bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 432: Establishment of reference samples for the detection of somatic variants in cancer
Authors: Fang Li Tai , Xiao Wenming ,   Somatic Mutation Working Group, SEQC2 Consortium
Published: August 2018

Abstract
The FDA is well aware of the crucial role that next generation sequencing (NGS) plays in precision medicine, and this technology is already leveraged in regulatory decision-making. However, lack of well-characterized and community-validated reference samples and data benchmarks creates a potential challenge for development and review of NGS applications.
To address this challenge, 60+ institutions and 160+ scientists have come together to form a somatic mutation working group within the FDA-led Sequencing Quality Control Phase II (SEQC2) consortium. We present genomic samples with high-confidence germline and somatic mutation data in order to establish a community standard against which new tools and platforms can be evaluated and benchmarked. Our initial reference samples are a triple-negative breast cancer cell line: HCC1395, and its B lymphocyte derived normal cell line: HCC1395BL. To minimize bias, we sequenced these two cell lines at up to 10 sequencing centers using multiple sequencing platforms. In totality, we have performed whole genome sequencing of the two cell lines to coverage depths of 2400X on Illumina HiSeq, 450X on NovaSeq, 600X on 10X Genomics and 50X on PacBio. Additionally, we performed whole exome sequencing at 1200X on HiSeq and 100X on Ion Torrent. Lastly, we sequenced (RNAseq) &gt;5000 single cells for cellular heterogeneity studies. We applied machine learning algorithms to define high confidence mutation calls with datasets from 8 NGS platforms combined with 9 bioinformatics analysis pipelines. Each mutation in the “gold standard” dataset was annotated with confidence scores and supporting evidence. To independently evaluate accuracy of our call set, we selected a subset of mutation calls for additional validation using orthogonal methods, including ddPCR.
To summarize, we present the first release of high-confidence germline variants and somatic mutations on a pair of well characterized cell lines. We plan to continuously advance accuracy and completeness of our reference sample data, in order to serve as a standard for the community for years to come.
Citation Format: Li Tai Fang, Wenming Xiao, Somatic Mutation Working Group, SEQC2 Consortium. Establishment of reference samples for the detection of somatic variants in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 432.
Abstract 4344: Low mitochondrial copy number induces resistance to chemotherapy in esophageal cancer
Authors: Yamada Moyuru , Tanaka Koji , Masuike Yasunori , Makino Tomoki , takahashi Tsuyoshi , Kurokawa Yukinori , Yamasaki Makoto , Nakajima Kiyokazu , Mori Masaki , Doki Yuichiro , Odagiri Kabuki 
Published: August 2018

Abstract
Introduction: Esophageal squamous cell carcinoma (ESCC) is the one of the deadliest gastrointestinal cancers. The important problem in treating ESCC is resistance to chemotherapy. A few previous reports showed that mitochondrial DNA (mtDNA) copy number was decreased in esophageal squamous cell carcinoma (ESCC). However, it is unclear whether alteration of mtDNA copy number affects the effect of chemotherapy for ESCC. In the present study, we investigated the relationship between mtDNA copy number and the effect of chemotherapy in ESCC.
Methods: To analyze the mtDNA copy number of surgically resected primary tumors from ESCC patients, qPCR for Cytochrome Oxidase I was performed. Human ESCC cells (TE8 and TE11) with decreased mtDNA copy number were established by knockdown of mitochondrial transcription factor A (TFAM). Those cells were treated with 5FU, cisplatin and docetaxel. The response of chemotherapy was accessed by cell viability assay (WST assay) and apoptosis assay (flow cytometry). To investigate the mechanism of resistance of chemotherapy, expression of EMT-related genes such as CDH1, CDH2, vimentin and zeb1 was measured by qPCR. Wound healing assay and invasion assay were performed to access the cell migration and invasion.
Results: Patients were categorized into higher and lower subgroups according to the median value of the mtDNA copy number. Lower mtDNA copy number group was significantly correlated with tumor depth and pathologic response of chemotherapy. ESCC patients with lower mtDNA copy number had significantly poorer 5-year recurrence-free and overall survival than higher group. By shRNA knockdown of TFAM gene expression, mtDNA copy number decreased to 40% in TE8 and 60% in TE11 compared with non-target control cells. Viability of mtDNA-depleted TE8 and TE11 treated with chemotherapy was higher than that of control cells. Apoptosis assay showed the percentages of apoptosis induced by chemotherapy in mtDNA-depleted TE8 and TE11 were lower than those of control cells. Invasion assay and wound healing migration assay showed that mtDNA-depleted TE8 and TE11 were significantly more invaded and migrated than the control-sh cells.
Conclusions: These results suggest that low mitochondrial copy number induces resistance to chemotherapy in esophageal cancer.
Citation Format: Moyuru Yamada, Koji Tanaka, Yasunori Masuike, Tomoki Makino, Tsuyoshi takahashi, Yukinori Kurokawa, Makoto Yamasaki, Kiyokazu Nakajima, Masaki Mori, Yuichiro Doki, Kabuki Odagiri. Low mitochondrial copy number induces resistance to chemotherapy in esophageal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4344.
Abstract 4413: DNA methylation of miR-7 is a mechanism involved in platinum response through MAFG overexpression in cancer cells
Authors: Vera Olga , Jimenez Julia , Rodriguez-Antolin Carlos , Pernia Olga , Rodriguez Carmen , Soto Javier , Rosas Rocio , Esteban-Rodriguez Isabel , Perona Rosario , Castro Javier de , Ibáñez-de-Cáceres Inmaculada 
Published: August 2018

Abstract
One of the major limitations associated with platinum use is the resistance that almost invariably develops in different tumor types. In the current study, we sought to identify epigenetically regulated microRNAs as novel biomarkers of platinum resistance in lung and ovarian cancers, the ones with highest ratios of associated chemo-resistance. Experimental procedures: We combined transcriptomic data from microRNA and mRNA under the influence of an epigenetic reactivation treatment in a panel of four paired cisplatin -sensitive and -resistant cell lines, followed by real-time expression and epigenetic validations for accurate candidate selection in 19 human cancer cell lines. To identify specific candidate genes under miRNA regulation, we assembled “in silico” miRNAs and mRNAs sequences by using ten different algorithms followed by qRT-PCR validation. Functional assays of site-directed mutagenesis and luciferase activity, miRNAs precursor overexpression, silencing by antago-miR and cell viability were performed to confirm their specificity in gene regulation. Results were further explored in 187 primary samples obtained from ovarian tumors and controls. Results: We identified 4 candidates, miR-7, miR-132, miR-335 and miR-148a, which deregulation seems to be a common event in the development of resistance to cisplatin in both tumor types. miR-7 presented specific methylation in resistant cell lines, and was associated with poorer prognosis in ovarian cancer patients. Our experimental results strongly support the direct regulation of MAFG through miR-7 and their involvement in the development of CDDP resistance in human tumor cells. Conclusion: The basal methylation status of miR-7 before treatment may be a potential clinical epigenetic biomarker, predictor of the chemotherapy outcome to CDDP in ovarian cancer patients. To the best of our knowledge, this is the first report linking the regulation of MAFG by miRNA-7 and its role in chemotherapy response to CDDP. Furthermore, this data highlights the possible role of MAFG as a novel therapeutic target for platinum resistant tumors.
Citation Format: Olga Vera, Julia Jimenez, Carlos Rodriguez-Antolin, Olga Pernia, Carmen Rodriguez, Javier Soto, Rocio Rosas, Isabel Esteban-Rodriguez, Rosario Perona, Javier de Castro, Inmaculada Ibáñez-de-Cáceres. DNA methylation of miR-7 is a mechanism involved in platinum response through MAFG overexpression in cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4413.
Abstract 4425: PARP1 inhibition impedes Warburg effect in breast cancer cells through modulation of the miR-98/STAT3 signaling axis
Authors: Shukla Nidhi 
Published: August 2018

Abstract
Cancer cells have increased metabolic autonomy and rewired cellular metabolism in order to meet the bioenergetics, biosynthetic, and redox demands during tumorigenesis. They tend to depend on glycolysis rather than oxidative metabolism to meet their energy demand. Therefore, elucidation of the key regulators of metabolism could potentially aid in devising selective and promising anti-cancer therapies. MicroRNAs (miRNAs) have recently attained prominence as key regulators of cancer cell metabolism. MiRNAs are known to regulate metabolism in cancer cells either through the direct regulation of key metabolic enzymes, tumor suppressors and oncogenes or the indirect modulation of master transcription factors and signalling pathways. Therefore dysregulation of cellular metabolism by miRNAs contributes significantly to cancer progression. Current therapeutic strategies include: (a) targeting metabolic pathways that are strictly required for cancer cells, or (b) impairing an oncogenic signalling axis involved in cancer metabolic rewiring. The poly (ADP-ribose) polymerase (PARP) inhibitors, used in the treatment of DNA repair deficient tumours are also known to facilitate oxidative metabolism. However, the effect of PARP inhibition on glycolytic metabolism is yet to be elucidated. In the present study we aimed to identify novel miRNAs involved in the regulation of glycolytic metabolism after PARP1 inhibition. MiRNA microarray analysis revealed upregulation of the tumor suppressor miR-98 in PARP1 inhibitor treated MDA-MB-231 breast cancer cells. Further mechanistic studies confirmed miR-98 regulation of STAT3 expression and downregulation of key glycolytic enzymes HK2 and PKM2 leading to decreased Warburg effect. MiR-98 overexpression or PARP1 inhibition in combination with miR-98 antagomir showed downregulation of STAT3, HK2 and PKM2. Glucose consumption and HK2 activity were decreased upon PARP1 inhibition associated miR-98 expression. Collectively, these results showed that miR-98 is a critical regulator of PARP1 inhibition associated reduction of Warburg effect in breast cancer cells.
Citation Format: Nidhi Shukla. PARP1 inhibition impedes Warburg effect in breast cancer cells through modulation of the miR-98/STAT3 signaling axis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4425.
Abstract 4548: Host immunogenetics and hyperprogression under PD1/PD-L1 checkpoint inhibitors
Authors: Refae Sadal , Ebran Nathalie , Gal Jocelyn , Otto Josiane , Giacchero Damien , Borchiellini Delphine , Guigay Joel , Peyrade Frederique , Milano Gerard , Saada Esma 
Published: August 2018

Abstract
Background: Hyperprogressive disease (HPD) has been described in advanced solid tumors patients treated with anti PD1 anti PDL1 monotherapy (Champiat, Clin Can Res 2016; Saada-Bouzid, Ann Oncol, 2017). Our aim was to explore whether host constitutional variations in the nucleotide sequence of genes involved in immune response might be associated with the occurrence of HPD in patients treated with anti PD-(L)1.
Methods : From April to August 2017, 98 patients were treated in the Centre Antoine Lacassagne (Nice, France) with anti PD-(L)1. Potential SNPs for four candidate genes with a minor allele frequency≥ 5% in caucasians were selected according to genome browser data-base: PD1 (rs10204525, rs11568821, rs2227981), PD-L1 (rs2282055, rs2297136, rs2297137, rs4143815, rs10815225), IDO1 (rs3739319, rs3808606, rs373931, rs9657182) and VEGR2 (rs2305948, rs1870377, rs2071559). High through-output genotyping was done by MassARRAY (AGENA). HPD was defined as a TGKR (ratio of the slope of tumor growth before treatment and the slope of tumor growth on treatment) ≥ 2.
Results: Patients were treated for head and neck squamous cell carcinoma (16/98), non-small cell lung cancer (48/98), melanoma (13/98), renal cell carcinoma (14/98) and 7 others. Median age was 66 years old, 33 were male. All tested SNPs were in Hardy-Weinberg equilibrium. Responses were associated with G3-G4 toxicities (10% vs 42%, p=0.001). TGKR was assessable in 80 patients. HPD was observed in 11/80 (14 %) patients. HPD was significantly associated with age≥70y (6% vs 25%, p=0.02) and genotype for PD1 rs 2227981 (8/32=35% G/G vs 2/43=5% A/G or A/A, p=0.02), PDL1 rs 2282055 (1/37=3% T/T vs 10/43=23% T/G or G/G,p=0.02) and VEGFR2 rs1870377 (2/48=5% T/T vs 9/32=28% T/A or A/A, p=0.005). Multivariate analysis confirmed the association between HPD and VEGFR2 rs1870377 T/A or A/A (OR=15.3, p=0.007), PDL1 rs 2282055 T/G or G/G (OR=18.7, p=0.01) and age≥70y (OR=14.4, p=0.006).). Combining the three alleles at risk for HPD gave an OR =12.4 (p=0.001).
Conclusion: In patients treated with anti PD-(L)1, HPD was independently associated with older age and host related gene variations. Host related immunogenetics could become an integrative part of predictive factor for immunotherapy outcome.
Citation Format: Sadal Refae, Nathalie Ebran, Jocelyn Gal, Josiane Otto, Damien Giacchero, Delphine Borchiellini, Joel Guigay, Frederique Peyrade, Gerard Milano, Esma Saada. Host immunogenetics and hyperprogression under PD1/PD-L1 checkpoint inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4548.
Abstract 4598: A comprehensive assessment of the impact of preanalytical variables on cell free DNA and circulating tumor cells in blood
Authors: Pottekat Anita , Allawi Hatim T. , Boragine Genna T. , Kaiser Michael W. , Sander Tamara , Krueger Chateen , Bruinsma Janelle J. , Murray Amber N. 
Published: August 2018

Abstract
Liquid biopsy continues to gain traction as a minimally invasive method to monitor biomarkers associated with malignancy and metastasis. A simple blood draw can reveal key biomarkers such as circulating tumor cells (CTCs) and cell-free DNA (cfDNA). However, these analytes are present in low quantities and are prone to rapid degradation and contamination, which presents challenges for the detection of rare CTCs and cfDNA targets. Higher molecular weight genomic DNA from poorly stabilized leukocytes can contaminate plasma, compromising liquid biopsy assay results by increasing the total amount of extracted DNA while diluting rare cfDNA targets. Preservation of CTCs and cfDNA over time is thus essential for the accuracy of downstream tests, and preanalytical variables that impact plasma volume, cfDNA yield and quality, and cell recovery in ex vivo blood must be understood. Here, we identified several preanalytical variables, including type of blood collection tube, storage time and conditions post-phlebotomy, and centrifugation conditions for plasma fractionation. We then carried out a series of studies to better understand the interplay between these preanalytical variables and plasma recovery, cell recovery, and cfDNA preservation in healthy donor blood, contrived samples, and patient samples. We found that choice of blood collection tube, in particular, has a significant impact on preservation of plasma volume, CTCs, cfDNA over time, particularly under real-world stress conditions including temperature excursions, sample shipping, and storage time post-draw. The work presented here demonstrates the importance of assessing preanalytical variables for the preservation of cancer biomarkers in whole blood without compromising sample integrity. This will ultimately help researchers make informed decisions on how best to stabilize their analytes of interest without introducing un-intended variables due to blood tube selection, shipping and storage conditions, and plasma isolation conditions.
Citation Format: Anita Pottekat, Hatim T. Allawi, Genna T. Boragine, Michael W. Kaiser, Tamara Sander, Chateen Krueger, Janelle J. Bruinsma, Amber N. Murray. A comprehensive assessment of the impact of preanalytical variables on cell free DNA and circulating tumor cells in blood [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4598.
Abstract 462: Hyperactivation of ERK/MAPK pathway reduces pancreatic cancer cells' proliferation and tumor progression through phosphoproteome reprogramming
Authors: Rowell Marie-Camille , Deschênes-Simard Xavier , Calvé Benjamin Le , Lopes-Paciência Stéphane , Ruiz Ana Fernandez , Kottakis Filippos , Bardeesy Nabeel , Ferbeyre Gerardo 
Published: August 2018

Abstract
This study aims to better understand the loss of tumor -uppression functions of ERK in pancreatic cancer progression. Pancreatic cancer is the 4th leading cause of death by cancer in Canada and USA with a 5-year survival rate below 7%. We have identified a high level of phosphorylation of the MAP kinase ERK in benign pancreatic intraepithelial neoplasms (PanIN), followed by a reduction in phospho-ERK levels in pancreatic ductal adenocarcinoma (PDAC) both in human patient samples and KRas-driven mouse models for pancreatic cancer. Since PanINs are considered senescent lesions, we hypothesized that phospho-ERK levels were reduced in PDAC to bypass oncogene-induced senescence and allow tumor initiation. We propose that reactivating high ERK in PDAC could restore tumor-suppression mechanisms lost during progression. To do so, we use a tamoxifen-inducible constitutive allele of RAF1 kinase, which acts upstream of ERK (ΔRAF1-ERT). In human (PANC-1, KP-4) and murine PDAC cell lines, activated RAF1 slows cell proliferation and induces cellular senescence in vitro in an ERK-dependent and p53/p16-independent manner. Activation of ERK kinases by this system in subcutaneous PDAC xenografts slows tumor growth in nude mice. To characterize key mediators of ERK-dependent tumor suppression, we did phosphoproteomics by mass spectrometry and identified a reprogramming of nuclear vs. cytoplasmic phosphoproteome, involving key ribosome biogenesis factors. Depletion of these nucleolar targets by shRNAs and nucleolar stress inducers such as RNA polymerase I inhibitor CX-5461 recapitulates ERK-dependent tumor suppression. At the same time, we are also investigating autophagy-related processes involved in RAF/MEK signaling blockade in PDAC cells. In summary, we suggest that high levels of p-ERK1/2 in early PanIN stage act as a tumor-suppressor mechanism, which is lost with cancer progression. Our future work aims to better understand the mechanism by which high ERK signaling exerts tumor suppression in order to find downstream effectors that could be used as therapeutic targets in pancreatic cancer.
Citation Format: Marie-Camille Rowell, Xavier Deschênes-Simard, Benjamin Le Calvé, Stéphane Lopes-Paciência, Ana Fernandez Ruiz, Filippos Kottakis, Nabeel Bardeesy, Gerardo Ferbeyre. Hyperactivation of ERK/MAPK pathway reduces pancreatic cancer cells' proliferation and tumor progression through phosphoproteome reprogramming [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 462.
Abstract 4637: Tumor treating fields (TTFields) have antiproliferative effects on high-grade pediatric brain tumor cell lines
Authors: Branter Joshua , Estevez-Cebrero Maria , Grundy Richard , Basu Surajit , Smith Stuart 
Published: August 2018

Abstract
Introduction Approximately 400 children in the UK are diagnosed with a CNS tumor each year, which represents a quarter of childhood cancer cases in the UK. The 5-year survival rate of paediatric brain tumor patients is approximately 75%, but survival remains much worse for some brain tumor patients, particularly high-grade gliomas. Pre-clinical and clinical studies have demonstrated efficacy of TTFields as a treatment for high-grade glioma leading to the approval of TTFields for adult Glioblastoma multiforme (GBM) patients. The lack of overlapping toxicities associated with TTFields has made electric field therapy an attractive treatment strategy for poor prognosis paediatric brain tumors.Methods The inovitro is the laboratory based testing system used to deliver TTFields to cell cultures. inovitro was used to deliver TTFields over 72 hours at a range of clinically relevant frequencies (100-400kHz) to our panel of paediatric GBM, Medulloblastoma and Ependymoma cell lines. The effects of TTFields on cell viability and cell cycle was assessed using Resazurin based metabolic viability tests and flow cytometry. The determined optimal frequency for each cell line was also combined with a mitotic inhibitor to explore synergistic effects. Gene expression changes of TTFields treated cells was investigated. Results TTFields treatment reduces cell viability of all cell lines tested within the frequency panel. The optimum frequencies were between 100 and 400kHz for all cell lines tested. TTFields treatment had effects on cell cycling with increased G2 accumulation of treated cells being observed. Combining TTFields with mitotic inhibitors increased efficacy in an additive fashion. Conclusions This preliminary study has demonstrated efficacy of TTFields on paediatric brain tumor cell lines. The optimal frequencies for all the paediatric GBM cell lines used did not match the 200kHz as previously reported for U-87 MG cells. This report warrants further study into the potential for TTFields therapy for paediatric brain tumor patients.
Citation Format: Joshua Branter, Maria Estevez-Cebrero, Richard Grundy, Surajit Basu, Stuart Smith. Tumor treating fields (TTFields) have antiproliferative effects on high-grade pediatric brain tumor cell lines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4637.