Functional heterogeneity of intestinal stem cells: molecular mechanisms and relevance in disease

• Applicant: Dr. Natalia Soshnikova
• Subject Area: General Genetics and Functional Genome Biology ; Developmental Biology ; Gastroenterology
• Term: since 2019
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 427330905

Gastrointestinal diseases involving disruptions in the epithelial cell compartment, such as inflammatory bowel disease (IBD), celiac disease (CeD), and small intestinal or colorectal cancer (CRC), are major public health concerns. Intestinal stem cells (ISCs) play a critical role in maintaining tissue homeostasis by continuously generating absorptive enterocytes, secretory goblet, enteroendocrine, tuft and Paneth cells. Traditionally, ISCs are viewed as a functionally homogeneous source for differentiated epithelial cells. However, the differentiation and neoplastic potential of individual ISCs and the molecular mechanisms behind these processes remain unexplored. In the first funding period, we discovered that adult ISCs are functionally heterogeneous. Based on the molecular characteristics of their embryonic progenitors, ISCs exhibit different capacities for generating secretory cell types. Specifically, ISCs derived from Axin2+ embryonic progenitors have an enhanced ability to differentiate into tuft and enteroendocrine cells but show a reduced capacity to produce Paneth cells. We found that ISC differentiation potential is established during embryogenesis through paracrine BMP signalling and cell-intrinsic transcription factors. Consequently, transient inhibition of BMP signalling during embryogenesis alters the differentiation potentials of both Axin2+- and Axin2neg-derived ISCs. Importantly, Axin2+-derived ISCs are the primary source of adenomas in the Apcmin/+ mouse model, and a marker of these cells, CSRNP3, is overexpressed in the inflamed and malignant epithelium of patients with IBD and intestinal cancer, respectively. Now, we aim to explore the mechanisms driving the differential cancer-promoting potential of genetically identical Axin2+- and Axin2neg-derived ISCs. Using the Apcmin/+:Axin2Cre-ERT:Rosa26tdTomato mouse model and applying CRISPR/Cas9 gene editing in organoid systems, we will investigate how cell-intrinsic factors and niche-derived signals contribute to tumour progression. Furthermore, we will use human organoids and tumoroids to translate findings from mouse models and identify factors influencing tumour development in humans. The results of this study will provide new insights into the cellular and molecular mechanisms that drive tumour progression, potentially revealing novel therapeutic targets. Our second goal is to investigate the role of Axin2+-derived epithelial cells in Crohn's disease. Using mouse models of acute and chronic ileitis, combined with CRISPR/Cas9-edited human and mouse organoids, we will assess epithelial barrier integrity and differential susceptibility to inflammatory signals in Axin2+ versus Axin2neg-derived clones. This research will identify the molecular mechanisms underlying barrier dysfunction and chronic inflammation in IBD, laying the groundwork for clonal-targeted therapies in Crohn’s disease.

• DFG Programme: Research Grants