A rapid and accurate closed-tube Methylation-Sensitive High Resolution Melting Analysis assay for the semi-quantitative determination of SOX17 promoter methylation in clinical samples.

INTRODUCTION: SOX17 promoter methylation can provide important prognostic information in cancer. We developed a novel semi-quantitative MS-HRMA assay for SOX17 promoter methylation. METHODS: The assay was optimized by using synthetic control samples and validated by analyzing 165 clinical samples: a) 107 formalin fixed paraffin embedded (FFPEs) samples of patients with early breast cancer, b) 27 FFPE samples of patients with metastatic breast cancer, c) 15 reduction mammoplasty specimens obtained from healthy women and d) 16 genomic DNA samples isolated from healthy blood donors. Comparison with real time MSP was also performed. RESULTS: The assay is highly specific and sensitive and provides a semi-quantitative estimation of SOX17 promoter methylation. SOX17 promoter was found methylated in 96/134 (71.6%) breast cancer samples, while none of the 31 non-cancerous samples tested was positive (0%). SOX17 promoter methylation levels varied significantly among samples. When 165 clinical samples were analyzed both by MS-HRMA and real time MSP results were significantly comparable (concordance: 146/165, 88.5%). CONCLUSIONS: This novel MS-HRMA assay for SOX17 promoter methylation is closed-tube, highly sensitive, specific, cost-effective, rapid and easy-to-perform. It gives comparable results to Real-Time MSP in less time, while it offers the advantage of additionally providing an estimation of SOX17 promoter methylation levels.

PIK3CA mutational status in circulating tumor cells can change during disease recurrence or progression in patients with breast cancer.

PURPOSE: Molecular characterization of circulating tumor cells (CTC) is crucial for the investigation of molecular-targeted therapies while PIK3CA somatic mutations play a crucial role in therapy response. We investigated the presence of PIK3CA mutations in CTC and whether this is associated with clinical outcome. EXPERIMENTAL DESIGN: We developed and validated an ultrasensitive methodology for the detection of PIK3CA mutations that is based on a combination of allele-specific, asymmetric rapid PCR and melting analysis. We analyzed PIK3CA hotspot mutations in: (i) a training group consisting of EpCAM-positive CTC fraction from 37 patients with clinically confirmed metastasis, and 26 healthy female volunteers and 15 primary breast tumor tissues and (ii) an independent group consisting of EpCAM-positive CTC fraction from 57 metastatic and 118 operable breast cancer patients and 76 corresponding primary tumors. RESULTS: The assay could detect 0.05% of mutated dsDNA in the presence of 99.95% wtDNA for both exons (9 and 20) and was highly specific (0/26 healthy donors). PIK3CA mutations were identified in EpCAM-positive CTC in 20 of 57(35.1%) and in 23 of 118 (19.5%) patients with metastatic and operable breast cancer, and in 45 of 76(59.2%) corresponding FFPEs. Our data indicate that PIK3CA mutational status in CTCs can change during disease progression and is associated with worse survival (P = 0.047). CONCLUSIONS: PIK3CA hotspot mutations are present at a relatively high frequency in CTCs and their presence is associated with worse survival in patients with breast cancer with metastasis. Evaluation of PIK3CA mutational status in CTCs is a strategy with potential clinical application.

Metadherin, p50, and p65 expression in epithelial ovarian neoplasms: an immunohistochemical study.

NF-κB signaling promotes cancer progression in a large number of malignancies. Metadherin, a coactivator of the NF-κB transcription complex, was recently identified to regulate different signaling pathways that are closely related to cancer. We assessed the immunohistochemical expression of p50, p65, and metadherin in 30 ovarian carcinomas, 15 borderline ovarian tumours, and 31 benign ovarian cystadenomas. Ovarian carcinomas exhibited significantly higher expression of all 3 markers compared to benign ovarian tumours. Borderline ovarian tumours demonstrated significantly higher expression for all 3 markers compared to benign cystadenomas. Ovarian carcinomas demonstrated significantly higher expression of p50 and metadherin compared to borderline ovarian tumours, whereas no significant difference was noted in p65 expression between ovarian carcinomas and borderline ovarian tumours. There was a strong correlation with the expression levels of p50, p65, and metadherin, whereas no correlation was observed with either grade or stage. Strong p50, p65, and metadherin expression was associated with a high probability to distinguish ovarian carcinomas over borderline and benign ovarian tumours, as well as borderline ovarian tumours over benign ovarian neoplasms. A gradual increase in the expression of these molecules is noted when moving across the spectrum of ovarian carcinogenesis, from borderline ovarian tumours to epithelial carcinomas.

Numerical aberrations of chromosomes 1 and 7 by fluorescent in situ hybridization and DNA ploidy analysis in breast cancer.

The goals of this study were to detect the numerical alterations of chromosomes 1 and 7 in breast cancer and to correlate the findings with DNA ploidy status as well as with parameters of prognostic significance. Fluorescence in situ hybridization (FISH) with centromeric probes for chromosomes 1 and 7 and cellular DNA content measurement by image analysis-based cytophotometry were applied on interface nuclei from fresh tissue imprints of 59 breast ductal carcinomas. Immunohistochemical stainings for estrogen receptor (ER), progesterone receptor (PR), HER-2, p53, and Ki67 were performed on paraffin tumor sections. The correlation between DNA ploidy and chromosomal aberrations revealed a significant association between aneuploidy and aneusomy for both chromosomes 1 (p=0.002) and 7 (p=0.00001), however, a number of diploid tumors were found to be aneusomic, especially for chromosome 1. Chromosome 7 polysomy was significantly associated with a higher incidence of axillary lymph node metastasis (p=0.05), poorly differentiated (grade III) tumors (p=0.03), negative ER and PR status (p=0.02 and 0.001, respectively), as well as p53 protein expression (p=0.05) and a higher Ki67 labeling index (p=0.004). Chromosome 1 aneusomy was only related with HER-2 protein overexpression (p=0.05). No association between chromosome alterations and tumor size was detected. In conclusion, the results of our study indicate that the detection of numerical aberrations of chromosomes 1 and 7 by FISH seems to be more sensitive than DNA ploidy status for the evaluation of abnormal cellular DNA and chromosome 7 aneusomy characterizes tumors with aggressive features and therefore might be a useful predictor of unfavorable biological behavior in breast cancer.

Evaluation of HER2 gene status in breast cancer by chromogenic in situ hybridization: comparison with immunohistochemistry.

BACKGROUND: The purpose of this study was to evaluate HER2 gene status in relation to chromosome 17 polysomy with the chromogenic in situ hybridization (CISH) technique and to compare the results with those of immunohistochemistry (IHC). METHODS AND RESULTS: Sixty six cases of breast carcinoma with an immunohistochemical HER2 protein score of 1+, 2+ 3+ (HercepTest) were investigated. HER2 gene status was evaluated on paraffin sections with the CISH technique using a digoxigenin-labeled DNA probe. In HER2 positive cases with low level amplification (LLA), the copy number of chromosome 17 was determined. Thirty four tumors (51.5%) were negative and 32 (48.5%) were positive for HER2 gene amplification. Of these 10 tumors (15%) showed LLA and 22 tumors (33.5%) high level amplification (HLA). Nine of ten tumors with LLA had an equal or greater than two ratio of HER2 to chromosome 17 signals. The correlation of the results obtained by CISH and IHC showed that the concordance of the two methods was highest in the 3+ group (100%) and lower in 1+ group (89%), whereas a high degree of discordance was found in the 2+ group (69%). CONCLUSIONS: CISH is an accurate and practical technique for the evaluation of both HER2 gene and chromosome 17 status and its application is considered necessary especially for the clarification of the 2+ results of IHC.

Immunohistochemical profile of cystosarcoma phyllodes of the breast: a study of 23 cases.

Cystosarcoma phyllodes (CP) of the breast is a rare biphasic tumor composed of benign epithelium and a spindle cell stroma. Biologic behavior of CP cannot be predicted with certainty on the basis of morphologic criteria only. We studied immunohistochemical expression of basic fibroblastic growth factor (bFGF), urokinase, Ki67, p53 protein, and microvessel density in stromal and epithelial components of 14 low-grade CP (LCP) and 9 high-grade CP (HCP). bFGF was more often positive in LCP than in HCP. The stroma was positive for bFGF in 86% of LCP and 67% of HCP, and the epithelium was positive in 64% of LCP and 14% of HCP. Urokinase was positive in stromal cells of 86% of LCP and 93% of HCP. The epithelial positivity for urokinase in both groups resembled closely that of the stroma. p53 protein was more often positive in stromal cells of HCP (67%) than in LCP (50%). Ki67 was positive in the stroma of 43% of LCP and 89% of HCP and in the epithelium of 14% of LCP and 33% of HCP. There was no significant difference in microvessel density (MVD) in low- and high-grade lesions. Our study demonstrates that stromal Ki67 and p53 immunohistochemical positivity are more often associated with high-grade tumors. The positive immunostaining for bFGF, urokinase, Ki67, and p53 in stroma and epithelium of the majority of CP supports the existence of epithelial-stromal interactions and recognizes epithelium as an integral part of this tumor.