The 30 kb deletion in the APOBEC3 cluster decreases APOBEC3A and APOBEC3B expression and creates a transcriptionally active hybrid gene but does not associate with breast cancer in the European population.

Katarzyna Klonowska,Cezary Cybulski,Magdalena Ratajska,Karol Czubak,Anna Jakubowska,Marzena Wojciechowska,Bogna Rusak,Piotr Kozlowski,Jan Lubinski,Natalia Krawczynska,Danuta Vasilevska,Wojciech Kluzniak

doi:10.18632/oncotarget.19400

Abstract

APOBEC3B, in addition to other members of the APOBEC3 gene family, has recently been intensively studied due to its identification as a gene whose activation in cancer is responsible for a specific pattern of massively occurring somatic mutations. It was recently shown that a common large deletion in the APOBEC3 cluster (the APOBEC3B deletion) may increase the risk of breast cancer. However, conflicting evidence regarding this association was also reported. In the first step of our study, using different approaches, including an in-house designed multiplex ligation-dependent probe amplification assay, we analyzed the structure of the deletion and showed that although the breakpoints are located in highly homologous regions, which may generate recurrent occurrence of similar but not identical deletions, there is no sign of deletion heterogeneity. This knowledge allowed us to distinguish transcripts of all affected genes, including the highly homologous canonical APOBEC3A and APOBEC3B, and the hybrid APOBEC3A/APOBEC3B gene. We unambiguously confirmed the presence of the hybrid transcript and showed that the APOBEC3B deletion negatively correlates with APOBEC3A and APOBEC3B expression and positively correlates with APOBEC3A/APOBEC3B expression, whose mRNA level is >10-fold and >1500-fold lower than the level of APOBEC3A and APOBEC3B, respectively. In the next step, we performed a large-scale association study in three different cohorts (2972 cases and 3682 controls) and showed no association of the deletion with breast cancer, familial breast cancer or ovarian cancer. Further, we conducted a meta-analysis that confirmed the lack of the association of the deletion with breast cancer in non-Asian populations.

Highlights

Breast cancer is the primary cause of cancerassociated death among women worldwide
In the first step of our study, using different approaches, including an in-house designed multiplex ligation-dependent probe amplification assay, we analyzed the structure of the deletion and showed that the breakpoints are located in highly homologous regions, which may generate recurrent occurrence of similar but not identical deletions, there is no sign of deletion heterogeneity
F is located on the border of APOBEC3A intron 3 and exon 4, upstream of the presumed 5’-breakpoint of the APOBEC3B deletion; R1 is located in the APOBEC3A exon 5 downstream of the presumed 5’-breakpoint of the deletion; and R2 is specific to the sequence within the APOBEC3B exon 8 downstream of the presumed 3’-breakpoint of the deletion (Figure 1A)

Summary

Introduction

Breast cancer is the primary cause of cancerassociated death among women worldwide. The probability of developing breast cancer is modulated by an interplay of lifestyle, environmental, and genetic factors. The overall heritability (h2) of breast cancer was estimated at approximately 30% [1]. Penetrant germline mutations in BRCA1 and BRCA2 and in several genes associated with various hereditary cancer syndromes explain 16-40% of all breast cancer cases that aggregate in families [2,3,4]. It is estimated that mutations in several susceptible genes of moderate penetrance, e.g., ATM, CHEK2 or NBN, account for another 5% of all familial breast cancer cases [2, 5, 6]. The genetic background of breast cancer predisposition in approximately 50% of breast cancer cases aggregated in families still remains to be explained [4, 7]

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