Lipidomic changes in persister cancer cells drive enhanced ferroptosis sensitivity

Persister cancer cells (PSs) are implicated in minimal residual disease from which cancer relapse occurs. PSs are sensitive to and present a critical point through which identification and targeting of PSs may be possible. To identify biomarkers for such cells, the drivers of ferroptosis sensitivity in PSs should be identified. Here, we first derived PSs from the lung carcinoma cell line PC9 (PSPC9), performed transcriptomic analysis, and observed enrichment of lipid and sugar metabolism gene expression in PSPC9. We performed untargeted and targeted lipidomics, revealing enrichment within PSPC9 for ferroptosis-driving diPUFA phospholipids (diPUFA-PL), as well as polyunsaturated free fatty acids (PUFA FFAs). Upon PSPC9 reversion to the ferroptosis-resistant parental state (PC9PS -> PC9), this lipid signature reverted. We generated two additional PS-like cell models: PS-like prostate carcinoma (PSLNCaP) from LNCaP and PS-like fibrosarcoma (PSHT1080) from HT1080. These PS-like models individually had features consistent with PS, including increased labile-iron pool, reversibility, and enhanced ferroptosis sensitivity. We performed lipidomics in these cell models, and identified lipid features consistent with those in PSPC9. Finally, we found that in PSHT1080, mitochondrial elimination partially abrogated ferroptosis sensitivity and altered the PSHT1080 lipid profile. In summary, we found that lipidomic changes dependent on the presence of mitochondria are key for the ferroptosis sensitivity of drug-tolerant persister cancer cells. Overall design: PC9 and 6 day erlotinib derived PS were submitted in triplicate per condition with follow on DGE analysis and GSEA to explore pathways that may be enriched between the persister vs parental state.