Abstract

TP53-mutated breast carcinomas are associated with specific array comparative hybridization (aCGH) patterns involving deletions of 3p, 4p, 4q and 5q.

HKM Vollan1, 2) , A Langerød1) , EU Due1) , R Kåresen2) , E Schlichting2) , A-L Børresen-Dale1) .

1) Dept of Genetics, Institute for Cancer Research, Norwegian Radium Hospital, Rikshospitalet University Hospital, Oslo, Norway.
2) Dept of Breast and Endocrine Surgery, Ullevål University Hospital, Oslo, Norway

The TP53 tumor suppressor protein acts as a major defense against cancer. Among its most distinctive features is the ability to elicit both apoptotic death and cell cycle arrest. TP53 plays a key role in mediating cell response to various stresses: one of these is DNA-repair. When TP53 is mutated the maintenance of DNA integrity may be reduced, resulting in copy number alterations (CNA) in the tumor. Aneuploidy is an important feature of cancer cells, and specific CNAs have shown to be of both prognostic and predictive value. Most of these alterations can be detected by use of array Comparative Genomic Hybridization (aCGH). The aim of this study was to investigate the CNAs in breast tumors, with a high resolution platform, in relation to TP53 mutation status.

Tumor tissues from a series of 212 primary breast cancer cases were sequentially collected at Ullevål University Hospital between 1990 and 94. Tissues were sampled at the time of primary surgery and snap frozen. TP53 mutation data from previous sequence analyses were available for 203 of the samples. We performed aCGH on 167 of these tumors. DNA was isolated using chloroform/phenol extraction, followed by ethanol precipitation. The aCGH-platform was the Agilent Human-Genome-CGH Microarray 244k. For detection of aberrations we used ACE (analysis of copy errors) and PCF (piecewise constant fit), both implemented in the CGH-explorer software. For visualization we used the software Nexus 2.0. Significance Analysis for Microarray (SAM) was performed using the R/BioConductor package “samr”.

Many significant genetic alterations were found, with a large heterogeneity between the different tumors. The most frequently observed alterations were amplification of 1q, 8q, 16 p and 17q and deletion of 1p, 8p, 16q and 17p. When grouping the tumors by TP53 mutation status we found a significant difference in the CNA patterns between TP53 mutated vs. none-mutated tumors. Overall the mutated group had more aberrations than the wild type group, and interestingly the aberrations were not evenly distributed along the genome, suggesting that some chromosomal areas are more prone to instability or selected for in the presence of a mutated TP53 protein. The most frequent losses associated with TP53 mutation status were regions on 3p, 4p, 4q, 5q and 8p, whereas significant gains were observed for 8q and 10p. A detailed structure of the CNAs and the involved genes will be presented in relation to type of mutations and to various clinical data.