DNA copy number changes detected by comparative genomic hybridization and their association with clinicopathologic parameters in breast tumors

https://doi.org/10.1016/S0165-4608(03)00094-3Get rights and content

Abstract

The purpose of this study was to use comparative genomic hybridization (CGH) to screen breast tumors for copy number changes: 22 ductal, 9 lobular, 7 mixed, 2 micropapillary carcinomas, and 2 ductal carcinoma in situ were studied and various regional genomic imbalances were detected. The majority of the aberrations identified in this study were in line with previous CGH findings. The most frequent DNA sequence copy number changes were 1q, 8q, and 20q gains. The frequency of 16q losses was significantly higher in lobular carcinomas. The nodal involvement was 10 times higher in cases showing losses of 13q than in cases having normal peak profile at this region. Estrogen receptor positivity was significantly higher in cases displaying 20q gains and 16q losses. Unambiguous high-level DNA amplifications have also been detected. These mapped to 4q31, 6q21∼q22, 8q21∼q24, 8p11.2∼p12, 11q13, 15q24∼qter, 20q13.1∼qter, and 20q12∼qter chromosomal locations. Our results highlight several chromosomal regions that may be important in the molecular genetics of distinct clinicopathologic breast cancer subgroups.

Introduction

Various cytogenetic changes are associated with tumor genesis and progression. Although breast cancer is the most common cancer in females worldwide, its cytogenetic features and the role of particular chromosomal changes in tumor progression and clinical outcome are not yet well established. The main obstacle is that it is hard to identify clonal cytogenetic aberrations via conventional techniques because of the complexity of genetic changes. Standard karyotype analyses have revealed extreme genetic heterogeneity of breast cancer, and various karyotypic subgroups have been identified [1], [2]. Because of the intratumoral heterogeneity of the chromosomal changes within tumor samples, it can be difficult to estimate selective advantage of individual changes and interpret their significance in tumor genesis by karyotyping. Only a limited number of dividing cells can be investigated by conventional chromosomal studies, and the detected mainline might not represent the overall tumor cell population. Although allelotyping is an alternative to karyotyping to define regional genomic alterations in breast tumors, analysis with all known markers is extremely labor intensive. Besides, the nature of the genetic events characterized by allelotyping may be ambiguous; allelic imbalances can represent either a gain or a loss [3].

Regional DNA copy number changes caused by aneuploidy and unbalanced structural aberrations predominantly represented in tumor cell population, as well as amplifications affecting certain chromosomal regions, can be detected by comparative genomic hybridization (CGH). A molecular cytogenetic technique [4], CGH has been applied to a number of breast cancer studies [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15]. Investigations of breast tumors have used CGH to characterize primary breast tumors [5], [6], [7], [11], [13], preinvasive intraductal carcinomas [8], [10], and infiltrating lobular carcinomas [16] and to compare primary tumors and their metastases [9], [17]. These studies revealed genomic imbalances involving chromosomal regions with DNA copy number gains on 1q, 6p, 8q, 11q, 12q, 17q, and 20q and losses on 6q, 12q, 13q, and 17p. Although some of the findings are discordant, the prognostic correlations of certain regions targeted to genomic imbalances and their relation to histologic subgroups have been found. Additional CGH findings are needed to establish unambiguous correlations to further define the prognostic significance of already defined genomic regions and to identify new chromosomal loci involved in the pathogenesis of breast cancer. In this study, 42 breast tumors were screened by CGH to identify commonly involved DNA copy number changes and their associations with clinicopathologic parameters.

Section snippets

Tumor specimens

Forty-two primary breast tumor cases diagnosed at Dokuz Eylül Medical School Hospital during 1997–2000 were included in this study. Clinicopathologic descriptions of the tumors studied are summarized in Table 1. After surgical removal, tumor tissues were immediately stored at −80°C until DNA isolation. The mean age of the patients was 52 years (range: 32–80). None of the patients received therapy prior to specimen collection. Twenty-seven tumors were node positive, 15 node negative.

Results

DNA copy number changes were detected in 37 of 42 (88%) of cases. The chromosomal localization of DNA sequence copy number changes in all tumors are given in Table 2. An example of the green-to-red CGH ratio peak profile pertaining to case 39 is shown in Fig. 1. The total number of regional DNA imbalances per tumor showed variation from case to case. A summary of the genomic imbalances detected in the 37 tumor samples is depicted in the ideogram in Fig. 2. Case 51 displayed maximum copy number

Discussion

Despite a wide spectrum of genetic changes underlying the development and progression of breast cancer identified by cytogenetic studies and molecular methods, the karyotypic features of breast cancer and their association with the clinical course remain poorly understood. When available for analyses with various conventional and molecular cytogenetic methods, breast carcinoma cells display complex and heterogeneous chromosomal changes, as is often the case with other types of carcinomas. It

Acknowledgements

This study was sponsored by Dokuz Eylül University Research Fund, project no. 0923.99.01.03 (to O.A.).

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