PhD position: pluripotent stem cell-derived gut-brain axis on a microfluidic chip.

The project
Brain disorders present a global debilitating burden to society urgently calling for in-depth molecular understanding of their pathological processes to propel the development of effective therapeutic targeting strategies forward. While many brain-localized aspects are known that regulate brain function, interestingly, a feature located nearly a meter away from the brain critically drives brain activity and cognition. This feature comprises the intestinal microbiota, or microbiome, which is considered to interact with the brain via the intestinal microbiome-gut-brain axis. Perturbations in the richness and diversity of the microbiome are a common feature in many brain-related disorders, including neurodegeneration, brain tumors, multiple sclerosis, autism spectrum disorders and schizophrenia. Nevertheless, the molecules, cell types and signaling pathways involved in this multi-tissue process remain enigmatic. Studies into this topic remain sparse as a result of multi-organ complexity and challenges to accurately recapitulate this complexity by means of current model systems of the human physiological microbiome-gut-brain axis. This project aims to provide fundamental mechanistic insights into how long distance interaction aids the communication between the microbiome and the brain health and disease by exploiting the differentiation potential of induced pluripotent stem cells into organoids. This project will generate an integrated microbiome-gut-brain axis from polycultured microbiome and stem cell-derived intestine, vagus nerve and brain connection that recapitulates key aspects of human physiology.

Your role
You will be generating human induced pluripotent stem cell-derived organoids of the intestine and vagus nerve along existing protocols. You will develop a differentiation procedure to create a brain stem organoid from pluripotent stem cells. Following their generation, you will validate the identity, stage of maturation, and functional activity of the organoids using biomarker (protein and mRNA) expression, imaging, epithelial barrier integrity and electrophysiological read-outs. Using CRISPR-Cas9-mediated gene editing you will modulate the genetic make-up of pluripotent stem cells to express potential features of interest to microbiome-gut-brain axis communication. Under the supervision of a highly skilled post-doctoral scientist and in collaboration with other groups at the University of Twente you will be creating microfluidic devices for organoid culture. You will generate bacterial cultures and use live cell stains to visualize their co-culture with intestinal organoids using microscopy. You will assess co-culture induced changes in specific marker expression using western blot, ELISA and confocal imaging.