Molecular mechanisms of intestinal organogenesis: A transcriptomic approach

Abstract

Organogenesis is a process normally reserved for developing organisms, however, some adult organisms are capable of such a feat. Adult sea cucumbers, in the highly regenerative clade Echinodermata, can undergo intestinal organogenesis after a process of evisceration where the intestine is severed then expelled through the cloaca. Studying this phenomenon has implications in regenerative biology to help discover the cellular and molecular processes that allow some species to regenerate better than others. Also, the field of regenerative medicine can benefit by enhancing existing biomedical applications, particularly that of intestinal tissue engineering. Thus, the sea cucumber <em>Holothuria glaberrima</em> is being used in this study to investigate intestinal organogenesis. The cellular properties of its regeneration have largely been elucidated, but the molecular mechanisms are now just starting to be unveiled. In this study we use a bioinformatic approach to investigate molecular mechanisms by collecting RNA-seq data from various early- and late-stage intestinal regenerate timepoints. These new timepoints not only contain newly sequenced tissue with luminal epithelium, but also samples that are spatially separated, i.e., anterior and posterior regenerates. Analyses from differential gene expression, gene set enrichment analyses, and weighted gene co-expression revealed differences in gene expression and molecular pathways operating at distinct temporal and spatial timepoints. For example, various signaling components of the Wnt/β-catenin pathway appear to be upregulated during early-stage rudiment regeneration, while signaling components of the Wnt/Planar Cell Polarity pathway are upregulated during late-stage regeneration in tissue that contains luminal epithelium. Even distinct gene ontological terms are functionally enriched in anterior regenerates that are not in posterior regenerates such as chromosome organization and cilium assembly. Altogether, this study demonstrates the diversity of molecular mechanism that occur during a dynamic process like intestinal organogenesis and serves as a baseline to guide future hypothesis-driven molecular studies.