CENTER FOR COOPERATIVERESEARCH IN BIOSCIENCES

CIC bioGUNEPLAYS A STRONG ROLEIN ADVANCINGBIOMEDICAL RESEARCHAND TECHNOLOGICALINNOVATION INTHE BASQUE COUNTRY

The conviction that fundamentalbiomedical research and technological

innovation can be brought together drivesour work at the Center for CooperativeResearch in Biosciences, CIC bioGUNE.

We live in a time of discovery. Every year, newdiscoveries bring us closer to answering ofthe crucial questions about life; improvedunderstanding and treatment of disease havenever been so tantalizingly close. At the sametime, science and technology have becomeglobal and it is undeniable that scientificknowledge plays a fundamental role in thegeneration of wealth. However, not allcountries know how to obtain the bestsocioeconomic benefit from this commonknowledge (the so-called European paradox).The conviction that fundamental biomedical

research and technological innovation canbe brought together drives our work atthe Center for Cooperative Research inBiosciences, CIC bioGUNE.

CIC bioGUNE, a non-profit biomedical researchorganization founded in 2002 by the Departmentof Industry of the Basque Government, openedits research installations at the TechnologyPark of Bizkaia in January 2005. Since then,CIC bioGUNE has played a strong role inadvancing biomedical research andtechnological innovation in the Basque Country.

CIC bioGUNE invested over 35 million €in state-of-the-art research infrastructures,including genomics, gene silencing,proteomics, metabolomics, NMR, electronmicroscopy, x-ray diffraction, computer andanimal facilities, to support the researchactivities of its faculty and students.The Center commits every year more than5.5 million € for research and dedicates 450thousand € to PhD training. It employs 22faculty investigators, more than 85 postdocs,technicians and engineers, and providestraining opportunities to more than 23 PhDstudents each year. Our 22 faculty investigators,recruited internationally, include 15 fellowsfrom Ikerbasque, Bizkaia:xede, and Ramón yCajal programs.

CIC bioGUNE research strategy is based onthe firm belief that if talented researchers aregiven the freedom and necessary meansthey will contribute to the solution of thefundamental biological questions. Followingthis policy, scientists at CIC bioGUNE haveestablished research projects in a variety ofareas, including cell growth anddifferentiation, cancer, the innate immuneresponse, liver disease, chromatinremodeling, intracellular trafficking processes,and the structure of proteins, ribosomes andviruses. The projects are summarized in thisannual report. We also firmly believe inthe necessity of creating a lively intellectualenvironment in collaboration with biotechcompanies that fosters creative and

innovative approaches to research andtechnological innovation. Following thisconcept, the Center has set up three jointresearch laboratories with companiesestablished in the Basque Country.

External funding represents a criticalcomponent of CIC bioGUNE’s strategic plan.Since 2006, CIC bioGUNE has received4.1 million € from competitive research grants(mainly from the European Union, NIH, theSpanish Plan Nacional I+D+I, FIS, CIBER andCONSOLIDER programs) and 1 million € fromfoundations (primarily from the BBVAFoundation and Genome Spain) and researchcontracts. Concerted efforts of theadministration of CIC bioGUNE have helpedthe faculty to succeed in the competition forexternal funding. Extramural funding,combined with the generous support of theBasque Government and the RegionalGovernment of Bizkaia, allowed facultyresearch projects to grow and prosper.In fact, in 2008 CIC bioGUNE’s investigatorsauthored 51 scientific publications, in journalswith an average impact factor of 7, andapplied for 3 international patents.

CIC bioGUNE collaborates with the Universityof the Basque Country in the Master ofMolecular Biology and Biomedicineprogramme, reflecting our commitment toinspire and educate a new generation ofscientists. The Center also combines theorganization of research seminars, workshops,and congresses directed to specialists withseries of lectures designed for the generalpublic. CIC bioGUNE, in collaboration withthe other CIC, publishes CIC Network, ajournal dedicated to promote a culture ofresearch and technological innovation in theBasque Country.

CIC bioGUNE research strategy resides inthe firm belief that if talented researchers

are given the freedom and necessarymeans they will contribute to the solution

of the fundamental biological questions.

Prof José M MatoGeneral Director

INTERDISCIPLINARYRESEARCH WILLADVANCE LIFE SCIENCESDISCOVERIES TOWARDPRACTICAL USESFOR SOCIETY

CIC bioGUNE wants to bringtogether under the same roof scientists

from the research centers and thosefrom private companies.

Convinced that the convergence of thelife sciences and the physical sciences,mathematics and engineering can providein the 21st-century an economic growthcomparable to that driven by theconvergence between the physical sciencesand engineering in the 20th-century,the Basque Government recognized lifescience and biotechnology to be an essentialpillar of its economy. To reach this aim, in2002 the Basque Government implementeda plan, known as BioBasque 2010(www.biobasque.org), to drive and

coordinate all efforts in this area.Both the Center for Cooperative Researchin Biosciences in Bizkaia (CIC bioGUNE,www.cicbiogune.es) and the Center forCooperative Research in Biomaterials inGipuzkoa (CIC biomaGUNE,www.cicbiomagune.es) represent thatcommitment. Founded in 2002, CIC bioGUNEestablished its research facilities in the TechnologyPark of Bizkaia (www.parque-tecnologico.net)in January 2005 with the aim to bring togetherunder the same roof scientists from the researchcenters and those from private companies.

The idea was to stimulate interdisciplinaryresearch that will advance life science discoveriestoward practical uses for society. Five yearslater CIC bioGUNE, with around 130 scientistsand technicians, has produced a brandstreamin the Basque Country. As one indicator ofsuccess, the number of companies relatedto bioscience and biotechnology in theBasque Country has increased from 41 in2002 to 72 in 2009 and the sector alreadyaccounts for some 1,500 direct jobs.

At CIC bioGUNE, most of its faculty membershave engaged in their research collaborationswith scientists, engineers and technologyexperts at the universities, other researchand technology centers and biotechcompanies, as well as with medical doctorsin hospitals. One collaborative projectlaunched by CIC bioGUNE, for example, seeksto develop a blood test for the early diagnosisof liver diseases. Another project is trying toidentify genetic variants implicated incommon human complex diseases such astype I diabetes and multiple sclerosis.CIC bioGUNE’s laboratories are also studyingcell-signaling mechanisms involved in cancerinitiation and metastases. These projectscould become a clinical reality within thenext few years.

CIC bioGUNE’s new Structural Biology Unit,which opened in 2007, includes biologists,chemists and engineers working togetherto study the relationships between the

structure of biological molecules and theirintrinsic function. One of the laboratories, forinstance, focuses on the “motors” involvedin universal biological functions whereinteractions between protein and nucleicacids are essential, such as ribosomes duringthe translation process. Another projectlaunched by CIC bioGUNE seeks thecharacterization of proteins and theirinteractions during chromatin remodelingand DNA replication and repair, while yetanother studies the atomic structure of virus.CIC bioGUNE’s laboratories also pursue theanalysis of complex processes such asintracellular trafficking or the structuralcharacterization of enzymes involved in rarediseases such as porfiria, homocystinuria andretinitis pigmentosa. These studies couldprovide new strategies for disease diagnosis,treatment and prevention.

Accelerating these innovations will be themost important challenge of CIC bioGUNEin the coming years. Above all, this will requirefinding more efficient ways to carry outinterdisciplinary work involving the lifesciences researchers, the physicists, physiciansmathematicians and engineers, as well ascollaboration between CIC bioGUNE and thehospitals, technology centers and biotechcompanies.

CarmenGaraizar

President

At CIC bioGUNE members haveengaged in their research

collaborations with scientists,engineers and technology expertsat the universities, other research

and technology centers and biotechcompanies, as well as with medical

doctors in hospitals.

“THE WORLD LOOKS SO DIFFERENT AFTER LEARNING SCIENCE”

Richard Feynman

SCIENTIFICADVISORYBOARD

SCIENTIFICADVISORY BOARD

· Richard H FinnellInstitute of Biosciences and Technology, Texas A&M Health Science Center, Houston, Texas, USA

· Angela GronenbornDepartment of Structural Biology, University of Pittsburg, USA

· Samir M HanashMolecular Diagnostics, Fred Hutchinson Cancer Research Center, Seattle, USA

· Shelly LuUSC Research Center for Liver Diseases, Keck School of Medicine USC, Los Angeles, California, USA

· Juan RodésLiver Unit, Hospital Clinic, Barcelona, Spain

· Rima RozenDepartment of Pediatrics, Human Genetics and Biology, Mc Gill University-Montreal, Quebec, Canada

· Margarita SalasSevero Ochoa Molecular Biology Center, CSIC, Autónoma University of Madrid, Canto Blanco, Madrid, Spain

· Roger M BurnettProfessor Emeritus, The Wistars Institute, Philadelphia, USA

· Tom BlundellProfessor Emeritus, Department of Biochemistry, University of Cambridge, UK

INDEXRESEARCHUNITS

01 RESEARCHAREAS

TECHNOLOGYPLATFORMS

RESEARCHSUPPORTUNITS

01.1

01.2

02.1

Functional Genomics

Proteomics

Metabolomics

Cell Biology & Stem Cells

Structural Biology

Structural Biology

Genome Analysis

Proteomics & Metabolomics

Gene Silencing

Animal Facilities

Biosafety & Radioactive Protection

Informatics

Maintenance

SERVICEAREAS

ADMINISTRATION &DIRECTOR’S OFFICE

02.2

ADDITIONALINFORMATION

02

03

Funding

Patents

Aids to Recruitment

General Assembly

RESEARCHUNITS

FUNCTIONALGENOMICSUNIT

Genetic analysis is being used to understand the

fundamental mechanisms that underlie hereditary

diseases. This will allow development of therapeutic

strategies and diagnostic systems, both for hereditary

diseases and to predict individual sensitivity to

particular drugs.

The Functional Genomics Unit is concerned with studying the

regulation of the gene expression, in different cell types and during

development. We use sophisticated molecular biology and genetics

techniques to study the genes that control normal biological

processes, like the activation of the innate immune response to

microbial infections and the mechanisms controlling the

development of higher organisms. We are investigating genetic

variants within human populations that are associated with

particular diseases and the possible contribution of nutritional

and environmental influences to the development of pathological

conditions.

FUNCTIONALGENOMICSUNIT

Development of multicellular organisms requires the strict control

of cell division and differentiation. In higher eukaryotes, this control

is exerted by highly conserved signalling pathways, such as the

Transforming Growth Factor-β pathway, and the genes regulated by

them. Among those, the genes encoding the Spalt protein family are

necessary for numerous biological processes and are implicated in

diverse inherited human syndromes, such as the Townes-Brocks or

the Okihiro syndromes, as well as the susceptibility to Ovarian

Carcinoma or Wilms' Tumors. These syndromes include various

malformations, such as dysplastic kidneys (a major cause of renal

failure in infants), supernumerary thumbs, dysplastic ears, sensorineural

hearing loss and severe growth retardation, that might indicate

pituitary dysfunction.

Spalt proteins act as transcriptional repressors and are associated

with chromosomal stability, but the details of their mechanism of

action are still unknown. In our laboratory we try to understand this

mechanism, using the fruit fly Drosophila melanogaster as a model

organism. We are investigating the importance of posttranslational

modifications by sumoylation on the role of Spalt. We have generated

transgenic flies expressing low levels of Sumo using RNA interference

technology. The knockdown flies are unable to move on to adult

stages and stop their growth due to the low levels of ecdysone, the

hormone needed for metamorphosis. We are particularly interested

on the contribution of Spalt to this phenotype, as well as other factors

involved in the synthesis of Ecdysone. The possible role of Spalt

proteins in the regulation of growth is especially intriguing

and constitutes the focus of our research.

Rosa Barrio

Principal Investigator

Collaborations· Dr Rafael Cantera (Stockholm University, Sweden and IIBCE,

Montevideo, Uruguay).

· 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).

· Dr James David Sutherland (CIC bioGUNE, Bizkaia, Spain).

Selected Publications1. Talamillo A, Sánchez J, Cantera R, Pérez C, Martín D, Caminero E

and Barrio R. Smt3 is required for Drosophila melanogaster

metamorphosis. Development 135: 1659-1668 (2008).

2. Talamillo A, Sánchez J and Barrio R. Functional analysis of the

SUMOylation pathway in Drosophila. Biochem Soc Trans 36: 868-873

(2008).

3. De Celis JF and Barrio R. Regulation and function of Spalt proteins

during animal development. Int J Dev Biol 52: 2408-2422 (2008).

4. Barrio R, López-Varea A, Casado M and de Celis JF. Characterization

of dSnoN and its relationship to Decapentaplegic signaling in

Drosophila. Dev Biol 306: 66-81 (2007).

Lab Members

Roland HjerpePostdoctoralResearcher

Coralia PérezFernándezTechnician

Ana TalamilloPostdoctoralResearcher

Lab. 1

Leire HerbosoPhD Student

The genetic polymorphisms are variants of the genome that appear

by mutation in some individuals, are transmitted to the descendants

and acquire certain frequency in the population after multiple

generations. It has been estimated that there is a variant for every

1,000 base pairs among the 3,000 million that make the human

genome. The polymorphisms are the base of the evolution and those

that consolidate can be silent or can provide advantages to the

individuals, although they can also contribute to diseases.

With this background in mind, the main objective of this research

group is the identification and validation of genetic variants implicated

in common human complex diseases, in collaboration with national

and international medical researchers.

Most of the projects carried out at the laboratory i) use high-

throughput genotyping or sequencing techniques for simultaneously

examining complete genomes of patients and control individuals to

identify genetic variants; ii) help to develop bioinformatics tools for

the efficient study of the polymorphisms associated with the

susceptibility to a particular disease; and iii) supply biological

interpretation of the obtained results by testing the functionality of

the identified genes, examining their involvement in the aetiology

of diseases and their possible mechanism of action.

The identification of new diagnostic methods for early stages of

certain diseases and of possible targets for the specific drug generation

is of great importance for the development of successful treatment

of many serious human disorders.

Our lab is leading a project for the detailed genetic characterization

of the Basque population in relation to the high incidence of some

inherited diseases in this isolated population. Furthermore, we are

the group responsible of the Genetics Work-Package within the

COEDUCA (Cognition and Education) Consolider–Ingenio 2010

CSD2008-00048 project. In addition, we are participating in several

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-throughput

genotyping of the MHC (6p21) and LCR (19q3.4) regions in HLA-B27

populations in order to spot genetic variants associated to Ankylosing

Spondylitis; iv) SNP analysis and haplotype structure of cytokine gene

clusters in Multiple Sclerosis patients; v) genetic polymorphisms

association study of Alzheimer Disease by means of high-throughput

SNP genotyping; vi) system biology of Non Alcoholic Fatty Liver

diseases; vii) clinical validation of genetic tests for the evaluation and

therapy selection in colorectal patients (COLOGENETICS); and viii)

EDGeS - Enabling Desktop Grids for e-Science (Grant from the

European Commission's FP7 IST Capacities programme under grant

agreement RI-211727).

Collaborations· Dr Luis Castaño, Dr José Ramón Bilbao and Dr Guiomar Pérez de

Nanclares (Cruces Hospital, Bizkaia, Spain).

· Dr Alfredo Antigüedad and Dr Juan Mari Uterga (Basurto Hospital,

Bizkaia, Spain).

· Dr Carlos López Larrea (Hospital Universitario Central de Asturias,

Asturias, Spain).

· Dr Koen Vandenbroeck and Dr Carlos Matute (Universidad del País

Vasco UPV/EHU, Bizkaia, Spain).

· Dr Manuel Carreiras (Basque Center of Cognition, Brain and Language,

Gipuzkoa, Spain).

· Dr José M Mato & Dr María Luz Martínez-Chantar (CIC bioGUNE,

Bizkaia, Spain).

· Gabriel Carasa (CIC bioGUNE, Bizkaia, Spain).

· Dr Juan Falcón (CIC bioGUNE, Bizkaia, Spain).

· BIOEF foundation (Sondika, Bizkaia, Spain).

· OWL Genomics (Derio, Bizkaia, Spain).

Ana Mª Aransay

Principal Investigator

Lab. 2

Iñaki MendibilTechnician

· Pharmakine (Derio, Bizkaia, Spain).

· AMPTEC (Hamburg, Germany).

· Atos Origin (Madrid, Spain).

Selected Publications1. Hackenberg M, Sturm M, Langenberger D, Falcón-Pérez JM, Aransay

AM. 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, Aransay

AM, Olaskoaga J, Marti-Masso JF, López de Munain A. Association

between SYNAPSIN III gene promoter SNPs and multiple sclerosis in

Basque 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, Matthiesen

R, Yang H, Calvisi DF, Esteller M, Fraga M, Lu SC, Wagner C, Mato JM.

Loss of the Glycine N-Methyltransferase Gene Leads to Steatosis and

Hepatocellular Carcinoma in Mice. Hepatology 47, 4, 1191-9 (2008).

4. Castellanos-Rubio A, Martín-Pagola A, Santín I, Hualde I, Aransay

AM, Castaño L, Vitoria JC, Bilbao JR. Combined functional and positional

genetic information for the identification of susceptibility genes in

celiac 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 is

associated with celiac disease. Tissue Antigens 71, 3, 247-9 (2008).

Lab MembersLiher ImazPhD Student

Karin SchlangenPostdoctoralResearcher

Models of the innate immune response and genetic diseases in the

fly Drosophila.

The fruit-fly, Drosophila melanogaster, represents a very powerful

model to study biological processes due to its ease of culture, rapid

generation time and the sophisticated genetic tools that have been

developed for this organism.

As an example, the Toll receptor in humans, which is involved in the

recognition of pathogens, was identified by homology to the

Drosophila Toll gene.

In humans, the immune response consists of an immediate “innate”

response (mediated via antimicrobial peptides) and a delayed

“acquired” response (mediated via antibodies). In response to microbial

challenge, insects sythesize antibiotic peptides, activate macrophage-

like cells and mount a melanization response, but the antibody

mediated response is absent.

The major objective of our laboratory is to understand the mechanisms

of activation and degradation of the Necrotic protein in Drosophila.

In 1999, we identified Necrotic as a member of the serpin (serine

protease inhibitor) family, closely resembling human protease

inhibitors involved in the inflammatory response. More specifically,

Necrotic controls initiation of the extracellular proteolytic cascade

which activates the immune response to microbial infections. Serpin

turnover in biological systems tends to be extremely rapid and serpin-

degradation mechanisms may share genetic components with

mechanisms of misfolded-peptide clearance that underlie

diseases such as Alzheimer's and Parkinson's. These diseases have in

Lab. 3common the over-accumulation of peptides which prevent the

normal functioning of nerves.

An additional interest of our laboratory is the cryopreservation of

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 method

of long-term cryopreservation of stocks.

Collaborations· Dr Jean-Marc Reichhart (ICBM, Strasbourg, France).

· Dr David Lomas (Department of Medicine, University of Cambridge, UK).

· Dr John Morris (Asymptote Ltd, Cambridge, UK).

Selected Publications1. Garrett M, Fullaondo A, Troxler L, Micklem G, Gubb D. Identification

and analysis of serpin-family genes by homology and synteny across

the 12 sequenced Drosophilid genomes. MBC Genomics, 10: 489

(2009).

2. Soukup S, Culi J, Gubb D. Uptake of the Necrotic Serpin in Drosophila

Melanogaster via the Lipophorin Receptor-1. PLoS Genet

5(6):e1000532 (2009).

3. Lin Y, Gubb D. Molecular dissection of Drosophila Prickle isoforms

distinguishes their essential and overlapping roles in planar cell

polarity. Dev Biol 325: 386-399 (2009).

4. Yan J, Huen D, Morely T, Johnson G, Gubb D, Roote J, Adler P. The

multiple-wing-hairs gene encodes a novel GBD-FH3 domain-

containing protein that functions both prior to and after wing hair

initiation. Genetics 180 219-28 (2008).

5. Pelte N, Robertson A, Zhou Z, Belorgey D, Dafforn T, Jiang H, Lomas

D, Reichhart J-M, Gubb D. Immune Challenge induces N-terminal

cleavage of the Drosophila serpin Necrotic. Insect Biochemistry Mol

Biol. l 36: 37-46 (2006).

David GubbPrincipal Investigator

Lab MembersVeronikaMikitovaPostdoctoralResearcher

Laura BárcenaTechnician

Arantza SanzParraTechnician

Ubiquitination of neuronal proteins is an essential regulatory

mechanism of brain function, and its failure is associated to a number

of neurodegenerative conditions, including Parkinson’s and Alzheimer’s

diseases. Over the last two decades, much has been learnt from

studies on yeast and mammalian cell culture regarding the regulation

of ubiquitination at the molecular level. However, our understanding

of ubiquitination pathways within the context of whole organisms

is still very poor.

Genetic studies using Drosophila as a model system have identified

a number of ubiquitination pathways essential for neuronal function,

but the evidence for actual ubiquitination of the candidate substrates

has at best been indirect. Whereas the anatomic complexity of

Drosophila is far simpler than ours, most molecular mechanisms

governing neuronal cell function are actually highly conserved.

However, due to its relative complexity and tissue heterogeneity,

even Drosophila labs have often used cell culture for validating

candidate substrates of ubiquitin, on the assumption that if a protein

can be ubiquitinated in a given cell line, it might be ubiquitinated as

well in any other cell type. However, ubiquitination is used to regulate

cell function in a context-specific manner, and its roles are very likely

to be regulated differently in different tissues. For example, it is well

known that E3 ligase expression patterns differ enormously. Since

most characterised genomes code for hundreds of E3 ligases, it is

expected that ubiquitination pathways will be tissue specific.

We are developing a novel strategy for the efficient isolation of

neuronal ubiquitin conjugates from flies. The approach is based on

the in vivo biotinylation of ubiquitin expressed in a tissue-specific

manner. Taking advantage of the strength of the streptavidin-biotin

Lab. 4interaction, we are capable of enriching the ubiquitinated proteins

from Drosophila neurons up to levels not achieved by any other

approach until now. This technique is allowing us to isolate and

identify all neuronal proteins that are ubiquitinated, to resolve whether

they are mono or polyubiquitinated, and even to quantify for each

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.

Our lab has a number of ongoing projects to take advantage of the

technology we have developed. We are comparing the ubiquitination

profile of the developing brain with that of the adult brain, as well

as with the ubiquitination profile of other tissues. We are looking at

the specific substrates of a few important E3 ligases, like Highwire,

Ariadne1 and dUbE3A, this last one being the E3 ligase whose loss

of function causes Angelman syndrome, a genetic neurological

disorder. We are also looking at the ubiquitination profile in fly models

of polyglutamine diseases, to try to discern whether the ubiquitination

associated with those neurodegenerative disorders is the cause or

the effect of the disease. Additionally, we are looking at SUMOylation

using a very similar approach.

Collaborations· Dr Junmin Peng (Emory University School of Medicine, Atlanta, GA, USA).

· Dr Andrea Brand (Wellcome Trust Cancer Research UK Gurdon

Institute, Cambridge, UK).

· Dr Catherine Lindon (Dept of Genetics, University of Cambridge,

Cambridge, UK).

· Dr Rosa Barrio (CIC bioGUNE, Bizkaia, Spain).

· Dr Alberto Ferrus (Instituto Cajal CSIC, Madrid, Spain).

· Dr Janice Fischer (University of Texas, Austin, TX, USA).

Selected Publications1. Religa TL, Markson JS, Mayor U, Freund SMV, Fersht AR. Solution

structure of a protein denatured state and folding intermediate.

Nature 437:1053-6 (2005).

Ugo MayorPrincipal InvestigatorIkerbasque Research Professor

So Young LeeTechnician

Lab MembersJuan ManuelRamírez SánchezPhD Student

Maribel FrancoPostdoctoralResearcher

2. Mayor U, Guydosh NR, Johnson CM, Grossmann JG, Sato S, Jas GS,

Freund SMV, Alonso DOV, Daggett V and Fersht AR. The complete

folding 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 denaturing

and native conditions. Journal of Molecular Biology 333:977-91 (2003).

4. Mayor U, Johnson CM, Daggett V and Fersht AR. Protein folding

and unfolding in microseconds to nanoseconds by experiment and

simulation. Proc. of the National Academy of Sciences of the USA

97:13518-22 (2000).

PROTEOMICSUNIT

The map of human proteins will make it possible to

find new diagnostic markers for different pathologies.

The availability of the complete sequence of certain genomes,

especially the human genome, offers new opportunities for

biological research.

The goal of the Proteomics Unit is to identify proteins involved in

some physiological processes and also to characterize the

interactions between them.

Such functional characterization may allow comparisons between

the protein pattern present in diseased tissue versus healthy tissue

and consequently, it may be possible to establish the specific

"proteomic fingerprint" of a pathological state. Detailed protein

studies may reveal potential molecular markers associated with

disease progression and lead to possible therapeutic targets.

PROTEOMICSUNIT

Lab. 1

Transmissible spongiform encephalopathies (TSEs) are fatal

neurodegenerative disorders affecting both humans and animals.

TSEs can be of genetic, sporadic or infectious origin. The infectious

agent associated with TSEs, termed prion, appears to consist of a

single protein, an abnormal conformer (PrPSc) of a natural host protein

(PrPC), which propagates by converting host PrPC into a replica of

itself. One of the characteristics of prions is their ability to infect some

species and not others. This phenomenon is known as transmission

barrier. Interestingly, prions occur in the form of different strains that

show distinct biological and physicochemical properties, even though

they are encoded by PrP with the same amino acid sequence, albeit

in presumably different conformations. In general, the transmission

barrier is expressed by an incomplete attack rate and long incubation

times (time from the animal inoculation until the onset of the clinical

signs) which become shorter after serial inoculation passages.

Compelling evidence indicates that the transmission barriers are

closely related to differences in PrP amino acid sequences between

the donor and recipients of infection, as well as the prion strain

conformation. Unfortunately, the molecular basis of the transmission

barrier phenomenon and its relationship to prion strain conformations

is currently unknown and we cannot predict the degree of a species

barrier simply by comparing the prion proteins from two species. We

have conducted a series of experiments using the Protein Misfolding

Cyclic Amplification (PMCA) technique that mimics in vitro some of

the fundamental steps involved in prion replication in vivo, albeit with

accelerated kinetics. The in vitro generated prions possess key prion

features, i.e., they are infectious in vivo and maintain their strain

specificity. We have used PMCA to efficiently replicate a variety of

prion strains from, among others, mice, hamsters, bank voles, deer,

cattle, sheep, and humans. The correlation between in vivo data and

our in vitro results suggest that PMCA is a valuable tool for assessing

the strength of the transmission barriers between diverse species

and for different prion strains; we are using the method to determine

which amino acids in the PrPC sequence contribute to the strength

of the transmission barrier. These studies are proving very useful in

evaluating the potential risks to humans and animals, of not only

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) propagated

in sheep does so efficiently. In addition, we have also generated

prions that are infectious to species hitherto considered to be resistant

to prion disease.

Collaborations· Dr Glenn Telling (Department of Microbiology, Immunology and

Molecular Genetics, University of Kentucky, Lexington, KY, USA).

· Dr Charles Weissmann (Department of Infectology, Scripps Research

Institute, Jupiter, FL, USA).

· Dr Adriano Aguzzi (Institute of Neuropathology, University Hospital

Zurich, Zurich, Switzerland).

· Dr Juan María Torres (Centro de Investigación en Sanidad Animal,

INIA, Madrid, Spain).

· Dr Enric Vidal and Dr Martí Pumarola (Departament de Medicina i

Cirugia Animals, Universitat Autònoma de Barcelona, Barcelona,

Spain).

Selected Publications1. Castilla J, Morales R, Saá P and Soto C. Propagation of prion strains

in vitro. EMBO J. 27, 2557-2566 (2008).

2. Castilla J, Gonzaléz D, Saá P, Morales R, de Castro J and Soto C.

Crossing species barrier by in vitro replication of protein misfolding

generates new infectious prions. Cell. 134, 757-768 (2008).

3. Green KM, Castilla J, Seward TS, Napier DL, Jewell JE, Soto C and

Telling GC. Accelerated High Fidelity Prion Amplification Within and

Across Prion Species Barriers. PLOS Pathogens. 4, 1-12 (2008).

Joaquín Castilla

Principal InvestigatorIkerbasque Research Professor

Alberto MarinaTechnician

4. Saá P, Castilla J and Soto C. Pre-symptomatic detection of prions in

blood. Science. 313, 92-4 (2006).

5. Soto C, Estrada L and Castilla J. Amyloids, prions and the inherent

infectious nature of misfolded protein aggregates. Trends in

Biochemical Sciences. 31, 150-155 (2006).

Lab Members

NataliaFernández-BorgesPostdoctoralResearcher

Nagore SacristánTechnician

Iker UriartePostdoctoralResearcher

Emma LovisaHelena JakobssonPostdoctoralResearcher

Adhesion between cells, as well as adhesion of cells to substrates, is

a fundamental property of multicellular organisms. Changes in cell

adhesion can give rise to defects in development and loss of tissue

integrity that contributes to human disease. During cancer metastasis,

transformed cells of a solid tumor can disperse and become more

motile, traveling to remote sites where they may form secondary

tumors. Cells must leave the primary tumor, enter and exit the

circulatory system by crossing endothelial layers, and populate the

secondary site - all steps that require remodelling and changes

in cell adhesion structures.

Our work focuses on PET-LIM proteins, a small family of scaffolding

proteins that may regulate the formation of protein complexes

involved in diverse cellular processes, including cell spreading,

adhesion and polarity. The testin protein (TES) exhibits dynamic

localisation within cells and shuttles between the nucleus and the

integrin-based focal adhesions formed between cells and substrates.

Loss of TES is observed in several tumor types and mice lacking TES

exhibit aggressive tumor growth, pointing to its role as a tumor

suppressor. We are using screening by RNAi to uncover additional

factors in the TES tumor suppression pathway. Also, to understand

how TES is regulated, we are using biochemistry, mutational analysis

and structure-based approaches to uncover intramolecular interactions

that control the ability to form complexes with known and novel TES

ligands. Lastly, several PET-LIM family members are farnesylated and

may regulate multiprotein complex assembly at the plasma membrane

or close to organelles. One of these, Prickle3, dynamically localises to

cell-cell adhesions. Further examination of this class of PET-LIMs will

reveal if they are also cancer-related or have novel roles in development

and disease.

Collaborations· Dr Puri Fortes, Dr Rubén Hernández (Centro de Investigación Médica

Aplicada, Universidad de Navarra, Pamplona, Spain).

· Dr Roberto Martínez, Dr Ricardo Rezola, Dr María Jesús Michelena

(Instituto Oncológico, San Sebastián, Gipuzkoa, Spain).

· Dr Rosa Barrio (CIC bioGUNE, Bizkaia, Spain).

Selected Publications1. Garvalov BK, Higgins TE, Sutherland JD, Zettl M, Scaplehorn N,

Köcher T, Piddini E, Griffiths G, Way M. The conformational state of

Tes regulates its zyxin-dependent recruitment to focal adhesions.

J Cell Biol. 161(1):33-39 (2003).

Lab MembersItziar Martín RuízTechnician

Lab. 2James D Sutherland

Principal Investigator

The covalent conjugation of ubiquitin and ubiquitin-like molecules

to different substrates has become one of the most widely investigated

post-translational modifications. Modified substrates include proteins

controlling an extensive array of essential processes, such as protein

degradation via the 26S proteasome, regulation of transcription, the

cell cycle and oncogenesis.

The ubiquitin family of molecules can be attached to protein substrates

as monomers and polymers. Although a considerable amount of

data on many aspects of ubiquitin and ubiquitin-like mediated

processes is available, many aspects regarding the modification-

specific and chain-type recognition of conjugated substrates, as well

as the molecular processes engaged after protein conjugation with

the various ubiquitin-like modifiers such as SUMO-1, SUMO-2, SUMO-

3 and NEDD8, remain obscure. To address these questions our main

models are: 1) Iκβα a and A20 proteins -both proteins are natural

inhibitors of the NF-κβ transcription factor, which conditions its

transcriptional activity during the immune and inflammatory responses

and 2) the tumour suppressor p53.

Our specific objectives are:

a. Identification of specificity motifs in the target proteins determining

the preferential recognition by modifier-protein ligases (E3s), and the

use of these motifs to isolate, identify and study the role of interacting

proteins participating in the response generated by such modifications.

b. Applying this knowledge to develop high troughput screenings

methods (HTS) to isolate new drugs that can be used to treat

pathologies where our protein models are implicated.

Manuel Rodríguez MedinaPrincipal Investigator

Lab. 3c. Developing new strategy and applications to isolate and identify

ubiquitylated proteins in vivo from cell cultures as well as for tissues

and organs from animal models where the Ubiquitin-Proteasome

Pathway appears to be at the origin of drug resistance or pathologies

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 and

disease.

Collaborations· Dr Patrick England (Pasteur Institute, Paris, France).

· Dr Ron Hay (Dundee University, Scotland, UK).

· Dr Rosa Farrás (Centro de Investigación Principe Felipe,

Valencia, Spain).

· Dr Carmen Rivas (CNB, CSIC, Madrid, Spain).

· Dr Rosa Barrio (Functional Genomics Unit, CIC bioGUNE, Bizkaia, Spain).

· Dr Edurne Berra (Cell Biology Unit, CIC bioGUNE, Bizkaia, Spain).

· Dr José M Mato (Metabolomics Unit, CIC bioGUNE, Bizkaia, Spain).

· Dr María Luz Martínez-Chantar (Metabolomics Unit, CIC bioGUNE,

Bizkaia, Spain).

Selected Publications1. Hjerpe R, Aillet F, Torres-Ramos M, Lang V, Farrás R, Hay RT and

Rodríguez MS. Mdm2 mediates multiple mono-ubiquitin-dependent

proteasomal degradation of p53. Submitted (2009).

2. Hjerpe R, Aillet F, Lopitz-Otsoa F, Lang V, England P and Rodríguez

MS. Using Tandem Ubiquitin Binding Entities (TUBEs) to isolate

polyubiquitylated proteins. EMBO rep Octubre 2009.

3. Hjerpe R and Rodríguez MS. Alternative UPS drug targets upstream

the 26S proteasome. International Journal of Biochemistry and Cell

Biology. 40, 1126-1140 (2008).

Fabienne AilletPostdoctoralResearcherCIBERehd Fellow Member

Fernando LopitzPostdoctoralResearcher

Valerie LangPostdoctoralResearcher

4. Rubio A, Guruceaga E, Vázquez-Chantada M, Sandoval J, Martínez-

Cruz LA, Segura V, Sevilla JL, Podhorski A, Corrales FJ, Torres L, Rodríguez

MS, Aillet F, Ariz U, Martínez Arrieta F, Caballería J, Martín-Duce A, Lu

SC, Martínez-Chantar ML, Mato JM. Identification of a Gene-pathway

associated with non-alcoholic esteatohepatitis. J. Hepatology 46,

708-718 (2007).

Lab Members

METABOLOMICSUNIT

Metabolomics provides knowledge to identify the

metabolites present in a biological sample, and is

the simplest, cheapest and most efficient method

to diagnose diseases.

Metabolomics focuses on the study of metabolites. These small

molecules are the last step in the biological process initiated with

gene expression. The study of human metabolome is a very efficient

method to identify possible markers and determine if an individual

person is going to suffer from a disease, helping to diagnose a

specific pathology.

In mammals, specially in human, the liver plays an important role

in metabolomic equilibrium. In a pathological situation like diabetes

mellitus, obesity, steatohepatitis or cirrhosis, a failure in the

regulation of the mechanism maintaining the metabolomic

equilibrium takes place. The aim of this unit is to identify the

essential metabolites involved in signaling pathway regulation

and analyze the mechanism of the progression and development

of liver diseases. This knowledge will help us to understand the

mechanism and the relationship existing between essential

metabolites and proliferation, cellular death and cellular

metabolism.

METABOLOMICSUNIT

Non-alcoholic fatty liver disease (NAFLD) is currently the most frequent

chronic liver disease in western countries affecting about 20-30% of

adults above age 20. NAFLD is characterized by the accumulation of

fat in the liver (steatosis). Although generally asymptomatic, 10-40%

of NAFLD patients, depending on the population selected, develop

non-alcoholic steatohepatitis (NASH), which is characterized by the

presence of steatosis with inflammation, necrosis and fibrosis. NASH

is a progressive disease of the liver that may progress to cirrhosis and

hepatocellular carcinoma (HCC). Obesity is a major risk factor for the

development of NAFLD. However, the observation that about half

the patients with NAFLD are not obese indicates that there are factors

(nutritional, genetic and environmental), independent of the ingestion

and lipid metabolism that strongly affect the accumulation of fat in

the liver.

In my laboratory we have used gene-knockout technology to study

how mouse genes regulate liver metabolism and fat accumulation

–a research that provides relevant information on the hepatic

metabolism in humans and how hepatic fat accumulates when there

is a metabolic imbalance–. Using this technology, we have identified

that S-adenosylmethionine (SAMe, a metabolite of methionine) plays

a crucial role as a regulator of liver metabolism and hepatocyte

proliferation and how both, a chronically low levels and excess of

hepatic SAMe leads to NASH and HCC. The mechanism by which

SAMe regulates liver function involves histone- and DNA-methylation

as well as regulation of AMP-activated protein kinase (AMPK), the

main enzyme involved in the regulation of hepatic metabolism.

Other research lines in my laboratory include: the identification of

non-invasive serum biomarkers that differentiate between steatosis

José M Mato

Principal Investigator

Lab. 1and NASH using high-throughput metabolic technology – at present

the gold standard for the diagnosis of NAFLD is histological

examination of a liver biopsy specimen, which is an expensive, invasive

and subjective procedure associated with potential complications

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 endocytic

origin secreted by most cell types that mediate communication

between cells, facilitating processes such as antigen presentation

and in trans-signaling to neighboring cells.

Collaborations

· Dr Shelly C Lu (University of Southern California, Los Angeles,

CA, USA).

· Dr Conrad Wagner (Vanderbilt University School of Medicine,

Nashville, TN, USA).

· Dr Richard H Finnell (Texas Institute for Genomic Medicine,

Houston, TX, USA).

· Dr Juan Caballería (Hospital Clínic de Barcelona, Barcelona, Spain).

· Dr CB Rountree (Penn State Children's Hospital, Hershey, PA, USA).

· Dr Jian-Min Yuan (University of Minnesota, Minneapolis, MN, USA).

· Dr Luis Torres (Universidad de Valencia, Valencia, Spain).

· Dr Yannick Le Marchand-Brustel (Universitaire Archimed, INSERM,

Nice, France).

· Dr Jonathan Barr (OWL Genomics, Derio, Bizkaia, Spain).

· Dr Carlos Simón (Fundación IVI, Valencia, Spain).

Selected Publications1. Varela-Rey M, Fernández-Ramos D, Martínez-López N, Embade N,

Gómez-Santos L, Vázquez-Chantada M, Rodríguez J, Luka Z, Wagner

C, Lu SC, Martínez-Chantar ML, Mato JM. Impired liver regeneration

in mice lacking glycine N-methyltransferase. Hepatology.

Aug;50(2):443-52 (2009).

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-activated

protein kinase/ endothelial nitric oxide synthase cascade regulated

by hepatocyte growth factor, S-adenosylmethionine, and nitric oxide

in 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 Adenosyl

Transferase 1A Deficient Mice Demonstrate Resistance to TGF-β

induced apoptosis. Hepatology; 49:1277-86 (2009).

4. Mato JM, Martínez-Chantar ML, Lu SC. Methionine Metabolism and

Liver Disease. Annu Rev Nutr. Aug 21;28:273-293 (2008).

Lab Members

Lab Members attachedto external projects

Richard H FinnellVisitingScientific

David FernándezRamosPhD Student

Juan Luis GarcíaRodríguezPhD Student

Mercedes VázquezChantadaPostdoctoralResearcher

Javier CondePhD Student

Juan ManuelFalcónPostdoctoralResearcher

EsperanzaGonzález JiménezTechnician

Nieves EmbadePostdoctoralResearcher

Marcella SiniVisitingResearcher

Miriam PérezCormenzanaPlatformSpecialist

Non-alcoholic fatty liver disease (NAFLD) is a clinical-pathological

term that includes a spectrum of alterations ranging from the simple

accumulation of triglycerides in the hepatocytes (steatosis) to steatosis

with hepatic inflammation (steatohepatitis or NASH). NASH, in turn,

also progresses to cirrhosis and HCC. The mechanisms that lead to

the manifestation of NASH are not clear, but it is a condition associated

with obesity, insulin resistance, and diabetes.

Since the incidence of these diseases is increasing, the prevalence of

NASH is also expected to increase in coming years (today it varies

between 13 to 15 % of the population). NASH is now considered as

an emerging disease in USA and occidental countries. Nowadays,

lacking accurate, sensitive diagnostic test, distinguishing steatosis

from steatohepatitis requires the use of invasive techniques like liver

biopsy. In summary, the lack of information about the factors

implicated in the NASH pathogenesis, as well as in the prognostics

characteristics and the treatment of this pathology, emphasize the

need of new approaches aimed at understanding the mechanisms

implicated in the development of NASH and HCC. In response to

these needs we propose a multidisciplinary research project to study

these pathologies.

Over the last few years, we have elucidated some of the molecular

mechanisms of SAMe regulated proliferation, regeneration and

apoptosis and identified downstream targets contributing to the

abnormal hepatic lipid metabolism and proliferation in both

MAT1A-KO and GNMT-KO mice, both with chronically abnormal levels

of SAMe. The most important projects proposed are the following

ones: 1) Examine SAMe’s regulation of HGF-mediated hepatocyte

proliferation. Hepatocyte growth factor (HGF) activates AMP-activated

Mª Luz Martínez Chantar

Principal Investigator

Lab. 2protein kinase (AMPK), which is required for hepatocyte proliferation.

Our new data also show cross-talks between AMPK and nitric oxide

synthase in modulating the proliferative effect of HGF. How SAMe

regulates these pathways will be elucidated. 2) We have isolated a

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 risk

of HCC is high. 3) Identify mechanisms of malignant degeneration

when SAMe metabolism is altered. Both chronic SAMe deficiency

and excess result in fatty liver and HCC. Successful completion of the

proposed tasks should greatly enhance our understanding of SAMe’s

role in liver health and pathology and help identify patients that will

benefit from its therapeutic use.

Collaborations· Dr Shelly C Lu (University of California, Los Angeles, CA, USA).

· Dr Myriam Gorospe (NIH, Baltimore, MD, USA).

· Dr Anna Maeh Diehl (Duke University Medical Center, Durham,

NC, USA).

· Dr Richard Finnell (Department of Nutrition and Food Science,

Houston, TX, USA).

Selected Publications1. Tomasi ML, Iglesias-Ara A, Yang H, Ramani K, Feo F, Pascale MR, Martínez-

Chantar ML, Mato JM, Lu SC. S-Adenosylmethionine Regulates

Apurinic/Apyrimidinic Endonuclease 1 Stability: Implication

Hepatocarcinogenesis. Gastroenterology. 136:1025-1036 (2009).

2. Vázquez-Chantada M , Ariz U, Varela-Rey M, Martínez-López Nuria,

Embade N, Fernández-Ramos D, Gómez-Santos, Lu SC, Martínez-Chantar

ML, Mato JM. Evidence for an LKB1/AMPK/eNOS Cascade

Regulated by HGF, S-Adenosylmethionine and NO. Hepatology 49:

608-617 (2009).

3. Varela-Rey M, Embade N, Ariz U, Lu SC, Mato JM, Martínez-Chantar

ML. Non-alcoholic steatohepatitis and animal models: Understanding

the human disease. Int J Biochem Cell Biol. 41:969-976 (2009).

4. Martínez-Chantar ML, Vázquez-Chantada M, Ariz U, Martínez N, Varela

M, 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 the

glycine N-methyltransferase gene leads to steatosis and hepatocellular

carcinoma in mice. Hepatology 47:1191-1199 (2008).

Lab Members

Naiara BerazaPostdoctoralResearcher

BegoñaRodríguezIruretagoyenaTechnician

Itziar FradesPhD Student

Nuria MartínezLópezPhD Student

Marta VarelaPostdoctoralResearcherCIBERehd Fellow Member

Ashwin WoodhooPostdoctoralResearcher

CELL BIOLOGY& STEM CELLSUNIT

We investigate the molecular changes that occur in

cells and their genomes in response to different

stimuli.

We work on projects of basic and applied research that investigate

important cellular processes such as cell proliferation,

differentiation, maintenance of pluripotency and adaptation to

low oxygen availability. Scientific interests of the laboratories in

the Unit include the signalling pathways activated by steroid

hormones, Wnt family growth factors and hypoxia, the genetic

changes occurring during carcinogenesis and the functional and

spatial organisation of the genome. Our aims are to understand

the relationship between these processes and pathologies such

as cancer, neurodegenerative disease and ischemia and to generate

new diagnostic and therapeutic tools.

CELL BIOLOGY &STEM CELLS UNIT

Bruno SimõesPhD Student

ValentineComaillsPhD Student

Oihana IriondoPhD Student

Marco PivaPhD Student

The main objective of the laboratory is to gain further insight into

the roles that steroid hormone receptors play in normal breast tissue

and during breast cancer development. Furthermore, the influences

of estrogen, other signalling factors and the microenvironment in

breast stem cells and in their transformation into cancer initiating

cells are being explored.

Following the interest of the laboratory in the initiation and progression

of breast cancer, three stem/progenitor cell populations were identified

in the human mammary gland. These populations are currently being

characterised in more detail and their responses to hormones and

other signals are being investigated. In addition, both normal breast

and breast tumour cells are being propagated as mammospheres to

facilitate comparative studies of stem/progenitor cell self-renewal

and differentiation in response to various treatments.

The cancer stem cell hypothesis implies that stem/progenitor cells

are more resistant to current therapies used to treat patients. Tamoxifen

is one of the most commonly used endocrine treatments for estrogen-

responsive breast cancer, although development of resistance is a

frequent clinical problem. Breast cancer stem/progenitor cells that

are resistant to tamoxifen have been generated and the responses

of these cells to chemotherapy drugs and other factors are currently

being studied.

The various approaches undertaken in the laboratory should

contribute to a better knowledge of the molecular profile of breast

stem cells and the responses of both normal and cancer breast

stem/progenitor cells to their cellular environment.

Lab. 1Collaborations· Dr José Antonio López Ruiz (PreteImagen, Bilbao, Bizkaia, Spain).

· Dr Shyamala Maheswaran (MGH, Harvard Medical School,

Boston, MA, USA).

· Dr José Luis Toca-Herrera (CIC biomaGUNE, Gipuzkoa, Spain).

Selected Publications1. Moreno-Flores S, Benitez R, Vivanco MdM, Toca-Herrera JL. Stress

relaxation microscopy: Imaging local stress in cells. J Biomech. [Epub

ahead of print] (2009).

2. Vivanco MdM. Biomarkers in breast cancer. Chapter 7 in:

Bioinformatics Methods in Clinical Research (2009). Eds. J Walker and

R Matthiesen, Humana Press (2009).

3. Krützfeldt M, Ellis M, Weekes DB, Bull JJ, Eilers M, Vivanco MdM,

Sellers WR, Mittnacht S. Selective ablation of retinoblastoma protein

function by the RET finger protein. Molecular Cell 18, 213-224 (2005).

4. Clayton H, Titley I and Vivanco MdM. Growth and differentiation

of progenitor/stem cells derived from the human mammary gland.

Exp Cell Res 297, 444-460 (2004).

Lab Members

María del Mar Vivanco

Principal Investigator

Gemma ReverterPostdoctoralResearcher

Mª ÁngelesRábanoTechnician

The Wnt signalling pathway plays an important role in cell growth

and differentiation and is frequently activated in cancer. Our goals

are to understand how Wnts, their antagonists and their effectors

control cell growth and differentiation and to use the technological

platforms at CIC bioGUNE to characterise the cellular responses to

Wnt ligands. We study these aspects in two contexts – prostate cancer

(PCa) progression and neuronal differentiation.

We examined Wnt gene expression in PCa and found that Wnt-11 is

upregulated in hormone-refractory PCa. Gene silencing and

overexpression were used to show that Wnt-11 alters the survival

and neuroendocrine-like differentiation of PCa cells. Wnt gene

expression was also analysed during retinoic acid induction of neural

differentiation of human embryonal carcinoma (hEC) cells. Three Wnts

were identified that might play roles in this process, one of which is

Wnt-11. Ongoing studies involve characterisation of the Wnt signals

that control survival and differentiation of PCa and hEC cells. The sFRP

and Dickkopf families of secreted Wnt antagonists have also been

characterized and Dkk3 and sFRP1 were found to be downregulated

in PCa. We are presently studying the function of Dkk3 in cell

differentiation in more detail.

Finally, we are characterising the Wnt effectors Axin and glycogen

synthase kinase-3 (GSK-3), which together act to inhibit Wnt/beta-

catenin signalling. Phosphorylation sites in Axin have been identified

that play a role in the regulation of GSK-3 activity. We are now analysing

the functions of the different isoforms of GSK-3 in PCa and in neuronal

differentiation.

Lab. 2

Zafira CastañoPostdoctoralResearcher

Mercedes CaroTechnician

Víctor ManuelCampaPostdoctoralResearcher

Collaborations· Dr Akira Kikuchi (Hiroshima University, Hiroshima, Japan).

· Dr Jonathan Waxman (Imperial College London, London, UK).

· Dr Phillip Gordon-Weeks (MRC Centre for Developmental

Neurobiology, Kings College London, London, UK).

· Dr María del Mar Vivanco (CIC bioGUNE, Bizkaia, Spain).

Selected Publications1. Kawano Y, Diez S, Uysal-Onganer P, Darrington RS, Waxman J,

Kypta R. sFRP1 is a negative regulator of androgen receptor activity

in prostate cancer. British Journal of Cancer, 100, 1165-1174 (2009).

2. Kypta R. Wnt signalling in The Encyclopedia of Cancer, 2nd Edition

Edited by Manfred Schwab, Springer Press (2009).

3. Castano Z, and Kypta R. Housekeeping Proteins: Limitations as

References During Neuronal Differentiation. The Open Neuroscience

Journal, 2, 36-40 (2008).

4. Kypta R. GSK-3 inhibitors and their potential in the treatment of

Alzheimer's disease. Expert Opinion in Therapeutic Patents 15, 1315-

1332 (2005).

Lab Members

Robert Kypta

Principal Investigator

Rocío JiménezAlonsoPhD Student

The laboratory of Cytogenomics is focused on studying genome

organization at the cellular level, in particular during liver

carcinogenesis. Our research project “Cytogenomics of benign and

malignant lesions of the liver”, aims to characterize the profile of

genome alterations of liver tumours arising in human and in different

mouse models of the disease. To this end, conventional and molecular

cytogenetic methods, such as FISH, SKY and array-CGH are currently

used in the laboratory.

The group is also interested in investigating the 3-dimensional

arrangements of chromosomes and genes in the interphase nucleus

during carcinogenesis. The project “Organization of the genome in

the interphase nucleus” intends to generate a 3D map of those

chromosomes and genes recurrently involved in abnormalities in

hepatomas using interphase FISH with whole-chromosome painting

and locus-specific probes combined with high-resolution microscopy

on normal and tumor cells.

Most importantly, we aim to understand how the spatial distribution

of chromosomes and genes is related to genome function. In this

regard, we are currently investigating the “role of the nucleolus on

the functional organization of Pol II dependent genes” and the

“Genome response to signalization events mediated by integrins”.

The nucleolus is the most prominent compartment of the nucleus,

where ribosomal genes are transcribed. We ask whether its activity

influences the spatial and functional organization of non-ribosomal

genes. To address this question we perform expression analysis of

genes mapping to chromosomes that harbour NOR, as well as

NOR-negative chromosomes, and RNA-FISH combined with nucleolus

immunostaining of nucleolar proteins to obtain single

cell expression profiles and in situ-loci mapping of genes

simultaneously. Since genomic events are also elicited by processes

in the extracellular microenvironment, we also study the organizational

changes of the genome associated with signalling events mediated

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.

Collaborations· Dr Alicia Lorenti (Laboratory of Tissue Engineering, University Hospital,

Austral University, Buenos Aires, Argentina).

· Dr África García-Orad (Dept. of Genetics, Universidad del País Vasco

UPV/EHU, Bizkaia, Spain).

· Dr María Luz Martínez-Chantar & Dr José M Mato (Metabolomics

Unit, CIC bioGUNE, Bizkaia, Spain).

· Dr Federico Garrido (Dept. of Clinical Chemistry & Immunology,

University Hospital Virgen de las Nieves, Granada, Spain).

Selected Publications1. Calvo A, Perez-Stable C, Segura V, Catena R, Garuceaga E, Nquewa P,

Blanco D, Parada LA, Green F. Molecular characterization of the

FG/Tag transgenic mouse model of hormone refractory prostate

cancer: comparison to human prostate cancer. The Prostate (2009

in press).

2. Royo F, Paz N, Espinosa L, Vellón L, Parada LA. Spatial link between

nucleoli and expression of the Zac1 gene. Chromosoma. Epub

DOI10.1007/s00412-009-0229-1 (2009).

3. Parada LA. Interphase genome organization and cancer.

Chromosome Research 17: 18-20 (2009).

4. Parada LA. Genome reorganization during invasive cell growth. Atlas

Genet Cytogenet Oncol Haematol, 12: 1-81 (2008).

5. Vellón L, Espinosa L, Royo F, Parada LA. α5β1 integrin-emanating

signals remodel nuclear architecture through the activation of

ERK1/2 and p38a MAPKs during invasive cell growth. Eur. J. Cancer

6: 36 (2008).

Lab. 3Luis Parada

Principal Investigator

Amaia ZabalaTechnician

Nerea PazPhD Student

Lab Members

Félix RoyoPostdoctoralResearcherCIBERehd Fellow Member

Luciano VellónPostdoctoralResearcher

Low oxygen availability or hypoxia is associated with several

physiopathological processes, like ischemia and cancer. This is why

the manipulation of the hypoxia-signalling cascade (by activating

and/or inhibiting) appears to be a very interesting therapeutic

approach. However, in order to do that, it is necessary to precisely

elucidate this signalling pathway and particularly, the mechanisms

regulating the α subunit of the Hypoxia Inducible Factor (HIF). Indeed,

HIFα is crucial in the hypoxia signalling pathway and the regulation

of its stability, the limiting step of this cascade.

HIFα stability is regulated by the PHDs (HIF Prolyl Hydroxylases or

Prolyl Hydroxylases Domain containing proteins). These enzymes

hydroxylate HIFα by using oxygen as a co-substrate and thus act as

veritable oxygen “sensors”. Three PHD isoforms have been identified:

PHD1, 2 and 3. The three isoforms are ubiquitously expressed but

their relative expression levels and localization are different. These

isoforms are able to hydroxylate HIFα in vitro, but our previous results

have shown that in cellulo, PHD2 plays a central and unique role in

well-oxygenated cells, whereas PHD1 and PHD3 only contribute to

the regulation of HIFα stability upon chronic hypoxia.

The aim of our group is to elucidate the PHDs regulatory mechanisms

and their physiological importance. We are planning to: i) study the

contribution of post-translational modifications like hydroxylation,

phosphorylation, acetylation, ubiquitination or sumoylation; ii) identify

new actors implicated in this regulatory pathway by performing a

high-throughput RNAi screening; iii) explore the impact of these new

actors on tumour growth and metastasis as well as in different

ischemia-models. This project will allow us to improve our basic

understanding of the hypoxia-signalling cascade and also to identify

new therapeutics targets in the pathologies in which hypoxia is

implicated.

The most important current projects

• Cascada de señalización activada por la hipoxia y cáncer

(SAF 2007-64597).

• Integration of Novel Nanoparticle based Technology for

Therapeutics and Diagnosis of different types of cancer;

NANOTHER (NMP4-LA-2008-213631).

Collaborations· Dr Sebastien Lecommandoux (LCPO-UMR5629-ENSCPB,

Bordeaux, France).

· Dr Javier Oliver (CSIC, Granada, Spain).

· Dr Alberto Pascual/José López-Barneo (IBiS, Sevilla, Spain).

· Dr Andrea Pichler (Max F. Perutz Laboratories, Vienna, Austria).

· Dr Tomás Santalucía/Anna Serra (IIBB-CSIC/IDIBAPS, Barcelona, Spain).

· Bioftalmik (Derio, Bizkaia, Spain).

· Colorobbia Italia Spa (Sovigliana, Vinci, Italy).

Selected Publications1. Loinard C, Ginouvès A, Vilar J, Cochain C, Zouggari Y, Recalde A,

Duriez M, Lévy B, Pouysségur J, Berra E, Silvestre JS. Inhibition of Prolyl

Hydroxylase Domain Proteins Promotes Therapeutic

Revascularization. Circulation, 120(1):50-59 (2009).

2. Ginouvès A, Ilc K, Macías N, Pouysségur J, Berra E. PHDs

overactivation during chronic hypoxia “desensitizes” HIFα and

protects cells from necrosis. Proc. Natl. Acad. Sci. USA 105: 4745-4750

(2008).

3. Trastour C, Benizri E, Ettore F, Ramaioli A., Chamorey E, Pouysségur

J, Berra E. HIF-1alpha and CA IX staining in invasive breast

carcinomas: Prognosis and treatment outcome. Int J Cancer,

120: 1443-1450 (2007).

Edurne Berra

Principal Investigator

Lab. 4

Analía NúñezO’MaraPhD Student

Francisco RGonzález-PachecoPostdoctoralResearcher

Nuria MacíasTechnician

Sara PozoTechnician

4. Berra E, Ginouvès A, Pouyssegur J. The hypoxia-inducible factor

hydroxylases 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. HIF

prolyl 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

STRUCTURALBIOLOGYUNIT

Structural Biology investigates the relationship

between structure and function of biological

macromolecules.

All cellular processes are maintained and regulated by biological

macromolecules. Structural Biology studies the relationship

between the three-dimensional structure of such molecules

and their specific function. The aim is to understand their role

in cellular pathways crucial to life. The aim of our unit is to

elucidate the three-dimensional structure of enzymes, proteins,

nucleic acids, as well as their complexes.

We try to understand the structural basis of biological processes

such as signal transduction, bacterial pathogenesis or gene

expression.

To this end we make use of biophysical techniques such as

Macromolecular Crystallography, Nuclear Magnetic Resonance,

Cryo-Electron Microscopy and Bioinformatic techniques.

STRUCTURALBIOLOGYUNIT

The laboratory is basically focused on two different projects. The first

one aims to understand how “cystathionine β-synthase (CBS) domains”

regulate the activity of their target proteins upon binding of different

ligands such as adenosyl groups or ions. The “CBS domain” proteins

comprise a large superfamily of evolutionarily-conserved proteins

which are present in all kingdoms of life. Mutations within these

motifs cause several hereditary diseases in humans, such as

homocystinuria, autosomic retinitis pigmentosa, myotonia congenital,

idyopatic epilepsy or hypercalciuric nephrolytiasis, among others.

Thus, they can be considered as promising targets for the development

of novel drugs. CBS domains are unusually abundant in archaea.

Organisms such as the hyperthermophile Methanococcus jannaschii

offer an excellent model for the characterization of the adenosyl

binding site of these proteins.

The second project is part of the CONSOLIDER program of the Spanish

Ion Channel Initiative, a multidisciplinar and cooperative initiative

aiming to understand the structure-function relationship in ionic

channels, headed by Prof. Antonio Ferrer Montiel from the University

Miguel Hernández in Elche, Spain. My group is involved in the 3D-

structure determination of selected targets using crystallographic

approaches.

Collaborations· Dr Sung-Hou Kim (University of California, Berkeley, CA, USA).

· Dr Liang Tong (Columbia University, New York, NY, USA).

· Dr Regine Herbst Irmer (Goteborg University, Goteborg, Germany).

· Dr George Sheldrick (Goteborg University, Germany).

· Dr Henri Blehaut (Institut Jerome Lejeune, Paris, France).

Alfonso Martínez de la Cruz

Principal Investigator

Lab. 1· Dr Martín Martínez-Ripoll (Instituto Rocasolano, CSIC, Madrid, Spain).

· Dr Armando Albert (Instituto Rocasolano, CSIC, Madrid, Spain).

· Dr Antonio Ferrer Montiel (Universidad Miguel Hernández,

Elche, Alicante, Spain).

· Dr José Luis Neira Faleiro (Universidad Miguel Hernández,

Elche, Alicante, Spain).

· Dr José Antonio Encinar Hidalgo (Universidad Miguel Hernández,

Elche, Alicante, Spain).

· Dr Jesús Prieto (CNIO, Madrid, Spain).

· Dr Javier Gómez (Universidad de Zaragoza, Zaragoza, Spain).

· Dr José Andrés Hernández (Universidad del País Vasco, UPV/EHU,

Bizkaia, Spain).

· Dr María Luz Martínez Chantar (CIC bioGUNE, Bizkaia, Spain).

· Dr José M Mato (CIC bioGUNE, Bizkaia, Spain).

Selected Publications1. Gómez García I, Kortázar D, Oyenarte I, Mato JM, Martínez-Chantar

ML, Martínez-Cruz LA. Purification, crystallization and preliminary

crystallographic analysis of protein MJ1225 from Methanocaldo-

coccus jannaschii, a putative archaeal homologue of gamma-AMPK.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 65, 813-817 (2009).

2. Martínez-Cruz LA, Encinar JA, Kortazar D, Prieto J, Gómez J,

Fernández-Millán P, Lucas M, Astigarraga E, Fernández JA, Martínez-

Chantar ML, Mato JM and Neira JL. The CBS-domain protein MJ0729

of Methanococcus jannaschii is a thermostable protein with a pH-

dependent self-oligomerization. Biochemistry 48 (12):2766-2776 (2009).

3. Lucas M, Kortazar D, Astigarraga E, Fernández JA, Mato JM, Martínez-

Chantar ML, Martínez-Cruz LA. Purification, crystallization and

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).

4. Fernández-Millán P, Kortazar D, Lucas M, Martínez-Chantar ML,

Astigarraga E, Fernández JA, Sabas O, Albert A, Mato JM, Martínez-

Cruz LA. Crystallization and preliminary crystallographic analysis of

merohedrally twinned crystals of MJ0729, a CBS-domain protein from

Methanococcus jannaschii. Acta Crystallogr Sect F Struct Biol Cryst

Commun. 64 (7):605-6 09 (2008).

Iker OyenarteTechnician

InmaculadaGómez García

PostdoctoralResearcher

Lab Members

Protein complexes of diverse nature are main subjects in our

crystallographic projects. We aim to understand if the knowledge of

structural principles of a biological intermolecular recognition can

be exploited to control and pharmacologically modulate protein

specificity. We focus our efforts on human neurodegenerative diseases,

and currently study complexes with RNA in project: “Structural Basis

for Suppression of Human Trinucleotide Repeat Expansion Diseases

(TREDs) ”and complexes with glycolipids in project: “ Molecular Basis

for Manipulating the Selectivity of Glycolipid Transfer”.

We are currently working on the two main projects:

• “Structural Basis for Suppression of Human Trinucleotide Repeat

Expansion Diseases”. Expanded tracts of repeated triplet sequences

in DNA cause many muscle- and neurodegenerative diseases. Our

central hypothesis [4] is that the mechanism of pathogenesis involves

a RNA interference pathway, which could be inhibited by means of

a viral suppressor of RNA interference p19. The protein p19 is known

to bind to small interfering RNAs (siRNAs) in a sequence non-specific

manner [6]. Our goal is to identify the p19 mutations, which make it

disease-repeat specific. We use the X-ray crystallographic approaches

to elucidate the structural principles for manipulating the p19/siRNA

binding specificity.

• “Molecular Basis for Manipulating the Selectivity of Glycolipid

Transfer”. Membrane lipids are increasingly being recognized as

regulators of numerous cellular processes. Much attention is focused

on the mechanisms by which cells impose selectivity and directionality

on lipid movement. Glycosphingolipids (GSLs), key regulators of

cellular differentiation, growth, development, and apoptosis, are

synthesized in the Golgi, and delivered to others membranes by both

Lucy Malinina

Principal Investigator

Lab. 2vesicular and non-vesicular mediated pathways. Glycolipid transfer

proteins (GLTPs) are small, soluble, and ubiquitous proteins that

selectively accelerate the intermembrane transfer of glycolipids.

The preliminary structural insights suggest a strict specificity of GLTP

for glycolipids, and the existence of a concerted sequence of events

during GSL transfer to/from membranes [2-3,5]. Our intention is

“to evolve” artificial GLTP species capable of distinguishing sugar

headgroups and lipid chain structures.

Collaborations· Dr Rhoderick E Brown (The Hormel Institute, Austin MN, USA).

· Dr Alexander Popov (ESRF, Grenoble, France).

· Dr Dinshaw J Patel (MSKCC, New York NY, USA).

Selected Publications1. Rechkoblit O, Malinina L, Cheng Y, Geacintov NE, Broyde S, Patel

DJ. Impact of Conformational Heterogeneity of OxoG Lesions and

Their Pairing Partners on Bypass Fidelity by Y Family Polymerases.

Structure.17:725-736 (2009).

2. Zhai X, Malakhova ML, Pike HM, Benson LM, Bergen HR 3rd, Sugár

IP, Malinina L, Patel DJ, Brown RE. Glycolipid Acquisition by Human

Glycolipid Transfer Protein Dramatically Alters Intrinsic Tryptophan

Fluorescence: INSIGHTS INTO GLYCOLIPID BINDING AFFINITY. J Biol

Chem. 284:13620-13628 (2009).

3. Malinina L, Malakhova ML, Kanak A, Lu M, Abagyan R, Brown RE

and Patel DJ. The liganding of glycolipid transfer protein is controlled

by glycolipid acyl structure. PLOS Biol. 4:e362 (2006).

4. Malinina L. Possible involvement of the RNAi pathway in trinucleotide

repeat expansion diseases. J. Biol. Struct. & Dynamics. 23:233-236 (2005).

5. Malinina L, Malakhova ML, Teplov A, Brown RE, Patel DJ. Structural

basis of glycosphingolipid transfer specificity. Nature. 430:1048-1053 (2004).

JevgeniaTamjarPhD Student

ElizavetaKatorchaPhD Student

ValeriyaSamyginaPostdoctoralResearcher

Borja OchoaDe EribeTechnician

Sandra DelgadoTechnician

Lab Members

Our research interest is focused on intracellular trafficking processes.

Eukaryotic cells have elaborate mechanisms of protein transport

through vesicular trafficking.

The Golgi is the major compartment at which different sorting

pathways diverge. Here, proteins undergo final modifications before

being directed into a variety of carrier vesicles for transport to the

cell surface, endosomal compartments or lysosomes. Vesicle targeting

and fusing with an acceptor membrane are regulated by a variety of

integral and peripheral membrane proteins that are highly conserved.

While fusion between vesicles is critical in pairing of integral membrane

SNARE proteins, peripheral multi-protein tethering complexes act

upstream by selecting and tethering target membranes in long-range

interaction.

My current research is focused on developing an understanding, on

the atomic level, of how tethering complexes contribute to specificity

of membrane fusion by recognizing vesicle features in both donor

and acceptor membranes.

To pursue these studies I use X-ray crystallography of protein

complexes in combination with cell biology and biochemistry.

Since vesicle tethering events play key roles in intracellular network,

studying tethering factors from a structural viewpoint represents a

crucial stage in understanding how protein-protein recognition and

protein-membrane interactions regulate the correct vesicle targets.

Many clinical manifestations of diseases are related to malfunction

or hijacking of these pathways, therefore detailed knowledge of these

interactions is necessary to search for possible therapies.

Aitor Hierro

Principal Investigator

Lab. 3Collaborations· Dr Juan S. Bonifacino (National Institute of Child Health and Human

Development, Bethesda, MD, USA).

Selected Publications1. Hierro A*, Rojas AL*, Rojas R, Murthy N, Effantin G, Kajava AV, Steven

AC, Bonifacino JS, Hurley JH. Functional architecture of the retromer

cargo-recognition complex. Nature. 25; 449(7165):1063-1067 Epub

2007 Sep 23 (2007).

2. Kostelansky MS, Sun J, Lee S, Kim J, Ghirlando R, Hierro A, Emr SD,

Hurley JH. Structural and functional organization of the ESCRT-I

trafficking complex. Cell. 7;125(1):113-126 (2006).

3. Kim J, Sitaraman S, Hierro A, Beach BM, Odorizzi G, Hurley JH.

Structural basis for endosomal targeting by the Bro1 domain. Dev

Cell. 8(6):937-947 (2005).

4. Hierro A, Sun J, Rusnak AS, Kim J, Prag G, Emr SD, Hurley JH. Structure

of the ESCRT-II endosomal trafficking complex. Nature 9;431

(7005):221-225 Epub 2004 Aug 25 (2004).

* These authors contributed equally.

Lab MembersAnderVidaurrazagaTechnician

María SerranoPostdoctoralResearcher

GuillermoAbascalPhD Student

Igor TascónPhD Student

Melisa LázaroTechnician

We observe working molecular motors to understand their

functioning. By means of cryo-electron microscopy we can obtain

3D maps of such motors in close to physiological conditions, even

within the cells. Our aim is to describe conformational changes of

macromolecules during their performance.

We focus on motors involved in universal biological functions where

interactions between protein and nucleic acids are essential. Structural

studies of ribosomes during translation allow the understanding of

the mechanisms which govern protein synthesis. In this line,

interactions with translation factors and interference by several

antibiotics in the process are especially important. Another working

interest concentrates on the structural characterization of p53 tumor

suppressor. This protein works as transcription factor of genes involved

in cell cycle control in vertebrates and hence functions as a tumor

suppressor. The protein has been found mutated in about half of

human tumors. We are interested in the structure of p53 tetramers

and their interaction with DNA and other cell cycle controlling proteins.

Collaborations· Dr Alan Fresht (Medical Research Council; University of

Cambridge, Cambridge, UK).

· Dr Marina V. Rodnina (Max Planck Institute for Biophysical

Chemistry, Göttingen, Germany).

· Dr Liang Tong (Columbia University, NY, USA).

Selected Publications1. Yu L, Xiang S, Lasso G, Gil D, Valle M, Tong L. A symmetrical tetramer

for S. aureus pyruvate carboxylase in complex with coenzyme A.

Structure 17 (6): 823-832 (2009).

Mikel Valle

Principal Investigator

Lab. 42. Scheres SH, Valle M, Grpb P, Nogales E, Carazo JM. Maximum

likelihood refinement of electron microsocpy data with normalization

errors. J Struct Biology; 166: 234-240 (2009).

3. Conde-Vancells J, Rodríguez-Suárez E, Embade N, Gil D, Matthiesen

R, Valle M, Elortza F, Lu SC, Mato JM, Falcón-Pérez JM. Characterization

and Comprehensive Proteome Profiling of Exosomes Secreted by

Hepatocytes. J Proteome Res. 7(12):5157-5166 (2008).

4. Julián P, Konevega AL, Scheres SH, Lázaro M, Gil D, Wintermeyer W,

Rodnina MV, Valle M. Structure of ratcheted ribosomes with tRNAs in

hybrid states. Proc Natl Acad Sci USA. 4;105(44):16924-16927 (2008).

5. Tidow H, Melero R, Mylonas E, Freund SM, Grossmann JG, Carazo

JM, Svergun DI, Valle M, Fersht AR. Quaternary structures of tumor

suppressor p53 and a specific p53 DNA complex. Proc Natl Acad Sci

USA. 24;104(30):12324-12329 (2007).

Lab Members

Gorka LassoPostdoctoralResearcher

Patricia JuliánPhD Student

Xabier AgirrezabalaPostdoctoralResearcher

Collaborations· Dr Dennis H Bamford (Finnish Centre of Excellence in Virus Research,

University of Helsinki, Finland).

· Dr Stephen D Bell (Sir William Dunn School of Pathology, University

of Oxford, UK).

Selected Publications1. Korkhin Y, Unligil UM, Littlefield O, Nelson PJ, Stuart DI, Sigler PB,

Bell SD and Abrescia, NGA. Evolution of Complex RNA Polymerases:

the Complete Archaeal RNA Polymerase Structure. Plos Biology 7(5):

e1000102. doi:10.1371/Journal.Pbio.1000102 (2009).

2. Kadlec J, Loureiro S, Abrescia NG, Stuart DI, and Jones IM. The

postfusion structure of baculovirus gp64 supports a unified view of

viral fusion machines. Nat. Struct. Mol. Biol. 15, 1024-1030 (2008).

3. Abrescia NG, Grimes JM, Kivelä HM, Assenberg R, Sutton G, Butcher

SJ, Bamford JKH., Bamford DH, Stuart DI. Insights into virus evolution

and membrane biogenesis from the structure of the marine lipid-

containing bacteriophage PM2. Mol. Cell. 5, 749-761 (2008).

4. Abrescia NG, Cockburn JJB, Grimes JM, Sutton GC, Diprose JM,

Butcher , Fuller SD, San Martín C, Burnett RM, Stuart DI, Bamford DH,

Bamford JKH. Insights into assembly from structural analysis of

bacteriophage PRD1. Nature 432, 68-74 (2004).

5. Cockburn JJB, Abrescia NG, Grimes JM, Bamford JKH, Benevides J,

Thomas GJr, Bamford DH, Stuart DI. Membrane structure and

interactions with protein and DNA in bacteriophage PRD1. Nature,

432, 122-125 (2004).

Lab Members

Biological complexity is often associated with processes which require

highly accurate and regulated protein interactions. Examples of such

complexity can be found in the assembly pathway of viruses or in

the molecular mechanism of “gene expression”. Our research aims

to understand how large multi-component proteins assemble,

function and interact in the cellular context.

One line of investigation is directed to the understanding of virus

structures, their assembly principles and to the virus-cell recognition

mechanisms. Indeed, viruses represent a source of wonder as

miniaturized entities that permeate and cross-interact with the entire

biosphere and are by far the most numerous organisms on earth.

Some of them are, however, pathogens and represent a threat to

human and animal health. The understanding of virus morphogenesis

and virus-host recognition mechanisms is fundamental in the

development of antiviral drugs. The second line of research is focused

on the elucidation of transcription initiation and regulation using

Archaea as a model system for Eukarya. Transcription can be divided

into three major steps: Initiation, Transcription/Elongation and

Termination. Initiation and Termination are the less understood

processes but relevant in many associated gene disorders.

Research in our group is focused on the structural analysis by cryo-

electron microscopy and crystallography techniques of biomedically

relevant non-infectious subviral particles (SVPs) of Flaviviruses and of

the pre-initiation-complex (PIC) of the archaeal RNA polymerase

transcription machinery.

Nicola G A Abrescia

Principal InvestigatorIkerbasque Research Professor

Lab. 5

Marina OndivielaTechnician

Bibiana PeraltaPostdoctoralResearcher

Magda WojtasPhD Student

Mutations in the primary sequence of enzymes are often ultimately

responsible for a large number of autosomal diseases. In our laboratory

we pursue the structural characterization of two enzymes involved

in heme group biosynthesis: uroporphyrinogen III synthase and

porphobilinogen deaminase. A decrease in their catalytic activity

results in the outbreak of a pathology called porphyria. Porphyria has

a low statistical incidence but very acute symptoms, usually inversely

proportional to the residual catalytic activity. This activity loss can be

produced by a perturbation in the active centre, a conformational

change or an overall thermodynamic destabilization of the enzyme.

A detailed structural characterization can provide useful therapeutical

and diagnostic information. We make use of nuclear magnetic

resonance (NMR) to understand the relationship between porphyria

and the structural determinants of the heme group biosynthesis.

The large catalytic efficiency and the exquisite enantioselectivity of

an enzyme has been employed in some industrial processes to

upgrade their properties towards an environmentally-friendly process.

However, large scale industrial implementation of biotechnological

reactions is often limited by the marginal stability of the enzyme in

the reactor conditions. In our laboratory we employ NMR and circular

dichroism to investigate the effect of external crowding agents to

improve the activity and stability for several enzymes. Furthermore,

we are interested in the relationship between the cosolute induced

stability changes and a rational modification of the protein surface

by means of site directed mutagenesis.

Proteins from halophilic organisms function in extreme saline

conditions and have evolved to remain folded at very high ionic

strengths. The surfaces of halophilic proteins show a biased aminoacid

composition with a high prevalence of aspartic and glutamic acids, a

low frequency of lysine and a high occurrence of aminoacids with small

side chains. In our laboratory we are investigating the mechanism for

protein haloadaptation by a combined use of site directed mutagenesis

and high-resolution NMR spectroscopy.

Collaborations· Dr Gloria del Solar (Centro de Investigaciones Biológicas,

Madrid, Spain).

· Dr Javier Sancho (Unidad de Biofísica BIFI, Zaragoza, Spain).

· Dr Miquel Pons (Parc Científic de Barcelona, Barcelona, Spain).

Selected Publications1. Tadeo X, López-Méndez B, Castaño D, Trigueros T, Millet O. Protein

stabilization and the Hofmeister effect: the role of hydrophobic solvation.

Biophysical Journal, 97, 2595-2603 (2009).

2. Fortian A, Castaño D, Ortega G, Laín A, Pons M, Millet O.

Uroporphyrinogen III synthase mutations related to congenital

erythropoietic porphyria identify a key helix for protein stability.

Biochemistry 20;48(2):454-461 (2009).

3. Tadeo X, Castaño D, Millet O. Anion modulation of the 1H/2H exchange

rates in backbone amide protons monitored by NMR spectroscopy. Protein

Science, 33, 2733-2740 (2007).

4. Blobel J, Schmidl S, Vidal D, Nisius L, Bernadó P, Millet O, Brunner E,

Pons M. Protein tyrosine phosphatase oligomerization studied by a

combination of 15N NMR relaxation and 129Xe NMR. Effect of buffer

containing arginine and glutamic acid. Journal of the American Chemical

Society 129, 5946-5953 (2007).

5. Tadeo X, Pons M, Millet O. Influence of the Hofmeister Anions on Protein

Stability As Studied by Thermal Denaturation and Chemical Shift

Perturbation. Biochemistry, 46, 917-923 (2007).

Oscar Millet

Principal Investigator

Lab. 7

Lab Members

Xabier TadeoPhD Student

David CastañoPhD Student

Blanca LópezMéndezPostdoctoralResearcher

Ana LaínTechnician

Our main research interest is the structural characterization of proteins

and their interactions with other molecules relevant to chromatin

remodeling, DNA replication and repair, and cell adhesion. Our main

tool is Nuclear Magnetic Resonance spectroscopy; we also use other

biophysical techniques.

ING4, a member of the Inhibitor of Growth family of tumor suppressor

proteins, contains a C-terminal Plant Homeo domain (PHD). The PHD

of ING4 binds to histone methylated tails and is involved in

transcription activation, through its interaction with the Histone

Acetyl transferase complex HBO1. The structure and dynamics of

ING4-PHD bound to histone 3 trimethylated at Lys4 has been

determined, and the specificity of binding to different methylated

histone fragments in solution has been analyzed. We found that

binding affects the PHD backbone dynamics, in contrast to previous

assumptions of histone binding being made by static protein modules.

The specificity for the methylated histone tail recognition is entropy

driven, in contrast to chromodomains. Our results highlight the

versatility of PHD fingers as readers of the histone code. We are

currently studying how the crowded, inner macromolecular

environment of cells affects the recognition of methylated histones.

Gadd45α (Growth Arrest and DNA damage-inducible gene) is a

nuclear protein transcriptionally regulated by the tumor suppressor

p53. The interactions of Gadd45α with other proteins play a central

role in DNA repair, cell cycle control and apoptosis. The solution

structure of human Gadd45α shows a α/β fold with a five stranded

mixed β-sheet at the core and five helices surrounding it. We are

currently investigating the interaction of GADD45α with PCNA

(Proliferating Cellular Nuclear Antigen) and other proteins involved

in cell cycle control and DNA repair.

Francisco Blanco

Principal InvestigatorIkerbasque Research Professor

Lab. 8Meganucleases recognize long DNA sequences (between 14 and

40 bp) and produce double strand breaks at single sites in whole

genomes. Engineered meganucleases can be used to induce

endogenous homologous recombination and repair defective genes

ex vivo without detectable genotoxicity. We are characterizing the

structure-function relationships of several of these highly specific

nucleases of biomedical interest.

We have characterized the binding of a group of small molecules

designed to compete for the binding to the I-domain of the integrin

lymphocyte function-associated antigen-1 (LFA-1) to the intercell

adhesion molecule-1 (ICAM-1). These interactions play a key role in

autoimmune diseases and cancer. We have found that these ligands

bind to the I-domain of LFA-1, but not to the MIDAS (metal ion

dependent adhesion site), the site of ICAM-1 binding. They bind

instead to the IDAS (I-domain allosteric site), suggesting that they

may act as allosteric inhibitors, in a way similar to lovastatin.

Collaborations· Dr Guillermo Montoya (CNIO, Madrid, Spain).

· Dr Frédéric Pâques (Cellectis SA, Romainville, France).

· Dr Fernando Cossío (Universidad del País Vasco UPV/EHU, Gipuzkoa,

Spain).

· Dr Ignacio Palmero (IIB-UAM-CSIC, Madrid, Spain).

· Dr Irene Luque (UG, Granada, Spain).

· Dr Ramón Campos-Olivas (CNIO, Madrid, Spain).

Selected Publications1. Palacios A, Muñoz IG, Pantoja-Uceda D, Marcaida MJ, Torres D,

Martín-García JM, Luque I, Montoya G, Blanco FJ. Molecular basis of

histone H3K4Me3 recognition by ING4. Journal of Biological Chemistry

283: 15946-15964 (2008).

2. Zimmerman T, Blanco FJ. Inhibitors targeting the LFA-1/ICAM-1 cell-

adhesion interaction: design and mechanism of action. Current

Pharmaceutical Design 14: 2128-2139 (2008).

SimoneCulurgionePhD Student

Alfredo De BiasioPostdoctoralResearcher

3. Sánchez R, Pantoja-Uceda D, Torres D, Prieto J, Campos-Olivas R,

Blanco FJ. NMR assignment and secondary structure of human growth

arrest and DNA damage protein Gadd45α. Biomolecular NMR

Assignments 2: 245-247 (2008).

4. Redondo P, Prieto J, Muñoz IG, Alibés A, Stricher F, Serrano L,

Cabaniols JP, Daboussi F, Arnould S, Pérez C, Duchateau P, Pâques F,

Blanco FJ, Montoya G. Molecular basis of xeroderma pigmentosum

group C DNA recognition and cleavage by engineered meganucleases.

Nature 456:107-111 (2008).

Lab Members

Maider VillateTechnician

Nekane MerinoTechnician

John AlexanderRodríguezBuitragoPhD Student

TECHNOLOGYPLATFORMS

STRUCTURALBIOLOGYPLATFORMS

Structural biology is a highly interactive and versatile

discipline dedicated to elucidating the function of

biomolecules by high-resolution analysis of their

3-dimensional structure. This may furthermore

include studies of molecular dynamics and

interactions, also with atomic resolution.

Structural biology relies on the combination and cooperation of

several complementary techniques: specialised biochemistry to

provide for the target molecules in the required purity, quantity

and with possible modifications; NMR spectroscopy, X-ray

crystallography and electron microscopy as the experimental core

STRUCTURALBIOLOGYPLATFORMS

techniques for structure analysis up to atomic resolution;

computational bioinformatics methods for structure prediction,

calculation and analysis; and various auxiliary biophysical methods

to further characterise the target molecules and complement the

structural information.

This multi-disciplinary approach can provide for a fundamental

understanding of complex biological phenomena at molecular

level. The resulting data on atomic distances, molecular shape, 

dynamics, charge distribution, interaction, etc., allow for a

comprehensive view on molecular mechanisms of action.

Such knowledge is of basic importance for various fields of research,

and particularly for rational drug development.

Atomic characterization of macromolecules and their interactions

with macro and small molecules is the cornerstone of understanding

many biological processes. X-ray crystallography is currently the most

powerful technique to study the structure of a wide range of biological

molecules such as nucleic acids, proteins, macromolecular complexes

and viruses.

CIC bioGUNE enjoys state-of-the-art X-ray crystallography facilities.

The platform is equipped with a X8-PROTEUM system (BRUKER) with

two detectors and a cryosystem for data collection, liquid handling

(TECAN), Crystallization robot (MOSQUITO) and a Crystal Farm (BRUKER)

image analysis platform. Other complementary techniques as Circular

Dichroism and Dynamic Light Scattering are also available. At the

Macromolecular Crystallography Platform we provide user support

from sample preparation to structure determination.

Selected Publications1. Golubev A M, Rojas AL, Nascimento AS, Bleicher L, Kulminskaya AA,

Eneyskaya EV, Polikarpov I. Crystallization and preliminary crystallographic

analysis of laminarinase from Rhodothermus marinus: a case of

pseudomerohedral twinning. Protein Pept Lett, 15(10): 1142-1144 (2008).

2. Rojas R, Vlijmen TV, Mardones G, Prabhu Y, Rojas AL, et al. Regulation

of Retromer Recruitment to Endosomes by Sequential Action of Rab5 and

Rab7. J Cell Biol ,183(3):513-526 (2008).

Adriana L RojasPlatform Manager

MACROMOLECULARCRYSTALLOGRAPHYPLATFORM

3. Hierro* A, Rojas* AL, Rojas R, et al. Functional Arquitecture of the retromer

cargo recognition complex. Nature, 449 (7165): 1063-1067 (2007).

4. Rojas AL, Fischer H, Eneiskaya EV, et al. Structural Insights into the beta-

Xylosidase from Trichoderma reesei Obtained by Synchrotron Small-Angle

X-ray Scattering and Circular Dichroism Spectroscopy. Biochemistry, 44:

15578-15584 (2005).

5. Nagem RPA, Ambrosio ALB, Rojas AL, et al. Getting the most of X-ray

home sources. Acta Crystallographica D. D61: 1022–1030 (2005).

* These authors contributed equally.

The mission of the Electron Microscopy Facility at CIC bioGUNE is to

offer state-of-the-art instrumentation, services and training for high-

resolution transmission electron microscopy to biomedical researchers.

To fulfil these goals, the Electron Microscopy Facility provides two

transmission electron microscopes, including a JEM-2200FS

transmission electron microscope equipped with a field emission

gun (FEG) and an in-column energy filter, as well as major auxiliary

equipment such as vitrification robots required for the preparation

and imaging of biological samples at cryogenic temperatures

(http://personal.cicbiogune.es/dcarton/).

This high-tech equipment allows us to make use of advanced methods

of image processing and computation to investigate at different

levels the biological complexity of large macromolecular structures

(c.f. ribosomes, virus-like-particles, etc.) by three-dimensional

reconstruction techniques.

Collaborations· Dr Mikel Valle (CIC bioGUNE, Bizkaia, Spain).

· Dr Nicola Abrescia (CIC bioGUNE, Bizkaia, Spain).

· Dr Juan M Falcón (CIC bioGUNE, Bizkaia, Spain).

· Dr Ilya Reviakine (CIC biomaGUNE, Gipuzkoa, Spain).

· Dr Itziar Alkorta (Universidad del País Vasco UPV/EHU, Bizkaia, Spain).

· Dr Arturo Muga (Universidad del País Vasco UPV/EHU, Bizkaia, Spain).

· Dr Diego M. A. Guérin (Universidad del País Vasco UPV/EHU, Bizkaia, Spain).

· Dr Juan Manuel González-Mañas (Universidad del País Vasco

UPV/EHU, Bizkaia, Spain).

· Dr África Barrientos (Midatech, Derio, Bizkaia, Spain).

· Dr Rubén Álvarez Rodríguez (BIOFORGE, Valladolid, Spain).

· Dr José Carlos Rodríguez Cabello (BIOFORGE, Valladolid, Spain).

· Dr María Moragues (NANOC LABEIN - Tecnalia, Derio, Bizkaia, Spain).

· Dr Yolanda de Miguel (NANOC LABEIN - Tecnalia, Derio,

Bizkaia, Spain).

· Dr Edurne Erkizia (NANOC LABEIN - Tecnalia, Derio, Bizkaia, Spain).

· Dr José Antonio Ibáñez (NANOC LABEIN - Tecnalia, Derio,

Bizkaia, Spain).

· Dr Sandra Rainieri (AZTI - Tecnalia / Food Research, Derio,

Bizkaia, Spain).

Selected Publications1. Yu L, Xiang S, Lasso G, Gil D, Valle M, Tong L. A symmetrical tetramer

for S. aureus pyruvate carboxylase in complex with coenzyme A.

Structure, 17 (6): 823-832 (2009).

2. Julián P, Konevega AL, Scheres SH, Lázaro M, Gil D, Wintermeyer W,

Rodnina MV, Valle M. Structure of ratcheted ribosomes with tRNAs in

hybrid states. Proc Natl Acad Sci USA, 105(44):16924-16927 (2008).

3. Conde-Vancells J, Rodríguez-Suárez E, Embade N, Gil D, Matthiesen

R, Valle M, Elortza F, Lu SC, Mato JM, Falcón-Pérez JM. Characterization

and Comprehensive Proteome Profiling of Exosomes Secreted by

Hepatocytes. J Proteome Res, 7, 12: 5157-5166 (2008).

David GilPlatform Manager

ELECTRONMICROSCOPYPLATFORM

The NMR equipment at CiC bioGUNE is highly complementary, and

ideally suited for a double-track strategy: a 600 MHz medium-field

spectrometer with flexible configuration and ample accessories allows

for a variety of highly specialised NMR experiments beyond standard

biomolecular applications; and a 800 MHz high-field spectrometer

with fixed configuration and a cryo-probe to run classical biomolecular

NMR applications with highest sensitivity. Both BRUKER spectrometers

are of the most modern AVANCE III generation.

To complement the modern NMR hardware, an ongoing project

of the NMR platform is the continuous optimisation of existing NMR

experiments with regard to user friendliness, robustness and maximum

sensitivity. Recent improvements have already yielded an average of

50% sensitivity gains with respect to conventional implementations

of NMR experiments. We are currently exploring the limits of these

sensitivity-enhancement schemes, and their broadness of application.

In collaboration with partners from the Max-Planck-Institutes

(Tuebingen), we are furthermore developing NMR methodology to

cleanse spectra from uninformative components or artifacts,

and to measure new NMR parameters required for a novel streamlined

protocol for fast protein structure analysis with highest resolution.

Exploiting the ample extra accessories available for the 600 MHz,

especially its set of dedicated probe-heads, we are also extending

Tammo DiercksPlatform Manager

NUCLEARMAGNETICRESONANCE(NMR)

the range of conventional biomolecular NMR applications to, e.g.,

study more exotic nuclei. In a collaboration project with partners

from the CIB (Madrid) and Ludwig-Maximilians-University (Munich)

we have, thus, developed a novel NMR approach to study

carbohydrate-protein interactions. This technique has already been

shown to yield unique new insight into binding kinetics and substrate

specificity, and is now being developed further and applied more

broadly.

Collaborations· Dr Hans-Joachim Gabius (Ludwig-Maximilians-Universitaet,

Muenchen, Germany).

· Dr Jesús Jiménez Barbero (Centro de Investigaciones Biológicas,

Madrid, Spain).

· Dr Murray Coles and Dr Vincent Truffault (Max-Planck Institute for

Developmental Biology, Tuebingen, Germany).

Selected Publications1. Diercks T, Ribeiro JP, Cañada FJ, André S, Jiménez-Barbero J, Gabius

H-J. Fluorinated Carbohydrates as Lectin Ligands: Versatile Sensors

in 19F-Detected Saturation Transfer Difference NMR Spectroscopy.

Chem. Eur. J. 15: 5666-5668 (2009).

2. Diercks T, AB E, Daniëls MA, de Jong, RN, Besseling R, Kaptein R,

Folkers GE. Solution Structure and Characterization of the DNA-Binding

Activity of the B3BP-Smr Domain. J. Mol. Biol. 383:1156-1170 (2008).

GENOMEANALYSISPLATFORM

The Genome Analysis Platform at CIC bioGUNE

offers services in the latest technologies for

high-throughput genome analysis.

GENOME ANALYSISPLATFORM

The national and international scientific communities can take

advantage of high-throughput genome analysis technologies offered

by Genome Analysis Platform at CIC bioGUNE:

* The BeadStation 500 GT/GX (Illumina, Inc., www.illumina.com), for

high-throughput standard and customized SNP genotyping, gene

expression and methylation analysis; and

* The Genome Analyzer (Illumina Inc., www.illumina.com), which

allows Sequencing-by-Synthesis (SBS) for multiple applications

including genome sequencing and re-sequencing, digital gene

expression (tag profiling and small-RNA discovery and analysis) and

in vivo protein-DNA interactions identification and quantification on

a genome-wide scale (ChiP-Seq methodology).

In addition to the technological set-up, several Bioinformatics tools

are being developed. Therefore, we can offer some assistance in the

designing of the customized SNP (for genotyping projects) or gene

panels (for differential expression projects) and in basic statistical

analyses of the resulting data.

Quotations for genotyping, transcriptomics, methylation analysis or

sequencing services can be requested at: "gap@cicbiogune.es" or

"http://genomics.cicbiogune.es/GAP/service".

Platform MembersAne FullaondoPlatformSpecialist

Naiara RodríguezEzpeletaPlatformSpecialist

Ewa Gubb *Technician

AintzaneGonzález LaheraTechnicianCIBERehd Fellow Member

Ana Mª AransayPlatform Manager

GENOME ANALYSISPLATFORM

* External

PROTEOMICS &METABOLOMICSPLATFORM

The proteomics and metabolomics platform is chiefly

focused on the analysis of proteins and metabolites

by mass spectrometry. This platform provides service

both to in-house and external research groups.

PROTEOMICS& METABOLOMICSPLATFORM

At the beginning of the XXI century, the biomedical research scenario

changed with the so called post-genomic era. Then, gene product

analysis, thus, protein analysis on a large scale became feasible.

The Proteomics platform provides protein identification and molecular

weight determination service by mass spectrometry (MS) using the

following equipment:

MALDI Platform:

A Proteineer DP robotic station for in-gel automatic digestion and

an Autoflex TOF/TOF smartbeam mass spectrometer (Bruker). Proteins

are identified by peptide mass fingerprinting and/or peptide fragment

fingerprinting.

Liquid chromatography tandem mass spectrometry systems:

Two nano flow liquid chromatography system are coupled to a

quadrupole time of flight hybrid instrument Q-TOF premier (Waters-

Micromass) and to an Orbitrap XL upgraded with the ETD module

(Thermo-Fisher), respectively. These high performance systems have

the latest features for optimal protein identification in complex protein

mixtures and for in depth protein post-translational modification

characterisation analysis.

Proteomics Core Facility works for the continuous development of

mass spectrometry based proteomic methods to better address

Felix ElortzaPlatform Manager

PROTEOMICS &METABOLOMICSPLATFORM

proteomic research related new challenges. Researchers at this

laboratory are actively involved in research projects such as HUPO´s

Human Liver Proteome Project. Different collaborative efforts are

carried out with groups from CIC bioGUNE, neighbouring proteomics

core facility in the UPV/EHU and also international laboratories.

With the aim of discovering new diagnostic biomarkers, the Proteomics

Platform works closely with the company OWL Genomics, whose

Metabolomics Platform is managed by Doctor Jonathan Barr,

responsible for metabolomics studies. OWL Genomics has established

a state-of-the-art mass spectrometry based metabolomics platform

ideally suited to studies in key areas such as biomarker discovery,

clinical studies, diagnostics and toxicology.

Mass spectrometry based metabolomics offers selective, sensitive

analyses with the potential to identify metabolites. The analytical

platform at OWL Genomics includes several liquid-chromatography

interfaced mass spectrometers:

UPLC TOF: This mass analyser delivers high full-scan sensitivity,

resolution, and exact mass measurements ideal for the high

throughput, selective analysis of hundreds to thousands of metabolites

found in biofluids and tissues.

UPLC Q-TOF: Possesses all the above features with the added benefits

of quadrupole precursor ion selection and controlled fragmentation

in a collision cell prior to TOF analysis. The unique design of this

instrument allows MS data to be captured with alternating low- and

high collision cell energy. This MSE approach can be used to obtain

both precursor and product ion information in the same analytical

run.

Selected Publications1. Casado-Vela J, Rodríguez-Suárez E, Iloro I, Ametzazurra A, Alkorta

N, García-Velasco JA, Matorras R, Prieto B, González S, Nagore D, Simón

L, Elortza F. Comprehensive proteomic analysis of human endometrial

fluid aspirate. Journal of Proteome Research 8, 10, 4622-4632 (2009).

Mikel AzkargortaTechnician

Juan CasadoPlatformSpecialist

2. Conde-Vancells J, Rodríguez-Suárez E, Embade N, Gil D, Matthiesen

R, Valle M, Elortza F, Lu SC, Mato JM, Falcón-Pérez JM. Characterization

and Comprehensive Proteome Profiling of Exosomes Secreted by

Hepatocytes. Journal of Proteome Research 7, 12 5157-5166 (2008).

3. Omaetxebarria MJ, Elortza F, Rodríguez-Suárez E, Aloria K,

Arizmendi JM, Jensen ON and Matthiesen R. Computational approach

for identification and characterization of gpi-anchored peptides in

proteomics experiments. Proteomics 7, 12, 1951-1960 (2007).

4. Elortza F, Mohammed S, Bunkenborg J, Foster LJ, Nühse TS,

Brodbeck U, Peck SC and Jensen ON. Modification-specific proteomics

of plasma membrane proteins: identification and characterization

of glycosylphosphatidylinositol-anchored proteins released upon

phospholipase D treatment. Journal of Proteome Research 5, 4,

935-943 (2006).

Platform Members

Ibon IloroPlatformSpecialist

Eva RodríguezSuárezPlatformSpecialist

Gene silencing by RNAi is ushering biological research

into a new age. Using the human genome sequence

and the ability of RNAi to systematically silence families

of genes or even all genes, we can expect to obtain a

functional genomic map that can give rise to novel

therapeutic approaches.

GENE SILENCINGPLATFORM

RNAi is an evolutionarily conserved, sequence-specific post-

transcriptional gene silencing mechanism induced by double stranded

RNA (dsRNA). The RNAi machinery can also be triggered by exogenous

delivery of dsRNAs providing an extremely powerful tool for genetic

analysis. Thus, gene silencing by RNAi is ushering biological research

in a new age. Using the human genome sequence and the ability of

RNAi to systematically silence families of genes or even all genes, we

can expect to obtain a functional genomic map that can give rise to

novel therapeutic approaches.

The GSP is a dedicated facility to develop and execute cell-based

screenings using RNAi with a dedicated staff to manage platform

resources and to help in assay development and analysis. The main

goal of the platform is to make RNAi-mediated gene silencing as

widely accessible as possible.

We are currently working with the human retroviral shRNAmir library

(developed in the Hannon-Elledge labs, Open Biosystems) offering

wide genome coverage, efficient silencing and flexible vector formats.

We also provide the Silencer® Drosophila RNAi Library distributed by

Ambion/Applied Biosystem. This library is a collection of 13.071 dsRNAs

targeting the best annotated Drosophila genome.

We facilitate in vitro and in vivo silencing of individual or families of

genes (sub-libraries) to elucidate their functions and also high-

throughput, high-content screening to identify new genes implicated

Edurne BerraPlatform Manager

GENE SILENCINGPLATFORM

Monika GonzálezLópezPostdoctoralResearcher

EncarnaciónPérez AndrésTechnician

in particular biological processes. We advise users on screen design

and can adapt our protocols (cellular models and biological assays)

to meet user needs: human, mouse, or Drosophila primary or tumor

cells, for the analysis of stem cell differentiation, tumor invasion, cellular

adhesion, angiogenesis, etc. The Platform is equipped with an

automated liquid handling system (Sciclone ALH3000), a robotic plate

delivery system (Twister II) and different peripheral systems: CO2

incubator with plate shuttling (Cytomat 2C), microplate reader (Synergy

HT), automated microscope and high-content analysis software

(ImageXpressMicro, MetaXpress, AcuityXpress, MDCShare data base).

Platform Members

RESEARCHSUPPORTUNITS

The CIC bioGUNE´s Animal Unit (AU) is an AAALAC

accredited facility which includes a Specific Pathogen

Free (SPF) area to house rodents from commercial

sources and to produce and keep some strains of

genetically engineered mice (GEM).

THE MAIN FUNCTIONS OF THE AU ARE:

• Covering the CIC bioGUNE user´s needs by providing them

with the assessment and equipment necessary to carry out

their research on laboratory animals.

• Providing the care and welfare of laboratory animals, and

carrying out periodic health monitoring.

• Ensuring observance of all legal and ethical standards

concerning the use of animals for research and other scientific

ends.

The AU works for the continuing improvement in their services

and also engages in the development of new services through

the collaboration with researchers from different areas of interest.

With this in mind, our main objective for the coming months is

focused on the use of ultrasounds (echography) to detect liver

lesions in murine models of steatosis and hepatic tumours. In

addition, preliminary echocardiography assays are being developed

in order to assess the heart function in new strains of GEM.

Selected Publications1. Varela-Rey M, Fernández-Ramos D, Martínez-López N, Embade N,

Gómez-Santos L, Vázquez-Chantada M, Rodríguez J, Luka Z, Wagner

C, Lu SC, Martínez-Chantar ML, Mato JM. Impaired Liver Regeneration

in Mice Lacking Glycine N-Methyltransferase. Hepatology 50(2):4443-

4452 (2009).

2. Martínez-Chantar ML, Vázquez-Chantada M, Ariz U, Martínez N,

Varela M, Luka Z, Capdevila A, Rodriguez J, Aransay AM, Matthiesen

R, Yang H, Calvisi DF, Esteller M, Fraga M, Lu SC, Wagner C, Mato JM.

Loss of the Glycine N-Methyltransferase Gene Leads to Steatosis and

Hepatocellular Carcinoma in Mice. Hepatology 47(4):1191-1199 (2008).

3. Rodríguez-Cuesta J, Vidal-Vanaclocha F, Mendoza L, Valcárcel M,

Gallot N, Martínez de Tejada G. Effect of asymptomatic natural

infections due to common mouse pathogens on the metastatic

progression of B16 murine melanoma in C57BL/6 mice. Clinical and

Experimental Metastasis 22(7):549-558 (2005).

ANIMALFACILITIES UNIT

Juan Rodríguez CuestaAnimal Unit Officer

Arantza PeñaTechnician

Virginia PérezLuenaTechnician

Nahia del TesoTechnician

Itziar FernándezDomínguezPhD Student

4. Vergara-Irigaray N, Chávarri-Martínez A, Rodríguez-Cuesta J, Miller

JF, Cotter PA, Martínez de Tejada G. Evaluation of the role of the Bvg

intermediate phase in Bordetella pertussis during experimental

respiratory infection. Infection and Immunity 73(2):748-760 (2005).

5. Lorenzo-Pajuelo B, Villanueva JL, Rodríguez-Cuesta J, Vergara-

Irigaray N, Bernabeu-Wittel M, Garcia-Curiel A, Martínez de Tejada G.

Cavitary pneumonia in an AIDS patient caused by an unusual

Bordetella bronchiseptica variant producing reduced amounts of

pertactin and other major antigens. Journal of Clinical Microbiology

40(9):3146-3154 (2002).

Lab Members

BIOSAFETY &RADIOACTIVEPROTECTION

Beatriz González CallejasBiosafety & RadioprotectionOfficer

This service is in charge of the proper operation of CIC bioGUNE´sRadioactive Facility including all activities carried out by theoperators and users, according to the rules provided by theOperation Authorization, the Protection Radiology Manual, theEmergency Plan and any other officially approved documentsobliging the users to observe such rules. As regards its biosafetyrole, the main duty of the service is to establish safe workingconditions by promoting good laboratory practices.

• Foreseeing needs of the center and fulfilling them.

• Supporting the strategic and corporate plan of the center.

Staff

Staff attachedto external projects

INFORMATICS

The service is responsible for providing scientific

and administrative computing, networking,

audiovisual and media services along with support

for centrally managed servers and applications.

High Performance Computing system has been implemented in

CIC bioGUNE to provide a huge boost in the computing capacity

available to researchers at the center. This accelerates projects

which already use HPC as a major tool and, in addition, will expand

the scope of researchers who are currently constrained to desktop

computing resources.

INFORMATICS SERVICE MAIN OBJECTIVES ARE:

• Offering a reliable and efficient service.

• Getting continuous improvement of services through

innovation and collaboration.

Gabriel CarasaInformatics Officer

Álvaro SáezGarcíaTechnician

Mónica Vega *Technician

Albano MartínezAlmeida *Technician

Itxaso UgarteTechnician

Maite GutiérrezCalzadaTechnician

Cristian PabloMankocTechnician

David ÁlvarezPeñarandaTechnician

Ewa Gubb *WebMaster

* External

The main task of this service is the development

and implementation of a preventive, predictive and

corrective maintenance in CIC bioGUNE.

Development of a predictive maintenance/external maintenance.

MAINTENANCE

José AntonioOvejeroTechnician

Sergio ÁlvarezRubioTechnician

Carles ChalauxMaintenance Officer

Staff

ADMINISTRATION& DIRECTOR’SOFFICE

The Administration Department at CIC bioGUNE is

responsible for the centre’s management and

administration functions and services, and reports

to the General Director and to the Board.

The Administration Department deals with all aspects of

governance of the centre, planning, organizing, coordinating and

maintaining supervision over the day-to-day administrative and

financial matters:

1. It manages purchases, budgeting control, administration of

grants and accounting for grants submission, and financial

forecasts to assist the General Director in the conduct of any

activity.

2. Administers personnel policies and functions related to human

resources, including recruitment, training and career

development.

3. Directs functions and coordinates activities of research-

supporting services.

4. Provides support for the exploitation of results and technology

transfer activities derived from research.

5. Coordinates the legal services and the development of the

adequate framework for all activities within the centre.

ADMINISTRATION& DIRECTOR’SOFFICE

The Administration Department works under the guides of

accountability, establishing criteria to measure the performance of

management and responding to the board from which they derive

their authority, and of transparency, which includes both the availability

of information and clarity about government rules, regulations, and

decisions.

CIC bioGUNE is commited to excellence at management levels placing

strong emphasis on enhancing the quality of professional administration

as part of our quest to achieve the best job performance.

Alfonso EgañaChief Financial Officer (CFO)

Mada RodríguezQuintanaHead ofAdministration

Bárbara MatoTechnician

LoliMontanosTechnician

José ManuelAparicioAccountingOfficer

Staff

Ana BarreiraTechnician

Alicia GonzálezGarcíaAssistant toGeneral Director

PROTEÍNAS DE FUSIÓN DE P53 SIN ACTIVIDAD DE TRANSCRIPCIÓN Y SUS APLICACIONES

METHOD FOR THE DIAGNOSIS OF NASH BASED ON METABOLIC PROFILES

UBIQUITIN BINDING POLYPETIDES 5’-METHYLTHIOADENOSINE (MTA) AS A MARKER OF LIVER INJURY

PROTEOMIC FINGERPRINT FOR THE DIAGNOSIS OF NON-ALCOHOLIC STEATOHEPATITIS (NASH) AND/OR STEATOSIS

SP1 AS A MARKER IN DIAGNOSIS AND PROGNOSIS OF NON-ALCOHOLIC STEATOHEPATITIS (NASH) AND TARGET IN DRUG SCREENING FOR NASH

PATENTS

0401

02 05

03 06

Centre: Centro de Investigación Cooperativa en Biociencias · CIC bioGUNE - OWL GenomicsDate: August 2008

Patent no.: EP08380249.6

Patented in: SPAIN/EUROPE

Exploitation: OWL Genomics

Centre: Centro de Investigación Cooperativaen Biociencias · CIC bioGUNEDate: June 2006

Patent no.: P200601537.0

Patented in: SPAIN

Exploitation: CIC bioGUNE · CI Príncipe Felipe

Centre: Centro de Investigación Cooperativa en Biociencias · CIC bioGUNEDate: February 2008 (EPO), February 2009 (USPTO)

Patent no.: EP08380059.9, US 12/389.660

Patented in: EUROPE/USA

Exploitation: Life Sensors

Centre: Centro de Investigación Cooperativa en Biociencias · CIC bioGUNE- University of VanderbiltDate: December 2006

Patent no.: US 11/963.691

Patented in: USA

Exploitation: OWL Genomics

Centre: Centro de Investigación Cooperativa en Biociencias · CIC bioGUNE - OWL GenomicsDate: July 2008

Patent no.: EP08380196.9

Patented in: SPAIN/EUROPEExploitation: OWL Genomics

Centre: Centro de Investigación Cooperativa en Biociencias · CIC bioGUNEDate: March 2005Patent no.: EP05075602.2/EP05077320.9/11/370068

Patented in: SPAIN/EUROPE/USA

Exploitation: OWL Genomics

DIAGNOSTIC AND PROGNOSTICMETHODS ON NON-ALCOHOLIC STEATOHEPATITIS(NASH)

Centre: Centro de Investigación Cooperativa en Biociencias · CIC bioGUNEDate: July 2004Patent no.: EP05780314.0/11/572.562

Patented in: EUROPE/USA

Exploitation: OWL Genomics

07

FUNDING

EUROPEAN UNION

BASQUE ADMINISTRATION

OTHER INSTITUTIONS

STATE GOVERNMENT

Postdoctoral ResearchersMINISTRY OF SCIENCE AND INNOVATIONNational Plan for Scientific Research, Development and Technological InnovationNational Program for Recruitment and Placement of Research Human Resources• Ramón y Cajal Subprogram Valerie Lang Juan Falcón Naiara Beraza

Xabier Aguirrezabala • Juan de la Cierva Subprogram Ashwin Woodhoo• University of Sassari Marcella Sini

National Plan for Scientific Research, Development and Technological InnovationResearch Activity and Complementary Actions Program• CONSOLIDER-INGENIO 2010 Research Activity Subprogram Mónika González López• Non-guided Basic Research Projects Subprogram Gorka Lasso

PROSTATE CANCER RESEARCH FOUNDATION Víctor Manuel Campa

NETWORK CENTRE FOR BIOMEDICAL RESEARCH IN LIVER AND GASTROINTESTINAL DISEASES. CIBERehd Marta Varela Félix Royo Fabienne Aillet

Platform SpecialistFOUNDATION FOR DEVELOPMENT OF RESEARCH IN GENOMICS AND PROTEOMICSSpanish National Institute Of Proteomics - PROTEORED Eva Rodríguez Suárez Ibon Iloro

AIDS TO RECRUITMENT FROM OTHER PUBLIC AND PRIVATE INSTITUTIONSPrincipal InvestigatorsMINISTRY OF SCIENCE AND INNOVATIONNational Plan for Scientific Research, Development and Technological InnovationNational Program for Recruitment and Placement of Research Human Resources• Ramón y Cajal Subprogram Manuel Rodríguez Medina James D Sutherland Aitor Hierro

IKERBASQUE FOUNDATIONFramework Agreement to Collaborate in the Promotion and Development of Research Nicola Abrescia Francisco Blanco Joaquín Castilla Ugo Mayor

BIZKAIA REGIONAL COUNCILAssociation for Mobility Supporting of Qualified People in Knowledge and innovation, Bizkaia:XEDE• GIZA:XEDE Program Mikel Valle Edurne Berra Lucy Malinina

Platform ManagersBIZKAIA REGIONAL COUNCILAssociation for Mobility Supporting of Qualified People in Knowledge and Innovation, Bizkaia:XEDE• GIZA:XEDE Program Tammo Diercks

TechniciansMINISTRY OF SCIENCE AND INNOVATIONNational Plan for Scientific Research, Development and Technological InnovationNational Program for Recruitment and Placement of Research Human Resources• Peer Technical Assistance (PTA) Subprogram Esperanza González Jiménez

Research Activity and Complementary Actions Program• Non-guided Basic Research Projects Subprogram Sara Pozo• CONSOLIDER-INGENIO 2010 Research Activity Subprogram Roland Hjerpe

NETWORK CENTRE FOR BIOMEDICAL RESEARCH IN LIVER AND GASTROINTESTINAL DISEASES. CIBERehd Aitziber González Lahera

PhD StudentsMINISTRY OF SCIENCE AND INNOVATIONNational Plan for Scientific Research, Developmentand Technological InnovationNational Program for Recruitment and Placement of Research Human Resources• Research Staff Training (FPI) Subprogram Valentine Comaills Rocío Jiménez Alonso Analía Elena Núñez O'Mara Leire Herboso Juan Luis García Rodríguez• Academic Staff Training (FPU) Subprogram Nuria Martínez López David Castaño

Research Activity and Complementary Actions Program• Non-guided Basic Research Projects Subprogram Elizaveta Katorcha

Carlos III Health Institute• Health Research Predoctoral Trainee Grants (PFIS) David Fernández Ramos• Biomedical and Health Sciences Research Promotion Program Javier Conde

BASQUE GOVERNMENT - EDUCATION, UNIVERSITIES AND RESEARCH DEPT.Program for Training and Improvement of the Research Staff• AE Modality: PhD Trainee Grants for staff researchers at R&D centres in Spain Guillermo Abascal Oihana Iriondo

SCIENCE AND TECHNOLOGY FOUNDATION Bruno Simões

LA CAIXA FOUNDATIONBiomedical Research Agreement Itziar Frades

BARCELONA SCIENCE PARK Xavier Tadeo

TECHNOLOGY CENTERS

PUBLIC ADMINISTRATION

COMPANIES

GENERAL ASSEMBLY

Parque Tecnológico de Bizkaia, Edificio 801A · 48160 DERIO · www.cicbiogune.es