Most types of cancer cells are characterized by aberrant methylation of promoter genes. In this study, we described a rapid, reproducible, and relatively inexpensive approach allowing the detection of multiple human methylated promoter genes from many tissue samples, without the need of bisulfite conversion. The Methylation Ligation-dependent Macroarray (MLM), an array-based analysis, was designed in order to measure methylation levels of 58 genes previously described as putative biomarkers of cancer. The performance of the design was proven by screening the methylation profile of DNA from esophageal cell lines, as well as microdissected formalin-fixed and paraffin-embedded (FFPE) tissues from esophageal adenocarcinoma (EAC). Using the MLM approach, we identified 32 (55%) hypermethylated promoters in EAC, and not or rarely methylated in normal tissues. Among them, 21promoters were found aberrantly methylated in more than half of tumors. Moreover, seven of them (ADAMTS18, APC, DKK2, FOXL2, GPX3, TIMP3 and WIF1) were found aberrantly methylated in all or almost all the tumor samples, suggesting an important role for these genes in EAC. In addition, dysregulation of the Wnt pathway with hypermethylation of several Wnt antagonist genes was frequently observed. MLM revealed a homogeneous pattern of methylation for a majority of tumors which were associated with an advanced stage at presentation and a poor prognosis. Interestingly, the few tumors presenting less methylation changes had a lower pathological stage. In conclusion, this study demonstrated the feasibility and accuracy of MLM for DNA methylation profiling of FFPE tissue samples.

Aberrant methylation of multiple promoter CpG islands could be related to the biology of ovarian tumors and its determination could help to improve treatment strategies. DNA methylation profiling was performed using the Methylation Ligation-dependent Macroarray (MLM), an array-based analysis. Promoter regions of 41 genes were analyzed in 102 ovarian tumors and 17 normal ovarian samples. An average of 29% of hypermethylated promoter genes was observed in normal ovarian tissues. This percentage increased slightly in serous, endometrioid, and mucinous carcinomas (32%, 34%, and 45%, respectively), but decreased in germ cell tumors (20%). Ovarian tumors had methylation profiles that were more heterogeneous than other epithelial cancers. Unsupervised hierarchical clustering identified four groups that are very close to the histological subtypes of ovarian tumors. Aberrant methylation of three genes (BRCA1, MGMT, and MLH1), playing important roles in the different DNA repair mechanisms, were dependent on the tumor subtype and represent powerful biomarkers for precision therapy. Furthermore, a promising relationship between hypermethylation of MGMT, OSMR, ESR1, and FOXL2 and overall survival was observed. Our study of DNA methylation profiling indicates that the different histotypes of ovarian cancer should be treated as separate diseases both clinically and in research for the development of targeted therapies.

Abstract. TBX15 is a gene involved in the development of mesodermal derivatives. As the ovaries and the female reproductive system are of mesodermal origin, the aim of the present study was to determine the methylation status of the TBX15 gene promoter and the expression levels of TBX15 in ovarian carcinoma, which is the most lethal and aggressive type of gynecological tumor, in order to determine the role of TBX15 in the pathogenesis of ovarian carcinoma. This alteration could be used to predict tumor development, progression, recurrence and therapeutic effects. The study was conducted on 80 epithelial ovarian carcinoma and 17 control cases (normal ovarian and tubal tissues). TBX15 promoter methylation was first determined by pyrosequencing following bisulfite modification, then by cloning and sequencing, in order to obtain information about the epigenetic haplotype. Immunohistochemical analysis was performed to evaluate the correlation between the methylation and protein expression levels. Data revealed a statistically significant increase of the TBX15 promoter region methylation in 82% of the tumor samples and in various histological subtypes. Immunohistochemistry showed an inverse correlation between methylation levels and the expression of the TBX15 protein. Furthermore, numerous tumor samples displayed varying degrees of intratumor heterogeneity. Thus, the present study determined that ovarian carcinoma typically expresses low levels of TBX15 protein, predominantly due to an epigenetic mechanism. This may have a role in the pathogenesis of ovarian carcinoma independent of the histological subtype. IntroductionOvarian cancer is the fourth most common type of cancer in the female genital tract, but has the highest mortality rate of all gynecological tumors. Ovarian carcinoma accounts for >90% of cases of ovarian cancer and may arise from relatively pluripotent cells of the coelomic epithelium or 'modified mesothelium' that covers the ovary (1). The coelomic epithelium is the mesodermal-derived epithelial lining of the intraembryonic coelom that invaginates to give rise to the mülllerian ducts, the primordia for the epithelia of the fallopian tube, the endometrium and the endocervix (1). There is now compelling evidence that certain carcinomas can also originate from the fallopian tubes and the endometriosis (1,2). Ovarian carcinoma are a heterogeneous group of neoplasms that exhibit a wide range of tumor morphologies and clinical manifestations (2). According to the World Health Organization classification, the most common tumor subtypes are serous, endometrioid and mucinous, and are characterized by their morphological resemblance to various mucosal tissues of the female reproductive tract (3). Cytogenetic and molecular analysis indicates that multiple genetic and epigenetic changes are involved in the pathogenesis of ovarian carcinoma (2,4); however, it remains unclear how these alterations lead to the development of ovarian cancer. Better understanding of the molecular mechanisms responsible for the diffe...

Abstract. [-2]pro-prostate-specific antigen (2pPSA), a proform of PSA, is a new marker in patients at risk of prostate cancer. We explored the potential role of 2pPSA in the identification of patients with metastatic progression following radical prostatectomy for prostate cancer. Seventy-six patients with biochemical (PSA) recurrence following radical prostatectomy were studied retrospectively. Diagnostic imaging performed at the time of biochemical recurrence confirmed metastatic disease in 31 of the 76 patients. Serum samples were collected and stored at the time of imaging-confirmed metastatic progression or at the most recent procedure for patients with negative imaging. Median values of PSA, free PSA (fPSA), %fPSA, 2pPSA and prostate health index (PHI) were compared between metastatic and non-metastatic patients by the Mann-Whitney U test. The results of each test were then correlated with metastatic status by univariate and multivariate logistic regression analysis. PSA, fPSA, %fPSA, 2pPSA serum concentrations and PHI values were statistically significantly higher in patients with metastatic disease. Results of the multivariate analysis revealed that 2pPSA remained a statistically significant predictor of imaging-proven metastatic prostate cancer among patients with biochemical recurrence. At a cut-off value of 12.25 pg/ml, 2pPSA outperformed the other markers in terms of sensitivity and specificity (97 and 80%, respectively) with respect to imaging-confirmed metastatic progression. This is the first study suggesting that 2pPSA predicts diagnostic imaging-proven metastatic disease in previously resected prostate cancer patients with biochemical recurrence. Our results merit validation in a prospective study.

Background: Ovarian cancer is the gynecological disease with the highest death rate. Efforts towards ovarian cancer research are needed to develop early detection tools, better therapies, cures and to prevent the disease. DNA methylation profiling of a large set of putative cancer biomarkers may help to identify relevant biological aspects of ovarian cancer. Materials and Methods: We selected 106 patients diagnosed for ovarian cancer (35 serous, 30 endometrioid, 32 mucinous and 8 germinal tumors) for which clinicopathological informations were available and 17 histologically normal ovarian tissues as control. In order to identify methylation signatures, a method called Methylation Ligation-dependant Macroarray (MLM) and developed in our laboratory was applied to DNA extracted from microdissected formalin-fixed and paraffin-embedded tissue sections. The MLM technology, derived from a multiplex ligation assay coupled with an array-based analysis of uniform size amplification products, permits the methylation status analysis of 60 promoter regions at the same time. Results: Each of the 106 ovarian tumor samples analyzed had a unique methylation profile. Hierarchical clustering identified mainly two groups of patients with distinct methylation profiles. The first group of tumors contained low levels of methylation, whereas the second group had higher methylation levels. The group 1 included normal ovarian tissues as well as a large number of ovarian serous tumors. Endometrioid and mucinous tumors were more represented in the group 2. When looking at the gene level, the highest methylation frequency was detected in the TAC1, SPARC, ADAMTS12 and hTERT promoter genes. The promoter of the BORIS/CTCFL cancer testis-antigen gene was found hypomethylated in several tumors, mainly in serous and germinal types. Located in the X-chromosome, the DAX1 promoter gene, which is partially methylated in normal ovarian tissues, was found hypomethylated or hypermethylated in tumors. Interestingly, the difference between the hypo- and hyper-methylated groups concerned mainly genes belonging to the WNT pathway. Conclusion: The marked differences in methylation profiles independently of histological subtypes underscore the importance of characterizing tumors at the molecular level. Further investigations are needed to evaluate the role of the WNT signaling pathway as a marker and putative target for cisplatin chemosensitivity in ovarian tumors. Citation Format: Sonia T. Chelbi, Lorena Losi, Sara Saponaro, Patricia Martin, Richard Braunschweig, Jean Benhattar. DNA methylation profiling of ovarian tumors by methylation ligation-dependant macroarray. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4254. doi:10.1158/1538-7445.AM2013-4254