Single cell sequencing reveals sex bias in autism associated cells and genes
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ABSTRACT:
PROVIDER: PRJNA694426 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13516500_1.fastq.gz | Fastqsanger.gz | |||
| SRR13516500_2.fastq.gz | Fastqsanger.gz | |||
| SRR13516501_1.fastq.gz | Fastqsanger.gz | |||
| SRR13516501_2.fastq.gz | Fastqsanger.gz | |||
| SRR13516502_1.fastq.gz | Fastqsanger.gz |
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Project description:Here we performed single-cell RNA sequencing to examine the transcriptomes of over 45,000 cells isolated from the hippocampus of an autistic mouse model. Each cell was assigned to one of twelve major cell types based on distinct expression profiles. Differential expression analysis identified cell type specific genes with altered expression after prenatal valproic acid exposure. The largest number of differentially expressed genes was detected in neurons, choroid plexus epithelial cells, and microglia. In microglia, there were more male-specific than female-specific inflammation-related pathways that were important to induce autistic-like behavior. Meanwhile, there were several X-linked genes among the male-specific DEGs of neurons, and the changes of those genes after prenatal VPA exposure may be another key reason why more male than female ASD patients are seen in clinic.
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Project description:Background: We have recently identified the nuclear hormone receptor RORA (retinoic acid-related orphan receptor-alpha) as a novel candidate gene for autism spectrum disorder (ASD). Our independent cohort studies have consistently demonstrated the reduction of RORA transcript and/or protein levels in blood-derived lymphoblasts as well as the postmortem prefrontal cortex and cerebellum of individuals with ASD. Moreover, we have also shown that RORA has the potential to be under negative and positive regulation by androgen and estrogen, respectively, suggesting the possibility that RORA may contribute to the male bias of ASD. However, little is known about transcriptional targets of this nuclear receptor, particularly in humans. Methods: Here we comprehensively identify transcriptional targets of RORA in human neuronal cells using chromatin immunoprecipitation (ChIP), followed by whole-genome promoter array (chip) analysis. Selected potential targets of RORA were then further validated by an independent chromatin immunoprecipitation, followed by qPCR analysis. To further demonstrate that reduced RORA expression results in aberrant transcription of RORA targets, we determined the expression levels of selected transcriptional targets in RORA-deficient human neuronal cells, as well as in postmortem brain tissues from individuals with ASD who exhibit reduced RORA expression. Results: The ChIP-on-chip analysis reveals that RORA1, a major isoform of RORA protein in human brain, can be recruited to as many as 1,338 genomic locations corresponding to promoter regions of 1,274 genes across the human genome. Among the genes potentially directly regulated by RORA1 are genes known to have biological functions negatively impacted in individuals with ASD, including neuronal adhesion and survival, synaptogenesis, and development of the cortex and the cerebellum. Independent ChIP-qPCR analyses confirm binding of RORA1 to promoter regions of several ASD-associated genes, including A2BP1, CYP19A1, HSD17B10, ITPR1, NLGN1, and NTRK2, whose expression levels are also decreased in RORA1-repressed human neuronal cells and in prefrontal cortex tissues from individuals with ASD. Conclusion: Findings from this study indicate that RORA transcriptionally regulates A2BP1, CYP19A1, HSD17B10, ITPR1, NLGN1, and NTRK2, and strongly suggest that reduction of this sex hormone-sensitive nuclear receptor in the brain causes dysregulated expression of these genes which, in turn, may contribute to the underlying pathobiology of ASD. Nuclear lysates from the human neuroblastoma cell line SH-SY5Y were chromatin-immunoprecipitated with goat anti-RORA1 antibody vs. normal goat IgG antibody
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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.
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Project description:Background: We have recently identified the nuclear hormone receptor RORA (retinoic acid-related orphan receptor-alpha) as a novel candidate gene for autism spectrum disorder (ASD). Our independent cohort studies have consistently demonstrated the reduction of RORA transcript and/or protein levels in blood-derived lymphoblasts as well as the postmortem prefrontal cortex and cerebellum of individuals with ASD. Moreover, we have also shown that RORA has the potential to be under negative and positive regulation by androgen and estrogen, respectively, suggesting the possibility that RORA may contribute to the male bias of ASD. However, little is known about transcriptional targets of this nuclear receptor, particularly in humans. Methods: Here we comprehensively identify transcriptional targets of RORA in human neuronal cells using chromatin immunoprecipitation (ChIP), followed by whole-genome promoter array (chip) analysis. Selected potential targets of RORA were then further validated by an independent chromatin immunoprecipitation, followed by qPCR analysis. To further demonstrate that reduced RORA expression results in aberrant transcription of RORA targets, we determined the expression levels of selected transcriptional targets in RORA-deficient human neuronal cells, as well as in postmortem brain tissues from individuals with ASD who exhibit reduced RORA expression. Results: The ChIP-on-chip analysis reveals that RORA1, a major isoform of RORA protein in human brain, can be recruited to as many as 1,338 genomic locations corresponding to promoter regions of 1,274 genes across the human genome. Among the genes potentially directly regulated by RORA1 are genes known to have biological functions negatively impacted in individuals with ASD, including neuronal adhesion and survival, synaptogenesis, and development of the cortex and the cerebellum. Independent ChIP-qPCR analyses confirm binding of RORA1 to promoter regions of several ASD-associated genes, including A2BP1, CYP19A1, HSD17B10, ITPR1, NLGN1, and NTRK2, whose expression levels are also decreased in RORA1-repressed human neuronal cells and in prefrontal cortex tissues from individuals with ASD. Conclusion: Findings from this study indicate that RORA transcriptionally regulates A2BP1, CYP19A1, HSD17B10, ITPR1, NLGN1, and NTRK2, and strongly suggest that reduction of this sex hormone-sensitive nuclear receptor in the brain causes dysregulated expression of these genes which, in turn, may contribute to the underlying pathobiology of ASD.
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