Revealing principles of cell fate conversion through Collide-seq

• Applicant: Professor Dr. Stefan Stricker
• Subject Area: General Genetics and Functional Genome Biology ; Cell Biology
• Term: since 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 529751041

Despite the therapeutic promise of direct reprogramming, a general concept on how cells resolve cell identity conflicts and gain a new identity is still lacking. We have recently developed Collide-seq, a single-cell protocol and computational strategy for the simultaneous initiation and analysis of multiple cell fate conversion events. With our already conducted experiments, we show that Collide-seq has the potential to address key issues in this field. Applying Collide-Seq on fibroblasts using five reprogramming factors (Oct4, Sox2, Ascl1, FoxA2, MyoD1) for five different fates reveals already several important insights, such as a surprising insignificance of reprogramming factor levels, and a clear hierarchy when fates collide. It remains however largely unclear, what determines this hierarchy. Expanding this approach will now allow to generalize findings, investigate questions that are still open and reveal overarching principles and rules concerning cell identity. We will mainly concentrate on two very concise and specific questions that have not been satisfyingly addressed before: How does the epigenetic landscape of the cell of origin influence the outcome of cell identity conflicts? And: How do reprogramming factors for the same developmental lineage cooperate? The answers for these questions are not only highly relevant for the application of therapeutic reprogramming, they will also contribute to our conceptual understanding of cell identity, cell identity protection and cell conflict resolution in general.

• DFG Programme: Research Grants