Mutation-specific dynamics of dedifferentiation trajectories and tumor–stromal interactions in thyroid cancer

Abstract

Progression from differentiated thyroid cancer to anaplastic thyroid cancer (ATC) involves profound epithelial plasticity and remodeling of the tumor microenvironment (TME), but how BRAFV600E and RAS driver mutations shape these processes remains unclear. Here, we integrated single-nucleus RNA-seq, spatial transcriptomics, and bulk RNA-seq across BRAFV600E- and RAS-driven thyroid tumors to delineate mutation-specific progression trajectories. BRAFV600E-driven tumors exhibited a gradual dedifferentiation trajectory with immune pathway activation, whereas RAS-driven tumors displayed abrupt transitions characterized by aneuploidy, epithelial–mesenchymal transition, hypoxia, and extracellular matrix remodeling. Cancer-associated fibroblasts (CAFs) emerged as key regulators, with mutation-specific ligand–receptor interactions: integrin-based signaling predominated in BRAFV600E-mutant ATCs, while PLAU–PLAUR, TNFSF10–TNFRSF10B, and AREG–EGFR were additionally enriched in RAS-driven ATCs. These CAF–epithelial circuits were spatially validated and associated with poor prognosis. Together, our findings reveal mutation-dependent epithelial and TME dynamics associated with thyroid cancer dedifferentiation and highlight the potential importance of molecular-tailored approaches in the management of advanced thyroid cancer.