Bioinformatics and system biology approach to identify the influences of HIV and LN on the regulation of gene expression

Analyze the molecular mechanisms related to oxidative stress (OS) and endoplasmic reticulum stress (ERS) shared by lupus nephritis (LN) and human immunodeficiency virus (HIV) infection. The sequencing data of LN (GSE81622) and HIV (GSE195434) were downloaded from the Gene Expression Omnibus (GEO) database. Co-expressed differentially expressed genes (DEGs) were identified, followed by immune infiltration and diagnostic receiver operating characteristic (ROC) analysis. Functional enrichment was performed using Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Set Enrichment Analysis (GSEA). Hub genes were screened via protein-protein interaction networks (PPIs), and interaction analyses were conducted focusing on miRNAs, transcription factors (TFs), pharmaceuticals, diseases, and RNA binding proteins (RBPs). Finally, qPCR expression validation was performed on the selected hub genes. The analysis revealed 22 common DEGs, among which 11 were identified as hub genes. Functional enrichment analysis indicated that these genes were primarily enriched in ribosome- and tumor-related pathways. The key gene, GINS2, demonstrated high diagnostic value for both diseases (AUC: 0.827–0.919). Furthermore, the study predicted 5 related microRNAs (miRNAs) and 5 TFs. This study provides shared molecular markers, therapeutic targets, and potential drugs for patients with concurrent HIV infection and LN.