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Single cell transcriptomics in blood of patients with chronic obstructive pulmonary disease

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE249584 | GEO | 2024/10/01

REPOSITORIES: GEO

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Project description:Rationale: Chronic Obstructive Pulmonary Disease (COPD) is considered a chronic inflammatory disease characterized by progressive airflow limitation and also has significant extrapulmonary (systemic) effects that lead to comorbid conditions. Very little is known about the pathomechanism of the disease. Objectives: Among inflammatory cell types, alveolar macrophages appear to have a key role in initiating and/or sustaining disease progression. These cells are derived from peripheral monocytes. Identification of disease and cell type specific gene expression profiles can be revealing and also practically useful in order to diagnose and characterize disease progression and the effect of drug treatment. Methods: We used Affymetrix microarrays to obtain gene expression data of alveolar macrophages and circulating monocytes of COPD and healthy control patients. The microarray results were confirmed by quantitative real-time polymerase chain reaction in multiple patient collections. Measurements and Main Results: We have identified gene sets specifically associated with COPD in alveolar macrophages and also in monocytes. Immune function, responses to stimuli, and cell death related genes appear to be impacted in both cell types. Remarkably, there is an overlapping gene set between the two cell types. Conclusions: Taken together, our data show that COPD-specific gene signatures can be identified and validated, and that the disease also affects peripheral monocytes. Moreover, monocytes and alveolar macrophages carry overlapping gene expression signatures. Our findings further support the notion that altered responsiveness to stimuli is the key characteristic of alveolar macrophages and also of their precursors, peripheral monocytes. Brochoalveolar lavage fluid samples were collected from of COPD and healthy control patients. Alveolar macrophages were isolated using Percoll gradient centrifugation, isolated using CD14+ magnetic beads, and total RNA was extracted using Qiagen RNeasy Kit. The monocyte samples represent a pool of RNA from 5 patients. Total RNA was labeled with biotin and individual samples were hybridized to Affymetrix HG U133A GeneChips. Affymetrix data files were analyzed using GeneSpring 7.3 software. Using a non-parametric statistical test, we compared the gene expression patterns of the COPD and the healthy control patients and identified a set a genes that showed differential expression between the two groups.

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Single cell transcriptomics in blood of patients with chronic obstructive pulmonary disease

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