Journal Article

Screening of hub genes for sepsis-induced myopathy by weighted gene co-expression network analysis and protein-protein interaction network construction

Wang, Jianhao, Lu, Jinshuai, Han, Kun

2024

Overview

Sepsis-induced myopathy is one of the serious complications of sepsis, which severely affects the respiratory and peripheral motor systems of patients, reduces their quality of life, and jeopardizes their lives, as evidenced by muscle atrophy, loss of strength, and impaired regeneration after injury. The pathogenesis of sepsis-induced myopathy is complex, mainly including cytokine action, enhances free radical production in muscle, increases muscle protein hydrolysis, and decreases skeletal muscle protein synthesis, etc. The above mechanisms have been demonstrated in existing studies. However, it is still unclear how the overall pattern of gene co-expression affects the pathological process of sepsis-induced myopathy. Therefore, we intend to identify hub genes and signaling pathways. Weighted gene co-expression network analysis was our main approach to study gene expression profiles: skeletal muscle transcriptome in ICU patients with sepsis-induced multi-organ failure (GSE13205). After data pre-processing, about 15,181 genes were used to identify 13 co-expression modules. Then, 16 genes (FEM1B, KLHDC3, GPX3, NIFK, GNL2, EBNA1BP2, PES1, FBP2, PFKP, BYSL, HEATR1, WDR75, TBL3, and WDR43) were selected as the hub genes including 3 up-regulated genes and 13 down-regulated genes. Then, Gene Set Enrichment Analysis was performed to show that the hub genes were closely associated with skeletal muscle dysfunction, necrotic and apoptotic skeletal myoblasts, and apoptosis in sepsis-induced myopathy. Overall, 16 candidate biomarkers were certified as reliable features for more in-depth exploration of sepsis-induced myopathy in basic and clinical studies.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Analysis / Apoptosis / Atrophy / Connectivity / Cytokines / Datasets / Diagnosis / Epidemiology / Free radicals / Gene expression / Gene Expression Profiling / Gene Regulatory Networks / Gene set enrichment analysis / Gene set enrichment analysis (GSEA) / Genes / Genetic aspects / Genotype & phenotype / Humans / Internal Medicine / Medicine / Medicine & Public Health / Mortality / Muscle diseases / Muscle, Skeletal - metabolism / Muscle, Skeletal - pathology / Muscular Diseases - diagnosis / Muscular Diseases - etiology / Muscular Diseases - genetics / Muscular dystrophy / Musculoskeletal system / Myoblasts / Myopathy / Orthopedics / Protein biosynthesis / Protein interaction / Protein Interaction Maps / Protein synthesis / Protein-protein interaction network (PPI) / Protein-protein interactions / Proteins / Quality of life / Rehabilitation / Rheumatology / Risk factors / Sepsis / Sepsis - complications / Sepsis - genetics / Sepsis - metabolism / Sepsis-induced myopathy (SIM) / Signal Transduction - genetics / Skeletal muscle / Sports Medicine / Transcriptome / Transcriptomes / Weighted gene co-expression network analysis (WGCNA)