A single-cell transcriptional roadmap of the mouse and human lymph node lymphatic vasculature
Authors: Xiang Menglan , Grosso Rubén Adrián , Takeda Akira , Pan Junliang , Bekkhus Tove , Brulois Kevin , Dermadi Denis , Nordling Sofia , Vanlandewijck Michael , Jalkanen Sirpa , Ulvmar Maria H. , Butcher Eugene C. 
Published: January 2020

AbstractSingle-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.HighlightsComputational alignments (“trajectories”) predict LN LEC organizationin situ, revealing a continuum of phenotypes punctuated by specialized clustersMultiple intermediate phenotypes suggest LEC malleabilityGene profiles define niche-specific functional specializationMedullary sinus LECs are comprised of Ptx3-LECs and Marco-LECsDistinct mechanisms for pathogen interactions and matrix modelingPtx3-LECs: paracortical and central medullary sinuses near hilus; enriched for genes driving lymphangiogenic responses and lymphocyte egressMarco-LECs: peri-follicular medullary sinuses; macrophage-associated genes, complement and coagulation cascadeNiche-specific responses to inflammationIFN gene responses in SCS floor and medullary sinus LECsSuppression of LEC identity genes in responding subsetsConserved and unique LEC subsets and gene programs across speciesCore subsets common to mouse and humanGreater diversity of subsets and intermediates in human LN LECs