Fig. 3
APOBEC3 gene expression is altered in OSCC. a The mRNA expression levels of all seven APOBEC3 genes in our paired OSCC samples were determined by RNA-Seq. The y-axis shows the TPM (transcripts per million) of each gene in paired tissue samples. N, adjacent normal tissue; T, tumor tissues. The expression profiles illustrate the tumor-specific up-regulations of A3A, A3B (p < 0.0001, Mann–Whitney U-test), and A3G (p = 0.02, Mann–Whitney U-test). In tumors, A3A was expressed at a higher level than A3B (p < 0.001). b A3A-specific peptides were identified in tissue proteomes using iTRAQ-mass spectrometry. The y axis represents the protein level relative to a common reference. A3A-specific peptides were significantly higher (~3 fold) in tumor tissues compared with corresponding normal tissues (p < 0.001, Mann-Whitney U-test). Of the 38 N/T paired tissues analyzed, we detected A3A peptides in 35 normal tissue samples and 36 tumor tissue samples. c Expression levels of A3A and A3B in different TCGA cancer types. Only cancers reported to have APOBEC-mutation signatures were included in this plot; they are ordered according to the A3A expression levels in their tumors. The y-axis shows the TPM of our RNA-Seq data for the A3A and A3B genes. The HNSC samples were further grouped into OSCC and ‘others’ (HNSC-non-OSCC). UCEC, DLBC, SKCM, STAD, PAAD, THCA, KIRP, CESC, BLCA, BRCA, ESCA, LUSC, and LUAD correspond to uterine corpus endometrial carcinoma, lymphoid neoplasm diffuse large B-cell lymphoma, skin cutaneous melanoma, stomach adenocarcinoma, pancreatic adenocarcinoma, thyroid carcinoma, kidney renal papillary cell carcinoma, cervical squamous cell carcinoma, bladder urothelial carcinoma, breast invasive carcinoma, esophageal carcinoma, lung squamous cell carcinoma and lung adenocarcinoma, respectively. Box plots show the distribution of expression of indicated APOBEC genes. Boxes extend from the third (Q3) to the first (Q1) quartile, with the line at the median; whiskers extend to 2.5 and 97.5 percentiles
