bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2183: High-throughput screening, identification and characterization of novel kinases involved in chemosensitization of breast cancer cells
Authors: Hsieh Charline , Lin Asha , Hsiao Michael 
Published: February 2011

Abstract
Background - Development of drug resistance is considered to be one of the most challenging issues in chemotherapy for cancer patients. As one of the conventional chemotherapeutic agent, paclitaxel was originally extracted from Pacific yew tree and has been applied widely in ovarian cancer, breast cancer and lung cancer. Resistance to paclitaxel has posed severe problems in cancer treatment. We are therefore interested in identifying the genes that render paclitaxel-resistant breast cancer cells to become more sensitive with the drug treatment. The mechanisms and signaling pathways of these kinases in relations to paclitaxel resistance and their molecular targets have been investigated. Methods - We have screened a shRNA library containing 592 novel kinase genes with 1306 clones for the chemosensitizer loci. DNA was extracted in a high throughput manner, and cell transfection/transduction was carried out on 384 well plates using a unique solid-phase DNA delivery method. The positive hits were selected according to the alteration on their IC50 values for the drug using cell viability assays. Quantitative PCR, Western blot, and caspase assays have been employed to elucidate the signaling pathways of these kinases in response to paclitaxel. Protein purification and interaction studies have also been carried out in attempt to elucidate the putative substrates for the kinases and their interaction partners. Results and Conclusions - We have established a high throughput screening platform for identification of the chemosensitizer loci. High transfection/transduction efficiencies can be achieved using our solid-phase gene delivery method. Several novel unknown kinase genes that render drug-resistant cancer cells to become sensitive have been selected. The positive shRNA hits were further verified by quantitative real-time PCR. Among the 20 hits that showed diminished IC50 values of paclitaxel in breast cancer cells, we have selected two candidates for further studies. Knocking down of TAOK3 or VRK3 in breast cancer cells resulted in reduction of IC50 of paclitaxel to half of the original value. Furthermore, we have investigated the signaling pathways of these 2 kinases in relation to paclitaxel resistance. The different signaling pathways elucidated have revealed the complex nature of drug resistance development in cancer cells.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2183.
Abstract 2184: SUMO-binding proteins as effectors and regulators of SUMO modification
Authors: Guzzo Catherine M. , Uzoma Ijeoma , Zhu Heng , Cox Eric , Blackshaw Seth , Matunis Michael J. 
Published: February 2011

Abstract
SUMOs (Small Ubiquitin-related Modifiers) are reversibly conjugated to other proteins in the cell, thereby regulating a wide range of essential functions. Many of the functions regulated by SUMOylation are intimately tied to processes directly relevant to cancer, including maintenance of genome integrity and cell cycle regulation. Studies in the past several years have in fact linked SUMOylation to a variety of human cancers, including leukemia, prostrate, breast, and colon cancers. Thus, developing a fundamental understanding of the signals and factors that regulate SUMOylation, as well as how SUMOylation affects protein function, has the potential to lead to important new insights into cancer development, diagnosis, and treatment. We hypothesize that the three SUMO paralogs expressed in vertebrate cells (SUMO-1, SUMO-2 and SUMO-3), as well as their polymeric forms, represent unique signals recognized by unique proteins. Moreover, we propose that SUMOylation often promotes interactions between modified proteins and downstream factors containing SUMO-interacting motifs (SIMs). To test this hypothesis, we have initiated high throughput studies to identify novel SUMO-1, SUMO-2 and SUMO-2 polymeric chain binding proteins. Using microarray analysis, we identified ∼400 mostly nuclear proteins, many with preferential affinity for specific SUMO paralogs. Among these 400 putative SUMO-binding proteins was a family of zinc finger proteins that we have determined to possess a novel SIM. This family of proteins contains a stretch of unique tandem zinc fingers called MYM (myeloproliferative and mental retardation) domains. Although the exact functions of MYM-type zinc finger domains are not known, proteins containing these domains are linked to myeloproliferative syndromes, X-linked mental retardation, and transcriptional regulation. We have found that the MYM-type zinc finger domains are both necessary and sufficient for SUMO-binding. MYM-type zinc finger domains represent only the second known class of SUMO-binding motifs.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2184.
Abstract 2189: Efficacy of combination therapies in lung cancer
Authors: Sos Martin L. , Weiss Jonathan , Peifer Martin , Thomas Roman K. 
Published: February 2011

Abstract
Genetically activated oncogenes induce dependency on the constitutively activated oncoprotein in cancer cells. Targeted therapeutics that shut down the oncogenic signaling, induce apoptosis and thus lead to tumor shrinkage in patients can exploit this dependency. However, efficacy of single-agent inhibition often is limited by release of negative feedback loops or incomplete suppression of its primary target at clinically relevant concentrations.
The lack of preclinical models that capture the genomic diversity of human tumors impedes the transition from preclinical drug discovery to clinical trials lies in and this diversity. We sought to overcome these limitations and therefore we established a panel of 84 non-small cell lung cancer cell lines and characterized in depth in gene copy number, gene expression and mutation space.
We applied a chemo-genomics approach in order to determine the efficacy of single-agent and combination treatment with PI3K-, MAPK- and receptor tyrosine kinase (RTK-) inhibitors in genotypically defined subsets of tumor cells. We found RTK-driven tumors to largely depend on PI3K and RAS-/ RAF-driven tumors to be addicted to the MAPK signaling pathways, respectively. However, release of negative feedback loops led to activation of the alternate pathway. Combined inhibition of PI3K- and MAPK-pathways potently suppressed release of negative feedback loops, thereby resulting in enhanced induction of apoptosis in tumor cells and tumor shrinkage in vivo. In the subset of EGFR mutated cells harboring the gatekeeper mutation T790M we found limited efficacy of single-agent treatment with irreversible EGFR inhibitors. This limited activity could be linked to decreased binding velocity to the mutant kinase. However combined treatment of T790M-mutant tumor cells with irreversible ERBB inhibitors, and PI3K/mTOR inhibitors led to induction of apoptosis. Recently we established a systematic screening pipeline for the study of combined inhibition of key nodules of oncogenic signaling pathways and preliminary results suggest a critical role of PI3K/mTOR-signaling for efficacy of combination therapies. Overall our approach builds a robust framework for the preclinical study of combination therapies and might help to direct future drug development and patient stratification in clinical trials.
Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2189.
Abstract 219: Treatment with survivin siRNA augments cytotoxicity of paclitaxel in primary ovarian cancer cells
Authors: Kar Rajarshi , Palanichamy Jayanth K. , Sharma Chandresh , Chattopadhyay Parthaprasad , Jain Sunesh K. , Kumar Lalit , Singh Neeta 
Published: February 2011

Abstract
Introduction
Chemoresistance is a major problem encountered during the treatment of ovarian cancer. Paclitaxel one of the first line drugs is less effective in patients whose cancer cells overexpress survivin. This study investigates whether reducing expression of survivin by siRNA treatment of primary cultures of ovarian cancer cells can increase sensitivity to paclitaxel.
Methodology
Five primary cultures were established from ascites obtained from untreated ovarian cancer patients. Ascites mixed with MCDB 105 and M199 medium (ratio 1:1) was plated in 75 mm2 flasks for establishment of primary cultures. Survivin siRNA was synthesized using in-vitro transcription technique and was quantified using pico green. A dose of 15 nM of Survivin siRNA was used for further experiments. Primary cultures were treated with survivin siRNA using olgofectamine as the transfecting agent. After 24 hours Survivin expression was quantified by RT-PCR. Cells plated in 96 well plates were treated with survivin siRNA (15nM). After 24 hours, paclitaxel treatment was given at four different doses (0.1, 1, 5 and 25 µg/ml) in separate wells. Untransfected cells, cells transfected with oligofectamine alone (mock transfection) and with universal control siRNA were also treated with same doses of paclitaxel after 24 hours. Cell survival was quantified using MTT assay. All experiments were done in triplicates.
Results
On treating the primary cultures with survivin siRNA there was a 6 fold decrease in Survivin expression. Survivin siRNA alone caused 23 ±3% cell deaths in the 5 primary cultures. When these cultures were treated with paclitaxel alone (untansfected cells) at different doses (0.1, 1, 5 and 25 µg/ml) the average cell death was 21.2%, 22.4%, 26% and 37.5% respectively. There was no significant difference in cell death in mock transfected and control siRNA transfected cells when compared to untransfected cells. However when the cells were pretreated with survivin siRNA and then followed by same doses of paclitaxel after 24 hours, cell death increased to 52.8%, 55.4%, 60% and 70% respectively. All the primary cultures were resistant to paclitaxel treatment as 62.5% of the cells survived the highest dose of paclitaxel. Survivin siRNA treatment could significantly increase the sensitivity of the primary ovarian cancer cell cultures to paclitaxel.
Conclusion
Survivin appears to play a major role in the response of ovarian cancer cells to paclitaxel treatment and knocking off survivin expression may prove beneficial in the treatment of ovarian cancer patients with paclitaxel whose tumors overexpress Survivin.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 219.
Abstract 2190: Yeast-based pharmacogenomics approaches to identify Cisplatin responsive genes
Authors: Ferrari Elisa , Lucca Chiara , Spitaleri Gianluca , de Braud Filippo , Foiani Marco 
Published: February 2011

Abstract
Platinum-based drugs are largely used in cancer treatment. Using genome-wide approaches we aimed at identifying cisplatin primary and secondary targets and at characterizing cisplatin responsive genes.
The yeast Saccharomyces cerevisiae is widely used to study a variety of eukaryotic cellular processes including those that are relevant for human health.
Yeast can be used for genetic, genomic and mechanistic studies as well as for pharmacogenomic approaches. Using yeast-based pharmacogenomic screens we identified novel genes relevant for the cisplatin response. In particular, we have identified genes involved in DNA repair pathways such as Nucleotide Excision Repair, Homologous Recombination and Post Replicative Repair, as well other genes.
We also used mechanistic approaches to further characterize those factors that have obvious human ortologues and whose functions are still elusive.
Altogether our approaches allowed us to unmask novel factors that contribute to cell viability and genome integrity in response to cisplatin treatment. Complementary studies on the human ortologues are ongoing.
Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2190.
Abstract 2198: Exome and transcriptome sequencing of human tumors and tumor-derived cell lines
Authors: Nickerson Michael L. , McGee Kate , Gold Bert , Lawley Cindy , Tran Bao , Stewart Claudia , Harkins Tim , Waldman Fred , Zbar Berton , Moore Lee , Dean Mike 
Published: February 2011

Abstract
Insight into the cancer genome has recently increased in an unprecedented way due to high throughput (HT) sequencing technology to examine the genome, exome, and transcriptome. We sought new genetic biomarkers for cancer by using HT sequencing to examine highly characterized primary sporadic tumors and tumor-derived cell lines. Several tumors/cell lines represented the most common subtype of kidney cancer, clear cell renal cell carcinoma, as well as NCI-60 panel cell lines from breast (MCF7) and prostate (PC3). Incorporation of NCI-60 panel cell lines was advantageous due to extensive prior characterization of these reagents, including gene expression, comparative genome hybridization, SNPs, and drug cytotoxicity. The study was performed using three major platforms (454, Illumina, ABI) to compare sequencing quality, cost, quantity, and computational amenability. Different methodologies were examined including exome, transcriptome, and whole genome sequencing. Alignment of sequence to a consensus genome (hg 18) allowed identification of novel and previously documented genomic variants. Various filters were implemented to sort the large number of variants detected, including dbSNP, personal genome variants, and 1000 genomes data. An average of 65 million 35-50 base pair sequences were generated from transcriptomes of two primary clear cell RCC tumors. Over 2 million 375 base pair sequences were generated from each of four cell line exomes. Differences were observed in extent and depth of coverage of a given target region by various experimental approaches. SNP array genotyping showed 1% discordance with sequencing. Previously characterized mutations were confirmed in HT sequences. We identified multiple regions of homozygosity at an unprecedented resolution. For example, in the clear cell renal cancer cell line, 786-0, a known mutation in VHL (311delG) was identified, and LOH at SNP positions across the entire length of chromosome 3 was confirmed.
Alignment to a reference genome (hg 18) permitted identification of 2583-5307 genomic sequence variants, including 92-297 novel non-synonymous variants in the exomes of each cell line. Variants include frameshift and nonsense mutations. Novel non-synonymous variants were identified in cancer-related genes and these are being examined in additional tumors. Potential functions of newly identified mutated genetic loci suggest perturbation of signaling pathways and are candidates for targeted therapy.
Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2198.
Abstract 2206: Distinct somatic mutation patterns in multiple human cancers and their subtypes
Authors: Kan Zhengyan , Stinson Jeremy , Bhatt Deeplai , Kaminker Joshua , Stern Howard , Faham Malek , Seshagiri Somasekar 
Published: February 2011

Abstract
We have systematic analyzed 4.5Mb of DNA representing 1507 genes in 450 human fresh frozen tumors covering four major human cancers and their subtypes for somatic mutations. For this analysis we used E. coli mismatch repair detection (MRD) for our primary mutation scans. All the identified variations were validated as somatic using nucleic acid mass spec and confirmed to be present in the original tumor and absent in the matched adjacent normal DNA. Of the all tumor samples analyzed ∼80% show somatic mutations in one or more genes studies. Of the genes analyzed we identified mutation in 842 genes. Applying statistical techniques and other measures we have identified 221 genes to be significantly mutated across all cancers studied. Further analysis of mutated genes by tumor types and subtypes revealed distinct patterns of significantly mutated genes. Besides the previously known mutated genes, we have identified several novel mutated genes with previously unknown role in cancers across the various cancer types studied. To further ascertain the relevance we have performed integrated analysis of mutation and copy number variations data from the samples studied and identified putative tumor supressors and oncogenes. Also, we have performed mutational analysis at the level of biological pathways and identified several mutated pathways.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2206.
Abstract 2209: Integrative analysis of DNA copy number and gene expression in metastatic tumor cells from oral squamous cell carcinoma for the identification of genes associated with survival
Authors: Xu Chang , Liu Yan , Wang Pei , Fan Wenhong , Rue Tessa C. , Upton Melissa P. , Houck John R. , Lohavanichbutr Pawadee , Doody David R. , Futran Neal D. , Zhao Lue P. , Schwartz Stephen M. , Chen Chu , Méndez Eduardo 
Published: February 2011

Abstract
To examine the impact of copy number aberrations (CNA) on gene expression in oral squamous cell carcinoma (OSCC) metastasis, we used Affymetrix 250K Nsp single nucleotide polymorphism arrays and U133 Plus 2.0 expression arrays, respectively, to interrogate the DNA and RNA from metastatic OSCC cells isolated using laser capture microdissection from lymph nodes of 20 patients. Overall, CNA accounted for expression changes in about 30% of the transcripts studied. With a false discovery rate &lt; 1%, 530 transcripts (461 genes) were identified as to have significantly correlated CNA and expression. When tested using an independent dataset with expression profiles for 148 primary OSCC and 45 normal oral mucosa, the genes were enriched with candidates associated with OSCC (vs. normal oral mucosa) (n=174 transcripts differentially expressed) and OSCC-specific survival (n=32 transcripts associated), as compared to a random gene set of the same size (p &lt; 0.001). We then fit two Cox models using the first two principal components derived from these two gene sets (‘174-transcript PCA’ or ‘32-transcript PCA’), and two other models that combined stage with either the 174- or the 32-transcript PCA score. The Area Under the Curve (AUC) for a model combining stage with 174-gene PCA was significantly higher than that for a model with stage alone (AUC=0.80 vs. 0.72, p = 0.042). Further investigation is warranted to confirm these findings and to examine the biologic role of these copy number-associated transcripts in OSCC metastasis and their potential as therapeutic targets.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2209.
Abstract 221: C6-ceramide sensitizes the aggressive L3-6 pancreatic cancer cell line to paclitaxel-mediated antitumor effects in vivo and in vitro
Authors: Cao Cong , Bowen Wayne , Wanebo Harold , Wan Yansheung , Ji Fran , Lu Su , Shrayer David 
Published: February 2011

Abstract
Key words: C6 Ceramide, Taxol, Gemcitabine, AMPK, AKT/mTOR, chemotherapy, pancreatic cancer
Background: Survival after therapy of pancreatic cancer is about &lt;5% with a strong need for new chemotherapy enhancing strategies. Our previous in vivo studies have demonstrated that C6 Ceramide has synergistic anti tumor effects on agents (Taxol, Oxaliplatin, Gemcitabine) against the aggressive pancreatic cancer cell line L3.6 in scid mice. The molecular mechanisms of this synergistic effect are our current focus.
Methods: The synergistic effects of C6 ceramide on Paclitaxel and Gemcitabine were studied both in vivo (by monitoring survival, tumor size, tumor growth rate, in heterografted L3-6 pancreatic cancer cells in scid mice) and in vitro (by MTT assay and apoptosis assays-(Caspase dependent/independent), and Western blot assays of signal transduction pathways to determine molecular mechanisms involved in the C6 Ceramide synergistic effects.
Results: In vivo and in vitro data confirmed significant C6 Ceramide synergistic enhancement of Paclitaxel (P) and Gemcitabine (G) in the L3-6 model. Basic findings: Paclitaxel alone activates pro-survival pathway PI3K/AKT/mTOR in L3.6 cells. C6 ceramide induces pharmacological and genetic inhibition of the PI3K/AKT/mTOR pathway sensitizing L3.6 cells to Paclitaxel induced cell death and apoptosis. C6 Ceramide also dramatically enhanced Paclitaxel induced AMPK activation, a key energy switch enzyme that is responsible for cell apoptosis in stress. PI3K/AKT/mTOR inhibition and AMPK induction may be major mechanisms of C6 synergistic effect on paclitaxel induced cell death. We also found that C6 Ceramide also promotes Paclitaxel induced activation of the mitochondrial mediated apoptosis pathway sensitizing L3.6 to chemotherapeutic induced cell death.
Conclusion: Our data suggests that combining C6 Ceramide with traditional chemotherapy drugs illustrated by paclitaxel may have potential as a new biologic therapeutic intervention against pancreatic cancer and merits continued study.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 221.