Fig. 4

Epigenomically-regulated protein biomarkers with prognostic value. Kaplan–Meier survival curves for immunohistochemical (IHC) results of three (out of five) selected markers with differential DNA methylation (OVOL1, AKT3, and TFAP2B; results for the other two markers can be found in Additional file 2: Figure S13A, B) in the independent validation tissue microarray cohort III. The selected candidates display methylation of the promoter regions, low (or high) initial methylation levels of nevi, and a consecutive increase (or decrease) of methylation during the subsequent stages of melanoma progression. Primary antibodies were validated prior to performing IHC (Additional file 2: Figures S1–S5). Image analysis software (IHC-Mark) was used to obtain H Scores for each biomarker, combining the percentage of melanoma cells stained and the intensity of the staining. Kaplan–Meier curves together with the Log-Rank confirm the prognostic power of the protein markers on (a) melanoma-specific and (b) progression-free survival (P < 0.05). Multivariate Cox regression analysis manifests the value of OVOL1 protein expression in predicting melanoma-specific survival, independent of Breslow thickness (right panel in a and b). For OVOL1, the median H Score was used as a cutoff point to define subgroups of high or low expressing melanomas with respect to immunohistochemical markers; for AKT3 and TFAP2B, the third and first quartile, respectively, was used (results for AKT3 and TFAP2B with the median H Score as cutoff can be found in Additional file 2: Figure S13)