DNA polymerase β deficiency is linked to aggressive breast cancer: a comprehensive analysis of gene copy number, mRNA and protein expression in multiple cohorts

Abstract

Short arm of chromosome 8 is a hot spot for chromosomal breaks, losses and amplifications in breast cancer. Although such genetic changes may have phenotypic consequences, the identity of candidate gene(s) remains to be clearly defined. Pol β gene is localized to chromosome 8p12-p11 and encodes a key DNA base excision repair protein. Pol β may be a tumour suppressor and involved in breast cancer pathogenesis. We conducted the first and the largest study to comprehensively evaluate pol β in breast cancer. We investigated pol β gene copy number changes in two cohorts (n = 128 &n = 1952), pol β mRNA expression in two cohorts (n = 249 &n = 1952) and pol β protein expression in two cohorts (n = 1406 &n = 252). Artificial neural network analysis for pol β interacting genes was performed in 249 tumours. For mechanistic insights, pol β gene copy number changes, mRNA and protein levels were investigated together in 128 tumours and validated in 1952 tumours. Low pol β mRNA expression as well as low pol β protein expression was associated high grade, lymph node positivity, pleomorphism, triple negative, basal-like phenotypes and poor survival (ps < 0.001). In oestrogen receptor (ER) positive sub-group that received tamoxifen, low pol β protein remains associated with aggressive phenotype and poor survival (ps < 0.001). Artificial neural network analysis revealed ER as a top pol β interacting gene. Mechanistically, there was strong positive correlation between pol β gene copy number changes and pol β mRNA expression (p < 0.0000001) and between pol β mRNA and pol β protein expression (p < 0.0000001). This is the first study to provide evidence that pol β deficiency is linked to aggressive breast cancer and may have prognostic and predictive significance in patients.

Keywords: Breast cancer; Pol β; Predictive factor; Prognostic factor.

Figure 1

Pol β mRNA expression in breast cancer. A. Kaplan Meier curves showing breast cancer specific survival in the Uppsala cohort. B. Kaplan Meier curves showing breast cancer specific survival in the Metabric cohort. C. Artificial neural network analysis. Top pair‐wise interactions for gene probe markers associated with Pol β expression in 249 breast cancers is shown here. Each gene probe is represented by a node and the interaction weight between them as an edge, the width being defined by the magnitude of the weight. Interactions are directed from a source gene to a target gene as indicated by arrows. Red interactions indicate an excitatory interaction and blue indicates an inhibitory interaction. Highly linked genes represent hubs that are indicated to be highly influential or highly regulated in the Pol β system. See Supplementary data 2 for the biological functions of individual genes.

Figure 2

Pol β protein expression in breast cancer. A. Western blot showing pol β in breast cancer cell lines (A1). Microphotographs of Pol β protein expression in breast cancer tissue (magnification × 200) showing tumour with low pol β expression (A2) and high pol β expression (A3). B. Kaplan Meier curves showing breast cancer specific survival in whole cohort (B1), ER + treated with tamoxifen (B2), ER + no tamoxifen (B3). C. Kaplan Meier curves showing breast cancer specific survival in luminal A sub‐group whole cohort (C1), luminal A treated with tamoxifen (C2), luminal A no tamoxifen (C3). D. Kaplan Meier curves showing breast cancer specific survival in luminal B sub‐group whole cohort (D1), luminal A treated with tamoxifen (D2), luminal A no tamoxifen (D3).

Figure 3

A. Correlation between Pol β gene copy number and Pol β mRNA expression in the Metabric cohort [AMP = amplification, NEUT = neutral, HETD = heterozygous deletion, HOMD = homozygous deletion]. B. Correlation between Pol β mRNA and Pol β protein expression in the Nottingham cohort.