Tumor-intrinsic programs of epithelial-mesenchymal transition and immune deregulation are linked to disease recurrence in papillary thyroid carcinoma

Introduction: Papillary thyroid carcinoma (PTC) is the most common subtype of differentiated thyroid cancer, predominantly affecting females and young adults. Current clinical models fail to capture its marked molecular heterogeneity and integrate this information into prognostic algorithms that would enable personalized care plans. Here, we identify tumor-intrinsic molecular programs contributing to thyroid cancer progression that may inform risk stratification. Methods: We performed single nuclei multiome (RNA and ATAC) sequencing of 16 fresh frozen samples from a PTC clinical cohort with varying risks of disease recurrence, as determined by the 2025 American Thyroid Association guidelines. Programs with distinct cellular activity were identified with consensus non-negative matrix factorization (cNMF). Cell-cell communication between the tumor and its microenvironment was assessed with MultiNicheNET. Active regulons within cell types of interest were identified using SCENIC. Chromatin accessibility analysis was performed using Signac. Results: We identified a novel, tumor-specific transcriptional program, defined by composite upregulation of epithelial-to-mesenchymal-transition (EMT) and TNF-alpha signaling, that was enriched in high-risk PTC. Top active regulons in this program included molecules involved in inflammatory response and immune modulation. Chromatin accessibility analysis revealed a significantly differentially accessible peak near CCL20, previously shown to promote thyroid cancer invasion via NF-kB signaling, in tumor cells with highest expression of the program. In thyroid cancer lines from the Broad Institute's Cancer Cell Line Encyclopedia (CCLE), expression of this program was significantly higher in the presence of BRAFV600E mutation ( p <0.001). Similarly, when projecting this program onto the Thyroid Cancer Genome Atlas (TCGA) database of 496 PTC samples, we observed a significant association between usage of this transcriptional program and both higher risk of recurrence and presence of BRAFV600E mutation ( p <0.001). This association remained independent in a multiple linear regression model and after adjusting for sex and tumor purity. Cell-cell interaction analyses demonstrated increased activity of thrombospondin-1, a key EMT mediator, signaling from cancer associated fibroblasts to tumor cells, that was unique to high-risk PTC samples. Conclusions: We identified a new, tumor-intrinsic transcriptional program through integrative multi-omic analysis that is characterized by EMT and immune deregulation, enriched in high-risk PTC, and validated its clinical relevance in TCGA. Evaluating the performance of this program in larger thyroid cancer cohorts will be essential to establish its prognostic value and potential to incorporate into clinical risk stratification models.