bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract A87: Targeting the mitochondrial quality control machinery in acute myeloid leukemia
Authors: Jeyaraju Danny V. , Voisin Veronique , Ramakrishnan Ashwin , Hurren Rose , Maclean Neil , Gronda Marcela , Minden Mark , Bader Gary , Schimmer Aaron D.
Published: May 2016

Recently, we demonstrated that a subset of AML cells and stem cells have metabolic vulnerabilities in the mitochondria and oxidative phosphorylation (OXPHOS) chain that could impact on the ability of AML and AML stem cells to handle increased electron flux in the respiratory chain (Sriskanthadevan et al., Blood, 2015). To identify additional vulnerabilities in the mitochondria of AML cells and AML stem cells, we analyzed RNA expression levels of a panel of mitochondrial quality control proteins using the nCounter Analysis System (Nanostring technologies) in bulk as well as the progenitor enriched fraction of AML patients and normal donors. Among the top hits was the mitochondrial processing peptidase (MPP) that was upregulated in AML cells and progenitors compared to normal hematopoietic cells. MPP is a metallopeptidase composed of a regulatoryα subunit and a proteolytic β subunit that cleaves presequences from several nuclear encoded and mitochondrially imported proteins. To further analyze the expression of MPP in AML, we analyzed publicly available datasets (Eppert et al., (GSE30377), Laurenti et al., (GSE42414) and Norversthen et al., (GSE24759)). GSEA (Gene Set Enrichment Analysis) on stem enriched as well as bulk AML cells demonstrated upregulation of MPPα and β as well as increased expression of the mitochondrial protein import pathway in a subset of AML cells and stem cells compared to normal hematopoietic cells and stem cells.

To understand the importance of MPP in AML cells, we knocked down MPPα and β using shRNA in lentiviral vectors and confirmed target knockdown by immunoblotting. Knockdown of MPPα or β reduced the growth and viability of OCI-AML2 cells. Mechanistically, knockdown of MPP β increased mitochondrial ROS generation.

Thus, the mitochondrial protein import pathway is upregulated in a subset of AML cells and stem cells. Moreover inhibition of this pathway at the level of MPPα and β is cytotoxic to AML cells and disrupts mitochondrial function.

Citation Format: Danny V. Jeyaraju, Veronique Voisin, Ashwin Ramakrishnan, Rose Hurren, Neil Maclean, Marcela Gronda, Mark Minden, Gary Bader, Aaron D. Schimmer. Targeting the mitochondrial quality control machinery in acute myeloid leukemia. [abstract]. In: Proceedings of the AACR Special Conference: Metabolism and Cancer; Jun 7-10, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(1_Suppl):Abstract nr A87.
Abstract A89: Glycolytic cancer cell metabolism suppressed by transplantation of exogenous normal mitochondria into human breast cancer cells
Authors: Elliott Robert L. , Jiang Xian-Peng , Head Jonathan F.
Published: May 2016

Most cancer cells switch metabolism from mitochondria-based glucose oxidation to cytoplasmic glycolysis even under normoxia (the Warburg effect). The effect promotes tumorigenesis, cancer growth, invasion and drug resistance. We hypothesize that introduction of normal mitochondria into cancer cells might suppress the Warburg effect. Normal human (MCF-12A) and mouse (EpH4-Ev) mammary epithelia, and human breast cancer (MCF-7) and mouse mammary adenocarcinoma (4T1) cell lines were used in this study. We found that isolated fluorescent probe-stained mitochondria of MCF-12A or EpH4-Ev could enter into cancer cells when co-cultured with MCF-7 or 4T1 cells respectively, confirmed by fluorescent and confocal microscopy. The mitochondria from MCF-12A cells inhibited the proliferation of breast cancer MCF-7 cells in a dose dependent pattern and increased drug sensitivity of MCF-7 cells to doxorubicin, paclitaxel and carboplatin. Real time qPCR showed that exogenous normal mitochondria suppressed the gene expression of 11 glycolytic enzymes, and glucose transporter 1 and 3 of MCF-7 cells. These results suggest that normal mitochondria suppress cancer proliferation and increase drug sensitivity by the mechanism of inhibition of cancer cell glycolysis and glucose consumption. Isolated mitochondria have remained viable in culture for over three weeks and still actively entered cancer cells and inhibited cancer proliferation. In mouse model bearing the 4T1 mammary adenocarcinoma, isolated MitoTracker orange dye-stained mitochondria of EpH4-Ev, when directly injected into tumor mass, entered into 4T1 cancer cells in 24 hours. Therefore, normal mitochondrial transfer could be a cell-based therapy for cancer and other mitochondrial disorders.

Citation Format: Robert L. Elliott, Xian-Peng Jiang, Jonathan F. Head. Glycolytic cancer cell metabolism suppressed by transplantation of exogenous normal mitochondria into human breast cancer cells. [abstract]. In: Proceedings of the AACR Special Conference: Metabolism and Cancer; Jun 7-10, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(1_Suppl):Abstract nr A89.
Abstract B31: Disruption of Folliculin interacting protein-1 modulates Myc-driven metabolism, increasing cell death following metabolic stress
Authors: Ramirez Julita A. , Tsang Mark , Park Heon , Margineantu Daciana , Gu Haiwei , Raftery Daniel , Hockenbery David M. , Iritani Brian M.
Published: May 2016

Folliculin interacting protein-1 (Fnip1) is a cytoplasmic protein originally discovered through its interaction with Folliculin (Flcn), a tumor suppressor mutated in the rare fibrofolliculoma disorder Birt-Hogg Dubé syndrome. Fnip1 and Flcn both interact with the master metabolic regulator AMP kinase (AMPK). Our previous studies have shown that Fnip1 is required for the development of B-cells past the late pre-B stage (Park et al Immunity 2012) and for the development invariant natural killer T (iNKT) cells in the thymus (Park et al PNAS 2014). Fnip1 deficiency also prevented the development of B cell lymphoma in Eµ-Myc transgenic mice. Fnip1 deficient immune cells exhibited hyperactivation of mTORC1 concurrent with increased activation of AMPK. In this study, we examined the potential efficacy of Fnip1 disruption in cancer by disrupting Fnip1 in primary mouse and human B cell lines overexpressing the Myc oncogene. We show that constitutive depletion of Fnip1 in primary pre-B cells, conditional knockdown of Fnip1 in primary mouse mature B cells using the Cre-loxP system, or siRNA-mediated depletion of endogenous FNIP1 from a human B cell line expressing a conditional Myc allele, increase oxidative phosphorylation and Myc-induced glycolysis, which support cell division. Disruption of Fnip1 increases death of primary murine pre-B Eµ-Myc cells and human B cell lines in response to nutrient deprivation and chemotherapeutic drugs in vitro. Mass spectrometric analysis of a human B cell line depleted of Fnip1 reveals significant alterations in metabolites involved in glutaminolysis, glycolysis, antioxidant and serine biosynthesis pathways. These results suggest that inhibition of Fnip1 may provide a novel strategy to increase death of lymphoma cells in response to cytotoxic and metabolic stress.

Citation Format: Julita A. Ramirez, Mark Tsang, Heon Park, Daciana Margineantu, Haiwei Gu, Daniel Raftery, David M. Hockenbery, Brian M. Iritani. Disruption of Folliculin interacting protein-1 modulates Myc-driven metabolism, increasing cell death following metabolic stress. [abstract]. In: Proceedings of the AACR Special Conference: Metabolism and Cancer; Jun 7-10, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(1_Suppl):Abstract nr B31.
Abstract B33: Assessing the role of DGAT activity on lipid homeostasis and cancer cell survival
Authors: Ackerman Daniel , Qiu Bo , Xie Hong , Kamphorst Jurre , Simon M. Celeste
Published: May 2016

Studies on the effects of modulating the lipid composition of cells have found that increases in saturated fatty acid levels can lead to ER stress, activation of the unfolded protein response (UPR) and cell death. These effects may occur through saturation of the phospholipid pool and subsequent deterioration of ER membrane function. Changes in the composition of the ER membrane can be sensed by the two UPR stress sensors IRE1 and PERK and lead to activation of UPR targets.

Rapidly proliferating cancer cells frequently exhibit elevated ER stress due to their increased protein translation rate. In addition, the tumor microenvironment is frequently hypoxic and a lack of oxygen can inhibit the activity of the fatty acid desaturase SCD1. This leads to saturation of the fatty acid pool and renders the ER less able to cope with high levels of protein synthesis, making the maintenance of adequate lipid homeostasis of paramount importance to cancer cells within hypoxic tumor domains. Tumor cells adapt to these conditions through a variety of mechanisms, including the uptake of exogenous unsaturated lipid. Both hypoxia and the presence of certain oncogenic drivers have been found to increase lipid uptake, which was found to protect cancer cells against inhibition of SCD1.

Since fatty acids can be converted to triglycerides and stored within lipid droplets, we asked whether cancer cells also cope with saturation of their fatty acid pool by storing excess saturated fatty acids as triglycerides. Clear cell renal cell carcinoma (ccRCC) tumors are very fatty and lipidomic analyses have found high levels of triglycerides in ccRCC compared to normal kidney tissue. We inhibited triglyceride synthesis in A498 ccRCC cells by shRNA –mediated knockdown of DGAT enzymes, which catalyze the final step in the synthesis of triglycerides from fatty acids. We tested whether loss of DGAT activity causes sensitivity to tumor-like stresses and investigated its effect on xenograft tumor growth. Remarkably, while loss of DGAT activity has little effect on cancer cell proliferation under oxygen- and nutrient-rich conditions, loss of DGAT activity has large effects on xenograft tumor growth. We also find that loss of DGAT activity is often accompanied by increases in markers of ER stress. We are currently assessing the lipid composition of these tumors and determining what aspects of the tumor microenvironment sensitize cells to loss of DGAT activity.

Citation Format: Daniel Ackerman, Bo Qiu, Hong Xie, Jurre Kamphorst, M. Celeste Simon. Assessing the role of DGAT activity on lipid homeostasis and cancer cell survival. [abstract]. In: Proceedings of the AACR Special Conference: Metabolism and Cancer; Jun 7-10, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(1_Suppl):Abstract nr B33.
Abstract B43: The utilization of extracellular proteins as nutrients is suppressed by mTORC1
Authors: Palm Wilhelm , Park Youngkyu , Wright Kevin , Pavlova Natalya N. , Tuveson David A. , Thompson Craig B.
Published: May 2016

To engage in growth and proliferation, cells require a continuous supply of precursors for macromolecular synthesis. Despite being surrounded by diverse nutrients, mammalian cells preferentially metabolize glucose and free amino acids. However, it was recently shown that Ras-induced macropinocytosis of extracellular proteins could reduce a transformed cell's dependence on extracellular amino acids. Here, we show that macropinocytosis and lysosomal catabolism of extracellular proteins can serve as a source of essential amino acids. Lysosomal degradation of internalized proteins can sustain cell survival and induce lysosomal recruitment and activation of mammalian target of rapamycin complex 1 (mTORC1), but fails to elicit significant cell accumulation. Surprisingly, we discovered that unlike its growth-promoting activity under amino acid-replete conditions, mTORC1 activation suppresses proliferation when cells rely on extracellular proteins as an amino acid source. Inhibiting mTORC1 results in increased catabolism of endocytosed proteins and enhances cell proliferation during nutrient-depleted conditions in vitro and within vascularly compromised tumors in vivo. Thus, by preventing consumption of extracellular proteins as nutrients, mTORC1 couples growth to availability of free amino acids. These results may have important implications for the use of mTOR inhibitors as therapeutics.

Citation Format: Wilhelm Palm, Youngkyu Park, Kevin Wright, Natalya N. Pavlova, David A. Tuveson, Craig B. Thompson. The utilization of extracellular proteins as nutrients is suppressed by mTORC1. [abstract]. In: Proceedings of the AACR Special Conference: Metabolism and Cancer; Jun 7-10, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(1_Suppl):Abstract nr B43.
Abstract IA16: Mapping metabolic drivers of cancer using chemoproteomic and metabolomic platforms
Authors: Nomura Daniel
Published: May 2016

Cancer cells possess fundamentally altered cellular metabolism that not only leads to a re-wiring of cellular biochemistry, but also drives nearly every aspect of cancer cell pathogenicity. While targeting dysregulated metabolism is a promising strategy for cancer treatment, much of cancer metabolism has focused on well-understood metabolic pathways in central carbon metabolism (e.g. glycolytic or glutamine metabolism) underlying cellular transformation and early-stages of cancer, and has largely ignored many of cellular metabolic pathways or those networks involved in cancer progression, despite clear genetic or metabolic evidence of their involvement in cancer. Here, we describe chemoproteomic and metabolomic technologies that we have utilized to identifying unique and novel dysregulated metabolic drivers of cancer. In particular, we have identified several unique nodes within lipid and sialic acid metabolism that are essential in driving cancer pathogenicity.

Citation Format: Daniel Nomura. Mapping metabolic drivers of cancer using chemoproteomic and metabolomic platforms. [abstract]. In: Proceedings of the AACR Special Conference: Metabolism and Cancer; Jun 7-10, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(1_Suppl):Abstract nr IA16.
Abstract IA23: Use of viruses to study cancer metabolism
Authors: Christofk Heather R.
Published: May 2016

Viruses are powerful tools to study cancer metabolism. They trigger major metabolic changes in host cells to meet the bioenergetic and biosynthetic demands of virus infection - changes similar to the enhanced glycolysis and anabolic metabolism widely observed in cancer cells. However, unlike cancer cells, viruses undergo intense selection for efficiency, and rapidly and robustly reprogram host cell metabolism through activation of specific key flux-altering nodes, rather than whole metabolic pathway gene sets. We recently reported that adenovirus infection increases host cell anabolic glucose metabolism via MYC activation of specific metabolic target genes, only a subset of those turned on by MYC in many cancers. We are now investigating how adenovirus-induced MYC activation leads to selective transcription of target genes. Additionally, we have generated a list of the specific metabolic genes altered by adenovirus infection and are examining their role in anabolic metabolism, virus replication, and cancer proliferation. Because viruses are so efficient at reprogramming host cell metabolism towards increased anabolism, they represent a powerful tool to identify the most important metabolic enzymes for anabolic metabolism, and potentially the most promising cancer metabolism drug targets.

Citation Format: Heather R. Christofk. Use of viruses to study cancer metabolism. [abstract]. In: Proceedings of the AACR Special Conference: Metabolism and Cancer; Jun 7-10, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(1_Suppl):Abstract nr IA23.
Abstract A44: Clinical value of immunohistochemical expression of EGFL7 within high-grade serous ovarian cancer tissue.
Authors: Sznurkowski Jacek Jan , Zawrocki Anton , Pawlowski Maciej
Published: May 2016

Epidermal growth factor like domain 7 (Egfl7) is expressed by endothelial cells in normal tissues and by malignant cells in various human tumors.

Aim: to analyze patterns of immunohistochemical (IHC) staining of Egfl7 within high grade serous ovarian cancer (HGSOC) tissue and to assess clinical value of this biomarker.

Material and methods:

The IHC staining and pathological analyses were performed on paraffin-embedded primary tumours collected from 73 HGSOC patients with verified clinical history. Mouse anti-human monoclonal antibody against Egfl7, was used.

Egfl7 expressing tumors were classified qualitatively in accordance to intense of staining (HSCORE). The appropriate statistical analyses were performed. P-values of <0.05 were regarded as significant.

Results: Egfl7 was expressed by the cancer cells within 63 of 73 primary HGSOC tumors (68.3%). Endothelial expression of this biomarker was sporadic. Cancer cells presented two patterns of staining: cytoplasmic only in 50/72 cases (69.4%) and nuclear/cytoplasmic in 13/72 cases (18%). Median duration of the follow-up was 47.25 months (range 17–79 months)

Cytoplasmic expression of Egfl7 was not correlated with any of clinico-pathological features as well as with prognosis.

The presence of nuclear/cytoplasmic staining within HGSOC predicts worse response for chemotherapy and correlates with increased preoperative levels of CA125.

Conclusion: Cancer endogenous expression of Egfl7 is frequent within HGSOC tissue.

Predictive value of nuclear/cytoplasmic staining of Egfl7 for chemoresistance should be further evaluated.

Citation Format: Jacek Jan Sznurkowski, Anton Zawrocki, Maciej Pawlowski. Clinical value of immunohistochemical expression of EGFL7 within high-grade serous ovarian cancer tissue. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: Exploiting Vulnerabilities; Oct 17-20, 2015; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(2 Suppl):Abstract nr A44.
Abstract A56: Inhibition of Snail-induced EMT promotes anti-tumor immune response in ovarian cancer.
Authors: Taki Mana , Abiko Kaoru , Matsumura Noriomi , Baba Tsukasa , Hamanishi Junzo , Horikawa Naoki , Konishi Ikuo
Published: May 2016

Background: Peritoneal dissemination is a common mode of tumor progression in ovarian cancer, and one of the most important unfavorable prognostic factors. Epithelial-mesenchymal transition (EMT) has been indicated to be a key process in tumor invasion and metastasis. Recent studies demonstrate that EMT suppresses anti-tumor immunity in some types of cancer. The aim of the current study is to elucidate the relationship between EMT-related gene Snail and local immunity in ovarian cancer.

Methods: The expression of Snail and patient survival was analyzed in two microarray datasets, TCGA, and KOV75 (75 ovarian cancer cases operated in our department).

Using mouse ovarian cancer cell line HM-1, the influence of Snail expression on EMT, peritoneal dissemination, survival, and local immunity was analyzed using both in vitro and in vivo models. Snail-silenced cell line, HM1-sh-snail was established, and compared with the control HM-1.

Results: Among 4 subtypes of high grade serous ovarian cancer, Mesenchymal subtype, which show marked stromal reaction in histopathology, shows the worst prognosis (TCGA, KOV75). Snail expression was significantly high in Mesenchymal subtype (TCGA, p<0.0001; KOV75, p<0.05). High Snail expression was significantly related to short overall survival in TCGA (p<0.05).

In HM1-sh-snail, expression of vimentin and fibronectin was decreased in RT-PCR analysis. Cell migration was inhibited in wound-healing assay (p<0.001), but the cell proliferation was not altered in WST assay. In mouse peritoneal dissemination model, HM1-sh-snail group demonstrated longer survival than the control group (p<0.05). In mouse subcutaneous tumor model, HM-1-sh-snail group revealed smaller tumor than the control group (p<0.05), although there was no difference between two groups in nude mouse model.

Flow cytometric analysis of mouse tumors revealed that infiltration of CD4+ T cells and CD8+ T cells were all increased and MDSCs were decreased in HM1-sh-snail group.

Conclusion: Snail-induced EMT inhibits local immune reaction and promotes peritoneal dissemination in ovarian cancer. Snail may be a potential therapeutic target in ovarian cancer.

Citation Format: Mana Taki, Kaoru Abiko, Noriomi Matsumura, Tsukasa Baba, Junzo Hamanishi, Naoki Horikawa, Ikuo Konishi. Inhibition of Snail-induced EMT promotes anti-tumor immune response in ovarian cancer. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: Exploiting Vulnerabilities; Oct 17-20, 2015; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(2 Suppl):Abstract nr A56.
Abstract B01: Mutagenic and tumorigenic effects of follicular fluid in the context of p53 loss: Initiation of fimbria carcinogenesis.
Authors: Chu Tang-Yuan , Huang Hsuan-Shun , Hsu Che-Fang
Published: May 2016

Ovulation is the strongest risk factor for ovarian high-grade serous carcinoma (HGSC) that largely originates from the fallopian tube fimbriae and always carries loss-of-function mutations of TP53 in both early and late lesions. Mature ovarian follicle contains high level of reactive oxygen species (ROS). When released from ovulation, follicular fluid (FF) bathes the fimbriae and may lead to DNA double strand break (DSB) and neoplastic transformation. In this study, we examined the mutagenic and tumorigenic activities of human pre-ovulatory FFs. A subset (6/11) of FFs was found with high levels of ROS whereas the antioxidant capacities were indifferent. These ROS-high FFs induced intracellular ROS and DSBs in the secretory cell population of fimbriae epithelium. In the context of p53 and Rb deficiency in an E6/E7 immortalized fimbria secretory cell line, FF-exposed secretory cells overcame apoptosis and maintained the population carrying ROS and DSB. The cancer initiation effects of FF were further recapitulated in Trp53-/- mice. When introduced into the mammary fat pad, ROS-high but not ROS-low FFs induced early-onset B-cell lymphoma. Cotreatment with physiological concentration of melatonin, a potent antioxidant, ameliorated the mutagenic and tumorigenic effect of ROS-high FF in vitro and in vivo. The study revealed ROS and mitogens in mature ovarian follicles could initiate the transformation of fimbria epithelium in the context of p53 loss and melatonin is a potent preventive agent.

Citation Format: Tang-Yuan Chu, Hsuan-Shun Huang, Che-Fang Hsu. Mutagenic and tumorigenic effects of follicular fluid in the context of p53 loss: Initiation of fimbria carcinogenesis. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: Exploiting Vulnerabilities; Oct 17-20, 2015; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(2 Suppl):Abstract nr B01.
Abstract B49: Giant cancer stem cells of high-grade ovarian serous carcinoma .
Authors: Liu Jinsong
Published: May 2016

Polyploid giant cancer cells (PGCCs) have been observed by pathologists for over a century. PGCCs or nuclear atypia are an important diagnosis feature for high grade serous carcinoma and frequently present in post-chemotherapy patients and contribute to tumor heterogeneity, but their functions are largely undefined. Little attention has been given to these cells, largely because PGCCs have been generally thought to originate from repeated mitosis/cytokinesis failure and have no capacity for long-term survival and cell proliferation. Here we report that we successfully purified and cultured PGCCs from human ovarian cancer cell lines and primary ovarian cancer. These cells are highly resistant to oxygen deprivation and could form through endoreduplication or cell fusion, generating regular-sized cancer cells through budding or burst. They are positive for normal and cancer stem cell markers, divided asymmetrically and cycled slowly. They can differentiate into adipose, cartilage, bone, and erythroid cells. A single PGCC formed cancer spheroids in vitro and generated tumors in immunodeficient mice. PGCC-derived tumor gained a mesenchymal phenotype with increased expression of cancer stem cell markers CD44 and CD133 and become more resistant to the treatment of cisplatin. Together, our results reveal that the PGCCs present a resistant form of human cancer cells like mother cancer stem cells that can contribute to generation of daughter cancer stem-like cells. The PGCCs may play a fundamental role in regulating tumor heterogeneity, stemness, and chemoresistance in human cancer. In contrast to the phenotype unstable cancer stem cells selected by cell surface markers, PGCCs can be stably passaged and maintained, thus these cells provide reproducible experimental system to study mechanisms involved in generation of ovarian cancer stem cells.

Citation Format: Jinsong Liu. Giant cancer stem cells of high-grade ovarian serous carcinoma . [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: Exploiting Vulnerabilities; Oct 17-20, 2015; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(2 Suppl):Abstract nr B49.
Abstract B64: Suboptimal cytoreduction in ovarian carcinoma is associated with molecular pathways characteristic of increased stromal activation.
Authors: Liu Zhenqiu , Beach Jessica A. , Agadjanian Hasmik , Jia Dongyu , Aspuria Paul-Joseph , Karlan Beth Y. , Orsulic Sandra
Published: May 2016

Suboptimal cytoreductive surgery in advanced epithelial ovarian cancer (EOC) is associated with poor survival but it is unknown if poor outcome is due to the intrinsic biology of unresectable tumors or insufficient surgical effort resulting in residual tumor-sustaining clones. Our objective was to identify the potential molecular pathway(s) and cell type(s) that may be responsible for suboptimal surgical resection. By comparing gene expression in optimally and suboptimally cytoreduced patients, we identified a gene network associated with suboptimal cytoreduction and explored the biological processes and cell types associated with this gene network. We show that primary tumors from suboptimally cytoreduced patients express molecular signatures that are typically present in a distinct molecular subtype of EOC characterized by increased stromal activation and lymphovascular invasion. Similar molecular pathways are present in EOC metastases, suggesting that primary tumors in suboptimally cytoreduced patients are biologically similar to metastatic tumors. We demonstrate that the suboptimal cytoreduction network genes are enriched in reactive tumor stroma cells rather than malignant tumor cells. Our data suggest that the success of cytoreductive surgery is dictated by tumor biology, such as extensive stromal reaction and increased invasiveness, which may hinder surgical resection and ultimately lead to poor survival.

Citation Format: Zhenqiu Liu, Jessica A. Beach, Hasmik Agadjanian, Dongyu Jia, Paul-Joseph Aspuria, Beth Y. Karlan, Sandra Orsulic. Suboptimal cytoreduction in ovarian carcinoma is associated with molecular pathways characteristic of increased stromal activation. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: Exploiting Vulnerabilities; Oct 17-20, 2015; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(2 Suppl):Abstract nr B64.
Abstract B68: Erythropoietin stimulates ovarian tumor growth via EphB4.
Authors: Pradeep Sunila , Huang Jie , Mora Edna , Wu Sherry Y. , Li Chun , Lopez-Berestein Gabriel , Jackson David , Sood Anil
Published: May 2016

Background: Recombinant human erythropoietin (rhEpo) has been widely used to treat anemia in cancer patients, concerns about its adverse effects on patient survival have emerged. However the lack of correlation between expression of the canonical EpoR and rhEpo's effects on cancer cells prompted us to consider the existence of an alternative Epo receptor.

Methods: We analyzed the membrane-bound portion of the proteome for candidate receptors possessing structural, regulatory, and functional features consistent with Epo binding and tumorigenic signaling. To examine the potential for EphB4 binding to Epo, we generated EpoR-/- MEFs from EpoR-/- mice. We injected A2780-shControl and-shEpoR cells, shEphB4 or -shEpoR/shEphB4 cells in nude mice to study rhEpo induced tumor progression. We also assessed potential effects of tumoral EpoR or EphB4 expression on the effects of ESA treatment in patients with ovarian (N = 175) or breast (N = 88) cancer. Results: Through systems-based approaches we identified EphB4 as an alternate Epo receptor. MST experiments with fluorophore labeled rhEpo demonstrated binding to EpoR with an apparent dissociation constant (KD,app) of 28.0 ± 14.0 nM and EphB4 with a KD,app value of 880.6 ± 128.6 nM. EphB4 and EphrinB2 bound with a KD,app value of 140.5 ± 28.3 nM. We showed that [I125]rhEpo can bind to these cells EpoR-/- MEFs cells.

EphB4 triggered the downstream signaling via STAT3 and promoted rhEpo-induced tumor growth and progression. rhEpo stimulated in vivo growth of A2780-shControl (p<0.01) and-shEpoR cells (p<0.01), but not -shEphB4 or -shEpoR/shEphB4 cells. In human ovarian and breast cancer samples, expression of EphB4 rather than the canonical EpoR correlated with decreased disease-specific survival in rhEpo-treated patients. Conclusion: In this study, we identified a new mechanism that EphB4 as a critical mediator of erythropoietin signaling, which induced tumor progression in ovarian cancer patients. Altogether our study provides a novel and clinically significant dimension to the biology of erythropoietin, which was not appreciated before.

Citation Format: Sunila Pradeep, Jie Huang, Edna Mora, Sherry Y. Wu, Chun Li, Gabriel Lopez-Berestein, David Jackson, Anil Sood. Erythropoietin stimulates ovarian tumor growth via EphB4. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: Exploiting Vulnerabilities; Oct 17-20, 2015; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(2 Suppl):Abstract nr B68.
Abstract B74: Can we repurpose anti-malarial drug quinacrine to treat ovarian cancer?
Authors: Roy Debarshi , Khurana Ashwani , Kalogera Eleftheria , Wen Xuyang , Mondal Susmita , Shridhar Viji
Published: May 2016

Resistance to chemotherapy is a major hurdle that results in the increased mortality associated with ovarian cancer (OvCa). New therapeutics that synergize with cis-carboplatin/paclitaxel in recurrent tumors will have an enormous impact in prolonging the survival of OvCa patients. Due to the enormous cost of designing and testing new drugs, we have adopted the drug repurposing approach and tested the effect of the antimalarial drug quinacrine (QC) in sensitizing drug resistant OvCa cells to carboplatin induced cytotoxicity and determined that it is autophagy dependent. We have discovered that QC, an autophagy modulator exhibited distinct anti-cancer properties in OvCa cell lines in contrast to other anti-malarial/autophagy inhibitor drugs such as hydroxyquinacrine, bafilomycin A and 3-MA. It is well established that autophagy can be a survival mechanism under stress in cancer or a death promoting phenomenon that is cell type and contextual dependent. Here we demonstrate that QC acts to promote chemotherapy induced cell death specifically more in resistant cells in an autophagy dependent manner. Our preliminary data both in vitro and in vivo indicate that QC induced autophagy downregulates p62 and upregulates cathepsin L levels to sensitize the chemoresistant cells to autophagic and caspase mediated cell death in a p53 independent manner. These unexpected findings led us to explore the mechanistic basis of QC-induced upregulation of the cell cycle inhibitor p21 in cells bearing mutant p53. We uncovered that irrespective of p53 status, QC induces p21 expression in an autophagy-dependent p62-Skp2 mediated ubiquitin pathway resulting in cell cycle arrest and cell death. Since QC is already in PhaseI Clinical trial, these studies may spur new treatment strategies to improve OvCa patient outcome and patient care.

Citation Format: Debarshi Roy, Ashwani Khurana, Eleftheria Kalogera, Xuyang Wen, Susmita Mondal, Viji Shridhar. Can we repurpose anti-malarial drug quinacrine to treat ovarian cancer? [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: Exploiting Vulnerabilities; Oct 17-20, 2015; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(2 Suppl):Abstract nr B74.
Abstract IA07: Targeting checkpoint signaling and DNA repair in ovarian cancer.
Authors: Karnitz Larry M.
Published: May 2016

DNA damage and replication stress activate the ATR-Chk1 checkpoint signaling pathway in which ATR phosphorylates multiple substrates including the kinase Chk1. The ATR-Chk1 signaling pathway regulates DNA repair and cell cycle arrest and promotes the survival of tumor cells exposed to genotoxic chemotherapies. Accordingly, the ATR-Chk1 pathway has emerged as an attractive therapeutic target to increase the antitumor activities of chemotherapy agents, and selective ATR and Chk1 inhibitors have been developed. However, it remains unclear whether ATR and Chk1 inhibition are equally effective with genotoxic chemotherapies that have different mechanisms of action. Here, we compared ATR versus Chk1 inhibition in ovarian cancer cells exposed to agents (cisplatin, topotecan, gemcitabine, and PARP inhibitor) with different mechanisms of action that are used to treat this disease. We found that Chk1 inhibition selectively sensitized to gemcitabine, whereas ATR inhibition broadly sensitized to all chemotherapy agents. Importantly, ATR inhibition also robustly sensitized to PARP inhibitors even in cells with defective HR. These findings suggest that combining ATR inhibitors with these chemotherapy agents may a viable therapeutic strategy in HR-proficient and-deficient tumors.

Citation Format: Larry M. Karnitz. Targeting checkpoint signaling and DNA repair in ovarian cancer. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: Exploiting Vulnerabilities; Oct 17-20, 2015; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(2 Suppl):Abstract nr IA07.
Abstract IA16: Endometriosis-related ovarian cancer.
Authors: Shih Ie-Ming
Published: May 2016

Endometriosis-related ovarian neoplasms (ERONs) include clear cell carcinoma, endometrioid carcinoma, and, least frequently, seromucinous carcinomas. They belong to a unique group of ovarian tumors in that unlike other histotypes of ovarian cancer, these tumors are frequently associated with endometriosis, especially the lesions presenting as ovarian endometriotic cysts or endometriomas. ERONs usually present as large, unilateral, cystic neoplasms. In general, ERONs tend to behave in an indolent fashion because many of the diseases present at early clinical stages. When confined to the ovary, they have an excellent prognosis, but advanced stage tumors have a poor outcome. It has been demonstrated that ERONs can develop from endometriotic cyst epithelium through sequential stages of tumor progression. The microenvironment of an endometriotic cyst is highly inflammatory, and the cyst contains abundant iron-induced reactive oxygen species that are thought to be genotoxic and mutagenic. Chronic exposure of cystic epithelium to this microenvironment likely facilitates the accumulation of somatic molecular genetic changes that ultimately transform the cells and lead to tumor development. Molecular analyses of ERONs, including genome-wide analysis, have identified several alterations associated with aberrant activation or inactivation of pathways involving ARID1A, PI3K, Wnt, PP2A and mismatch repair. Specifically, canonical Wnt signaling pathway defects and microsatellite instability are more frequently detected in endometrioid carcinomas than in clear cell carcinomas. Among all of the molecular genetic changes identified to date, inactivating mutations of the ARID1A tumor suppressor gene are most common in ERON. Interestingly, ARID1A mutations are rarely observed in other types of ovarian cancer. ARID1A participates in the SWI/SNF chromatin remodeling complex, which plays a fundamental role in a variety of cellular processes, including DNA damage repair, telomere maintenance, transcription and DNA synthesis and methylation. The molecular events that dictate the development of different ERONs remain elusive, but studies using genetically engineered mouse models demonstrate that co-deletion of ARID1A and PTEN results in ovarian endometrioid carcinoma, while co-deletion of ARID1A and PIK3CA leads to formation of clear cell-like ovarian neoplasms in mice. However, deletion of ARID1A by itself is insufficient to drive ovarian tumor formation. Understanding the molecular changes and pathogenesis involved in the development of ERON is fundamental for future translational studies aimed at designing new diagnostic tests for outcome prediction and at identifying critical molecular features for target-based therapy.

Citation Format: Ie-Ming Shih. Endometriosis-related ovarian cancer. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: Exploiting Vulnerabilities; Oct 17-20, 2015; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(2 Suppl):Abstract nr IA16.
Abstract IA20: Biomarkers for risk prediction, screening, and early diagnostics.
Authors: Urban Nicole , Hawley Sarah , Janes Holly , Karlan Beth Y. , Drescher Charles W. , Daly Mary B. , Anderson Garnet L.
Published: May 2016

Objective: We developed and validated a hybrid risk classifier combining serum markers and epidemiologic risk factors to identify post-menopausal women at elevated risk for invasive fallopian tube, primary peritoneal, and ovarian epithelial carcinoma. The marker component of the classifier uses HE4 in addition to CA125. We have previously reported that HE4 may be useful as a confirmatory test for early diagnosis of ovarian cancer, when rising CA125 is used as a first-line screen.

Methods: To select epidemiologic risk factors for use in the classifier, Cox proportional hazards analyses were conducted using 74,786 Women's Health Initiative (WHI) Observational Study (OS) participants. To construct a combination classifier, 210 WHI OS cases and 536 matched controls with serum marker measurements were analyzed; validation employed 143 cases and 725 matched controls from the WHI Clinical Trial (CT) with similar data.

Results: Analyses identified a combination risk classifier composed of two elevated-risk groups: 1) women with either CA125 or HE4 exceeding a 98% specificity threshold; and 2) women with intact fallopian tubes, prior use of menopausal hormone therapy for at least two years, and either a first degree relative with breast or ovarian cancer or a personal history of breast cancer. In the WHI OS population, it classified 13% of women as elevated risk, identifying 30% of ovarian cancers diagnosed up to 7.8 years post-enrollment (Hazard Ratio [HR]=2.6, p<0.001). In the WHI CT validation population, it classified 8% of women as elevated risk, identifying 31% of cancers diagnosed within 7 years of enrollment (HR=4.6, p<0.001).

Conclusion: CA125 and HE4 contributed significantly to risk prediction in a classifier combining serum markers with epidemiologic risk factors. The hybrid risk classifier may be useful to identify post-menopausal women who would benefit from timely surgical intervention to prevent epithelial ovarian cancer.

Citation Format: Nicole Urban, Sarah Hawley, Holly Janes, Beth Y. Karlan, Charles W. Drescher, Mary B. Daly, Garnet L. Anderson. Biomarkers for risk prediction, screening, and early diagnostics. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: Exploiting Vulnerabilities; Oct 17-20, 2015; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(2 Suppl):Abstract nr IA20.
Abstract 03: The impact of chromosomal translocation locus and fusion oncogene coding sequence in synovial sarcomagenesis
Authors: Jones Kevin B. , Barrott Jared J. , Jin Huifeng , Haldar Malay , Capecchi Mario R.
Published: May 2016

Synovial sarcoma, the most common soft-tissue sarcoma in young adults bears a t(X;18) translocation that generates a fusion between SS18 (formerly SYT) and an SSX gene. SS18-SSX1 and SS18-SSX2 differ by only 13 amino acids. Clinically, SS18-SSX1 is more common, portends a worse prognosis, and demonstrates increased prevalence of biphasic histology. We conditionally expressed each fusion in otherwise identical mouse models, unexpectedly finding SS18-SSX2 to be more sarcomagenic than SS18-SSX1 and equally prone to biphasic histology. This suggested that coding sequence does not account for clinical differences between the fusions. Reanalysis of patient series found a gender bias in the prevalence of SS18-SSX2-expressing tumors, suggesting an X-linked effect and implicating the loss of native SSX2 by translocation as a hinderance to SS18-SSX2-driven synovial sarcomagenesis in males. Next, we confirmed that human synovial sarcomas almost universally express native SSX2, but not SSX1 and knock-down of native SSX2 in human synovial sarcoma cell lines blunted proliferation whereas overexpression of SSX2 enhances cell proliferation. In conclusion, we hypothesize that SSX2 facilitates sarcomagenesis in SS18-SSX1-expressing tumors and because our model of SS18-SSX2-expressing mice does not disrupt native SSX2 it recapitulates the prevalence and phenotype of SS18-SSX1 tumors.

Citation Format: Kevin B. Jones, Jared J. Barrott, Huifeng Jin, Malay Haldar, Mario R. Capecchi. The impact of chromosomal translocation locus and fusion oncogene coding sequence in synovial sarcomagenesis. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Integrating Clinical Genomics and Cancer Therapy; Jun 13-16, 2015; Salt Lake City, UT. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(1_Suppl):Abstract nr 03.
Abstract 44: Building patient-specific predictors of drug responses from cell line genomics
Authors: Szeto Christopher W. , Benz Stephen , Vaske Charlies
Published: May 2016

Hundreds of model cancer cell lines from diverse tissues have now been comprehensively assayed using several different genome-scale technologies. Additionally, many of these model lines have been challenged with dozens of clinically available oncotherapies. Here we present a set of high-throughput technologies suitable for turning these diverse datasources into actionable, patient-specific diagnostic predictors of response.

First, we computationally integrate diverse -omics data from the DNA, mRNA and protein levels into a pathway model of the cellular state. Next, parallel compute clusters are used to develop and evaluate accurate predictive models upon these pathway activity levels. Finally, these predictive models are used to suggest therapies in a patient-specific manner.

Here we show results from applying these technologies to learning a simple 50-gene signature for response to the the tyrosine kinase inhibitor Dasatinib. This signature utilizes features from the TP53/FOXM1, FOS/JUN & MYC pathways. We note that the exceptional responders to Dasatinib are enriched for nervous-system cancer cell lines. We applied our predictive signature to glioblastoma multiforme samples to correctly indicate which specific GBM patients may have respond to Dasatinib.

Citation Format: Christopher W. Szeto, Stephen Benz, Charlies Vaske. Building patient-specific predictors of drug responses from cell line genomics. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Integrating Clinical Genomics and Cancer Therapy; Jun 13-16, 2015; Salt Lake City, UT. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(1_Suppl):Abstract nr 44.
Abstract 45: Detection of focal somatic copy number variants in whole genome, whole exome, and targeted next-generation sequencing data of tumor/normal pairs
Authors: Aldrich Jessica , Keats Jonathan J. , Liang Winnie S. , Carpten John D. , Craig David W.
Published: May 2016

We describe the development and validation of an analysis pipeline for detection of focal somatic copy number aberrations from next-generation sequencing (NGS) data. In the clinical setting, tumor samples may be derived from historical tissue or from recently collected fresh frozen biopsies. DNA extracted from samples preserved as formalin-fixed, paraffin-embedded (FFPE) tissue are often highly degraded. We describe challenges inherent to sequencing different tissue sources and algorithmic approaches for optimizing detection of focal alterations in these samples with a high degree of accuracy. The first area of optimization takes into account clonal or fragment coverage based on user-defined intervals by accounting for coverage between paired-end reads. Normalized log2 fold-changes between tumor and normal samples are then calculated and a smoothing window is applied. In addition, we utilize tumor allele frequencies of known heterozygous germline SNPs identified within the normal to both evaluate potential false positives and correct biases. Lastly, a segmentation algorithm (circular binary segmentation as implemented in DNAcopy package1) is applied to summarize the individual log2 fold-changes into intervals with a constant copy number state. The results from the segmentation algorithm are then annotated and reformatted into the VCF format. We have analytically optimized and validated our algorithm across a series of samples with known alterations for implementation on both clinical and research samples.

1. Seshan VE and Olshen A. DNAcopy: DNA copy number data analysis. R package version 1.40.0.

Citation Format: Jessica Aldrich, Jonathan J. Keats, Winnie S. Liang, John D. Carpten, David W. Craig. Detection of focal somatic copy number variants in whole genome, whole exome, and targeted next-generation sequencing data of tumor/normal pairs. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Integrating Clinical Genomics and Cancer Therapy; Jun 13-16, 2015; Salt Lake City, UT. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(1_Suppl):Abstract nr 45.
Abstract IA10: Extracellular RNA: A next frontier of biomarker research for precision medicine
Authors: Tewari Muneesh
Published: May 2016

Development of effective, minimally invasive biomarker approaches for cancer is critical for enabling precision oncology. Whereas circulating tumor DNA (ctDNA) is one such approach that is now beginning to reach the clinic after an extended period of development, circulating extracellular RNA (exRNA) is a more recent discovery and represents a new frontier for precision medicine biomarker development. I will review the recent history of extracellular circulating RNA, beginning with the discovery of circulating microRNAs and extending to consider other classes of RNA found in human plasma. I will compare and contrast ctDNA and exRNA approaches, and highlight current challenges as well as possibilities for development of circulating exRNAs as biomarkers for precision oncology.

Citation Format: Muneesh Tewari. Extracellular RNA: A next frontier of biomarker research for precision medicine. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Integrating Clinical Genomics and Cancer Therapy; Jun 13-16, 2015; Salt Lake City, UT. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(1_Suppl):Abstract nr IA10.