Evidence for APOBEC3B mutagenesis in multiple human cancers

Abstract

Thousands of somatic mutations accrue in most human cancers, and their causes are largely unknown. We recently showed that the DNA cytidine deaminase APOBEC3B accounts for up to half of the mutational load in breast carcinomas expressing this enzyme. Here we address whether APOBEC3B is broadly responsible for mutagenesis in multiple tumor types. We analyzed gene expression data and mutation patterns, distributions and loads for 19 different cancer types, with over 4,800 exomes and 1,000,000 somatic mutations. Notably, APOBEC3B is upregulated, and its preferred target sequence is frequently mutated and clustered in at least six distinct cancers: bladder, cervix, lung (adenocarcinoma and squamous cell carcinoma), head and neck, and breast. Interpreting these findings in the light of previous genetic, cellular and biochemical studies, the most parsimonious conclusion from these global analyses is that APOBEC3B-catalyzed genomic uracil lesions are responsible for a large proportion of both dispersed and clustered mutations in multiple distinct cancers.

Figure 1. APOBEC3B is upregulated in numerous cancer types

Each data point represents one tumor or normal sample, and the Y-axis is log-transformed for better data visualization. Red, blue, and yellow horizontal lines indicate the median APOBEC3B/TBP value for each cancer type (Table 1), the median value for each set of normal tissue RNAseq data (Supplementary Table 1), and individual RT-qPCR data points, respectively. Asterisks indicate significant upregulation of APOBEC3B in the indicated tumor type relative to the corresponding normal tissues (p<0.0001 by Mann-Whitney U-test). P-values for negative or insignificant associations are not shown.

Figure 2. Mutation types and signatures in 19 human cancers

(a) Stacked bar graph summarizing the 6 types of base substitution mutations as proportions of the total mutations per cancer. (b) Median APOBEC3B relative to TBP expression levels plotted against the proportion of mutations at C/G base pairs (Spearman p = 0.0031, r = 0.64). Dashed grey line is the best-fit for visualization.

Figure 3. Cytosine mutation spectra for 19 cancers

(a) Dendrogram with weblogos indicating the relationship among cancer types determined by the trinucleotide contexts of mutations occurring at C nucleotides for the top 50% APOBEC3B expressing samples within each cancer type. Font size of the bases at the 5’ and 3’ positions are proportional to their observed occurrence in exome mutation datasets. The preferred mutation context for recombinant APOBEC3B from Ref. is included in the hierarchical clustering in order to determine how closely each cancers’ actual mutation spectrum matches the preferred motif for APOBEC3B in vitro. The pattern expected if the mutations were to occur at random C bases in the exome is included as an inset at the bottom left. (b) Stacked bars indicate the observed proportion of cytosine mutations at each unique trinucleotide [5’-NCN-to-N(T/G/A)N]. Bar color indicates each mutation type: red: C-to-T, black: C-to-G, and blue: C-to-A. The top 6 cancer types (highlighted by solid line box) show clear biases toward mutations within 5’TCN motifs, at frequencies that resemble the preferences of recombinant APOBEC3B in vitro (Ref. 33). Skin cancer and the bottom 7 cancers (highlighted by dashed line boxes) have obviously different cytosine mutation spectra.

Figure 4. APOBEC3B expression levels correlate with total mutation loads and kataegis events

(a) A dot plot showing the total mutation loads for each tumor exome from each of the indicated cancers. Each data point represents one tumor, and the Y-axis is log-transformed for better visualization. A red horizontal line shows the median mutation load for each cancer type. (b) Median mutation loads per tumor exome for each cancer type plotted against the median APOBEC3B relative to TBP expression values (Spearman p = 0.0013, r = 0.68). Dashed grey line is the best-fit for visualization. (c) The mean number of cytosine mutation clusters per exome for each cancer type plotted against median APOBEC3B relative to TBP expression values (Spearman p = 0.0017, r = 0.54). Dashed grey line is the best-fit for visualization.