Abstract P5-06-03: A solution to the APOBEC mutation paradox in breast cancer

Abstract

Abstract Breast cancer has a major genetic component, and individual tumors can have thousands to tens-of-thousands of mutations. Large proportions are cytosine mutations in TCA and TCT trinucleotide motifs. A variety of studies have attributed this mutation signature to the APOBEC family of DNA cytosine deaminases, with previous literature favoring APOBEC3B as the most likely enzyme to bee responsible (from a total of nine active family members). However, breast tumor genomic DNA sequences from patients with a naturally occurring germline deletion of the entire APOBEC3B gene still show an intact APOBEC mutation signature. To resolve this paradox, we tested the hypothesis that the only other functionally dimorphic APOBEC family member, APOBEC3H, may be responsible. First, we performed an unbiased genetic analysis of TCGA data sets and showed that APOBEC3B-null tumors with this mutational bias have at least one copy of the haplotype-I variant of APOBEC3H, despite weak genetic linkage between these two genes (n=14/14). Remarkably, breast tumors without APOBEC3B and APOBEC3H haplotype-I showed no evidence for an APOBEC mutation signature (n=3/3). The proportion of APOBEC signature mutations between the cohort with and the cohort without APOBEC3H haplotype-I was highly significant (p<0.00001 and lower), indicating that these two enzymes alone may be fully responsible (and casting serious doubt on the potential role of APOBEC3A). Second, although deemed inactive in prior studies, we discovered that APOBEC3H haplotype-I has robust activity in biochemical assays with mutation of TCA-containing single-stranded DNA and in cellular assays with hypermutation of HIV-1 cDNA and mutation of a genomic DNA eGFP reporter gene. Third, the subcellular localization APOBEC3H haplotype-I and other expressed variants of this enzyme differed with only the latter showing significant nuclear localization in a panel of cell lines. The genomic mutagenicity and localization of APOBEC3H haplotype-I is attributable to a glycine at position 105, whereas other variants of this enzyme that have an arginine at this position, suggesting a general molecular mechanism. These studies combine to offer a parsimonious solution to the APOBEC mutation paradox with APOBEC3B and APOBEC3H haplotype-I, together, accounting for the strong “APOBEC mutation signature” observed in many breast cancers. Citation Format: Harris RS, Starrett GJ, McCann JL, Carpenter MA. A solution to the APOBEC mutation paradox in breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P5-06-03.