Identification of novel breast cancer susceptibility genes through exome sequencing: a population-specific approach based on Slavic founder mutations
Gynaecology and Obstetrics
Hematology, Oncology
Final Report Abstract
This project was set up to bring together two groups from Russia, one group from Belarus and one group from Hannover for a coordinated effort to identify and validate novel breast cancer susceptibility genes in Slavic populations. Our exome-sequencing study of familial breast cancer patients from Belarus uncovered 84 loss-of-function variants in 82 prioritized candidate genes involved in cell cycle, DNA repair, apoptosis or estrogen-related pathways. 42 gene variants were then genotyped in breast cancer case-control studies from Belarus, Russia and Germany, comprising a total of 4,602 breast cancer cases and 3,079 healthy women. We identified two truncating variants that were associated with increased breast cancer risk in Belarus and Russia at overall significance of p=0.01, but were very rare in the German population. We also obtained evidence for a truncating variant that may be associated with decreased breast cancer risk (p=0.02). We identified a splicing variant that was present in both Belarusian and Russian exomes and was associated with breast cancer across the three populations (p=0.035) with no evidence of heterogeneity between the studies. This variant in USP39 affects a regulatory exon in the 3´-UTR that was found active in breast epithelial cells and could be modulated with antisense oligonucleotides. In a subsequent sequencing study of the coding regions of 60 prioritized candidate genes in 811 German breast cancer cases and 975 German female controls, one additional gene was identified that showed evidence of an increased prevalence of truncating variants in breast cancer cases versus controls (p=0.04). None of these results withstands statistical correction for multiple testing and, therefore, novel candidates need to be replicated and further characterised at the molecular level. During the funding period, we have taken part in large replication studies from multinational consortia to corroborate BARD1, FANCC and FANCM as susceptibility genes for ER-negative breast cancer. We also have generated a breast epithelial cell culture model that stably expresses Cas9(D10A) nickase and, in initial experiments, could be successfully modified through single-base genome editing to functionally characterise a gene variant in APOBEC3B. In summary, this project has uncovered promising novel candidate breast cancer susceptibility genes through founder variants in Slavic populations, has helped to fully establish three previously proposed candidates, and has provided a novel biological tool for the in vitro functional assessment of selected risk variants.
Publications
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A Splice Site Variant of CDK12 and Breast Cancer in Three Eurasian Populations. Frontiers Oncol 2019 Jun 14;9:493
Bogdanova NV, et al.
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BARD1 is A Low/Moderate Breast Cancer Risk Gene: Evidence Based on An Association Study of the Central European p.Q564X Recurrent Mutation. Cancers 2019;11(6):740
Suszynska M, et al.
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Two truncating variants in FANCC and breast cancer risk. Sci Rep 2019; 9(1):12524
Dörk T, et al.
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Exome sequencing study of Russian breast cancer patients suggests a predisposing role for USP39. Breast Cancer Res Treat 2020;179(3):731-742
Kuligina ES, et al.
