bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2938: Inhibition of PI3K/AKT and MEK/ERK pathways act independently on p27 upregulation induced by downregulation of cathepsin B and uPAR in glioma
Authors: Gopinath Sreelatha , Alapati Kiranmai , Malla Rama Rao , Gondi Christopher S. , Mohanam Sanjeeva , Dinh Dzung H. , Rao Jasti S. 
Published: June 2012

Abstract
Cathepsin B and urokinase plasminogen activator receptor (uPAR) are overexpressed in gliomas. Deregulation of the G1 phase cell cycle machinery is a common feature of cancers. The abundance of cyclin-dependent kinase inhibitor p27Kip1 (p27) during the cell cycle determines whether cells will proliferate or become quiescent. In the present study, we carried out transfections using shRNA against cathepsin B and uPAR. We assessed cell cycle arrest using FACS analysis and used Western blot analysis to detect expression of ERK, AKT, p27, cyclin E, cyclin D, CDK4, CDK2, EGFR, β1 integrins, and the pocket proteins (p-Rb, p107 and p130). Specific inhibitors like Wortmanin (10 µM) and U0126 (10 µM) were used to further determine the roles of the AKT and ERK pathways. We used immunoprecipitation analysis to detect the respective interactions between EGFR and β1, p27 and CDK4, and p27 and CDK2. CHIP analysis was used to check for the recruitment of transcription factors FOXO3a, E2F1 and AP-1 to the p27 promoter. The results of the present study show that shRNA treatment efficiently downregulated expression of cathepsin B and uPAR and induced G0/G1 arrest through upregulation of p27. Downregulation of both p-ERK and p-AKT downstream of EGFR and β1 are involved, but independently, in p27 upregulation. Multiple transcription factors (namely, AP-1, E2F1 and FOXO3a) were involved in upregulation of p27 as determined by luciferase expression under the influence of promoter regions to which these transcription factors bind individually. Also, cathepsin B and uPAR downregulation reduced tumor growth and increased p27 nuclear expression in vivo. In summary, the reduction of p-ERK and AP-1, the increased expression of E2F1 and FOXO3a, and the reduced association of cyclin D-CDK4 and cyclin E-CDK2 complexes contributed to p27 upregulation as well as G0/G1 arrest induced by downregulation of cathepsin B and uPAR.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2938. doi:10.1158/1538-7445.AM2011-2938
Abstract 2941: Defining novel pathways that arrest genetically unstable tetraploid cells
Authors: Ganem Neil J. , O'Rourke Kevin P. , Pellman David 
Published: June 2012

Abstract
Tetraploid cells, which are a common byproduct of cell division failures, are genetically unstable and have the capacity to facilitate tumorigenesis. Consequently, p53-dependent tumor suppression mechanisms exist to limit the continued proliferation of these cells by promoting G1 cell cycle arrest. However, unlike other common cellular insults that activate p53 and promote G1 arrest, such as the DNA damage response, the mechanisms governing G1 arrest in response to tetraploidy remain largely unexplored. To gain insight into these mechanisms, we have developed a novel genome-wide RNAi screening assay to comprehensively identify proteins that are necessary to activate or maintain G1 cell cycle arrest after the induction of tetraploidy. Results from this screen, in combination with complementary bioinformatic approaches, have begun to illuminate the nature of the stresses associated with tetraploidy. More importantly, this work is shedding light on the adaptive mechanisms that tetraploid and near-tetraploid tumors may have evolved in order to overcome these stresses. These findings have the potential to lead to the identification of new pathways that can be targeted by chemotherapeutics to specifically reinforce G1 arrest in grossly aneuploid cancer cells.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2941. doi:10.1158/1538-7445.AM2011-2941
Abstract 2960: A combined bioinformatics and proteomics approach identifies DNA repair factors regulated by the APC/C
Authors: van Vugt Marcel A. , Fehrmann Rudolf S.N. , Ong Shao-En 
Published: June 2012

Abstract
Our genome is constantly challenged by endogenous and exogenous factors that induce a variety of DNA lesions. DNA double strand breaks are considered to most toxic type of DNA damage, and cells have evolved powerful mechanisms that can detect and repair such lesions. Two main mechanisms responsible for repair of DNA double strand breaks are Non-Homologous End Joining (NHEJ) and Homologous Recombination (HR). The choice between these two types of DNA double strand break repair is strongly influenced by the cell cycle. Only cells in late S and G2 phase of the cell cycle can employ HR and this differential activity is underscored by a strict requirement for Cdk activity for HR. Mechanisms that enable HR during S-phase have been previously identified, but how exactly HR DNA repair is inactivated during the mitosis-to-G1 transition is poorly understood. Based on the observed strict cell-cycle regulation of HR repair, a role for the mitotic E3 ligase APC/C was suggested.
Here we present a combined proteomics and bioinformatics approach to identify APC/C targets and reveal components of DNA double strand break repair that are potential targets of the APC/C. Firstly, proteins were identified that contain evolutionary conserved and sterically accessibly APC/C targeting domains (KEN and D-boxes) using bioinformatics. Within this group of proteins with a known role in DNA repair were highlighted. Subsequently, a quantitative mass-spec approach was used to identify those proteins, whose abundance was readily lost upon mitotic exit. Reassuringly, we could identify many previously identified APC/C targets, that all showed loss of abundance during mitotic exit. We subsequently searched for DNA repair-associated factors that were down-regulated during mitotic exit and among those, we identified multiple topoisomerase subunits as likely APC/C substrates. We could subsequently confirm a role for the APC/C in regulating protein levels of these novel substrates using RNAi-mediated depletion of Cdh1 and live cell microscopy. In conclusion, we here present a novel method to identify APC/C targets and used this approach to uncover novel regulatory aspects of cell cycle-regulated DNA repair.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2960. doi:10.1158/1538-7445.AM2011-2960
Abstract 2967: Nucleolin phosphorylation by CK2 modulates its role in cell cycle checkpoint activation
Authors: Caglar Elif , Das Dibash , Borowiec James , Saxena Anjana 
Published: June 2012

Abstract
Nucleolin is a multifunctional abundant nucleolar protein and its gene expression is transactivated by the proto-oncogene c-myc during exponential cellular growth. This non-ribosomal protein is a major nucleolar phosphoprotein which is involved in ribosomal RNA processing, RNA polymerase I-catalyzed transcription, and the regulation of apoptosis, demonstrating both positive and negative effects on cell proliferation. During an unperturbed cell-cycle, interphase (CK2) and mitotic (Cdc2) kinases regulate nucleolin phosphorylation, modulating its function and nucleolar localization. Following cellular stress, nucleolin has been shown to inhibit chromosomal replication and to relay nucleolar stress signals mediated by its re-localization within the nucleus. Nucleolin also interacts with prominent components of the ARF (Alternate Reading Frame)/p53 checkpoint pathway that controls growth upon oncogenic stress signals. We have previously demonstrated that nucleolin binds to the p53-antagonist Hdm2, inhibits Hdm2-mediated degradation of p53 and causes p53-mediated apoptosis in an ARF-independent manner. Here we further dissect role/s of nucleolin phosphorylation in regulating the ARF/p53 checkpoint. We have generated a novel system by engineering human osteocarcinoma (NARF6) cells to induce expression of nucleolin-wt (wild-type) or -S6A (a phospho-mutant with six consensus site serines mutated to alanine, impairing phosphorylation by CK2). This novel system can control expression of both nucleolin and ARF by different promoters, allowing us to dissect the downstream events that are solely nucleolin- or ARF- dependent, or regulated by both. We found that increased levels of nucleolin-S6A significantly decreased ARF protein levels as compared to nucleolin-wt. Nucleolin-S6A was significantly more nucleoplasmic and, interestingly, cells that express S6A lacked nucleolar ARF expression. Although a dramatic loss in both ARF and p21 protein levels is evident with nucleolin-S6A expression, there was a net increase in p53 levels. Significantly, nucleolin-S6A expression caused an increase in the fraction of G1 cells in an ARF-independent manner. Thus, reduction of nucleolin phosphorylation by CK2 acts as a molecular switch causing the sub-nuclear re-localization of both nucleolin and ARF. These events lead to p53 activation, and the control of growth in both normal and stressed cells. These results also provide validation of our unique cellular system that allows us to manipulate nucleolin wt and mutant levels, facilitating the study of its physiological functions.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2967. doi:10.1158/1538-7445.AM2011-2967
Abstract 2996: DNA-damaging agents disrupt telomere structure
Authors: Samassekou Oumar 
Published: June 2012

Abstract
Telomeres are found at chromosome ends. When these ends are not protected by telomeric capping, the telomeres are recognized as double-strand breaks and the consequent recruitment of DNA repair machinery may affect cellular fate. Furthermore, telomeric capping proteins have been shown to interact with some of the proteins involved in DNA repair. A direct link thus exists between DNA repair and telomeres. However, few data are available on the changes in telomere structure associated with the different modes of DNA repair. To study the effects of three DNA-damaging agents on telomere structure, we exposed normal human primary fibroblasts to H202, gamma radiation, or UVB rays. The cells were then harvested at different times over a period of 24 hours. First the telomere nuclear architecture was studied by quantitative fluorescence in situ hybridization with a telomere-specific peptide nucleic acid probe followed by 3D telomere imaging. H202 treatment induced a significant reduction of telomere signals and a disruption of the nuclear volume that became normal after 24 hours of recovery. Also, telomere positioning was positively correlated to nuclear volume that disrupted over time. For gamma irradiation, the nuclear volume was positively correlated to the number of telomere signals and negatively correlated to telomere average intensity for each time point. UVB lead to a significant formation of telomeric aggregates and disruption of telomere nuclear shape by forming ellipsoid instead of circular shape.
Next, we studied the effects of these different DNA damage agents on the expression profile of telomere shelterin genes. The most affected genes were TRF1, POT1, TIN2 and Rap1. For instance, while the three agents showed a high induction of TIN2, gamma and H202 treatments presented high induction for POT1 and only H202 treatment induced significant increase of TRF1.
In conclusion, certain DNA-damaging events alter telomere structure by acting on nuclear telomere architecture and the expression profile of some telomere shelterin genes. The disruption of telomere structure due to acute insults might have an influence on cell homeostasis and the pathways involved can shed light for a better understanding of some pathological and therapeutic processes.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2996. doi:10.1158/1538-7445.AM2011-2996
Abstract 3: Induction of mitochondrial autophagy in leukemia by the Bcl-2 quadruplex-forming sequence
Authors: Sedoris Kara C. , Clarkson Cortney R. , Thomas Shelia D. , Miller Donald M. 
Published: June 2012

Abstract
Bcl-2 (B-cell CLL/lymphoma 2), a mitochondrial membrane oncoprotein functioning as an inhibitor of apoptosis, is commonly overexpressed in a variety of hematological malignancies promoting apoptotic resistance. Inhibition of Bcl-2 may result in sustained regression of leukemia/lymphoma. The promoters of several cancer-related oncogenes, including Bcl-2, contain sequences within nuclease hypersensitivity regions capable of forming quadruplex (four-stranded) DNA. The Bcl-2 quadruplex-forming sequence (Bcl-2 q, 23 bp) is located upstream of the P1 promoter of the Bcl-2 gene and is implicated in negative regulation of Bcl-2 transcription, however, the biological role of this sequence remains unclear. We hypothesize that treatment of leukemia cells with an oligonucleotide encoding Bcl-2 q induces cell death by inhibiting Bcl-2 gene expression. To determine the biological role of the Bcl-2 q on leukemic cell proliferation, U937 cells were treated with Bcl-2 q or the corresponding mutant sequence (MutBcl-2), which lacks runs of two or more guanines. Our results demonstrate that Bcl-2 q formed a stable parallel quadruplex structure and showed remarkable serum and intracellular stability. Treatment of leukemia cells with Bcl-2 q caused a significant dose and time-dependent decrease in cell proliferation after 3 and 6 days (IC50&lt;5µM), which was not a result of cell cycle arrest. No change in growth of non-transformed stromal cells occurred in response to Bcl-2 q indicating the effect is specific for malignant cells. Confocal and flow cytometry analysis of cells treated with FITC-labeled Bcl-2 q or MutBcl-2 showed prominent uptake and nuclear localization of Bcl-2 q in contrast to MutBcl-2. Inhibition of cell proliferation corresponded with decreased Bcl-2 protein expression and increased expression of pro-apoptotic proteins Bax and Bak. This resulted in decreased mitochondrial transmembrane potential and significant autophagic degradation of mitochondria, characteristic of mitophagy. Induction of mitophagy was associated with increased Beclin-1 and LC3B expression and disruption of Bcl-2/Beclin-1 interaction. These results demonstrate striking growth inhibition in response to Bcl-2 q related to inhibition of Bcl-2 expression and induction of mitochondrial autophagy and shows considerable therapeutic potential.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3. doi:10.1158/1538-7445.AM2011-3
Abstract 30: Identification of genomic and epigenetic features of tumor suppressors and oncogenes in ovarian cancer
Authors: Wrzeszczynski Kazimierz O. , Varadan Vinay , Kamalakaran Sitharthan , Levine Douglas A. , Dimitrova Nevenka , Zhang Michael Q. , Lucito Robert 
Published: June 2012

Abstract
The identification of genetic and epigenetic alterations from primary tumor cells has become a common method to identify genes critical to the development and progression of cancer. We provide a bioinformatic analysis of copy number variation and DNA methylation covering the genetic landscape of ovarian cancer tumor cells. We individually examined the copy number variation and DNA methylation for 42 primary ovarian cancer samples using our MOMA-ROMA technology and 379 tumor samples analyzed by The Cancer Genome Atlas. We have identified 346 genes with significant deletions or amplifications among the tumor samples. Utilizing associated gene expression data we predict 156 genes with significantly altered copy number and correlated changes in expression. Among these genes CCNE1, POP4, UQCRB, PHF20L1 and C19orf2 were identified within both datasets. We were specifically interested in copy number variation as our base genomic property in the prediction of tumor suppressors and oncogenes in the altered ovarian tumor. We therefore identify changes in DNA methylation and expression for all amplified and deleted genes. We predicted 615 potential oncogene and tumor suppressor candidates by integrating these multiple genomic and epigenetic data types. Genes with a strong correlation for methylation dependent expression exhibited at varying copy number aberrations include CDCA8, ATAD2, CDKN2A, RAB25, AURKA, BOP1 and EIF2C3. Moreover, well characterized tumor suppressors and oncogenes exhibit varying CNV, methylation and expression features within cancers. We therefore compared significant copy number variation and methylation effects on expression for many known tumor suppressors, oncogenes and cancer related genes in order to identify altered gene function properties specific to primary ovarian tumors. Here, we present the analysis of multiple genomic modalities from two primary ovarian tumor datasets for the identification of candidate genes. We predict genes with epigenetic and genomic tumor suppressor and oncogenic properties having both analyzed and identified known validated ovarian cancer genes and identifying new candidates.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 30. doi:10.1158/1538-7445.AM2011-30
Abstract 3002: Multiplexing ChIP-Seq and rapid chromatin preparation from solid mammalian tissues for low cell ChIP assays
Authors: Tobler Andreas R. , Pickle Loni , Marnellos George , Chen Tom Z. 
Published: June 2012

Abstract
Currently, the chromatin immunoprecipitation assay (ChIP) is the most powerful method utilized to selectively enrich for DNA sequences bound by a particular protein in living cells. We developed a SOLiD™ ChIP-seq kit, which offers an optimized ChIP workflow and an efficient SOLiD™ ChIP-seq library construction from relatively low cell number samples. ChIP procedure is usually laborious, time consuming, and typically requires large starting cell numbers. We use MAGnify™ Chromatin Immunoprecipitation System, which is suitable for fast enrichment of chromatin complexes and DNA recovery. It is able to use lower starting cell numbers for ChIP and allows faster throughput to investigate different chromatin and transcription time-course events as well as enable antibody screening to determine ChIP compatibility. In addition, we develop a sensitive ChIP-seq library construction procedure which enables users to construct a complex library using as low as 1 ng ChIP DNA. Combining with SOLiD™'s ultra high sequencing throughput, SOLiD™ ChIP-seq offers a highly sensitive, hypothesis-neutral approach to accurately characterize protein-DNA interactions at genome-wide scale. Here we paired the SOLiD™ Fragment Library Barcoding Kit, which enables users to pool fragment libraries prior to emulsion PCR and then conduct multiplexed sequencing analysis, with the SOLiD™ ChIP-Seq Kit to characterize Estrogen Receptor alpha binding sites in breast cancer cells utilizing the SOLiD™ platform. In addition, we demonstrate a novel, rapid, and low input per ChIP tissue collection protocol for researchers utilizing solid mammalian tissue to study protein-DNA interaction via the MAGnify™ ChIP System. The 50 cent assay is reduced to less than 1 cent per reaction and it reduces reported homebrew amount of tissue from approximately 30mg to less than 1mg per ChIP reaction when paired with the powerful MAGnify™ ChIP system.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3002. doi:10.1158/1538-7445.AM2011-3002
Abstract 3010: Evaluation of genome wide analysis platforms for chromatin immunoprecipitation
Authors: Ma Lin 
Published: June 2012

Abstract
Chromatin states can influence transcription directly by altering the packaging of DNA to allow or prevent access to DNA-binding proteins, or they can modify the nucleosome surface to enhance or impede recruitment of effector protein complexes. Genome-wide mapping of protein-DNA interaction and epigenetic marks helps to better understand the transcriptional regulation. Prior to the development of next gen sequencing technologies, chip on chip or location analysis was the method of choice for exploring genome wide protein:DNA occupancy patterns. ChIP-seq is increasing in popularity due to the data density and lack of interrogation bias that this platform provides. While this application is becoming more popular, few studies have been performed which explore differences in binding site profiles obtained from both methods.
Here we present data which compares the performance of ChIP antibodies by ChIP-chip as well as by ChIP-seq. For theses studies, chIP-chip using Agilent microarrays and ChIP-seq using the Illumina Genome Analyzer platform were performed. These studies may serve as a basis to allow the development of specifications for acceptable performance on these genome wide platforms to facilitate the comparison of data sets in shared databases and in published research.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3010. doi:10.1158/1538-7445.AM2011-3010