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Translatome analysis in postmortem brain-derived samples from Autism Spectrum Disorder affected individuals

ABSTRACT: Translatome analysis in postmortem brain-derived samples from Autism Spectrum Disorder affected individuals

PROVIDER: PRJNA992390 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25182927.fastq.gz	Fastqsanger.gz
	SRR25182928.fastq.gz	Fastqsanger.gz
	SRR25182929.fastq.gz	Fastqsanger.gz
	SRR25182930.fastq.gz	Fastqsanger.gz
	SRR25182931.fastq.gz	Fastqsanger.gz

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Translatome analysis in postmortem brain-derived samples from Autism Spectrum Disorder affected individuals

Project description:Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with a strong genetic link, but no single well-established cause. This suggests that perturbed regulatory network may better explain its heterogeneity of phenotypes and multiple gene associations. Consistently, our previous study provided evidence of abnormal alternative polyadenylation in transcripts from distinct brain regions suggesting a potential imbalance in the protein synthesis in the postsynaptic density. To test this hypothesis, we studied transcriptome-wide alterations of mRNA translation in post-mortem brain samples from neurotypical and ASD-affected young males subjects. To this end, we employed an optimised polysome profiling technique amendable for small tissue samples and analyzed changes in the translatome using the anota2seq algorithm. The analysis revealed bolstered translation of mRNAs whose translational efficiency was previously reported to be sensitive to eIF4E, a key factor for synaptic protein synthesis modulated by Ras/ERK and PI3K/mTOR signaling pathways. This observation is consistent with previous findings linking hyperactive eIF4E to increased translation of neuroligins, a disturbed excitation/inhibition ratio in synapses and autistic-like phenotypes in mice. In summary, we reveal a link between eIF4E-dependent translation and human autism, indicating a potential pharmacy-therapeutical target for the prevention of behavioral impairments in ASD.

2023-10-27 | GSE236761 | GEO

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Project description:To assess the clinical impact of splice-altering noncoding mutations in autism spectrum disorder (ASD), we used a deep learning framework (SpliceAI) to predict the splice-altering potential of de novo mutations in 3,953 individuals with ASD from the Simons Simplex Collection. To validate these predictions, we selected 36 individuals that harbored predicted de-novo cryptic splice mutations; each individual represented the only case of autism within their immediate family. We obtained peripheral blood-derived lymphoblastoid cell lines (LCLs) and performed high-depth mRNA sequencing (approximately 350 million 150 bp single-end reads per sample). We used OLego to align the reads against a reference created from hg19 by substituting de novo variants of each individual with the corresponding alternate allele.

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5-hydroxymethylcytosine alterations in the human postmortem brains of autism spectrum disorder

Project description:5-hydroxymethylcytosine alterations in the human postmortem brains of autism spectrum disorder

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5-hydroxymethylcytosine alterations in the human postmortem brains of autism spectrum disorder

Project description:Autism spectrum disorders (ASD) comprise a group of disorders characterized by impaired language, social, and communication skills, in addition to restrictive behaviors or stereotypies. However, with a prevalence of 1.5% in developed countries and relatively high comorbidity rates, no clear underlying mechanism that unifies the heterogeneous phenotypes of ASD is known. 5-hydroxymethylcytosine (5hmC) has been reported highly enriched in brain, and is now recognized as an important epigenetic mark in developmental and neurological disorders. To explore the role of 5hmC in ASD, we utilized the genomic DNA isolated from the postmortem cerebellum of both ASD patients and age-matched controls to profile genome-wide distribution of 5hmC. We identified 797 age-dependent differential hydroxymethylated regions (DhMRs) (q-value < 0.05, FDR adjusted) in young group (age ≤ 18), while no significant DhMR was identified in the groups over 18-year-old. Pathway and disease association analyses indicated that the intragenic DhMRs were located in the genes that involved in cell-cell communication and neurological disorders. By comparing the 5hmC counts (ASD vs. Control) in each psychiatric gene (±10kb), we observed significant 5hmC changes in larger fraction of psychiatric genes than in reference genes. Interestingly, we found that the predicted cis functions of non-coding intergenic DhMRs strikingly associated with ASD and intellectual disorders. A significant fraction of intergenic DhMRs were overlapped with topologically associating domains (TAD). These results together suggest that 5hmC dynamic alteration is associated with ASD, particularly in the early development stage, and could contribute to the pathogenesis of ASD.

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Project description:H3K27ac ChIP-seq were performed on postmortem samples from autism spectrum disorder and matched control brains. Tissues were chosen from three brain regions: prefrontal cortex, temporal cortex and cerebellum.

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