Germline polymorphisms in an enhancer of PSIP1 are associated with progression-free survival in epithelial ovarian cancer.
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ABSTRACT:
SUBMITTER: French JD
PROVIDER: S-EPMC4872719 | biostudies-literature | 2016 Feb
REPOSITORIES: biostudies-literature
Publications
Germline polymorphisms in an enhancer of PSIP1 are associated with progression-free survival in epithelial ovarian cancer.
French Juliet D JD Johnatty Sharon E SE Lu Yi Y Beesley Jonathan J Gao Bo B Kalimutho Murugan M Henderson Michelle J MJ Russell Amanda J AJ Kar Siddhartha S Chen Xiaoqing X Hillman Kristine M KM Kaufmann Susanne S Sivakumaran Haran H O'Reilly Martin M Wang Chen C Korbie Darren J DJ Lambrechts Diether D Despierre Evelyn E Van Nieuwenhuysen Els E Lambrechts Sandrina S Vergote Ignace I Karlan Beth B Lester Jenny J Orsulic Sandra S Walsh Christine C Fasching Peter A PA Beckmann Matthias W MW Ekici Arif B AB Hein Alexander A Matsuo Keitaro K Hosono Satoyo S Pisterer Jacobus J Hillemanns Peter P Nakanishi Toru T Yatabe Yasushi Y Goodman Marc T MT Lurie Galina G Matsuno Rayna K RK Thompson Pamela J PJ Pejovic Tanja T Bean Yukie Y Heitz Florian F Harter Philipp P du Bois Andreas A Schwaab Ira I Hogdall Estrid E Kjaer Susanne K SK Jensen Allan A Hogdall Claus C Lundvall Lene L Engelholm Svend Aage SA Brown Bob B Flanagan James M JM Metcalf Michelle D MD Siddiqui Nadeem N Sellers Thomas T Fridley Brooke B Cunningham Julie J Schildkraut Joellen M JM Iversen Ed E Weber Rachel Palmieri RP Brennan Donal D Berchuck Andrew A Pharoah Paul P Harnett Paul P Norris Murray D MD Haber Michelle M Goode Ellen L EL Lee Jason S JS Khanna Kum Kum KK Meyer Kerstin B KB Chenevix-Trench Georgia G deFazio Anna A Edwards Stacey L SL MacGregor Stuart S
Oncotarget 20160201 6
Women with epithelial ovarian cancer (EOC) are usually treated with platinum/taxane therapy after cytoreductive surgery but there is considerable inter-individual variation in response. To identify germline single-nucleotide polymorphisms (SNPs) that contribute to variations in individual responses to chemotherapy, we carried out a multi-phase genome-wide association study (GWAS) in 1,244 women diagnosed with serous EOC who were treated with the same first-line chemotherapy, carboplatin and pacl ...[more]
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Project description:BackgroundThe mechanisms of recurrence have been under-studied in rare histologies of invasive epithelial ovarian cancer (EOC) (endometrioid, clear cell, mucinous, and low-grade serous). We hypothesised the existence of an expression signature predictive of outcome in the rarer histologies.MethodsIn split discovery and validation analysis of 131 Mayo Clinic EOC cases, we used clustering to determine clinically relevant transcriptome classes using microarray gene expression measurements. The signature was validated in 967 EOC tumours (91 rare histological subtypes) with recurrence information.ResultsWe found two validated transcriptome classes associated with progression-free survival (PFS) in the Mayo Clinic EOC cases (P=8.24 × 10(-3)). This signature was further validated in the public expression data sets involving the rare EOC histologies, where these two classes were also predictive of PFS (P=1.43 × 10(-3)). In contrast, the signatures were not predictive of PFS in the high-grade serous EOC cases. Moreover, genes upregulated in Class-1 (with better outcome) were showed enrichment in steroid hormone biosynthesis (false discovery rate, FDR=0.005%) and WNT signalling pathway (FDR=1.46%); genes upregulated in Class-2 were enriched in cell cycle (FDR=0.86%) and toll-like receptor pathways (FDR=2.37%).ConclusionsThese findings provide important biological insights into the rarer EOC histologies that may aid in the development of targeted treatment options for the rarer histologies.
| S-EPMC4984456 | biostudies-literature
Project description:PurposeThis study was conducted to evaluate the prognostic significance of pre-treatment complete blood cell count (CBC), including white blood cell (WBC) differential, in epithelial ovarian cancer (EOC) patients with primary debulking surgery (PDS) and to develop nomograms for platinum sensitivity, progression-free survival (PFS), and overall survival (OS).Materials and methodsWe retrospectively reviewed the records of 757 patients with EOC whose primary treatment consisted of surgical debulking and chemotherapy at Samsung Medical Center from 2002 to 2012. We subsequently created nomograms for platinum sensitivity, 3-year PFS, and 5-year OS as prediction models for prognostic variables including age, stage, grade, cancer antigen 125 level, residual disease after PDS, and pre-treatment WBC differential counts. The models were then validated by 10-fold cross-validation (CV).ResultsIn addition to stage and residual disease after PDS, which are known predictors, lymphocyte and monocyte count were found to be significant prognostic factors for platinum-sensitivity, platelet count for PFS, and neutrophil count for OS on multivariate analysis. The area under the curves of platinum sensitivity, 3-year PFS, and 5-year OS calculated by the 10-fold CV procedure were 0.7405, 0.8159, and 0.815, respectively.ConclusionPrognostic factors including pre-treatment CBC were used to develop nomograms for platinum sensitivity, 3-year PFS, and 5-year OS of patients with EOC. These nomograms can be used to better estimate individual outcomes.
| S-EPMC5512372 | biostudies-literature
Project description:Previous studies have identified common germline variants nominally associated with breast cancer survival. These associations have not been widely replicated in further studies. The purpose of this study was to evaluate the association of previously reported SNPs with breast cancer-specific survival using data from a pooled analysis of eight breast cancer survival genome-wide association studies (GWAS) from the Breast Cancer Association Consortium.A literature review was conducted of all previously published associations between common germline variants and three survival outcomes: breast cancer-specific survival, overall survival and disease-free survival. All associations that reached the nominal significance level of P value <0.05 were included. Single nucleotide polymorphisms that had been previously reported as nominally associated with at least one survival outcome were evaluated in the pooled analysis of over 37,000 breast cancer cases for association with breast cancer-specific survival. Previous associations were evaluated using a one-sided test based on the reported direction of effect.Fifty-six variants from 45 previous publications were evaluated in the meta-analysis. Fifty-four of these were evaluated in the full set of 37,954 breast cancer cases with 2,900 events and the two additional variants were evaluated in a reduced sample size of 30,000 samples in order to ensure independence from the previously published studies. Five variants reached nominal significance (P <0.05) in the pooled GWAS data compared to 2.8 expected under the null hypothesis. Seven additional variants were associated (P <0.05) with ER-positive disease.Although no variants reached genome-wide significance (P <5 x 10(-8)), these results suggest that there is some evidence of association between candidate common germline variants and breast cancer prognosis. Larger studies from multinational collaborations are necessary to increase the power to detect associations, between common variants and prognosis, at more stringent significance levels.
| S-EPMC4484708 | biostudies-literature
Project description:Epithelial ovarian cancer (EOC) has an innate susceptibility to become chemoresistant. Up to 30% of patients do not respond to conventional chemotherapy [paclitaxel (Taxol®) in combination with carboplatin] and, of those who have an initial response, many patients relapse. Therefore, an understanding of the molecular mechanisms that regulate cellular chemotherapeutic responses in EOC cells has the potential to impact significantly on patient outcome. The mitotic arrest deficiency protein 2 (MAD2), is a centrally important mediator of the cellular response to paclitaxel. MAD2 immunohistochemical analysis was performed on 82 high-grade serous EOC samples. A multivariate Cox regression analysis of nuclear MAD2 IHC intensity adjusting for stage, tumour grade and optimum surgical debulking revealed that low MAD2 IHC staining intensity was significantly associated with reduced progression-free survival (PFS) (p = 0.0003), with a hazard ratio of 4.689. The in vitro analyses of five ovarian cancer cell lines demonstrated that cells with low MAD2 expression were less sensitive to paclitaxel. Furthermore, paclitaxel-induced activation of the spindle assembly checkpoint (SAC) and apoptotic cell death was abrogated in cells transfected with MAD2 siRNA. In silico analysis identified a miR-433 binding domain in the MAD2 3' UTR, which was verified in a series of experiments. Firstly, MAD2 protein expression levels were down-regulated in pre-miR-433 transfected A2780 cells. Secondly, pre-miR-433 suppressed the activity of a reporter construct containing the 3'-UTR of MAD2. Thirdly, blocking miR-433 binding to the MAD2 3' UTR protected MAD2 from miR-433 induced protein down-regulation. Importantly, reduced MAD2 protein expression in pre-miR-433-transfected A2780 cells rendered these cells less sensitive to paclitaxel. In conclusion, loss of MAD2 protein expression results in increased resistance to paclitaxel in EOC cells. Measuring MAD2 IHC staining intensity may predict paclitaxel responses in women presenting with high-grade serous EOC.
| S-EPMC3593171 | biostudies-literature
Project description:Objective(s)The Gynecologic Oncology Group (GOG) examined the association between ERBB2 amplification and clinical covariates, tumor response, disease status post-chemotherapy, progression-free survival (PFS), and overall survival (OS) in epithelial ovarian cancer (EOC).MethodsWomen with suboptimally-resected, advanced stage EOC who participated in GOG-111, a multi-center randomized phase III trial of cyclophosphamide+cisplatin versus paclitaxel+cisplatin, and provided a tumor block through the companion protocol GOG-9404 were eligible. ERBB2 amplification was examined using fluorescence in situ hybridization (FISH) with probes for ERBB2 and the centromere of chromosome 17 (CEP17).ResultsERBB2 amplification, defined as >2 copies of ERBB2/CEP17, was a rare event in EOC with 7% (9/133) of women exhibiting between 2.2 and 33.7 copies of ERBB2/CEP17, and was not associated with patient age, race, GOG performance status, stage, cell type, grade, measurable disease status, volume of ascites, tumor response or disease status post-chemotherapy. Women with >2 verses < or =2 copies of ERBB2/CEP17 did not have a reduced risk of disease progression (hazard ratio [HR]=0.56; 95% confidence interval [CI]=0.27-1.16; p=0.120) or death (HR=0.57; 95% CI=0.26-1.23; p=0.152), and ERBB2 amplification was not an independent prognostic factor for PFS or OS. ERBB2 amplification, defined as >4 copies of ERBB2/nuclei, was observed in 9% (12/133) of women with levels ranging from 4.2 to 49.2 copies of ERBB2/nuclei, and was associated with older age and volume of ascites, but not with the other clinical covariates or outcome.Conclusion(s)ERBB2 amplification is a rare event and has no predictive or prognostic value in suboptimally-resected, advanced stage EOC treated with platinum-based combination chemotherapy.
| S-EPMC6944288 | biostudies-literature
Project description:Purpose: The majority of patients with epithelial ovarian cancer (EOC) is diagnosed at advanced stage and has a poor prognosis. A proportion of these patients though will fare well, with a prognosis similar to patients with early stage disease while others die very quickly. Clinicopathological prognostic factors do not allow precise identification of these subgroups. Thus we have validated a molecular subclassification as prognostic factor in EOC. Experimental Design: One hundred ninety-four patients with EOC stage II to IV were characterized by whole-genome expression profiling of tumor tissues and classified using a published 112 gene-set, derived from a FIGO stage directed supervised classification approach. Results: The 194 tumor samples were classified into two subclasses of 95 (subclass 1) and 99 (subclass 2) tumors, grouping all 9 FIGO II tumors in subclass 1 (p=0.001). Subclass 2 (54% of advanced stage tumors) correlated significantly with peritoneal carcinomatosis and non-optimal debulking. Patients with subclass 2 tumors had a worse progression free survival (HR 1.67, p=0.005) by univariate analysis, but it was not an independent factor in multiple analysis. However, overall survival was impaired both, univariate (HR 3.68, p<0.001) and in models corrected for relevant clinicopathologic parameters (HR 3.13, p<0.001). Significance analysis of microarrays revealed 2,115 genes differentially expressed in both subclasses (FDR 5%). Conclusion: In this validation study we showed that in advanced-stage epithelial ovarian cancer two approximately equally large molecular subtypes exist, independent from classical clinocopathological parameters presenting with highly different whole genome expression profiles and an impressively different overall survival. Purpose: The majority of patients with epithelial ovarian cancer (EOC) is diagnosed at advanced stage and has a poor prognosis. A proportion of these patients though will fare well, with a prognosis similar to patients with early stage disease while others die very quickly. Clinicopathological prognostic factors do not allow precise identification of these subgroups. Thus we have validated a molecular subclassification as prognostic factor in EOC. Experimental Design: One hundred ninety-four patients with EOC stage II to IV were characterized by whole-genome expression profiling of tumor tissues and classified using a published 112 gene-set, derived from a FIGO stage directed supervised classification approach. Results: The 194 tumor samples were classified into two subclasses of 95 (subclass 1) and 99 (subclass 2) tumors, grouping all 9 FIGO II tumors in subclass 1 (p=0.001). Subclass 2 (54% of advanced stage tumors) correlated significantly with peritoneal carcinomatosis and non-optimal debulking. Patients with subclass 2 tumors had a worse progression free survival (HR 1.67, p=0.005) by univariate analysis, but it was not an independent factor in multiple analysis. However, overall survival was impaired both, univariate (HR 3.68, p<0.001) and in models corrected for relevant clinicopathologic parameters (HR 3.13, p<0.001). Significance analysis of microarrays revealed 2,115 genes differentially expressed in both subclasses (FDR 5%). Conclusion: In this validation study we showed that in advanced-stage epithelial ovarian cancer two approximately equally large molecular subtypes exist, independent from classical clinocopathological parameters presenting with highly different whole genome expression profiles and an impressively different overall survival. Targeted therapies in second line treatment gain more and more importance in managing recurrent or progressive carcinomas, particularly in ovarian cancer, a cancer entity characterized by a very high recurrence rate. One step ahead, it is necessary to define new therapeutic targets and to select patients who might benefit from these therapies already in first line settings. A robust molecular subclassification could provide both, an adequate patient selection and potential new targets. Notably, the validation of such a subclassification is of outstanding importance to obtain a reliable basis for a specific clinical decision and a rational for the expensive development of new targeted therapies. This work provides a comprehensive basis for both. The expression values of 204 epithelial ovarian cancer tissues are determined and used for the validation of a subclassification approach (Cancer Sci. 2009 Aug;100(8):1421-8.)
2014-01-01 | E-GEOD-49997 | biostudies-arrayexpress
Project description:OBJECTIVE:To investigate the association of tumor glucocorticoid receptor (GR) expression and patient outcome in ovarian cancer. METHODS:GR expression was evaluated by immunohistochemistry using tissue microarrays of specimens from 481 patients with ovarian cancer and 4 patients with benign conditions. Low GR expression was defined as an intensity of 0 or 1+ and high GR as 2+ or 3+ in >1% of tumor cells. Analyses were performed to evaluate the relationship of GR expression with clinical characteristics, progression-free survival (PFS) and overall survival (OS). RESULTS:GR protein was highly expressed in 133 of 341 (39.0%) tumors from patients who underwent upfront cytoreduction surgery followed by adjuvant chemotherapy. High GR expression was more common in serous tumors (p<0.001), high grade tumors (p<0.001), and advanced stage tumors (p=0.037). Median PFS was significantly decreased in cases with high GR (20.4months) compared to those with low GR (36.0months, HR=1.66, 95% CI 1.29-2.14, p<0.001). GR remained an independent prognostic factor for PFS in multivariate analysis. OS was not associated with GR status. CONCLUSIONS:These data suggest that high GR expression correlates with poor prognosis and support the hypothesis that modulating GR activity in combination with chemotherapy may improve outcomes.
| S-EPMC5955699 | biostudies-literature
Project description:PURPOSE:Wnt pathways control key biological processes that potentially impact on tumor progression and patient survival. We aimed to evaluate DNA methylation at promoter CpG islands (CGI) of Wnt pathway genes in ovarian tumors at presentation and identify biomarkers of patient progression-free survival (PFS). EXPERIMENTAL DESIGN:Epithelial ovarian tumors (screening study n = 120, validation study n = 61), prospectively collected through a cohort study, were analyzed by differential methylation hybridization at 302 loci spanning 189 promoter CGIs at 137 genes in Wnt pathways. The association of methylation and PFS was examined by Cox proportional hazards model. RESULTS:DNA methylation is associated with PFS at 20 of 302 loci (P < 0.05, n = 111), with 5 loci significant at false discovery rate (FDR) less than 10%. A total of 11 of 20 loci retain significance in an independent validation cohort (n = 48, P ? 0.05, FDR ? 10%), and 7 of these loci, at FZD4, DVL1, NFATC3, ROCK1, LRP5, AXIN1, and NKD1 genes, are independent from clinical parameters (adjusted P < 0.05). Increased methylation at these loci associates with increased hazard of disease progression. A multivariate Cox model incorporates only NKD1 and DVL1, identifying two groups differing in PFS [HR = 2.09; 95% CI (1.39-3.15); permutation test P < 0.005]. Methylation at DVL1 and NFATC3 show significant association with response. Consistent with their epigenetic regulation, reduced expression of FZD4, DVL1, and ROCK1 is an indicator of early-disease relapse in an independent ovarian tumor cohort (n = 311, adjusted P < 0.05). CONCLUSION:The data highlight the importance of epigenetic regulation of multiple promoter CGIs of Wnt pathway genes in ovarian cancer and identify methylation at NKD1 and DVL1 as independent predictors of PFS.
| S-EPMC3431504 | biostudies-literature
Project description:BackgroundTo date, no predictive or prognostic molecular biomarkers except BRCA mutations are clinically established for epithelial ovarian cancer (EOC) despite being the deadliest gynecological malignancy. Aim of this biomarker study was the analysis of DNA methylation biomarkers for their prognostic value independent from clinical variables in a heterogeneous cohort of 203 EOC patients from two university medical centers.ResultsThe marker combination CAMK2N1/RUNX3 exhibited a significant prognostic value for progression-free (PFS) and overall survival (OS) of sporadic platinum-sensitive EOC (n?=?188) both in univariate Kaplan-Meier (LogRank p?<?0.05) and multivariate Cox regression analysis (p?<?0.05; hazard ratio HR?=?1.587). KRT86 methylation showed a prognostic value only in univariate analysis because of an association with FIGO staging (Fisher's exact test p?<?0.01). Thus, it may represent a marker for EOC staging. Dichotomous prognostic values were observed for KATNAL2 methylation depending on BRCA aberrations. KATNAL2 methylation exhibited a negative prognostic value for PFS in sporadic EOC patients without BRCA1 methylation (HR 1.591, p?=?0.012) but positive prognostic value in sporadic EOC with BRCA1 methylation (HR 0.332, p?=?0.04) or BRCA-mutated EOC (HR 0.620, n.s.).ConclusionThe retrospective analysis of 188 sporadic platinum-sensitive EOC proved an independent prognostic value of the methylation marker combination CAMK2N1/RUNX3 for PFS and OS. If validated prospectively this combination may identify EOC patients with worse prognosis after standard therapy potentially benefiting from intensive follow-up, maintenance therapies or inclusion in therapeutic studies. The dichotomous prognostic value of KATNAL2 should be validated in larger sample sets of EOC.
| S-EPMC7824928 | biostudies-literature
Project description:Purpose: The majority of patients with epithelial ovarian cancer (EOC) is diagnosed at advanced stage and has a poor prognosis. A proportion of these patients though will fare well, with a prognosis similar to patients with early stage disease while others die very quickly. Clinicopathological prognostic factors do not allow precise identification of these subgroups. Thus we have validated a molecular subclassification as prognostic factor in EOC. Experimental Design: One hundred ninety-four patients with EOC stage II to IV were characterized by whole-genome expression profiling of tumor tissues and classified using a published 112 gene-set, derived from a FIGO stage directed supervised classification approach. Results: The 194 tumor samples were classified into two subclasses of 95 (subclass 1) and 99 (subclass 2) tumors, grouping all 9 FIGO II tumors in subclass 1 (p=0.001). Subclass 2 (54% of advanced stage tumors) correlated significantly with peritoneal carcinomatosis and non-optimal debulking. Patients with subclass 2 tumors had a worse progression free survival (HR 1.67, p=0.005) by univariate analysis, but it was not an independent factor in multiple analysis. However, overall survival was impaired both, univariate (HR 3.68, p<0.001) and in models corrected for relevant clinicopathologic parameters (HR 3.13, p<0.001). Significance analysis of microarrays revealed 2,115 genes differentially expressed in both subclasses (FDR 5%). Conclusion: In this validation study we showed that in advanced-stage epithelial ovarian cancer two approximately equally large molecular subtypes exist, independent from classical clinocopathological parameters presenting with highly different whole genome expression profiles and an impressively different overall survival. Purpose: The majority of patients with epithelial ovarian cancer (EOC) is diagnosed at advanced stage and has a poor prognosis. A proportion of these patients though will fare well, with a prognosis similar to patients with early stage disease while others die very quickly. Clinicopathological prognostic factors do not allow precise identification of these subgroups. Thus we have validated a molecular subclassification as prognostic factor in EOC. Experimental Design: One hundred ninety-four patients with EOC stage II to IV were characterized by whole-genome expression profiling of tumor tissues and classified using a published 112 gene-set, derived from a FIGO stage directed supervised classification approach. Results: The 194 tumor samples were classified into two subclasses of 95 (subclass 1) and 99 (subclass 2) tumors, grouping all 9 FIGO II tumors in subclass 1 (p=0.001). Subclass 2 (54% of advanced stage tumors) correlated significantly with peritoneal carcinomatosis and non-optimal debulking. Patients with subclass 2 tumors had a worse progression free survival (HR 1.67, p=0.005) by univariate analysis, but it was not an independent factor in multiple analysis. However, overall survival was impaired both, univariate (HR 3.68, p<0.001) and in models corrected for relevant clinicopathologic parameters (HR 3.13, p<0.001). Significance analysis of microarrays revealed 2,115 genes differentially expressed in both subclasses (FDR 5%). Conclusion: In this validation study we showed that in advanced-stage epithelial ovarian cancer two approximately equally large molecular subtypes exist, independent from classical clinocopathological parameters presenting with highly different whole genome expression profiles and an impressively different overall survival. Targeted therapies in second line treatment gain more and more importance in managing recurrent or progressive carcinomas, particularly in ovarian cancer, a cancer entity characterized by a very high recurrence rate. One step ahead, it is necessary to define new therapeutic targets and to select patients who might benefit from these therapies already in first line settings. A robust molecular subclassification could provide both, an adequate patient selection and potential new targets. Notably, the validation of such a subclassification is of outstanding importance to obtain a reliable basis for a specific clinical decision and a rational for the expensive development of new targeted therapies. This work provides a comprehensive basis for both.
2014-01-01 | GSE49997 | GEO