bluuebunny/crossref_metadata_2025 huggingface dataset:
Matching effective few-nucleon theories to QCD
Authors: Kirscher J.
Published: May 2016

The emergence of complex macroscopic phenomena from a small set of parameters and microscopic concepts demonstrates the power and beauty of physical theories. A theory which relates the wealth of data and peculiarities found in nuclei to the small number of parameters and symmetries of quantum chromodynamics is by that standard of exceptional beauty.

Decade-long research on computational physics and on effective field theories facilitate the assessment of the presumption that quark masses and strong and electromagnetic coupling constants suffice to parametrize the nuclear chart. By presenting the current status of that enterprise, this article touches the methodology of predicting nuclei by simulating the constituting quarks and gluons and the development of effective field theories as appropriate representations of the fundamental theory.

While the nuclear spectra and electromagnetic responses analyzed computationally so far with lattice QCD are in close resemblance to those which intrigued experimentalists a century ago, they also test the theoretical understanding which was unavailable to guide the nuclear pioneers but developed since then. This understanding is shown to be deficient in terms of correlations amongst nuclear observables and their sensitivity to fundamental parameters. By reviewing the transition from one effective field theory to another, from QCD to pionful chiral theories to pionless and eventually to cluster theories, we identify some of those deficiencies and conceptual problems awaiting a solution before QCD can be identified as the high-energy theory from which the nuclear landscape emerges.
An Operational Matrix Method for Solving Delay Fredholm and Volterra Integro–Differential Equations
Authors: Shahmorad Sedaghat , Ostadzad Mohammad Hossein
Published: May 2016

In this paper, we develop the operational approach to the Tau method to solve delay integro-differential equations (DIDEs). The differential and integral parts appearing in the equations are replaced by their operational Tau matrix representations. Some numerical results are given to demonstrate the superior performance of the method.
A molecule for all seasons: The heme
Authors: Ascenzi Paolo , Brunori Maurizio
Published: May 2016

If life without heme-Fe were at all possible, it would definitely be different. Indeed this complex and versatile iron-porphyrin macrocycle upon binding to different “globins” yields hemeproteins crucial to sustain a variety of vital functions, generally classified, for convenience, in a limited number of functional families. Over-and-above the array of functions briefly outlined below, the spectacular progress in molecular genetics seen over the last 30 years led to the discovery of many hitherto unknown novel hemeproteins in prokaryotes and eukaryotes. Here, we highlight a few basic aspects of the chemistry of the hemeprotein universe, in particular those that are relevant to the control of heme-Fe reactivity and specialization, as sculpted by a variety of interactions with the protein moiety.
Restoring Haptic Feedback in NOTES Procedures with a Novel Wireless Tissue Stiffness Probe
Authors: Beccani Marco , Natali Christian Di , Valdastri Pietro , Obstein Keith L.
Published: May 2016

In the past two decades, several instruments have been developed to overcome the loss of haptic sensation in minimally invasive surgery (MIS). Unfortunately, none of the proposed instruments has been clinically adopted or utilized in natural orifice translumenal endoscopic surgery (NOTES) procedures. The challenge is that NOTES instruments require mounting upon flexible endoscopes thus altering endoscope flexibility and dexterity. We have developed a novel wireless tissue stiffness probe (WTSP) that can be used with a flexible endoscope and create a real-time stiffness distribution map with potential to restore haptic sensation in NOTES. The aim of our study was to assess the performance and feasibility of the WTSP in an ex vivo trial (three phantom models of different elasticity; comparing discrimination of human touch with the WTSP) and in an in vivo trans-colonic access NOTES procedure. Overall, the WTSP was able to detect the stiffness of the three phantoms with a relative error smaller than 3% and a success rate of 100% versus 95% when compared to human perception. The novel WTSP was successful in providing the operator with tactile and kinesthetic feedback for accurate discrimination between tissue phantoms. In vivo tissue palpation was feasible using the WTSP in a trans-colonic NOTES procedure. The WTSP did not encumber the maneuverability or dexterity of the flexible endoscope. This innovative approach to tissue palpation has the potential to open a new paradigm in the field of NOTES where no mechanical link between the external platform and the target region exists.
Regulatory T Cells: Molecular Actions on Effector Cells in Immune Regulation
Authors: Arce-Sillas Asiel , Álvarez-Luquín Diana Denisse , Tamaya-Domínguez Beatriz , Gomez-Fuentes Sandra , Trejo-García Abel , Melo-Salas Marlene , Cárdenas Graciela , Rodríguez-Ramírez Juan , Adalid-Peralta Laura
Published: May 2016

T regulatory cells play a key role in the control of the immune response, both in health and during illness. While the mechanisms through which T regulatory cells exert their function have been extensively described, their molecular effects on effector cells have received little attention. Thus, this revision is aimed at summarizing our current knowledge on those regulation mechanisms on the target cells from a molecular perspective.
Effects of Transcranial Alternating Current Stimulation on Cognitive Functions in Healthy Young and Older Adults
Authors: Antonenko Daria , Faxel Miriam , Grittner Ulrike , Lavidor Michal , Flöel Agnes
Published: May 2016

Recently, transcranial alternating current stimulation (tACS) has emerged as a tool to enhance human cognitive processes. Here, we provide a brief summary of the rationale behind tACS-induced effects on task-relevant brain oscillations and associated cognitive functions and review previous studies in young subjects that have applied tACS in cognitive paradigms. Additionally, we present pilot data where we administered theta-tACS (6 Hz) over the temporoparietal cortex and a supraorbital reference for 20 min during implicit language learning in healthy young (mean/SD age: 22/2) and older (mean/SD age: 66/4) adults, in a sham-controlled crossover design. Linear mixed models revealed significantly increased retrieval accuracy following tACS-accompanied associative learning, after controlling for session order and learning success. These data provide the first implementation of tACS during cognitive performance in older adults and support recent studies suggesting that tACS in the theta frequency range may serve as a tool to enhance cognition, possibly through direct modulation of task-relevant brain oscillations. So far, studies have been heterogeneous in their designs, leaving a number of issues to be addressed in future research, including the setup of electrodes and optimal stimulation frequencies to be employed, as well as the interaction with age and underlying brain pathologies in specific patient populations.
Experimental and Numerical Investigations on Feasibility and Validity of Prismatic Rock Specimen in SHPB
Authors: Li Xibing , Zhou Tao , Li Diyuan , Wang Zewei
Published: May 2016

The paper presents experimental and numerical studies on the feasibility and validity of using prismatic rock specimens in split Hopkinson pressure bar (SHPB) test. Firstly, the experimental tests are conducted to evaluate the stress and strain uniformity in the prismatic specimens during impact loading. The stress analysis at the ends of the specimen shows that stress equilibrium can be achieved after about three wave reflections in the specimen, and the balance can be well maintained for a certain time after peak stress. The strain analysis reveals that the prismatic specimen deforms uniformly during the dynamic loading period. Secondly, numerical simulation is performed to further verify the stress and strain uniformity in the prismatic specimen in SHPB test. It indicates that the stress equilibrium can be achieved in prismatic specimen despite a certain degree of stress concentration at the corners. The comparative experiments demonstrate that the change of specimen shape has no significant effect on dynamic responses and failure patterns of the specimen. Finally, a dynamic crack propagation test is presented to show the application of the present work in studying fracturing mechanisms under dynamic loading.
Automatic Detection of Cervical Cancer Cells by a Two-Level Cascade Classification System
Authors: Su Jie , Xu Xuan , He Yongjun , Song Jinming
Published: May 2016

We proposed a method for automatic detection of cervical cancer cells in images captured from thin liquid based cytology slides. We selected 20,000 cells in images derived from 120 different thin liquid based cytology slides, which include 5000 epithelial cells (normal 2500, abnormal 2500), lymphoid cells, neutrophils, and junk cells. We first proposed 28 features, including 20 morphologic features and 8 texture features, based on the characteristics of each cell type. We then used a two-level cascade integration system of two classifiers to classify the cervical cells into normal and abnormal epithelial cells. The results showed that the recognition rates for abnormal cervical epithelial cells were 92.7% and 93.2%, respectively, when C4.5 classifier or LR (LR: logical regression) classifier was used individually; while the recognition rate was significantly higher (95.642%) when our two-level cascade integrated classifier system was used. The false negative rate and false positive rate (both 1.44%) of the proposed automatic two-level cascade classification system are also much lower than those of traditional Pap smear review.
Detection of Common Problems in Real-Time and Multicore Systems Using Model-Based Constraints
Authors: Beamonte Raphaël , Dagenais Michel R.
Published: May 2016

Multicore systems are complex in that multiple processes are running concurrently and can interfere with each other. Real-time systems add on top of that time constraints, making results invalid as soon as a deadline has been missed. Tracing is often the most reliable and accurate tool available to study and understand those systems. However, tracing requires that users understand the kernel events and their meaning. It is therefore not very accessible. Using modeling to generate source code or represent applications’ workflow is handy for developers and has emerged as part of the model-driven development methodology. In this paper, we propose a new approach to system analysis using model-based constraints, on top of userspace and kernel traces. We introduce the constraints representation and how traces can be used to follow the application’s workflow and check the constraints we set on the model. We then present a number of common problems that we encountered in real-time and multicore systems and describe how our model-based constraints could have helped to save time by automatically identifying the unwanted behavior.
Aromatase Expression in the Hippocampus of AD Patients and 5xFAD Mice
Authors: Prange-Kiel Janine , Dudzinski Danuta A. , Pröls Felicitas , Glatzel Markus , Matschke Jakob , Rune Gabriele M.
Published: May 2016

Numerous studies show that 17β-estradiol (E2) protects against Alzheimer’s disease (AD) induced neurodegeneration. The E2-synthesizing enzyme aromatase is expressed in healthy hippocampi, but although the hippocampus is severely affected in AD, little is known about the expression of hippocampal aromatase in AD. To better understand the role of hippocampal aromatase in AD, we studied its expression in postmortem material from patients with AD and in a mouse model for AD (5xFAD mice). In human hippocampi, aromatase-immunoreactivity was observed in the vast majority of principal neurons and signal quantification revealed higher expression of aromatase protein in AD patients compared to age- and sex-matched controls. The tissue-specific first exons of aromatase I.f, PII, I.3, and I.6 were detected in hippocampi of controls and AD patients by RT-PCR. In contrast, 3-month-old, female 5xFAD mice showed lower expression of aromatase mRNA and protein (measured by qRT-PCR and semiquantitative immunohistochemistry) than WT controls; no such differences were observed in male mice. Our findings stress the importance of hippocampal aromatase expression in neurodegenerative diseases.
Abstract C201: Activity of the GlaxoSmithKline kinase inhibitor set on glioblastoma stem cells
Authors: Khagi Simon , Sengupta Sejuti , Tabtieng Tate , Cochran Brent H.
Published: May 2016

Despite significant advances in our understanding glioblastoma (GBM) in recent years, it remains a deadly cancer with a very poor prognosis. There is an urgent need for new therapies. Kinases are well known regulators of cellular growth and survival and there are many compounds available that are capable of inhibiting specific kinases. Recently, GlaxoSmithKline has made available a library of over 350 kinase inhibitors in a public-private partnership to facilitate the discovery of new drugs and targets in multiple disease settings (Nature Chemical Biology 9:3 (2013)). Together these compounds have been shown to inhibit over 100 different kinases by in vitro kinase assay at 1 uM. We have screened these compounds against 3 different GBM stem cell lines under normoxic and hypoxic conditions. Over 40 compounds were strongly inhibitory for least one cell line and condition. However, only 9 of these compounds were capable of inhibiting the growth all three cell lines by 90% at 1 uM in both conditions. Seven of the 9 common inhibitors had IC50's under 100 nM and 4 had IC50's under 10 nM in at least one oxygen condition. In vitro kinase assays indicate that these compounds each have multiple kinase targets. Based on an analysis of common targets, it is likely that one of the targets is PLK1 which is well known GBM inhibitor. Two compounds that don't inhibit PLK1 both inhibit CLK2 and KIT strongly. IC50 analysis demonstrated wide variability among cell lines and oxygen concentrations. The effectiveness of a single compound could vary more then tenfold between cell lines and more than fiftyfold between normoxia and hypoxia. Some compounds were more effective under hypoxia and some were less. These results strengthen the case for personalized therapies and indicate that hypoxia (which is prevalent in GBM) can significantly alter the effectiveness of inhibitors.

Citation Format: Simon Khagi, Sejuti Sengupta, Tate Tabtieng, Brent H. Cochran. Activity of the GlaxoSmithKline kinase inhibitor set on glioblastoma stem cells. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr C201.
Abstract A22: Cell growth regulation of gain-of-function mutant p53 via miRNAs on metabolic inhibition
Authors: Jo Se-Young , Moon Hae-Min , Lee ChuHee , Jang Se Jin , Suh Young-Ah
Published: May 2016

There is growing evidence that tumor cells depend on unique metabolism for their continued growth and survival, and that cancer cells are peculiarly addicted to the rapacious uptake of glucose and glutamine. Due to the gain-of-function, mutant p53 protein contributes to tumor metastasis and shortening the latency of tumor progression, and thereby activated K-ras/mutant p53 mouse is preferentially used as lung adenocarcinoma preclinical model. Epigenetic regulation through histone modification or miRNA also plays a pivotal role on gene regulation, as regarded as global epigenetic markers, especially in tumor related genes. Hence, chemical approaches targeting histone-modifying enzymes have emerged onto the main stage of anticancer drug discovery. Here, we have investigated the involvement of miRNAs in cell growth regulation upon the treatment of metabolic inhibitors. We have generated different genotypes of mouse tumor cells derived from activated mutant p53 and/or K-ras mutant mice. We have tested whether inhibitors regulating metabolism induce adverse effect on cell growth and changes of miRNA expression through microarray analysis, with the hint of enormous demands for nutrients in fast growing tumor cells. We then analyzed affected genes and miRNAs via quantitative RT-PCR to confirm the involvement of miRNAs on cell growth when tumor metabolic environment were damaged.

Citation Format: Se-Young Jo, Hae-Min Moon, ChuHee Lee, Se Jin Jang, Young-Ah Suh. Cell growth regulation of gain-of-function mutant p53 via miRNAs on metabolic inhibition. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr A22.
Abstract IA06: SWI/SNF chromatin remodeling complex mutations in cancer: Mechanisms and potential therapeutic insights
Authors: Roberts Charles W.M.
Published: May 2016

Data emerging over the last several years implicate the SWI/SNF (BAF) chromatin remodeling complex as a major tumor suppressor as frequent inactivating mutations in at least eight SWI/SNF subunits have been identified in a variety of cancers. These include inactivating mutations of the gene encoding the ARID1A (BAF250a) subunit in ovarian, endometrioid, bladder, stomach, colorectal and pancreatic cancers; of the PBRM1 (BAF180) subunit in renal carcinomas; of the ARID2 subunit in hepatocellular, lung, and pancreas carcinomas as well as melanomas; of the BRD7 subunit in breast cancers; and of the BRG1 (SMARCA4) subunit in non-small cell lung cancers, medulloblastomas and ovarian small cell carcinomas. The SWI/SNF complex includes both core and lineage-specific subunits and utilizes the energy of ATP to modulate chromatin structure and regulate transcription.

My laboratory began studying the SWI/SNF complex when the SNF5 (SMARCB1/INI1/BAF47) subunit was first identified as a tumor suppressor over a decade ago when it was found to be recurrently and specifically inactivated in a highly aggressive type of pediatric cancer called malignant rhabdoid tumor. We now study the complex using mouse models, cell lines and primary human tumor samples. Our goals are to elucidate the normal function of the complex, identify the mechanisms by which subunit mutations drive cancer formation, and utilize this insight to identify and develop novel therapeutic approaches. Insights into the normal function of SWI/SNF complexes, the mechanisms by which mutation of the complexes drive cancer formation, and potential therapeutic vulnerabilities created by mutation of the complex will be presented.

Citation Format: Charles W.M. Roberts. SWI/SNF chromatin remodeling complex mutations in cancer: Mechanisms and potential therapeutic insights. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr IA06.
Abstract A08: Telomerase inhibition brings metabolic compromises in glioblastoma multiforme (GBM)
Authors: Ahmad Fahim , Sen Ellora
Published: May 2016

Introduction: A defining characteristic of cancer cells is their ability to circumvent multiple regulatory mechanisms that normally restrict cell proliferation. Understanding the links between aberrant metabolic adaptation and prosurvival responses in glioma cells is crucial towards the development of new anti-glioma therapies. Human telomerase reverse transcriptase (hTERT) is the catalytic subunit of the telomerase holoenzyme. The telomere maintenance or telomerase activity is mainly driven by hTERT and hTERC. A large number of reports suggest an ever increasing role of telomere maintenance in cancer progression. We sought to evaluate its involvement in the regulation of metabolic status in these cells.

Methods: Human glioma cell lines A172 and U87MG Cells were grown in DMEM supplemented with 10% FBS. On attaining semi confluence, cells were switched to SFM (serum free media) for 4 hrs and further treated with Telomerase inhibitor for 24hrs. Glioma cell lines were transiently transfected with lipofectamine 2000 and lipofectamine RNAi max reagents. Cells were harvested 48hrs post transfection. Heterotropic glioma xenografts were generated upon injecting U87MG cells subcutaneously in flank region of nude mice. After 20 days of injection, prominent tumor volume was visible. Thereafter, mice were grouped and administered either with PBS or Telomerase inhibitor for 20 days on every alternate day. Mice were sacrificed and tissues were processed for subsequent experiments. Histochemically identified TERT mutant and wild type human glioma samples were also used to unravel the ongoing signaling cascades.

Results: Inhibition of telomerase resulted in metabolic compromises. TERT was found to regulate the expression of an important transcription factor responsibe for maintenance of metabolic and antioxidant proteins. The expression of this transcription factor was concomitant with altered metabolic profile as characterized by decreased pentose phosphate pathway. TERT regulated expression of PPP genes seemed to have its effect on prosurvival and antioxidant molecules.

Conclusions: hTERT plays a key role in survival responses by modulating the metabolic status of glioma cells both in vitro and in vivo. By switching the signals under the control of a metabolic sensor (transcription factor) that modifies energy status to govern anti proliferative environment, hTERT regulates both survival responses and energy status.

Citation Format: Fahim Ahmad, Ellora Sen. Telomerase inhibition brings metabolic compromises in glioblastoma multiforme (GBM). [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr A08.
Abstract A15: Different stem-like characteristics of diffuse and intestinal type gastric cancer spheroids
Authors: Lee Jong Won , Sung Jae Sook , Chung Seok , Kim Yeul Hong
Published: May 2016

Cancer Stem Cells (CSCs) have been hypothesized to drive the tumor initiation, metastasis and chemo-resistance. Identification of this subpopulation is important to understand the CSCs characteristics and the development of treatment strategy. Spheroid forming ability is the character of CSCs. Thus, sphere culture can be utilized for isolation of CSCs in cancer cell lines. Here, we applied Spheroid Film as a limiting dilution assay platform to isolate gastric CSCs from single cell sphere culture. Gastric cancer cell lines MKN28, MKN74, SNU484 and SNU638 was seeded as single cell in non-attached 361 micro-wells culture dish with serum free condition. After 2 weeks, each well was evaluated whether single cell formed spheroid or not. The population of spheroids was increased in sub-spheroid culture. The spheroids showed higher expression levels of stemness marker, such as OCT4, SOX2 and NANOG than parent cells. Moreover, they exhibited up-regulation of CSC related gene ALDH1A1 and CD44v8-10 compared with parent cells. Spheroids cell were more resistant to drug inducing apoptosis (5FU, Cisplatin and Paclitaxel) than parent cells. When spheroids injected in to skin of nude mice, it showed larger size of tumor than parent cells. Especially, the expression of stemness gene was higher in diffuse type (SNU484 and SNU638) than intestinal type (MKN28 and MKN74). Besides, diffuse type has lower IC50 value of anti-cancer drugs than intestinal type. In conclusion, cancer stem-like cells were isolated efficiently by single cell spheroid culture methods from gastric cancer cell lines. We have shown that different stem-like characteristics in spheroids cell, and it may be related with their histological type. Further investigation of difference between diffuse and intestinal type gastric cancer sphroids may provide novel insights to understand gastric cancer stem cells.

Citation Format: Jong Won Lee, Jae Sook Sung, Seok Chung, Yeul Hong Kim. Different stem-like characteristics of diffuse and intestinal type gastric cancer spheroids. [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr A15.
Abstract A30: Two faces of YAP: Oncogene in malignant progression but barrier for phenotypic transition in LKB1-deficient lung cancer
Authors: Zhang Wenjing , Gao Yijun , Han Xiangkun , Li Fuming , Ji Hongbin
Published: May 2016

Hippo signaling is actively involved in adult tissue homeostasis and cell fate determination. Previous studies have linked the activation of YAP (the major downstream effector of Hippo pathway) with LKB1 deficiency. Here, we characterize the function of YAP in the malignant progression and phenotypic plasticity of LKB1-deficient lung tumors.

Using various lung cancer mouse models, we show that YAP expression significantly accelerates lung adenocarcinoma (ADC) malignant progression in KrasG12D mice whereas YAP deletion dramatically delays the process in Lkb1L/L/KrasG12D mice, suggesting that YAP functions as an essential mediator of malignant progression of Lkb1-deficient lung ADC. Further mechanistic studies identified Survivin as the mediator downstream of YAP in promoting malignant progression of Lkb1-deficient lung ADC. Knockdown of Survivin mimics the inhibitory phenotype of YAP knockdown whereas ectopic expression of Survivin rescues the inhibitory function of YAP knockdown. Our previous work has shown LKB1 inactivation confers lung ADC with strong plasticity to progressively change the cell fate and transit to squamous cell carcinoma (SCC). We find that ectopic YAP expression dramatically inhibits ADC to SCC transdifferentiation whereas knockdown of YAP conversely accelerates the transition process. YAP is initially activated by LKB1 loss in ADC, leading to ZEB2 up-regulation in ADC cells, which binds to DNp63 gene promoter to repress DNp63 transcription. During the transition process, extracellular matrix (ECM) depletion in ADC inactivates YAP, thus relieves ZEB2 mediated default repression on DNp63 transcription in ADC, leading to the initiation of squamous differentiation program.

Together, these findings uncover the two faces of YAP in lung tumor malignant progression and phenotypic plasticity. YAP is an essential mediator of malignant progression of Lkb1-deficient lung ADC via regulating Survivin whereas an important barrier for lung cancer transdifferentiation through ZEB2 dependent DNp63 repression. Those works shed light on the fundamental role of YAP in regulating cancer progression and lineage phenotypic transition in LKB1 deficient lung tumors, which might help future development of better therapeutic strategies.

Citation Format: Wenjing Zhang, Yijun Gao, Xiangkun Han, Fuming Li, Hongbin Ji. Two faces of YAP: Oncogene in malignant progression but barrier for phenotypic transition in LKB1-deficient lung cancer. [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr A30.
Abstract A31: Monitoring the activity of various classes of methylltransferases in vitro using a universal, homogenous and bioluminescent assay
Authors: Goueli Said A.
Published: May 2016

Post transcriptional modifications of proteins and nucleic acids are well-recognized to play major role in mediation of extensive and broad range of cellular functions. Such modifications that include phosphorylation, acetylation, methylation, etc. are known to be critical for normal and abnormal cell growth, and thus, the enzymes involved in these reactions have been validated as drug targets resulting in the development of several drugs. Recent biochemical and biological data suggest that the enzymatic activities of several of these enzymes have pathogenic roles in cancer, inflammation, and neurodegenerative diseases. Thus, pharmacological modulation of these enzymes by small molecules will be beneficial in the development of novel therapeutics for multiple unmet medical needs. Of these, methyltransferases are known to alter the epigenome by altering the methylation status of nucleic acids or proteins resulting in changes in cellular phenotypes. Towards this goal of searching for activators/inhibitors of these enzymes for the development of next generation of drugs, screening assays for these modulators are urgently needed. To address these unmet needs, we have developed a novel assay that monitors the activities of these enzymes and their modulation by small molecules. The assay is bioluminescent based, HTS formatted and highly sensitive. The assay is universal since it is based on monitoring the formation of the universal product S-adenosylhomocysteine (SAH), i.e., capable of detecting changes in activity of a broad range of methyltransferases such as DNA, protein, RNA, and small molecules methyltransferases. In addition, the assay has been validated for all classes of protein methyltransferases (Lysine and Arginine), and with different types of substrates (small peptides, large proteins, or even nucleosomes). This enables determining the specificity of these enzymes and their substrate requirements. The assay has high signal to background and low C.V. The assay is robust (Z’ value > 0.7) and has been validated using various plate densities such as 96-, 384, and 1536-well plates. A strong feature of this assay is its utility with broad range of substrates with no limitations on the use of high concentrations of substrates or the composition of the substrates (short vs. long peptides), thus enabling the generation of kinetic data and determining the mechanism of action of various modulators of methyltransferases of interest.

Citation Format: Said A. Goueli. Monitoring the activity of various classes of methylltransferases in vitro using a universal, homogenous and bioluminescent assay. [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr A31.
Abstract B08: Inflammasome components caspase-1, IL1β, IL18 and NLRP3 (NOD-like receptor family, pyrin domain containing 3) are increased in a spontaneous model (chicken: Gallus gallus) of human ovarian cancer
Authors: Luborsky Judith , Edassery Seara , Edassery Seby L. , Barua Animesh , Bahr Janice M.
Published: May 2016

Chronic inflammation is associated with cancer risk and development. There is increasing evidence that a chronic, pro-inflammatory environment is mediated by multi-protein inflammasome complexes that promote activation of IL1β and IL18, which are apex cytokines for regulation of inflammation. The objective was to determine if the inflammasome components NLRP3, caspase-1, IL1β and IL18 were expressed in ovarian cancer and if the expression differed between normal ovary and ovarian tumors using the hen, an animal model of spontaneous ovarian cancer. mRNA was measured by qRT-PCR using primers based on chicken orthologs of human genes from the NCBI database as follows, NLRP3 XM_001233261.3; Caspase-1 XM_003642384.2; IL1β NM_204524.1; IL18 NM_204608; IL17 NM_204460.1. mRNA expression (mean fold change compared to normal ovary = mFC) was increased significantly (t -test) compared to normal ovaries for caspase-1 (mFC=14.6±12.6; p=0.01), IL1β (mFC=6.5±5.3 p=0.01) and IL18 (mean fold change=4.9±3.4; p=0.01) with a moderate increase in NLRP3 (mFC=1.7±0.98; p=0.04) in cancer (n=8) compared to normal ovary (n=6). Expression of the pro-inflammatory cytokine, IL17 was increased (mFC=4.0±6.0; p=0.1) but not significantly in this limited sample set. Moderate protein expression of the same components was evident by immunohistochemistry in groups of tumor cells but not in all tumor cells. Expression also occurred in tumor immune cells; the number of immunohistochemically reactive immune cells varied among tumors. Differences in invading immune cells with an activated inflammasome could account for the range of total mRNA values; differences among tumor expression of inflammasomes infers a potential basis for differences in response to immunotherapies. The results demonstrate expression of inflammasome components in a spontaneous model resembling human ovarian cancer and suggest a mechanism by which a chronic pro-inflammatory, pro-tumor environment is maintained. Improved understanding of the role of inflammasomes could lead to methods for management of the tumor immune environment and responses to immunotherapy.

Citation Format: Judith Luborsky, Seara Edassery, Seby L. Edassery, Animesh Barua, Janice M. Bahr. Inflammasome components caspase-1, IL1β, IL18 and NLRP3 (NOD-like receptor family, pyrin domain containing 3) are increased in a spontaneous model (chicken: Gallus gallus) of human ovarian cancer. [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr B08.
Abstract B33: The oligoclonal antibody MM-151 overcomes acquired resistance to cetuximab and panitumumab in colorectal cancer cells harboring EGFR extracellular domain mutations
Authors: Arena Sabrina , Siravegna Giulia , Mussolin Benedetta , Kearns Jeffrey D. , Wolf Beni B. , Misale Sandra , Lazzari Luca , Bertotti Andrea , Trusolino Livio , Adjei Alex , Montagut Clara , Nicolantonio Federica Di , Nering Rachel , Bardelli Alberto
Published: May 2016

The anti-EGFR antibodies cetuximab and panitumumab are used to treat ‘RAS’ wild type colorectal cancers (CRCs), but their efficacy is limited by development of drug resistance. At relapse, approximately 20% of tumors carry EGFR extracellular domain (ECD) mutations (S492R, R451C, S464L, G465R, G465E, K467T, I491M) that impair antibody binding. We find that these EGFR genetic variants are effectively targeted by the oligoclonal anti-EGFR antibody MM-151. Both EGFR mediated signaling and proliferation of colorectal cancer (CRC) cells carrying EGFR ECD mutations are impaired by MM-151. Notably, EGFR extracellular domain mutations, which are found in circulating free tumor DNA (ctDNA) of CRC patients who relapsed upon anti-EGFR antibodies treatment, decline during MM-151 therapy. In conclusion, MM-151 based therapy may be valuable for the treatment of secondary resistance to cetuximab and panitumumab driven by EGFR ECD mutations. Further prospective clinical evaluation is warranted.

Citation Format: Sabrina Arena, Giulia Siravegna, Benedetta Mussolin, Jeffrey D. Kearns, Beni B. Wolf, Sandra Misale, Luca Lazzari, Andrea Bertotti, Livio Trusolino, Alex Adjei, Clara Montagut, Federica Di Nicolantonio, Rachel Nering, Alberto Bardelli. The oligoclonal antibody MM-151 overcomes acquired resistance to cetuximab and panitumumab in colorectal cancer cells harboring EGFR extracellular domain mutations. [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr B33.
Abstract B34: Quantitative systems pharmacology and immunotherapy: accelerating lead generation and optimization of a PD-1 x TIM-3 biotherapeutic in immuno-oncology
Authors: Apgar Joshua F. , Wong Jamie , Phennicie Ryan , Briskin Mike , Burke John M.
Published: May 2016

The goal of this collaboration was to provide early quantitative decision making guidance for the project team by developing and interrogating a quantitative systems pharmacology (QSP) model of the co-modulation inhibitory receptors PD-1 and TIM-3 in immuno-oncology. The QSP model was to: (1) provide predictions of the best-in-class profile for a PD-1 and TIM-3 dual antagonist biologic(s), (2) accelerate project timelines, (3) provide biological insights, and (4) reduce experimental costs.

The QSP model was based on first principles as a system of elementary mass-action, mechanistic PKPD, ordinary differential equations. The model parameters and reactions were based on biophysics, and are interpretable. The model reactions include protein synthesis and elimination, ligand-receptor and drug-target formation and turnover, and drug administration and first order clearance. There were four versions of the model: PD-1 monospecific, TIM-3 monospecific, PD-1 x TIM-3 bispecific and fixed dose combination (FDC) targeting PD-1 and TIM-3. The monospecific models were then benchmarked against published data such that model parameter values were set to known values and unknown parameters were estimated. Once benchmarked, the FDC and bispecific models were analyzed by systematically investigating how tuning the model parameters (e.g., affinity, avidity, dose, half-life, target expression, etc.) impacted target inhibition, and to simulate patient variability.

The model was in good agreement with published clinical data from nivolumab and pembrolizumab, and data from RMT3-23 in the TIM-3 driven mouse model. QSP model analysis predicted: (1) there would be diminishing returns on very tight binding biologics due to Target Mediated Drug Disposition (TMDD) that offsets potency, and (2) there is no advantage between FDC, 2-2 bispecific, and 2-1 bispecific formats, which are predicted to be roughly equivalent. As a result of these analyses, there was a significant reduction in the number of experiments, and acceleration of project timelines by (1) eliminating rounds of affinity maturation, as drug leads were in predicted optimal drug parameter ranges, and (2) eliminating the need to construct and evaluate bi-specific constructs and proceed with FDCs.

Citation Format: Joshua F. Apgar, Jamie Wong, Ryan Phennicie, Mike Briskin, John M. Burke. Quantitative systems pharmacology and immunotherapy: accelerating lead generation and optimization of a PD-1 x TIM-3 biotherapeutic in immuno-oncology. [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr B34.
Abstract IA15: Functional diversity of the pancreas tumor stroma
Authors: LeBleu Valerie S. , Özdemir Berna C. , Pentcheva-Hoang Tsvetelina , Carstens Julienne L. , Zheng Xiaofeng , Wu Chin-Chia , Simpson Tyler , Laklai Hanane , Sugimoto Hikaru , Kahlert Christoph , Novitskiy Sergey V. , Acosta Ana DeJesus , Sharma Padmanee , Heidari Pedram , Mahmood Umar , Chin Lynda , Moses Harold , Weaver Valerie , Maitra Anirban , Allison James P. , Kalluri Raghu
Published: May 2016

The desmoplastic reaction in pancreatic ductal adenocarcinoma (PDAC) is composed of functionally diverse cellular components embedded in a complex and dynamic fibrotic matrix. In this context, the marked accumulation of stromal myofibroblasts has long been associated with pro-tumorigenic functions, by enhancing tumor cell growth, and limiting immune infiltration and chemotherapeutic drug delivery. Testing of some of these concepts in the clinical care of PDAC patients was however met with paradoxical results. Precise functional auditing of the stromal fibroblasts using genetic targeting in genetically engineered mouse models of PDAC depicted a more complex picture, wherein myofibroblast emerged in this context as tumor-limiting stromal cells. Depletion of the stromal fibroblasts in the early and late stages of PDAC in mice led to more invasive tumors with a negative impact on overall survival, and failed to improve response to Gemcitabine therapy. While our result indicated that suppression of the desmoplastic reaction was associated with decreased tumor angiogenesis, increased intratumoral hypoxia, and epithelial-to-mesenchymal transition of cancer cells with heightened tumorigenicity, our study also informed on the immunomodulatory functions of myofibroblasts in murine PDAC. Depletion of myofibroblasts supported an enhanced response to anti-CTLA4 checkpoint blockade therapy with prolonged survival of mice.

Citation Format: Valerie S. LeBleu, Berna C. Özdemir, Tsvetelina Pentcheva-Hoang, Julienne L. Carstens, Xiaofeng Zheng, Chin-Chia Wu, Tyler Simpson, Hanane Laklai, Hikaru Sugimoto, Christoph Kahlert, Sergey V. Novitskiy, Ana DeJesus Acosta, Padmanee Sharma, Pedram Heidari, Umar Mahmood, Lynda Chin, Harold Moses, Valerie Weaver, Anirban Maitra, James P. Allison and Raghu Kalluri. Functional diversity of the pancreas tumor stroma. [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr IA15.
Abstract IA20: Chromatin looping factors and breast cancer
Authors: Treloar Aislinn , Wu Xue , Penrod Nadia , Bailey Swneke D. , Zhang Xiaoyang , Desai Kinjal , Gyorffy Balazs , Lupien Mathieu
Published: May 2016

Estrogen signaling in breast cancer cells relies on chromatin interactions connecting distal regulatory elements bound by the estrogen receptor alpha (ER) to target gene promoters. This ensures stimulus and subtype-specific transcriptional responses. Chromatin looping factors, including CTCF, ZNF143 and RAD21, are genetically altered in breast cancer. However, the impact of these alterations on breast cancer development is ill defined. Here we demonstrate that ZNF143 directly regulates the formation of chromatin interactions by marking promoters connecting with distal regulatory elements. ZNF143 occupies the promoter of most early-response estrogen target genes in ER-positive breast cancer cells. Its chromatin occupancy is unaffected by estrogen stimulation suggesting that chromatin interactions are stable as opposed to modulated by stimulus. ZNF143 overexpression within ER-positive breast cancer patients associates with a worse outcome. Its loss abrogates the estrogen response in breast cancer cells. Overall, these results suggest that ZNF143 is a critical effector of the estrogen response and highlights the contribution of the chromatin looping machinery to ER-positive breast cancer development.

Citation Format: Aislinn Treloar, Xue Wu, Nadia Penrod, Swneke D. Bailey, Xiaoyang Zhang, Kinjal Desai, Balazs Gyorffy, Mathieu Lupien. Chromatin looping factors and breast cancer. [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr IA20.
Abstract IA27: Retooling CRISPR to turn genes on and off
Authors: Gilbert Luke A. , Horlbeck Max A. , Villalta Jacqueline , Hao Shao , Gestwicki Jason E. , Weissman Jonathan S.
Published: May 2016

CRISPR (clustered regularly interspaced short palindromic repeats) is an adaptive genome defense system in bacteria and archaea. CRISPR has been widely repurposed as an RNA-guided genome editing method. We have shown that the endonuclease domains of the Cas9 protein can be mutated to create a programmable RNA-guided DNA-binding protein. In human cells, we have shown we can control transcription of endogenous coding and non-coding genes over a wide range (up to 1000 fold) by using dCas9 chimeras to deliver protein domains that either repress (CRISPRi) or activate (CRISPRa) transcription. These experiments provide proof of principle that we can use dCas9 as an RNA-guided DNA binding platform to deliver in theory any protein to a specific genomic location, which may be useful for studying transcription, epigenetic regulation, DNA replication and DNA repair.

We have developed a genome-scale CRISPRi/a functional genomics platform for loss- and gain-of-function screening in human cells. We have demonstrated that our CRISPRi/a screening platform can robustly identify pathways and proteins required for cancer cell growth and survival. Gain-of-function CRISPRa screens promise to reveal a layer of genetic information missing from previous efforts. We have shown in a cell growth screen that CRISPRa reveals latent tumor suppressors and transcription factors that regulate cancer cell state in chronic myeloid leukemia cells. In proof of principle, we have also used CRISPRi/a screens to determine the mechanism of cellular uptake, trafficking, retro-translocation, and toxicity for a chimeric bacterial toxin. These experiments establish CRISPRi and CRISPRa as powerful tools that provide rich and complementary information for mapping complex pathways.

Recently, we have used our CRISPRi/a functional genomics platform to determine the genetics of cellular response to HSP70 inhibitors, which are a new class of anti-cancer drugs targeting a non-oncogene addiction. Together, our experiments demonstrate the utility of our CRISPRi/a functional genomics approach for studying principles of oncogene and non-oncogene addiction in cancer biology and cancer therapy.

Citation Format: Luke A. Gilbert, Max A. Horlbeck, Jacqueline Villalta, Shao Hao, Jason E. Gestwicki, Jonathan S. Weissman. Retooling CRISPR to turn genes on and off. [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr IA27.
Abstract IA34: Clinical proof of concept for the first-in-class BCL-2-selective inhibitor venetoclax (ABT-199/GDC-0199)
Authors: Leverson Joel D.
Published: May 2016

Many cancer cells maintain survival through over-expression of anti-apoptotic BCL-2 family proteins, which sequester high levels of their pro-apoptotic counterparts. While this makes BCL-2 proteins compelling targets for the development of cancer therapeutics, synthesizing small molecules capable of disrupting these protein-protein interactions has been a major challenge for the field. Structure-based drug design led to the discovery of navitoclax (ABT-263), a dual inhibitor of BCL-2 and BCL-XL. Navitoclax has shown promising activity in the clinic but its efficacy has been limited by thrombocytopenia caused by BCL-XL inhibition. To avoid this toxicity, we designed a BCL-2-selective inhibitor, venetoclax (ABT-199/GDC-0199), that maintains efficacy in hematologic malignancies while sparing platelets. In this presentation, I will review the preclinical work that led to the discovery of venetoclax, the translational studies that have pointed to utility for venetoclax in a variety of cancers, and the results from ongoing clinical studies, in which venetoclax has demonstrated clear signs of activity. I will discuss what we have learned from multiple iterations of translational work between the bench and the bedside, and how we are using a toolkit of highly selective BCL-2 family inhibitors to parse the roles of BCL-2 family proteins in cancer cell survival.

JDL is an AbbVie employee. The design, study conduct and financial support was provided by AbbVie and Genentech. AbbVie and Genentech participated in the data generation, interpretation of data, review and approval of this publication (A5107572).

Citation Format: Joel D. Leverson. Clinical proof of concept for the first-in-class BCL-2-selective inhibitor venetoclax (ABT-199/GDC-0199). [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr IA34.