Breast carcinomas are characterized by DNA copy number alterations (CNAs) with biological and clinical significance. This explorative study integrated CNA, expression, and germline genotype data of 112 early-stage breast cancer patients. Recurrent CNAs differed substantially between tumor subtypes classified according to expression pattern. Deletion of 16q was overrepresented in Luminal A, and a predictor of good prognosis, both overall and for the nonluminal A subgroups. The deleted region most significantly associated with survival mapped to 16q22.2, harboring the genes TXNL4B and DXH38, whose expression was strongly correlated with the deletion. The area most frequently deleted resided on 16q23.1, 3.5 MB downstream of the area most significantly associated with survival, and included the tumor suppressor gene ADAMTS18 and the cell recognition gene CNTNAP4. Whole-genome association analysis identified germline single nucleotide polymorphisms (SNPs) and their corresponding haplotypes, residing on several different chromosomes, to be associated with deletion of 16q. The genes where these SNPs reside encode proteins involved in the extracellular matrix (CHST3 and SPOCK2), in regulation of the cell cycle (JMY, PTPRN2, and Cwf19L2) and chromosome stability (KPNB1).

The CpG island spanning the transcription start of the glutathione S-transferase P1 becomes methylated in a variety of human cancers including breast cancer. To study the effect of sequence variation on hypermethylation of the GSTP1 promoter, we analyzed the genetic and epigenetic variability in 90 tumors from patients with locally advanced breast cancer. High-resolution quantitative analysis revealed large variability in the DNA methylation levels. Lack of methylation was more often observed in the basal and normal-like estrogen receptor (ER)-negative tumors, and methylated GSTP1 was associated with better overall survival (P = 0.00063). Studies of the genetic variation identified 14 different haplotypes. The distribution of methylation levels of tumors homozygous for the most frequent haplotype was significantly different from other haplotype combinations (P = 0.011), the difference being more pronounced in ER-positive (P = 0.005) and progesterone receptor-positive (P = 0.008) tumors. Regression modeling identified the ER status and haplotype as the main determinants of DNA methylation variability. We identified a putative c-Myb response element (MRE) that was present in one of two minimal promoter haplotypes. In vitro analysis showed that c-Myb binds to the MRE, but binding was weakened by the two polymorphisms. Transient cotransfections in luminal-type and basal-like breast cancer cell lines confirmed cell-specific differential binding of c-Myb to the polymorphic sites, leading to a change in the expression from the GSTP1 promoter in vivo. GSTP1 expression was moderately but significantly (P = 0.01) reduced after siRNA-mediated knockdown of c-Myb. Our results indicate that haplotype structure of a promoter is important for the extent of DNA methylation. [Cancer Res 2008;68(14):5562-71]

Background: Microarray Comparative Genomic Hybridization (array CGH) provides a means to examine DNA copy number aberrations. Various platforms, brands and underlying technologies are available, facing the user with many choices regarding platform sensitivity and number, localization, and density distribution of probes.

Recently, genome-wide association studies of breast cancer revealed single nucleotide polymorphisms (SNPs) in five genes with novel association to susceptibility. While there is little doubt that the novel susceptibility markers produced from such highly powered studies are true, the mechanisms by which they cause the susceptibility remain undetermined. We have looked at the expression levels of the identified genes in tumours and found that they are highly significantly differentially expressed between the five established breast cancer subtypes. Also, a significant association between SNPs in these genes and their expression in tumours was seen as well as a significantly different frequency of the SNPs between the subtypes. This suggests that the observed genes are associated with different breast cancer subtypes, and may exert their effect through their expression in the tumours. Thus, future studies stratifying patients by their molecular subtypes may give much more power to classic case control studies, and genes of no or borderline significance may appear to be high-penetrant for certain subtypes and, therefore, be identifiable.A genome-wide association study of breast cancer has revealed single nucleotide polymorphisms (SNPs) in five genes with novel association to susceptibility: TNRC9, FGFR2, MAP3K1, H19 and LSP1 [1]. The results were confirmed for FGFR2 and TNRC9 in two independent studies [2,3]. However, these studies revealed little of the mechanisms underlying these associations. Pooling of such a large amount of cases, as performed in these studies, inevitably leads to concealment of the various histological and clinico-pathological subtypes. This suggests that the observed genes are either of universal importance for breast cancer development, are associated with a subgroup that dominates the overall pool or are associated with any subgroup but with an association sufficiently strong to dominate the overall result. Breast cancer patients can be divided into five distinct molecular subtypes based on their expression profiles [4]. The existence of these five subtypes, luminal A, luminal B, basal-like, ErbB2 + , and normal-like, have been confirmed in independent datasets [5] and they are associated with different clinical outcomes [6]. If the probability to develop a given subtype of breast cancer is genetically determined, we might expect to find that the newly discovered susceptibility genes [1] are differentially expressed in the various tumour subtypes, and that their transcription is regulated in cis by SNPs within them. With this in mind, we retrieved the mRNA expression data of TNRC9, FGFR2, MAP3K1, H19 and LSP1 from 112 breast tumours representing all five subtypes [7]. Significantly different mRNA levels between the subtypes were found for all the five genes by ANOVA analysis (Table 1). For instance, TNRC9 was up-regulated in luminal A, luminal B and ErbB2 + subtypes and down-regulated in the basal-like subtype (p = 4.5 × 10 -7 ). FGFR2 was up-regulated in luminal A and basal-like s...