Constitutive PD-L1 expression in melanoma

Treatment of melanoma based on targeted therapy and immunotherapy has dramatically advanced over the past decade. Advances in targeted therapy have been based on inhibition of the MAPK pathway while for immunotherapy, advances have been based on blocking immune checkpoint proteins such as the PD-1/PD-L1 axis. PD-L1 serves as a potent immune suppressor of the immune response enabling cancer cells to escape the immune surveillance. Recently, it was reported in several studies that resistance to MAPK pathway inhibitors can be accompanied by increases in constitutive PD-L1 expression in melanoma, highlighting the importance of understanding the underlying regulation of PD-L1 expression. However, the mechanism regulating constitutive PD-L1 expression remains unclear in melanoma. In this study, one of the aims was to investigate whether DNA methylation plays a role in PD-L1 expression. Firstly, it was found that melanoma cell lines with constitutive PD-L1 expression have a marked loss of global DNA methylation (hypomethylation), particularly in the intergenic regions and repeat elements, which suggested an altered epigenomic landscape. A number of endogenous retrovirus (ERV) elements that reside in the intergenic region were increased in expression in the constitutive PD-L1 cell lines. This was accompanied by activation of the innate immune response and transcription factors that can upregulate PD-L1 levels. Intergenic lncRNAs that are in close proximity to immune related genes were also upregulated in the constitutive PD-L1 cell lines. Moreover, DNMTi (global demethylation) mediated PD-L1 upregulation was revealed to increase many of the same innate immune response genes and transcription factors that were upregulated in the constitutive PD-L1 samples supporting the role of DNA hypomethylation in PD-L1 expression. Furthermore, how PD-L1 expression is associated with resistance to MAPK targeted inhibitors remains unclear. Here, it was found that constitutive PD-L1 expression is associated with a transcriptomic state that is characteristic for dedifferentiation which is mediated by the loss of SOX10 expression and upregulation of other transcription factors such as SOX9. Moreover, constitutive PD-L1 samples were associated with a reduced expression of genes involved in oxidative phosphorylation demonstrating an altered metabolic program. Overall, we found evidence that supports constitutive PD-L1 expression in melanoma is regulated by the viral mimicry pathway via global hypomethylation. Furthermore, constitutive PD-L1 expression is closely associated with dedifferentiation mediated by loss of SOX10 which provides insight as to why PD-L1 expression increases upon development of therapy resistance