In the current study, we used a genome-wide aCGH approach to profile CNAs from breast cancers for 259 young women from a previously reported population-based case-control study in Atlanta, GA [22
]. We identified characteristic CNAs associated with breast cancer subtypes (ER+/−, HER2+/−, TN) and found statistically significant differences in the average overall frequency of genome-wide CNAs in subtype comparisons, as well as frequency differences in CNAs occurring at specific genomic sites. We also observed differences in the frequency (>20%) and genomic locations of CNA events for TN tumors in AA and CA women.
Our results demonstrate that TN tumors had marked genomic instability with the highest average frequency of genome-wide CNAs compared to the other breast cancer subtypes. Chin et al. and Bergamaschi et al. also reported similar findings, with TN/basal tumors having the highest frequency of both copy number gains and losses compared to other subtypes [18
]. Fridlyand et al. observed a subset of ER- tumors associated with poor outcomes and extensive genomic instability, classifying this molecular subtype as the “complex” subtype. These “complex” tumors were found to have a high degree of similarity for CNA profiles when compared to BRCA1 hereditary tumors [20
]. We also observe our TN tumor samples to have CNAs in genomic regions that are characteristically altered in BRCA1 hereditary tumors specifically at 5q, 10p, 12p, 12q, and 20q [30
Copy number gain at 10p has been reported to be a distinguishing CNA for TN/basal tumors compared to other breast cancer subtypes [32
]. We observed a copy number gain in the region of 10p spanning 10p15-10p12 in our set of TN tumors. There are numerous genes spanning this region, with several confirmed to have increased protein expression associated with TN/basal tumors. Up-regulation of gene expression for several genes in this region (10p13), specifically, C10orf7, UPF2, HSPA14, RPP38 and CAMK1D has been confirmed to correlate with copy number gain [32
]. The region of 10p13 also contains the gene for vimentin (VIM) that has been associated with increased expression with TN/basal tumors and plays a role in the epithelial-mesenchymal transition [35
]. Although we do not present corresponding gene expression data for our samples, we see a significantly higher frequency of copy number gain at 10p13, corresponding to the genomic region containing the gene for VIM in TN tumors.
Amplification at 8q24 is common in breast cancer and has been previously observed in TN/basal and BRCA1 breast tumors and associated with poor outcomes [36
]. We observed a significant difference in the frequency of gain events in the genomic region (8q24) containing the C-MYC gene in ER-negative, primarily TN tumors, with >50% of the TN tumors compared to non-TN tumors (30%) having copy number gain in this region. We also compared the frequency of CNAs in TN tumors of AA and CA at 8q24, and observed a negligible CNA frequency difference between AA women (54%) and CA women (52%) for gains in this region, indicating that copy number gain in this region, containing the C-MYC, is not a distinguishing feature between tumors of AA and CA women.
There was twice the frequency of copy number gain in 13q31-13q34 for TN tumors for AA (20%) versus CA (9%) women. Amplification in the region of 13q31-13q34 has been previously reported to be associated with TN/basal tumors (20%) and BRCA1-associated breast tumors (8.1%) in a study reported by Melchor et al. [38
]. They identified two “driver” genes in 13q34 that facilitate tumor progression, cullin4A (CUL4A) and transcription factor Dp-1 (TFDP1). Both were demonstrated to have increased protein expression in tumors with amplification at 13q34. Both CUL4A and TFDP1 overexpression in breast cancers have been associated with shorter overall and disease-free survival [39
]. The study conducted by Melchor et al. included a total of 188 familial and 277 sporadic breast cancer samples, most of which came from cancer centers of predominantly Latino/Hispanic patients in Spain and Ecuador. Both AA and Hispanic women with TN/basal tumors have poorer outcomes compared to CA women [9
]. Additional studies are needed to evaluate events associated with amplification of 13q31-13q34 in relation to race and ethnicity and clinical outcome for AA, Latino/Hispanic, and Caucasian women.
ER-negative, specifically TN tumors, had a statistically significant differential frequency of copy number loss at 14q32.2 (p=0.001) when compared to the ER-positive and non-TN tumors, respectively and rarely occurred in HER2-positive tumors (5%) (). In addition, this CNA occurred more than twice as often in TN tumors of AA women compared to TN tumors of CA women (59% vs. 21%, respectively). The 14q32.2 region contains the gene for the microRNA, miR-342. MiR-342 has a critical role in proliferation, differentiation, development, and metabolism (reviewed in [42
]) and functions as a pro-apoptotic tumor suppressor in colon tumors [43
]. For breast cancer, a recent study demonstrated that miR-342 expression was highest in ER-positive and HER2-positive breast tumors and lowest in TN/basal tumors. This expression pattern is consistent with the CNA profiles they we found at 14q32.2 for the breast tumor subtypes, suggesting that copy number loss at 14q32.2 in TN tumors may lead to the downregulation of miR-342 expression, particularly in tumors of AA women.
Although the current literature has been inconsistent with respect to biological differences between tumors of AA and CA women, two recent reports support the hypothesis that biological differences exist and find that in women with breast tumors of similar ER status, AA women have poorer survival than CA women, even after adjustment for socioeconomic factors [44
]. In addition, a separate study showed that there are biological differences impacting angiogenesis, chemotaxis, and immunobiology pathways in breast tumors of AA and CA women based on the comparison of gene expression profiles of tumor and stromal tissue from breast tumors of these two racial populations [46
]. Our preliminary findings of differences in CNA frequencies in TN tumors from AA and CA women support the observations that there may be biological differences in the TN tumors. It is still unknown how these differences contribute to prognosis for AA and CA women.
One potential study limitation was selection bias in the array-tested samples. Therefore, we conducted a weighted analysis to address the issue of selection bias, but cannot be certain that this weighting completely addressed that issue. In addition, although there were limitations in the use of the moderate resolution BAC array for the identification of CNAs, we successfully demonstrated that we could confirm previously identified CNAs associated with specific breast cancer subtypes and identify additional novel CNAs not previously reported, particularly for the TN/basal subtype.
In this report we found characteristic genomic alterations associated with subtypes of breast cancer. The breast cancer samples included in this study were a part of a larger cohort of young women, and included the largest aCGH study on both breast tumors from young women and on number of TN tumors analyzed by aCGH. Further replication studies will need to be performed to confirm these findings. These results can be applied to future studies to increase our understanding of the biology of the different breast cancer subtypes, particularly TN tumors, and differences by race, ultimately leading towards the identification of improved targeted therapeutic strategies and breast cancer survival.