Dissecting residual disease in spheroids reveals pan-cancer persistence signatures and a therapeutic window for oncolytic viruses

Drug resistance remains a major burden in clinical care, often emerging from a subpopulation of cells in a drug-tolerant state. In this study, we aimed to characterize the transcriptional features of persistent non-small cell lung cancer (NSCLC) cells following cisplatin-pemetrexed chemotherapy and explore the therapeutic potency of oncolytic viruses to eliminate these cells. We established a 3D spheroid model of NSCLC and applied long-term chemotherapy to induce a reversible, non-proliferative persistent state associated with lower sensitivity to treatment. Single-cell RNA sequencing coupled with comparative analysis of multiple human datasets sheds light on a core transcriptional signature of persistence. This signature was enriched in patient-derived minimal residual disease (MRD) datasets, highlighting the clinical relevance of persistent preclinical models. Furthermore, transcriptomic analyses suggested a vulnerability of persister cells to oncolytic viruses, a finding validated in spheroid and patient-derived organoids. Altogether, these results define a conserved persistence signature and support the use of virotherapy as a promising option to target MRD.