bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4487: A critical role of PARylation in regulating the functions of OVOL2
Authors: Zhang Rui , Li Boan , Liou Yih-Cherng 
Published: July 2017

Abstract
Poly(ADP-ribosyl)ation (PARylation) is one of the post-translational modifications, by which the ADP-ribose (PAR) polymers are added to the specific protein by a PAR polymerase (PARP). In the about 50 years' studies, this specific modification has been verified to be related to multiple important biological functions including cell death, cell differentiation, histone modification, transcriptional regulation, DNA repair and genome stability. Ovo-like 2 (OVOL2), a novel zinc finger transcriptional factor, contains a Snail/Gli (SNAG) motif at the N-terminal to possess a transcriptional regulatory activity and four DNA-binding Cys2-His2 (C2H2) zinc finger domains at the C-terminal to bind with DNA. OVOL2 is demonstrated to be involved in the cranial neural tube, angiogenesis, heart and placental development. In addition, OVOL2 can also suppress cell cycle and terminate differentiation of keratinocyte by directly inhibiting of c-Myc and Notch1. However, the regulation and biological function of OVOL2 are still largely unknown. In this study, we identify the binding targets, PARP1 and NPM1, of OVOL2. In addition, we report that the function of OVOL2 is regulated by PARP1 through PARylation, which modifies on C2H2 zinc finger domains and plays an important role in the regulation of OVOL2 functions. PARylated OVOL2, but not the 3K mutant, alters focal adhesion and cell cycle, resulting in the formation of polyploidy in cells. Our findings not only have significant implications for the cellular functions of OVOL2, but also provide a better understanding on the multiple biological functions of the PARylation.
Citation Format: Rui Zhang, Boan Li, Yih-Cherng Liou. A critical role of PARylation in regulating the functions of OVOL2 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4487. doi:10.1158/1538-7445.AM2017-4487
Abstract 449: Reduced argininosuccinate synthetase expression in refractory sarcomas: impacts on therapeutic potential and drug resistance
Authors: Kobayashi Eisuke , Kim Youngji , Kubota Daisuke , Suehara Yoshiyuki , Kawai Akira , Kitano Shigehisa 
Published: July 2017

Abstract
Introduction: Treating drug-resistant sarcomas remain a major challenge. The present study aimed to identify a novel therapy for drug-resistant sarcomas based on a metabolic errors involving argininosuccinate synthetase1 (ASS1).
Methods: We assessed the expression of ASS1 and P-glycoprotein (P-gp) in osteosarcoma (KHOS), doxorubicin (Dox)-resistant osteosarcoma (KHOSR2), epithelioid sarcomas (ES-X and VAESBJ), alveolar soft part sarcoma (ASPS-KY), and each clinical specimen. Each cell was cultured in arginine-containing and arginine-free media. Cell growth was assessed using an XTT assay and flow cytometry. We analyzed the induction of autophagy in arginine-free medium. Moreover, we assessed the expression of P-gp in after suppressing ASS1 in Dox-sensitive cells (MCF-7, KHOS) and in after transfecting the ASS1 into Dox-resistant cells (ES-X, VAESBJ, ASPS-KY and KHOSR2).
Results: The expression of ASS1 was reduced in Dox-resistant sarcoma cells. Immunohistochemistry (IHC) and real-time PCR showed that there was interestingly an inverse relationship between the expression of ASS1 and the expression of P-gp. The inhibition of cellular proliferation with G1-arrest was shown to lead to autophagy with arginine deprivation. In addition, the combination of autophagy inhibitor plus arginine deprivation was more effective than arginine deprivation alone. In cells in which the expression of ASS1 was suppressed, the expression of P-gp was upregulated in comparison to negative controls.
Discussion: These results indicate that the reduced expression of ASS1 expression in Dox-resistant sarcomas may contribute to drug resistance. ASS1 deficiency is a potential target for novel drug therapies. The combination of arginine deprivation therapy and an autophagy inhibitor may have anti-tumor effects in refractory sarcomas.
Significance: As the induction of autophagy by the deprivation arginine may have a pro-survival role in patients with ASS1-deficient sarcomas, the combination of arginine deprivation therapy with autophagy modulators might potentiate anti-tumor effects in patients with drug-resistant sarcomas.
Citation Format: Eisuke Kobayashi, Youngji Kim, Daisuke Kubota, Yoshiyuki Suehara, Akira Kawai, Shigehisa Kitano. Reduced argininosuccinate synthetase expression in refractory sarcomas: impacts on therapeutic potential and drug resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 449. doi:10.1158/1538-7445.AM2017-449
Abstract 4497: Single-cell protein-mRNA co-detection to reveals subpopulation-specific correlation patterns
Authors: Gong Haibiao , Wang Xiaohui , Liu Benjamin , Holcomb Ilona , Dakshinamoorthy Gajalakshmi , Ooi Aik , Sun Gang , Ramakrishnan Ramesh 
Published: July 2017

Abstract
We have developed a streamlined workflow for multiplexed co-detection of proteins and mRNAs in single reactions at single-cell resolution. This workflow couples OER for protein detection with reverse transcription (RT) for mRNA detection. In this study, we examined 31 overlapping targets, from a panel of 84 protein and 40 mRNA assays, across three different cell lines (A549, SKBR3 and K562). Unsupervised gene expression profiling analysis, including principal component analysis and hierarchical clustering revealed different aspects of the protein-mRNA relationship. The top 10 genes contributing to cell differentiation were identified for both proteins and mRNAs, and eight of them overlap. This result implies an overall concordance of certain protein and mRNA expression in different cell lines. Our results also demonstrate that cells can be classified into subpopulations based on protein-mRNA expression profiles, and different subpopulations have distinct correlation coefficient values. The correlation between CCNB1 protein and mRNA was low (R = 0.2884) in the whole population. However, there was a subpopulation in which CCNB1 protein correlated strongly with its mRNA. When this subpopulation was analyzed, the R value was 0.8350, while therest of the cells had an R value of 0.0233. More interestingly, in subpopulation I CCNB1 protein level correlated positively with CCNA2 protein (R = 0.9102) but negatively with CCNE1 protein(R = - 0.5249). The observed correlation patterns of these genes match their known expression profiling at cell-cycle phases of S, G2 and M, suggesting that this subpopulation may represent actively dividing cells. This study further indicated that systematic comparisons of protein and mRNA expression data in single cells can reveal additional layers of complexity which are not attainable at bulk levels.
Citation Format: Haibiao Gong, Xiaohui Wang, Benjamin Liu, Ilona Holcomb, Gajalakshmi Dakshinamoorthy, Aik Ooi, Gang Sun, Ramesh Ramakrishnan. Single-cell protein-mRNA co-detection to reveals subpopulation-specific correlation patterns [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4497. doi:10.1158/1538-7445.AM2017-4497
Abstract 4517: A CRISPR approach to monitoring hypoxia-inducible proteins in real-time
Authors: Schwinn Marie K. , Machleidt Thomas , Binkowski Brock F. , Eggers Christopher T. , Wood Keith V. 
Published: July 2017

Abstract
Hypoxia-inducible factor 1A (HIF1A) regulates expression of genes implicated in various aspects of oncogenesis, including angiogenesis, cell survival, metastasis, and glucose metabolism. Overexpression or hypoxia-induced stabilization of HIF1A has been associated with poor prognosis in cancer patients, making HIF1A and its associated pathway a high-profile target for anticancer therapies. We sought to develop a live-cell assay to monitor abundance of endogenous HIF1A and HIF1A-inducible proteins that could be used to identify potent and specific inhibitors of the hypoxia signaling pathway. To accomplish this goal, mammalian cell lines were edited by CRISPR using a Cas9:crRNA ribonucleoprotein complex with a single-stranded oligonucleotide donor DNA to introduce the HiBiT tag at the C-terminus of HIF1A and a number of known hypoxia-inducible proteins, including BNIP3, ANKRD37, HILDPA and KLF10. The 11 amino acid HiBiT peptide and its complementing 18 kDa polypeptide, known as LgBiT, spontaneously reconstitute into an active luciferase derived from the NanoLuc enzyme. Co-expression of LgBiT in edited cells, followed by addition of the cell-permeable luciferase substrate, leads to generation of a bright, steady luminescent signal that directly correlates with abundance of the HiBiT fusion. The edited cells were treated with several known modulators of the HIF1A signaling pathway, and changes in the abundance of the protein fusions were followed in real-time by monitoring luminescence. The HiBiT tag was also used to validate size and subcellular localization of the fusion proteins using bioluminescence imaging and antibody-free blotting. As expected, all tested compounds induced HIF1A accumulation. However, the downstream targets of HIF1A generated differing response to the chemical modulators, warranting further investigation into the modes by which these compounds act. By coupling the speed and efficiency of CRISPR-mediated editing with the small size and brightness of HiBiT, it was possible to generate a live-cell assay to monitor abundance of proteins along the HIF1A pathway. This assay could easily be adapted to screen for compound-induced effects on protein levels of HIF1A, as well as HIF1A- induced changes in expression patterns.
Citation Format: Marie K. Schwinn, Thomas Machleidt, Brock F. Binkowski, Christopher T. Eggers, Keith V. Wood. A CRISPR approach to monitoring hypoxia-inducible proteins in real-time [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4517. doi:10.1158/1538-7445.AM2017-4517
Abstract 4520: Hepatitis B virus X protein regulates hypoxia-inducible factor-1alpha (HIF-1 alpha) and lysyl oxidase like 2 (LOXL2) pathway in hepatocellular carcinoma
Authors: Chan Cerise Yuen-Ki , Tse Aki Pui-Wah , Chiu Elley Yong-Tuen , Sze Karen Man-Fong , Koh Hui-Yu , Ng Irene Oi-Lin , Wong Carmen Chak-Lui 
Published: July 2017

Abstract
Hepatocellular carcinoma (HCC), the most common form of primary liver cancer, is a fatal malignancy and is prevalent in HBV-endemic geographical areas. Hepatitis B virus (HBV) infection is a major etiologic factor of HCC. HBV is a double-stranded DNA virus and encodes for a viral onco-protein called transactivator protein X (HBx) which interacts with the host proteins to enhance proliferative potential of the host cells. Here, using Tet-ON and Tet-OFF HBx inducible systems in HBV-negative HCC cell lines, we showed that induced expression of HBx stabilizes hypoxia-inducible factor-1α (HIF-1α) protein under hypoxia. Reversely, knockdown of HBx in HBV-positive HCC cell lines reduced HIF-1α protein stabilization under hypoxia. More intriguingly, we found that induced HBx expression up-regulated the mRNA and protein expression a known HIF-1α transcriptional target, lysyl oxidase like 2 (LOXL2) in HCC. Our previous study showed that LOXL2 cross-linked collagen in the extracellular matrix to promote HCC metastasis. Scanning electron microscopy demonstrated that knockdown of HBx in HCC cell lines markedly reduced formation of collagen fibers in vitro. Transwell invasion assay showed that knockdown of HBx reduced HCC invasive ability. Picrosirius red staining further showed that knockdown of HBx reduced collagen cross-linking in vivo and repressed HCC growth and metastasis. Taken together, our study unprecedentedly show the HBx remodels the ECM through HIF-1α/LOXL2 pathway to promote HCC metastasis.
Citation Format: Cerise Yuen-Ki Chan, Aki Pui-Wah Tse, Elley Yong-Tuen Chiu, Karen Man-Fong Sze, Hui-Yu Koh, Irene Oi-Lin Ng, Carmen Chak-Lui Wong. Hepatitis B virus X protein regulates hypoxia-inducible factor-1alpha (HIF-1 alpha) and lysyl oxidase like 2 (LOXL2) pathway in hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4520. doi:10.1158/1538-7445.AM2017-4520
Abstract 4541: Understanding the dose and schedule dependence of efficacy for the Wee1 inhibitor AZD1775 in xenograft and patient derived explant models by mathematical modelling
Authors: Yates James W. , Cadogan Elaine , Hare Jennifer , Hughes Adina , Polanska Urszula M. , O'Connor Mark , Critchlow Susan E. 
Published: July 2017

Abstract
AZD1775 is a highly selective, small-molecule inhibitor of WEE1 being developed to treat patients with advanced solid tumors, as monotherapy and in combination with olaparib.
Experimental Procedures Patient-derived explant (PDX) and xenografted models with a range of sensitivities to AZD1775 were tested for response to different doses and schedules of AZD1775. WEE1 inhibition was assessed by pCDK1 as a direct substrate of Wee1 and RRM2 as a surrogate of CDK2 activity. Concentration of AZD1775 in plasma was measured in the same animals. Mathematical models were developed to describe the relationship between drug exposure, biomarker modulation and resulting tumour growth inhibition.
Results The PKPD relationship of both pCDK1 and RRM2 could be described by the mathematical model with significant delay between PK and RRM2 reduction due to this being a protein degradation event. Three factors influenced anti-tumour activity in the A427 xenograft and three TNBC PDX models, namely the AZD1775 dose, the number of consecutive days of dosing and the number of days between AZD1775 doses. The minimally effective preclinical dose with anti-tumour activity was 60 mg/kg od. TGI was seen to increase with increased days of consecutive AZD1775 dosing from 3 days on, such that a 5 days on/9 days off schedule was more efficacious than 3 days on/4 days off schedule for two weeks. A mathematical model successfully described this efficacy by using the predicted dose and schedule dependent reduction in pCDK1.
Conclusions The insights from this predictive modelling informed the starting dose of 125mg BID AZD1775 on a 5 day on/9 day off schedule; with the clinical goal to optimize the days of consecutive AZD1775 dosing as well as the maximum tolerated dose.
Citation Format: James W. Yates, Elaine Cadogan, Jennifer Hare, Adina Hughes, Urszula M. Polanska, Mark O'Connor, Susan E. Critchlow. Understanding the dose and schedule dependence of efficacy for the Wee1 inhibitor AZD1775 in xenograft and patient derived explant models by mathematical modelling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4541. doi:10.1158/1538-7445.AM2017-4541
Abstract 4546: Structural evaluation of mutations identified on Cue domain of FANCD2
Authors: Siddiqui Mohd Quadir , Varma Ashok K. 
Published: July 2017

Abstract
Fanconi anemia complementation group D2 (FANCD2) protein plays pivotal role in DNA interstrand crosslink (ICL) repair and genome stability. FANCD2 comprises conserved CUE domain at N terminus, which is important for DNA ICL repair and protein stability. However, molecular mechanism associated to genetic alteration has not well characterized. Here, we have carried out multimodal approaches to explore folding pattern of FANCD2 Cue domain and functionally relevant mutations. Dynamic Light Scattering and Mass Spectrometry data of purified proteins could revealed that wild- type protein is predominantly monomeric, but mutated counterparts are exhibiting oligomeric properties. Secondary, tertiary structure assessment and their thermal stability of wild- type, mutants were studied by Circular Dichroism (CD) and Fluorescence spectroscopy. Furthermore, binding affinity and kinetics of Cue domain and mutants with monoubiquitin was evaluated by surface plasmon resonance (SPR). Molecular modelling, simulation, normal mode analysis, principal component analysis and docking studies were carried out to understand in-depth conformational dynamics and interactions. References:- 1. Regulation of the Fanconi anemia pathway by a CUE ubiquitin-binding domain in the FANCD2 protein. Rego, M. A. et al, Blood 120: 2109-2117,(2012). 2. Hypomorphic mutations in the gene encoding a key Fanconi anemia protein, FANCD2, sustain a significant group of FA-D2 patients with severe phenotype. Kalb et al, Am J Hum Genet 80: 895-910, (2007)
Citation Format: Mohd Quadir Siddiqui, Ashok K. Varma. Structural evaluation of mutations identified on Cue domain of FANCD2 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4546. doi:10.1158/1538-7445.AM2017-4546
Abstract 4552: ssCOPA: a novel method with improved sensitivity to assess statistical significance for cancer outlier profile analysis of gene expression
Authors: Gao Hong , Ng Sam , Gierman Hinco J. 
Published: July 2017

Abstract
To understand the genetic mechanism of disease, finding biomarkers and drug targets are a major focus of academic and pharmaceutical research. However, it has become clear that many important genes driving diseases like cancer, are deregulated in a relatively small group of outliers, e.g. amplified and fusion genes. Cancer outlier profile analysis (COPA), introduced by Tomlins et al, has raised interest in detecting genes with outlier expression within a group, particularly in cancer patients. However, the magnitudes of the COPA scores are not directly comparable across different studies or with different input parameters. Also, integrating COPA scores across multiple studies in a meta-analysis is problematic. Current solutions to performing meta-analyses, including rank-based methods and binomial test, require large study numbers without adjustment for the differences in study size. Also, within a single study COPA scores alone do not provide a P-value, and it is impossible to know which outlier genes are statistically significant. Here we developed three novel methods to address these problems by computing a significance for COPA scores, including Bootstrap resampling, Bootstrap + generalized Pareto distribution (GPD) and Binomial method for statistical significance of COPA (ssCOPA), to enable the comparison of COPA score across studies or parameters. We first evaluated our methods using two breast cancer studies. The P-values generated by Binomial method match closely to Bootstrap resampling using 10,000 randomizations, better than Bootstrap + GPD. In addition, the Binomial method requires significantly less computing time than the other methods. We further validated our methods with a meta-analysis of five breast cancer studies and compared the results with the top-ranking genes of a large-scale meta-analysis of 31 breast cancer studies by ONCOMINE. We show that our P-value-based approaches (P = 10-17~10-24) achieves significantly better concordance than the Binomial test (P = 10-14). Data and methods are available for use on the Illumina BaseSpace® CohortAnalyzer platform (formerly known as NextBio Clinical).
Citation Format: Hong Gao, Sam Ng, Hinco J. Gierman. ssCOPA: a novel method with improved sensitivity to assess statistical significance for cancer outlier profile analysis of gene expression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4552. doi:10.1158/1538-7445.AM2017-4552
Abstract 4554A: Simple, efficient, and quantitative approach for determination of synergism, additive effect, and antagonism of drugs in vivo using combination index method: a proposition for clinical protocol design and regulatory synergy claims
Authors: Fu Jianing , Chou Ting-Chao 
Published: July 2017

Abstract
Based on the systematic dynamic rate derivations with the mass-action principle and mathematical induction-deduction, the median-effect equation of Chou, and the combination index (CI) equation and their algorithm allow quantitative determination of synergism (CI&lt;1), additive effect (CI=1) and antagonism (CI&gt;1) (Pharmacol Rev 58:621-681, 2006). Based on Google Scholar Citations, the CI simulation has been cited 7,712 times in &gt;800 bio-medical journals as of 10.19.2016. However, most citing papers were with experiments in vitro, relative few in vivo and rarely in clinical trials. This is despite the fact that the CI method equation, algorithm, and the CompuSyn software are the same for in vitro and in vivo, although the practical aspects such as sample size, time and cost, the readiness of the end-point measurement, and the ethical considerations are different. Our recent publication (in Fu J et al. Synergy 3: 15-30, 2016) of two-drug combination (docetaxel and T-607 compound, 1:2) against HCT-116 colon carcinoma xenograft in nude mice has demonstrated very desirable synergy. We now illustrate the experimental and data-analytical details of the experimental planning and design, execution, measurements, for docetaxel and T-Compound combination against MX-1 mammary carcinoma xenograft in nude mice. Treatment Q3Dx4 i.v. starting Day 7, and the tumor sizes and bodyweight changes measured on Days 16, 19, and 22. A total of 50 nude mice were used (each drug and combinations, 3 doses each (n=5) plus a control group of 5). Full spectrum of synergism (CI=0.79 to 0.93) were observed on Days 19 and 22. Automated simulation were carried out for dose-effect curve, ME plot, Fa-CI plot, isobologram, and Fa-DRI (Dose-Reduction Index) plot with CompuSyn software (Free download available upon registration via www.combosyn.com). This simple, efficient, “econo-green” bio-research paves the way for drug combination clinical trial design and regulatory synergy claims.
Citation Format: Jianing Fu, Ting-Chao Chou. Simple, efficient, and quantitative approach for determination of synergism, additive effect, and antagonism of drugs in vivo using combination index method: a proposition for clinical protocol design and regulatory synergy claims [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4554A. doi:10.1158/1538-7445.AM2017-4554A