The role of Myc in interferon-γ signaling inhibition and immunotherapy resistance in advanced melanoma patients

Novel immunotherapies have revolutionized the treatment of melanoma. As the pathways mediating resistance to immunotherapy are largely unknown, we conducted transcriptome profiling of pre-immunotherapy tumor biopsies from melanoma patients that received either PD-1 blockade (n=36) or adoptive cell therapy with tumor infiltrating lymphocytes (n=37).

We identified 1952 differentially expressed genes (FDR<0.05) between responders and non-responders that segregated into 3 distinct clusters, which were enriched for leukocyte markers, response to interferon-γ (IFNγ⁺) and oncogenic pathways (Onco⁺) such as dedifferentiation and mitotic cell cycle. The IFNγ⁺ and Onco⁺ gene clusters were inversely correlated in melanoma cells and significantly associated with good and poor immunotherapy outcome in two external melanoma immunotherapy cohorts (GSE91061 and GSE100797), thus suggesting two opposing gene expression programs that govern the response to immunotherapy. IPA transcription factor analysis identified Myc as the main upstream regulator associated with the IFNγ^- Onco⁺ phenotype. Indeed, immunohistochemistry showed increased nuclear Myc staining among non-responding patients.

Myc and Mock stably transfected cells from patient-derived melanoma cell cultures were exposed for 48h to IFNγ. Remarkably, Myc overexpression rendered cells from non-responders resistant to IFNγ, as it hindered the induction of 6 IFNγ-responsive genes and MHC class I and PD-L1 protein upregulation, compared to Mock-transfected cells. In contrast, Myc did not confer IFNγ-resistance in melanoma cells from responders. This suggests that Myc-responsive cells can utilize Myc to oppose IFNγ signaling and thereby become immuno-resistant.

In summary, we suggest a potential major mechanistic role for Myc in resistance to immunotherapy by impairing the tumoral response to IFNγ.