskaya et al., 2010) and Harbin Medical University (HMUIRB2012006). The protocol symptomatic ASD such as Rett syndrome and Fragile X was approved by the Institutional Research Board of Harbin syndrome. However, environmental modulation of epigenetic Medical University. Safety and fairness principle has been fully states is poorly understood. Since, monozygotic twins have a considered in the study plans. All subjects gave written informed DNA sequence in common, the study of discordant monozygotic consent in accordance with the Declaration of Helsinki and the (MZ) twins provides an ideal model to investigate the value content of the research have no harm or risk. of epigenetic factors in the field of disease etiology. DNA methylation, as the most widely investigated process in epigenetic DNA Extraction and Bisulfite Conversion mechanisms, was considered as a key element that mediates Genomic DNA was extracted from whole blood using the reversible changes in gene expression regardless of DNA QIAamp DNA Mini Kit (Qiagen, Darmstadt, German), and sequence variation (Henikoff and Matzke, 1997). Recent advances assessed for integrity, quantity, purity and concentration in high-throughput genomic technology expand our knowledge by electrophoresis in a 1% agarose gel and Nanodrop2000 of DNA methylation. As a result, uncovering this complex spectrophotometer. Bisulfite conversion of 500 ng of genomic relationship will be important for understanding the mechanism DNA was performed using EZ 96-DNA methylation kit (Zymo of DNA methylation in ASD. Lately, two studies have dissected Research, Irvine, CA, United States) consistent of manufacturer’s several ASD-associated differentially methylated loci (Nguyen standard protocol. The bisulfite conversion reaction was et al., 2010; Wong et al., 2014), and further support that the conducted in duplicate to minimize potential bias caused by peripherally derived DNA can be used to identify disease- variable conversion efficiency, and pooled bisulfite-treated DNA associated epigenetic changes. Nonetheless, to date, no study was used for subsequent array experiments. has been reported for the methylomic profile in the samples of Chinese ASD-discordant MZ twins, and it is necessary to investigate the significance of epigenetic mechanism in the Infinium Human-Methylation Chinese population. 450BeadChip (450K) Array This study was designed to identify the genome-wide DNA Three pairs of ASD-discordant MZ twins for Genome-wide DNA methylation patterns in Chinese MZ twins discordant for methylation were measured via the Illumina Infinium Human ASD, and further provide the evidence for ASD associated Methylation 450BeadChip assay (Illumina, San Diego, CA, epigenetic alterations. United States), which interrogated the DNA methylation profile of more than 485,000 methylation sites per sample at single- nucleotide resolution. Arrays were scanned by HiScan 2000 MATERIALS AND METHODS (Illumina). Illumina Genome Studio software (Illumina) was used to extract signal intensities for each probe and to perform Samples Recruitment initial control quality checks. There were no failed samples which All the participants were recruited from the Children needed to be excluded by examined 450K array control probes Development and Behavior Research Center (CDBRC), to assess
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