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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 3

Human pulmonary artery possesses a specific smooth muscle cell–fibroblast intermediary cluster.

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Human pulmonary artery possesses a specific smooth muscle cell–fibroblas...
(A) Hierarchical clustering heatmap of top 10 genes enriched in smooth muscle cell (SMC) and fibroblast clusters. Wilcoxon rank sum test with Bonferroni adjustment, P < 0.05 and |log2(fold change)| > 0.25. (B) Uniform manifold approximation and projection (UMAP) expression plots of ACTA2, TAGLN, MYH11 and PDGFRA, and DCN and COL1A1. The color gradient represents the average expression across the fibroblasts and SMC clusters. (C) Representative immunofluorescence staining of ACTA2 (red, medial layer), PDGFRA (green, adventitial layer), VWF (gray, intima layer), and DAPI (blue, nuclei) in human formalin-fixed, paraffin-embedded (FFPE) lung tissue. Scale bar = 20 μm (n = 5 vessels). (D) Trajectory inference overlaid on 3-dimensional (3D) UMAP of the extracted SMC and fibroblast clusters. (E and F) Color-coded pseudotime calculation overlaid on 3D UMAP of the extracted SMC and fibroblast subset using fibroblasts (E) and SMC1 (F) as root nodes (left panel). Scatterplots illustrating the different expression of canonical markers for fibroblasts (DCN), SMC2 (VCAN), and SMC (ACTA2) going along with the increase of pseudotime along the trajectory from fibroblast to SMC1 (E, right panel) or from SMC1 to fibroblast (F, right panel). (G) RNA velocity overlaid on UMAP of the extracted SMC and fibroblast subset. RNA velocity analysis identified 317 velocity genes across the data set. (H) RNA velocity of canonical markers for SMC (ACTA2), SMC2 (VCAN), and fibroblasts (DCN). (I) Integration of human and murine pulmonary artery single-cell RNA-Seq data set, showing the extracted fibroblast-SMC subset (left) with associated bar plot depicting cell composition (Fibroblasts, SMC1,2,3,4, right) in the 2 data sets. (J) UMAP expression plots of CFH and VCAN in integrated human and mouse fibroblast-SMC data set. The color gradient represents the average expression across the extracted fibroblast and SMC subset.

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