Periodic Reporting for period 1 - InterYAP (Dissecting the molecular mechanisms underlying YAP activation in intestinal tissue repair)
Okres sprawozdawczy: 2021-09-01 do 2023-08-31
During intestinal organogenesis, equipotent epithelial progenitors mature into phenotypically distinct stem cells that are responsible for lifelong maintenance of the tissue. While the morphological changes associated with the transition are well characterized, the molecular mechanisms underpinning the maturation process are not fully understood. In this project, the main goal was to define transcriptional and epigenetic landscapes that define the embryonic and adult cellular states in order to identify cell-intrinsic mechanisms regulating tissue maturation.
This project generated a comprehensive datasets that provide a framework for investigation of determinants of epithelial maturation, allowing scientists in the field to further investigate and better understand the developmental processes and associated congenital disorders of the intestinal epithelium. Given the emerging evidence that similar mechanisms operate in the context of tissue repair and cancer, the findings of the project are also of interest for regenerative medicine and oncology research fields. Finally, the identification cell-intrinsic mechanisms regulating cellular maturation might also assist the development of more robust embryonic stem cell/induced pluripotent stem cell differentiation in vitro protocols, which often result in the generation of immature cell types that are ill-suited for functional studies or cell-replacement therapies for a variety of human disorders.
Thus, in summary, the knowledge generated in the project might assist the future development of more effective therapies for a variety of conditions affecting the gastrointestinal tract (e.g congenital disorders, inflammatory bowel diseases, colorectal cancer) and, therefore, benefit society at large.
This project generated a comprehensive datasets that provide a framework for investigation of determinants of epithelial maturation, allowing scientists in the field to further investigate and better understand the developmental processes and associated congenital disorders of the intestinal epithelium. Given the emerging evidence that similar mechanisms operate in the context of tissue repair and cancer, the findings of the project are also of interest for regenerative medicine and oncology research fields. Finally, the identification cell-intrinsic mechanisms regulating cellular maturation might also assist the development of more robust embryonic stem cell/induced pluripotent stem cell differentiation in vitro protocols, which often result in the generation of immature cell types that are ill-suited for functional studies or cell-replacement therapies for a variety of human disorders.
Thus, in summary, the knowledge generated in the project might assist the future development of more effective therapies for a variety of conditions affecting the gastrointestinal tract (e.g congenital disorders, inflammatory bowel diseases, colorectal cancer) and, therefore, benefit society at large.
In this project, I leveraged intestinal organoid cultures to profile transcriptional, chromatin accessibility, DNA methylation, and three-dimensional (3D) chromatin conformation landscapes in fetal and adult epithelial cells. In collaboration with other members of the Jensen team, we observed prominent differences in gene expression and enhancer activity, which are accompanied by local changes in 3D organization, DNA accessibility, and methylation between the two cellular states. Using integrative analyses, we identified sustained Yes-Associated Protein (YAP) transcriptional activity as a major gatekeeper of the immature fetal state. We found the YAP-associated transcriptional network to be regulated at various levels of chromatin organization and likely to be coordinated by changes in extracellular matrix composition.
Our functional and transcriptomic analyses indicate that activated YAP signaling, however, is not the sole determinant of the fetal program. Additional pathways are likely to play key roles in safeguarding the fetal progenitor state and/or driving maturation into adult, functionally specified cells. Thus, the comprehensive datasets generated in project provide a framework for investigation of further determinants of epithelial maturation and help shed light on conserved mechanisms of tissue maturation, repair, and neoplasia. The major findings and associated datasets have been recently published as open access article in Science Advances (Pikkupeura and Bressan et al., 2023). To further allow exploitation of the data, the transcriptomic and epigenetic profiling datasets have been made freely available to the research community. All raw and processed sequencing data generated in this study have been submitted to the NCBI Gene Expression Omnibus (GEO; https://ncbi.nlm.nih.gov/geo/(odnośnik otworzy się w nowym oknie)) under accession numbers GSE228519 and GSE183671. To facilitate the access to the community, we generated a user-friendly webpage that allows visualization of differentially expressed promoters and enhancers, as well as DNA methylation and chromatin structure patterns. The page can be accessed through the link: https://shiny.binf.ku.dk/fetal_adult_regulatory_app/(odnośnik otworzy się w nowym oknie). The datasets are already being further exploited by other members of the Jensen lab and by external collaborators working on related projects.
Our functional and transcriptomic analyses indicate that activated YAP signaling, however, is not the sole determinant of the fetal program. Additional pathways are likely to play key roles in safeguarding the fetal progenitor state and/or driving maturation into adult, functionally specified cells. Thus, the comprehensive datasets generated in project provide a framework for investigation of further determinants of epithelial maturation and help shed light on conserved mechanisms of tissue maturation, repair, and neoplasia. The major findings and associated datasets have been recently published as open access article in Science Advances (Pikkupeura and Bressan et al., 2023). To further allow exploitation of the data, the transcriptomic and epigenetic profiling datasets have been made freely available to the research community. All raw and processed sequencing data generated in this study have been submitted to the NCBI Gene Expression Omnibus (GEO; https://ncbi.nlm.nih.gov/geo/(odnośnik otworzy się w nowym oknie)) under accession numbers GSE228519 and GSE183671. To facilitate the access to the community, we generated a user-friendly webpage that allows visualization of differentially expressed promoters and enhancers, as well as DNA methylation and chromatin structure patterns. The page can be accessed through the link: https://shiny.binf.ku.dk/fetal_adult_regulatory_app/(odnośnik otworzy się w nowym oknie). The datasets are already being further exploited by other members of the Jensen lab and by external collaborators working on related projects.
The project findings highlight the value of unbiased profiling of regulatory landscapes for the identification of key mechanisms underlying tissue development and provide a framework for exploration of determinants of cellular maturation. Given that similar mechanisms operate in process of tissue repair and cancer, these findings are also of interest for regenerative medicine and oncology research fields. Finally, the identification cell-intrinsic mechanisms regulating cellular maturation might also assist the development of more robust embryonic stem cell/induced pluripotent stem cell differentiation in vitro protocols for functional studies and/or cell-replacement therapies for a variety of human disorders (e.g inflammatory bowel diseases).