EZH2 Inhibition Restores Tumor Suppressor SFRP1 Activity by Reprogramming Extrachromosomal Circular DNA Dynamics in Ovarian Cancer

Extrachromosomal circular DNA (eccDNA) has emerged as a pivotal contributor to cancer progression, facilitating oncogene amplification, dysregulated gene expression, and tumor heterogeneity. Despite its significance in cancer, the interplay between eccDNA and key epigenetic regulators such as EZH2 remains largely unexplored. In this study, we systematically investigate the correlation between Tazemetostat, a highly selective EZH2 inhibitor, and alterations in the eccDNA landscape and transcriptional programs in ovarian cancer. Through integrated profiling using Circle-seq and RNA sequencing, we demonstrate that EZH2 inhibition is associated with markedly reprogrammed eccDNA dynamics. Furthermore, multi-omics integration identified that 67 genes exhibited concordant changes in both eccDNA abundance and transcript expression. Subsequent analyses also pinpointed 11 genes as putative effectors of drug response. Notably, spatial single-cell transcriptomics identified SFRP1 as the most consistently reactivated tumor suppressor across eccDNA, bulk expression, and spatial datasets, based on predefined statistical and biological criteria, by Tazemetostat. Moreover, SFRP1 was one of the genes that varied the most within cancer-associated fibroblast populations, exhibiting distinct spatial expression patterns. Taken together, this study establishes the first potential evidence that EZH2 inhibition may reprogram eccDNA dynamics to potentially restore SFRP1 tumor suppressor expression in ovarian cancer. By integrating multi-omics and spatial single-cell transcriptomics, we uncovered a novel epigenetic–eccDNA axis that may contribute to oncogenic plasticity and therapeutic resistance. This could result in a paradigm shift in targeting eccDNA-driven malignancies.