Integrating single-cell sequencing and metabolomics reveals the macrophages heterogeneity in glucocorticoids-induced immunocompromised mice during Pneumocystis infection

With the extensive use of glucocorticoids (GCs), the occurrence of immunocompromised patients is increasingly raised. Pneumonia, caused by opportunistic pathogens including Pneumocystis (PC), is a major cause of morbidity and mortality. The loss of adaptive immune responses have been demonstrated as a key reason for the infection of Pneumocystis. Nevertheless, the alterations of innate immunity by GCs treatment and the subsequent effects remain unclear. Here we integrated the single-cell RNA sequencing and metabolomic analysis to decipher the alterations of the innate immunity in immunocompromised mice with PC infection. Our results have shown that a group of Mmp12+ macrophages was enriched in lung tissues of the immunocompetent mice upon PC infection. Pathway enrichment analysis showed obviously up-regulated pro-inflammatory pathways, suggesting that these Mmp12+ macrophages may be essential for the protection against PC infection. In the dexamethasone (DEX)-treated mice, the monocyte differentiation towards Mmp12+ macrophages was dramatically hampered via downregulating the granulocyte/macrophage colony-stimulating factor (GM-CSF) signaling. Further, DEX treatment simultaneously impaired the metabolic and functional integrity of resident macrophages through down-regulating lysophosphatidylcholine and GM-CSF. These induced suppressed host antimicrobial capacities. The results of our study provides a rich resource for understanding the heterogeneity and changes in macrophages and also provides novel insights into immune response take place in GCs-induced immunosuppressed mice during PC infection. Overall design: Single-cell RNA profiles of immunocompetent or Dexamethasone(DEX)-induced immunocompromised mices with or without Pneumocystis infection for 2 weeks.