bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 3957: Optimized plasma collection procedures for liquid biopsy analyses in cancer
Authors: Parpart-Li Sonya T. , Bartlett Bjarne , Popoli Maria , Adleff Vilmos , Brahmer Julie , Azad Nilo , Bonerigo Sarah , Browner Ilene , Ryan Amy , Velculescu Victor , Sausen Mark , Diaz Luis A. 
Published: July 2016

Abstract
Analyses of genomic alterations in cell-free DNA (cfDNA) shed from tumors into the blood stream is rapidly advancing as a method to detect and genotype cancer. Liquid biopsy analyses are a favorable alternative to invasive tissue approaches, particularly for cancers in organs where tissue is difficult to obtain. As these methods become a clinical standard, the method for blood collection and plasma isolation will be an important consideration to ensure optimal assay performance with limited degradation of circulating tumor DNA (ctDNA). We compared blood collection and plasma isolation using both K2EDTA and cell-free DNA Streck™ BCT tubes to determine the stability of cfDNA and ctDNA in blood at room temperature or at 4°C. Blood was collected from nine cancer patients with KRAS mutations using K2EDTA and Streck™ BCT tubes. Over the course of seven days, cell lysis occurred in K2EDTA tubes at room temperature, releasing germline DNA into the blood (1300% increase over seven days), which significantly increased the number of total genomic equivalents. Additionally, we found that the volume of plasma collected from both tube types during blood fractionation decreased over time when tubes were at room temperature (an average of 3.5 mL vs. 1.0 mL, respectively). To evaluate the effect of storage conditions on performance of each tube type, blood was also collected from six cancer patients with KRAS or EGFR mutations and either maintained at room temperature or stored at 4°C for up to three days. Taken together, K2EDTA tubes stored at 4°C prevented cell lysis and preserved the ctDNA in a manner equivalent to Streck™ BCT tubes. These data demonstrate that liquid biopsies can be collected using either tube type with similar performance and appropriate consideration of storage conditions.
Citation Format: Sonya T. Parpart-Li, Bjarne Bartlett, Maria Popoli, Vilmos Adleff, Julie Brahmer, Nilo Azad, Sarah Bonerigo, Ilene Browner, Amy Ryan, Victor Velculescu, Mark Sausen, Luis A. Diaz. Optimized plasma collection procedures for liquid biopsy analyses in cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3957.
Abstract 3979: Metabolic pathways associated with urinary metabolite biomarkers differentiate bladder cancer patients from healthy controls
Authors: Kim Won Tae , Yun Seok Joong , Yan Chunri , Jeong Pildu , Kim Ye Hwan , Lee Il-Seok , Park Sunghyouk , Moon Sung-Kwon , Choi Yung-Hyun , Choi Young Deuk , Kim Jayoung , Kim Wun-Jae 
Published: July 2016

Abstract
Our high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry study identified bladder cancer (BCA)-specific urine metabolites, including carnitine, acylcarnitines, and melatonin. The objective of the current study was to determine which metabolic pathways are perturbed in BCA based on our previously identified urinary metabolome. Significant alterations in the carnitine-acylcarnitine and tryptophan metabolic pathways were detected in urine specimens from BCA patients compared to those of healthy controls. The expression of eight genes involved in the carnitine-acylcarnitine metabolic pathway (CPT1A, CPT1B, CPT1C, CPT2, SLC25A20, and CRAT) or tryptophan metabolism (TPH1 and IDO1) was assessed by RT-PCR in our BCA cohort (n = 135). CPT1B, CPT1C, SLC25A20, CRAT, TPH1, and IOD1 were significantly downregulated in tumor tissues compared to adjacent normal bladder tissues (p &lt; 0.05 all) of patients with non-muscle invasive bladder cancer, whereas CPT1B, CPT1C, CRAT, and TPH1 were downregulated in those with muscle invasive bladder cancer (p &lt; 0.05), with no changes in IDO1 expression. In this study, alterations in the expression of genes associated with the carnitine-acylcarnitine and tryptophan metabolic pathways, the most perturbed pathways in BCA, were determined. Our findings provide insight into the mechanisms underlying BCA-associated metabolic flux perturbation.
Citation Format: Won Tae Kim, Seok Joong Yun, Chunri Yan, Pildu Jeong, Ye Hwan Kim, Il-Seok Lee, Sunghyouk Park, Sung-Kwon Moon, Yung-Hyun Choi, Young Deuk Choi, Jayoung Kim, Wun-Jae Kim. Metabolic pathways associated with urinary metabolite biomarkers differentiate bladder cancer patients from healthy controls. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3979.
Abstract 3990: FGFR3 mutations as novel oncogenic targets
Authors: Martinez Cardona Gabriela , Gaffney Dana , Bell Katherine , Portale Joseph , Dunworth Matthew , Lorenzi Matthew , Platero Suso , Karkera Jayaprakash 
Published: July 2016

Abstract
Fibroblast growth factors (FGFs) are a family of homologous secreted glycoproteins involved in signaling pathways responsible for embryonic development, cell proliferation, survival, and migration. FGF activity is mediated by four transmembrane fibroblast growth factor receptors (FGFRs) which are receptor tyrosine kinases. Typically, FGF binding induces FGFR dimerization, leading to phosphorylation of the intracellular tyrosine kinase domain. This leads to downstream activation of multiple signaling pathways, including the mitogen-activated protein kinase (MAPK), PI3K/AKT, signal transducer and activator of transcription (STAT), and phospholipase-C-γ cascades. Deregulated FGFR activity, through mutations or translocations, is often associated with oncogenic events. Aberrations in FGFR genes have been observed in several tumor types including bladder, gastric, colorectal, ovarian, and hematologic cancers. To date, several FGFR3 mutations have been identified in bladder cancer. In this study, we developed a TaqMan qRT-PCR-based approach to detect four FGFR3 mutations in formalin-fixed paraffin embedded tissue (FFPET) samples. Cell lines overexpressing FGFR3 mutations were generated to determine impact on cell signaling, and sensitivity to the small-molecule pan-FGFR inhibitor JNJ-42756493. To determine the role and significance of these FGFR3 mutations in cancer, mutation expression constructs were designed and individually transfected into normal rat kidney epithelial cells. Cells harboring the FGFR3 mutations exhibited anchorage-independent growth, increased proliferation, and showed increased sensitivity to the FGFR inhibitor JNJ-42756493 in vitro compared to parental lines. These findings underline the oncogenic potential of the FGFR3 mutation genes and highlight their unique potential as predictive biomarkers in the selection of patients for FGFR-targeted therapy.
Citation Format: Gabriela Martinez Cardona, Dana Gaffney, Katherine Bell, Joseph Portale, Matthew Dunworth, Matthew Lorenzi, Suso Platero, Jayaprakash Karkera. FGFR3 mutations as novel oncogenic targets. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3990.
Abstract 4004: Development of a successful combination therapy for hepatocellular cancer by targeting Treg and PD-1
Authors: Liu Dai , Li Guangfu , Cooper Timothy , Kimchi Eric , Qi Xiaoqiang , Li Ningfei , Rockey Don , Schell Todd , Staveley-O’Carroll Kevin 
Published: July 2016

Abstract
We have established a clinically relevant murine model to reveal tumor-induced immunotoerance in hepatocellular carcinoma (HCC). Critical factors are targeted to develop immune-based therapies for HCC control.
Intrasplenic (ISPL) inoculation of oncogenic hepatocytes and intraperitoneal (IP) injection of carbon tetrachloride (CCl4) are combined to induce progressive HCCs in fibrotic livers of immunocompetent mice. We characterize the features of this model, examine tumor-antigen-specific (TAS) immunity during tumor initiation and progression, and identify the critical factors in tumor-induced immune tolerance. The established murine model recapitulates human HCC and reflects its typical features. TAS CD8+ T cells initially maintain a naive phenotype and function in early-stage tumor-bearing mice, then become profound exhaustion with the tumor progression to the advanced stage. The deep immunosuppression is associated with the significant upregulation of Programmed cell death protein 1(PD-1), Cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) and the increase of Tregs. While the changes in Tregs and PD-1 are systemic, they are particularly pronounced in the tumor microenvironment. Sunitinib-mediated reduction of Treg together with antibody-mediated blockade of PD-1 synergistically suppress tumor growth and activate anti-tumor immunity.
Our data provide evidence that oncogenic hepatocytes escape immune surveillance during tumor initiation via immune ignorance, while later-stage established HCCs evade immune destruction via tumor-induced immunotolerance. Synergy of sunitinib and anti-PD-1 Ab generates favorable effect on suppressing tumor growth and activating anti-tumor immunity. This combinational strategy has high translational potential in HCC treatment.
Citation Format: Dai Liu, Guangfu Li, Timothy Cooper, Eric Kimchi, Xiaoqiang Qi, Ningfei Li, Don Rockey, Todd Schell, Kevin Staveley-O’Carroll. Development of a successful combination therapy for hepatocellular cancer by targeting Treg and PD-1. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4004.
Abstract 401: Preservation of cells in blood and culture
Authors: Browne Cecille , Lu Dan , Roth Daniela , Liberal Vasco 
Published: July 2016

Abstract
Introduction: Liquid biopsies and cell-based therapies are emerging approaches for the treatment of cancer. Accuracy of diagnosis using liquid biopsies and effectiveness of treatment using cell-based therapies will rely upon the preservation cells for both viability and the information contained in them.
Experimental procedures: Biomatrica's proprietary chemical library was used to develop formulations that could preserve cells in multiple formats. Cell preservation was assessed by a variety of cell-based and molecular techniques such as microscopy, flow cytometry and real-time PCR.
Results: Blood samples spiked with circulating tumor cells (CTCs) were preserved for several days at room temperature to allow for downstream morphological and transcriptomic analyses. CTC recoveries in preserved samples were as much as 4 times those in non-protected samples over 4 days. Changes in RNA expression of CTC-specific genes in preserved samples ranged from 0 to +/- 2 delta Ct values, while in non-protected samples, changes ranged from 0 to +/-5 delta Ct values over 4 days. In some formulations, CTC viabilities were as much as twice the viabilities of CTCs in non-protected samples. Supporting these viability results was a demonstrated culturability of isolated CTCs. Furthermore, cell-free DNA in plasma of preserved blood samples changed by less than 2 Ct values over 4 days, whereas in control samples, plasma DNA changed by as much as 10 Ct values. Hemolysis in preserved blood samples was also lower by as much as 69% compared to non-protected samples.
In a separate set of experiments, activated T-cells were stored in the presence of common buffers (RPMI, PBS) or formulations at room temperature. T-cells cultured with formulations displayed greater 40 to 60% greater cell viability after 3 days compared to those stored in common buffers.
Conclusions: Biomatrica has developed a library of cell preservatives that can be used to preserve cells in blood samples and in cell culture. The ability to recover cells in blood samples and determine their genetic information would enable monitoring of a patient's cancer status and personalizing drug treatments. In addition, cell preservation may allow further advances in cell-based therapies as cells could be more reliably recovered from patients, modified (e.g. CAR-T, stem cells), and administered to patients.
Citation Format: Cecille Browne, Dan Lu, Daniela Roth, Vasco Liberal. Preservation of cells in blood and culture. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 401.
Abstract 4015: Exposure of lymphatic endothelial cells to ionizing radiation increases the surface expression levels of integrin ligands
Authors: Rodriguez-Ruiz Maria E. , Garasa Saray , Rodriguez Inmaculada , Yanguas Alba , Teijeira Álvaro , Melero Ignacio , Rouzaut Ana 
Published: July 2016

Abstract
Radiotherapy has been proven an efficacious tool to combat cancer by directly destroying tumor cells. However, effects of radiotherapy have been also described that occur through the re-education of the immune tumor microenvironment, being leukocyte traffic regulation across the tumor vasculature of key importance.
Here, we address the effects that radiotherapy may be causing on the adhesive properties of the tumor lymphatic vasculature. To study this, we irradiated primary and immortalized human and murine lymphatic endothelial cells grown in vitro, and fresh tumor explants obtained from colon cancer patients. As a result, we observed dose- and time- dependent increases in the expression of the integrin counter-receptors ICAM-1 and VCAM on the surface of the tumor lymphatic endothelial cells. These effects are also observed in vivo on colon (MC38) and melanoma (B16) tumors transplanted into syngeneic mice and irradiated with a single dose of 20 Gy. These findings are consistent with increased ICAM-1 and VCAM expression levels on Lymphatic endothelial cells in tumor biopsies from cancer patients which were taken before and four weeks after fractionated radiotherapy, including head and neck, colon and oropharyngeal human carcinomas. While the TGFβ pathway was found to be involved in these effects, NF-κB inhibitors did not hamper ICAM-1 or VCAM induction.
In summary, these results show ICAM-1 and VCAM surface expression was enhanced on lymphatic vessels after radiotherapy and may explain differential leukocyte traffic following irradiation.
Citation Format: Maria E. Rodriguez-Ruiz, Saray Garasa, Inmaculada Rodriguez, Alba Yanguas, Álvaro Teijeira, Ignacio Melero, Ana Rouzaut. Exposure of lymphatic endothelial cells to ionizing radiation increases the surface expression levels of integrin ligands. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4015.
Abstract 402: Multiplex TaqMan assays for rare mutation analysis using digital PCR
Authors: Laig Marion -. , Chan Frances , Lac Le , Straub Ted , Varma Kamini , Keys David 
Published: July 2016

Abstract
Introduction
Detection of rare mutations for research purposes in tumor tissue and cell free DNA (cfDNA) allows for monitoring of tumor progression and regression. cfDNA isolated from plasma combined with a sensitive detection method like digital PCR is non-invasive and enables earlier detection compared to conventional imaging techniques.
Building on the TaqMan based Rare Mutation assay set for detection of rare mutations using digital PCR on the QuantStudio 3D Digital PCR System, we are now developing multiplex assays for simultaneous detection of several mutations. We selected relevant mutations in the EGFR and KRAS genes for our initial multiplex application: EGFR G719, EGFR exon 19 deletions, and KRAS G12/G13. These mutations may have implications for potential future targeted therapy.
Methods
Primers and probes of singleplex Rare Mutation Assays were reformulated to generate multiplex assays detecting the EGFR and KRAS mutations. All multiplex assays were tested on template composed of wild-type genomic DNA background mixed with mutant plasmid reflecting each of the mutations detected by the multiplex assays.
Summary
Initial experimental results were successful and showed excellent signal intensity and clear cluster separation when analyzed with the QuantStudio 3D AnalysisSuite™ Cloud Software. The EGFR G719 mutations (COSM6239, COSM6253, COSM6252) were detected using a 3plex assay, EGFR exon 19 deletions (COSM12383, COSM12422, COSM12678, COSM6223, COSM6254, COSM6255) were detected using a 6plex assay, and KRAS G12/G13 mutations (COSM516, COSM517, COSM518, COSM520, COSM521, COSM522, COSM527, COSM532) were detected using an 8plex.
Conclusion
Multiplexing assays for three relevant mutation loci proved feasible and presents an efficient way to assess the presence and the percentage of mutations at these loci.
Citation Format: Marion -. Laig, Frances Chan, Le Lac, Ted Straub, Kamini Varma, David Keys. Multiplex TaqMan assays for rare mutation analysis using digital PCR. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 402.
Abstract 4029: MEK pathway inhibition upregulates PD-L1 and MHC class I expression levels in head and neck squamous cell carcinoma
Authors: Kang Seong-Ho , Keam Bhumsuk , Kim Soyeon , Kim Miso , Ahn Yong-Oon , Kim Tae Min , Kim Dong-Wan , Heo Dae Seog 
Published: July 2016

Abstract
Background: Expression of programmed death-ligand 1 (PD-L1) and down-regulation of MHC class I are well known tumor immune evasion mechanisms. The purpose of this study is to investigate the regulation of PD-L1 and MHC class I expression in head and neck squamous cell carcinoma (HNSCC) cell lines by MEK inhibitor trametinib.
Methods: Six HNSCC cell lines (SNU-1041, SNU-1066, SNU-1076, PCI-13, Detroit 562, and FaDu) were used. Trametinib was purchased from Selleckchem. Growth inhibition of trametinib was measured using MTT assay. Trametinib was dosed at 10 - 640 nM for investigating their effect on PD-L1 and MHC class I molecule expression. Changes of PD-L1 and MHC class I (including HLA-A2) expression levels were analyzed by flow cytometry after treatment with trametinib (20 nM) and/or IFN-γ (1 - 10 ng/ml). Total and phosphorylated STAT1 and STAT3 were analyzed by western blot.
Results: Overall IC50 values of trametinib were over 10 μM in cell lines except SNU-1066 and Detroit 562 with IC50 values still higher than 100 nM. All the six cell lines have no upstream RAS or RAF mutation. Although trametinib treatment did not inhibit growth of these cells, it up-regulated MHC class I expression level in all cells. Furthermore, trametinib enhanced exogenous IFN-γ-induced MHC class I up-regulation in four out of six cell lines. Mechanistically, trametinib treatment increased phosphorylated STAT1 levels by IFN-γ in all cells, and subsequent total STAT1 levels in two out of six cell lines. Interestingly, trametinib treatment directly phosphorylated STAT3 although total STAT3 level was not changed. Either trametinib alone or with IFN-γ induce PD-L1 expression, but the effect was various in these cells. These results imply that blockade of MAPK pathway may alternatively activate JAK/STAT pathway in HNSCC cells, and MHC class I and PD-L1 expression levels were changed as the results
Conclusion: Our results suggest that MEK pathway is closely related with regulation of PD-L1 and MHC class I expression. Up-regulated levels of PD-L1 and MHC class I by inhibiting MEK pathway suggest a possible synergistic role of MEK inhibitor with anti-PD-1/PD-L1 immunotherapy in HNSCC.
Citation Format: Seong-Ho Kang, Bhumsuk Keam, Soyeon Kim, Miso Kim, Yong-Oon Ahn, Tae Min Kim, Dong-Wan Kim, Dae Seog Heo. MEK pathway inhibition upregulates PD-L1 and MHC class I expression levels in head and neck squamous cell carcinoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4029.
Abstract 4041: Glioma cells display a prognostically significant hematopoietic phenotype
Authors: Moncayo Gerald 
Published: July 2016

Abstract
Glioblastoma multiforme (GBM) is one of the most aggressive human cancers. Glioma cells expressed immunoreceptor tyrosine-based activation motif (ITAM) bearing molecules, such as Fc receptors, T cell receptor components and C-type lectins and expression was up regulated in two distinct tumor-derived prognostic signatures identified in GBM and low-grade gliomas. Targeting SYK, downstream of ITAM molecules, attenuated GBM tumor growth and invasiveness, and reduced B and CD11b+ cell mobility and infiltration resulting in improved survival. In addition, GBM tumor cells were found to display phagocytic characteristics in vitro and in vivo by flow cytometry and two photon imaging. Our data demonstrate that gliomas are hematopoietic-like tumors that express an immune signaling network important in glioma progression, and identify targets for therapeutic intervention.
Citation Format: Gerald Moncayo. Glioma cells display a prognostically significant hematopoietic phenotype. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4041.