bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4897: Genome-wide analysis of CGIs in bladder cancer identifies novel epigenetic biomarkers for diagnosis and follow-up
Authors: Kandimalla Raju , Tilborg Angela Van , Kompier Lucie , Stumpel Dominique J.P.M , Zwarthoff Ellen C. 
Published: February 2011

Abstract
Epigenetic modifications have been shown to contribute to the pathogenesis of various cancers including bladder cancer. Hypermethylation in cancer is often found in CGIs in the 5′ regions of genes. These DNA modifications may serve as useful biomarkers, both for diagnostic and prognostic purposes. Although the list of aberrantly methylated genes in cancer is expanding, only a few genes so far were investigated for their usefulness as tumor biomarkers for early diagnosis and risk assessment of bladder cancer. Thus, a large scale (genome wide) screening of aberrant methylation of CGIs is needed to identify bladder-specific epigenetic markers.
In this study, we performed a genome wide screening for DNA methylation in different subtypes of bladder cancer using differential methylation hybridization (DMH) coupled with Agilent 244k human CpG island microarrays. We next validated the genome-wide data on a 384-plex custom Illumina Golden Gate Methylation Assay (GGMA), which is based on bisulfite conversion.
We found and validated a large number of possible novel epigenetic biomarkers for early detection and prognosis of bladder cancer. We also observed that subgroups of bladder tumors cluster separately due to their different methylation patterns suggesting possible differences in pathogenesis. Our data clearly shown that the adjacent CpG loci within a CGI were co-methylated. In contrast, CGIs neighboring a methylated island were usually not methylated. The data showed no bias toward promoter methylation as the relative proportion of methylated islands in genes was similar to those encompassing promoter regions. We observed that 70% of the methylated genes are downregulated in bladder cancer. Moreover, gene body methylation also seems to be negatively correlated with gene expression. Interestingly, we found an overrepresentation of methylated genes in those genes that are the target of polycomb group protein complexes in embryonic stem cells. Further validation of selected CGIs on a separate group of bladder cancers on a custom Illumina Golden Gate Methylation assay (GGMA) allowed us to confirm 70 % of CGIs differentiating bladder cancers from normal cells, besides validating CGIs discriminating subgroups of bladder tumors.
In conclusion, this is the first genome-wide study on bladder cancer which identified potential methylation target genes that provides putative biomarkers that may be correlated with disease course as well as insight into the pathogenesis of bladder cancer subtypes.
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 4897.
Abstract 490: Different localization of epidermal growth factor receptor affects the response of Cetuximab in the irradiated NSCLC cell lines
Authors: Ryu Seung-Hee , Yang Youn-Joo , Moon Soo Young , Oh Jeong-Yoon , Song Si Yeol , Kim Jong Hoon , Choi Eun Kyung , Ahn Seung Do , Lee Sang-wook 
Published: February 2011

Abstract
The overexpressed epidermal growth factor receptor (EGFR) mediates resistance of tumor cells to chemo- and radiotherapy resulting from the induction of DNA repair by DNA-PK activation. The blockage of EGFR by a specific antibody (cetuximab) or tyrosine kinase inhibitor can inhibit the nuclear import of EGFR and consequently increase cellular sensitivity to ionizing radiation. Even though cetuximab combined with radiation showed encouraging response rates in locally advanced head and neck cancer, there are negative results in a recent trials comparing cetuximab and chemotherapy to chemotherapy alone. Thus it is critical to preselect patients based on their biologic factors to predict sensitivity for combination of cetuximab and radiation. The human non-small cell lung cancer (NSCLC) cell lines, A549 and H1299 which contain wild type EGFR, were used to demonstrate the different response to cetuximab in the combination with radiotherapy. Localization of EGFR was detected by confocal microscope and radiosensitivity was measured by clonogenic assay. Treatment of cetuximab inhibited colony formation in a dose-dependent manner in A549 cell line, while did not affect that in H1299 cell line. Microscopic images revealed that EGFR localized in cytosolic fraction especially around golgi body in H1299 cell line instead of the localization in membrane fraction in A549 cell line. After irradiation nuclear EGFR was detected in A549 cell line, however EGFR did not translocate to nucleus in H1299 cell. Even though decreased EGFR expression both A549 and H1299 cell lines was detected in the combination with cetuximab and radiation, radiosensitivity was increased only in A549 cells, not in H1299 cells. Our data indicated that localization of EGFR is evident marker to determine the efficacy of cetuximab and may relate sensitivity/resistance of cells treated cetuximab in the combination with radiotherapy. We suggest that EGFR status can be used for preselection of patients to predict treatment sensitivity in the combination therapy. *Grant Support : This study was supported by a grant (A090401) of Korea Healthcare Technology R&D Project, Ministry for Health, Welfare & Family Affairs, Republic of Korea.
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 490.
Abstract 4905: Quantitative high resolution detection of O6-MGMT methylation in routinely processed human glioblastoma specimens
Authors: Lehmann Ulrich , Weidner Jenny , Albrecht David , Schipper Elisa , Brandis Almuth , Kreipe Hans H. 
Published: February 2011

Abstract
Hypermethylation of the DNA repair gene 06-Methylguanosinemethyltransferase (06-MGMT) is an important prognostic and predictive marker for the management of glioblastoma patients. However, assessment of O6-MGMT gene methylation is not yet standardized and a comprehensive comparison of different methods described in the literature is missing.
Therefore, the methylation status of the MGMT gene was analyzed in a large series of glioblastoma specimens, WHO grade IV (n = 92) using nested conventional methylation-specific PCR (MSP), real-time PCR using either SybrGreen or a sequence specific probe for detection and pyrosequencing. All specimens were routinely processed formalin-fixed paraffin-embedded tumor biopsies. For a subset of samples (n = 30) three different protocols for the treatment of genomic DNA with bisulfite were compared. As a control, 20 brain biopsies from 10 patients without glioblastoma were analyzed. MGMT mRNA level was measured using quantitative real-time RT-PCR in n = 39 samples and the mRNA expression levels were correlated to the methylation status of these samples.
The three different bisulfite protocols did not show statistically significant differences concerning quality and yield of recovered DNA. A region in the MGMT promoter in which many published primers bind, displayed constitutively elevated methylation levels also in healthy brain tissue samples, thereby leading to false-positivity under many circumstances. Nested MSP and pyrosequencing correlate fairly well in scoring samples as “methylated” versus “unmethylated”, but a considerable number of samples scored “methylated” by nested MSP (n = 7) displayed only background methylation when analyzed by pyrosequencing. Only methylation levels measured by pyrosequencing correlated with mRNA expression levels (r2 = 0.32, p = 0.0002). Also, threshold definition was much more straightforward and easier to standardize using pyrosequencing. Real-time PCR based methods did not correlate very well with nested PCR or pyrosequencing.
In conclusion, pyrosequencing is the most reliable methodology for methylation analysis of O6-MGMT gene methylation analysis in routinely processed glioblastoma specimens.
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 4905.
Abstract 4911: HPV-independent methylation of specific TGF-B pathway-relevant genes in head and neck squamous cell carcinomas associated with prior radiation therapy and exposure to alcohol and tobacco
Authors: Bennett Kristi L. , Romigh Todd , Lee Walter , Lamarre Eric , Zhang Xiatong , Seth Rahul , Scharpf Joseph , Hunt Jennifer , Eng Charis 
Published: February 2011

Abstract
Head and neck squamous cell carcinoma (HNSCC) is an aggressive malignancy with more than half a million people being diagnosed with the disease annually. Therefore, it is critical to identify early detection markers, such as DNA methylation, for more timely diagnosis. In a recent study, we identified five tumor suppressive genes (IRX1, EBF3, SLC5A8, SEPT9, and FUSSEL18) as frequently methylated in HNSCC biopsies using a global methylation analysis via restriction landmark genomic scanning (RLGS). Interestingly, we found these candidates are all potentially involved in the TGF-B signaling pathway, which is often disrupted in HNSCC. Therefore, we sought to determine coordinated epigenetic silencing of these candidate genes in HNSCC as potential key disruptors of TGF-B signaling, which could ultimately result in HNSCC progression. Through immunoprecipitation studies, all five of the investigated candidate genes were found to interact with components of the TGF-B pathway. Also, overexpression of SLC5A8, EBF3, and IRX1 resulted in decreased mitotic activity and increased apoptosis. These findings are significant because they reveal a set of genes that interact with components of the TGF-B pathway, and their silencing via methylation in HNSCC results in coordinated decrease in apoptosis, increased proliferation, and decreased differentiation. We went on to define the methylation of these genes in relationship to HPV16-positivity, radiation therapy, and alcohol and tobacco exposure. By utilizing the available clinical information linked to the patient specimens, we found a strong association between promoter methylation of FUSSEL18, IRX1, and EBF3 and prior radiation therapy (P &lt; 0.0001) irrespective of HPV status. Also, promoter methylation of FUSSEL18 and SEPTIN9 were found to correlate significantly with exposure to alcohol and tobacco (P = 0.021). Importantly, in this study we preliminarily show a trend between HPV16 positivity and specific target gene hypermethylation of IRX1, EBF3, SLC5A8, and SEPT9. Equally notable and independent of HPV status, hypermethylation of the promoters of a subset of these genes in recurrences especially in the setting of prior radiation or in the setting of alcohol and tobacco use might help guide adjunctive inclusion or exclusion or epigenetic therapy.
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 4911.
Abstract 4924: Gene-specific hyper and hypomethylation in follicular lymphoma progression
Authors: Saggese Matilde , Thodima Venkata , Heguy Adriana , Chan Timothy A. , Chaganti Raju S. K. 
Published: February 2011

Abstract
Epigenetic mechanisms involved in the origin and transformation of indolent lymphomas to aggressive forms are poorly understood. Based on the comparison of methylation states of follicular lymphoma (FL) pre and post- transformation, it has been suggested that DNA methylation changes occur during the early stages of lymphomagenesis. To obtain a more complete understanding of methylation aberrations responsible for progression and transformation of FL, we analyzed 20 untreated FL biopsies (10 low grade, 10 high grade), 5 diffuse large B cell lymphoma (DLBCL) biopsies, and 5 benign reactive lymph node (RLN) biopsies by using methyl-DNA immunoprecipitation coupled with analysis with Agilent 244K human promoter ChIP-on-chip microarrays. Our analysis revealed statistically significant differences in methylation status for 120 genes between FL samples and RLN samples and for 23 genes between low and high grade FL samples. To investigate the biological significance of these findings, we used DAVID functional annotation clustering algorithms and Gominer software. We found that the most methylation-enriched functional groups were comprised of genes with roles in cell cycle control, adhesion and motility, transcription regulation, homeobox, and developmental genes. In order to validate the DNA methylation differences of the significant gene regions, we utilized the MassARRAY EpiTYPER assay. Our data identified 13 genes (CYP26B1, GRM7, HS3ST2, DOCK5, GRB10, SST, TAC1, PALM2-AKAP, FLJ40125, ST6GAL2, WDR35, NCAM1, SATB2) with increased levels of DNA methylation in FL samples compared to controls; 3 of these genes (ST6GAL2, WDR35, NCAM1) exhibited increased methylation in high grades FLs and 1 gene (SATB2) in low grades FLs. We are currently investigating gene specific DNA hypomethylation in low versus high grade FL and FL versus DLBCL. Our data are the first to characterize the global changes in methylation that occur in FL progression. Our findings suggest that high grade FL are associated with hypermethylation of a specific subset of genes compared to low grade subtypes. Ongoing efforts include investigating the functional relevance of these methylation changes by treating, in vitro, FL cell lines with demethylating agents to evaluate changes in gene expression levels and correlating with phenotype alterations.
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 4924.
Abstract 4952: Study of mouse tumor models with an IRDye 800CW SNAP-tag imaging probe
Authors: Zhang Aihua , Sun Luo , Kovar Joy , Gong Haibiao , Oliver D. Michael , Correa Ivan , Russello Salvatore , Noren Christopher , Xu Ming Qun 
Published: February 2011

Abstract
Non-invasive optical analysis of molecular targets inside living animals has become an important tool for disease progression and treatment assessment. One of the essential elements of molecular imaging is the development of specific, sensitive imaging contrast agents to investigate these biological processes. The use of longer wavelength dyes, i.e. near-infrared (NIR) dyes, presents distinct advantages over inherently fluorescent protein tags, including reduced autofluorescence background and increased sensitivity in imaging small animals. In addition, the adoption of efficient and specific labeling techniques is a key step in the generation of protein-based fluorescent imaging agents. In the present study, we explore the versatility of a self-labeling protein termed SNAP-tag, derived from human O6-alkylguanine-DNA alkyltransferase, in tagging polypeptides with a near-infrared dye, IRDye® 800CW. In cell-based assays, an IRDye 800CW conjugated SNAP-tag successfully labeled cells transiently transfected with a pSNAP-ADRB2 plasmid. For in vivo experiments, a synthetic epidermal growth factor receptor (EGFR)-binding ligand was used to construct an IRDye 800CW-EGFR-SNAP-tag. Following injection of the agent into nude mice bearing EGFR-overexpressing A431 xenografts, tumors were clearly visualized with a Pearl® Imaging system. Furthermore, the specificity of binding was demonstrated in competition experiments with unlabeled EGF. Similar probes labeled with visible fluorophores were used to image EGFR-expressing cultured cells by confocal microscopy. This fluorescent imaging system using a self-labeling protein tag and highly sensitive organic dyes provides versatile tools for cancer research, drug discovery and small animal imaging.
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 4952.
Abstract 4959: Multispectral imaging of chromogenic multiplex IHC assays as an alternative to fluorescent methods
Authors: Kerfoot Christopher A. , Girees Sherif , Dauffenbach Lisa M. 
Published: February 2011

Abstract
Detection and analysis of two or more co-localized antigens by light microscopy has been hindered by the difficulty in discerning and quantifying overlaying chromogens. Performing multi-analyte immunohistochemistry has many potential benefits and applications in the field of drug target evaluation and patient screening, including: 1) determination and quantification of immunoreactivity co-localization; 2) evaluation of spatial relationships between immunoreactive cell types; 3) signal transduction pathway activation studies; 4) reduction in tissue depletion; and 5) decreased reagent utilization. Multiplex immunofluorescence is not widely used as an analytical technique for clinical samples due to its lower sensitivity than chromogenic methods and concerns about autofluorescence in formalin-fixed tissue. Through the use of multispectral imaging, the absorption pattern of overlapping chromogens can be spectrally unmixed into quantitative individual dye components. This process works accurately when chromogens are developed to a lower intensity than typical for most standard pathology laboratories. The chromogens must be developed to a point where they do not scatter light or block subsequent chromogenic development. The current study was performed to define the accuracy of spectral unmixing of chromogens and evaluate whether interference existed between chromogens. Stained samples were imaged using multispectral imaging, and quantitative grayscale images for each analyte were created by spectral unmixing. The grayscale images were analyzed using image analysis software to determine the overall expression levels of each analyte. Development with Vulcan Red followed by DAB produced little interference, while high density development with DAB decreased the subsequent Vulcan Red staining intensity. Vulcan Red, DAB and hematoxylin unmixed properly and quantitatively. In summary, when multiplexed chromogenic IHC assays were developed using methods optimized for multispectral imaging, the technique demonstrated excellence performance characteristics without suffering from drawbacks commonly associated with fluorescence-based techniques.
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 4959.
Abstract 4968: Modes of co-factor recruitment by an oncogenic fusion protein
Authors: Schwentner Raphaela , Kauer Maximilian O. , Bilke Sven , Jug Gunhild , Walker Robert L. , Meltzer Paul S. , Kovar Heinrich 
Published: February 2011

Abstract
Ewing's sarcoma (ESFT) is a highly aggressive pediatric cancer of the bone and characterized by the chimeric ETS transcription factor EWS-FLI1 as a result of a chromosomal translocation. By whole genome gene expression and ChIP-seq analyses we obtained evidence that EWS-FLI1 directly regulates E2F target genes and possibly cooperates with E2F transcription factors. Furthermore, several E2F factors were themselves inferred to be direct targets of EWS-FLI1. To unravel the hierarchical structure of this EWS-FLI1 transcriptional network module we performed luciferase reporter gene assays in combination with DNA motif mutation analyses. The promoter regions of nine candidates for direct target genes of EWS-FLI1 and E2F factors were chosen for in-depth analysis. Corroborating the transcriptomic data, promoter activity of all 9 genes showed reduced levels upon knockdown of EWS-FLI1. The strongest modulatory effect of EWS-FLI1 silencing was observed for the E2F3 promoter, and mutation of a single ETS binding site lead to a comparable reduction of luciferase activity as knockdown of EWS-FLI1. These results validate E2F3 as a directly EWS-FLI1 regulated gene in Ewing's sarcoma. For the other EWS-FLI1 target candidates mutation analysis lead to more complex results. In the RAD51 promoter simultaneous mutation of two ETS binding sites was necessary to obtain a significant reduction of luciferase activity. Furthermore, mutation of a single E2F binding site abolished the effect of EWS-FLI1 knockdown. In promoters of two other candidates, GEMIN4 and ATAD2, mutation of the ETS site resulted in only a moderate reduction of reporter activity, and additional destruction of an E2F binding site was required to achieve a significant decrease in promoter activity. Our results imply that EWS-FLI1 uses several modes of interaction with E2F factors to control common target genes. First, EWS-FLI1 directly activates E2F3 and other E2F factors which, in turn, co-operate with EWS-FLi1 on target gene promoters in a feed-forward loop. Second, results for the RAD51 promoter are compatible with a mechanism where a repressive E2F factor is exchanged for an activating E2F factor via binding of EWS-FLI1. Finally, EWS-FLI1 might have a more indirect role in the regulation of ATAD2 and GEMIN4 where most of the transcriptional effect seems to be exerted by E2F factors.
Acknowledgement: This study was funded by the 6th framework program of the European Commission, (“E.E.T. Pipeline” contract LSHC-CT-2006-037260) and by the Austrian genome research program “GEN-AU Ch.I.L.D.“ (GZ 200.136/1 - VI/1/2005). R. Schwentner is a recipient of a DOC-fFORTE-fellowship of the Austrian Academy of Sciences.
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 4968.