Analysis of candidate biomarkers and related transcription factors involved in the development and restoration of stress-induced gastric ulcer by transcriptomics

• Published in: Cell stress & chaperones 2020-03, Vol.25 (2), p.265-275
• Main Authors: Huang, Pan, Tang, Weihong, Shen, Rong, Ju, Xiaoli, Shao, Genbao, Xu, Xiao, Jiang, Anqi, Qian, Xiaobin, Chen, Miao, Zhou, Zhengrong, Ren, Caifang
• Format: Article
• Language: English
• Subjects: Animals; Apoptosis; Biochemistry; Bioinformatics; Biomarkers; Biomarkers - metabolism; Biomedical and Life Sciences; Biomedicine; Bleeding; Cancer Research; Cell Biology; Complications; Computational Biology; EGR-1 protein; FosB protein; Gene Expression; Gene Regulatory Networks; Gene sequencing; Genes; Immunology; Interleukin 17; JunB protein; Male; Neurosciences; ORIGINAL PAPER; Oxygen enrichment; Peroxisome proliferator-activated receptors; Protein Interaction Maps; Proteins; Rats; Rats, Sprague-Dawley; Restoration; Ribonucleic acid; RNA; Signal transduction; Signaling; Stomach Ulcer - metabolism; Stress; Transcription factors; Transcription Factors - metabolism; Transcriptome; Trauma; Ulcers
• ISSN: 1355-8145; 1466-1268
• DOI: 10.1007/s12192-020-01070-8

Stress-induced gastric ulcer is one of the common complications affecting patients after trauma, mainly leading to gastrointestinal bleeding and perforation, and severe cases may be life-threatening. However, the molecular mechanism of stress-induced gastric ulcer remains unclear. In the present study, RNA-sequencing was performed on gastric tissues of normal rats (C), stress-induced gastric ulcer rats (T0), and rats recovered from gastric ulcer for 3 days (T3), and bioinformatics analysis was performed to determine changes in gene expression and biological pathways. The protein–protein interaction (PPI) networks of differentially expressed genes (DEGs) were constructed by STRING and visualized by the Cytoscape software. The associated transcriptional factor (TFs)–gene regulatory network of the hub DEGs was also constructed. Pairwise comparisons obtained 103 (T0_C), 127 (T3_T0), and 13 (T3_C) DEGs, respectively. Gene ontology (GO) enrichment analysis indicated DEGs in T0_C and T3_T0 were significantly enriched in response to oxygen-containing compound, response to organic substance, and response to external stimulus. Pathway analysis suggested that DEGs were enriched in TNF signaling pathway, PPAR signaling pathway, apoptosis, and IL-17 signaling pathway. Seven hub genes (Fos, Jun, Nfkbia, Dusp1, Pim3, Junb, and Fosb) were obtained from the PPI networks of T0_C and T3_T0. Key TFs with close interactions, such as Fos, Jun, Nfkbia, Junb, Egr1, and Fosb, were screened This study used RNA-sequencing and bioinformatics analysis to screen out genes associated with gastric ulcer, which can help reveal the molecular mechanism of gastric ulcer development and restoration, and provide reference for the treatment of human gastric ulcers.