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non conding rna

Alain Casanova, Shyan H Low, Mario Emmenlauer, Raquel Conde-Alvarez, Suzana P Salcedo, Jean-Pierre Gorvel, Christoph Dehio
Brucella species are facultative intracellular pathogens that infect animals as their natural hosts. Transmission to humans is most commonly caused by direct contact with infected animals or by ingestion of contaminated food and can lead to severe chronic infections. Brucella can invade professional and non-professional phagocytic cells and replicates within endoplasmic reticulum (ER)-derived vacuoles. The host factors required for Brucella entry into host cells, avoidance of lysosomal degradation, and replication in the ER-like compartment remain largely unknown...
2016: Journal of Visualized Experiments: JoVE
Daouda Sissoko, Cedric Laouenan, Elin Folkesson, Abdoul-Bing M'Lebing, Abdoul-Habib Beavogui, Sylvain Baize, Alseny-Modet Camara, Piet Maes, Susan Shepherd, Christine Danel, Sara Carazo, Mamoudou N Conde, Jean-Luc Gala, Géraldine Colin, Hélène Savini, Joseph Akoi Bore, Frederic Le Marcis, Fara Raymond Koundouno, Frédéric Petitjean, Marie-Claire Lamah, Sandra Diederich, Alexis Tounkara, Geertrui Poelart, Emmanuel Berbain, Jean-Michel Dindart, Sophie Duraffour, Annabelle Lefevre, Tamba Leno, Olivier Peyrouset, Léonid Irenge, N'Famara Bangoura, Romain Palich, Julia Hinzmann, Annette Kraus, Thierno Sadou Barry, Sakoba Berette, André Bongono, Mohamed Seto Camara, Valérie Chanfreau Munoz, Lanciné Doumbouya, Souley Harouna, Patient Mumbere Kighoma, Fara Roger Koundouno, Réné Lolamou, Cécé Moriba Loua, Vincent Massala, Kinda Moumouni, Célia Provost, Nenefing Samake, Conde Sekou, Abdoulaye Soumah, Isabelle Arnould, Michel Saa Komano, Lina Gustin, Carlotta Berutto, Diarra Camara, Fodé Saydou Camara, Joliene Colpaert, Léontine Delamou, Lena Jansson, Etienne Kourouma, Maurice Loua, Kristian Malme, Emma Manfrin, André Maomou, Adele Milinouno, Sien Ombelet, Aboubacar Youla Sidiboun, Isabelle Verreckt, Pauline Yombouno, Anne Bocquin, Caroline Carbonnelle, Thierry Carmoi, Pierre Frange, Stéphane Mely, Vinh-Kim Nguyen, Delphine Pannetier, Anne-Marie Taburet, Jean-Marc Treluyer, Jacques Kolie, Raoul Moh, Minerva Cervantes Gonzalez, Eeva Kuisma, Britta Liedigk, Didier Ngabo, Martin Rudolf, Ruth Thom, Romy Kerber, Martin Gabriel, Antonino Di Caro, Roman Wölfel, Jamal Badir, Mostafa Bentahir, Yann Deccache, Catherine Dumont, Jean-François Durant, Karim El Bakkouri, Marie Gasasira Uwamahoro, Benjamin Smits, Nora Toufik, Stéphane Van Cauwenberghe, Khaled Ezzedine, Eric D'Ortenzio, Eric Dortenzio, Louis Pizarro, Aurélie Etienne, Jérémie Guedj, Alexandra Fizet, Eric Barte de Sainte Fare, Bernadette Murgue, Tuan Tran-Minh, Christophe Rapp, Pascal Piguet, Marc Poncin, Bertrand Draguez, Thierry Allaford Duverger, Solenne Barbe, Guillaume Baret, Isabelle Defourny, Miles Carroll, Hervé Raoul, Augustin Augier, Serge P Eholie, Yazdan Yazdanpanah, Claire Levy-Marchal, Annick Antierrens, Michel Van Herp, Stephan Günther, Xavier de Lamballerie, Sakoba Keïta, France Mentre, Xavier Anglaret, Denis Malvy
BACKGROUND: Ebola virus disease (EVD) is a highly lethal condition for which no specific treatment has proven efficacy. In September 2014, while the Ebola outbreak was at its peak, the World Health Organization released a short list of drugs suitable for EVD research. Favipiravir, an antiviral developed for the treatment of severe influenza, was one of these. In late 2014, the conditions for starting a randomized Ebola trial were not fulfilled for two reasons. One was the perception that, given the high number of patients presenting simultaneously and the very high mortality rate of the disease, it was ethically unacceptable to allocate patients from within the same family or village to receive or not receive an experimental drug, using a randomization process impossible to understand by very sick patients...
March 2016: PLoS Medicine
Ana B Larque, Laura Conde, Sofia Hakim, Llucia Alos, Pedro Jares, Isabel Vilaseca, Antonio Cardesa, Alfons Nadal
We studied the expression of p16(INK4a) in a series of HPV-negative laryngeal squamous cell carcinomas and assessed its association with prognosis. Forty-five patients with laryngeal carcinoma were included in the study. Clinicopathological features and prognosis were reviewed. p16(INK4a) protein expression was analysed through immunohistochemistry. We analysed messenger RNA (mRNA) in 25 cases through quantitative reverse transcription polymerase chain reaction. HPV status was assessed by PCR using three different protocols based on MY09/11 and GP5/6 primers...
April 2015: Virchows Archiv: An International Journal of Pathology
Pauli Rämö, Anna Drewek, Cécile Arrieumerlou, Niko Beerenwinkel, Houchaima Ben-Tekaya, Bettina Cardel, Alain Casanova, Raquel Conde-Alvarez, Pascale Cossart, Gábor Csúcs, Simone Eicher, Mario Emmenlauer, Urs Greber, Wolf-Dietrich Hardt, Ari Helenius, Christoph Kasper, Andreas Kaufmann, Saskia Kreibich, Andreas Kühbacher, Peter Kunszt, Shyan Huey Low, Jason Mercer, Daria Mudrak, Simone Muntwiler, Lucas Pelkmans, Javier Pizarro-Cerdá, Michael Podvinec, Eva Pujadas, Bernd Rinn, Vincent Rouilly, Fabian Schmich, Juliane Siebourg-Polster, Berend Snijder, Michael Stebler, Gabriel Studer, Ewa Szczurek, Matthias Truttmann, Christian von Mering, Andreas Vonderheit, Artur Yakimovich, Peter Bühlmann, Christoph Dehio
BACKGROUND: Large-scale RNAi screening has become an important technology for identifying genes involved in biological processes of interest. However, the quality of large-scale RNAi screening is often deteriorated by off-targets effects. In order to find statistically significant effector genes for pathogen entry, we systematically analyzed entry pathways in human host cells for eight pathogens using image-based kinome-wide siRNA screens with siRNAs from three vendors. We propose a Parallel Mixed Model (PMM) approach that simultaneously analyzes several non-identical screens performed with the same RNAi libraries...
2014: BMC Genomics
Lucia Conde, Jacques Riby, Jianqing Zhang, Paige M Bracci, Christine F Skibola
Recent GWAS have identified several susceptibility loci for NHL. Despite these successes, much of the heritable variation in NHL risk remains to be explained. Common copy-number variants are important genomic sources of variability, and hence a potential source to explain part of this missing heritability. In this study, we carried out a CNV analysis using GWAS data from 681 NHL cases and 749 controls to explore the relationship between common structural variation and lymphoma susceptibility. Here we found a novel association with diffuse large B-cell lymphoma (DLBCL) risk involving a partial duplication of the C-terminus region of the LOC283177 long non-coding RNA that was further confirmed by quantitative PCR...
2014: PloS One
Y Huang, J P Wang, X L Yu, Z V Wang, T S Xu, X C Cheng
With the completion of large scale genomic sequencing, a great number of non-conding RNAs (ncRNAs) have been discovered and capture the attention of the biological sciences community. All known ncRNAs may be divided into two groups, namely: i) small ncRNAs, which comprise microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs) and short interfering RNAs (siRNAs), and ii) several thousands of long ncRNAs (IncRNAs). NcRNAs were shown to be involved in eukaryotic growth and development, cell proliferation and differentiation, apoptosis, epigenetic modifications, and also the complex control and pathogenesis of various diseases...
July 2013: Molekuliarnaia Biologiia
Pablo Palma, Marta Cuadros, Raquel Conde-Muíño, Carmen Olmedo, Carlos Cano, Inmaculada Segura-Jiménez, Armando Blanco, Pablo Bueno, J Antonio Ferrón, Pedro Medina
Preoperative chemoradiation significantly improves oncological outcome in locally advanced rectal cancer. However there is no effective method of predicting tumor response to chemoradiation in these patients. Peripheral blood mononuclear cells have emerged recently as pathology markers of cancer and other diseases, making possible their use as therapy predictors. Furthermore, the importance of the immune response in radiosensivity of solid organs led us to hypothesized that microarray gene expression profiling of peripheral blood mononuclear cells could identify patients with response to chemoradiation in rectal cancer...
2013: PloS One
Felix Royo, Karin Schlangen, Laura Palomo, Esperanza Gonzalez, Javier Conde-Vancells, Agustin Berisa, Ana M Aransay, Juan M Falcon-Perez
The discovery that the cells communicate through emission of vesicles has opened new opportunities for better understanding of physiological and pathological mechanisms. This discovery also provides a novel source for non-invasive disease biomarker research. Our group has previously reported that hepatocytes release extracellular vesicles with protein content reflecting the cell-type of origin. Here, we show that the extracellular vesicles released by hepatocytes also carry RNA. We report the messenger RNA composition of extracellular vesicles released in two non-tumoral hepatic models: primary culture of rat hepatocytes and a progenitor cell line obtained from a mouse foetal liver...
2013: PloS One
Eva Pros, Sylvie Lantuejoul, Lydia Sanchez-Verde, Sandra D Castillo, Ester Bonastre, Ana Suarez-Gauthier, Esther Conde, Juan C Cigudosa, Fernando Lopez-Rios, Juan Torres-Lanzas, Josep Castellví, Santiago Ramon y Cajal, Elisabeth Brambilla, Montse Sanchez-Cespedes
Growth factor receptors (GFRs) are amenable to therapeutic intervention in cancer and it is important to select patients appropriately. One of the mechanisms for activation of GFRs is gene amplification (GA) but discrepancies arising from the difficulties associated with data interpretation and the lack of agreed parameters confound the comparison of results from different laboratories. Here, we attempt to establish appropriate conditions for standardization of the determination of GA in a panel of GFRs. A NSCLC tissue microarray panel containing 302 samples was screened for alterations at ALK, FGFR1, FGFR2, FGFR3, ERBB2, IGF1R, KIT, MET and PDGFRA by FISH, immunostaining and/or real-time quantitative RT-PCR...
August 15, 2013: International Journal of Cancer. Journal International du Cancer
Marta Conde-Sieira, Rosa Alvarez, Marcos A López-Patiño, Jesús M Míguez, Gert Flik, José L Soengas
To assess the hypothesis that cortisol release in rainbow trout is modulated by glucose levels, we first evaluated cortisol release [basal and adrenocorticotropic hormone (ACTH)-regulated] by head kidney tissue superfused with medium reflecting hypoglycaemic, normoglycaemic or hyperglycaemic conditions. Next, cortisol release from head kidney fragments in static incubations was assessed in parallel with changes in parameters related to cortisol synthesis (mRNA abundance of StAR, P450scc, 3βHSD and 11βH) and the GK-mediated glucosensing mechanism (levels of glycogen and glucose, activities of GK, GSase and PK, and mRNA levels of GK, GLUT-2, Kir6...
February 15, 2013: Journal of Experimental Biology
João Conde, Gonçalo Doria, Jesus M de la Fuente, Pedro Viana Baptista
Nanotechnology provides new tools for gene expression analysis that allow for sensitive and specific characterization of prognostic signatures related to cancer. Cancer is a multigenic complex disease where multiple gene loci contribute to the phenotype. The ability to simultaneously monitor differential expression originating from each locus allows for a more accurate indication of degree of cancerous activity than either locus alone. Metal nanoparticles have been widely used as labels for in vitro identification and quantification of target sequences...
2012: Methods in Molecular Biology
Marta Conde-Sieira, Marcos A López Patiño, Jesús M Míguez, José L Soengas
To assess whether the glucosensing capacity in peripheral (liver and Brockmann bodies) and central (hypothalamus and hindbrain) locations of rainbow trout displays day-night variations in its response to changes in circulating glucose levels, we evaluated the response of parameters related to glucosensing [glucose, glycogen and glucose 6-phosphate levels, activities of glucokinase (GK), glycogen synthetase (GSase) and pyruvate kinase (PK), and mRNA abundance of GK, glucose transporter 2 (GLUT2), and K(ATP) channel subunits Kir6...
September 1, 2012: Journal of Experimental Biology
Sergio Ruiz-Llorente, Enrique Carrillo Santa de Pau, Ana Sastre-Perona, Cristina Montero-Conde, Gonzalo Gómez-López, James A Fagin, Alfonso Valencia, David G Pisano, Pilar Santisteban
BACKGROUND: The transcription factor Pax8 is essential for the differentiation of thyroid cells. However, there are few data on genes transcriptionally regulated by Pax8 other than thyroid-related genes. To better understand the role of Pax8 in the biology of thyroid cells, we obtained transcriptional profiles of Pax8-silenced PCCl3 thyroid cells using whole genome expression arrays and integrated these signals with global cis-regulatory sequencing studies performed by ChIP-Seq analysis RESULTS: Exhaustive analysis of Pax8 immunoprecipitated peaks demonstrated preferential binding to intragenic regions and CpG-enriched islands, which suggests a role of Pax8 in transcriptional regulation of orphan CpG regions...
2012: BMC Genomics
Carolina Castilla, M Luz Flores, José M Conde, Rafael Medina, Francisco J Torrubia, Miguel A Japón, Carmen Sáez
PTPL1, a non-receptor type protein tyrosine phosphatase, has been involved in the regulation of apoptosis and invasiveness of various tumour cell types, but its role in prostate cancer remained to be investigated. We report here that downregulation of PTPL1 by small interfering RNA in PC3 cells decreases cell proliferation and concomitantly reduces the expression of cell cycle-related proteins such as cyclins E and B1, PCNA, PTTG1 and phospho-histone H3. PTPL1 downregulation also increases the invasion ability of PC3 cells through Matrigel coated membranes...
April 2012: Clinical & Experimental Metastasis
Mario Pérez-Sayáns, Gayoso-Diz Pilar, Francisco Barros-Angueira, José Manuel Suárez-Peñaranda, Alexia Conde Fernández, José Manuel Gándara-Rey, Abel García-García
A micro RNA (miRNA) is a single-stranded endogenous, non-coding RNA, with length ranging between 18 and 24 nucleotides and the ability of regulating the expression of other genes on a post-transcriptional level by means of various processes, degradation or repression of target mRNA. miRNAs play a crucial role in regulating fundamental processes such as cell cycle, differentiation and apoptosis; thus, their deregulation can affect normal cell growth and development, and even participate in carcinogenesis. The goals of this paper are: to outline the formation and functions of miRNAs; to determine their role in oral squamous cell carcinoma; to analyze the different miRNAs described and their roles as oncogenes or tumor suppressor genes, depending on their overexpression or subexpression; to describe the different polymorphisms and epigenetic alterations identified; and to determine their role in multidrug resistance...
July 2012: Journal of Oral Pathology & Medicine
Virginia P Ronchi, Ana M Giudici, Julieta R Mendieta, Veronica J Caballero, Andrea N Chisari, Pedro M Sanllorenti, Rubén D Conde
The aim of this work was to evaluate the effects of a diet depleted of amino acids (protein-free diet, or PFD), as well as the supplementation with methionine (PFD+Met), on the antioxidant status of the female mouse liver. With this purpose, cytosolic protein spots from two-dimensional non-equilibrium pH gel electrophoresis were identified by several procedures, such as mass spectrometry, Western blot, gel matching and enzymatic activity. PFD decreased the contents of catalase (CAT), peroxiredoxin I (Prx-I), and glutathione peroxidase (GPx) by 67%, 37% and 45%, respectively...
June 2010: Journal of Physiology and Biochemistry
D A MacIntyre, B Jiménez, E Jantus Lewintre, C Reinoso Martín, H Schäfer, C García Ballesteros, J Ramón Mayans, M Spraul, J García-Conde, A Pineda-Lucena
Chronic lymphocytic leukaemia (CLL) is a heterogeneous disease exhibiting variable clinical course and survival rates. Mutational status of the immunoglobulin heavy chain variable regions (IGHVs) of CLL cells offers useful prognostic information for high-risk patients, but time and economical costs originally prevented it from being routinely used in a clinical setting. Instead, alternative markers of IGHV status, such as zeta-associated protein (ZAP70) or messenger RNA levels are often used. We report a (1)H-NMR-based metabolomics approach to examine serum metabolic profiles of early stage, untreated CLL patients (Binet stage A) classified on the basis of IGHV mutational status or ZAP70...
April 2010: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
Samuel García, Antonio Mera, Juan J Gómez-Reino, Carmen Conde
OBJECTIVES: To investigate the effect of poly(ADP-ribose) polymerase 1 (PARP-1) suppression on CD95/Apo-1 (Fas)-induced apoptosis in fibroblast-like synoviocytes (FLS) from RA patients. METHODS: Apoptosis, determined by Hoechst staining and quantification of nucleosomal release by ELISA, was induced by stimulation with anti-Fas antibody with or without pre-treatment with cycloheximide (CHX). PARP-1 and poly(ADP-ribose) glycohydrolase (PARG) were suppressed in RA FLS by small interfering RNA (siRNA) transfection...
May 2009: Rheumatology
Mariano Bisbal, Cecilia Conde, Maribel Donoso, Flavia Bollati, Juliana Sesma, Santiago Quiroga, Alberto Díaz Añel, Vivek Malhotra, Maria Paz Marzolo, Alfredo Cáceres
In non-neuronal cells, inactivation of protein kinase D (PKD) blocks fission of trans-Golgi network (TGN) transport carriers, inducing the appearance of long tubules filled with cargo. We now report on the function of PKD1 in neuronal protein trafficking. In cultured hippocampal pyramidal cells, the transferrin receptor (TfR) and the low-density receptor-related protein (LRP) are predominantly transported to dendrites and excluded from axons. Expression of kinase-inactive PKD1 or its depletion by RNA interference treatment dramatically and selectively alter the intracellular trafficking and membrane delivery of TfR- and LRP-containing vesicles, without inhibiting exit from the TGN or inducing Golgi tubulation...
September 10, 2008: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
Joke Reumers, Lucia Conde, Ignacio Medina, Sebastian Maurer-Stroh, Joost Van Durme, Joaquin Dopazo, Frederic Rousseau, Joost Schymkowitz
Single nucleotide polymorphisms (SNPs) are, together with copy number variation, the primary source of variation in the human genome. SNPs are associated with altered response to drug treatment, susceptibility to disease and other phenotypic variation. Furthermore, during genetic screens for disease-associated mutations in groups of patients and control individuals, the distinction between disease causing mutation and polymorphism is often unclear. Annotation of the functional and structural implications of single nucleotide changes thus provides valuable information to interpret and guide experiments...
January 2008: Nucleic Acids Research
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