Extended Data Fig. 4: p53 mutations are associated with decreased ERAP1 expression in other cancers.
From: RETRACTED ARTICLE: Tumor necrosis factor overcomes immune evasion in p53-mutant medulloblastoma
a,b, Expression of ERAP1 and TAP1 in p53-mutant relative to p53 wild type tumors in TCGA datasets. Cancer sites are indicated along the X-axis. Each column represents the fold change in expression in p53 mutant relative to p53 WT tumors. Positive values indicate increased expression of ERAP1 a, or TAP1 b, mRNA levels in p53 mutant tumors compared to p53 wild-type (WT) tumors; negative values indicate decreased expression of ERAP1 or TAP1 in p53 mutant tumors compared to WT tumors; 0 indicates no change in expression. Error bars indicate standard error of the mean. *P<0.05; **P<0.01; ***P<0.001; ns, not significant, based on two-sided Wilcoxon Rank Sum test. Precise p-/q-values and sample sizes are provided in Supplemental Table 1. (c,d) Box plots describing mRNA expression of ERAP1 c, and TAP1 d, in patient tumors from TCGA datasets (AML, Head and Neck, lung and stomach cancer) with p53-mutant samples shown in red and p53-wild type (WT) samples shown in blue. Box plot center lines show median, box limits indicate the 25th and 75th percentiles, lower and upper whiskers extend 1.5 times the interquartile range from the 25th and 75th percentiles, respectively. p-values represent significance, based on two-sided Wilcoxon Rank Sum test. (e, f) Erap1 (e) and Tap1 (f) expression in p53-WT (blue) and mutant (red) human AML cell lines. (g, h) Erap1 (g) and Tap1 (h) expression in p53-WT (blue) and mutant (red) murine and human DIPG cell lines. Erap1 and Tap1 expression were measured by qRT-PCR. Quantification of 3 independent experiments is shown. Error bars represent means ± SD. p-values were determined by two-sided unpaired t-test comparing p53 WT and mutant lines. In (e) * P= 0.0457 ; in (f) NS, not significant, P= 0.7724 ; in (g) **P= 0.007 (murine) and *P= 0.033 (human) ; in (h) **P= 0.0009 (murine) and *P= 0.028 (human). (I, j) Erap2 (i) and Tap2 (j) expression in MP tumors (n = 3), MG tumors (n = 3), MG tumors overexpressing DNp53 (MG+P) (n = 3) were measured by qRT-PCR. Error bars represent means ± SD. p-values were determined by two-sided unpaired t-test. In (j) NS, not significant, P= 0.21 (MG vs MP), P = 0.394 (MG vs MG+P) ; In (j) NS, P= 0.112 (MG vs MP) and P= 0.149 (MG vs MG+P).
