DFFB suppresses interferon to enable cancer persister cell regrowth

Oncogene targeted cancer therapies can provide deep responses but frequently suffer from acquired resistance. Therapeutic approaches to treat tumours which have acquired drug resistance are complicated by continual tumour evolution and multiple co-occurring resistance mechanisms. Rather than treating resistance after it emerges, it may possible to prevent it by inhibiting the adaptive processes which initiate resistance but these are poorly understood. Here we report that residual cancer persister cells that survive oncogene targeted therapy are growth arrested by drug stress-induced intrinsic Type I interferon (IFN) signaling. To escape growth arrest, persister cells leverage apoptotic machinery to transcriptionally suppress interferon-stimulated genes (ISGs). Mechanistically, persister cells sublethally engage apoptotic caspases to activate DNA endonuclease DNA Fragmentation Factor B (DFFB, also known as Caspase-Activated DNase (CAD)) which induces DNA damage, mutagenesis, and stress response factor Activating Transcription Factor 3 (ATF3). ATF3 limits Activator Protein-1 (AP1)-mediated ISG expression sufficiently to allow persister cell regrowth. Persister cells deficient in DFFB or ATF3 exhibit high ISG expression and are consequently unable to regrow. Therefore, sublethal apoptotic stress paradoxically promotes regrowth of residual cancer cells that survive drug treatment. Bulk and single cell RNA sequencing data. Bulk RNA sequencing with Illumina Stranded mRNA. A375 WT, DFFB KO, and ATF3 KO cells in triplicate were untreated (parental), treated for 14 days with 250 nM dabrafenib and 25 nM trametinib (persister), or persisters were co-treated with 20 uM AP-1 inhibitor T-5224 for the duration of persister formation. Single cell RNA sequencing of PC9 and A375 cells with 10X Genomics. For single cell RNA sequencing, PC9 WT lung cancer cells were untreated (parental) or treated with 2.5 µM erlotinib for 14 days (persister cells). A375 WT or DFFB KO cells were untreated (parental) or treated with 250 nM dabrafenib and 25 nM trametinib in combination for 14 days (persister cells). A375 WT and DFFB KO drug tolerant expanded persister cells (DTEPs) were treated with 250 nM dabrafenib and 25 nM trametinib for 9 weeks.