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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 5

Identification of the proliferative lung EC subpopulation during the regeneration phase.

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Identification of the proliferative lung EC subpopulation during the reg...
(A) UMAP of 5318 individual lung ECs isolated at 3 days after systemic LPS injury. (B) The GO terms indicate the enriched biological processes of proEC. P values are indicated on the left in a color scale. (C) The expression levels of representative marker genes are visualized by UMAP. The color bars in UMAP indicate gene expression level in log2 scale. (D) Confocal images of RNA-FISH of mouse lung sections obtained at 3 days after LPS injury. The lung structures are shown in D by enhancing autofluorescence of lung tissues. The lung ECs express tdTomato (Td). The RNAs of Ccne1 were probed and labeled with gray. Scale bar: 20 μm. Nuclei were stained by DAPI. (E) The quantification of cell number of Td+/Ccne1+ cells in lung sections of mice at baseline, LPS 24 hours, LPS 2 days, and LPS 3 days. Data are shown as mean ± SE from 3 independent mice at different time points. ****P < 0.0001 compared with baseline by 1-way ANOVA. (F) Pseudo-time trajectory of devECs from baseline, LPS 6 hours, LPS 1 day, LPS 2 days, and proEC of LPS 3 days. Colored by time points of LPS treatment.

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