Genomic alterations in sporadic synchronous primary breast cancer using array and metaphase comparative genomic hybridization

Abstract

Synchronous primary breast cancer describes the occurrence of multiple tumors affecting one or both breasts at initial diagnosis. This provides a unique opportunity to identify tissue-specific genomic markers that characterize each tumor while controlling for the individual genetic background of a patient. The aim of this study was to examine the genomic alterations and degree of similarity between synchronous cancers. Using metaphase comparative genomic hybridization and array comparative genomic hybridization (aCGH), the genomic alterations of 23 synchronous breast cancers from 10 patients were examined at both chromosomal and gene levels. Synchronous breast cancers, when compared to their matched counterparts, were found to have a common core set of genetic alterations, with additional unique changes present in each. They also frequently exhibited features distinct from the more usual solitary primary breast cancers. The most frequent genomic alterations included chromosomal gains of 1q, 3p, 4q, and 8q, and losses of 11q, 12q, 16q, and 17p. aCGH identified copy number amplification in regions that are present in all 23 tumor samples, including 1p31.3-1p32.3 harboring JAK1. Our findings suggest that synchronous primary breast cancers represent a unique type of breast cancer and, at least in some instances, one tumor may give rise to the other.

Figure 1

Frequency graph of aberrations in 15 cases of synchronous breast cancer obtained by mCGH. The green marks on the right side of the chromosome ideograms indicate the frequency of chromosomal gains, and the red marks on the left show the frequency of losses. The cutoff values for chromosomal gain and losses were 1.2 and 08, respectively. The graph was created with the Progenetix software [21].

Figure 2

Comparison of mCGH profiles of synchronous tumors in patient 1 with four synchronous breast tumors. Tumors P₁T₁ and P₁T₂ show no gain on 1q, whereas tumors 3 and 4 are similar in showing gains on chromosome 1q. Tumors P₁T₁ and P₁T₂ have high gains of 8q, whereas tumors P₁T₃ and P₁T₄ show normal profiles for chromosome 8. Chromosome 13 in tumor 4 shows a low-level gain in the q region. Although tumors P₁T₁, P₁T₂, and P₁T₃ have not been (marked to have) scored as having this chromosomal gain, this region in these cases has “spikes” just below the threshold, suggesting a possible gradual increase in chromosomal instability in this region. For each profile, the black vertical line on the middle represents a ratio of 1.0; the red line on the left represents a ratio of 0.8; and the green line on the right represents a ratio of 1.2. Alterations to the right represent chromosomal gains, and alterations to the left are chromosomal losses. Gains and deletions are marked next to chromosome ideograms as green and red bars, respectively.

Figure 3

Comparison of aCGH profiles of synchronous tumors from patient 9. Profiles of P₉T₁ (green) and P₉T₂ (red) were generated by Normalise Suite software and superimposed to facilitate comparison. Note the dissimilar regions in chromosomes 6, 8, 9, 12, 17, and 20 (arrows). For each profile, the vertical line on the middle represents a ratio of 1.0. By convention, alterations to the right are copy number amplifications, and alterations to the left are copy number deletions. Thresholds are marked on the graph (top) and indicate 3 SD from the mean. Yellow dotted lines are data points.

Figure 4

Cluster analysis of array data showing the relative relationship between synchronous breast cancer tumors. Tumor samples with a high degree of similarity are connected to the tree by very short branches. Tumors with decreased similarity are joined by increasingly longer branches. Tumors in patient 8 (P₈T₁ and P₈T₂) and patient 3 (P₃T₁ and P₃T₂) show the greatest degree of similarity to their synchronous counterparts. In patient 6, only tumors P₆T₁ and P₆T₂ are clustered closely, whereas P₆T₃ is only distantly related. Tumors P₁T₃ and P₁T₄ (left breast) from patient 1 also clustered closely but separated from P₁T₁ and P₁T₂ (right breast). Note that not all tumors are matched to their synchronous counterparts. The clustering map was created with Eisen cluster.

Figure 5

Shown is a schematic model used to explain the genomic relationships of synchronous breast cancers arising from a common progenitor. In the first model, the progenitor breast cancer cell 1 (left) contains the “core” genomic information, and genomic divergence during tumor growth leads to synchronous tumors possessing related genomic signatures (shown as a different gray tone). The expansion of clones from this common progenitor, through either selection of the microenvironment or karyotypic viability, results in clones that will accumulate unique genomic changes. The second model implicates the presence of a progenitor breast cancer cell 2 shown in gray, also possessing the “core” genomic information for breast cancers. Collectively, it can be seen that tumors (1 and 2) can evolve independently from the progenitor cell with no common lineage, but may possess common changes.