Mutational impact of APOBEC3B and APOBEC3A in a human cell line

Abstract

AbstractA prominent source of mutation in cancer is single-stranded DNA cytosine deamination by cellular APOBEC3 enzymes, which results in C-to-T and C-to-G mutations in TCA and TCT motifs. Although multiple enzymes have been implicated, reports conflict and it is unclear which enzyme(s) are responsible. Here we develop a selectable system to quantify genome mutation and compare the mutagenic activities of three leading candidates - APOBEC3A, APOBEC3B, and APOBEC3H. The human cell line, HAP1, is engineered to express the thymidine kinase (TK) gene of HSV-1, which confers sensitivity to ganciclovir. Clonal expression of APOBEC3A and APOBEC3B, but not catalytic mutant controls or APOBEC3H, trigger elevated DNA damage responses and increased frequencies of TK mutation. Mutant TK DNA sequences reveal nearly indistinguishable cytosine mutation patterns. Whole genome sequences from TK mutant clones confirm these results and enable broader bioinformatic analyses. Most importantly, comparisons of APOBEC3A- and APOBEC3B-inflicted mutation signatures in this system and the actual APOBEC3 signature from breast cancer indicate that most tumors are likely to manifest a composite signature. These studies help resolve a long-standing etiologic debate in the cancer field and indicate that future diagnostic and therapeutic efforts should focus on both APOBEC3A and APOBEC3B.