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Cellular cartography of the intestine in health and inflammation

Project description

In situ sequencing to map cell interactions in the intestinal mucosa

Under physiological conditions, the intestinal epithelium constitutes a dynamic physical barrier serving as the first line of immune defence. Damage of the monolayer of specialised intestinal epithelial cells induces disruption of intestinal immune homeostasis and leads to inflammatory bowel diseases (IBD), such as ulcerative colitis and Crohn’s disease. Given the rising incidence of IBD in modern societies, scientists of the EU-funded GUTMAPS project aim to investigate the intestinal tissue in unprecedented resolution. To do so, they will perform in situ sequencing to profile individual cells, map cell–cell interactions and help to create a better understanding of this organ in health and disease.


The intestinal epithelium is the first line of defence of the mucosal immune system because it acts as a dynamic physical barrier segregating the luminal content from the underlying mucosal tissue. This barrier is mainly formed by a monolayer of specialised intestinal epithelial cells (IECs) that are crucial in maintaining intestinal homeostasis. Damage to this epithelial layer can increase intestinal permeability and lead to abnormalities in interactions between IECs, stromal cells and immune cells in the underlying lamina propria thereby disturbing the intestinal immune homeostasis, all of which are a hallmark of several intestinal disorders including inflammatory bowel diseases (IBD). Ulcerative colitis (UC) and Crohn’s disease (CD) are the two major forms of IBD, affecting an estimated 4 million people in the United States and Europe and have a rising incidence in the developing world. Recent single cell RNA seq (scRNAseq) studies of the intestine have allowed us to understand this organ in unprecedented detail, however, such studies still require the dissociation of tissue and loss of spatial resolution. With this project, I would like to take advantage of recent advances in in-situ sequencing to study intestinal tissue in toto and by combining this with the available scRNA-seq data, generate spatial maps of the intestine (GUTMAPS). The results obtained here will allow us to look at tissue composition and cell-cell interactions with unprecedented resolution in normal and diseased mucosa.


Net EU contribution
€ 187 572,48
3015 GD Rotterdam

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West-Nederland Zuid-Holland Groot-Rijnmond
Activity type
Higher or Secondary Education Establishments
Total cost
€ 187 572,48