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A comprehensive bioinformatics analysis of circRNA expression in the brain of distinct mouse models of Autism Spectrum Disorder / Guilherme Cordenonsi DA FONSECA ; Carmem GOTTFRIED in Research in Autism Spectrum Disorders, 109 (November 2023)
[article]
Titre : A comprehensive bioinformatics analysis of circRNA expression in the brain of distinct mouse models of Autism Spectrum Disorder Type de document : Texte imprimé et/ou numérique Auteurs : Guilherme Cordenonsi DA FONSECA, Auteur ; Carmem GOTTFRIED, Auteur Article en page(s) : 102261 Langues : Anglais (eng) Mots-clés : Autism spectrum disorder Animal models Circular RNA Bioinformatics NcRNAs Index. décimale : PER Périodiques Résumé : Background Autism Spectrum Disorder (ASD) is a neurodevelopmental condition estimated to affect 1% of individuals worldwide. Its etiology is still not fully understood, but several molecular alterations in ASD are related to noncoding RNAs (ncRNAs). Recently, gene expression of circular RNAs (circRNAs) has been shown to be altered in the brains of autistic individuals and two animal models of ASD. Here we use bioinformatics methods to analyze the gene expression of circRNAs in the brain of six distinct animal models of ASD and identify possible alterations shared between models and between models and humans. Method: six publicly available RNA-Seq data sets were used. CircRNAs were identified by a combination of algorithms using CirComPara2 software. Differentially expressed circRNAs (DECs) were evaluatedwith the Limma Voom method, and the functional profile was evaluated with clusterProfiler. Databases of risk genes and circRNAs altered in ASD were used for translational comparison. Results: We have identified over 130,000 unique circRNAs. DECs per se are shared by a few animal models. However, functional analysis revealed that the DECs from distinct models share a similar profile of changes, mostly related to synaptic structure and function. Regarding translational alterations, around 2% of DECs in mice are orthologous to DECs in autistic individuals. Conclusions: We provide an overview of the expression of circRNAs in mouse models of ASD. The analyses indicate that synaptic circRNAs may be central to the alterations found. We hope the broad identification of circRNAs can help researchers further explore their selected mouse models. En ligne : https://doi.org/10.1016/j.rasd.2023.102261 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=517
in Research in Autism Spectrum Disorders > 109 (November 2023) . - 102261[article] A comprehensive bioinformatics analysis of circRNA expression in the brain of distinct mouse models of Autism Spectrum Disorder [Texte imprimé et/ou numérique] / Guilherme Cordenonsi DA FONSECA, Auteur ; Carmem GOTTFRIED, Auteur . - 102261.
Langues : Anglais (eng)
in Research in Autism Spectrum Disorders > 109 (November 2023) . - 102261
Mots-clés : Autism spectrum disorder Animal models Circular RNA Bioinformatics NcRNAs Index. décimale : PER Périodiques Résumé : Background Autism Spectrum Disorder (ASD) is a neurodevelopmental condition estimated to affect 1% of individuals worldwide. Its etiology is still not fully understood, but several molecular alterations in ASD are related to noncoding RNAs (ncRNAs). Recently, gene expression of circular RNAs (circRNAs) has been shown to be altered in the brains of autistic individuals and two animal models of ASD. Here we use bioinformatics methods to analyze the gene expression of circRNAs in the brain of six distinct animal models of ASD and identify possible alterations shared between models and between models and humans. Method: six publicly available RNA-Seq data sets were used. CircRNAs were identified by a combination of algorithms using CirComPara2 software. Differentially expressed circRNAs (DECs) were evaluatedwith the Limma Voom method, and the functional profile was evaluated with clusterProfiler. Databases of risk genes and circRNAs altered in ASD were used for translational comparison. Results: We have identified over 130,000 unique circRNAs. DECs per se are shared by a few animal models. However, functional analysis revealed that the DECs from distinct models share a similar profile of changes, mostly related to synaptic structure and function. Regarding translational alterations, around 2% of DECs in mice are orthologous to DECs in autistic individuals. Conclusions: We provide an overview of the expression of circRNAs in mouse models of ASD. The analyses indicate that synaptic circRNAs may be central to the alterations found. We hope the broad identification of circRNAs can help researchers further explore their selected mouse models. En ligne : https://doi.org/10.1016/j.rasd.2023.102261 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=517 Annual Research Review: Threats to the validity of child psychiatry and psychology / Michael RUTTER in Journal of Child Psychology and Psychiatry, 57-3 (March 2016)
[article]
Titre : Annual Research Review: Threats to the validity of child psychiatry and psychology Type de document : Texte imprimé et/ou numérique Auteurs : Michael RUTTER, Auteur ; Andrew PICKLES, Auteur Article en page(s) : p.398-416 Langues : Anglais (eng) Mots-clés : Classification diagnosis genetics epigenetics bioinformatics brain imaging biomarkers neural networks Index. décimale : PER Périodiques Résumé : Background Suggestions have been made that many claims concern false-positive findings in the field of child psychology and psychiatry. Findings The literature was searched for concepts and findings on the validity of child psychiatry and psychology. Substantial progress has been made in some, but not all, areas and considerable challenges remain in all. Conclusions The two major threats to validity concern the inability to examine brain tissues in life and the evidence that there is a high overlap among disorders. We emphasize the need to follow published guidelines on preplanned analyses and we note the dangers associated with unregulated flexibility in data analysis. We note the very important clinical and developmental findings that have been ignored, perhaps partly because of an excessive focus on technologies. Nevertheless, we are positive about both the accomplishments and the ways in which challenges are being met. En ligne : http://dx.doi.org/10.1111/jcpp.12461 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=282
in Journal of Child Psychology and Psychiatry > 57-3 (March 2016) . - p.398-416[article] Annual Research Review: Threats to the validity of child psychiatry and psychology [Texte imprimé et/ou numérique] / Michael RUTTER, Auteur ; Andrew PICKLES, Auteur . - p.398-416.
Langues : Anglais (eng)
in Journal of Child Psychology and Psychiatry > 57-3 (March 2016) . - p.398-416
Mots-clés : Classification diagnosis genetics epigenetics bioinformatics brain imaging biomarkers neural networks Index. décimale : PER Périodiques Résumé : Background Suggestions have been made that many claims concern false-positive findings in the field of child psychology and psychiatry. Findings The literature was searched for concepts and findings on the validity of child psychiatry and psychology. Substantial progress has been made in some, but not all, areas and considerable challenges remain in all. Conclusions The two major threats to validity concern the inability to examine brain tissues in life and the evidence that there is a high overlap among disorders. We emphasize the need to follow published guidelines on preplanned analyses and we note the dangers associated with unregulated flexibility in data analysis. We note the very important clinical and developmental findings that have been ignored, perhaps partly because of an excessive focus on technologies. Nevertheless, we are positive about both the accomplishments and the ways in which challenges are being met. En ligne : http://dx.doi.org/10.1111/jcpp.12461 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=282 Germ-cell-specific transcriptome analysis illuminates the chromatin and ubiquitin pathway in autism spectrum disorders / Sawako Furukawa in Autism Research, 16-6 (June 2023)
[article]
Titre : Germ-cell-specific transcriptome analysis illuminates the chromatin and ubiquitin pathway in autism spectrum disorders Type de document : Texte imprimé et/ou numérique Auteurs : Sawako Furukawa, Auteur ; Jun NOMURA, Auteur ; Hiroaki Hanafusa, Auteur ; Hiroko Maegawa, Auteur ; Toru TAKUMI, Auteur Article en page(s) : p.1101-1110 Langues : Anglais (eng) Mots-clés : autism spectrum disorder bioinformatics copy number variants embryonic stem cells germ cells single-cell analysis Index. décimale : PER Périodiques Résumé : Abstract Accumulating epidemiological studies have suggested a positive association between advanced paternal age at conception and the increased risk of neurodevelopmental outcomes such as autism spectrum disorder (ASD) in their children. Recent biological studies using human sperm have identified increased de novo mutations in aged fathers, and hyper- or hypomethylation has been identified in the sperm from aged rodents. Dysregulation of DNA methylation in sperm may explain the transgenerational effects on the pathogenesis of ASD. However, compared to these epigenetic changes in the sperm of aged males, the effects of inherited predisposition from germ cells are largely unknown. Here, we use single-cell transcriptome data sets from 13 cell lines, including 12 ASD-associated CNVs models and control, that are performed neural differentiation from mouse embryonic stem cells. This study performed comprehensive bioinformatic analyses such as gene ontology (GO), network, pathway, and upstream regulator analyses. Through these analyses, we identify several susceptible pathways, such as chromatin and ubiquitin, in addition to translational and oxidative phosphorylation. Our results suggest that dysregulation of epigenetic chromosome remodeling and ubiquitin-proteasome pathway in the germ cell is a possible modulator for subsequent differentiated cells, sperm, and egg, as a risk factor for the neurodevelopmental disorder. En ligne : https://doi.org/10.1002/aur.2939 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=507
in Autism Research > 16-6 (June 2023) . - p.1101-1110[article] Germ-cell-specific transcriptome analysis illuminates the chromatin and ubiquitin pathway in autism spectrum disorders [Texte imprimé et/ou numérique] / Sawako Furukawa, Auteur ; Jun NOMURA, Auteur ; Hiroaki Hanafusa, Auteur ; Hiroko Maegawa, Auteur ; Toru TAKUMI, Auteur . - p.1101-1110.
Langues : Anglais (eng)
in Autism Research > 16-6 (June 2023) . - p.1101-1110
Mots-clés : autism spectrum disorder bioinformatics copy number variants embryonic stem cells germ cells single-cell analysis Index. décimale : PER Périodiques Résumé : Abstract Accumulating epidemiological studies have suggested a positive association between advanced paternal age at conception and the increased risk of neurodevelopmental outcomes such as autism spectrum disorder (ASD) in their children. Recent biological studies using human sperm have identified increased de novo mutations in aged fathers, and hyper- or hypomethylation has been identified in the sperm from aged rodents. Dysregulation of DNA methylation in sperm may explain the transgenerational effects on the pathogenesis of ASD. However, compared to these epigenetic changes in the sperm of aged males, the effects of inherited predisposition from germ cells are largely unknown. Here, we use single-cell transcriptome data sets from 13 cell lines, including 12 ASD-associated CNVs models and control, that are performed neural differentiation from mouse embryonic stem cells. This study performed comprehensive bioinformatic analyses such as gene ontology (GO), network, pathway, and upstream regulator analyses. Through these analyses, we identify several susceptible pathways, such as chromatin and ubiquitin, in addition to translational and oxidative phosphorylation. Our results suggest that dysregulation of epigenetic chromosome remodeling and ubiquitin-proteasome pathway in the germ cell is a possible modulator for subsequent differentiated cells, sperm, and egg, as a risk factor for the neurodevelopmental disorder. En ligne : https://doi.org/10.1002/aur.2939 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=507