Analysis of the response of AXL and/or MITF melanoma subpopulations to immunotherapy

Abstract

BackgroundTumor heterogeneity is a hurdle to effective therapy, as illustrated by the “mixed responses” frequently seen in immunotherapy-treated patients. Previously, AXL+ tumor cells were identified to be highly resistant to targeted therapy, whereas more differentiated MITF+ tumor cells do respond to RAF and MEK inhibitors. MethodsIn this study we analyzed tumor heterogeneity, and explored the presence of the previously described AXL+ or MITF+ melanoma subpopulations, both at the mRNA and protein level, in metastatic tissues by Nanostring gene expression analysis, single-cell RNA sequencing, and by in situ multiplex immunofluorescence, respectively. Furthermore, we analyzed how these subpopulations correlate with immunological pressure and response to immunotherapy (immunomodulating antibodies or autologous tumor lysate-loaded dendritic cell vaccination). ResultsOur data demonstrate large inter patient variability and variable therapy-induced changes independent of the type of therapy. We identify the presence of previously described AXL+ and MITF+ subpopulations in metastatic tissues both at the mRNA and in situ at the protein level, and demonstrate that MITF+ melanoma cells are significantly decreased upon immunotherapy, while AXL+ melanoma cells numbers are stable. MITF+ tumor cells showed the most significant inverse correlation with CD8+ T cells. Our patient cohort also shows that immunotherapy-induced changes in the abundance of AXL+ or MITF+ tumor cells did not correlate with improved survival. ConclusionOverall, this study suggests that more differentiated MITF+ tumors are efficiently targeted by immunotherapy, while AXL+ tumor cells may be more resistant, analogous to their response to targeted therapy.