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Analysis of mRNA transcriptomic changes in ethanol-exposed human embryonic stem cell (hESC)-derived cortical interneurons using ribosome depletion RNA sequencing

ABSTRACT: Purpose: The goal of this study to use ethanol-exposed human embryonic stem cell (hESC)-derived neural cells as models to investigate mRNA expression changes in the brains of subjects with alcohol use disorder (AUD). Methods: hESCs were differentiated into neural cells (mainly cortical interneurons), which were then cultured in media with or without ethanol (50-100 mM) for 7 days (by duplicate experiments). Total RNAs were extracted from hESC-derived neural cells (with or without ethanol exposure) for mRNA sequencing. The sequence reads were processed using the RNA-seq processing pipeline Pipeliner [Front Genet. 2019; 10:614] workflow. Ethanol-induced mRNA transcriptomic changes were analyzed by the Limma-Voom method. Results: When the significance level was set at FC>2.0 & P<0.01, 19 coding genes showed differential expression, and all of them were downregulated after a 7-day ethanol exposure. Conclusions: The hESC-derived neural cell model study can partially validate mRNA transcriptomic changes in postmortem brains of subjects with alcohol use disorder.

ORGANISM(S): Homo sapiens

PROVIDER: GSE181049 | GEO | 2021/10/13

REPOSITORIES: GEO

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Analysis of microRNA transcriptomic changes in ethanol-exposed human embryonic stem cell (hESC)-derived cortical interneurons using small RNA sequencing

Project description:Purpose: The goal of this study to use ethanol-exposed human embryonic stem cell (hESC)-derived neural cells as models to investigate microRNA expression changes in the brains of subjects with alcohol use disorder (AUD). Methods: hESCs were differentiated into neural cells (mainly cortical interneurons), which were then cultured in media with or without ethanol (50-100 mM) for 7 days (by duplicate experiments). Total RNAs were extracted from hESC-derived neural cells (with or without ethanol exposure) for small RNA sequencing. The sequence reads were processed using the Comprehensive Analysis Pipeline for miRNA Sequencing Data (CAP-miRseq) workflow. Ethanol-induced miRNA transcriptomic changes were analyzed by the Limma-Voom method. Results: A 7-day ethanol exposure led to differential expression of six miRNAs (absolute FC>2.0 & P<0.05) in hESC-derived cortical interneurons. Three miRNAs were upregulated (>2-fold increase & P<0.05), while three other miRNAs were downregulated (> 2-fold decrease & P < 0.05) due to ethanol exposure. Conclusions: The hESC-derived neural cell model study can partially validate miRNA transcriptomic changes in postmortem brains of subjects with alcohol use disorder.

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