Broadly, tissue regeneration is achieved in two ways: by proliferation of common differentiated cells and/or by deployment of specialized stem/progenitor cells. Which of these pathways applies is both organ and injury-specific1–4. Current paradigms in the lung posit that epithelial repair can be attributed to cells expressing mature lineage markers5–8. In contrast we here define the regenerative role of previously uncharacterized, rare lineage-negative epithelial stem/progenitor (LNEPs) cells present within normal distal lung. Quiescent LNEPs activate a ΔNp63/cytokeratin 5 (Krt5+) remodeling program after influenza or bleomycin injury. Activated cells proliferate and migrate widely to occupy heavily injured areas depleted of mature lineages, whereupon they differentiate toward mature epithelium. Lineage tracing revealed scant contribution of pre-existing mature epithelial cells in such repair, whereas orthotopic transplantation of LNEPs, isolated by a definitive surface profile identified through single cell sequencing, directly demonstrated the proliferative capacity and multipotency of this population. LNEPs require Notch signaling to activate the ΔNp63/Krt5+ program whereas subsequent Notch blockade promotes an alveolar cell fate. Persistent Notch signaling post-injury led to parenchymal micro-honeycombing, indicative of failed regeneration. Lungs from fibrosis patients show analogous honeycomb cysts with evidence of hyperactive Notch signaling. Our findings indicate distinct stem/progenitor cell pools repopulate injured tissue depending on the extent of injury, and the outcomes of regeneration or fibrosis may ride in part on the dynamics of LNEP Notch signaling.

SUMMARY After influenza infection, lineage-negative epithelial progenitors (LNEPs) exhibit a binary response to reconstitute epithelial barriers: activating a Notch-dependent ΔNp63/cytokeratin 5(Krt5) remodeling program or differentiating into alveolar type II cells (AEC2s). Here we show that local lung hypoxia, via hypoxia inducible factor (HIF1α), drives Notch signaling and Krt5pos basal-like cell expansion. Single cell transcriptional profiling of human AEC2s from fibrotic lungs revealed a hypoxic subpopulation with activated Notch, suppressed surfactant protein C (SPC), and trans-differentiation toward a Krt5pos basal-like state. Activated murine Krt5pos LNEPs and diseased human AEC2s upregulate strikingly similar core pathways underlying migration and squamous metaplasia. While robust, HIF1α-driven metaplasia is ultimately inferior to AEC2 reconstitution in restoring normal lung function. HIF1α deletion or enhanced Wnt/β-catenin activity in Sox2+ LNEPs blocks Notch and Krt5 activation, instead promoting rapid AEC2 differentiation and migration and improving the quality of alveolar repair.

H1N1 influenza virus infection induces dramatic and permanent alveolar remodeling mediated by p63+ progenitor cell expansion in both mice and some patients with acute respiratory distress syndrome. This persistent lung epithelial dysplasia is accompanied by chronic inflammation, but the driver(s) of this pathology are unknown. This work identified de novo appearance of solitary chemosensory cells (SCCs), as defined by the tuft cell marker doublecortin-like kinase 1, in post-influenza lungs, arising in close proximity with the dysplastic epithelium, whereas uninjured lungs are devoid of SCCs. Interestingly, fate mapping demonstrated that these cells are derived from p63-expressing lineage-negative progenitors, the same cell of origin as the dysplastic epithelium. Direct activation of SCCs with denatonium + succinate increased plasma extravasation specifically in post-influenza virus-injured lungs. Thus we demonstrate the previously unrecognized development and activity of SCCs in the lung following influenza virus infection, implicating SCCs as a central feature of dysplastic remodeling.

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Red blood cells detect and bind cell-free nucleic acids, contributing to anemia and immune cell activation during acute inflammation.

Alveolar type-2 (AT2) cells are necessary for the lung’s regenerative response to epithelial insults such as influenza. However, current methods to expand these cells rely on mesenchymal co-culture, complicating the possibility of transplantation following acute injury. Here we developed several mesenchyme-free culture conditions that promote growth of murine AT2 organoids. Transplanting dissociated AT2 organoids into influenza-infected mice demonstrated that organoids engraft and either proliferate as AT2 cells or unexpectedly adopt a basal cell-like fate associated with maladaptive regeneration. Alternatively, transplanted primary AT2 cells also robustly engraft, maintaining their AT2 lineage while replenishing the alveolar type-1 (AT1) cell population in the epithelium. Importantly, pulse oximetry revealed significant increase in blood-oxygen saturation in primary AT2 recipients, indicating that transplanted cells also confer increased pulmonary function after influenza. We further demonstrated that both acid installation and bleomycin injury models are also amenable to AT2 transplantation. These studies provide additional methods to study AT2 progenitor potential, while serving as proof-of-principle for adoptive transfer of alveolar progenitors in potential therapeutic applications.

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Lung epithelial cells use remarkably adaptive sensing and signaling systems to maintain a physiological state supporting gas exchange and minimizing environmental insults. One facet of epithelial adaptability is the reversible acquisition of mesenchymal features, a process termed epithelial-mesenchymal transition (EMT). Although in the adult, permanent and complete EMT appears rare or non-existent, a growing body of evidence implicates a critical role for the activation of EMT signaling in tissue remodeling, including fibrotic lung disease. The specific phenotypes of cells undergoing EMT re-programming during epithelial responses to injury continue to be defined and are reviewed here. Several recent studies implicate epithelial expression of canonical EMT transcription factors, such as Snail and Twist1, with the acquisition of a less differentiated, more proliferative stem-like state, providing an additional link between activation of EMT signaling and tissue repair. In lung airways, proliferating variant clara cells rely upon Snail for effective epithelial repair, and in the breast, cells possessing the greatest regenerative capacity also express Snail2. The ongoing elucidation of signaling underlying epithelial stem/progenitor expansion coincides with recent discoveries implicating regenerative activity in the lung, possibly including de novo regeneration of airway and alveolar units. It remains largely unknown what signals drive organization of epithelial progenitor cells that expand after lung injury, to what degree such organization is ever functionally relevant, and whether the lung regenerative potential recently observed in mouse models extends to humans. Yet these unknowns with clinical potential bring future mechanistic studies of EMT and lung repair directly into the field of regenerative medicine. This article is part of a Special Issue entitled: Fibrosis: Translation of basic research to human disease.