Genomic analysis of the HER2/TOP2A amplicon in breast cancer and breast cancer cell lines

Abstract

HER2 and TOP2A are targets for the therapeutic agents trastuzumab and anthracyclines and are frequently amplified in breast cancers. The aims of this study were to provide a detailed molecular genetic analysis of the 17q12-q21 amplicon in breast cancers harbouring HER2/TOP2A co-amplification and to investigate additional recurrent co-amplifications in HER2/ TOP2A-co-amplified cancers. In total, 15 breast cancers with HER2 amplification, 10 of which also harboured TOP2A amplification, as defined by chromogenic in situ hybridisation, and 6 breast cancer cell lines known to be amplified for HER2 were subjected to high-resolution microarray-based comparative genomic hybridisation analysis. This revealed that the genomes of 12 cases were characterised by at least one localised region of clustered, relatively narrow peaks of amplification, with each cluster confined to a single chromosome arm (ie 'firestorm' pattern) and 3 cases displayed many narrow segments of duplication and deletion affecting the vast majority of chromosomes (ie 'sawtooth' pattern). The smallest region of amplification (SRA) on 17q12 in the whole series extended from 34.73 to 35.48 Mb, and encompassed HER2 but not TOP2A. In HER2/TOP2A-co-amplified samples, the SRA extended from 34.73 to 36.54 Mb, spanning a region of B1.8 Mb. Apart from HER2 and TOP2A, this region encompassed four additional genes whose expression levels as defined by quantitative real-time PCR are significantly higher in HER2/TOP2A-co-amplified vs HER2-amplified breast cancers: CASC3, CDC6, RARA and SMARCE1. Of the cell lines studied, SKBR3 and UACC812 showed HER2/TOP2A co-amplification. In conclusion, this is the first detailed genome-wide characterisation of HER2/TOP2A-amplified breast cancers; cell lines were identified that can be used to model these cancers in vitro. The 17q12 amplicon is complex and harbours multiple genes that may be associated with breast cancer development and progression, and potentially exploitable as therapeutic targets.

Genomic and immunohistochemical analysis of adenosquamous carcinoma of the breast

“…Copy number changes were categorized as gains, losses or amplifications according to previously validated thresholds for each clone. 15 Threshold values were chosen to correspond to three standard deviations of the normal ratios obtained from the filtered clones mapping to chromosomes 1-22, assessed in multiple hybridizations between DNA extracted from a pool of male and female blood donors as previously described 16,17 (Log2 ratio of ±0.12). Low-level gain was defined as a smoothed Log2 ratio of between 0.12 and 0.45, corresponding to approximately 3-5 copies of the locus, whereas gene amplification was defined as having a Log2 ratio 40.45, corresponding to more than five copies.…”

Targeting anthracyclines in early breast cancer: new candidate predictive biomarkers emerge

“…Owing to the high level of coordinated genetic aberrations within this region, it may prove challenging to pinpoint the gene(s) responsible for driving the response to chemotherapeutic agents. HER2 is the most recognized and studied gene within the region, with amplification of HER2 being associated with amplifications and deletions of neighbouring genes including GRB7, RARA, THRA1, CDC6 and TOP2A (Arriola et al, 2008). It has recently been shown that the patterns of coordinated genetic aberrations are inconsistent between HER2-amplified tumours (Arriola et al, 2008).…”

“…HER2 is the most recognized and studied gene within the region, with amplification of HER2 being associated with amplifications and deletions of neighbouring genes including GRB7, RARA, THRA1, CDC6 and TOP2A (Arriola et al, 2008). It has recently been shown that the patterns of coordinated genetic aberrations are inconsistent between HER2-amplified tumours (Arriola et al, 2008). However, Arriola et al (2008) only considered 19 HER2-amplified tumours and did not consider genetic alterations in HER2 non-amplified tumours.…”

“…It has recently been shown that the patterns of coordinated genetic aberrations are inconsistent between HER2-amplified tumours (Arriola et al, 2008). However, Arriola et al (2008) only considered 19 HER2-amplified tumours and did not consider genetic alterations in HER2 non-amplified tumours. Previous to the work by Arriola et al (2008), Orsetti et al (2004) assessed genomic gains and losses on chromosome 17 in 22 breast cancers irrespective of HER2 amplification status.…”

“…However, Arriola et al (2008) only considered 19 HER2-amplified tumours and did not consider genetic alterations in HER2 non-amplified tumours. Previous to the work by Arriola et al (2008), Orsetti et al (2004) assessed genomic gains and losses on chromosome 17 in 22 breast cancers irrespective of HER2 amplification status. Genomic gains and losses varied markedly between tumours with only 18% of tumours showing no genomic alterations.…”