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RNA sequencing of RBP4 or control treated cells

ABSTRACT: Purpose: The purpose of this study was to find the differentially expressed genes in RBP4 and control treated cells by transcriptome analysis (RNA-seq) for subsequent mechanism study. Methods: Illumina Novaseq™ 6000 was used to sequencing RBP4 and control-treated human umbilical vein endothelial cells.Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.GO enrichment analysis provides all GO terms that significantly enriched in DEGs comparing to the genome background. Firstly all DEGs were mapped to GO terms in the Gene Ontology database (http://www.geneontology.org/), gene numbers were calculated for every term, significantly enriched GO terms in DEGs comparing to the genome background were defined by hypergeometric test. Results:The RNA-seq results showed that compared to the untreated HUVECs, RBP4 treatment resulted in significant changes in the gene expression, including 180 up-regulated and 53 down-regulated genes among a total number of 233 DEGs. GO enrichment were analyzed for relationships among all DEGs. Conclusions: Our study analyzed the mechanism of RBP4 on human umbilical vein endothelial cells and its possible pathway in detail by RNA-seq technique, and provided a basis for elucidating the damage of RBP4 on endothelial cells through large-scale gene screening.

ORGANISM(S): Homo sapiens

PROVIDER: GSE197314 | GEO | 2025/02/22

REPOSITORIES: GEO

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	GSE197314_genes_fpkm_expression.txt.gz	Txt

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Project description:Background: We investigated the effect of PPIA overexpression on downstream gene expression at the cellular level. Methods: The PPIA gene was overexpressed in human umbilical vein endothelial cells. Then, transcriptome sequencing was performed. The differentially expressed genes and genes with alternative splicing were screened. GO and KEGG analyses were performed. Nine differentially expressed genes and 7 genes with alternative splicing were validated by real-time quantitative PCR. Results: After PPIA overexpression, 328 genes were differentially expressed, including 157 up-regulated genes and 171 down-regulated genes. GO enrichment analysis of up-regulated genes found that the enriched GO terms included extracellular region, protein binding and metal ion binding, etc. For down-regulated genes, the enriched GO terms included neuron projection, protein binding, endoplasmic reticulum unfolded protein response, etc. KEGG showed that the up-regulated genes were mainly enriched in gastric acid secretion, AMPK signaling pathway, etc; and, the down-regulated genes were enriched in transcriptional misregulation in cancer, TNF signaling pathway, etc. Real-time quantitative PCR analysis of ATF4 (activating transcription factor 4), PPP1R15A (protein phosphatase 1, regulatory (inhibitor) subunit 15A protein phosphate 1, regulatory (inhibitor) subunit 15A), GADD45B (growth arrest and DNA damage inducible protein 45B), SGK1 (serum/glucocorticoid regulated kinase 1), DDIT3 (Recombinant DNA Damage Inducible Transcript 3), PMAIP1 (Phorbol-12-myristate-13-acetate-induced Protein 1), SULF1 (Sulfatase 1), GDF6 (Growth Differentiation Factor 6), and XBP1 (X-Box Binding Protein 1) obtained consistent results with the sequencing results. On the other hand, multiple genes with alternative splicing were identified and analyzed with KEGG and GO. Real-time quantitative PCR validation showed that the probability of alternative splicing in LHPP, APH1A, BRD1, and ORAI3 was increased. However, the changes of NFX1, SERGEF, and PCBP4 were inconsistent with the sequencing results. Conclusion: The overexpression of PPIA in human umbilical vein endothelial cells causes changes in the expression of downstream genes, and induces alternative splicing in multiple genes. PPIA may be involved in the development of atherosclerosis by regulating the expression of downstream genes and causing endothelial cell dysfunction.

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RNA sequencing of RBP4 or control treated cells

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