Genetic and environmental factors affect our chances of being and staying healthy, as well as our susceptibility to disease development and treatment. At 3GI, we do translational and interdisciplinary research to foster the development of novel personalised treatments, in order to prevent or treat complex, immune-mediated diseases affecting the gastrointestinal tract.

To explain how health and treatment efficacy are regulated in an individual, we analyse big data generated from samples of healthy donors and patients obtained from population and patient cohorts.

We focus on complex diseases of the gastrointestinal tract such as celiac disease (CeD), inflammatory bowel disease (IBD: Crohn’s disease and ulcerative colitis), irritable bowel syndrome (IBS), non-alcoholic fatty liver disease (NAFLD), and systemic candidemia.

  • We apply genomics technology to understand the role of the genome (DNA genotyping, exome-sequencing, single-cell RNA-seq, single-cell ATAC-seq, targeted proteomics, metabolomics) and metagenomic sequencing to investigate the role of the microbiome in health and disease.
  • The big data generated is analysed and the different data layers are integrated by application of statistical genetics and bioinformatics methods.
  • To validate our findings we apply novel experimental model systems and techniques such as CRISPR/Cas, patient-derived adult stem cells (ASCs) and induced pluripotent stem cells (iPSCs), organoid culturing, and organ-on-chip systems.
Relevance

We aim to develop novel treatments or personalised treatment approaches for complex, immune-mediated diseases

With a greying population in the Netherlands, the health burden of complex, immune mediated diseases of the gastro-intestinal tract is rapidly increasing.  We aim to uncover how the genetic or gut microbial  make-up or the environment of an individual contributes to the development of complex, immune-mediated diseases. This knowledge enables the pinpointing of novel targets for personalised prevention and treatment using either existing approved drugs (drug repurposing) or innovative (e.g. microbiome directed) treatment protocols.

We focus on the mechanisms of complex, immune-mediated diseases of the gastro-intestinal tract, but similar or identical mechanisms and factors (both genetical, microbial and environmental) are involved in other complex diseases such as type 1 diabetes (T1D), rheumatoid arthritis (RA), multiple sclerosis (MS), and others. Because of this, our research results will contribute to the understanding and treatment of complex diseases in a broader sense.

  • We generated public awareness on the influence of non-antibiotic drugs on the gut microbiome (specifically proton pump inhibitors, which are taken by > 2 million people in the Netherlands).
  • We published a cahier on Organs-on-chip
  • We established large-scale public-private collaborations (e.g. with Takeda, DSM, Winclove)