Paired-cell RNA sequencing enables spatial gene expression mapping of liver endothelial cells

Spatially resolved single-cell RNA sequencing (scRNAseq) is a powerful approach for inferring connections between a cell’s identity and its position in a tissue. Researchers at the Weizmann Institute of Science recently combined scRNAseq with spatially mapped landmark genes to infer the expression zonation of hepatocytes. However, determining zonation of small cells with low mRNA content, or without highly expressed landmark genes, remains challenging. Here they used paired-cell sequencing, in which mRNA from pairs of attached mouse cells were sequenced and gene expression from one cell type was used to infer the pairs’ tissue coordinates. The researchers applied this method to pairs of hepatocytes and liver endothelial cells (LECs). Using the spatial information from hepatocytes, they reconstructed LEC zonation and extracted a landmark gene panel that they used to spatially map LEC scRNAseq data. This approach revealed the expression of both Wnt ligands and the Dkk3 Wnt antagonist in distinct pericentral LEC sub-populations. This approach can be used to reconstruct spatial expression maps of non-parenchymal cells in other tissues.

Single-cell RNAseq reveals the expression signatures of liver non-parenchymal cells

(a) T-distributed stochastic neighbor embedding (tSNE) map showing the identified seven clusters: endothelial cells (1,203 cells, b), T cells (958 cells, c), pDCs (119 cells, d), Kupffer cells (340 cells, e), LCMs (164 cells, f), B cells (307 cells, g) and neutrophils (60 cells, h). Blue represents high expression and gray represents low expression in b–h.