M. Asaoka1,2, S. K. Patnaik1, A. L. Butash1, E. Katsuta1, T. Ishikawa2, K. Takabe1,2 1Roswell Park Cancer Institute,Surgical Oncology,Buffalo, NY, USA 2Tokyo Medical University,Department Of Breast Surgery And Oncology,Shinjuku, Tokyo, Japan
Introduction:
APOBEC enzymes are known as strong mutagenic factors, particularly in breast cancer. APOBEC3B (A3B) gene expression is significantly increased in breast cancer and associated with tumor mutation load and intra-tumor heterogeneity. The relevance of the other APOBEC3s (A3A, C-H) is not yet clear in breast cancer. Therefore, we analyzed these genes, looking at their association with survival, mutations, and immune activity.
Methods:
We collected gene expression data for primary tumors (1091) and adjacent normal tissues (113) from The Cancer Genome Atlas (TCGA). Patients were divided into 3 equal groups by gene expression to compare high and low expressors. Tumor immune features like cytolytic activity and T cell receptor (TCR) diversity were quantified from gene expression data. Data for some of these features, mutation-related aspects, and survival were obtained from TCGA publications. Gene expression data for 55 breast cancer cell-lines was from Cancer Cell Line Encyclopedia. Cox regression and Spearman methods were used for survival and correlation analyses, resp. Welch t test was used for group comparison, with P <0.05 deemed significant. Hallmark gene-sets were used for enrichment analysis.
Results:
A3B and A3C represented 91% of A3 gene expression in breast cancer cell-lines. In patients, expression of A3B was higher in tumors compared to normal tissue (4.5x), while that of A3C was lower (0.5x). A3B or A3A levels had no effect on overall (OS) or disease-specific survival (DSS). But, higher expression for each of A3C-H was significantly associated with improved OS (HR, 0.45-0.66) or DSS (0.43-0.61). The prognostic value of high A3C-H expression was validated in two gene expression meta-datasets (KMPlot and SurvExpress). A3A and A3B expression levels correlated with both tumor mutation burden and neoantigen load (ρ = 0.28-0.34), which resp. were 2.0-2.9x more in high expressors. There was no association of tumor mutation burden or neoantigen load with A3C-H. A3C-H expression levels correlated positively with both total immune cell and lymphocyte populations in tumor (ρ = 0.29-0.70 & 0.20-0.50, resp.), whereas the correlations were poor for A3B (0.10 & -0.01, resp.). Expression of genes related to immune function like interferon response and complement activation was enriched in high A3C-H expressors, which also had significantly more CD4 and CD8 T cells, and TCR diversity (2.3-4.0x, 2.1-5.4x & 1.3-2.1x, resp.). Concordantly, for each of A3C-H, expression correlated with tumor immune cytolytic activity (ρ = 0.31-0.79), which was increased 3.1-7.9x in high expressors.
Conclusion:
APOBEC3s are DNA mutators. However, unlike A3B, whose expression is associated with poor survival, increased expression of A3C-H confers a survival benefit. Further studies are warranted to explore if the increased A3C-H expression reflects a heightened anti-cancer immune response, and if A3C-H can be used as prognostic biomarkers.