Brochure CIC bioGUNE

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Brochure CIC bioGUNE

  1. 1. CENTER FOR COOPERATIVERESEARCH IN BIOSCIENCES
  2. 2. CIC bioGUNEPLAYS A STRONG ROLEIN ADVANCINGBIOMEDICAL RESEARCHAND TECHNOLOGICALINNOVATION INTHE BASQUE COUNTRY The conviction that fundamental We live in a time of discovery. Every year, new research and technological innovation can biomedical research and technological discoveries bring us closer to answering of be brought together drives our work atinnovation can be brought together drives the crucial questions about life; improved the Center for Cooperative Research in our work at the Center for Cooperative understanding and treatment of disease have Biosciences, CIC bioGUNE. Research in Biosciences, CIC bioGUNE. never been so tantalizingly close. At the same time, science and technology have become CIC bioGUNE, a non-profit biomedical research global and it is undeniable that scientific organization founded in 2002 by the Department knowledge plays a fundamental role in the of Industry of the Basque Government, opened generation of wealth. However, not all its research installations at the Technology countries know how to obtain the best Park of Bizkaia in January 2005. Since then, socioeconomic benefit from this common CIC bioGUNE has played a strong role in knowledge (the so-called European paradox). advancing biomedical research and The conviction that fundamental biomedical technological innovation in the Basque Country.
  3. 3. innovative approaches to research and Prof José M Mato technological innovation. Following this General Director concept, the Center has set up three joint research laboratories with companies established in the Basque Country. External funding represents a critical component of CIC bioGUNE’s strategic plan. Since 2006, CIC bioGUNE has received CIC bioGUNE invested over 35 million € 4.1 million € from competitive research grants in state-of-the-art research infrastructures, (mainly from the European Union, NIH, the including genomics, gene silencing, Spanish Plan Nacional I+D+I, FIS, CIBER and proteomics, metabolomics, NMR, electron CONSOLIDER programs) and 1 million € from CIC bioGUNE research strategy resides in microscopy, x-ray diffraction, computer and foundations (primarily from the BBVAthe firm belief that if talented researchers animal facilities, to support the research Foundation and Genome Spain) and research are given the freedom and necessary activities of its faculty and students. contracts. Concerted efforts of themeans they will contribute to the solution The Center commits every year more than administration of CIC bioGUNE have helped of the fundamental biological questions. 5.5 million € for research and dedicates 450 the faculty to succeed in the competition for thousand € to PhD training. It employs 22 external funding. Extramural funding, faculty investigators, more than 85 postdocs, combined with the generous support of the technicians and engineers, and provides Basque Government and the Regional training opportunities to more than 23 PhD Government of Bizkaia, allowed faculty students each year. Our 22 faculty investigators, research projects to grow and prosper. recruited internationally, include 15 fellows In fact, in 2008 CIC bioGUNE’s investigators from Ikerbasque, Bizkaia:xede, and Ramón y authored 51 scientific publications, in journals Cajal programs. with an average impact factor of 7, and applied for 3 international patents. CIC bioGUNE research strategy is based on the firm belief that if talented researchers are CIC bioGUNE collaborates with the University given the freedom and necessary means of the Basque Country in the Master of they will contribute to the solution of the Molecular Biology and Biomedicine fundamental biological questions. Following programme, reflecting our commitment to this policy, scientists at CIC bioGUNE have inspire and educate a new generation of established research projects in a variety of scientists. The Center also combines the areas, including cell growth and organization of research seminars, workshops, differentiation, cancer, the innate immune and congresses directed to specialists with response, liver disease, chromatin series of lectures designed for the general remodeling, intracellular trafficking processes, public. CIC bioGUNE, in collaboration with and the structure of proteins, ribosomes and the other CIC, publishes CIC Network, a viruses. The projects are summarized in this journal dedicated to promote a culture of annual report. We also firmly believe in research and technological innovation in the the necessity of creating a lively intellectual Basque Country. environment in collaboration with biotech companies that fosters creative and
  4. 4. INTERDISCIPLINARYRESEARCH WILLADVANCE LIFE SCIENCESDISCOVERIES TOWARDPRACTICAL USESFOR SOCIETY CIC bioGUNE wants to bring Convinced that the convergence of the coordinate all efforts in this area.together under the same roof scientists life sciences and the physical sciences, Both the Center for Cooperative Research from the research centers and those mathematics and engineering can provide in Biosciences in Bizkaia (CIC bioGUNE, from private companies. in the 21st-century an economic growth www.cicbiogune.es) and the Center for comparable to that driven by the Cooperative Research in Biomaterials in convergence between the physical sciences Gipuzkoa (CIC biomaGUNE, and engineering in the 20th-century, www.cicbiomagune.es) represent that the Basque Government recognized life commitment. Founded in 2002, CIC bioGUNE science and biotechnology to be an essential established its research facilities in the Technology pillar of its economy. To reach this aim, in Park of Bizkaia (www.parque-tecnologico.net) 2002 the Basque Government implemented in January 2005 with the aim to bring together a plan, known as BioBasque 2010 under the same roof scientists from the research (www.biobasque.org), to drive and centers and those from private companies.
  5. 5. structure of biological molecules and their Carmen intrinsic function. One of the laboratories, for Garaizar instance, focuses on the “motors” involved President in universal biological functions where interactions between protein and nucleic acids are essential, such as ribosomes during the translation process. Another project launched by CIC bioGUNE seeks the characterization of proteins and their The idea was to stimulate interdisciplinary interactions during chromatin remodeling research that will advance life science discoveries and DNA replication and repair, while yet toward practical uses for society. Five years another studies the atomic structure of virus. later CIC bioGUNE, with around 130 scientists CIC bioGUNE’s laboratories also pursue the At CIC bioGUNE members have and technicians, has produced a brandstream analysis of complex processes such as engaged in their research in the Basque Country. As one indicator of intracellular trafficking or the structural collaborations with scientists, success, the number of companies related characterization of enzymes involved in rare engineers and technology experts to bioscience and biotechnology in the diseases such as porfiria, homocystinuria and at the universities, other research Basque Country has increased from 41 in retinitis pigmentosa. These studies couldand technology centers and biotech 2002 to 72 in 2009 and the sector already provide new strategies for disease diagnosis, companies, as well as with medical accounts for some 1,500 direct jobs. treatment and prevention. doctors in hospitals. At CIC bioGUNE, most of its faculty members Accelerating these innovations will be the have engaged in their research collaborations most important challenge of CIC bioGUNE with scientists, engineers and technology in the coming years. Above all, this will require experts at the universities, other research finding more efficient ways to carry out and technology centers and biotech interdisciplinary work involving the life companies, as well as with medical doctors sciences researchers, the physicists, physicians in hospitals. One collaborative project mathematicians and engineers, as well as launched by CIC bioGUNE, for example, seeks collaboration between CIC bioGUNE and the to develop a blood test for the early diagnosis hospitals, technology centers and biotech of liver diseases. Another project is trying to companies. identify genetic variants implicated in common human complex diseases such as type I diabetes and multiple sclerosis. CIC bioGUNE’s laboratories are also studying cell-signaling mechanisms involved in cancer initiation and metastases. These projects could become a clinical reality within the next few years. CIC bioGUNE’s new Structural Biology Unit, which opened in 2007, includes biologists, chemists and engineers working together to study the relationships between the
  6. 6. “THE WORLD LOOKS SO DIFFERENT AFTER LEARNING SCIENCE”Richard Feynman
  7. 7. SCIENTIFICADVISORYBOARD
  8. 8. SCIENTIFICADVISORY BOARD · Tom Blundell Professor Emeritus, Department of Biochemistry, University of Cambridge, UK · Roger M Burnett Professor Emeritus, The Wistars Institute, Philadelphia, USA · Richard H Finnell Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, Texas, USA · Angela Gronenborn Department of Structural Biology, University of Pittsburg, USA · Samir M Hanash Molecular Diagnostics, Fred Hutchinson Cancer Research Center, Seattle, USA · Shelly Lu USC Research Center for Liver Diseases, Keck School of Medicine USC, Los Angeles, California, USA · Juan Rodés Liver Unit, Hospital Clinic, Barcelona, Spain · Rima Rozen Department of Pediatrics, Human Genetics and Biology, Mc Gill University-Montreal, Quebec, Canada · Margarita Salas Severo Ochoa Molecular Biology Center, CSIC, Autónoma University of Madrid, Canto Blanco, Madrid, Spain
  9. 9. INDEX 01 RESEARCH AREAS 01.1 RESEARCH UNITS Functional Genomics Proteomics Metabolomics Cell Biology & Stem Cells Structural Biology 01.2 TECHNOLOGY Structural Biology PLATFORMS Genome Analysis Proteomics & Metabolomics Gene Silencing SERVICE 02 AREAS RESEARCH 02.1 SUPPORT Animal Facilities UNITS Biosafety & Radioactive Protection Informatics Maintenance 02.2 ADMINISTRATION & DIRECTOR’S OFFICE ADDITIONAL 03 INFORMATION Patents Funding Aids to Recruitment General Assembly
  10. 10. RESEARCHUNITS
  11. 11. FUNCTIONALGENOMICSUNIT
  12. 12. FUNCTIONALGENOMICSUNITGenetic analysis is being used to understand the techniques to study the genes that control normal biological processes, like the activation of the innate immune response tofundamental mechanisms that underlie hereditary microbial infections and the mechanisms controlling thediseases. This will allow development of therapeutic development of higher organisms. We are investigating geneticstrategies and diagnostic systems, both for hereditary variants within human populations that are associated with particular diseases and the possible contribution of nutritionaldiseases and to predict individual sensitivity to and environmental influences to the development of pathologicalparticular drugs. conditions.The Functional Genomics Unit is concerned with studying theregulation of the gene expression, in different cell types and duringdevelopment. We use sophisticated molecular biology and genetics
  13. 13. Collaborations Lab. 1 · Dr Rafael Cantera (Stockholm University, Sweden and IIBCE, Rosa Barrio Montevideo, Uruguay). Principal Investigator · Dr José Félix de Celis (CBMSO, Madrid, Spain). · Dr David Martín (Institut de Biologia Molecular de Barcelona, CSIC, Barcelona, Spain). · Dr Manuel Salvador Rodríguez (CIC bioGUNE, Bizkaia, Spain).Development of multicellular organisms requires the strict control · Dr James David Sutherland (CIC bioGUNE, Bizkaia, Spain).of cell division and differentiation. In higher eukaryotes, this controlis exerted by highly conserved signalling pathways, such as theTransforming Growth Factor-β pathway, and the genes regulated bythem. Among those, the genes encoding the Spalt protein family are Selected Publicationsnecessary for numerous biological processes and are implicated in 1. Talamillo A, Sánchez J, Cantera R, Pérez C, Martín D, Caminero Ediverse inherited human syndromes, such as the Townes-Brocks or and Barrio R. Smt3 is required for Drosophila melanogasterthe Okihiro syndromes, as well as the susceptibility to Ovarian metamorphosis. Development 135: 1659-1668 (2008).Carcinoma or Wilms Tumors. These syndromes include various 2. Talamillo A, Sánchez J and Barrio R. Functional analysis of themalformations, such as dysplastic kidneys (a major cause of renal SUMOylation pathway in Drosophila. Biochem Soc Trans 36: 868-873failure in infants), supernumerary thumbs, dysplastic ears, sensorineural (2008).hearing loss and severe growth retardation, that might indicate 3. De Celis JF and Barrio R. Regulation and function of Spalt proteinspituitary dysfunction. during animal development. Int J Dev Biol 52: 2408-2422 (2008).Spalt proteins act as transcriptional repressors and are associated 4. Barrio R, López-Varea A, Casado M and de Celis JF. Characterizationwith chromosomal stability, but the details of their mechanism of of dSnoN and its relationship to Decapentaplegic signaling inaction are still unknown. In our laboratory we try to understand this Drosophila. Dev Biol 306: 66-81 (2007).mechanism, using the fruit fly Drosophila melanogaster as a modelorganism. We are investigating the importance of posttranslationalmodifications by sumoylation on the role of Spalt. We have generated Lab Memberstransgenic flies expressing low levels of Sumo using RNA interference Coralia Pérez Ana Talamillotechnology. The knockdown flies are unable to move on to adult Fernández Postdoctoralstages and stop their growth due to the low levels of ecdysone, the Technician Researcherhormone needed for metamorphosis. We are particularly interestedon the contribution of Spalt to this phenotype, as well as other factors Roland Hjerpe Leire Herbosoinvolved in the synthesis of Ecdysone. The possible role of Spalt Postdoctoral PhD Studentproteins in the regulation of growth is especially intriguing Researcherand constitutes the focus of our research.
  14. 14. inherited diseases in this isolated population. Furthermore, we are Lab. 2 the group responsible of the Genetics Work-Package within the COEDUCA (Cognition and Education) Consolider–Ingenio 2010 Ana Mª Aransay CSD2008-00048 project. In addition, we are participating in several Principal Investigator collaborative projects, namely: i) high density genotyping in the region 6p21 for the identification of polymorphisms associated with the susceptibility to Type 1 Diabetes mellitus; ii) identification of new genes associated with Monogenic Diabetes; iii) high-throughputThe genetic polymorphisms are variants of the genome that appear genotyping of the MHC (6p21) and LCR (19q3.4) regions in HLA-B27by mutation in some individuals, are transmitted to the descendants populations in order to spot genetic variants associated to Ankylosingand acquire certain frequency in the population after multiple Spondylitis; iv) SNP analysis and haplotype structure of cytokine genegenerations. It has been estimated that there is a variant for every clusters in Multiple Sclerosis patients; v) genetic polymorphisms1,000 base pairs among the 3,000 million that make the human association study of Alzheimer Disease by means of high-throughputgenome. The polymorphisms are the base of the evolution and those SNP genotyping; vi) system biology of Non Alcoholic Fatty Liverthat consolidate can be silent or can provide advantages to the diseases; vii) clinical validation of genetic tests for the evaluation andindividuals, although they can also contribute to diseases. therapy selection in colorectal patients (COLOGENETICS); and viii) EDGeS - Enabling Desktop Grids for e-Science (Grant from theWith this background in mind, the main objective of this research European Commissions FP7 IST Capacities programme under grantgroup is the identification and validation of genetic variants implicated agreement RI-211727).in common human complex diseases, in collaboration with nationaland international medical researchers.Most of the projects carried out at the laboratory i) use high- Collaborationsthroughput genotyping or sequencing techniques for simultaneously · Dr Luis Castaño, Dr José Ramón Bilbao and Dr Guiomar Pérez deexamining complete genomes of patients and control individuals to Nanclares (Cruces Hospital, Bizkaia, Spain).identify genetic variants; ii) help to develop bioinformatics tools for · Dr Alfredo Antigüedad and Dr Juan Mari Uterga (Basurto Hospital,the efficient study of the polymorphisms associated with the Bizkaia, Spain).susceptibility to a particular disease; and iii) supply biological · Dr Carlos López Larrea (Hospital Universitario Central de Asturias,interpretation of the obtained results by testing the functionality of Asturias, Spain).the identified genes, examining their involvement in the aetiology · Dr Koen Vandenbroeck and Dr Carlos Matute (Universidad del Paísof diseases and their possible mechanism of action. Vasco UPV/EHU, Bizkaia, Spain). · Dr Manuel Carreiras (Basque Center of Cognition, Brain and Language, The identification of new diagnostic methods for early stages of Gipuzkoa, Spain).certain diseases and of possible targets for the specific drug generation · Dr José M Mato & Dr María Luz Martínez-Chantar (CIC bioGUNE,is of great importance for the development of successful treatment Bizkaia, Spain).of many serious human disorders. · Gabriel Carasa (CIC bioGUNE, Bizkaia, Spain). · Dr Juan Falcón (CIC bioGUNE, Bizkaia, Spain).Our lab is leading a project for the detailed genetic characterization · BIOEF foundation (Sondika, Bizkaia, Spain).of the Basque population in relation to the high incidence of some · OWL Genomics (Derio, Bizkaia, Spain).
  15. 15. · Pharmakine (Derio, Bizkaia, Spain).· AMPTEC (Hamburg, Germany).· Atos Origin (Madrid, Spain).Selected Publications1. Hackenberg M, Sturm M, Langenberger D, Falcón-Pérez JM, AransayAM. miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Nucl. Acids Res. 37, W68-W76(2009).2. Otaegui D, Zuriarrain O, Castillo-Triviño T, Ruíz-Martínez J, AransayAM, Olaskoaga J, Marti-Masso JF, López de Munain A. Associationbetween SYNAPSIN III gene promoter SNPs and multiple sclerosis inBasque patients. Multiple Sclerosis Journal 15, 1, 124-8 (2009).3. Martínez-Chantar ML, Vázquez-Chantada M, Ariz U, Martínez N,Varela M, Luka Z, Capdevila A, Rodríguez J, Aransay AM, MatthiesenR, Yang H, Calvisi DF, Esteller M, Fraga M, Lu SC, Wagner C, Mato JM.Loss of the Glycine N-Methyltransferase Gene Leads to Steatosis andHepatocellular Carcinoma in Mice. Hepatology 47, 4, 1191-9 (2008).4. Castellanos-Rubio A, Martín-Pagola A, Santín I, Hualde I, AransayAM, Castaño L, Vitoria JC, Bilbao JR. Combined functional and positionalgenetic information for the identification of susceptibility genes inceliac disease. J. Gastroenterology 134, 3, 738-746 (2008).5. Santín I, Castellanos-Rubio A, Aransay AM, Castaño L, Vitoria JC,Bilbao JR. The functional R620W variant of the PTPN22 gene isassociated with celiac disease. Tissue Antigens 71, 3, 247-9 (2008).Lab Members Iñaki Mendibil Liher Imaz Technician PhD Student Karin Schlangen Postdoctoral Researcher
  16. 16. common the over-accumulation of peptides which prevent the Lab. 3 normal functioning of nerves. David Gubb An additional interest of our laboratory is the cryopreservation of Principal Investigator Drosophila stocks. The maintenance of genetic strains has reached a crisis point in the Drosophila community, due to the lack of a practical method for long-term storage of the many thousands of unique fly strains. For this reason we are trying to develop a methodModels of the innate immune response and genetic diseases in the of long-term cryopreservation of stocks.fly Drosophila.The fruit-fly, Drosophila melanogaster, represents a very powerful Collaborationsmodel to study biological processes due to its ease of culture, rapid · Dr Jean-Marc Reichhart (ICBM, Strasbourg, France).generation time and the sophisticated genetic tools that have been · Dr David Lomas (Department of Medicine, University of Cambridge, UK).developed for this organism. · Dr John Morris (Asymptote Ltd, Cambridge, UK).As an example, the Toll receptor in humans, which is involved in therecognition of pathogens, was identified by homology to theDrosophila Toll gene. Selected Publications 1. Garrett M, Fullaondo A, Troxler L, Micklem G, Gubb D. IdentificationIn humans, the immune response consists of an immediate “innate” and analysis of serpin-family genes by homology and synteny acrossresponse (mediated via antimicrobial peptides) and a delayed the 12 sequenced Drosophilid genomes. MBC Genomics, 10: 489“acquired” response (mediated via antibodies). In response to microbial (2009).challenge, insects sythesize antibiotic peptides, activate macrophage- 2. Soukup S, Culi J, Gubb D. Uptake of the Necrotic Serpin in Drosophilalike cells and mount a melanization response, but the antibody Melanogaster via the Lipophorin Receptor-1. PLoS Genetmediated response is absent. 5(6):e1000532 (2009). 3. Lin Y, Gubb D. Molecular dissection of Drosophila Prickle isoformsThe major objective of our laboratory is to understand the mechanisms distinguishes their essential and overlapping roles in planar cellof activation and degradation of the Necrotic protein in Drosophila. polarity. Dev Biol 325: 386-399 (2009).In 1999, we identified Necrotic as a member of the serpin (serineprotease inhibitor) family, closely resembling human protease 4. Yan J, Huen D, Morely T, Johnson G, Gubb D, Roote J, Adler P. Theinhibitors involved in the inflammatory response. More specifically, multiple-wing-hairs gene encodes a novel GBD-FH3 domain-Necrotic controls initiation of the extracellular proteolytic cascade containing protein that functions both prior to and after wing hairwhich activates the immune response to microbial infections. Serpin initiation. Genetics 180 219-28 (2008).turnover in biological systems tends to be extremely rapid and serpin- 5. Pelte N, Robertson A, Zhou Z, Belorgey D, Dafforn T, Jiang H, Lomasdegradation mechanisms may share genetic components with D, Reichhart J-M, Gubb D. Immune Challenge induces N-terminalmechanisms of misfolded-peptide clearance that underlie cleavage of the Drosophila serpin Necrotic. Insect Biochemistry Moldiseases such as Alzheimers and Parkinsons. These diseases have in Biol. l 36: 37-46 (2006).
  17. 17. Lab Members Laura Bárcena Veronika Technician Mikitova Postdoctoral Researcher Arantza Sanz Parra Technician
  18. 18. interaction, we are capable of enriching the ubiquitinated proteins Lab. 4 from Drosophila neurons up to levels not achieved by any other approach until now. This technique is allowing us to isolate and Ugo Mayor identify all neuronal proteins that are ubiquitinated, to resolve whether Principal Investigator they are mono or polyubiquitinated, and even to quantify for each Ikerbasque Research Professor ubiquitin substrate which percentage was ubiquitinated in the neuronal tissue of the living fly. We are also identifying the position at which those proteins are being ubiquitin-modified.Ubiquitination of neuronal proteins is an essential regulatorymechanism of brain function, and its failure is associated to a number Our lab has a number of ongoing projects to take advantage of the technology we have developed. We are comparing the ubiquitinationof neurodegenerative conditions, including Parkinson’s and Alzheimer’s profile of the developing brain with that of the adult brain, as welldiseases. Over the last two decades, much has been learnt from as with the ubiquitination profile of other tissues. We are looking atstudies on yeast and mammalian cell culture regarding the regulation the specific substrates of a few important E3 ligases, like Highwire,of ubiquitination at the molecular level. However, our understanding Ariadne1 and dUbE3A, this last one being the E3 ligase whose lossof ubiquitination pathways within the context of whole organisms of function causes Angelman syndrome, a genetic neurologicalis still very poor. disorder. We are also looking at the ubiquitination profile in fly models of polyglutamine diseases, to try to discern whether the ubiquitinationGenetic studies using Drosophila as a model system have identified associated with those neurodegenerative disorders is the cause ora number of ubiquitination pathways essential for neuronal function, the effect of the disease. Additionally, we are looking at SUMOylationbut the evidence for actual ubiquitination of the candidate substrates using a very similar approach.has at best been indirect. Whereas the anatomic complexity ofDrosophila is far simpler than ours, most molecular mechanismsgoverning neuronal cell function are actually highly conserved.However, due to its relative complexity and tissue heterogeneity, Collaborationseven Drosophila labs have often used cell culture for validating · Dr Junmin Peng (Emory University School of Medicine, Atlanta, GA, USA).candidate substrates of ubiquitin, on the assumption that if a protein · Dr Andrea Brand (Wellcome Trust Cancer Research UK Gurdoncan be ubiquitinated in a given cell line, it might be ubiquitinated as Institute, Cambridge, UK).well in any other cell type. However, ubiquitination is used to regulate · Dr Catherine Lindon (Dept of Genetics, University of Cambridge,cell function in a context-specific manner, and its roles are very likely Cambridge, UK).to be regulated differently in different tissues. For example, it is well · Dr Rosa Barrio (CIC bioGUNE, Bizkaia, Spain).known that E3 ligase expression patterns differ enormously. Since · Dr Alberto Ferrus (Instituto Cajal CSIC, Madrid, Spain). · Dr Janice Fischer (University of Texas, Austin, TX, USA).most characterised genomes code for hundreds of E3 ligases, it isexpected that ubiquitination pathways will be tissue specific.We are developing a novel strategy for the efficient isolation of Selected Publicationsneuronal ubiquitin conjugates from flies. The approach is based on 1. Religa TL, Markson JS, Mayor U, Freund SMV, Fersht AR. Solutionthe in vivo biotinylation of ubiquitin expressed in a tissue-specific structure of a protein denatured state and folding intermediate.manner. Taking advantage of the strength of the streptavidin-biotin Nature 437:1053-6 (2005).
  19. 19. 2. Mayor U, Guydosh NR, Johnson CM, Grossmann JG, Sato S, Jas GS,Freund SMV, Alonso DOV, Daggett V and Fersht AR. The completefolding pathway of a protein from nanoseconds to microseconds.Nature 421:863-7 (2003).3. Mayor U, Grossmann JG, Foster NW, Freund SMV and Fersht AR.The denatured state of Engrailed homeodomain under denaturingand native conditions. Journal of Molecular Biology 333:977-91 (2003).4. Mayor U, Johnson CM, Daggett V and Fersht AR. Protein foldingand unfolding in microseconds to nanoseconds by experiment andsimulation. Proc. of the National Academy of Sciences of the USA97:13518-22 (2000).Lab Members So Young Lee Juan Manuel Technician Ramírez Sánchez PhD Student Maribel Franco Postdoctoral Researcher
  20. 20. PROTEOMICSUNIT
  21. 21. PROTEOMICSUNITThe map of human proteins will make it possible to Such functional characterization may allow comparisons between the protein pattern present in diseased tissue versus healthy tissuefind new diagnostic markers for different pathologies. and consequently, it may be possible to establish the specific "proteomic fingerprint" of a pathological state. Detailed proteinThe availability of the complete sequence of certain genomes, studies may reveal potential molecular markers associated withespecially the human genome, offers new opportunities for disease progression and lead to possible therapeutic targets.biological research.The goal of the Proteomics Unit is to identify proteins involved insome physiological processes and also to characterize theinteractions between them.
  22. 22. our in vitro results suggest that PMCA is a valuable tool for assessing Lab. 1 the strength of the transmission barriers between diverse species and for different prion strains; we are using the method to determine Joaquín Castilla which amino acids in the PrPC sequence contribute to the strength of the transmission barrier. These studies are proving very useful in Principal Investigator evaluating the potential risks to humans and animals, of not only Ikerbasque Research Professor established prion strains, but also new (atypical) strains. For example, while classical sheep scrapie is unable to cross the human transmission barrier in vitro, bovine spongiform encephalopathy (BSE) propagatedTransmissible spongiform encephalopathies (TSEs) are fatal in sheep does so efficiently. In addition, we have also generatedneurodegenerative disorders affecting both humans and animals. prions that are infectious to species hitherto considered to be resistantTSEs can be of genetic, sporadic or infectious origin. The infectious to prion disease.agent associated with TSEs, termed prion, appears to consist of asingle protein, an abnormal conformer (PrPSc) of a natural host protein(PrPC), which propagates by converting host PrPC into a replica ofitself. One of the characteristics of prions is their ability to infect some Collaborationsspecies and not others. This phenomenon is known as transmission · Dr Glenn Telling (Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington, KY, USA).barrier. Interestingly, prions occur in the form of different strains that · Dr Charles Weissmann (Department of Infectology, Scripps Researchshow distinct biological and physicochemical properties, even though Institute, Jupiter, FL, USA).they are encoded by PrP with the same amino acid sequence, albeit · Dr Adriano Aguzzi (Institute of Neuropathology, University Hospitalin presumably different conformations. In general, the transmission Zurich, Zurich, Switzerland).barrier is expressed by an incomplete attack rate and long incubation · Dr Juan María Torres (Centro de Investigación en Sanidad Animal,times (time from the animal inoculation until the onset of the clinical INIA, Madrid, Spain).signs) which become shorter after serial inoculation passages. · Dr Enric Vidal and Dr Martí Pumarola (Departament de Medicina iCompelling evidence indicates that the transmission barriers are Cirugia Animals, Universitat Autònoma de Barcelona, Barcelona,closely related to differences in PrP amino acid sequences between Spain).the donor and recipients of infection, as well as the prion strainconformation. Unfortunately, the molecular basis of the transmissionbarrier phenomenon and its relationship to prion strain conformations Selected Publicationsis currently unknown and we cannot predict the degree of a species 1. Castilla J, Morales R, Saá P and Soto C. Propagation of prion strainsbarrier simply by comparing the prion proteins from two species. We in vitro. EMBO J. 27, 2557-2566 (2008).have conducted a series of experiments using the Protein Misfolding 2. Castilla J, Gonzaléz D, Saá P, Morales R, de Castro J and Soto C.Cyclic Amplification (PMCA) technique that mimics in vitro some of Crossing species barrier by in vitro replication of protein misfoldingthe fundamental steps involved in prion replication in vivo, albeit with generates new infectious prions. Cell. 134, 757-768 (2008).accelerated kinetics. The in vitro generated prions possess key prion 3. Green KM, Castilla J, Seward TS, Napier DL, Jewell JE, Soto C andfeatures, i.e., they are infectious in vivo and maintain their strain Telling GC. Accelerated High Fidelity Prion Amplification Within andspecificity. We have used PMCA to efficiently replicate a variety of Across Prion Species Barriers. PLOS Pathogens. 4, 1-12 (2008).prion strains from, among others, mice, hamsters, bank voles, deer,cattle, sheep, and humans. The correlation between in vivo data and
  23. 23. 4. Saá P, Castilla J and Soto C. Pre-symptomatic detection of prions inblood. Science. 313, 92-4 (2006).5. Soto C, Estrada L and Castilla J. Amyloids, prions and the inherentinfectious nature of misfolded protein aggregates. Trends inBiochemical Sciences. 31, 150-155 (2006).Lab Members Alberto Marina Natalia Technician Fernández-Borges Postdoctoral Researcher Nagore Sacristán Iker Uriarte Technician Postdoctoral Researcher
  24. 24. Collaborations Lab. 2 · Dr Puri Fortes, Dr Rubén Hernández (Centro de Investigación Médica James D Sutherland Aplicada, Universidad de Navarra, Pamplona, Spain). Principal Investigator · Dr Roberto Martínez, Dr Ricardo Rezola, Dr María Jesús Michelena (Instituto Oncológico, San Sebastián, Gipuzkoa, Spain). · Dr Rosa Barrio (CIC bioGUNE, Bizkaia, Spain).Adhesion between cells, as well as adhesion of cells to substrates, isa fundamental property of multicellular organisms. Changes in cell Selected Publicationsadhesion can give rise to defects in development and loss of tissue 1. Garvalov BK, Higgins TE, Sutherland JD, Zettl M, Scaplehorn N,integrity that contributes to human disease. During cancer metastasis, Köcher T, Piddini E, Griffiths G, Way M. The conformational state oftransformed cells of a solid tumor can disperse and become more Tes regulates its zyxin-dependent recruitment to focal adhesions.motile, traveling to remote sites where they may form secondary J Cell Biol. 161(1):33-39 (2003).tumors. Cells must leave the primary tumor, enter and exit thecirculatory system by crossing endothelial layers, and populate thesecondary site - all steps that require remodelling and changesin cell adhesion structures. Lab Members Itziar Martín Ruíz Emma Lovisa Technician Helena JakobssonOur work focuses on PET-LIM proteins, a small family of scaffolding Postdoctoralproteins that may regulate the formation of protein complexes Researcherinvolved in diverse cellular processes, including cell spreading,adhesion and polarity. The testin protein (TES) exhibits dynamiclocalisation within cells and shuttles between the nucleus and theintegrin-based focal adhesions formed between cells and substrates.Loss of TES is observed in several tumor types and mice lacking TESexhibit aggressive tumor growth, pointing to its role as a tumorsuppressor. We are using screening by RNAi to uncover additionalfactors in the TES tumor suppression pathway. Also, to understandhow TES is regulated, we are using biochemistry, mutational analysisand structure-based approaches to uncover intramolecular interactionsthat control the ability to form complexes with known and novel TESligands. Lastly, several PET-LIM family members are farnesylated andmay regulate multiprotein complex assembly at the plasma membraneor close to organelles. One of these, Prickle3, dynamically localises tocell-cell adhesions. Further examination of this class of PET-LIMs willreveal if they are also cancer-related or have novel roles in developmentand disease.
  25. 25. c. Developing new strategy and applications to isolate and identify Lab. 3 ubiquitylated proteins in vivo from cell cultures as well as for tissues and organs from animal models where the Ubiquitin-Proteasome Manuel Rodríguez Medina Pathway appears to be at the origin of drug resistance or pathologies Principal Investigator such as cancer or neurodegenerative disorders. The knowledge obtained using these approaches will most certainly contribute significantly to generating new concepts of the role of members of the ubiquitin family in the regulation of molecular events, in an important number of essential cellular processes in health andThe covalent conjugation of ubiquitin and ubiquitin-like molecules disease.to different substrates has become one of the most widely investigatedpost-translational modifications. Modified substrates include proteinscontrolling an extensive array of essential processes, such as proteindegradation via the 26S proteasome, regulation of transcription, the Collaborationscell cycle and oncogenesis. · Dr Patrick England (Pasteur Institute, Paris, France). · Dr Ron Hay (Dundee University, Scotland, UK).The ubiquitin family of molecules can be attached to protein substrates · Dr Rosa Farrás (Centro de Investigación Principe Felipe,as monomers and polymers. Although a considerable amount of Valencia, Spain).data on many aspects of ubiquitin and ubiquitin-like mediated · Dr Carmen Rivas (CNB, CSIC, Madrid, Spain).processes is available, many aspects regarding the modification- · Dr Rosa Barrio (Functional Genomics Unit, CIC bioGUNE, Bizkaia, Spain).specific and chain-type recognition of conjugated substrates, as well · Dr Edurne Berra (Cell Biology Unit, CIC bioGUNE, Bizkaia, Spain).as the molecular processes engaged after protein conjugation with · Dr José M Mato (Metabolomics Unit, CIC bioGUNE, Bizkaia, Spain).the various ubiquitin-like modifiers such as SUMO-1, SUMO-2, SUMO- · Dr María Luz Martínez-Chantar (Metabolomics Unit, CIC bioGUNE,3 and NEDD8, remain obscure. To address these questions our main Bizkaia, Spain).models are: 1) Iκβα a and A20 proteins -both proteins are naturalinhibitors of the NF-κβ transcription factor, which conditions itstranscriptional activity during the immune and inflammatory responses Selected Publicationsand 2) the tumour suppressor p53. 1. Hjerpe R, Aillet F, Torres-Ramos M, Lang V, Farrás R, Hay RT and Rodríguez MS. Mdm2 mediates multiple mono-ubiquitin-dependentOur specific objectives are: proteasomal degradation of p53. Submitted (2009).a. Identification of specificity motifs in the target proteins determining 2. Hjerpe R, Aillet F, Lopitz-Otsoa F, Lang V, England P and Rodríguezthe preferential recognition by modifier-protein ligases (E3s), and the MS. Using Tandem Ubiquitin Binding Entities (TUBEs) to isolateuse of these motifs to isolate, identify and study the role of interacting polyubiquitylated proteins. EMBO rep Octubre 2009.proteins participating in the response generated by such modifications. 3. Hjerpe R and Rodríguez MS. Alternative UPS drug targets upstreamb. Applying this knowledge to develop high troughput screenings the 26S proteasome. International Journal of Biochemistry and Cellmethods (HTS) to isolate new drugs that can be used to treat Biology. 40, 1126-1140 (2008).pathologies where our protein models are implicated.
  26. 26. 4. Rubio A, Guruceaga E, Vázquez-Chantada M, Sandoval J, Martínez-Cruz LA, Segura V, Sevilla JL, Podhorski A, Corrales FJ, Torres L, RodríguezMS, Aillet F, Ariz U, Martínez Arrieta F, Caballería J, Martín-Duce A, LuSC, Martínez-Chantar ML, Mato JM. Identification of a Gene-pathwayassociated with non-alcoholic esteatohepatitis. J. Hepatology 46,708-718 (2007).Lab Members Fabienne Aillet Fernando Lopitz Postdoctoral Postdoctoral Researcher Researcher CIBERehd Fellow Member Valerie Lang Postdoctoral Researcher
  27. 27. METABOLOMICSUNIT
  28. 28. METABOLOMICSUNITMetabolomics provides knowledge to identify the In mammals, specially in human, the liver plays an important role in metabolomic equilibrium. In a pathological situation like diabetesmetabolites present in a biological sample, and is mellitus, obesity, steatohepatitis or cirrhosis, a failure in thethe simplest, cheapest and most efficient method regulation of the mechanism maintaining the metabolomicto diagnose diseases. equilibrium takes place. The aim of this unit is to identify the essential metabolites involved in signaling pathway regulationMetabolomics focuses on the study of metabolites. These small and analyze the mechanism of the progression and developmentmolecules are the last step in the biological process initiated with of liver diseases. This knowledge will help us to understand thegene expression. The study of human metabolome is a very efficient mechanism and the relationship existing between essentialmethod to identify possible markers and determine if an individual metabolites and proliferation, cellular death and cellularperson is going to suffer from a disease, helping to diagnose a metabolism.specific pathology.
  29. 29. and NASH using high-throughput metabolic technology – at present Lab. 1 the gold standard for the diagnosis of NAFLD is histological examination of a liver biopsy specimen, which is an expensive, invasive José M Mato and subjective procedure associated with potential complications Principal Investigator and prone to sampling error – the identification of gene variants associated with the development of NASH; and the characterization and comprehensive proteome profiling of exosomes secreted by hepatocytes. Exosomes are 40-100 nm membrane vesicles of endocyticNon-alcoholic fatty liver disease (NAFLD) is currently the most frequent origin secreted by most cell types that mediate communicationchronic liver disease in western countries affecting about 20-30% of between cells, facilitating processes such as antigen presentationadults above age 20. NAFLD is characterized by the accumulation of and in trans-signaling to neighboring cells.fat in the liver (steatosis). Although generally asymptomatic, 10-40%of NAFLD patients, depending on the population selected, developnon-alcoholic steatohepatitis (NASH), which is characterized by thepresence of steatosis with inflammation, necrosis and fibrosis. NASH Collaborationsis a progressive disease of the liver that may progress to cirrhosis and · Dr Shelly C Lu (University of Southern California, Los Angeles,hepatocellular carcinoma (HCC). Obesity is a major risk factor for the CA, USA).development of NAFLD. However, the observation that about half · Dr Conrad Wagner (Vanderbilt University School of Medicine,the patients with NAFLD are not obese indicates that there are factors Nashville, TN, USA).(nutritional, genetic and environmental), independent of the ingestion · Dr Richard H Finnell (Texas Institute for Genomic Medicine,and lipid metabolism that strongly affect the accumulation of fat in Houston, TX, USA).the liver. · Dr Juan Caballería (Hospital Clínic de Barcelona, Barcelona, Spain). · Dr CB Rountree (Penn State Childrens Hospital, Hershey, PA, USA).In my laboratory we have used gene-knockout technology to study · Dr Jian-Min Yuan (University of Minnesota, Minneapolis, MN, USA).how mouse genes regulate liver metabolism and fat accumulation · Dr Luis Torres (Universidad de Valencia, Valencia, Spain).–a research that provides relevant information on the hepatic · Dr Yannick Le Marchand-Brustel (Universitaire Archimed, INSERM,metabolism in humans and how hepatic fat accumulates when there Nice, France).is a metabolic imbalance–. Using this technology, we have identified · Dr Jonathan Barr (OWL Genomics, Derio, Bizkaia, Spain).that S-adenosylmethionine (SAMe, a metabolite of methionine) plays · Dr Carlos Simón (Fundación IVI, Valencia, Spain).a crucial role as a regulator of liver metabolism and hepatocyteproliferation and how both, a chronically low levels and excess ofhepatic SAMe leads to NASH and HCC. The mechanism by whichSAMe regulates liver function involves histone- and DNA-methylation Selected Publicationsas well as regulation of AMP-activated protein kinase (AMPK), the 1. Varela-Rey M, Fernández-Ramos D, Martínez-López N, Embade N,main enzyme involved in the regulation of hepatic metabolism. Gómez-Santos L, Vázquez-Chantada M, Rodríguez J, Luka Z, Wagner C, Lu SC, Martínez-Chantar ML, Mato JM. Impired liver regenerationOther research lines in my laboratory include: the identification of in mice lacking glycine N-methyltransferase. Hepatology.non-invasive serum biomarkers that differentiate between steatosis Aug;50(2):443-52 (2009).
  30. 30. 2. Vázquez-Chantada M, Ariz U, Varela-Rey M, Embade N, Martínez-López N, Fernández-Ramos D, Gómez-Santos L, Lamas S, Lu SC,Martínez-Chantar ML, Mato JM. Evidence for LKB1/AMP-activatedprotein kinase/ endothelial nitric oxide synthase cascade regulatedby hepatocyte growth factor, S-adenosylmethionine, and nitric oxidein hepatocyte proliferation. Hepatology. Feb;49(2):608-17 (2009).3. Ding W, Mouzaki M, You H, Laird J, Mato JM, Lu SC, Rountree CB.CD 133 + Liver Cancer Stem Cells from Methionine AdenosylTransferase 1A Deficient Mice Demonstrate Resistance to TGF-βinduced apoptosis. Hepatology; 49:1277-86 (2009).4. Mato JM, Martínez-Chantar ML, Lu SC. Methionine Metabolism andLiver Disease. Annu Rev Nutr. Aug 21;28:273-293 (2008).Lab Members Esperanza Javier Conde González Jiménez PhD Student Technician Nieves Embade Juan Luis García Postdoctoral Rodríguez Researcher PhD Student Juan Manuel David Fernández Falcón Ramos Postdoctoral PhD Student Researcher Marcella Sini Richard H Finnell Visiting Visiting Researcher ScientificLab Members attachedto external projects Mercedes Vázquez Miriam Pérez Chantada Cormenzana Postdoctoral Platform Researcher Specialist
  31. 31. protein kinase (AMPK), which is required for hepatocyte proliferation. Lab. 2 Our new data also show cross-talks between AMPK and nitric oxide synthase in modulating the proliferative effect of HGF. How SAMe Mª Luz Martínez Chantar regulates these pathways will be elucidated. 2) We have isolated a Principal Investigator cancerous cell line (SAMe-D) from MAT1A-KO HCC. Our aim is to characterize this cell line to learn more about how cancer develops in MAT1A-KO mice liver. This is highly relevant in cases with liver cirrhosis where MAT1A expression is often low or absent and the riskNon-alcoholic fatty liver disease (NAFLD) is a clinical-pathological of HCC is high. 3) Identify mechanisms of malignant degenerationterm that includes a spectrum of alterations ranging from the simple when SAMe metabolism is altered. Both chronic SAMe deficiencyaccumulation of triglycerides in the hepatocytes (steatosis) to steatosis and excess result in fatty liver and HCC. Successful completion of thewith hepatic inflammation (steatohepatitis or NASH). NASH, in turn, proposed tasks should greatly enhance our understanding of SAMe’salso progresses to cirrhosis and HCC. The mechanisms that lead to role in liver health and pathology and help identify patients that willthe manifestation of NASH are not clear, but it is a condition associatedwith obesity, insulin resistance, and diabetes. benefit from its therapeutic use.Since the incidence of these diseases is increasing, the prevalence ofNASH is also expected to increase in coming years (today it varies Collaborationsbetween 13 to 15 % of the population). NASH is now considered as · Dr Shelly C Lu (University of California, Los Angeles, CA, USA).an emerging disease in USA and occidental countries. Nowadays, · Dr Myriam Gorospe (NIH, Baltimore, MD, USA).lacking accurate, sensitive diagnostic test, distinguishing steatosis · Dr Anna Maeh Diehl (Duke University Medical Center, Durham,from steatohepatitis requires the use of invasive techniques like liver NC, USA).biopsy. In summary, the lack of information about the factors · Dr Richard Finnell (Department of Nutrition and Food Science,implicated in the NASH pathogenesis, as well as in the prognosticscharacteristics and the treatment of this pathology, emphasize the Houston, TX, USA).need of new approaches aimed at understanding the mechanismsimplicated in the development of NASH and HCC. In response tothese needs we propose a multidisciplinary research project to study Selected Publicationsthese pathologies. 1. Tomasi ML, Iglesias-Ara A, Yang H, Ramani K, Feo F, Pascale MR, Martínez- Chantar ML, Mato JM, Lu SC. S-Adenosylmethionine RegulatesOver the last few years, we have elucidated some of the molecular Apurinic/Apyrimidinic Endonuclease 1 Stability: Implicationmechanisms of SAMe regulated proliferation, regeneration and Hepatocarcinogenesis. Gastroenterology. 136:1025-1036 (2009).apoptosis and identified downstream targets contributing to theabnormal hepatic lipid metabolism and proliferation in both 2. Vázquez-Chantada M , Ariz U, Varela-Rey M, Martínez-López Nuria,MAT1A-KO and GNMT-KO mice, both with chronically abnormal levels Embade N, Fernández-Ramos D, Gómez-Santos, Lu SC, Martínez-Chantarof SAMe. The most important projects proposed are the following ML, Mato JM. Evidence for an LKB1/AMPK/eNOS Cascadeones: 1) Examine SAMe’s regulation of HGF-mediated hepatocyte Regulated by HGF, S-Adenosylmethionine and NO. Hepatology 49:proliferation. Hepatocyte growth factor (HGF) activates AMP-activated 608-617 (2009).
  32. 32. 3. Varela-Rey M, Embade N, Ariz U, Lu SC, Mato JM, Martínez-ChantarML. Non-alcoholic steatohepatitis and animal models: Understandingthe human disease. Int J Biochem Cell Biol. 41:969-976 (2009).4. Martínez-Chantar ML, Vázquez-Chantada M, Ariz U, Martínez N, VarelaM, Luka Z, Capdevila A, Rodríguez J, Aransay AM, Matthiesen R, Yang H,Calvisi DF, Esteller M, Fraga M, Lu SC, Wagner C, Mato JM. Loss of theglycine N-methyltransferase gene leads to steatosis and hepatocellularcarcinoma in mice. Hepatology 47:1191-1199 (2008).Lab Members Begoña Ashwin Woodhoo Rodríguez Postdoctoral Iruretagoyena Researcher Technician Naiara Beraza Itziar Frades Postdoctoral PhD Student Researcher Marta Varela Nuria Martínez Postdoctoral López Researcher PhD Student CIBERehd Fellow Member
  33. 33. CELL BIOLOGY& STEM CELLSUNIT
  34. 34. CELL BIOLOGY &STEM CELLS UNITWe investigate the molecular changes that occur in the Unit include the signalling pathways activated by steroid hormones, Wnt family growth factors and hypoxia, the geneticcells and their genomes in response to different changes occurring during carcinogenesis and the functional andstimuli. spatial organisation of the genome. Our aims are to understand the relationship between these processes and pathologies suchWe work on projects of basic and applied research that investigate as cancer, neurodegenerative disease and ischemia and to generateimportant cellular processes such as cell proliferation, new diagnostic and therapeutic tools.differentiation, maintenance of pluripotency and adaptation tolow oxygen availability. Scientific interests of the laboratories in
  35. 35. Collaborations Lab. 1 · Dr José Antonio López Ruiz (PreteImagen, Bilbao, Bizkaia, Spain). María del Mar Vivanco · Dr Shyamala Maheswaran (MGH, Harvard Medical School, Principal Investigator Boston, MA, USA). · Dr José Luis Toca-Herrera (CIC biomaGUNE, Gipuzkoa, Spain).The main objective of the laboratory is to gain further insight into Selected Publicationsthe roles that steroid hormone receptors play in normal breast tissue 1. Moreno-Flores S, Benitez R, Vivanco MdM, Toca-Herrera JL. Stressand during breast cancer development. Furthermore, the influences relaxation microscopy: Imaging local stress in cells. J Biomech. [Epubof estrogen, other signalling factors and the microenvironment in ahead of print] (2009).breast stem cells and in their transformation into cancer initiatingcells are being explored. 2. Vivanco MdM. Biomarkers in breast cancer. Chapter 7 in: Bioinformatics Methods in Clinical Research (2009). Eds. J Walker andFollowing the interest of the laboratory in the initiation and progression R Matthiesen, Humana Press (2009).of breast cancer, three stem/progenitor cell populations were identified 3. Krützfeldt M, Ellis M, Weekes DB, Bull JJ, Eilers M, Vivanco MdM,in the human mammary gland. These populations are currently being Sellers WR, Mittnacht S. Selective ablation of retinoblastoma proteincharacterised in more detail and their responses to hormones and function by the RET finger protein. Molecular Cell 18, 213-224 (2005).other signals are being investigated. In addition, both normal breast 4. Clayton H, Titley I and Vivanco MdM. Growth and differentiationand breast tumour cells are being propagated as mammospheres to of progenitor/stem cells derived from the human mammary gland.facilitate comparative studies of stem/progenitor cell self-renewal Exp Cell Res 297, 444-460 (2004).and differentiation in response to various treatments.The cancer stem cell hypothesis implies that stem/progenitor cells Lab Membersare more resistant to current therapies used to treat patients. Tamoxifenis one of the most commonly used endocrine treatments for estrogen- Mª Ángeles Oihana Iriondo Rábano PhD Studentresponsive breast cancer, although development of resistance is a Technicianfrequent clinical problem. Breast cancer stem/progenitor cells thatare resistant to tamoxifen have been generated and the responsesof these cells to chemotherapy drugs and other factors are currently Gemma Reverter Marco Piva Postdoctoral PhD Studentbeing studied. ResearcherThe various approaches undertaken in the laboratory should Valentine Bruno Simõescontribute to a better knowledge of the molecular profile of breast Comaills PhD Studentstem cells and the responses of both normal and cancer breast PhD Studentstem/progenitor cells to their cellular environment.
  36. 36. Collaborations Lab. 2 · Dr Akira Kikuchi (Hiroshima University, Hiroshima, Japan). Robert Kypta · Dr Jonathan Waxman (Imperial College London, London, UK). Principal Investigator · Dr Phillip Gordon-Weeks (MRC Centre for Developmental Neurobiology, Kings College London, London, UK). · Dr María del Mar Vivanco (CIC bioGUNE, Bizkaia, Spain).The Wnt signalling pathway plays an important role in cell growth Selected Publicationsand differentiation and is frequently activated in cancer. Our goals 1. Kawano Y, Diez S, Uysal-Onganer P, Darrington RS, Waxman J,are to understand how Wnts, their antagonists and their effectors Kypta R. sFRP1 is a negative regulator of androgen receptor activitycontrol cell growth and differentiation and to use the technological in prostate cancer. British Journal of Cancer, 100, 1165-1174 (2009).platforms at CIC bioGUNE to characterise the cellular responses to 2. Kypta R. Wnt signalling in The Encyclopedia of Cancer, 2nd EditionWnt ligands. We study these aspects in two contexts – prostate cancer Edited by Manfred Schwab, Springer Press (2009).(PCa) progression and neuronal differentiation. 3. Castano Z, and Kypta R. Housekeeping Proteins: Limitations as References During Neuronal Differentiation. The Open NeuroscienceWe examined Wnt gene expression in PCa and found that Wnt-11 is Journal, 2, 36-40 (2008).upregulated in hormone-refractory PCa. Gene silencing andoverexpression were used to show that Wnt-11 alters the survival 4. Kypta R. GSK-3 inhibitors and their potential in the treatment ofand neuroendocrine-like differentiation of PCa cells. Wnt gene Alzheimers disease. Expert Opinion in Therapeutic Patents 15, 1315- 1332 (2005).expression was also analysed during retinoic acid induction of neuraldifferentiation of human embryonal carcinoma (hEC) cells. Three Wntswere identified that might play roles in this process, one of which is Lab MembersWnt-11. Ongoing studies involve characterisation of the Wnt signals Mercedes Caro Zafira Castañothat control survival and differentiation of PCa and hEC cells. The sFRP Technician Postdoctoraland Dickkopf families of secreted Wnt antagonists have also been Researchercharacterized and Dkk3 and sFRP1 were found to be downregulatedin PCa. We are presently studying the function of Dkk3 in cell Víctor Manuel Rocío Jiménezdifferentiation in more detail. Campa Alonso Postdoctoral PhD Student ResearcherFinally, we are characterising the Wnt effectors Axin and glycogensynthase kinase-3 (GSK-3), which together act to inhibit Wnt/beta-catenin signalling. Phosphorylation sites in Axin have been identifiedthat play a role in the regulation of GSK-3 activity. We are now analysingthe functions of the different isoforms of GSK-3 in PCa and in neuronaldifferentiation.
  37. 37. cell expression profiles and in situ-loci mapping of genes Lab. 3 simultaneously. Since genomic events are also elicited by processes in the extracellular microenvironment, we also study the organizational Luis Parada changes of the genome associated with signalling events mediated Principal Investigator by cell-surface proteins. More specifically we wish to learn the nature of the nuclear changes, and how integrins-mediated signalling participates in the spatial genome reorganization during invasion and metastasis.The laboratory of Cytogenomics is focused on studying genomeorganization at the cellular level, in particular during livercarcinogenesis. Our research project “Cytogenomics of benign and Collaborationsmalignant lesions of the liver”, aims to characterize the profile of · Dr Alicia Lorenti (Laboratory of Tissue Engineering, University Hospital,genome alterations of liver tumours arising in human and in different Austral University, Buenos Aires, Argentina).mouse models of the disease. To this end, conventional and molecular · Dr África García-Orad (Dept. of Genetics, Universidad del País Vascocytogenetic methods, such as FISH, SKY and array-CGH are currently UPV/EHU, Bizkaia, Spain).used in the laboratory. · Dr María Luz Martínez-Chantar & Dr José M Mato (Metabolomics Unit, CIC bioGUNE, Bizkaia, Spain).The group is also interested in investigating the 3-dimensional · Dr Federico Garrido (Dept. of Clinical Chemistry & Immunology,arrangements of chromosomes and genes in the interphase nucleus University Hospital Virgen de las Nieves, Granada, Spain).during carcinogenesis. The project “Organization of the genome inthe interphase nucleus” intends to generate a 3D map of thosechromosomes and genes recurrently involved in abnormalities in Selected Publicationshepatomas using interphase FISH with whole-chromosome painting 1. Calvo A, Perez-Stable C, Segura V, Catena R, Garuceaga E, Nquewa P,and locus-specific probes combined with high-resolution microscopy Blanco D, Parada LA, Green F. Molecular characterization of theon normal and tumor cells. FG/Tag transgenic mouse model of hormone refractory prostate cancer: comparison to human prostate cancer. The Prostate (2009Most importantly, we aim to understand how the spatial distribution in press).of chromosomes and genes is related to genome function. In this 2. Royo F, Paz N, Espinosa L, Vellón L, Parada LA. Spatial link betweenregard, we are currently investigating the “role of the nucleolus on nucleoli and expression of the Zac1 gene. Chromosoma. Epubthe functional organization of Pol II dependent genes” and the DOI10.1007/s00412-009-0229-1 (2009).“Genome response to signalization events mediated by integrins”. 3. Parada LA. Interphase genome organization and cancer.The nucleolus is the most prominent compartment of the nucleus, Chromosome Research 17: 18-20 (2009).where ribosomal genes are transcribed. We ask whether its activity 4. Parada LA. Genome reorganization during invasive cell growth. Atlasinfluences the spatial and functional organization of non-ribosomal Genet Cytogenet Oncol Haematol, 12: 1-81 (2008).genes. To address this question we perform expression analysis of 5. Vellón L, Espinosa L, Royo F, Parada LA. α5β1 integrin-emanatinggenes mapping to chromosomes that harbour NOR, as well as signals remodel nuclear architecture through the activation ofNOR-negative chromosomes, and RNA-FISH combined with nucleolus ERK1/2 and p38a MAPKs during invasive cell growth. Eur. J. Cancerimmunostaining of nucleolar proteins to obtain single 6: 36 (2008).
  38. 38. Lab Members Amaia Zabala Luciano Vellón Technician Postdoctoral Researcher Félix Royo Nerea Paz Postdoctoral PhD Student Researcher CIBERehd Fellow Member
  39. 39. understanding of the hypoxia-signalling cascade and also to identify Lab. 4 new therapeutics targets in the pathologies in which hypoxia is implicated. Edurne Berra Principal Investigator The most important current projects • Cascada de señalización activada por la hipoxia y cáncer (SAF 2007-64597). • Integration of Novel Nanoparticle based Technology forLow oxygen availability or hypoxia is associated with several Therapeutics and Diagnosis of different types of cancer;physiopathological processes, like ischemia and cancer. This is why NANOTHER (NMP4-LA-2008-213631).the manipulation of the hypoxia-signalling cascade (by activatingand/or inhibiting) appears to be a very interesting therapeuticapproach. However, in order to do that, it is necessary to precisely Collaborationselucidate this signalling pathway and particularly, the mechanisms · Dr Sebastien Lecommandoux (LCPO-UMR5629-ENSCPB,regulating the α subunit of the Hypoxia Inducible Factor (HIF). Indeed, Bordeaux, France).HIFα is crucial in the hypoxia signalling pathway and the regulation · Dr Javier Oliver (CSIC, Granada, Spain).of its stability, the limiting step of this cascade. · Dr Alberto Pascual/José López-Barneo (IBiS, Sevilla, Spain). · Dr Andrea Pichler (Max F. Perutz Laboratories, Vienna, Austria).HIFα stability is regulated by the PHDs (HIF Prolyl Hydroxylases or · Dr Tomás Santalucía/Anna Serra (IIBB-CSIC/IDIBAPS, Barcelona, Spain).Prolyl Hydroxylases Domain containing proteins). These enzymes · Bioftalmik (Derio, Bizkaia, Spain).hydroxylate HIFα by using oxygen as a co-substrate and thus act as · Colorobbia Italia Spa (Sovigliana, Vinci, Italy).veritable oxygen “sensors”. Three PHD isoforms have been identified:PHD1, 2 and 3. The three isoforms are ubiquitously expressed buttheir relative expression levels and localization are different. These Selected Publicationsisoforms are able to hydroxylate HIFα in vitro, but our previous results 1. Loinard C, Ginouvès A, Vilar J, Cochain C, Zouggari Y, Recalde A,have shown that in cellulo, PHD2 plays a central and unique role in Duriez M, Lévy B, Pouysségur J, Berra E, Silvestre JS. Inhibition of Prolylwell-oxygenated cells, whereas PHD1 and PHD3 only contribute to Hydroxylase Domain Proteins Promotes Therapeuticthe regulation of HIFα stability upon chronic hypoxia. Revascularization. Circulation, 120(1):50-59 (2009).The aim of our group is to elucidate the PHDs regulatory mechanisms 2. Ginouvès A, Ilc K, Macías N, Pouysségur J, Berra E. PHDsand their physiological importance. We are planning to: i) study the overactivation during chronic hypoxia “desensitizes” HIFα andcontribution of post-translational modifications like hydroxylation, protects cells from necrosis. Proc. Natl. Acad. Sci. USA 105: 4745-4750phosphorylation, acetylation, ubiquitination or sumoylation; ii) identify (2008).new actors implicated in this regulatory pathway by performing a 3. Trastour C, Benizri E, Ettore F, Ramaioli A., Chamorey E, Pouysségurhigh-throughput RNAi screening; iii) explore the impact of these new J, Berra E. HIF-1alpha and CA IX staining in invasive breastactors on tumour growth and metastasis as well as in different carcinomas: Prognosis and treatment outcome. Int J Cancer,ischemia-models. This project will allow us to improve our basic 120: 1443-1450 (2007).
  40. 40. 4. Berra E, Ginouvès A, Pouyssegur J. The hypoxia-inducible factorhydroxylases bring fresh air into hypoxia signalling. EMBO Rep.7: 41-45 (2006).5. Berra E, Benizri E, Ginouvès A, Volmat V, Roux D, Pouysségur J. HIFprolyl hydroxylase 2 is the key oxygen sensor setting low steady-state levels of HIF-1alpha in normoxia. EMBO J. 22: 4082-4090 (2003).Lab Members Nuria Macías Francisco R Technician González-Pacheco Postdoctoral Researcher Sara Pozo Analía Núñez Technician O’Mara PhD Student
  41. 41. STRUCTURALBIOLOGYUNIT
  42. 42. STRUCTURALBIOLOGYUNITStructural Biology investigates the relationship We try to understand the structural basis of biological processes such as signal transduction, bacterial pathogenesis or genebetween structure and function of biological expression.macromolecules. To this end we make use of biophysical techniques such asAll cellular processes are maintained and regulated by biological Macromolecular Crystallography, Nuclear Magnetic Resonance,macromolecules. Structural Biology studies the relationship Cryo-Electron Microscopy and Bioinformatic techniques.between the three-dimensional structure of such moleculesand their specific function. The aim is to understand their rolein cellular pathways crucial to life. The aim of our unit is toelucidate the three-dimensional structure of enzymes, proteins,nucleic acids, as well as their complexes.
  43. 43. · Dr Martín Martínez-Ripoll (Instituto Rocasolano, CSIC, Madrid, Spain). Lab. 1 · Dr Armando Albert (Instituto Rocasolano, CSIC, Madrid, Spain). · Dr Antonio Ferrer Montiel (Universidad Miguel Hernández, Alfonso Martínez de la Cruz Elche, Alicante, Spain). · Dr José Luis Neira Faleiro (Universidad Miguel Hernández, Principal Investigator Elche, Alicante, Spain). · Dr José Antonio Encinar Hidalgo (Universidad Miguel Hernández, Elche, Alicante, Spain).The laboratory is basically focused on two different projects. The first · Dr Jesús Prieto (CNIO, Madrid, Spain).one aims to understand how “cystathionine β-synthase (CBS) domains” · Dr Javier Gómez (Universidad de Zaragoza, Zaragoza, Spain).regulate the activity of their target proteins upon binding of different · Dr José Andrés Hernández (Universidad del País Vasco, UPV/EHU,ligands such as adenosyl groups or ions. The “CBS domain” proteins Bizkaia, Spain).comprise a large superfamily of evolutionarily-conserved proteins · Dr María Luz Martínez Chantar (CIC bioGUNE, Bizkaia, Spain).which are present in all kingdoms of life. Mutations within these · Dr José M Mato (CIC bioGUNE, Bizkaia, Spain).motifs cause several hereditary diseases in humans, such ashomocystinuria, autosomic retinitis pigmentosa, myotonia congenital,idyopatic epilepsy or hypercalciuric nephrolytiasis, among others. Selected PublicationsThus, they can be considered as promising targets for the development 1. Gómez García I, Kortázar D, Oyenarte I, Mato JM, Martínez-Chantarof novel drugs. CBS domains are unusually abundant in archaea. ML, Martínez-Cruz LA. Purification, crystallization and preliminaryOrganisms such as the hyperthermophile Methanococcus jannaschii crystallographic analysis of protein MJ1225 from Methanocaldo-offer an excellent model for the characterization of the adenosyl coccus jannaschii, a putative archaeal homologue of gamma-AMPK.binding site of these proteins. Acta Crystallogr Sect F Struct Biol Cryst Commun. 65, 813-817 (2009). 2. Martínez-Cruz LA, Encinar JA, Kortazar D, Prieto J, Gómez J,The second project is part of the CONSOLIDER program of the Spanish Fernández-Millán P, Lucas M, Astigarraga E, Fernández JA, Martínez-Ion Channel Initiative, a multidisciplinar and cooperative initiative Chantar ML, Mato JM and Neira JL. The CBS-domain protein MJ0729aiming to understand the structure-function relationship in ionic of Methanococcus jannaschii is a thermostable protein with a pH-channels, headed by Prof. Antonio Ferrer Montiel from the University dependent self-oligomerization. Biochemistry 48 (12):2766-2776 (2009).Miguel Hernández in Elche, Spain. My group is involved in the 3D- 3. Lucas M, Kortazar D, Astigarraga E, Fernández JA, Mato JM, Martínez-structure determination of selected targets using crystallographic Chantar ML, Martínez-Cruz LA. Purification, crystallization andapproaches. preliminary X-ray diffraction analysis of the CBS-domain pair from the Methanococcus jannaschii protein MJ0100. Acta Crystallogr Sect F Struct Biol Cryst Commun. 64 (10):936-941 (2008).Collaborations 4. Fernández-Millán P, Kortazar D, Lucas M, Martínez-Chantar ML,· Dr Sung-Hou Kim (University of California, Berkeley, CA, USA). Astigarraga E, Fernández JA, Sabas O, Albert A, Mato JM, Martínez-· Dr Liang Tong (Columbia University, New York, NY, USA). Cruz LA. Crystallization and preliminary crystallographic analysis of· Dr Regine Herbst Irmer (Goteborg University, Goteborg, Germany). merohedrally twinned crystals of MJ0729, a CBS-domain protein from· Dr George Sheldrick (Goteborg University, Germany). Methanococcus jannaschii. Acta Crystallogr Sect F Struct Biol Cryst· Dr Henri Blehaut (Institut Jerome Lejeune, Paris, France). Commun. 64 (7):605-6 09 (2008).
  44. 44. Lab Members Iker Oyenarte Inmaculada Technician Gómez García Postdoctoral Researcher

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