Background Cancer can recur when a subset of tumor cells, termed persister cells, survive therapy and re-enter the cell cycle. The cellular origins that give rise to persister cells and the mechanisms that confer the persister state remain poorly understood. We hypothesize that an epigenetic signature underlies the drug-tolerant persister state, characterized by transcriptional and chromatin accessibility changes that promote survival of residual cancer following chemotherapy.

Methods To identify clinically relevant features of persister cells in untreated tumors and residual disease, we performed single-cell multiomic profiling (scRNA+scATAC) on a cohort of treatment-naïve and neoadjuvant chemotherapy (NACT)-treated high-grade serous ovarian cancer (HGSOC) samples. Additionally, we sought to validate the features that give rise to a persister state experimentally by performing single-cell multiomic profiling on HGSOC patient-derived xenograft (PDX) models before and after platinum-based chemotherapy.

Results We identified differences in gene expression and DNA binding factor - transcription factors (TF) and chromatin regulators - enrichment between naïve and residual patient tumors following chemotherapy. Notably, the changes in chromatin accessibility present in residual NACT tumors were also found in treatment-naive samples from patients who later developed resistance. This suggests that a pre-existing epigenetic signature may be driving the chemotherapy-tolerant state in persister cells. This epigenetic signature independently predicted chemotherapy response in PDX models of HGSOC and in a separate patient cohort of metastatic HGSOC. Cells enriched in the persister state arose from multiple tumor lineages and displayed activation of oncogenic pathways, including altered stress responses, epithelial to mesenchymal transition, and changes to the cell cycle promoting quiescence. Additionally, we identified a subset of genes that are epigenetically primed for expression before treatment and are upregulated after treatment. These genes stay dormant or lowly expressed before chemotherapy but are significantly upregulated after treatment, which could explain the mechanism by which persister cells gain resistance to chemotherapy.

Conclusion Our study reveals an intrinsic epigenetic program that primes tumor cells towards chemotherapy tolerance and identifies new vulnerabilities that could be exploited to delay or prevent cancer recurrence. The ability of the epigenetic signature to stratify treatment-naïve patient tumors into chemotherapy-sensitive and -resistant groups suggests that epigenetic profiling could be used as a predictive biomarker to guide therapeutic decisions and reduce cancer recurrence.