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Epigenome analysis of autism spectrum disorder samples

ABSTRACT: The aim of this study was to identify ASD vulnerability components, explore possible vulnerability subgroups, and evaluate environmental contribution to phenotypic variability. We performed PCA and cluster analysis using ASD risk factor data. We found that PC1 had a higher correlation with psychosocial stress (maternal stress, maternal education, and social class), and PC2 a higher correlation with biological factors (Psychiatric Family History and Gestational Complications). Clustering analysis of PCA scores using bootstrap approach showed two clusters. Comparing the methylome between clusters we found 11.879 DMPs (p<0.05), and their CpG sites were enriched in VMRs, most showing environmental and genetic influences. Hypermethylated probes presented higher rates in different regulatory regions associated with functional SNPs, indicating that the subgroups may have different affected regulatory regions and their liability to disease explained by common variations. Vulnerability score moderated by epigenetic clock was associated with Vineland Total score (p=0.0036, adjR2=0.31), suggesting risk factors with stress burden can influence phenotype.

ORGANISM(S): Homo sapiens

PROVIDER: GSE164563 | GEO | 2021/10/01

REPOSITORIES: GEO

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Project description:Autism spectrum disorders (ASD) are neurodevelopmental disorders characterized by delayed/abnormal language development, deficits in social interaction, repetitive behaviors and restricted interests. The heterogeneity in clinical presentation of ASD, likely due to different etiologies, complicates genetic/biological analyses of these disorders. DNA microarray analyses were conducted on 116 lymphoblastoid cell lines (LCL) from individuals with idiopathic autism who are divided into 3 phenotypic subgroups according to severity scores from the commonly used Autism Diagnostic Interview-Revised questionnaire and age-matched, nonautistic controls. Statistical analyses of gene expression data from control LCL against that of LCL from ASD probands identify genes for which expression levels are either quantitatively or qualitatively associated with phenotypic severity. Comparison of the significant differentially expressed genes from each subgroup relative to the control group reveals differentially expressed genes unique to each subgroup as well as genes in common across subgroups. Among the findings unique to the most severely affected ASD group are genes that regulate circadian rhythm, which has been shown to have multiple effects on neurological as well as metabolic functions commonly dysregulated in autism. Among the genes common to all 3 subgroups of ASD are 5 novel genes which appear to associate with androgen sensitivity, which may underlie the strong 4:1 bias towards affected males. Gene expression profiling of 116 LCL from autistic (87) and nonautistic (29) individuals were obtained using a custom-printed DNA microarray containing 39,936 elements (TIGR 40K Human array, GPL3427) and a reference design in which each sample was compared to the Stratagene Universal Human RNA standard. The 87 autistic samples were divided into phenotypic subgroups (language, mild, savant) on the basis of cluster analyses of scores from an autism diagnostic questionnaire, the Autism Diagnostic Interview-Revised instrument. Differentially expressed genes were determined for all autistic vs. control groups, as well as for each of 3 phenotypic ASD groups and controls.

Project description:The highly intra-tumoral heterogeneity and complex cell origination of PCa greatly limited the significance of traditional bulk RNA sequencing in finding better biomarker for disease stratification. In the context of these sequencing strategies, significant gene expression differences in specific cell population might be normalized or even shaded by genes in those less “important” but large in amount cells. Tissue specimens based single-cell RNA sequencing holds great promise for identification of novel stratification biomarkers. However, the preparation of enough viable cells for sequencing, in particular for prostate cancer (PCa), is very challenging when using this technique. In the current study, we, for the first time, employed single-cell RNA sequencing of PCa cells isolated from cancerous prostate tissues of two patients and identified fifteen cell groups including three luminal clusters with different expression profiles. One of these luminal clusters had the highest copy number variation level and marker genes mainly enriched in PCa-related metabolic process, thereafter, was considered as the malignant luminal cells in PCa. Further analysis indicates that the fifth subgroup of these cells highly expressed genes significantly correlated with PCa initiation and early development. In addition, we found this subgroup highly expressed PCa prognosis biomarkers such as AMACR and PCA3. These findings suggest that this cell subgroup might be a critical cell population for PCa diagnosis and stratification. Moreover, by further deciphering the gene expression of this subgroup, we identified another marker gene, HPN, with a 0.930 area under the curve (AUC) score distinguishing normal tissue from PCa lesion using the RNA-seq data from The Cancer Genome Atlas (TCGA). This finding was further validated by immunostaining of HPN in PCa tissue array. The expression of HPN in PCa with Gleason score > 6 is significantly higher than those in Gleason score = 6. Taken together, we provide a valuable resource for interpreting the tumor heterogeneity in PCa, and a novel candidate marker for PCa management.

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Epigenome analysis of autism spectrum disorder samples

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