Series test of cluster and network analysis for lupus nephritis, before and after IFN-K-immunosuppressive therapy

The purpose was to screen potential targets of IFN-K-immunosuppressive therapy, which was used to offer effective information and resources for molecular targeted therapy.

The gene expression profile of GSE72747 was used to screen out significant differently expressed genes (DEGs). Series Test of Cluster (STC) analysis for DEGs was performed. For all DEGs, the Database for Annotation, Visualization, and Integrated Discovery was performed for Gene Ontology (GO) enrichment analysis. Pathway enrichment analysis of DEGs was performed based on Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Pathway was constructed based on the interactions in the KEGG database. The coexpression network and gene signal expression networks were constructed and analyzed.

A total of 2193 DEGs were screened and eight significant profiles were identified. Significant GO terms included small molecule metabolic process, translation and apoptotic process. Metabolic pathways and Alzheimer's disease were significant KEGG pathways. Pathway relationship network of DEGs was constructed. MAPK signalling pathway, apoptosis and pathways in cancer were hub nodes. Gene co-expression network analysis was performed. VCP-interacting membrane protein and NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex, 1, 8 kDa were the hub nodes. Gene signal network was constructed with 162 nodes and 254 edges. Hub nodes were phospholipase C, beta 2.

Screened DEGs including VIMP, NDUFAB1, SEC61G, PSMC2 might be potential targets for lupus nephritis treatment by involving in different functions and pathways, such as metabolic process and immune process.