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

## TL;DR

This study shows that inhibiting EZH2 can restore the tumor suppressor SFRP1 by altering circular DNA in ovarian cancer, offering a new approach to treat such cancers.

## Contribution

The study reveals a novel epigenetic–eccDNA pathway linking EZH2 inhibition to SFRP1 reactivation in ovarian cancer.

## Key findings

- EZH2 inhibition reprograms extrachromosomal circular DNA (eccDNA) dynamics in ovarian cancer.
- SFRP1 is the only tumor suppressor gene uniformly reactivated by Tazemetostat treatment.
- SFRP1 expression varies significantly in cancer-associated fibroblasts, indicating context-dependent tumor niche function.

## Abstract

Extrachromosomal circular DNA (eccDNA) contributes significantly to cancer progression through oncogene amplification and increased tumor heterogeneity. However, its regulatory interplay with epigenetic modulators such as EZH2 is not well characterized. Here, the effect of Tazemetostat, a specific EZH2 inhibitor, is examined on both the eccDNA repertoire and gene expression profiles in ovarian cancer. By combining Circle-seq with RNA-seq, we demonstrate that EZH2 suppression leads to substantial reprogramming of eccDNA. Integrated multi-omics revealed 67 genes with changes in eccDNA levels that correlated with altered transcription; among these genes, 11 were identified as potential drivers of drug response. Spatial single-cell RNA sequencing further highlighted that SFRP1 is the only tumor suppressor gene uniformly reactivated following Tazemetostat treatment. SFRP1 also showed pronounced expression heterogeneity in cancer-associated fibroblasts, suggesting that its function within the tumor niche is context-dependent. Our results provide initial evidence that targeting EZH2 restructures eccDNA architecture and reinstates SFRP1-mediated tumor suppression. These findings define a previously unrecognized epigenetics–eccDNA pathway that promotes malignant plasticity and treatment resistance, providing a new conceptual basis for addressing eccDNA-driven cancers.

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.