A ceRNA regulatory network in systemic lupus erythematosus and its molecular interplay with cancer.

ABSTRACT

Background: Systemic lupus erythematosus (SLE) is an autoimmune disease defined by the production of autoantibodies and involves multiple organs and systems. Although there are reports on SLE, data on its pathogenesis is limited. Methods: Using R language software, we constructed a competing endogenous RNA (ceRNA) network. We then utilized the Search Tool for Recurring Instances of Neighbouring Genes (STRING) and cytoHubba databases to generate a protein-protein interaction (PPI) network, which led to the identification of hub genes. The top two hub genes with the highest Maximal Clique Centrality (MCC) score in the PPI network were further validated via quantitative real-time polymerase chain reaction (qRT-PCR) using in-house clinical samples. Also, weighted gene co-expression network analysis (WGCNA) with genes from the Gene Expression Omnibus Series (GSE)121239 dataset identified hub modules that were associated with clinical indicators. In addition, the genes contained in key modules as obtained by WGCNA were enriched and analyzed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) online tool. The top hub gene, X-linked apoptosis inhibitory protein-associated factor (XAF1), was then identified by intersection of the PPI and WGCNA outcomes, and a pan-cancer analysis of this hub gene was subsequently performed. Results: We comprehensively profiled the expression of Circular RNAs (circRNAs), MicroRNAs (miRNAs), and messenger RNAs (mRNAs) in SLE. We identified a hub gene, XAF1, based on evidence from the ceRNA network, WGCNA key module genes, and PPI network analyses. Moreover, qRT-PCR analysis demonstrated that the expression of XAF1 was significantly upregulated in SLE. Through the pan-cancer analysis, we demonstrated the common molecular roles of XAF1 in the pathogenesis of SLE and tumors, especially cutaneous melanoma. Conclusions: XAF1 is a key molecular biomarker in SLE. The pan-cancer analysis in this study provided shared genomic characteristics in SLE and cancers, especially for skin cutaneous melanoma (SKCM).