Epithelial-mesenchymal crosstalk is essential in lung development and repair upon injury. Such crosstalk occurs in specific subtissular niches, in which niche-specific epithelial cell states interact with their mesenchymal counterparts, either driving alveologenesis or re-epithelialization. IPF is characterized by a fulminant profibrotic niche, the fibroblast focus, in which CTHRC1+ myofibroblasts reside in close contact with KRT17+/KRT5- basaloid cells. Although it is currently unknown how these fibrosis-specific cell states evolve, it probably occurs through various preceding injury associated profibrotic cell states (IAPCS). In this study, we aimed to: 1) identify IAPCS in the alveolar space, 2) characterize their distinct niche environments, and 3) study how such niche environments change during the progression of fibrotic disease. 
 
To study the progression of human fibrogenesis, we microCT-staged 90 IPF explant lung samples (mild, moderate and severe disease) and compared these with 45 control samples. Using snRNAseq, laser-capture microdissection-based spatial proteomics and multiplexed immunofluorescence (4i) imaging, we identified a spectrum of IAPCS residing in distinct niches with unique proteomic profiles. Cell-cell communication analysis uncovered niche-specific ligand-receptor interactions putatively driving disease progression.
 
In conclusion, our multimodal analysis provides a (1) map of the evolution of epithelial and mesenchymal cell states throughout disease progression in IPF, and (2) predicts critical cell-cell communication events in the alveolar and terminal airway niches.