Identification of Five Candidate Genes and Development of an Exploratory Diagnostic Nomogram for COPD Using Integrative Single-Cell and Bulk Transcriptomic Analyses

Integrative transcriptomic analyses can prioritize genes associated with chronic obstructive pulmonary disease (COPD), but expression associations require experimental assessment.

Single-cell GSE173896 and bulk GSE57148 data were analyzed using clustering, co-expression networks, CellChat, differential expression, immune deconvolution, pseudotime, and virtual knockout analysis. A five-gene logistic nomogram was developed in GSE57148. Clinical RT-qPCR included 30 participants with COPD and 30 without COPD. Two independent IL6-targeting siRNAs were examined in HBEC3-KT and BEAS-2B cells using epithelial-macrophage co-culture, cytokine measurements, and wound-healing assays.

NHSL2, CDKL5, CRIP1, TNNI2, and IL6 were prioritized as candidate genes. Clinical RT-qPCR supported higher CDKL5, IL6, and NHSL2 expression and lower CRIP1 and TNNI2 expression in COPD. IL6 knockdown reduced epithelial IL6 expression and attenuated several macrophage-associated transcriptional responses in co-culture after epithelial cigarette smoke extract exposure. Secretory responses varied by cell line and siRNA; co-culture IL-10 reductions were significant in the HBEC3-KT system but not in the BEAS-2B system. IL6 knockdown also reduced epithelial wound closure. The nomogram was evaluated within its development cohort and lacked independent external validation.

The study identifies five COPD-associated candidate genes and provides experimental evidence linking epithelial IL6 perturbation to selected co-culture responses and wound closure. These findings do not establish a COPD-specific mechanism or therapeutic benefit. The nomogram remains exploratory and requires independent validation.