IBDome – A Platform for Research on Chronic Inflammatory Bowel Diseases
IBDome integrates genetic, molecular, and clinical data from patients with Crohn’s disease and ulcerative colitis into a unified database. Researchers of TRR 241 use this platform to gain new insights into disease mechanisms and to develop more targeted therapies.
In the first project phase, we have already:
- Established a joint biobank in Erlangen and Berlin
- Analyzed over 300 patient samples comprehensively (e.g., gene expression, microbiome)
- Developed a web-based platform for data analysis (IBDome Explorer)
In the next phase, we aim to include more patients, investigate long-term disease courses, and apply innovative analysis methods such as single-cell sequencing. Our long-term goal is to establish one of the world’s largest publicly accessible IBD databases.
SEPIA – A Database for Mouse Models in IBD Research
SEPIA is a central platform of TRR 241 that consolidates sequencing data from various mouse models of chronic inflammatory bowel diseases. Researchers within the consortium can use these data to gain insights into disease mechanisms and to compare mouse models with clinical data from IBDome.
Since 2021, the first datasets have been available, and in the next project phase, SEPIA will be integrated into a web-based tool to facilitate data access and analysis. In the long term, SEPIA aims to become publicly accessible to:
- Analyze target gene expression in the gut and during inflammation induction
- Develop new hypotheses on IBD pathogenesis
- Reduce unnecessary animal experiments and support the 3R principle
SEPIA exemplifies the close collaboration within TRR 241 and demonstrates how synergies between basic research and clinical application can be leveraged.
IEC-Atlas
The IEC-Atlas is a resource for researchers analyzing transcriptomic data from intestinal epithelial organoids stimulated with various microbial, immunological, and neuronal factors. These organoids were derived from mouse intestinal crypts as well as patient biopsies. The platform enables visualization and investigation of intestinal epithelial cell (IEC) responses to diverse microbial, host-intrinsic, and extrinsic stimuli.
In the long term, the IEC-Atlas aims to help researchers:
- Better understand the molecular mechanisms of IEC responses to inflammatory stimuli
- Develop new hypotheses about the role of IECs in intestinal inflammation
- Promote the translation of experimental findings into clinical contexts
The IEC-Atlas exemplifies close collaboration among several research labs in Erlangen and Berlin, demonstrating how shared expertise can create specialized resources for analyzing epithelial immune responses and advance translational research.
Simultaneously, the IEC-Atlas shows how surplus funds within TRR 241 have been competitively and effectively allocated to support small collaborative projects at different TRR 241 sites. This led to the creation of a valuable resource that strengthens the motto “IEC in IBD” and benefits both the local and international scientific communities.