An interferon-induced survival program in dedifferentiated cancer cells drives resistance to immuno-virotherapy

Oncolytic virotherapies are currently being explored to improve cancer immunotherapies. How the complex roles of interferons (IFNs) for host defenses against cancer cells and viruses shape responses to immuno-virotherapies is poorly understood. Here, we experimentally show that IFN-unresponsive melanoma cell subpopulations in heterogeneous tumors resist T-cell control but are efficiently eradicated with oncolytic virotherapy. Unexpectedly, T-cell immunity and viral oncolysis were abrogated by the emergence of dedifferentiated, IFN-responsive tumor cell subpopulations. On the molecular level, we discovered that the melanocyte master transcription factor MITF counter-regulates IFNα-mediated anti-viral responses in melanoma cells by dampening the upregulation of IFNα-stimulated anti-viral genes. A subset of these genes overlaps with the IFN-related DNA damage resistance signature (IRDS). The baseline expression of this subset in human melanoma cells is associated with non-response to immune checkpoint blockade in patients. Our results support current approaches targeting cancer cell dedifferentiation and chronic activation of IFN-signaling to advance immunotherapies. To gain insight into the molecular mechanisms how MITF might regulate IFN-mediated anti-viral responses, we employed a functional genomics approach by assessing transcriptomic changes (bulk RNA-seq). We used the MaMel65-tet-on-MITF-eGFP melanoma cell line that was genetically engineered to express MITF tagged with the fluorescent protein eGFP in a doxycycline-inducible manner. Treatment of this cell line with doxycyline for 24 hours induces MITF expression as confirmed by fluorescence microscopy for the eGFP tag. Doxycycline- and vehicle-treated cells were then exposed to 100 IU/ml recombinant human IFNα or to vehicle control for 5 hours and infected with SFV-VA7-mCherry. The experiment was performed by utilizing biological triplicates per condition.