miRNA expression in spatially-sorted hepatocytes

The mammalian liver is composed of repeating hexagonal units termed lobules. Spatially-resolved single-cell transcriptomics revealed that about half of hepatocyte genes are differentially expressed across the lobule. Technical limitations impede reconstructing similar global spatial maps of other hepatocyte features. Here, we used zonated surface markers to sort hepatocytes from defined lobule zones with high spatial resolution. We applied transcriptomics, miRNA array measurements and Mass spectrometry proteomics to reconstruct spatial atlases of multiple zonated hepatocyte features. We found that protein zonation largely overlapped mRNA zonation, with the periportal HNF4α as an exception. We identified zonation of miRNAs such as miR-122, and inverse zonation of miRNAs and their hepatocyte target genes, implying potential regulation through zonated mRNA degradation. These targets included the pericentral Wnt receptors Fzd7 and Fzd8 and the periportal Wnt inhibitors Tcf7l1 and Ctnnbip1. Our approach facilitates reconstructing spatial atlases of multiple cellular features in the liver and other structured tissues. Single tetraploid hepatocytes were isolated from three mice, and FACS-sorted according to expression of the surface markers Nt5e (CD73) and Cdh1 (E-cadherin), yielding 8 subpopulations of hepatocytes originating from distinct positions in the liver lobule.