Deciphering functional intra-tumoral heterogeneity in BRAFV600E-driven mouse thyroid cancer reveals EMT trajectory and metabolic remodeling

Within BRAFV600E thyrocytes, we identified distinct subpopulations exhibiting varying degrees of mesenchymal transformation and stability. Further analysis uncovered an epithelial-mesenchymal transition (EMT) trajectory, where malignant subpopulations progress from an intermediate to a more mesenchymal and malignant state. The EMT-related phenotype of each subpopulation was validated with an organoid culture system. Further analysis demonstrated that major malignant subpopulations maintain distinct EMT states through subpopulation-specific pathway usage, whereas transitioning cells undergo a dynamic shift in molecular strategy by using different pathway combinations or distinct gene sets within the same EMT-related pathways along the EMT trajectory. Moreover, metformin diminished the most malignant subpopulation in the PTC mouse model and inhibited EMT potential in both regular and organoid cultures. Importantly, the functional heterogeneity of tumor cells identified in PTC mouse model have clinical relevance. Furthermore, transcriptome dynamics analysis revealed an EMT trajectory-related gene module with substantial predictive value for human PTCs with BRAFV600E. Lastly, our analysis reveals that p53 deficiency lowers the tumorigenic threshold for BRAFV600E and promotes cell state transition towards a more malignant state, rather than altering cellular heterogeneity or the transition trajectory. Subsequent analysis in vitro demonstrated that p53 loss might confer more malignant potential to BRAFV600E thyrocytes through modulating metabolic plasticity. Collectively, our work not only deciphers the functional intra-tumoral heterogeneity of BRAFV600E-drieven PTC but also thereby provides a theoretical foundation for developing EMT-targeted treatment.