IDENTIFICATION OF DIFFERENTIALLY EXPRESSED GENES IN PATIENTS WITH SYSTEMIC LUPUS ERYTHEMATOSUS

Abstract

Background Characterizing differentially expressed genes (DEGs) of systemic lupus erythematosus (SLE) is necessary to understand immunogenic interactions, and how several key immune genes were closely associated with the susceptibility of SLE.

Objectives This study aimed to identify DEGs of SLE using gene expression-based computational methodologies to analyze disease-immune interactions, which affect the development and progression of SLE.

Methods Twenty-six patients with SLE and 46 healthy controls were selected from the Gene Expression Omnibus database. The significantly enriched immune and virus related gene lists were computed and visualized by using the DEGs from the Gene Set Enrichment Analysis. Quantification of 38 immune cells were performed in determining the impact of immune cells on the virus mediated immunity in SLE by using ImmQaunt algorithm.

Results Thirty nine upregulated and 57 downregulated were identified in SLE patient compared to the healthy controls. Upregulated genes were significantly implicated in Gene Ontology gene sets as cytokine mediated signaling, secretion, and exocytosis in immune response pathways. In addition, these genes were enriched in hepatitis C, influenza A, measles, Epstein–Barr virus, and herpes simplex virus 1 infection in Kyoto Encyclopedia of Genes and Genomes pathways. Especially, FCGR1A, IRF7, OAS2, CAMP, MX1, OAS3, OAS1, DEFA3, ISG15, and RSAD2 were involved in virus mediated SLE mechanism, and the expression for OAS1, OAS2, and IRF7 was closely associated with the quantities of colony forming unit-monocyte and colony forming unit-granulocyte.

Conclusion Identifying virus mediated SLE genes and quantifies of immune cells were used to understand the pathological process and perform early diagnosis of SLE, and will lead to clinical tools for treating SLEs in patients.