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Effect of Pf-Rel/poI-κB RNA interference on gene expression in mantle tissue in Pinctada fucata

ABSTRACT: Pinctada fucata is an important pearl production shellfish in aquaculture. The formation of shells and pearls is a hot research topic in biomineralization, and matrix proteins secreted by the mantle tissues play the key role in this process. However, upstream regulatory mechanisms of transcription factors on the matrix protein genes remain unclear. Previous studies have shown that NF-κB signaling pathway regulated biomineralization process through expression regulation of specific matrix proteins.In this study, we systematically investigated the effect of the NF-κB signaling pathway key factor Pf-Rel and inhibitory protein poI-κB on the biomineralization and shell regeneration process. RNA-seq was conducted based on RNA interference animal model to identify potential regulatory genes by transcription factor Pf-Rel. We extracted total RNA from the whole tissue samples of the pericardium 7 days after dsRNA injection, and named them as the Rel-RNAi group, IκB-RNAi group and control group, respectively. We first calculated the Pearson correlation coefficient between each pair of samples, which reflects the similarity in overall gene expression patterns among the samples. The calculation results showed a high correlation coefficient of 0.954 between the Rel-RNAi group and IκB-RNAi group. We performed Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses on differentially expressed genes (DEGs) from two groups. The top three enriched GO terms for DEGs were: extracellular region, peptidase inhibitor activity and peptidase regulator activity. In addition, immune receptor activity and integrin-mediated signaling pathways terms were significantly enriched. The KEGG Pathway classification showed that a large number of DEGs were classified as signal transduction and immune system terms. Biomineralization is also an important natural immune pathway in shellfish, which suggests that the NF-κB signaling pathway in P. fucata is closely related to natural immunity. KEGG pathway enrichment analysis indicated that substantial DEGs were attributed to PI3K-Akt signaling pathway term, which plays a vital role in cell survival

ORGANISM(S): Pinctada fucata

PROVIDER: GSE236891 | GEO | 2023/07/07

REPOSITORIES: GEO

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Project description:Objectives: To analyze the gene expression profile of peripheral blood monocytes in different stages of coronary artery disease (CAD) by transcriptome sequencing, and to explore potential genes and pathway involved in CAD pathogenesis. Methods: According to the screening of coronary angiography and quality control of blood samples, 8 intermediate coronary lesion patients were selected, then 8 patients with acute myocardial infarction and 8 patients with normal coronary angiography were matched by age and gender. Transcriptomics sequencing was conducted for the peripheral blood monocytes of these 24 samples by using Illumina HiSeq high-throughput platform. Then differentially expressed genes (DEGs) were analyzed. Gene Ontology (GO) functional annotation, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation and protein-protein interaction (PPI) network were applied to annotate the potential functions of DEGs. Results: Compared with the normal coronary angiography group, we identified a total of 169 DEGs in the intermediate coronary lesion group, which were significantly enriched in 59 GO terms and 17 KEGG pathways. Compared with the normal coronary angiography group, we found a total of 2028 DEGs, which were significantly enriched in 311 GO terms and 20 KEGG pathways in the acute myocardial infarction group. The cross-comparison between normal versus intermediate coronary lesion group, and normal versus acute myocardial infarction group included 98 differential genes with 65 up regulated and 33 down regulated genes, which were significantly enriched in 46 GO terms and 10 KEGG pathways. During the progression of CAD, there was a significant up-regulated expression of CSF3、IL-1A、CCR7 and IL-18, and down-regulated expression of MAPK14. Besides GO items such as inflammatory response was significantly enriched, KEGG analysis showed the most remarkable enrichments in IL-17 signaling pathway and cytokine-cytokine receptor interactions. Conclusions: Transcriptomics profiles vary in patients with different severity of CAD. CSF3、IL-1A、CCR7、IL-18 and MAPK14, as well as IL-17 signaling pathway and cytokines and cytokine receptor interaction signaling pathway related with inflammatory response might be the potential biomarker and targets for the treatment of coronary artery disease.

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Effect of Pf-Rel/poI-κB RNA interference on gene expression in mantle tissue in Pinctada fucata

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