ArticleCell stem cell2025
Longitudinal single-cell profiles of lung regeneration after viral infection reveal persistent injury-associated cell states.
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Article in Cell stem cell, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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33citing papers in PubMed
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33 citing papers in PubMed.
- Spatial Total RNA Sequencing of Formalin-Fixed Paraffin-Embedded Tissue by spRandom-seq.Small (Weinheim an der Bergstrasse, Germany) · 2026Article
- LATS1/2 inactivation drives a distinct venous endothelial cell response that contributes to fibrotic remodeling of the lung.Science advances · 2026Article
- Ferroptosis-Senescence Crosstalk in Sepsis-Associated Acute Lung Injury: Mechanisms and Therapeutic Opportunities.Biomedicines · 2026Review
- Early cell-autonomous and niche-mediated epithelial response to influenza infection in primary alveolar organoids.JCI insight · 2026Article
- Co-optation of the regenerative role of type 2 alveolar cells in distal lung repair in mice by terminal airway epithelial cells in humans.bioRxiv : the preprint server for biology · 2026Article
- An immune-poised state of human bronchial epithelial cells mediates defense against RSV in adults.Nature communications · 2026Article
- Single-cell and spatial transcriptomic profiling reveals distinct immune landscapes in murine lungs infected with H1N1 versus H5N1 influenza viruses.Journal of virology · 2026Article
- The cell with many faces: lung macrophage plasticity and function in response to environmental and pathogenic insults.Physiological reviews · 2026Review
- Defective alveolar regeneration in emphysema: identifying dysfunctional cellular crosstalk and novel therapeutic opportunities for tissue repair.European respiratory review : an official journal of the European Respiratory Society · 2026Review
- Rebalancing the Neurovascular Axis: NTRK2 Isoform Equilibrium as a Determinant of Pulmonary Endothelial Regeneration.Cell proliferation · 2026Article
- From Heterogeneity to Plasticity: Endothelial Dynamics in Lung Disease.Pulmonary circulation · 2026Review
- Article
- The chromatin remodeling complex PRC2 safeguards cell fate in alveolar epithelial type 2 cells.bioRxiv : the preprint server for biology · 2026Article
- SEA CDM: Study-Experiment-Assay Common Data Model and Databases for Cross-Domain Data Integration and Analysis.Scientific data · 2026Article
- A Transcriptional Atlas of Endothelial Cell Zonation Along the Pulmonary Vascular Tree.bioRxiv : the preprint server for biology · 2026Article
- Rebalancing NTRK2 isoforms promotes vascular regeneration in bronchopulmonary dysplasia.Cell stem cell · 2026Article
- Cellular plasticity and regenerative mechanisms in the lung.European respiratory review : an official journal of the European Respiratory Society · 2026Review
- Endothelial Heterogeneity in Pulmonary Hypertension.Arteriosclerosis, thrombosis, and vascular biology · 2026Review
- Article
- A Brief Overview of Biomechanics and Mechanobiology of the Pulmonary Circulation.Advances in experimental medicine and biology · 2026Review
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Authors and funding
17 authors.
Terren K NiethamerDepartment of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn-Children's Hospital of Philadelphia Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Cancer and Developmental Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA. Electronic address: terren.niethamer@nih.gov.
Joseph D PlanerDepartment of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn-Children's Hospital of Philadelphia Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
Michael P MorleyDepartment of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn-Children's Hospital of Philadelphia Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
Apoorva BabuPenn-Children's Hospital of Philadelphia Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
Gan ZhaoPenn-Children's Hospital of Philadelphia Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Maria C BasilDepartment of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn-Children's Hospital of Philadelphia Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
Edward CantuPenn-Children's Hospital of Philadelphia Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Cardiovascular Surgery, Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
David B FrankPenn-Children's Hospital of Philadelphia Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Pediatric Cardiology, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USA.
Joshua M DiamondDepartment of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Ana N NottinghamPenn-Children's Hospital of Philadelphia Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
Shanru LiDepartment of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
Arnav SharmaCancer and Developmental Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
Hannah HallquistDepartment of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn-Children's Hospital of Philadelphia Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
Lillian I LevinDepartment of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
Su ZhouDepartment of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
Andrew E VaughanPenn-Children's Hospital of Philadelphia Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Edward E MorriseyDepartment of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn-Children's Hospital of Philadelphia Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address: emorrise@pennmedicine.upenn.edu.
Funding
TRAINING IN PULMONARY IMMUNOLOGYT32HL007586 · NHLBI · UNIVERSITY OF PENNSYLVANIA · PI MEYER, NUALA JENNINGS · 1985 to 2025
$8.8MGenetic Investigation of Covid 19 in Lung DiseaseR01HL164929 · NHLBI · UNIVERSITY OF PENNSYLVANIA · PI MARK L KAHN, EDWARD E MORRISEY · 2022 to 2026
$4.7MMolecular pathways controlling alveolar epithelial remodeling in development and regenerationR01HL132999 · NHLBI · UNIVERSITY OF PENNSYLVANIA · PI MORRISEY, EDWARD E · 2016 to 2023
$4.6MMechanical signaling through the nuclear membrane in lung alveolar healthR01HL168803 · NHLBI · UNIVERSITY OF PENNSYLVANIA · PI EDWARD E MORRISEY · 2023 to 2026
$3.1MObjective Lung Assessment Tools for Improved Organ Use in Lung TransplantationR01HL155821 · NHLBI · UNIVERSITY OF PENNSYLVANIA · PI CANTU, EDWARD · 2021 to 2025
$3.0MEndothelial plasticity and signaling in development and regeneration of the lungZIABC012165 · NCI · DIVISION OF BASIC SCIENCES - NCI · PI NIETHAMER, TERREN · 2024 to 2025
$2.4MThe Penn LungMAP 3 team: Defining chronic lung diseaseU01HL175409 · NHLBI · UNIVERSITY OF PENNSYLVANIA · PI EDWARD E MORRISEY · 2024 to 2026
$2.3MTranscriptional Regulation of Lung Alveolar RegenerationR01HL152194 · NHLBI · UNIVERSITY OF PENNSYLVANIA · PI MORRISEY, EDWARD E · 2021 to 2024
$2.3MControl of lung alveolar regeneration by Dot1L/H3K79 methylationR01HL162683 · NHLBI · UNIVERSITY OF PENNSYLVANIA · PI EDWARD E MORRISEY · 2023 to 2026
$2.3MMolecular regulation of cell fate and progenitor function in the distal human respiratory airwaysK08HL163398 · NHLBI · UNIVERSITY OF PENNSYLVANIA · PI Maria Ciocca Basil · 2022 to 2026
$834kEndothelial cell signaling in regeneration of the lungK99HL164960 · NHLBI · UNIVERSITY OF PENNSYLVANIA · PI NIETHAMER, TERREN KATHRYN · 2022 to 2023
$323kIntramural NIH HHS ZIA BC012165NHLBI NIH HHS K08 HL163398NHLBI NIH HHS K99 HL164960NHLBI NIH HHS R01 HL132999NHLBI NIH HHS R01 HL152194NHLBI NIH HHS R01 HL155821NHLBI NIH HHS R01 HL162683NHLBI NIH HHS R01 HL164929NHLBI NIH HHS R01 HL168803NHLBI NIH HHS T32 HL007586NHLBI NIH HHS U01 HL175409
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.
Indexed as
LungLung InjuryOrthomyxoviridae InfectionsRegenerationSingle-Cell AnalysisAnimalsEndothelial CellsHumansMiceMice, Inbred C57BLalveolarendothelial plasticityinfluenzainjurylineage tracinglungpulmonary endotheliumregeneration
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