Stem Cells and Organoid Biology

ESR project

1.9

Title of project

Epithelial based diagnostics for Very Early-Onset Inflammatory Bowel Disease (VEO-IBD)

We offer

A 4-year PhD student position in the interdisciplinary area of regenerative medicine. Your project will focus on developing and use of intestinal organoid-based diagnostic pipeline. This pipeline will be used to identify patients with a pathological epithelial phenotype and to predict patient-specific drug responses.

We ask

You hold a Master’s degree in cellular, molecular biology, biomedical sciences or in a related area. You have affinity with advanced cell and tissue culture techniques and molecular biology techniques and thrive in a multidisciplinary research environment. Experience with computational/bioinformatic data analysis are of benefit.

Department

The Department of Gastroenterology at WKZ UMC Utrecht and RMCU

Description

Despite the availability of numerous drugs that can be used for the treatment of IBD, we still do not have distinctive and effective treatments for many of the very early onset inflammatory bowel disease (VEOIBD) patients. This discrepancy is mainly the result of the fact that most of these therapies were established as beneficial upon testing in large cohort trials.  Therefore, it is almost impossible to reliably predict which medicine will be effective in which specific patient. In this respect, VEOIBD patients are particularly relevant, as these pathologies are thought to result from rare and mostly unknown gene defects.

The intestinal epithelium is a one of the key players in the (VEO) IBD pathogenesis. Our group has developed a method to culture the intestinal epithelial layer in vitro –called intestinal organoids or “mini-guts”.  Our research has enabled us to culture, analyze and store these organoids in a highly controlled fashion. This unique model system may, therefore, replicate the patient’s own epithelial pathology in IBD. Specifically, epithelial barrier function and microbial responsiveness will be studied. We will use this model system to develop intestinal organoid-based assays that will be used to identify patients with an intestinal epithelial phenotype and to predict patient-specific drug responses.

This project is part of VEOIBD consortium (http://veoibd.org/). Project is supervised by prof. Edward Nieuwenhuis (WKZ UMC Utrecht) and prof. Hans Clevers (Hubrecht Institute). Lab work will be performed at Mokry/Nieuwenhuis lab at RMCU.

Requirements

  • You have a Master in in cellular, molecular biology, biomedical sciences or in a related area.
  • You have affinity with advanced cell and tissue culture techniques and molecular biology techniques (molecular cloning, Crisp/Cas, PCR, WB, immunostaining, etc), and thrive in a dynamic and multidisciplinary research environment.  
  • You are motivated, creative and hard-working,
  • Experience with intestinal organoids and computational/bioinformatic data analysis are of benefit.

Contact person & more information

Dr. Michal Mokry, UMC Utrecht 
m.mokry@umcutrecht.nl

RESCUE

This project is part of RESCUE, a multidisciplinary, intersectoral and interdisciplinary PhD training programme in Regenerative Medicine and Stem Cells organised by UMC Utrecht (coordinator) and Utrecht University. RESCUE is partly funded by the European Commission under Horizon 2020's Marie Skłodowska-Curie Actions COFUND scheme. There are specific requirements with regards to English language and mobility for candidates who would like to take part in this programme. More information