bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2085: MMP-2 knockdown leads to anoikis and inhibits migration and invasion by attenuating αvβ3/EGFR/Pak4 survival signaling in human glioma xenograft cells in vitro and in vivo
Authors: Kesanakurti Divya , Chetty Chandramu , Maddirela Dilip , Dinh Dzung H. , Rao Jasti S. 
Published: August 2012

Abstract
MMP-2 plays a key role in the degradation of the extracellular matrix and thereby enhances the proliferative, invasive and metastatic potential of cancer cells. MMP-2 knockdown using siRNA (pM) in human glioma xenograft cell lines, 4910 and 5310, sensitized cells to anoikis associated with cleavage of PARP, and caspases 8 and 3. pM-inhibited cell adhesion, invasion and migration correlated with attenuation of EGFR, c-Src and Pak4 phosphorylation. High expression of Pak4 in human glioma cell lines and tumor tissues implicated its essential role in increasing glioma malignancy. Co-immunoprecipitation studies implied that MMP-2 directly interacts by complex formation with EGFR, p130CAS and Pak4 along with αvβ3 integrin and pM treatment disrupted this direct binding. Vitronectin-mediated αvβ3 activation and EGF and rhMMP-2 supplementation counteracted pM-inhibited, Pak4-mediated migration and invasion. Conversely, αvβ3 blocking antibody and ErbB-2/EGFR inhibitor (GW2974) further reduced pM-inhibited, Pak4-mediated invasiveness and migration, thereby suggesting a role of αvβ3 and EGFR in the regulation of Pak4 survival signaling. Individual treatments of pM and Pak4.si led to considerable anoikis in both 4910 and 5310 cells and simultaneous co-depletion MMP-2 and Pak4 resulted in robust increase in anoikis levels. In vivo orthotopic experiments in nude mice revealed decreased tumor size with pM treatment. Immunofluorescence analysis of pSV-tumor sections showed high expression and co-localization of MMP-2/αvβ3, which decreased upon treatment with pM along with significant decrease in phospho-EGFR, phospho-Pak4, Bcl2 and Bcl-xL levels. Our results imply a possible crosstalk between MMP-2 and Pak4 and suggest the potential of targeting both MMP-2 and Pak4 as a future therapeutic approach in glioma therapy.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2085. doi:1538-7445.AM2012-2085
Abstract 2086: Evaluation of a promoter methylation panel in plasma cell-free DNA to screen for colorectal cancer in Hispanics
Authors: del Mar Gonzalez-Pons Maria , Rodríguez Heriberto M. , Delgado Patricia , Velazquez Francisco , Lacourt Mercedes Y. Y. , Cardona Alberto , Bernabe Raúl D. , Cruz-Correa Marcia R. 
Published: August 2012

Abstract
Introduction: Detection of quantitative and qualitative changes in cell-free, tumor-derived nucleic acids in cancer patients are being evaluated as potential screening, monitoring and diagnostic tools. Genetic and epigenetic changes in cell-free plasma DNA (cfpDNA) have been studied as non-invasive colorectal cancer (CRC) diagnostic markers, but a gene panel with the diagnostic accuracy necessary for clinical use has not been defined. The CpG island methylator phenotype (CIMP), characterized by hypermethylation in promoter-associated regions, is one of the molecular mechanisms resulting in CRC. We evaluated the detection of promoter hypermethylation in a gene panel previously used to define CIMP in CRC tumors, as plasma biomarkers. Methods: Methylation specific PCR was used to analyze eight CIMP-specific gene promoters (CACNA1G, IGF2, NEUROG1, RUNX3, SOCS1, hMLH1, p16, CRABP1) in cfpDNA. Forty age-and-gender matched plasma samples (20 CRC and 20 controls) were evaluated. Samples were classified as methylated, unmethylated or not detected if not amplified by either primer set. Results: Methylation patterns of eight genes in 40 subjects (20 CRC and 20 controls; mean age 67 ± 12.2 years; 20 females) were examined. Five genes revealed a 100% unmethylation pattern. p16 was found to be more likely methylated in controls (11%) whereas NEUROG1 and CRABP1 were more likely to be methylated in CRC cases (6% and 33%, respectively). 53.3% of CRC and 48% controls had β1 methylated genes (OR = 1.24, 95% CI 0.34-4.46). The use of β1 methylated genes detected CRC with 40% sensitivity and 65% specificity. Discussion: We report the first evaluation of the methylation pattern of an eight-gene panel as CRC biomarkers in Hispanics. Our preliminary findings showed that genes were mostly unmethylated in cases and controls. NEUROG1 and CRAP1 were found to be most likely methylated in CRC patients, but the diagnostic accuracy of this panel was poor as a CRC screening biomarker.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2086. doi:1538-7445.AM2012-2086
Abstract 2088: Detection of PIK3CA somatic mutations in cell-free DNA of breast cancer patients by high-resolution melting curve analysis
Authors: Schiza Christina , Farkona Sofia , Chimonidou Maria , Vorkas Panos , Malamos Nikos , Georgoulias Vasilis , Lianidou Evi S. 
Published: August 2012

Abstract
Introduction: Somatic mutations in the gene encoding for the phosphatidyl-inositol 3-kinase (PI3K) catalytic subunit, PIK3CA, have been discovered in many different human cancers. We have recently developed a high-resolution melting curve analysis method for the detection of the three hotspot mutations of PIK3CA gene (Vorkas et al, J of Mol Diagn 2010). The aim of our study was to evaluate this method for the presence of PIK3CA mutations in cell-free DNA (cfDNA) circulating in plasma of breast cancer patients and healthy individuals. Patients and methods: cfDNA was isolated from plasma (200μL) of 30 patients with operable breast cancer, 45 patients with metastatic breast cancer and 12 healthy donors. After DNA extraction, real-time PCR was performed in triplicate for all samples in the LightCycler (Roche), in the presence of LC-Green Plus saturating dye (Idaho Technology Inc.). High-resolution melting curves were obtained with HR-1 High Resolution Melter (Idaho Technology Inc.). Results: We identified 15 cfDNA samples mutated out of 75 tested (20%). 3/75 (4%) cfDNA samples were mutated within the exon 9 amplified region, and 12/75 (16%) cfDNA samples were mutated within exon 20 (31.6%). In operable breast cancer 1/30 (3.3%) cfDNA sample was mutated in exon 9 and 3/30 (10%) cfDNA samples were mutated in exon 20, while in metastatic breast cancer 2/45 (4.4%) cfDNA samples wer mutated in exon 9 and 9/45 (20%) cfDNA samples were mutated in exon 20. PIK3CA mutations were not detected in any of the 12 cfDNA samples from healthy donors, used as negative controls. Conclusions: Using High-Resolution Melting curve Analysis (HRMA) PIK3CA gene mutations were detected in cfDNA circulating in plasma of patients with operable and metastatic breast cancer, but not in plasma of healthy individuals. The prognostic significance of this finding will be evaluated when a longer follow up period will be completed for these patients and a larger number of clinical samples will be analyzed.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2088. doi:1538-7445.AM2012-2088
Abstract 2090: Mutational analysis in circulating tumor cells (CTC):ScreenCell MB Filtration Unit and ICE COLD-PCR
Authors: Richardson Katherine A. , Wu Grant , Kuang Yanan , Wang Lilin , Legendre Benjamin , Lin Rui , Shi Yanggu , Eastlake Phil , Cayre Yvon , Janne Pasi , Distel Robert 
Published: August 2012

Abstract
The aim of this study was to validate the use of the ScreenCell® MB Filtration Unit for detection of mutations in Circulating Tumor Cells. This device allows physicians to easily isolate any CTCs using a simple blood draw which can be performed at a local doctor's office. This is especially important when trying to analyze CTCs in elderly patient populations and in regions where the large medical centers are far away. Once isolated, the filter containing the CTCs can be sent to a laboratory for DNA isolation and the mutation analysis. Mutational analysis using ICE COLD-PCR can then be performed without the use of expensive or specialized equipment. The mutation was characterized using standard Sanger DNA sequencing with a detection limit of 0.5 - 0.1% mutant sequence in the wild-type background. Results will be presented from a mock experiment where PC9 cells (EGFR exon 19 deletion: p.E746_A750del) or H1975 cells (EGFR exon 21: p.L858R) were spiked into blood and then these mock CTCs were collected on the ScreenCell Molecular Filter Device. Following DNA isolation, the mutations were easily detected at the lowest number of cells spiked in to the blood samples (10 cells). Additional data from CTCs collected from NSCLC patients detected the L858R point mutation, an exon 19 E746_A750del mutation, and an exon 19 E746_S752delinsV. Mutations in these same samples could not be detected in DNA sequencing following standard PCR amplification. These data show that the ScreenCell MB Filtration Unit coupled to mutational analysis using ICE COLD-PCR can be an easy, cost-effective method for collection and analysis of CTCs in patient blood samples. Moreover, the device is simple enough to be used in any doctor's office.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2090. doi:1538-7445.AM2012-2090
Abstract 2092: Integrated genetic analysis of clear cell renal cell carcionoma
Authors: Sato Yusuke , Mekawa Shigekatsu , Nagata Yasunobu , Yoshida Kenichi , Sato Aiko , Okuno Yusuke , Shiraishi Yuichi , Yoshizato Tetsuichi , Suzuki Hiromichi , Sanada Masashi , Kume Haruki , Homma Yukio , Ogawa Seishi 
Published: August 2012

Abstract
Renal cell carcinoma (RCC) is the most common form of adult kidney cancer and accounts for 2-3% of all adult malignancies, in which clear cell carcinoma accounts for more than 80% of the cases. As for the pathogenesis of clear cell RCC, inactivation of the VHL gene has been reported in 80% of clear cell RCC and more recently, frequent mutations of epigenetic regulators, including PBRM1, SETD2, KDM5C and UTX, have been demonstrated through high-throughput mutation studies, including PBRM1 has been demonstrated in ∼40% of the cases. Nevertheless, probably, our knowledge of the full spectrum of gene mutations in RCC is still incomplete. In this study, to obtain a better understanding of molecular pathogenesis of clear cell RCC, we performed an integrated genetic study of clear cell RCC, where a total of 93 paired specimens were analyzed by massively parallel sequencing of SureSelect (Agilent)-enriched whole exomes, SNP array-based copy number analysis (Affymetrix), as well as gene expression profiling (Agilent). In whole exome sequencing, 42 somatic mutations per sample were identified on average, which involved not only previously reported genes, but also a number of novel gene targets. Among these, mutations of genes involved in chromatin regulation or histone modification were preferentially found in advanced cases. To understand whole picture of gene mutations of epigenetic mechanism in clear cell RCC, mutation analysis of 85 genes involved in chromatin regulation or histone modification were performed in 180 cases using multiplexed barcode sequencing. A total of 201 somatic mutations were validated and 74% cases had at least one somatic mutation. PBRM1 mutations were found in 43% cases and SETD2 were mutated in 10% of cases. When comparing clinical picture with mutation status, SETD2 mutation was associated with the risk of metastasis, while PBRM1 mutations had no impact on prognosis. Our results showed that in clear cell RCC, multiple component of complexes involved in epigenetic regulation undergo gene mutations, confirming that deregulated epigenetic apparatus play important roles in pathogenesis of clear cell RCC. In this meeting, we will present the result of our integrated genetic analysis of RCC and discuss the genetic basis of RCC in terms of copy number alterations, gene mutations, as well as gene expression profiles.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2092. doi:1538-7445.AM2012-2092
Abstract 2093: Next-gen deep sequencing improves FGFR3 mutation detection in the urine of bladder cancer patients
Authors: Millholland John M. , Li Shuqiang , Fernandez Cecilia A. , Shuber Anthony P. 
Published: August 2012

Abstract
FGFR3 mutations have been identified in ∼60-70% of low-stage, non-invasive tumors. Our group and others have developed assays to detect FGFR3 mutations in the urine of bladder cancer patients. However, urine-based assays have been limited by the technical ability to detect rare events in a dilute medium where there is a high background of normal DNA. In these assays, FGFR3 mutations are generally found in ∼30% of the urine samples, which is &lt; 50% concordance with the expected detection in tissue. We have now developed an ultra-deep amplicon sequencing technique that increases FGFR3 mutation detection in urine to ∼67%, near the expected detection if every mutation found in tissue could be detected in urine. Amplicons were designed against FGFR3 exons 7, 10, and 15 using PCR primers containing the adapter sequences for unidirectional sequencing. Taqman probes were used to determine if sufficient DNA was present in each sample. Primary amplification was performed from DNA isolated from 4 ml of urine. The resulting PCR products were used as template for emulsion PCR and these were then sequenced using the Roche 454 GS Junior. Samples were analyzed for total DNA reads per sample and number of mutant sequencing reads to determine percent mutation. Urine samples from 29 patients with stage Ta bladder cancer were analyzed by both our previously described qPCR method and the new ultra-deep sequencing approach. Of the 29 samples, 2 did not have sufficient DNA for analysis by sequencing. Using ultra-deep amplicon sequencing, 18 out of 27 (66.7%) were positive for FGFR3 mutations, while only 3 out of 27 (11.1%) were positive for mutations by qPCR. The urine samples from the 15 newly identified mutations using deep sequencing contained FGFR3 mutations as low as 0.05%. Using matched tissue and urine samples, we demonstrate that the sensitivity in urine approximates the FGFR3 mutations observed in tissue. We have developed a highly sensitive non-invasive urine based assay that can detect FGFR3 mutant DNA when present at &lt; 1% of the sample and that achieves &gt; 90% concordance with tumor tissues. To our knowledge, this is the first practical application of next generation sequencing technology for diagnostic use.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2093. doi:1538-7445.AM2012-2093
Abstract 2095: A virtual pyrogram generator to resolve ambiguity of pyrosequencing results
Authors: Chen Guoli , Olson Matthew T. , O'Neill Alan , Norris-Kirby Alexis , Beierl Katie , Harada Shuko , Debeljak Marija , Rivera-Roman Keila , Finley Samantha , Stafford Amanda , Gocke Christopher D. , Lin Ming-Tseh , Eshleman James R. 
Published: August 2012

Abstract
We report a freely available software program, Pyromaker, which generates simulated pyrosequencing traces based on user inputs and aids in analysis of complex pyrosequencing results. To achieve this goal, simulated pyrograms are generated based on the hypothesized mutations and matched with the actual pyrogram. We validated the software testing common KRAS gene mutations and several mutations in the BRAF, GNAS and, p53 genes. We demonstrate that all eighteen possible single base mutations within codons 12 and 13 of KRAS gene generate unique simulated pyrosequencing traces and highlight the distinctions between them. We further verify that all reported codon 12 and 13 complex mutations produce unique pyrograms. However, some complex pyrograms are indistinguishable from single base mutations, using a standard dispensation order. Pyromaker was used in two strategies, one in which hypothesis-based simulated pyrograms were pattern-matched with the actual pyrograms. In a second mode, with only the pyrogram, Pyromaker was used to identify the underlying mutation by iteratively reconstructing the mutant pyrogram. Either strategy was able to successfully identify the complex mutations, which were confirmed by cloning and subsequent sequencing. With two examples of KRAS codon 12 mutations, (GGTαTTT, G12F and GGTαGAG, G12E), we report optimal combinations of the five analysis approaches that permit unambiguous mutation identification. The most efficient one is pyrosequencing with Pyromaker.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2095. doi:1538-7445.AM2012-2095
Abstract 2097: In situ mutation detection in cancer tissue sections for research and diagnostics in clinical oncology
Authors: Grundberg Ida , Kiflemariam Sara , Imgenberg-Kreuz Juliana , Edlund Karolina , Micke Patrick , Sundström Magnus , Botling Johan , Nilsson Mats 
Published: August 2012

Abstract
Activating oncogenic mutations are targets for a new generation of cancer drugs. Current mutation assays for clinical diagnostics are based on DNA-extracts from tissue sections that often contain morphologically heterogeneous neoplastic regions with variable mixtures of normal stromal and inflammatory cells. We have developed an RNA-based in situ mutation assay that can target oncogenic mutations in a multiplex fashion on tissue slides by the use of multiple mutation-specific padlock probes and rolling-circle amplification. For EGFR therapy prediction, we demonstrate reliable in situ detection of KRAS mutations in codon 12 and 13 in colon and lung cancer - on cytologic tumor imprints as well as on fresh frozen and formalin-fixed, paraffin-embedded tissue sections. High throughput screening of KRAS mutation status was successfully performed on a tissue microarray. Moreover, we show how the pattern of expressed mutated and wild-type alleles can be studied in situ from tumors with complex combinations of mutated EGFR, KRAS and TP53. This in situ method holds great promise as a tool to investigate the role of somatic mutations during tumor progression and for prediction of response to targeted therapy.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2097. doi:1538-7445.AM2012-2097
Abstract 21: Gastrokine 1 functions as a tumor suppressor by regulating inflammatory mediators
Authors: Yoon Junghwan , Choi Yoo Jin , Han Lin , Lee Suk Woo , Park Won Sang 
Published: August 2012

Abstract
Gastrokine 1 (GKN1) plays an important role in the gastric mucosal defense mechanisms and also acts as a functional gastric tumor suppressor. The specific aim of this study was to determine the inflammatory mediator regulation underlying GKN1 activity in the tumor development/progression of gastric cancer. We examined the effect of GKN1 on expression of inflammatory mediators including NF-κB, COX-2, and cytokines in GKN1-transfected and recombinant GKN1-treated AGS gastric cancer cells by western blot and real time RT-PCR. Lymphocyte migration and cell viability were also analyzed in AGS cells after being treated with GKN1 and inflammatory mediators by transwell chemotaxis and MTT assay, respectively. In GKN1-transfected AGS cells, we observed inactivation and reduced expression of NF-κB and COX-2. Ectopic GKN1 expression induced the production of inflammatory mediators including IL-8 and -17A, but decreased IL-6 and IL-10 expressions. GKN1 also functions as a chemoattractant in migration of Jurkat T cells and peripheral B lymphocytes in transwell assay. In addition, GKN1 significantly inhibited cell viability, whereas treatment of IL-10, IL-17 and TNF-α in AGS cells did not show significant difference in cell viability. These data suggest that the GKN1 gene may play an important role in the regulation of inflammatory mediators in the tumor development/progression of gastric cancer.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 21. doi:1538-7445.AM2012-21
Abstract 2100: Cancer biomarker research using castPCR technology
Authors: Bao Yun , Ching Bonnie , Mouanoutoua Mokang , Yu Wang , Keys David , Desai Sejal , Stevens Junko 
Published: August 2012

Abstract
Cancer Biomarkers have applications in the diagnosis, staging, prognosis and monitoring of disease progression, as well as in the predication and monitoring of drug response. Profiling and validation research tools are needed that exhibit the combined features of high sensitivity and high specificity for cancers. However, the sensitivity of molecular methods such as DNA sequencing and conventional genotyping in tumor samples is limited, typically ranging from 5-20%. We have recently developed TaqMan® Mutation Detection Assays using our competitive allele specific TaqMan® PCR (castPCR) technology for cancer biomarker research. castPCR assays were tested with &gt;300 tumor research samples (either fresh/frozen or formalin-fixed, paraffin-embedded samples) and cell lines to assess mutation status. The results showed that castPCR technology can robustly detect mutations as low as 0.1% and has &gt;99% concordance to other technologies including PCR-based technology and sequencing. In this study, a large panel of castPCR assays for AKT1, APC, BRAF, CTNNB1, HRAS, KRAS, NRAS, PIK3CA, PTEN and TP53 genes were used for investigating somatic mutations in breast tumor research samples. Initially, 4 model FFPE cell lines were used to validate the assays. Mutant DNAs were titrated in the wild type DNAs from 50% to 0.1%. Mutations were identified down to 0.1% titration with high reproducibility. No false positives were found in non-tumor samples. The results obtained by castPCR assays for 20 breast tumor samples were concordant to those reported by other methods. Our data showed that castPCR technology provides an excellent tool for identifying cancer biomarkers or confirming potential cancer markers such as those obtained by next-generation sequencing and other technologies.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2100. doi:1538-7445.AM2012-2100