Identification of Dendritic Cell-Associated Genes in COPD Based on Bioinformatics

The activation of dendritic cells, which is atypical, is vital for triggering the acquired immune response in people afflicted with chronic obstructive pulmonary disease (COPD). This research seeks to pinpoint significant genes linked to dendritic cells within the lung tissues of COPD patients by utilizing bioinformatics predictions and experimental validation.

Differentially expressed genes of classical dendritic cells (cDCs) were identified using single-cell RNA sequencing (scRNA-seq) data from GSE196638, and their biological functions and regulatory signaling pathways were thoroughly explored. Additionally, RNA sequencing (RNA-seq) data from GSE26296 was utilized to analyze differentially expressed genes in myeloid dendritic cells (mDCs) of emphysema patients. The RNA-seq data from GSE38974 underwent weighted gene co-expression network analysis (WGCNA) along with differential analysis to pinpoint genes that are differentially expressed and modules linked to COPD. Validation was performed using a mouse model of emphysema induced by cigarette smoke (CS) and bone marrow-derived dendritic cells (BMDCs) exposed to 3% cigarette smoke extract (CSE).

The genes that showed differential expression in cDCs and mDCs were mainly associated with immune responses, the reaction to interferon-gamma, the differentiation of Th1 and Th2 cells, along with the signaling pathways of TNF and IL-17. The WGCNA results revealed that the green-yellow and red modules exhibited the highest correlation coefficients with the COPD phenotype. An assessment of the genes that are expressed differently between cDCs and mDCs, combined with the intersection of GSE38974 module genes and differentially expressed genes, results in the identification of four dendritic cells (DCs)-related genes: one upregulated signature gene (RASGRP3) and three downregulated signature genes (C1QB, BLOC1S2, VSIG4). In both the lung tissues of mice with CS-induced emphysema and in CSE-treated BMDCs, RT-qPCR validated the expression trends of these four genes. Concomitantly, Western blot revealed a reduction in VSIG4 protein level in the lung tissues of emphysema mice compared with the control group.

RASGRP3, C1QB, BLOC1S2, and VSIG4 may represent DCs-related genes in the lung tissue of COPD patients, potentially involved in the development and progression of emphysema.