Frequent genetic differences between matched primary and metastatic breast cancer provide an approach to identification of biomarkers for disease progression

Abstract

Breast cancer is a major cause of morbidity and mortality in women and its metastatic spread is the principal reason behind the fatal outcome. Metastasis-related research of breast cancer is however underdeveloped when compared with the abundant literature on primary tumors. We applied an unexplored approach comparing at high resolution the genomic profiles of primary tumors and synchronous axillary lymph node metastases from 13 patients with breast cancer. Overall, primary tumors displayed 20% higher number of aberrations than metastases. In all but two patients, we detected in total 157 statistically significant differences between primary lesions and matched metastases. We further observed differences that can be linked to metastatic disease and there was also an overlapping pattern of changes between different patients. Many of the differences described here have been previously linked to poor patient survival, suggesting that this is a viable approach toward finding biomarkers for disease progression and definition of new targets useful for development of anticancer drugs. Frequent genetic differences between primary tumors and metastases in breast cancer also question, at least to some extent, the role of primary tumors as a surrogate subject of study for the systemic disease.

Figure 1

The examples of four classes of global genome CNV pattern comparing matched primary tumor and metastasis of patients 67, 23, 26 and 127 affected by breast cancer. The panel for each case represents a summary of four hybridizations using the 32K BAC array: two for primary tumor DNA and two for metastases. Each hybridization of cancer-derived DNA was carried out against DNA from peripheral blood of a normal healthy female control. Red and blue dots represent data from the merging of two hybridizations for metastasis and primary tumor, respectively. The X-axis denotes chromosome mapping and the Y-axis represents a straight fluorescent ratio from hybridization of tumor-derived DNA against a normal female control. The ‘no. spots' value represents the sum of array features from merged duplicate hybridizations that passed the quality control criteria for scoring. Only spots that had a standard deviation of ⩽15% of ratios in regular and dye-swap hybridizations were subject to further statistical analysis (see Materials and Methods)., On the basis of statistically significant differences in the level of changes between profiles of primary tumors and metastases, a combination of bioinformatics and statistical tools resulted in the division of array-CGH profiles into four classes. For a detailed definition of the four classes, see Results. In panel displaying case ID 23, an enlarged view of chromosome 1 is shown with a reversed order of color layers for red (metastasis) and blue (primary tumor).

Figure 2

Two high-resolution images of the amplicon from 11q13.1–11q14.1 (64.47–78.3 Mb) in four patients. In two of these (IDs 22 and 67), the profiles of primary tumor (blue dots) and metastasis are highly correlated. In two cases (IDs 23 and 140), these amplicons are pronounced in metastases. The X-axis describes the position on chromosome 11 and the Y-axis represents a straight fluorescent ratio from hybridization of tumor-derived DNA against a normal female control. For example, a straight fluorescent ratio of five corresponds to ∼10 DNA copies at a given locus. The ‘no. spots' value represents the sum of the displayed array features from merged duplicate hybridizations that passed the quality control criteria for scoring.