Investigating molecular mechanisms of chronic inflammatory signaling during intestinal fibrosis by mechanosensing pathways

• Applicant: Andrew G. Clark, Ph.D.
• Subject Area: Cell Biology ; Biophysics
• Term: since 2025
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 569500933

Cellular mechanosensing mechanisms have been shown to play a major role in regulating various biological processes, including stem cell maintenance, differentiation, cell division and cell death. One of the long-term consequences of chronic inflammation, for example in inflammatory bowel diseases (IBDs) such as Crohn’s disease or ulcerative colitis, is a mechanical stiffening of the tissue, culminating in fibrosis. However, little is known about how fibrosis affects cellular function or modulates inflammatory signaling in this context. In the proposed work, we seek to understand how mechanosensing influences the response of intestinal epithelial cells to inflammatory cytokines. In preliminary experiments using intestinal organoids, we have identified Interleukin (IL)-13, a cytokine commonly upregulated in IBDs, as a regulator of intestinal barrier function and intestinal stem cell differentiation. Our further preliminary data using intestinal organoid monolayers suggest that substrate mechanosensing and IL-13 signaling behave synergistically to modulate differentiation, biasing differentiation toward secretory cell lineages. Blocking either mechanosensing or downstream IL-13 effectors rescues stiffness- or IL-13-dependent changes, suggesting that these pathways may also be co-dependent. Based on these preliminary findings, we propose an interdisciplinary research programme combining state-of-the-art primary organoid culture techniques, quantitative high-resolution microscopy, mechanobiology assays and in vivo mouse models to elucidate the mechanisms underlying synergy between mechanosensing and IL-13 signaling. To address this, we will use a combination of genetic and chemical perturbation and fluorescently-tagged IL-13 signaling components in organoids to investigate the molecular mechanisms of IL-13 mechanosensing. Next, we will perform mechanobiology assays including traction force microscopy, laser ablation and mechanical tension biosensors combined with functional inhibition experiments to determine direct and indirect mechanotransduction pathways responsible for the mechanosensing response. Finally, we will use fluorescent biosensors of downstream signaling pathways in organoids to link mechanosensing and IL-13 signaling with changes in cell differentiation. We will validate our mechanistic findings from organoid monolayers using 3D organoids embedded in tunable hybrid synthetic polymer/ECM networks and using a mouse model of colitis and organoids extracted from these mice. Together, this work will uncover fundamental mechanisms of mechanosensing in epithelial cells and provide future perspectives to address IBDs by targeting mechanotransduction pathways.

• DFG Programme: Research Grants