Transcriptomic analysis of papillary thyroid cancer: a focus on immune-subtyping, oncogenic fusion, and recurrence

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Transcriptomic analysis of papillary thyroid cancer: a focus on immune-subtyping, oncogenic fusion, and recurrence
Seung Jin Park; Y E Kang; Jeong Hwan KimJong Lyul ParkSeon-Kyu Kim; Seung Woo Baek; In-Sun Chu; S Yi; S E Lee; Y J Park; E J Chung; J M Kim; H M Ko; J R Kim; S N Jung; H R Won; J W Chang; B S Koo; Seon-Young Kim
Bibliographic Citation
Clinical and Experimental Otorhinolaryngology, vol. 15, no. 2, pp. 183-193
Publication Year
Objectives: Thyroid cancer is the most common endocrine tumor, with rapidly increasing incidence worldwide. However, its transcriptomic characteristics associated with immunological signatures, driver fusions, and recurrence markers remain unclear. We aimed to investigate the transcriptomic characteristics of advanced papillary thyroid cancer. Methods: This study included 282 papillary thyroid cancer tumor samples and 155 normal samples from Chungnam National University Hospital and Seoul National University Hospital. Transcriptomic quantification was determined by high-throughput RNA sequencing. We investigated the associations of clinical parameters and molecular signatures using RNA sequencing. We validated predictive biomarkers using the Cancer Genome Atlas database. Results: Through a comparison of differentially expressed genes, gene sets, and pathways in papillary thyroid cancer compared to normal tumor-adjacent tissue, we found increased immune signaling associated with cytokines or T cells and decreased thyroid hormone synthetic pathways. In addition, patients with recurrence presented increased CD8+ T-cell and Th1-cell signatures. Interestingly, we found differentially overexpressed genes related to immune-escape signaling such as CTLA4, IDO1, LAG3, and PDCD1 in advanced papillary thyroid cancer with a low thyroid differentiation score. Fusion analysis showed that the PI3K and mitogen-activated protein kinase (MAPK) signaling pathways were regulated differently according to the RET fusion partner genes (CCDC6 or NCOA4). Finally, we identified HOXD9 as a novel molecular biomarker that predicts the recurrence of thyroid cancer in addition to known risk factors (tumor size, lymph node metastasis, and extrathyroidal extension). Conclusion: We identified a high association with immune-escape signaling in the immune-hot group with aggressive clinical characteristics among Korean thyroid cancer patients. Moreover, RET fusion differentially regulated PI3K and MAPK signaling depending on the partner gene of RET, and HOXD9 was found to be a recurrence marker for advanced papillary thyroid cancer.
Thyroid cancerKorean thyroid cancerAdvanced papillary thyroid cancerRNA sequencingImmune subtypingImmune-escape signalingFusion outlierPredictive biomarkerRETHOXD9
Korea Soc-Assoc-Inst
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Aging Convergence Research Center > 1. Journal Articles
Division of Biomedical Research > Metabolic Regulation Research Center > 1. Journal Articles
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