1,721,013 research outputs found
Abstract 1247: Identifying novel regulators of the Unfolded Protein Response (UPR) by genome-scale CRISPR-Cas9 knockout screens
No full textAbstract
Development and growth of a tumor as well as its ability to metastasize involves a complex relationship with its tissue microenvironment. A proliferating tumor encounters several microenvironmental stress conditions such as hypoxia, lack of nutrients and acidosis. To cope with these conditions, cancer cells have developed elaborate cytoprotective mechanisms which provide them with distinct advantages to thrive. Thus, deciphering the signaling pathways which get activated in the tumor microenvironment has been paramount to develop new therapeutic strategies for treatment. The Unfolded Protein Response (UPR) is an adaptive prosurvival pathway elicited by stresses in the tumor microenvironment (e.g., hypoxia, low glucose) and involves translational and transcriptional activation of effector genes which act to relieve cellular stress and block cancer cell death. We developed a strategy to comprehensively analyze critical mediators of cell fate in response to UPR activation. We have delivered a lentiviral genome-scale CRISPR Cas9 knockout (GeCKOv2) library to Sq20B cells (human squamous head and neck carcinoma) and A375 (human melanoma) cells. The library is targeting 19,050 genes with 123,411 unique guide sequences and enables both negative and positive selection screening. We used the GeCKO v2 library to identify genes essential for triggering the UPR in response to thapsigargin and tunicamycin, known specific activators of ER stress. Our highest-ranking candidates include BIRC5/Survivin, a well-studied molecule that acts as an inhibitor of apoptosis and is highly expressed in cancer cells and eukaryotic translation initiation factor eIF6, whose overexpression increases motility and invasiveness of cancer cells. Our preliminary results indicate that loss of Survivin and eIF6 dramatically enhance sensitization of cells to various ER stress conditions. Moreover, this synergistic outcome is observed when cells are treated with YM155, a small molecule that selectively suppresses Survivin and is used in phase I/II clinical trials. Lastly, morphological changes like endoreduplication are observed after long term absence of Survivin indicating its endogenous ER stress inducing role. Taken together, Survivin and eIF6 are important mediators of survival following ER stress and characterizing the pathways involved can lead to the development of novel targeted agents and therapeutic approaches.
Citation Format: Nektaria Maria Leli, Souvik Dey, Lauren Brady, Constantinos Koumenis. Identifying novel regulators of the Unfolded Protein Response (UPR) by genome-scale CRISPR-Cas9 knockout screens [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 1247. doi:10.1158/1538-7445.AM2017-1247</jats:p
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Finite Sum Representations of Elements in R and R2
Get PDFIn February 2017, a number theoretic problem was posed in Mathematics Magazine by Souvik Dey, a master’s student in India. The problem asked whether it was possible to represent a real number by a finite sum of elements in an open subset of the real numbers that contained one positive and one negative number. This paper not only provides a solutionto the original problem, but proves an analogous statement for elements of R2
Finite Sum Representations of Elements in R and R2
Get PDFIn February 2017, a number theoretic problem was posed in Mathematics Magazine by Souvik Dey, a master’s student in India. The problem asked whether it was possible to represent a real number by a finite sum of elements in an open subset of the real numbers that contained one positive and one negative number. This paper not only provides a solutionto the original problem, but proves an analogous statement for elements of R2
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
Abstract 4500: Inhibition of PERK by small molecule inhibitors enhances the response to ionizing radiation in vitro and animal tumor models
No full textAbstract
Endoplasmic reticulum (ER) is a well organized membranous network, responsible for synthesis and folding of secretory and membrane proteins, lipid and sterol biosynthesis and intracellular calcium storage. Perturbations in ER lumen caused by depletion of Ca2+ levels, hypoxia, nutrient deprivation, affect the ER homeostasis, a condition known as an ER stress. In order to cope with this stress, cells have developed an orchestrated biochemical response, termed Unfolded Protein Response (UPR). Hypoxia, an ER stress inducer, is an important and unique characteristic of the solid tumor microenvironment, promotes resistance to radiotherapy and contributes to poor patient prognosis. Cancer cells overcome these stress conditions through activation the PERK-eIF2α arm of the UPR, leading to inhibition of global protein synthesis and cell survival. We hypothesize that the use of small molecule PERK inhibitors will decrease the survival of hypoxic cells and eventually sensitize them to irradiation. In this study we used highly radioresistant melanoma and head and neck squamous cell carcinoma cell lines B16F10-ova and SQ20B, under nomroxia and hypoxia, respectively. We used two specific PERK inhibitors (PERKi) and tested for their efficacy both in vitro and in vivo. Induction of ER stress in both cell lines, either by treatment with the pharmacologic agents thapsigargin (TG) and tunicamycin (TN), or by exposure to hypoxic conditions (0.2%), was evaluated by activation of PERK and its downstream targets. Pre-treatment of stressed B16F10-ova and SQ20B cells for 2h with PERKi (1μM), caused complete inhibition of PERK-eIF2a-ATF4-CHOP arm of the UPR. Moreover, both cell lines pre-treated with PERKi presented a significant decrease in survival fraction under ER-stress induced by TG (0.5μM) as well as under hypoxia (0.2%) along with increasing doses of irradiation (IR). For the in vivo experiments, nude and C57BL/6 mice were treated with either 100mg/kg of PERKi by oral gavage, twice a day for 3weeks, or IR or a combination of PERKi and IR. Mice treated with PERKi showed a small but not significant delay of tumor growth in both backgrounds of mice. However, combined treatment with IR (12 and 15Gy) caused a significant reduction of tumor volume as well as a delayed tumor growth which was significantly more pronounced in the immunocompetent mice. Data from flow cytometry analysis of one of the the PERKi+IR treated tumors from C57BL/6 mice showed that there is a significant infiltration of CD3+ cells as well as significant higher number of CD3+CD8+ cells compared to the untreated mice or mice treated with either PERKi or IR alone. Collectively, our results show that PERKi effectively reduces the survival of hypoxic B16F10-ova and SQ20B cells and sensitize them to IR in vitro and in tumors. Further experiments will clarify whether PERKi have a dual role on reducing the hypoxic fraction and direct recruitment of the cytotoxic T-cells.
Citation Format: Ioannis Verginadis, Joel Encarnación, Souvik Dey, Constantinos Koumenis. Inhibition of PERK by small molecule inhibitors enhances the response to ionizing radiation in vitro and animal tumor models [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 4500. doi:10.1158/1538-7445.AM2017-4500</jats:p
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