Abstract 2103: Genome-wide DNA methylation profiling uncovers epigenetic alterations in key oncogenic pathways and prognostic biomarkers of metastatic thyroid cancer.

Abstract Background: Thyroid cancer is the most prevalent endocrine malignancy with its incidence rising worldwide. Distant metastases are the leading cause of patient morbidity and mortality. While aberrant DNA methylation is known to drive thyroid cancer progression, the methylation landscape of metastatic thyroid cancer cells remains poorly characterized. This study aims to investigate DNA methylation dynamics in metastatic cells and to identify aberrantly methylated genes with potential clinical significance. Methods: Whole-genome bisulfite sequencing (WGBS) was performed on four paired primary and metastatic thyroid cancer cell lines, each derived from genetically engineered mouse models of PTC, FTC, PDTC, and ATC. GO and KEGG analyses were conducted to annotate the functions and pathways associated with differentially methylated regions (DMRs). The cBioPortal for Cancer Genomics was utilized to access the TCGA-ThCa database for biomarker screening and to construct a prognostic multi-gene signature. Results: DNA hypomethylation was markedly increased in metastatic cells. Comparative methylome analysis identified more than 3,500 DMRs in each cancer pair. Among these, 133 hypomethylated and 20 hypermethylated regions were consistently detected across all metastatic cancer types, representing a set of common metastatic DMRs. Pathway enrichment analysis revealed that the hypomethylated genes were significantly overrepresented in several key signaling pathways implicated in cancer progression, including focal adhesion, ECM-receptor interaction, PI3K-Akt, Wnt, and MAPK pathways. Notably, these epigenetic alterations were positively correlated with the transcriptional upregulation of the corresponding genes as determined by RNA-Seq analysis. Several metastasis-driven genes were found to be hypomethylated, such as Col4a1, lamc1, Il6ra, Rptor, Tcf7l2, and Nfatc1, suggesting their potential as therapeutic targets. Furthermore, a five-gene hypomethylation signature comprising DEDD, TJAP1, CAVIN4, YWHAG, and FABP4 was identified, the overexpression of which was significantly associated with poor overall survival (p < 10-10), poor disease-specific survival (p < 10-10), and poor progression-free survival. Clinically, overexpression of these genes exhibited a statistically significant correlation with older age at diagnosis, higher aneuploidy and hypoxia scores, and advanced disease stage. Conclusions: Metastatic thyroid cancer cells demonstrated significant global DNA hypomethylation, resulting in the transcriptional activation of numerous metastasis-driving genes. The hypomethylated gene signature may serve as a potential prognostic biomarker to stratify patients at elevated risk for distant metastasis and to guide individualized therapeutic strategies. Citation Format: Sara Alnassar, Jana Almusallam, Nada Almutairi, Najla Albader, Amal Qattan, Yufei Shi. Genome-wide DNA methylation profiling uncovers epigenetic alterations in key oncogenic pathways and prognostic biomarkers of metastatic thyroid cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 2103.