Bioinformatics Analysis for Identifying Pertinent Pathways and Genes in Sepsis.

Yiran Li,Feixiang Wu,Tiancheng Zhang,Hongyan Zhang,Guangzhi Jin,Ruiqing Zong,Jindong Chen,Xiaoyan Meng,Jinyan Shao,Tao Huang

doi:10.1155/2021/2085173

Abstract

Purpose Sepsis becomes the main death reason in hospitals with rising incidence, causing a growing economic and medical burden. However, the genes related to the pathogenesis and prognosis of sepsis are still unclear, which is a problem that needs to be solved urgently. Materials and Methods Gene expression profiles of GSE69528 were obtained from the National Center for Biotechnology Information. Limma software package got employed to search for differentially expressed genes (DEGs). Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) were used for enrichment analysis. Protein-protein interaction (PPI) network was built by the Search Tool for the Retrieval of Interacting Genes (STRING) database. Results We screened 101 DEGs, containing 81 upregulated DEGs and 20 downregulated DEGs. GO analysis demonstrated that the upregulated DEGs were chiefly concentrated in negative regulation of response to interferon-gamma and regulation of granulocyte differentiation. KEGG analysis revealed that the pathways of upregulated DEGs were concentrated in prion diseases, complement and coagulation cascades, and Staphylococcus aureus infection. The PPI network constructed by upregulated DEGs contained 67 nodes (proteins) and 110 edges (interactions). Analysis of bioinformatics results showed that CEACAM8, MPO, and RETN were hub genes of sepsis. Conclusion Our analysis reveals a series of signal pathways and key genes related to the mechanism of sepsis, which are promising biotargets and biomarkers of sepsis.

Highlights

Sepsis is a serious syndrome characterized by infection changes in physiology, pathology, and biochemical life [1]
Microarray data were acquired from Gene Expression Omnibus (GEO), an accessible functional genomics database of high-throughput resources, which was one of the most commonly used sequencing databases in the National Center for Biotechnology Information (NCBI)
Through DAVID online database enrichment analysis, we found that the biological processes (BPs) of upregulated differentially expressed genes (DEGs) were majorly enriched in negative regulation of response to interferon-gamma, negative regulation of interferon-gamma-mediated signaling pathway, and regulation of granulocyte differentiation (Figure 2)

Summary

Introduction

Sepsis is a serious syndrome characterized by infection changes in physiology, pathology, and biochemical life [1]. It has become a main death reason for hospital deaths in intensive care unit (ICU) patients and millions of deaths worldwide every year [2]. In the United States, 10% of ICU patients have sepsis, and about 25% of ICU beds are occupied by sick patients [3]. The advancement of medicine career has increased the rate of survivors after primary sepsis injury. Acute death is not the main reason for sepsis death. 70% of sepsis-related deaths happen in the first three days after its onset, which is caused by secondary infection [5]

Methods

Findings

Discussion

Conclusion