Probing cell identity hierarchies by fate titration and collision during direct reprogramming

Area of Science:

• Cell biology
• Molecular biology
• Genetics

Background:

• Direct reprogramming holds therapeutic potential but lacks understanding of fate erasure and cell identity conflict resolution.
• Current reprogramming methods face challenges in controlling cell fate transitions and understanding underlying mechanisms.

Purpose of the Study:

• To investigate fundamental principles of cell fate erasure and identity conflict resolution during direct reprogramming.
• To develop and apply a novel single-cell protocol for simultaneous analysis of multiple cell fate conversion events.

Main Methods:

• Development of Collide-seq, a single-cell protocol enabling combinatorial and traceable reprogramming factor expression analysis.
• Simultaneous induction of multiple competing reprogramming factors to study cell fate titrations and collisions.

Main Results:

• Identified a lack of a common mechanism for initiating fibroblast-specific gene expression loss.
• Observed abrupt transcriptome changes in converting cells upon reaching critical reprogramming factor levels.
• Demonstrated a deterministic system where competing factors lead to dominant or colliding fates, independent of target gene binding.

Conclusions:

• Collide-seq provides novel insights into the fundamental principles governing cell fate conversion.
• Findings may help refine and improve current direct reprogramming strategies for therapeutic applications.