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Quantitative Analysis of Transcriptomes of Control and BP-3 exposure embryos (zebrafish) by RNA-sequencing

ABSTRACT: Purpose: The goals of this study are to quantitatively compare the expression difference of embryos incubated with or without benzophenone-3（BP-3） at the transcriptome level and find the underlying mechanism how could BP-3 impede the development of enteric nervous system. Methods: Intestinal RNA profiles of 5dpf Wide Type (WT) and BP-3 exposure groups of zebrafish embryos were generated by paired-end sequencing, in triplicate, using Illumina HiSeqTM 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level. The PossionDis algorithm was applied to perform differential gene detection and screened |log2 (FoldChange)| > 1 & qvalue<0.05 as the DEGs. Gene Set Enrichment Analysis (GSEA) comparing WT and BP-3 exposure groups was performed by GSEA software (version 4.0.03). A nominal p-value < 0.05 and false discovery rate (FDR) q-value < 0.25 were considered statistically significant for GSEA analyses. Results: The PossionDis algorithm was applied to perform differential gene detection and screened |log2 (FoldChange)| > 1 & qvalue<0.05 as the DEGs. RNA-seq data confirmed 159 up-regulated and 73 down-regulated genes in BP-3 exposure groups. Some MAPK/ERK signaling pathway related terms were enriched in molecular function and biological process and MAPK/ERK signaling pathway reached notable enrichment based on KEGG analysis. Conclusions: Our study represented the first detailed analysis of BP-3 exposure zebrafish intestinal transcriptomes, with biologic replicates, generated by RNA-sequencing technology. Our results showed that 159 genes were up-regulated and 73 were down-regulated in BP-3 exposure groups. Some MAPK/ERK signaling pathway related terms were enriched in molecular function and biological process. MAPK/ERK signaling pathway reached notable enrichment based on KEGG analysis.

ORGANISM(S): Danio rerio

PROVIDER: GSE171619 | GEO | 2021/04/08

REPOSITORIES: GEO

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Project description:Bis-2-chloroethyl sulfide (sulfur mustard, SM) is a potent alkylating agent and vesicant. Exposure to SM results in activation of numerous signaling cascades, including mitogen-activated protein kinase (MAPK) signaling pathways. These pathways include the Erk, p38, and JNK pathways, which are involved in cell growth, inflammation, and stress signaling. However, the precise roles of these pathways in SM toxicity have not been fully elucidated. We used Western blotting and microarray analysis to examine the activation and role of each pathway following SM exposure in primary human epidermal keratinocytes. Western blotting revealed increased phosphorylation of p38 and JNK following SM exposure; however, phosphorylation of Erk was equivocal, suggesting that growth conditions may impact activation of Erk by SM. We used pharmacologic inhibitors to target each MAPK and then compared the gene expression profiles to identify SM-induced gene networks regulated by each MAPK. Cells were pretreated with 10 µM SB 203580 (p38 inhibitor), PD 98059 (Erk inhibitor), or SP 600125 (JNK inhibitor) 60 minutes before exposure to 200 µM SM. Cells were harvested at 1h, 4h, and 8h post-exposure, and RNA was extracted for synthesis of microarray probes. Probes were hybridized to Affymetrix U133 Plus 2.0 arrays for gene expression profiling. Analysis of variance was performed to identify genes significantly modulated due to pharmacologic inhibition in SM-exposed cells. Pathway mapping confirmed alterations in SM-induced Erk, JNK, and p38 MAPK signaling due to pharmacologic inhibition. SM-induced expression of IL-8, IL-6, and TNF-alpha was decreased by p38 MAPK inhibition, but not by inhibition of other MAPKs. Based on the number of significant pathways mapped to each MAPK in the presence and absence of inhibitors, the p38 MAPK pathway appeared to be the MAPK pathway most responsive to SM exposure. Interestingly, pathway mapping of the microarray data identified potential cross-talk between MAPK signaling pathways and other pathways involved in SM-induced signaling. Mining of these results will increase our understanding of the role of MAPK pathways in SM-induced signal transduction and may identify potential therapeutic targets for medical countermeasure development.

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Quantitative Analysis of Transcriptomes of Control and BP-3 exposure embryos (zebrafish) by RNA-sequencing

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