Abstract Rationale Small airway disease is a hallmark of COPD and recent work has defined distinct small airway lesions, that emerge with disease progression, and include “web”, “occlusion”, and “collapse” (Geudens et al., AJRCCM, 2025). However, despite a growing appreciation of the structural heterogeneity of small airway disease, the cellular microenvironments and underlying biology that drive these lesions is unknown. Objective To define the cellular pathology underlying structurally distinct small airway lesions in COPD. Methods We performed an integrated radiological and molecular analysis combining microCT, spatial transcriptomics, and single-nuclear RNA sequencing (snRNA-seq) on inflated and frozen lung tissue cylinders from nine human lungs: three control donor lungs without emphysema, three lungs with emphysema (5-20% based on radiologist assessment), and three COPD GOLD IV explants. A 10-µm-resolution microCT scan was used to map distinct small-airway lesions, after which individual lesions were sectioned, allowing precise isolation of both diseased and normal small airways. Airways were profiled using Xenium spatial transcriptomics with a 480-gene custom panel; data underwent quality control and were analyzed with Seurat v5.1. Results MicroCT identified 45 individual small airways: normal (n = 14), web (n = 9), occlusion (n = 4), and collapse (n = 18) lesions. Small airways were confirmed histopathologically and registered to spatial transcriptomic maps (28.071.607 transcripts and 659.051 cells) (Fig. 1a-c). Across compartments, we identified 53 distinct canonical cell types and previously validated cell states (Zhang et al., Nature Genetics, in press), including fibroblast/perivascular (n = 6), endothelial (n = 11), epithelial (n = 12), myeloid (n = 8), and lymphoid/dendritic (n = 12) populations. In addition to the tissue, also associated mucus plugs were profiled and found to consist predominantly of accumulated macrophages and epithelial cells (Fig. 1d). Across samples, we identified distinct lesion-specific patterns of cellular co-occurrence and an evolution from web to occlusion to collapse. Conclusions This study establishes a proof of concept for integrating microCT-based lesion mapping, precision microdissection and spatial transcriptomics to define the cellular architecture of small airway disease. Together with ongoing snRNA-seq analyses from the same samples, these data will refine our understanding of lesion subtypes in early-stage COPD and may ultimately guide the development of targeted interventions to prevent disease progression. This abstract is funded by: DOD
Geudens et al. (Fri,) studied this question.