Single-Cell Transcriptome Atlas of Murine Endothelial Cells

Kalucka, Joanna; Rooij, Laura P.M.H. de; Goveia, Jermaine; Rohlenová, Kateřina; Dumas, Sébastien J.; Meta, Elda; Conchinha, Nadine V.; Taverna, Federico; Teuwen, Laure-Anne; Veys, Koen; García-Caballero, Melissa; Khan, Shawez; Geldhof, Vincent; Sokol, Liliana; Chen, Rongyuan; Treps, Lucas; Borri, Mila; Zeeuw, Pauline de; Dubois, Charlotte; Karakach, Tobias K.; Falkenberg, Kim D.; Parys, Maciej; Yin, Xiaokang; Vinckier, Stefan; Du, Yi; Fenton, Robert A.; Schoonjans, Luc; Dewerchin, Mieke; Eelen, Guy; Thienpont, Bernard; Lin, Lin; Bolund, Lars; Li, Xuri; Luo, Yonglun; Carmeliet, Peter

doi:10.1016/j.cell.2020.01.015

Cited by 902 publications

(1,211 citation statements)

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“…Thus CRP may contribute widely to vascular homeostasis, providing a distributed pool of regenerative cells for local vascular maintenance and replenishment. Consistent with this thesis, a recent scRNAseq study also reported rare Apln + “angiogenic” EC in normal tissues 74 .…”

Section: Discussionsupporting

confidence: 76%

A molecular map of lymph node blood vascular endothelium at single cell resolution

Brulois

Rajaraman

Szade

et al. 2020

Preprint

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48 49 Blood vascular endothelial cells (BECs) control the immune response by regulating immune 50 cell recruitment, metabolite exchange and blood flow in lymphoid tissues. However, the 51 diversity of BEC and their origins during immune angiogenesis remain poorly understood. 52Here we profile transcriptomes of BEC from mouse peripheral lymph nodes and map key 53 phenotypes to the vasculature. Our analysis identifies multiple novel subsets including a 54 venous population whose gene signature predicts an unexpectedly selective role in myeloid 55 cell (vs lymphocyte) recruitment to the medulla, confirmed by 2 photon videomicroscopy. 56We define five phenotypes of capillary lining BEC including a capillary resident regenerative 57 population (CRP) that displays stem cell and migratory gene signatures and contributes to58 homeostatic BEC turnover and to vascular neogenesis after immunization. Trajectory 59 analyses reveal retention of developmental programs along a progression of cellular 60 phenotypes from CRP to mature venous and arterial BEC subsets. Overall, our single cell 61 atlas provides a molecular blueprint of the lymph node blood vasculature and defines subset 62 specialization for immune cell recruitment and vascular homeostasis. 63 64 Introduction 65The vascular endothelium lining blood vessels regulates exchange of oxygen and 66 metabolites between the blood vascular compartment and tissues. In lymph nodes (LN), 67 additionally, the endothelium plays essential roles in controlling immune cell access. The 68 organization of the vasculature in LN is well characterized: Arteries entering at the hilus lead to 69 capillary arcades in the LN cortex; capillaries link to 'high endothelial venules' (HEV), the post 70 capillary venules that recruit lymphocytes from the blood 1 ; and the vasculature exits the lymph 71 node at the hilus. Upon immune challenge, lymph nodes increase in volume up to 10-fold or more 72 within days, and the vascular endothelium expands roughly proportionally from local precursors 1,2 . 73Vessel expansion involves extensive proliferation of both capillary and high endothelial cells 74 (HEC) 3 , without contribution from blood borne progenitors 4 ; and an increase in vessel numbers 75 through intussusceptive (splitting) angiogenesis 5 . However, the nature and extent of endothelial 76 cell diversity within LN remains incompletely understood. 77Single cell RNA profiling is a transformative technology for the identification of cell 78 diversity and elucidation of developmental and physical relationships. Here we provide a survey 79 of blood vessel endothelial cells (BEC) from mouse peripheral lymph nodes (PLN). We confirm 80 known features of high endothelium 6,7 , identify novel endothelial subsets, uncover unexpected 81 diversity among capillary cells and demonstrate a distinctive role of medullary veins in selective 82 myeloid cell recruitment. We define gene signatures and transcription regulatory factors for these 83 subsets, and map key subsets to the vasculature. We also identify a p...

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Section: Discussionsupporting

confidence: 76%

A molecular map of lymph node blood vascular endothelium at single cell resolution

Brulois

Rajaraman

Szade

et al. 2020

Preprint

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“…Our data define a human intestinal EC signature that includes almost 150 genes that are enriched in intestinal ECs relative to lung and kidney ECs. Recent work described an adult murine EC atlas spanning 11 organ systems at single cell resolution, and provides a foundational resource to compliment the work presented here, aimed at understanding human intestinal EC patterning (Kalucka et al, 2020). Several of the validated human organ-specific markers identified in our dataset demonstrated similar expression patterns in adult mouse atlas, suggesting that organ-specific signatures established during development are retained into adulthood, although future work should confirm these findings in both developing and adult human and murine tissue.…”

Section: Discussionmentioning

confidence: 99%

“…Several studies have demonstrated that vasculature patterning is organ-specific (Daniel et al, 2018; Ding et al, 2010; Feng et al, 2019; Kalucka et al, 2020; Lee et al, 2014; Marcu et al, 2018; Nolan et al, 2013); however, whether or not organoids are programmed with this patterning information in vitro was not known. Furthermore, profiling of organ-specific ECs has not included human intestinal ECs prior to this work.…”

Section: Discussionmentioning

confidence: 99%

“…Since organ-specific morphology in vascular beds has long been appreciated (Aird, 2007), and organ-specific transcriptional signatures and functions have been described in mouse (Ding et al, 2011; Kalucka et al, 2020; Lee et al, 2014; Nolan et al, 2013) and human tissues (Chi et al, 2003; Marcu et al, 2018), we further sought to determine if HIO ECs were properly patterned by interrogating human fetal intestine, lung, and kidney tissue to identify and validate organ enriched EC gene signatures and individual genes. These data were then used to assess the extent to which HIO ECs resembled human intestinal ECs.…”

Section: Introductionmentioning

confidence: 99%

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Differentiation of human intestinal organoids with endogenous vascular endothelial cells

Holloway

Czerwinkski

et al. 2020

Preprint

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22Human pluripotent stem cell (hPSC)-derived intestinal organoids (HIOs) generated using directed 23 differentiation lack some cellular populations found in the native organ, including vasculature. Using 24 single cell RNA sequencing (scRNAseq), we have identified a transient population of endothelial cells 25 (ECs) present early in HIO differentiation that are lost over time in culture. Here, we have developed a 26 method to enhance co-differentiation and maintenance of ECs within HIOs (vHIOs). Given that ECs are 27 known to possess organ specific gene expression, morphology and function, we used bulk RNAseq 28 and scRNAseq to interrogate the developing human intestine, lung, and kidney in order to identify 29 organ-enriched EC-gene signatures in these organ systems. By comparing organ-specific gene 30 signatures along with markers validated by fluorescent in situ hybridization to HIO ECs, we find that 31 HIO ECs grown in vitro share the highest similarity with native intestinal ECs relative to kidney and 32 lung. Together, these data show that HIOs can co-differentiate a native EC population that are properly 33 patterned with an intestine-specific EC transcriptional signature in vitro. 34 35 36 37 38 39 40 41 42 43 44 65highly vascularized regions of immunocompromised mice (Cortez et al., 2018; Watson et al., 2014). In 66 these environments, HIOs undergo extensive vascularization by the murine host tissue, and increase in 67 complexity to resemble mature intestinal tissue (Finkbeiner et al., 2015b; Watson et al., 2014). 68However, co-culture approaches or co-differentiating HIOs with a native vasculature prior to in vivo 69 engraftment has not yet been achieved. 71Here, we performed single cell RNA sequencing (scRNAseq) at various timepoints across HIO 72 differentiation in vitro and observed a transient population of endothelial-like cells (ECs) present within 73 HIOs early during differentiation; however, these cells are not maintained during prolonged culture 74 under standard growth conditions. This suggested that early during HIO differentiation, cells within the 75 culture are capable of giving rise to EC-like cells. Based on these observations, we hypothesized that a 76 modified directed differentiation approach would allow the induction and maintenance of a more robust 77 EC population within HIOs (termed vHIO). Our findings demonstrate that modified culture conditions 78 allow a ~13-fold increase in the induction of EC-like cells within HIOs without impacting the other HIO 79 cell populations present (i.e. epithelium, mesenchyme), and support the survival of this population of 80 ECs within HIOs in culture for months. 82Since organ-specific morphology in vascular beds has long been appreciated (Aird, 2007), and 83 organ-specific transcriptional signatures and functions have been described in mouse (Ding et al., 84 2011; Kalucka et al., 2020; Lee et al., 2014; Nolan et al., 2013) and human tissues (Chi et al., 2003; 85 Marcu et al., 2018), we further sought to determine if HIO ECs were properly...

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“…Endothelial cells, defined by pan-EC markers PECAM1 , CDH5 and VWF, were highly heterogeneous, consisting of eight subpopulations (Figure 3A). The most abundant subpopulation (53.0% of all EC) was annotated as capillary EC (EC_cap) given the enrichment of RGCC and CA4, marker genes of microvascular endothelium in the mouse endothelial cell atlas36 . A separate cluster, expressing endothelial capillary markers, was largely represented by cells ( Supplementary…”

mentioning

confidence: 99%

Cells and gene expression programs in the adult human heart

Litviňuková

Talavera-López

Maatz

et al. 2020

Preprint

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SummaryCardiovascular disease is the leading cause of death worldwide. Advanced insights into disease mechanisms and strategies to improve therapeutic opportunities require deeper understanding of the molecular processes of the normal heart. Knowledge of the full repertoire of cardiac cells and their gene expression profiles is a fundamental first step in this endeavor. Here, using large-scale single cell and nuclei transcriptomic profiling together with state-of-the-art analytical techniques, we characterise the adult human heart cellular landscape covering six anatomical cardiac regions (left and right atria and ventricles, apex and interventricular septum). Our results highlight the cellular heterogeneity of cardiomyocytes, pericytes and fibroblasts, revealing distinct subsets in the atria and ventricles indicative of diverse developmental origins and specialized properties. Further we define the complexity of the cardiac vascular network which includes clusters of arterial, capillary, venous, lymphatic endothelial cells and an atrial-enriched population. By comparing cardiac cells to skeletal muscle and kidney, we identify cardiac tissue resident macrophage subsets with transcriptional signatures indicative of both inflammatory and reparative phenotypes. Further, inference of cell-cell interactions highlight a macrophage-fibroblast-cardiomyocyte network that differs between atria and ventricles, and compared to skeletal muscle. We expect this reference human cardiac cell atlas to advance mechanistic studies of heart homeostasis and disease.

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Single-Cell Transcriptome Atlas of Murine Endothelial Cells

Abstract: Highlights d A single-cell EC atlas of healthy murine tissues d This study provides an interactive webtool for comparative analyses and data exploration d Characterization of inter-and intra-tissue EC heterogeneity d Discovery tool for characterization of ECs in other datasets

Cited by 902 publications

References 91 publications

A molecular map of lymph node blood vascular endothelium at single cell resolution

A molecular map of lymph node blood vascular endothelium at single cell resolution

Differentiation of human intestinal organoids with endogenous vascular endothelial cells

Cells and gene expression programs in the adult human heart

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