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

Spatially resolved single-cell RNA sequencing (scRNAseq) is a powerful approach to infer connections between a cell’s identity and its position within a tissue. We 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, we present paired-cell sequencing, whereby mRNA from pairs of attached cells are sequenced and gene expression from one cell type is used to infer the pairs’ tissue coordinates. We apply the method to pairs of hepatocytes and liver endothelial cells (LECs). Using the spatial information from hepatocytes, we reconstruct LEC zonation and extract a landmark gene panel that we use to spatially map LEC scRNAseq data. Our approach reveals 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.