Image-based spatial transcriptomics identifies molecular niche dysregulation associated with distal lung remodeling in pulmonary fibrosis [Xenium]

Large-scale changes in the structure and cellular makeup of the distal lung are a hallmark of pulmonary fibrosis (PF), but the spatial contexts that contribute to disease pathogenesis have remained uncertain. Using image-based spatial transcriptomics, we analyzed the gene expression of 1.6 million cells from 35 unique lungs. Through complementary cell-based and innovative cell-agnostic analyses, we characterized the localization of PF-emergent cell types, established the cellular and molecular basis of classical PF histopathologic features and identified a diversity of distinct molecularly defined spatial niches in control and PF lungs. Using machine learning and trajectory analysis to segment and rank airspaces on a gradient of remodeling severity, we identified compositional and molecular changes associated with progressive distal lung pathology, beginning with alveolar epithelial dysregulation and culminating with changes in macrophage polarization. Together, these results provide a unique, spatially resolved view of PF and establish methods that could be applied to other spatial transcriptomic studies. Sample names were generated based on their collection site (Vanderbilt University-'VU'; Translational Genomics Research Institute-'T'), disease status (healthy donor-'HD'; interstitial lung disease-'ILD'), unique number assigned to the patient and where applicable, whether the sample was taken from a 'less affected' or 'more affected' tissue section as determined by percent pathology scores. Replicate healthy samples were labeled 'A' and 'B' to distinguish (for example, VUHD116A and VUHD116B), and replicate disease samples with the same 'less affected' or 'more affected' designation were labeled '1' and '2' (for example, VUILD105MA1 and VUILD105MA2). UPDATE [May-08-2025]: - GSM7990534_output-XETG00048__0003400__TILD117MA__20230313__191400_transcripts.csv.gz was replaced by GSM7990534_output-XETG00048__0003400__TILD117MA1__20230313__191400_transcripts.csv.gz - GSM8505453_TILD117MA_transcripts.csv.gz was replaced by GSM8505453_TILD117MA2_transcripts.csv.gz UPDATE [June-06-2025]: The processed data were updated.