Extended Data Fig. 8: HLA-A methylated primary tumors and prognostic value of HLA-A in TCGA data. | Nature Cancer

Extended Data Fig. 8: HLA-A methylated primary tumors and prognostic value of HLA-A in TCGA data.

From: Multiomics in primary and metastatic breast tumors from the AURORA US network finds microenvironment and epigenetic drivers of metastasis

Extended Data Fig. 8

a. Oncoprint diagram depicting HLA-A and HLA-B methylated cases using 761 primary tumors of TCGA-BRCA dataset according to PAM50 molecular subtype. b. Proportion of each molecular subtype found in HLA-A (68) and HLA-B (8) methylated tumors. c. Hypermethylated CpG sites in HLA-A (9 CpG sites) using 761 TCGA primary breast tumors and 74 tumor-adjacent breast tissues (n = 835 samples). d. Boxplots of HLA-A mRNA gene expression levels according to DNA methylation status (n = 761 tumors). Comparisons between 2 paired groups were performed by t-test, two-sided. e. Scatter plot showing the correlation between HLA-A mRNA expression values and DNA methylation levels (ꞵ-values) (n = 761 tumors). f. Boxplots of gene expression signature B cell/T cell cooperation and IgG scores according to DNA methylation status in tumors and tumor-adjacent breast tissues in TCGA-BRCA (n = 761 tumors). Comparison between 2 groups was performed by ANOVA with post hoc Tukey’s test, one-sided. Statistically significant values are highlighted in red. Each mark represents the value of a single sample. g. Kaplan-Meier plots using the log-rank test of overall survival from primary tumors according to HLA-A methylation status (n = 760 tumors). h. Multivariable Cox proportional hazards analyses of TCGA BRCA patients for overall survival prediction using the covariates of HLA-A methylation status, PAM50 subtypes, and tumor stage (10 Stage IV patients were removed from the analysis) (n = 744). Hazard ratio (HR) = 1: no effect. HR < 1: reduction in hazard. HR > 1: increase in hazard. Statistically significant values are highlighted in red. All Box-and-whisker plots display the median value on each bar, showing the lower and upper quartile range of the data (Q1 to Q3) and data outliers. The whiskers represent the lines from the minimum value to Q1 and Q3 to the maximum value. Unme, unmethlylated; HyperMe, hypermethylated. LumA, Luminal A; LumB, Luminal B.

Back to article page