bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2482: A portable bioinformatics pipeline for the FDA authorized IMPACT DNAseq assay
Authors: Tang Zuojian , Kumar Nikhil , Bolipata Allan , Song Timothy , Kandoth Cyriac , Liu Feng , Mcmanamon David , Hampton Oliver , Socci Nicholas , Solit David 
Published: August 2019

Abstract
On November 2017, the US Food and Drug Administration (FDA) authorized Memorial Sloan Kettering Cancer Center's (MSKCC) IMPACT (Integrated Mutation Profiling of Actionable Cancer Targets) tumor profiling assay and bioinformatics pipeline for clinical decisions in treating all solid tumors. The IMPACT test uses next-generation sequencing (NGS) to identify the presence of mutations in 468 unique genes, fusions at known sites, copy-number alterations, and microsatellite instability (MSI). A version freeze of the bioinformatics pipeline was made public in May 2017 in Zehir et al. "Mutational Landscape of Metastatic Cancer Revealed from Prospective Clinical Sequencing of 10,000 Patients", Nat Med. 23(6): 703-713. Active development of the pipeline has continued in its CLIA-compliant computing environment, and the resulting improvements have been incorporated into an open-source portable research-grade bioinformatics pipeline. Here, we present results from Roslin, our research bioinformatics pipeline built to be functionally equivalent to the IMPACT clinical reporting workflow that includes manual filtering/annotation and signout by molecular oncologists. Roslin can be installed and executed on laptops, workstations, local compute clusters, or cloud compute servers. As a research-grade pipeline it is flexible enough to handle new assays including exomes/genomes, and extensible enough to add or replace components like reference genomes, sequence aligners, variant callers, false-positive filters, and functional/clinical annotation. Tracking all components and parameters used in each pipeline run allows researchers to easily generate method sections for manuscripts that are sufficiently detailed for peer-review and reproducibility of published results. Roslin has been deployed and tested on multiple high-performance clusters and cloud computing resources. It offers end users GUI driven workflow logging, run reporting, and real-time tracking (https://github.com/mskcc/roslin). Evaluated on NGS data from 128 tumors with signed out IMPACT clinical reports, Roslin achieves a recall rate of 98% for both somatic substitutions and indels, and 60% for fusions. Precision was 96% for substitutions, and 86% for indels. We present our work in maximizing precision and recall rates while retaining the portability, modularity, and reproducibility of Roslin.
Citation Format: Zuojian Tang, Nikhil Kumar, Allan Bolipata, Timothy Song, Cyriac Kandoth, Feng Liu, David Mcmanamon, Oliver Hampton, Nicholas Socci, David Solit. A portable bioinformatics pipeline for the FDA authorized IMPACT DNAseq assay [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2482.
Abstract 2495: Glucosamine enhances TRAIL-induces apoptosis in DU145 and Hela cancer cell lines
Authors: Sun Chao , Chesnokov Viktor , Itakura Keiichi 
Published: August 2019

Abstract
Tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) has attracted wide attention and extensive research because of selective apoptosis of tumor cells but not of normal cells. However, the clinical trials using TRAIL alone were disappointed due to the resistance of cancer cells to the TRAIL-treatment. Several resistant mechanisms, such as low expression of death receptors, and overexpression of cFLIP, BCL-2 antiapoptotic family members and XIAP were proposed. Tunicamycin was reported to enhance the expression of death receptor 5 through the activation of CHOP. Similar to tunicamycin, glucosamine is known to increase the expression of CHOP by inducing ER stress. We thus investigated whether glucosamine could increase the expression of death receptor 5 to overcome TRAIL-resistance. We found that glucosamine treatment of DU145 cells did not increase the expression of death receptor 5 on the cell surface, even though the overall expression was increased. However, glucosamine significantly increased TRAIL-induced apoptosis in DU145 and Hela cells. Our investigation revealed that glucosamine sensitized cancer cells to TRAIL-induced apoptosis through both intrinsic and extrinsic apoptosis pathways, as evidenced by the cleavage of both caspase 9 and caspase 8. Our data further showed that the combination of TRAIL with glucosamine suppressed the expression of cFLIP, BCL-2 and XIAP, translocated BAK to the mitochondrial outer membrane, and released cytochrome C and SMAC from mitochondrial. Interestingly, in addition to the activation of apoptotic pathways, TRAIL-mediated inflammatory responses were attenuated by glucosamine treatment. Pretreatment of glucosamine reduced the TRAIL-induced nuclear NF-kB level and the expression of IL-6 and IL-8. Together, these results demonstrated that the combination treatment, TRAIL with glucosamine, may provide a promising novel strategy for treating different human cancers by overcoming TRAIL-resistance and inhibiting TRAIL-induced inflammation.
Citation Format: Chao Sun, Viktor Chesnokov, Keiichi Itakura. Glucosamine enhances TRAIL-induces apoptosis in DU145 and Hela cancer cell lines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2495.
Abstract 25: Identifying new inhibitors of ABCG2 by high-throughput screening
Authors: Kokubo Shoji , Ohnuma Shinobu , Karasawa Hideaki , Yamamura Akihiro , Suzuki Hideyuki , Murakami Megumi , Sugisawa Norihiko , Kanehara Keigo , Sato Keisuke , Ishida Takanori , Kamei Takashi , Naitoh Takeshi , Unno Michiaki 
Published: August 2019

Abstract
Background: ABCG2, also known as breast cancer resistance protein (BCRP), is a member of the ATP-binding cassette (ABC)-family of membrane transport proteins associated with multidrug resistance (MDR). No ABCG2 inhibitor has shown clinical significance yet.
Aim: To identify novel inhibitors of ABCG2 by high-throughput screening.
Material & Methods: After higher expression of ABCG2 in HCT-116/BCRP cells was confirmed by flow cytometry (FACSVerse) using 5D3 antibody, high-throughput fluorescent cell-based assay was performed with the original chemical library of Tohoku University containing about 6000 compounds using ABCG2-specific fluorescent substrate, Pheophorbide a (PhA) in HCT-116/BCRP cells overexpressing ABCG2. Ko143, a potent ABCG2 inhibitor, was used as positive control. Fluorescence intensity in the cells was read by a fluorescence plate reader (SpectraMax M2e) in bottom read mode, with 395 nm excitation, 670 nm emission. To validate the results, flow cytometry assay was performed with 10 µM PhA in HCT-116/BCRP cells. The fluorescence intensity was analyzed by flow cytometry (FACSVerse).
Results: Fluorescenct cell-based assay with high-throughput screening could detect 23 candidate compounds, which showed higher fluorescence intensity as positive control Ko143 showed. Then, these 23 compounds were validated with flow cytometry assays. The flow cytometry assays revealed that 16 compounds increased fluorescence intensity of PhA in HCT-116/BCRP cells in dose dependent manner, suggesting that these candidate compounds inhibited transport function of ABCG2. Among 16 compounds, 6 compounds showed further inhibitory effect for transport function of ABCG2 as equivalent to that of Ko143.
Conclusion: These 6 compounds may provide a basis for further investigation of ABCG2 function.
Citation Format: Shoji Kokubo, Shinobu Ohnuma, Hideaki Karasawa, Akihiro Yamamura, Hideyuki Suzuki, Megumi Murakami, Norihiko Sugisawa, Keigo Kanehara, Keisuke Sato, Takanori Ishida, Takashi Kamei, Takeshi Naitoh, Michiaki Unno. Identifying new inhibitors of ABCG2 by high-throughput screening [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 25.
Abstract 2536: O-GlcNAcylation of Ewing sarcoma EWSR1/FLI1 protein impairs relocation of Aurora B to the midzone during mitosis
Authors: Azuma Mizuki 
Published: August 2019

Abstract
Ewing sarcoma is a pediatric bone cancer expressing chimeric EWSR1/FLI1 protein derived from a t(22;11)(q24;12) translocation. Our previous study demonstrated that EWSR1/FLI1 impairs the relocation of Aurora B kinase from the centromere to the midzone during the metaphase-anaphase transition (referred to as “Aurora B-relocation”). Aurora B-relocation to the midzone is essential for faithful cell division, whereas compromising this process will lead to formation of a binucleated cell or chromosomal mis-segregation. This cellular activity might play a role in the pathogenesis of Ewing sarcoma; however, how EWSR1/FLI1 impairs Aurora B-relocation remains unclear. In the present study, we tested the hypothesis that O-GlcNAcylation of EWSR1/FLI1 impairs Aurora B-relocation. The results showed that the increase in cellular O-GlcNAc levels in Ewing sarcoma A673 cells induced by treatment with the O-GlcNAcase inhibitor Thiamet-G (TMG) increased the level of aberrant Aurora B-relocation, and the O-GlcNAcylation level of endogenously expressed EWSR1/FLI1. To map the amino acid(s) required for O-GlcNAcylation of EWSR1/FLI1, HeLa cells were used because they do not express EWSR1/FLI1 endogenously. Among the putative point mutant constructs of EWSR1/FLI1, the substitution of Thr79 of EWSR1/FLI1 by Asp (phosphor mimic mutant) significantly reduced the O-GlcNAcylation level of EWSR1/FLI1, suggesting that Thr79 is the site of O-GlcNAcylation. Finally, the EWSR1/FLI1-T79D and EWSR1/FLI1-T79A mutant constructs failed to induce aberrant Aurora B-relocation in HeLa and A673 cells. Therefore, we propose that O-GlcNAcylated EWSR1/FLI1-T79 is required for the induction of aberrant Aurora B-relocation. In addition, EWSR1/FLI1-dependent disruption of Aurora B-relocation leads to defects in chromosome instability (CIN). Here, we demonstrate a unique role of EWSR1/FLI1 that may be a part of the pathogenesis of Ewing sarcoma.
Citation Format: Mizuki Azuma. O-GlcNAcylation of Ewing sarcoma EWSR1/FLI1 protein impairs relocation of Aurora B to the midzone during mitosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2536.
Abstract 2543: Cyclin-dependent kinase 1(CDK1)-mediated phosphorylation of SET in mitosis inhibits its oncogenic activity
Authors: Yin Ling , Zeng Yongji , Dong Jixin 
Published: August 2019

Abstract
SET is a protein phosphatase 2A (PP2A) inhibitor and functions as an oncogene in multiple human cancer types. Here we revealed a novel phosphorylation site of SET in mitosis and its biological significance in tumorigenesis. We found that the mitotic kinase cyclin-dependent kinase 1 (CDK1) phosphorylates SET in vitroand in vivo at serine 7 during antimitotic drug-induced G2/M phase arrest and in normal mitosis. SET deletion resulted in massive mitotic defects including centrosome amplification, multipolar spindles, and chromosome missregregation. Moreover, we revealed that SET mitotic phosphorylation is required for proper mitotic progression and its oncogenic function in vitro and in xenograft animal models. Furthermore, we found STAT3 and p53 signaling are regulated by SET. Collectively, our findings suggest a novel layer of regulation for SET in mitosis and its role in tumorigenesis. (This is supported by Fred and Pamela Buffett Cancer Center Support Grant P30 CA036727)
Citation Format: Ling Yin, Yongji Zeng, Jixin Dong. Cyclin-dependent kinase 1(CDK1)-mediated phosphorylation of SET in mitosis inhibits its oncogenic activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2543.
Abstract 2549: Allostatic conditions in human glioblastoma stem cells are maintained with the contribution of CLIC1 membrane protein functional expression
Authors: Verduci Ivan , Carlini Valentina , Barbieri Federica , Daga Antonio , Florio Tullio , Mazzanti Michele 
Published: August 2019

Abstract
Allostasis is a cellular condition physiologically occurring during transient hyper-activated state of the cell. When stress is persistent, cells are unable to restore a basal homeostatic state and allostasis become chronic. Most of the cells are not able to cope with these prolonged conditions and die. Conversely, solid tumors reveal a persistent stress state strengthen by chronic overexpression of several elements and hyper-activation of intracellular pathways. In glioblastoma stem cells (GSCs), the most evident allostatic outcome is a high rate of cell division. Several proteins present in the allostatic GSC plasma membrane are deregulated in either expression or function. Altering any of these proteins disrupts the allostatic equilibrium, causing drastic functional changes and, in some cases, cell death. Several of these proteins, potentially used as valuable pharmacological targets, are also crucial for the physiological activity of the cells. Consequently, modifying their functions would affect the survival of both cancer and healthy cell population. On the contrary, chloride intracellular protein 1 (CLIC1) is active as a membrane charge carrier only during periods of chronic stress, while during homeostatic conditions it is essentially irrelevant. Inhibition of NADPH oxidase or the NHE1 proton pump, both overexpressed in CSCs, causes death of both GSCs and normal mesenchymal stem cells. Conversely, impairing CLIC1 activity delays GSC cycle progression but leaves healthy cells functions unaltered. Our work suggests that CLIC1 protein and its associated chloride permeability are a crucial element involved in the stabilization of GB CSC allostasis. (This work is supported by a GRANT from AIRC to MM)
Citation Format: Ivan Verduci, Valentina Carlini, Federica Barbieri, Antonio Daga, Tullio Florio, Michele Mazzanti. Allostatic conditions in human glioblastoma stem cells are maintained with the contribution of CLIC1 membrane protein functional expression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2549.
Abstract 2555: Modulation of protein interaction states in the cell cycle and during cancer drug action
Authors: Nordlund Pär 
Published: August 2019

Abstract
The cellular thermal shift assay (CETSA) is a biophysical technique allowing direct studies of ligand binding to proteins in cells and tissues. The proteome-wide implementation of CETSA with mass spectrometry detection (MS-CETSA) is an efficient method to discover targets for orphan clinical drugs and hits from phenotypic screens, as well as to identify off-targets, explain poly-pharmacology and toxicity. Recently implemented highly sensitive multidimensional MS-CETSA techniques can now also access binding of physiological ligands to proteins, such as metabolites, nucleic acids and other proteins. MS-CETSA can thereby provide comprehensive information on modulations of protein interaction states in cellular processes, including downstream effects of drugs and transitions between different physiological cell states (Dai, Cell 2018, Tan, Science 2018). Such horizontal information on ligand modulation in cells is largely orthogonal to vertical information on the levels of different proteins, and therefore opens novel opportunities to understand operational aspects of cellular proteomes in more detail. We will discuss recent application of MS-CETSA to understand the cell cycle as well as cancer drug action and resistance.
References:
- Modulation of Protein-Interaction States through the Cell Cycle. Dai L, Zhao T, Bisteau X, Sun W, Prabhu N, Lim YT, Sobota RM, Kaldis P, Nordlund P. Cell. 2018 173(6):1481-1494.
- Thermal proximity coaggregation for system-wide profiling of protein complex dynamics in cells. Tan CSH, Go KD, Bisteau X, Dai L, Yong CH, Prabhu N, Ozturk MB, Lim YT, Sreekumar L, Lengqvist J, Tergaonkar V, Kaldis P, Sobota RM, Nordlund P. Science. 2018 359(6380):1170-1177.
Citation Format: Pär Nordlund. Modulation of protein interaction states in the cell cycle and during cancer drug action [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2555.
Abstract 2557: X-ray repair cross complementing 1 (XRCC1) is a critical factor in response to DNA damaging agents in triple negative breast cancer
Authors: Lee Kevin J. , Andrews Joel , Gassman Natalie R. 
Published: August 2019

Abstract
Triple negative breast cancer (TNBC) is a breast cancer subtype that is characterized by the lack of expression of estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2). The lack of these targetable molecules makes cytotoxic chemotherapies a first-line choice, thus there is a pressing need to better understand how TNBC will respond to alternative or emerging treatments. Base excision repair (BER) proteins play an essential role in DNA damage response and repair, yet they have been overlooked in the analysis of chemotherapeutic treatment response. XRCC1 is a critical scaffold protein that mediates the protein-protein and protein-DNA interactions involved in BER and single-strand break repair. Several studies have linked single nucleotide polymorphisms (SNPs) within XRCC1 to increases in breast cancer incidence, yet XRCC1’s role in modulating treatment response is unknown. Here we show XRCC1 expression in a panel of TNBC cell lines correlates to an increase in basal DNA damage levels. DNA damage was analyzed using the Repair Assisted Damage Detection (RADD) assay which measures the broadest spectrum of DNA damage in vitro. We show MDA-MB-157 with low levels of XRCC1 correlate to low levels of basal DNA damage, MDA-MB-231 and HCC1806 have moderate levels of XRCC1 and DNA damage, and MDA-MB-468 contain high expression levels of XRCC1 that correlate with high levels of DNA damage. XRCC1 localization is also variable across the panel of TNBC cell lines with XRCC1 being mislocalized to the cytoplasm in the HCC1806 cells and highly localized to the nuclear compartment in the MDA-MB-468. These expression and localization changes in XRCC1 alter the ability of cells to repair single strand break (SSB) lesions induced by 355 nM laser microirradiation and DNA damaging chemicals. Here we show that TNBC cell lines respond differently to alkylating damage (methyl methanesulfonate) and PARP inhibition (olaparib) based on XRCC1 expression and localization in combination with levels of basal DNA damage. Taken together it is important to consider XRCC1 in context with DNA damage levels and expression of other BER proteins in TNBC in order to effectively design experiments utilizing DNA damaging agents or chemotherapeutics targeting DNA repair pathways.
Citation Format: Kevin J. Lee, Joel Andrews, Natalie R. Gassman. X-ray repair cross complementing 1 (XRCC1) is a critical factor in response to DNA damaging agents in triple negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2557.
Abstract 2561: DNA-PKCS deacetylation by SIRT2 promotes DNA double-strand break repair by non-homologous end joining
Authors: Head PamelaSara E. , Ganji Nagaraju P. , Wang Shi-Ya , Duong Duc , Zhang Hui , Daddacha Waaqo , Li Shuyi , Seyfried Nicholas T. , Smalley David M. , Wang Ya , Deng Xingming , Dynan William S. , El-Rayes Bassel , Davis Anthony J. , Yu David S. 
Published: August 2019

Abstract
DNA-dependent protein kinase (DNA-PK) plays a critical role in non-homologous end joining (NHEJ), the predominant pathway that repairs DNA double-strand breaks (DSB) in response to ionizing radiation (IR) to govern genome integrity. How DNA-PK is activated in response to DSBs has remained elusive. Here, we show that the SIRT2 sirtuin deacetylase and tumor suppressor directs the activation of DNA-PK through deacetylation of its catalytic subunit (DNA-PKcs). SIRT2 deacetylase activity governs cellular resistance to DSB-inducing agents and promotes NHEJ. SIRT2 furthermore interacts with and deacetylates DNA-PKcs in response to IR, which facilitates its interaction with Ku and recruitment to DSBs, thereby leading to DNA-PKcs autophosphorylation and DNA-PK signaling to downstream NHEJ substrates. Moreover, SIRT2 inhibitor sensitizes resistant cancer cells and tumors to IR. Our findings define a mechanism for DNA-PK activation by SIRT2-mediated deacetylation, elucidating a critical upstream signaling event initiating the repair of DSBs by NHEJ to promote genome integrity and govern IR resistance, which can be exploited for improvements in cancer therapy.
Citation Format: PamelaSara E. Head, Nagaraju P. Ganji, Shi-Ya Wang, Duc Duong, Hui Zhang, Waaqo Daddacha, Shuyi Li, Nicholas T. Seyfried, David M. Smalley, Ya Wang, Xingming Deng, William S. Dynan, Bassel El-Rayes, Anthony J. Davis, David S. Yu. DNA-PKCS deacetylation by SIRT2 promotes DNA double-strand break repair by non-homologous end joining [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2561.