bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 5411: Demonstrated improvements in tumor profiling with enzymatic ribosomal RNA depletion and streamlined RNA-sequencing library preparation
Authors: Nabilsi Nancy H. , Cheney Drew , Cloete Leendert , Jaarsveld Ida van , Kasinskas Rachel , Pavlica Jennifer 
Published: July 2017

Abstract
High resolution RNA analysis using next-generation sequencing (RNA-seq) is a rapidly growing application in cancer research. Formalin-fixed paraffin-embedded (FFPE) tissue is a ubiquitous resource for clinical studies. However, the ability to generate high quality libraries is confounded by the low quality and yield of RNA extracted from FFPE specimen. To enable optimal interrogation of such a clinically-relevant tissue resource, it is critical to identify RNA-seq library construction workflows that improve performance using challenging and degraded sample types. In this study, the effects of RNA type, quality, and quantity on RNA-seq library construction are assessed, and expectations regarding sequencing data quality are addressed. Included are recommendations for quality control measures and input-specific modifications that may improve performance Three workflows employing either bead-based or enzymatic strategies for the removal of ribosomal RNA content were used to prepare RNA-seq libraries from degraded paired breast normal and tumor samples. Enzymatic depletion followed by library preparation using the KAPA RNA HyperPrep1 workflow identified the highest number of transcripts for each sample, translating to a 4.9-fold increase in number of differentially expressed transcripts detected between normal and tumor samples. Of the transcripts identified as differentially expressed exclusively by Kapa, 174 are protein-coding RNAs, many of which are frequently dysregulated in breast cancer. In contrast, only two protein-coding RNAs were identified exclusively by the alternative workflows. RealTime Ready Custom panels were used for independent quantitative rt-PCR assessment. Of a subset of 71 transcripts identified exclusively by Kapa, up to 69 (97%) were validated as differentially expressed. Additional performance improvements of the KAPA RNA HyperPrep workflow include coverage balance across transcripts, lower duplication rate, technical replicate reproducibility, agreement across input quantities, and gene expression concordance between paired fresh frozen and FFPE samples. 1For Research Use Only. Not for use in diagnostic procedures.
Citation Format: Nancy H. Nabilsi, Drew Cheney, Leendert Cloete, Ida van Jaarsveld, Rachel Kasinskas, Jennifer Pavlica. Demonstrated improvements in tumor profiling with enzymatic ribosomal RNA depletion and streamlined RNA-sequencing library preparation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5411. doi:10.1158/1538-7445.AM2017-5411
Abstract 5412: Expression and inhibition of monocarboxylate transporters in canine osteosarcoma
Authors: Gardner Heather L. , Fenger Joelle M. , Sandanayaka Vincent P. , London Cheryl A. 
Published: July 2017

Abstract
Background: A distinguishing feature of cancer cells is their ability to undergo aerobic glycolysis, even in the presence of oxygen. This process generates lactic acid, which must be removed from the cell in order to maintain proliferation and survival. Monocarboxylate transporters (MCTs) move lactic acid across the plasma membrane, providing a mechanism for tumor cells to meet their bioenergetic needs during glycolysis in a variety of limiting microenvironments. The objective of this work is to determine the biologic effects of modulating cellular metabolism through inhibition of MCT1 and MCT4 in canine osteosarcoma (OS), a well-established spontaneous large animal model of the human disease.
Methods: MCT1 and MCT4 expression was assessed in canine OS cell lines using qRT-PCR and western blotting. Immunohistochemistry and qRT-PCR were performed to determine relative MCT1 and MCT4 expression in primary canine OS tissues. The effects of small molecule inhibitors (NGY066 and NGY008) and shRNA approaches targeting MCT1 and MCT4 on proliferation and survival of canine OS were examined using the CyQUANT Cell Proliferation and Caspase-3/7 assays, respectively. The impact of MCT1/4 inhibition on cellular oxygen consumption was evaluated using the Seahorse Cell Mito Stress Test. Lastly, potential synergistic effects of combining metformin and doxorubicin with MCT1/4 inhibition in canine OS cell lines were investigated using the CyQUANT Assay.
Results: We found that while both MCT1 and MCT4 are expressed in canine OS lines and tissues, MCT1 is expressed at higher levels relative to MCT4 in the cell lines. Small molecule inhibitors directed against MCT1 and MCT4 did not significantly inhibit cell proliferation or induce apoptosis even in the presence of limiting cell culture conditions. Maximal respiratory capacity was not increased in canine OS cell lines following inhibition of MCT1 and MCT4 function. However, synergistic anti-proliferative activity was observed when OS cells were treated with doxorubicin or metformin in the presence of MCT1 and MCT4 inhibitors.
Conclusions: MCT1 and MCT4 are expressed in canine OS, and therefore represent a good model to evaluate the therapeutic potential of manipulating lactic acid transport. Importantly, drug combinations with synergistic activity may be necessary to realize the full potential of MCT1/4 inhibition.
Citation Format: Heather L. Gardner, Joelle M. Fenger, Vincent P. Sandanayaka, Cheryl A. London. Expression and inhibition of monocarboxylate transporters in canine osteosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5412. doi:10.1158/1538-7445.AM2017-5412
Abstract 5416: Downregulation of PRMT6 promotes the Warburg effect in hepatocellular carcinoma via PKM2
Authors: Wong Tin Lok , Chan Lok Hei , Ma Stephanie 
Published: July 2017

Abstract
Hepatocellular carcinoma (HCC) is one of the top ranked causes of cancer death in the world, accounting for more than 740,000 deaths in 2012. Treatment of HCC is hindered by recurrence and resistance to chemotherapy. Altered metabolism in cancer has been linked to increased tumorigenicity and resistance to chemotherapeutics. One of the main features of altered metabolism is the Warburg effect, which is widely observed in solid tumor including HCC. Recently, our group have identified protein arginine methyltransferase 6 (PRMT6) as a tumor suppressor protein in HCC. Protein arginine methylation is a post-translational modification implicated in a variety of cellular functions including signaling and regulation of gene expression.Downregulation of PRMT6 expression was observed in HCC patients and knockdown of PRMT6 in HCC cell lines increased the tumorigenicity and sensitivity to both chemo- and molecular-targeted therapies. Other members of the Type 1 PRMT protein has previously been reported to be involved in glucose metabolism. Microarray profiling of HCC cells stably knockdown and overexpressed of PRMT6 showed enrichment of genes in glycolysis. We therefore hypothesize that reduced expression of PRMT6 in HCC drives the Warburg effect to support cancer progression. Metabolome profiling of HCC cells stably knockdown and overexpressed of PRMT6 showed enrichment of metabolites in glycolysis. Using Seahorse Extracellular Flux Analyzer, we show that stable knockdown of PRMT6 in HCC cell line drives glycolysis. This enhanced glycolysis rate is coupled with increased uptake of glucose, lactate production and pyruvate kinase activity. mRNA expression level of several glycolysis-related genes was screened by real-time quantitative PCR and we identified PKM2, a well-known regulator of the Warburg effect, as a potential link between PRMT6 and enhanced glycolysis. Knockdown of PRMT6 leads to an increase in mRNA and protein expression level of PKM2, but not PKM1 and PKLR, suggesting that PKM2 is the sole contributor for enhanced pyruvate kinase activity. In addition, by immunofluorescence staining, PKM2 is shown to accumulate in the nucleus following PRMT6 knockdown, where it has been shown to drive the expression of other glycolysis-related genes. In conclusion, PRMT6 regulates the expression level PKM2 and glycolysis of HCC cell. Ongoing studies are in progress to delineate the underlying mechanisms by which PRMT6 regulates PKM2 to drive Warburg effect.
Citation Format: Tin Lok Wong, Lok Hei Chan, Stephanie Ma. Downregulation of PRMT6 promotes the Warburg effect in hepatocellular carcinoma via PKM2 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5416. doi:10.1158/1538-7445.AM2017-5416
Abstract 5421: Differential expression of lysosomal acid lipase (LAL) between benign and malignant tissues among human organs
Authors: Gassim Mohamed EI , Mao Jinghe , Ma Tangen , Zhou Xinchun 
Published: July 2017

Abstract
Background: Lysosomal acid lipase (LAL), a lysosomal enzyme is able to degrade cholesteryl esters to free fatty acids and cholesterol. The information on the association of LAL with malignancies is limited. This study is to determine the difference in expression level of LAL between benign and malignant tissues among human organs.
Method: Immunohistochemistry (IHC) for human LAL was performed on A tissue microarray (TMA) containing 360 benign and malignant tissues from 36 human organs. The expression level of LAL was represented by an IHC score calculated by multiplying area score (0-3) with intensity score (0-3), ranged from 0 to 9. Student’s t-test was used to compare the mean IHC score between benign and malignant tissues in same organs.
Results: Eighteen out of 36 human organs have IHC stains on both benign and malignant tissues. As shown in Table 1, LAL expression level was higher in malignancy than in benign tissues in 9 organs. The difference in LAL expression level was significantly (or nearly lower in malignant tissues of adrenal gland, stomach, liver, testis and kidney.
Conclusion: The expression level of LAL varies among human organs. As compared with elevation of LAL expression level, decreased expression level of LAL in malignancies could be of more significance.
Table 1Difference in expression level of LALOrganmalignantBenignpM/BnMeanSEnMeanSEvalueRatioAdrenal Gland31.670.73560.950.02-1.36Stomach131.170.4583.130.820.035-2.7Liver131.350.3483.560.490.001-2.6Larynx80.250.0940.630.380.22-2.5Testis41.630.4743.750.750.054-2.3Uterus131.620.4272.570.970.302-1.6Kidney122.920.3134.50.870.051-1.5Prostate152.970.51441.22.389-1.3Urinary Bladder110.680.1750.70.30.9561Cervix41.630.4751.250.560.6361.3Colon162.340.3991.50.280.1451.6Esophagus41.630.992100.6951.6Ovary43.631.0741.940.930.2781.9Skin83.591.3251.850.720.3491.9Breast142.860.5861.380.550.1392.1Pancreas101.80.5590.830.140.1262.2Brain32.170.4450.80.560.144`2.7Lung81.970.7450.600.290.193.3
Citation Format: Mohamed EI Gassim, Jinghe Mao, Tangen Ma, Xinchun Zhou. Differential expression of lysosomal acid lipase (LAL) between benign and malignant tissues among human organs [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5421. doi:10.1158/1538-7445.AM2017-5421
Abstract 5426: LPA stimulates glycolytic shift in ovarian cancer
Authors: Ha Ji Hee , Radhakrishnan Rangasudhagar , Ward Jeremy D. , Jayaraman Muralidharan , Dhanasekaran Danny N. 
Published: July 2017

Abstract
Cancer cells resort to aerobic glycolysis to meet the increased energy consumption and growth requirement during active proliferation. While it has been observed that the cancer cells preferentially shift to aerobic glycolysis, the extraneous growth factors involved in this process is largely unknown. Since our previous studies have shown that lysophosphatidic acid (LPA) plays a critical role in the pathophysiology of ovarian cancers, we investigated the role of LPA in the metabolic reprogramming of ovarian cancer cells. Our results using XFe96 analyzer indicate that LPA stimulates aerobic glycolysis in multiple ovarian cancer cell lines as well as in patient-derived ovarian cancer cells. Physiological role for LPA in this process is demonstrated by the observation that the inhibitors of LPA-receptors attenuate the glycolytic shift stimulated by the ascitic fluid derived cancer patients. We further demonstrate that the silencing Gαi2, a downstream signaling mediator for LPA, inhibits LPA-stimulated glycolytic shift in ovarian cancer cells. Further analyses indicated that LPA-stimulated metabolic reprogramming involves the generation of reactive oxygen species (ROS). Treatment of cells with N-Acetyl Cysteine (NAC), a ROS-scavenger, inhibited the glycolytic shift stimulated by LPA. In addition, our studies point to a role for LPA-stimulated HIF1α activation in this process. These results indicate that LPA-stimulated metabolic reprogramming in ovarian cancer cells involve ROS-generation via LPA-Gαi2-HIF1α-dependent signaling pathway. Together with the findings that the glycolytic shift is crucially involved in tumor cell survival our studies point to LPA-Gαi2-HIF1α signaling axis as a potential target for therapy in ovarian cancer.
Citation Format: Ji Hee Ha, Rangasudhagar Radhakrishnan, Jeremy D. Ward, Muralidharan Jayaraman, Danny N. Dhanasekaran. LPA stimulates glycolytic shift in ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5426. doi:10.1158/1538-7445.AM2017-5426
Abstract 5431: Androgen receptor regulates the mitochondrial pyruvate carrier to fuel oncometabolism in prostate cancer
Authors: Bader David A. , Putluri Nagireddy , Hartig Sean M. , McGuire Sean E. 
Published: July 2017

Abstract
The metabolic underpinnings of androgen receptor (AR)-driven growth in prostate cancer (PCa) are underexplored, hindering the development of strategies to leverage the metabolic properties differentiating PCa from normal tissue. To this end, we discovered a subunit of the mitochondrial pyruvate carrier (MPC), MPC2, is a direct AR target gene that is increased in PCa specimens and associated with clinical outcomes. Our observation suggests a targetable link between AR signaling and carbon trafficking in PCa. Indeed, MPC inhibition delays proliferation and alters metabolic properties in hormone sensitive and castrate resistant AR-driven PCa models. Next, using 13C metabolic flux analysis coupled with a reverse phase protein array, we determined MPC inhibition results in activation of the eIF2α/ATF4 integrated stress response pathway to partially compensate for MPC inhibition by coordinating increased glutamine incorporation into the citric acid cycle. Therefore, to amplify the effect of MPC inhibition, we restricted glutamine availability during MPC inhibition and found this combination resulted in proliferative arrest. Last, we extended our efforts in-vivo and demonstrated combinatorial MPC/glutaminase inhibition resulted in a significant reduction in castrate-resistant prostate tumor xenograft growth in mice with no overt host toxicity. We anticipate our findings will accelerate the development of clinical strategies to therapeutically manipulate carbon flux to starve clinically lethal castrate-resistant PCa.
Citation Format: David A. Bader, Nagireddy Putluri, Sean M. Hartig, Sean E. McGuire. Androgen receptor regulates the mitochondrial pyruvate carrier to fuel oncometabolism in prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5431. doi:10.1158/1538-7445.AM2017-5431
Abstract 5432: Characterization of metabolic fuel dependency in multidrug resistant breast cancer cells
Authors: Kam Yoonseok , Romero Natalia , Swain Pamela , Dranka Brian P. 
Published: July 2017

Abstract
Multidrug resistance (MDR) is a common resistant mechanism of cancer cells to cytotoxic drugs in systemic therapy. MDR is characterized by increased expression of ATP-dependent drug exporting pumps which remove cytotoxic compounds from the cytosol. However, the mechanism whereby cancer cells rapidly respond to this increased ATP demand is not fully understood although the glycolytic nature of MDR phenotype has been evidenced repeatedly by previous reports. We thus hypothesized that flexibility and dependency on mitochondrial fuels would be altered in concert with the switch to glycolysis. In order to more accurate analyze glycolytic pathway, we newly developed an assay to improve glycolytic rate measurements by accounting for TCA-dependent CO2 contribution to extracellular acidification and to correlate Seahorse extracellular flux data with lactate production. In a comparison of glycolytic rates between MCF7 breast cancer cell line and its MDR variant MCF7/Dox using this new assay, we confirmed that in MCF7/Dox cells glycolysis rate under basal conditions is significantly increased compared to wild type cells. Furthermore, MCF7Dox presents a significant increase in compensatory glycolysis when mitochondrial ATP production is blocked. This metabolic profile switch is accompanied by a decreased dependency on glutamine to fuel mitochondrial respiration an increased tolerance of the MCF7/Dox cells to glutamine deprivation as compared to the MCF7 wild type. In contrast, dependency on glucose and fatty acids mitochondrial-oxidation was largely unchanged in MDR cells. Additionally, an increase in long chain fatty acid oxidation is observed when glucose and glutamine oxidation is blocked indicating that MDR cells has higher mitochondrial flexibility to compensate for inhibition of alternative fuels utilization although it preferentially uses glucose. Together these data demonstrate that acquisition of multidrug resistance in MCF7 cells fundamentally changes their metabolism from a glutamine-driven, oxidative phosphorylation dependent phenotype to a highly glycolytic and glucose-dependent phenotype. These findings have potential therapeutic relevance in the context of inhibition of specific mitochondrial fuel pathways to prevent therapy resistance.
Citation Format: Yoonseok Kam, Natalia Romero, Pamela Swain, Brian P. Dranka. Characterization of metabolic fuel dependency in multidrug resistant breast cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5432. doi:10.1158/1538-7445.AM2017-5432
Abstract 5433: β-Tubulin inhibitors reduce GLUT1 membrane trafficking to attenuate tumorigenesis in glioblastoma subtypes
Authors: Labak Collin M. , Guda Maheedhara R. , Asuthkar Swapna , Jain Neha , Lu Yining , Purvis Ian , Tuszynski Jack , Nakano Ichiro , Tsung Andrew J. , Velpula Kiran K. 
Published: July 2017

Abstract
Glioblastoma is an aggressive, high-grade tumor with poor prognosis due to lack of sound therapeutic options. Mesenchymal subtype GBMs are particularly difficult to treat because they tend to proliferate in the sub ventricular zone, an area that breeds stem-like neural cells and proves nearly impossible to access for surgical resection. They also contribute to creating a hypoxic microenvironment and switch to glycolytic metabolism in what is known as the Warburg Effect. Here, we hypothesize that strategically inhibiting the glucose transporter, GLUT1, through cytoskeletal components that traffic it to the cell membrane may reverse the Warburg Effect, attenuating further tumorigenesis and decreasing the stemness of such cells. Datamining studies and immunoblot analysis conducted on human glioblastoma patient specimens (hGBM) demonstrated that GLUT1 is highly upregulated. Limiting dilution assay conducted using GLUT1 inhibitors- fasentin and 2-Deoxy-D-glucose reduced the proliferation in mesenchymal cancer stem cell (CSC) subtype in in vitro culture. Simultaneously, mass spectrometric analysis revealed significant association between GLUT1 and β-tubulin 4 (TUBB4) in mesenchymal subtyped cells. This association was further confirmed by large-sample datamining and in immunoprecipitation studies from hGBM specimens, suggesting that TUBB4 may be a viable target in deterring the trafficking of upregulated GLUT1 to the membrane. Collectively, these studies confirm that GLUT1 is associated with TUBB4, and that targeting TUBB4 via siRNA or colchicine derivatives could prove effective in reversing the Warburg Effect in GBM cells and ultimately improve patient outcomes.
Citation Format: Collin M. Labak, Maheedhara R. Guda, Swapna Asuthkar, Neha Jain, Yining Lu, Ian Purvis, Jack Tuszynski, Ichiro Nakano, Andrew J. Tsung, Kiran K. Velpula. β-Tubulin inhibitors reduce GLUT1 membrane trafficking to attenuate tumorigenesis in glioblastoma subtypes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5433. doi:10.1158/1538-7445.AM2017-5433
Abstract 5434: Tumor necrosis factor receptor-associated protein 1 (TRAP1) as a potential target for glutamine addicted cancer cells
Authors: Vo Vu T. , Phan Ai N. , Hua Tuyen N. , Jeong Yangsik , Kang Byoung Heon , Kim Hyun-Won , Choi Jong-Whan 
Published: July 2017

Abstract
Glutamine, a non-essential amino acid, is an important nutrient which is involved in many biochemical pathways such as energy production, macromolecular synthesis, and oxidative stress scavenging. Glutamine metabolism is dysregulated in many cancers which mostly display glutamine addiction for cell proliferation. Thus, glutamine metabolism has become a potential target for treating cancer. Here we report that glutamine-dependent cancer cells are more susceptible for inhibiting cell proliferation with inhibitor treatment of Tumor Necrosis Factor Receptor-Associated Protein 1 (TRAP1), a downstream factor of oncogenic c-Myc involved in glutamine metabolism. Using cell proliferation and cell viability assays, we examined growth inhibitory effects of TRAP1 inhibitor, gamitrinib-triphenylphosphonium (G-TPP), on two groups of cell lines, glutamine-deprivation sensitive versus resistant cell lines. Included are cell lines for each group: HCC827 acquired gefitinib resistance and A549 for the sensitive; HuH7 for the resistant group. Glutamine-deprivation sensitive cell lines showed significant growth inhibition with TRAP1 inhibitor treatment while the corresponding resistant group of cell lines showed no growth inhibitory effects in the same treatment condition. This suggests a potential mechanistic connection of TRAP1 to c-Myc regulation in glutamine metabolism. Taken together, this finding provides a better understanding of oncogene-driven glutamine metabolism as well as evidence that TRAP1 is a promising therapeutic target for glutamine addicted cancer cells.
Citation Format: Vu T. Vo, Ai N. Phan, Tuyen N. Hua, Yangsik Jeong, Byoung Heon Kang, Hyun-Won Kim, Jong-Whan Choi. Tumor necrosis factor receptor-associated protein 1 (TRAP1) as a potential target for glutamine addicted cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5434. doi:10.1158/1538-7445.AM2017-5434