COVID-19 imprints airway basal cells to impair epithelium regeneration

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PROJECT SUMMARY COVID-19 (CoV19) is caused by SARS-CoV-2 infection of the airway epithelium resulting in extensive damage in the lower respiratory tract. Since 2020, CoV19 has claimed over 1 million lives in the United States surpassing the death toll of the 1918 H1N1 influenza pandemic. Clinical studies show that the mortality and morbidity of CoV19 is associated with secondary infection. Given a central role of the airway epithelium as a barrier against pathogens, preliminary studies tested whether airway basal stem cells (BSCs) are impaired in their regenerative function in CoV19 patients. Of note, BSCs are a major type of stem cells responsible for epithelium regeneration following respiratory viral infection in humans. In preliminary studies, we derived 6 lines of BSCs from severe cases of CoV19 using tracheal aspirate (TA) as a source of bronchial BSCs. These CoV19-exposed BSCs were tested free of virus; however, they show early cell cycle arrest, sustained STAT3 hyperactivity, and defective differentiation in air-liquid interface. In contract, BSCs derived from TA of control patients with neurogenic and cardiogenic respiratory failure have no such defects. Similar to our findings in vitro, antibody staining of fatal CoV19 lung sections revealed increased senescence and defective differentiation of BSCs. In addition, CoV19- exposed BSCs in vitro maintained, at least partially, an inflammatory gene signature that was found in BSCs in vivo by single cell-seq of lung samples from CoV19 patients. As such, BSCs derived from TA of CoV19 patients provide a viable cell model to investigate how CoV19 impairs epithelial regeneration by inducing an inflammatory memory in BSCs. Mechanistically, CoV19-exposed BSCs exhibit unique chromatin opening at sites enriched for transcriptional factors mediating the inflammatory pathways, such as STAT3. Based on these preliminary findings, we hypothesize that inflammation in CoV19 causes an epigenetic memory in BSCs to impair epithelium regeneration. Leveraging our ability to derive TA BSCs, Aim1 will test whether CoV19 uniquely reprograms BSCs compared to other acute respiratory infections. Aim 2 will identify the molecular mediators of the inflammatory memory in CoV19-exposed BSCs using complementary assays. The rescue assay will test whether blocking STAT3 hyperactivity and reversing epigenetic modification in CoV19-exposed BSCs will normalize their role in epithelial regeneration. The disease-mimicking assay will assess the activity of inflammatory signals in memory induction in healthy control BSCs. The proposed exploratory studies will lay the foundation for future delineation of inflammatory signals and intracellular mediators in the disease memory of BSCs using genetic approaches and animal models of SARS-CoV-2 infection. Our findings will inform therapeutics to facilitate epithelial regeneration in severe cases of CoV19.