Dynamic control of metabolic zonation and liver repair by endothelial cell Wnt2 and Wnt9b revealed by single cell spatial transcriptomics using Molecular Cartography

Abstract

The conclusive identity of Wnt proteins regulating liver zonation (LZ) and regeneration (LR) remains unclear despite an undisputed role of b-catenin. Using single-cell analysis of liver cells from various species, a conserved Wnt2 and Wnt9b expression in endothelial cells (ECs) in zone 3 shown to be the major Wnt cell source, was identified. Conditional EC-elimination of Wnt2 and Wnt9b led to perturbation of LZ with not only loss of b-catenin targets in zone 3, but also re-appearance of zone 1 genes in zone 3, unraveling dynamicity as revealed by single-cell spatial transcriptomics using Molecular Cartography. Defective LR observed in the knockouts phenocopied other models of defective hepatic Wnt signaling. Administration of a tetravalent antibody to activate Wnt signaling rescued LZ and LR in the knockouts. Molecular Cartography on the livers of the agonist-treated animal revealed changes in LZ. Administration of the agonist also promoted LR in acetaminophen overdose acute liver failure (ALF) fulfilling an unmet clinical need. Overall, we report an unequivocal role of EC-Wnt2 and Wnt9b in LZ and LR and show the role of Wnt activators as regenerative therapy for ALF.

Liver macrophages in health and disease

“…These cell-cell interactions are highly conserved across species (Guilliams et al, 2022) and humans carrying ALK1 mutations develop Hereditary Hemorrhagic Telangiectasia, which is associated with severe vascular malformations in the liver, necessitating liver transplantation (Lerut et al, 2006). The WNT signals produced by peri-central LSECs are also conserved across species and are essential to control the peri-central function of hepatocytes (Hu et al, 2022). Altogether, this suggests that throughout evolution hepatocytes, LSECs, stellate cells and KCs have become genetically integrated to function together as one intercellular functional module, highlighting that these cells represent one another's niche.…”

Bento: A toolkit for subcellular analysis of spatial transcriptomics data

“…In order to facilitate a flexible workflow, Bento is generally compatible with molecule-level resolution spatial transcriptomics data ( Fig. 1A ), such as datasets produced by MERFISH 13 , seqFISH+ 14 , CosMx (NanoString) 34 , Xenium (10x Genomics) 15,35 , and Molecular Cartography (Resolve Biosciences) 36 . Bento’s workflow takes as input 1) 2D spatial coordinates of transcripts annotated by gene, 2) cell segmentation boundaries and 3) nuclear segmentation boundaries ( Fig.…”

Bento: a toolkit for subcellular analysis of spatial transcriptomics data

“…In order to facilitate a flexible workflow, Bento is generally compatible with moleculelevel resolution spatial transcriptomics data (Fig. 1A), such as datasets produced by MERFISH [13], seqFISH + [14], CosMx (NanoString) [33], Xenium (10 × Genomics) [15,34], and Molecular Cartography (Resolve Biosciences) [35]. Bento's workflow takes as input (1) 2D spatial coordinates of transcripts annotated by gene and (2) segmentation boundaries (e.g., cell membrane, nuclear membrane, and any other regions of interest) (Fig.…”