Multiple mutations are required for cancer development, and genome sequencing has revealed that several cancers, including breast, have somatic mutation spectra dominated by C-to-T transitions1–9. Most of these mutations occur at hydrolytically disfavored10 non-methylated cytosines throughout the genome, and are sometimes clustered8. Here, we show that the DNA cytosine deaminase APOBEC3B (A3B) is a likely source of these mutations. A3B mRNA is up-regulated in the majority of primary breast tumors and breast cancer cell lines. Tumors that express high levels of A3B have twice as many mutations as those that express low levels and are more likely to have mutations in TP53. Endogenous A3B protein is predominantly nuclear and the only detectable source of DNA C-to-U editing activity in breast cancer cell line extracts. Knockdown experiments show that endogenous A3B correlates with elevated levels of genomic uracil, increased mutation frequencies, and C-to-T transitions. Furthermore, induced A3B over-expression causes cell cycle deviations, cell death, DNA fragmentation, γ-H2AX accumulation, and C-to-T mutations. Our data suggest a model in which A3B-catalyzed deamination provides a chronic source of DNA damage in breast cancers that could select TP53 inactivation and explain how some tumors evolve rapidly and manifest heterogeneity.

Thousands of somatic mutations accrue in most human cancers and causes are largely unknown. We recently showed that the DNA cytosine 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, totaling over 4,800 exomes and 1,000,000 somatic mutations. Remarkably, APOBEC3B is upregulated and its preferred target sequence is frequently mutated and clustered in at least 6 distinct cancers: bladder, cervix, lung (adeno- and squamous cell), head/neck, and breast. Interpreted in light of prior genetic, cellular, and biochemical studies, the most parsimonious conclusion based on 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.

After gene rearrangement, immunoglobulin variable genes are diversified by somatic hypermutation or gene conversion, whereas the constant region is altered by class-switch recombination. All three processes depend on activation-induced cytidine deaminase (AID), a B-cell-specific protein that has been proposed (because of sequence homology) to function by RNA editing. But indications that the three gene diversification processes might be initiated by a common type of DNA lesion, together with the proposal that there is a first phase of hypermutation that targets dC/dG, suggested to us that AID may function directly at dC/dG pairs. Here we show that expression of AID in Escherichia coli gives a mutator phenotype that yields nucleotide transitions at dC/dG in a context-dependent manner. Mutation triggered by AID is enhanced by a deficiency of uracil-DNA glycosylase, which indicates that AID functions by deaminating dC residues in DNA. We propose that diversification of functional immunoglobulin genes is triggered by AID-mediated deamination of dC residues in the immunoglobulin locus with the outcome--that is, hypermutation phases 1 and 2, gene conversion or switch recombination--dependent on the way in which the initiating dU/dG lesion is resolved.