2 recherche sur le mot-clé 'gene set enrichment analysis'

Integrative analysis of transcriptome-wide association study and mRNA expression profiles identifies candidate genes associated with autism spectrum disorders / Hong HUANG in Autism Research, 12-1 (January 2019)  

Public ISBD [article]  inAutism Research > 12-1 (January 2019) . - p.33-38 Titre : Integrative analysis of transcriptome-wide association study and mRNA expression profiles identifies candidate genes associated with autism spectrum disorders Type de document : texte imprimé Auteurs : Hong HUANG, Auteur ; Shiqiang CHENG, Auteur ; Miao DING, Auteur ; Yan WEN, Auteur ; Mei MA, Auteur ; Liang ZHANG, Auteur ; Pengli LI, Auteur ; Bastian CHENG, Auteur ; Xingmei LIANG, Auteur ; Li LIU, Auteur ; Yanan DU, Auteur ; Yan ZHAO, Auteur ; Om Prakash KAFLE, Auteur ; Bei HAN, Auteur ; Feng ZHANG, Auteur Article en page(s) : p.33-38 Langues : Anglais (eng) Mots-clés : autism spectrum disorders  gene set enrichment analysis  mRNA expression profiles  transcriptome-wide association study Index. décimale : PER Périodiques Résumé : Autism spectrum disorders (ASD) are a group of highly heritable psychiatric syndromes with high prevalence. The genetic mechanism of ASD remains elusive now. Here we conducted a transcriptome-wide association study (TWAS) of ASD. The GWAS summary data of ASD was driven from the Psychiatric Genomics Consortium (PGC) portal, totally involving 5,305 ASD cases and 5,305 controls. FUSION software was applied to the GWAS summary data for tissue-related TWAS of ASD considering brain and blood. The ASD associated genes identified by TWAS were further validated by mRNA expression profiling of ASD and the Simons Foundation for Autism Research (SFARI) Gene tool. DAVID 6.8 was used to perform gene ontology (GO) enrichment analysis of ASD associated genes identified by TWAS. TWAS identified 85 genes with TWAS P value <0.05 for ASD. Further comparing the 85 genes with the differentially expressed genes identified by mRNA expression profiling of ASD patients found 5 overlapped genes, including MUTYH (PTWAS = 0.0460, PmRNA = 0.0040), ARHGAP27 (PTWAS = 0.0100, PmRNA = 0.0016), GCA (PTWAS = 0.0480, PmRNA = 0.0063), CCDC14 (PTWAS = 0.0067, PmRNA = 0.0035), and MED15 (PTWAS = 0.0324, PmRNA = 0.0092). Gene Ontology (GO) enrichment analysis of the genes identified by TWAS detected 10 significant GO terms, such as mitochondrion (P = 0.0051), NAD or NADH binding (P = 0.0169), mitochondrial part (P = 0.0386) and 2-oxoglutarate metabolic process (P = 0.0399). In conclusion, this study identified multiple ASD associated genes and gene sets, providing novel clues for revealing the pathogenesis of ASD. Autism Research 2019, 12: 33-38. (c) 2018 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY: Recent genetic studies of autism spectrum disorders (ASD) have found multiple ASD related genes. However, the results of these studies were hardly replicated with each other, providing limited clues for exploring the genetic mechanism of ASD. This study detected a group of candidate genes showing transcriptome-wide associations with ASD. These results may provide novel clues for revealing the pathogenesis of ASD. En ligne : http://dx.doi.org/10.1002/aur.2048 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=376 [article] Integrative analysis of transcriptome-wide association study and mRNA expression profiles identifies candidate genes associated with autism spectrum disorders [texte imprimé] / Hong HUANG, Auteur ; Shiqiang CHENG, Auteur ; Miao DING, Auteur ; Yan WEN, Auteur ; Mei MA, Auteur ; Liang ZHANG, Auteur ; Pengli LI, Auteur ; Bastian CHENG, Auteur ; Xingmei LIANG, Auteur ; Li LIU, Auteur ; Yanan DU, Auteur ; Yan ZHAO, Auteur ; Om Prakash KAFLE, Auteur ; Bei HAN, Auteur ; Feng ZHANG, Auteur . - p.33-38. Langues : Anglais (eng) in Autism Research > 12-1 (January 2019) . - p.33-38 Mots-clés : autism spectrum disorders  gene set enrichment analysis  mRNA expression profiles  transcriptome-wide association study Index. décimale : PER Périodiques Résumé : Autism spectrum disorders (ASD) are a group of highly heritable psychiatric syndromes with high prevalence. The genetic mechanism of ASD remains elusive now. Here we conducted a transcriptome-wide association study (TWAS) of ASD. The GWAS summary data of ASD was driven from the Psychiatric Genomics Consortium (PGC) portal, totally involving 5,305 ASD cases and 5,305 controls. FUSION software was applied to the GWAS summary data for tissue-related TWAS of ASD considering brain and blood. The ASD associated genes identified by TWAS were further validated by mRNA expression profiling of ASD and the Simons Foundation for Autism Research (SFARI) Gene tool. DAVID 6.8 was used to perform gene ontology (GO) enrichment analysis of ASD associated genes identified by TWAS. TWAS identified 85 genes with TWAS P value <0.05 for ASD. Further comparing the 85 genes with the differentially expressed genes identified by mRNA expression profiling of ASD patients found 5 overlapped genes, including MUTYH (PTWAS = 0.0460, PmRNA = 0.0040), ARHGAP27 (PTWAS = 0.0100, PmRNA = 0.0016), GCA (PTWAS = 0.0480, PmRNA = 0.0063), CCDC14 (PTWAS = 0.0067, PmRNA = 0.0035), and MED15 (PTWAS = 0.0324, PmRNA = 0.0092). Gene Ontology (GO) enrichment analysis of the genes identified by TWAS detected 10 significant GO terms, such as mitochondrion (P = 0.0051), NAD or NADH binding (P = 0.0169), mitochondrial part (P = 0.0386) and 2-oxoglutarate metabolic process (P = 0.0399). In conclusion, this study identified multiple ASD associated genes and gene sets, providing novel clues for revealing the pathogenesis of ASD. Autism Research 2019, 12: 33-38. (c) 2018 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY: Recent genetic studies of autism spectrum disorders (ASD) have found multiple ASD related genes. However, the results of these studies were hardly replicated with each other, providing limited clues for exploring the genetic mechanism of ASD. This study detected a group of candidate genes showing transcriptome-wide associations with ASD. These results may provide novel clues for revealing the pathogenesis of ASD. En ligne : http://dx.doi.org/10.1002/aur.2048 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=376

Prospective association of the infant gut microbiome with social behaviors in the ECHO consortium / Hannah E. LAUE in Molecular Autism, 15 (2024)  

Public ISBD [article]  inMolecular Autism > 15 (2024) . - 21p. Titre : Prospective association of the infant gut microbiome with social behaviors in the ECHO consortium Type de document : texte imprimé Auteurs : Hannah E. LAUE, Auteur ; Kevin S. BONHAM, Auteur ; Modupe O. COKER, Auteur ; Yuka MOROISHI, Auteur ; Wimal PATHMASIRI, Auteur ; Susan MCRITCHIE, Auteur ; Susan SUMNER, Auteur ; Anne G. HOEN, Auteur ; Margaret R. KARAGAS, Auteur ; Vanja KLEPAC-CERAJ, Auteur ; Juliette C. MADAN, Auteur Article en page(s) : 21p. Langues : Anglais (eng) Mots-clés : Humans  Gastrointestinal Microbiome  Female  Male  Infant  Feces/microbiology  Social Behavior  Prospective Studies  Child, Preschool  Autism Spectrum Disorder/microbiology  Autism  Gene set enrichment analysis  Gut metagenome  Microbiome  Social behavior  funder had no role in (1) the study design, (2) data collection, analysis, or  interpretation, 3) writing the report, 4) the decision to submit the manuscript  for publication. The content is solely the responsibility of the authors and does  not necessarily represent the official views of the National Institutes of  Health. HEL, KSB, MOC, YM, MRK, VKC, and JCM wrote the first draft of the  manuscript. No authors received an honorarium, grant, or other form of payment to  produce the manuscript. Index. décimale : PER Périodiques Résumé : BACKGROUND: Identifying modifiable risk factors of autism spectrum disorders (ASDs) may inform interventions to reduce financial burden. The infant/toddler gut microbiome is one such feature that has been associated with social behaviors, but results vary between cohorts. We aimed to identify consistent overall and sex-specific associations between the early-life gut microbiome and autism-related behaviors. METHODS: Utilizing the Environmental influences on Children Health Outcomes (ECHO) consortium of United States (U.S.) pediatric cohorts, we gathered data on 304 participants with fecal metagenomic sequencing between 6-weeks to 2-years postpartum (481 samples). ASD-related social development was assessed with the Social Responsiveness Scale (SRS-2). Linear regression, PERMANOVA, and Microbiome Multivariable Association with Linear Models (MaAsLin2) were adjusted for sociodemographic factors. Stratified models estimated sex-specific effects. RESULTS: Genes encoding pathways for synthesis of short-chain fatty acids were associated with higher SRS-2 scores, indicative of ASDs. Fecal concentrations of butyrate were also positively associated with ASD-related SRS-2 scores, some of which may be explained by formula use. LIMITATIONS: The distribution of age at outcome assessment differed in the cohorts included, potentially limiting comparability between cohorts. Stool sample collection methods also differed between cohorts. Our study population reflects the general U.S. population, and thus includes few participants who met the criteria for being at high risk of developing ASD. CONCLUSIONS: Our study is among the first multicenter studies in the U.S. to describe prospective microbiome development from infancy in relation to neurodevelopment associated with ASDs. Our work contributes to clarifying which microbial features associate with subsequent diagnosis of neuropsychiatric outcomes. This will allow for future interventional research targeting the microbiome to change neurodevelopmental trajectories. En ligne : https://dx.doi.org/10.1186/s13229-024-00597-2 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=538 [article] Prospective association of the infant gut microbiome with social behaviors in the ECHO consortium [texte imprimé] / Hannah E. LAUE, Auteur ; Kevin S. BONHAM, Auteur ; Modupe O. COKER, Auteur ; Yuka MOROISHI, Auteur ; Wimal PATHMASIRI, Auteur ; Susan MCRITCHIE, Auteur ; Susan SUMNER, Auteur ; Anne G. HOEN, Auteur ; Margaret R. KARAGAS, Auteur ; Vanja KLEPAC-CERAJ, Auteur ; Juliette C. MADAN, Auteur . - 21p. Langues : Anglais (eng) in Molecular Autism > 15 (2024) . - 21p. Mots-clés : Humans  Gastrointestinal Microbiome  Female  Male  Infant  Feces/microbiology  Social Behavior  Prospective Studies  Child, Preschool  Autism Spectrum Disorder/microbiology  Autism  Gene set enrichment analysis  Gut metagenome  Microbiome  Social behavior  funder had no role in (1) the study design, (2) data collection, analysis, or  interpretation, 3) writing the report, 4) the decision to submit the manuscript  for publication. The content is solely the responsibility of the authors and does  not necessarily represent the official views of the National Institutes of  Health. HEL, KSB, MOC, YM, MRK, VKC, and JCM wrote the first draft of the  manuscript. No authors received an honorarium, grant, or other form of payment to  produce the manuscript. Index. décimale : PER Périodiques Résumé : BACKGROUND: Identifying modifiable risk factors of autism spectrum disorders (ASDs) may inform interventions to reduce financial burden. The infant/toddler gut microbiome is one such feature that has been associated with social behaviors, but results vary between cohorts. We aimed to identify consistent overall and sex-specific associations between the early-life gut microbiome and autism-related behaviors. METHODS: Utilizing the Environmental influences on Children Health Outcomes (ECHO) consortium of United States (U.S.) pediatric cohorts, we gathered data on 304 participants with fecal metagenomic sequencing between 6-weeks to 2-years postpartum (481 samples). ASD-related social development was assessed with the Social Responsiveness Scale (SRS-2). Linear regression, PERMANOVA, and Microbiome Multivariable Association with Linear Models (MaAsLin2) were adjusted for sociodemographic factors. Stratified models estimated sex-specific effects. RESULTS: Genes encoding pathways for synthesis of short-chain fatty acids were associated with higher SRS-2 scores, indicative of ASDs. Fecal concentrations of butyrate were also positively associated with ASD-related SRS-2 scores, some of which may be explained by formula use. LIMITATIONS: The distribution of age at outcome assessment differed in the cohorts included, potentially limiting comparability between cohorts. Stool sample collection methods also differed between cohorts. Our study population reflects the general U.S. population, and thus includes few participants who met the criteria for being at high risk of developing ASD. CONCLUSIONS: Our study is among the first multicenter studies in the U.S. to describe prospective microbiome development from infancy in relation to neurodevelopment associated with ASDs. Our work contributes to clarifying which microbial features associate with subsequent diagnosis of neuropsychiatric outcomes. This will allow for future interventional research targeting the microbiome to change neurodevelopmental trajectories. En ligne : https://dx.doi.org/10.1186/s13229-024-00597-2 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=538