bluuebunny/crossref_metadata_2025 huggingface dataset:
Index Based Hidden Outlier Detection in Metric Space
Authors: Xu Honglong , Mao Rui , Liao Hao , Zhang He , Lu Minhua , Chen Guoliang
Published: July 2016

Useless and noise information occupies large amount of big data, which increases our difficulty to extract worthy information. Therefore outlier detection attracts much attention recently, but if two points are far from other points but are relatively close to each other, they are less likely to be detected as outliers because of their adjacency to each other. In this situation, outliers are hidden by each other. In this paper, we propose a new perspective of hidden outlier. Experimental results show that it is more accurate than existing distance-based definitions of outliers. Accordingly, we exploit a candidate set based hidden outlier detection (HOD) algorithm. HOD algorithm achieves higher accuracy with comparable running time. Further, we develop an index based HOD (iHOD) algorithm to get higher detection speed.
A Critical Review on Wind Turbine Power Curve Modelling Techniques and Their Applications in Wind Based Energy Systems
Authors: Sohoni Vaishali , Gupta S. C. , Nema R. K.
Published: July 2016

Power curve of a wind turbine depicts the relationship between output power and hub height wind speed and is an important characteristic of the turbine. Power curve aids in energy assessment, warranty formulations, and performance monitoring of the turbines. With the growth of wind industry, turbines are being installed in diverse climatic conditions, onshore and offshore, and in complex terrains causing significant departure of these curves from the warranted values. Accurate models of power curves can play an important role in improving the performance of wind energy based systems. This paper presents a detailed review of different approaches for modelling of the wind turbine power curve. The methodology of modelling depends upon the purpose of modelling, availability of data, and the desired accuracy. The objectives of modelling, various issues involved therein, and the standard procedure for power performance measurement with its limitations have therefore been discussed here. Modelling methods described here use data from manufacturers’ specifications and actual data from the wind farms. Classification of modelling methods, various modelling techniques available in the literature, model evaluation criteria, and application of soft computing methods for modelling are then reviewed in detail. The drawbacks of the existing methods and future scope of research are also identified.
Abstract 101: Identification of pancreatobilliary cancer specific fusion genes in patient tissues
Authors: Kim Kahee , Jung Dawoon E. , Seo Mi-kyoung , Kim Sang Woo , Song Si Young
Published: July 2016

Gene fusion occurs when a part of one gene fuses with or attaches to a part of another gene by genome rearrangement and the result in gene fusion may possess oncogenic properties; fused gene may be translated into a unique protein that may promotes cancer properties. Pancreatic cancer and bile duct cancer are one of the most lethal cancer types with low 5-year survival rates, but lack of proper diagnostic or prognostic markers. Our aim was to investigate pancreatobilliary- specific fusion genes found in patient's specimens. We used TRIzol to extract total RNA from seven pancreatic cancer tissues and normal tissues from the same patients, and five bile duct cancer tissues and normal tissues from the same patients. Total RNA was assessed for RNA sequencing and the result data was analyzed using ChimeraScan to detect gene fusion. To identify the cancer somatic fusion gene, the fusion occurred in normal tissues and previously reported fusion genes found in normal tissues were excluded and the fusion occurred in coding region was included. As a result, we found 87 pancreatic cancer tissue specific- and 52 bile duct cancer tissue specific- fusion genes. We then selected fusion genes that either one of the gene has been reported to express in cancer tissues. We confirmed the expression of selected fusion genes by RT-PCR in cancer and normal tissues as well as in cancer cell lines. As a result we observed novel pancreatobilliary cancer specific fusion genes. These findings indicate the presence of novel fusion genes as well as its possible application for the early diagnosis or prognosis of pancreatic and bile duct cancer.

Citation Format: Kahee Kim, Dawoon E. Jung, Mi-kyoung Seo, Sang Woo Kim, Si Young Song. Identification of pancreatobilliary cancer specific fusion genes in patient tissues. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 101.
Abstract 1011: Endostatin regulates androgen receptor-mediated metabolic and oxido-reductive pathways in prostate cancer cells
Authors: Lee Joo Hyoung , Kang Minsung , Mobley James A. , Sonpavde Guru , Garvey W. Timothy , Darley-Usmar Victor M. , Ponnazhagan Selvarangan
Published: July 2016

Endostatin (ES) has been recognized for decades as an endogenous protein with antiangiogenic function. Recent findings, however, indicate the pleiotropic effects of ES in different tissue and cell types, ensuing further investigation on unidentified molecular mechanisms of action. Previously, we have shown that ES exerts a direct role in suppressing prostate cancer cell proliferation by inhibiting androgen receptor (AR) activity, signifying therapeutic potential of ES for targeting both tumor epithelia and endothelia. Subsequent to this finding, we identified robust glucose influx and significant reduction of intracellular ROS levels in LNCaP cells upon ES treatment. The ES mutants with low AR binding did not promote glucose uptake through GLUT1 augmentation, suggesting that AR-targeted effects of ES include modulation of downstream metabolic pathways. Surprisingly, global proteome analysis showed that the levels of major metabolic enzymes either in glycolytic pathway or TCA cycle were not changed upon ES treatment. Instead, ES markedly increased the levels of G6PD (5-fold), NAMPT (2.5-fold), and NAPRT (5-fold), indicating upregulation of the late-limiting steps in NAD biosynthesis and pentose phosphate pathway (PPP). Further proteome analysis of ES-treated LNCaP cells strongly indicated upregulation of ROS scavenging machinery, including SOD2 (3- fold), CAT (2-folds), GSS (2-fold), GSR (1.8-fold), and POR (4.6-fold). Overall, these data suggest that ES can modulate intracellular ROS levels by augmenting glucose uptake, NAD biosynthesis, and the NADPH levels by shunting metabolic pathways to PPP. Given that basal ROS levels are known to increase upon disease progression to higher grade prostate tumors, ES effect of promoting ROS scavenging machinery can be employed as an adjuvant to re-sensitize prostate cancer cells to ROS-inducing chemo- and radiation therapies.

Abbreviations: CAT: catalase, GLUT1: glucose transporter isoform 1, G6PD: glucose-6-phosphate dehydrogenase, GSS: glutathione synthase, GSR: glutathione reductase, NAMPT: nicotinamide phosphoribosyltransferase, NAPRT: nicotinate phosphoribosyltransferase, POR: NADPH-cytochrome P450 reductase, ROS: reactive oxygen species, SOD2: manganese superoxide dismutase, TCA: tricarboxylic acid

Citation Format: Joo Hyoung Lee, Minsung Kang, James A. Mobley, Guru Sonpavde, W. Timothy Garvey, Victor M. Darley-Usmar, Selvarangan Ponnazhagan. Endostatin regulates androgen receptor-mediated metabolic and oxido-reductive pathways in prostate cancer cells. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1011.
Abstract 1016: Variants in autophagy related genes and clinical characteristics in melanoma: a population-based study
Authors: White Kirsten A. m. , Luo Li , Thompson Todd A. , Torres Salina , Hu Chien-An A. , Thomas Nancy E. , Anton-Culver Hoda , Gruber Stephen B. , From Lynn , Busam Klaus J. , Orlow Irene , Kanetsky Peter A. , Marrett Lorraine D. , Gallagher Richard P. , Zanetti Roberto , Rosso Stefano , Dwyer Terry , Cust Anne E. , Venn Allison , Begg Colin B. , Berwick Marianne , Lillyquist Jenna
Published: July 2016

Autophagy has been linked with melanoma, but no polymorphisms in autophagy related (ATG) genes have been investigated for association with melanoma prognostic indicators and survival. We examined 5 ATG gene single nucleotide polymorphisms (SNPs) in a large international multicenter population-based case-control study of melanoma. DNA from 911 melanoma patients was genotyped for five SNPs with a known or suspected impact on autophagic flux. While we did not identify an association with survival, a significant association was identified between the minor allele for an ATG16L polymorphism (rs2241880) and a decrease in Breslow thickness (p = 0.03), earlier tumor stage at diagnosis (OR 0.47, 95% CI 0.27-0.81, p = 0.02) and younger age at diagnosis (p = 0.02). In addition, two SNPs in ATG5 (rs2245214 and rs510432) were found to be significantly associated with increased tumor stage of melanoma (OR 1.84 95% CI 1.12-3.02, p = 0.05; OR 1.47 95% CI 1.11-1.94, p = 0.03). Finally, we identified inverse associations between the minor allele of rs2245214 and melanomas on the scalp or neck (OR 0.20, 95% CI 0.05-0.86, p = 0.03); rs1864182 (OR 0.42, 95% CI 0.21-0.88, p = 0.02) and brisk TILs, and rs510432 (OR 0.55 95% CI 0.34-0.87, p = 0.01) with non-brisk TILs, although they were not globally significant. In summary, our data suggests that ATG SNPs, while not associated with survival, may be associated with Breslow thickness, tumor stage, age at diagnosis, and aggressive histopathological factors. These associations could contribute to our current understanding of the significant role of autophagy in melanoma progression.

Citation Format: Kirsten A. m. White, Li Luo, Todd A. Thompson, Salina Torres, Chien-An A. Hu, Nancy E. Thomas, Hoda Anton-Culver, Stephen B. Gruber, Lynn From, Klaus J. Busam, Irene Orlow, Peter A. Kanetsky, Lorraine D. Marrett, Richard P. Gallagher, Roberto Zanetti, Stefano Rosso, Terry Dwyer, Anne E. Cust, Allison Venn, Colin B. Begg, Marianne Berwick, Jenna Lillyquist. Variants in autophagy related genes and clinical characteristics in melanoma: a population-based study. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1016.
Abstract 1021: Lipidomic analysis: a powerful tool for evaluating lipid metabolism in cultured cancer cells
Authors: Eiríksson Finnur F. , Magnusdottir Manuela , Halldorsson Skarphedinn , Thorsteinsdottir Margret , Ögmundsdottir Helga M.
Published: July 2016

Lipids have numerous functions in biological processes, structural as well as regulatory. Cancer cells show differences from healthy normal cells in their metabolism, including lipid metabolism, which contribute to their survival and growth. Overexpression of fatty acid synthase (FASN) is commonly observed in cancer cells and there is also evidence of other lipid pathways being changed in tumor cells. The general aim of this project is to establish a lipidomic based UPLC-QToF method for evaluation of lipid composition in cultured cells of normal and cancerous origin using electrospray quadrupole traveling wave ion mobility Q-ToF mass spectrometry. Cell lines were selected based on their lipid metabolism, including three breast cancer cell lines: SK-Br-3 (overexpresses FASN), T47D (TP53-mutated), MCF7 (estrogen receptor-positive); and one pancreatic cancer cell line, ASPC-1(overexpresses 5-and 12-lipoxygenases). Furthermore, we analyzed the immortalized breast epithelial stem cell line D492 along with its subline, D492M, that has undergone epithelial to mesenchymal transition (EMT). Principal component analysis (PCA) revealed distinct differences in lipid composition between all the cell lines tested, each cell line showed a clear cluster of lipid components and patterns that were reproducible between experiments. The Sk-Br-3 was most clearly separated from the other two breast cancer cell lines. Further analysis revealed significant differences in levels of phosphocholins (PC) that are elevated in Sk-Br-3compared to other cell lines. Further investigations of the data have led to identification of certain PC that are different between cell lines. Significant differences were detected in the lipid composition of D492 and D492M. In conclusion, different levels of lipid-synthesizing enzymes are reflected in distinct lipid profiles in breast cancer cells. The observed differences in lipid profiles of the breast epithelial cell line and its mesenchymal-like subline may provide an insight into membrane changes associated with EMT and help evaluate lipidomes of tumor samples from patients in terms of invasive potential.

Citation Format: Finnur F. Eiríksson, Manuela Magnusdottir, Skarphedinn Halldorsson, Margret Thorsteinsdottir, Helga M. Ögmundsdottir. Lipidomic analysis: a powerful tool for evaluating lipid metabolism in cultured cancer cells. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1021.
Abstract 1022: The ketone body β-hydroxybutyrate down regulates c-Myc signaling in a malignant glioma model
Authors: Rossi Alex P. , Silva-Nichols Helena B. , Woolf Eric C. , Scheck Adrienne C.
Published: July 2016

Glioblastoma (GB) is the most common primary malignant brain tumor with a dismal median survival of 1.5 years. To address the need for novel therapeutics for the treatment of GB, investigations into high fat, low carbohydrate ketogenic diets (KD) have been explored as potential adjuvant therapeutic modalities. Preclinical studies of the KD in a mouse model of malignant glioma demonstrated that the KD extended median survival when used alone and substantially potentiated both radiotherapy and chemotherapy. However, the underlying mechanisms by which the KD exerts its therapeutic benefits remain poorly understood. A key result of the KD is the production of the ketone bodies β-hydroxybutyrate (βHB), acetoacetate, and acetone. Of these, BHB is the most prevalent ketone body produced. In order to elucidate the underlying molecular mechanisms of the KD, we have examined the interactions between BHB and the mouse glioma cell line GL261-Luc2. Previously, we demonstrated the ability of βHB to recapitulate the in vivo effects of the KD in tumor cells in an in vitro model. In the present study, we demonstrate that the ketone βHB is able to significantly down regulate the master transcription factor c-Myc, which is intimately involved in cell cycle progression, apoptosis, proliferation, DNA damage and repair, and metabolism. Overexpression of c-Myc is tied to a variety of human malignancies. In GB, upregulation of c-Myc signaling has been connected to an increase in tumor glucose metabolism. Furthermore, downregulating c-Myc expression has been demonstrated to confer sensitivity to tumors. We show that doses of both 5mM and 10mM βHB significantly reduced the expression of c-Myc in the GL261-Luc2 cell line when evaluated by both immunocytochemistry and western blot. Downregulation of c-Myc may, in part, be a mechanism by which βHB and thus the KD exert their radiosensitizing and antiproliferative effects on tumors. We intend to further investigate the role of c-Myc in the KD by investigating downstream targets of c-Myc as well as potential regulators of c-Myc transcription that are affected by BHB.

Citation Format: Alex P. Rossi, Helena B. Silva-Nichols, Eric C. Woolf, Adrienne C. Scheck. The ketone body β-hydroxybutyrate down regulates c-Myc signaling in a malignant glioma model. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1022.
Abstract 1028: A mouse model of allelic loss of the core autophagy gene BECN1 in ovarian cancer
Authors: Delaney Joe R. , Patel Chandni , Stupack Dwayne G.
Published: July 2016

Autophagy, a process of protein and organelle recycling, can both suppress and promote tumors. Gliomas, KRAS mutant, and BRAF driven tumor models require functional autophagy for maximal tumorigenicity and/or tumor progression. Inhibition of autophagy is able to eliminate many human cancer cell lines. However, allelic loss of the autophagy gene BECN1 is present in the majority of ovarian cancers, and BECN1 loss incurs early tumorigenesis in mouse models free of other oncogenic stimuli. Recent sequencing efforts and analyses, depending on the study, have both supported and refuted the relevance of BECN1 allelic loss in ovarian and breast cancers. To directly address the role of BECN1 allelic loss in ovarian cancer, we crossed BECN1 heterozygous knockout dams with MISIIR-TAg sires. In this model, the MISIIR promoter induces expression of large T antigen specifically in the ovarian and fallopian epithelium, inhibiting p53 activity and driving ovarian cancers in a manner befitting its human analogue. Here we present our pre-publication findings relating to the oncogenesis and progression of this murine BECN1 allelic loss model of ovarian cancer. We compare the in vivo murine results to those of in vitro human cell line models of beclin depletion, which exhibit higher basal dsDNA break repair signaling, mitochondrial stress, and reactive oxygen species generation.

Citation Format: Joe R. Delaney, Chandni Patel, Dwayne G. Stupack. A mouse model of allelic loss of the core autophagy gene BECN1 in ovarian cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1028.
Abstract 1041: Glutamine drives glutathione synthesis and contributes to radiation sensitivity of A549 and H460 lung cancer cell lines
Authors: Sappington Daniel , Penney Rosalind , Siegel Eric , Boysen Gunnar
Published: July 2016

Increased glutamine uptake is known to drive cancer cell proliferation, making tumor cells glutamine-dependent. Glutamine provides additional carbon and nitrogen sources for cell growth. The first step in glutamine utilization is its conversion to glutamate by glutaminase (GLS). Glutamate is a precursor for glutathione synthesis, and we investigated the hypothesis that glutamine drives glutathione synthesis and thereby contributes to cellular defense systems. The importance of glutamine for glutathione synthesis was studied in H460 and A549 lung cancer cell lines using glutamine-free medium and BPTES a GLS inhibitor. Metabolic activities were determined by targeted mass spectrometry. A significant correlation between glutamine consumption and glutathione excretion was demonstrated in H460 and A549 tumor cells. Culturing in the presence of [13C5]glutamine demonstrated that by 12 hrs >50% of excreted glutathione is derived from glutamine. Culturing in glutamine-free medium or treatment with Bis-2-(5-phenyl-acetamido-1,3,4-thiadiazol-2-yl)ethyl sulfide (BPTES), a glutaminase (GLS)-specific inhibitor, reduced cell proliferation and viability, and abolished glutathione excretion. Treatment with glutathione-ester prevented BPTES induced cytotoxicity. Inhibition of GLS markedly radiosensitized the lung tumor cell lines, suggesting an important role of glutamine-derived glutathione in determining radiation sensitivity. We demonstrate here for the first time that a significant amount of extracellular glutathione is directly derived from glutamine. This finding adds yet another important function to the already known glutamine dependence of tumor cells and probably tumors as well.

Citation Format: Daniel Sappington, Rosalind Penney, Eric Siegel, Gunnar Boysen. Glutamine drives glutathione synthesis and contributes to radiation sensitivity of A549 and H460 lung cancer cell lines. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1041.
Abstract 1048: Modulation of lipid metabolism through inhibition of acetyl-CoA carboxylase with ND-646 leads to potent inhibition of breast cancer cell growth in vitro and in vivo
Authors: Rocnik Jennifer L. , Miao Wenyan , Harriman Geraldine , Greenwood Jeremy , Bhat Sathesh , Harwood H. James , Kapeller Rosana , Westlin William F.
Published: July 2016

Metabolic attenuation is a promising approach to cancer therapy and rate-limiting steps in key biosynthetic pathways are particularly attractive targets. Many cancer types are dependent on fatty acid synthesis as a primary source of energy and for providing lipids for expansion of cell and nuclear membranes in rapidly proliferating cells. The rate-limiting enzyme in fatty acid synthesis, acetyl-CoA carboxylase (ACC), has been shown to be highly expressed in human breast cancer. ACC is thought to be critical for the growth and survival of cancer cells, especially within a tumor microenvironment where exogenous fatty acids might be limited. Effective therapeutic options for triple negative breast cancer are limited and identification of robust targeted agents without overt toxicity for this indication are especially needed. Dual inhibition of the ACC isozymes, ACC1 and ACC2, results in concomitant inhibition of fatty acid synthesis and stimulation of fatty acid oxidation. We have identified ND-646, a potent, selective, allosteric inhibitor of ACC with broad tissue distribution that binds to the ACC biotin carboxylase domain and potently inhibits the dimerization and enzymatic activity of both ACC1 (IC50 = 3.5nM) and ACC2 (IC50 = 4.1nM). Profiling the potency of ND-646 in vitro in a panel of breast cancer cell lines including triple negative and BRCA1 mutant cell lines demonstrated potent inhibition of cell proliferation with IC50s<100nM. The anti-proliferative effects were more pronounced when cells were cultured in media containing delipidated serum. Daily oral dosing of ND-646 at 25 mg/kg BID, 50 mg/kg QD, and 50 mg/kg BID in mice bearing orthotopic triple negative MDA-MB-468 breast cancer xenografts led to tumor growth inhibition of 60-70% that correlated with compound exposure and target engagement in the tumor. Analysis of ND-646 treated tumors demonstrated disruption of tumor tissue architecture and induction of apoptosis and necrosis suggesting a direct effect on cell survival. These results provide further evidence that de novo lipogenesis is an important mediator of breast cancer cell growth and survival, and that selective inhibition of ACC is a viable therapeutic strategy for treatment of breast cancer.

Citation Format: Jennifer L. Rocnik, Wenyan Miao, Geraldine Harriman, Jeremy Greenwood, Sathesh Bhat, H. James Harwood, Rosana Kapeller, William F. Westlin. Modulation of lipid metabolism through inhibition of acetyl-CoA carboxylase with ND-646 leads to potent inhibition of breast cancer cell growth in vitro and in vivo. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1048.
Abstract 1050: Inhibition of the polyamine synthesis pathway is synthetically lethal with loss of argininosuccinate synthase 1 in cancer
Authors: Szlosarek Peter W. , Locke Matthew , Ghazaly Essam , Lattanzio Laura , Lo Nigro Cristiana , Martin Sarah A.
Published: July 2016

Argininosuccinate synthetase 1 (ASS1) is the rate-limiting enzyme for arginine biosynthesis. ASS1 expression is lost in a range of different tumour types, including 50% of malignant pleural mesotheliomas. Starving ASS1-deficient cells of arginine with arginine blockers such as ADI-PEG20 can induce selective lethality and has shown great promise in the clinic. However, recent data has shown that ASS1-deficient tumours can become resistant to this therapy although the mechanisms behind this resistance remain unclear. We have generated the first model of ADI-PEG20 resistance in mesothelioma cells whereby we observe re-expression of ASS1, via demethylation of the ASS1 promoter. Through coordinated transcriptomic and metabolomic profiling, we have shown that ASS1-deficient cells have decreased levels of acetylated polyamines, resulting in an increased activation of the polyamine synthesis pathway. Upon arginine deprivation, we observe a decrease in polyamine metabolites in the ASS1-deficient cells only, suggesting that exogenous arginine is required to maintain polyamine biosynthesis in the absence of ASS1. We identify for the first time a compensatory increase in polyamine synthesis gene expression upon ASS1 loss and highlight a synthetic lethal dependence between ASS1-deficiency and polyamine metabolism, which could potentially be exploited for the treatment of ASS1-negative cancers.

Citation Format: Peter W. Szlosarek, Matthew Locke, Essam Ghazaly, Laura Lattanzio, Cristiana Lo Nigro, Sarah A. Martin. Inhibition of the polyamine synthesis pathway is synthetically lethal with loss of argininosuccinate synthase 1 in cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1050.
Abstract 1051: Activation of PI3K pathway in breast cancer associates with tumor phospholipid fatty acid composition
Authors: Hajjaji Nawale , Arbion Flavie , Fautrel Alain , Villalva Claire , Karayan-Tapon Lucie , Jourdan Marie-Lise
Published: July 2016

Background

Ever since the discovery of the PI3K/Akt/mTOR pathway key role in breast cancer resistance, several molecules have been developed to target this pathway. However, mechanisms of resistance restrain their efficacy. An in-depth understanding of the interactions of PI3K pathway is essential to improve its blockade and avoid resistance. Preclinical studies reported that lipid composition of cancer cells altered the activation of PI3K pathway, thus suggesting another possible molecular interaction with lipid metabolism. The aim of this study was to analyze the relationship between the activation of PI3K pathway and tumor lipid composition in breast cancer patients.

Methods

Frozen and formalin-fixed paraffin-embedded tumor specimens were retrieved for 50 French patients with stage I to III primary breast cancer treated uniformly with surgery, adjuvant chemotherapy, radiation therapy and endocrine therapy. The tumor specimens were analyzed for PIK3CA gene mutation, PTEN protein expression by immunohistochemistry, and pAktS473, pAktT308, mTOR, pS6K, and S6RP by protein array. Tumor total fatty acid (FA) and phospholipid FA compositions were analysed using mass spectroscopy. Pearson test was used for correlation analyses.

Results

Mean age was 53 years. All tumors were ER or PR positive and HER-2 negative, and 76% were node positive. PI3K mutation was observed in 14% of cases, and 34% were PTEN negative or had low PTEN expression. Mean tumor satured fatty acid (SFA) level was 33.78 mol%, monounsaturated FA (MUFA) level was 46.46 mol%, n-6 polyunsaturated FA (PUFA) level was 18.08 mol%, and n-3 PUFA level was 1.68 mol%. Large and high grade tumors had a higher SFA content. MUFA rich tumors were frequently low grade. There was a positive correlation between d18:1/C20:0 ceramide level and Akt, mTOR and p70S6K expression. mTOR expression also correlated with 18:0 lysophosphatidylserine (lysoPS), 36:1 PS, 38:3 PS, 38:5 PS, 40:5 PS, 40:6 PS, 34:0 phosphatidylcholine (PC), 34:1 PC, and 38:3 PC.

Conclusions

Our results show that SFA associated with a more aggressive tumor phenotype and that PI3K pathway activation significantly correlated with fatty acid composition of specific tumor phospholipids. These results suggest a potential role of tumor lipid metabolism in PI3K pathway activation.

Citation Format: Nawale Hajjaji, Flavie Arbion, Alain Fautrel, Claire Villalva, Lucie Karayan-Tapon, Marie-Lise Jourdan. Activation of PI3K pathway in breast cancer associates with tumor phospholipid fatty acid composition. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1051.
Abstract 1064: MicroRNA-based diagnosis and therapy in NRF2-stabilized tumor
Authors: Inoue Jun , Fujiwara Naoto , Yamamoto Shinsuke , Kawano Tatsuyuki , Inazawa Johji
Published: July 2016

NRF2 is a master transcriptional regulator that integrates cellular stress responses and is negatively regulated by KEAP1 at the posttranslational level. In human cancers, aberrantly stabilized NRF2, either by mutation of NRF2 or KEAP1, plays a vital role in chemoresistance and tumor cell growth through the transcriptional activation of target genes, suggesting that targeted inhibition of NRF2 is a potential therapy for NRF2-stabilized tumors. Some tumor-suppressing microRNAs (miRNAs) target multiple oncogenes concurrently and therefore may be useful as cancer therapeutic agents. Further, such miRNAs may be useful to address chemotherapeutic resistance in cancer, which remains a primary clinical challenge in need of solutions. Thus, cytoprotective processes upregulated in cancer cells that are resistant to chemotherapy are a logical target for investigation.

By using a reporter-coupled miRNA library screening, we have recently identified four miRNAs (miR-507, -634, -450a, and -129-5p) that negatively regulate the NRF2 activity by directly targeting. Importantly, downregulation of these miRNAs, in addition to the somatic mutation of NRF2 or KEAP1, is associated with stabilized NRF2 and poor prognosis in esophageal squamous cell carcinoma (ESCC). Interestingly, we found that overexpression of miR-634 activates the mitochondrial apoptotic pathway by direct concurrent targeting of genes associated with mitochondrial homeostasis, antiapoptosis, and autophagy, together with NRF2-mediated antioxidant ability. In particular, we showed how enforced expression of miR-634 enhanced chemotherapy-induced cytotoxicity in a model of ESCC, where resistance to chemotherapy remains clinically problematic. Our findings illustrate how reversing miRNA-mediated cytoprotective processes may offer a broadly useful approach to improving cancer therapy.

Citation Format: Jun Inoue, Naoto Fujiwara, Shinsuke Yamamoto, Tatsuyuki Kawano, Johji Inazawa. MicroRNA-based diagnosis and therapy in NRF2-stabilized tumor. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1064.
Abstract 1088: Efficient detection of germ cell cancer related miRNAs in serum using the TaqMan miRNA ABC purification bead kit in combination with the Taqman advanced miRNA assays
Authors: Looijenga Leendert HJ , Van Agthoven Ton , Gillis Ad
Published: July 2016

Malignant germ cell tumors, also known as germ cell cancers (GCC), are the most frequent cancer in young Caucasian males, with an increasing incidence during the last decades. They are clinically and histologically subdivided into seminomas and nonseminomas. The last can be composed of different elements, including embryonal carcinoma (the stem cell component), teratoma (TE) (somatic lineage) as well as yolk sac tumor (YST) and choriocarcinoma (CHC) (extra-embryonic lineages). The currently used serum markers, informative for both diagnosis as well as follow-up are AFP and hCG, predominantly indicative for the presence of the YST and CHC components. Recently, we reported that a selected set of miRNAs are highly expressed in all histological elements of GCC, with the exception of TE, including the miR 371-3 cluster. In addition to the presence in the primary cancers, they can also be identified in the serum of patients with such a malignancy, outperforming the classical markers AFP and hCG (Gillis and Rijlaarsdam et al. Molec. Oncol. 2013; Rijlaarsdam et al. Andrology, 2015). Here we demonstrate the power of the TaqMan Advanced miRNA Assays (PN 478007, Applied Biosystems) in combination with the use of the TaqMan miRNA ABC Purification Kit (PN 4473087, Applied Biosystems), starting with 50 μL human serum. The protocol includes polyadenylation of the miRNA targets at the 3’ end, followed by an adapter ligation at the 5’ end. Universal forward and reverse primers are used for amplification, followed by detection using the Applied Biosystems 7500 RealTime PCR System. Quality controls were added using dilution experiments of the cell lines, also included as inter-plate control, as well as for cDNA synthesis and RT-PCR efficiency. The non-human spike-ins ath-miR159a and cel-miR-39-3p were added as exogenous controls, while hsa-miR-30b-5p was used as endogenous control for normalization (reference). In total 30 GCC-related sera as well as 10 normal controls proved the informativity as well as efficiency of the developed pipeline in a standardized laboratory setting.

Citation Format: Leendert HJ Looijenga, Ton Van Agthoven, Ad Gillis. Efficient detection of germ cell cancer related miRNAs in serum using the TaqMan miRNA ABC purification bead kit in combination with the Taqman advanced miRNA assays. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1088.
Abstract 1109: AAGUGC-microRNAs are an integral part of an oncogenic signaling network driving non-small cell lung cancer proliferation
Authors: Zhou Yan , Frings Oliver , Fredlund Erik , Boekel Jorrit , Branca Rui M. , Orre Lukas M.
Published: July 2016

microRNA dysregulation is a common feature of cancer cells, but the complex roles of microRNAs in cancer are not fully elucidated. Here we used functional genomics to identify oncogenic microRNAs in non-small cell lung cancer (NSCLC) and to evaluate their impact on response to EGFR targeting therapy. Our data demonstrates that microRNAs with an AAGUGC-motif in their seed-sequence increase both cancer cell proliferation and sensitivity to EGFR inhibitors.

Using miR-372 as a prototypic AAGUGC-miRNA we set out to identify target mRNAs and an explanation to the discovered phenotype. Global transcriptomics, proteomics and target prediction, resulted in the identification of more than 500 candidate target mRNAs, including several tumor suppressors involved in the G1/S transition. The clinical relevance of our findings were evaluated by analysis of public domain data of NSCLC patients, revealing that almost 200 of the candidate target mRNAs showed a negative correlation to AAGUGC-miRNAs. In addition, the analysis of NSCLC clinical data supported the link between this microRNA seed-family and cancer cell proliferation and indicated that high expression of this type of microRNAs is associated with shorter relapse free survival.

Expanding the analysis to include additional types of cancer revealed large differences in expression of AAGUGC-miRNA both within and between cancer types. In general the results from the analysis of NSCLC was replicated in other cancer types, where expression of AAGUGC-miRNAs was associated with decreased mRNA levels of tumor suppressor targets and increased expression of genes involved in proliferation.

In conclusion we propose that AAGUGC-microRNAs are an integral part of an oncogenic signaling network, and that these findings have potential therapeutic implications, especially in selecting patients for EGFR-targeting therapy.

Citation Format: Yan Zhou, Oliver Frings, Erik Fredlund, Jorrit Boekel, Rui M. Branca, Lukas M. Orre. AAGUGC-microRNAs are an integral part of an oncogenic signaling network driving non-small cell lung cancer proliferation. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1109.
Abstract 1128: Role of STAT3 in pediatric sarcoma cell lines
Authors: Hariharan Seethalakshmi , Phelps Doris A. , Houghton Peter J.
Published: July 2016

Signal transducer and activator of transcription-3 (STAT3) is a transcription factor that plays a major role in embryonic development, cell growth, differentiation and apoptosis. STAT3 becomes activated in the cytosol via phosphorylation at tyrosine-705 by JAK-1/2 kinases, in response to stimulation of either cytokine receptors or receptor tyrosine kinases. Phospho-STAT3 forms dimers, which then translocate into the nucleus to function as a transcription factor. Various pro-survival and anti-apoptotic genes including VEGF, Bcl-xL, Bcl-2 and survivin have been identified as STAT3 gene targets. Constitutive activation of STAT3 is observed in various cancers including breast, lung, pancreatic cancers and sarcomas. Since our studies indicate that STAT3 is upregulated in a number of pediatric sarcomas as well, we set out to understand the functional significance of STAT3 activation in these tumors in the context of tumor cell proliferation, survival, migration and resistance to apoptosis.

High basal expression levels of phospho-STAT3 (Tyr705) were detected in a number of rhabdomyosarcoma, Ewing's sarcoma and osteosarcoma xenografts and cell lines. Interleukin-6 (IL-6) was capable of inducing STAT3 (Tyr705) phosphorylation in these cell lines in a time-dependent manner. On the other hand, stimulation with insulin-like growth factors-1 and 2 or IGF-1/2 resulted only in a weak induction in STAT3 phosphorylation during early timepoints. Treatment with a potent JAK-1/2 inhibitor, ruxolitinib suggested that STAT3 phosphorylation in these cell lines is dependent on JAK-1/2 activities.

To understand the role of STAT3 in tumorigenesis, STAT3 was either knocked down using siRNAs or STAT3 phosphorylation was attenuated using ruxolitinib in sarcoma cell lines that express constitutively activated STAT3. Neither complete knockdown of STAT3, nor inhibition of STAT3 phosphorylation by ruxolitinib inhibited proliferation or decreased survival. These results indicate that activation of STAT3 may not have a significant role in tumor cell proliferation and survival under culture conditions. However, STAT3 inhibition resulted in decreased cell migration implicating STAT3 in regulation of tumor cell migration and invasion.

Overall, our data demonstrates a role for STAT3 activation in sarcoma cell migration and invasion and we speculate that targeting STAT3 might serve as a useful therapeutic approach to control tumor invasion and metastasis. Supported by USPHS grant CA165995.

Citation Format: Seethalakshmi Hariharan, Doris A. Phelps, Peter J. Houghton. Role of STAT3 in pediatric sarcoma cell lines. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1128.
Abstract 1138: Prognostic impact of BRAF-V600E expression and correlation with mutation status in cutaneous melanoma
Authors: Hugdahl Emilia , Kalvenes May Britt , Puntervill Hanne , Ladstein Rita , Akslen Lars A.
Published: July 2016

Around 50% of primary cutaneous melanomas harbour BRAF mutations, but their prognostic impact has not been clear. Recently, a BRAF-V600E mutation-specific antibody has become available for immunohistochemistry (IHC). Here, we investigated for the first time the prognostic impact of BRAF-V600E protein expression in primary melanoma. In a patient series of 248 nodular melanomas, BRAF-V600E and total BRAF expression were assessed by IHC using tissue microarray sections of paraffin-embedded archival tissue. Mutation status was assessed by real-time PCR. Positive BRAF-V600E expression was present in 86 (35%) of the cases and was significantly associated with increased tumor thickness, presence of tumor ulceration and reduced survival. Further, BRAF-V600E expression was an independent prognostic factor by multivariate survival analysis. There was 88% concordance between BRAF-V600E expression and mutation status. Our findings indicate that BRAF-V600E expression is a novel prognostic marker in primary melanoma.

Citation Format: Emilia Hugdahl, May Britt Kalvenes, Hanne Puntervill, Rita Ladstein, Lars A. Akslen. Prognostic impact of BRAF-V600E expression and correlation with mutation status in cutaneous melanoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1138.
Abstract 1142: E2F1 impairs all-trans retinoic acid-induced osteogenic differentiation of osteosarcoma by promoting ubiquitination-mediated degradation of RARa
Authors: Zhou Qian , Ying Meidan , Yang Bo , He Qiaojun
Published: July 2016

Objective: All-trans retinoic acid (ATRA) is a widely-used differentiation drug that can effectively induce osteogenic differentiation of osteosarcoma cells, but the underlying mechanism remains elusive, which limits the clinical application for ATRA in osteosarcoma patients. In this study, we identified E2F1 as a novel regulator involved in ATRA induced osteogenic differentiation of osteosarcoma cells.

Methods: Osteosarcoma cell lines were used as our research models. (1) Protein levels were detected by Western blotting; (2) The interactions between E2F1 and RARalpha were determined by immunofluorescence, immunoprecipitation and GST pull-down assay; (3) The mRNA levels were determined by RT-PCR; (4) Related proteins and genes were investigated via transfection; (5) RARE activity were detected by luciferase reporter assay. (6) Alkaline phosphatase activity was assessed by colorimetric assay using BCIP/NBT Alkaline Phosphatase Color Development kit. Results: We observed that osteosarcoma cells are coupled with individual differences in the expression levels of E2F1 in patients, and E2F1 impairs ATRA-induced differentiation of osteosarcoma cells. Moreover, remarkable anti-proliferative and differentiation-inducing effects of ATRA treatment are only observed in E2F1 low to negative expressed primary osteosarcoma cultures. These results strongly suggested that E2F1 may serve as a potent indicator for the effectiveness of ATRA treatment in osteosarcoma. Interestingly, E2F1 is found to down-regulate retinoic acid receptor (RAR), a key factor determines the effectiveness of ATRA. E2F1 specifically binds to RAR and promotes its ubiquitination-mediated degradation; as a consequence, RAR-mediated differentiation is inhibited in osteosarcoma.

Conclusion: E2F1 may serve as a potent biomarker as well as a therapeutic target for ATRA-based differentiation therapeutics, and raise the hope of using differentiation-based approaches for osteosarcoma patients.

Citation Format: Qian Zhou, Meidan Ying, Bo Yang, Qiaojun He. E2F1 impairs all-trans retinoic acid-induced osteogenic differentiation of osteosarcoma by promoting ubiquitination-mediated degradation of RARa. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1142.
Abstract 1143: Pro-proliferative function of SIRT3 in a human melanoma xenograft mouse model
Authors: George Jasmine , Nihal Minakshi , Ndiaye Mary A. , Ahmad Nihal
Published: July 2016

Melanoma is one of the most aggressive forms of skin cancer and is often lethal, if not treated early. Therefore, it is necessary to try to develop novel target-based strategies to combat this neoplasm. SIRT3 is a nicotinamide adenine dinucleotide (NAD+) -dependent mitochondrial protein deacetylase involved in metabolism- and aging- related disorders, including certain cancers. Interestingly, studies have suggested both tumor suppressor as well as tumor promoter roles of SIRT3 in cancer. However, its role in melanoma is not well-established. Previously, we have shown that SIRT3 was upregulated in human melanoma cells and its lentiviral knockdown resulted in anti-proliferative effects in human melanoma cells. We also found that SIRT3 knockdown resulted in the G1-phase arrest of the cell cycle, induction of senescence, and decrease in cell migration. This study was designed to determine the relevance of our in vitro findings to the in vivo situation, in human melanoma xenograft models. Employing immunodeficient mice (Crl:NU-Foxn1nu, homozygous; Strain 088), we first determined the effect of SIRT3-knockdown on melanoma tumorigenesis. The mice were subcutaneously implanted with shNS-SK-MEL-2 (control) and shSIRT3-SK-MEL-2 (SIRT3-knockdown) melanoma cells, followed by assessing tumorigenesis of melanoma cells. We found that compared to shNS-SK-MEL-2 cells, shSIRT3-SK-MEL-2 cells showed a significantly decreased tumorigenic potential in these mice, in terms of average tumor volume (measured weekly) and average tumor weight (measured at termination of the study). Further, the Kaplan-Meier analysis showed that SIRT3 knockdown resulted in a significant survival advantage, in terms of reaching the cutoff tumor size (2.0 cm in one dimension). In an additional strategy, we determined the tumorigenicity of SIRT3 overexpressing melanoma cells (Hs294T-SIRT3) in NU/NU mice. Our data demonstrated that compared to control Hs294T-pcDNA cells, the SIRT3 overexpressing Hs294T-SIRT3 cells demonstrated a significantly enhanced tumorigenic potential (average tumor volume and tumor weight) in NU/NU mice. Overall, our study provides evidence supporting a pro-proliferative role of SIRT3 in melanoma and suggests that SIRT3 needs to be further evaluated as a potential druggable therapeutic target for melanoma management. However, detailed mechanistic and in vivo studies in relevant melanoma models are needed to further validate our findings.

Citation Format: Jasmine George, Minakshi Nihal, Mary A. Ndiaye, Nihal Ahmad. Pro-proliferative function of SIRT3 in a human melanoma xenograft mouse model. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1143.