• intestinal organoid
• metabolism
• regeneration
• single-cell decision-making

From the smallest cell to the whole body, thousands of gears work in concert in space and time to ensure the utmost expression of human physiology. How in the absence of a hierarchical control, single cells coordinate and give rise to complex tissues is a mystery of multicellular organisms. Borrowing from the science of complex systems, it has been hypothesized that a set of local rules govern the life of a single cell and that emergent properties stem from complex interactions at the population level. Here we study single-cell decision-making in the context of a complex self-organising eukaryotic tissue.
With one of the highest turnover rates in the body, intestinal epithelium is a flourishing and dynamical territory where regenerative cell-types constantly sense the environment and need to decide which fate to acquire and which mature cell-type to become. To quantitatively track the single cells whilst keeping a holistic view of the emergent patterns at the population levels, we made use of organoid techniques which allow the in-vitro three-dimensional reproduction of the microanatomy and functions observed in-vivo. We studied the process of intestinal organoid regeneration, whereby a single cell rapidly grows into a symmetrical sphere of cells which ultimately buds into an asymmetrical mature organoid, with its crypts and villi that morphologically and functionally recapitulate the intestinal epithelium.
Through the transcriptomic analysis at the single cell resolution, we characterized the metabolic fingerprints that support intestinal organoid regeneration and cell lineage acquisition. We further confirmed our results through high-throughput imaging in fixed and living single cells from mature intestinal organoids. Through manipulation experiments targeting newly found metabolic markers we generated organoids with different proportions of mature cell-types. Altogether, our findings suggest an instructive role for metabolism in cell decision-making, suggesting cell metabolic state as a putative candidate for understanding the coordination and collective behaviour at the system level.