bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 453: Immune cell profile of sentinel lymph nodes in melanoma patients .
Authors: Mohos Anita , Sebestyen Timea , Liszkay Gabriella , Plotar Vanda , Horvath Szabolcs , Gaudi Istvan , Ladanyi Andrea 
Published: August 2014

Abstract
Besides being a preferential site of early metastasis, the sentinel lymph node (SLN) is also a privileged site of T-cell priming, and may thus be an appropriate target for investigating cell types involved in antitumor immune reactions. We determined the prevalence of OX40+ activated T lymphocytes, FOXP3+ regulatory T cells, DC-LAMP+ mature dendritic cells (DCs) and CD123+ plasmacytoid DCs by immunohistochemistry in 100 SLNs from 60 melanoma patients. Density values of each cell type in SLNs were compared to those in non-sentinel nodes obtained from block dissections (n=37), and analyzed with regard to associations with clinicopathological parameters and disease outcome. Sentinel nodes showed elevated amount of all cell types studied in comparison to non-sentinel nodes. Metastatic SLNs had higher density of OX40+ lymphocytes compared to tumor-negative nodes, while no significant difference was observed in the case of the other cell types studied. Within the sentinel-positive group, FOXP3+ cell density was higher in patients showing disease progression and &gt;5 years survival than in those without progression and &lt;5 years survival, respectively, or in sentinel-negative cases. High amount of FOXP3+ cells in SLNs was associated with shorter progression-free (P=0.0203) and overall survival (P=0.0238), while no significant correlation was found in the case of the other immune cell types. In multivariate analysis, SLN status, ulceration, Breslow index and patient gender, but not the density values of the immune cell types, proved significant independent predictors of survival. Taken together, our results are compatible with the hypothesis of functional competence of sentinel lymph nodes based on the prevalence of the studied immune cells. The density of FOXP3+ lymphocytes showed association with progression and survival, but none of the immune markers emerged as independent prognostic factor. These results, together with our previous findings on the prognostic value of activated T cells and mature DCs infiltrating primary melanomas, suggest that immune cells residing in the primary tumor, rather than those in sentinel lymph nodes, may be crucial in the development of antitumor immune response reflected in influencing the outcome of the disease. This work was supported by the National Scientific Research Fund OTKA 72836. *The first two authors contributed equally to the work.
Citation Format: Anita Mohos, Timea Sebestyen, Gabriella Liszkay, Vanda Plotar, Szabolcs Horvath, Istvan Gaudi, Andrea Ladanyi. Immune cell profile of sentinel lymph nodes in melanoma patients . [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 453. doi:10.1158/1538-7445.AM2013-453
Abstract 4538: A novel assay platform for the detection of kinase-inhibitor binding in intact mammalian cells.
Authors: Saharia Abhi , Raab William , Bassoni Daniel , Hunt Jeremy , Treiber Daniel K. , Wehrmann Tom 
Published: August 2014

Abstract
Kinase binding assays have become an integral part of inhibitor characterization. These tools have been applied in KINOME-wide screening systems as well as the detailed characterization of inhibitor residence time for lead optimization and MOA studies. However in cells, assays are limited to monitoring kinase activity and downstream substrate phosphorylation events. Although these types of cellular assays are critical to move programs forward, their ability to characterize inhibitor function is limited, requires targeted antibody reagents, and knowledge of specific substrates which are often not available. To circumvent these issues and apply the power of binding assays to a cellular format we have devised a method for monitoring compound binding to kinase targets in intact mammalian cells termed InCELL Hunter. The assay is shown to retain the benefits of cellular assays such as assessing compound permeability, toxicity, and target engagement; while exhibiting the generic applicability of a kinase binding assay. The InCELL hunter assay correctly describes type I, type II, and Type III inhibitors with the expected rank order cellular potencies. The assay is activity and substrate independent making it amenable to previously intractable targets and provides novel cellular information that complements both biochemical and existing cellular formats.
Citation Format: Abhi Saharia, William Raab, Daniel Bassoni, Jeremy Hunt, Daniel K. Treiber, Tom Wehrmann. A novel assay platform for the detection of kinase-inhibitor binding in intact mammalian cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4538. doi:10.1158/1538-7445.AM2013-4538
Abstract 4541: Highly sensitive kinase assays combining Carna Biosciences QSS Assist ELISA reagents with the Meso Scale Discovery MULTI-ARRAY platform.
Authors: Jacobi Carsten , Schilb Alain , Kawase Yusuke , Kirii Yasuyuki , Boldyreff Brigitte 
Published: August 2014

Abstract
We developed a sensitive kinase asay using a QSS Assist ELISA kinase assay kit from Carna Biosciences, Inc. and the detection method from Meso Scale Discovery. The QSS Assist ELISA kit is optimized for screening of compounds. Comparing to most other kinase assay kits, QSS Assist ELISA kits are available for both peptide and protein substrates and several ELISA kits developed by Carna Biosciences employ a naturally occurring protein substrate, e.g. MAP kinases for MAPK kinases.
Detection of kinase activity is achieved with a primary anti-phosphoserine/threonine or tyrosine antibody and a secondary anti-Ig-antibody. Commonly, such secondary antibodies are coupled to horseradish peroxidase (HRP), which allows for signal detection by adding a color reagent, i.e. an HRP substrate which can be detected upon reaction by measuring optical density. Here we applied an MSD SULFO-TAG labeled secondary antibody. These antibodies emit light upon electrochemical stimulation initiated at the electrode surfaces of MULTI-ARRAY microplates, and thus detect the primary antibody with ultimate sensitivity without direct labeling it.
We have sucessfully miniaturized the highly sensitive assay and this new assay technology has been validated with published kinase inhibitors from AstraZeneca and Tocris Bioscience.
Citation Format: Carsten Jacobi, Alain Schilb, Yusuke Kawase, Yasuyuki Kirii, Brigitte Boldyreff. Highly sensitive kinase assays combining Carna Biosciences QSS Assist ELISA reagents with the Meso Scale Discovery MULTI-ARRAY platform. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4541. doi:10.1158/1538-7445.AM2013-4541
Abstract 4551: Identification of TRPM7 kinase inhibitors.
Authors: Kaoud Tamer S. , Park Jihyun , Mitra Shreya , Tavares Clint D.J. , Tseng Anna , Dalby Kevin N. 
Published: August 2014

Abstract
TRPM7 (transient receptor potential melastatin 7) encodes a calcium permeable non-selective cation channel implicated in cell adhesion and magnesium homoeostasis. The TRPM7 gene encodes for a protein kinase whose activity is linked to the control of actomyosin contractility. TRPM7 mediates adhesion and migration of MDA-MB-231 breast cancer cells and recently has been reported to promote breast tumor cell metastasis. The lack of cell-permeable pharmacological inhibitors of the kinase domain represent a barrier to fully understanding kinase function. Herein, we describe the discovery of several compounds that target TRPM7 kinase activity and which were shown to decrease the binding of Myosin IIB to TRPM7 in HEK293 cells transfected with pCMV6-TRPM7. Magnesium starvation, which promotes TRPM7 kinase activity, induces phosphorylation of eEF2. Treatment of cells with several of the compounds decreased eEF2 phosphorylation under conditions of magnesium starvation, consistent with the notion that they inhibit TRPM7 kinase activity in cells.
Citation Format: Tamer S. Kaoud, Jihyun Park, Shreya Mitra, Clint D.J. Tavares, Anna Tseng, Kevin N. Dalby. Identification of TRPM7 kinase inhibitors. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4551. doi:10.1158/1538-7445.AM2013-4551
Abstract 4558: Discovery and mechanistic studies of novel class of CXCR2 inhibitors.
Authors: Ha Helen , Neamati Nouri 
Published: August 2014

Abstract
Background: Chemokine receptor, CXCR2 is expressed on various immune cells and is essential for neutrophil recruitment and angiogenesis at sites of acute and chronic inflammation caused by tissue injury or infection. Due to its role in inflammation, it has been implicated in a number of inflammation-mediated diseases such as psoriasis, arthritis, COPD, cystic fibrosis, and asthma. More recently, it is also implicated in various types of cancer. CXCR2 and its ligands are up-regulated in cancer cells as well as the tumor microenvironment and have been shown to promote tumor growth, angiogenesis and invasiveness. Though pharmaceutical companies have pursued the development of CXCR2-specific small-molecule inhibitors as anti-inflammatory agents within the two past decades, there are currently no clinically approved CXCR2 inhibitors.
Methodology/Principal Findings: Using a high-throughput, cell-based, CXCR2 assay, we screened an in-house library of structurally diverse compounds and identified a novel class of CXCR2 biased ligand. Our lead compound, CX797, inhibited IL8-mediated cyclic AMP signaling and receptor degradation, while specifically up-regulating IL8-mediated β-arrestin recruitment and MAP kinase signaling. CX797 also inhibited Jurkat cell proliferation via G0/G1 cell cycle arrest.
Conclusions/Significance: In our studies we have identified a novel class of CXCR2 ligand, CX797, and the first to report biased CXCR2 ligand signaling. Mechanistic studies of CX797 and previously reported CXCR2 inhibitor, SB265610, show these two classes have distinct mechanism of action on CXCR2. CX797 is a potential candidate for further optimization and development for various inflammatory diseases and CXCR2-expressing cancer.
Citation Format: Helen Ha, Nouri Neamati. Discovery and mechanistic studies of novel class of CXCR2 inhibitors. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4558. doi:10.1158/1538-7445.AM2013-4558
Abstract 4591: Whole genome sequencing of SHH medulloblastomas predicts molecular groups of responders and non-responders to SMO-inhibition .
Authors: Kool Marcel , Jones David TW , Jaeger Natalie , Northcott Paul A. , Hovestadt Volker , Schueller Ulrich , Remke Marc , Cho Yoon-Jae , Pomeroy Scott , Taylor Michael D. , Eils Roland , Korshunov Andrey , Lichter Peter , Pfister Stefan M. 
Published: August 2014

Abstract
Recently, we and others analyzed large series of pediatric medulloblastomas (MB) and identified a number of recurrent aberrations in each of the four major subgroups (WNT, SHH, Group 3 and Group 4). However, due to their infrequent occurrence not much is known about genetic aberrations in adult MBs. We now have analyzed a large series of adult SHH MBs (age ≥ 16) by whole genome sequencing and compared them with pediatric SHH MBs. We sequenced tumor and blood of 26 adult SHH MBs and compared them with 30 pediatric SHH MBs. A replication cohort of 28 adult and 29 pediatric SHH MBs was sequenced for 414 genes by targeted sequencing. We also performed expression profiling and DNA methylation analyses on most of these cases. Whole genome sequencing revealed a clear correlation between mutation rate and age of the patient (r = 0.69). Furthermore, the genomic data showed that SHH MBs can be split up in three distinct subgroups: infants, children and adults. They all have mutations in the SHH pathway, mostly in PTCH1 (infants and adults), SUFU (infants) and SMO (adults). Children almost completely lack the classical upstream SHH pathway mutations but instead have more downstream aberrations such as MYCN and GLI2 mplifications, and have frequent TP53 mutations, often in the germline, whilst all of these were extraordinarily rare in infants and adults. We also identified several recurrent mutations in adult MBs that were not found in pediatric MBs. Moreover, the three SHH subgroups were different in their transcriptome and methylome with the TP53 mutated SHH MBs in children being more similar to adult MBs. Collectively, this data will help to better understand the biology of pediatric and adult SHH-medulloblastoma, but most importantly may help selecting patients for targeted SHH inhibition and new treatment strategies for TP53 mutated SHH MBs in a clinical setting.
Citation Format: Marcel Kool, David TW Jones, Natalie Jaeger, Paul A. Northcott, Volker Hovestadt, Ulrich Schueller, Marc Remke, Yoon-Jae Cho, Scott Pomeroy, Michael D. Taylor, Roland Eils, Andrey Korshunov, Peter Lichter, Stefan M. Pfister. Whole genome sequencing of SHH medulloblastomas predicts molecular groups of responders and non-responders to SMO-inhibition . [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4591. doi:10.1158/1538-7445.AM2013-4591
Abstract 4600: Analysis of clonal evolution in cancer using whole exome sequence data reveals that subclonal driver mutations predict poor prognosis in chronic lymphocytic leukemia.
Authors: Carter Scott L. , Landau Dan-Avi , Stojanov Petar , McKenna Aaron , Cibulskis Kristian , Lawrence Michael S. , Lohr Jens , Stevenson Kristen , Neuberg Donna , Meyerson Matthew , Wu Catherine J. , Getz Gad 
Published: August 2014

Abstract
Clonal evolution is a key feature of cancer progression and relapse. We present a computational technique for analyzing whole exome sequence data to measure the fraction of cancer cells harboring each somatic mutation and resolve subclonal cell populations. We applied our methods to 149 chronic lymphocytic leukemia (CLL) samples to classify driver mutations as predominantly clonal or subclonal, corresponding to initiating and progression events in CLL evolution. We identified driver mutations as predominantly clonal (e.g., MYD88, trisomy 12 and del(13q)) or subclonal (e.g., SF3B1, TP53), corresponding to earlier and later events in CLL evolution. We sampled leukemia cells from 18 patients at two timepoints and found that 10 of 12 CLL cases treated with chemotherapy (but only 1 of 6 without treatment) underwent clonal evolution, predominantly involving subclones with driver mutations (e.g., SF3B1, TP53) that expanded over time. Furthermore, presence of a subclonal driver mutation was an independent risk factor for rapid disease progression. Our methods uncover patterns of clonal evolution in cancer, providing insights into its stepwise transformation and linking the presence of subclones with adverse clinical outcome. Because our methods require only whole exome sequence data, they are readily applicable to a large corpus of approximately 6,000 sequenced cancer exomes, and are ideally suited for application in future exome-based clinical cancer sequencing pipelines. We present additional application of our methods to analysis of prostate cancer, multiple myeloma, and glioblastoma multiforme datasets.
Citation Format: Scott L. Carter, Dan-Avi Landau, Petar Stojanov, Aaron McKenna, Kristian Cibulskis, Michael S. Lawrence, Jens Lohr, Kristen Stevenson, Donna Neuberg, Matthew Meyerson, Catherine J. Wu, Gad Getz. Analysis of clonal evolution in cancer using whole exome sequence data reveals that subclonal driver mutations predict poor prognosis in chronic lymphocytic leukemia. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4600. doi:10.1158/1538-7445.AM2013-4600
Abstract 4609: Novel phosphorylation and ubiquitination sites regulate ROS-dependent degradation of c-FLIP and sensitization of cancer cells to TRAIL.
Authors: Wilkie-Grantham Rachel P. , Matsuzawa Shu-Ichi , Reed John C. 
Published: August 2014

Abstract
The cytosolic protein c-FLIP (cellular Fas-associated death domain-like interleukin 1β-converting enzyme inhibitory protein) is an inhibitor of death receptor-mediated apoptosis that is up-regulated in a variety of cancers, contributing to apoptosis resistance. Several compounds found to restore sensitivity of cancer cells to TRAIL, a TNF family death ligand with promising therapeutic potential, act by targeting c-FLIP ubiquitination and degradation by the proteasome. The generation of reactive oxygen species (ROS) has been implicated in c-FLIP protein degradation. However, the mechanism by which ROS post-transcriptionally regulate c-FLIP protein levels is not well understood. We show here that treatment of prostate cancer PPC-1 cells with the superoxide generators menadione or paraquat down-regulates c-FLIP long (c-FLIPL) protein levels, which is prevented by the proteasome inhibitor MG132. Furthermore, pretreatment of PPC-1 cells with a ROS scavenger prevented ubiquitination and loss of c-FLIPL protein induced by menadione or paraquat. We identified lysine 167 as a novel ubiquitination site of c-FLIPL important for ROS-dependent degradation. We also identified threonine 166 as a novel phosphorylation site and demonstrate that T166 phosphorylation is required for ROS-induced K167 ubiquitination. The mutation of either T166 or K167 was sufficient to stabilize c-FLIP protein levels in PPC-1, HEK293T, and HeLa cancer cells treated with menadione or paraquat. Accordingly, expression of c-FLIP T166A or K167R mutants protected cells from ROS-mediated sensitization to TRAIL-induced cell death. Our findings reveal novel ROS-dependent post-translational modifications of c-FLIP that regulate c-FLIP protein degradation and subsequent sensitization of cancer cells to TRAIL.
Citation Format: Rachel P. Wilkie-Grantham, Shu-Ichi Matsuzawa, John C. Reed. Novel phosphorylation and ubiquitination sites regulate ROS-dependent degradation of c-FLIP and sensitization of cancer cells to TRAIL. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4609. doi:10.1158/1538-7445.AM2013-4609
Abstract 4627: Role of intratumoral cell heterogeneity on therapeutic efficacy in glioblastoma.
Authors: Chakravarty Debyani , Pedraza Alicia , Liu Angela H. , Cotari Jesse , Altan-Bonnet Grégoire , Brennan Cameron W. 
Published: August 2014

Abstract
Glioblastoma (GBM), the most common and lethal malignancy of the brain, is typified by high degrees of histologic and molecular heterogeneity. The majority of GBM harbor amplification and/or mutations of receptor tyrosine kinases (RTKs), most frequently EGFR (40-50%) or PDGFRA (∼15%). We recently documented that a subset of glioblastoma harbors independent focal amplification of two or more RTKs, most commonly PDGFRA and EGFR. This phenomenon lends genetic evidence to support that co-expression of more than one RTK in the same cell serves a functional purpose in conferring selective growth advantage to GBM.
In this study we demonstrate that EGF stimulates endogenous interaction between activated EGFR and PDGFRA, assessed using reciprocal coimmunoprecipitation and proximity ligation assays in patient-derived GBM tumor-sphere lines of multiple genotypes. EGF leads to phosphorylation of PDGFRA Y720. This transactivation and subsequent activation of Shp2 are abolished by EGFR inhibitors gefitinib or lapatinib at low concentrations. Evidence of EGFR-PDGFRA interaction was found in the majority of GBM tumorsphere lines where both receptors were expressed. We used multichannel phospho-FACS in a panel of tumorsphere lines to characterize the cell-to-cell heterogeneity of EGFR and PDGFRA expression levels and how these levels affect p-Akt and p-ERK baseline activity, response to ligands and response to targeted receptor inhibition. Indeed, high expression of both EGFR and PDGFRA identifies tumor cells with elevated MAPK and PI3K pathway activity. Notably, these tumor cells have high downstream pathway activation in the absence of explicit stimulation by ligand and appear to be refractory to dual RTK inhibition. Taken together, these data underscore the role of tumor cell RTK heterogeneity in therapeutic resistance to RTK inhibitors in GBM. This study also highlights a possible mechanism that heterotypic RTKs in the same cell may utilize to achieve growth advantage.
Citation Format: Debyani Chakravarty, Alicia Pedraza, Angela H. Liu, Jesse Cotari, Grégoire Altan-Bonnet, Cameron W. Brennan. Role of intratumoral cell heterogeneity on therapeutic efficacy in glioblastoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4627. doi:10.1158/1538-7445.AM2013-4627