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In order to obtain a comprehensive DNA methylation signature of HER2-positive breast cancer (HER2+ breast cancer), we performed a genome-wide methylation analysis on 17 HER2+ breast cancer and compared with ten normal breast tissue samples using the Illumina Infinium HumanMethylation450 BeadChip (450K). In HER2+ breast cancer, we found altered DNA methylation in genes involved in multicellular development, differentiation and transcription. Within these genes, we observed an overrepresentation of homeobox family genes, including several genes that have not been previously reported in relation to cancer (DBX1, NKX2–6, SIX6). Other affected genes included several belonging to the PI3K and Wnt signaling pathways. Notably, HER2, AKT3, HK1, and PFKP, genes for which altered methylation has not been previously reported, were also identified in this analysis. In total, we report 69 candidate biomarker genes with maximum differential methylation in HER2+ breast cancer. External validation of gene expression in a selected group of these genes (n = 13) revealed lowered mean gene expression in HER2+ breast cancer. We analyzed DNA methylation in six top candidate genes (AKR1B1, INA, FOXC2, NEUROD1, CDKL2, IRF4) using EpiTect Methyl II Custom PCR Array and confirmed the 450K array findings. Future clinical studies focusing on these genes, as well as on homeobox-containing genes and HER2, AKT3, HK1, and PFKP,are warranted which could provide further insights into the biology of HER2+ breast cancer.

Solute carrier family 25A member 43 (SLC25A43) gene is a putative tumor suppressor gene that undergoes loss of heterozygosity (LOH) in human epidermal growth factor receptor 2 (HER2) positive breast cancer. Also, knockdown of SLC25A43in cell lines influences cell turnover and metabolism. Absence of mutations in this gene in breast cancers prompted us to study methylation as an alternate mechanism for gene inactivation of this X encoded gene. Quantification of CpG site methylation using pyrosequencing was performed upstream of the SLC25A43gene and at its 5′ end in a cohort of breast tumor tissues (n = 80, HER2 positive or negative) with different SLC25A43gene deletion status. Compared with control tissue, cancer tissues had lower levels of methylation at the 5′ and 3′ shores of the gene. Cancer tissues with no deletion in the SLC25A43gene (Del -)had higher methylation in the CpG island (CGI) of the gene than cancers carrying the deletion (Del+). Methylation in the CGI of the SLC25A43gene was negatively correlated with age at diagnosis. In HER2 positive breast cancer, ER negativity and lymph node positivity was associated with higher methylation in the CGI and in the adjacent shores of this gene. Our results suggest that methylation in the CGI of the SLC25A43gene could be an alternate mechanism of gene silencing in the absence of LOH. Also, associations between site-specific methylation and clinicopathological parameters suggest that epigenetic changes in SLC25A43gene could be of importance in breast carcinogenesis.

Tamoxifen therapy reduces the risk of recurrence and prolongs the survival of oestrogen-receptor-positive patients with breast cancer. Even if most patients benefit from tamoxifen, many breast tumours either fail to respond or become resistant. Because tamoxifen is extensively metabolised by polymorphic enzymes, one proposed mechanism underlying the resistance is altered metabolism. In the present study we investigated the prognostic and/or predictive value of functional polymorphisms in cytochrome P450 3A5 CYP3A5 (*3), CYP2D6 (*4), sulphotransferase 1A1 (SULT1A1; *2) and UDP-glucuronosyltransferase 2B15 (UGT2B15; *2) in tamoxifen-treated patients with breast cancer. In all, 677 tamoxifen-treated postmenopausal patients with breast cancer, of whom 238 were randomised to either 2 or 5 years of tamoxifen, were genotyped by using PCR with restriction fragment length polymorphism or PCR with denaturing high-performance liquid chromatography. The prognostic evaluation performed in the total population revealed a significantly better disease-free survival in patients homozygous for CYP2D6*4. For CYP3A5, SULT1A1and UGT2B15no prognostic significance was observed. In the randomised group we found that for CYP3A5, homozygous carriers of the *3allele tended to have an increased risk of recurrence when treated for 2 years with tamoxifen, although this was not statistically significant (hazard ratio (HR) = 2.84, 95% confidence interval (CI) = 0.68 to 11.99, P= 0.15). In the group randomised to 5 years' tamoxifen the survival pattern shifted towards a significantly improved recurrence-free survival (RFS) among CYP3A5*3-homozygous patients (HR = 0.20, 95% CI = 0.07 to 0.55, P= 0.002). No reliable differences could be seen between treatment duration and the genotypes of CYP2D6, SULT1A1or UGT2B15. The significantly improved RFS with prolonged tamoxifen treatment in CYP3A5*3homozygotes was also seen in a multivariate Cox model (HR = 0.13, CI = 0.02 to 0.86, P= 0.03), whereas no differences could be seen for CYP2D6, SULT1A1and UGT2B15. The metabolism of tamoxifen is complex and the mechanisms responsible for the resistance are unlikely to be explained by a single polymorphism; instead it is a combination of several mechanisms. However, the present data suggest that genetic variation in CYP3A5may predict response to tamoxifen therapy.

Adjuvant therapy of breast cancer patients reduces the risk of recurrence and mortality, although, a substantial proportion of patients acquire resistance and relapse in the disease. Predictors of therapeutic response are therefore important to avoid both therapy resistance and the side effects of inefficient regimes. The p53 protein is a key determinant to induce either growth arrest or apoptosis in response to cytotoxic stress.

Tamoxifen is widely used as endocrine therapy for oestrogen-receptor-positive breast cancer. However, many of these patients experience recurrence despite tamoxifen therapy by incompletely understood mechanisms. In the present report we propose that tamoxifen resistance may be due to differences in activity of metabolic enzymes as a result of genetic polymorphism. Cytochrome P450 2D6 (CYP2D6) and sulfotransferase 1A1 (SULT1A1) are polymorphic and are involved in the metabolism of tamoxifen. The CYP2D6*4and SULT1A1*2genotypes result in decreased enzyme activity. We therefore investigated the genotypes of CYP2D6and SULT1A1in 226 breast cancer patients participating in a trial of adjuvant tamoxifen treatment in order to validate the benefit from the therapy. The patients were genotyped using PCR followed by cleavage with restriction enzymes. Carriers of the CYP2D6*4allele demonstrated a decreased risk of recurrence when treated with tamoxifen (relative risk = 0.28, 95% confidence interval = 0.11–0.74, P= 0.0089). A similar pattern was seen among the SULT1A1*1homozygotes (relative risk = 0.48, 95% confidence interval = 0.21–1.12, P= 0.074). The combination of CYP2D6*4and/or SULT1A1*1/*1genotypes comprised 60% of the patients and showed a 62% decreased risk of distant recurrence with tamoxifen (relative risk = 0.38, 95% confidence interval = 0.19–0.74, P= 0.0041). The present study suggests that genotype of metabolic enzymes might be useful as a guide for adjuvant endocrine treatment of postmenopausal breast cancer patients. However, results are in contradiction to prior hypotheses and the present sample size is relatively small. Findings therefore need to be confirmed in a larger cohort.

Frequent allelic deletions at chromosome 11q24-q25 have been described in both early and late onset breast cancers, suggesting the existence of a gene locus implicated in the initiation and/or progression of the disease. In the present study we fine mapped this region further by loss of heterozygosity (LOH) analysis in a population of early onset breast cancer cases (n = 102, 22 to 36 years old). Loss of chromosomal material was assessed for possible association with patient survival as well as Nottingham histologic grade (NHG). Additionally, we investigated the involvement of the 11q24-q25 locus in a group of familial breast cancer cases with no detectable BRCA1 or BRCA2 gene alterations (n = 32, ages 28 to 40 years). Among the consecutive patients, extensive LOH was observed for all markers at 11q24-q25, with frequencies ranging from 42% to 54%. Deletion at the D11S4125 marker was found to be associated with reduced survival (p = 0.026), whereas the adjacent D11S387 marker correlated with higher histologic grade (p = 0.042). In the familial cases, the most telomeric markers showed substantially lower proportions of LOH, ranging from 10% to 21%. Comparison of the two patient groups demonstrated that this difference in LOH frequency was statistically significant for the D11S4098, D11S968, D11S387 and D11S4125 markers (p = 0.020, p = 0.029, p = 0.0070 and p = 0.0030, respectively). We conclude that 11q25 may harbor a gene implicated in early onset breast cancer. Our data suggest that the most probable position for this locus is defined by the markers D11S387 and D11S4125 and furthermore that it may play a less significant role in familial breast cancer cases not linked to either of the BRCA genes. © 2001 Wiley-Liss, Inc.

Young breast cancer patients have a decreased survival rate and it has been demonstrated that young age is an independent predictor of adverse prognosis. Overexpression of c-erbB-2 protein (also known as HER-2/neu) has been shown to be a prognostic indicator in breast cancer in general and especially among patients with axillary nodal metastases. The present study was initiated to determine the prognostic significance of c-erbB-2 protein overexpression in early onset breast cancer. A population consisting of 110 young breast cancer patients, ≤ 36-year-old at diagnosis, was analyzed with immunohistochemical staining for c-erbB-2 protein. Thirty patients (27%) were found to overexpress the c-erbB-2 protein. C-erbB-2 positivity was significantly associated with poor survival when all patients were included in the analysis (P= 0.002) and for patients with axillary nodal metastases (P= 0.0007). No such association was found for node-negative patients. Furthermore, the difference in prognosis in relation to c-erbB-2among node-positive patients was maintained, when these were stratified in groups treated or not treated with adjuvant chemotherapy. The study indicates that overexpression of c-erbB-2 protein is a strong prognostic factor in young breast cancer patients with axillary nodal metastases. Moreover, the adverse prognosis associated with c-erbB-2overexpression in node-positive patients was observed whether or not the patients had received adjuvant chemotherapy.

Long-term exposure to oestrogens is a well-recognised risk factor for breast cancer, whereas little is known about the influence of polymorphisms of genes involved in oestrogen biosynthesis and metabolism. A candidate, containing a single bp polymorphism, T→C, (designated, A2 allele), might be the CYP17 gene, which codes for an enzyme involved in oestrogen synthesis. This polymorphism creates an additional Sp1-type promoter site (CCACC box), which has been shown to be associated with increased serum oestrogen levels. We performed a case-control study, to evaluate association of the CYP17 gene polymorphism with risk of breast cancer in young women (younger than 37 years). We found a statistically significant increased risk in carriers of at least 1 A2 allele [odds ratio (OR), 2.0; 95% confidence interval (CI), 1.1–3.5, p = 0.027], and a trend toward a gene-dose effect illustrated by a slightly higher risk for A2-homozygous subjects (OR, 2.8) than for heterozygous women (OR, 1.9). Furthermore, when we investigated the CYP17 genotype in relation to tumour characteristics, breast cancer patients with 1 or 2 A2 alleles tended to have lower oestrogen receptor levels (risk ratio, 0.70; CI, 0.41–1.2, p = 0.44). Our findings suggest that CYP17 gene polymorphism influences breast carcinogenesis in young women. Int. J. Cancer (Pred. Oncol.) 84:350–353, 1999. © 1999 Wiley-Liss, Inc.

Estimation of S-phase fraction in breast carcinomas with single parameter flow cytometry may include errors due to dilution of cancer cells by host cells. Use of tissue specific markers may to some extent correct for the effect of dilution. S-phase fraction was estimated by flow cytometry with and without immunoselection in 80 DNA-euploid breast carcinomas in stage I-II. The tumor tissue was mechanically disintegrated and fixed in ethanol. A primary antibody, specific for cytokeratins 8 and 18, was added before incubation with the secondary FITC-conjugated antibody. S-phase fraction was calculated for both the gated (cytokeratin-positive) and the ungated cell population. An increasing proportion of tetraploid cells compared to diploid cells was found when the immunoselection method was used. The gated population tended to have a higher S-phase fraction than the ungated population. In univariate analysis S-phase fraction estimated from both ungated and gated cell populations yielded significant information for predicting recurrence when stratified for tumor size and nodal status. In bivariate analysis S-phase fraction of the gated population contributed prognostic information in addition to S-phase fraction of the ungated population when both variables were included in the analysis. Our conclusion is that S-phase fraction calculated from cytokeratin-positive cells provides prognostic information in addition to ungated S-phase values in DNA euploid breast carcinomas.

Flow cytometry was performed on frozen specimens from the primary tumour of 184 women with recurrent breast cancer. No significant association was seen between DNA ploidy and the other prognostic factors investigated. Patients with a high S-phase fraction had more often a negative estrogen receptor (ER) status and a short disease-free interval. A shorter survival after disease recurrence was seen both in patients with DNA aneuploid tumours and among those with a high S-phase fraction. Patients with DNA tetraploid tumours showed the longest survival after recurrence. In this subgroup, half of the patients survived more than 3 years after recurrence and the estimated survival rate at 10 years was 17%. In a Cox's regression analysis including 116 patients, site of recurrence, number of positive nodes at time of primary operation, size and ER content of the primary tumour as well as DNA ploidy showed additional prognostic value.

To evaluate the degree of intratumoral DNA ploidy heterogeneity in endometrial carcinoma, the authors examined curettage specimens from 30 patients with clinical stage I and II endometrial carcinoma. The curettage material was obtained before the onset of treatment. A representative sample from each tumour was chosen and a 50 urn section was cut. The paraffin block of tumor was then divided into 4 equal parts and a 50 urn section was cut from each part. All tumour samples were analysed separately by flow cytometry. DNA ploidy heterogeneity was noted in 5/29 cases (17%). In three cases DNA-aneuploid stem cell lines were found only among the 4-part sections and were not detected when the whole tumor section was analysed.

Functional p53 protein is essential for the cellular response to drug-induced DNA damage. We investigated p53 accumulation in tumour specimens from premenopausal breast cancer patients who were randomised to adjuvant chemotherapy (CMF) or postoperative radiotherapy. Of the tumours from 139 patients, 20 showed abnormal accumulation as judged with immunohistochemistry (>10% positive tumour cells). The risk of distant recurrence was similar in the two treatment groups for patients whose primary tumours lacked p53 accumulation, whereas there was a significant benefit from CMF for patients showing abnormal accumulation (relative risk 0.18, 95% CI, 0.04-0.93). This result suggests that p53-dependent apoptosis is not a general mechanism by which breast cancer cells respond during CMF chemotherapy.

Eighty-five male breast carcinomas limited to the breast, diagnosed between 1958 and 1967 in Sweden, were investigated by flow cytometry using paraffin-embedded tissue. DNA ploidy and S-phase fraction (SPF) were studied in relation to lymph node status, tumour size and malignancy grade, and with respect to clinical outcome. Median age at diagnosis was 65.5 years. Median survival time related to breast cancer was 78.7 months, and 37 patients died from the disease. Forty-nine (57.6%) carcinomas were aneuploid or had multiple stemlines. Median SPF was 8.9% for all tumours, for diploid and tetraploid (diploid) together 6.6%, and for aneuploid tumours 14.3% (p < 0.001). Ploidy was significantly related to the tumour size (p = 0.03), but no significant correlations with node status or malignancy grade were observed. In univariate survival analysis, node status, tumour size and malignancy grade predicted breast cancer mortality significantly. In a multivariate Cox's model, only node status and tumour size were independent prognostic factors. In contrast to females with breast cancer, ploidy and SPF had no significant relation to prognosis in males. This lack of predictive value of DNA analysis needs further evaluation. Studies based on extended materials are necessary to further investigate the role of DNA analysis as a predictor of outcome in male breast cancer patients.