Interferon Signaling Is Frequently Downregulated in Melanoma

Abstract

Immune checkpoint inhibitors that block the programmed cell death protein 1/PD-L1 pathway have significantly improved the survival of patients with advanced melanoma. Immunotherapies are only effective in 15–40% of melanoma patients and resistance is associated with defects in antigen presentation and interferon signaling pathways. In this study, we examined interferon-γ (IFNγ) responses in a large panel of immune checkpoint inhibitor-naïve melanoma cells with defined genetic drivers; BRAF-mutant (n = 11), NRAS-mutant (n = 10), BRAF/NRAS wild type (n = 10), and GNAQ/GNA11-mutant uveal melanomas (UVMs) (n = 8). Cell surface expression of established IFNγ downstream targets PD-L1, PD-L2, HLA-A, -B, and -C, HLA-DR, and nerve growth factor receptor (NGFR) were analyzed by flow cytometry. Basal cellular expression levels of HLA-A, -B, -C, HLA-DR, NGFR, and PD-L2 predicted the levels of IFNγ-stimulation, whereas PD-L1 induction was independent of basal expression levels. Only 13/39 (33%) of the melanoma cell lines tested responded to IFNγ with potent induction of all targets, indicating that downregulation of IFNγ signaling is common in melanoma. In addition, we identified two well-recognized mechanisms of immunotherapy resistance, the loss of β-2-microglobulin and interferon gamma receptor 1 expression. We also examined the influence of melanoma driver oncogenes on IFNγ signaling and our data suggest that UVM have diminished capacity to respond to IFNγ, with lower induced expression of several targets, consistent with the disappointing response of UVM to immunotherapies. Our results demonstrate that melanoma responses to IFNγ are heterogeneous, frequently downregulated in immune checkpoint inhibitor-naïve melanoma and potentially predictive of response to immunotherapy.

Tumor MHC Expression Guides First-Line Immunotherapy Selection in Melanoma

“…Rodig et al also found that melanoma MHC-II but not MHC-I expression by immunohistochemistry (IHC) was predictive of week-13 response to anti-PD-1 monotherapy in the CheckMate 064 trial [ 18 ]. We now confirm that expression of MHC-I and MHC-II proteins on tumor cell surface is highly correlated, as was previously observed at both the transcript and protein levels [ 19 ]. While it is difficult to directly compare flow cytometric- and immunohistochemistry-based estimates of MHC expression, we found that IHC-defined thresholds associated with immunotherapy response, 30% for MHC-I [ 18 ] and 1% [ 18 ] or 5% for MHC-II [ 20 ], identified only 43% of MHC-I low tumors in our study and 50% or 83% of MHC-II low tumors, respectively.…”

Efficient Induction of Cytotoxic T Cells by Viral Vector Vaccination Requires STING-Dependent DC Functions

“…Previous research has shown that many melanoma cells and cell lines have variable defects in interferon signaling pathways (74)(75)(76), which was also observed in the melanoma cell line that we used as feeder cells for this study (77,78). Moreover, compared to infected BMDCs, we observed in MVAinfected S91 feeder cells a severely limited cytokine/chemokine response with a complete lack of type I and II interferons ( Supplementary Figure 7).…”

Melanoma Stem Cell-Like Phenotype and Significant Suppression of Immune Response within a Tumor Are Regulated by TRIM28 Protein

“…Interestingly, we observed significant downregulation of the IRF transcription factor family members (IRF1, IRF2, IRF5, IRF8) corresponding to attenuated interferon signaling in TRIM28 HIGH melanomas, probably as a consequence of low immune cell infiltration. Recently, Alavi S. et al [ 50 ] have reported that downregulation of interferon signaling occurred in almost 70% of immunotherapy-naïve melanomas, although they did not link this phenomenon with TRIM28 expression. As TRIM28 is a well-known transcriptional co-repressor, we suggest that low IRF1 , IRF2 , IRF5 , and IRF8 expression (in the absence of stimulating signaling) result from TRIM28-mediated epigenetic modifications within the IRF promoters.…”