Spatial transcriptomic and morpho-functional information derived from single mouse FFPE slides allows in-depth fingerprinting of lung fibrosis

RNA sequencing can provide insightful information on the molecular processes underlying development and progression of multiple diseases, including idiopathic pulmonary fibrosis (IPF) and its bleomycin (BLM)-induced preclinical model. We investigated the feasibility of applying RNAseq analysis to formalin-fixed and paraffin-embedded (FFPE) lung slides from control and BLM-treated mice. The results were validated by comparison with public bulk data from fresh-frozen mouse tissue and human IPF biopsies. Unsupervised cluster analysis on Differentially Expressed Genes revealed gene clusters associated with extracellular matrix organization, tissue remodeling and inflammatory response pathways, distinguishing untreated and BLM-treated fibrotic lung samples. For each sample, expression levels of individual gene clusters were highly correlated with 2D histology readouts and aeration compartments determined on matched 2D coronal slices by micro-CT imaging. This combined approach can produce a precise, spatially oriented picture of pulmonary disease development, paving the way to the identification of novel translationally relevant biomarkers and therapeutic targets.