Transcriptomic Signature of Asthma-Chronic Obstructive Pulmonary Disease Overlap in Whole Blood

ACDC: a general approach for detecting phenotype or exposure associated co-expression

Background

Existing module-based differential co-expression methods identify differences in gene-gene relationships across phenotype or exposure structures by testing for consistent changes in transcription abundance. Current methods only allow for assessment of co-expression variation across a singular, binary or categorical exposure or phenotype, limiting the information that can be obtained from these analyses.

Methods

Here, we propose a novel approach for detection of differential co-expression that simultaneously accommodates multiple phenotypes or exposures with binary, ordinal, or continuous data types.

Results

We report an application to two cohorts of asthmatic patients with varying levels of asthma control to identify associations between gene co-expression and asthma control test scores. Results suggest that both expression levels and covariances of ADORA3, ALOX15, and IDO1 are associated with asthma control.

Conclusion

ACDC is a flexible extension to existing methodology that can detect differential co-expression across varying external variables.

Genetic Determinants in Airways Obstructive Diseases: The Case of Asthma Chronic Obstructive Pulmonary Disease Overlap

Genome-wide association studies (GWAS) of asthma and chronic obstructive pulmonary disease (COPD) with ever-increasing sample sizes have found multiple genetic loci associated with either disease. However, there are few intersecting loci between asthma and COPD. GWAS specifically focused on asthma-COPD overlap (ACO) have been limited by smaller sample sizes and the lack of a consistent definition of ACO that has also hampered clinical and epidemiologic studies. Other genomic techniques, such as gene expression profiling, are feasible with smaller sample sizes. Genetic analyses of objective measures of airway reactivity and allergy/T2 inflammation biomarkers in COPD studies may be another strategy to overcome limitations in ACO definitions.

Blood RNA sequencing shows overlapping gene expression across COPD phenotype domains

RATIONALE

COPD can be assessed using multidimensional grading systems with components from three domains: pulmonary function tests, symptoms and systemic features. Clinically, measures may be used interchangeably, though it is not known if they share similar pathobiology.

OBJECTIVE

To use RNA sequencing (RNA-seq) to determine if there is an overlap in the underlying biological mechanisms and consequences driving different components of the multidimensional grading systems.

METHODS

Whole blood was collected for RNA-seq from current and former smokers in the Genetic Epidemiology of COPD study. We tested the overlap in gene expression and biological pathways associated with case-control status and quantitative COPD phenotypes within and between the three domains.

RESULTS

In 2647 subjects, there were 3030 genes differentially expressed in any of the three domains or case-control status. There were five genes that overlapped between the three domains and case-control status, including G protein-coupled receptor 15(GPR15), sestrin 1 (SESN1) and interferon-induced guanylate-binding protein 1 (GBP1), which were associated with longitudinal decline in FEV1. The overlap between the three domains was enriched for pathways related to cellular components.

CONCLUSIONS

We identified gene sets and pathways that overlap between 12 COPD-related phenotypes and case-control status. There were no pathways represented in the overlap between the three domains and case-control status, but we identified multiple genes that demonstrated a consistent pattern of expression across several of the phenotypes. Patterns of gene expression correlation were generally similar to the correlation of clinical phenotypes in the PFT and symptom domains but not the systemic features.

Asthma-COPD Overlap: What Are the Important Questions?

Asthma-COPD overlap (ACO) is a heterogeneous condition that describes patients who show persistent airflow limitation with clinical features that support both asthma and COPD. Although no single consensus definition exists to diagnose this entity, common major criteria include a strong bronchodilator reversibility or bronchial hyperreactivity, a physician diagnosis of asthma, and a ≥ 10-pack-year cigarette smoking history. The prevalence of ACO ranges from 0.9% to 11.1% in the general population, depending on the diagnostic definition used. Notably, patients with ACO experience greater symptom burden, worse quality of life, and more frequent and severe respiratory exacerbations than those with asthma or COPD. The underlying pathophysiologic features of ACO have been debated. Although emerging evidence supports the role of environmental and inhalational exposures in its pathogenesis among patients with a pre-existing airway disease, biomarker profiling and genetic analyses suggest that ACO may be a heterogeneous condition, but with definable characteristics. Early-life factors including childhood-onset asthma and cigarette smoking may interact to increase the risk of airflow obstruction later in life. For treatment options, the population with ACO historically has been excluded from therapeutic trials; therefore strong, evidence-based recommendations are lacking beyond first-line inhaler therapies. Advanced therapies in patients with ACO are selected according to disease phenotypes and are based on extrapolated data from asthma and COPD. Research focused on defining biomarkers and evidence-based treatment options for ACO is needed urgently.