bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1147: High-throughput nanofluidic PCR-based preparation of 454 sequencing libraries for identifying mutations in EGFR and MET
Authors: Wang Jun , Anderson Megan J. , Kaper Fiona , Stewart Claudia , Soppet Daniel , Bere Bill , Hartley Todd , Chen Peilin , Lin Min , Pieprzyk Martin , Jones Robert C. , May Andrew P. 
Published: February 2011

Abstract
The epidermal growth factor receptor (EGFR) and mesenchymal-epithelial transition factor (MET) play important roles in cancer development and are promising targets for anticancer therapies. Mutations in the EGFR and MET genes are associated with multiple types of cancer and the ability to detect variants in these genes is crucial for a better understanding of disease progression and response to targeted therapeutics. Next-generation sequencers (e.g. 454, Illumina) hold great potential for detecting disease-specific alterations within patient populations for a given cancer type. However, current approaches for targeted resequencing of specific genetic regions are not well suited to studying the hundreds or thousands of patient samples required to assign significance to mutations.
We have developed a novel nanofluidic platform, the Access Array™ system, which enables the robust, simultaneous amplification of 48 PCR products (amplicon) from 48 samples in parallel using only 50ng input DNA per sample. In addition, we have developed a primer design strategy that incorporates sample-specific barcodes and 454 sequencing adaptors into each amplicon, removing the need for library preparation before sequencing. We will present sequencing data collected from amplicon libraries prepared using the Access Array system to amplify 48 exon regions of the EGFR and MET genes from the NCI-60 cell lines. Sequencing data from these libraries demonstrates excellent uniformity in representation between amplicons and across samples. We will present data mapping mutations within these genes across the NCI-60, and discuss the use of Access Array enrichment panels in monitoring mutations across large patient populations.
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 1147.
Abstract 1154: Direct detection of DNA methylation and mutagenic damage through single-molecule, real-time (SMRTTM) DNA sequencing
Authors: Flusberg Benjamin , Webster Dale , Travers Kevin , Olivares Eric , Korlach Jonas , Turner Stephen 
Published: February 2011

Abstract
Changes in genomic methylation patterns are often associated with cancer processes. The development of new, high-throughput techniques for mapping aberrant methylation patterns, along with various forms of DNA damage, will be important for advancing cancer research. Single-molecule real-time (SMRTTM) sequencing yields a rich set of information about nucleic acid structure that allows direct detection of various forms of modified nucleotides, including 5-methylcytosine, 5-hydroxymethylcytosine, N6-methyladenosine, and 8-oxoguanosine. We have studied DNA templates with a range of CpG methylation patterns, and we describe how this approach, in combination with circular consensus sequencing of individual DNA molecules, can be used for base-pair resolution identification of epigenetic modifications. Unlike current bisulfite-sequencing techniques, which are limited by short read lengths and by the reduction in genomic complexity, our method will enable mapping of methylation patterns within even highly repetitive genomic regions. Overall, these results highlight the potential applications of the SMRTTM technology to high-throughput sequencing of methylation and mutagenic DNA lesions.
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 1154.
Abstract 1162: RNA expression analysis of rare tumor cells by laser-mediated lysis
Authors: Kamme Fredrik , Bright Gary 
Published: February 2011

Abstract
Molecular analysis of live rare cells, such as circulating tumor cells (CTCs) is challenging. Current strategies include antibody-mediated capture and size selection and are limited in the purity and recovery of the cells of interest. We have developed a novel approach for rare cell analysis based on the specific lysis of targeted cells in a background of a vast majority of other cell using a precisely targeted laser pulse. Instantly lysed cells release their contents into the medium, including mRNA, providing a method to analyze mRNA content in selected cells. Using a high throughput plate cytometer equipped with lasers for in situ cell manipulation (LEAP Cell Processing and Purification Workstation), we have analyzed RNA from individual tumor cells in a model of CTCs consisting of carcinoma cells spiked into human PBMCs. A 5-gene panel was measured by RT-PCR from single tumor cells and was detected in 94% of the cases with 0% false positives. RNA analysis of single tumor cells via laser-mediated lysis represents a new principle for the analysis of rare cells, as the specificity of analysis is dependent on imaging and laser targeting only and free of any limitations imposed by an antibody- or size-dependent purification strategy.
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 1162.
Abstract 1167: The GNAS1 T393C polymorphism is a predictor of clinical outcome in esophageal cancer
Authors: Effenberger Katharina E. , Musici Safije , Yekebas Emre F. , Kutup Asad , Kamradt Till , Mina Sormeh , Kalinin Viacheslav , Brandt Burkhard , Pantel Klaus , Izbicki Jakob R. , Vashist Yogesh K. 
Published: February 2011

Abstract
Background: There is a paucity of prognostic markers in esophageal cancer (EC). Genetic variations determined in the germline DNA of cancer patients may serve as important prognostic factors of clinical outcome since genomic DNA remains unbiased by instability occurring in tumor DNA and is easily accessible in the peripheral blood. G-protein α subunit (Gαs) polymorphism has been identified as a prognostic marker of tumor recurrence and survival in various tumor entities. We genotyped the single nucleotide T393C polymorphism in the GNAS1 gene encoding Gαs, and focused on three different genotypes, TT, TC, and CC. The aim of this study was to evaluate the potential prognostic value of the GNAS1 polymorphism in EC.
Methods: Genomic DNA was extracted from peripheral blood leucocytes of 190 patients who underwent complete resection for esophageal cancer and did not receive any neoadjuvant or adjuvant therapy. The GNAS1 genotypes were correlated with clinicopathological parameters, tumor cell dissemination in bone marrow and clinical outcome.
Results: The TT and TC genotypes correlated with advanced disease, predominantly characterized by the presence of lymph node metastases (p&lt;0.001) and tumor cell dissemination (p=0.01). In line with this, significantly more TT and TC genotype patients displayed disseminated tumor cells in bone marrow compared to the CC genotype group (p=0.01). Accordingly, the disease recurrence rate was higher in TT and TC than in CC patients. Kaplan-Meier estimates for disease-free (DFS) and overall survival (OS) displayed better outcome in CC compared to TT and TC genotypes. Furthermore, in multivariate Cox proportional hazard analysis, GNAS1 polymorphism independently predicted disease progression with the CC group presenting the best outcome (OS: p=0.001, DFS p=0.002).
Conclusion: The GNAS1 polymorphism was identified as a strong independent prognostic factor for DFS and OS in EC patients supporting a functional role of Gαs in this tumor entity. Preoperative determination of the GNAS1 polymorphism will allow allocation of patients into different risk profiles as well as stratification into individual therapy regimen.
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 1167.
Abstract 1170: NFE2L2 gene mutation in Japanese lung cancer patients
Authors: Sasaki Hidefumi , Hikosaka Yu , Kawano Osamu , Okuda Katsuhiro , Moriyama Satoru , Yano Motoki , Fujii Yoshitaka 
Published: February 2011

Abstract
Recently, the nuclear factor (erythroid derived 2)-like 2 (NFE2L2, former NRF2) gene mutation was identified in lung cancers. The constitutive activation of NFE2L2 in lung cancer cells promotes tumorigenicity. However, the correlation between NFE2L2 mutation status and clinico-pathological features of lung cancer was not well reported. We have investigated NFE2L2 gene mutation status in 263 surgically treated lung cancer cases from Nagoya City University Hospital. The presence or absence of NFE2L2 mutation was analyzed by direct sequences. EGFR mutations status was already investigated and reported. We detected 13 case (5.1%) of NFE2L2 mutation in our cohort, especially in male and squamous histology (p&lt;0.0001). Total EGFR mutations were present in 78 patients (30.8%). The NFE2L2 mutation was exclusive with EGFR mutations. The NFE2L2 mutation occurred tendency towards more frequent in patients with advanced stages. The patient with NFE2L2 mutation (n=13, 8 were dead) was significantly worse prognosis than the patient with wild type NFE2L2 (n=250, 72 were dead) (Log-rank test, p=0.0035, Breslow-Gehan-Wilcoxon test; p=0.0030). In our study, NFE2L2 mutations might play a role in tumor prognosis of squamous cell carcinoma of the lung.
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 1170.
Abstract 1171: Gastrointestinal stromal tumors (GIST) cell proliferation inhibition with combined adenoviral and molecular targeted therapy
Authors: Allen Derron E. , Arnoletti J. Pablo , Heslin Martin J. , Taguchi Takahiro , Kashentseva Elena A. , Dmitriev Igor , Frolov Andrey 
Published: February 2011

Abstract
Introduction: GIST, the most common mesenchymal malignancies of the GI tract, are characterized by gain-of-function mutations in KIT and PDGFRα receptors. Imatinib and sunitinib are tyrosine kinase inhibitors (TKI) currently approved for the treatment of GIST. Recent evidence suggests that GIST cells acquire secondary resistance to TKI through activation of alternative signaling pathways. We hypothesize that gene therapy with replicative vector oncolysis (virotherapy) can be utilized to improve efficacy of TKI and overcome GIST resistance to treatment.
Objectives: To determine if a panel of oncolytic adenoviruses in combination with imatinib and sunitinib, results in synergistic inhibition of GIST cell proliferation.
Results: GIST882 and GIST-T1 cells were subjected to imatinib and sunitinib treatment in combination with a panel of oncolytic adenoviruses (Ad5, Ad5RGD, Ad5pK7, and Ad5 - Ad3 fiber knob), to assess their inhibitory effects on cell proliferation. The Ad5/3 vector had the best rate of gene transfer and cytolytic effect. The greatest anti-proliferative effects were observed with 100 viral particles/cell of the Ad5/3 vector combined with TKI concentrations of 0.1 µM in GIST-T1 cell line. The combination of TKI and oncolytic adenoviruses showed greater inhibition of GIST cell proliferation (78% decrease) when compared to TKI alone (58% decrease) and viral therapy alone (23% decrease, p&lt;0.01). Successful ex vivo infection and oncolysis of GIST by Ad5/3 particles was confirmed in cells obtained from patient surgical specimens (n=4).
Conclusions: The oncolytic adenovirus Ad5/3 infects and inhibits GIST cell proliferation both in vitro and ex vivo. Virotherapy with Ad5/3 has synergistic anti-proliferative effects with TKI and may help overcome GIST resistance to KIT 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 1171.
Abstract 1180: MicroRNAs and their target messenger RNAs associated with progression of breast cancer
Authors: Schultz Silke , Petat-Dutter Karina , Walter Michael , Poths Sven , Vogel Ulrich , Bonin Michael , Sotlar Karl , Neuburger Christina , Wallwiener Diethelm , Fehm Tanja , Neubauer Hans J. 
Published: February 2011

Abstract
Background
Based on own results using laser micro dissected cells of invasive ductal (IDC) and ductal in situ (DCIS) breast cancer of the same tumor combined with Affymetrix microarray technology 445 differentially transcribed candidate genes have been identified (Schütz et al., Cancer Research 2006, 66:5278-5286). In this project differential expression of miRNAs and mRNAs was investigated in the same DCIS/IDC breast cancers and pure DCIS fixed in formalin and embedded in paraffin (FFPE).
Aims
The aim was (1) to identify miRNAs and their target mRNAs to serve as progression markers between DCIS and IDC and (2) to find an miRNA/mRNA set to characterize aggressive DCIS with a high invasive potential.
Material and Methods
Bioinformatic analysis using support vector machine and principle component analyses was applied to extract a prognostic gene set from the set of differentially expressed genes and qRT-PCR validation was carried out on micro dissected FFPE epithelial cells. Additionally, Illumina microarray technology was applied for mRNA and miRNA expression analysis. For functional analysis transmigration assays were performed in combination with siRNA mediated knock down of target genes.
Results
We obtained a 9-gene progression set which is able to correctly classify DCIS and IDC in 23 out of 24 cases (95.8%). Eight of the 9 possible marker genes were correctly validated in FFPE tissues. Further, expression of these genes also varied between pure DCIS and DCIS areas of DCIS/IDC mixed tumors - expression validation is currently done with qRT-PCR. Nineteen miRNAs were differentially expressed between DCIS and IDC, of which 4 had already been described in tumors. These 4 miRNAs have binding sites on 5 of the 9 candidate genes. Microarray analysis of mRNA from FFPE tissues confirmed differential expression of LRRC15 which has been found to be functionally relevant for breast cancer cell invasion and of LRRC32. An siRNA mediated knock down of LRRC32 reduced invasive potential of MDA-MB-231 breast cancer cells in transmigration assays.
Conclusions
A small gene set of potential progression markers obtained by microarray analysis of native breast carcinomas was successfully validated on FFPE tissues. In addition, a set of targeting miRNAs was identified that might thus serve as prognostic markers. Further analyses are still ongoing.
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 1180.
Abstract 1181: Expression of epithelial splicing regulatory protein 1 and 2 in ovarian cancer
Authors: Shoji Yutaka , Chirumamilla Siri , Chandramouli GVR , Risinger John I. 
Published: February 2011

Abstract
Epithelial Splicing Regulatory Proteins (ESRP1 and ESRP2) have recently been reported as RNA binding proteins that regulate epithelial specific splicing. We identified over-expression of ESRP1 and ESRP2 in ovarian cancer. The aim of this study was to determine the extent of expression of ESRP1 and ESRP2 in ovarian cancers and to examine whether its expression affects the abundance of the epithelial isoform of the Fibroblast Growth Factor receptor 2 (FGFR2) in ovarian cancer. Furthermore, we studied the regulation of FGFR2 splicing following knock-down of ESRPs in ovarian cancer cells. Affymetrix U133 Plus2.0 Array and quantitative real-time polymerase chain reactions (qRT-PCR) were used to measure gene expression levels in ovarian cancers and normal ovaries. ESRP1, ESRP2, epithelial specific FGFR2 IIIb and mesenchymal isoform FGFR2 IIIc mRNA levels were determined via qRT-PCR. RNA interference (RNAi) was used to knock-down ESRP1 and/or ESRP2 to examine its function on determining FGFR2 isoform expression in ovarian cancer cell line OVCAR3. Affymetrix GeneChip expression array analysis of 20 Stage IIIC serous ovarian cancers and 8 normal ovary surface epithelium brushings identified over-expression of ESRP1 (235 fold) and ESRP2 (33 fold). qRT-PCR confirmed that ESRP1 (7586 fold, p &lt; 0.00001) and ESRP2 (21 fold, p &lt;0.00001) were over-expressed in an independent set of 27 ovarian cancers compared to 11 normals. Since ESRP1 and ESRP2 function to drive the epithelial specific splicing of FGFR2, we examined the relative expression of FGFR2 IIIb and FGFR2 IIIc via qRT-PCR. The epithelial specific FGFR2 IIIb was over-expressed (313 fold; p &lt; 0.00001), whereas the mesenchymal isoform FGFR2 IIIc was down-regulated (75 fold). RNAi knock-down of ESRP1 in OVCAR3 cells resulted in increased levels of mesenchymal specific FGFR2 IIIc (6 fold), but had a minimal effect on FGFR2 IIIb expression (−1 fold). ESRP2 knock-down had no detectable effect on FGFR2 IIIc and IIIb expression. However, ESRP1 and ESRP2 double knock-down results in the predominant expression of FGFR2 IIIc (25 fold) and down-regulation of FGFR2 IIIb (−3 fold) when standardized to a scramble control. Our results confirmed that ESRP1, ESRP2 and FGFR2 IIIb are over-expressed and FGFR2 IIIc is down-regulated in ovarian cancers. Also, results of RNAi double knock-down of ESRP1 and ESRP2 indicate that ESRPs drive the expression of the epithelial isoform FGFR2 IIIb in ovarian cancer cells. These data have implications on the ligand specificity of the FGFR2 receptor and for potential individualized therapies targeting FGF signaling in ovarian cancer.
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 1181.
Abstract 1184: Prognostic significance of genetic alterations detected by high-density single nucleotide polymorphism (SNP) array in gastrointestinal cancer
Authors: Tada Motohisa , Kanai Fumihiko , Asaoka Yoshinari , Tanaka Yasuo , Tateishi Keisuke , Ijichi Hideaki , Ohta Miki , Seto Motoko , Sanada Masashi , Nannya Yasuhito , Imazeki Fumio , Yokosuka Osamu , Ogawa Seishi , Omata Masao 
Published: February 2011

Abstract
(Background and aims) We sought to identify specific gene that would be useful for predicting the prognosis of gastrointestinal cancer by the use of high-density single nucleotide polymorphism (SNP) array.
(Materials and Methods) We performed genome-wide analysis of 35 colorectal cancer (CC), 34 gastric cancer (GC), 17 Liver cancer and 26 pancreatic cancer cell lines using Affymetrix GeneChip Human mapping 100K Set. These analyses showed 10 remarkably recurrent homozygous deleted regions. These 10 regions were fine and contained only 1-2 genes, respectively. So, we chose 10 genes from these 10 regions and performed loss of heterozygosity (LOH) analyses using 64 CC (38 men and 26 women; mean age; 65.8±10.4 yr) and 42 GC (29 men and 13 women; mean age; 64.8±11.7 yr) tissues. For precise evaluation of LOH, laser capture microdissection was performed, minimizing the chance of contamination by non-tumor tissues. These 10 genes included the genes that have been not reported to be deleted in cancer besides FHIT and CDKN2A gene, which were known to be deleted in several cancers.
(Results) LOH of these 10 genes was detected in 35.5 %-74.6 % of CC and 39.0 %-67.5 % of GC tissues, respectively. We divided CC and GC into two groups (LOH-H; showing LOH of 5 genes or more, LOH-L; showing LOH of less than 5 genes), respectively. In CC, LOH-H showed a significant positive association with lymphatic invasion and lymph nodes metastasis (p = 0.007 and 0.04). On the other hand, LOH-H showed a significant positive association with lymph nodes metastasis (p = 0.019) in GC. The prognosis of the patients with LOH-L was significantly better than that of those with LOH-H in all CC cases (p = 0.038), while subgroup analysis showed that the prognosis of CC patients with LOH-L tended to be better than that of those with LOH-H in stage I + II CC cases (p = 0.057). Similarly, the prognosis of the patients with LOH-L was significantly better than that of those with LOH-H in all GC cases (p = 0.048). Subgroup analysis showed that the prognosis of the patients with LOH-L was also significantly better than that of those with LOH-H in stage I + II GC cases (p = 0.037). Multivariate analyses showed that stage and the LOH status were independent significant prognostic factors in CC and size and the LOH status were independent prognostic factors in GC.
(Conclusion)
LOH of these 10 genes might be a novel molecular signature of CC and GC with malignant phenotype.
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 1184.