Journal Article

Bioinformatics analyses of combined databases identify shared differentially expressed genes in cancer and autoimmune disease

Fu, Xue-Qi, Xing, Shu, Sui, Yuan, Li, Shuping, Zhao, Zhizhuang Joe

2023

Overview

Background Inadequate immunity caused by poor immune surveillance leads to tumorigenesis, while excessive immunity due to breakdown of immune tolerance causes autoimmune genesis. Although the function of immunity during the onset of these two processes appears to be distinct, the underlying mechanism is shared. To date, gene expression data for large bodies of clinical samples are available, but the resemblances of tumorigenesis and autoimmune genesis in terms of immune responses remains to be summed up. Methods Considering the high disease prevalence, we chose invasive ductal carcinoma (IDC) and systemic lupus erythematosus (SLE) to study the potential commonalities of immune responses. We obtained gene expression data of IDC/SLE patients and normal controls from five IDC databases (GSE29044, GSE21422, GSE22840, GSE15852, and GSE9309) and five SLE databases (GSE154851, GSE99967, GSE61635, GSE50635, and GSE17755). We intended to identify genes differentially expressed in both IDC and SLE by using three bioinformatics tools including GEO2R, the limma R package, and Weighted Gene Co-expression Network Analysis (WGCNA) to perform function enrichment, protein-protein network, and signaling pathway analyses. Results The mRNA levels of signal transducer and activator of transcription 1 (STAT1), 2'-5'-oligoadenylate synthetase 1 (OAS1), 2'-5'-oligoadenylate synthetase like (OASL), and PML nuclear body scaffold (PML) were found to be differentially expressed in both IDC and SLE by using three different bioinformatics tools of GEO2R, the limma R package and WGCNA. From the combined databases in this study, the mRNA levels of STAT1 and OAS1 were increased in IDC while reduced in SLE. And the mRNA levels of OASL and PML were elevated in both IDC and SLE. Based on Kyoto Encyclopedia of Genes and Genomes pathway analysis and QIAGEN Ingenuity Pathway Analysis, both IDC and SLE were correlated with the changes of multiple components involved in the Interferon (IFN)-Janus kinase (JAK)-signal transducer and activator of transcription (STAT) signaling pathway. Conclusion The expression levels of STAT1 and OAS1 manifest the opposite expression tendency across cancer and autoimmune disease. They are components in the IFN-JAK-STAT signaling pathway related to both tumorigenesis and autoimmune genesis. STAT1 and OAS1-associated IFN-JAK-STAT signaling could explain the commonalities during tumorigenesis and autoimmune genesis and render significant information for more precise treatment from the point of immune homeostasis.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Analysis / Apoptosis / Autoimmune diseases / Autoimmune genesis / Bioinformatics / Biomedical and Life Sciences / Biomedicine / Breast cancer / Cancer / Carcinogenesis / Computational Biology / Cytotoxicity / Data collection / Disease / Gene expression / Genetic aspects / Genomes / Health aspects / Homeostasis / Humans / Immune response / Immune system / Immunobiology and immunotherapy / Immunological tolerance / Immunosurveillance / Interferon / Invasive ductal carcinoma / Janus kinase / Janus Kinases - therapeutic use / Lupus / Lupus Erythematosus, Systemic - genetics / Lymphocytes / Medicine/Public Health / Neoplasms / OAS1 / Pathogens / Prevention / Proteins / Risk factors / RNA, Messenger - metabolism / Signal transduction / STAT1 / Stat1 protein / Systemic lupus erythematosus / Tumorigenesis