Identification of Potential Biomarkers and Immune Features of Sepsis Using Bioinformatics Analysis

• Published in: Mediators of inflammation 2020-10, Vol.2020 (2020), p.1-12
• Main Authors: Chen, Er-Zhen, Chen, Ying, Yang, Zhi-Tao, Wang, Yu-Ming, Ji, Ran, Gong, Fang-Chen, Mao, En-Qiang
• Format: Article
• Language: English
• Subjects: Antigen presentation; Antigens; Bioinformatics; Biological markers; Biomarkers; Cells; Computational biology; Datasets; DNA microarrays; Fyn protein; Gene expression; Genes; Health aspects; Immune response; Infection; Innate immunity; Itk protein; Lck protein; Lymphocytes T; Molecular modelling; Morbidity; Natural killer cells; Neutrophils; p53 Protein; Protein interaction; Protein-protein interactions; Ribonucleic acid; RNA; Sepsis; T cells; Transcriptomics; Tumor proteins; ZAP-70 protein
• ISSN: 0962-9351; 1466-1861
• DOI: 10.1155/2020/3432587

Sepsis remains a major global concern and is associated with high mortality and morbidity despite improvements in its management. Markers currently in use have shortcomings such as a lack of specificity and failures in the early detection of sepsis. In this study, we aimed to identify key genes involved in the molecular mechanisms of sepsis and search for potential new biomarkers and treatment targets for sepsis using bioinformatics analyses. Three datasets (GSE95233, GSE57065, and GSE28750) associated with sepsis were downloaded from the public functional genomics data repository Gene Expression Omnibus. Differentially expressed genes (DEGs) were identified using R packages (Affy and limma). Functional enrichment of the DEGs was analyzed with the DAVID database. Protein-protein interaction networks were derived using the STRING database and visualized using Cytoscape software. Potential biomarker genes were analyzed using receiver operating characteristic (ROC) curves in the R package (pROC). The three datasets included 156 whole blood RNA samples from 89 sepsis patients and 67 healthy controls. Between the two groups, 568 DEGs were identified, among which 315 were upregulated and 253 were downregulated in the septic group. These genes were enriched for pathways mainly involved in the innate immune response, T-cell biology, antigen presentation, and natural killer cell function. ROC analyses identified nine genes—LRG1, ELANE, TP53, LCK, TBX21, ZAP70, CD247, ITK, and FYN—as potential new biomarkers for sepsis. Real-time PCR confirmed that the expression of seven of these genes was in accordance with the microarray results. This study revealed imbalanced immune responses at the transcriptomic level during early sepsis and identified nine genes as potential biomarkers for sepsis.