bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 3183: Breast Cancer MethylSeq: Analysis of bisulfite converted breast cancer genomes using microdroplet-based targeted sequencing
Authors: Samuels Michael L. , Wu Chia-Chin , Brayer James , Warner Jason , Link Darren , Harris Alan , Oesterreichs Steffi , Lee Adrian , Milosavljevic Aleksandar 
Published: August 2012

Abstract
Targeted sequencing using microdroplet-based PCR provides a method to selectively and uniformly amplify thousands of genomic regions of interest (ROIs) for efficient next generation sequencing (NGS). Recently, this approach has been adapted for the analysis of bisulfite-treated DNA, enabling strand-specific determination of cytosine methylation status with single-base pair resolution. This droplet PCR-based targeted approach significantly reduces cost and improves sequencing depth compared to whole-genome sequencing, allowing researchers to power larger studies to discover and validate how methylation and genomic aberrations affect cancer development. Here we report results from our ongoing work using a breast cancer targeted panel (Breast Cancer MethylSeq Panel) for sequence specific analysis of both epigenomic methylation and genomic mutation in breast tumor samples. The panel includes PCR primer pairs designed to target ∼2,700 ROIs, leaving room for an additional 1,300 target ROIs of interest to be added by individual researchers. Use of this single panel will provide information about CpG methylation and genomic sequence enabling analysis of multiple content types including: A) cell subtype; B) genomic mutation; C) surrogate gene expression subtypes using promoter CpG islands or other methylation markers; D) copy-number variation (CNV); E) Loss of Heterozygosity (LOH); F) methylation-mediated gene silencing and loss of imprinting. The Breast Cancer MethylSeq microdroplet library, comprising individual primer pairs for PCR in droplets, will be tested and validated using a set of 64 bisulfite-converted samples including 8 breast cancer cell lines, a range of ER positive and negative tumors and TCGA samples, and a set of 8 metastatic tumors from a single individual. We will report overall sequencing success metrics, as well as concordance with metadata on the various ROI classes (A-F above). The deep and comprehensive breast tumor sequencing enabled by this targeting panel will allow researchers to identify epigenomic alterations and genomic mutations across a range of assay types using just one assay. The goal for development and validation of this panel is to provide the breast cancer research community a unique tool for identifying and correlating cancer subtypes with clinical outcomes.
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 3183. doi:1538-7445.AM2012-3183
Abstract 3190: Capture and molecular characterization of ovarian cancer-derived exosomes
Authors: Ruf Ingrid K. , Briggs Hilary , Tewari Muneesh 
Published: August 2012

Abstract
Exosomes are secreted, membrane-bound vesicles of 50-100 nm known to carry cellular messenger RNAs (mRNA) and microRNAs (miRNA). Several reports have indicated that tumor-derived exosomes are released into the circulation of patients with a variety of cancer types, including epithelial ovarian cancer. The goals of this study are (i) to develop methods for specific capture and molecular profiling of ovarian cancer tumor-derived exosomes from blood plasma and (ii) determine whether information carried in tumor-derived exosomes can serve as a reliable surrogate for tumor tissue for measurement of key miRNA and mRNA biomarkers. In our work to date, we have used exosomes derived from conditioned media of ovarian cancer cell lines to develop and optimize methods for the isolation and physical characterization of exosomes. Using Nanoparticle Tracking Analysis (NTA) technology (NanoSight, Inc.) to directly count and accurately size exosome populations, our initial data indicates that traditional ultracentrifugation protocols may fail to recover a major fraction of exosomes present in conditioned media. The basis for this finding is currently under investigation and the latest results will be presented. In parallel, we are developing affinity capture approaches to isolate specific subpopulations of exosomes using antibodies directed against epithelial cell adhesion molecule (EpCAM) and other exosomal surface proteins. Initial results indicate that a subpopulation of ovarian cancer-derived exosomes can be purified in this manner; molecular characterization of exosomal contents is in progress. Finally, we are analyzing clinical plasma specimens from patients and controls to: (i) test whether bulk properties of exosomes (e.g., size and number) differ between cases and controls, and (ii) perform specific capture of tumor-derived plasma exosomes and compare exosomal mRNA/miRNA profiles to matched tumor tissue to determine the degree of concordance between exosomal and tissue RNA profiles. Latest results from these studies will be presented. Ultimately, we anticipate that this work will lead to methods for molecular phenotyping of epithelial ovarian cancers in individual patients using a blood-based approach. This work was supported in part by a Stand Up To Cancer/AACR Innovative Research Grant to M. Tewari.
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 3190. doi:1538-7445.AM2012-3190
Abstract 3193: A new approach for colocalization of proteins using HRP and AP enzyme detection in paraffin embedded tissues
Authors: Gonzalez Rachel M. , Ding Li , Xiao Ming , Zhang Xiaoping 
Published: August 2012

Abstract
Co-localization of two proteins is a powerful tool in immunofluorescence, however the stability of the fluorescence limits the ability to screen large sample sets. Double and triple staining with the ability to visualize co-localization of proteins using HRP and AP enzymes in paraffin embedded tissue may prove to be a useful tool for discovery and functional analysis of gene and protein expression. Here we present a novel chromogen mix by GBILabs.com of Emerald and Red that yields a third color (Dark Blue/Purple) when proteins are co-localized using HRP and AP enzymes for detection. Initial tests evaluated combinations of ER, Her2, CEA, Keratin, PR, p53, PCNA, and Ki67 in 10 breast and 10 colon cancer cases to screen the percentage of co-localized proteins in these cases. In addition, a 70 case breast cancer tissue array containing duplicate samples and known diagnosis of ER, PR, and Her2 for each case were screened with ER, PR, Her2, p53, PCNA, or Ki67and keratin antibodies. The core tumors sections showed co-localization of PCNA, Ki67 and p53 proteins. This new double and triple staining protocols in combination with tissue arrays, will allow researchers to rapidly determine the association between expression of two or more proteins in the tissue and if proteins co-localize within the cell.
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 3193. doi:1538-7445.AM2012-3193
Abstract 3200: The AKT inhibitor AZD5363 is selectively active in PIK3CA mutant gastric cancer cell lines, and sensitizes a gastric cancer explant model to docetaxel
Authors: Li Jing , Davies Barry R. , Zhou Minhua , Zhang Jingchuan , Xu Yan , Tang Lili , Wang Huiying , Liu Charles , Yin Xiaolu , Ji Qunsheng , Yu Derek Dehua 
Published: August 2012

Abstract
Activation of the phosphatidylinositol 3-kinase (PI3K)/AKT pathway is a common phenomenon in cancer due to multiple mechanisms, including mutation of PI3KCA, loss or mutation of PTEN, or over-expression of receptor tyrosine kinases. We recently developed a novel AKT kinase inhibitor, AZD5363. To explore the activity of AZD5363 and elucidate the correlation between AZD5363 response and genetic alterations in gastric cancer, we investigated the effects of pharmacological inhibition of AKT on a panel of 20 gastric cancer cell lines. We demonstrated that gastric cancer cells with PIK3CA mutations were selectively sensitive to AZD5363. Interestingly, we found that HGC27, a cell line harboring both PI3KCA mutation and PTEN loss, displayed the greatest sensitivity to this AKT inhibitor, suggesting possible synergy between these two genetic alterations. To further dissect the role of PI3KCA mutation and PTEN loss in response to AKT inhibition, we tested, using in vivo xenografts, the antitumor activity of AZD5363 in HGC27 and two other primary gastric cancer models containing either PI3KCA mutation or PTEN loss. Our data indicated that AZD5363 monotherapy treatment led to complete tumor regression in the HGC27 xenograft model, correlating with the induction of cell apoptosis and inhibition of PI3K/AKT pathway. On the other hand, the same treatment evoked only a moderate response (∼60% TGI) in the PI3KCA mutant primary xenograft model. Whilst monotherapy AZD5363 or docetaxel were not active in the PTEN negative, PIK3CA wild-type primary xenograft model, significant anti-tumor activity was seen when AZD5363 was combined with docetaxel. These results suggest that PI3KCA mutation is an important determinant of response to AKT inhibition in gastric cancer. Moreover, combination with AZD5363 can overcome innate resistance to docetaxel in a gastric cancer explant model.
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 3200. doi:1538-7445.AM2012-3200
Abstract 3203: High quality DNA obtained with an automated DNA Extraction method with 15 to 40 year old formalin fixed paraffin embedded (FFPE) blocks from normal and cancer tissues
Authors: Niland Erin , McGuire Audrey D. , Cox Mary L. , Sandusky George E. 
Published: August 2012

Abstract
DNA and RNA have been used as markers of tissue quality and integrity in tissues the last decade. In this research study, kidney, liver, colon, lung, and breast genomic quality were analyzed in tissues from surgical cancer patients and post-mortem cases obtained with an IRB approved protocol and informed/or next of kin consent. DNA extraction was performed on formalin-fixed paraffin-embedded tissues (FFPE) from both groups of cases from the 1970's through the 2000's and formalin fixed / long term 70% ethanol storage(15 + years). To extract the DNA from the FFPE tissues, we soaked all tissues in xylene to remove the paraffin, digested the tissue with a proteinase K solution, and used an automated extraction machine to extract the DNA. A similar SOP was used for the formalin fixed/ 70% long term ethanol-stored tissue, except the tissue was first homogenized rather than soaked in xylene. DNA quality and yield were evaluated using a spectrophotometer. Gel electrophoresis was used to evaluate the length of the DNA in about 20% of the 200 samples. Samples that had optical density (OD) readings above 1.60 and below 2.10 with a DNA yield above 100 µg/mL were deemed to be high quality DNA. FFPE tissues yielded the highest DNA concentration and quality (OD reading of 1.87 and yield of 625 ug/ml) with greater than 95% of the samples meeting the above specifications, while the formalin fixed/long term 70% ethanol stored tissue yielded both the lowest DNA concentration and quality (yield of 52 ug/ml and OD reading of 1.48). In conclusion, the results show that high quality DNA can be extracted from FFPE tissue using an automated DNA extraction procedure with paraffin blocks from the early 1970's to present, and the DNA extracted is useful for clinical and experimental studies. The DNA from tissues stored in aqueous media (formalin fixed / long term 70% ethanol storage) may be useful in some research applications, but the DNA is partially degraded compared to the tissue stored in paraffin blocks.
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 3203. doi:1538-7445.AM2012-3203
Abstract 3263: Expression of Bim, Noxa, and Puma in non-small cell lung cancer
Authors: Sakakibara-Konishi Jun , Oizumi Satoshi , Kikuchi Junko , Kikuchi Eiki , Mizugaki Hidenori , Kinoshita Ichiro , Dosaka-Akita Hirotoshi , Nishimura Masaharu 
Published: August 2012

Abstract
Background: The BH3-only members of the Bcl-2 protein family have been proposed to play a key role in the control of apoptosis and in the initiation of the apoptotic pathways. In this study, we evaluated the expression of Bim, Noxa, and Puma in non-small cell lung cancer (NSCLC). Methods: A total of 135 surgically resected NSCLCs were immunohistochemically assessed for Bim, Noxa, and Puma expression. The immunoscores were determined, and then its correlation with either the clinicopathological variables or the survival outcomes were analyzed. Results: Immunohistochemical reactivity for Bim, Noxa, and Puma was detected in the cytoplasm of the tumor cells. Bim expression was associated with several clinicopathological factors, including sex (p&lt;0.001), smoking habit (p=0.03), pathological histology (p=0.001), pathological T stage (p=0.03), pathological disease stage (p=0.02), and differentiation of tumor (p&lt;0.001). Multivariate logistic regression analysis showed a significant correlation between low Bim expression and squamous cell carcinoma (p=0.04), in addition to a correlation between high Bim expression and well differentiated tumors (p=0.02). Analysis of cellular biological expression demonstrated a link between low Bim expression and high Ki67. While Noxa expression was also shown to be correlated with both smoking habit (p=0.02) and the pathological histology (p=0.03), there was no strong association observed between the expression and the clinical features when they were examined by a multivariate logistic regression analysis. No correlations were noted between Puma expression and any of the variables. Our analyses also indicated that the expression levels of the BH3-only proteins were not pertinent to the survival outcome. Conclusions: The current analyses demonstrated that Bim expression in the NSCLCs was associated with both squamous cell carcinoma histology and tumor proliferation.
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 3263. doi:1538-7445.AM2012-3263
Abstract 33: Implementing CAD cells quantify the relationships between Ig-CAM-mediated adhesion, force transduction, and actin dynamics
Authors: Fuller Miles H. , Schaefer Andrew , Mejean Cecile , Forscher Paul 
Published: August 2012

Abstract
Several neuro-degenerative diseases and motor defects have been linked to malfunctions in the motility of neurons. This project is focused on the determining whether the roles of the transmembrane proteins NCAM and L1-CAM can be studied using the CAD cell line as a model. CAD cells are a cancer cell line that come from mice and can be stimulated to grow as either neurons or glial cells. In addition, this cell line has been shown to be an easily transfected line. In order to determine usefulness of this cell line several techniques were used. Western blots were implemented in order to determine if the NCAM and/or L1-CAM and proteins known to be involved in their signaling pathways were present in the cell line. Western blots were then confirmed by immunocytochemistry staining. Next, the CAD cell line was transfected with photoactivateable actin. Finally, immuno beads were attached to the membranes of these CAD cells and then holographic optical tweezers were used to determine whether or not thsee ligands coupled to the retrograde actin flow in the cells. The combination of these experiments should provide the evidence for whether or not the CAD cells would be a feasible model to study the nature of the NCAM and L1-CAM proteins and their relationship to the movement of actin in the cytoskeleton of neurons.
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 33. doi:1538-7445.AM2012-33
Abstract 3328: Targeted inactivation of EZH2 by CDF inhibits pancreatic tumor growth mediated by re-expression of lost miRNAs in tumors
Authors: Bao Bin , Ali Shadan , Banerjee Sanjeev , Logna Farah , Azmi Asfar , Kong Dejuan , Ahmad Aamir , Li Yiwei , Padhye Subhash , Sarkar Hazlul H. 
Published: August 2012

Abstract
EZH2 plays a critical role in the regulation of cell survival, proliferation and cancer stem cell (CSC) function, contributing to tumor aggressiveness. Increased expression of EZH2 has been found in human pancreatic cancer (PC); however, the mechanism(s) by which EZH2 mediates its biological effects is not known, and there is no avenue for inactivation of EZH2. In this study, we examined the effect of CDF, a novel Curcumin analogue, on tumor cell growth in vitro and in vivo and assessed whether the effect of CDF is due to inactivation of EZH2 and CSC function mediated by deregulation of microRNAs (miRNAs). We found that CDF decreased cell survival, clonogenicity, formation of pancreatospheres, cell migration and invasion, and attenuated CSC function in human PC cells, which was associated with inactivation of EZH2 expression and NF-κB activity, and increased expression of miRNAs such as let-7a, b, c, d, miR-26a, miR-101, miR-146a, and miR-200b, c. Further mechanistic studies showed that the re-expression of miR-101 led to decreased expression of EZH2 and EpCAM. Moreover, CDF inhibited tumor growth in a mouse orthotopic model of PC, which was associated with decreased expression of EZH2, Notch-1, CD44, EpCAM and Nanog, and increased expression of let-7, miR-26a and miR-101 in tumor remnant. From these results, we conclude that the inhibition of tumor growth and tumor cell aggressiveness by CDF is in part due to down-regulation of EZH2, which was mediated by up-regulation of specific miRNAs, suggesting that CDF could be useful for the prevention of tumor progression and/or treatment of PC.
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 3328. doi:1538-7445.AM2012-3328
Abstract 3335: The potential role of lateral inhibition in the maintenance of glioblastoma cancer stem cells
Authors: Lim Kah Jing , Eberhart Charles G. , Bar Eli E. 
Published: August 2012

Abstract
Glioblastoma (GBM) is a malignant cancer of the central nervous system. Tumor cells are highly resistant to conventional therapies and tumors always recur. Cancer stem cells are thought to be critical for long-term growth and therapeutic resistance of GBM. It is therefore important to understand the signaling mechanisms maintaining GBM cancer stem cells. Notch is known to be an important signaling pathway during neural development, and can promote the maintenance of stem and progenitor cells via the process of lateral inhibition. Lateral inhibition is a contact-dependent signaling mechanism by which some cells within a field remain stem-like while others differentiate. In normal development, Notch ligands initiate this process by binding to the receptor on an adjacent cell, signaling to this neighbor to remain undifferentiated. Although Notch is known to be a critical player in the maintenance of stem-like cancer cells in various tumor types, including GBM, it is not known if the mechanism of lateral inhibition is also conserved in neural cancer stem cells. To test this hypothesis, we engineered a model system where isogenic cells expressing low and high levels of the Jag1 ligand are co-cultured followed by flow-based separation and determination of Notch pathway activity in each respective population. These experiments suggest that lateral inhibition is conserved in GBM. In the GBM neurosphere lines HSR-GBM1 and 040821, co-culture induced expression of Notch targets Hes5 and Hey1 in Jag1-low “signal receiving” cells and inhibited expression of these targets in Jag1-overexpressing “signal sending” isogenic cells. Preliminary experiments suggest that the ligand intracellular domain (ICD) is involved in this process. Our data suggest conservation of a developmental mechanism regulating Notch activation in cancer, and may affect our understanding of how to treat Notch-dependent tumors.
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 3335. doi:1538-7445.AM2012-3335
Abstract 334: Identification of novel regulatory genes controlling epithelial to mesenchymal transition in cultured breast cancer cells
Authors: Lehtinen Laura , Mäkelä Rami , Kallioniemi Olli , Iljin Kristiina 
Published: August 2012

Abstract
Breast cancer prognosis is tightly correlated with the degree of spread beyond the primary tumor. A prerequisite for breast cancer cell dissemination is activation of a process called “epithelial - mesenchymal transition” (EMT). During EMT, epithelial cells lose epithelial characteristics, such as E-cadherin expression and gain mesenchymal properties, such as vimentin expression. The reversal process to EMT is mesenchymal-epithelial transition (MET), which occurs during colonization of the disseminated cancer cells to distant sites. Thus, EMT should be considered as a transient and reversible process in cancer progression. Despite the clinical importance, EMT and MET have been largely studied from a focused signalling standpoint, which may provide a biased view of the biological processes involved. In this study, RNAi technology followed up by lysate microarray analysis (LMA) using E-cadherin and vimentin as endpoint markers was performed to identify novel EMT and MET regulatory genes in cultured breast cancer cells. The screening conditions were optimized for the estrogen receptor (ER) positive E-cadherin expressing luminal MCF-7 breast cancer cells and for ER negative vimentin expressing mesenchymal bone metastatic MDA-MB 231 cells. The results from the replicate screens with &gt;1012 siRNAs targeting 599 genes (1-3 siRNAs / gene) amplified and /or over-expressed in breast cancer cells were found to correlate (r &gt; 0.9), and the validated siRNAs targeting E-cadherin and vimentin were among the top repressing hits for the corresponding endpoints, indicating reliability of the protocol. Interestingly, several novel putative E-cadherin (E-cadherin reducing siRNAs, genes inducing loss of metastatic potential) and vimentin (vimentin reducing siRNAs, metastasis-promoting candidate genes) regulators were identified and validated using secondary assays, indicating that our knowledge on EMT and MET is still far from comprehensive. Functional characterization of the identified candidate regulators in cultured breast cancer cells is on-going. Since modulation of the differentiation state of breast cancer cells is a promising therapeutic strategy, better understanding of EMT and MET may provide novel therapeutic opportunities to block breast cancer cell dissemination.
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 334. doi:1538-7445.AM2012-334