Integrated analysis of whole-exome sequencing and transcriptome profiling in males with autism spectrum disorders

BACKGROUND: Autism spectrum disorders (ASD) are a group of neurodevelopmental disorders with high heritability. Recent findings support a highly heterogeneous and complex genetic etiology including rare de novo and inherited mutations or chromosomal rearrangements as well as double or multiple hits. METHODS: We performed whole-exome sequencing (WES) and blood cell transcriptome by RNAseq in a subset of male patients with idiopathic ASD (n = 36) in order to identify causative genes, transcriptomic alterations, and susceptibility variants. RESULTS: We detected likely monogenic causes in seven cases: five de novo (SCN2A, MED13L, KCNV1, CUL3, and PTEN) and two inherited X-linked variants (MAOA and CDKL5). Transcriptomic analyses allowed the identification of intronic causative mutations missed by the usual filtering of WES and revealed functional consequences of some rare mutations. These included aberrant transcripts (PTEN, POLR3C), deregulated expression in 1.7% of mutated genes (that is, SEMA6B, MECP2, ANK3, CREBBP), allele-specific expression (FUS, MTOR, TAF1C), and non-sense-mediated decay (RIT1, ALG9). The analysis of rare inherited variants showed enrichment in relevant pathways such as the PI3K-Akt signaling and the axon guidance. CONCLUSIONS: Integrative analysis of WES and blood RNAseq data has proven to be an efficient strategy to identify likely monogenic forms of ASD (19% in our cohort), as well as additional rare inherited mutations that can contribute to ASD risk in a multifactorial manner. Blood transcriptomic data, besides validating 88% of expressed variants, allowed the identification of missed intronic mutations and revealed functional correlations of genetic variants, including changes in splicing, expression levels, and allelic expression. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13229-015-0017-0) contains supplementary material, which is available to authorized users

Epigenetic alterations in autism spectrum disorders (ASD)

The aetiology of autism spectrum disorders (ASD), a group of neurodevelopmental conditions with early onset, characterized by social and communication impairment and restricted interests, is unknown in about a third of the patients. The intense research done over the past decade has revealed a genetic contribution, while the epigenetic contribution barely begins to show. The epigenetic marks can exert an effect in gene expression without altering the underlying genetic sequence. In turn, these marks can be impaired by genetic mutations in their target sequence. Therefore, research in genomic, epigenomic and transcriptomic fields will provide convergent information to unravel the causes of ASD, necessary to establish improved diagnostic protocols and therapeutic strategies, allowing an earlier diagnosis and personalized treatment crucial for a better prognosis. Our data reveal variants associated to the phenotype which shows genetic-epigenetic interplay along with gene expression consequences. It also reveals region epigenetic variants, which follow a polygenic or complex model. Finally, we found ASD genotype-specific epigenetic marks. In the future, the progress in cost-efficiency technologies assessing epigenomics, and the availability of a reference epigenome in various tissues and cell types will provide the background to set a step-forward in establishing the developmental stage, cell types and tissues involved in the epigenetic mechanisms of the disorder.L'etiologia dels trastorns de l'espectre autista (TEA), un grup de malalties del neurodesenvolupament d’aparició primerenca caracteritzades per problemes de comunicació, relació social, i per la presencia d’interessos restringits, és desconeguda per un terç dels individus afectats. La intensa investigació feta durant l'última dècada ha revelat una gran contribució genètica en aquesta malaltia, mentre que de l’epigenètica tot just es comença a evidenciar. Les marques epigenètiques, sense alterar la seqüència genètica subjacent, tenen un efecte en l'expressió dels gens. A la vegada, aquestes marques epigenètiques es poden veure afectades per mutacions genètiques a la seqüència. Així doncs, la recerca en genòmica, epigenòmica i transcriptòmica proporcionarà informació convergent per determinar les causes dels TEA, indispensable per establir millores en els protocols de diagnòstic i en estratègies terapèutiques, facilitant el diagnòstic precoç i el tractament personalitzat, crucial per a un millor pronòstic. Les nostres dades mostren que hi ha alteracions genètiques i epigenètiques associades al fenotip, que interactuen i tenen conseqüències sobre l’expressió gènica. També hem trobat regions amb alteracions epigenètiques, que sembla que contribueixen de manera additiva i seguint un model complex. Finalment, trobem marques epigenètiques específiques de grups de genotips TEA. En el futur, la millora de les tecnologies disponibles per avaluar l’epigenòmica, i la disponibilitat d'un epigenoma de referència en diversos teixits i tipus cel•lulars, serviran com a base per fer un pas cap endavant en l'establiment de l’etapa del desenvolupament, dels tipus cel•lulars i els teixits involucrats en els mecanismes epigenètics del trastorn

DNA methylation abnormalities in congenital heart disease

Congenital heart defects represent the most common malformation at birth, occurring also in ∼50% of individuals with Down syndrome. Congenital heart defects are thought to have multifactorial etiology, but the main causes are largely unknown. We have explored the global methylation profile of fetal heart DNA in comparison to blood DNA from control subjects: an absolute correlation with the type of tissue was detected. Pathway analysis revealed a significant enrichment of differential methylation at genes related to muscle contraction and cardiomyopathies in the developing heart DNA. We have also searched for abnormal methylation profiles on developing heart-tissue DNA of syndromic and non-syndromic congenital heart defects. On average, 3 regions with aberrant methylation were detected per sample and 18 regions were found differentially methylated between groups. Several epimutations were detected in candidate genes involved in growth regulation, apoptosis and folate pathway. A likely pathogenic hypermethylation of several intragenic sites at the MSX1 gene, involved in outflow tract morphogenesis, was found in a fetus with isolated heart malformation. In addition, hypermethylation of the GATA4 gene was present in fetuses with Down syndrome with or without congenital heart defects, as well as in fetuses with isolated heart malformations. Expression deregulation of the abnormally methylated genes was detected. Our data indicate that epigenetic alterations of relevant genes are present in developing heart DNA in fetuses with both isolated and syndromic heart malformations. These epimutations likely contribute to the pathogenesis of the malformation by cis-acting effects on gene expression.This work was supported by grants of the Spanish Fondo de Investigación Sanitaria of the Ministry of Economy and Competitiveness and FEDER funds [FIS PI10/2512 and PI13/2812], an intramural project of the CIBERER, the Catalan Government [SGR2009/1274, SGR2014/1468 and ICREA Acadèmia] and a predoctoral fellowship of the Fondo de Investigación Sanitaria [FIS FI08/00365] to CS-J

DNA methylation abnormalities in congenital heart disease

Congenital heart defects represent the most common malformation at birth, occurring also in ∼50% of individuals with Down syndrome. Congenital heart defects are thought to have multifactorial etiology, but the main causes are largely unknown. We have explored the global methylation profile of fetal heart DNA in comparison to blood DNA from control subjects: an absolute correlation with the type of tissue was detected. Pathway analysis revealed a significant enrichment of differential methylation at genes related to muscle contraction and cardiomyopathies in the developing heart DNA. We have also searched for abnormal methylation profiles on developing heart-tissue DNA of syndromic and non-syndromic congenital heart defects. On average, 3 regions with aberrant methylation were detected per sample and 18 regions were found differentially methylated between groups. Several epimutations were detected in candidate genes involved in growth regulation, apoptosis and folate pathway. A likely pathogenic hypermethylation of several intragenic sites at the MSX1 gene, involved in outflow tract morphogenesis, was found in a fetus with isolated heart malformation. In addition, hypermethylation of the GATA4 gene was present in fetuses with Down syndrome with or without congenital heart defects, as well as in fetuses with isolated heart malformations. Expression deregulation of the abnormally methylated genes was detected. Our data indicate that epigenetic alterations of relevant genes are present in developing heart DNA in fetuses with both isolated and syndromic heart malformations. These epimutations likely contribute to the pathogenesis of the malformation by cis-acting effects on gene expression.This work was supported by grants of the Spanish Fondo de Investigación Sanitaria of the Ministry of Economy and Competitiveness and FEDER funds [FIS PI10/2512 and PI13/2812], an intramural project of the CIBERER, the Catalan Government [SGR2009/1274, SGR2014/1468 and ICREA Acadèmia] and a predoctoral fellowship of the Fondo de Investigación Sanitaria [FIS FI08/00365] to CS-J

Genetic and epigenetic methylation defects and implication of the ERMN gene in autism spectrum disorders.

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.The funding source for the study was received from the Spanish Ministry of Economy and Competitivity (FIS PI1002512, PI1302481 and PI1300823 co-financed by FEDER), Fundación Alicia Koplowitz, Generalitat de Catalunya (2014SGR1468), and Fundación Ramón Areces. AH had a predoctoral fellowship of Ministry of Education, Culture and Sport (FPU AP2009-4795)

Integrated analysis of whole-exome sequencing and transcriptome profiling in males with autism spectrum disorders.

BACKGROUND: Autism spectrum disorders (ASD) are a group of neurodevelopmental disorders with high heritability. Recent findings support a highly heterogeneous and complex genetic etiology including rare de novo and inherited mutations or chromosomal rearrangements as well as double or multiple hits. METHODS: We performed whole-exome sequencing (WES) and blood cell transcriptome by RNAseq in a subset of male patients with idiopathic ASD (n = 36) in order to identify causative genes, transcriptomic alterations, and susceptibility variants. RESULTS: We detected likely monogenic causes in seven cases: five de novo (SCN2A, MED13L, KCNV1, CUL3, and PTEN) and two inherited X-linked variants (MAOA and CDKL5). Transcriptomic analyses allowed the identification of intronic causative mutations missed by the usual filtering of WES and revealed functional consequences of some rare mutations. These included aberrant transcripts (PTEN, POLR3C), deregulated expression in 1.7% of mutated genes (that is, SEMA6B, MECP2, ANK3, CREBBP), allele-specific expression (FUS, MTOR, TAF1C), and non-sense-mediated decay (RIT1, ALG9). The analysis of rare inherited variants showed enrichment in relevant pathways such as the PI3K-Akt signaling and the axon guidance. CONCLUSIONS: Integrative analysis of WES and blood RNAseq data has proven to be an efficient strategy to identify likely monogenic forms of ASD (19% in our cohort), as well as additional rare inherited mutations that can contribute to ASD risk in a multifactorial manner. Blood transcriptomic data, besides validating 88% of expressed variants, allowed the identification of missed intronic mutations and revealed functional correlations of genetic variants, including changes in splicing, expression levels, and allelic expression.This work was funded by grants from the Spanish Ministry of Health (FIS PI1002512, PI1302481, and PI1300823 cofunded by FEDER), Fundación Alicia Koplowitz and Generalitat de Catalunya (2014SGR1468). The ‘Medical Genome Project’ is a joint initiative of the Consejería de Salud de la Junta de Andalucía and Roche, supported by the ‘Programa Nacional de Proyectos de investigación Aplicada’, I + D + i 2008, ‘Subprograma de actuaciones Científicas y Tecnológicas en Parques Científicos y Tecnológicos’ (ACTEPARQ 2009) and FEDER. The CIBER de Enfermedades Raras is an initiative of the ISCIII. CDTI FEDER-Innterconecta EXP00052887/ITC-20111037

Integrated analysis of whole-exome sequencing and transcriptome profiling in males with autism spectrum disorders.

BACKGROUND: Autism spectrum disorders (ASD) are a group of neurodevelopmental disorders with high heritability. Recent findings support a highly heterogeneous and complex genetic etiology including rare de novo and inherited mutations or chromosomal rearrangements as well as double or multiple hits. METHODS: We performed whole-exome sequencing (WES) and blood cell transcriptome by RNAseq in a subset of male patients with idiopathic ASD (n = 36) in order to identify causative genes, transcriptomic alterations, and susceptibility variants. RESULTS: We detected likely monogenic causes in seven cases: five de novo (SCN2A, MED13L, KCNV1, CUL3, and PTEN) and two inherited X-linked variants (MAOA and CDKL5). Transcriptomic analyses allowed the identification of intronic causative mutations missed by the usual filtering of WES and revealed functional consequences of some rare mutations. These included aberrant transcripts (PTEN, POLR3C), deregulated expression in 1.7% of mutated genes (that is, SEMA6B, MECP2, ANK3, CREBBP), allele-specific expression (FUS, MTOR, TAF1C), and non-sense-mediated decay (RIT1, ALG9). The analysis of rare inherited variants showed enrichment in relevant pathways such as the PI3K-Akt signaling and the axon guidance. CONCLUSIONS: Integrative analysis of WES and blood RNAseq data has proven to be an efficient strategy to identify likely monogenic forms of ASD (19% in our cohort), as well as additional rare inherited mutations that can contribute to ASD risk in a multifactorial manner. Blood transcriptomic data, besides validating 88% of expressed variants, allowed the identification of missed intronic mutations and revealed functional correlations of genetic variants, including changes in splicing, expression levels, and allelic expression.This work was funded by grants from the Spanish Ministry of Health (FIS PI1002512, PI1302481, and PI1300823 cofunded by FEDER), Fundación Alicia Koplowitz and Generalitat de Catalunya (2014SGR1468). The ‘Medical Genome Project’ is a joint initiative of the Consejería de Salud de la Junta de Andalucía and Roche, supported by the ‘Programa Nacional de Proyectos de investigación Aplicada’, I + D + i 2008, ‘Subprograma de actuaciones Científicas y Tecnológicas en Parques Científicos y Tecnológicos’ (ACTEPARQ 2009) and FEDER. The CIBER de Enfermedades Raras is an initiative of the ISCIII. CDTI FEDER-Innterconecta EXP00052887/ITC-20111037