Identification of abnormal airway niches in the fibrotic lung using spatial transcriptomics - 20/03/24

Currently, there is no information about the cellular and molecular mechanism underlying long COVID-associated lung parenchymal abnormalities. Even if a relatively low fraction of these abnormalities persists, or worse, progress to fibrosis, we will be facing a substantial healthcare challenge with detrimental implications for patients and society. Thus, using cellular resolution spatial transcriptomic technology, we analyzed and compared the tissue from patient with long COVID and IPF patients.

We performed COSmx technology on 7 FFPE slides obtained from 7 patients with early IPF, long COVID or ILA (interpreted as normal). The lung tissue was sampled via a cryobiopsy performed in Forly hospital (Dr Ravaglia, Italy). 3 tissues sections were placed on a slide, stained (Pancytokeratine, CD45, CD3) and imaged. A cellular segmentation was performed in region of interest selected from the stained tissue and the transcriptomic expression pattern obtained from a 1000 genes panel was aligned on each segmented cell.

In all, 139,182 cells were analyzed, the mean number of transcripts per cell was 125. All the major cell types were identified on the integrated UMAP including airway epithelial cells, alveolar epithelial cells, stromal cells vascular endothelial cells and immune cells. As compared to controls, lung tissue one long COVID and IPF patients showed an increased proportion fibroblast and pro fibrotic macrophages (SPP1+, MMP9+, CHI3L1+) proportion in the distal lung (Fig. 1A). Long COVID patients showed an increased proportion of plasmocytes near the proximal airways as compared to IPF and Control patients (Fig. 1B). Aberrant basaloid cells were identified in one long COVID patients, predominantly located near the basal cells (Fig. 1B and C). Analysis of the vascular endothelial cells revealed an enrichment of veinous cells COL15A1+ in the IPF lung and in one long COVID patients (Fig. 1D).

These preliminary results suggest abnormal cell population described in the IPF lung can be identified in the long COVID lung. We will confirm these data with a single cell analysis from frozen sample in a larger cohort.