FIBROTARGET Training Academy
FIBROTARGET has developed a training academy with material for early career researchers working in IBD across Europe. Explore our first module below and stay tuned for detailed protocols and webinars of essential in vitro, in vivo, ex vivo and in silico immunological techniques!
Module 1: in vitro fibrosis models
This video provides an overview of inflammatory bowel disease (IBD) pathology and experimental methods to study intestinal fibrosis using human primary fibroblasts and induced pluripotent stem cells (iPSCs)–derived models. We outline the dissociation of human ileum into viable single-cell suspensions for flow cytometry and primary cell culture, including mechanical and enzymatic digestion, filtration, and immunophenotyping of stromal populations.
We further describe approaches to evaluate pro-fibrotic phenotypes in primary human intestinal fibroblasts and iPSC-derived organoids. Functional assays include pro-inflammatory cytokines stimulation, assessment of extracellular matrix production, and analysis of fibrosis markers by qPCR, immunostaining, and functional assays. Together, these methods provide a platform to investigate mechanisms of fibrosis in IBD.
Module 2: in vivo fibrosis models induction and monitoring of fibrosis in mice
This module presents in detail the most commonly used in-vivo models for fibrosis induction, including chemically induced colitis using DSS and TNBS, as well as a novel model of intestinal fibrosis based on the TNFΔARE mouse strain. Specifically, we describe induction and monitoring of disease development and available tools and techniques for fibrosis assessment, ranging from histological and colorimetric assays to non-invasive MRI-based approaches.
Module 3: ex vivo fibrosis models
This module provides an overview of methodologies for studying fibrosis using ex vivo human intestinal explants, with a particular focus on biopsy-based techniques and ex vivo organ culture approaches
Module 4: Omics-based annotation
This session provides a comprehensive overview of high-resolution transcriptomics in the context of gut fibrosis. We will explore the fundamental differences between Single-cell RNA sequencing and Spatial Transcriptomics, moving from data acquisition to the computational strategies used to interpret complex datasets. The presentation outlines the standard analysis pipeline—from processing raw data to identifying cell clusters—and demonstrates how these tools are applied to annotate mesenchymal cell dynamics in health, inflammation, and stenosis.
FIBROTARGET Training Academy Modules
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