Integrating Single-Cell RNA sequencing analysis to assess functional plasticity alterations of airway epithelial cells during sepsis - 09/05/26

Sepsis is a life-threatening condition caused by a dysregulated immune response to infection, often leading to organ dysfunction. While >85% of patients now survive the primary episode due to advances in treatment, they remain highly susceptible to ICU-acquired pneumonia. The airway epithelium, a key regulator of lung immune responses, may undergo sepsis-induced alterations that impair anti-infective defense.

We analyzed publicly available single-cell RNA sequencing data set (GSE207651) from a murine model of extra-pulmonary polymicrobial sepsis to investigate epithelial cell-specific transcriptional alterations during sepsis. Bioinformatic analyses were performed in R using Seurat for data preprocessing, integration, and clustering and clusterProfiler (enrichGO function) for functional enrichment analysis based on Gene Ontology Biological Processes.

ScRNA-seq analysis of lung tissues obtained 24 h and 48 h after Ceacal ligation and puncture (CLP) or sham-operated mice revealed epithelial cell type–specific transcriptomic alterations. Alveolar Type I cells (AT I) showed no transcriptional changes. In contrast, ciliated, club, and alveolar type II (AT II) cells exhibited upregulation of S100a8 and S100a9 , consistent with enhanced inflammatory signaling post-sepsis. Club cells showed increased expression of Fmo2 , Pdk4 , and Cyp2b10 , indicating altered fatty acid metabolism and oxidation. Both ciliated and AT II cells exhibited downregulation of genes involved in chaperone-mediated protein folding (e.g. Hsp8 , Hsp90ab1 , St13 ) and upregulation of Lcn2 (ROS biosynthesis). Specifically in ciliated cells, we observed downregulation of cellular respiration and mitochondrial organization related genes (e.g. Cox8a , Cox17 and Hmgb1 ), and of the Ptn gene, which encodes pleiotrophin, suggesting an impaired epithelial repair process. Additionally, ciliated cells showed reduced expression of genes associated with microtubule and ciliary movement (e.g. Dnaj1 , Tubb4b , and Tuba1a ). AT II-specific changes included increased expression of Slpi (inhibition of serine proteases such as neutrophil elastase), and Rgcc , Ngp , Foxp1 (endothelial proliferation/VEGF regulation) and reduced Cd36 , Slc12a2 (wound healing), Scgb1a1 (immune modulation and epithelial repair), surfactant genes ( Sftpc , Sftpa ) and Cldn18 (barrier integrity).

Together, these findings indicate that sepsis induces a profound and cell type–specific transcriptional reprogramming of respiratory epithelial cells potentially contributing to impaired inflammatory response, cellular respiration and energy, metabolism, mucociliary clearance, epithelial repair, and barrier function in the post-septic lung.