Abstract P3-04-04: Identification of a “BRCAness” signature in triple negative breast cancer by Comparative Genomic Hybridization
Authors: Toffoli S , Bar I , Abdulsater F , Delrée P , Hilbert P , Cavallin F , Moreau F , Clark J , Lacroix-Triki M , Campone M , Martin A-L , Roché H , Machiels J-P , Carrasco J , Canon J-L 
Published: August 2014

Abstract
Background: Triple Negative Breast Cancers (TNBC) represent 12% to 20% of total Breast Cancers (BC) and have a worse outcome compared with other breast cancer subtypes. TNBC often show a deficiency in DNA double strand break repair mechanisms. This deficiency is generally related to inactivation of a repair enzymatic complex involving BRCA1 caused either by genetic mutations, epigenetic modifications, or by post-transcriptional regulations. The identification of BC presenting a BRCA1 deficiency could be useful to select patients that could benefit from PARP inhibitors, alkylant agents or platinum-based chemotherapy.
In this study, we have identified by Comparative Genomic Hybridization array (CGH-array) a recurrent gain in 17q25.3 characteristic of BRCA1 mutated or methylated TNBC.
Methods: 130 formalin-fixed paraffin embedded (FFPE) tumours including TNBC (unknown-BRCA1-status, BRCA1 mutated and non-mutated), Luminal A, Luminal B, Her2-neu amplified (Her2+) BC and BRCA1-mutated non-TNBC (mutated-Luminal A, Luminal B, Her2+) were obtained from our local tumour collection. DNA was extracted and genomic copy-number alterations were analysed by CGH-array (Agilent, SuperPrint G3 Human CGH 8×60K Oligo Microarrays). FISH analyses were performed on section from FFPE samples to validate some chromosomal aberrations belonging to the 17q25.3 amplified region evidenced by CGH-array. The study of BRCA1 promoter methylation status in all tumours was carried out by MDxHealth (Liege, Belgium).
Results: In this study, we have identified by CGH-array a genomic region (17q25.3) amplified in 90% of the BRCA1 mutated tumours (29/32). This chromosomal gain was studied in other subtypes of BC by CGH-array and it was only evidenced in 30% (6/20) of BRCA1 non-mutated TNBC, 26.67% (4/15) of unknown-BRCA1-status TNBC, 13.64% (3/22) of Luminal B, 19.05% (4/21) of Her2+ and 0% (0/20) of Luminal A breast cancers. FISH assays confirmed these chromosomal amplifications and evidenced like CGH array analyses a significant difference between BRCA1 mutated and non-mutated BC for the 17q25.3 gain.
BRCA1 methylation was found only in TNBC (11/58) and was not found in the BRCA1-mutated BC cohort, nor in the Luninal A, Luminal B and Her2+ samples. In BRCA1 non-mutated TNBC, the methylation was found in 8 cases including 4 with 17q25.3 amplification. In the unknown-BRCA1-status TNBC, 3 methylated samples were found with 1 case with co-amplification of the 17q25.3 region.
Recurrence of 17q25.3 amplification in BRCA1 mutated tumours as well as its detection in BC having a methylation in BRCA1 promoter suggests that the 17q25.3 gain could be a marker of the BRCA1 deficiency. Identification of relevant genes whose expression is up-regulated within the recurrently gained region is underway.
Conclusions: The CGH signature observed in 17q25.3 chromosomal region and FISH assay developed in this study could allow the identification of “BRCAness” breast tumours, improving the diagnostic performance and orienting the selection of the appropriate therapy. The up-regulated genes themselves might also represent potential therapeutic targets.
Acknowledgements: This work was financed through the “Plan National Cancer-Action 29” (Belgium) and supported by the UNICANCER-PACS08 trial (France).
Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P3-04-04.