Abstract P3-08-05: High APOBEC3C-H gene expression in tumor associates with better survival in breast cancer
Authors: Asaoka M , Patnaik SK , Katsuta E , Kawaguchi T , Ishikawa T , Takabe K 
Published: May 2019

Background

APOBEC3 (A3) enzymes are strong mutagenic factors. A3B has been well described as an active mutator in breast cancer, whereas the roles of the other APOBEC3s (A3A, C-H) are unclear. While mutations may directly drive cancer progression, they can indirectly suppress cancer growth by generating neoantigens. To elucidate this, we comprehensively analyzed all APOBEC3s for their association with mutations and immune activity in breast cancer.

Methods

RNA seq.-based gene expression data for 1091 primary carcinomas and 113 adjacent normal tissues was from TCGA. Patients were divided into high and low groups by top and bottom gene expression tertiles. Tumor immune features like cytolytic activity, T cell receptor (TCR) diversity, and cell fractions were quantified from gene expression data. Data for some of these features, mutation-related aspects, and survival outcomes were obtained from the Pan-Cancer Atlas. Gene expression data for 55 breast cancer cell-lines was from Cancer Cell Line Encycolpedia. Cox regression and Spearman methods were respectively used for survival and correlation analyses. Welch's t test was used for group comparison. P &lt;0.05 was deemed significant. Hallmark gene-sets were used for enrichment analysis with recommended 25% FDR.

Results

A3B and A3C together represented most (91%) of A3 gene expression in breast cancer cell-lines. In TCGA patients, expression of only A3B was increased by 4.5x in tumors compared to normal tissue, whereas levels for other A3 genes were unchanged. Surprisingly, tumor A3B or A3A levels had no significant association with overall (OS) or disease-specific survival (DSS), whereas for each of A3C-H, higher expression was significantly associated with improved OS (hazard ratios of 0.45-0.66) or DSS (0.43-0.61). The prognostic benefit of high A3C-H expression was also seen in survival analyses of two meta-datasets of microarray-based gene expression (KMPlot and SurvExpress). A3A and A3B levels correlated with both mutation burden and neoantigen load (Spearman ρ = 0.28-0.34), which respectively were 2.0-2.9x higher in high compared to low expressors. But there was no association of expression with mutation burden or neoantigen load for A3C-H. On the other hand, A3C-H levels correlated positively with tumor leukocyte fraction (ρ = 0.29-0.70) and its lymphocyte subset (ρ = 0.20-0.50), whereas the correlation was poor for A3B (ρ = 0.10 & -0.01 respectively). Expression of genes of immune function like interferon response and complement activation was enriched in high A3C-H expressors. It was not so for A3B, for which enrichment was instead observed for cell proliferation. Both CD4 and CD8 T cells were significantly more (2.3-4.0x & 2.1-5.4x resp.), and TCR diversity significantly higher (1.3-2.1x) in A3C-H high expressors. 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 compared to low expressors.

Conclusions

These findings suggest that in spite of A3C-H being known as DNA mutators, an increase in their expression confers a survival benefit in breast cancer. Their increased expression likely reflects a heightened anti-cancer immune response, and may be useful for disease prognosis and monitoring immunotherapy.

Citation Format: Asaoka M, Patnaik SK, Katsuta E, Kawaguchi T, Ishikawa T, Takabe K. High APOBEC3C-H gene expression in tumor associates with better survival in breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-08-05.