bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 3406: Activity of catechol-O-methyltransferase gene promoter polymorphisms in renal cancer cells
Authors: Chang Inik , Fukuhara Shinichiro , Wong Darryn K. , Gill Ankurpreet , Shahryari Varahram , Yamamura Soichiro , Majid Shahana , Saini Sharanjot , Hirata Hiroshi , Ueno Koji , Deng Guoren , Dahiya Rajvir , Tanaka Yuichiro 
Published: May 2015

Abstract
Catechol-compounds such as 4-hydroxy-estrogen have been shown to play a role in the renal carcinogenesis process. To counter the effects of the highly reactive and mutagenic catechol-estrogens, the catechol-O-methyltransferase (COMT) gene detoxifies these compounds by forming methoxy compounds, which have been shown to be biologically inactive. Proper COMT function is thus vital for cells and a mechanism by which activity levels can be affected is through polymorphisms. The Val(158)Met polymorphism that correlates with renal cancer has been shown to reduce COMT enzymatic activity, but also of importance are those variants in the promoter region which can lead to alterations in gene expression levels. The aim of this study was to determine if polymorphisms of the COMT promoter can influence their transcription levels. To examine this, plasmids containing wildtype regions of the COMT promoter were obtained and site-directed mutagenesis used to create polymorphic variants. Constructs were then transfected into the Caki-1 renal cell line to measure their effects on gene expression by using a luciferase reporter assay. A total of 8 polymorphic sites covering the distal and proximal promoter region were evaluated. Results indicate that the variant at polymorphic sites rs2020917 (C to T), rs13306278 (C to T), and rs6269 (A to G) caused a significant reduction (P&lt;0.01) whereas rs165656 (G to C) and rs165722 (C to T) caused a significant increase (P&lt;0.01) in luciferase activity. No differences were observed for rs737865 (A to G), 4646312 (T to C), and rs3810595 (G to C). These results demonstrate polymorphisms of the COMT promoter region to cause altered expression levels in renal cells and warrant further studies with clinical case-control specimens to determine their associations for renal cell cancer.
Citation Format: Inik Chang, Shinichiro Fukuhara, Darryn K. Wong, Ankurpreet Gill, Varahram Shahryari, Soichiro Yamamura, Shahana Majid, Sharanjot Saini, Hiroshi Hirata, Koji Ueno, Guoren Deng, Rajvir Dahiya, Yuichiro Tanaka. Activity of catechol-O-methyltransferase gene promoter polymorphisms in renal cancer cells. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3406. doi:10.1158/1538-7445.AM2014-3406
Abstract 3423: The genomic evolution of prostate cancer under the selective pressure of anti-androgen therapy
Authors: Gsponer Joël Roman , Dietsche Tanja , Rufle Alexander , Lorber Thomas , Juskevicius Darius , Perrina Valeria , Lenkiewicz Elisabeth , Zellweger Tobias , Bachmann Alexander , Barrett Michael T. , Rentsch Cyrill A. , Ruiz Christian , Bubendorf Lukas 
Published: May 2015

Abstract
Background
The implementation of novel technologies such as array comparative genomic hybridization (aCGH) and next-generation sequencing has led to a deeper understanding of the genomic nature of cancer. However, these analyses have classically been done without respecting intra-tumor heterogeneity. Here, we applied a methodology that allows us analyzing the genomic profile of distinct tumor populations from individual tumors and their clonal evolution during the progression to castration-resistant disease, thus enabling the discovery of novel genetic alterations in the course of the development of therapy resistance.
Methods
Matched pre- and post- hormone treated fresh frozen and/or formalin fixed prostate cancer samples were selected from our biobank. Clonal tumor populations were flow-sorted according to their nuclear DNA content. Sorted tumor populations were subjected to whole genome CGH and to full exome sequencing analyses by the use of Agilent SurePrint 2x400k microarrays and the SureSelect All Exon Kit, respectively. Target aberrations were evaluated using a prostate cancer tissue micro array (TMA) and fluorescence in situ hybridization as well as immunohistochemistry.
Results
The de-convolution of the genomic evolution in the investigated tumors shows that genetic aberrations and mutations are newly occurring under the selective pressure of anti-androgen therapy. More importantly, judging on the temporal dynamics of changes in allelic frequencies, we cannot only observe events that become more abundant, but also cancer associated mutations that are negatively selected for. We are currently following up several of these targets, of which at least one shows significant association with overall survival and differences in its expression pattern between hormone naïve and castration resistant cancer.
Conclusions
Genomic profiling of distinct clonal tumor populations during prostate cancer progression allows for analysis of intra-tumoral heterogeneity and the underlying clonal evolution. Importantly, this approach identifies genomic aberrations that were selected for under the pressure of hormone ablation therapy.
Citation Format: Joël Roman Gsponer, Tanja Dietsche, Alexander Rufle, Thomas Lorber, Darius Juskevicius, Valeria Perrina, Elisabeth Lenkiewicz, Tobias Zellweger, Alexander Bachmann, Michael T. Barrett, Cyrill A. Rentsch, Christian Ruiz, Lukas Bubendorf. The genomic evolution of prostate cancer under the selective pressure of anti-androgen therapy. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3423. doi:10.1158/1538-7445.AM2014-3423
Abstract 3431: Functional characterization of ARID2 in melanoma and melanocytes
Authors: Luo Flora , Garraway Levi 
Published: May 2015

Abstract
In a recent exome sequencing study conducted by our laboratory, AT-rich interaction 2 (ARID2) was found to be mutated in 9% of melanoma samples. Of all the novel melanoma genes identified, ARID2 had the highest loss of function mutation burden—suggesting that ARID2 is likely inactivated in melanoma. Although it is well-established that ARID2 is a member of the ATP-dependent SWI/SNF chromatin remodeling complex, the mechanisms by which ARID2 functions as a tumor suppressor remain unclear, and its role in melanoma is completely unknown. The goal of this project is to characterize the role of ARID2 in melanoma genesis. Our preliminary data indicates that ARID2-mutant melanoma cells express low levels of both ARID2 and MITF—the master regulator of melanocyte differentiation and a lineage oncogene. On the other hand, other SWI/SNF components appear necessary for survival of an ARID2-mutant cell line. Ongoing efforts in the laboratory include soft agar assays and mouse xenografts to determine whether knockout of ARID2 via CRISPR technology can transform immortalized primary melanocytes. We are also investigating the larger SWI/SNF dependency of these mutant cell lines. By studying ARID2 inactivation in melanoma, we ultimately seek to pinpoint targetable vulnerabilities of ARID2-mutant cells from many cancer types.
Citation Format: Flora Luo, Levi Garraway. Functional characterization of ARID2 in melanoma and melanocytes. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3431. doi:10.1158/1538-7445.AM2014-3431
Abstract 346: Differentiation induced apoptosis in AML cells: The role of p73 in p53-independent versus p53-mediated apoptosis
Authors: Roberts Michael , Saffie Rizwan , Salmons Harold , Ghoto Mansoor , Schneider Juliana , Forrester Jeffrey 
Published: May 2015

Abstract
Human acute myeloid cell lines can be induced to differentiate into macrophage-like cells by phorbol esters. Differentiation is accompanied by cessation of cell proliferation and initiation of apoptosis. Many of these cell lines, like HL-60, are p53 deficient and therefore execute a differentiation-induced, p53-independent program of cell death. Evaluating changes in gene expression during a time course of PMA-induced HL-60 cell differentiation by DNA microarray analyses and RT-qPCR reveals up-regulation of several pro-apoptotic genes (ex. TNF, MCL1, EGR2, BCL3) and down-regulation of several anti-apoptotic genes (ex. BCL2, ANXA3, TSC22D3). Interestingly, RNA levels of p73 are unchanged, suggesting p73 does not substitute for the missing p53 function via activation of p73 gene transcription, however, we report here that p73 protein levels increase dramatically during the differentiation time course. By reintroducing p53 into HL-60 cells, we compare the changing gene expression profile during p53-mediated apoptosis versus that which occurs during phorbol ester-induced p73 accumulation through protein stabilization. Common and unique gene expression changes define the putative p73-dependent apoptosis program compared to p53-dependent apoptosis.
Citation Format: Michael Roberts, Rizwan Saffie, Harold Salmons, Mansoor Ghoto, Juliana Schneider, Jeffrey Forrester. Differentiation induced apoptosis in AML cells: The role of p73 in p53-independent versus p53-mediated apoptosis. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 346. doi:10.1158/1538-7445.AM2014-346
Abstract 3483: A centrifugal ultrafiltration-based method for rapid purification of exosomes from biological samples
Authors: Cappione Amedeo , Gutierrez Sara , Mabuchi Masaharu , Smith Janet , Strug Ivona , Nadler Timothy 
Published: May 2015

Abstract
Exosomes represent a subset of small particles secreted by many types of cells under both normal and pathological conditions. The release of microvesicles has demonstrated biological relevance; these particles act as mediators of intercellular communication both within the local microenvironment of the release site as well as systemically. Moreover, since exosomes contain RNA (messenger and miRNA) and protein (membrane-bound and cytosolic) from their cells of origin, and given that this content can be influenced by cell state, they also potentially represent a burgeoning target for biomarker discovery. Critical to understanding the physiological significance of these particles is the development of preparative techniques permitting reliable isolation of purified fractions. While numerous methods of exosome purification exist, including ultracentrifugation, immunoaffinity-based isolation using magnetic beads, precipitation, and ultrafiltration, most are plagued by sample limitations or require long and tedious workflows to achieve success. Here we present a rapid alternative method for the selective fractionation of exosomes from biological samples using an ultrafiltration device. Since the method is spin-based and dependent on size exclusion, the device has broad applications with regards to sample volume and/or type. Optimization of the protocol was aided through use of a mid infrared (MIR)-based spectroscopy platform that permits simultaneous monitoring of lysis conditions, protein quantitation, and analysis of total lipid content during exosome fractionation. Given the ultrafiltration device's capacity for buffer exchange and sample concentration, purified fractions can be easily formatted to meet the requirements of any downstream analysis platform. To demonstrate this, resulting fractions were assayed by numerous techniques including flow cytometry, western blotting, ELISA-based assays, and electron microscopy.
Citation Format: Amedeo Cappione, Sara Gutierrez, Masaharu Mabuchi, Janet Smith, Ivona Strug, Timothy Nadler. A centrifugal ultrafiltration-based method for rapid purification of exosomes from biological samples. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3483. doi:10.1158/1538-7445.AM2014-3483
Abstract 3485: Efficient transfection of cancer cell lines using the 4D-NucleofectorTM System
Authors: Schroeder Jenny , Altrogge Ludger , Lorbach Elke , Kokatam Srinivasan , Schaepermeier Sabine , Weigel Meike , Andretta-Beu Gina , Buesch Stefanie , Grabeck Tamara , Krumnow Alexandra , Spicker Sonja , Kallol Sampada , Kapoor Preeti , Toell Andrea 
Published: May 2015

Abstract
Cell lines isolated from tumors are an important tool to study cancer in vitro. They can be used for drug development as well as for understanding the basic mechanisms underlying cancer. Transfection of cancer cell lines with different molecules like plasmid DNA, siRNA or mRNA is often an integral part for this kind of research.
Lonza's 4D-Nucleofector™ System is a modular system for the efficient transfection of primary cells and cell lines with a variety of substrates including plasmid DNA and siRNA. The 4D-Nucleofector™ X Unit supports the Nucleofection™ in two different formats. The aluminum-free 20µl Nucleocuvette™ Strip allows the transfection of low cell numbers down to 2x104 cells per reaction. As 16 reactions can be performed in parallel it is well suited for optimizing Nucleofection™ Conditions for cells lacking a ready-to-use Optimized Protocol. For higher cell numbers of up to 2x107 cells per reaction the same Nucleofection™ Conditions can be applied in the 100μl single Nucleocuvette™ Vessel. For higher throughput needs the 96-well Shuttle™ Add-on can be connected to the 4D-Nucleofector™ System. With this add-on six 20µl Nucleocuvette™ Strips can be processed in parallel allowing for screening applications or accelerating the optimization of transfection parameters for many cell types.
In this study we used the 4D-Nucleofector™ System in combination with the 96-well Shuttle™ Add-on for optimizing transfection conditions for multiple cancer cell lines. An exemplary optimization process is depicted for the human prostate carcinoma cell line DU 145 and for the human colorectal adenocarcinoma cell line COLO 205. Optimization steps included the selection of the appropriate Nucleofector™ Solution, Nucleofector™ Program and plasmid DNA concentration.
Transfection parameters were thereby optimized for a variety of adherent and non-adherent human cancer cell lines resulting in transfection efficiencies of up to 99%; while maintaining high cell viability.
Citation Format: Jenny Schroeder, Ludger Altrogge, Elke Lorbach, Srinivasan Kokatam, Sabine Schaepermeier, Meike Weigel, Gina Andretta-Beu, Stefanie Buesch, Tamara Grabeck, Alexandra Krumnow, Sonja Spicker, Sampada Kallol, Preeti Kapoor, Andrea Toell. Efficient transfection of cancer cell lines using the 4D-NucleofectorTM System. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3485. doi:10.1158/1538-7445.AM2014-3485
Abstract 3499: Funding innovative technologies for cancer research at the National Cancer Institute
Authors: Dickherber Anthony 
Published: May 2015

Abstract
In the fall of 2013, the National Cancer Institute re-launched the Innovative Molecular Analysis Technologies (IMAT) program, committing up to $10.5 million through unique funding mechanisms (3 year R21s and R33s) to better support investigators through both the early and advanced stages of technology development over traditional funding mechanisms for exploratory research. The IMAT program has supported the development of various analytical and sample processing platforms that have made substantial contributions across the cancer research continuum, and the process of winning an award remains highly competitive. A variety of IMAT-supported research projects will be highlighted to demonstrate the variety and high level of innovation evident in the IMAT portfolio of supported research. An emphasis will be placed on recently completed projects so that investigators interested in next generation tools may become aware of possible developments through NCI-funded projects for their research. In addition, trends from recently awarded projects will be described to provide insight for potential applicants on the nature of the program and the competition. Potential projects of interest and identified technology gaps will also be discussed. The IMAT program continues to represent a unique resource for highly innovative technology development.
Citation Format: Anthony Dickherber. Funding innovative technologies for cancer research at the National Cancer Institute. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3499. doi:10.1158/1538-7445.AM2014-3499
Abstract 3536: Roles of miR-215 and regulatory mechanisms for its biogenesis in response to hypoxia in glioblastoma stem cells
Authors: Hu Jing , Sun Tao , Wang Hui , Wang Pingping , Fu Xiang-Dong , Li Qi-Jing , Wang Xiao-Fan 
Published: May 2015

Abstract
Glioblastoma (GBM) is the most common and aggressive primary brain tumor in adults, which is highly resistant to conventional therapies. In GBM, glioblastoma stem cells (GSCs) are critical for the tumor progression and resistance. The hypoxic tumor microenvironment has been reported to help maintain GSCs. However, the mechanism regulating responses of GSCs to hypoxia remains elusive. Abnormal microRNA processing is a contributing factor in various types of cancer including GBM. Using small RNA deep sequencing and Real-time PCR array, we found a group of miRNAs altered in the expression levels under hypoxia in the CD133+ GSCs. Further through a functional screen, we identified miR-215 as an important mediator for GSC growth and tumor progression in response to hypoxia. In addition, we also investigated the regulatory mechanisms for the biogenesis of the altered miRNAs under hypoxia. Interestingly, we found that hypoxia could regulate miRNA processing both transcriptionally and post-transcriptionally. These findings suggest that de-regulated miRNA biogenesis may have significant impacts on the activities of GSCs under hypoxia.
Citation Format: Jing Hu, Tao Sun, Hui Wang, Pingping Wang, Xiang-Dong Fu, Qi-Jing Li, Xiao-Fan Wang. Roles of miR-215 and regulatory mechanisms for its biogenesis in response to hypoxia in glioblastoma stem cells. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3536. doi:10.1158/1538-7445.AM2014-3536
Abstract 3558: The role of miRNA in PAX3-FKHR positive rhabdomyosarcoma
Authors: Muir Shannon , Nathanson Jason , Wilbert Melissa , Yeo Gene , Furnari Frank , Arden Karen , Cavenee Webster 
Published: May 2015

Abstract
Rhabdomyosarcoma is the most commonly diagnosed pediatric soft tissue cancer. Tumors may develop in several locations, but all tumors express markers of undifferentiated skeletal muscle tissue. Of the two main rhabdomyosarcoma subtypes, the alveolar subtype leads to a much poorer prognosis than the embryonal subtype. Alveolar rhabdomyosarcoma is characterized by a chromosomal translocation between either chromosomes 1 and 13, or more commonly 2 and 13, which creates the fusion genes PAX7-FKHR or PAX3-FKHR, respectively. The fusion genes encode a protein that contains the PAX DNA binding domain and the FKHR transactivation domain, but the mechanism of disease of the fusion protein has not yet been fully elucidated. Here we use gain of function and loss of function techniques to study the effect of PAX3-FKHR on miRNA expression. Using small RNA-seq, we show that PAX3-FKHR expression leads to an upregulation of microRNAs mir-495 and miR-543. Examination of the mir-495 and mir-543 genes revealed conserved PAX3 binding sites. We further investigate the effect of the microRNAs on rhabdomyosarcoma cell differentiation and tumorigenicity.
Citation Format: Shannon Muir, Jason Nathanson, Melissa Wilbert, Gene Yeo, Frank Furnari, Karen Arden, Webster Cavenee. The role of miRNA in PAX3-FKHR positive rhabdomyosarcoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3558. doi:10.1158/1538-7445.AM2014-3558
Abstract 3566: A robust and rapid targeted sequencing technology for iterative multiple genomic features in cancer
Authors: Lau Billy , Cushing Anna , Ji Hanlee 
Published: May 2015

Abstract
Targeted resequencing has enabled researchers and clinicians to analyze specific genomic regions of interest from cancer. For example, deep sequencing of cancer genes has allowed for the sensitive detection of rare somatic variants as well as oncogenic rearrangements that are otherwise difficult to observe with shotgun resequencing. Deep targeted resequencing of these regions can potentially provide prognostic information as well as guide treatment regimens. Current targeted resequencing methods, however, suffer from poor on-target performance, slow capture rates on the order of days, and significant manual effort. Existing commercial kits are extremely restricted for targeting custom regions of interest. Furthermore, libraries prepared for targeted resequencing purposes generally cannot be reused, thus limiting the number of replicates and follow-up experiments that can be performed for cancer samples.
We present APEX (attachment-based porous extension) capture, a platform that rapidly and robustly generates targeted DNA fragments for next-generation sequencing on the Illumina platform in as little as two hours. It is based on the principle that chemical reactions are rapidly enhanced in high surface-to-area ratio microenvironments when one reaction component is surface-bound. As a proof of concept, we covalently tethered next-generation sequencing compatible DNA libraries to a silica membrane found in conventional spin columns, performed target-specific primer extension, and eluted them for next-generation sequencing. Through serial dilutions of cytomegalovirus (CMV) and human DNA admixtures, we demonstrate CMV target enrichment down to single genome equivalents. In addition, using a tiling primer strategy we were able to robustly capture and resequence entire bacterial genomes.
Because our targeted resequencing technology preserves the original sample library, we can sequentially target different regions of interest in a series of guided experiments. We performed multi-tiered analyses of colon biopsies, where we deep resequence cancer genes as well as survey fro cancer-related pathogens such as bacterial genomes that are co-purified in the sample. APEX capture therefore enables researchers to aggressively and rapidly characterize cancer genomic material, where large-scale targeting panels are followed by precise discriminatory ones that can guide diagnosis and treatment.
Citation Format: Billy Lau, Anna Cushing, Hanlee Ji. A robust and rapid targeted sequencing technology for iterative multiple genomic features in cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3566. doi:10.1158/1538-7445.AM2014-3566