Blood Gene Expression and Immune Cell Subtypes Associated with Chronic Obstructive Pulmonary Disease Exacerbations

Abstract

Rationale: Acute exacerbations of chronic obstructive pulmonary disease (AE-COPDs) are associated with a significant disease burden. Blood immune phenotyping may improve our understanding of a COPD endotype at increased risk of exacerbations. Objective: To determine the relationship between the transcriptome of circulating leukocytes and COPD exacerbations. Methods: Blood RNA sequencing data (n = 3,618) from the COPDGene (Genetic Epidemiology of COPD) study were analyzed. Blood microarray data (n = 646) from the ECLIPSE (Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints) study were used for validation. We tested the association between blood gene expression and AE-COPDs. We imputed the abundance of leukocyte subtypes and tested their association with prospective AE-COPDs. Flow cytometry was performed on blood in SPIROMICS (Subpopulations and Intermediate Outcomes in COPD Study) (n = 127), and activation markers for T cells were tested for association with prospective AE-COPDs. Measurements and Main Results: Exacerbations were reported 4,030 and 2,368 times during follow-up in COPDGene (5.3 ± 1.7 yr) and ECLIPSE (3 yr), respectively. We identified 890, 675, and 3,217 genes associated with a history of AE-COPDs, persistent exacerbations (at least one exacerbation per year), and prospective exacerbation rate, respectively. In COPDGene, the number of prospective exacerbations in patients with COPD (Global Initiative for Chronic Obstructive Lung Disease stage ⩾2) was negatively associated with circulating CD8⁺ T cells, CD4⁺ T cells, and resting natural killer cells. The negative association with naive CD4⁺ T cells was replicated in ECLIPSE. In the flow-cytometry study, an increase in CTLA4 on CD4⁺ T cells was positively associated with AE-COPDs. Conclusions: Individuals with COPD with lower circulating lymphocyte counts, particularly decreased CD4⁺ T cells, are more susceptible to AE-COPDs, including persistent exacerbations.

Keywords: COPD exacerbation; RNA sequencing; chronic obstructive pulmonary disease; circulating leukocytes; immune phenotyping.

Figure 1.

Volcano plots for differentially expressed genes in COPDGene (Genetic Epidemiology of COPD) whole-blood RNA-sequencing analysis. (A) History of exacerbation was defined as having one or more exacerbations in the year before the study visit. (B) Prospective exacerbation rate was defined as log(total number of exacerbation + 0.5) – log(years followed + 1). (C) Persistent exacerbators were participants with at least one prospective exacerbation per year in the follow-up years. For differential gene-expression analyses, linear models were adjusted for age, race, sex, current smoking status, smoking pack-years, library generation batch, and surrogate variables for technical variation.

Figure 2.

Numbers of genes and pathways significantly associated with exacerbation measures. (A) Venn diagram showing overlap between differentially expressed genes in the three separate analyses. Persistent exacerbators were participants with at least one prospective exacerbation per year in the follow-up years. History of exacerbation was defined as having one or more exacerbations in the year prior to the study visit. Prospective exacerbation rate was defined as log(total number of exacerbation + 0.5) – log(years followed + 1). For differential gene expression analyses, linear models were adjusted for age, race, sex, current smoking status, smoking pack-years, library generation batch, and surrogate variables for technical variation. (B) Venn diagram showing the number of overlaps between significantly enriched Kyoto Encyclopedia of Genes and Genomes pathways identified in Signature Overrepresentation Analysis. DEG = differentially expressed gene.