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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
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Research Article Infectious disease Pulmonology

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

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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

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Figure 4

Identifying inflammatory and developmental lung EC subpopulations of lung ECs during the late immune phase (24 hours after LPS injury).

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Identifying inflammatory and developmental lung EC subpopulations of lun...
(A) UMAP of 5158 individual lung ECs isolated 24 hours after systemic LPS injury with different colors presenting distinct clusters. The immuneEC (cluster 1) and devEC (cluster 2) are indicated. (B and C) The GO terms of immuneEC (B) and devEC (C) indicate the enriched biological processes in each cluster. (D) Heatmap of the most differentially expressed genes from immuneEC and devEC clusters with the color bar showing gene expression levels on a log2 scale. (E) The box plot of top differentially expressed genes in immuneEC compared with devEC. Data are presented as log2 fold changes. (F and G) Confocal images (F) and quantification (G) of protein immunostaining of mouse lung sections for Irf7 (gray) and Sox17 (green) after LPS treatment for 24 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 small region in the white square is shown at higher magnification on the right. Scale bars: 50 μm on the left; 20 μm on the right. Nuclei were stained by DAPI. The quantification of Td+/Irf7+, Td+/Sox17+, and Td+/Sox17+/Irf7+ cells in lung sections of mice are shown in F. 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.

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