Single cell transcriptomics in blood of patients with chronic obstructive pulmonary disease
Background Chronic obstructive pulmonary disease (COPD) is a leading cause of morbidity and mortality worldwide. Single-cell RNA sequencing (scRNA-seq) provides gene expression profiles at the single-cell level. Hence, we evaluated gene expression in the peripheral blood of patients with COPD. Methods Peripheral blood samples from seven healthy controls and eight patients with COPD were obtained in this study. The 10X Genomics Chromium Instrument and cDNA synthesis kit was utilized to generate a barcoded cDNA library for single cell RNA-sequencing. We compared the scRNA-seq data between the COPD and control groups using computational analysis. Functional analyses were performed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses. Results scRNA-seq was used to analyze the transcriptome of peripheral blood mononuclear cells from seven normal controls and eight patients with COPD. We found increased numbers of monocyte macrophages in the COPD group compared to those in the normal control group. Among the differentially expressed genes (DEGs) in monocyte-macrophages, we identified five upregulated genes (HLA-DRB5, ITGB2, EGR1, CXCL8, and CCL4) and seven downregulated genes (FOLR3, RPS4Yq, CD52, LY6E, HLA-DQB1, G0S2, and CCL3L1) in the COPD group compared to the normal control group. Conclusions Using scRNA-seq, we found differences in cell type distribution, especially in monocyte macrophages. Several upregulated and downregulated genes were found in the monocyte-macrophages of the COPD groups. Overall design: Data from the Chronic Obstructive Pulmonary Disease in Dusty Areas (CODA) cohort were analyzed. The CODA cohort enrolled participants living in six cities (Gangneung, Donghae, Samcheok, Yeongwol, Danyang, and Jecheon) near cement plants in the Kangwon and Chungbuk provinces of South Korea between 2012 and 2017. Among the COPD group and the heath group who participated in the CODA cohort, patients who agreed to participate in our study were divided into two groups and scRNA sequencing was performed on peripheral blood samples. We obtained data from seven healthy participants and eight participants with COPD from the CODA cohort. Peripheral blood samples were obtained by dividing the patients living in two cities (Samcheok and Yeongwol) into two groups: COPD and normal control. Peripheral blood mononuclear cells (PBMCs) were isolated by density centrifugation and processed directly or after frozen storage, labeled with cell hashing antibodies and loaded on droplet-based (10x) scRNA-seq platforms