bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 3600: Next generation high capacity DNA damage detection assay for chemotherapy and genotoxic compound screening
Authors: Sykora Peter , Woodgate Sandra , George Jay , Sobol Robert W. 
Published: July 2016

Abstract
The mechanism of action of many classes of chemotherapeutic agents involves either the repression of DNA repair or an increase in DNA damage. However the measurement of DNA damage levels within a cell has been notoriously difficult and current methods to asses DNA damage potential of new chemotherapeutics have major technical flaws. The single cell gel electrophoresis (SCGE) assay is a long-standing method for measuring levels of DNA damage within a cell. The principle of SCGE is that DNA damage can cause DNA strand breaks in cells. These breaks cause the relaxation of the compact highly supercoiled DNA. The application of an electric field while the cells are embedded in agarose allows damaged DNA to migrate faster than intact DNA. The more breaks in the DNA, the further it will travel in the agarose resulting in the formation of a “comet” tail, the size and length of which directly correlates to the amount of DNA damage. The SCGE method benefits from both technical simplicity and high sensitivity. The major drawback is the assay is extremely laborious, lacks appropriate controls and has poor reproducibility. We have recently overcome these drawbacks by developing a 96-well plate format of the SCGE, aptly named “CometChip”. The CometChip uses micro-pillar technology to create an agarose 96-well chip where each well has approximately 300 micro-wells used to capture individual cells. Using this technology we can incorporate multiple treatments, controls and time points on a single CometChip which can then be rapidly analyzed using a fluorescence based imaging instrument. The utility of the new technology was tested using 75 different chemical compounds considered either genotoxic, non-genotoxic or unknown. The compounds were tested on two lymphocyte cell lines with different p53 status to compare the accumulation and repair of DNA damage. We report that the CometChip gives highly reproducible and accurate results without loss of sensitivity. In the high throughput screening approach using multiple CometChip apparatus, we estimate the throughput of the assay to be approximately 10,000% greater than doing traditional slide based comet analysis. The massive increase in processivity brings new opportunity for large-scale compound screening. The increased sensitivity coupled with large sample sizes will allow researchers the option to measure minor changes in DNA damage with unparalleled accuracy.
Citation Format: Peter Sykora, Sandra Woodgate, Jay George, Robert W. Sobol. Next generation high capacity DNA damage detection assay for chemotherapy and genotoxic compound screening. [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 3600.
Abstract 3635: Performance of the Agilent D5000 and high sensitivity D5000 ScreenTape assays for the Agilent 4200 TapeStation system
Authors: Nitsche Rainer , Prieto-Lafuente Lidia , MacDonald Claire , Pechtl Isabell 
Published: July 2016

Abstract
The Agilent 4200 TapeStation system provides automated, fast, and reliable DNA and RNA electrophoresis for up to 96 samples using prepackaged reagents and minimal manual handling. The Agilent D5000 ScreenTape and High Sensitivity D5000 ScreenTape assays have been developed for the separation and analysis of DNA fragments from 100 bp to 5,000 bp, a size range that complements and resides between the Agilent D1000 ScreenTape and the Genomic DNA ScreenTape assays. The 4200 TapeStation system and the DNA ScreenTape assays can be used at several steps of the Next Generation Sequencing (NGS) workflow. With the emergence of methodologies, such as the use of Transposomes, NGS library sizes are tending to increase beyond 1,000 bp, even for the short-read NGS technologies. This Poster focuses on the performance of both D5000 ScreenTape assays with respect to the accuracy and precision of quantification and sizing, as well as the sensitivity of these assays. Data analysis for quantification and molarity determination was compared against the corresponding assay for the Agilent 2100 Bioanalyzer system. Additionally, performance of both the D5000 and High Sensitivity D5000 assays on the 4200 TapeStation was compared to the 2200 TapeStation system.
Citation Format: Rainer Nitsche, Lidia Prieto-Lafuente, Claire MacDonald, Isabell Pechtl. Performance of the Agilent D5000 and high sensitivity D5000 ScreenTape assays for the Agilent 4200 TapeStation system. [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 3635.
Abstract 3657: ZBTB7A is a tumor suppressor and novel therapeutic target in triple-negative breast cancer
Authors: Molloy Mary Ellen , Lewinska Monika , Liu Xue-Song , Wang Angela A. , Yuan Zhi-Min 
Published: July 2016

Abstract
Due to lack of targeted therapies triple-negative breast cancers (TNBC) are the deadliest form of breast cancer, raising a pressing need to develop new therapeutic strategies. Recent advances in tumor metabolism have created exciting therapeutic opportunities by unveiling many previously unrecognized therapeutic targets. Like other tumor types, TNBCs also feature elevated glucose and glutamine metabolism (Shen, L., et al. 2015; McCleland, M., et al. 2012). A better understanding of the underlying mechanisms may uncover novel therapeutic targets for TNBC. Our lab has recently discovered that ZBTB7A suppresses glycolysis by transcriptionally repressing key genes within the glycolytic pathway in various cancer types (Liu, X.S., et al. 2014). Currently, ZBTB7A is proposed as an oncogene in breast cancer (Zu, X., et al. 2011), however our data suggest that ZBTB7A acts as a tumor suppressor specifically in TNBC. The purpose of this study was to determine the potential therapeutic value of targeting ZBTB7A in TNBC. Using publicly available databases, we find that low ZBTB7A expression is associated with poor prognosis in patients with hormone receptor-negative breast cancers. Our studies corroborate with patient derived data by demonstrating that reduced expression of ZBTB7A in TNBC cell lines leads to increased proliferation and resistance to radiation and chemotherapy. Differential gene expression analysis across human breast cancer samples in TCGA database revealed an inverse correlation between ZBTB7A and glycolytic genes. Overexpression of ZBTB7A in TNBC cells leads to decreased MCT1, LDHB and GLUT3 expression at the transcript level, consistent with our published data. Modulation of ZBTB7A expression also leads to changes in lactate production and glucose consumption in TNBC cells. Results from this study support ZBTB7A as a novel tumor suppressor and perspective therapeutic target in TNBC.
Citation Format: Mary Ellen Molloy, Monika Lewinska, Xue-Song Liu, Angela A. Wang, Zhi-Min Yuan. ZBTB7A is a tumor suppressor and novel therapeutic target in triple-negative breast 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 3657.
Abstract 3664: RARRES2 functions as a direct tumor suppressor by promoting beta-catenin phosphorylation and degradation independent of CMKLR1 and CMKLR1-mediated antitumor immune response in adrenocortical carcinoma
Authors: Liu-Chittenden Yi , Gaskins Kelli , Wang Sophie , Kebebew Electron 
Published: July 2016

Abstract
Tumor suppressors and the immune system are critical players in tumor suppression. However, little is known about whether a tumor suppressor can function through both immune-dependent and immune-independent mechanisms. RARRES2 is a small secreted protein that is down-regulated in multiple human cancer types such as adrenocortical carcinoma (ACC), hepatocellular carcinoma (HCC) and melanoma. It has been shown that RARRES2 can play an indirect tumor-suppressive role by acting as a chemoattractant to recruit anti-cancer immune cells expressing its receptor CMKLR1 to sites of tumor. In this study, we show that epigenetic CpG hypermethylation of RARRES2 in vivo and in vitro in ACC causes RARRES2 down-regulation. We also found that RARRES2 can function as a direct tumor suppressor and that its tumor suppressive effect does not depend on the recruitment of CMKLR1-expressing immune cells. We show that although exogenous treatment of cultured cells with recombinant human RARRES2 protein did not show any tumor-suppressive effect, transient overexpression of RARRES2 significantly inhibited cellular invasion. Stable overexpression of RARRES2 in ACC cell line NCI-H295R led to significantly reduced cell proliferation, cell invasion, and tumorigenecity in a RARRES2 dose-dependent manner. Using xenografts of stable NCI-H295R cell lines in two immunodeficient mouse models (athymic nude mice and NSG mice), we found that in the absence of functional immune cells, stable RARRES2 overexpression can still significantly suppress tumor growth in vivo. RARRES2 overexpression promoted beta-catenin phosphorylation and degradation, reduced the phosphorylation of p38 MAP kinase and inhibited the secretion of matrix metalloprotease protein 10 (MMP10) from cancer cells in a RARRES2 dose-dependent manner. Taken into account that CMKLR1 expression is barely detectable in all the cell lines tested, our results present the first evidence that RARRES2 can function as a direct tumor suppressor independent of CMKLR1 and CMKLR1-mediated anti-tumor immune response.
Citation Format: Yi Liu-Chittenden, Kelli Gaskins, Sophie Wang, Electron Kebebew. RARRES2 functions as a direct tumor suppressor by promoting beta-catenin phosphorylation and degradation independent of CMKLR1 and CMKLR1-mediated antitumor immune response in adrenocortical carcinoma. [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 3664.
Abstract 3671: Polarity and tumor development: Regulation by adenomatous polyposis coli
Authors: Lesko Alyssa C. , Chandra Madeline , Prosperi Jenifer R. 
Published: July 2016

Abstract
The process of epithelial polarity is tightly regulated by multiple complexes including aPKC, PAR, and Crumbs proteins. Our laboratory has recently investigated loss of Adenomatous Polyposis Coli (APC) in the MDCK 3D culture system. We have observed a lack of hollow lumens and mislocalization of podocalyxin (gp135) to the basal surface, both of which are independent of the canonical Wnt/β-catenin signaling pathway. We further showed that the c-terminus of APC, which contains binding domains for polarity proteins (Dlg and Scrib) and cytoskeletal proteins (microtubules and actin), is responsible for the observed phenotypes. In the current study, we have investigated the molecular mechanisms required for the inversion of polarity and the potential impact on tumorigenesis. We have made the novel observation that different mechanisms are responsible for the increased size versus altered polarity observed in cysts derived from APC-KD cells. Alterations in size, although independent of changes in proliferation and/or apoptosis, are regulated by the c-terminal domain, focal adhesion kinase (FAK), Src, and β1-integrin. Despite this, the mis-localization of gp135 is only rescued by the c-terminal domain of APC, suggesting a unique molecular mechanism. As loss of epithelial polarity is an early marker for tumor development, we investigated tumor-associated phenotypes. APC-KD cells were found to grow larger colonies in soft agar, and have increased migration in wound-filling assays, which appeared to be regulated through similar molecular mechanisms. These data suggest that APC regulates polarity and associated disease phenotypes (including kidney development, cardiovascular disease, and cancer) through pathways independent of Wnt signaling.
Citation Format: Alyssa C. Lesko, Madeline Chandra, Jenifer R. Prosperi. Polarity and tumor development: Regulation by adenomatous polyposis coli. [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 3671.
Abstract 3673: BVES dependent regulation of YAP1 in colorectal cancer cells
Authors: Mittal Mukul K. , Bilotta Anthony , Keating Cody E. , Short Sarah P. , Williams Christopher S. 
Published: July 2016

Abstract
Colorectal cancer (CRC) has a US incidence rate of almost 150,000 cases and accounts for over 10% of new cancer diagnoses. Dysfunction of epithelial adherens junctions and tight junctions (TJs) have long been implicated in CRC growth and metastasis The Popeye domain containing family of proteins are TJ-associated and appear to nucleate TJ formation. BVES or POPDC1 is one member of this family and is under-expressed in all stages of human colorectal carcinoma (CRC). On the other hand, YAP1 a novel oncogene in the Hippo pathway is up-regulated in many cancers including colon cancer. In the present study, we report an inverse correlation between tumor suppressor protein BVES and oncogene YAP1 in human colorectal carcinoma tumor samples and human colon cancer cell lines. We demonstrate that ectopic expression of BVES in BVES deficient cells decreases YAP1 protein while knocking down BVES in cells expressing BVES increases YAP1 levels. Cycloheximide (CHX) experiments indicate that this is likely occurring at the level of protein stability. CDK6 is a cell cycle regulator and YAP1 transcriptional target, and its levels are increased in the setting of BVES-knockdown in CACO2 cells. Concurrent with this there is increased cell growth. Conversely, when BVES is overexpressed, CDK6 transcription is reduced. Further knocking down of YAP1 in BVES knocked down cells reverses the cell growth advantage suggesting that BVES regulation of cell growth in part is dependent upon YAP1 protein levels. Co-immunoprecipitation (Co-IP) and yeast-2-hybrid (Y2H) assay also shows a direct interaction of BVES and YAP1. In sum, these findings suggest a novel mechanism underlying BVES tumor-suppressive function through regulation of a potential growth modulator, YAP1 in colorectal cancer.
Citation Format: Mukul K. Mittal, Anthony Bilotta, Cody E. Keating, Sarah P. Short, Christopher S. Williams. BVES dependent regulation of YAP1 in colorectal 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 3673.
Abstract 3678: The tumor suppressive small GTPase DiRas3 (ARHI) inhibits proliferation and activation of NF-κB in glioblastoma
Authors: Rymaszewski Amy , Straza Michael , Frei Anne , Bergom Carmen 
Published: July 2016

Abstract
Glioblastoma (GB) is the most aggressive malignancy affecting the central nervous system (CNS) with a median survival of 12 to 15 months even with surgery, radiation and chemotherapy. Previous research demonstrates that increased activation of NF-κB is critical for GB growth, proliferation and the up regulation of genes involved in cytokine production, cell cycle regulation, apoptosis and cell adhesion. Understanding the molecular targets that regulate NF-κB may provide more effective therapeutic targets for GB. DiRas family small GTPases, which are homologous to pro-oncogenic Ras GTPases, are tumor suppressive rather than tumor promoting and include DiRas1, DiRas2 and DiRas3 (ARHI). DiRas1 and DiRas2 have been suggested to be tumor suppressive in CNS malignancies, but the role of DiRas3 in CNS malignancies remains unknown. Here we demonstrate that expression of DiRas3 protein in GB cell lines is absent, although DiRas3 is expressed in non-malignant glial cells. Re-expression of DiRas3 in U-87 cells reduces cell proliferation by 20%. Using a NF-κB transcriptional activity luciferase reporter assay demonstrates that DiRas3 expression reduces NF-κB transcriptional activity by 70% compared to vector control. Further experiments demonstrate that decreased NF- κB activity occurs via reduced phosphorylation of the NF-κB inhibitor IκBα. The reduced phosphorylation of IκBα could be a result of decreased AKT and ERK activity, as increased ERK and AKT activity can stimulate NF-κB pathways. Our lab has previously demonstrated that the most common binding partner for DiRas1 and DiRas2 was the small GTPase binding protein SmgGDS, and DiRas1 and DiRas2 also reduce NF- κB activation. However, DiRas3 does not interact with SmgGDS, suggesting that DiRas3 can reduce NF-κB in a SmgGDS-independent manner. Understanding the role of DiRas3 and its binding partners in mediating NF- κB activation may lead to novel therapeutics for glioblastoma.
Citation Format: Amy Rymaszewski, Michael Straza, Anne Frei, Carmen Bergom. The tumor suppressive small GTPase DiRas3 (ARHI) inhibits proliferation and activation of NF-κB in glioblastoma. [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 3678.
Abstract 3686: Elephant TP53 (ep53) retrogene protein expression enhances cellular apoptosis in response to DNA damage
Authors: Abegglen Lisa M. , Robinson Rosann , Donovan Lauren , Caulin Aleah F. , Goldfeder Mor , Schroeder Avi , Maley Carlo C. , Schiffman Joshua D. 
Published: July 2016

Abstract
We previously reported that compared with other mammalian species, elephants have a lower than expected rate of cancer (Abegglen JAMA 2015). While exploring cancer resistance in elephants, we discovered that elephants have 20 copies of TP53 (1 ancestral gene with introns and 19 retrogenes) compared to humans with 1 copy. TP53 amplification was associated with increased p53-mediated apoptosis induced by DNA damage in elephant cells compared to human cells. As a follow up to this study, we further explored the function of these elephant TP53 retrogenes by expressing their protein (ep53) in cells with 2 functional TP53 alleles. NIH/3T3 cells were transfected with a mammalian expression construct encoding TP53 retrogene 9 fused to an epitope tag (myc). Western blot analysis probing for myc confirmed expression of retrogene 9. To measure the functional consequence of expression, we compared apoptosis of cells transfected with empty vector to cells transfected with myc-tagged retrogene 9 after doxorubicin treatment. Apoptosis was measured with a triplex assay that assesses viability, cytotoxicity and apoptosis (Apo Tox-Glo, Promega). We observed a significant increase in apoptosis of NIH/3T3 cells expressing retrogene 9 compared to empty vector transfected control cells (10μM doxorubicin, P&lt;0.001). These results suggest that ep53 is a functional protein contributing to cancer resistance in elephants, and that elephant retrogenes can function in cells from other species to enhance their apoptotic response to DNA damage. These findings may hold significance for human cancer prevention and treatment.
Citation Format: Lisa M. Abegglen, Rosann Robinson, Lauren Donovan, Aleah F. Caulin, Mor Goldfeder, Avi Schroeder, Carlo C. Maley, Joshua D. Schiffman. Elephant TP53 (ep53) retrogene protein expression enhances cellular apoptosis in response to DNA damage. [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 3686.
Abstract 369: Automating recovery of spiked tumor cells from blood
Authors: Sarinana Mark , Truong Ky , Cannon Keith , Guia Antonio 
Published: July 2016

Abstract
The isolation and study of circulating tumor cells (CTC) enables personalized medicine solutions, monitoring of therapeutics (theragnostics), and monitoring of minimal residual disease (MRD); culturing these rare cells is a frequent goal in cancer research, however the common methods for their isolation (gradient centrifugation, lysis buffer) are damaging to these cells, and many emerging technologies leave the cells bound in a consumable, bound to a biomarker or in a state that is difficult to use in cell culture. Further, the anuclear cells in blood greatly outnumber nucleated cells and present significant challenges to the study of the nucleated cells, for example, erythrocytes can absorb excitation or emission wavelengths in fluorescence studies, and their shape promotes rouleaux formation which can sequester the cells of interest; platelets also have a tendency to be activated by physical handling and cause aggregation that can also sequester and damage the cells of interest, and these all contain the greatest content of RNA and other markers that increase background noise in many assays. We demonstrate a new technology that automates the depletion of erythrocytes, thrombocytes, and plasma markers from, initially, small volumes of blood, using a micromachined membrane filter. We spiked small counts (10 to 1000 estimated from dilution) of tumor cell lines BT474 (breast cancer), DLD1 (colorectal cancer), and K562 (myelogenous leukemia) and other cell types into aliquots of blood. Using calcein-AM-loading to distinguish the spiked cells from blood cells, the recovery rates were determined in a flow cytometer, indicating an average of 80% ±4% (SE, N = 27) recovery of the rare cells after depletion of anuclear cells and plasma. The technology is amenable to use of beads for initial negative depletion of common nucleated cells by magnetic beads and has a recovery capacity of a few to as much as 3 million cells per specimen. Tumor cell lines alone that were run through this automation process then seeded for cell culture demonstrated growth rates indistinguishable from those seeded in similar counts in a regular cell passage. In further studies we demonstrate depletion of leukocytes with magnetic beads and of anuclear cells by filtration to handle larger blood volumes. The filtration system may be used for automated recovery of nucleated cells or cell clusters from blood or other fluid samples (liquid biopsies) without use of harsh chemicals or centrifugation, removing a common barrier for emerging analytical approaches.
Citation Format: Mark Sarinana, Ky Truong, Keith Cannon, Antonio Guia. Automating recovery of spiked tumor cells from blood. [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 369.