Increased expression of BCL11B and its recruited chromatin remodeling factors during highly active antiretroviral therapy synergistically represses the transcription of human immunodeficiency virus type 1 and is associated with residual immune activation

Identification of Biomarkers for Sarcoidosis and Tuberculosis of the Lung Using Systematic and Integrated Analysis

Background

Sarcoidosis (SARC) is a multisystem inflammatory disease of unknown etiology and pulmonary tuberculosis (PTB) is caused by Mycobacterium tuberculosis. Both of these diseases affect lungs and lymph nodes and share similar clinical manifestations. However, the underlying mechanisms for the similarities and differences in genetic characteristics of SARC and PTB remain unclear.

Material/Methods

Three datasets (GSE16538, GSE20050, and GSE19314) were retrieved from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) in SARC and PTB were identified using GEO2R online analyzer and Venn diagram software. Functional enrichment analysis was performed using Database for Annotation, Visualization and Integrated Discovery (DAVID) and R packages. Two protein–protein interaction (PPI) networks were constructed using Search Tool for the Retrieval of Interacting Genes database, and module analysis was performed using Cytoscape. Hub genes were identified using area under the receiver operating characteristic curve analysis.

Results

We identified 228 DEGs, including 56 common SARC-PTB DEGs (enriched in interferon-gamma-mediated signaling, response to gamma radiation, and immune response) and 172 SARC-only DEGs (enriched in immune response, cellular calcium ion homeostasis, and dendritic cell chemotaxis). Potential biomarkers for SARC included CBX5, BCL11B, and GPR18.

Conclusions

We identified potential biomarkers that can be used as candidates for diagnosis and/or treatment of patients with SARC.