Paired-cell sequencing enables spatial gene expression mapping of liver endothelial cells.
IF: 68.164
Cited by: 172


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. 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 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. We applied this method to pairs of hepatocytes and liver endothelial cells (LECs). Using the spatial information from hepatocytes, we reconstructed LEC zonation and extracted a landmark gene panel that we used to spatially map LEC scRNAseq data. Our 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.


Spatial Transcriptomics
Spatial reconstruction
Spatial Gene Expression

MeSH terms

Base Sequence
Endothelial Cells
Gene Expression Regulation
Protein Transport
RNA, Messenger
Sequence Analysis, RNA
Wnt Signaling Pathway


Halpern, Keren Bahar
Shenhav, Rom
Massalha, Hassan
Toth, Beata
Egozi, Adi
Massasa, Efi E
Medgalia, Chiara
David, Eyal
Giladi, Amir
Moor, Andreas E
Porat, Ziv
Amit, Ido
Itzkovitz, Shalev

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