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Single-cell transcriptomics reveals skewed cellular communication and phenotypic shift in pulmonary artery remodeling
Slaven Crnkovic, Francesco Valzano, Elisabeth Fließer, Jürgen Gindlhuber, Helene Thekkekara Puthenparampil, Maria Basil, Mike P. Morley, Jeremy Katzen, Elisabeth Gschwandtner, Walter Klepetko, Edward Cantu, Heimo Wolinski, Horst Olschewski, Jörg Lindenmann, You-Yang Zhao, Edward E. Morrisey, Leigh M. Marsh, Grazyna Kwapiszewska
Slaven Crnkovic, Francesco Valzano, Elisabeth Fließer, Jürgen Gindlhuber, Helene Thekkekara Puthenparampil, Maria Basil, Mike P. Morley, Jeremy Katzen, Elisabeth Gschwandtner, Walter Klepetko, Edward Cantu, Heimo Wolinski, Horst Olschewski, Jörg Lindenmann, You-Yang Zhao, Edward E. Morrisey, Leigh M. Marsh, Grazyna Kwapiszewska
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Research Article Pulmonology Vascular biology

Single-cell transcriptomics reveals skewed cellular communication and phenotypic shift in pulmonary artery remodeling

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Abstract

A central feature of progressive vascular remodeling is altered smooth muscle cell (SMC) homeostasis; however, the understanding of how different cell populations contribute to this process is limited. Here, we utilized single-cell RNA sequencing to provide insight into cellular composition changes within isolated pulmonary arteries (PAs) from pulmonary arterial hypertension and donor lungs. Our results revealed that remodeling skewed the balanced communication network between immune and structural cells, in particular SMCs. Comparative analysis with murine PAs showed that human PAs harbored heterogeneous SMC populations with an abundant intermediary cluster displaying a gradient transition between SMCs and adventitial fibroblasts. Transcriptionally distinct SMC populations were enriched in specific biological processes and could be differentiated into 4 major clusters: oxygen sensing (enriched in pericytes), contractile, synthetic, and fibroblast-like. End-stage remodeling was associated with phenotypic shift of preexisting SMC populations and accumulation of synthetic SMCs in neointima. Distinctly regulated genes in clusters built nonredundant regulatory hubs encompassing stress response and differentiation regulators. The current study provides a blueprint of cellular and molecular changes on a single-cell level that are defining the pathological vascular remodeling process.

Authors

Slaven Crnkovic, Francesco Valzano, Elisabeth Fließer, Jürgen Gindlhuber, Helene Thekkekara Puthenparampil, Maria Basil, Mike P. Morley, Jeremy Katzen, Elisabeth Gschwandtner, Walter Klepetko, Edward Cantu, Heimo Wolinski, Horst Olschewski, Jörg Lindenmann, You-Yang Zhao, Edward E. Morrisey, Leigh M. Marsh, Grazyna Kwapiszewska

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Figure 4

Pulmonary artery pericytes represent a minor group of ACTA2-positive cells.

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Pulmonary artery pericytes represent a minor group of ACTA2-positive cel...
(A) Uniform manifold approximation and projection (UMAP) expression plots of PDGFRB and NDUFA4L2. Color gradient represents the average expression across the fibroblasts and smooth muscle cell (SMC) clusters. (B) UMAP of the extracted fibroblast, SMC, and pericyte subsets. (C) Dot plot of the top 8 genes from the pericyte cluster (NDUFA4L2, GJA4, APOLD1, HIGD1B, LGI4, COX4I2, FABP4, and PDGFRB). Dot size represents percentage of cells expressing the gene; color gradient represents the average expression across the data set. (D) UMAP gene expression plot of NDUFA4L2. The color gradient represents the average expression across the entire pulmonary artery (PA) data set. (E) Representative immunofluorescence staining of the expression of NDUFA4L2-positive cells (in gray) embedded in different locations of the PA medial layer in human formalin-fixed, paraffin-embedded (FFPE) lung tissue (ACTA2, red; VWF, green; and DAPI, blue). Scale bar = 20 μm (n = 4). (F) UMAP of the extracted SMC subset resulting in 4 subclusters (SMC1,2,3,4, smooth muscle cell 1,2,3,4). (G) Hierarchical clustering heatmap of the top 50 marker genes across the SMC subset. Wilcoxon rank sum test with Bonferroni adjustment, P < 0.05. (H) Gene Ontology (GO) analysis performed on cluster-enriched genes. Fisher’s exact test with Benjamini-Hochberg adjustment, P < 0.05. (I) GO-based new nomenclature of the 4 SMC clusters (contractile, oxygen sensing, synthetic, fibroblast-like) with associated violin plot of 5 most enriched genes per cluster (ACTG2, CNN1, RAMP1, RGS5, TPM2 for contractile; APOE, FBLN1, LUM, TIMP1, VCAN for synthetic; FABP4, MT1M, MT2A, RGS16, SOCS3 for oxygen sensing; APOD, CFD, DCN, LUM, S100A10 for fibroblast-like).

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