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Al-Sarraj Y, Taha RZ, Al-Dous E, Ahram D, Abbasi S, Abuazab E, Shaath H, Habbab W, Errafii K, Bejaoui Y, AlMotawa M, Khattab N, Aqel YA, Shalaby KE, Al-Ansari A, Kambouris M, Abouzohri A, Ghazal I, Tolfat M, Alshaban F, El-Shanti H, Albagha OME. The genetic landscape of autism spectrum disorder in the Middle Eastern population. Front Genet 2024; 15:1363849. [PMID: 38572415 PMCID: PMC10987745 DOI: 10.3389/fgene.2024.1363849] [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: 12/31/2023] [Accepted: 03/04/2024] [Indexed: 04/05/2024] Open
Abstract
Introduction: Autism spectrum disorder (ASD) is characterized by aberrations in social interaction and communication associated with repetitive behaviors and interests, with strong clinical heterogeneity. Genetic factors play an important role in ASD, but about 75% of ASD cases have an undetermined genetic risk. Methods: We extensively investigated an ASD cohort made of 102 families from the Middle Eastern population of Qatar. First, we investigated the copy number variations (CNV) contribution using genome-wide SNP arrays. Next, we employed Next Generation Sequencing (NGS) to identify de novo or inherited variants contributing to the ASD etiology and its associated comorbid conditions in families with complete trios (affected child and the parents). Results: Our analysis revealed 16 CNV regions located in genomic regions implicated in ASD. The analysis of the 88 ASD cases identified 41 genes in 39 ASD subjects with de novo (n = 24) or inherited variants (n = 22). We identified three novel de novo variants in new candidate genes for ASD (DTX4, ARMC6, and B3GNT3). Also, we have identified 15 de novo variants in genes that were previously implicated in ASD or related neurodevelopmental disorders (PHF21A, WASF1, TCF20, DEAF1, MED13, CREBBP, KDM6B, SMURF1, ADNP, CACNA1G, MYT1L, KIF13B, GRIA2, CHM, and KCNK9). Additionally, we defined eight novel recessive variants (RYR2, DNAH3, TSPYL2, UPF3B KDM5C, LYST, and WNK3), four of which were X-linked. Conclusion: Despite the ASD multifactorial etiology that hinders ASD genetic risk discovery, the number of identified novel or known putative ASD genetic variants was appreciable. Nevertheless, this study represents the first comprehensive characterization of ASD genetic risk in Qatar's Middle Eastern population.
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Affiliation(s)
- Yasser Al-Sarraj
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Rowaida Z. Taha
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Eman Al-Dous
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Dina Ahram
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
- Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, United States
| | - Somayyeh Abbasi
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Eman Abuazab
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Hibah Shaath
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Wesal Habbab
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Khaoula Errafii
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Yosra Bejaoui
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Maryam AlMotawa
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Namat Khattab
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Yasmin Abu Aqel
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Karim E. Shalaby
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Amina Al-Ansari
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Marios Kambouris
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
- Pathology & Laboratory Medicine Department, Genetics Division, Sidra Medicine, Doha, Qatar
| | - Adel Abouzohri
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Iman Ghazal
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Mohammed Tolfat
- The Shafallah Center for Children with Special Needs, Doha, Qatar
| | - Fouad Alshaban
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Hatem El-Shanti
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Omar M. E. Albagha
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
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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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3
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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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4
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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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5
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Nishizaki SS, Boyle AP. SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions. BMC Bioinformatics 2022; 23:317. [PMID: 35927613 PMCID: PMC9351228 DOI: 10.1186/s12859-022-04865-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 07/28/2022] [Indexed: 12/02/2022] Open
Abstract
MOTIVATION Aberrant DNA methylation in transcription factor binding sites has been shown to lead to anomalous gene regulation that is strongly associated with human disease. However, the majority of methylation-sensitive positions within transcription factor binding sites remain unknown. Here we introduce SEMplMe, a computational tool to generate predictions of the effect of methylation on transcription factor binding strength in every position within a transcription factor's motif. RESULTS SEMplMe uses ChIP-seq and whole genome bisulfite sequencing to predict effects of methylation within binding sites. SEMplMe validates known methylation sensitive and insensitive positions within a binding motif, identifies cell type specific transcription factor binding driven by methylation, and outperforms SELEX-based predictions for CTCF. These predictions can be used to identify aberrant sites of DNA methylation contributing to human disease. AVAILABILITY AND IMPLEMENTATION SEMplMe is available from https://github.com/Boyle-Lab/SEMplMe .
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Affiliation(s)
- Sierra S Nishizaki
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Alan P Boyle
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA.
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6
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Pourtavakoli A, Ghafouri-Fard S. Calcium signaling in neurodevelopment and pathophysiology of autism spectrum disorders. Mol Biol Rep 2022; 49:10811-10823. [PMID: 35857176 DOI: 10.1007/s11033-022-07775-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/05/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUND Autism spectrum disorder (ASD) covers a group of neurodevelopmental disorders with complex genetic background. Several genetic mutations, epigenetic alterations, copy number variations and single nucleotide polymorphisms have been reported that cause ASD or modify its phenotype. Among signaling pathways that influence pathogenesis of ASD, calcium signaling has a prominent effect. METHODS We searched PubMed and Google Scholar databases with key words "Calcium signaling" and "Autism spectrum disorder". CONCLUSION This type of signaling has essential roles in the cell physiology. Endoplasmic reticulum and mitochondria are the key organelles involved in this signaling. It is vastly accepted that organellar disorders intensely influence the central nervous system (CNS). Several lines of evidence indicate alterations in the function of calcium channels in polygenic disorders affecting CNS. In the current review, we describe the role of calcium signaling in normal function of CNS and pathophysiology of ASD.
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Affiliation(s)
- Ashkan Pourtavakoli
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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7
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Khogeer AA, AboMansour IS, Mohammed DA. The Role of Genetics, Epigenetics, and the Environment in ASD: A Mini Review. EPIGENOMES 2022; 6:15. [PMID: 35735472 PMCID: PMC9222497 DOI: 10.3390/epigenomes6020015] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/12/2022] [Accepted: 06/16/2022] [Indexed: 01/21/2023] Open
Abstract
According to recent findings, variances in autism spectrum disorder (ASD) risk factors might be determined by several factors, including molecular genetic variants. Accumulated evidence has also revealed the important role of biological and chemical pathways in ASD aetiology. In this paper, we assess several reviews with regard to their quality of evidence and provide a brief outline of the presumed mechanisms of the genetic, epigenetic, and environmental risk factors of ASD. We also review some of the critical literature, which supports the basis of each factor in the underlying and specific risk patterns of ASD. Finally, we consider some of the implications of recent research regarding potential molecular targets for future investigations.
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Affiliation(s)
- Asim A. Khogeer
- Research Department, The Strategic Planning Administration, General Directorate of Health Affairs of Makkah Region, Ministry of Health, Makkah 24382, Saudi Arabia
- Medical Genetics Unit, Maternity & Children Hospital, Makkah Healthcare Cluster, Ministry of Health, Makkah 24382, Saudi Arabia;
- Scientific Council, Molecular Research and Training Center, iGene, Jeddah 3925, Saudi Arabia
| | - Iman S. AboMansour
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah 24382, Saudi Arabia;
- Neurogenetic Section, Department of Pediatrics, King Faisal Specialist Hospital and Research Center, Jeddah 2865, Saudi Arabia
| | - Dia A. Mohammed
- Medical Genetics Unit, Maternity & Children Hospital, Makkah Healthcare Cluster, Ministry of Health, Makkah 24382, Saudi Arabia;
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8
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LaSalle JM. X Chromosome Inactivation Timing is Not e XACT: Implications for Autism Spectrum Disorders. Front Genet 2022; 13:864848. [PMID: 35356429 PMCID: PMC8959653 DOI: 10.3389/fgene.2022.864848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
The etiology of autism spectrum disorders (ASD) is complex, involving different combinations of genetic and environmental factors. My lab's approach has been to investigate DNA methylation as a tractable genome-wide modification at the interface of these complex interactions, reflecting past and future events in the molecular pathogenesis of ASD. Since X-linked genes were enriched in DNA methylation differences discovered from cord blood from newborns later diagnosed with ASD, this has prompted me to review and revisit the recent advancements in the field of X chromosome inactivation (XCI), particularly in humans and other primates. In this Perspective, I compare XCI mechanisms in different mammalian species, including the finding of the noncoding transcript XACT associated with X chromosome erosion in human pluripotent stem cells and recent findings from non-human primate post-implantation embryos. I focus on the experimentally challenging peri- and post-implantation stages of human development when the timing of XCI is prolonged and imprecise in humans. Collectively, this research has raised some important unanswered questions involving biased sex ratios in human births and the male bias in the incidence of ASD.
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Affiliation(s)
- Janine M. LaSalle
- Department of Medical Microbiology and Immunology, Perinatal Origins of Disparities Center, MIND Institute, Genome Center, Environmental Health Sciences Center, University of California, Davis, Davis, CA, United States
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9
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Erden S, Akbaş İleri B, Sadıç Çelikkol Ç, Nalbant K, Kılınç İ, Yazar A. Serum B12, homocysteine, and anti-parietal cell antibody levels in children with autism. Int J Psychiatry Clin Pract 2022; 26:8-13. [PMID: 33823740 DOI: 10.1080/13651501.2021.1906906] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AIMS To compare vitamin B12, homocysteine, and anti-parietal cell antibody (APCA) levels between children with ASD and controls, paired in terms of age, sex, and socioeconomic level. METHODS The research group consisted of 69 children, 36 with ASD and 33 controls. The severity of ASD was determined using the Childhood Autism Rating Scale (CARS). Serum vitamin B12, homocysteine and human anti-parietal cell levels were analysed using enzyme-linked immunosorbent assay. RESULTS The serum vitamin B12 and homocysteine levels in children with ASD were lower than in the control group, but there was no significant difference in terms of APCA levels. CONCLUSIONS Deficiencies in micronutrients, such as B12, may play a role in the pathogenesis and clinical symptoms of autism. However, it is believed that these parameters should be analysed in a wider population to clarify their effect on the aetiology of ASD.KEY POINTWe hypothesised that low levels of vitamin B12 and homocysteine levels reported in previous studies might be associated with APCA levels.The homocysteine and B12 levels were found to be significantly lower in children with ASD. There was no significant difference in serum APCA levels.No significant relationship was found between B12 levels and APCA.Given all these findings, it can be stated that vitamin B12 deficiency is not associated with an absorption-related mechanism due to the presence of APCA.Deficiencies in micronutrients, such as B12, may play a role in the pathogenesis and clinical symptoms of autism.In future studies, it will be beneficial to investigate other mechanisms that may cause vitamin B12 deficiency.
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Affiliation(s)
- Semih Erden
- Department of Child and Adolescent Psychiatry, Necmettin Erbakan University Faculty of Medicine, Konya, Turkey
| | - Betül Akbaş İleri
- Department of Child and Adolescent Psychiatry, Necmettin Erbakan University Faculty of Medicine, Konya, Turkey
| | - Çağla Sadıç Çelikkol
- Department of Child and Adolescent Psychiatry, Necmettin Erbakan University Faculty of Medicine, Konya, Turkey
| | - Kevser Nalbant
- Department of Child and Adolescent Psychiatry, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - İbrahim Kılınç
- Department of Biochemistry, Necmettin Erbakan University Faculty of Medicine, Konya, Turkey
| | - Abdullah Yazar
- Department of Child Health and Diseases, Necmettin Erbakan University Faculty of Medicine, Konya, Turkey
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10
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Recent ultra-rare inherited variants implicate new autism candidate risk genes. Nat Genet 2021; 53:1125-1134. [PMID: 34312540 DOI: 10.1038/s41588-021-00899-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/18/2021] [Indexed: 01/28/2023]
Abstract
Autism is a highly heritable complex disorder in which de novo mutation (DNM) variation contributes significantly to risk. Using whole-genome sequencing data from 3,474 families, we investigate another source of large-effect risk variation, ultra-rare variants. We report and replicate a transmission disequilibrium of private, likely gene-disruptive (LGD) variants in probands but find that 95% of this burden resides outside of known DNM-enriched genes. This variant class more strongly affects multiplex family probands and supports a multi-hit model for autism. Candidate genes with private LGD variants preferentially transmitted to probands converge on the E3 ubiquitin-protein ligase complex, intracellular transport and Erb signaling protein networks. We estimate that these variants are approximately 2.5 generations old and significantly younger than other variants of similar type and frequency in siblings. Overall, private LGD variants are under strong purifying selection and appear to act on a distinct set of genes not yet associated with autism.
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11
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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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12
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Abstract
The prevalence of autism spectrum disorder (ASD) has been increasing steadily over the last 20 years; however, the molecular basis for the majority of ASD cases remains unknown. Recent advances in next-generation sequencing and detection of DNA modifications have made methylation-dependent regulation of transcription an attractive hypothesis for being a causative factor in ASD etiology. Evidence for abnormal DNA methylation in ASD can be seen on multiple levels, from genetic mutations in epigenetic machinery to loci-specific and genome-wide changes in DNA methylation. Epimutations in DNA methylation can be acquired throughout life, as global DNA methylation reprogramming is dynamic during embryonic development and the early postnatal period that corresponds to the peak time of synaptogenesis. However, technical advances and causative evidence still need to be established before abnormal DNA methylation and ASD can be confidently associated.
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Affiliation(s)
- Martine W Tremblay
- Program in Genetics and Genomics, Duke University, Durham, North Carolina 27710, USA
| | - Yong-Hui Jiang
- Program in Genetics and Genomics, Duke University, Durham, North Carolina 27710, USA.,Departments of Pediatrics and Neurobiology, Duke University School of Medicine, Durham, North Carolina 27710, USA;
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13
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Rylaarsdam L, Guemez-Gamboa A. Genetic Causes and Modifiers of Autism Spectrum Disorder. Front Cell Neurosci 2019; 13:385. [PMID: 31481879 PMCID: PMC6710438 DOI: 10.3389/fncel.2019.00385] [Citation(s) in RCA: 241] [Impact Index Per Article: 48.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/06/2019] [Indexed: 12/18/2022] Open
Abstract
Autism Spectrum Disorder (ASD) is one of the most prevalent neurodevelopmental disorders, affecting an estimated 1 in 59 children. ASD is highly genetically heterogeneous and may be caused by both inheritable and de novo gene variations. In the past decade, hundreds of genes have been identified that contribute to the serious deficits in communication, social cognition, and behavior that patients often experience. However, these only account for 10-20% of ASD cases, and patients with similar pathogenic variants may be diagnosed on very different levels of the spectrum. In this review, we will describe the genetic landscape of ASD and discuss how genetic modifiers such as copy number variation, single nucleotide polymorphisms, and epigenetic alterations likely play a key role in modulating the phenotypic spectrum of ASD patients. We also consider how genetic modifiers can alter convergent signaling pathways and lead to impaired neural circuitry formation. Lastly, we review sex-linked modifiers and clinical implications. Further understanding of these mechanisms is crucial for both comprehending ASD and for developing novel therapies.
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Affiliation(s)
| | - Alicia Guemez-Gamboa
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
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14
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Alex AM, Saradalekshmi KR, Shilen N, Suresh PA, Banerjee M. Genetic association of DNMT variants can play a critical role in defining the methylation patterns in autism. IUBMB Life 2019; 71:901-907. [PMID: 30786140 DOI: 10.1002/iub.2021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/29/2018] [Accepted: 01/14/2019] [Indexed: 12/15/2022]
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder with impairments in social communication, restricted, repetitive and stereotyped behaviors. Both genetic and environmental factors are known to contribute toward pathophysiology of Autism. Environmental influences on gene expression can be mediated by methylation patterns which are established and maintained by DNA methyltransferases. Several studies in the past have investigated the role of global methylations in Autism. The present study is aimed to investigate the role of genetic variations in the DNA methyltransferase which might be critical in defining the threshold for environmental factors toward susceptibility to autism. Polymorphisms in DNA methyltransferases, DNMT1, DNMT3A, DNMT3B, and DNMT3L were screened for association with ASD in 180 autistic patients and 260 healthy controls from a south Indian population. DNMT1 rs10418707 and rs10423341, and DNMT3A rs2289195 were found to be significantly associated at genotypic and allelic level with ASD. Functional prediction indicates that these SNPs have a role in transcriptional regulation and increased expression, indicating that hypermethylation might be induced by its genotype status. The study might reflect the role of genetics variants in DNMTs in defining the threshold of environmental impact in influencing the disease or phenotype variations in ASD. © 2019 IUBMB Life, 2019.
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Affiliation(s)
- Ann Mary Alex
- Human Molecular Genetics Laboratory, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, India
| | | | | | - Poovathinal A Suresh
- Institute for Communicative and Cognitive Neuro-Science, Shoranur, Kerala, India
| | - Moinak Banerjee
- Human Molecular Genetics Laboratory, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, India
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15
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Dall'Aglio L, Muka T, Cecil CAM, Bramer WM, Verbiest MMPJ, Nano J, Hidalgo AC, Franco OH, Tiemeier H. The role of epigenetic modifications in neurodevelopmental disorders: A systematic review. Neurosci Biobehav Rev 2018; 94:17-30. [PMID: 30067938 DOI: 10.1016/j.neubiorev.2018.07.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/21/2018] [Accepted: 07/20/2018] [Indexed: 02/07/2023]
Abstract
Epigenetic processes have been suggested as key mechanisms in the etiology of neurodevelopmental disorders. This systematic review summarizes the current evidence for an association between epigenetics and Autism Spectrum Disorder (ASD) and Attention/Deficit-Hyperactivity Disorder (ADHD). Six databases were searched until the 24th of October 2017. Of the 2169 retrieved articles, 29 met our inclusion criteria. While generally associations between epigenetics and neurodevelopmental disorders were reported, only a few findings were consistent across independent analyses. Differential epigenetic markers were repeatedly identified in OR2L13, C11orf21/TSPAN32, PRRT1 and H3K27 for autism, and in VIPR2 for ADHD. Overall, evidence of an association between epigenetic modifications and ASD or ADHD should be considered preliminary and based on studies suffering from numerous caveats. We highlight the need for carefully designed investigations and for greater homogeneity and provide specific recommendations for future research. Despite the current limited understanding, the suggestive findings and rapid advances in the field hold the promise of a forthcoming elucidation of the role of epigenetic modifications in neurodevelopmental disorders.
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Affiliation(s)
- Lorenza Dall'Aglio
- Department of Epidemiology, Erasmus University Medical Center-Sophia Children's Hospital, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Taulant Muka
- Department of Epidemiology, Erasmus University Medical Center-Sophia Children's Hospital, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Charlotte A M Cecil
- Department of Epidemiology, Erasmus University Medical Center-Sophia Children's Hospital, PO Box 2040, 3000 CA, Rotterdam, The Netherlands; Department of Child and Adolescent Psychiatry, Erasmus University Medical Center-Sophia Children's Hospital, PO Box 2040, 3000 CA, Rotterdam, The Netherlands; Department of Psychology, Institute of Psychiatry, Psychology & Neuroscience, King's College London, 10 Cutcombe Road, SE5 9RJ, London, UK
| | - Wichor M Bramer
- Medical Library, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Michael M P J Verbiest
- Department of Internal Medicine, University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Jana Nano
- Department of Epidemiology, Erasmus University Medical Center-Sophia Children's Hospital, PO Box 2040, 3000 CA, Rotterdam, The Netherlands; Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02115, USA
| | - Andrea Cortes Hidalgo
- Department of Epidemiology, Erasmus University Medical Center-Sophia Children's Hospital, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Oscar H Franco
- Department of Epidemiology, Erasmus University Medical Center-Sophia Children's Hospital, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Henning Tiemeier
- Department of Epidemiology, Erasmus University Medical Center-Sophia Children's Hospital, PO Box 2040, 3000 CA, Rotterdam, The Netherlands; Department of Child and Adolescent Psychiatry, Erasmus University Medical Center-Sophia Children's Hospital, PO Box 2040, 3000 CA, Rotterdam, The Netherlands; Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02115, USA.
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16
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Bruner-Tran KL, Mokshagundam S, Herington JL, Ding T, Osteen KG. Rodent Models of Experimental Endometriosis: Identifying Mechanisms of Disease and Therapeutic Targets. CURRENT WOMEN'S HEALTH REVIEWS 2018; 14:173-188. [PMID: 29861705 PMCID: PMC5925870 DOI: 10.2174/1573404813666170921162041] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/03/2017] [Accepted: 08/10/2017] [Indexed: 12/13/2022]
Abstract
BACKGROUND Although it has been more than a century since endometriosis was initially described in the literature, understanding the etiology and natural history of the disease has been challenging. However, the broad utility of murine and rat models of experimental endometriosis has enabled the elucidation of a number of potentially targetable processes which may otherwise promote this disease. OBJECTIVE To review a variety of studies utilizing rodent models of endometriosis to illustrate their utility in examining mechanisms associated with development and progression of this disease. RESULTS Use of rodent models of endometriosis has provided a much broader understanding of the risk factors for the initial development of endometriosis, the cellular pathology of the disease and the identification of potential therapeutic targets. CONCLUSION Although there are limitations with any animal model, the variety of experimental endometriosis models that have been developed has enabled investigation into numerous aspects of this disease. Thanks to these models, our under-standing of the early processes of disease development, the role of steroid responsiveness, inflammatory processes and the peritoneal environment has been advanced. More recent models have begun to shed light on how epigenetic alterations con-tribute to the molecular basis of this disease as well as the multiple comorbidities which plague many patients. Continued de-velopments of animal models which aid in unraveling the mechanisms of endometriosis development provide the best oppor-tunity to identify therapeutic strategies to prevent or regress this enigmatic disease.
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Affiliation(s)
- Kaylon L. Bruner-Tran
- Department of Obstetrics and Gynecology, Women’s Reproductive Health Research Center, Nashville, TN37232, USA
| | - Shilpa Mokshagundam
- Department of Obstetrics and Gynecology, Women’s Reproductive Health Research Center, Nashville, TN37232, USA
| | - Jennifer L. Herington
- Division of Neonatology, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN37232, USA
| | - Tianbing Ding
- Department of Obstetrics and Gynecology, Women’s Reproductive Health Research Center, Nashville, TN37232, USA
| | - Kevin G. Osteen
- Department of Obstetrics and Gynecology, Women’s Reproductive Health Research Center, Nashville, TN37232, USA
- VA Tennessee Valley Healthcare System, NashvilleTN37212, USA
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17
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Turner TN, Coe BP, Dickel DE, Hoekzema K, Nelson BJ, Zody MC, Kronenberg ZN, Hormozdiari F, Raja A, Pennacchio LA, Darnell RB, Eichler EE. Genomic Patterns of De Novo Mutation in Simplex Autism. Cell 2017; 171:710-722.e12. [PMID: 28965761 PMCID: PMC5679715 DOI: 10.1016/j.cell.2017.08.047] [Citation(s) in RCA: 227] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/03/2017] [Accepted: 08/25/2017] [Indexed: 12/22/2022]
Abstract
To further our understanding of the genetic etiology of autism, we generated and analyzed genome sequence data from 516 idiopathic autism families (2,064 individuals). This resource includes >59 million single-nucleotide variants (SNVs) and 9,212 private copy number variants (CNVs), of which 133,992 and 88 are de novo mutations (DNMs), respectively. We estimate a mutation rate of ∼1.5 × 10-8 SNVs per site per generation with a significantly higher mutation rate in repetitive DNA. Comparing probands and unaffected siblings, we observe several DNM trends. Probands carry more gene-disruptive CNVs and SNVs, resulting in severe missense mutations and mapping to predicted fetal brain promoters and embryonic stem cell enhancers. These differences become more pronounced for autism genes (p = 1.8 × 10-3, OR = 2.2). Patients are more likely to carry multiple coding and noncoding DNMs in different genes, which are enriched for expression in striatal neurons (p = 3 × 10-3), suggesting a path forward for genetically characterizing more complex cases of autism.
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Affiliation(s)
- Tychele N Turner
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Bradley P Coe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Diane E Dickel
- Functional Genomics Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Bradley J Nelson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | - Zev N Kronenberg
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Fereydoun Hormozdiari
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA 95817, USA
| | - Archana Raja
- 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
| | - Len A Pennacchio
- Functional Genomics Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Robert B Darnell
- New York Genome Center, New York, NY 10013, USA; Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, 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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Siu MT, Weksberg R. Epigenetics of Autism Spectrum Disorder. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 978:63-90. [PMID: 28523541 DOI: 10.1007/978-3-319-53889-1_4] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Autism spectrum disorder (ASD), one of the most common childhood neurodevelopmental disorders (NDDs), is diagnosed in 1 of every 68 children. ASD is incredibly heterogeneous both clinically and aetiologically. The etiopathogenesis of ASD is known to be complex, including genetic, environmental and epigenetic factors. Normal epigenetic marks modifiable by both genetics and environmental exposures can result in epigenetic alterations that disrupt the regulation of gene expression, negatively impacting biological pathways important for brain development. In this chapter we aim to summarize some of the important literature that supports a role for epigenetics in the underlying molecular mechanism of ASD. We provide evidence from work in genetics, from environmental exposures and finally from more recent studies aimed at directly determining ASD-specific epigenetic patterns, focusing mainly on DNA methylation (DNAm). Finally, we briefly discuss some of the implications of current research on potential epigenetic targets for therapeutics and novel avenues for future work.
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Affiliation(s)
- Michelle T Siu
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1X8, Canada
| | - Rosanna Weksberg
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1X8, Canada. .,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1X8, Canada. .,Department of Paediatrics, University of Toronto, Toronto, ON, M5S 1A1, Canada. .,Institute of Medical Science, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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19
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McGee SL, Walder KR. Exercise and the Skeletal Muscle Epigenome. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a029876. [PMID: 28320830 DOI: 10.1101/cshperspect.a029876] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
An acute bout of exercise is sufficient to induce changes in skeletal muscle gene expression that are ultimately responsible for the adaptive responses to exercise. Although much research has described the intracellular signaling responses to exercise that are linked to transcriptional regulation, the epigenetic mechanisms involved are only just emerging. This review will provide an overview of epigenetic mechanisms and what is known in the context of exercise. Additionally, we will explore potential interactions between metabolism during exercise and epigenetic regulation, which serves as a framework for potential areas for future research. Finally, we will consider emerging opportunities to pharmacologically manipulate epigenetic regulators and mechanisms to induce aspects of the skeletal muscle exercise adaptive response for therapeutic intervention in various disease states.
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Affiliation(s)
- Sean L McGee
- Metabolic Research Unit, School of Medicine and Centre for Molecular and Medical Research, Deakin University, Geelong, Victoria 3216, Australia
| | - Ken R Walder
- Metabolic Research Unit, School of Medicine and Centre for Molecular and Medical Research, Deakin University, Geelong, Victoria 3216, Australia
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20
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Reilly J, Gallagher L, Chen JL, Leader G, Shen S. Bio-collections in autism research. Mol Autism 2017; 8:34. [PMID: 28702161 PMCID: PMC5504648 DOI: 10.1186/s13229-017-0154-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/23/2017] [Indexed: 01/06/2023] Open
Abstract
Autism spectrum disorder (ASD) is a group of complex neurodevelopmental disorders with diverse clinical manifestations and symptoms. In the last 10 years, there have been significant advances in understanding the genetic basis for ASD, critically supported through the establishment of ASD bio-collections and application in research. Here, we summarise a selection of major ASD bio-collections and their associated findings. Collectively, these include mapping ASD candidate genes, assessing the nature and frequency of gene mutations and their association with ASD clinical subgroups, insights into related molecular pathways such as the synapses, chromatin remodelling, transcription and ASD-related brain regions. We also briefly review emerging studies on the use of induced pluripotent stem cells (iPSCs) to potentially model ASD in culture. These provide deeper insight into ASD progression during development and could generate human cell models for drug screening. Finally, we provide perspectives concerning the utilities of ASD bio-collections and limitations, and highlight considerations in setting up a new bio-collection for ASD research.
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Affiliation(s)
- Jamie Reilly
- Regenerative Medicine Institute, School of Medicine, BioMedical Sciences Building, National University of Ireland (NUI), Galway, Ireland
| | - Louise Gallagher
- Trinity Translational Medicine Institute and Department of Psychiatry, Trinity Centre for Health Sciences, St. James Hospital Street, Dublin 8, Ireland
| | - June L Chen
- Department of Special Education, Faculty of Education, East China Normal University, Shanghai, 200062 China
| | - Geraldine Leader
- Irish Centre for Autism and Neurodevelopmental Research (ICAN), Department of Psychology, National University of Ireland Galway, University Road, Galway, Ireland
| | - Sanbing Shen
- Regenerative Medicine Institute, School of Medicine, BioMedical Sciences Building, National University of Ireland (NUI), Galway, Ireland
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21
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Abstract
Recent technological advances have made it possible to decode DNA methylomes at single-base-pair resolution under various physiological conditions. Many aberrant or differentially methylated sites have been discovered, but the mechanisms by which changes in DNA methylation lead to observed phenotypes, such as cancer, remain elusive. The classical view of methylation-mediated protein-DNA interactions is that only proteins with a methyl-CpG binding domain (MBD) can interact with methylated DNA. However, evidence is emerging to suggest that transcription factors lacking a MBD can also interact with methylated DNA. The identification of these proteins and the elucidation of their characteristics and the biological consequences of methylation-dependent transcription factor-DNA interactions are important stepping stones towards a mechanistic understanding of methylation-mediated biological processes, which have crucial implications for human development and disease.
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22
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Vogel Ciernia A, LaSalle J. The landscape of DNA methylation amid a perfect storm of autism aetiologies. Nat Rev Neurosci 2016; 17:411-23. [PMID: 27150399 PMCID: PMC4966286 DOI: 10.1038/nrn.2016.41] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Increasing evidence points to a complex interplay between genes and the environment in autism spectrum disorder (ASD), including rare de novo mutations in chromatin genes such as methyl-CpG binding protein 2 (MECP2) in Rett syndrome. Epigenetic mechanisms such as DNA methylation act at this interface, reflecting the plasticity in metabolic and neurodevelopmentally regulated gene pathways. Genome-wide studies of gene sequences, gene pathways and DNA methylation are providing valuable mechanistic insights into ASD. The dynamic developmental landscape of DNA methylation is vulnerable to numerous genetic and environmental insults: therefore, understanding pathways that are central to this 'perfect storm' will be crucial to improving the diagnosis and treatment of ASD.
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Affiliation(s)
- Annie Vogel Ciernia
- Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, California 95616, USA
| | - Janine LaSalle
- Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, California 95616, USA
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23
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Homs A, Codina-Solà M, Rodríguez-Santiago B, Villanueva CM, Monk D, Cuscó I, Pérez-Jurado LA. Genetic and epigenetic methylation defects and implication of the ERMN gene in autism spectrum disorders. Transl Psychiatry 2016; 6:e855. [PMID: 27404287 PMCID: PMC5545709 DOI: 10.1038/tp.2016.120] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 04/01/2016] [Accepted: 05/08/2016] [Indexed: 12/11/2022] Open
Abstract
Autism spectrum disorders (ASD) are highly heritable and genetically complex conditions. Although highly penetrant mutations in multiple genes have been identified, they account for the etiology of <1/3 of cases. There is also strong evidence for environmental contribution to ASD, which can be mediated by still poorly explored epigenetic modifications. We searched for methylation changes on blood DNA of 53 male ASD patients and 757 healthy controls using a methylomic array (450K Illumina), correlated the variants with transcriptional alterations in blood RNAseq data, and performed a case-control association study of the relevant findings in a larger cohort (394 cases and 500 controls). We found 700 differentially methylated CpGs, most of them hypomethylated in the ASD group (83.9%), with cis-acting expression changes at 7.6% of locations. Relevant findings included: (1) hypomethylation caused by rare genetic variants (meSNVs) at six loci (ERMN, USP24, METTL21C, PDE10A, STX16 and DBT) significantly associated with ASD (q-value <0.05); and (2) clustered epimutations associated to transcriptional changes in single-ASD patients (n=4). All meSNVs and clustered epimutations were inherited from unaffected parents. Resequencing of the top candidate genes also revealed a significant load of deleterious mutations affecting ERMN in ASD compared with controls. Our data indicate that inherited methylation alterations detectable in blood DNA, due to either genetic or epigenetic defects, can affect gene expression and contribute to ASD susceptibility most likely in an additive manner, and implicate ERMN as a novel ASD gene.
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Affiliation(s)
- A Homs
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain,Institut Hospital del Mar d’Investigacions Mèdiques, Barcelona, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras, Barcelona, Spain
| | - M Codina-Solà
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain,Institut Hospital del Mar d’Investigacions Mèdiques, Barcelona, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras, Barcelona, Spain
| | | | - C M Villanueva
- Center for Research in Environmental Epidemiology, Barcelona, Spain,Consorcio de Investigación Biomédica de Epidemiología y Salud Pública, Barcelona, Spain
| | - D Monk
- Cancer Epigenetics Group, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
| | - I Cuscó
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain,Institut Hospital del Mar d’Investigacions Mèdiques, Barcelona, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras, Barcelona, Spain,Genetics Unit, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Dr. Aiguader 88, Barcelona 08003, Spain. E-mails: and
| | - L A Pérez-Jurado
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain,Institut Hospital del Mar d’Investigacions Mèdiques, Barcelona, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras, Barcelona, Spain,Genetics Unit, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Dr. Aiguader 88, Barcelona 08003, Spain. E-mails: and
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24
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Irwin RE, Pentieva K, Cassidy T, Lees-Murdock DJ, McLaughlin M, Prasad G, McNulty H, Walsh CP. The interplay between DNA methylation, folate and neurocognitive development. Epigenomics 2016; 8:863-79. [PMID: 27319574 DOI: 10.2217/epi-2016-0003] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
DNA methylation provides an attractive possible means for propagating the effects of environmental inputs during fetal life and impacting subsequent adult mental health, which is leading to increasing collaboration between molecular biologists, nutritionists and psychiatrists. An area of interest is the potential role of folate, not just in neural tube closure in early pregnancy, but in later major neurodevelopmental events, with consequences for later sociocognitive maturation. Here, we set the scene for recent discoveries by reviewing the major events of neural development during fetal life, with an emphasis on tissues and structures where dynamic methylation changes are known to occur. Following this, we give an indication of some of the major classes of genes targeted by methylation and important for neurological and behavioral development. Finally, we highlight some cognitive disorders where methylation changes are implicated as playing an important role.
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Affiliation(s)
- Rachelle E Irwin
- EpiFASSTT study, Biomedical Sciences, Ulster University, Coleraine, UK
| | - Kristina Pentieva
- EpiFASSTT study, Biomedical Sciences, Ulster University, Coleraine, UK
| | - Tony Cassidy
- EpiFASSTT study, Psychology, Ulster University, Coleraine, UK
| | | | | | - Girijesh Prasad
- EpiFASSTT study, Computer Sciences Research Institutes, Ulster University, Londonderry, UK
| | - Helene McNulty
- EpiFASSTT study, Biomedical Sciences, Ulster University, Coleraine, UK
| | - Colum P Walsh
- EpiFASSTT study, Biomedical Sciences, Ulster University, Coleraine, UK
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25
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Kim KC, Gonzales EL, Lázaro MT, Choi CS, Bahn GH, Yoo HJ, Shin CY. Clinical and Neurobiological Relevance of Current Animal Models of Autism Spectrum Disorders. Biomol Ther (Seoul) 2016; 24:207-43. [PMID: 27133257 PMCID: PMC4859786 DOI: 10.4062/biomolther.2016.061] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 04/05/2016] [Indexed: 12/24/2022] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by social and communication impairments, as well as repetitive and restrictive behaviors. The phenotypic heterogeneity of ASD has made it overwhelmingly difficult to determine the exact etiology and pathophysiology underlying the core symptoms, which are often accompanied by comorbidities such as hyperactivity, seizures, and sensorimotor abnormalities. To our benefit, the advent of animal models has allowed us to assess and test diverse risk factors of ASD, both genetic and environmental, and measure their contribution to the manifestation of autistic symptoms. At a broader scale, rodent models have helped consolidate molecular pathways and unify the neurophysiological mechanisms underlying each one of the various etiologies. This approach will potentially enable the stratification of ASD into clinical, molecular, and neurophenotypic subgroups, further proving their translational utility. It is henceforth paramount to establish a common ground of mechanistic theories from complementing results in preclinical research. In this review, we cluster the ASD animal models into lesion and genetic models and further classify them based on the corresponding environmental, epigenetic and genetic factors. Finally, we summarize the symptoms and neuropathological highlights for each model and make critical comparisons that elucidate their clinical and neurobiological relevance.
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Affiliation(s)
- Ki Chan Kim
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Center for Neuroscience Research, SMART Institute of Advanced Biomedical Sciences, Konkuk University, Seoul 05029, Republic of Korea
| | - Edson Luck Gonzales
- Center for Neuroscience Research, SMART Institute of Advanced Biomedical Sciences, Konkuk University, Seoul 05029, Republic of Korea.,School of Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - María T Lázaro
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Chang Soon Choi
- Center for Neuroscience Research, SMART Institute of Advanced Biomedical Sciences, Konkuk University, Seoul 05029, Republic of Korea.,School of Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Geon Ho Bahn
- Department of Neuropsychiatry, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Hee Jeong Yoo
- Department of Neuropsychiatry, Seoul National University Bungdang Hospital, Seongnam 13620, Republic of Korea
| | - Chan Young Shin
- Center for Neuroscience Research, SMART Institute of Advanced Biomedical Sciences, Konkuk University, Seoul 05029, Republic of Korea.,School of Medicine, Konkuk University, Seoul 05029, Republic of Korea
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26
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Lahiri DK, Maloney B, Bayon BL, Chopra N, White FA, Greig NH, Nurnberger JI. Transgenerational latent early-life associated regulation unites environment and genetics across generations. Epigenomics 2016; 8:373-87. [PMID: 26950428 DOI: 10.2217/epi.15.117] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The origin of idiopathic diseases is still poorly understood. The latent early-life associated regulation (LEARn) model unites environmental exposures and gene expression while providing a mechanistic underpinning for later-occurring disorders. We propose that this process can occur across generations via transgenerational LEARn (tLEARn). In tLEARn, each person is a 'unit' accumulating preclinical or subclinical 'hits' as in the original LEARn model. These changes can then be epigenomically passed along to offspring. Transgenerational accumulation of 'hits' determines a sporadic disease state. Few significant transgenerational hits would accompany conception or gestation of most people, but these may suffice to 'prime' someone to respond to later-life hits. Hits need not produce symptoms or microphenotypes to have a transgenerational effect. Testing tLEARn requires longitudinal approaches. A recently proposed longitudinal epigenome/envirome-wide association study would unite genetic sequence, epigenomic markers, environmental exposures, patient personal history taken at multiple time points and family history.
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Affiliation(s)
- Debomoy K Lahiri
- Department of Psychiatry, Stark Neurosciences Research Institute, Indiana University School of Medicine, 320 West 15th Street, Indianapolis, IN 46202, USA.,Department of Medical & Molecular Genetics, Indiana University School of Medicine, 320 West 15th Street, Indianapolis, IN 46202, USA
| | - Bryan Maloney
- Department of Psychiatry, Stark Neurosciences Research Institute, Indiana University School of Medicine, 320 West 15th Street, Indianapolis, IN 46202, USA
| | - Baindu L Bayon
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, 320 West 15th Street, Indianapolis, IN 46202, USA
| | - Nipun Chopra
- Department of Psychiatry, Stark Neurosciences Research Institute, Indiana University School of Medicine, 320 West 15th Street, Indianapolis, IN 46202, USA
| | - Fletcher A White
- Department of Anesthesia, Stark Neurosciences Research Institute, Indiana University School of Medicine, 320 West 15th Street, Indianapolis, IN 46202, USA
| | - Nigel H Greig
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - John I Nurnberger
- Department of Psychiatry, Stark Neurosciences Research Institute, Indiana University School of Medicine, 320 West 15th Street, Indianapolis, IN 46202, USA.,Department of Medical & Molecular Genetics, Indiana University School of Medicine, 320 West 15th Street, Indianapolis, IN 46202, USA
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27
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Nava C, Rupp J, Boissel JP, Mignot C, Rastetter A, Amiet C, Jacquette A, Dupuits C, Bouteiller D, Keren B, Ruberg M, Faudet A, Doummar D, Philippe A, Périsse D, Laurent C, Lebrun N, Guillemot V, Chelly J, Cohen D, Héron D, Brice A, Closs EI, Depienne C. Hypomorphic variants of cationic amino acid transporter 3 in males with autism spectrum disorders. Amino Acids 2015. [PMID: 26215737 PMCID: PMC4633447 DOI: 10.1007/s00726-015-2057-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Cationic amino acid transporters (CATs) mediate the entry of L-type cationic amino acids (arginine, ornithine and lysine) into the cells including neurons. CAT-3, encoded by the SLC7A3 gene on chromosome X, is one of the three CATs present in the human genome, with selective expression in brain. SLC7A3 is highly intolerant to variation in humans, as attested by the low frequency of deleterious variants in available databases, but the impact on variants in this gene in humans remains undefined. In this study, we identified a missense variant in SLC7A3, encoding the CAT-3 cationic amino acid transporter, on chromosome X by exome sequencing in two brothers with autism spectrum disorder (ASD). We then sequenced the SLC7A3 coding sequence in 148 male patients with ASD and identified three additional rare missense variants in unrelated patients. Functional analyses of the mutant transporters showed that two of the four identified variants cause severe or moderate loss of CAT-3 function due to altered protein stability or abnormal trafficking to the plasma membrane. The patient with the most deleterious SLC7A3 variant had high-functioning autism and epilepsy, and also carries a de novo 16p11.2 duplication possibly contributing to his phenotype. This study shows that rare hypomorphic variants of SLC7A3 exist in male individuals and suggest that SLC7A3 variants possibly contribute to the etiology of ASD in male subjects in association with other genetic factors.
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Affiliation(s)
- Caroline Nava
- Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, ICM, 75013, Paris, France.,INSERM, U 1127, 75013, Paris, France.,CNRS, UMR 7225, 75013, Paris, France.,Institut du cerveau et de la moelle épinière (ICM), 75013, Paris, France.,Département de Génétique et de Cytogénétique, Hôpital de la Pitié-Salpêtrière, AP-HP, 75013, Paris, France
| | - Johanna Rupp
- Department of Pharmacology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Jean-Paul Boissel
- Department of Pharmacology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Cyril Mignot
- Département de Génétique et de Cytogénétique, Hôpital de la Pitié-Salpêtrière, AP-HP, 75013, Paris, France.,Centre de Référence "déficiences intellectuelles de causes rares", Paris, France.,Groupe de Recherche Clinique (GRC) "déficience intellectuelle et autisme" UPMC, Paris, France.,Service de neuropédiatrie, Hôpital Trousseau, AP-HP, Paris, France
| | - Agnès Rastetter
- Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, ICM, 75013, Paris, France.,INSERM, U 1127, 75013, Paris, France.,CNRS, UMR 7225, 75013, Paris, France.,Institut du cerveau et de la moelle épinière (ICM), 75013, Paris, France
| | - Claire Amiet
- Service de psychiatrie de l'enfant et de l'adolescent, Hôpital Pitié-Salpêtrière, AP-HP, 75013, Paris, France
| | - Aurélia Jacquette
- Département de Génétique et de Cytogénétique, Hôpital de la Pitié-Salpêtrière, AP-HP, 75013, Paris, France.,Centre de Référence "déficiences intellectuelles de causes rares", Paris, France.,Groupe de Recherche Clinique (GRC) "déficience intellectuelle et autisme" UPMC, Paris, France
| | - Céline Dupuits
- Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, ICM, 75013, Paris, France.,INSERM, U 1127, 75013, Paris, France.,CNRS, UMR 7225, 75013, Paris, France.,Institut du cerveau et de la moelle épinière (ICM), 75013, Paris, France
| | - Delphine Bouteiller
- Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, ICM, 75013, Paris, France.,INSERM, U 1127, 75013, Paris, France.,CNRS, UMR 7225, 75013, Paris, France.,Institut du cerveau et de la moelle épinière (ICM), 75013, Paris, France
| | - Boris Keren
- Département de Génétique et de Cytogénétique, Hôpital de la Pitié-Salpêtrière, AP-HP, 75013, Paris, France
| | - Merle Ruberg
- Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, ICM, 75013, Paris, France.,INSERM, U 1127, 75013, Paris, France.,CNRS, UMR 7225, 75013, Paris, France.,Institut du cerveau et de la moelle épinière (ICM), 75013, Paris, France
| | - Anne Faudet
- Département de Génétique et de Cytogénétique, Hôpital de la Pitié-Salpêtrière, AP-HP, 75013, Paris, France
| | - Diane Doummar
- Service de neuropédiatrie, Hôpital Trousseau, AP-HP, Paris, France
| | - Anne Philippe
- Service de psychiatrie de l'enfant et de l'adolescent, Hôpital Pitié-Salpêtrière, AP-HP, 75013, Paris, France
| | - Didier Périsse
- Service de psychiatrie de l'enfant et de l'adolescent, Hôpital Pitié-Salpêtrière, AP-HP, 75013, Paris, France.,Centre Diagnostic Autisme de l'Hôpital Pitié-Salpêtrière, 75013, Paris, France
| | - Claudine Laurent
- Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, ICM, 75013, Paris, France.,INSERM, U 1127, 75013, Paris, France.,CNRS, UMR 7225, 75013, Paris, France.,Institut du cerveau et de la moelle épinière (ICM), 75013, Paris, France.,Service de psychiatrie de l'enfant et de l'adolescent, Hôpital Pitié-Salpêtrière, AP-HP, 75013, Paris, France
| | - Nicolas Lebrun
- Institut Cochin, Inserm U567, UMR 8104, Université René Descartes, Paris 5, France
| | - Vincent Guillemot
- Bioinformatics and Biostatistics Core Facility (iCONICS), Institut du cerveau et de la moelle épinière (ICM), Paris, France
| | - Jamel Chelly
- Institut Cochin, Inserm U567, UMR 8104, Université René Descartes, Paris 5, France
| | - David Cohen
- Service de psychiatrie de l'enfant et de l'adolescent, Hôpital Pitié-Salpêtrière, AP-HP, 75013, Paris, France.,Institut des Systèmes Intelligents et Robotiques, CNRS UMR 7222, UPMC-Paris-6, Paris, France
| | - Delphine Héron
- Département de Génétique et de Cytogénétique, Hôpital de la Pitié-Salpêtrière, AP-HP, 75013, Paris, France.,Centre de Référence "déficiences intellectuelles de causes rares", Paris, France.,Groupe de Recherche Clinique (GRC) "déficience intellectuelle et autisme" UPMC, Paris, France.,Service de neuropédiatrie, Hôpital Trousseau, AP-HP, Paris, France
| | - Alexis Brice
- Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, ICM, 75013, Paris, France.,INSERM, U 1127, 75013, Paris, France.,CNRS, UMR 7225, 75013, Paris, France.,Institut du cerveau et de la moelle épinière (ICM), 75013, Paris, France.,Département de Génétique et de Cytogénétique, Hôpital de la Pitié-Salpêtrière, AP-HP, 75013, Paris, France
| | - Ellen I Closs
- Department of Pharmacology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Christel Depienne
- Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, ICM, 75013, Paris, France. .,INSERM, U 1127, 75013, Paris, France. .,CNRS, UMR 7225, 75013, Paris, France. .,Institut du cerveau et de la moelle épinière (ICM), 75013, Paris, France. .,Département de Génétique et de Cytogénétique, Hôpital de la Pitié-Salpêtrière, AP-HP, 75013, Paris, France.
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28
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MTHFR Gene C677T Polymorphism in Autism Spectrum Disorders. GENETICS RESEARCH INTERNATIONAL 2014; 2014:698574. [PMID: 25431675 PMCID: PMC4241316 DOI: 10.1155/2014/698574] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 10/22/2014] [Accepted: 10/23/2014] [Indexed: 11/18/2022]
Abstract
Aim. Autism is a subgroup of autism spectrum disorders, classified as a heterogeneous neurodevelopmental disorder and symptoms occur in the first three years of life. The etiology of autism is largely unknown, but it has been accepted that genetic and environmental factors may both be responsible for the disease. Recent studies have revealed that the genes involved in the folate/homocysteine pathway may be risk factors for autistic children. In particular, C677T polymorphism in the MTHFR gene as a possible risk factor for autism is still controversial. We aimed to investigate the possible effect of C677T polymorphism in a Turkish cohort. Methods. Autism patients were diagnosed by child psychiatrists according to DSM-IV and DSM-V criteria. A total of 98 children diagnosed as autistic and 70 age and sex-matched children who are nonautistic were tested for C677T polymorphism. This polymorphism was studied by using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) methods. Results. MTHFR 677T-allele frequency was found to be higher in autistic children compared with nonautistic children (29% versus 24%), but it was not found statistically significant. Conclusions. We conclude that other MTHFR polymorphisms such as A1298C or other folate/homocysteine pathway genes may be studied to show their possible role in autism.
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29
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Kalkbrenner AE, Schmidt RJ, Penlesky AC. Environmental chemical exposures and autism spectrum disorders: a review of the epidemiological evidence. Curr Probl Pediatr Adolesc Health Care 2014; 44:277-318. [PMID: 25199954 PMCID: PMC4855851 DOI: 10.1016/j.cppeds.2014.06.001] [Citation(s) in RCA: 183] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 06/09/2014] [Accepted: 06/12/2014] [Indexed: 12/11/2022]
Abstract
In the past decade, the number of epidemiological publications addressing environmental chemical exposures and autism has grown tremendously. These studies are important because it is now understood that environmental factors play a larger role in causing autism than previously thought and because they address modifiable risk factors that may open up avenues for the primary prevention of the disability associated with autism. In this review, we covered studies of autism and estimates of exposure to tobacco, air pollutants, volatile organic compounds and solvents, metals (from air, occupation, diet, dental amalgams, and thimerosal-containing vaccines), pesticides, and organic endocrine-disrupting compounds such as flame retardants, non-stick chemicals, phthalates, and bisphenol A. We included studies that had individual-level data on autism, exposure measures pertaining to pregnancy or the 1st year of life, valid comparison groups, control for confounders, and adequate sample sizes. Despite the inherent error in the measurement of many of these environmental exposures, which is likely to attenuate observed associations, some environmental exposures showed associations with autism, especially traffic-related air pollutants, some metals, and several pesticides, with suggestive trends for some volatile organic compounds (e.g., methylene chloride, trichloroethylene, and styrene) and phthalates. Whether any of these play a causal role requires further study. Given the limited scope of these publications, other environmental chemicals cannot be ruled out, but have not yet been adequately studied. Future research that addresses these and additional environmental chemicals, including their most common routes of exposures, with accurate exposure measurement pertaining to several developmental windows, is essential to guide efforts for the prevention of the neurodevelopmental damage that manifests in autism symptoms.
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Affiliation(s)
- Amy E Kalkbrenner
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI
| | - Rebecca J Schmidt
- Department of Public Health Sciences, University of California Davis School of Medicine, Davis, CA; Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, University of California Davis, Sacramento, CA
| | - Annie C Penlesky
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI
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30
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Jiang YH, Wang Y, Xiu X, Choy KW, Pursley AN, Cheung SW. Genetic diagnosis of autism spectrum disorders: the opportunity and challenge in the genomics era. Crit Rev Clin Lab Sci 2014; 51:249-62. [PMID: 24878448 PMCID: PMC5937018 DOI: 10.3109/10408363.2014.910747] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A genetic etiology for autism spectrum disorders (ASDs) was first suggested from twin studies reported in the 1970s. The identification of gene mutations in syndromic ASDs provided evidence to support a genetic cause of ASDs. More recently, genome-wide copy number variant and sequence analyses have uncovered a list of rare and highly penetrant copy number variants (CNVs) or single nucleotide variants (SNVs) associated with ASDs, which has strengthened the claim of a genetic etiology for ASDs. Findings from research studies in the genetics of ASD now support an important role for molecular diagnostics in the clinical genetics evaluation of ASDs. Various molecular diagnostic assays including single gene tests, targeted multiple gene panels and copy number analysis should all be considered in the clinical genetics evaluation of ASDs. Whole exome sequencing could also be considered in selected clinical cases. However, the challenge that remains is to determine the causal role of genetic variants identified through molecular testing. Variable expressivity, pleiotropic effects and incomplete penetrance associated with CNVs and SNVs also present significant challenges for genetic counseling and prenatal diagnosis.
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Affiliation(s)
- Yong-Hui Jiang
- Department of Pediatrics and Neurobiology, Duke University School of Medicine, Durham, NC, USA
- Division of Neurology, The Children’s Hospital of Fudan University, Shanghai, People’s Republic of China
| | - Yi Wang
- Division of Neurology, The Children’s Hospital of Fudan University, Shanghai, People’s Republic of China
| | - Xu Xiu
- Division of Child Development and Health, The Children’s Hospital of Fudan University Shanghai, People’s Republic of China
| | - Kwong Wai Choy
- Department of Obstetrics and Gynecology, and Joint Centre with Utrecht University Genetic core, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, People’s Republic of China
| | - Amber Nolen Pursley
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sau W. Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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31
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Common DNA methylation alterations in multiple brain regions in autism. Mol Psychiatry 2014; 19:862-71. [PMID: 23999529 PMCID: PMC4184909 DOI: 10.1038/mp.2013.114] [Citation(s) in RCA: 221] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2013] [Revised: 07/03/2013] [Accepted: 07/25/2013] [Indexed: 12/13/2022]
Abstract
Autism spectrum disorders (ASD) are increasingly common neurodevelopmental disorders defined clinically by a triad of features including impairment in social interaction, impairment in communication in social situations and restricted and repetitive patterns of behavior and interests, with considerable phenotypic heterogeneity among individuals. Although heritability estimates for ASD are high, conventional genetic-based efforts to identify genes involved in ASD have yielded only few reproducible candidate genes that account for only a small proportion of ASDs. There is mounting evidence to suggest environmental and epigenetic factors play a stronger role in the etiology of ASD than previously thought. To begin to understand the contribution of epigenetics to ASD, we have examined DNA methylation (DNAm) in a pilot study of postmortem brain tissue from 19 autism cases and 21 unrelated controls, among three brain regions including dorsolateral prefrontal cortex, temporal cortex and cerebellum. We measured over 485,000 CpG loci across a diverse set of functionally relevant genomic regions using the Infinium HumanMethylation450 BeadChip and identified four genome-wide significant differentially methylated regions (DMRs) using a bump hunting approach and a permutation-based multiple testing correction method. We replicated 3/4 DMRs identified in our genome-wide screen in a different set of samples and across different brain regions. The DMRs identified in this study represent suggestive evidence for commonly altered methylation sites in ASD and provide several promising new candidate genes.
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32
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Lee SY, Ramirez J, Franco M, Lectez B, Gonzalez M, Barrio R, Mayor U. Ube3a, the E3 ubiquitin ligase causing Angelman syndrome and linked to autism, regulates protein homeostasis through the proteasomal shuttle Rpn10. Cell Mol Life Sci 2014; 71:2747-58. [PMID: 24292889 PMCID: PMC11113982 DOI: 10.1007/s00018-013-1526-7] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 11/15/2013] [Indexed: 01/31/2023]
Abstract
Ubiquitination, the covalent attachment of ubiquitin to a target protein, regulates most cellular processes and is involved in several neurological disorders. In particular, Angelman syndrome and one of the most common genomic forms of autism, dup15q, are caused respectively by lack of or excess of UBE3A, a ubiquitin E3 ligase. Its Drosophila orthologue, Ube3a, is also active during brain development. We have now devised a protocol to screen for substrates of this particular ubiquitin ligase. In a neuronal cell system, we find direct ubiquitination by Ube3a of three proteasome-related proteins Rpn10, Uch-L5, and CG8209, as well as of the ribosomal protein Rps10b. Only one of these, Rpn10, is targeted for degradation upon ubiquitination by Ube3a, indicating that degradation might not be the only effect of Ube3a on its substrates. Furthermore, we report the genetic interaction in vivo between Ube3a and the C-terminal part of Rpn10. Overexpression of these proteins leads to an enhanced accumulation of ubiquitinated proteins, further supporting the biochemical evidence of interaction obtained in neuronal cells.
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Affiliation(s)
- So Young Lee
- CIC bioGUNE, Bizkaia Teknologia Parkea, Building 801-A, Derio, 48160 Derio, Basque Country Spain
| | - Juanma Ramirez
- CIC bioGUNE, Bizkaia Teknologia Parkea, Building 801-A, Derio, 48160 Derio, Basque Country Spain
| | - Maribel Franco
- CIC bioGUNE, Bizkaia Teknologia Parkea, Building 801-A, Derio, 48160 Derio, Basque Country Spain
- Present Address: Instituto de Neurociencias CSIC/UMH, 03550 Sant Joan d’Alacant, Spain
| | - Benoît Lectez
- CIC bioGUNE, Bizkaia Teknologia Parkea, Building 801-A, Derio, 48160 Derio, Basque Country Spain
| | - Monika Gonzalez
- CIC bioGUNE, Bizkaia Teknologia Parkea, Building 801-A, Derio, 48160 Derio, Basque Country Spain
| | - Rosa Barrio
- CIC bioGUNE, Bizkaia Teknologia Parkea, Building 801-A, Derio, 48160 Derio, Basque Country Spain
| | - Ugo Mayor
- CIC bioGUNE, Bizkaia Teknologia Parkea, Building 801-A, Derio, 48160 Derio, Basque Country Spain
- Ikerbasque, Basque Foundation for Science, 48011 Bilbao, Spain
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33
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Zhubi A, Cook EH, Guidotti A, Grayson DR. Epigenetic Mechanisms in Autism Spectrum Disorder. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2014; 115:203-44. [DOI: 10.1016/b978-0-12-801311-3.00006-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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34
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Meng L, Person RE, Huang W, Zhu PJ, Costa-Mattioli M, Beaudet AL. Truncation of Ube3a-ATS unsilences paternal Ube3a and ameliorates behavioral defects in the Angelman syndrome mouse model. PLoS Genet 2013; 9:e1004039. [PMID: 24385930 PMCID: PMC3873245 DOI: 10.1371/journal.pgen.1004039] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 11/04/2013] [Indexed: 11/18/2022] Open
Abstract
Angelman syndrome (AS) is a severe neurodevelopmental disorder caused by maternal deficiency of the imprinted gene UBE3A. Individuals with AS suffer from intellectual disability, speech impairment, and motor dysfunction. Currently there is no cure for the disease. Here, we evaluated the phenotypic effect of activating the silenced paternal allele of Ube3a by depleting its antisense RNA Ube3a-ATS in mice. Premature termination of Ube3a-ATS by poly(A) cassette insertion activates expression of Ube3a from the paternal chromosome, and ameliorates many disease-related symptoms in the AS mouse model, including motor coordination defects, cognitive deficit, and impaired long-term potentiation. Studies on the imprinting mechanism of Ube3a revealed a pattern of biallelic transcription initiation with suppressed elongation of paternal Ube3a, implicating transcriptional collision between sense and antisense polymerases. These studies demonstrate the feasibility and utility of unsilencing the paternal copy of Ube3a via targeting Ube3a-ATS as a treatment for Angelman syndrome. Angelman syndrome (AS) is a devastating neurodevelopmental disorder diagnosed in young children, currently with no effective treatments. It is characterized by absence of speech, ataxia, intellectual disability, epilepsy, and a characteristic behavior of frequent laughter and smiling. The disease is caused by loss of the maternal allele of UBE3A, which is preferentially silenced on the paternal chromosome and expressed on the maternal chromosome in neurons due to genomic imprinting. It has been long proposed that by activating the originally silenced paternal allele of UBE3A, the disease may be cured. Here in our research, we demonstrated the feasibility of activating paternal Ube3a in mice by terminating the transcription of its antisense RNA Ube3a-ATS genetically. In the AS mouse model who additionally receives the terminated Ube3a-ATS allele from the paternal side, we observed restoration of Ube3a expression, amelioration of behavioral defects and reversal of the impaired long-term potentiation. We further studied the imprinting mechanisms of Ube3a and proposed a novel transcriptional collision model. These results provide solid in vivo evidence for a key regulatory role of Ube3a-ATS in the disease and open up an exciting possibility of a gene-specific treatment for Angelman syndrome.
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Affiliation(s)
- Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard Erwin Person
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Wei Huang
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ping Jun Zhu
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, United States of America
| | - Mauro Costa-Mattioli
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, United States of America
| | - Arthur L. Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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35
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Zhu L, Wang X, Li XL, Towers A, Cao X, Wang P, Bowman R, Yang H, Goldstein J, Li YJ, Jiang YH. Epigenetic dysregulation of SHANK3 in brain tissues from individuals with autism spectrum disorders. Hum Mol Genet 2013; 23:1563-78. [PMID: 24186872 DOI: 10.1093/hmg/ddt547] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The molecular basis for the majority of cases of autism spectrum disorders (ASD) remains unknown. We tested the hypothesis that ASD have an epigenetic cause by performing DNA methylation profiling of five CpG islands (CGI-1 to CGI-5) in the SHANK3 gene in postmortem brain tissues from 54 ASD patients and 43 controls. We found significantly increased overall DNA methylation (epimutation) in three intragenic CGIs (CGI-2, CGI-3 and CGI-4). The increased methylation was clustered in the CGI-2 and CGI-4 in ∼15% of ASD brain tissues. SHANK3 has an extensive array of mRNA splice variants resulting from combinations of five intragenic promoters and alternative splicing of coding exons. Altered expression and alternative splicing of SHANK3 isoforms were observed in brain tissues with increased methylation of SHANK3 CGIs in ASD brain tissues. A DNA methylation inhibitor modified the methylation of CGIs and altered the isoform-specific expression of SHANK3 in cultured cells. This study is the first to find altered methylation patterns in SHANK3 in ASD brain samples. Our finding provides evidence to support an alternative approach to investigating the molecular basis of ASD. The ability to alter the epigenetic modification and expression of SHANK3 by environmental factors suggests that SHANK3 may be a valuable biomarker for dissecting the role of gene and environment interaction in the etiology of ASD.
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Lahiri DK, Sokol DK, Erickson C, Ray B, Ho CY, Maloney B. Autism as early neurodevelopmental disorder: evidence for an sAPPα-mediated anabolic pathway. Front Cell Neurosci 2013; 7:94. [PMID: 23801940 PMCID: PMC3689023 DOI: 10.3389/fncel.2013.00094] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Accepted: 05/27/2013] [Indexed: 12/27/2022] Open
Abstract
Autism is a neurodevelopmental disorder marked by social skills and communication deficits and interfering repetitive behavior. Intellectual disability often accompanies autism. In addition to behavioral deficits, autism is characterized by neuropathology and brain overgrowth. Increased intracranial volume often accompanies this brain growth. We have found that the Alzheimer's disease (AD) associated amyloid-β precursor protein (APP), especially its neuroprotective processing product, secreted APP α, is elevated in persons with autism. This has led to the "anabolic hypothesis" of autism etiology, in which neuronal overgrowth in the brain results in interneuronal misconnections that may underlie multiple autism symptoms. We review the contribution of research in brain volume and of APP to the anabolic hypothesis, and relate APP to other proteins and pathways that have already been directly associated with autism, such as fragile X mental retardation protein, Ras small GTPase/extracellular signal-regulated kinase, and phosphoinositide 3 kinase/protein kinase B/mammalian target of rapamycin. We also present additional evidence of magnetic resonance imaging intracranial measurements in favor of the anabolic hypothesis. Finally, since it appears that APP's involvement in autism is part of a multi-partner network, we extend this concept into the inherently interactive realm of epigenetics. We speculate that the underlying molecular abnormalities that influence APP's contribution to autism are epigenetic markers overlaid onto potentially vulnerable gene sequences due to environmental influence.
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Affiliation(s)
- Debomoy K. Lahiri
- Department of Psychiatry, Indiana University School of MedicineIndianapolis, IN USA
- Laboratory of Medical and Molecular Genetics, Indiana University School of MedicineIndianapolis, IN, USA
- Institute of Psychiatric Research, Indiana University School of MedicineIndianapolis, IN, USA
| | - Deborah K. Sokol
- Department of Neurology, Indiana University School of MedicineIndianapolis, IN, USA
| | - Craig Erickson
- Cincinnati Children’s Hospital Medical CenterCincinnati, OH, USA
| | - Balmiki Ray
- Department of Psychiatry, Indiana University School of MedicineIndianapolis, IN USA
- Institute of Psychiatric Research, Indiana University School of MedicineIndianapolis, IN, USA
| | - Chang Y. Ho
- Department of Radiology and Imaging Sciences, Indiana University School of MedicineIndianapolis, IN, USA
| | - Bryan Maloney
- Department of Psychiatry, Indiana University School of MedicineIndianapolis, IN USA
- Institute of Psychiatric Research, Indiana University School of MedicineIndianapolis, IN, USA
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Flashner BM, Russo ME, Boileau JE, Leong DW, Gallicano GI. Epigenetic factors and autism spectrum disorders. Neuromolecular Med 2013; 15:339-50. [PMID: 23468062 DOI: 10.1007/s12017-013-8222-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 02/13/2013] [Indexed: 12/28/2022]
Abstract
Autism is a complex neurodevelopmental disorder that has significant phenotypic overlap with several diseases, many of which fall within the broader category of autism spectrum disorders (ASDs). The etiology of the disorder is unclear and seems to involve a complex interplay of polygenic as well as environmental factors. We discuss evidence that suggests that epigenetic dysregulation is highly implicated as a contributing cause of ASDs and autism. Specifically, we examine neurodevelopmental disorders that share significant phenotypic overlap with ASDs and feature the dysregulation of epigenetically modified genes including UBE3A, GABA receptor genes, and RELN. We then look at the dysregulated expression of implicated epigenetic modifiers, namely MeCP2, that yield complex and varied downstream pleiotropic effects. Finally, we examine epigenetically mediated parent-of-origin effects through which paternal gene expression dominates that of maternal contributing to contrasting phenotypes implicated in ASDs. Such preliminary evidence suggests that elucidating the complex role of epigenetic regulations involved in ASDs could prove vital in furthering our understanding of the complex etiology of autism and ASDs.
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Affiliation(s)
- Bess M Flashner
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University School of Medicine, 3900 Reservoir Rd. NW, Washington, DC 20057, USA
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38
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Ronchi VP, Klein JM, Haas AL. E6AP/UBE3A ubiquitin ligase harbors two E2~ubiquitin binding sites. J Biol Chem 2013; 288:10349-60. [PMID: 23439649 DOI: 10.1074/jbc.m113.458059] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
By exploiting (125)I-polyubiquitin chain formation as a functional readout of enzyme activity, we have quantitatively examined the mechanism of human E6AP/UBE3A for the first time. Initial rate studies identify UbcH7 as the cognate E2 carrier protein for E6AP, although related Ubc5 isoforms and the ISG15-specific UbcH8 paralog also support E6AP with reduced efficacy due to impaired binding and catalytic competence. Initial rates of polyubiquitin chain formation displayed hyperbolic kinetics with respect to UbcH7 concentration (K(m) = 57.6 ± 5.7 nM and kcat = 0.032 ± 0.001 s(-1)) and substrate inhibition above 2 μM. Competitive inhibition by an isosteric UbcH7C86S-ubiquitin oxyester substrate analog (K(i) = 64 ± 18 nM) demonstrates that Km reflects intrinsic substrate affinity. In contrast, noncompetitive inhibition by a UbcH7C86A product analog (K(i) = 7 ± 0.7 μM) and substrate inhibition at high concentrations require two functionally distinct E2∼ubiquitin substrate binding sites. The kinetics of polyubiquitin chain formation reflect binding at a cryptic Site 1 not previously recognized that catalyzes E6AP∼ubiquitin thioester formation. Subsequent binding of E2∼ubiquitin at the canonical Site 2 present in the extant crystal structure is responsible for polyubiquitin chain elongation. Other rate studies show that the conserved -4 Phe(849) residue is required for polyubiquitin chain formation rather than target protein conjugation as originally suggested. The present studies unambiguously preclude earlier models for the mechanism of Hect domain-catalyzed conjugation through the canonical binding site suggested by the crystal structure and define a novel two-step mechanism for formation of the polyubiquitin degradation signal.
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Affiliation(s)
- Virginia P Ronchi
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans, Louisiana 70112, USA
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39
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Daily J, Smith AG, Weeber EJ. Spatial and temporal silencing of the human maternal UBE3A gene. Eur J Paediatr Neurol 2012; 16:587-91. [PMID: 22560727 PMCID: PMC3419305 DOI: 10.1016/j.ejpn.2012.03.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Revised: 02/10/2012] [Accepted: 03/17/2012] [Indexed: 01/21/2023]
Abstract
Angelman syndrome (AS) is characterized by severe cognitive disruption, seizures, difficulty speaking and ataxia. Nearly all cases are attributed to the disruption or absence of the imprinted maternal copy of UBE3A, transcribing an E3-type ubiquitin ligase. Much of what is known about the molecular and biochemical changes in the CNS associated with AS has been obtained through this murine model. This widely used mouse model created by a null mutation of the maternal UBE3A gene recapitulates the major phenotypes characteristic of AS patients. The imprinting of maternal UBE3A was originally believed to be brain region specific; however recent reports using the AS mouse model have revealed a more wide-spread absence of the protein. The present study is the first to determine that the Ube3a protein ablation seen in the AS mouse model is also characteristic of AS patients and the silencing of the paternal UBE3A allele appears to be lifelong.
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Affiliation(s)
- Jennifer Daily
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, FL, USA
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40
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Understanding the pathogenesis of Angelman syndrome through animal models. Neural Plast 2012; 2012:710943. [PMID: 22830052 PMCID: PMC3399338 DOI: 10.1155/2012/710943] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 05/10/2012] [Accepted: 05/11/2012] [Indexed: 01/08/2023] Open
Abstract
Angelman syndrome (AS) is a neurodevelopmental disorder characterized by severe mental retardation, lack of speech, ataxia, susceptibility to seizures, and unique behavioral features such as easily provoked smiling and laughter and autistic features. The disease is primarily caused by deletion or loss-of-function mutations of the maternally inherited UBE3A gene located within chromosome 15q11-q13. The UBE3A gene encodes a 100 kDa protein that functions as ubiquitin ligase and transcriptional coactivator. Emerging evidence now indicates that UBE3A plays a very important role in synaptic function and in regulation of activity-dependent synaptic plasticity. A number of animal models for AS have been generated to understand the disease pathogenesis. The most widely used model is the UBE3A-maternal-deficient mouse that recapitulates most of the essential features of AS including cognitive and motor abnormalities. This paper mainly discusses various animal models of AS and how these models provide fundamental insight into understanding the disease biology for potential therapeutic intervention.
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Melnyk S, Fuchs GJ, Schulz E, Lopez M, Kahler SG, Fussell JJ, Bellando J, Pavliv O, Rose S, Seidel L, Gaylor DW, James SJ. Metabolic imbalance associated with methylation dysregulation and oxidative damage in children with autism. J Autism Dev Disord 2012; 42:367-77. [PMID: 21519954 DOI: 10.1007/s10803-011-1260-7] [Citation(s) in RCA: 167] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Oxidative stress and abnormal DNA methylation have been implicated in the pathophysiology of autism. We investigated the dynamics of an integrated metabolic pathway essential for cellular antioxidant and methylation capacity in 68 children with autism, 54 age-matched control children and 40 unaffected siblings. The metabolic profile of unaffected siblings differed significantly from case siblings but not from controls. Oxidative protein/DNA damage and DNA hypomethylation (epigenetic alteration) were found in autistic children but not paired siblings or controls. These data indicate that the deficit in antioxidant and methylation capacity is specific for autism and may promote cellular damage and altered epigenetic gene expression. Further, these results suggest a plausible mechanism by which pro-oxidant environmental stressors may modulate genetic predisposition to autism.
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Affiliation(s)
- Stepan Melnyk
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA
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Abstract
Rett syndrome is an X-linked autism-spectrum disorder caused by mutations in MECP2, encoding methyl CpG-binding protein 2. Since the discovery of MECP2 mutations as the genetic cause of Rett syndrome, the understanding of MeCP2 function has evolved. Although MeCP2 was predicted to be a global transcriptional repressor of methylated promoters, large-scale combined epigenomic approaches of MeCP2 binding, methylation and gene expression have demonstrated that MeCP2 binds preferentially to intergenic and intronic regions, and sparsely methylated promoters of active genes. This review compares the evolution of thought within two ‘classic’ epigenetic mechanisms of parental imprinting and X chromosome inactivation to that of the MeCP2 field, and considers the future relevance of integrated epigenomic databases to understanding autism and Rett syndrome.
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Affiliation(s)
- Janine M LaSalle
- Medical Microbiology and Immunology and Rowe Program in Human Genetics, University of California Davis School of Medicine, Davis, CA 95616, USA.
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The Role of Endocrine Disruptors in the Epigenetics of Reproductive Disease and Dysfunction: Potential Relevance to Humans. CURRENT OBSTETRICS AND GYNECOLOGY REPORTS 2012; 1:116-123. [PMID: 24932427 DOI: 10.1007/s13669-012-0014-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In a murine model, we have linked early life toxicant exposure to reduced uterine sensitivity to progesterone, a phenotype we had previously associated with inflammation in endometriosis patients. Subsequent studies revealed that developmental toxicant exposure not only reduces fertility in male and female mice but also negatively impacts pregnancy leading to spontaneous preterm birth (PTB). An epigenetic alteration of the progesterone receptor gene correlated with reduced fertility and adverse pregnancy outcomes and persisted in multiple generations of mice in the absence of an additional toxicant exposure. Gene-environment interactions in women may explain why some patients "at risk" for PTB deliver at term while others without known risks deliver early. Our model provides a unique system to unravel the interactive influences of inflammation and reduced progesterone responsiveness on PTB and suggests that therapy needs to begin prior to pregnancy (and involve both partners) rather than once the inflammatory cascade has been initiated.
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Meng L, Person RE, Beaudet AL. Ube3a-ATS is an atypical RNA polymerase II transcript that represses the paternal expression of Ube3a. Hum Mol Genet 2012; 21:3001-12. [PMID: 22493002 DOI: 10.1093/hmg/dds130] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Angelman syndrome gene, UBE3A, is subject to genomic imprinting controlled by mechanisms that are only partially understood. Its antisense transcript, UBE3A-ATS, is also imprinted and hypothesized to suppress UBE3A in cis. In this research, we showed that the mouse antisense ortholog, Ube3a-ATS, was transcribed by RNA polymerase (RNAP) II. However, unlike typical protein-coding transcripts, Ube3a-ATS was not poly-adenylated and was localized exclusively in the nucleus. It was relatively unstable with a half-life of 4 h, shorter than most protein-coding RNAs tested. To understand the role of Ube3a-ATS in vivo, a mouse model with a 0.9-kb genomic deletion over the paternal Snrpn major promoter was studied. The mice showed partial activation of paternal Ube3a, with decreased expression of Ube3a-ATS but not any imprinting defects in the Prader-Willi syndrome/Angelman syndrome region. A novel cell culture model was also generated with a transcriptional termination cassette inserted downstream of Ube3a on the paternal chromosome to reduce Ube3a-ATS transcription. In neuronally differentiated embryonic stem (ES) cells, paternal Ube3a was found to be expressed at a high level, comparable with that of the maternal allele. To further characterize the antisense RNA, a strand-specific microarray was performed. Ube3a-ATS was detectable across the entire locus of Ube3a and extended beyond the transcriptional start site of Ube3a. In summary, we conclude that Ube3a-ATS is an atypical RNAPII transcript that represses Ube3a on the paternal chromosome. These results suggest that the repression of human UBE3A-ATS may activate the expression of UBE3A from the paternal chromosome, providing a potential therapeutic strategy for patients with Angelman syndrome.
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Affiliation(s)
- Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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45
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Miyake K, Hirasawa T, Koide T, Kubota T. Epigenetics in autism and other neurodevelopmental diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 724:91-8. [PMID: 22411236 DOI: 10.1007/978-1-4614-0653-2_7] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Autism was previously thought to be caused by environmental factors. However, genetic factors are now considered to be more contributory to the pathogenesis of autism, based on the recent findings of mutations in the genes which encode synaptic molecules associated with the communication between neurons. Epigenetic is a mechanism that controls gene expression without changing DNA sequence but by changing chromosomal histone modifications and its abnormality is associated with several neurodevelopmental diseases. Since epigenetic modifications are known to be affected by environmental factors such as nutrition, drugs and mental stress, autistic diseases are not only caused by congenital genetic defects, but may also be caused by environmental factors via epigenetic mechanism. In this chapter, we introduce autistic diseases caused by epigenetic failures and discuss epigenetic changes by environmental factors and discuss new treatments for neurodevelopmental diseases based on the recent epigenetic findings.
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Affiliation(s)
- Kunio Miyake
- Department of Epigenetics Medicine, University of Yamanashi, Yamanashi, Japan
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46
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Abstract
A literature review was conducted on the genetic and developmental bases of autism in relation to genes and pathways associated with cancer risk. Convergent lines of evidence from four types of analysis: (1) recent theoretical studies on the causes of autism, (2) epidemiological studies, (3) genetic analyses linking autism with mutations in tumor suppressor genes and other cancer-associated genes and pathways, and (4) contrasts with schizophrenia, Parkinson's, and Alzheimer's disease indicate that autism may involve altered cancer risk. This evidence should motivate further epidemiological studies, and it provides useful insights into the nature of the genetic, epigenetic, and environmental factors underlying the etiologies of autism, other neurological conditions, and carcinogenesis.
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Affiliation(s)
- B Crespi
- Department of Biological Sciences, Simon Fraser University, Burnaby (B.C.), British Columbia, Canada.
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47
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Meguro-Horike M, Yasui DH, Powell W, Schroeder DI, Oshimura M, Lasalle JM, Horike SI. Neuron-specific impairment of inter-chromosomal pairing and transcription in a novel model of human 15q-duplication syndrome. Hum Mol Genet 2011; 20:3798-810. [PMID: 21725066 DOI: 10.1093/hmg/ddr298] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Although the etiology of autism remains largely unknown, cytogenetic and genetic studies have implicated maternal copy number gains of 15q11-q13 in 1-3% of autism cases. In order to understand how maternal 15q duplication leads to dysregulation of gene expression and altered chromatin interactions, we used microcell-mediated chromosome transfer to generate a novel maternal 15q duplication model in a human neuronal cell line. Our 15q duplication neuronal model revealed that by quantitative RT-PCR, transcript levels of NDN, SNRPN, GABRB3 and CHRNA7 were reduced compared with expected levels despite having no detectable alteration in promoter DNA methylation. Since 15q11-q13 alleles have been previously shown to exhibit homologous pairing in mature human neurons, we assessed homologous pairing of 15q11-q13 by fluorescence in situ hybridization. Homologous pairing of 15q11-q13 was significantly disrupted by 15q duplication. To further understand the extent and mechanism of 15q11-q13 homologous pairing, we mapped the minimal region of homologous pairing to a ∼500 kb region at the 3' end of GABRB3 which contains multiple binding sites for chromatin regulators MeCP2 and CTCF. Both active transcription and the chromatin factors MeCP2 and CTCF are required for the homologous pairing of 15q11-q13 during neuronal maturational differentiation. These data support a model where 15q11-q13 genes are regulated epigenetically at the level of both inter- and intra-chromosomal associations and that chromosome imbalance disrupts the epigenetic regulation of genes in 15q11-q13.
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Affiliation(s)
- Makiko Meguro-Horike
- Frontier Science Organization, Kanazawa University, 13-1 Takaramachi, Kanazawa, Japan.
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Amaral DG. The promise and the pitfalls of autism research: an introductory note for new autism researchers. Brain Res 2011; 1380:3-9. [PMID: 21129367 PMCID: PMC3307796 DOI: 10.1016/j.brainres.2010.11.077] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Revised: 11/07/2010] [Accepted: 11/21/2010] [Indexed: 10/18/2022]
Abstract
The last decade has seen an enormous growth in the quantity of research directed at understanding the biological underpinnings of autism spectrum disorders. This increase has been spurred on, in part, by research funding provided through private, parent advocacy groups. While increased funding and entry into autism research by scientists from many disciplines has facilitated the speed of discoveries germane to establishing the etiologies of autism, there remain a number of roadblocks to understanding autism sufficiently well to foster new treatments. This short article provides a brief overview of some of the achievements and some of the difficulties in conducting autism research.
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Affiliation(s)
- David G Amaral
- Department of Psychiatry and Behavioral Sciences, The MIND Institute, University of California, Davis, Sacramento, CA 95817, USA.
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49
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Peters SU, Bird LM, Kimonis V, Glaze DG, Shinawi LM, Bichell TJ, Barbieri-Welge R, Nespeca M, Anselm I, Waisbren S, Sanborn E, Sun Q, O'Brien WE, Beaudet AL, Bacino CA. Double-blind therapeutic trial in Angelman syndrome using betaine and folic acid. Am J Med Genet A 2010; 152A:1994-2001. [PMID: 20635355 DOI: 10.1002/ajmg.a.33509] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Angelman syndrome (AS) is caused by reduced or absent expression of the maternally inherited ubiquitin protein ligase 3A gene (UBE3A), which maps to chromosome 15q11-q13. UBE3A is subject to genomic imprinting in neurons in most regions of the brain. Expression of UBE3A from the maternal chromosome is essential to prevent AS, because the paternally inherited gene is not expressed, probably mediated by antisense UBE3A RNA. We hypothesized that increasing methylation might reduce expression of the antisense UBE3A RNA, thereby increasing UBE3A expression from the paternal gene and ameliorating the clinical phenotype. We conducted a trial using two dietary supplements, betaine and folic acid to promote global levels of methylation and attempt to activate the paternally inherited UBE3A gene. We performed a number of investigations at regular intervals including general clinical and developmental evaluations, biochemical determinations on blood and urine, and electroencephalographic studies. We report herein the data on 48 children with AS who were enrolled in a double-blind placebo-controlled protocol using betaine and folic acid for 1 year. There were no statistically significant changes between treated and untreated children; however, in a small subset of patients we observed some positive trends.
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Affiliation(s)
- Sarika U Peters
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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Liu X, Solehdin F, Cohen IL, Gonzalez MG, Jenkins EC, Lewis MES, Holden JJA. Population- and Family-Based Studies Associate the MTHFR Gene with Idiopathic Autism in Simplex Families. J Autism Dev Disord 2010; 41:938-44. [DOI: 10.1007/s10803-010-1120-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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