Single cell RNA sequencing of the small intestine epithelium during Xenopus tropicalis metamorphosis reveals the involvement of epithelial-mesenchymal transition in the development of adult epithelial stem cells

ABSTRACT: Intestinal remodeling during thyroid hormone-dependent Xenopus metamorphosis involves degeneration of the larval epithelium through apoptosis and de novo formation of adult stem cells followed by their proliferation and differentiation to establish a multi-fold adult epithelium. This offers an opportunity to study how adult organ-specific stem cells are formed during vertebrate development. Here, we have carried out single cell RNA-sequencing (scRNA-seq) analyses of the intestinal epithelium at stage 56, a larval stage, and stage 61, a climax stage when larval epithelial cells undergo apoptosis and adult epithelial stem cells are formed and proliferating, and stage 66, the completion of metamorphosis. By distributing cells on a UMAP, where the locations of individual cells on a 2-dimensional plot are dictated by their transcriptomes relative to other cells, we found that most known cell types in the intestinal epithelium, such as goblet and enteroendocrine cells, are colocalized at the two stages, suggesting little changes in the transcriptomes of these cells between the two stages. On the other hand, the location of the major cell type, the enterocytes, shifts significantly at stage 61. Importantly, stem cells and a novel cell type, epithelial-mesenchymal transition (EMT) cells, are found almost exclusively at stage 61. Bioinformatics analyses of the differentially expressed genes (DEGs) between stages 56 and 61 for the enterocytes, EMT cells, and stem cells reveal that many more DEGs are for EMT cells and stem cells compared to the enterocytes. Interestingly, nearly 40% of the DEGs are common between EMT cells and stem cells. Pathway analyses of these common DEGs suggest that the EMT cells are the precursors of the adult stem cells and are derived from larval epithelial cells, most likely the enterocytes.

ORGANISM(S): Xenopus tropicalis

PROVIDER: GSE328891 | GEO | 2026/08/14

REPOSITORIES: GEO