Tumor-infiltrating T Lymphocytes Recognize Thyroid-specific Proteins and Neo-antigens in Follicular Cell-derived Thyroid Cancers.

Abstract

Thyroid cancers are among the growing list of cancer types that are resistant to immune-checkpoint inhibitor monotherapy. Although T-cell infiltration is common in follicular cell-derived thyroid cancers, tumor mutation burden is low. The antigenic potential of thyroid cancers is unknown. To investigate the anti-tumor T-cell response in thyroid cancer, we expanded tumor-infiltrating lymphocytes (TIL) from primary thyroid tumors and tumor-involved lymph nodes (TILN). Putative neoantigens and both tissue-associated and tumor-associated antigens were identified by targeted sequencing and RNA-seq. HLA typing was performed for all patients, and neoantigen binding potential was predicted for each patient using NetMHCpan 4.1 and NetMHCIIpan 4.0 algorithms. In parallel, T-cell receptor β sequencing was performed to detect T-cell clonal expansions in patient-matched primary tumors and TILN. TIL reactivity to tumor-associated antigens and neoantigens was determined in vitro by interferon γ ELISA and flow cytometry. Tumor-infiltrating T cells were evident in all thyroid tumors and readily expanded ex vivo. Shared clones were present in primary thyroid tumors and matched TILN in all patients tested, constituting 1% to 10% of the sequenced clones in 6/8 patients. T-cell reactivity to thyroid tissue-specific proteins, thyroid peroxidase and thyroglobulin, was observed in 84.6% (11/13) and 69.2% (9/13) patients, respectively. A BrafV600E-specific T-cell response was evident in 80% (4/5) BrafV600E+ patients. T cells reactive to gene fusion-derived neoantigens were detected in patients with TPR-NTRK1+ and CCDC6-RET+ thyroid cancer. Our studies confirm the presence of tumor antigen-specific T cells in patients with thyroid cancer and encourage further exploration of T cell-targeted immunotherapies for patients with progressive, treatment refractory thyroid cancer.