Abstract Rationale Influenza A virus (IAV) infection severely disrupts mucociliary clearance (MCC), the airway’s primary defense mechanism, and can lead to persistent lung injury and characteristic respiratory symptoms such as productive cough and sputum overproduction in recovering patients. However, the mechanisms underlying this chronic morbidity, particularly the MCC damage-repair cycle, cell fate transitions, and virus-host interactions post IAV infection—remain poorly understood, posing a critical barrier to the development of targeted therapies. Methods Human ALI culture and mice were utilized to track the MCC damage-repair cycle post IAV infection, in vitro and in vivo. A μOCT-based functional imaging analysis were performed to quantify MCC dynamics, including ciliary dyskinesia and mucus hypersecretion. Lineage tracing of infected cells was combined with single cell RNA-seq and proteomics to understand cell fate transition, cellular and virus-epithelium interactions. Genetic and chemical perturbations were performed to elucidate the mechanism behind MCC disorders. Results μOCT imaging revealed prolonged MCC damage— after viral clearance, characterized by ciliary loss and mucin hypersecretion, which was not repaired until 14 days post infection in human ALI culture and mice in vivo. Lineage tracing combined with multiomics demonstrated a ciliated-to-mucous cell fate transition, which was promoted by the IAV-hijacked IFN response pathway, contributing to persistent mucus hypersecretion. We further identified viral protein as a key disruptor of host ciliogenesis: IAV downregulates the master regulator TP73, suppressing FOXJ1 and RFX3, while viral protein promotes proteasomal degradation of FOXJ1, creating a feed-forward loop that perpetuates ciliary dysfunction. Conclusions Our findings reveal the damage-repair cycle of MCC after IAV infection. We uncovered a ciliated-to-mucous cell fate transition responsible for mucus hypersecretion, and reveal a novel strategy by which IAV exploits host repair mechanisms to change cell fate. We identify two key targetable pathways that are central to post-influenza mucus hypersecretion and ciliary injury, respectively. These findings reveal promising therapeutic targets to restore mucosal homeostasis and prevent post-viral complications. This abstract is funded by: National Natural Science Foundation of China (82301945, 22HAA00617); the Pearl River Talent Recruitment Program (2024QN11Y223)
Ye et al. (Fri,) studied this question.