Identification and Mapping of Human Lymph Node Stromal Cell Subsets by Combining Single-Cell RNA Sequencing with Spatial Transcriptomics.

Lymph node stromal cells (LNSCs) have a crucial immunomodulatory function, but their heterogeneity in humans is incompletely understood. Here, we report the single-cell RNA sequencing (scRNA-seq) of 9267 LNSCs isolated from a human lymph node (LN). This study comprehensively defines the gene signatures of 10 fibroblast subtypes: CCL21+ SC, CCL19+ SC, CD34+CXCL14+ SC, pericytes, DES+ SC, LAMP5+ SC, NR4A1+BCAM+ SC, HLA-DR+ SC, SEPT4+ SC and GLDN+ SC. The existence of these subtypes was validated across 13 LN donors using 2 publicly available datasets and our dataset. To explore the heterogeneous stromal compartment within the complex LN tissue architecture, we integrated the scRNA-seq profiles of the identified LNSC subsets with a publicly available human spatial transcriptomic LN dataset and predicted their location within the complex LN tissue architecture. Each LNSC subtype was spatially restricted to specific LN regions, indicating different LNSC-lymphocyte interactions, which were further investigated using NicheNet. The positioning of distinct LNSC subtypes within different LN regions sets the stage for future research on the relationship between LNSC-specific niches and immunomodulatory function during health and disease.