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A systems biology approach to investigate cell fate switches in intestinal organoids

Periodic Reporting for period 2 - SysOrganoid (A systems biology approach to investigate cell fate switches in intestinal organoids)

Reporting period: 2020-04-01 to 2021-09-30

Every day, billions of new cells are produced in the intestine of a mouse. The generation of these cells is driven by adult stem cells, which residue in the intestinal epithelium. These stem cells divide every day, but they also differentiate towards distinct cell types that are involves in processes such as nutrient uptake and secretion of mucus and hormones. Intestinal organoid cultures recently emerged as a paradigm to study adult stem cell maintenance and differentiation. These ‘miniguts’ can be cultured in vitro and contain all the different cell types that present in the mouse small intestinal epithelium. Recently it was shown that small-molecule driven perturbations can be used to obtain organoids, which are strongly enriched for specific intestinal cell types. This system thus provides a perfect opportunity to study, for the first time, adult stem cell maintenance and (de)differentiation in a controlled manner.
Using small molecule-driven perturbations and a unique combination of ‘omics’ technologies, which are embedded in our department, we will provide a systems-wide view of the molecular (epigenetic) mechanisms that orchestrate cell fate changes in intestinal organoids. This integrative approach will identify the major regulatory networks that define the remarkable cellular plasticity of the mouse small intestinal epithelium. Beyond this basic scientific goal, our work will also have profound implications for cancer research and regenerative medicine, both of which are characterized by changes in adult stem cell homeostasis.
So far in the project we have uncovered differentiation trajectories and associated gene expression dynamics for various cell types in the mouse intestinal epithelium, including enterocytes, Paneth cells and M cells. We have also developed various technologies in the context of the project, including a new method te profile genome-wide transcription factor binding affinities. We have recently filed a patent for this method.
Several innovative technologies are being developed in the project, including a miniaturised interaction proteomics platform on a microfluidics chip and, as mentioned, a new genomics method to profile genome-wide transcription factor binding affinities. Our multi-omics analyses of cellular differentiation and dedifferentiation in the mouse small intestinal epithelium will uncover new regulators of cell fate, which will have profound implications from a fundamental and applied scientific perspective.