APOBEC3B expression in breast cancer reflects cellular proliferation, while a deletion polymorphism is associated with immune activation

Abstract

Genomic sequencing studies of breast and other cancers have identified patterns of mutations that have been attributed to the endogenous mutator activity of APOBEC3B (A3B), a member of the AID/APOBEC family of cytidine deaminases. A3B gene expression is increased in many cancers, but its upstream drivers remain undefined. Furthermore, there exists a common germ-line deletion polymorphism (A3B^del), which has been associated with a paradoxical increase in breast cancer risk. To examine causes and consequences of A3B expression and its constitutive absence in breast cancer, we analyzed two large clinically annotated genomic datasets [The Cancer Genome Atlas (TCGA) and the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC)]. We confirmed that A3B expression is associated with aggressive clinicopathologic characteristics and adverse outcomes and show that A3B expression is highly correlated with proliferative features (mitosis and cell cycle-related gene expression) in breast and 15 of 16 other solid tumor types. However, breast cancers arising in homozygous A3B^del individuals with A3B absent did not differ in these features, indicating that A3B expression is a reflection rather than a direct cause of increased proliferation. Using gene set enrichment analysis (GSEA), we detected a pattern of immune activation in A3B^del breast cancers, which seems to be related to hypermutation arising in A3B^del carriers. Together, these results provide an explanation for A3B overexpression and its prognostic effect, giving context to additional study of this mutator as a cancer biomarker or putative drug target. In addition, although immune features of A3B^del require additional study, these findings nominate the A3B^del polymorphism as a potential predictor for cancer immunotherapy. Significance Somatic mutagenesis is fundamental to the development and evolution of cancers. APOBEC3B (A3B) is a cellular deaminase, which is overexpressed in cancers and believed to be an important cause of cancer-associated mutations. The factors responsible for A3B up-regulation are unknown. Interestingly, a germ-line deletion polymorphism exists, such that a significant proportion of the global population does not express A3B protein. Using large human cancer datasets, we show that A3B expression is strongly associated with cellular proliferation. Furthermore, we identify a pattern of immune activation related to hypermutation in tumors arising in A3B deletion carriers suggesting that these patients could respond differently to immune-directed therapies. These results provide important context for the ongoing study of A3B as a therapeutic target or biomarker.