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. 2025 Feb 6;32(2):302-321.e6.
doi: 10.1016/j.stem.2024.12.002. Epub 2025 Jan 15.

Longitudinal single-cell profiles of lung regeneration after viral infection reveal persistent injury-associated cell states

Terren K Niethamer  1 , Joseph D Planer  2 , Michael P Morley  2 , Apoorva Babu  3 , Gan Zhao  4 , Maria C Basil  2 , Edward Cantu  5 , David B Frank  6 , Joshua M Diamond  7 , Ana N Nottingham  8 , Shanru Li  9 , Arnav Sharma  10 , Hannah Hallquist  2 , Lillian I Levin  9 , Su Zhou  9 , Andrew E Vaughan  4 , Edward E Morrisey  11
Affiliations

Longitudinal single-cell profiles of lung regeneration after viral infection reveal persistent injury-associated cell states

Terren K Niethamer et al. Cell Stem Cell. .

Abstract

Functional regeneration of the lung's gas exchange surface following injury requires the coordination of a complex series of cell behaviors within the alveolar niche. Using single-cell transcriptomics combined with lineage tracing of proliferating progenitors, we examined mouse lung regeneration after influenza injury, demonstrating an asynchronously phased response across different cellular compartments. This longitudinal atlas of injury responses has produced a catalog of transient and persistent transcriptional alterations in cells as they transit across axes of differentiation. These cell states include an injury-induced capillary endothelial cell (iCAP) that arises after injury, persists indefinitely, and shares hallmarks with developing lung endothelium and endothelial aberrations found in degenerative human lung diseases. This dataset provides a foundational resource to understand the complexity of cellular and molecular responses to injury and correlations to responses found in human development and disease.

Keywords: alveolar; endothelial plasticity; influenza; injury; lineage tracing; lung; pulmonary endothelium; regeneration.

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Conflict of interest statement

Declaration of interests The authors declare no competing interests.

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