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Wang Y, Riaz F, Wang W, Pu J, Liang Y, Wu Z, Pan S, Song J, Yang L, Zhang Y, Wu H, Han F, Tang J, Wang X. Functional significance of DNA methylation: epigenetic insights into Sjögren's syndrome. Front Immunol 2024; 15:1289492. [PMID: 38510251 PMCID: PMC10950951 DOI: 10.3389/fimmu.2024.1289492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024] Open
Abstract
Sjögren's syndrome (SjS) is a systemic, highly diverse, and chronic autoimmune disease with a significant global prevalence. It is a complex condition that requires careful management and monitoring. Recent research indicates that epigenetic mechanisms contribute to the pathophysiology of SjS by modulating gene expression and genome stability. DNA methylation, a form of epigenetic modification, is the fundamental mechanism that modifies the expression of various genes by modifying the transcriptional availability of regulatory regions within the genome. In general, adding a methyl group to DNA is linked with the inhibition of genes because it changes the chromatin structure. DNA methylation changes the fate of multiple immune cells, such as it leads to the transition of naïve lymphocytes to effector lymphocytes. A lack of central epigenetic enzymes frequently results in abnormal immune activation. Alterations in epigenetic modifications within immune cells or salivary gland epithelial cells are frequently detected during the pathogenesis of SjS, representing a robust association with autoimmune responses. The analysis of genome methylation is a beneficial tool for establishing connections between epigenetic changes within different cell types and their association with SjS. In various studies related to SjS, most differentially methylated regions are in the human leukocyte antigen (HLA) locus. Notably, the demethylation of various sites in the genome is often observed in SjS patients. The most strongly linked differentially methylated regions in SjS patients are found within genes regulated by type I interferon. This demethylation process is partly related to B-cell infiltration and disease progression. In addition, DNA demethylation of the runt-related transcription factor (RUNX1) gene, lymphotoxin-α (LTA), and myxovirus resistance protein A (MxA) is associated with SjS. It may assist the early diagnosis of SjS by serving as a potential biomarker. Therefore, this review offers a detailed insight into the function of DNA methylation in SjS and helps researchers to identify potential biomarkers in diagnosis, prognosis, and therapeutic targets.
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Affiliation(s)
- Yanqing Wang
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Farooq Riaz
- Center for Cancer Immunology, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology (SIAT), Chinese Academy of Sciences (CAS), Shenzhen, China
| | - Wei Wang
- Department of Radiology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jincheng Pu
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yuanyuan Liang
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhenzhen Wu
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Shengnan Pan
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jiamin Song
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Lufei Yang
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Youwei Zhang
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Huihong Wu
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Fang Han
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jianping Tang
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xuan Wang
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
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Viola TW, Danzer C, Mardini V, Szobot C, Chrusciel JH, Stertz L, Schmitz JM, Walss-Bass C, Fries GR, Grassi-Oliveira R. Prenatal cocaine exposure and its influence on pediatric epigenetic clocks and epigenetic scores in humans. Sci Rep 2024; 14:1946. [PMID: 38253635 PMCID: PMC10803757 DOI: 10.1038/s41598-024-52433-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/18/2024] [Indexed: 01/24/2024] Open
Abstract
The investigation of the effects of prenatal cocaine exposure (PCE) on offspring has been inconsistent, with few studies investigating biological outcomes in humans. We profiled genome-wide DNA methylation (DNAm) of umbilical cord blood (UCB) from newborns with (n = 35) and without (n = 47) PCE. We used DNAm data to (1) assess pediatric epigenetic clocks at birth and (2) to estimate epigenetic scores (ES) for lifetime disorders. We generated gestational epigenetic age estimates (DNAmGA) based on Knight and Bohlin epigenetic clocks. We also investigated the association between DNAmGA and UCB serum brain-derived neurotrophic factor (BDNF) levels. Considering the large-scale DNAm data availability and existing evidence regarding PCE as a risk for health problems later in life, we generated ES for tobacco smoking, psychosis, autism, diabetes, and obesity. A gene ontology (GO) analysis on the CpGs included in the ES with group differences was performed. PCE was associated with lower DNAmGA in newborns, and this effect remained significant when controlling for potential confounders, such as blood cell type composition predicted by DNAm and obstetric data. DNAmGA was negatively correlated with BDNF levels in the serum of UCB. Higher tobacco smoking, psychosis, and diabetes ES were found in the PCE group. The GO analysis revealed GABAergic synapses as a potential pathway altered by PCE. Our findings of decelerated DNAmGA and ES for adverse phenotypes associated with PCE, suggest that the effects of gestational cocaine exposure on the epigenetic landscape of human newborns are detectable at birth.
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Affiliation(s)
- Thiago Wendt Viola
- School of Medicine, Developmental Cognitive Neuroscience Lab, Pontifical Catholic University of Rio Grande Do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Christina Danzer
- Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 11, A701-129, 8200, Aarhus, Denmark
| | - Victor Mardini
- Clinical Hospital of Porto Alegre, Porto Alegre, RS, Brazil
| | - Claudia Szobot
- Clinical Hospital of Porto Alegre, Porto Alegre, RS, Brazil
| | - João Henrique Chrusciel
- School of Medicine, Developmental Cognitive Neuroscience Lab, Pontifical Catholic University of Rio Grande Do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Laura Stertz
- Faillace Department of Psychiatry and Behavioral Sciences, Translational Psychiatry Program, The University of Texas Health Science Center at Houston, Houston, USA
| | - Joy M Schmitz
- Faillace Department of Psychiatry and Behavioral Sciences, Translational Psychiatry Program, The University of Texas Health Science Center at Houston, Houston, USA
| | - Consuelo Walss-Bass
- Faillace Department of Psychiatry and Behavioral Sciences, Translational Psychiatry Program, The University of Texas Health Science Center at Houston, Houston, USA
| | - Gabriel R Fries
- Faillace Department of Psychiatry and Behavioral Sciences, Translational Psychiatry Program, The University of Texas Health Science Center at Houston, Houston, USA
| | - Rodrigo Grassi-Oliveira
- School of Medicine, Developmental Cognitive Neuroscience Lab, Pontifical Catholic University of Rio Grande Do Sul (PUCRS), Porto Alegre, RS, Brazil.
- Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 11, A701-129, 8200, Aarhus, Denmark.
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Singh M, Saxena S, Mohan KN. DNMT1 downregulation as well as its overexpression distinctly affect mostly overlapping genes implicated in schizophrenia, autism spectrum, epilepsy, and bipolar disorders. Front Mol Neurosci 2023; 16:1275697. [PMID: 38125006 PMCID: PMC10731955 DOI: 10.3389/fnmol.2023.1275697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/15/2023] [Indexed: 12/23/2023] Open
Abstract
Data on schizophrenia (SZ), epilepsy (EPD) and bipolar disorders (BPD) suggested an association of DNMT1 overexpression whereas certain variants of the gene were predicted to result in its increased expression in autism spectrum disorder (ASD). In addition, loss of DNMT1 in frontal cortex resulted in behavioral abnormalities in mice. Here we investigated the effects of increased as well as lack of DNMT1 expression using Dnmt1tet/tet neurons as a model for abnormal neurogenesis and 10,861 genes showing transcript level dysregulation in datasets from the four disorders. In case of overexpression, 3,211 (∼ 30%) genes were dysregulated, affecting pathways involved in neurogenesis, semaphorin signaling, ephrin receptor activity, etc. A disproportionately higher proportion of dysregulated genes were associated with epilepsy. When transcriptome data of Dnmt1tet/tet neurons treated with doxycycline that downregulated DNMT1 was used, 3,356 genes (∼31%) were dysregulated with a significant proportion involved in pathways similar to those in untreated cells. Both conditions resulted in ∼68% of dysregulated genes wherein a majority showed similar patterns of transcript level changes. Among the genes with transcripts returning to normal levels, ribosome assembly/biogenesis was most significant whereas in absence of DNMT1, a new set of 903 genes became dysregulated and are involved in similar pathways as mentioned above. These findings provide support for overexpression of DNMT1 as well as its downregulation as risk factor for the four disorders and that its levels within a tight range are essential for normal neurodevelopment/mental health.
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Affiliation(s)
- Minali Singh
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad, India
| | - Sonal Saxena
- Centre for Human Disease Research, Birla Institute of Technology and Science, Pilani, Hyderabad, India
| | - Kommu Naga Mohan
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad, India
- Centre for Human Disease Research, Birla Institute of Technology and Science, Pilani, Hyderabad, India
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Strathearn L, Momany A, Kovács EH, Guiler W, Ladd-Acosta C. The intersection of genome, epigenome and social experience in autism spectrum disorder: Exploring modifiable pathways for intervention. Neurobiol Learn Mem 2023; 202:107761. [PMID: 37121464 PMCID: PMC10330448 DOI: 10.1016/j.nlm.2023.107761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 02/22/2023] [Accepted: 04/22/2023] [Indexed: 05/02/2023]
Abstract
The number of children diagnosed with autism spectrum disorder (ASD) has increased substantially over the past two decades. Current research suggests that both genetic and environmental risk factors are involved in the etiology of ASD. The goal of this paper is to examine how one specific environmental factor, early social experience, may be correlated with DNA methylation (DNAm) changes in genes associated with ASD. We present an innovative model which proposes that polygenic risk and changes in DNAm due to social experience may both contribute to the symptoms of ASD. Previous research on genetic and environmental factors implicated in the etiology of ASD will be reviewed, with an emphasis on the oxytocin receptor gene, which may be epigenetically altered by early social experience, and which plays a crucial role in social and cognitive development. Identifying an environmental risk factor for ASD (e.g., social experience) that could be modified via early intervention and which results in epigenetic (DNAm) changes, could transform our understanding of this condition, facilitate earlier identification of ASD, and guide early intervention efforts.
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Affiliation(s)
- Lane Strathearn
- Stead Family Department of Pediatrics, Carver College of Medicine, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA; Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, 51 Newton Road 2-471 Bowen Science Building, Iowa City, IA 52241, USA; Interdisciplinary Graduate Program in Neuroscience, University of Iowa, 356 Medical Research Center, Iowa City, IA 52242, USA; Center for Disabilities and Development, University of Iowa Stead Family Children's Hospital, 100 Hawkins Drive, Iowa City, IA 52242, USA; Hawkeye Intellectual and Developmental Disabilities Research Center (Hawk-IDDRC), University of Iowa, 100 Hawkins Drive, Iowa City, IA 52242, USA.
| | - Allison Momany
- Stead Family Department of Pediatrics, Carver College of Medicine, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA; Hawkeye Intellectual and Developmental Disabilities Research Center (Hawk-IDDRC), University of Iowa, 100 Hawkins Drive, Iowa City, IA 52242, USA.
| | - Emese Hc Kovács
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, 51 Newton Road 2-471 Bowen Science Building, Iowa City, IA 52241, USA.
| | - William Guiler
- Interdisciplinary Graduate Program in Neuroscience, University of Iowa, 356 Medical Research Center, Iowa City, IA 52242, USA.
| | - Christine Ladd-Acosta
- Department of Epidemiology and the Wendy Klag Center for Autism and Developmental Disabilities, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe Street, Baltimore, MD 21205, USA.
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Gevezova M, Sbirkov Y, Sarafian V, Plaimas K, Suratanee A, Maes M. Autistic spectrum disorder (ASD) - Gene, molecular and pathway signatures linking systemic inflammation, mitochondrial dysfunction, transsynaptic signalling, and neurodevelopment. Brain Behav Immun Health 2023; 30:100646. [PMID: 37334258 PMCID: PMC10275703 DOI: 10.1016/j.bbih.2023.100646] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 06/03/2023] [Indexed: 06/20/2023] Open
Abstract
Background Despite advances in autism spectrum disorder (ASD) research and the vast genomic, transcriptomic, and proteomic data available, there are still controversies regarding the pathways and molecular signatures underlying the neurodevelopmental disorders leading to ASD. Purpose To delineate these underpinning signatures, we examined the two largest gene expression meta-analysis datasets obtained from the brain and peripheral blood mononuclear cells (PBMCs) of 1355 ASD patients and 1110 controls. Methods We performed network, enrichment, and annotation analyses using the differentially expressed genes, transcripts, and proteins identified in ASD patients. Results Transcription factor network analyses in up- and down-regulated genes in brain tissue and PBMCs in ASD showed eight main transcription factors, namely: BCL3, CEBPB, IRF1, IRF8, KAT2A, NELFE, RELA, and TRIM28. The upregulated gene networks in PBMCs of ASD patients are strongly associated with activated immune-inflammatory pathways, including interferon-α signaling, and cellular responses to DNA repair. Enrichment analyses of the upregulated CNS gene networks indicate involvement of immune-inflammatory pathways, cytokine production, Toll-Like Receptor signalling, with a major involvement of the PI3K-Akt pathway. Analyses of the downregulated CNS genes suggest electron transport chain dysfunctions at multiple levels. Network topological analyses revealed that the consequent aberrations in axonogenesis, neurogenesis, synaptic transmission, and regulation of transsynaptic signalling affect neurodevelopment with subsequent impairments in social behaviours and neurocognition. The results suggest a defense response against viral infection. Conclusions Peripheral activation of immune-inflammatory pathways, most likely induced by viral infections, may result in CNS neuroinflammation and mitochondrial dysfunction, leading to abnormalities in transsynaptic transmission, and brain neurodevelopment.
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Affiliation(s)
- Maria Gevezova
- Department of Medical Biology, Medical University of Plovdiv, Bulgaria
- Research Institute at MU-Plovdiv, Bulgaria
| | - Yordan Sbirkov
- Department of Medical Biology, Medical University of Plovdiv, Bulgaria
- Research Institute at MU-Plovdiv, Bulgaria
| | - Victoria Sarafian
- Department of Medical Biology, Medical University of Plovdiv, Bulgaria
- Research Institute at MU-Plovdiv, Bulgaria
| | - Kitiporn Plaimas
- Advanced Virtual and Intelligent Computing (AVIC) Center, Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Apichat Suratanee
- Department of Mathematics, Faculty of Applied Science, King Mongkut's University of Technology North Bangkok, Bangkok, 10800, Thailand
| | - Michael Maes
- Research Institute at MU-Plovdiv, Bulgaria
- Department of Psychiatry, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
- Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, South Korea
- Department of Psychiatry, Medical University of Plovdiv, Plovdiv, Bulgaria
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Stoccoro A, Conti E, Scaffei E, Calderoni S, Coppedè F, Migliore L, Battini R. DNA Methylation Biomarkers for Young Children with Idiopathic Autism Spectrum Disorder: A Systematic Review. Int J Mol Sci 2023; 24:ijms24119138. [PMID: 37298088 DOI: 10.3390/ijms24119138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/19/2023] [Accepted: 05/21/2023] [Indexed: 06/12/2023] Open
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental condition, the underlying pathological mechanisms of which are not yet completely understood. Although several genetic and genomic alterations have been linked to ASD, for the majority of ASD patients, the cause remains unknown, and the condition likely arises due to complex interactions between low-risk genes and environmental factors. There is increasing evidence that epigenetic mechanisms that are highly sensitive to environmental factors and influence gene function without altering the DNA sequence, particularly aberrant DNA methylation, are involved in ASD pathogenesis. This systematic review aimed to update the clinical application of DNA methylation investigations in children with idiopathic ASD, investigating its potential application in clinical settings. To this end, a literature search was performed on different scientific databases using a combination of terms related to the association between peripheral DNA methylation and young children with idiopathic ASD; this search led to the identification of 18 articles. In the selected studies, DNA methylation is investigated in peripheral blood or saliva samples, at both gene-specific and genome-wide levels. The results obtained suggest that peripheral DNA methylation could represent a promising methodology in ASD biomarker research, although further studies are needed to develop DNA-methylation-based clinical applications.
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Affiliation(s)
- Andrea Stoccoro
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56100 Pisa, Italy
| | - Eugenia Conti
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, 56128 Pisa, Italy
| | - Elena Scaffei
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, 56128 Pisa, Italy
- Department of Neuroscience, Psychology, Drug Research and Child Health NEUROFARBA, University of Florence, 50139 Florence, Italy
| | - Sara Calderoni
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, 56128 Pisa, Italy
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
| | - Fabio Coppedè
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56100 Pisa, Italy
| | - Lucia Migliore
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56100 Pisa, Italy
| | - Roberta Battini
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, 56128 Pisa, Italy
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
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7
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Budkina A, Medvedeva YA, Stupnikov A. Assessing the Differential Methylation Analysis Quality for Microarray and NGS Platforms. Int J Mol Sci 2023; 24:ijms24108591. [PMID: 37239934 DOI: 10.3390/ijms24108591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 04/28/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
Differential methylation (DM) is actively recruited in different types of fundamental and translational studies. Currently, microarray- and NGS-based approaches for methylation analysis are the most widely used with multiple statistical models designed to extract differential methylation signatures. The benchmarking of DM models is challenging due to the absence of gold standard data. In this study, we analyze an extensive number of publicly available NGS and microarray datasets with divergent and widely utilized statistical models and apply the recently suggested and validated rank-statistic-based approach Hobotnica to evaluate the quality of their results. Overall, microarray-based methods demonstrate more robust and convergent results, while NGS-based models are highly dissimilar. Tests on the simulated NGS data tend to overestimate the quality of the DM methods and therefore are recommended for use with caution. Evaluation of the top 10 DMC and top 100 DMC in addition to the not-subset signature also shows more stable results for microarray data. Summing up, given the observed heterogeneity in NGS methylation data, the evaluation of newly generated methylation signatures is a crucial step in DM analysis. The Hobotnica metric is coordinated with previously developed quality metrics and provides a robust, sensitive, and informative estimation of methods' performance and DM signatures' quality in the absence of gold standard data solving a long-existing problem in DM analysis.
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Affiliation(s)
- Anna Budkina
- Department of Biomedical Physics, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Yulia A Medvedeva
- Department of Biomedical Physics, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
- Federal State Institution «Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences», 119071 Moscow, Russia
| | - Alexey Stupnikov
- Department of Biomedical Physics, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
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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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Perini S, Filosi M, Domenici E. Candidate biomarkers from the integration of methylation and gene expression in discordant autistic sibling pairs. Transl Psychiatry 2023; 13:109. [PMID: 37012247 PMCID: PMC10070641 DOI: 10.1038/s41398-023-02407-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 03/18/2023] [Accepted: 03/21/2023] [Indexed: 04/05/2023] Open
Abstract
While the genetics of autism spectrum disorders (ASD) has been intensively studied, resulting in the identification of over 100 putative risk genes, the epigenetics of ASD has received less attention, and results have been inconsistent across studies. We aimed to investigate the contribution of DNA methylation (DNAm) to the risk of ASD and identify candidate biomarkers arising from the interaction of epigenetic mechanisms with genotype, gene expression, and cellular proportions. We performed DNAm differential analysis using whole blood samples from 75 discordant sibling pairs of the Italian Autism Network collection and estimated their cellular composition. We studied the correlation between DNAm and gene expression accounting for the potential effects of different genotypes on DNAm. We showed that the proportion of NK cells was significantly reduced in ASD siblings suggesting an imbalance in their immune system. We identified differentially methylated regions (DMRs) involved in neurogenesis and synaptic organization. Among candidate loci for ASD, we detected a DMR mapping to CLEC11A (neighboring SHANK1) where DNAm and gene expression were significantly and negatively correlated, independently from genotype effects. As reported in previous studies, we confirmed the involvement of immune functions in the pathophysiology of ASD. Notwithstanding the complexity of the disorder, suitable biomarkers such as CLEC11A and its neighbor SHANK1 can be discovered using integrative analyses even with peripheral tissues.
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Affiliation(s)
- Samuel Perini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento (TN), Italy
| | - Michele Filosi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento (TN), Italy
- EURAC Research, Bolzano, Italy
| | - Enrico Domenici
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento (TN), Italy.
- Fondazione The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy.
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Apte M, Kumar A. Correlation of Mutated gene and Signalling pathways in ASD. IBRO Neurosci Rep 2023; 14:384-392. [PMID: 37101819 PMCID: PMC10123338 DOI: 10.1016/j.ibneur.2023.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Autism is a complicated spectrum of neurodevelopmental illnesses characterized by repetitive and constrained behaviors and interests, as well as social interaction and communication difficulties that are first shown in infancy. More than 18 million Indians, according to the National Health Portal of India, and 1 in 160 children worldwide, according to the WHO, are diagnosed with autism spectrum disorders. This review aims to discuss the complex genetic architecture that underlies autism and summarizes the role of proteins likely to play in the development of autism. We also consider how genetic mutations can affect convergent signaling pathways and hinder the development of brain circuitry and the role of cognition development and theory of mind with Cognition-behavior therapy benefits in autism.
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Affiliation(s)
- Madhavi Apte
- Quality Assurance and Pharmacognosy and Phytochemistry, SVKM’s Dr. Bhanuben Nanavati College of Pharmacy, Vile Parle, 400056 Mumbai, India
- Correspondence to: SVKM’s Dr. Bhanuben Nanavati College of Pharmacy, Mithibai Campus, V.M. Road, Vile Parle West, 400056 Mumbai, India.
| | - Aayush Kumar
- Quality Assurance, SVKM’s Dr. Bhanuben Nanavati College of Pharmacy, Vile Parle, 400056 Mumbai, India
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11
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Davide G, Rebecca C, Irene P, Luciano C, Francesco R, Marta N, Miriam O, Natascia B, Pierluigi P. Epigenetics of Autism Spectrum Disorders: A Multi-level Analysis Combining Epi-signature, Age Acceleration, Epigenetic Drift and Rare Epivariations Using Public Datasets. Curr Neuropharmacol 2023; 21:2362-2373. [PMID: 37489793 PMCID: PMC10556384 DOI: 10.2174/1570159x21666230725142338] [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: 09/20/2022] [Revised: 12/09/2022] [Accepted: 12/17/2022] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND Epigenetics of Autism Spectrum Disorders (ASD) is still an understudied field. The majority of the studies on the topic used an approach based on mere classification of cases and controls. OBJECTIVE The present study aimed at providing a multi-level approach in which different types of epigenetic analysis (epigenetic drift, age acceleration) are combined. METHODS We used publicly available datasets from blood (n = 3) and brain tissues (n = 3), separately. Firstly, we evaluated for each dataset and meta-analyzed the differential methylation profile between cases and controls. Secondly, we analyzed age acceleration, epigenetic drift and rare epigenetic variations. RESULTS We observed a significant epi-signature of ASD in blood but not in brain specimens. We did not observe significant age acceleration in ASD, while epigenetic drift was significantly higher compared to controls. We reported the presence of significant rare epigenetic variations in 41 genes, 35 of which were never associated with ASD. Almost all genes were involved in pathways linked to ASD etiopathogenesis (i.e., neuronal development, mitochondrial metabolism, lipid biosynthesis and antigen presentation). CONCLUSION Our data support the hypothesis of the use of blood epi-signature as a potential tool for diagnosis and prognosis of ASD. The presence of an enhanced epigenetic drift, especially in brain, which is linked to cellular replication, may suggest that alteration in epigenetics may occur at a very early developmental stage (i.e., fetal) when neuronal replication is still high.
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Affiliation(s)
- Gentilini Davide
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, 27100, Italy
- Bioinformatics and Statistical Genomics Unit, IRCCS Istituto Auxologico Italiano, Milan, 20090, Italy
| | - Cavagnola Rebecca
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, 27100, Italy
| | - Possenti Irene
- Department of Statistical Sciences Paolo Fortunati, University of Bologna, Bologna, Italy
| | - Calzari Luciano
- Bioinformatics and Statistical Genomics Unit, IRCCS Istituto Auxologico Italiano, Milan, 20090, Italy
| | - Ranucci Francesco
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, 27100, Italy
| | - Nola Marta
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, 27100, Italy
| | - Olivola Miriam
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, 27100, Italy
| | - Brondino Natascia
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, 27100, Italy
| | - Politi Pierluigi
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, 27100, Italy
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12
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Anna S, Magdalena J. Editorial: Epigenomic contributions to autism spectrum disorders. Front Neurosci 2023; 17:1177378. [PMID: 37144095 PMCID: PMC10151758 DOI: 10.3389/fnins.2023.1177378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/27/2023] [Indexed: 05/06/2023] Open
Affiliation(s)
- Starnawska Anna
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, CGPM, and Center for Integrative Sequencing, iSEQ, Aarhus, Denmark
- *Correspondence: Starnawska Anna
| | - Janecka Magdalena
- Seaver Autism Center, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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13
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Qureshi F, Hahn J. Towards the Development of a Diagnostic Test for Autism Spectrum Disorder: Big Data Meets Metabolomics. CAN J CHEM ENG 2023; 101:9-17. [PMID: 36591338 PMCID: PMC9799131 DOI: 10.1002/cjce.24594] [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: 02/27/2022] [Accepted: 04/06/2022] [Indexed: 01/05/2023]
Abstract
Autism spectrum disorder (ASD) is defined as a neurodevelopmental disorder which results in impairments in social communications and interactions as well as repetitive behaviors. Despite current estimates showing that approximately 2.2% of children are affected in the United States, relatively little about ASD pathophysiology is known in part due to the highly heterogenous presentation of the disorder. Given the limited knowledge into the biological mechanisms governing its etiology, the diagnosis of ASD is performed exclusively based on an individual's behavior assessed by a clinician through psychometric tools. Although there is no readily available biochemical test for ASD diagnosis, multivariate statistical methods show considerable potential for effectively leveraging multiple biochemical measurements for classification and characterization purposes. In this work, markers associated with the folate dependent one-carbon metabolism and transulfuration (FOCM/TS) pathways analyzed via both Fisher Discriminant Analysis and Support Vector Machine showed strong capability to distinguish between ASD and TD cohorts. Furthermore, using Kernel Partial Least Squares regression it was possible to assess some degree of behavioral severity from metabolomic data. While the results presented need to be replicated in independent future studies, they represent a promising avenue for uncovering clinically relevant ASD biomarkers.
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Affiliation(s)
- Fatir Qureshi
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy NY 12180
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy NY 12180
| | - Juergen Hahn
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy NY 12180
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy NY 12180
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy NY 12180
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14
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Song AY, Bakulski K, Feinberg JI, Newschaffer C, Croen LA, Hertz-Picciotto I, Schmidt RJ, Farzadegan H, Lyall K, Fallin MD, Volk HE, Ladd-Acosta C. Associations between accelerated parental biologic age, autism spectrum disorder, social traits, and developmental and cognitive outcomes in their children. Autism Res 2022; 15:2359-2370. [PMID: 36189953 PMCID: PMC9722613 DOI: 10.1002/aur.2822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 09/19/2022] [Indexed: 01/11/2023]
Abstract
Parental age is a known risk factor for autism spectrum disorder (ASD), however, studies to identify the biologic changes underpinning this association are limited. In recent years, "epigenetic clock" algorithms have been developed to estimate biologic age and to evaluate how the epigenetic aging impacts health and disease. In this study, we examined the relationship between parental epigenetic aging and their child's prospective risk of ASD and autism related quantitative traits in the Early Autism Risk Longitudinal Investigation study. Estimates of epigenetic age were computed using three robust clock algorithms and DNA methylation measures from the Infinium HumanMethylation450k platform for maternal blood and paternal blood specimens collected during pregnancy. Epigenetic age acceleration was defined as the residual of regressing chronological age on epigenetic age while accounting for cell type proportions. Multinomial logistic regression and linear regression models were completed adjusting for potential confounders for both maternal epigenetic age acceleration (n = 163) and paternal epigenetic age acceleration (n = 80). We found accelerated epigenetic aging in mothers estimated by Hannum's clock was significantly associated with lower cognitive ability and function in offspring at 12 months, as measured by Mullen Scales of Early Learning scores (β = -1.66, 95% CI: -3.28, -0.04 for a one-unit increase). We also observed a marginal association between accelerated maternal epigenetic aging by Horvath's clock and increased odds of ASD in offspring at 36 months of age (aOR = 1.12, 95% CI: 0.99, 1.26). By contrast, fathers accelerated aging was marginally associated with decreased ASD risk in their offspring (aOR = 0.83, 95% CI: 0.68, 1.01). Our findings suggest epigenetic aging could play a role in parental age risks on child brain development.
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Affiliation(s)
- Ashley Y. Song
- Department of Mental Health, Johns Hopkins Bloomberg School
of Public Health, Baltimore, MD
- Wendy Klag Center for Autism and Developmental
Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Kelly Bakulski
- Department of Epidemiology, University of Michigan, Ann
Arbor, MI
| | - Jason I. Feinberg
- Department of Mental Health, Johns Hopkins Bloomberg School
of Public Health, Baltimore, MD
- Wendy Klag Center for Autism and Developmental
Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Craig Newschaffer
- Department of Mental Health, Johns Hopkins Bloomberg School
of Public Health, Baltimore, MD
- College of Health and Human Development, Pennsylvania State
University, State College, PA
| | - Lisa A. Croen
- Division of Research, Kaiser Permanente, Oakland, CA
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences and The MIND
Institute, School of Medicine, University of California-Davis, Davis, CA
| | - Rebecca J. Schmidt
- Department of Public Health Sciences and The MIND
Institute, School of Medicine, University of California-Davis, Davis, CA
| | - Homayoon Farzadegan
- Department of Epidemiology, Johns Hopkins Bloomberg School
of Public Health, Baltimore, MD
| | - Kristen Lyall
- A.J. Drexel Autism Institute, Drexel University,
Philadelphia, PA
| | - M. Daniele Fallin
- Rollins School of Public Health, Emory University, Atlanta,
Georgia, USA
| | - Heather E. Volk
- Department of Mental Health, Johns Hopkins Bloomberg School
of Public Health, Baltimore, MD
- Wendy Klag Center for Autism and Developmental
Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Christine Ladd-Acosta
- Department of Mental Health, Johns Hopkins Bloomberg School
of Public Health, Baltimore, MD
- Wendy Klag Center for Autism and Developmental
Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
- Department of Epidemiology, Johns Hopkins Bloomberg School
of Public Health, Baltimore, MD
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15
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Liang J, Jia Y, Yu H, Yan H, Shen Q, Xu Y, Li Y, Yang M. 5-Aza-2'-Deoxycytidine Regulates White Adipocyte Browning by Modulating miRNA-133a/Prdm16. Metabolites 2022; 12:1131. [PMID: 36422269 PMCID: PMC9695087 DOI: 10.3390/metabo12111131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/03/2022] [Accepted: 11/15/2022] [Indexed: 01/27/2024] Open
Abstract
The conversion of white adipocytes into brown adipocytes improves their thermogenesis and promotes energy consumption. Epigenetic modifications affect related genes and interfere with energy metabolism, and these are the basis of new ideas for obesity treatment. Neonatal mice show high levels of DNA hypermethylation in white adipose tissue early in life and low levels in brown adipose tissue. Thus, we considered that the regulation of DNA methylation may play a role in the conversion of white adipose to brown. We observed growth indicators, lipid droplets of adipocytes, brown fat specific protein, and miRNA-133a after treatment with 5-Aza-2'-deoxycytidine. The expression of Prdm16 and Ucp-1 in adipocytes was detected after inhibiting miRNA-133a. The results showed a decrease in total lipid droplet formation and an increased expression of the brown fat specific proteins Prdm16 and Ucp-1. This study indicated that 5-Aza-2'-deoxycytidine promotes white adipocyte browning following DNA demethylation, possibly via the modulation of miR-133a and Prdm16.
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Affiliation(s)
- Jia Liang
- Department of Pharmacology, Binzhou Medical University, Yantai 264003, China
| | - Ying Jia
- Department of Pharmacology, Binzhou Medical University, Yantai 264003, China
| | - Huixin Yu
- Department of Pharmacology, Binzhou Medical University, Yantai 264003, China
| | - Haijing Yan
- Department of Pharmacology, Binzhou Medical University, Yantai 264003, China
| | - Qingyu Shen
- Department of Pharmacology, Binzhou Medical University, Yantai 264003, China
| | - Yong Xu
- Department of Pharmacology, Binzhou Medical University, Yantai 264003, China
| | - Yana Li
- Department of Pathophysiology, Binzhou Medical University, Yantai 264003, China
| | - Meizi Yang
- Department of Pharmacology, Binzhou Medical University, Yantai 264003, China
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16
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Anne A, Saxena S, Mohan KN. Genome-wide methylation analysis of post-mortem cerebellum samples supports the role of peroxisomes in autism spectrum disorder. Epigenomics 2022; 14:1015-1027. [PMID: 36154275 DOI: 10.2217/epi-2022-0184] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: We tested the hypothesis that a subset of patients with autism spectrum disorder (ASD) contains candidate genes with high DNA methylation differences (effective values) that potentially affect one of the two alleles. Materials & methods: Genome-wide DNA methylation comparisons were made on cerebellum samples from 30 patients and 45 controls. Results: 12 genes with high effective values, including GSDMD, MMACHC, SLC6A5 and NKX6-2, implicated in ASD and other neuropsychiatric disorders were identified. Monoallelic promoter methylation and downregulation were observed for SERHL (serine hydrolase-like) and CAT (catalase) genes associated with peroxisome function. Conclusion: These data are consistent with the hypothesis implicating impaired peroxisome function/biogenesis for ASD. A similar approach holds promise for identifying rare epimutations in ASD and other complex disorders.
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Affiliation(s)
- Anuhya Anne
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, Birla Institute of Technology & Science, Pilani - Hyderabad Campus, 500 078, India.,Centre for Human Disease Research, Birla Institute of Technology & Science, Pilani - Hyderabad Campus, 500 078, India
| | - Sonal Saxena
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, Birla Institute of Technology & Science, Pilani - Hyderabad Campus, 500 078, India
| | - Kommu Naga Mohan
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, Birla Institute of Technology & Science, Pilani - Hyderabad Campus, 500 078, India.,Centre for Human Disease Research, Birla Institute of Technology & Science, Pilani - Hyderabad Campus, 500 078, India
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17
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Wang T, Zhao PA, Eichler EE. Rare variants and the oligogenic architecture of autism. Trends Genet 2022; 38:895-903. [PMID: 35410794 PMCID: PMC9378350 DOI: 10.1016/j.tig.2022.03.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/08/2022] [Accepted: 03/14/2022] [Indexed: 12/12/2022]
Abstract
Most large-scale genetic studies of autism have focused on the discovery of genes by proving an enrichment of de novo mutations (DNMs) in autism probands or characterizing polygenic risk based on the association of common variants. We present evidence in support of an oligogenic model where two or more ultrarare mutations of more modest effect are preferentially transmitted to children with autism. Such private gene-disruptive mutations are enriched in families where there are multiple affected individuals, emerged two or three generations ago, and map to genes not previously associated with autism. Although no single gene has reached statistical significance, this class of variation should be considered along with genetic and nongenetic factors to better explain the etiology of this complex trait.
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Affiliation(s)
- Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Peiyao A Zhao
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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18
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Saeliw T, Permpoon T, Iadsee N, Tencomnao T, Hu VW, Sarachana T, Green D, Sae-Lee C. LINE-1 and Alu methylation signatures in autism spectrum disorder and their associations with the expression of autism-related genes. Sci Rep 2022; 12:13970. [PMID: 35978033 PMCID: PMC9385849 DOI: 10.1038/s41598-022-18232-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022] Open
Abstract
Long interspersed nucleotide element-1 (LINE-1) and Alu elements are retrotransposons whose abilities cause abnormal gene expression and genomic instability. Several studies have focused on DNA methylation profiling of gene regions, but the locus-specific methylation of LINE-1 and Alu elements has not been identified in autism spectrum disorder (ASD). Here we interrogated locus- and family-specific methylation profiles of LINE-1 and Alu elements in ASD whole blood using publicly-available Illumina Infinium 450 K methylation datasets from heterogeneous ASD and ASD variants (Chromodomain Helicase DNA-binding 8 (CHD8) and 16p11.2del). Total DNA methylation of repetitive elements were notably hypomethylated exclusively in ASD with CHD8 variants. Methylation alteration in a family-specific manner including L1P, L1H, HAL, AluJ, and AluS families were observed in the heterogeneous ASD and ASD with CHD8 variants. Moreover, LINE-1 and Alu methylation within target genes is inversely related to the expression level in each ASD variant. The DNA methylation signatures of the LINE-1 and Alu elements in ASD whole blood, as well as their associations with the expression of ASD-related genes, have been identified. If confirmed in future larger studies, these findings may contribute to the identification of epigenomic biomarkers of ASD.
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Affiliation(s)
- Thanit Saeliw
- The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Tiravut Permpoon
- Research Division, SiMR, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nutta Iadsee
- Research Division, SiMR, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Tewin Tencomnao
- Natural Products for Neuroprotection and Anti-Ageing Research Unit, Chulalongkorn University, Bangkok, Thailand.,Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Valerie W Hu
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Tewarit Sarachana
- Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand.,SYstems Neuroscience of Autism and PSychiatric Disorders (SYNAPS) Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Daniel Green
- Institute of Life Course and Medical Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Chanachai Sae-Lee
- Research Division, SiMR, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
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19
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Epigenetic profiling of social communication trajectories and co-occurring mental health problems: a prospective, methylome-wide association study. Dev Psychopathol 2022; 34:854-863. [PMID: 33494854 PMCID: PMC8622455 DOI: 10.1017/s0954579420001662] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
While previous studies suggest that both genetic and environmental factors play an important role in the development of autism-related traits, little is known about potential biological mechanisms underlying these associations. Using data from the Avon Longitudinal Study of Parents and Children (ALSPAC), we examined prospective associations between DNA methylation (DNAm: nbirth = 804, nage 7 = 877) and trajectories of social communication deficits at age 8-17 years. Methylomic variation at three loci across the genome (false discovery rate = 0.048) differentiated children following high (n = 80) versus low (n = 724) trajectories of social communication deficits. This differential DNAm was specific to the neonatal period and not observed at 7 years of age. Associations between DNAm and trajectory membership remained robust after controlling for co-occurring mental health problems (i.e., hyperactivity/inattention, conduct problems). The three loci identified at birth were not replicated in the Generation R Study. However, to the best of our knowledge, ALSPAC is the only study to date that is prospective enough to examine DNAm in relation to longitudinal trajectories of social communication deficits from childhood to adolescence. Although the present findings might point to potentially novel sites that differentiate between a high versus low trajectory of social communication deficits, the results should be considered tentative until further replicated.
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20
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Doi M, Li M, Usui N, Shimada S. Genomic Strategies for Understanding the Pathophysiology of Autism Spectrum Disorder. Front Mol Neurosci 2022; 15:930941. [PMID: 35813066 PMCID: PMC9263364 DOI: 10.3389/fnmol.2022.930941] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/06/2022] [Indexed: 11/25/2022] Open
Abstract
Recent breakthroughs in sequencing technology and technological developments have made it easier to analyze the entire human genome than ever before. In addition to disease-specific genetic mutations and chromosomal aberrations, epigenetic alterations in individuals can also be analyzed using genomics. Autism spectrum disorder (ASD) is a neurodevelopmental disorder (NDD) caused by genetic and/or environmental factors. More than a thousand genes associated with ASD have been identified which are known to be involved in brain development. However, it is difficult to decode the roles of ASD-associated genes without in vitro and in vivo validations, particularly in the process of brain development. In this review, we discuss genomic strategies for understanding the pathological mechanisms underlying ASD. For this purpose, we discuss ASD-associated genes and their functions, as well as analytical strategies and their strengths and weaknesses in cellular and animal models from a basic research perspective.
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Affiliation(s)
- Miyuki Doi
- Department of Neuroscience and Cell Biology, Graduate School of Medicine, Osaka University, Suita, Japan
- Addiction Research Unit, Osaka Psychiatric Research Center, Osaka Psychiatric Medical Center, Osaka, Japan
| | - Mengwei Li
- Department of Neuroscience and Cell Biology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Noriyoshi Usui
- Department of Neuroscience and Cell Biology, Graduate School of Medicine, Osaka University, Suita, Japan
- Addiction Research Unit, Osaka Psychiatric Research Center, Osaka Psychiatric Medical Center, Osaka, Japan
- United Graduate School of Child Development, Osaka University, Suita, Japan
- Global Center for Medical Engineering and Informatics, Osaka University, Suita, Japan
- *Correspondence: Noriyoshi Usui
| | - Shoichi Shimada
- Department of Neuroscience and Cell Biology, Graduate School of Medicine, Osaka University, Suita, Japan
- Addiction Research Unit, Osaka Psychiatric Research Center, Osaka Psychiatric Medical Center, Osaka, Japan
- United Graduate School of Child Development, Osaka University, Suita, Japan
- Global Center for Medical Engineering and Informatics, Osaka University, Suita, Japan
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21
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Taeubert MJ, de Prado-Bert P, Geurtsen ML, Mancano G, Vermeulen MJ, Reiss IKM, Caramaschi D, Sunyer J, Sharp GC, Julvez J, Muckenthaler MU, Felix JF. Maternal iron status in early pregnancy and DNA methylation in offspring: an epigenome-wide meta-analysis. Clin Epigenetics 2022; 14:59. [PMID: 35505416 PMCID: PMC9066980 DOI: 10.1186/s13148-022-01276-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 04/11/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Unbalanced iron homeostasis in pregnancy is associated with an increased risk of adverse birth and childhood health outcomes. DNA methylation has been suggested as a potential underlying mechanism linking environmental exposures such as micronutrient status during pregnancy with offspring health. We performed a meta-analysis on the association of maternal early-pregnancy serum ferritin concentrations, as a marker of body iron stores, and cord blood DNA methylation. We included 1286 mother-newborn pairs from two population-based prospective cohorts. Serum ferritin concentrations were measured in early pregnancy. DNA methylation was measured with the Infinium HumanMethylation450 BeadChip (Illumina). We examined epigenome-wide associations of maternal early-pregnancy serum ferritin and cord blood DNA methylation using robust linear regression analyses, with adjustment for confounders and performed fixed-effects meta-analyses. We additionally examined whether associations of any CpGs identified in cord blood persisted in the peripheral blood of older children and explored associations with other markers of maternal iron status. We also examined whether similar findings were present in the association of cord blood serum ferritin concentrations with cord blood DNA methylation. RESULTS Maternal early-pregnancy serum ferritin concentrations were inversely associated with DNA methylation at two CpGs (cg02806645 and cg06322988) in PRR23A and one CpG (cg04468817) in PRSS22. Associations at two of these CpG sites persisted at each of the follow-up time points in childhood. Cord blood serum ferritin concentrations were not associated with cord blood DNA methylation levels at the three identified CpGs. CONCLUSION Maternal early-pregnancy serum ferritin concentrations were associated with lower cord blood DNA methylation levels at three CpGs and these associations partly persisted in older children. Further studies are needed to uncover the role of these CpGs in the underlying mechanisms of the associations of maternal iron status and offspring health outcomes.
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Affiliation(s)
- M J Taeubert
- The Generation R Study Group, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Pediatric Oncology, Hematology and Immunology, University Medical Center Heidelberg, Heidelberg, Germany
| | - P de Prado-Bert
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - M L Geurtsen
- The Generation R Study Group, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Pediatrics, Sophia's Children's Hospital, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - G Mancano
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Bristol Medical School Population Health Sciences, University of Bristol, Bristol, UK
| | - M J Vermeulen
- Department of Pediatrics, Sophia's Children's Hospital, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - I K M Reiss
- Department of Pediatrics, Sophia's Children's Hospital, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - D Caramaschi
- College of Life and Environmental Sciences, Psychology, University of Exeter, Exeter, UK
| | - J Sunyer
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - G C Sharp
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Bristol Medical School Population Health Sciences, University of Bristol, Bristol, UK
- School of Oral and Dental Sciences, University of Bristol, Bristol, UK
| | - J Julvez
- ISGlobal, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Institut d'Investigació Sanitària Pere Virgili, Hospital Universitari Sant Joan de Reus, Reus, Spain
| | - M U Muckenthaler
- Department of Pediatric Oncology, Hematology and Immunology, University Medical Center Heidelberg, Heidelberg, Germany
| | - J F Felix
- The Generation R Study Group, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.
- Department of Pediatrics, Sophia's Children's Hospital, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
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22
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Gupta C, Chandrashekar P, Jin T, He C, Khullar S, Chang Q, Wang D. Bringing machine learning to research on intellectual and developmental disabilities: taking inspiration from neurological diseases. J Neurodev Disord 2022; 14:28. [PMID: 35501679 PMCID: PMC9059371 DOI: 10.1186/s11689-022-09438-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 04/07/2022] [Indexed: 12/31/2022] Open
Abstract
Intellectual and Developmental Disabilities (IDDs), such as Down syndrome, Fragile X syndrome, Rett syndrome, and autism spectrum disorder, usually manifest at birth or early childhood. IDDs are characterized by significant impairment in intellectual and adaptive functioning, and both genetic and environmental factors underpin IDD biology. Molecular and genetic stratification of IDDs remain challenging mainly due to overlapping factors and comorbidity. Advances in high throughput sequencing, imaging, and tools to record behavioral data at scale have greatly enhanced our understanding of the molecular, cellular, structural, and environmental basis of some IDDs. Fueled by the "big data" revolution, artificial intelligence (AI) and machine learning (ML) technologies have brought a whole new paradigm shift in computational biology. Evidently, the ML-driven approach to clinical diagnoses has the potential to augment classical methods that use symptoms and external observations, hoping to push the personalized treatment plan forward. Therefore, integrative analyses and applications of ML technology have a direct bearing on discoveries in IDDs. The application of ML to IDDs can potentially improve screening and early diagnosis, advance our understanding of the complexity of comorbidity, and accelerate the identification of biomarkers for clinical research and drug development. For more than five decades, the IDDRC network has supported a nexus of investigators at centers across the USA, all striving to understand the interplay between various factors underlying IDDs. In this review, we introduced fast-increasing multi-modal data types, highlighted example studies that employed ML technologies to illuminate factors and biological mechanisms underlying IDDs, as well as recent advances in ML technologies and their applications to IDDs and other neurological diseases. We discussed various molecular, clinical, and environmental data collection modes, including genetic, imaging, phenotypical, and behavioral data types, along with multiple repositories that store and share such data. Furthermore, we outlined some fundamental concepts of machine learning algorithms and presented our opinion on specific gaps that will need to be filled to accomplish, for example, reliable implementation of ML-based diagnosis technology in IDD clinics. We anticipate that this review will guide researchers to formulate AI and ML-based approaches to investigate IDDs and related conditions.
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Affiliation(s)
- Chirag Gupta
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA.,Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Pramod Chandrashekar
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA.,Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ting Jin
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA.,Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Chenfeng He
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA.,Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Saniya Khullar
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA.,Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Qiang Chang
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA.,Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA.,Department of Neurology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Daifeng Wang
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA. .,Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA. .,Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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23
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An epigenetic association analysis of childhood trauma in psychosis reveals possible overlap with methylation changes associated with PTSD. Transl Psychiatry 2022; 12:177. [PMID: 35501310 PMCID: PMC9061740 DOI: 10.1038/s41398-022-01936-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 11/20/2022] Open
Abstract
Patients with a severe mental disorder report significantly higher levels of childhood trauma (CT) than healthy individuals. Studies have suggested that CT may affect brain plasticity through epigenetic mechanisms and contribute to developing various psychiatric disorders. We performed a blood-based epigenome-wide association study using the Childhood Trauma Questionnaire-short form in 602 patients with a current severe mental illness, investigating DNA methylation association separately for five trauma subtypes and the total trauma score. The median trauma score was set as the predefined cutoff for determining whether the trauma was present or not. Additionally, we compared our genome-wide results with methylation probes annotated to candidate genes previously associated with CT. Of the patients, 83.2% reported CT above the cutoff in one or more trauma subtypes, and emotional neglect was the trauma subtype most frequently reported. We identified one significant differently methylated position associated with the gene TANGO6 for physical neglect. Seventeen differentially methylated regions (DMRs) were associated with different trauma categories. Several of these DMRs were annotated to genes previously associated with neuropsychiatric disorders such as post-traumatic stress disorder and cognitive impairments. Our results support a biomolecular association between CT and severe mental disorders. Genes that were previously identified as differentially methylated in CT-exposed subjects with and without psychosis did not show methylation differences in our analysis. We discuss this inconsistency, the relevance of our findings, and the limitations of our study.
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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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25
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Okazaki S, Kimura R, Otsuka I, Funabiki Y, Murai T, Hishimoto A. Epigenetic clock analysis and increased plasminogen activator inhibitor-1 in high-functioning autism spectrum disorder. PLoS One 2022; 17:e0263478. [PMID: 35113965 PMCID: PMC8812940 DOI: 10.1371/journal.pone.0263478] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/19/2022] [Indexed: 12/23/2022] Open
Abstract
Background Autism spectrum disorder (ASD) is characterized by impaired social communication and behavioral problems. An increased risk of premature mortality has been observed in individuals with ASD. Therefore, we hypothesized that biological aging is accelerated in individuals with ASD. Recently, several studies have established genome-wide DNA methylation (DNAm) profiles as ‘epigenetic clocks’ that can estimate biological aging. In addition, ASD has been associated with differential DNAm patterns. Methods We used two independent datasets from blood samples consisting of adult patients with high-functioning ASD and controls: the 1st cohort (38 ASD cases and 31 controls) and the 2nd cohort (6 ASD cases and 10 controls). We explored well-studied epigenetic clocks such as HorvathAge, HannumAge, SkinBloodAge, PhenoAge, GrimAge, and DNAm-based telomere length (DNAmTL). In addition, we investigated seven DNAm-based age-related plasma proteins, including plasminogen activator inhibitor-1 (PAI-1), and smoking status, which are the components of GrimAge. Results Compared to controls, individuals with ASD in the 1st cohort, but not in the 2nd cohort, exhibited a trend for increased GrimAge acceleration and a significant increase of PAI-1 levels. A meta-analysis showed significantly increased PAI-1 levels in individuals with ASD compared to controls. Conclusion Our findings suggest there is no epigenetic age acceleration in the blood of individuals with ASD. However, this study provides novel evidence regarding increased plasma PAI-1 levels in individuals with high-functioning ASD. These findings suggest PAI-1 may be a biomarker for high-functioning ASD, however, larger studies based on epigenetic clocks and PAI-1 will be necessary to confirm these findings.
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Affiliation(s)
- Satoshi Okazaki
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Ryo Kimura
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ikuo Otsuka
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yasuko Funabiki
- Department of Cognitive and Behavioral Science, Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
- Department of Psychiatry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Toshiya Murai
- Department of Psychiatry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akitoyo Hishimoto
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
- Department of Psychiatry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- * E-mail:
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26
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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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27
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Bakulski KM, Dou JF, Feinberg JI, Aung MT, Ladd-Acosta C, Volk HE, Newschaffer CJ, Croen LA, Hertz-Picciotto I, Levy SE, Landa R, Feinberg AP, Fallin MD. Autism-Associated DNA Methylation at Birth From Multiple Tissues Is Enriched for Autism Genes in the Early Autism Risk Longitudinal Investigation. Front Mol Neurosci 2021; 14:775390. [PMID: 34899183 PMCID: PMC8655859 DOI: 10.3389/fnmol.2021.775390] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/28/2021] [Indexed: 12/30/2022] Open
Abstract
Background: Pregnancy measures of DNA methylation, an epigenetic mark, may be associated with autism spectrum disorder (ASD) development in children. Few ASD studies have considered prospective designs with DNA methylation measured in multiple tissues and tested overlap with ASD genetic risk loci. Objectives: To estimate associations between DNA methylation in maternal blood, cord blood, and placenta and later diagnosis of ASD, and to evaluate enrichment of ASD-associated DNA methylation for known ASD-associated genes. Methods: In the Early Autism Risk Longitudinal Investigation (EARLI), an ASD-enriched risk birth cohort, genome-scale maternal blood (early n = 140 and late n = 75 pregnancy), infant cord blood (n = 133), and placenta (maternal n = 106 and fetal n = 107 compartments) DNA methylation was assessed on the Illumina 450k HumanMethylation array and compared to ASD diagnosis at 36 months of age. Differences in site-specific and global methylation were tested with ASD, as well as enrichment of single site associations for ASD risk genes (n = 881) from the Simons Foundation Autism Research Initiative (SFARI) database. Results: No individual DNA methylation site was associated with ASD at genome-wide significance, however, individual DNA methylation sites nominally associated with ASD (P < 0.05) in each tissue were highly enriched for SFARI genes (cord blood P = 7.9 × 10-29, maternal blood early pregnancy P = 6.1 × 10-27, maternal blood late pregnancy P = 2.8 × 10-16, maternal placenta P = 5.6 × 10-15, fetal placenta P = 1.3 × 10-20). DNA methylation sites nominally associated with ASD across all five tissues overlapped at 144 (29.5%) SFARI genes. Conclusion: DNA methylation sites nominally associated with later ASD diagnosis in multiple tissues were enriched for ASD risk genes. Our multi-tissue study demonstrates the utility of examining DNA methylation prior to ASD diagnosis.
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Affiliation(s)
- Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - John F Dou
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Jason I Feinberg
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States.,Wendy Klag Center for Autism and Developmental Disabilities, Baltimore, MD, United States.,Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Max T Aung
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Christine Ladd-Acosta
- Wendy Klag Center for Autism and Developmental Disabilities, Baltimore, MD, United States.,Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Heather E Volk
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States.,Wendy Klag Center for Autism and Developmental Disabilities, Baltimore, MD, United States
| | - Craig J Newschaffer
- College of Health and Human Development, Penn State University, State College, PA, United States
| | - Lisa A Croen
- Kaiser Permanente Division of Research, Oakland, CA, United States
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences, School of Medicine, University of California, Davis, Davis, CA, United States.,MIND Institute, University of California, Davis, Davis, CA, United States
| | - Susan E Levy
- Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Rebecca Landa
- Kennedy Krieger Institute Center for Autism and Related Disorders, Baltimore, MD, United States
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD, United States.,Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, United States.,Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Margaret D Fallin
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States.,Wendy Klag Center for Autism and Developmental Disabilities, Baltimore, MD, United States.,Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD, United States
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28
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Dean DD, Agarwal S, Muthuswamy S, Asim A. Brain exosomes as minuscule information hub for Autism Spectrum Disorder. Expert Rev Mol Diagn 2021; 21:1323-1331. [PMID: 34720032 DOI: 10.1080/14737159.2021.2000395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Autism spectrum disorder (ASD) is a neurodevelopmental disorder initiating in the first three years of life. Early initiation of management therapies can significantly improve the health and quality of life of ASD subjects. Thus, indicating the need for suitable biomarkers for the early identification of ASD. Various biological domains were investigated in the quest for reliable biomarkers. However, most biomarkers are in the preliminary stage, and clinical validation is yet to be defined. Exosome based research gained momentum in various Central Nervous System disorders for biomarker identification. However, the utility and prospect of exosomes in ASD is still underexplored. AREAS COVERED In the present review, we summarized the biomarker discovery current status and the future of brain-specific exosomes in understanding pathophysiology and its potential as a biomarker. The studies reviewed herein were identified via systematic search (dated: June 2021) of PubMed using variations related to autism (ASD OR autism OR Autism spectrum disorder) AND exosomes AND/OR biomarkers. EXPERT OPINION As exosomess are highly relevant in brain disorders like ASD, direct access to brain tissue for molecular assessment is ethically impossible. Thus investigating the brain-derived exosomes would undoubtedly answer many unsolved aspects of the pathogenesis and provide reliable biomarkers.
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Affiliation(s)
- Deepika Delsa Dean
- Deptartment of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences (Sgpgims), Lucknow, India
| | - Sarita Agarwal
- Deptartment of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences (Sgpgims), Lucknow, India
| | | | - Ambreen Asim
- Deptartment of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences (Sgpgims), Lucknow, India
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29
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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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30
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Smyth LJ, Cruise SM, Tang J, Young I, McGuinness B, Kee F, McKnight AJ. An investigation into DNA methylation patterns associated with risk preference in older individuals. Epigenetics 2021; 17:1159-1172. [PMID: 34696705 PMCID: PMC9542846 DOI: 10.1080/15592294.2021.1992910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Risk preference is a complex trait governed by psycho-social, environmental and genetic determinants. We aimed to examine how an individual’s risk preference associates with their epigenetic profile. Risk preferences were ascertained by asking participants of the Northern Ireland COhort for the Longitudinal study of Ageing to make a series of choices between hypothetical income scenarios. From these, four risk preference categories were derived, ranging from risk-averse to risk-seeking. Illumina’s Infinium High-Density Methylation Assay was used to evaluate the status of 862,927 CpGs. Risk preference and DNA methylation data were obtained for 1,656 individuals. The distribution of single-site DNA methylation levels between risk-averse and risk-seeking individuals was assessed whilst adjusting for age, sex and peripheral white cell counts. In this discovery cohort, 55 CpGs were identified with significantly different levels of methylation (p≤x10−5) between risk-averse and risk-seeking individuals when adjusting for the maximum number of covariates. No CpGs were significantly differentially methylated in any of the risk preference groups at an epigenome-wide association level (p<9x10−8) following covariate adjustment. Protein-coding genes NWD1 and LRP1 were among the genes in which the top-ranked dmCpGs were located for all analyses conducted. Mutations in these genes have previously been linked to neurological conditions. Epigenetic modifications have not previously been linked to risk-aversion using a population cohort, but may represent important biomarkers of accumulated, complex determinants of this trait. Several striking results from this study support further analysis of DNA methylation as an important link between measurable biomarkers and health behaviours.
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Affiliation(s)
- Laura J Smyth
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University Belfast, Northern Ireland, UK
| | - Sharon M Cruise
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University Belfast, Northern Ireland, UK
| | - Jianjun Tang
- School of Agricultural Economics and Rural Development, Renmin University of China, Beijing, China
| | - Ian Young
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University Belfast, Northern Ireland, UK
| | - Bernadette McGuinness
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University Belfast, Northern Ireland, UK
| | - Frank Kee
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University Belfast, Northern Ireland, UK
| | - Amy Jayne McKnight
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University Belfast, Northern Ireland, UK
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31
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Coppedè F. The diagnostic potential of the epigenome in autism spectrum disorders. Epigenomics 2021; 13:1587-1590. [PMID: 34617447 DOI: 10.2217/epi-2021-0338] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Tweetable abstract The diagnostic application of genome-wide methylation signatures is increasing in various syndromic forms of autism, but further studies are warranted to clarify whether epigenetic biomarkers can be of diagnostic utility in idiopathic ASD.
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Affiliation(s)
- Fabio Coppedè
- Department of Translational Research & of New Surgical & Medical Technologies, University of Pisa, Via Roma 55, Pisa, 56126, Italy
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32
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Havdahl A, Niarchou M, Starnawska A, Uddin M, van der Merwe C, Warrier V. Genetic contributions to autism spectrum disorder. Psychol Med 2021; 51:2260-2273. [PMID: 33634770 PMCID: PMC8477228 DOI: 10.1017/s0033291721000192] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 01/14/2021] [Accepted: 01/18/2021] [Indexed: 12/12/2022]
Abstract
Autism spectrum disorder (autism) is a heterogeneous group of neurodevelopmental conditions characterized by early childhood-onset impairments in communication and social interaction alongside restricted and repetitive behaviors and interests. This review summarizes recent developments in human genetics research in autism, complemented by epigenetic and transcriptomic findings. The clinical heterogeneity of autism is mirrored by a complex genetic architecture involving several types of common and rare variants, ranging from point mutations to large copy number variants, and either inherited or spontaneous (de novo). More than 100 risk genes have been implicated by rare, often de novo, potentially damaging mutations in highly constrained genes. These account for substantial individual risk but a small proportion of the population risk. In contrast, most of the genetic risk is attributable to common inherited variants acting en masse, each individually with small effects. Studies have identified a handful of robustly associated common variants. Different risk genes converge on the same mechanisms, such as gene regulation and synaptic connectivity. These mechanisms are also implicated by genes that are epigenetically and transcriptionally dysregulated in autism. Major challenges to understanding the biological mechanisms include substantial phenotypic heterogeneity, large locus heterogeneity, variable penetrance, and widespread pleiotropy. Considerable increases in sample sizes are needed to better understand the hundreds or thousands of common and rare genetic variants involved. Future research should integrate common and rare variant research, multi-omics data including genomics, epigenomics, and transcriptomics, and refined phenotype assessment with multidimensional and longitudinal measures.
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Affiliation(s)
- A. Havdahl
- Nic Waals Institute, Lovisenberg Diaconal Hospital, Oslo, Norway
- Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway
- Department of Psychology, PROMENTA Research Center, University of Oslo, Oslo, Norway
| | - M. Niarchou
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, TN, USA
| | - A. Starnawska
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
- Department of Biomedicine, Aarhus University, Denmark
- Center for Genomics for Personalized Medicine, CGPM, and Center for Integrative Sequencing, iSEQ, Aarhus, Denmark
| | - M. Uddin
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - C. van der Merwe
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, MA, USA
| | - V. Warrier
- Department of Psychiatry, Autism Research Centre, University of Cambridge, UK
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Shirvani-Farsani Z, Maloum Z, Bagheri-Hosseinabadi Z, Vilor-Tejedor N, Sadeghi I. DNA methylation signature as a biomarker of major neuropsychiatric disorders. J Psychiatr Res 2021; 141:34-49. [PMID: 34171761 DOI: 10.1016/j.jpsychires.2021.06.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/27/2021] [Accepted: 06/09/2021] [Indexed: 02/07/2023]
Abstract
DNA methylation is a broadly-investigated epigenetic modification that has been considered as a heritable and reversible change. Previous findings have indicated that DNA methylation regulates gene expression in the central nervous system (CNS). Also, disturbance of DNA methylation patterns has been associated with destructive consequences that lead to human brain diseases such as neuropsychiatric disorders (NPDs). In this review, we comprehensively discuss the mechanism and function of DNA methylation and its most recent associations with the pathology of NPDs-including major depressive disorder (MDD), schizophrenia (SZ), autism spectrum disorder (ASD), bipolar disorder (BD), and attention/deficit hyperactivity disorder (ADHD). We also discuss how heterogeneous findings demand further investigations. Finally, based on the recent studies we conclude that DNA methylation status may have implications in clinical diagnostics and therapeutics as a potential epigenetic biomarker of NPDs.
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Affiliation(s)
- Zeinab Shirvani-Farsani
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University G.C., Tehran, IR, Iran.
| | - Zahra Maloum
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University G.C., Tehran, IR, Iran.
| | - Zahra Bagheri-Hosseinabadi
- Department of Clinical Biochemistry, School of Medicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran.
| | - Natalia Vilor-Tejedor
- BarcelonaBeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Carrer Wellington 30, 08005, Barcelona, Spain; Center for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain; Erasmus University Medical Center, Department of Clinical Genetics, Rotterdam, the Netherlands; Pompeu Fabra University, Barcelona, Spain.
| | - Iman Sadeghi
- BarcelonaBeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Carrer Wellington 30, 08005, Barcelona, Spain; Center for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.
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35
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Abdolmaleky HM, Zhou JR, Thiagalingam S. Cataloging recent advances in epigenetic alterations in major mental disorders and autism. Epigenomics 2021; 13:1231-1245. [PMID: 34318684 PMCID: PMC8738978 DOI: 10.2217/epi-2021-0074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/12/2021] [Indexed: 11/21/2022] Open
Abstract
During the last two decades, diverse epigenetic modifications including DNA methylation, histone modifications, RNA editing and miRNA dysregulation have been associated with psychiatric disorders. A few years ago, in a review we outlined the most common epigenetic alterations in major psychiatric disorders (e.g., aberrant DNA methylation of DTNBP1, HTR2A, RELN, MB-COMT and PPP3CC, and increased expression of miR-34a and miR-181b). Recent follow-up studies have uncovered other DNA methylation aberrations affecting several genes in mental disorders, in addition to dysregulation of many miRNAs. Here, we provide an update on new epigenetic findings and highlight potential origin of the diversity and inconsistencies, focusing on drug effects, tissue/cell specificity of epigenetic landscape and discuss shortcomings of the current diagnostic criteria in mental disorders.
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Affiliation(s)
- Hamid Mostafavi Abdolmaleky
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, 02118 MA, USA
- Department of Surgery, Nutrition/Metabolism Laboratory, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, 02215 MA, USA
| | - Jin-Rong Zhou
- Department of Surgery, Nutrition/Metabolism Laboratory, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, 02215 MA, USA
| | - Sam Thiagalingam
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, 02118 MA, USA
- Genetics & Genomics Graduate Program, Boston University School of Medicine, Boston, 02118 MA, USA
- Department of Pathology & Laboratory Medicine, Boston University School of Medicine, Boston, 02218 MA, USA
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36
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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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Stanton JE, Malijauskaite S, McGourty K, Grabrucker AM. The Metallome as a Link Between the "Omes" in Autism Spectrum Disorders. Front Mol Neurosci 2021; 14:695873. [PMID: 34290588 PMCID: PMC8289253 DOI: 10.3389/fnmol.2021.695873] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 06/14/2021] [Indexed: 12/26/2022] Open
Abstract
Metal dyshomeostasis plays a significant role in various neurological diseases such as Alzheimer's disease, Parkinson's disease, Autism Spectrum Disorders (ASD), and many more. Like studies investigating the proteome, transcriptome, epigenome, microbiome, etc., for years, metallomics studies have focused on data from their domain, i.e., trace metal composition, only. Still, few have considered the links between other "omes," which may together result in an individual's specific pathologies. In particular, ASD have been reported to have multitudes of possible causal effects. Metallomics data focusing on metal deficiencies and dyshomeostasis can be linked to functions of metalloenzymes, metal transporters, and transcription factors, thus affecting the proteome and transcriptome. Furthermore, recent studies in ASD have emphasized the gut-brain axis, with alterations in the microbiome being linked to changes in the metabolome and inflammatory processes. However, the microbiome and other "omes" are heavily influenced by the metallome. Thus, here, we will summarize the known implications of a changed metallome for other "omes" in the body in the context of "omics" studies in ASD. We will highlight possible connections and propose a model that may explain the so far independently reported pathologies in ASD.
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Affiliation(s)
- Janelle E Stanton
- Department of Biological Sciences, University of Limerick, Limerick, Ireland.,Bernal Institute, University of Limerick, Limerick, Ireland
| | - Sigita Malijauskaite
- Bernal Institute, University of Limerick, Limerick, Ireland.,Department of Chemical Sciences, University of Limerick, Limerick, Ireland
| | - Kieran McGourty
- Bernal Institute, University of Limerick, Limerick, Ireland.,Department of Chemical Sciences, University of Limerick, Limerick, Ireland.,Health Research Institute, University of Limerick, Limerick, Ireland
| | - Andreas M Grabrucker
- Department of Biological Sciences, University of Limerick, Limerick, Ireland.,Bernal Institute, University of Limerick, Limerick, Ireland.,Health Research Institute, University of Limerick, Limerick, Ireland
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38
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Novel treatments for autism spectrum disorder based on genomics and systems biology. Pharmacol Ther 2021; 230:107939. [PMID: 34174273 DOI: 10.1016/j.pharmthera.2021.107939] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 06/03/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a highly heterogeneous neurodevelopmental disorder with a complex underlying genetic architecture. There are currently no known pharmacologic treatments for the core ASD symptoms of social deficits and restricted/ repetitive behavior. However, there are dozens of clinical trials currently underway that are testing the impact of novel and existing agents on core and associated symptoms in ASD. METHODS We present a narrative synthesis of the historical and contemporary challenges to drug discovery in ASD. We then provide an overview of novel treatments currently under investigation from a genomics and systems biology perspective. RESULTS Data driven network and cluster analyses suggest alterations in transcriptional regulation, chromatin remodelling, synaptic transmission, neuropeptide signalling, and/or immunological mechanisms may contribute to or underlie the development of ASD. Agents and upcoming trials targeting each of the above listed systems are reviewed. CONCLUSION Identifying effective pharmacologic treatments for the core and associated symptom domains in ASD will require further collaboration and innovation in the areas of outcome measurement, biomarker research, and genomics, as well as systematic efforts to identify and treat subgroups of individuals with ASD who may be differentially responsive to specific treatments.
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39
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Jangjoo M, Goodman SJ, Choufani S, Trost B, Scherer SW, Kelley E, Ayub M, Nicolson R, Georgiades S, Crosbie J, Schachar R, Anagnostou E, Grunebaum E, Weksberg R. An Epigenetically Distinct Subset of Children With Autism Spectrum Disorder Resulting From Differences in Blood Cell Composition. Front Neurol 2021; 12:612817. [PMID: 33935932 PMCID: PMC8085304 DOI: 10.3389/fneur.2021.612817] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/15/2021] [Indexed: 12/23/2022] Open
Abstract
Background: Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder that often involves impaired cognition, communication difficulties and restrictive, repetitive behaviors. ASD is extremely heterogeneous both clinically and etiologically, which represents one of the greatest challenges in studying the molecular underpinnings of ASD. While hundreds of ASD-associated genes have been identified that confer varying degrees of risk, no single gene variant accounts for >1% of ASD cases. Notably, a large number of ASD-risk genes function as epigenetic regulators, indicating potential epigenetic dysregulation in ASD. As such, we compared genome-wide DNA methylation (DNAm) in the blood of children with ASD (n = 265) to samples from age- and sex-matched, neurotypical controls (n = 122) using the Illumina Infinium HumanMethylation450 arrays. Results: While DNAm patterns did not distinctly separate ASD cases from controls, our analysis identified an epigenetically unique subset of ASD cases (n = 32); these individuals exhibited significant differential methylation from both controls than the remaining ASD cases. The CpG sites at which this subset was differentially methylated mapped to known ASD risk genes that encode proteins of the nervous and immune systems. Moreover, the observed DNAm differences were attributable to altered blood cell composition, i.e., lower granulocyte proportion and granulocyte-to-lymphocyte ratio in the ASD subset, as compared to the remaining ASD cases and controls. This ASD subset did not differ from the rest of the ASD cases in the frequency or type of high-risk genomic variants. Conclusion: Within our ASD cohort, we identified a subset of individuals that exhibit differential methylation from both controls and the remaining ASD group tightly associated with shifts in immune cell type proportions. This is an important feature that should be assessed in all epigenetic studies of blood cells in ASD. This finding also builds on past reports of changes in the immune systems of children with ASD, supporting the potential role of altered immunological mechanisms in the complex pathophysiology of ASD. The discovery of significant molecular and immunological features in subgroups of individuals with ASD may allow clinicians to better stratify patients, facilitating personalized interventions and improved outcomes.
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Affiliation(s)
- Maryam Jangjoo
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Sarah J Goodman
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Sanaa Choufani
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Brett Trost
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Stephen W Scherer
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,McLaughlin Centre, University of Toronto, Toronto, ON, Canada
| | - Elizabeth Kelley
- Department of Psychiatry, Queen's University, Kingston, ON, Canada
| | - Muhammad Ayub
- Department of Psychiatry, Queen's University, Kingston, ON, Canada
| | - Rob Nicolson
- Department of Psychiatry, University of Western Ontario, London, ON, Canada
| | - Stelios Georgiades
- Department of Psychiatry and Behavioural Neurosciences, Offord Centre for Child Studies, McMaster University, Hamilton, ON, Canada
| | - Jennifer Crosbie
- Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Russell Schachar
- Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Psychiatry, University of Toronto, Toronto, ON, Canada.,Institute of Medical Science, School of Graduate Studies, University of Toronto, Toronto, ON, Canada
| | - Evdokia Anagnostou
- Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON, Canada.,Department of Pediatrics, University of Toronto, Toronto, ON, Canada
| | - Eyal Grunebaum
- Institute of Medical Science, School of Graduate Studies, University of Toronto, Toronto, ON, Canada.,Division of Immunology and Allergy, The Hospital for Sick Children, Toronto, ON, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rosanna Weksberg
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Institute of Medical Science, School of Graduate Studies, University of Toronto, Toronto, ON, Canada.,Department of Pediatrics, University of Toronto, Toronto, ON, Canada.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
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40
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Sabit H, Tombuloglu H, Rehman S, Almandil NB, Cevik E, Abdel-Ghany S, Rashwan S, Abasiyanik MF, Yee Waye MM. Gut microbiota metabolites in autistic children: An epigenetic perspective. Heliyon 2021; 7:e06105. [PMID: 33553761 PMCID: PMC7848646 DOI: 10.1016/j.heliyon.2021.e06105] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/18/2021] [Accepted: 01/22/2021] [Indexed: 12/18/2022] Open
Abstract
Gut microbiota has become an issue of great importance recently due to its major role in autism spectrum disorder (ASD). Over the past three decades, there has been a sustained research activity focused to explain the actual mechanism by which gut microbiota triggers/develops autism. Several genetic and epigenetic factors are involved in this disorder, with epigenetics being the most active area of research. Although the constant investigation and advancements, epigenetic implications in ASD still need a deeper functional/causal analysis. In this review, we describe the major gut microbiota metabolites and how they induce epigenetic changes in ASD along with interactions through the gut-brain axis.
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Affiliation(s)
- Hussein Sabit
- Department of Genetics, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P. O. Box 1982, Dammam, 31441 Saudi Arabia
| | - Huseyin Tombuloglu
- Department of Genetics, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P. O. Box 1982, Dammam, 31441 Saudi Arabia
| | - Suriya Rehman
- Department of Epidemic Diseases, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P. O. Box 1982, Dammam, 31441 Saudi Arabia
| | - Noor B Almandil
- Department of Clinical Pharmacy Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, P. O. Box 1982, Dammam, 31441 Saudi Arabia
| | - Emre Cevik
- Department of Genetics, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P. O. Box 1982, Dammam, 31441 Saudi Arabia
| | - Shaimaa Abdel-Ghany
- Department of Environmental Biotechnology, College of Biotechnology, Misr University for Science and Technology, P. O. Box 77, Giza, Egypt
| | - Sanaa Rashwan
- Pediatrics Department, Madinat Zayed Hospital, SEHA, Abu Dhabi, United Arab Emirates
| | - Mustafa Fatih Abasiyanik
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA.,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Mary Miu Yee Waye
- The Nethersole School of Nursing, The Croucher Laboratory for Human Genomics, The Chinese University of Hong Kong, Shatin, N.T. Hong Kong
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41
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Mesleh AG, Abdulla SA, El-Agnaf O. Paving the Way toward Personalized Medicine: Current Advances and Challenges in Multi-OMICS Approach in Autism Spectrum Disorder for Biomarkers Discovery and Patient Stratification. J Pers Med 2021; 11:jpm11010041. [PMID: 33450950 PMCID: PMC7828397 DOI: 10.3390/jpm11010041] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 02/06/2023] Open
Abstract
Autism spectrum disorder (ASD) is a multifactorial neurodevelopmental disorder characterized by impairments in two main areas: social/communication skills and repetitive behavioral patterns. The prevalence of ASD has increased in the past two decades, however, it is not known whether the evident rise in ASD prevalence is due to changes in diagnostic criteria or an actual increase in ASD cases. Due to the complexity and heterogeneity of ASD, symptoms vary in severity and may be accompanied by comorbidities such as epilepsy, attention deficit hyperactivity disorder (ADHD), and gastrointestinal (GI) disorders. Identifying biomarkers of ASD is not only crucial to understanding the biological characteristics of the disorder, but also as a detection tool for its early screening. Hence, this review gives an insight into the main areas of ASD biomarker research that show promising findings. Finally, it covers success stories that highlight the importance of precision medicine and the current challenges in ASD biomarker discovery studies.
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Affiliation(s)
- Areej G. Mesleh
- Division of Genomics and Precision Medicine (GPM), College of Health & Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Doha 34110, Qatar;
| | - Sara A. Abdulla
- Neurological Disorder Center, Qatar Biomedical Research Institute (QBRI), HBKU, Doha 34110, Qatar
- Correspondence: (S.A.A.); (O.E.-A.)
| | - Omar El-Agnaf
- Division of Genomics and Precision Medicine (GPM), College of Health & Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Doha 34110, Qatar;
- Neurological Disorder Center, Qatar Biomedical Research Institute (QBRI), HBKU, Doha 34110, Qatar
- Correspondence: (S.A.A.); (O.E.-A.)
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42
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Starnawska A, Demontis D. Role of DNA Methylation in Mediating Genetic Risk of Psychiatric Disorders. Front Psychiatry 2021; 12:596821. [PMID: 33868039 PMCID: PMC8049112 DOI: 10.3389/fpsyt.2021.596821] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 02/16/2021] [Indexed: 12/28/2022] Open
Abstract
Psychiatric disorders are common, complex, and heritable conditions estimated to be the leading cause of disability worldwide. The last decade of research in genomics of psychiatry, performed by multinational, and multicenter collaborative efforts on hundreds of thousands of mental disorder cases and controls, provided invaluable insight into the genetic risk variants of these conditions. With increasing cohort sizes, more risk variants are predicted to be identified in the near future, but there appears to be a knowledge gap in understanding how these variants contribute to the pathophysiology of psychiatric disorders. Majority of the identified common risk single-nucleotide polymorphisms (SNPs) are non-coding but are enriched in regulatory regions of the genome. It is therefore of great interest to study the impact of identified psychiatric disorders' risk SNPs on DNA methylation, the best studied epigenetic modification, playing a pivotal role in the regulation of transcriptomic processes, brain development, and functioning. This work outlines the mechanisms through which risk SNPs can impact DNA methylation levels and provides a summary of current evidence on the role of DNA methylation in mediating the genetic risk of psychiatric disorders.
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Affiliation(s)
- Anna Starnawska
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Center for Genomics and Personalized Medicine (CGPM), Center for Integrative Sequencing, iSEQ, Aarhus, Denmark
| | - Ditte Demontis
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Center for Genomics and Personalized Medicine (CGPM), Center for Integrative Sequencing, iSEQ, Aarhus, Denmark
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43
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García-Ortiz MV, de la Torre-Aguilar MJ, Morales-Ruiz T, Gómez-Fernández A, Flores-Rojas K, Gil-Campos M, Martin-Borreguero P, Ariza RR, Roldán-Arjona T, Perez-Navero JL. Analysis of Global and Local DNA Methylation Patterns in Blood Samples of Patients With Autism Spectrum Disorder. Front Pediatr 2021; 9:685310. [PMID: 34676183 PMCID: PMC8524094 DOI: 10.3389/fped.2021.685310] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 09/06/2021] [Indexed: 01/04/2023] Open
Abstract
The goal of this investigation was to determine whether there are alterations in DNA methylation patterns in children with autism spectrum disorder (ASD). Material and Methods: Controlled prospective observational case-control study. Within the ASD group, children were sub-classified based on the presence (AMR subgroup) or absence (ANMR subgroup) of neurodevelopmental regression during the first 2 years of life. We analyzed the global levels of DNA methylation, reflected in LINE-1, and the local DNA methylation pattern in two candidate genes, Neural Cell Adhesion Molecule (NCAM1) and Nerve Growth Factor (NGF) that, according to our previous studies, might be associated to an increased risk for ASD. For this purpose, we utilized blood samples from pediatric patients with ASD (n = 53) and their corresponding controls (n = 45). Results: We observed a slight decrease in methylation levels of LINE-1 in the ASD group, compared to the control group. One of the CpG in LINE-1 (GenBank accession no.X58075, nucleotide position 329) was the main responsible for such reduction, highly significant in the ASD subgroup of children with AMR (p < 0.05). Furthermore, we detected higher NCAM1 methylation levels in ASD children, compared to healthy children (p < 0.001). The data, moreover, showed higher NGF methylation levels in the AMR subgroup, compared to the control group and the ANMR subgroup. These results are consistent with our prior study, in which lower plasma levels of NCAM1 and higher levels of NGF were found in the ANMR subgroup, compared to the subgroup that comprised neurotypically developing children. Conclusions: We have provided new clues about the epigenetic changes that occur in ASD, and suggest two potential epigenetic biomarkers that would facilitate the diagnosis of the disorder. We similarly present with evidence of a clear differentiation in DNA methylation between the ASD subgroups, with or without mental regression.
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Affiliation(s)
- María Victoria García-Ortiz
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain.,Department of Genetics, University of Córdoba, Córdoba, Spain.,Reina Sofía University Hospital, Córdoba, Spain
| | - María José de la Torre-Aguilar
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain.,Department of Pediatrics, Reina Sofia University Hospital, University of Córdoba, Córdoba, Spain
| | - Teresa Morales-Ruiz
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain.,Department of Genetics, University of Córdoba, Córdoba, Spain.,Reina Sofía University Hospital, Córdoba, Spain
| | - Antonio Gómez-Fernández
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain.,Department of Pediatrics, Reina Sofia University Hospital, University of Córdoba, Córdoba, Spain
| | - Katherine Flores-Rojas
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain.,Pediatric Metabolism Unit, Reina Sofia University Hospital, University of Córdoba, Córdoba, Spain.,Physiopathology of Obesity and Nutrition Networking Biomedical Research Center (CIBEROBN), Córdoba, Spain
| | - Mercedes Gil-Campos
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain.,Pediatric Metabolism Unit, Reina Sofia University Hospital, University of Córdoba, Córdoba, Spain.,Physiopathology of Obesity and Nutrition Networking Biomedical Research Center (CIBEROBN), Córdoba, Spain
| | - Pilar Martin-Borreguero
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain.,Department of Child and Adolescent Clinical Psychiatry and Psychology, Reina Sofia University Hospital, Córdoba, Spain
| | - Rafael R Ariza
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain.,Department of Genetics, University of Córdoba, Córdoba, Spain.,Reina Sofía University Hospital, Córdoba, Spain
| | - Teresa Roldán-Arjona
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain.,Department of Genetics, University of Córdoba, Córdoba, Spain.,Reina Sofía University Hospital, Córdoba, Spain
| | - Juan Luis Perez-Navero
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain.,Department of Pediatrics, Reina Sofia University Hospital, University of Córdoba, Córdoba, Spain.,Biomedical Research Center-Rare Diseases (CIBERER), Carlos III Health Institute, Madrid, Spain
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44
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Pauly R, Ziats CA, Abenavoli L, Schwartz CE, Boccuto L. New Strategies for Clinical Trials in Autism Spectrum Disorder. Rev Recent Clin Trials 2020; 16:131-137. [PMID: 33222679 DOI: 10.2174/1574887115666201120093634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/10/2020] [Accepted: 10/22/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a complex neurodevelopmental condition that poses several challenges in terms of clinical diagnosis and investigation of molecular etiology. The lack of knowledge on the pathogenic mechanisms underlying ASD has hampered the clinical trials that so far have tried to target ASD behavioral symptoms. In order to improve our understanding of the molecular abnormalities associated with ASD, a deeper and more extensive genetic profiling of targeted individuals with ASD was needed. METHODS The recent availability of new and more powerful sequencing technologies (third-generation sequencing) has allowed to develop novel strategies for the characterization of comprehensive genetic profiles of individuals with ASD. In particular, this review will describe integrated approaches based on the combination of various omics technologies that will lead to a better stratification of targeted cohorts for the design of clinical trials in ASD. RESULTS In order to analyze the big data collected by assays such as the whole genome, epigenome, transcriptome, and proteome, it is critical to develop an efficient computational infrastructure. Machine learning models are instrumental to identify non-linear relationships between the omics technologies and, therefore, establish a functional informative network among the different data sources. CONCLUSION The potential advantage provided by these new integrated omics-based strategies is better characterization of the genetic background of ASD cohorts, to identify novel molecular targets for drug development, and ultimately offer a more personalized approach in the design of clinical trials for ASD.
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Affiliation(s)
- Rini Pauly
- Greenwood Genetic Center, Greenwood, SC, United States
| | | | - Ludovico Abenavoli
- Department of Health Sciences, University "Magna Graecia", Catanzaro, Italy
| | | | - Luigi Boccuto
- Greenwood Genetic Center, Greenwood, SC, United States
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Masini E, Loi E, Vega-Benedetti AF, Carta M, Doneddu G, Fadda R, Zavattari P. An Overview of the Main Genetic, Epigenetic and Environmental Factors Involved in Autism Spectrum Disorder Focusing on Synaptic Activity. Int J Mol Sci 2020; 21:ijms21218290. [PMID: 33167418 PMCID: PMC7663950 DOI: 10.3390/ijms21218290] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/28/2020] [Accepted: 10/30/2020] [Indexed: 12/11/2022] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder that affects social interaction and communication, with restricted interests, activity and behaviors. ASD is highly familial, indicating that genetic background strongly contributes to the development of this condition. However, only a fraction of the total number of genes thought to be associated with the condition have been discovered. Moreover, other factors may play an important role in ASD onset. In fact, it has been shown that parental conditions and in utero and perinatal factors may contribute to ASD etiology. More recently, epigenetic changes, including DNA methylation and micro RNA alterations, have been associated with ASD and proposed as potential biomarkers. This review aims to provide a summary of the literature regarding ASD candidate genes, mainly focusing on synapse formation and functionality and relevant epigenetic and environmental aspects acting in concert to determine ASD onset.
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Affiliation(s)
- Elena Masini
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, 09042 Cagliari, Italy; (E.M.); (E.L.); (A.F.V.-B.)
| | - Eleonora Loi
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, 09042 Cagliari, Italy; (E.M.); (E.L.); (A.F.V.-B.)
| | - Ana Florencia Vega-Benedetti
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, 09042 Cagliari, Italy; (E.M.); (E.L.); (A.F.V.-B.)
| | - Marinella Carta
- Center for Pervasive Developmental Disorders, Azienda Ospedaliera Brotzu, 09121 Cagliari, Italy;
| | - Giuseppe Doneddu
- Centro per l’Autismo e Disturbi correlati (CADc), Nuovo Centro Fisioterapico Sardo, 09131 Cagliari, Italy;
| | - Roberta Fadda
- Department of Pedagogy, Psychology, Philosophy, University of Cagliari, 09123 Cagliari, Italy;
| | - Patrizia Zavattari
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, 09042 Cagliari, Italy; (E.M.); (E.L.); (A.F.V.-B.)
- Correspondence:
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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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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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48
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Yuan R, Chen S, Wang Y. Computational Prediction of Drug Responses in Cancer Cell Lines From Cancer Omics and Detection of Drug Effectiveness Related Methylation Sites. Front Genet 2020; 11:917. [PMID: 32849855 PMCID: PMC7426400 DOI: 10.3389/fgene.2020.00917] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 07/23/2020] [Indexed: 12/13/2022] Open
Abstract
Accurately predicting the response of a cancer patient to a therapeutic agent remains an important challenge in precision medicine. With the rise of data science, researchers have applied computational models to study the drug inhibition effects on cancers based on cancer genomics and transcriptomics. Moreover, a common epigenetic modification, DNA methylation, has been related to the occurrence and development of cancer, as well as drug effectiveness. Therefore, it is helpful for improvement of drug response prediction through exploring the relationship between DNA methylation and drug effectiveness. Here, we proposed a computational model to predict drug responses in cancers through integration of cancer genomics, transcriptomics, epigenomics, and compound chemical properties. Meanwhile, we applied a regularized regression model (Least Absolute Shrinkage and Selection Operator, lasso) to detect the methylation sites that were closely related to drug effectiveness. The prediction models were trained on a well-known pharmacogenomics data resource, Genomics of Drug Sensitivity in Cancer (GDSC). The cross-validation indicates that the performance of the prediction model using DNA methylation is comparable to that of using other cancer omics, including oncogene mutation and gene expression data. It indicates the important role of DNA methylation in prediction of drug responses. Encyclopedia of DNA Elements (ENCODE) and Transcriptional Regulatory Relationships Unraveled by Sentence-based Text mining (TRRUST2) database analyses suggest that the methylation sites associated with drug effectiveness are mainly located in the transcription factor (TF) binding region. Therefore, we hypothesized that the sensitivity of cancer cells to drugs could be regulated by changing the methylation modification of TF binding region. In conclusion, we confirmed the important role of DNA methylation in prediction of drug responses, and provided some methylation sites that closely related to the drug effectiveness, which may be a great regulatory target for improvement of drug treatment effects on cancer patients.
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Affiliation(s)
- Rui Yuan
- Key Laboratory of Plateau Biological Adaptation and Evolution, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shilong Chen
- Key Laboratory of Plateau Biological Adaptation and Evolution, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
| | - Yongcui Wang
- Key Laboratory of Plateau Biological Adaptation and Evolution, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
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49
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Gui A, Jones EJH, Wong CCY, Meaburn E, Xia B, Pasco G, Lloyd-Fox S, Charman T, Bolton P, Johnson MH. Leveraging epigenetics to examine differences in developmental trajectories of social attention: A proof-of-principle study of DNA methylation in infants with older siblings with autism. Infant Behav Dev 2020; 60:101409. [PMID: 32623100 DOI: 10.1016/j.infbeh.2019.101409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 12/15/2022]
Abstract
Preliminary evidence suggests that changes in DNA methylation, a widely studied epigenetic mechanism, contribute to the etiology of Autism Spectrum Disorder (ASD). However, data is primarily derived from post-mortem brain samples or peripheral tissue from adults. Deep-phenotyped longitudinal infant cohorts are essential to understand how epigenetic modifications relate to early developmental trajectories and emergence of ASD symptoms. We present a proof-of-principle study designed to evaluate the potential of prospective epigenetic studies of infant siblings of children with ASD. Illumina genome-wide 450 K DNA methylation data from buccal swabs was generated for 63 male infants at multiple time-points from 8 months to 2 years of age (total N = 107 samples). 11 of those infants received a diagnosis of ASD at 3 years. We conducted a series of analyses to characterize DNA methylation signatures associated with categorical outcome and neurocognitive measures from parent-report questionnaire, eye-tracking and electro-encephalography. Effects observed across the entire genome (epigenome-wide association analyses) suggest that collecting DNA methylation samples within infant-sibling designs allows for the detection of meaningful signals with smaller sample sizes than previously estimated. Mapping networks of co-methylated probes associated with neural correlates of social attention implicated enrichment of pathways involved in brain development. Longitudinal modelling found covariation between phenotypic traits and DNA methylation levels in the proximity of genes previously associated with cognitive development, although larger samples and more complete datasets are needed to obtain generalizable results. In conclusion, assessment of DNA methylation profiles at multiple time-points in infant-sibling designs is a promising avenue to comprehend developmental origins and mechanisms of ASD.
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Affiliation(s)
- Anna Gui
- Department of Psychological Sciences, Birkbeck College, University of London, UK.
| | - Emily J H Jones
- Department of Psychological Sciences, Birkbeck College, University of London, UK
| | - Chloe C Y Wong
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, UK
| | - Emma Meaburn
- Department of Psychological Sciences, Birkbeck College, University of London, UK
| | - Baocong Xia
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, UK
| | - Greg Pasco
- Department of Psychology, Institute of Psychiatry, Psychology & Neuroscience, King's College London, UK
| | | | - Tony Charman
- Department of Psychology, Institute of Psychiatry, Psychology & Neuroscience, King's College London, UK
| | - Patrick Bolton
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, UK
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50
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Vasu MM, Sumitha PS, Rahna P, Thanseem I, Anitha A. microRNAs in Autism Spectrum Disorders. Curr Pharm Des 2020; 25:4368-4378. [PMID: 31692427 DOI: 10.2174/1381612825666191105120901] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 10/31/2019] [Indexed: 01/10/2023]
Abstract
BACKGROUND Efforts to unravel the extensive impact of the non-coding elements of the human genome on cell homeostasis and pathological processes have gained momentum over the last couple of decades. miRNAs refer to short, often 18-25 nucleotides long, non-coding RNA molecules which can regulate gene expression. Each miRNA can regulate several mRNAs. METHODS This article reviews the literature on the roles of miRNAs in autism. RESULTS Considering the fact that ~ 1% of the human DNA encodes different families of miRNAs, their overall impact as critical regulators of gene expression in the mammalian brain should be immense. Though the autism spectrum disorders (ASDs) are predominantly genetic in nature and several candidate genes are already identified, the highly heterogeneous and multifactorial nature of the disorder makes it difficult to identify common genetic risk factors. Several studies have suggested that the environmental factors may interact with the genetic factors to increase the risk. miRNAs could possibly be one of those factors which explain this link between genetics and the environment. CONCLUSION In the present review, we have summarized our current knowledge on miRNAs and their complex roles in ASD, and also on their therapeutic applications.
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Affiliation(s)
- Mahesh Mundalil Vasu
- Department of Neurogenetics, Institute for Communicative and Cognitive Neurosciences (ICCONS), Kavalappara, Shoranur, Palakkad - 679 523, Kerala, India
| | - Puthiripadath S Sumitha
- Department of Neurogenetics, Institute for Communicative and Cognitive Neurosciences (ICCONS), Kavalappara, Shoranur, Palakkad - 679 523, Kerala, India
| | - Parakkal Rahna
- Department of Neurogenetics, Institute for Communicative and Cognitive Neurosciences (ICCONS), Kavalappara, Shoranur, Palakkad - 679 523, Kerala, India
| | - Ismail Thanseem
- Department of Neurogenetics, Institute for Communicative and Cognitive Neurosciences (ICCONS), Kavalappara, Shoranur, Palakkad - 679 523, Kerala, India
| | - Ayyappan Anitha
- Department of Neurogenetics, Institute for Communicative and Cognitive Neurosciences (ICCONS), Kavalappara, Shoranur, Palakkad - 679 523, Kerala, India
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