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Mouat JS, Krigbaum NY, Hakam S, Thrall E, Mellis J, Yasui DH, Cirillo PM, Ludena Y, Schmidt RJ, La Merrill MA, Hertz-Picciotto I, Cohn BA, LaSalle JM. Females with autism spectrum disorders show stronger DNA methylation signatures than males in perinatal tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.11.603098. [PMID: 39026708 PMCID: PMC11257592 DOI: 10.1101/2024.07.11.603098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Autism spectrum disorder (ASD) comprises a group of neurodevelopmental conditions currently diagnosed by behavioral assessment in childhood, with reported underdiagnosis in females. Though diagnosis in early life is linked to improved outcomes, we currently lack objective screening tools for newborns. To address this gap, we sought to identify a sex-specific DNA methylation signature for ASD using perinatal tissues that reflect dysregulation in the brain. DNA methylation was assayed from ASD and typically developing (TD) newborn blood, umbilical cord blood, placenta, and post-mortem cortex samples using whole genome bisulfite sequencing (WGBS) in a total of 511 samples. We found that methylation levels of differentially methylated regions (DMRs) differentiated samples by ASD diagnosis in females more than males across the perinatal tissues. We tested three theories for ASD sex differences in newborn blood, finding epigenetic support for an X chromosome-related female protective effect, as well as a high replication rate of DMRs (48.1%) in females across two independent cohorts. In our pan-tissue analysis, three genes (X-linked BCOR, GALNT9, OPCML) mapped to ASD DMRs replicated in all four female tissues. ASD DMRs from all tissues were enriched for neuro-related processes (females) and SFARI ASD-risk genes (females and males). Overall, we found a highly replicated methylation signature of ASD in females across perinatal tissues that reflected dysregulation in the brain and involvement of X chromosome epigenetics. This comparative study of perinatal tissues shows the promise of newborn blood DNA methylation biomarkers for early detection of females at risk for ASD and emphasizes the importance of sex-stratification in ASD studies.
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Affiliation(s)
- Julia S Mouat
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA USA
- Genome Center, University of California, Davis, CA USA
- MIND Institute, University of California, Davis, CA USA
| | - Nickilou Y Krigbaum
- Child Health and Development Studies, Public Health Institute, Berkeley, CA USA
| | - Sophia Hakam
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA USA
- Genome Center, University of California, Davis, CA USA
- MIND Institute, University of California, Davis, CA USA
| | - Emily Thrall
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA USA
- Genome Center, University of California, Davis, CA USA
- MIND Institute, University of California, Davis, CA USA
| | - Julia Mellis
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA USA
- Genome Center, University of California, Davis, CA USA
- MIND Institute, University of California, Davis, CA USA
| | - Dag H Yasui
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA USA
- Genome Center, University of California, Davis, CA USA
- MIND Institute, University of California, Davis, CA USA
| | - Piera M Cirillo
- Child Health and Development Studies, Public Health Institute, Berkeley, CA USA
| | - Yunin Ludena
- MIND Institute, University of California, Davis, CA USA
- Department of Public Health Sciences, University of California, Davis, CA USA
| | - Rebecca J Schmidt
- Perinatal Origins of Disparities Center, University of California, Davis, CA USA
- MIND Institute, University of California, Davis, CA USA
- Department of Public Health Sciences, University of California, Davis, CA USA
| | - Michele A La Merrill
- Perinatal Origins of Disparities Center, University of California, Davis, CA USA
- Genome Center, University of California, Davis, CA USA
- Department of Environmental Toxicology, University of California, Davis, CA USA
- Environmental Health Sciences Center, University of California, Davis, CA USA
| | - Irva Hertz-Picciotto
- Perinatal Origins of Disparities Center, University of California, Davis, CA USA
- MIND Institute, University of California, Davis, CA USA
- Department of Public Health Sciences, University of California, Davis, CA USA
- Environmental Health Sciences Center, University of California, Davis, CA USA
| | - Barbara A Cohn
- Child Health and Development Studies, Public Health Institute, Berkeley, CA USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA USA
- Genome Center, University of California, Davis, CA USA
- MIND Institute, University of California, Davis, CA USA
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Eaves LA, Harrington CE, Fry RC. Epigenetic Responses to Nonchemical Stressors: Potential Molecular Links to Perinatal Health Outcomes. Curr Environ Health Rep 2024; 11:145-157. [PMID: 38580766 DOI: 10.1007/s40572-024-00435-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/06/2024] [Indexed: 04/07/2024]
Abstract
PURPOSE OF REVIEW We summarize the recent literature investigating exposure to four nonchemical stressors (financial stress, racism, psychosocial stress, and trauma) and DNA methylation, miRNA expression, and mRNA expression. We also highlight the relationships between these epigenetic changes and six critical perinatal outcomes (preterm birth, low birth weight, preeclampsia, gestational diabetes, childhood allergic disease, and childhood neurocognition). RECENT FINDINGS Multiple studies have found financial stress, psychosocial stress, and trauma to be associated with DNA methylation and/or miRNA and mRNA expression. Fewer studies have investigated the effects of racism. The majority of studies assessed epigenetic or genomic changes in maternal blood, cord blood, or placenta. Several studies included multi-OMIC assessments in which DNA methylation and/or miRNA expression were associated with gene expression. There is strong evidence for the role of epigenetics in driving the health outcomes considered. A total of 22 biomarkers, including numerous HPA axis genes, were identified to be epigenetically altered by both stressors and outcomes. Epigenetic changes related to inflammation, the immune and endocrine systems, and cell growth and survival were highlighted across numerous studies. Maternal exposure to nonchemical stressors is associated with epigenetic and/or genomic changes in a tissue-specific manner among inflammatory, immune, endocrine, and cell growth-related pathways, which may act as mediating pathways to perinatal health outcomes. Future research can test the mediating role of the specific biomarkers identified as linked with both stressors and outcomes. Understanding underlying epigenetic mechanisms altered by nonchemical stressors can provide a better understanding of how chemical and nonchemical exposures interact.
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Affiliation(s)
- Lauren A Eaves
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Cailee E Harrington
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Rebecca C Fry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA.
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA.
- Curriculum in Toxicology and Environmental Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, USA.
- Department of Pediatrics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA.
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Denomme MM, McCallie BR, Haywood ME, Parks JC, Schoolcraft WB, Katz-Jaffe MG. Paternal aging impacts expression and epigenetic markers as early as the first embryonic tissue lineage differentiation. Hum Genomics 2024; 18:32. [PMID: 38532526 PMCID: PMC10964547 DOI: 10.1186/s40246-024-00599-4] [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: 12/27/2023] [Accepted: 03/14/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND Advanced paternal age (APA) is associated with adverse outcomes to offspring health, including increased risk for neurodevelopmental disorders. The aim of this study was to investigate the methylome and transcriptome of the first two early embryonic tissue lineages, the inner cell mass (ICM) and the trophectoderm (TE), from human blastocysts in association with paternal age and disease risk. High quality human blastocysts were donated with patient consent from donor oocyte IVF cycles from either APA (≥ 50 years) or young fathers. Blastocysts were mechanically separated into ICM and TE lineage samples for both methylome and transcriptome analyses. RESULTS Significant differential methylation and transcription was observed concurrently in ICM and TE lineages of APA-derived blastocysts compared to those from young fathers. The methylome revealed significant enrichment for neuronal signaling pathways, as well as an association with neurodevelopmental disorders and imprinted genes, largely overlapping within both the ICM and TE lineages. Significant enrichment of neurodevelopmental signaling pathways was also observed for differentially expressed genes, but only in the ICM. In stark contrast, no significant signaling pathways or gene ontology terms were identified in the trophectoderm. Despite normal semen parameters in aged fathers, these significant molecular alterations can adversely contribute to downstream impacts on offspring health, in particular neurodevelopmental disorders like autism spectrum disorder and schizophrenia. CONCLUSIONS An increased risk for neurodevelopmental disorders is well described in children conceived by aged fathers. Using blastocysts derived from donor oocyte IVF cycles to strategically control for maternal age, our data reveals evidence of methylation dysregulation in both tissue lineages, as well as transcription dysregulation in neurodevelopmental signaling pathways associated with APA fathers. This data also reveals that embryos derived from APA fathers do not appear to be compromised for initial implantation potential with no significant pathway signaling disruption in trophectoderm transcription. Collectively, our work provides insights into the complex molecular mechanisms that occur upon paternal aging during the first lineage differentiation in the preimplantation embryo. Early expression and epigenetic markers of APA-derived preimplantation embryos highlight the susceptibility of the future fetus to adverse health outcomes.
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Affiliation(s)
| | - Blair R McCallie
- CCRM Genetics, 10290 Ridgegate Circle, Lone Tree, CO, 80124, USA
| | - Mary E Haywood
- CCRM Genetics, 10290 Ridgegate Circle, Lone Tree, CO, 80124, USA
| | - Jason C Parks
- CCRM Genetics, 10290 Ridgegate Circle, Lone Tree, CO, 80124, USA
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Willinger Y, Friedland Cohen DR, Turgeman G. Exogenous IL-17A Alleviates Social Behavior Deficits and Increases Neurogenesis in a Murine Model of Autism Spectrum Disorders. Int J Mol Sci 2023; 25:432. [PMID: 38203599 PMCID: PMC10779042 DOI: 10.3390/ijms25010432] [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: 10/25/2023] [Revised: 12/17/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Among the proposed mechanisms for autism spectrum disorders (ASD) is immune dysregulation. The proinflammatory cytokine Interleukine-17A (IL-17A) was shown to play a key role in mediating immune-related neurodevelopmental impairment of social behavior. Nevertheless, post-developmental administration of IL-17A was found to increase social behavior. In the present study, we explored the effect of post-developmental administration of IL-17A on ASD-like behaviors induced by developmental exposure to valproic acid (VPA) at postnatal day 4. At the age of seven weeks, VPA-exposed mice were intravenously injected twice with recombinant murine IL-17A (8 μg), and a week later, they were assessed for ASD-like behavior. IL-17A administration increased social behavior and alleviated the ASD-like phenotype. Behavioral changes were associated with increased serum levels of IL-17 and Th17-related cytokines. Exogenous IL-17A also increased neuritogenesis in the dendritic tree of doublecortin-expressing newly formed neurons in the dentate gyrus. Interestingly, the effect of IL-17A on neuritogenesis was more noticeable in females than in males, suggesting a sex-dependent effect of IL-17A. In conclusion, our study suggests a complex role for IL-17A in ASD. While contributing to its pathology at the developmental stage, IL-17 may also promote the alleviation of behavioral deficits post-developmentally by promoting neuritogenesis and synaptogenesis in the dentate gyrus.
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Affiliation(s)
- Yehoshua Willinger
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel; (Y.W.); (D.R.F.C.)
| | - Daniella R. Friedland Cohen
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel; (Y.W.); (D.R.F.C.)
| | - Gadi Turgeman
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel; (Y.W.); (D.R.F.C.)
- The Adelson School of Medicine, Ariel University, Ariel 40700, Israel
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5
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Shorey-Kendrick LE, Roberts VHJ, D'Mello RJ, Sullivan EL, Murphy SK, Mccarty OJT, Schust DJ, Hedges JC, Mitchell AJ, Terrobias JJD, Easley CA, Spindel ER, Lo JO. Prenatal delta-9-tetrahydrocannabinol exposure is associated with changes in rhesus macaque DNA methylation enriched for autism genes. Clin Epigenetics 2023; 15:104. [PMID: 37415206 PMCID: PMC10324248 DOI: 10.1186/s13148-023-01519-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/12/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND With the growing availability of cannabis and the popularization of additional routes of cannabis use beyond smoking, including edibles, the prevalence of cannabis use in pregnancy is rapidly increasing. However, the potential effects of prenatal cannabis use on fetal developmental programming remain unknown. RESULTS We designed this study to determine whether the use of edible cannabis during pregnancy is deleterious to the fetal and placental epigenome. Pregnant rhesus macaques consumed a daily edible containing either delta-9-tetrahydrocannabinol (THC) (2.5 mg/7 kg/day) or placebo. DNA methylation was measured in 5 tissues collected at cesarean delivery (placenta, lung, cerebellum, prefrontal cortex, and right ventricle of the heart) using the Illumina MethylationEPIC platform and filtering for probes previously validated in rhesus macaque. In utero exposure to THC was associated with differential methylation at 581 CpGs, with 573 (98%) identified in placenta. Loci differentially methylated with THC were enriched for candidate autism spectrum disorder (ASD) genes from the Simons Foundation Autism Research Initiative (SFARI) database in all tissues. The placenta demonstrated greatest SFARI gene enrichment, including genes differentially methylated in placentas from a prospective ASD study. CONCLUSIONS Overall, our findings reveal that prenatal THC exposure alters placental and fetal DNA methylation at genes involved in neurobehavioral development that may influence longer-term offspring outcomes. The data from this study add to the limited existing literature to help guide patient counseling and public health polices focused on prenatal cannabis use in the future.
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Affiliation(s)
- Lyndsey E Shorey-Kendrick
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA.
| | - Victoria H J Roberts
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA
| | - Rahul J D'Mello
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Elinor L Sullivan
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA
- Department of Psychiatry, Oregon Health and Science University, Portland, OR, 97239, USA
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, 27701, USA
| | - Owen J T Mccarty
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Danny J Schust
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, 27701, USA
| | - Jason C Hedges
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA
- Department of Urology, Oregon Health and Science University, Portland, OR, 97239, USA
| | - A J Mitchell
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA
| | - Jose Juanito D Terrobias
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA
| | - Charles A Easley
- Department of Environmental Health Science, University of Georgia College of Public Health, Athens, GA, 30602, USA
| | - Eliot R Spindel
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA
| | - Jamie O Lo
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, Oregon Health and Science University, Portland, OR, 97239, USA
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Tran MTMT, Kuo FC, Low JT, Chuang YM, Sultana S, Huang WL, Lin ZY, Lin GL, Wu CF, Li SS, Suen JL, Hung CH, Wu MT, Chan MWY. Prenatal DEHP exposure predicts neurological disorders via transgenerational epigenetics. Sci Rep 2023; 13:7399. [PMID: 37149698 PMCID: PMC10164151 DOI: 10.1038/s41598-023-34661-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/05/2023] [Indexed: 05/08/2023] Open
Abstract
Recent experimental and observational research has suggested that childhood allergic asthma and other conditions may be the result of prenatal exposure to environmental contaminants, such as di-(2-ethylhexyl) phthalate (DEHP). In a previous epidemiological study, we found that ancestral exposure (F0 generation) to endocrine disruptors or the common plasticizer DEHP promoted allergic airway inflammation via transgenerational transmission in mice from generation F1 to F4. In the current study, we employed a MethylationEPIC Beadchip microarray to examine global DNA methylation in the human placenta as a function of maternal exposure to DEHP during pregnancy. Interestingly, global DNA hypomethylation was observed in placental DNA following exposure to DEHP at high concentrations. Bioinformatic analysis confirmed that DNA methylation affected genes related to neurological disorders, such as autism and dementia. These results suggest that maternal exposure to DEHP may predispose offspring to neurological diseases. Given the small sample size in this study, the potential role of DNA methylation as a biomarker to assess the risk of these diseases deserves further investigation.
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Affiliation(s)
- Mita T M T Tran
- Department of Biomedical Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chia-Yi, 621, Taiwan
- Epigenomics and Human Disease Research Center, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
- Center for Innovative Research on Aging Society (CIRAS), National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Fu-Chen Kuo
- Research Center for Precision Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung, Taiwan
- Department of Obstetrics & Gynecology, E-Da Hospital, Kaohsiung, Taiwan
| | - Jie-Ting Low
- Department of Biomedical Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chia-Yi, 621, Taiwan
- Epigenomics and Human Disease Research Center, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Yu-Ming Chuang
- Department of Biomedical Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chia-Yi, 621, Taiwan
- Epigenomics and Human Disease Research Center, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
- Center for Innovative Research on Aging Society (CIRAS), National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Sofia Sultana
- Department of Biomedical Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chia-Yi, 621, Taiwan
- Epigenomics and Human Disease Research Center, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
- Center for Innovative Research on Aging Society (CIRAS), National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Wen-Long Huang
- Department of Biomedical Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chia-Yi, 621, Taiwan
- Epigenomics and Human Disease Research Center, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
- Center for Innovative Research on Aging Society (CIRAS), National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Zhe-Young Lin
- Department of Chemical Engineering, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Guan-Ling Lin
- Department of Biomedical Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chia-Yi, 621, Taiwan
- Epigenomics and Human Disease Research Center, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
- Center for Innovative Research on Aging Society (CIRAS), National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Chia-Fang Wu
- Research Center for Precision Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- International Master Program of Translational Medicine, National United University, Miaoli, Taiwan
| | - Sih-Syuan Li
- Research Center for Precision Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jau-Ling Suen
- Research Center for Precision Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Chih-Hsing Hung
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Department of Pediatrics, Kaohsiung Municipal Hsiao-Kang Hospital, Kaohsiung, Taiwan
| | - Ming-Tsang Wu
- Research Center for Precision Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
- PhD Program in Environmental and Occupational Medicine, Kaohsiung Medical University, Room 721, CS Building, No.100, Shih-Chuan 1St Road, Kaohsiung, 807, Taiwan.
- Department of Public Health, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan.
- Department of Family Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Michael W Y Chan
- Department of Biomedical Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chia-Yi, 621, Taiwan.
- Epigenomics and Human Disease Research Center, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.
- Center for Innovative Research on Aging Society (CIRAS), National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.
- Research Center for Precision Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
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Ravaei A, Emanuele M, Nazzaro G, Fadiga L, Rubini M. Placental DNA methylation profile as predicting marker for autism spectrum disorder (ASD). Mol Med 2023; 29:8. [PMID: 36647002 PMCID: PMC9843962 DOI: 10.1186/s10020-022-00593-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/15/2022] [Indexed: 01/18/2023] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder that impairs normal brain development and socio-cognitive abilities. The pathogenesis of this condition points out the involvement of genetic and environmental factors during in-utero life. Placenta, as an interface tissue between mother and fetus, provides developing fetus requirements and exposes it to maternal environment as well. Therefore, the alteration of DNA methylation as epigenetic consequence of gene-environmental interaction in the placenta could shed light on ASD pathogenesis. In this study, we reviewed the current findings on placental methylation status and its association with ASD. Differentially methylated regions (DMRs) in ASD-developing placenta were found to be mainly enriched in ASD gene loci affecting synaptogenesis, microtubule dynamics, neurogenesis and neuritogenesis. In addition, non-genic DMRs in ASD-placenta proposes an alternative contributing mechanism for ASD development. Our study highlights the importance of placental DNA methylation signature as a biomarker for ASD prediction.
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Affiliation(s)
- Amin Ravaei
- grid.8484.00000 0004 1757 2064Medical Genetics Laboratory, Department of Neuroscience and Rehabilitation, University of Ferrara, Via Fossato di Mortara 74, 44121 Ferrara, Italy
| | - Marco Emanuele
- grid.8484.00000 0004 1757 2064Section of Physiology, Department of Neuroscience and Rehabilitation, University of Ferrara, Ferrara, Italy ,grid.25786.3e0000 0004 1764 2907IIT@UniFe Center for Translational Neurophysiology of Speech and Communication (CTNSC), Istituto Italiano di Tecnologia, Ferrara, Italy
| | - Giovanni Nazzaro
- grid.8484.00000 0004 1757 2064Section of Physiology, Department of Neuroscience and Rehabilitation, University of Ferrara, Ferrara, Italy ,grid.25786.3e0000 0004 1764 2907IIT@UniFe Center for Translational Neurophysiology of Speech and Communication (CTNSC), Istituto Italiano di Tecnologia, Ferrara, Italy
| | - Luciano Fadiga
- grid.8484.00000 0004 1757 2064Section of Physiology, Department of Neuroscience and Rehabilitation, University of Ferrara, Ferrara, Italy ,grid.25786.3e0000 0004 1764 2907IIT@UniFe Center for Translational Neurophysiology of Speech and Communication (CTNSC), Istituto Italiano di Tecnologia, Ferrara, Italy
| | - Michele Rubini
- grid.8484.00000 0004 1757 2064Medical Genetics Laboratory, Department of Neuroscience and Rehabilitation, University of Ferrara, Via Fossato di Mortara 74, 44121 Ferrara, Italy
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8
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Cell-free DNA in maternal blood and artificial intelligence: accurate prenatal detection of fetal congenital heart defects. Am J Obstet Gynecol 2023; 228:76.e1-76.e10. [PMID: 35948071 DOI: 10.1016/j.ajog.2022.07.062] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 01/26/2023]
Abstract
BACKGROUND DNA cytosine nucleotide methylation (epigenomics and epigenetics) is an important mechanism for controlling gene expression in cardiac development. Combined artificial intelligence and whole-genome epigenomic analysis of circulating cell-free DNA in maternal blood has the potential for the detection of fetal congenital heart defects. OBJECTIVE This study aimed to use genome-wide DNA cytosine methylation and artificial intelligence analyses of circulating cell-free DNA for the minimally invasive detection of fetal congenital heart defects. STUDY DESIGN In this prospective study, whole-genome cytosine nucleotide methylation analysis was performed on circulating cell-free DNA using the Illumina Infinium MethylationEPIC BeadChip array. Multiple artificial intelligence approaches were evaluated for the detection of congenital hearts. The Ingenuity Pathway Analysis program was used to identify gene pathways that were epigenetically altered and important in congenital heart defect pathogenesis to further elucidate the pathogenesis of isolated congenital heart defects. RESULTS There were 12 cases of isolated nonsyndromic congenital heart defects and 26 matched controls. A total of 5918 cytosine nucleotides involving 4976 genes had significantly altered methylation, that is, a P value of <.05 along with ≥5% whole-genome cytosine nucleotide methylation difference, in congenital heart defect cases vs controls. Artificial intelligence analysis of the methylation data achieved excellent congenital heart defect predictive accuracy (areas under the receiver operating characteristic curve, ≥0.92). For example, an artificial intelligence model using a combination of 5 whole-genome cytosine nucleotide markers achieved an area under the receiver operating characteristic curve of 0.97 (95% confidence interval, 0.87-1.0) with 98% sensitivity and 94% specificity. We found epigenetic changes in genes and gene pathways involved in the following important cardiac developmental processes: "cardiovascular system development and function," "cardiac hypertrophy," "congenital heart anomaly," and "cardiovascular disease." This lends biologic plausibility to our findings. CONCLUSION This study reported the feasibility of minimally invasive detection of fetal congenital heart defect using artificial intelligence and DNA methylation analysis of circulating cell-free DNA for the prediction of fetal congenital heart defect. Furthermore, the findings supported an important role of epigenetic changes in congenital heart defect development.
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Folate in maternal rheumatoid arthritis-filial autism spectrum disorder continuum. Reprod Toxicol 2023; 115:29-35. [PMID: 36402436 DOI: 10.1016/j.reprotox.2022.11.004] [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: 10/01/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022]
Abstract
Rheumatoid Arthritis (RA) is an inflammatory autoimmune disease that affects women three times more than men. Epidemiological studies found that the incidence of Autism Spectrum Disorder (ASD), a neurological and developmental disorder, in children born to mothers suffering from RA is higher compared with the control population. Considering that the pathogenesis of ASD could be traced back to pregnancy and in uterine conditions, and the evidence of reduced folate levels in the brain of ASD-affected children, we aimed to study the role of folate, as an important nutritional factor during pregnancy, in associating maternal RA to ASD development in the offspring. Folate balance during RA could be influenced twice, initially during the immune activation associated with disease onset, and later during the treatment with anti-folate drugs, with a potential consequence of folate deficiency. Maternal folate deficiency during pregnancy could increase homocysteine levels, oxidative stress, and global DNA hypomethylation, all known risk factors in ASD pathogenesis. These effects could be intensified by genetic polymorphisms in the folate system, which were also found as genetic risk factors for both RA and ASD. The available evidence suggests that folate level as an important factor during RA, pregnancy and ASD could have pathological and therapeutical significance and should be carefully monitored and investigated in the RA-pregnancy-ASD axis.
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10
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DNA Methylation Profiles of GAD1 in Human Cerebral Organoids of Autism Indicate Disrupted Epigenetic Regulation during Early Development. Int J Mol Sci 2022; 23:ijms23169188. [PMID: 36012452 PMCID: PMC9408997 DOI: 10.3390/ijms23169188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/05/2022] [Accepted: 08/14/2022] [Indexed: 11/17/2022] Open
Abstract
DNA methylation profiling has become a promising approach towards identifying biomarkers of neuropsychiatric disorders including autism spectrum disorder (ASD). Epigenetic markers capture genetic risk factors and diverse exogenous and endogenous factors, including environmental risk factors and complex disease pathologies. We analysed the differential methylation profile of a regulatory region of the GAD1 gene using cerebral organoids generated from induced pluripotent stem cells (iPSCs) from adults with a diagnosis of ASD and from age- and gender-matched healthy individuals. Both groups showed high levels of methylation across the majority of CpG sites within the profiled GAD1 region of interest. The ASD group exhibited a higher number of unique DNA methylation patterns compared to controls and an increased CpG-wise variance. We detected six differentially methylated CpG sites in ASD, three of which reside within a methylation-dependent transcription factor binding site. In ASD, GAD1 is subject to differential methylation patterns that may not only influence its expression, but may also indicate variable epigenetic regulation among cells.
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11
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Dockx Y, Bijnens E, Saenen N, Aerts R, Aerts JM, Casas L, Delcloo A, Dendoncker N, Linard C, Plusquin M, Stas M, Van Nieuwenhuyse A, Van Orshoven J, Somers B, Nawrot T. Residential green space in association with the methylation status in a CpG site within the promoter region of the placental serotonin receptor HTR2A. Epigenetics 2022; 17:1863-1874. [PMID: 35723001 DOI: 10.1080/15592294.2022.2088464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Green space could influence adult cognition and childhood neurodevelopment , and is hypothesized to be partly driven by epigenetic modifications. However, it remains unknown whether some of these associations are already evident during foetal development. Similar biological signals shape the developmental processes in the foetal brain and placenta.Therefore, we hypothesize that green space can modify epigenetic processes of cognition-related pathways in placental tissue, such as DNA-methylation of the serotonin receptor HTR2A. HTR2A-methylation was determined within 327 placentas from the ENVIRONAGE (ENVIRonmental influence ON early AGEing) birth cohort using bisulphite-PCR-pyrosequencing. Total green space exposure was calculated using high-resolution land cover data derived from the Green Map of Flanders in seven buffers (50 m-3 km) and stratified into low (<3 m) and high (≥3 m) vegetation. Residential nature was calculated using the Land use Map of Flanders. We performed multivariate regression models adjusted for several a priori chosen covariables. For an IQR increment in total green space within a 1,000 m, 2,000 m and 3,000 m buffer the methylation of HTR2A increased with 1.47% (95%CI:0.17;2.78), 1.52% (95%CI:0.21;2.83) and 1.42% (95%CI:0.15;2.69), respectively. Additionally,, we found 3.00% (95%CI:1.09;4.91) and 1.98% (95%CI:0.28;3.68) higher HTR2A-methylation when comparing residences with and without the presence of nature in a 50 m and 100 m buffer, respectively. The methylation status of HTR2A in placental tissue is positively associated with maternal green space exposure. Future research is needed to understand better how these epigenetic changes are related to functional modifications in the placenta and the consequent implications for foetal development.
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Affiliation(s)
- Yinthe Dockx
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Esmée Bijnens
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Nelly Saenen
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Raf Aerts
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium.,Division Forest, Nature and Landscape, Department Earth and Environmental Sciences, KU Leuven, Leuven, Belgium.,Risk and Health Impact Assessment, Sciensano (Belgian Institute of Health), Brussels, Belgium.,Division Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium.,Mycology and Aerobiology, Sciensano (Belgian Institute of Health), Brussels, Belgium
| | - Jean-Marie Aerts
- Division Animal and Human Health Engineering, Department of Biosystems (BIOSYST), KU LeuvenMeasure, Model & Manage Bioresponses (M3-BIORES), Leuven, Belgium
| | - Lidia Casas
- Center for Environment and Health, Department of Public Health, Leuven University (KU Leuven), Leuven, Belgium.,Social Epidemiology and Health Policy, Department of Family Medicine and Population Health, University of Antwerp, Antwerp, Belgium.,Institute for Environment and Sustainable Development (IMDO), University of Antwerp, Antwerp, Belgium
| | - Andy Delcloo
- Royal Meteorological Institute of Belgium, Brussels, Belgium.,Department of Physics and Astronomy, Ghent University, Gent, Belgium
| | - Nicolas Dendoncker
- Department of Geography, University of Namur, Namur, Belgium.,Institute for Life, Earth and Environment (ILEE), University of Namur, Namur, Belgium
| | - Catherine Linard
- Department of Geography, University of Namur, Namur, Belgium.,Institute for Life, Earth and Environment (ILEE), University of Namur, Namur, Belgium
| | - Michelle Plusquin
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Michiel Stas
- Division Forest, Nature and Landscape, Department Earth and Environmental Sciences, KU Leuven, Leuven, Belgium.,Division Animal and Human Health Engineering, Department of Biosystems (BIOSYST), KU LeuvenMeasure, Model & Manage Bioresponses (M3-BIORES), Leuven, Belgium
| | - An Van Nieuwenhuyse
- Center for Environment and Health, Department of Public Health, Leuven University (KU Leuven), Leuven, Belgium.,Department of Health Protection, Laboratoire national de santé (LNS), Dudelange, Luxembourg
| | - Jos Van Orshoven
- Division Forest, Nature and Landscape, Department Earth and Environmental Sciences, KU Leuven, Leuven, Belgium
| | - Ben Somers
- Division Forest, Nature and Landscape, Department Earth and Environmental Sciences, KU Leuven, Leuven, Belgium
| | - Tim Nawrot
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium.,Center for Environment and Health, Department of Public Health, Leuven University (KU Leuven), Leuven, Belgium
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12
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Williams LA, LaSalle JM. Future Prospects for Epigenetics in Autism Spectrum Disorder. Mol Diagn Ther 2022; 26:569-579. [PMID: 35962910 PMCID: PMC9626414 DOI: 10.1007/s40291-022-00608-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2022] [Indexed: 12/30/2022]
Abstract
Despite decades of investigation into the genetics of autism spectrum disorder (ASD), a current consensus in the field persists that ASD risk is too heterogeneous to be diagnosed by a single set of genetic variants. As such, ASD research has broadened to include assessment of other molecular biomarkers implicated in the condition that may be reflective of environmental exposures or gene by environment interactions. Epigenetic variance, and specifically differential DNA methylation, have emerged as areas of particularly high interest to ASD, as the epigenetic markers from specific chromatin loci collectively can reflect influences of multiple genetic and environmental factors and can also result in differential gene expression patterns. This review examines recent studies of the ASD epigenome, detailing common gene pathways found to be differentially methylated in people with ASD, and considers how these discoveries may inform our understanding of ASD etiology. We also consider future applications of epigenetics in ASD research and clinical practice, focusing on substratification, biomarker development, and experimental preclinical models of ASD that test causality. In combination with other -omics approaches, epigenomics allows an improved conceptualization of the multifactorial nature of ASD, and opens future lines of inquiry for both basic research and clinical practice.
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Affiliation(s)
- Logan A. Williams
- grid.27860.3b0000 0004 1936 9684Department of Medical Microbiology and Immunology, University of California Davis School of Medicine, Davis, CA USA ,grid.27860.3b0000 0004 1936 9684Perinatal Origins of Disparities Center, University of California Davis, Davis, CA USA ,grid.27860.3b0000 0004 1936 9684MIND Institute, University of California Davis, Davis, CA USA ,grid.27860.3b0000 0004 1936 9684Genome Center, University of California Davis, Davis, CA USA
| | - Janine M. LaSalle
- grid.27860.3b0000 0004 1936 9684Department of Medical Microbiology and Immunology, University of California Davis School of Medicine, Davis, CA USA ,grid.27860.3b0000 0004 1936 9684Perinatal Origins of Disparities Center, University of California Davis, Davis, CA USA ,grid.27860.3b0000 0004 1936 9684MIND Institute, University of California Davis, Davis, CA USA ,grid.27860.3b0000 0004 1936 9684Genome Center, University of California Davis, Davis, CA USA
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13
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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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14
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Zhang S, Wang S, Liu R, Dong H, Zhang X, Tai X. A bibliometric analysis of research trends of artificial intelligence in the treatment of autistic spectrum disorders. Front Psychiatry 2022; 13:967074. [PMID: 36104988 PMCID: PMC9464861 DOI: 10.3389/fpsyt.2022.967074] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVE Autism Spectrum Disorder (ASD) is a serious neurodevelopmental disorder that has become the leading cause of disability in children. Artificial intelligence (AI) is a potential solution to this issue. This study objectively analyzes the global research situation of AI in the treatment of ASD from 1995 to 2022, aiming to explore the global research status and frontier trends in this field. METHODS Web of Science (WoS) and PubMed databese were searched for Literature related to AI on ASD from 1995 to April 2022. CiteSpace, VOSviewer, Pajek and Scimago Graphica were used to analyze the collaboration between countries/institutions/authors, clusters and bursts of keywords, as well as analyses on references. RESULTS A total of 448 literature were included, the total number of literature has shown an increasing trend. The most productive country and institution were the USA, and Vanderbilt University. The authors with the greatest contributions were Warren, Zachary, Sakar, Nilanjan and Swanson, Amy. the most prolific and cited journal is Journal of Autism and Developmental Disorders, the highest cited and co-cited articles were Dautenhahn (Socially intelligent robots: dimensions of human-robot interaction 2007) and Scassellati B (Robots for Use in Autism Research 2012). "Artificial Intelligence", "Brain Computer Interface" and "Humanoid Robot" were the hotspots and frontier trends of AI on ASD. CONCLUSION The application of AI in the treatment of ASD has attracted the attention of researchers all over the world. The education, social function and joint attention of children with ASD are the most concerned issues for global researchers. Robots shows gratifying advantages in these issues and have become the most commonly used technology. Wearable devices and brain-computer interface (BCI) were emerging AI technologies in recent years, which is the direction of further exploration. Restoring social function in individuals with ASD is the ultimate aim and driving force of research in the future.
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Affiliation(s)
- Shouyao Zhang
- School of Second Clinical Medicine/The Second Affiliated Hospital, Yunnan University of Chinese Medicine, Kunming, China
| | - Shuang Wang
- School of Second Clinical Medicine/The Second Affiliated Hospital, Yunnan University of Chinese Medicine, Kunming, China
| | - Ruilu Liu
- School of Second Clinical Medicine/The Second Affiliated Hospital, Yunnan University of Chinese Medicine, Kunming, China
| | - Hang Dong
- School of Second Clinical Medicine/The Second Affiliated Hospital, Yunnan University of Chinese Medicine, Kunming, China
| | - Xinghe Zhang
- School of Second Clinical Medicine/The Second Affiliated Hospital, Yunnan University of Chinese Medicine, Kunming, China
| | - Xiantao Tai
- School of Second Clinical Medicine/The Second Affiliated Hospital, Yunnan University of Chinese Medicine, Kunming, China
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