Abstract 5135: Effect of EZH2 inhibition in anaplastic thyroid cancer epithelial-mesenchymal transition revealed by transcriptome analysis

Abstract Introduction: Anaplastic thyroid cancer (ATC) is a rare but highly aggressive endocrine malignancy characterized by rapid tumor growth, early metastasis (>40%), and resistance to standard therapies like radioiodine. The epithelial-mesenchymal transition (EMT) is a critical process driving ATC progression and metastasis, underscoring the urgency of identifying its molecular regulators. In that sense, EZH2, the catalytic subunit of the Polycomb Repressive Complex 2, promotes transcriptional silencing by deposition of trimethylation of histone H3 at lysine 27 (H3K27me3) at target genes. Previously, we demonstrated that CRISPR/Cas9-mediated EZH2 inhibition suppresses ATC cell dedifferentiation, growth, migration, and invasion by downregulating EMT markers. However, the mechanisms through which EZH2 regulates EMT in ATC are not fully understood. Objective: To investigate the impact of EZH2 inhibition in the transcriptomic landscape of coding genes and miRNAs involved in EMT in ATC biology. Methods: RNAseq analysis was performed on EZH2-inhibited SW1736-ClE cells to identify differentially expressed genes (DEGs), with sequencing conducted on an Illumina Nextseq 2000 (paired-end 2 × 100 bp), yielding up to 42 million reads for SW1736-CTR and SW1736-ClE. Functional enrichment and protein-protein interaction (PPI) analyses were carried out using Enrichr and STRING web tools, respectively. EZH2/H3K27me3 targets were predicted using the Cistrome Database. A miRNome analysis (Qiagen miScript Arrays) assessed the expression of 1, 008 human miRNAs, and predicted miRNA targets were overlapped with DEGs for enrichment analysis. To explore the EZH2/Wnt/β-catenin/miR-200 axis in EMT regulation, Wnt signaling and miR-200 promoter activity were evaluated using β-catenin and miR-200 family overexpression models. Results: RNAseq analysis identified 1, 024 downregulated and 939 upregulated DEGs in SW1736-ClE. EZH2 inhibition suppressed EMT programs by downregulating canonical Wnt signaling genes, including CTNNB1, FZD4, and ZEB1, as shown by Enrichr and PPI analyses. Using Cistrome database, we observed that EZH2/H3K27me3 enrichment was observed at loci of negative Wnt signaling regulators (WNT5A/7A, FZD2/7), which were upregulated in SW1736-ClE cells. Suppressing canonical Wnt signaling reduced EMT-promoting factors and increased epithelial markers. miRNome analysis revealed significant upregulation of tumor suppressor miRNAs, notably the miR-200 family. The overexpression of the miR-200c or miR-200a alone in SW1736 cells did not independently inhibit Wnt signaling activity. Conversely, β-catenin overexpression impaired miR-200 promoter activity. Conclusions: EZH2 is a key regulator of ATC oncogenesis, driving EMT through a mechanistic link between Wnt signaling and miR-200 family regulation, highlighting potential therapeutic targets in ATC. Citation Format: Diego Claro de Mello, Kelly Cristina Saito, Marcella Maringolo Cristovão, Edna Teruko Kimura, Cesar Seigi Fuziwara. Effect of EZH2 inhibition in anaplastic thyroid cancer epithelial-mesenchymal transition revealed by transcriptome analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 5135.