Subtypes Of Serous Ovarian Cancer Research Articles

Outcome and prognostic factors of low‑grade serous ovarian cancer: An observational retrospective study.

Low-grade serous ovarian cancer (LGSOC) is a very rare histological subtype of serous ovarian cancer, representing ~2% of all epithelial ovarian cancer cases. LGSOC has a better prognosis but a lower response rate to chemotherapy in comparison to high-grade serous ovarian carcinoma (HGSOC). The present study is a retrospective review of the medical records of all patients with histologically proven LGSOC diagnosed and treated in a single institute between January 2003 and December 2019. A total of 23 patients diagnosed with LGSOC and treated at King Faisal Specialist Hospital and Research Center (Riyadh, Saudi Arabia) were identified. The median age at diagnosis was 45.5 years (range, 26-66 years) and the median body mass index was 26.1 (range, 18-43). A total of 21 patients (91.3%) had de novo LGSOC, whereas only 2 patients (8.7%) had LGSOC that had transformed from serous borderline ovarian tumors and recurred. A total of 8 patients (34.8%) were diagnosed with International Federation of Gynecology and Obstetrics stage IV, whereas 3 (13.0%), 3 (13.0%) and 9 (39.1%) were diagnosed with stages I, II and III, respectively. In addition, 10 (43.5%), 5 (21.7%), and 3 (13.0%) patients had complete response, stable disease and partial response statuses after first-line therapy, respectively. At a median follow-up time of 34 months [95% confidence interval (CI), 25.32-42.69], the median progression-free survival (PFS) time was 75.2 months (95% CI, 17.35-133.05) and the median overall survival (OS) time was not reached. In conclusion, LGSOC exhibited better PFS and OS times than HGSOC as compared with data from the literature, and there is the option for systemic treatment (chemotherapy or hormonal therapy). Optimal cytoreduction showed numerically higher, but non-significant, PFS and OS times compared with suboptimal debulking; however, the optimal systemic chemotherapy or hormonal treatment remains controversial.

Multi-omics-based analysis of high grade serous ovarian cancer subtypes reveals distinct molecular processes linked to patient prognosis.

Despite advancements in treatment, high-grade serous ovarian cancer (HGSOC) is still characterized by poor patient outcomes. To understand the molecular heterogeneity of this disease, which underlies the challenge in selecting optimal treatments for HGSOC patients, we have integrated genomic, transcriptomic, and epigenetic information to identify seven new HGSOC subtypes using a multiscale clustering method. These subtypes not only have significantly distinct overall survival, but also exhibit unique patterns of gene expression, microRNA expression, DNA methylation, and copy number alterations. As determined by our analysis, patients with similar clinical outcomes have distinct profiles of activated or repressed cellular processes, including cell cycle, epithelial-to-mesenchymal transition, immune activation, interferon response, and cilium organization. Furthermore, we performed a multiscale gene co-expression network analysis to identify subtype-specific key regulators and predicted optimal targeted therapies based on subtype-specific gene expression. In summary, this study provides new insights into the cellular heterogeneity of the HGSOC genomic, epigenetic, and transcriptomic landscapes and provides a basis for future studies into precision medicine for HGSOC patients.

Abstract 5202: AMG 794, a Claudin 6-targeted half-life extended (HLE) bispecific T cell engager (BITE®) molecule for non-small cell lung cancer and epithelial ovarian cancer

Abstract AMG 794 is a half-life extended BiTE® immune therapy targeting the oncofetal antigen Claudin 6 (CLDN6). AMG 794 redirects T cells to kill CLDN6-expressing tumor cells and is being developed for the treatment of non-small cell lung cancer (NSCLC) and epithelial ovarian cancer (EOC). CLDN6 is a compelling tumor antigen that is expressed during embryonic and fetal development, transcriptionally silenced in adult tissues, and re-expressed on the surface of NSCLC and EOC cells. By immunohistochemistry, CLDN6 staining of the cell membrane was observed in 27% of non-squamous NSCLC (n = 63) and 69% of EOC (n = 92) samples, the majority of which were of the high-grade serous ovarian cancer subtype. Expression of CLDN6 protein was not detected in most normal adult tissues, with rare CLDN6 immunostaining limited to individual cells in the pituitary, pancreas, small intestine, kidney, and female reproductive organs. AMG 794 is a fully human BiTE® molecule that binds both human and cynomolgus monkey CLDN6 and CD3. AMG 794 binds human CLDN6 and CD3 with equilibrium dissociation constant (KD) of 13 nM and 36 nM, respectively. In vitro, AMG 794 redirects human T cells to kill CLDN6-expressing cancer cells with a half-maximal lysis concentration (EC50) of 2.6 ± 1.1 pM to 127.4 ± 53.4 pM. Consistent with the mechanism of action of BiTE® immune therapy, AMG 794 induces T cell activation and transient production of cytokines in co-cultures of T cells and CLDN6-expressing tumor cells. Remarkably, AMG 794 binding and cytotoxic activity is selective for CLDN6 over other claudin family proteins, despite high homology in the extracellular loops with CLDN9. Weekly dosing of AMG 794 significantly inhibited the growth of established lung and ovarian xenograft tumors in immunocompromised mice injected with human T cells. Anti-tumor activity was associated with an increase in tumor-infiltrating T cells. AMG 794 was well tolerated in a one-month repeat-dose toxicology study in cynomolgus monkey, with evidence for target engagement. The potent, selective activity of AMG 794 for CLDN6-expressing NSCLC and EOC cells, together with an acceptable nonclinical safety profile, supported the advancement of AMG 794 into clinical development. A first-in-human study to explore the safety, tolerability, pharmacokinetics, and anti-tumor activity of AMG 794 in patients with CLDN6-positive advanced/metastatic non-squamous NSCLC or EOC will be enrolling patients in March 2022. Citation Format: Elizabeth Pham, Anja Henn, Beate Sable, Joachim Wahl, Kip Conner, Katja Matthes, Shivani Gupta, Rodolfo Yabut, Famke Aeffner, Kristin Lewis Wilson, Jonas Anlahr, Christoph Dahlhoff, Vijay Kale, Matthias Friedrich, Tobias Raum, Peter Kufer, Angela Coxon, Sabine Stienen, Julie M. Bailis. AMG 794, a Claudin 6-targeted half-life extended (HLE) bispecific T cell engager (BITE®) molecule for non-small cell lung cancer and epithelial ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5202.

Patient-Derived Xenografts of High-Grade Serous Ovarian Cancer Subtype as a Powerful Tool in Pre-Clinical Research.

(1) Background. PDX models have become the preferred tool in research laboratories seeking to improve development and pre-clinical testing of new drugs. PDXs have been shown to capture the cellular and molecular characteristics of human tumors better than simpler cell line-based models. More recently, however, hints that PDXs may change their characteristics over time have begun to emerge, emphasizing the need for comprehensive analysis of PDX evolution. (2) Methods. We established a panel of high-grade serous ovarian carcinoma (HGSOC) PDXs and developed and validated a 300-SNP signature that can be successfully utilized to assess genetic drift across PDX passages and detect PDX contamination with lymphoproliferative tissues. In addition, we performed a detailed histological characterization and functional assessment of multiple PDX passages. (3) Results. Our data show that the PDXs remain largely stable throughout propagation, with marginal genetic drift at the time of PDX initiation and adaptation to mouse host. Importantly, our PDX lines retained the major histological characteristics of the original patients' tumors even after multiple passages in mice, demonstrating a strong concordance with the clinical responses of their corresponding patients. (4) Conclusions. Our data underline the value of defined HGSOC PDXs as a pre-clinical tumor model.

The Platelet-Activating Factor Receptor's Association with the Outcome of Ovarian Cancer Patients and Its Experimental Inhibition by Rupatadine.

The platelet-activating factor receptor (PAFR) and its ligand (PAF) are important inflammatory mediators that are overexpressed in ovarian cancer. The receptor is an important player in ovarian cancer development. In this study, we aimed to evaluate the prognostic value of PAFR in epithelial ovarian cancer (EOC) and the potential use of its antagonist, rupatadine, as an experimental treatment. Tissue microarrays of ovarian cancer patients, most markedly those with a non-mucinous subtype, immunohistochemically overexpressed PAFR. Elevated cytoplasmic PAFR expression was found to significantly and independently impair patients’ overall and recurrence-free survival (OS: median 83.48 vs. 155.03 months; p = 0.022; RFS: median 164.46 vs. 78.03 months; p = 0.015). In vitro, the serous ovarian cancer subtypes especially displayed an elevated PAFR gene and protein expression. siRNA knockdown of PAFR decreased cell proliferation significantly, thus confirming the receptor’s protumorigenic effect on ovarian cancer cells. The clinically approved PAFR antagonist rupatadine effectively inhibited in vitro cell proliferation and migration of ovarian cancer cells. PAFR is a prognostic marker in ovarian cancer patients and its inhibition through rupatadine may have important therapeutic implications in the therapy of ovarian cancer patients.

Abstract 453: The neoantigen and immune landscape of low and high grade serous ovarian cancers

Abstract Background: Within serous ovarian cancer (SOC), high-grade serous carcinoma (HGSC) demonstrates a worse prognosis compared to low-grade serous carcinoma (LGSC). Molecular analysis of SOC has revealed a distinct pattern of mutations found between the two pathologic subtypes, with TP53 as the main driver for HGSC. We analyzed the neoantigen and immune landscape of different SOC subtypes according to pathological grades and mutation status. Methods: The analysis was done using the SOC cohort of The Cancer Genome Atlas (TCGA). The neoantigen prediction was done through the CloudNeo pipeline. CIBERSORT was applied to derive the tumor-infiltrating immune cells. Patients were grouped by their pathological grades (high vs. low) and the molecular features (type 1 vs. 2). For further subgroup analysis, high-grade samples were stratified by their TP53 mutation status. Results: Among 585 SOC patients, a subset of 254 patients with available mutation counts and predicted neoantigen counts were included. There was no significant difference in neoantigen count between low and high grades (median 50.50 vs. 62.50, p=0.84). However, there was a trend for differential numbers in the neoantigen count between type 1 and type 2 (median 29 vs. 66.50, p=0.07). No notable differences were detected in immune landscapes of low vs. high grade and type 1 vs. type 2. Conclusions: Our study is the first to describe the neoantigen and immune landscape of SOC. There were no significant differences in the immune landscape between the subtypes. It seems that molecular subtyping is more related to neoantigen differences than histologic subtyping. It is likely that the neoantigen differences are not defined by the histologic grade but rather by molecular trait. The immunologic characteristics of EMT low and high SOCNumber of ptientsNeoantigen countp-valueMutation countp-valueCytolytic scorep-valuePD-L1 expressionp-valueLow grade1250.500.84700.8757.120.4812.340.28High grade8062.5085.571.0919.66Type 117290.07114.60.98125.10.7824.940.77Type 222066.50115.3119.526.3High grade(TP53 wild type)744.000.06620.08163.20.0629.770.5High grade(TP53 mutated)7364.0086110.126.47TCGA cohort provided the data of low(GB, G1, G2) and high(G3, G4) grade SOCsType 1: Defined as mutations in KRAS, BRAF, PTEN, PIK3CA, CTNNB1 and ARID1A irrespective of histologic gradeType 2: Defined as mutation in TP53 irrespective of histologic gradeThe samples that had intersecting mutations were excluded in type 1 and type 2.The cytolytic activity score was defined as a geometric mean of mRNA expression of perforin and granzyme. Citation Format: Won Kyung Hur, Jin Young Hwang, Leeseul Kim, Myungwoo Nam, William H. Bae, Yoonhee Choi, Yeun Ho Lee, William Cheng, Heayoon S. Cho, Emma Yu, Chan Mi Jung, Eugene Kim, Christmann Low, Victor Wang, Jeff Chuang, Young Kwang Chae. The neoantigen and immune landscape of low and high grade serous ovarian cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 453.

Orthogonal Proteomic Platforms and Their Implications for the Stable Classification of High-Grade Serous Ovarian Cancer Subtypes.

SummaryThe National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) established a harmonized method for large-scale clinical proteomic studies. SWATH-MS, an instance of data-independent acquisition (DIA) proteomic methods, is an alternate proteomic approach. In this study, we used SWATH-MS to analyze remnant peptides from the original retrospective TCGA samples generated for the CPTAC ovarian cancer proteogenomic study. The SWATH-MS results recapitulated the confident identification of differentially expressed proteins in enriched pathways associated with the robust Mesenchymal high-grade serous ovarian cancer subtype and the homologous recombination deficient tumors. Hence, SWATH/DIA-MS presents a promising complementary or orthogonal alternative to the CPTAC proteomic workflow, with the advantages of simpler and faster workflows and lower sample consumption, albeit with shallower proteome coverage. In summary, both analytical methods are suitable to characterize clinical samples, providing proteomic workflow alternatives for cancer researchers depending on the context-specific goals of the studies.

Tumour immune cell infiltration and survival after platinum-based chemotherapy in high-grade serous ovarian cancer subtypes: A gene expression-based computational study.

BackgroundIncreasing evidence supports that the immune infiltration of tumours is associated with prognosis. Here, we sought to assess the relevance of the cellular composition of the immune infiltrate to survival after platinum-based chemotherapy amongst patients with high-grade serous ovarian cancer and evaluate these effects by molecular subtype.MethodsWe searched publicly available databases and identified 13 studies with more than 2000 patients. We estimated the proportions of 22 immune cell subsets by using a computational approach (CIBERSORT). Then, we investigated the associations between each immune cell subset and progression-free survival (PFS) and overall survival (OS), with cellular proportions modelled as quartiles.FindingsA high fraction of M1 [hazard ratio (HR) = 0.92, 95% confidence interval (CI) = 0.86–0.99] and M0 (HR = 0.93, 95% CI = 0.87–0.99) macrophages emerged as the most closely associated with favourable OS. Neutrophils were associated with poor OS (HR = 1.06, 95% CI = 1.00–1.13) and PFS (HR = 1.10, 95% CI = 1.02–1.13). Amongst the immunoreactive tumours, the M0 macrophages and the CD8+ T cells were associated with improved OS, whereas the M2 macrophages conferred worse OS. Interestingly, PD-1 was associated with good OS (HR=0.89, 95% CI = 0.80–1.00) and PFS (HR=0.89, 95% CI = 0.79–1.01) in this subtype. Four subgroups of tumours with distinct survival patterns were identified using immune cell proportions with unsupervised clustering.InterpretationFurther investigations of the quantitative cellular immune infiltrations in tumours may contribute to therapeutic advances.

Tumor-Immune Infiltration and Survival after Platinum-Based Chemotherapy in High Grade Serous Ovarian Cancer Subtypes

Background: Increasing evidence supporting that immune infiltration of tumors is associated with prognosis. Here, we sought to access the relevance of cellular composition of the immune infiltrate to survival after platinum-based chemotherapy among high grade serous ovarian cancer patients, and evaluate these effects by molecular subtypes. Methods: We searched for publicly available database and identified 13 studies with >2,000 patients. We estimated the proportions of 22 immune cell subsets using a proposed computational approach (CIBERSORT), then investigated associations between each cell type and progression-free survival (PFS) and overall survival (OS), with cellular proportions be modelled as quartiles. Findings: A higher fraction of M0 macrophages (hazard ratio [HR] = 0.86, 95% CI=0.80 to 0.92) and activated natural killer (NK) cells (HR = 0.89, 95% CI=0.84 to 0.96) emerged as the most closely associated with favorable OS. Monocytes was associated with poor OS (HR = 1.11, 95% CI=1.04 to 1.18) and PFS (HR = 1.11, 95% CI=1.04 to 1.19;), as well as neutrophils (HR = 1.10, 95% CI =1.03 to 1.17 for OS; HR = 1.12, 95% CI=1.04 to 1.21 for PFS. Among immunoreactive tumors, M0 macrophages, activated NK and CD8+ T cells were conferred improved OS, while M2 macrophages and monocytes were conferred worse OS. T cell gamma delta conferred poor PFS in proliferative subtype. Four subgroups of tumors with distinct survival patterns were identified using immune cell proportions with unsupervised clustering. Interpretation: Further investigations of the quantitative of cellular immune infiltrations in tumors may make contributions for therapeutic advances. Funding Statement: This study was supported by the National Scientific Foundation of China (No. 31801121, 81522048 and 81573511), Scientific Foundation of Xiang Ya hospital (2016Q04) and the National Key Research and Development Program (No. 2016YFC0905000, 2016YFC0905001). Declaration of Interests: The authors stated: None. Ethics Approval Statement: This study has been approved by the Institute of Clinical Pharmacology, Central South University.

Abstract 1761: Serous ovarian cancer risk factors by grade: Evidence for etiologic heterogeneity

Abstract Background: Growing evidence suggests that high grade serous ovarian carcinomas may arise from the fallopian tube, while low-grade serous ovarian cancer may develop on the ovaries. Previous studies have suggested differences in ovarian cancer risk factors by histologic subtypes, but few have evaluated differences in risk factors for high- vs. low-grade serous cancers. In the Ovarian Cancer Cohort Consortium (OC3), a pooling project of individual-level data from 23 prospective cohort studies, we evaluated associations of hormonal, reproductive, demographic and lifestyle factors, and family history of cancer with for serous ovarian cancer subtypes. Methods: Among 16 studies that abstracted grade information from pathology reports, 3,095 serous ovarian cancers were identified during follow-up (125 well differentiated, 506 moderately differentiated, 1671 poorly differentiated, 793 undetermined). We used competing risks Cox proportional hazards regression to compute relative risks (RRs) and 95% confidence intervals (CIs) for differences in association by grade. Models were stratified on study and year of birth and adjusted for age, parity and OC use; subtype heterogeneity was evaluated by likelihood ratio tests. Results: Although sample sizes were small for low-grade tumors, there was evidence for heterogeneity in the associations for oral contraceptive (OC) use, age at menopause, endometriosis, and family history of ovarian cancer. For example, each 5-year increase in OC use was associated with a 21% decrease in risk of low-grade serous ovarian cancer (RR: 0.79; 95% CI: 0.62-1.00), but only a 10% decrease in risk of high-grade serous cancers (RR: 0.90; 95% CI: 0.84-0.96; p-heterogeneity = 0.09). Consistent with a prior report in the Ovarian Cancer Association Consortium, endometriosis was associated with increased risk of low-grade serous tumors (RR: 3.77; 95% CI: 1.24-11.48), but not with high-grade serous tumors (RR: 1.11; 95% CI: 0.70-1.74; p-heterogeneity = 0.12). Conclusion: Our results demonstrate heterogeneous associations of risk factors with subtypes of serous ovarian cancer, supporting the idea that the high- and low-grade serous tumors develop through different pathways. Despite the small sample size for low-grade serous tumors, most risk factors were more strongly associated with low-grade tumors compared to high-grade serous carcinomas, suggesting that risk prediction may be more challenging for the most fatal subtype. Identifying subtype-specific risk factor and biomarkers is important both for better understanding ovarian cancer etiology and for targeted development of novel prevention approaches. These results underscore the importance of consortial projects to evaluate rare subtypes (low-grade serous cancers) for the better understanding of etiologic heterogeneity of this deadly disease. Citation Format: Elizabeth M. Poole, Nicolas A. Wentzensen, Britton Trabert, Shelley S. Tworoger, The Ovarian Cancer Cohort Consortium. Serous ovarian cancer risk factors by grade: Evidence for etiologic heterogeneity. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1761.

Abstract 3008: Preclinical characterization of AMG 900, a pan-aurora kinase inhibitor, alone and in combination with taxanes in ovarian cancer

Abstract BACKGROUND: Aurora kinases (AK) A and B play essential roles in multiple stages of mitosis and are frequently overexpressed in a subset of human cancers, including ovarian cancer (OC). AMG 900, a potent and highly selective small molecule inhibitor of AKs, showed promising single-agent activity in heavily pretreated patients with advanced OC in a Phase 1b clinical trial. In this study, we report the preclinical effects of AMG 900 in a panel of well-characterized human cancer cell lines representing clinically-relevant OC subtypes. METHODS: The anti-proliferative effects of AMG 900 were evaluated using a 5-day cell count assay. Cell lines were classified as sensitive to AMG 900 when lethality was > 15% at 10 nM. Molecular markers were profiled including TP53 mutation status, AURKA, CCNE1, MYC copy number, and p53, p21 and cyclin E1 protein by reverse phase protein array. Flow cytometry and imaging methods were used to evaluate the mechanism of action of AMG 900 alone and in combination with chemotherapy. The combination of AMG 900 plus docetaxel was evaluated in an IGROV-1 ovarian endometrioid carcinoma xenograft model. RESULTS: One third of the cell lines (11 of 35) were classified as sensitive to AMG 900 and showed enrichment for TP53 mutations and serous OC subtype. However, 10 of 24 resistant cell lines harbored TP53 mutations, indicating that TP53 mutational status alone was not sufficient for predicting AMG 900 sensitivity. Inhibition of AK activity by AMG 900 in OC cells resulted in aborted cell division leading to polyploidy and cell death (suggestive of aurora-B dominant phenotype). Re-plating of remnant cells after AMG 900 treatment showed an attenuation of cell regrowth, where TP53mut IGROV-1 cells showed minimal regrowth compared to TP53wt OVCAR-5 cells. AMG 900 inhibited proliferation at low nanomolar concentrations in the majority of OC cell lines and enhanced the effects of paclitaxel, carboplatin, and doxorubicin in IGROV-1 cells. In tumor-bearing mice, administration of AMG 900 at 7.5 mg/kg (PO) for two days per week or docetaxel at 10 mg/kg (IP) weekly for four cycles significantly inhibited the growth of IGROV-1 tumor xenografts (P < .0001 vs. vehicle alone). Notably, co-administration of AMG 900 with docetaxel enhanced efficacy and induced a delay in tumor regrowth compared to docetaxel alone. Single-agent-treated mice showed minimal body weight loss (BWL), whereas combination-treated mice showed moderate BWL (average < 10%) that was largely reversible (2 of 12 animals removed due to toxicity). CONCLUSIONS: AMG 900 alone or in combination with chemotherapy such as paclitaxel may be a promising clinical strategy to treat patients with ovarian cancer. Citation Format: Ondrej Kalous, Dylan Conklin, Kanthinh Manivong, William Wayne, Kelly Hanestad, Jude Canon, Robert Loberg, Gregory Friberg, Erick Gamelin, Florian D. Vogl, Gloria Juan, Angela Coxon, Dennis Slamon, Richard Finn, Marc Payton. Preclinical characterization of AMG 900, a pan-aurora kinase inhibitor, alone and in combination with taxanes in ovarian cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3008.

Abstract 1928: High-grade serous ovarian cancer subtypes are similar across diverse populations

Abstract The most common and lethal type of invasive epithelial ovarian cancer is high grade serous (HGSC). Three to four gene expression-based HGSC subtypes have been identified in prior studies. In contrast to most previous studies, which have assessed the performance of survival classifiers in validation sets, we sought to determine the degree of similarity of gene expression patterns in subtypes between populations using systematic unsupervised clustering within populations. We analyzed publically-available mRNA expression data from studies with >200 HGSC tumors: The Cancer Genome Atlas (TCGA, US, n = 519, Affymetrix HT U133a), Tothill et al. (GSE9891, Australia, n = 242, Affymetrix U133 Plus 2.0) and Yoshihara et al. (GSE32062, Japan, n = 258, Agilent G4112a). We restricted analyses to the 12,249 genes shared across all datasets and selected from these the union of the 1,500 most variant genes per population (2,824). Using these datasets, we performed k-means clustering within each population for k = 3 and k = 4. We compared each cluster to all other clusters using Significance Analysis of Microarrays, which outputs an F score for all 12,249 genes, measuring cluster-specific differential expression. We then calculated the correlation of the resulting F score vectors across populations and within populations across both numbers of centroids (k = 3 or k = 4). We identified analogous clusters by high F score correlations and determined each cluster's similarity to the TCGA subtypes based on cluster-specific differentially expressed genes. We observed high concordance of gene expression patterns for clusters across populations and across k-means runs, suggesting that analogous clusters exist in most analyses. For k = 3, F score correlations across populations for clusters 1, 2 and 3, respectively, ranged between 0.77-0.85, 0.80-0.90, and 0.66-0.72. For k = 4, F score correlations for clusters 1-4 were, respectively: 0.76-0.85, 0.82-0.85, 0.65-0.78, and 0.52-0.78. Across k = 3 and k = 4, correlations for cluster 1 within TCGA, Tothill, and Yoshihara were 0.99, 1.00 and 1.00, and correlations for cluster 2 were 0.96, 0.98, and 0.95, respectively. Correlations for cluster 3 were less strong: 0.56, 0.88, and 0.60, respectively. For k = 4, cluster 4 was composed mainly of samples that belonged to cluster 3 for k = 3; 88% for TCGA, 54% for Tothill, and 95% for Yoshihara. When compared to TCGA subtypes, cluster 1 corresponded most strongly to mesenchymal, cluster 2 to proliferative, cluster 3 to differentiated, and cluster 4 to immunoreactive. Our observation of highly correlated gene expression patterns between clusters across populations, across platforms, and across the number of centroids provides strong evidence that at least three biological HGSC subtypes exist. The mesenchymal-like and proliferative-like subtypes are particularly consistent across populations, and could be uniquely targeted for treatment. Citation Format: Gregory P. Way, James Rudd, Casey S. Greene, Jennifer A. Doherty. High-grade serous ovarian cancer subtypes are similar across diverse populations. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1928. doi:10.1158/1538-7445.AM2015-1928

Key nodes of a microRNA network associated with the integrated mesenchymal subtype of high-grade serous ovarian cancer.

Metastasis is the main cause of cancer mortality. One of the initiating events of cancer metastasis of epithelial tumors is epithelial-to-mesenchymal transition (EMT), during which cells dedifferentiate from a relatively rigid cell structure/morphology to a flexible and changeable structure/morphology often associated with mesenchymal cells. The presence of EMT in human epithelial tumors is reflected by the increased expression of genes and levels of proteins that are preferentially present in mesenchymal cells. The combined presence of these genes forms the basis of mesenchymal gene signatures, which are the foundation for classifying a mesenchymal subtype of tumors. Indeed, tumor classification schemes that use clustering analysis of large genomic characterizations, like The Cancer Genome Atlas (TCGA), have defined mesenchymal subtype in a number of cancer types, such as high-grade serous ovarian cancer and glioblastoma. However, recent analyses have shown that gene expression-based classifications of mesenchymal subtypes often do not associate with poor survival. This “paradox” can be ameliorated using integrated analysis that combines multiple data types. We recently found that integrating mRNA and microRNA (miRNA) data revealed an integrated mesenchymal subtype that is consistently associated with poor survival in multiple cohorts of patients with serous ovarian cancer. This network consists of 8 major miRNAs and 214 mRNAs. Among the 8 miRNAs, 4 are known to be regulators of EMT. This review provides a summary of these 8 miRNAs, which were associated with the integrated mesenchymal subtype of serous ovarian cancer.

Kallikrein family proteases KLK6 and KLK7 are potential early detection and diagnostic biomarkers for serous and papillary serous ovarian cancer subtypes.

BackgroundEarly detection of ovarian cancer remains a challenge due to widespread metastases and a lack of biomarkers for early-stage disease. This study was conducted to identify relevant biomarkers for both laparoscopic and serum diagnostics in ovarian cancer.MethodsBioinformatics analysis and expression screening in ovarian cancer cell lines were employed. Selected biomarkers were further validated in bio-specimens of diverse cancer types and ovarian cancer subtypes. For non-invasive detection, biomarker proteins were evaluated in serum samples from ovarian cancer patients.ResultsTwo kallikrein (KLK) serine protease family members (KLK6 and KLK7) were found to be significantly overexpressed relative to normal controls in most of the ovarian cancer cell lines examined. Overexpression of KLK6 and KLK7 mRNA was specific to ovarian cancer, in particular to serous and papillary serous subtypes. In situ hybridization and histopathology further confirmed significantly elevated levels of KLK6 and KLK7 mRNA and proteins in tissue epithelium and a lack of expression in neighboring stroma. Lastly, KLK6 and KLK7 protein levels were significantly elevated in serum samples from serous and papillary serous subtypes in the early stages of ovarian cancer, and therefore could potentially decrease the high “false negative” rates found in the same patients with the common ovarian cancer biomarkers human epididymis protein 4 (HE4) and cancer antigen 125 (CA-125).ConclusionKLK6 and KLK7 mRNA and protein overexpression is directly associated with early-stage ovarian tumors and can be measured in patient tissue and serum samples. Assays based on KLK6 and KLK7 expression may provide specific and sensitive information for early detection of ovarian cancer.Electronic supplementary materialThe online version of this article (doi:10.1186/s13048-014-0109-z) contains supplementary material, which is available to authorized users.

Kallikrein family proteases KLK6 and KLK7 are potential early detection and diagnostic biomarkers for serous and papillary serous ovarian cancer subtypes

Kallikrein family proteases KLK6 and KLK7 are potential early detection and diagnostic biomarkers for serous and papillary serous ovarian cancer subtypes

Angiogenic mRNA and microRNA gene expression signature predicts a novel subtype of serous ovarian cancer.

Ovarian cancer is the fifth leading cause of cancer death for women in the U.S. and the seventh most fatal worldwide. Although ovarian cancer is notable for its initial sensitivity to platinum-based therapies, the vast majority of patients eventually develop recurrent cancer and succumb to increasingly platinum-resistant disease. Modern, targeted cancer drugs intervene in cell signaling, and identifying key disease mechanisms and pathways would greatly advance our treatment abilities. In order to shed light on the molecular diversity of ovarian cancer, we performed comprehensive transcriptional profiling on 129 advanced stage, high grade serous ovarian cancers. We implemented a, re-sampling based version of the ISIS class discovery algorithm (rISIS: robust ISIS) and applied it to the entire set of ovarian cancer transcriptional profiles. rISIS identified a previously undescribed patient stratification, further supported by micro-RNA expression profiles, and gene set enrichment analysis found strong biological support for the stratification by extracellular matrix, cell adhesion, and angiogenesis genes. The corresponding “angiogenesis signature” was validated in ten published independent ovarian cancer gene expression datasets and is significantly associated with overall survival. The subtypes we have defined are of potential translational interest as they may be relevant for identifying patients who may benefit from the addition of anti-angiogenic therapies that are now being tested in clinical trials.

Deregulation of MYCN, LIN28B and LET7 in a Molecular Subtype of Aggressive High-Grade Serous Ovarian Cancers

Molecular subtypes of serous ovarian cancer have been recently described. Using data from independent datasets including over 900 primary tumour samples, we show that deregulation of the Let-7 pathway is specifically associated with the C5 molecular subtype of serous ovarian cancer. DNA copy number and gene expression of HMGA2, alleles of Let-7, LIN28, LIN28B, MYC, MYCN, DICER1, and RNASEN were measured using microarray and quantitative reverse transcriptase PCR. Immunohistochemistry was performed on 127 samples using tissue microarrays and anti-HMGA2 antibodies. Fluorescence in situ hybridisation of bacterial artificial chromosomes hybridized to 239 ovarian tumours was used to measure translocation at the LIN28B locus. Short interfering RNA knockdown in ovarian cell lines was used to test the functionality of associations observed. Four molecular subtypes (C1, C2, C4, C5) of high-grade serous ovarian cancers were robustly represented in each dataset and showed similar pattern of patient survival. We found highly specific activation of a pathway involving MYCN, LIN28B, Let-7 and HMGA2 in the C5 molecular subtype defined by MYCN amplification and over-expression, over-expression of MYCN targets including the Let-7 repressor LIN28B, loss of Let-7 expression and HMGA2 amplification and over-expression. DICER1, a known Let-7 target, and RNASEN were over-expressed in C5 tumours. We saw no evidence of translocation at the LIN28B locus in C5 tumours. The reported interaction between LIN28B and Let-7 was recapitulated by siRNA knockdown in ovarian cancer cell lines. Our results associate deregulation of MYCN and downstream targets, including Let-7 and oncofetal genes, with serous ovarian cancer. We define for the first time how elements of an oncogenic pathway, involving multiple genes that contribute to stem cell renewal, is specifically altered in a molecular subtype of serous ovarian cancer. By defining the drivers of a molecular subtype of serous ovarian cancers we provide a novel strategy for targeted therapeutic intervention.

DNA methylation markers associated with serous ovarian cancer subtypes

Objective: Ovarian cancer is the most deadly of the gynecologic malignancies. Several clinicopathologic factors have been used to prognosticate clinical outcome and select therapy, but none has provided sufficient insight into the biology of the disease. Even within a single histology, there may be variability in outcome and exposure history. DNA methylation is an epigenetic modification that consists of the addition of a methyl group to a cytosine followed by a guanine (mCpG). DNA methylation is important for gene transcription and in cancer cells, DNA methylation patterns are altered and this may lead to transcriptional changes.

Two subtypes of serous ovarian cancer with different gene expression pattern

Two subtypes of serous ovarian cancer with different gene expression pattern

Intraepithelial T cells and prognosis in ovarian carcinoma: novel associations with stage, tumor type, and BRCA1 loss

Intraepithelial tumor-infiltrating T cells have been correlated with improved outcomes in ovarian carcinoma, however, it is not known whether there is an association with disease stage, histological subtype, or BRCA mutation/expression. Two case series of ovarian carcinomas were included in the study; a retrospective series of 500 patients, and 40 prospectively collected cases fully characterized for BRCA1 mutation status and expression. Intraepithelial immune cells were assessed as present or absent by immunohistochemical staining of tissue microarrays. In the retrospective case series, the presence of intraepithelial CD8+ T-cells correlated with improved disease-specific survival (P=0.027), whereas intraepithelial CD3+ T cells did not (P=0.49). For serous ovarian carcinomas, the presence of intraepithelial CD3+ and CD8+ T-cells correlated with improved disease-specific survival (P=0.0016 and P≤0.0001, respectively). The presence of intraepithelial CD8+ T cells was not associated with improved survival in endometrioid or clear cell carcinomas. On multivariate analysis, disease stage and CD8+ T cells were found to be independently predictive of improved disease-specific survival, whereas grade, age at surgery, and type of adjuvant treatment were not. In the prospective patient cohort, intraepithelial CD8+ T-cells correlated with the presence of mutation or loss of expression of BRCA1 through promoter methylation (P=0.019). Intraepithelial CD8+ tumor-infiltrating T-cells correlate with improved clinical outcomes for all stages of ovarian cancer; this association is restricted to the serous ovarian cancer subtype, and is an independent prognostic factor on multivariate analysis. The presence of intraepithelial CD8+ T cells also significantly correlates with loss of BRCA1.