tbuckley/cabot-search huggingface dataset:
Abstract 4375: High hydrostatic pressure modified potato patatin induces apoptosis like cell death in human colorectal adenocarcinoma (HT-29) cell line
Authors: Rizwan Elahi, Tai Hua MU
Journal: Cancer Research (2018)

Abstract The current study assessed the anticancer activity of HHP-induced potato patatin on human colorectal adenocarcinoma (HT 29) cell line in vitro. Cell proliferation, apoptosis, necrosis and autophagy were investigated. HHP treatment inhibited HT-29 cell line proliferation in a dose a dependent manner. IC50 values showed antiproliferative activity (59.1%) at 4 mg mL-1 for HHP-induced patatin at 450 MPa. Flow cytometric analysis indicated that HHP-induced patatin at 450 MPa was the potent inducer of in vitro apoptotic cell death and showed significant (p&amp;lt;0.05) accumulation in S-phase followed by patatin pressurized at 550 MPa. Surface charge of patatin decreased with the increase in pressurization up to 350 MPa level, while at 450 MPa zeta potential value increased to (-13 mV) and (-11 mV) respectively. Overall, results indicated that 450 MPa patatin is a strong inhibitor of HT-29 and a potent inducer of apoptotic cell death. Thus, HHP treatment is an effective method for structural modification of patatin which ultimately enhance the anticancer potential against colorectal cancer cells. Citation Format: Rizwan Elahi, Tai Hua MU. High hydrostatic pressure modified potato patatin induces apoptosis like cell death in human colorectal adenocarcinoma (HT-29) cell line [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 4375.
Abstract 5774: Novel cell-based high-throughput hybridoma screening method using the Celigo image cytometer for antibody discovery
Authors: Leo L. Chan, Haohai Zhang, William Rice, Nasim Kassam, Maria S. Longhi, Haitao Zhao, Simon C. Robson, Wenda Gao, Yan Wu
Journal: Cancer Research (2018)

Abstract Hybridoma screening is a highly important process for antibody discovery, which can identify potential clones from hundreds to thousands of hybridoma cultures against the desired target antigen. Traditional screening methods using ELISA and flow cytometry presented technical issues such as limited accuracy, reduced high-throughput capability, increased time and cost. Conventional ELISA screening with coated antigen can also be impractical for difficult to express hydrophobic membrane antigens or multi-chain protein complexes. Here, we demonstrate novel cell-based high-throughput screening methodology using plate-based Celigo Image Cytometer, which avoids nonspecific signals by contrasting antibody binding signals directly on living cells, with and without recombinant antigen expression. The image cytometry-based high-throughput screening method was optimized by detecting the binding of hybridoma supernatants to the recombinant antigen CD39 expressed on Chinese hamster ovary (CHO) cells. Both target CHO and CFSE-stained wild type were co-cultured to simultaneously detect target antibodies (Alexa Fluor 594) and nonspecific binding, which can eliminate the need to produce a separate control sample for each hybridoma supernatant. Next, the image cytometer was used to screen 672 unique hybridoma supernatants to develop the high-throughput screening workflow. The Celigo was used to quickly image and analyze antibody binding of 672 samples, using Hoechst, Alexa Fluor 594 and CFSE fluorescence to identify high, medium, and low binding hits. Finally, the sensitivity of the image cytometer was demonstrated by serial dilution of purified CD39 antibody. Celigo was used to measure antibody affinities of commercial and in-house antibodies to membrane-bound CD39. This cell-based screening procedure can be completely accomplished within one day, significantly improving throughput and efficiency of hybridoma screening. Furthermore, measuring direct antibody binding to living cells eliminated both false positive and false negative hits. The image cytometry method was highly sensitive and versatile, and could detect positive antibody in supernatants at concentrations as low as ~5 ng/mL, with concurrent Kd binding affinity coefficient determination. We propose that this screening method will greatly improve screening technologies and facilitate more efficient antibody discovery. Citation Format: Leo L. Chan, Haohai Zhang, William Rice, Nasim Kassam, Maria S. Longhi, Haitao Zhao, Simon C. Robson, Wenda Gao, Yan Wu. Novel cell-based high-throughput hybridoma screening method using the Celigo image cytometer for antibody discovery [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 5774.
Insulin-Like Growth Factor-1 Receptor Deficiency in Macrophages Accelerates Atherosclerosis and Induces an Unstable Plaque Phenotype in Apolipoprotein E–Deficient Mice
Authors: YusukeHigashi, SergiySukhanov, Shaw-YungShai, SvitlanaDanchuk, RichardTang, PatriciaSnarski, ZhaohuiLi, PatriciaLobelle-Rich, MeifangWang, DerekWang, HongYu, RonaldKorthuis, PatriceDelafontaine
Journal: Circulation (2016)

Background—We have previously shown that systemic infusion of insulin-like growth factor-1 (IGF-1) exerts anti-inflammatory and antioxidant effects and reduces atherosclerotic burden in apolipoprotein E (Apoe)–deficient mice. Monocytes/macrophages express high levels of IGF-1 receptor (IGF1R) and play a pivotal role in atherogenesis, but the potential effects of IGF-1 on their function are unknown. Methods and Results—To determine mechanisms whereby IGF-1 reduces atherosclerosis and to explore the potential involvement of monocytes/macrophages, we created monocyte/macrophage–specific IGF1R knockout (MΦ-IGF1R-KO) mice on an Apoe−/− background. We assessed atherosclerotic burden, plaque features of stability, and monocyte recruitment to atherosclerotic lesions. Phenotypic changes of IGF1R-deficient macrophages were investigated in culture. MΦ-IGF1R-KO significantly increased atherosclerotic lesion formation, as assessed by Oil Red O staining of en face aortas and aortic root cross-sections, and changed plaq...
Anti-Obesity Therapy: from Rainbow Pills to Polyagonists
Authors: T. D. Müller, C. Clemmensen, B. Finan, R. D. DiMarchi, M. H. Tschöp
Journal: Pharmacological Reviews (2018)

With their ever-growing prevalence, obesity and diabetes represent major health threats of our society. Based on estimations by the World Health Organization, approximately 300 million people will be obese in 2035. In 2015 alone there were more than 1.6 million fatalities attributable to hyperglycemia and diabetes. In addition, treatment of these diseases places an enormous burden on our health care system. As a result, the development of pharmacotherapies to tackle this life-threatening pandemic is of utmost importance. Since the beginning of the 19th century, a variety of drugs have been evaluated for their ability to decrease body weight and/or to improve deranged glycemic control. The list of evaluated drugs includes, among many others, sheep-derived thyroid extracts, mitochondrial uncouplers, amphetamines, serotonergics, lipase inhibitors, and a variety of hormones produced and secreted by the gastrointestinal tract or adipose tissue. Unfortunately, when used as a single hormone therapy, most of these drugs are underwhelming in their efficacy or safety, and placebo-subtracted weight loss attributed to such therapy is typically not more than 10%. In 2009, the generation of a single molecule with agonism at the receptors for glucagon and the glucagon-like peptide 1 broke new ground in obesity pharmacology. This molecule combined the beneficial anorectic and glycemic effects of glucagon-like peptide 1 with the thermogenic effect of glucagon into a single molecule with enhanced potency and sustained action. Several other unimolecular dual agonists have subsequently been developed, and, based on their preclinical success, these molecules illuminate the path to a new and more fruitful era in obesity pharmacology. In this review, we focus on the historical pharmacological approaches to treat obesity and glucose intolerance and describe how the knowledge obtained by these studies led to the discovery of unimolecular polypharmacology.
Abstract 4531: Development of a companion diagnostic assay for the detection of phosphatase and tensin (PTEN) protein loss and treatment with ipatasertib in metastatic castration-resistant prostatic cancer (mCRPC)
Authors: Crystal Stephens, Erica Harnish, Rebecca Bowermaster, Azita Djalilvand, Dustin Smith, Doris Kim, Steven Gendreau, Edmundo Del Valle
Journal: Cancer Research (2018)

Abstract Background: Ventana Medical Systems, Inc. is developing in collaboration with Genentech, Inc., an immunohistochemical (IHC) companion diagnostic to aid in selecting patients with metastatic castration-resistant prostate cancer (mCRPC) that may benefit from ipatasertib, an Akt inhibitor therapy. The phosphatase and tensin (PTEN) protein plays an important role in controlling cell survival and cell cycle progression as a negative regulator of the phosphoinositide 3-kinase/AKT pathway. Methods: PTEN (SP218) rabbit monoclonal primary antibody was optimized for use with the VENTANA OptiView DAB IHC Detection Kit on the automated BenchMark ULTRA platform (PTEN (SP218) RxDx Assay). The PTEN (SP218) RxDx Assay was developed for use in formalin-fixed, paraffin-embedded tissue samples of mCRPC in a series of studies addressing sensitivity, specificity, robustness and precision. The scoring algorithm was defined using statistical analysis of clinical outcome data analysis, and the PTEN (SP218) RxDx Assay staining pattern and prevalence of PTEN loss of expression in a set of tissue samples. Inter-reader precision was established by 3 pathologists evaluating 90 mCRPC samples across the range of PTEN expression levels. Results: The Ventana PTEN (SP218) RxDx Assay met all pre-defined acceptance criteria. mCRPC tissue samples are designated with PTEN-Loss status when ≥ 50% of viable malignant cells have no specific cytoplasmic staining with PTEN (SP218) in the presence of acceptable internal controls. Inter-reader precision in determining PTEN status resulted in agreement rates greater than 97%. Conclusion: These results highlight the robustness and reproducibility of the Ventana PTEN (SP218) RxDx Assay. In the clinical outcome analysis, patients identified to have PTEN-loss status demonstrated clinically meaningful improvements when treated with ipatasertib. The clinical utility of the PTEN (SP218) RxDx assay will be further validated in additional patients in subsequent ipatasertib studies, including a Phase 3 study (IPATential150) beginning in 2017. Citation Format: Crystal Stephens, Erica Harnish, Rebecca Bowermaster, Azita Djalilvand, Dustin Smith, Doris Kim, Steven Gendreau, Edmundo Del Valle. Development of a companion diagnostic assay for the detection of phosphatase and tensin (PTEN) protein loss and treatment with ipatasertib in metastatic castration-resistant prostatic cancer (mCRPC) [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 4531.
Mitochondrial STAT3 Activation and Cardioprotection by Ischemic Postconditioning in Pigs With Regional Myocardial Ischemia/Reperfusion
Authors: GerdHeusch, JudithMusiolik, NilguenGedik, AndreasSkyschally
Journal: Circulation Research (2011)

Rationale:Timely restoration of coronary blood flow is the only way to salvage myocardium from infarction, but reperfusion per se brings on additional injury. Such reperfusion injury and the resulting size of myocardial infarction is attenuated by ischemic postconditioning, ie, the repeated brief interruption of coronary blood flow during early reperfusion. The signal transduction of ischemic postconditioning is under intense investigation, but no signaling step has yet been identified as causal for such protection in larger mammals in situ. Objective:We have now in an in situ pig model of regional myocardial ischemia/reperfusion addressed the role of mitochondrial signal transducer and activator of transcription 3 (STAT3). Methods and Results:We demonstrated reduction of infarct size by ischemic postconditioning (26±3% of area at risk versus 38±2% in controls with immediate full reperfusion) along with more markedly increased tyrosine705 phosphorylation of STAT3 in myocardial biopsies (at 10 minutes repe...
Usefulness of 18F Fluorodeoxyglucose Positron Emission Tomography/Computed Tomography in Infective Endocarditis in Daily Practice
Authors: Cristina Sánchez-Enrique, Carmen Olmos, Ana Jiménez-Ballvé, Cristina Fernández-Pérez, Carlos Ferrera, María Jesús Pérez-Castejón, Aida Ortega Candil, Roberto Delgado-Bolton, Manuel Carnero, Luis Maroto, José Luis Carreras, Isidre Vilacosta
Journal: JACC. Cardiovascular imaging (2018)
Retrospective validation of whole genome sequencing-enhanced surveillance of listeriosis in Europe, 2010 to 2015
Authors: Ivo Van Walle, Jonas Torgny Björkman, Martin Cormican, Timothy Dallman, Joël Mossong, Alexandra Moura, Ariane Pietzka, Werner Ruppitsch, Johanna Takkinen
Journal: Eurosurveillance (2018)

Background and aimThe trend in reported case counts of invasive Listeria monocytogenes (Lm), a potentially severe food-borne disease, has been increasing since 2008. In 2015, 2,224 cases were reported in the European Union/European Economic Area (EU/EEA). We aimed to validate the microbiological and epidemiological aspects of an envisaged EU/EEA-wide surveillance system enhanced by routine whole genome sequencing (WGS). Methods: WGS and core genome multilocus sequence typing (cgMLST) were performed on isolates from 2,726 cases from 27 EU/EEA countries from 2010-15. Results: Quality controls for contamination, mixed Lm cultures and sequence quality classified nearly all isolates with a minimum average coverage of the genome of 55x as acceptable for analysis. Assessment of the cgMLST variation between six different pipelines revealed slightly less variation associated with assembly-based analysis compared to reads-based analysis. Epidemiological concordance, based on 152 isolates from 19 confirmed outbreaks and a cluster cutoff of seven allelic differences, was good (sensitivity > 95% for two cgMLST schemes of 1,748 and 1,701 loci each; PPV 58‒68%). The proportion of sporadic cases was slightly below 50%. Of remaining isolates, around one third were in clusters involving more than one country, often spanning several years. Detection of multi-country clusters was on average several months earlier when pooling the data at EU/EEA level, compared with first detection at national level. Conclusions: These findings provide a good basis for comprehensive EU/EEA-wide, WGS-enhanced surveillance of listeriosis. Time limits should not be used for hypothesis generation during outbreak investigations, but should be for analytical studies.
Age at puberty and risk of asthma: A Mendelian randomisation study
Authors: Cosetta Minelli, Diana A. van der Plaat, Bénédicte Leynaert, Raquel Granell, Andre F. S. Amaral, Miguel Pereira, Osama Mahmoud, James Potts, Nuala A. Sheehan, Jack Bowden, John Thompson, Debbie Jarvis, George Davey Smith, John Henderson
Journal: PLoS Medicine (2018)

Background Observational studies on pubertal timing and asthma, mainly performed in females, have provided conflicting results about a possible association of early puberty with higher risk of adult asthma, possibly due to residual confounding. To overcome issues of confounding, we used Mendelian randomisation (MR), i.e., genetic variants were used as instrumental variables to estimate causal effects of early puberty on post-pubertal asthma in both females and males. Methods and findings MR analyses were performed in UK Biobank on 243,316 women using 254 genetic variants for age at menarche, and on 192,067 men using 46 variants for age at voice breaking. Age at menarche, recorded in years, was categorised as early (<12), normal (12–14), or late (>14); age at voice breaking was recorded and analysed as early (younger than average), normal (about average age), or late (older than average). In females, we found evidence for a causal effect of pubertal timing on asthma, with an 8% increase in asthma risk for early menarche (odds ratio [OR] 1.08; 95% CI 1.04 to 1.12; p = 8.7 × 10−5) and an 8% decrease for late menarche (OR 0.92; 95% CI 0.89 to 0.97; p = 3.4 × 10−4), suggesting a continuous protective effect of increasing age at puberty. In males, we found very similar estimates of causal effects, although with wider confidence intervals (early voice breaking: OR 1.07; 95% CI 1.00 to 1.16; p = 0.06; late voice breaking: OR 0.93; 95% CI 0.87 to 0.99; p = 0.03). We detected only modest pleiotropy, and our findings showed robustness when different methods to account for pleiotropy were applied. BMI may either introduce pleiotropy or lie on the causal pathway; secondary analyses excluding variants associated with BMI yielded similar results to those of the main analyses. Our study relies on self-reported exposures and outcomes, which may have particularly affected the power of the analyses on age at voice breaking. Conclusions This large MR study provides evidence for a causal detrimental effect of early puberty on asthma, and does not support previous observational findings of a U-shaped relationship between pubertal timing and asthma. Common biological or psychological mechanisms associated with early puberty might explain the similarity of our results in females and males, but further research is needed to investigate this. Taken together with evidence for other detrimental effects of early puberty on health, our study emphasises the need to further investigate and address the causes of the secular shift towards earlier puberty observed worldwide.
Abstract 4590: Larger family sizes improve stochastic error correction during untargeted searches of very-low frequency variant alleles in circulating cell-free DNA (ccfDNA)
Authors: Preetida J. Bhetariya, David Nix, Sabine Hellwig, Gabor Marth, Mary Bronner, Hunter Underhill
Journal: Cancer Research (2018)

Abstract Detection of ccfDNA derived from non-metastatic solid tumors requires discrimination of very-low frequency true variants from NGS library preparation and sequencing noise that commonly occurs at a similar frequency (&amp;lt;1%). Correction of NGS-related errors is particularly important during searches of unknown tumor-associated variants with multi-gene panels. Unique molecular identifiers (UMIs) have been used during in silico error correction by molecular barcoding and performing a consensus base calling at each position from DNA labelled with the same UMI (i.e., PCR duplicates). In this study, we sought to determine the utility of UMIs for error correction of stochastic noise in ccfDNA. ccfDNA was isolated from the plasma of 11 healthy participants. An eight base-pair random barcode (UMI) was ligated prior to library amplification. Libraries were enriched using a custom capture probe set (128 genes; 128 kb) and then sequenced (HiSeq 2500). Reads were aligned, grouped based on UMI similarity, and a consensus read sequence was determined. The number of PCR duplicates that yielded a single consensus sequence was defined as family size (FS). For non-reference alleles detected at a variant allele frequency (VAF) ≥ 0.1% and ≤ 1.0%, there was a significant reduction in observed counts with increasingly larger FSs (Table 1). This effect was observed for both unique and common non-reference allele counts (Table 1). Of note, counts of unique non-reference alleles (stochastic noise) were consistently greater than the common non-reference alleles regardless of family size (Table 1). The use of larger family sizes reduced the stochastic noise that may confound detection of very-low frequency variants present in ccfDNA during searches for unknown tumor-associated variants. Strategies that generate larger family sizes or suppress early PCR errors may further improve NGS specificity to broaden liquid biopsy clinical applications. Table 1. Mean (SD) Non-Reference Allele Counts with a VAF between 0.1% and 1.0% in Cell-Free DNAFS &amp;gt;= 1FS &amp;gt;= 5FS &amp;gt;= 10FS &amp;gt;= 15FS &amp;gt;= 20ANOVA Results F(4,50)P-valueAll Variants5536 (1230)3988 (881)2621 (805)1028 (552)1028 (552)49.8&amp;lt;0.001Unique Variants3597 (1107)2635 (766)1112 (526)709 (434)709 (434)27.6&amp;lt;0.001Common Variants1939 (161)1353 (188)521 (141)318 (121)318 (121)186.1&amp;lt;0.001 Citation Format: Preetida J. Bhetariya, David Nix, Sabine Hellwig, Gabor Marth, Mary Bronner, Hunter Underhill. Larger family sizes improve stochastic error correction during untargeted searches of very-low frequency variant alleles in circulating cell-free DNA (ccfDNA) [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 4590.
Abstract 4699: Identification of novel potential biomarkers of response to sunitinib in glioblastoma
Authors: Abu Shadat Mohammod Noman, Bassam Abdulkarim, Siham Sabri
Journal: Cancer Research (2018)

Abstract Introduction: Glioblastoma multiforme (GBM) is the most advanced and aggressive form of primary malignant brain tumors in adults. O6-Methylguanine methyltransferase (MGMT) is a DNA repair protein well known for its role in resistance to temozolomide used in standard treatment of patients newly diagnosed with GBM. Sunitinib is an oral multitargeting receptor tyrosine kinase (RTK) inhibitor with antiangiogenic and antiproliferative activities targeting several RTKs. Our group has previously shown the role of MGMT as a negative regulator of angiogenesis and invasion and the differential antiproliferative effect of sunitinib based on expression of MGMT in GBM. Recent gene expression profiling (GEP) studies showed that besides its effects on RTKs, sunitinib affects the expression level of other genes at the transcriptional level in different cancer types. We hypothesized that: (i) the mechanism of action of sunitinib may not be limited to direct inhibition of its known targets (RTKs) in GBM and (ii) expression of MGMT may affect response of GBM tumor cells to sunitinib. We performed GEP analysis to identify genes that could be potentially modulated in response to sunitinib in GBM cell lines isogenic for MGMT. Empty vector (EV)-transfected T98/EV cells with constitutive expression of MGMT and its knockdown counterpart T98/MGMT-shRNA were treated with sunitinib or vehicle control. Treatment of T98/EV and T98/MGMT-shRNA cell lines with sunitinib significantly changed the expression of over 2,000 gene transcripts (analysis performed at Genome Quebec Innovation center, McGill University). Lists of significant genes were fitted into previously known biochemical pathways, available among the canonical pathways from various databases provided by ConsensusPathDB (CPDB). Strikingly, immune system was among the top significantly enriched pathways (p-value&amp;lt;10-3), with some immune pathways not previously reported for response to sunitinib. Conclusion: Our study opens new avenues to further understand the mechanisms of action of sunitinib, investigate its immunomodulatory effects, and identify biomarkers for selection of patients who might benefit from the combination of antiangiogenic and immunebased strategies in GBM. Funding Acknowledgment: Cancer Research Society Operating Grant Competition #22716, and Higher Education Quality Enhancement Project (HEQEP)- Window -4 (Grant Id. CP-4023), University Grant Commission (UGC), Bangladesh. Citation Format: Abu Shadat Mohammod Noman, Bassam Abdulkarim, Siham Sabri. Identification of novel potential biomarkers of response to sunitinib in glioblastoma [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 4699.