bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract A11: Common links suggest a shared embryologic origin for pancreatic and ovarian mucinous tumors
Authors: Labidi-Galy Intidhar , Elias Kevin M. , Vitonis Allison F. , Hornick Jason L. , Doyle Leona A. , Hirsch Michelle S. , Cramer Daniel W. , Drapkin Ronny
Published: August 2014

Background: Mucinous ovarian tumors (MOT) have been linked to mucinous colorectal and appendiceal adenocarcinomas. However, recent molecular studies suggest MOT may share more in common with pancreatic mucinous cystic neoplasms (MCN). Commonalities between these seemingly disparate tumors are explored.

Methods: Epidemiologic features of MOT and mucinous gastrointestinal tumors were compared using the SEER database. Regional cases of 287 mucinous ovarian tumors were examined against 2,339 age-matched controls to delineate MOT risk factors. A case series of MCN was identified by chart review. Protein expression patterns among tumors were examined using seven immunohistochemical markers.

Results: SEER revealed that among GI neoplasms the epidemiology of MCN was most similar to MOT by age, race, and stage. MCN occurred almost exclusively in women, with a sex ratio of 19:1, compared to 1•1:1 and 1•2:1 for mucinous colorectal and appendiceal adenocarcinomas. In the case-control study, appendectomy and cervical conization did not reduce the risk of MOT, while smoking (OR 2•68, 95% CI 1•85-3•89, p<0•001), was associated with an increased risk of MOT. Smoking was similarly common among MCN patients. Histologically, MOT and MCN were CK7+, CK20-, MUC2-, and CDX2-, whereas mucinous colorectal and appendiceal adenocarcinomas were CK7-, CK20+, MUC2+, and CDX2+.

Interpretation: Clinical and morphologic similarities between MOT and MCN suggest a common pathogenesis, potentially a shared precursor such as embryologic rests that stopped in the pancreatic buds during migration of the primordial follicles to the gonads during development. This implies mucinous ovarian tumors may originate from primordial follicles, not the ovarian surface epithelium, offering a novel explanation for their pathogenesis.

Citation Format: Intidhar Labidi-Galy, Kevin M. Elias, Allison F. Vitonis, Jason L. Hornick, Leona A. Doyle, Michelle S. Hirsch, Daniel W. Cramer, Ronny Drapkin. Common links suggest a shared embryologic origin for pancreatic and ovarian mucinous tumors. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; Sep 18-21, 2013; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2013;19(19 Suppl):Abstract nr A11.
Abstract A19: Comparison of genomic alteration patterns between ovarian clear cell carcinoma and renal cell carcinoma
Authors: Asada Kayo , Koso Takahiro , Oda Katsutoshi , Uehara Yuriko , Yamamoto Shogo , Tatsuno Kenji , Ueda Hiroki , Kurikawa Reiko , Ikeda Yuji , Hiraike Osamu , Kawana Kei , Yano Tetsu , Osuga Yutaka , Fujii Tomoyuki , Aburatani Hiroyuki
Published: August 2014

Background: Ovarian clear cell carcinoma (OCCC) is a distinct histopathological subtype in epithelial ovarian cancer, and its pathological features and gene expression profiles are similar to those of clear cell renal cell carcinoma (ccRCC), including HIF pathway activation. Methods: We performed whole exome sequencing and/or SNP typing array in 45 OCCC clinical samples, and obtained the data of ccRCC from TCGA. Results: We identified several genetic mutations in SWI/SNF complex and PI3K/mTOR pathway, which had been reported in ccRCC, but not in OCCC. Mutations of ARID1A (BAF250a) were predominant in OCCC (55% vs 4%), whereas PBRM1 (BAF180) mutations were detected only in ccRCC at 35%. Mutations of PIK3CA (60% vs 3.0%) and the genetic alterations in the PI3K/mTOR pathway (65% vs 30%, p<0.05 by Fisher's exact test) were more common in OCCC. Distinct from ccRCC, we did not detect any mutations in VHL and copy number losses at chr 3p in OCCC. Conclusions: Genetic alteration patterns in the SWI/SNF complex and the PI3K/mTOR pathway are distinct between OCCC and ccRCC. Our data suggest that targeting mTOR pathway might be a promising therapeutic strategy in OCCC, as well as in ccRCC.

Citation Format: Kayo Asada, Takahiro Koso, Katsutoshi Oda, Yuriko Uehara, Shogo Yamamoto, Kenji Tatsuno, Hiroki Ueda, Reiko Kurikawa, Yuji Ikeda, Osamu Hiraike, Kei Kawana, Tetsu Yano, Yutaka Osuga, Tomoyuki Fujii, Hiroyuki Aburatani. Comparison of genomic alteration patterns between ovarian clear cell carcinoma and renal cell carcinoma. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; Sep 18-21, 2013; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2013;19(19 Suppl):Abstract nr A19.
Abstract A2: Novel serum biomarkers for histotype specific ovarian cancer diagnosis
Authors: Lehtinen Laura , Iljin Kristiina , Hynninen Johanna , Auranen Annika , Haglund Caj , Grenman Seija , Carpén Olli
Published: August 2014

Current diagnostic methods for ovarian cancer include gynecological inspection, ultrasound-imaging and detection of the serum tumor marker CA-125. Even combined, these methods are insufficient in specificity and sensitivity for detection of early disease. Since the majority of ovarian carcinomas are of epithelial origin, the carcinogenesis has thought to be induced in the epithelial layer of the ovaries or fallopian tubes. However, recent findings indicate that many ovarian cancers originate from non-ovarian tissues and therefore different ovarian cancer histotypes should be regarded as distinct diseases. Currently the histotype of ovarian carcinomas can be determined only during surgery. There is an increasing need for more sensitive and specific biomarkers for ovarian cancer diagnosis as well as for prediction of biological tumor behavior.

In this study, genes with ovarian cancer specific expression profile were identified from publicly available gene-expression databases. In order to find potential serum biomarker candidates, further in silico data mining was performed utilizing the GeneSapiens database. The identified ovarian cancer specific and potentially secreted or surface-expressed genes were validated in vitro in patient samples and primary ovarian cancer cells lines with qRT-PCR, western blotting and immunohistochemical staining of tumor tissue microarrays. The presence of the candidate biomarkers in patient serum samples was studied with dot blotting and immunoprecipitation. Finally, the expression levels of the candidate genes were compared to the pre-operative CA-125 and HE-4 levels in a cohort of prospective collected advanced ovarian cancer patients.

The in silico data analyses resulted in identification of altogether six novel serum biomarker candidates for serous, mucinous and clear cell ovarian tumors. Analysis of tumor samples and primary cell lines derived from ovarian cancer patient samples confirmed the expression of the candidate genes in ovarian carcinomas. Furthermore, the mRNA analysis showed evidence of histotype specificity, especially in the case of potential biomarkers for mucinous ovarian carcinoma. Immunohistochemical staining of several tumor tissue samples showed distinctive cytoplasmic expression pattern characteristic for secreted proteins. Further analysis of the presence of the biomarkers in the sera of the patients and matched controls is in progress.

Citation Format: Laura Lehtinen, Kristiina Iljin, Johanna Hynninen, Annika Auranen, Caj Haglund, Seija Grenman, Olli Carpén. Novel serum biomarkers for histotype specific ovarian cancer diagnosis. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; Sep 18-21, 2013; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2013;19(19 Suppl):Abstract nr A2.
Abstract A25: PPP2R1A mutations affect PP2A complex formation, and novel protein interactions in gynecological carcinoma cell lines
Authors: McConechy Melissa K. , Chen Vincent , Morin Gregg , Brenton James , Huntsman David G.
Published: August 2014

Gynecological malignancies (ovarian clear cell and endometrioid carcinomas, endometrial serous, endometrioid and clear cell carcinomas) harbor somatic mutations in the gene PPP2R1A, the scaffolding subunit of the serine/threonine protein phosphatase 2A (PP2A) complex. The PP2A complex is composed of an A (scaffold), C (catalytic) subunit, and different B (regulatory) subunits. The PPP2R1A mutations are proposed to play a role in PP2A B-subunit binding, and thus formation of a functional PP2A phosphatase complex. The aim of this study is to determine how PPP2R1A mutations affect the binding of B-subunits and other novel interactions within the context of ovarian and endometrial carcinomas.

The ovarian clear cell line RMG2 and endometrial carcinoma cell lines Hec-1-A and Hec50 all harbor PPP2R1A mutations. The mismatch repair deficient cell line Hec-1-A express a PPP2R1A W257L heterozygous mutation; therefore somatic cell knockout technology was used to generate isogenic PPP2R1A clones that express only mutant PPP2R1A, and clones that express more wild-type than mutant. These Hec-1-A isogenic cell lines were used for PPP2R1A co-immunoprecipiation (Co-IP) followed by MS/MS-SWATHTM analysis to identify PP2A B-subunits and other novel protein interactions.

Our preliminary results using Hec-1-A isogenic cell lines suggest that some PP2A B-subunits (PPP2R5D and PPP2R2A) are found to be decreased in abundance in the mutant cell lines. We were able to identify the catalytic subunit (PPP2CA) in PPP2R1A Co-IPs in all cell lines. We also show that PPP2R1A interacts with novel proteins such as histones (Histone 1, Histone H2B type 1-N), ubiquitin ligases (TRIM21) and proteins involved in mitotic control (ANKLE2). Of particular interest we have identified the cancer gene nucleophosmin (NPM1) as a potential novel interactor of PP2A.

We have established the isogenic Hec-1-A cell lines as a model system to determine the functional effects of a somatic PPP2R1A mutation. These cell lines have shown that the PPP2R1A mutation affects the ability of some B-subunits to interact and form the PP2A complex. We have also shown that PP2A may interact with novel proteins such as NPM1 and histones. Ongoing work will be completed to determine how these interactions function in the context of ovarian and endometrial carcinomas.

Citation Format: Melissa K. McConechy, Vincent Chen, Gregg Morin, James Brenton, David G. Huntsman. PPP2R1A mutations affect PP2A complex formation, and novel protein interactions in gynecological carcinoma cell lines. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; Sep 18-21, 2013; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2013;19(19 Suppl):Abstract nr A25.
Abstract A36: Protein markers of tumor-initiating cells and mitochondrial function in ovarian cancer
Authors: Gabrielson Marike , Björklund My , Carlson Joseph , Shoshan Maria
Published: August 2014

Background: Epithelial ovarian carcinoma (EOC) is the 5th leading cause of total cancer death in women. Despite initial responsiveness to treatment, >75% of patients relapse into metastatic and essentially incurable chemoresistant disease. In carcinomas, metastasis is associated with the dedifferentiation process termed epithelial-to-mesenchymal transition (EMT). EMT is molecularly related to a cancer stem cell phenotype. Cancer stem cells, or tumor-initiating cells (TICs) as they are now called, are increasingly believed to underlie relapse, and are by definition highly chemoresistant and able to give rise to metastases. By repeated cisplatin treatment of the EOC cell line SKOV-3, originating from malignant ascites, we have created a stable subline (SKOV-3-R) expressing TIC markers, and showing EMT, increased motility, sphere formation in stem cell medium. They also show increased mitochondrial content and expression of mitochondrial VDAC, and hexokinase-II (HK-II) known to be upregulated in glycolytic tumor cells [1]. The chemoresistance of SKOV-3-R was found to depend on HK-II [1]. The role of altered mitochondrial functions in tumor progression and in TICs is attracting increased attention.

Aim: To examine and correlate expression of TIC markers and mitochondrial markers in clinical samples, and to relate these to EOC subtype and hormone receptor status.

Results: SKOV-3-R expresses TIC markers CD117, CD44 and ALDH1. Cells freshly isolated from malignant EOC ascites were analysed for TIC markers CD117, CD44, EpCAM and Nanog, and loss of E-cadherin as a marker of EMT. In an immunohistochemical pilot study on 60 patient samples we now examine expression of CD117, CD44, ALDH1, and VDAC and HK-II.

Discussion: The SKOV-3-R results indicate that these cells constitute an in vitro model of TICs and that they have increased mitochondrial content. The analysis of malignant ascites shows potentially high levels of TICs in ascites. Results of immunhistochemical analysis of tumors are pending (August, 2013).

1. Wintzell M, Lofstedt L, Johansson J, Pedersen AB, Fuxe J, Shoshan M: Repeated cisplatin treatment can lead to a multiresistant tumor cell population with stem cell features and sensitivity to 3-bromopyruvate. Cancer Biol Ther 2012, 13(14):1454-1462.

Citation Format: Marike Gabrielson, My Björklund, Joseph Carlson, Maria Shoshan. Protein markers of tumor-initiating cells and mitochondrial function in ovarian cancer. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; Sep 18-21, 2013; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2013;19(19 Suppl):Abstract nr A36.
Abstract A52: Targeting c-MYC in cisplatin-resistant ovarian cancer
Authors: Reyes Jeyshka , Ivan Cristina , Sood Anil K. , Vivas-Mejia Pablo E.
Published: August 2014

Cisplatin has been the most active drug for the treatment of ovarian cancer for the last four decades. Although the majority of patients with ovarian cancer respond to front-line platinum combination chemotherapy, relapse occurs in over 70% of patients, resulting in chemoresistant, fatal disease. Therefore, there is an urgent need to find new therapies focused on targets within cancer cell survival pathways for advanced stage drug resistant ovarian cancer. Evidence indicates that activation of the oncogenic transcription factor c-MYC is involved in such resistance. Furthermore, it has been found that there is a significant association between increasing c-MYC expression and poor survival. Our previous findings indicate that cisplatin-resistant cells express higher c-MYC protein levels when compared to their sensitive counterparts. Importantly, targeting of c-MYC with small interference RNA (siRNA) in the cisplatin-resistant ovarian cancer cell line, A2780CP20, induced a significant cell growth arrest and inhibition of cell proliferation. Apoptosis and arrest of cell cycle progression were also observed after siRNA-based silencing of c-MYC. The mRNA expression of c-MYC and clinical data for 373 patients with high grade serous ovarian cancer were downloaded from “The Cancer Genome Atlas” (TCGA) data portal. The log-rank test revealed a significant relationship between the expression of c-MYC and the time of progression/recurrence of the tumor. These data suggests c-MYC as a potential therapeutic target for overcoming cisplatin resistance in ovarian cancer.

Citation Format: Jeyshka Reyes, Cristina Ivan, Anil K. Sood, Pablo E. Vivas-Mejia. Targeting c-MYC in cisplatin-resistant ovarian cancer. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; Sep 18-21, 2013; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2013;19(19 Suppl):Abstract nr A52.
Abstract A62: Imaging the tumor micro-environment to monitor ovarian cancer metastasis
Authors: Slack-Davis Jill K. , Scalici Jennifer M. , Thomas Stephanie , Harrer Christine , Raines Timothy A. , Curran Joanna , Atkins Kristen A. , Conaway Mark R. , Duska Linda , Kelly Kimberly A.
Published: August 2014

The inability to successfully treat women with ovarian cancer is due in large part to the advanced stage of disease at diagnosis, the development of platinum resistance, and the lack of sensitive methods to monitor tumor progression and response to treatment. Vascular cell adhesion molecule-1 (VCAM-1) is expressed on the mesothelium of ovarian cancer patients. We investigated VCAM-1 expression as a marker of peritoneal metastasis and tumor response to platinum-based chemotherapy. Immunohistochemical staining of peritoneal or omental biopsies obtained from women diagnosed with Stage I, Stage II or Stage III/IV ovarian cancer demonstrated that VCAM-1 expression correlated with tumor stage. All specimens from Stage I patients were negative, while 29% of Stage II patients and the 73% of Stage III/IV patients were positive. While the majority of women with advanced stage disease expressed VCAM-1, the incidence of expression was reduced among women who received neoadjuvant chemotherapy, suggesting a role for chemotherapy in regulating VCAM-1 expression. The effects of carboplatin on mesothelial VCAM-1 expression were determined in a mouse model of ovarian cancer peritoneal metastasis using radiolabeled VCAM-1-specific peptide imaging probes and single photon emission computed tomography (SPECT). This approach showed that 1) VCAM-1 is a viable imaging target in ovarian cancer metastasis, 2) maximal expression was detected with microscopic tumor burden, and 3) VCAM-1 expression reflected the effect of platinum-based treatment on tumor burden. Specifically, carboplatin treatment of mice with platinum-sensitive tumors showed reduced VCAM-1 expression, which correlated with reduced tumor burden; mice with platinum-resistant tumors retained elevated VCAM-1 expression and tumor burden following treatment. These observations support testing the utility of VCAM-1 imaging probes to monitor treatment response in ovarian cancer patients, thus providing the potential to improve management of women with this disease.

Citation Format: Jill K. Slack-Davis, Jennifer M. Scalici, Stephanie Thomas, Christine Harrer, Timothy A. Raines, Joanna Curran, Kristen A. Atkins, Mark R. Conaway, Linda Duska, Kimberly A. Kelly. Imaging the tumor micro-environment to monitor ovarian cancer metastasis. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; Sep 18-21, 2013; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2013;19(19 Suppl):Abstract nr A62.
Abstract B19: Functional genomics approach links anchorage-independence with tumor dormancy in ovarian cancer
Authors: Matsumura Noriomi , Yamanoi Koji , Amano Yasuaki , Hamanishi Junzo , Baba Tsukasa , Murphy Susan K. , Konishi Ikuo
Published: August 2014

Although a number of genes are aberrantly regulated in ovarian cancer, little is known about which genes are functionally important. The aim of this study was to identify new genes relevant to anchorage-independent growth of ovarian cancer cells through a genome-wide functional screening approach. We performed lentiviral transduction of a library of 81,000 shRNAs (Cellecta, Inc.) targeting 15,000 genes into an immortalized human ovarian surface epithelium cell line and 7 ovarian cancer cell lines (OVCA420, OVCA433, OVCA429, CAOV3, SKOV8, Tyk-nu and DOV13) which do not generate anchorage-independent colonies in soft agar. Among these, only OVCA420 generated colonies larger than 100 micrometers after shRNA library transduction. We extracted DNA from these colonies, amplified the shRNA constructs with PCR, and inserted the amplicons back into the original lentiviral vector, thus generating a secondary library of 68 shRNAs. Subsequent analysis, performed to examine the reproducible formation of anchorage-independent colonies using the secondary library, identified 5 shRNAs targeting ABHD2, CYB5R3, MR1, ELAC2 and CCL22. Interestingly, population doubling time was increased following transduction of these shRNAs (44.8, 50.1, 43.9, 28.0 and 33.2 hours, respectively) compared to the original or control shRNA-transducted OVCA420 cells (22.4 and 23.7 hours, respectively). Furthermore, side populations detected by efflux of Hoechst 33342 dye were drastically increased (50.5, 46.6, 55.5, 76.5 and 41.1%, respectively) compared to the original or control shRNA-transducted OVCA420 cells (7.3 and 10.4%, respectively). Although these data are not conclusive, they support that a phenotypic change occurs as ovarian cancer cells leave the primary tumor and are suspended in ascites. We found that repression of any one of these particular genes was sufficient to avoid anoikis. This change was accompanied by suppression of cell proliferation and increased efflux of Hoechst 33342 dye, which indicates activation of pumping function, suggesting a change to chemoresistant dormant cells. In summary, our functional genomics approach suggests a molecular mechanism underlying the process of anchorage independence, tumor dormancy and chemoresistance in ovarian cancer.

Citation Format: Noriomi Matsumura, Koji Yamanoi, Yasuaki Amano, Junzo Hamanishi, Tsukasa Baba, Susan K. Murphy, Ikuo Konishi. Functional genomics approach links anchorage-independence with tumor dormancy in ovarian cancer. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; Sep 18-21, 2013; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2013;19(19 Suppl):Abstract nr B19.
Abstract B35: Target discovery: Using VBIM technique to identify carboplatin resistance genes in ovarian cancer cells
Authors: Wei Han , Lu Tao
Published: August 2014

Among gynecological cancers, ovarian cancer is the leading cause of death each year. Women are often diagnosed with an advanced stage of the disease as it is frequently without overt or specific symptoms until late in its development. One of the major chemotherapy drugs used to treat ovarian cancer is carboplatin. Carboplatin was introduced in the late 1980s and has since gained popularity in clinical treatment due to its vastly reduced side-effects compared to its parent compound, cisplatin. Although resistance to carboplatin remains a major barrier to the successful treatment of ovarian cancer, the mechanisms of its resistance are poorly understood.

In this study, we used the novel validation-based insertional mutagenesis (VBIM) technique to identify carboplatin resistance genes in ovarian cancer cells and to further confirm and evaluate their role in mediating carboplatin resistance in ovarian cancer cells. In a preliminary screen, we identified three novel proteins whose functions have never been previously linked to carboplatin resistance in ovarian cancer. We name them ovarian cancer carboplatin resistance genes OCCRP-1, 2 and 3. By generating stable A2780 cells in which OCCRP-1 is either overexpressed or knocked down, we confirmed that OCCRP-1 is a carboplatin resistance gene in ovarian cancer cells. Similar work is carrying on for OCCRP-2 and 3 as well.

Our study promises to discover novel mechanisms of gene-mediated carboplatin resistance so that reversal or bypass of this resistance in ovarian cancer can be achieved by developing small chemical inhibitors which ultimately will lead to novel therapeutic approaches for ovarian cancer treatment.

Citation Format: Han Wei, Tao Lu. Target discovery: Using VBIM technique to identify carboplatin resistance genes in ovarian cancer cells. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; Sep 18-21, 2013; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2013;19(19 Suppl):Abstract nr B35.
Abstract B47: microRNA-181a plays a critical role in ovarian cancer progression through the regulation of epithelial-mesenchymal transition
Authors: Parikh Aditya , Lee Christine , Joseph Peronne , Marchini Sergio , Baccarini Alessia , Kolev Valentin , Romualdi Chiara , Fruscio Robert , Shah Hardik , Feng Wang , Mullokandov Gavriel , Fishman David , D'Incalci Maurizio , Rahaman Jamal , Kalir Tamara , Redline Raymond , Brown Brian D. , Narla Goutham , DiFeo Analisa
Published: August 2014

Ovarian cancer is the most lethal gynecological cancer primarily due to advanced stage of disease at diagnosis. Effective therapeutic targets and prognostic biomarkers are still lacking due to insufficient knowledge of the pathways that regulate ovarian cancer progression. Here, we identify miR-181a as a mediator of disease dissemination through the induction of EMT and direct activation of the TGF-β signaling pathway via repression of its functional target, Smad7. High expression of miR-181a and phospho-Smad2 were associated with poor patient outcome and were enriched in recurrent compared to matched-primary tumors. Ectopic expression of miR-181a resulted in increased cellular survival, migration, drug resistance, and in vivo tumor burden, and dissemination. Conversely, targeting this miRNA using a decoy vector resulted in significant decreases in cell survival, migration, and MET in ovarian cancer cell lines. Combined, our findings identify miR-181a as a novel modulator of ovarian cancer dissemination through the induction of EMT and highlight its role as a potential biomarker and therapeutic target for aggressive late-stage ovarian cancer.

Citation Format: Aditya Parikh, Christine Lee, Peronne Joseph, Sergio Marchini, Alessia Baccarini, Valentin Kolev, Chiara Romualdi, Robert Fruscio, Hardik Shah, Wang Feng, Gavriel Mullokandov, David Fishman, Maurizio D'Incalci, Jamal Rahaman, Tamara Kalir, Raymond Redline, Brian D. Brown, Goutham Narla, Analisa DiFeo. microRNA-181a plays a critical role in ovarian cancer progression through the regulation of epithelial-mesenchymal transition. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; Sep 18-21, 2013; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2013;19(19 Suppl):Abstract nr B47.
Abstract B57: Continuous exposure to epidermal growth factor in ovarian cancer cells causes a persistent increase in N-cadherin expression which then results in multicellular aggregate compaction
Authors: Samudio-Ruiz Sabrina L. , Hudson Laurie G.
Published: August 2014

Ovarian cancer is the leading cause of death arising from gynecological malignancies. Overexpression of the epidermal growth factor receptor (EGFR) or its ligands is associated with poor prognosis. The presence of EGFR activators in patient ascites fluid may lead to constitutive activation of the EGFR and thereby contribute to metastasis and/or resistance to therapy. Acquired chemoresistance following initial chemotherapeutic treatment prevents clinical effectiveness and occurs in a large majority of patients. Thus, our studies evaluated the cellular consequences to prolonged EGF exposure/EGFR activation and how this could contribute to metastasis or chemoresistance. We found that extended exposure to EGF (10 nM, ~40 days) resulted in a change in cell phenotype that was retained even when the EGF ligand was removed for at least 7 days (removal). There was a persistent increase in N-cadherin and vimentin levels in EGF treated and removal cells. This increase in mesenchymal markers in EGF treated cells is associated with a significant increase in multicellular aggregate (MCA) compaction. Furthermore, EGF treated MCAs displayed a significant increase in cell spreading when allowed to adhere to collagen. MCA compaction and enhanced spreading were largely due to elevated N-cadherin levels as we found that knock down of N-cadherin resulted in less compact MCAs and reduced spreading on collagen. MCAs have been shown to be chemoresistant and the compact MCA structure due to prolonged EGF treatment conferred resistance to cisplatin treatment. Our results indicate that prolonged EGFR activation causes a persistent change in mesenchymal marker expression, which regulates MCA compaction and sensitivity to chemotherapeutics. This finding suggests that activators of the EGFR in the tumor environment may drive changes in ovarian cancer cells that contribute to the low patient survival rates.

Citation Format: Sabrina L. Samudio-Ruiz, Laurie G. Hudson. Continuous exposure to epidermal growth factor in ovarian cancer cells causes a persistent increase in N-cadherin expression which then results in multicellular aggregate compaction. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; Sep 18-21, 2013; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2013;19(19 Suppl):Abstract nr B57.
Abstract IA1: Mining the TCGA
Authors: Levine Douglas A.
Published: August 2014

The Cancer Genome Atlas (TCGA) has recently completed its first formal analysis of the genomic and clinical data from the ovarian carcinoma project. This analysis has confirmed previous knowledge and discovered new insights into this challenging disease. Now is the time for the research community to take hold of this high-quality, robust data set and apply it to translational and basic biologic questions. This session will review the nuts and bolts of The Cancer Genome Atlas comprehensive genomic profiling projects with special emphasis on the completed ovarian project. The sample inclusion criteria, clinical data, and molecular platforms will be reviewed in detail. The TCGA biospecimens pipeline will be discussed. Numerous analytical tools for individuals to download raw data and use previously processed data will be provided. Case studies of individual research projects that use TCGA data will be examined. This session will be useful for any scientists, surgeons, or physicians who are interested in learning more about the NIH-sponsored TCGA project. This session will also be beneficial for individuals interested in figuring out how to practically use the large volumes of data generated by TCGA to enhance ongoing and planned research projects. The goal of this session is to demonstrate how TCGA data can serve as a reliable resource for the greater research community.

Citation Format: Douglas A. Levine. Mining the TCGA. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; Sep 18-21, 2013; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2013;19(19 Suppl):Abstract nr IA1.
Abstract IA14: Exploiting the translational and functional opportunities for homologous recombination deficiency
Authors: Edmondson Richard John
Published: August 2014

Cancer is a disease of DNA, and the processes by which cells repair DNA damage are critical, not only in causing the disease but also in determining how the cancer cell will respond to treatment. Of the six major pathways by which DNA damage is repaired, homologous recombination (HR) is perhaps the best studied in ovarian cancer. This pathway is responsible for repairing double strand breaks and uses at least forty proteins, including both BRCA1 and BRCA2.

We have shown that 50% of high grade serous cancers are defective in homologous recombination and this group are more likely to be sensitive to platinum chemotherapy and have a better prognosis than tumours which are competent for the pathway. As may be expected, this group also includes all the tumours occurring in women with germline mutations of BRCA1 and BRCA2.

HR status has also been suggested to be predictive of response to PARP inhibitors and it is proposed that this is an example of synthetic lethality in which inactivation of one pathway is not harmful to a cell but inhibition of two (one by the PARP inhibitor and the other the underlying HR defectiveness) will render the cell non viable. We have confirmed in a large panel of ovarian cancer primary cultures and cell lines that HR defectiveness is indeed a very strong predictor of ex vivo drug sensitivity with positive and negative predictive values close to 100%. These data provide the basis for developing biomarker directed therapy for PARP inhibitors and provide a rationale for increasing the indication for these drugs to tumours other than those caused by germline mutations.

Challenges still exist however and current work is seeking to investigate the interplay of the different DNA damage repair pathways and how these may be used to further refine the biomarkers currently available.

Citation Format: Richard John Edmondson. Exploiting the translational and functional opportunities for homologous recombination deficiency. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; Sep 18-21, 2013; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2013;19(19 Suppl):Abstract nr IA14.
Abstract IA2: Cell lines as ovarian cancer models: Insights from molecular profiles in TCGA and CCLE
Authors: Schultz Nikolaus
Published: August 2014

Cancer cell lines are frequently used as in vitro tumor models. Recent molecular profiles of hundreds of cell lines from the Cancer Cell Line Encyclopedia (CCLE) and thousands of tumor samples from The Cancer Genome Atlas (TCGA) now allow a systematic genomic comparison of cell lines and tumors. We analyzed a panel of 47 ovarian cancer cell lines and identified those that have the highest genetic similarity to ovarian tumors. Our comparison of copy-number changes, mutations and mRNA expression profiles revealed pronounced differences in molecular profiles between commonly used ovarian cancer cell lines and high-grade serous ovarian cancer tumor samples. We identified several rarely used cell lines that more closely resemble cognate tumor profiles than commonly used cell lines, and we propose these lines as the most suitable models of ovarian cancer. Our results indicate that the gap between cell lines and tumors can be bridged by genomically informed choices of cell line models for all tumor types. The genomic profiles of these ovarian cancer cell lines and tumor samples can be explored and analyzed via the cBioPortal for Cancer Genomics (cbioportal.org).

Citation Format: Nikolaus Schultz. Cell lines as ovarian cancer models: Insights from molecular profiles in TCGA and CCLE. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; Sep 18-21, 2013; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2013;19(19 Suppl):Abstract nr IA2.
Abstract IA9: Pathway-directed therapy
Authors: Levine Douglas A.
Published: August 2014

The Cancer Genome Atlas (TCGA) has recently completed its first formal analysis of the genomic and clinical data from the ovarian carcinoma project. The landscape of ovarian cancer is changing due to our improved understanding of risk factors, histopathology, and cancer genomics. Ovarian cancer is a unique disease with extensive activation of canonical cancer pathways. This session will update the latest advances in ovarian cancer research with a focus on pathway-based therapeutics. The incorporation of biomarkers to predict clinical outcome and for the selection of molecularly targeted agents will be examined. Throughout the session examples will be provided from recent literature and clinical trials. At the conclusion of the session, the participants should have a better understanding of the latest molecular progress and the application to screening, prevention, and therapeutic stratification.

Citation Format: Douglas A. Levine. Pathway-directed therapy. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; Sep 18-21, 2013; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2013;19(19 Suppl):Abstract nr IA9.
The CDK4/6 Inhibitor LY2835219 Overcomes Vemurafenib Resistance Resulting from MAPK Reactivation and Cyclin D1 Upregulation
Authors: Yadav Vipin , Burke Teresa F. , Huber Lysiane , Van Horn Robert D. , Zhang Youyan , Buchanan Sean G. , Chan Edward M. , Starling James J. , Beckmann Richard P. , Peng Sheng-Bin
Published: August 2014

B-RAF selective inhibitors, including vemurafenib, were recently developed as effective therapies for melanoma patients with B-RAF V600E mutation. However, most patients treated with vemurafenib eventually develop resistance largely due to reactivation of MAPK signaling. Inhibitors of MAPK signaling, including MEK1/2 inhibitor trametinib, failed to show significant clinical benefit in patients with acquired resistance to vemurafenib. Here, we describe that cell lines with acquired resistance to vemurafenib show reactivation of MAPK signaling and upregulation of cyclin D1 and are sensitive to inhibition of LY2835219, a selective inhibitor of cyclin-dependent kinase (CDK) 4/6. LY2835219 was demonstrated to inhibit growth of melanoma A375 tumor xenografts and delay tumor recurrence in combination with vemurafenib. Furthermore, we developed an in vivo vemurafenib-resistant model by continuous administration of vemurafenib in A375 xenografts. Consistently, we found that MAPK is reactivated and cyclin D1 is elevated in vemurafenib-resistant tumors, as well as in the resistant cell lines derived from these tumors. Importantly, LY2835219 exhibited tumor growth regression in a vemurafenib-resistant model. Mechanistic analysis revealed that LY2835219 induced apoptotic cell death in a concentration-dependent manner in vemurafenib-resistant cells whereas it primarily mediated cell-cycle G1 arrest in the parental cells. Similarly, RNAi-mediated knockdown of cyclin D1 induced significantly higher rate of apoptosis in the resistant cells than in parental cells, suggesting that elevated cyclin D1 activity is important for the survival of vemurafenib-resistant cells. Altogether, we propose that targeting cyclin D1–CDK4/6 signaling by LY2835219 is an effective strategy to overcome MAPK-mediated resistance to B-RAF inhibitors in B-RAF V600E melanoma. Mol Cancer Ther; 13(10); 2253–63. ©2014 AACR.
Abstract A05: Functional genetic approach identifies cancer-specific requirement for BUB1B/BubR1 in human brain tumor isolates and genetically transformed cells
Authors: Ding Yu , Hubert Christopher , Herman Jacob , DeLuca Jennifer , Olson James , Paddison Patrick
Published: August 2014

Cancer cells give rise to distinctive and complimentary capabilities that enable them to continuously grow. These capabilities may as well generate additional vulnerabilities and can be targeted for therapy. To identify new candidate therapeutic targets for glioblastoma multiforme, we combined functional genetics and glioblastoma network modeling to identify kinases required for the growth of patient-derived brain tumor-initiating cells (BTIC) but that are dispensable to proliferating human neural stem cells (NSC). This approach yielded BUB1B/BUBR1, a critical mitotic spindle checkpoint player, as the top-scoring glioblastoma lethal kinase. Knockdown of BUB1B inhibited expansion of BTIC isolates, both in vitro and in vivo, without affecting proliferation of NSCs or astrocytes. Mechanistic studies revealed that BUB1B's GLE2p-binding sequence (GLEBS) domain activity is required to suppress lethal kinetochore-microtubule (KT-MT) attachment defects in glioblastoma isolates and genetically transformed cells with altered sister KT dynamics, which likely favor KT-MT instability. These results indicate that glioblastoma tumors have an added requirement for BUB1B to suppress lethal consequences of altered KT function and further suggest that sister KT measurements may predict cancer-specific sensitivity to BUB1B inhibition and perhaps other mitotic targets that affect KT-MT stability.

Significance: Currently, no effective therapies are available for glioblastoma, the most frequent and aggressive brain tumor. Our results suggest that targeting the GLEBS domain activity of BUB1B may provide a therapeutic window for glioblastoma, as the GLEBS domain is nonessential in untransformed cells. Moreover, the results further suggest that sister KT distances at metaphase may predict sensitivity to anticancer therapeutics targeting KT function.

Citation Format: Yu Ding, Christopher Hubert, Jacob Herman, Jennifer DeLuca, James Olson, Patrick Paddison. Functional genetic approach identifies cancer-specific requirement for BUB1B/BubR1 in human brain tumor isolates and genetically transformed cells. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr A05.
Abstract A20: Genome-wide RNAi screens in human brain tumor isolates reveal a novel viability requirement for PHF5A
Authors: Hubert Christopher G. , Bradley Robert K. , Ding Yu , Chad Toledo M. , Skutt-Kakaria Kyobi , Girard Emily J. , Davison Jerry , Berndt Jason , Corrin Philip , Basom Ryan , Delrow Jeffery J. , Webb Thomas , Pollard Steven M. , Lee Jeongwu , Olson James M. , Paddison Patrick J.
Published: August 2014

To identify key regulators of human brain tumor maintenance and initiation, we performed multiple genome-wide RNAi screens in patient-derived glioblastoma multiforme (GBM) stem cells (GSCs). These screens identified the PHD-finger domain protein PHF5A as differentially required for GSC expansion gene, as compared to untransformed neural stem cells (NSCs) and fibroblasts. Given PHF5A's known involvement in facilitating interactions between the U2 snRNP complex and ATP-dependent helicases, we examined cancer-specific roles in RNA splicing. We find that in GSCs, but not untransformed controls, PHF5A facilitates recognition of exons with unusual C-rich 3' splice sites in thousands of essential genes. PHF5A knockdown in GSCs, but not untransformed NSCs, astrocytes, or fibroblasts, inhibited splicing of these genes, leading to cell cycle arrest and loss of viability. Notably, pharmacologic inhibition of U2 snRNP activity phenocopied PHF5A knockdown both in GSCs and in multiple genetically transformed cell types, suggesting that a cancer-specific requirement for PHF5A activity may be generalizable to a wide range of cancers. Furthermore, PHF5A inhibition compromises GSC tumor formation in vivo and dramatically inhibits the growth of established GBM patient-derived xenograft tumors. Together, this work demonstrates an additional mechanism for maintaining splicing fidelity in cancer cells and also suggests that PHF5A activity may provide new in-roads for novel anti-GBM therapeutic strategies.

Citation Format: Christopher G. Hubert, Robert K. Bradley, Yu Ding, Toledo M. Chad, Kyobi Skutt-Kakaria, Emily J. Girard, Jerry Davison, Jason Berndt, Philip Corrin, Ryan Basom, Jeffery J. Delrow, Thomas Webb, Steven M. Pollard, Jeongwu Lee, James M. Olson, Patrick J. Paddison. Genome-wide RNAi screens in human brain tumor isolates reveal a novel viability requirement for PHF5A. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr A20.
Abstract A23: Genome-wide discovery of synthetic lethal interactions in PTEN-deficient human mammary epithelial cells
Authors: Tang Yew Chung , McPherson John , Tan Elisabeth , Goh Germaine , Bard Frederic , Rozen Steve
Published: August 2014

PTEN is one of the most frequently dysregulated tumor suppressor genes in human cancers, and PTEN deficiency is common in breast tumors, particularly those that belong to the aggressive basal-like breast cancer (BLBC) subtype. Because the BLBC subtype is itself very heterogeneous and basal-like tumors lack expression of cancer drug targets like HER2, there is currently no targeted therapy available for effective treatment. To systematically and comprehensively explore potential vulnerabilities in PTEN-deficient BLBC, we sought to discover genes that are synthetic lethal to PTEN loss using a functional genomics approach. We carried out a synthetic lethal siRNA screen in a pair of isogenic cell lines: an untransformed, non-tumorigenic human mammary epithelial cell line with molecular characteristics that closely mimic BLBCs (MCF10A), and a derivative cell line that harbored a targeted deletion of exon 2 in the PTEN gene (MCF10A-PTEN-/-). For greater sensitivity in detecting synthetic lethal effects, we used a high content screening system to determine total cell numbers by direct counting of stained cell nuclei after siRNA knock-down. Through the discovery of synthetic lethal interactions in these PTEN-deficient cell lines, we aim to identify novel components of the PTEN signaling network and uncover vulnerabilities in PTEN-deficient tumors. We first completed a pilot screen of kinase and phosphatase genes and identified synthetic lethal hits which were subsequently confirmed using multiple siRNA sequences for each gene. Our top candidate synthetic lethal genes were not directly involved in the PI3K-Akt signaling pathway, consistent with studies showing that therapeutic targeting of the PI3K pathway in PTEN-deficient cancers is not always effective. Using the strongest hit from the pilot screen as a positive synthetic lethal control, we further completed a whole-genome screen in the same pair of isogenic cell lines. We are currently validating the top candidate synthetic lethal genes and will explore if these putative synthetic lethal interactions are present in other PTEN-deficient breast cancer cell lines belonging to the BLBC subtype.

Citation Format: Yew Chung Tang, John McPherson, Elisabeth Tan, Germaine Goh, Frederic Bard, Steve Rozen. Genome-wide discovery of synthetic lethal interactions in PTEN-deficient human mammary epithelial cells. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr A23.
Abstract A27: Dissecting the functional landscape of triple-negative breast cancer
Authors: Maxfield Kimberly , Prat Aleix , Corcoran Kathleen , Whitehurst Angelique
Published: August 2014

Our group employed a pangenomic loss of function screening approach to systematically dissect the molecular architecture that functionally supports Triple Negative Breast Cancer (TNBC). Given that treatment options for this disease are typically limited to cytotoxic therapies, we applied a paclitaxel-based synthetic lethal approach to identify those molecular components that modulate chemoresponsiveness. To account for heterogeneity within the patient population, we screened 4 triple negative tumor-derived breast cancer cell lines that represent the spectrum of TNBC oncogenic aberrations and chemoresponse profiles. We also accounted for the two molecular subtypes, Claudin-Low and Basal-Like, that comprise the majority of TNBC cases. These screens revealed a number of core modulators of tumor cell viability and paclitaxel-induced cellular stress that have not been previously appreciated for supporting TNBC biology at the cell autonomous level. For example, this strategy implicated AMPK family member, SIK2, as a key nutrient sensor that may inhibit excessive autophagy. Inhibition of SIK2 leads to enhanced autophagic flux and a loss of cell viability in a variety of TNBC genetic backgrounds. In addition, we discovered the signaling supported by the cytokine receptor, CXCR3, and its ligand, CXCL9, to be repurposed to promote mitotic fidelity and thus, tumor cell fitness specifically in the Basal-Like TNBC molecular subtype. Finally, we uncovered a requirement for the transcription factor, ZNF165, in specifying the gene expression profiles activated by TGFβ signaling. In particular, the TGFβ target protein, SERPINE1, is required to promote prosurvival signaling in the Claudin-Low TNBC molecular subtype. Given that the expression of ZNF165 is otherwise restricted to the male testes, ZNF165 may represent a mechanism by which tumors engage anomaly-expressed proteins to promote survival. Taken together, we have uncovered novel tumor cell vulnerabilities in TNBC that could be therapeutically leveraged to enhance current therapeutic approaches.

Citation Format: Kimberly Maxfield, Aleix Prat, Kathleen Corcoran, Angelique Whitehurst. Dissecting the functional landscape of triple-negative breast cancer. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr A27.