SAT-353 - Oncogenic Driver Mutations Program Distinct Immune Ecosystems in Papillary Thyroid Cancer

Introduction
Immunotherapy responses in thyroid cancer are heterogeneous and poorly predicted by current biomarkers. We hypothesized that oncogenic driver mutations establish distinct tumor immune ecosystems by independently regulating immune activation and macrophage mediated immunosuppression, rather than a simple immune hot-cold continuum.

Methods
Primary PTC samples (n = 11) from our institution underwent RNA sequencing and were stratified into BRAF V600E, RAS, and RET–PTC fusions. Results were validated with the PanCancer Atlas (BRAF n = 284, RAS n = 59, RET n = 33). Transcriptomic structure was assessed by PCA, immune and myeloid gene heatmaps, and pathway scoring by UCell. Composite indices included an Immune Hotness Score (IHS; leukocyte infiltration, cytotoxic T/NK activity, Interferon gamma (IFN-G) signaling, antigen presentation) and a Macrophage Suppression Score (MSS; macrophage and TGFβ pathways), with an Immune Dysfunction Index (IDI) defined as MSS - IHS. Group differences were tested using Kruskal-Wallis and pairwise Wilcoxon tests with balanced subsampling.

Results
PCA revealed mutation-specific immune transcriptomic separation, with RAS tumors distinct from BRAF and RET-fusion tumors. Immune heatmaps showed suppression of antigen presentation, interferon signaling, and leukocyte markers in RAS tumors, whereas BRAF and RET-fusion tumors exhibited broad immune activation. RET-fusion tumors showed enrichment of MHCII, INF-G responsive, but no macrophage-associated transcripts. These patterns defined three immune architectures: RAS tumors were immune-cold, BRAF tumors were macrophage-dominant with strong TGFβ-associated suppression, and RET-fusion tumors were highly immune-activated but concurrently macrophage suppressive.

IHS differed significantly across groups (p = 1.55 × 10⁻²³), with RAS tumors showing reduced immune activation compared with BRAF and RET tumors (p < 0.001). MSS also differed significantly (p = 1.01 × 10⁻¹⁹), identifying RAS tumors as macrophage-poor relative to BRAF and RET tumors (p < 0.001). In contrast, IDI showed weak separation (p = 0.054), indicating that immune activation and immunosuppression coexist rather than lie on a single axis. Findings were consistent across exploratory and validation cohorts.

Conclusion
Oncogenic driver mutations define distinct immune ecosystems in thyroid cancer through independent regulation of immune activation and macrophage-mediated suppression. RET-fusion tumors represent an immune-infiltrated but macrophage-constrained phenotype, BRAF tumors exhibit macrophage-dominant inflammatory states, and RAS tumors are true immune deserts. This two-dimensional immune architecture provides a mechanistic framework for heterogeneous immunotherapy responses and supports genotype-directed strategies targeting macrophage and TGFβ-mediated immunosuppression.

*Unless otherwise noted, all abstracts presented at ENDO must not be released to the press or the public until the date and time of presentation. For oral presentations, the abstracts are embargoed until the session begins. The Endocrine Society reserves the right to lift the embargo on specific abstracts that are selected for promotion prior to or during ENDO.*