Differential DARC/ACKR1 expression distinguishes venular from non-venular endothelial cells in murine tissues

Thiriot, Aude; Perdomo, Carolina; Cheng, George; Novitzky‐Basso, Igor; McArdle, Sara; Kishimoto, Jamie K.; Barreiro, Olga; Mazo, Irina B.; Triboulet, Robinson; Ley, Klaus; Rot, Antal; Andrian, Ulrich H. von

doi:10.1186/s12915-017-0381-7

Cited by 120 publications

(117 citation statements)

References 73 publications

(98 reference statements)

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“…Using the differentially expressed gene ACKR1 (aka DARC), we identified C19 as the endothelium of the collector channels downstream from Schlemm Canal (Figure 3G). ACKR1 has been identified as a marker to distinguish venular from non-venular endothelial cells, which is consistent with the pre/perivenular location of the channels (Thiriot et al,2017). Other DE genes for collector channel cells include SELE, SELP, COL15A1.…”

Section: Introductionsupporting

confidence: 62%

Cell Atlas of Aqueous Humor Outflow Pathways in Eyes of Humans and Four Model Species Provides Insights into Glaucoma Pathogenesis

Zyl

Yan

McAdams

et al. 2020

Preprint

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ABSTRACTIncreased intraocular pressure (IOP) represents a major risk factor for glaucoma, a prevalent eye disease characterized by death of retinal ganglion cells that carry information from the eye to the brain; lowering IOP is the only proven treatment strategy to delay disease progression. The main determinant of IOP is the equilibrium between production and drainage of aqueous humor, with compromised drainage generally viewed as the primary contributor to dangerous IOP elevations. Drainage occurs through two pathways in the anterior segment of the eye, called conventional and uveoscleral. To gain insights into the cell types that comprise these pathways, we used high-throughput single cell RNA sequencing (scRNA-seq). From ∼24,000 single cell transcriptomes, we identified 19 cell types with molecular markers for each and used histological methods to localize each type. We then performed similar analyses on four organisms used for experimental studies of IOP dynamics and glaucoma: cynomolgus macaque (Macaca fascicularis), rhesus macaque (Macaca mulatta), pig (Sus scrofa) and mouse (Mus musculus). Many human cell types had counterparts in these models, but differences in cell types and gene expression were evident. Finally, we identified the cell types that express genes implicated in glaucoma in all five species. Together, our results provide foundations for investigating the pathogenesis of glaucoma, and for using model systems to assess mechanisms and potential interventions.

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Section: Introductionsupporting

confidence: 62%

Cell Atlas of Aqueous Humor Outflow Pathways in Eyes of Humans and Four Model Species Provides Insights into Glaucoma Pathogenesis

Zyl

Yan

McAdams

et al. 2020

Preprint

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“…Further, we sought to understand the distribution of vascular addressins expressed by DARC + endothelial sub-populations, the site primary site of lymphocyte egress into tissues ( Figure S5E ) (Thiriot et al, 2017). Notably, across sub-populations of CD93 + endothelial cells (Venule sub-clusters 1-4), we observe variation in expression of vascular addressins ( Figure S5E ).…”

Section: Resultsmentioning

confidence: 99%

Highly Efficient, Massively-Parallel Single-Cell RNA-Seq Reveals Cellular States and Molecular Features of Human Skin Pathology

Tk¹,

Mh²,

Tm³

et al. 2019

Preprint

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1The development of high-throughput single-cell RNA-sequencing (scRNA-Seq) methodologies 2 has empowered the characterization of complex biological samples by dramatically increasing the 3 number of constituent cells that can be examined concurrently. Nevertheless, these approaches 4 typically recover substantially less information per-cell as compared to lower-throughput microtiter 5 plate-based strategies. To uncover critical phenotypic differences among cells and effectively link 6 scRNA-Seq observations to legacy datasets, reliable detection of phenotype-defining transcripts 7 -such as transcription factors, affinity receptors, and signaling molecules -by these methods is 8 essential. Here, we describe a substantially improved massively-parallel scRNA-Seq protocol we 9 term Seq-Well S^3 ("Second-Strand Synthesis") that increases the efficiency of transcript capture 10 and gene detection by up to 10-and 5-fold, respectively, relative to previous iterations, surpassing 11 best-in-class commercial analogs. We first characterized the performance of Seq-Well S^3 in cell 12 lines and PBMCs, and then examined five different inflammatory skin diseases, illustrative of 13 distinct types of inflammation, to explore the breadth of potential immune and parenchymal cell 14 states. Our work presents an essential methodological advance as well as a valuable resource 15 for studying the cellular and molecular features that inform human skin inflammation. 109Mann-Whitney U Test & Linear Regression; Figure 1B-C). To confirm that these overall 110 improvements were not driven by changes in the relative frequencies of different cell types 111 captured by each technology, we also examined each subset independently (Figure S2A-B). For 112 each cell type detected, we observed significant increases in the numbers of transcripts captured 113 and genes detected using S^3 for each pairwise comparison between techniques (P < 0.05, 114 Mann-Whitney U Test; CD4 + T cells, Seq-Well V1: 1,044 ± 62.3 UMIs/cell; 10x v2: 7,671 ± 103.9 115 UMIs/cell; Seq-Well S^3: 13,390 ± 253.4 UMIs/cell; Mean ± Standard Error of the Median (SEM); 116 Figure S2). Both Seq-Well S^3 and 10x v2 displayed increased sensitivity for transcripts and 117 genes relative to Seq-Well v1, but Seq-Well S^3 showed the greatest efficiency (defined as genes 118 recovered at matched read depth) to detect genes for each cell type (Figure 1D-E; Figure S2). 119We sought to further understand whether these improvements resulted in enhanced 120 detection of biologically relevant genes typically under-represented in high-throughput single-cell 121 sequencing libraries (Tabula Muris Consortium et al., 2018). Importantly, genes that were 122 differentially detected (i.e., higher in S^3) within each cell type include numerous transcription 123 factors, cytokines and cell-surface receptors (Figure 1D-E). For example, among CD4 + T cells, 124we observe significantly increased detection of cytokines (e.g., TGFB1 and TNF), surface 125 receptors (e.g., TGFBR and CCR4) and transcription fact...

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“…ACKR1 , also known as DARC (Duffy Antigen Receptor for Chemokines) marks human fLECs and Marco-LECs; but Ackr1 has very low expression in mouse LN LECs, without clear subset selectivity (Figure S8B). Consistent with this, endothelial ACKR1 in mouse is restricted to venular blood vessels, with only sparse and low detection in LECs [88]. ACKR1 is a chemokine “interceptor”, which can serve as a sink for a large range of inflammatory chemokines [89]: its expression could reflect a greater need to moderate inflammatory chemokines in the human.…”

Section: Species-specific Gene Expressionmentioning

confidence: 88%

A single-cell transcriptional roadmap of the mouse and human lymph node lymphatic vasculature

Xiang

Grosso

Pan

et al. 2020

Preprint

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Single-cell transcriptomics promises to revolutionize our understanding of the vasculature. Emerging computational methods applied to high dimensional single cell data allow integration of results between samples and species, and illuminate the diversity and underlying developmental and architectural organization of cell populations. Here, we illustrate these methods in analysis of mouse lymph node (LN) lymphatic endothelial cells (LEC) at single cell resolution. Clustering identifies five well-delineated subsets, including two medullary sinus subsets not recognized previously as distinct. Nearest neighbor alignments in trajectory space position the major subsets in a sequence that recapitulates known and suggests novel features of LN lymphatic organization, providing a transcriptional map of the lymphatic endothelial niches and of the transitions between them. Differences in gene expression reveal specialized programs for (1) subcapsular ceiling endothelial interactions with the capsule connective tissue and cells, (2) subcapsular floor regulation of lymph borne cell entry into the LN parenchyma and antigen presentation, and (3) medullary subset specialization for pathogen interactions and LN remodeling. LEC of the subcapsular sinus floor and medulla, which represent major sites of cell entry and exit from the LN parenchyma respectively, respond robustly to oxazolone inflammation challenge with enriched signaling pathways that converge on both innate and adaptive immune responses. Integration of mouse and human single-cell profiles reveals a conserved cross-species pattern of lymphatic vascular niches and gene expression, as well as specialized human subsets and genes unique to each species. The examples provided demonstrate the power of single-cell analysis in elucidating endothelial cell heterogeneity, vascular organization and endothelial cell responses. We discuss the findings from the perspective of LEC functions in relation to niche formations in the unique stromal and highly immunological environment of the LN.

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Differential DARC/ACKR1 expression distinguishes venular from non-venular endothelial cells in murine tissues

Cited by 120 publications

References 73 publications

Cell Atlas of Aqueous Humor Outflow Pathways in Eyes of Humans and Four Model Species Provides Insights into Glaucoma Pathogenesis

Cell Atlas of Aqueous Humor Outflow Pathways in Eyes of Humans and Four Model Species Provides Insights into Glaucoma Pathogenesis

Highly Efficient, Massively-Parallel Single-Cell RNA-Seq Reveals Cellular States and Molecular Features of Human Skin Pathology

A single-cell transcriptional roadmap of the mouse and human lymph node lymphatic vasculature

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