Mutational impact of APOBEC3A and APOBEC3B in a human cell line and comparisons to breast cancer

by Michael A. Carpenter, Nuri A. Temiz, Mahmoud A. Ibrahim, Matthew C. Jarvis, Margaret R. Brown, Prokopios P. Argyris, William L. Brown, Gabriel J. Starrett, Douglas Yee, Reuben S. Harris A prominent source of mutation in cancer is single-stranded DNA cytosine deamination by cellular APOBEC3 enzymes, which results in signature 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 protein(s) are responsible. Here we report the development of a selectable system to quantify genome mutation and demonstrate its utility by comparing the mutagenic activities of three leading candidates —APOBEC3A, APOBEC3B, and APOBEC3H. The human cell line, HAP1, is engineered to express thethymidine kinase (TK) gene of HSV-1, which confers sensitivity to ganciclovir. Expression of APOBEC3A and APOBEC3B, but not catalytic mutant controls or APOBEC3H, triggers increased frequencies ofTK mutation and similar TC-biased cytosine mutation profiles in the selectableTK reporter gene. Whole genome sequences from independent clones enabled an analysis of thousands of single base substitution mutations and extraction of local sequence preferences with APOBEC3A preferring YTCW motifs 70% of the time and APOBEC3B 50% of the time (Y = C/T; W = A/T). Signature comparisons with breast tumor whole genome sequences indicate that most malignancies manifest intermediate percentages of APOBEC3 signature mutations in YTCW motifs, ...
Source: PLoS Genetics - Category: Genetics & Stem Cells Authors: Source Type: research