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.

Highlights d Supervised scRNA-seq uncovers unexpected heterogeneity within club-like cells d Specialized epithelial progenitors with unique features hide among mature cells d Different stem/progenitors are activated in region and injurydependent manner d Transplantation of expanded progenitors rescues lung function of injured mice

No abstract

Antiretroviral therapy suppresses but does not cure HIV-1 infection due to the existence of a long-lived reservoir of latently infected cells. The reservoir has an estimated half-life of 44 mo and is largely composed of clones of infected CD4+ T cells. The long half-life appears to result in part from expansion and contraction of infected CD4+ T cell clones. However, the mechanisms that govern this process are poorly understood. To determine whether the clones might result from and be maintained by exposure to antigen, we measured responses of reservoir cells to a small subset of antigens from viruses that produce chronic or recurrent infections. Despite the limited panel of test antigens, clones of antigen-responsive CD4+ T cells containing defective or intact latent proviruses were found in seven of eight individuals studied. Thus, chronic or repeated exposure to antigen may contribute to the longevity of the HIV-1 reservoir by stimulating the clonal expansion of latently infected CD4+ T cells.

Conflict of interest: CDW, AR, and JC are inventors on a patent application (no. WO2019070407) for eicosanoids as biomarkers of senescence. AV is currently an employee at UNITY Biotechnology. HAC is the scientific founder of Pliant Therapeutics, which develops antifibrotic drugs and owns equity in the company. JC is the scientific founder of UNITY Biotechnology, which develops senolytic and other drugs to combat aging, owns equity in the company, and receives research funding from the company. JC is also named on several planned, pending, and awarded patents on the use of small molecules to eradicate senescent cells. CJLS has served as a consultant for UNITY Biotechnology and Gordian.