bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4845: Tumor cell line profiling of eighteen cancer therapeutics to evaluate relationships between tumor genotypes and cancer cell sensitivities
Authors: Ovechkina Yulia Y. , O'Day Christine , Marcoe Karen , Keyser Robert , Bernards Karen , Chesnut-Speelman Jessica , Nguyen Phuong , Mulligan Janine , Lin Teddy , Shively Rodney , Hnilo Jim , Nelson Brian 
Published: June 2012

Abstract
In vitro cellular response profiling of tumor human cell lines has become a widely used approach for the targeted cancer therapeutics development. Correlation of the drug sensitivity and resistance cellular response with genomic data offers a robust and sensitive system for predicting clinical efficacy and identifying more efficacious patient populations. We have developed a high throughput cellular approach to evaluate the relationship between tumor genotypes and drug sensitivity over 240 human tumor cell lines. A panel of the cancer therapeutic agents was tested for proliferative, apoptotic and cell cycle arrest responses using multiplexed high content screening with automated fluorescence microscopy and image analysis based technology. Growth index was measured using nuclear dye. Activated caspase 3 antibodies were used for the apoptosis induction detection. Phospho-histone H3 antibodies were used to measure the cell cycle block. The eighteen cancer therapeutics were used in this study: BMS-387032 (SNS-032), PD0325901, PD173074, API-2 (Triciribine), Lapatinib (Tykerb), BMS-536924, Geldanamycin, Sorafenib, Dasatinib, Erlotinib, VX-680, Sunitinib, Everolimus, Tandutinib, Cl 1040, Doxorubicin, Paclitaxel and Staurosporine. We generated cell line profiles to reveal drug sensitivity and resistance patterns and identified markers associated with a specific response. It was found that Raf/Ras mutations confer sensitivity to MEK inhibitors, PD0325901 and Cl 1040, while PIK3CA and RB mutations were associated with resistance. Resistance to IGF-1R, FGFR, and EGFR inhibitors correlated with PI3K/PTEN/Akt or Raf/Ras pathway activation. EGFR mRNA overexpression was associated with resistance to FGFR and IGF-1R inhibitors. Resistance to AKT inhibitor, API-2 (Triciribine) was associated with PTEN mutations and amplification of AKT. APC mutations were associated with resistance to Aurora kinase inhibitor, VX-680, while mutations in the beta-catenin gene were linked with a sensitive phenotype. This approach could provide insight into the mechanisms of enhanced susceptibility or resistance which in turn could be used for the optimization of the targeted cancer therapeutics.
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 4845. doi:10.1158/1538-7445.AM2011-4845
Abstract 4850: Paired-end RNA-sequencing based identification of 24 novel fusion genes in breast cancer
Authors: Edgren Henrik , Murumägi Astrid , Kangaspeska Sara , Nicorici Daniel , Hongisto Vesa , Kleivi Kristine , Rye Inga Hansine , Wolf Maija , Børresen-Dale Anne-Lise , Kallioniemi Olli 
Published: June 2012

Abstract
Fusion genes have recently been described in common solid tumors, revealing an important class of mutations that contribute to cancer development and progression. Next-generation sequencing technologies allow systematic characterization of cancer cell transcriptomes, including the fusion genes resulting from underlying chromosomal translocations. Using paired-end RNA-sequencing in conjunction with high-resolution chromosomal copy number analyses we characterized 24 novel and 3 previously known fusion genes in breast cancer cell lines. An improved bioinformatic approach allowed fusion gene validation with a 95% success rate by RT-PCR, Sanger sequencing and FISH. Among the identified fusions, partner genes were found to contribute both promoters (5′UTR; e.g. TATDN1-GSDMB), coding sequences (e.g. ACACA-STAC2) as well as 3′UTRs (e.g. CSE1L-ENSG00000236127). Most fusion genes (82%) were associated with copy number transitions, such as high level amplifications at e.g. 8q21, 17q12, 17q23 and 20q13, implying that fusion gene formation may contribute to the selective advantage provided by copy number amplifications. Although no prevalent single fusion gene was detected, the functional importance of the multiple fusion genes is supported by several lines of evidence. First, some of the fusion partner genes were expressed exclusively as fusion transcripts, e.g. TATDN1-GSDMB, indicating that the fusion event lead to the activation of a latent gene. Second, several fusion gene partners, including ACACA, NOTCH1 and RARA, have been previously found to be involved in oncogenic fusions in leukemias and lymphomas. Third, functional analysis using RNAi-mediated knockdown suggested a potential role for two fusion genes in controlling cancer cell proliferation. In conclusion, using RNA-sequencing together with improved bioinformatics and genomic copy number profiling, we have discovered multiple novel fusion genes in breast cancer, which may provide new insights on breast cancer, and provide therapeutic and diagnostic clues.
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 4850. doi:10.1158/1538-7445.AM2011-4850
Abstract 4854: Mutations activating proliferation pathways in ovarian cancer
Authors: Uhrhammer Nancy A. , Bidet Yannick , Chene Gautier , Viala Sandrine , Communal Yves , Raoelfils Inès , Penault-Llorca Frédérique , Bignon Yves-Jean 
Published: June 2012

Abstract
Ovarian malignancies may arise through different mechanisms of oncogenesis, which influence their treatment and are important for prognosis. Essential to carcinogenesis is the activation of proliferation pathways such as those directed by PI3 kinase or KRAS. New sequencing technologies may improve the detection of somatic mutations in tumor tissue, which is complicated by the low representation of a mutation within a tissue sample inevitably containing normal cells and subpopulations of malignant cells.
We analyzed selected exons in PIK3CA, PIK3R, KRAS, BRAF, EGFR and ERBB2 in 34 primary malignant ovarian tumors, including 10 serous, 4 borderline, 11 endometrioid, and 9 mixed or rare subtypes. DNA was extracted from flash-frozen tumor tissues, amplified, and sequenced on a 454-GS-Flx Genome Sequencer. Expression of PTEN, p53, Bcl2, ALDH and Ki67 were assessed by immunohistochemistry on formalin-fixed tissues.
Nine mutations were observed in PIK3CA, 5 in BRAF, 4 in KRAS, and 2 in EGFR. SNPs present in the amplicons analyzed allowed allelic imbalance to be estimated, showing possible amplification of EGFR in 9 of 20 informative samples, and of PIK3CA in 6 of 19 informative samples, none of which contained a point mutation.
Endometrioid tumors frequently showed anomalies in PIK3CA, Bcl2 expression, and not p53 overexpression. P53 overexpression was typical of serous tumors, and was associated with the absence of mutations in any of the genes sequenced. Borderline and low grade tumors were characterized by BRAF mutation, no imbalance at EGFR, no anomalies at PIK3CA, and less frequent p53 overexpression. The absence of BRAF mutations in high grade tumors suggested that they do not evolve from borderline tumors. PIK3CA mutations were not mutually exclusive with KRAS mutations, confirming the non-redundancy of these intertwined signaling pathways. PTEN extinction was not significantly negatively associated with either point mutations or allelic imbalance at PIK3CA, consistent with different roles for PTEN loss and PI3-kinase activation at different stages of tumorogenesis, in spite of the close association of PTEN with the PI3-kinase pathway. No significant associations were observed between ALDH and Ki67 and any parameters measured.
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 4854. doi:10.1158/1538-7445.AM2011-4854
Abstract 4862: Whole genome amplification allows for testing of valuable specimens by array comparative genomic hybridization
Authors: Edelman Daniel C. , Stevenson Holly , Suuriniemi Miiia , Singh Parvati , Rodriguez-Canales Jamie , Hanson Jeffery C. , Walker Robert , Emmert-Buck Michael R. , Meltzer Paul 
Published: June 2012

Abstract
Many cancer clinical specimens are obtained in minute quantities and in varying states of degradation; for example, when they are formalin or ethanol fixed. In addition, many investigators seek tests on multiple genomic analytes and frequently insufficient DNA remains for all inquiries after the initial priority testing. To accommodate all clinical scientific inquiries, the Sigma GenomePlex whole genome amplification (WGA) protocol has been evaluated as a means to produce sufficient genomic material for array comparative genomic hybridization (aCGH) downstream testing. However previous studies, including our own, have shown that testing degraded samples with WGA coupled to oligo CGH arrays resulted in decreased data quality. We contend this could be due to unequal genomic representation in the WGA product. Our objective was to assess the importance and efficacy of using correctly matched reference DNA and to compensate for the WGA amplification bias, potentially improving aCGH results.
We obtained DNA from ethanol-fixed prostate tissues in which both tumor and normal tissue compartments were separately isolated by laser capture microdissection or by directed needle-core sampling from formalin-fixed paraffin embedded blocks. We sought to optimize the Sigma WGA protocol by testing the following parameters: source of reference DNA (commercial versus matched normal), WGA cycle number, and the use of size-exclusion columns post-WGA. Quality control measures for the purified WGA product included electrophoresis (gel and Agilent Bioanalyzer), and a multiplex PCR to determine the extent of DNA genomic representation across the WGA product. ChromaSpin columns were used to reduce the number of smaller WGA amplicons prior to aCGH. WGA products were assayed with Agilent 8×60K CGH microarrays and chromosomal aberrations and data quality were assessed using BioDiscovery Nexus software.
Data will be presented comparing the effectiveness of using sheared reference DNA as opposed to matched normal DNA, the use of QC methods prior to hybridization, any benefit in removing small WGA DNA products, and varying the WGA cycle number. We continue to evaluate how these modifications can bring improvement to WGA when coupled to aCGH, because there is promise that this method could expand the genomic testing opportunities for valuable and rare clinical specimens.
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 4862. doi:10.1158/1538-7445.AM2011-4862
Abstract 4864: Antibody detection of translocations (ADOT) in Ewing's sarcoma
Authors: Luo Wen , Milash Brett , Dalley Brian , Smith Richard , Dutrow Natalie , Cairns Brad , Lessnick Stephen 
Published: June 2012

Abstract
Objective: The detection and identification of chromosomal translocations has important implications in the diagnosis, prognosis, and treatment of patients with cancer. Current approaches to translocation detection often have significant shortcomings, including limited sensitivity and/or specificity, and can be difficult to apply to formalin-fixed paraffin-embedded (FFPE) clinical samples. We developed a new approach, antibody detection of translocations (ADOT), that avoids many of the shortcomings of current techniques.
Methods: ADOT combines a transcriptional microarray-based approach with a novel antibody-based detection method. Microarrays were designed that probe for every possible fusion transcript in Ewing's sarcoma, both previously identified and theoretical. These include EWS/FLI, EWS/ERG, EWS/ETV1, EWS/ETV4, EWS/FEV and others. Total RNA, purified from Ewing's sarcoma cells or tumors (that express different types of translocations), is hybridized to the custom microarrays. A high-affinity antibody (S9.6) that binds to RNA-DNA duplexes formed during hybridization is used as a detection reagent.
Results: We demonstrate the feasibility of ADOT by examples in which both known, and unknown, translocation fusion transcripts are identified from cell lines, tumor xenografts, and primary tumor samples. Translocation fusion points identified by ADOT were confirmed using traditional RT-PCR and sequencing. Furthermore, ADOT is able to detect translocations in FFPE tumor samples in which case RT-PCR fails. The sensitivity of ADOT to detection of translocations is also determined.
Conclusion: ADOT allows for the accurate and sensitive identification of translocations and also provides exon-level information about the specific fusion transcript produced. Furthermore, the technique is readily generalizable to any potential fusion transcript, and can also detect previously undescribed fusions. This suggests that ADOT may be used as a diagnostic tool for pediatric sarcoma or other translocation-based cancers.
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 4864. doi:10.1158/1538-7445.AM2011-4864
Abstract 4867: Whole transcript expression microarray profiling of normal colon and adenocarcinoma total RNA
Authors: Mullinax Becky , Bergstrom-Lucas Anne , Venneri Jennifer , Kulkarni Vinayak , Janis Michael , Ghosh Jayati , Gao Jing , Fulmer-Smentek Stephanie 
Published: June 2012

Abstract
Whole transcript expression profiling by microarray analysis is an important tool for understanding biological mechanisms and development, classifying tissue and tumor types, and identifying indicators for diagnosis and prognosis. This analysis measures the alternative splicing of exons from a given RNA transcript leading to the translation of a variety of proteins from a single RNA transcript. To address the need for whole transcriptome expression profiling from low quantities of total RNA, we have developed an exon expression workflow which includes custom and catalog human, mouse, and rat exon microarrays, a whole transcript labeling method, and analysis software. This fast and simple microarray-based method employs a modified linear amplification procedure to generate Cy-labeled cRNA representing the whole transcript. The labeling method, available in the Low Input Quick Amp Labeling WT Kit (LIQA WT), employs a mixture of oligo dT- and random nucleotide-based T7 promoter primers (WT Primer Mix) resulting in high cRNA yields and specific activities from low RNA inputs. The probes on the human, mouse, and rat SurePrint G3 exon microarrays were designed from the high quality content of the public databases, primarily RefSeq and Ensembl. Exon array results are analyzed for gene and exon-level expression using GeneSpring GX 11.5 software. The exon gene expression workflow allowed whole transcript gene expression profile comparisons to be made in fewer than two days. Comparisons of probe signals from technical replicate samples demonstrated high reproducibility with a wide dynamic range and comparable signals across a broad range of input amounts. High correlations were demonstrated in platform comparisons to both qRT-PCR and RNA-Seq. This new workflow was used to detect alternative splicing of exons between cancerous and normal cells resulting in gene and exon expression profiles consistent with the current literature. These results demonstrate the value of the new exon expression workflow in identifying known exons, alternative start and stop sites, mutually exclusive exons, and cassette exons in cancer 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 4867. doi:10.1158/1538-7445.AM2011-4867
Abstract 4873: Protein complexes in cancer: A novel strategy to identify protein complexes through reduction of false discovery rate
Authors: Das Sudipto , Xiao Zhen , Bosley Allen D. , Chan King C. , Issaq Haleem J. , Veenstra Timothy D. , Andresson Thorkell , Green Jeffery E. 
Published: June 2012

Abstract
Most cellular processes are controlled by protein-protein interactions, and aberrant protein-protein interactions can lead to human diseases such as cancer. Hence a comprehensive understanding of a protein interaction network and its dynamics response to different physiological conditions is essential for understanding a protein's function and may reveal novel therapeutic opportunities for fighting cancer.
Affinity purification coupled with mass spectrometry has become the method of choice to study in vivo protein interactions and formation of protein complexes. However, the methodology has some limitations that reduce it application such as, under sampling of low abundant proteins and high background leading to an elevated false discovery rate (FDR).
Herein we describe a strategy utilizing differential expression of the target protein followed by analysis using quantitative proteomics. By performing affinity purification on cells expressing increasing amounts of the polycomb complex protein Bmi-1, we show that known interacting proteins could be distinguished very efficiently from the background proteins based on their abundance profile. Applying this method to the data set significantly reduced the FDR and allowed us to identify potentially new interacting proteins for Bmi-1 that otherwise would have been considered non-specifically bound proteins.
The method was also applied to characterize the interactome for Snail I, II and III a family of Zn-finger proteins thought to be involved in transcriptional repression. These proteins have been implicated in diverse biological function such as regulation of epithelial to mesenchymal transition, formation and maintenance of embryonic mesoderm, generation and migration of neural crest cells and metastasis.
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 4873. doi:10.1158/1538-7445.AM2011-4873
Abstract 4877: High throughput proteomic applications using protein A/G magnetic beads
Authors: Doyle Joanna , Ray Matthew , Ouyang Anlong , Benton Betsy , Bell Peter A. 
Published: June 2012

Abstract
Speed and sample purity are key issues for proteomics researchers. Sample and data-processing throughputs are current bottlenecks in proteomic analysis. Magnetic separations can provide greater consistency and automation of proteomic sample preparation. We report here the development of a novel 1µm protein A/G magnetic bead that enables fast and convenient isolation of proteins via immunoenrichment. Thermo Scientific Pierce Protein A/G Magnetic Beads use a recombinant protein A/G that combines the IgG binding domains of both protein A and protein G. Protein A/G contains four Fc-binding domains from protein A and two from protein G, making it a convenient tool for capture of immunoglobulins from a variety of species and isotypes. Recombinant protein A/G was covalently coupled to 1 μm, blocked double-shelled magnetic particles with a polymeric core. The beads had a binding capacity of &gt;60 μg rabbit IgG per mg bead along with low non-specific binding. Using a Thermo Scientific KingFisher Flex Magnetic Particle Processor, antibodies were purified from serum or ascites with high yield using the Pierce Protein A/G Magnetic Beads. The beads were also used to immunoprecipitate and co-immunoprecipitate multiple proteins significant to different phases of the cell cycle, including cyclin B, Cdk1, cyclin E, and cyclin D. U2OS and HeLa cell lines were first synchronized in serum starved media. The media was replaced with enriched media and cells were harvested at 4 hours (beginning of G1 phase), 6 hours (end of G1 phase), and 18 hours (end of G2 phase). Proteins were effectively isolated from the cell lysates using Pierce Protein A/G Magnetic Beads and identified by Western blot. In addition, these beads were successfully used in a chromatin-immunoprecipitation (ChIP) assay to measure binding of RNA Polymerase II to the proximal myc promoter in A431 lung carcinoma cells treated with and without EGF. In Conclusion, the results indicate that Pierce Protein A/G Magnetic Beads can effectively isolate protein targets in a variety of proteomic applications.
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 4877. doi:10.1158/1538-7445.AM2011-4877
Abstract 4880: Monitoring tumor response to chemotherapy by in vivo real-time imaging of phosphatidylserine targeting antibodies
Authors: Gong Jian , Him Linda , Hughes Christopher , Freimark Bruce 
Published: June 2012

Abstract
Phosphatidylserine (PS) is a phospholipid normally residing in the inner leaflet of the plasma membrane that becomes exposed on tumor vascular endothelial cells and tumor cells in response to chemotherapy, irradiation and oxidative stresses in the tumor microenvironment. Binding of antibodies targeting PS on the tumor endothelial cells recruit immune cells and engage the immune system to destroy tumor vasculature. The antibodies also enhance anti-tumor immunity by blocking the immunosuppressive action of PS. A chimeric anti-PS antibody, bavituximab, is being used in combination with chemotherapy to treat patients with solid tumors in randomized Phase IIb clinical trials. In the present study, we demonstrate in vivo tumor imaging of PS expression using real-time, near infrared fluorescence imaging of antibodies that specifically target PS. Human prostate PC-3 tumors expressing luciferase were orthotopically transplanted in SCID mice and tumor growth was monitored by bioluminescence. Targeting antibodies used in this study bind PS through the interaction of beta-2-glycoprotein 1 (β2GP1) in the same manner as bavituximab binding to β2GP1 in humans. Specific localization of fluorescence-labeled PS targeting antibodies after a single dose was observed in tumors compared to an isotype control antibody. Persistence of antibody localization was prolonged using intact IgG compared to F(ab’)2 fragment. Chemotherapy was shown to enhance the binding of PS targeting antibodies to tumors. These data provide a rationale to image PS expression to localize tumors or metastases and to monitor chemotherapy-induced PS expression during the course of bavituximab therapy.
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 4880. doi:10.1158/1538-7445.AM2011-4880