# Urokinase System in Pathogenesis of Pulmonary Fibrosis: A Hidden Threat of COVID-19
## 2 Results  
### uPA and uPAR Were Differentially Expressed in Lung Tissue of COVID-19 Patients  
We first addressed the role of uPA and uPAR in COVID-19-induced lung fibrosis through data-mining of scRNA-seq datasets from (i) warm postmortem lung biopsies of patients diseased from COVID-19-associated pneumonia and lung fibrosis, (ii) lung biopsies from individuals with pulmonary fibrosis (PF) and (iii) control samples (control) from healthy donors reported in [PERSON] et al. and [PERSON] et al. (GSE158127, GSE135893 [35; 36]). Among epithelial cells, only the basal cells expressed _PLAU_ and _PLAUR_ (mean and median normalized expression \(>0\)) (Figure 1A, Table S1). In COVID-19 and PF patients, the expression of _PLAU_ and _PLAUR_ in these cells was significantly decreased as compared to the control (\(p<0.0001\) vs. control, Figure 1B,C). _PLAU_ and _PLAUR_ expression was also observed in a fraction of cells from a pro-fibrogenic KRT17+ KRT5- population in COVID-19 and PF patients (Figure 1B,C), though the overall number of _PLAU_+ and _PLAUR_+ cells in this population was still low (median normalized expression 0) (Figure 1B,C). Figure 1: _PLAU_ and _PLAUR_ expression in epithelial cells of control, COVID-19 and pulmonary fibrosis (PF) lung samples: (**A**) Uniform Manifold Approximation and Projection (UMAP) embedding of jointly analyzed single-cell transcriptomes annotated by cell type (color) and disease status. Lung tissue transcriptomes of patients with COVID-19-associated pneumonia, PF and control lung samples from healthy donors, reported in [PERSON] et al. and [PERSON] et al. (GSE158127, GSE135893 [35; 36]) were analyzed. Normalized expression levels of _PLAU_ (**B**) and _PLAUR_ (**C**) grouped by different types of epithelial cells and disease status (control, COVID-19 and PF from left to right); statistics were calculated only for cell types with the median normalized expression value \(>0\) with the exception of KRT17+ KRT5- cells, where the median expression value equaled to 0, but a subpopulation of _PLAU_- and _PLAUR_-positive cells still existed. ***\(P_{\textit{adjusted}}<0.0001\) as assessed by false discovery rate (FDR). AT1 and AT2, alveolar type I and type II cells; IPF/other PF, idiopathic pulmonary fibrosis and other pulmonary fibrosis; umap, Uniform Manifold Approximation and Projection. In control mesenchymal cells, _PLAU_ expression was not normally detected (median normalized expression 0 in all cell types), and the median expression of _PLAUIR_\(>\) 0 was detected only in type 4 fibroblasts (Figure 2A). Of note, type 3 fibroblasts exhibited an elevated expression of both _PLAU_ and _PLAUIR_ in pulmonary fibrosis, while in mesothelial cells, only _PLAUIR_ expression was elevated (_p_ < 0.0001 vs. control, Figure 2B,C). The same effect was not observed in COVID-19, and it might be accounted for the unequal representation of mesenchymal cell types in tissue samples (type 3 fibroblast population was mostly lacking in the samples obtained from COVID-19 patients) (Figure 2A). The highest level of _PLAUIR_ expression was detected in the lung monocytes/macrophages within all the studied cells (Figure 3A,C), and its expression was significantly decreased in alveolar macrophages AM1-2, monocyte-derived macrophages MoM1-2, and monocytes of COVID-19 patients (_p_ < 0.001 for AM2 and \(p\) < 0.0001 for other cells vs. control, Figure 3A,C). A similar decrease in _PLAUIR_ expression was found in MoM2 cells and monocytes of PF  
Figure 2: _PLAU_ and _PLAUIR_ expression in the mesenchymal cells of control, COVID-19 and PF lung samples: (**A**) UMAP embedding of jointly analyzed single-cell transcriptomes annotated by cell type (color) and disease status. Lung tissue transcriptomes of patients with COVID-19-associated pneumonia, pulmonary fibrosis (PF) and control lung samples from healthy donors, reported in [PERSON] et al. and [PERSON] et al. (GSE158127, GSE135893 [35; 36]), were analyzed.