Go to The Journal of Clinical Investigation
  • About
  • Editors
  • Consulting Editors
  • For authors
  • Journal stats
  • Publication ethics
  • Publication alerts by email
  • Transfers
  • Advertising
  • Job board
  • Contact
  • Physician-Scientist Development
  • Current issue
  • Past issues
  • By specialty
    • COVID-19
    • Cardiology
    • Immunology
    • Metabolism
    • Nephrology
    • Oncology
    • Pulmonology
    • All ...
  • Videos
  • Collections
    • In-Press Preview
    • Resource and Technical Advances
    • Clinical Research and Public Health
    • Research Letters
    • Editorials
    • Perspectives
    • Physician-Scientist Development
    • Reviews
    • Top read articles

  • Current issue
  • Past issues
  • Specialties
  • In-Press Preview
  • Resource and Technical Advances
  • Clinical Research and Public Health
  • Research Letters
  • Editorials
  • Perspectives
  • Physician-Scientist Development
  • Reviews
  • Top read articles
  • About
  • Editors
  • Consulting Editors
  • For authors
  • Journal stats
  • Publication ethics
  • Publication alerts by email
  • Transfers
  • Advertising
  • Job board
  • Contact
Single-cell transcriptomic profiling of lung endothelial cells identifies dynamic inflammatory and regenerative subpopulations
Lianghui Zhang, Shang Gao, Zachary White, Yang Dai, Asrar B. Malik, Jalees Rehman
Lianghui Zhang, Shang Gao, Zachary White, Yang Dai, Asrar B. Malik, Jalees Rehman
View: Text | PDF
Research Article Infectious disease Pulmonology

Single-cell transcriptomic profiling of lung endothelial cells identifies dynamic inflammatory and regenerative subpopulations

  • Text
  • PDF
Abstract

Studies have demonstrated the phenotypic heterogeneity of vascular endothelial cells (ECs) within a vascular bed; however, little is known about how distinct endothelial subpopulations in a particular organ respond to an inflammatory stimulus. We performed single-cell RNA-Seq of 35,973 lung ECs obtained during baseline as well as postinjury time points after inflammatory lung injury induced by LPS. Seurat clustering and gene expression pathway analysis identified 2 major subpopulations in the lung microvascular endothelium, a subpopulation enriched for expression of immune response genes such as MHC genes (immuneEC) and another defined by increased expression of vascular development genes such as Sox17 (devEC). The presence of immuneEC and devEC subpopulations was also observed in nonhuman primate lungs infected with SARS-CoV-2 and murine lungs infected with H1N1 influenza virus. After the peak of inflammatory injury, we observed the emergence of a proliferative lung EC subpopulation. Overexpression of Sox17 prevented inflammatory activation in ECs. Thus, there appeared to be a “division of labor” within the lung microvascular endothelium in which some ECs showed propensity for inflammatory signaling and others for endothelial regeneration. These results provide underpinnings for the development of targeted therapies to limit inflammatory lung injury and promote regeneration.

Authors

Lianghui Zhang, Shang Gao, Zachary White, Yang Dai, Asrar B. Malik, Jalees Rehman

×

Figure 3

Divergence of inflammatory and developmental lung EC subpopulations during early immune injury (LPS response at 6 hours).

Options: View larger image (or click on image) Download as PowerPoint
Divergence of inflammatory and developmental lung EC subpopulations duri...
(A) UMAP of 6527 individual lung ECs isolated at 6 hours after LPS injury. Different colors indicate distinct clusters. The immuneEC (cluster 1) and devEC (cluster 2) are shown. (B and C) The GO terms of immuneEC (B) or devEC (C) indicate enriched biological processes in each cluster. P values are indicated on the left in a color scale. (D) Heatmap of the most differentially expressed genes of immuneEC and devEC. The color bar indicates the gene expression levels using a log2 scale. (E and F) The expression levels of representative genes (arrows labeled in D) of immuneEC (E) and devEC (F) visualized by UMAP. (G and H) Confocal images (G) and quantification (H) of RNA-FISH of mouse lung paraffin-embedded tissues after LPS treatment for 6 hours. The lung structures are shown in G by enhancing autofluorescence of lung tissues. The lung ECs expressed tdTomato (Td) in tamoxifen-treated tdTomatofl/fl Cdh5-CreERT(+) mice. The mRNA levels of Irf7 and Sox17 were probed and labeled in gray and green respectively. Nuclei were stained by DAPI. The small region in a white square is zoomed in as shown on the right. Scale bars: 50 μm on the left; 10 μm on the right. The statistical analysis of numbers of Td+/Irf7+, Td+/Sox17+, and Td+/Sox17+/Irf7+ cells in lung sections of mice are shown in H. Data are shown as mean ± SE from 3 independent mice. ***P < 0.001 compared with Td+/Sox17+/Irf7+ cells, ##P < 0.01 compared with Td+/Sox17+ by 1-way ANOVA.

Copyright © 2026 American Society for Clinical Investigation
ISSN 2379-3708

Sign up for email alerts