Functional Analysis of Promoter Variants in Genes Involved in Sex Steroid Action, DNA Repair and Cell Cycle Control.

Yosr Hamdi,Stéphane Dubois,Jacques Simard,Daniel Sinnett,Penny Soucy,Manon Ouimet,M'Hamed Lajmi Lakhal Chaieb,Guy Reimnitz,Martine Tranchant,Martin Leclerc,Martine Dumont,Pauline Cassart

doi:10.3390/genes10030186

Yosr Hamdi, Stéphane Dubois + Show 10 more

Open Access

https://doi.org/10.3390/genes10030186

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Abstract

Genetic variants affecting the regulation of gene expression are among the main causes of human diversity. The potential importance of regulatory polymorphisms is underscored by results from Genome Wide Association Studies, which have already implicated such polymorphisms in the susceptibility to complex diseases such as breast cancer. In this study, we re-sequenced the promoter regions of 24 genes involved in pathways related to breast cancer including sex steroid action, DNA repair, and cell cycle control in 60 unrelated Caucasian individuals. We constructed haplotypes and assessed the functional impact of promoter variants using gene reporter assays and electrophoretic mobility shift assays. We identified putative functional variants within the promoter regions of estrogen receptor 1 (ESR1), ESR2, forkhead box A1 (FOXA1), ubiquitin interaction motif containing 1 (UIMC1) and cell division cycle 7 (CDC7). The functional polymorphism on CDC7, rs13447455, influences CDC7 transcriptional activity in an allele-specific manner and alters DNA–protein complex formation in breast cancer cell lines. Moreover, results from the Breast Cancer Association Consortium show a marginal association between rs13447455 and breast cancer risk (p = 9.3 × 10−5), thus warranting further investigation. Furthermore, our study has helped provide methodological solutions to some technical difficulties that were encountered with gene reporter assays, particularly regarding inter-clone variability and statistical consistency.

Highlights

Over the last two decades since the discovery of the first high-risk breast cancer susceptibility genes breast cancer 1 (BRCA1) and BRCA2, an extensive body of literature has grown regarding theGenes 2019, 10, 186; doi:10.3390/genes10030186 www.mdpi.com/journal/genesGenes 2019, 10, 186 causes of hereditary and familial breast cancer [1]
Using a panel of 60 unrelated Caucasian individuals from families registered at the Centre d’Etude du Polymorphisme Humain (CEPH)/Utah, we amplified and sequenced a region of ~2.5 kb, upstream of the transcription start site of 24 genes involved in sex steroid action, DNA repair and cell cycle control (Table S2)
For the mediator of DNA damage checkpoint 1 (MDC1) gene, only one major haplotype (95%) was estimated and this gene was excluded from further functional analysis

Summary

Introduction

Over the last two decades since the discovery of the first high-risk breast cancer susceptibility genes breast cancer 1 (BRCA1) and BRCA2, an extensive body of literature has grown regarding theGenes 2019, 10, 186; doi:10.3390/genes10030186 www.mdpi.com/journal/genesGenes 2019, 10, 186 causes of hereditary and familial breast cancer [1]. One of the major observations that was derived from these studies is the marked variability in the penetrance of these genes among carriers sharing the same mutation, suggesting that breast cancer risk may be modified by multiple genetic and non-genetic factors. It is well-established that the genetic component of breast cancer risk is due to a combination of rare variants conferring high to intermediate risk of breast cancer with more common variants conferring a lower risk. Additional susceptibility variants might still be identified, and the molecular mechanisms accounting for the role of single nucleotide polymorphisms (SNPs) in the risk of cancer are still currently investigated

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