Pulmonary Epithelial Injury Impairs Innate Defense and Reprograms Macrophage Function, Reducing Early Mycobacterium tuberculosis Clearance

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a significant global health burden, characterized by complex host–pathogen interactions that drive heterogeneous clinical outcomes. While pulmonary epithelial cells are increasingly recognized as active participants in innate immunity during Mtb infection, how host defences are altered when the epithelial barrier is compromised remains unclear . In this study, we developed a murine model combining naphthalene-induced airway epithelial injury with Mtb infection, and found a pronounced impairment in pulmonary bacterial clearance. Through single-cell RNA sequencing (scRNA-seq), we mapped the pulmonary cells landscape and identified widespread suppression of epithelial immune functions. Notably, we observed macrophages transition from an antimicrobial to an antigen-presenting phenotype, indicating waning pulmonary innate defenses and heightened adaptive immune activation. These findings highlight the pivotal role of pulmonary epithelial integrity in shaping host immunity against Mtb and offer new insights into potential therapeutic strategies targeting barrier–immune crosstalk. Overall design: This study analyzed lung tissues from four groups of C57BL/6 mice to investigate the impact of pulmonary epithelial injury on immune responses during Mycobacterium tuberculosis (Mtb) infection. The groups included: (1) untreated healthy controls (Control), (2) mice infected with Mtb H37Rv (H37Rv), (3) mice with naphthalene-induced epithelial injury alone (Naph), and (4) mice subjected to both epithelial injury and subsequent Mtb infection (Naph+H37Rv). One mouse per group was used for single-cell RNA sequencing. Lung cells were enzymatically dissociated from each mouse and processed individually. The design incorporates both infection and injury conditions to enable comparison between baseline, injury alone, infection alone, and combined injury-infection states. No technical replicates were included, and all samples were analyzed separately without pooling.