Articles

Distinct COPD subtypes in former smokers revealed by gene network perturbation analysis

Buschur, Kristina L.; Riley, Craig; Saferali, Aabida; Castaldi, Peter; Zhang, Grace; Aguet, Francois; Ardlie, Kristin G.; Durda, Peter; Craig Johnson, W.; Kasela, Silva; Liu, Yongmei; Manichaikul, Ani; Rich, Stephen S.; Rotter, Jerome I.; Smith, Josh; Taylor, Kent D.; Tracy, Russell P.; Lappalainen, Tuuli; Graham Barr, R.; Sciurba, Frank; Hersh, Craig P.; Benos, Panayiotis V.

Background
Chronic obstructive pulmonary disease (COPD) varies significantly in symptomatic and physiologic presentation. Identifying disease subtypes from molecular data, collected from easily accessible blood samples, can help stratify patients and guide disease management and treatment.
Methods
Blood gene expression measured by RNA-sequencing in the COPDGene Study was analyzed using a network perturbation analysis method. Each COPD sample was compared against a learned reference gene network to determine the part that is deregulated. Gene deregulation values were used to cluster the disease samples.
Results
The discovery set included 617 former smokers from COPDGene. Four distinct gene network subtypes are identified with significant differences in symptoms, exercise capacity and mortality. These clusters do not necessarily correspond with the levels of lung function impairment and are independently validated in two external cohorts: 769 former smokers from COPDGene and 431 former smokers in the Multi-Ethnic Study of Atherosclerosis (MESA). Additionally, we identify several genes that are significantly deregulated across these subtypes, including DSP and GSTM1, which have been previously associated with COPD through genome-wide association study (GWAS).
Conclusions
The identified subtypes differ in mortality and in their clinical and functional characteristics, underlining the need for multi-dimensional assessment potentially supplemented by selected markers of gene expression. The subtypes were consistent across cohorts and could be used for new patient stratification and disease prognosis.

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Also Published In

Title
Respiratory Research
DOI
https://doi.org/10.1186/s12931-023-02316-6

More About This Work

Published Here
July 22, 2024

Notes

COPD, Graphical models, Gene expression, Disease subtypes