bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4234: The use of a synthetic peptide-DNA complex as an internal reference for chromatin immunoprecipitation.
Authors: Li Zirong , Thyagarajan Bhaskar , Rosenfeld John , Solache Alejandra , Sturges Michael 
Published: August 2014

Abstract
Chromatin immunoprecipitation (ChIP) is an analytical method used to investigate interaction of proteins with specific genomic DNA regions in vivo to provide a better understanding of mechanisms of gene regulation, DNA replication and DNA repair. However, variations in the efficiency of immunoprecipitation, background signals from carryover in immunoprecipitation, and loss of material during immunoprecipitation and purification of the ChIP DNA are sources of variability that restrict the use of ChIP as a quantitative tool. To address these limitations, we have developed a simple spike-in control that enables labs to generate results that are more consistent and more quantitative. The approach we have developed uses a synthetic peptide-DNA reagent that is spiked into chromatin immunoprecipitation reactions. Because this reagent mimics the behavior of cross-linked chromatin and can be quantitatively recovered by immunoprecipitation, it can be readily incorporated in to virtually any ChIP protocol. To utilize this internal control, a fixed amount of the synthetic peptide-DNA complex is spiked into the chromatin and co-ChIPed simultaneously with the antibody of interest. The recovered synthetic DNA is then used to normalize the results obtained with the antibody of interest. This spike-in control can be designed using a peptide specific to the ChIP antibody of interest and recovered using a single antibody. Alternatively, a universal spike-in control can be designed using a peptide that is recognized by an epitope tag antibody. This universal spike-in control and epitope tagged antibody are used along with the antibody of interest in a standard ChIP reaction. Our data show that the inclusion of our internal control significantly reduces variability between ChIP assays, thus increasing the accuracy of the ChIP data. Because of the universal feature, this method can also be used to compare ChIP data between different antibodies or to normalize data variations that often result between users and multiple experiments.
Citation Format: Zirong Li, Bhaskar Thyagarajan, John Rosenfeld, Alejandra Solache, Michael Sturges. The use of a synthetic peptide-DNA complex as an internal reference for chromatin immunoprecipitation. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4234. doi:10.1158/1538-7445.AM2013-4234
Abstract 4242: Methylation, SNP and expression analysis of the Vitamin D receptor (VDR) gene in different tumor tissues.
Authors: Poulin Matthew L. , Meyer Ann , Gonzalez Gregory , Bi Kevin , Yan Liying 
Published: August 2014

Abstract
The vitamin D receptor gene encodes the nuclear hormone receptor for vitamin D3 and belongs to the family of trans-acting transcriptional regulatory factors and shows sequence similarity to the steroid and thyroid hormone receptors. Downstream targets of this nuclear hormone receptor are principally involved in mineral metabolism though the receptor regulates a variety of other metabolic pathways, such as those involved in the immune response and cancer. In light of evidence for promoter methylation of the vitamin D receptor in the control of the expression of this gene, we have designed methylation assays that cover many regions of this gene in order to determine its methylation profile in normal individuals, ovarian tumors and ovarian cell lines. We have isolated the DNA from ten tumor tissues and their adjacent normal tissue from four different tumor types; ovarian, breast, colon and cervical. By utilizing a combination of bisulfite sequencing, SNP genotyping, and expression analysis, we show that there are distinct patterns of methylation levels between different regions of the VDR gene in each of the cancers observed. We have also analyzed a number of SNPs within these genes and show a possible correlation with the methylation and /or expression of the genes and the SNP genotypes. These data may provide information that could lead to the development of biomarkers for different cancers.
Citation Format: Matthew L. Poulin, Ann Meyer, Gregory Gonzalez, Kevin Bi, Liying Yan. Methylation, SNP and expression analysis of the Vitamin D receptor (VDR) gene in different tumor tissues. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4242. doi:10.1158/1538-7445.AM2013-4242
Abstract 4249: Landscape of DNA methylation status of human hepatocellular carcinoma revealed by Human Methylation BeadChip 450K.
Authors: Nishimura Takafumi , Mori Yukiko , Nishida Naoshi 
Published: August 2014

Abstract
&lt;Background and aim&gt; Global DNA hypomethylation and regional hypermethylation in CpG island has been recognized as common feature of cancer DNA, including that of hepatocellular carcinoma (HCC). However, precise mechanism underlying the alteration of methylation is still unclear. We conducted a genome-wide methylation analysis to elucidate distribution and characteristics of genes that subject to cancer-related DNA methylation in human HCC. &lt;Materials and methods&gt; With written informed consent, 20 HCC and 3 corresponding matched non-cancerous liver tissues were obtained at the time of hepatectomy (2 tumors) or orthotopic living-donor liver transplantation (17 tumors and 3 non-tumors). After bisulfite modification, the converted DNA was subject to hybridization on Infinium Human Methylation BeadChip 450K (Illumina, Inc., San Diego, CA) that contained 485,577 CpGs of the human genome including gene promoters and repetitive DNA elements. The methylation level for each CpG was represented as a beta value according to the fluorescent intensity ratio. In order to identify alteration of methylation profile between HCC and non-tumor liver, difference of average beta values between tumor and non-tumor was calculated. &lt;Results&gt; Of 485,577 CpG loci, differences of average beta values of 460,036 loci (94.7%) were within 30%. These were considered as constitutively methylated or unmethylated. Tumor-specific hypomethylation was found at 18,807 loci. Of these, 65.1% were located outside CpG islands, shore or shelf (so-called ‘open sea’). Tumor-specific demethylation rarely occurred within CpG islands (6.5%). On the other hand, tumor-specific DNA methylation was found at 6734 loci. Of these, 77.6% were located within CpG islands. Interestingly, normally methylated CpGs (average beta value &lt; 0.20) were mainly located in CpG islands (95,943 of 138,081, 69.0%), and many of normally unmethylated or variably methylated CpGs were located in the open sea (165,209 of 347,496, 47.5%). &lt;Conclusion&gt; Tumor-specific methylation occurring at CpG islands, may simply be dependent on the distribution of normally unmethylated CpGs. This finding may help us target epigenetically silenced tumor suppressor genes.
Citation Format: Takafumi Nishimura, Yukiko Mori, Naoshi Nishida. Landscape of DNA methylation status of human hepatocellular carcinoma revealed by Human Methylation BeadChip 450K. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4249. doi:10.1158/1538-7445.AM2013-4249
Abstract 425: Fractionated radiation-induced tumor suppressor microRNAs in human prostate carcinoma cells.
Authors: Coleman C. Norman , John-Aryankalayil Molykutty , Makinde Adeola Y. , Palayoor Sanjeewani T. 
Published: August 2014

Abstract
To understand the role of microRNAs (miRNA) in regulation of radiation-induced gene expression and to help define potential radiation-inducible targets, miRNA expression was studied in wild type p53 LNCaP and p53-mutated PC3 and DU145 cells. We have previously investigated the changes in the molecular profiles of tumor cells that were exposed to single dose (SD) versus fractionated radiation (MF) in vitro, and identified immune and stress response pathways that were induced by fractionated but not single dose radiation. Methods: Cells were exposed to 5Gy and 10Gy either as SD or MF radiation radiation. Microarray analyses were done using human Agilent miRNA Microarray Kit (V2). Data were analyzed using Gene Spring software. Validation of the miRNA expression and gene expression of miRNA targets was evaluated by real-time RT-PCR analysis. Target filter analysis of differentially expressed miRNAs (&gt;1.5 fold change and p value&lt;0.05) and their mRNA targets were done. Results: Microarray analyses revealed that radiation differentially expressed 84, 68 and 8 miRNAs with high confidence (&gt;1.5fold change, p&lt;0.05) in LNCaP, PC3 and DU145 cells, respectively. MF radiation affected more miRNAs than SD radiation in all cell lines. In LNCaP and PC3 cells, MF radiation upregulated tumor suppressor microRNAs miR-34a, miR-200, miR-135, miR-221 and let7. Baseline expression of miR-34a was markedly reduced in PC3 cells and DU145 cells compared to LNCaP cells. However, miR-34a was upregulated by fractionated irradiation in LNCaP and PC3 cells, but not in DU145 cells. RT_PCR analysis of 22 experimentally verified miR-34a targets, showed distinct expression patterns in PC3 and LNCaP cells 6 and 24 hours after radiation. An inverse correlation of NOTCH1, E2F5 and MDM4 expression was observed in PC3 cells 6 and 24 hours after MF but not in LNCaP cells. On the other hand, IFNB1 showed an inverse correlation only in LNCaP cells. Majority of the differences in the expression patterns of miR-34a targets were at 24 hours after MF. Conclusion: Differences in the miRNA expression exist between cell lines and after varying radiation regimens. Among the three prostate carcinoma cell lines, tumor suppressor miRNAs are upregulated after MF radiation in LNCaP and PC3 cells. Currently, we are in the process of modulating miRNAs and their targets to examine their effects on radio sensitivity.
This work was supported by the Intramural Research Program of the NIH, NCI, CCR.
Citation Format: C. Norman Coleman, Molykutty John-Aryankalayil, Adeola Y. Makinde, Sanjeewani T. Palayoor. Fractionated radiation-induced tumor suppressor microRNAs in human prostate carcinoma cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 425. doi:10.1158/1538-7445.AM2013-425
Abstract 4265: Derivation and characterization of endometrial cancer cells resistant to phosphatidylinositol-3-kinase (PI3K) pathway inhibitors.
Authors: Klempner Samuel J. , Myers Andrea P. , Li Jane , Mills Gordon , Cantley Lewis C. 
Published: August 2014

Abstract
Endometrial cancer remains the most common gynecologic malignancy in the United States with an estimated 43,000 cases annually. Limited options exist for patients with recurrent endometrial cancer after tumor progression following platinum/taxane combinations, and newer therapies are needed. Endometrial cancers have among the highest rates of oncogenic aberrations in the phosphatidylinositol-3-kinase (PI3K) pathway with frequencies approaching 75%, and clinical trials targeting components on the PI3K pathway are ongoing. Despite the clinical observation that many responses to PI3K inhibitors are short lived an understanding of the molecular mechanisms of resistance is lacking. We have derived endometrial cancer cell lines resistant to a panel of PI3K/AKT/mTOR inhibitors in clinical development in an effort to understand molecular mechanisms and signaling changes underlying resistance to PI3K-targeted therapy. All lines have previously undergone mutational analysis of the PI3K and RAS-ERK pathways. Representative compounds inhibiting each node in the canonical class I PI3K signaling cascade have been chosen. These agents have been synthesized base on the published structures and include a pan-p110 inhibitor, an allosteric AKT inhibitor, a dual p110-mTOR, and a MEK inhibitor. Using parallel high-throughput intracellular phospho-kinase and phospho-receptor tyrosine kinase (RTK) arrays for screening we have identified candidate common resistance mechanisms to inhibition of signaling nodes in the PI3K pathway. The phospho-screening approach has highlighted the interplay between PI3K/AKT/mTOR signaling and the Ras/Raf/MEK/ERK pathways in the development of resistance. We have begun to validate ERK upregulation as an activated escape pathway in patient samples from an AKT inhibitor clinical trial. Conserved resistance profiles may ultimately be used to define a subset of endometrial cancer patients unlikely to respond to PI3K/Akt/mTOR inhibitors and may inform more rational early phase combination strategies.
Citation Format: Samuel J. Klempner, Andrea P. Myers, Jane Li, Gordon Mills, Lewis C. Cantley. Derivation and characterization of endometrial cancer cells resistant to phosphatidylinositol-3-kinase (PI3K) pathway inhibitors. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4265. doi:10.1158/1538-7445.AM2013-4265
Abstract 4267: MUC1 increases epidermal growth factor receptor levels and signaling in endometrial cancer cell lines.
Authors: Engel Brian J. , Carson Daniel D. 
Published: August 2014

Abstract
Endometrial cancer is the most common gynecological cancer, affecting over 600,000 women in the United States. Furthermore, increased incidence of endometrial cancer is observed among obese and premenopausal women. Currently, the standard of care is hysterectomy with the addition of radiation and chemotherapy for late stage cancers. Novel therapies are required to avoid surgical complications associated with obese patients and to preserve the fertility of young patients. MUC1 is a large, heavily glycosylated transmembrane protein that functions to lubricate mucosal surfaces, protect cells from external insult and modulates the embryo implantation process. Recent evidence suggests that the C-terminus of MUC1 is involved in intracellular signaling through interaction with several cancer-associated proteins. One of these proteins is the epidermal growth factor receptor (EGFR), a receptor tyrosine kinase that influences cellular proliferation, migration and apoptosis. Elevated MUC1 levels are associated with increased levels and signaling of EGFR in breast cancer; however, this phenomenon has not been described in the context of endometrial cancer and the mechanisms involved are not well understood in any context. To this end, human endometrial cancer cell lines were subjected to siRNA knockdown of MUC1 followed by qRT-PCR, western blotting, EGFR promoter-driven luciferase assays, proliferation and migration assays. These assays demonstrate a correlation of MUC1 levels with EGFR mRNA levels, protein levels, signaling, gene expression and cellular proliferation and migration. These results demonstrate that MUC1 control of EGFR levels and signaling also occurs in endometrial cancer-derived cell lines. Future experiments will elucidate the mechanisms by which MUC1 promotes EGFR gene expression and signaling in endometrial cancer. These insights may provide novel MUC1-based targets for endometrial cancer therapies which when used in conjunction with current non-surgical treatments may provide a therapeutic strategy that avoids surgical complications and preserves fertility. (Work supported by NIH grants RO1 HD 29963 and NCI 2P5098258-06 as well as Rice University funds to DDC).
Citation Format: Brian J. Engel, Daniel D. Carson. MUC1 increases epidermal growth factor receptor levels and signaling in endometrial cancer cell lines. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4267. doi:10.1158/1538-7445.AM2013-4267
Abstract 4269: Human Epidermal Growth Factor (EGF) supresses Tumor Necrosis Factor-a (TNF-a)-mediated induction of Caspase-1, STAT1 and Apoptosis in human cervical carcinoma cells.
Authors: Ozes Osman N. 
Published: August 2014

Abstract
Background: Members of Human Epidermal Growth
Factor Receptors are over-expressed in variety of cancers. The EGFR-mediated activation of signal transduction pathways ultimately induce cellular growth, supress apoptosis and can cause tumor malignancy. On the contrary, TNF-α induces the expression of numerous genes which contribute to the inhibition of growth and the induction of apoptosis. Therefore, we tested the impact of EGF on TNF-α-induced expression of Caspase-1, activation of STAT1 and induction of apoptosis on human cervical carcinoma cells, (ME180).
Results: Treatment of ME180 cells with TNF-α (10 ng/ml) induced the expression of Caspase-1 in a time dependent manner. Also, pre-treatment of these cells with EGF (10ng/ml) completely inhibited
TNF-induced Caspase-1 induction. Since Caspase-1 induction is mediated by
STAT1, the levels of STAT1 activation by
TNF was determined. It was found that TNF induces STAT1 activation in these cells. However, pre-treatment of ME180 cells with EGF completely inhibited TNF-α-mediated activation of STAT1. Parallel to these findings, pre-treatment of ME180 cells with EGF for 1 hour completely inhibited TNF-induced apoptosis in these cells.
Conclusion: These results suggest that tumor microenvironment created by the tumor or surrounding cells are important in controlling the growth and apoptosis of cancer cells. Therefore, abundance of growth factors and pro-apoptotic cytokines may determine the fate of tumor behavior.
Citation Format: Osman N. Ozes. Human Epidermal Growth Factor (EGF) supresses Tumor Necrosis Factor-a (TNF-a)-mediated induction of Caspase-1, STAT1 and Apoptosis in human cervical carcinoma cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4269. doi:10.1158/1538-7445.AM2013-4269
Abstract 4272: NanoLucTM as an improved BRET donor to monitor EGFR interactions within living cells.
Authors: Robers Matthew B. , Machleidt Thomas , Kirkland Thomas , Woodroofe Carolyn , Fan Frank , Cong Mei , Wood Keith 
Published: August 2014

Abstract
As a small, versatile protein fusion reporter, NanoLuc™ luciferase offers superior brightness and sensitivity compared to any luciferase described to date. The small size and enhanced brightness of NanoLuc™ makes it ideally suited as an energy donor for Bioluminescence Resonance Energy Transfer (BRET) to a variety of fluorescent acceptors within living cells. By combining genetic reporters such as NanoLuc™ luciferase and HaloTag™ fluorescent labelling technology, it is possible to monitor the interactions of cell surface receptors such as EGFR with adapter proteins in response to growth factor stimulation. In addition to demonstrating inducible protein interactions, it may also be possible to apply this foundational BRET system to the measurement of ligand or small molecule binding events within living cells.
Citation Format: Matthew B. Robers, Thomas Machleidt, Thomas Kirkland, Carolyn Woodroofe, Frank Fan, Mei Cong, Keith Wood. NanoLucTM as an improved BRET donor to monitor EGFR interactions within living cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4272. doi:10.1158/1538-7445.AM2013-4272
Abstract 4281: Nedd4 controls cell migration by regulating PDGF receptor signaling.
Authors: Tanaka Nobuyuki , Oyama Kyoko , Tamai Keiichi 
Published: August 2014

Abstract
The ubiquitin ligase Nedd4 is an ubuiquitin ligase (E3) which belongs to the HECT family. Like other member of this family members, such as Itch and Smurf, Nedd4 has been proposed to regulate a number of signaling pathways, as well as the traffic of several cell surface molecules, however, its physiological role in mammals has not been well characterized. Former reports identified reduction in the mitogenic activity and increase of the adaptor protein Grb10, aberrant IGF-1, VEGF and FGF receptor localization and / or signaling. In the present study, we performed an analysis of Nedd4-null murine embryonal fibroblastoid cells (MEFs) to show that loss of Nedd4 may affect any additional growth factor signaling. Surface expression of PDGF receptor was significantly increased in homozygous mutant mouse embryonic fibroblasts. Accordingly, PDGF-BB stimulation induced enhanced signaling as judged by MAP kinase p42/44 and Akt phosphorylation. Knockdown of Nedd4 in cell lines also induced similar phenotype. Nedd4, when transiently expressed, ubiquitinated PDGF receptor, which lead to degradation. Under the presence of lysosome inhibitors, PDGF receptor down regulation was at least partially blocked, suggesting its lysosome-dependent degradation. Subcellular localization of the PDGF receptor was also analyzed, but apparent difference was not observed. In the scratch assay, Nedd4 knockout cells showed enhanced migration activity, suggesting their active movement. Thus, Nedd4 appears to negatively control PDGF signaling partly through the regulation of its lysosome dependent degradation.
Citation Format: Nobuyuki Tanaka, Kyoko Oyama, Keiichi Tamai. Nedd4 controls cell migration by regulating PDGF receptor signaling. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4281. doi:10.1158/1538-7445.AM2013-4281