Fig. 4

Identification of the mechanism of abnormal CEA expression in COVID-19 patients’ and healthy volunteers’ bronchoalveolar lavage fluid (BALF). scRNA-seq data of bronchoalveolar lavage fluid (BALF) from three patients with moderate COVID-19 (C141, C142 and C144), six patients with severe or critical infection (C143, C145, C146, C148, C149 and C152) and three healthy controls (C51, C52 and C100) (accession no. GSE145926) were download from the GEO database. A UAMP analysis was performed in 63,010 cells in BALF and clearly identified 20 clusters and 11 cell types (B cell, CD4 + T cell, CD8 + T cell, dendritic cell, macrophage, monocyte, natural killer cell, neutrophil, T cell: gamma–delta, type I pneumocyte, type II pneumocyte) (A, B). All other immune cells (B cell, CD4 + T cell, CD8 + T cell, dendritic cell, monocyte, natural killer cell, neutrophil and T cell: gamma–delta) except for macrophages and type I and type II pneumocytes were dominantly differentiated and chemotactic in COVID-19 patients’ BALF compared to healthy volunteer’s BALF (C). Furthermore, in terms of the expression and distribution of CRGs, CEACAM1, CEACAM3, CEACAM5, CEACAM6, CEACAM7, CEACAM8 and CEACAM21 were differentially expressing among moderate, severe/critical COVID-19 patients and healthy controls while CEACAM5 and CEACAM6 were significantly localized in the type II pneumocytes of COVID-19 patients (D, E). In particular, F summarized the absolute quantification of 50 hallmark gene sets calculated the GSVA in type I and type II pneumocytes, suggesting that the interferon response and cell proliferation signaling pathways were significantly activated in type II pneumocytes highly expressing CRGs of COVID-19 patients (F)