Microarray-based comparative genomic hybridisation of breast cancer patients receiving neoadjuvant chemotherapy

Abstract

We analysed the molecular genetic profiles of breast cancer samples before and after neoadjuvant chemotherapy with combination doxorubicin and cyclophosphamide (AC). DNA was obtained from microdissected frozen breast core biopsies from 44 patients before chemotherapy. Additional samples were obtained before the second course of chemotherapy (D21) and after the completion of the treatment (surgical specimens) in 17 and 21 patients, respectively. Microarray-based comparative genome hybridisation was performed using a platform containing B5800 bacterial artificial chromosome clones (genome-wide resolution: 0.9 Mb). Analysis of the 44 pretreatment biopsies revealed that losses of 4p, 4q, 5q, 12q13.11 -12q13.12, 17p11.2 and 17q11.2; and gains of 1p, 2p, 7q, 9p, 11q, 19p and 19q were significantly associated with oestrogen receptor negativity. 16q21 -q22.1 losses were associated with lobular and 8q24 gains with ductal types. Losses of 5q33.3 -q4 and 18p11.31 and gains of 6p25.1 -p25.2 and Xp11.4 were associated with HER2 amplification. No correlations between DNA copy number changes and clinical response to AC were found. Microarray-based comparative genome hybridisation analysis of matched pretreatment and D21 biopsies failed to identify statistically significant differences, whereas a comparison between matched pretreatment and surgical samples revealed a statistically significant acquired copy number gain on 11p15.2 -11p15.5. The modest chemotherapy-driven genomic changes, despite profound loss of cell numbers, suggest that there is little therapeutic selection of resistant non-modal cell lineages.

Changes in allelic imbalances in locally advanced breast cancers after chemotherapy

“…The most likely explanation for our observations is chemotherapy-driven selection of tumour subclones: breast cancer tumour cells are well known to be highly heterogeneous (Shipitsin et al, 2007) and those already bearing genetic alterations may be more sensitive to chemotherapy and enter apoptosis more rapidly than unaltered cells. Another recent report also showed that such post-treatment changes do exist but, as in our study, seem to be rare (Pierga et al, 2007). Whether specific molecular abnormalities can facilitate or impede response to therapy is a crucial issue in oncology (Tanner et al, 2006).…”

“…Alkylating agents transfer alkyl groups to cellular constituents, inducing DNA adducts as well as DNA crosslinking that may lead to point mutations (Sanderson and Shield, 1996;Hunter et al, 2006). A recent study using microarray-based CGH on 21 breast tumours before and after epirubicin/cyclophosphamide chemotherapy showed a significant acquired copy number gain on 11p15.2 -11p15.5 after treatment (Pierga et al, 2007). In 30 patients with breast cancers treated with alkylating agents, microsatellite instability and LOH were found in peripheral blood mononuclear cells, respectively, in 27 and in 6 patients (Fonseca et al, 2005), illustrating how acute chemotherapy-induced DNA damage can also affect normal cells.…”

High rates of breast conservation for large ductal and lobular invasive carcinomas combining multimodality strategies

“…This result is therefore in agreement with the Nomograms's design proposed online, which does not take into account the histological type of the tumour when deciding on the therapeutic option (Rouzier et al, 2005b). There is room to better define biological predictive factors of response to neoadjuvant chemotherapy to screen patients who would benefit most from this therapeutic option (Sotiriou et al, 2002;Chang et al, 2005;Gianni et al, 2005;Rouzier et al, 2005a;Pierga et al, 2007). Lobular carcinomas had reduced clinical responses to neoadjuvant chemotherapy, while responses to breast-conserving treatments were fewer, although not significantly (54% (42 out of 78) vs 65% (434 out of 672); P ¼ 0.07).…”

A high-resolution integrated analysis of genetic and expression profiles of breast cancer cell lines

“…Thresholds for gain and loss in aCGH were estimated as previously described [17,18,21,22]. Smoothed log2 ratio values less than -0.08 were categorised as losses (i.e., heterozygous deletions), those greater than 0.08 as gains, and those in between as unchanged.…”

“…Thresholded data for each clone were also used for categorical analysis, using a Fisher's exact test adjusted for multiple testing using the stepdown permutation procedure maxT, thus providing strong control of the family-wise type I error rate (FWER) [17,18,21,22]. …”