Single-Cell RNA Sequencing Unveils Unique Transcriptomic Signatures of Organ-Specific Endothelial Cells

Abstract

Background: Endothelial cells (ECs) display considerable functional heterogeneity depending on the vessel and tissue in which they are located. While these functional differences are presumably imprinted in the transcriptome, the pathways and networks which sustain EC heterogeneity have not been fully delineated. Methods: To investigate the transcriptomic basis of EC specificity, we analyzed single-cell RNA-sequencing (scRNA-seq) data from tissue-specific mouse ECs generated by the Tabula Muris consortium. We employed a number of bioinformatics tools to uncover markers and sources of EC heterogeneity from scRNA-seq data. Results: We found a strong correlation between tissue-specific EC transcriptomic measurements generated by either scRNA-seq or bulk RNA-seq, thus validating the approach. Using a graph-based clustering algorithm, we found that certain tissue-specific ECs cluster strongly by tissue (e.g. liver, brain) whereas others (i.e. adipose, heart) have considerable transcriptomic overlap with ECs from other tissues. We identified novel markers of tissue-specific ECs and signaling pathways that may be involved in maintaining their identity. Sex was a considerable source of heterogeneity in the endothelial transcriptome and we discovered Lars2 to be a gene that is highly enriched in ECs from male mice. In addition, we found that markers of heart and lung ECs in mice were conserved in human fetal heart and lung ECs. Finally, we identified potential angiocrine interactions between tissue-specific ECs and other cell types by analyzing ligand and receptor expression patterns. Conclusions: In summary, we use scRNA-seq data generated by the Tabula Muris consortium to uncover transcriptional networks that maintain tissue-specific EC identity and to identify novel angiocrine and functional relationships between tissue-specific ECs.

Single-Cell Transcriptomics Reveals Endothelial Plasticity During Diabetic Atherogenesis

“…The EC heterogeneity across healthy tissues has been characterized using scRNA-seq technology ( Feng et al, 2019 ; Kalluri et al, 2019 ; Kalucka et al, 2020 ; Paik et al, 2020 ). However, the EC plasticity in pathological conditions remains unexplored.…”

“…Endothelial cells exist in the whole body and play an essential role in tissue homeostasis by assisting vessel formation and function, and building a barrier between blood and tissue cells ( Cines et al, 1998 ). ECs exhibit considerable structural and functional heterogeneity depending on the tissue in which they reside, which have been demonstrated by recent single-cell RNA sequencing (scRNA-seq) studies ( Feng et al, 2019 ; Kalluri et al, 2019 ; Kalucka et al, 2020 ; Paik et al, 2020 ). In cardiac development, specifically, certain ECs within the endocardium undergo a process named endothelial-mesenchymal transition (EndMT) to give rise to mesenchymal cells, which play a crucial role in endocardial cushion formation ( Camenisch et al, 2002 ; Dejana et al, 2017 ).…”

Emerging Role of AP-1 Transcription Factor JunB in Angiogenesis and Vascular Development

“…There is accumulating evidence regarding gene expression in vascular endothelial cells. Recently, a large-scale transcriptome analysis of tissue-type vascular endothelial cells isolated from various tissues identified various tissue-specific vascular endothelial cell gene transcriptomes [ 3 , 4 , 5 ]. These data are available in the public vascular endothelial cell transcriptome database EndDB, hosted by VIB-KU Leuven Center for Cancer Biology (Leuven, Belgium; URL: , accessed on 1 February 2021) [ 6 ].…”

Human Induced Pluripotent Stem Cells as a Screening Platform for Drug-Induced Vascular Toxicity

“…While these HUVEC-based models are useful as a generic representation of vasculatures, they are not ideal models for organ-specific blood vessels. In fact, it is well-known that ECs in distinct organs differ in both molecular signature and function ( Marcu et al, 2018 ; Paik et al, 2020b ). By contrast, human iPSCs can be differentiated into organ-specific ECs, allowing us to manufacture more specialized and physiologically representative vasculatures.…”