Low-risk susceptibility alleles in 40 human breast cancer cell lines

Background: Low-risk breast cancer susceptibility alleles or SNPs confer only modest breast cancer risks ranging from just over 1.0 to 1.3 fold. Yet, they are common among most populations and therefore are involved in the development of essentially all breast cancers. The mechanism by which the low-risk SNPs confer breast cancer risks is currently unclear. The breast cancer association consortium BCAC has hypothesized that the low-risk SNPs modulate expression levels of nearby located genes. Methods: Genotypes of five low-risk SNPs were determined for 40 human breast cancer cell lines, by direct sequencing of PCR-amplified genomic templates. We have analyzed expression of the four genes that are located nearby the low-risk SNPs, by using real-time RT-PCR and Human Exon microarrays. Results: The SNP genotypes and additional phenotypic data on the breast cancer cell lines are presented. We did not detect any effect of the SNP genotypes on expression levels of the nearby-located genes MAP3K1, FGFR2, TNRC9 and LSP1. Conclusion: The SNP genotypes provide a base line for functional studies in a well-characterized cohort of 40 human breast cancer cell lines. Our expression analyses suggest that a putative disease mechanism through gene expression modulation is not operative in breast cancer cell lines

Promoter hypermethylation and BRCA1 inactivation in sporadic breast and ovarian tumors

Background: Inherited mutations in the BRCA1 gene may be responsible for al-most half of inherited breast carcino-mas. However, somatic (acquired) mu-tations in BRCA1 have not been reported, despite frequent loss of het-erozygosity (LOH or loss of one copy of the gene) at the BRCA1 locus and loss of BRCA1 protein in tumors. To ad-dress whether BRCA1 may be inacti-vated by pathways other than muta-tions in sporadic tumors, we analyzed the role of hypermethylation of the gene’s promoter region. Methods: Methylation patterns in the BRCA1 promoter were assessed in breast can-cer cell lines, xenografts, and 215 pri-mary breast and ovarian carcinomas by methylation-specific polymerase chain reaction (PCR). BRCA1 RNA ex-pression was determined in cell lines and seven xenografts by reverse tran-scription–PCR. P values are two-sided. Results: The BRCA1 promoter was found to be unmethylated in all normal tissues and cancer cell lines tested. However, BRCA1 promoter hyper-methylation was present in two breast cancer xenografts, both of which had loss of the BRCA1 transcript. BRCA1 promoter hypermethylation was pres-ent in 11 (13%) of 84 unselected pri-mary breast carcinomas. BRCA1 meth-ylation was strikingly associated with the medullary (67 % methylated; P =.0002 versus ductal) and mucinous (55 % methylated; P =.0033 versus duc-tal) subtypes, which are overrepre-sented in BRCA1 families. In a second series of 66 ductal breast tumors infor-mative for LOH, nine (20%) of 45 tu-mors with LOH had BRCA1 hyper-methylation, while one (5%) of 21 without LOH was methylated (P =.15). In ovarian neoplasms, BRCA1 methyl-ation was found only in tumors with LOH, four (31%) of 13 versus none of 18 without LOH (P =.02). The BRCA1 promoter was unmethylated in other tumor types. Conclusion: Silencing of the BRCA1 gene by promoter hyper-methylation occurs in primary breast and ovarian carcinomas, especially in the presence of LOH and in specific histopathologic subgroups. These find-ings support a role for this tumor sup-pressor gene in sporadic breast and ovarian tumorigenesis. [J Natl Cance