Defining spatiotemporal gene modules in liver regeneration using Analytical Dynamic Visual Spatial Omics Representation (ADViSOR)

Abstract

Background: The liver is the only organ with the ability to regenerate following surgical or toxicant insults, and partial hepatectomy serves as an experimental model of liver regeneration (LR). Dynamic changes in gene expression occur from the periportal to pericentral regions of the liver following partial hepatectomy; thus, spatial transcriptomics, combined with a novel computational pipeline (ADViSOR [Analytic Dynamic Visual Spatial Omics Representation]), was employed to gain insights into the spatiotemporal molecular underpinnings of LR. Methods: ADViSOR, comprising Time-Interval Principal Component Analysis and sliding dynamic hypergraphs, was applied to spatial transcriptomics data on 100 genes assayed serially through LR, including key components of the Wnt/β-catenin pathway at critical timepoints after partial hepatectomy. Results: This computational pipeline identified key functional modules demonstrating cell signaling and cell-cell interactions, inferring shared regulatory mechanisms. Specifically, ADViSOR analysis suggested that macrophage-mediated inflammation is a critical component of early LR and confirmed prior studies showing that Ccnd1, a hepatocyte proliferative gene, is regulated by the Wnt/β-catenin pathway. These findings were subsequently validated through protein localization, which provided further confirmation and novel insights into the spatiotemporal changes in the Wnt/β-catenin pathway during LR. Conclusions: Thus, ADViSOR may yield novel insights in other complex, spatiotemporal contexts.