Multiscale functional mapping of cell identity decisions in PDAC initiation

• Applicants: Professorin Alessandra Moretti, Ph.D.; Professor Dr. Roland Rad
• Subject Area: Gastroenterology
• Term: since 2024
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 544205465

Pancreatic cancer development is characterized by consecutive cellular fate changes through molecular reprogramming, for example during acinar to ductal metaplasia (ADM). Cell identity transitions are orchestrated by the iterative interplay between transcription factors (TFs), 3D genome conformation, the epigenome and the transcriptome. Our understanding of the molecular programs underlying (and resulting) from these interactions is, however, fragmented. Insertional mutagenesis screens performed in the first funding period reinforced the importance of developmental TFs in oncogenesis and highlighted that orthogonal profiling and functional studies are needed to advance the field, which we propose here through 4 work-packages. In WP1, we will create global stage-specific reference maps of transcriptional, epigenetic and topological changes during KRAS-related initiation of tumorigenesis. Utilizing a series of cellular models and mice, we will characterize the dynamic changes of the coding and non-coding transcriptome, the linear epigenome (histone modifications, chromatin accessibility) and the 3D genome (HiC-based connectome). Integrative analyses will aim at charting super-enhancer linked core TFs driving early cell-fate transition programs. In WP2, we will functionalize new players using somatic ADM screening in mice, based on new CRISPR engineering approaches that we developed for this purpose. The focus of WP3 will be mechanistic studies on newly discovered TFs, including Foxp1 which emerged recently as an ADM driver in our in vivo screens. Using a series of new mouse models and functional genomic approaches, we will study the downstream molecular mechanisms through which Foxp1 exerts its effects as well as the upstream triggers engaging Foxp1 in vivo. Finally, in WP4, we will combine the complementary expertise of the two applicants in genetic and cellular engineering to develop new technology for scalable interrogation of state-transition in pancreatic development and cancer, including mouse models and human iPSC-based platforms. This project will (1) create global functional maps of the molecular programs driving early cell state transitions during ADM, (2) give mechanistic insights into the biology of key players, and (3) fuel technology-driven discovery in the field through new genetic tools, methods and models.

• DFG Programme: Research Grants