Identification of biomarkers and pathways for focal segmental glomerulosclerosis using next generation sequencing data and bioinformatics analysis

Abstract

AbstractFocal segmental glomerulosclerosis (FSGS) is a renal disease leading threat to human health around the world. Here we aimed to explore novel molecular and potential therapeutic targets in FSGS through adopting integrated bioinformatics tools. Next generation sequencing (NGS) data of GSE197307 was available from Gene Expression Omnibus (GEO) database. Furthermore, differentially expressed genes (DEGs) were screened using the DESeq2 package in R software. Gene ontology (GO) and REACTOME pathway enrichment analyses of DEGs were performed via g:Profiler. Then, the protein-protein interaction (PPI) network, miRNA-hub gene regulatory network and TF-hub gene regulatory network were constructed using the HIPPIE, miRNet and NetworkAnalyst databases. Hub genes were validated using the receiver operating characteristic curve (ROC) analysis. By performing DEGs analysis, 488 up regulated genes and 488 down regulated genes were successfully identified from GSE197307, respectively. And they were mainly enriched in the terms of multicellular organismal process, cell periphery, protein binding, metabolism, immune system process, signaling receptor binding and immune system. Based on the data of protein–protein interaction (PPI), miRNA-hub gene regulatory network and TF-hub gene regulatory network, the top hub genes were ranked, including ILK, DDX5, MATR3, ALB, FOS, MKI67, PLK1, TNF, LCK and GTSE1. Bioinformatics analysis of NGS data identified signaling pathways and hub genes, potentially representing molecular mechanisms for the occurrence, progression, and risk prediction in FSGS.