Periodic Reporting for period 1 - TOP-GUT (Training for Organoids modelling Physiology and Pathology in the human gastrointestinal tract)
Período documentado: 2023-11-01 hasta 2025-10-31
The gastrointestinal system (GI) is a major barrier in our body that protects us from, but also interacts with, environmental cues. Every day we introduce several kilograms of food and liquid to our body, and with that bacteria, viruses and toxins. A failure in equilibrium can result in infection and cancer. The study of the GI tract has relied on cancer cell lines or animal models, but these fail to accurately mimic human physiology and offer poor predictive value. This is a general concern in current drug development, as fewer than 1 out of 10 drugs enter the market after showing effectiveness in traditional models. For these reasons, together with a rising societal interest in animal welfare and ethical awareness, the European Union encourages the development of alternatives to animal models to address gaps in the pipeline where such models are lacking or ineffective.
The last decade has witnessed a leap forward in the development of new human model systems, driven by breakthroughs in stem cell biology and perfusable organ-on-chip (OoC) technologies. A small biopsy of healthy or tumor tissue can now be embedded in a biological matrix in a plastic plate and grown in vitro, forming a ´´mini-organ´´ known as organoid. While healthy patient-derived organoids (PDOs) recapitulate key organ functions, cancer PDOs reproduce patient-specific pathologies and help predict individual responses to cancer therapies. PDOs can be integrated into OoC platforms to mimic the GI tract flow and to combine different organoids. Within TOP-GUT, we aim to train the next generation of scientist to understand and build model complexity, address future applications for personalized medicine, and manage ethical, regulatory and legal aspects, as well as effective science communication.
The last decade has witnessed a leap forward in the development of new human model systems, driven by breakthroughs in stem cell biology and perfusable organ-on-chip (OoC) technologies. A small biopsy of healthy or tumor tissue can now be embedded in a biological matrix in a plastic plate and grown in vitro, forming a ´´mini-organ´´ known as organoid. While healthy patient-derived organoids (PDOs) recapitulate key organ functions, cancer PDOs reproduce patient-specific pathologies and help predict individual responses to cancer therapies. PDOs can be integrated into OoC platforms to mimic the GI tract flow and to combine different organoids. Within TOP-GUT, we aim to train the next generation of scientist to understand and build model complexity, address future applications for personalized medicine, and manage ethical, regulatory and legal aspects, as well as effective science communication.
TOP-GUT is a highly interdisciplinary and intersectoral training network that brings together world-leading institutes, seven Universities and two companies, in the fields of PDOs, immunology, glycobiology, and OoC technology. Each host supervises one or two doctoral candidates (DCs), supported by thirteen associated partners, including companies, startups and a National Health Executive Agency. TOP-GUT is further supported by three internationally recognized experts who form an external advisory board to foster excellence.
The consortium has recruited eleven excellent students from diverse backgrounds: biochemistry, molecular biology, biotechnology, biomedical engineering, and international law. Each DC is enrolled in a graduate school or university and has begun a research project focus within one of TOP-GUT´s work packages: (i) understanding biology, (ii) building complexity or (iii) application. PDOs and methodologies have been exchanged between institutions and DCs have established PDO cultures in their host laboratories. They have learned about the GI tract and the immune system, and cutting-edge analysis techniques. Secondments have enabled hands-on training with the consortium experts, while active communication within the network has promoted the sharing of knowledge and expertise. Training events have complemented their scientific education on good scientific practice, diversity and inclusion in science, translational medicine, entrepreneurship, patenting and commercialisation.
The consortium has recruited eleven excellent students from diverse backgrounds: biochemistry, molecular biology, biotechnology, biomedical engineering, and international law. Each DC is enrolled in a graduate school or university and has begun a research project focus within one of TOP-GUT´s work packages: (i) understanding biology, (ii) building complexity or (iii) application. PDOs and methodologies have been exchanged between institutions and DCs have established PDO cultures in their host laboratories. They have learned about the GI tract and the immune system, and cutting-edge analysis techniques. Secondments have enabled hands-on training with the consortium experts, while active communication within the network has promoted the sharing of knowledge and expertise. Training events have complemented their scientific education on good scientific practice, diversity and inclusion in science, translational medicine, entrepreneurship, patenting and commercialisation.
PDOs are current state-of-the-art models with significant advances, but important limitations remain. First, the layer of complex sugars (glycans) decorating the cells and mucus is not well understood, despite its essential role demonstrated on the interaction with microbiota and pathogens and its importance as a cancer biomarker and therapeutic target. Second, the cellular microenvironment is essential for maintaining a healthy epithelium, interacting with immune cells, and shaping how cancer develops and responds to therapy. However, incorporating key microenvironmental components, such as immune cells, fibroblasts and vasculature, into PDO cultures is still in its early stages.
Glycomics is an emerging field whose specialized analytical techniques are still being developed. Within TOP-GUT we used established growth factor cocktails to drive differentiation towards mucus-producing secretory cell lineages and analyzed the secreted mucus by cutting-edge mass spectrometry. We also adapted spatial proteomics to visualize the local immune cell composition along the GI tract. Together, these approaches begin to build a region-resolved glycan and immune cell atlas of the human GI tract in vitro, providing a basis for further mechanistic analysis in glycosylation, host defence and disease.
The cellular microenvironment is largely defined by the physical scaffold surrounding the cells (extracellular matrix), the neighbouring support cells (such as fibroblasts) and the presence of small blood vessels. In TOP-GUT, we have fine-tuned biological hydrogels to support healthy and cancer-associated fibroblast, the formation of (perfusable) vasculature, and the development of crypt-villi-like structures. PDOs and co-cultures have been incorporated into two commercially available OoC platforms and a third, new chip is being developed, that better captures the three-dimensional architecture of the intestinal wall. Overall, this work advances PDOs from simple epithelial spheres towards complex, vascularized and stromal-rich GI tissue models.
Besides the understanding and development of more advanced in vitro models, ethical and regulatory routes must be considered to enable their clinical use in personalized medicine. One TOP-GUT project specifically addresses European and national legislations, using the Norwegian Directorate of Health’s regulations on stem cell-based embryo models as a case study to show how conceptual definitions can shape legal boundaries. Similar conceptual discussions are emerging for organoids. However, unlike embryo models, GI PDOs are structurally and functionally more limited and not viewed as embryo-like or organism-level hybrid entities. At the same time, PDOs are a novel technology and terminology; definitions and specific guidelines for clinical purpose and research are still being developed. Through its legal and ethical work, TOP-GUT contributes to shaping this emerging regulatory framework.
Glycomics is an emerging field whose specialized analytical techniques are still being developed. Within TOP-GUT we used established growth factor cocktails to drive differentiation towards mucus-producing secretory cell lineages and analyzed the secreted mucus by cutting-edge mass spectrometry. We also adapted spatial proteomics to visualize the local immune cell composition along the GI tract. Together, these approaches begin to build a region-resolved glycan and immune cell atlas of the human GI tract in vitro, providing a basis for further mechanistic analysis in glycosylation, host defence and disease.
The cellular microenvironment is largely defined by the physical scaffold surrounding the cells (extracellular matrix), the neighbouring support cells (such as fibroblasts) and the presence of small blood vessels. In TOP-GUT, we have fine-tuned biological hydrogels to support healthy and cancer-associated fibroblast, the formation of (perfusable) vasculature, and the development of crypt-villi-like structures. PDOs and co-cultures have been incorporated into two commercially available OoC platforms and a third, new chip is being developed, that better captures the three-dimensional architecture of the intestinal wall. Overall, this work advances PDOs from simple epithelial spheres towards complex, vascularized and stromal-rich GI tissue models.
Besides the understanding and development of more advanced in vitro models, ethical and regulatory routes must be considered to enable their clinical use in personalized medicine. One TOP-GUT project specifically addresses European and national legislations, using the Norwegian Directorate of Health’s regulations on stem cell-based embryo models as a case study to show how conceptual definitions can shape legal boundaries. Similar conceptual discussions are emerging for organoids. However, unlike embryo models, GI PDOs are structurally and functionally more limited and not viewed as embryo-like or organism-level hybrid entities. At the same time, PDOs are a novel technology and terminology; definitions and specific guidelines for clinical purpose and research are still being developed. Through its legal and ethical work, TOP-GUT contributes to shaping this emerging regulatory framework.