Marked Global DNA Hypomethylation Is Associated with Constitutive PD-L1 Expression in Melanoma

Abstract

SummaryConstitutive expression of the immune checkpoint, PD-L1, inhibits anti-tumor immune responses in cancer, although the factors involved in PD-L1 regulation are poorly understood. Here we show that loss of global DNA methylation, particularly in intergenic regions and repeat elements, is associated with constitutive (PD-L1CON), versus inducible (PD-L1IND), PD-L1 expression in melanoma cell lines. We further show this is accompanied by transcriptomic up-regulation. De novo epigenetic regulators (e.g., DNMT3A) are strongly correlated with PD-L1 expression and methylome status. Accordingly, decitabine-mediated inhibition of global methylation in melanoma cells leads to increased PD-L1 expression. Moreover, viral mimicry and immune response genes are highly expressed in lymphocyte-negative plus PD-L1-positive melanomas, versus PD-L1-negative melanomas in The Cancer Genome Atlas (TCGA). In summary, using integrated genomic analysis we identified that global DNA methylation influences PD-L1 expression in melanoma, and hence melanoma's ability to evade anti-tumor immune responses. These results have implications for combining epigenetic therapy with immunotherapy.

DNA hypermethylation is associated with invasive phenotype of malignant melanoma

“…Neural cell adhesion molecule L1 (CHL1) is frequently down‐regulated in different types of tumors, and it is verified to inhibit invasive growth and able to suppress further metastatic spread . It seems that down‐regulation of CHL1 in association with methylation change was also observed in melanoma cells by Chatterjee et al indicating that differentially methylated CHL1 is a marked alteration in melanoma cells as well.…”

“…Based on our results, methylation of EGFR gene body in correlation with up‐regulated expression was revealed in the invasive cells. Epigenetic activation of EGFR upon resistant development to BRAF inhibitors has been previously described in melanoma, as well EGFR showed methylation difference in metastatic cell lines compared with its matched primary cell lines . Recent studies indicated RBP4 serum levels as biomarker in colorectal cancer, and its overexpression was associated with ovarian cancer cell migration .…”

“…Recent studies indicated that increased expression of UHRF1 and/or UHRF2 negatively regulates de novo DNA methylation, and their decreased expression has been observed to correlate with hypermethylation pattern in different tumors . Consistent with the recent findings, both UHRF1 and UHRF2 genes showed down‐regulation in invasive cells, and however, this mechanism need additional investigations . Interestingly, the hypermethylation of TET2 promoter region along with the down‐regulation of gene was characteristic for the invasive melanoma cell population, which may contribute to the accumulation of 5mC and therefore plays a role in the global hypermethylation pattern of melanoma invasiveness; this observation need further investigations.…”

Targeting DNA Methylation and EZH2 Activity to Overcome Melanoma Resistance to Immunotherapy

“…As shown in Figure 2, these trigger well-known pathways involving adaptor proteins such as TRIF, myD88, mitochondrial antiviral signaling protein (MAVS), or stimulator of IFN genes (STING) associated with the endoplasmic reticulum [30,31] to generate endogenous IFN responses. Similar upregulation of PD-L1 (CD274) in human melanoma cell lines treated by DNMTi was achieved, suggesting a possible role for DNA methylation in suppressing PD-L1 expression [23].…”

“…It was questioned whether low PD-L1 expression could be attributed to methylation of the promoter region encoding PD-L1, as prior studies in lung carcinoma have linked resistance to anti-PD1 antibody treatment with DNA methylation at the promoter region [22]. Previous analysis of the Skin Cutaneous Melanoma (SKCM) TCGA data revealed two CpG sites in the proximal promoter region encoding PD-L1, which were not methylated [23,24]. These observations suggested that a distal enhancer similar to an enhancer previously described might be involved in the epigenetic regulation of PD-L1 [25].…”