The Gut Cell Atlas Project: Normal & Crohn’s Disease

This project will build a Gut Cell Atlas from human tissue samples, from which single-cell gene expression data and histopathological image cellular localization data will be generated These will be correlated with some clinical, pathological and radiological data. The project is funded by The Helmsley Charitable Trust

The goal of this study is to provide an integrated dataset of single-cell gene expression data mapped onto a high-resolution 3-dimensional framework model of the small and large intestines, focussing particularly on the terminal ileum, caecum and ascending colon. There will be mapping to both a 2D model (anatomogram) and a 1D linear model of healthy gut. Normal gut samples will be collected from appropriate subjects, as will samples from Crohn’s disease patients undergoing intestinal resections for complex fibrostenotic stricturing disease.

Data collected will include single cell RNA expression data, histopathological  images, and radiological studies of both normal and Crohn's Disease affected intestines.  All data will be published on open access online platforms, with all software and models accessible via Github.

The research  will deliver a gut-centric common coordinate framework to map anatomical locations of cells providing novel insights into Crohn’s disease mechanisms, crucial to developing personalized therapeutic strategies, and new analytical tools for querying the Gut Cell Atlas database.

This is a component project within a suite of projects to build a Gut Cell Atlas, supported by a grant of $3.1M from The Helmsley Charitable Trust.  The team is based in Edinburgh (Universities of Edinburgh and Heriot-Watt) and Cambridge (Wellcome Trust Sanger Institute and European Bioinformatics Institute).

The Gut Cell Atlas is a component of the Human Cell Atlas, which seeks to create comprehensive reference maps of all cells – the fundamental units of life – as a basis for both understanding human health and diagnosing, monitoring, and treating disease.