Research groups:
GENYO is a mixed centre with stakes
held by the Regional Ministry of Innovation, Science and Enterprise, the Regional Ministry of Health, the University of Granada and the pharmaceutical company Pfizer. This centre has been devised as a space for excellence research in genomic medicine, focusing on the Genomic Oncology Area
comprehensive study and understanding of the genetic basis of human diseases in general, This area focuses on research into those genetic placing special emphasis on cancer and its abnormalities that give rise to the process of genetic disorders related to inheritance. carcinogenesis and its progression. In addition to advancing in the knowledge of the bases of GENYO was created as a multidisciplinary disease, and in particular cancer, GENYO, due research space, where different professionals to its character of research centre with a clear from the healthcare, university and business translational vocation, should orientate part of its areas interact, making it possible to generate lines to development of new therapeutic issues new systems to diagnose, prevent and treat which respond to health problems. diseases based on the joint and coordinated Research groups:
application of first-rate knowledge in the different areas of genetics. This centre is the benchmark centre of the Andalusian Program for Research in Clinical Genetics and Genomic Medicine, a program which, together with those of Cel Therapy and Regenerative Medicine, and Nanomedicine have the main objective of supporting and fostering translational research in Advanced Therapies. The activities performed within these three research programs are developed in coordination with the Andalusian Initiative for The objective of pharmacogenomics is the Advanced Therapies (IATA), an initiative of the creation of drugs tailor-made for each patient Andalusian Government promoted by the and adapted to their genetic conditions. Regional Ministries of Health and Innovation, Science and Enterprise. This area has a special interest in a centre which, like GENYO, has a clear applied and RESEARCH AREAS
translational vocation, since it is one of the pillars of so-called individualized or personalized Human DNA Variability Area
medicine, which not only supposes adaptation to the patient of the best drugs, achieving a The Human Variability Area of GENYO is devised better and faster improvement or cure, but also as a scientific production structure which will involves a decrease in morbidity and mortality preferably include research groups centred on due to adverse risks, which leads to a better and work in the area of genetic epidemiology of more efficient management in public and private some of the main public health problems


Marta E. Alarcón Riquelme, MD, PhD

 Identification of the functional genetic variants for systemic lupus  Professor in Genetic Epidemiology of Chronic  Understand how risk variants affect cell differentiation and function.
Inflammatory Diseases  Develop assays to define patient subclasses or treatment responses based on genetic and cellular information.  Head of the Human DNA  Develop assays to detect cellular status reliable as clinical biomarkers. Variability Department, GENYO  Develop assays to test potential therapeutic compounds. MOST RELEVANT PUBLICATIONS
 Associate Member, Oklahoma Medical Research Foundation  Delgado-Vega, A.M., Dozmorov, M.G., Bernal Quirós, M., Wu, Y.Y.,
Martínez-García, B., Frostegård, J., Truedsson, L., De Ramón, E., Wren, J.D., Martin, J., Castil ejo-López, C., and Alarcón-Riquelme, M.E. Fine
Human Samples: DNA from 4000
Mapping and Conditional Analysis Identify a New Mutation in the SLE patients genotyped and with Autoimmunity Susceptibility Gene BLK that Leads to Reduced Half-Life of detailed clinical information. the BLK Protein. Ann Rheum Dis 71(7):1219-26, 2012  Castillejo-López, C., Delgado-Vega, A.M., Wojcik, J., Kozyrev, S.V., Available cell lines: proprietary
Sanchez, E., Thavathiru, E., Wu, Y.Y., Pöl man, D., López-Egido, J.R., cell lines containing mutants from James, J.A., Merril , J.T., Kel y, J.A., Kaufman, K.M., Moser, K., Gilkeson, various key genes, EBV cell lines of G., Frostegård, J., Pons-Estel, B.A., D'Alfonso, S., Witte, T., Cal ejas, J.L., genotyped individuals. Harley, J.B., Gaffney, P., Martin, J., Guthridge, J.M., and Alarcón-
Riquelme, M.E. Genetic and Physical Interaction of the B-cell SLE-
Associated Genes BANK1 and BLK. Ann Rheum Dis 71(1):136-42, 2012  Delgado-Vega, A.M., Sanchez, E., Löfgren, S., Castil ejo-López, C., and Alarcón-Riquelme, M.E. Recent Advances in the Genetics of Systemic
Autoimmune Diseases. Curr Opin Immunol 22(6):698-705, 2010
 SLEGEN* (*Members: John B. Harley, Carl D. Langefeld, Marta E.

Alarcón-Riquelme, Lindsey A. Criswel , Chaim O. Jacob, Robert P.
Kimberly, Kathy L. Moser, Betty P. Tsao and Timothy J. Vyse). A genome
wide association scan in women with systemic lupus erythematosus (SLE) identifies ITGAM, PXK, KIAA1542 and rs10798268 and other loci Nat Genet 40(2):204-10, 2008.  Kozyrev, S.V*., Abelson, A.K*., Wojcik, J., Zaghlool, A., Linga Reddy, P.M.V., Sanchez, E., Yin, H., Gunnarsson, I., Svenungsson, E., Sturfelt, G., Jönsen, A., Truedsson, L., Pons-Estel, B., Witte, T., D'Alfonso, S., Momigliano-Richiardi, P., Danieli, M.G., Gutierrez, C., Suárez, A., Junker, P., Laustrup, H., González-Escribano, M.F., Martin, J., Abderrahim, H., and Alarcón-Riquelme, M.E. The B Cell Gene BANK1 is Associated
with Systemic Lupus Erythematosus Through the Effect of Several
Functional Variants Nat Genet 40(2):211-6, 2008

 Hospital Virgen del Rocío, Sevilla  Fine Mapping and Replication of Genome-Wide Association Scans for SLE: Towards the Identification. Instituto de Salud Carlos III, Spain.
 Hospital Virgen de las Nieves, Period 2009-2012 (On renewal)  Dissecting Molecular Genetic B-Cell Pathway in Lupus Swedish
Research Council. Period: 2010-2013
Hospital Virgen de la Macarena,  Identification of Novel Genes and Biomarkers for Systemic Lupus Erythematosus. European Science Foundation. Period: 2010-2014.
 Hospital Negrín, Gran Canaria  Dissecting a Novel Molecular B-Cell Pathway in Lupus. Alliance for
Lupus Research, USA. Period: 2010-2013.
 Fundación Marqués de Valdecilla,  Complete Exome Sequencing of SLE Patients from Multiplex Families: Identification of Rare Mutations and their Functional Consequences. Fundación Ramón Areces, Spain. Period: 2012-2015.
SLEGEN Consortium (9
SLE is a chronic inflammatory autoimmune disease affecting primarily members in Europe and the women. Nearly 35 genes have been identified, and the group of Dr Alarcón- Riquelme has been at the forefront of these discoveries. Despite such  BIOLUPUS network (25
success, little is known about how risk variants alter gene and cell function. members in Europe) Our projects aim at defining the functional genetic variants using case-control MEMBERS OF THE RESEARCH
analyses as well as exome sequencing of family members with the disease and analyze the effects of the genetic risk variants or the mutations in B lymphocyte and plasmacytoid dendritic cell function.  Casimiro Castillejo López, senior The information will be used to: a) define how the variants affect gene function; b) identify cellular abnormalities that correlate with specific variation  Concepción Marañón Lizana, to determine subgroups of patients; c) associate genetic variants with clinical senior researcher, Miguel Servet outcomes in the largest study of its kind in Europe, with follow-up data for 2000 European SLE cases; d) produce cell lines that contain SLE susceptibility genes in wild-type and mutated form, to analyze how variants  Ina Georg, postdoc, Sara Borrel alter gene function or interactions with other proteins; and e) produce robust assays that measure the protein-protein interactions that may serve as  Manuel Martínez Bueno, postdoc biomarkers of disease progression and activity; f) identify compounds that modulate such interactions such that it leads to reduction in B or pDC cell  Manuel Bernal Quirós, PhD activity and consequently to a reduction in antibody and interferon secretion,  Alejandro Díaz Barreiro, PhD  2 technicians

1.- Creation of a custom Array covering 64 lupus susceptibility loci
and genotyping for the BIOLUPUS follow-up study
Chairman: Marta E. Alarcón-Riquelme Within the BIOLUPUS network that I coordinate we have performed the largest Centers involved:
GWAS to date made for lupus. In this study we identify 25 new susceptibility genes. To date we have 65 new loci, representing a 20% of the genetic  University of Birmingham, UK contribution to the disease. We propose to produce a new Custom Array to type all possible European lupus patients to combine the data with our flow  University College, London, UK cytometry analyses to identify groups of individuals that share risk variants. As  Hospital San Cecilio, Granada, several (but not all) susceptibility genes are shared among other systemic autoimmune diseases, this custom array will be useful to study those as well (rheumatoid arthritis, Sjögren's syndrome, Scleroderma). This study would also  University of Szeged, Hungary fine map some of the loci to uncover the true genes and functional variants and use genetic data to define the impact of genetic risk variants in clinical  Ospedale San Camilo, Rome, Italy outcomes and disease activity. Until now this study has been funded partly by  Cyprus Society of Rheumatology the European Science Foundation until 2014. We require a more extensive fol ow-up of the patients to cover at least 2 more years. We have 23 groups  Hospital San Antonio, Porto, across Europe, and the study requires support for the yearly inclusion of patients by clinical groups into a database, and database licenses. Most of the patients have been genotyped for the GWAS, but a more targeted genotyping is  University of Brescia, Italy required to avoid imputation data and also to homogenize the information.  University of Hannover, Germany Genotyping of the HLA would also be necessary.  University of Padova, Italy 2.- Perform flow cytometry measurements from whole blood to
detect abnormalities that associate with risk variants
 Hospital Carlos Haya, Málaga, We are optimizing flow cytometry measurements to detect lymphoid and myeloid cell subpopulation differences that relate to risk variants. Initially we wil  R igshospitalet, Copenhagen, DK detect these correlating with individual risk variants, but later we will combine these to identify the groups of individuals that statistically cluster. The project  U niversity of Siena, Italy aims at using these measurements in a way similar to those performed to  U niversité Catholique du Louvain, detect subclasses of leukemias in hemato-oncology. Our preliminary results are very promising, particularly for the gene BLK. We also will perform, when required studies for the intracellular detection of cytokines and kinase  Karolinska Institutet, Sweden activation. Correlations will be done with disease activity and ongoing therapy.  Hospital Universitario Sierral ana, Santander , Spain HUMAN DNA VARIABILITY
3.- Validation of protein-protein interaction assays in groups of SLE

 Odense University Hospital, DK We have performed studies with the gene BANK1, where we have identified several proteins that interact with it, leading to the chronicity of B-cell activation  Ospedale Maggiore Policlinico, and potentially of other non-T cells. This project aims at analyzing the status of these interactions using a robust assay we have designed in patients and controls, relate to their ongoing therapy and to the activity of their disease. If the assay is Hospital Clinic, Barcelona validated, we will then require the production of new, specific antibodies or affinity  Medical University of Vienna reagents if the assays are to be commercialized. The assay does require optimization for its use in primary cells. We also aim at developing these using  King's College, London  Hospital Virgen del Rocío, Sevilla, 4.- Use of Cellular Assays to Validate New Compounds
We have developed cellular assays containing mutants of the genes we are  Hospital Negrín, Gran Canaria, studying. These assays are very informative as the mutations do result in changes in cell function and activity. We would like to validate their use in the identification of potential new therapeutic compounds directed towards the inhibition of cel activity, cytokine production, etc. in the presence of the mutations or functional variants. The protein-protein interaction assays can also be used as biomarkers of compound efficacy. In fact, we have optimized these assays in several cell lines. HUMAN DNA VARIABILITY
Otology & Neurotology
Jos e Antonio López Escá mez, MD, PhD

 Member of the COST Action
 Definition of novel genes and biochemical pathways associated with European Network for the Study Meniere's disease. of Vestibular Disorders (in  Identification of rare allelic variants associated with familial cases of Meniere's disease. Member of The Spanish Immunogenetic profile and endophenotypes in Meniere's disease as a model Network for the study of for autoimmune inner ear disease. Meniere's disease (MEN)  Identification of genetic markers for hearing loss progression in Meniere's  Member of the International Classification of Vestibular MOST RELEVANT PUBLICATIONS
Disorders Committee of the Barany Society  Lopez-Escamez JA,* Saenz-Lopez P, Acosta L, Moreno A, Gazquez I, Perez- Garrigues H, Lopez-Nevot A, Lopez-Nevot MA. Association of a functional  Vocal of the Andalusian polymorphism of PTPN22 encoding a lymphoid protein phosphatase in Committee for R+D+I on Health bilateral Meniere s disease. Laryngoscope 2010; 120: 103-7. IF – Quartile (JCR) 2.096 – Q1 Vocal of the Ethics for Research Committee in Almeria.  Gazquez I, Lopez-Escamez JA*, Moreno A, Campbel CA, Meyer NC, Carey JP, Minor LB, Gantz BJ, Hansen MR, Del aSantina CC, Aran I, Soto-Varela A, BIOLOGICAL MATERIAL
Santos S, Batuecas A, Perez-Garrigues H, Lopez-Nevot A, Smith RJH, Lopez- Nevot MA. Functional variants in NOS1 and NOS2A are not associated with
Human Samples: >2000 DNA
progressive hearing loss in Menière's disease in a European Caucasian samples from European sporadic population. DNA Cell Biol 2011 30 (9): 699-708. IF – Quartile (JCR) 2.159 – and familial cases of Meniere's  Gazquez I, Lopez-Escamez JA*. Genetics of recurrent vertigo and vestibular disorders. Current Genomics 2011; 12 (6): 443-50. IF (JCR) – Quartile (JCR) 2.487 – Q3  Gazquez I, Soto-Varela A, Aran I, Santos S, Batuecas A, Trinidad G, Perez- Garrigues H, Gonzalez-Oller C, Acosta L, Lopez-Escamez JA*. High prevalence SUMMARY OF RESEARCH
of systemic autoimmune diseases in patients with Meniere's disease. PloS PRODUCTION (last 5 years)
ONE 2011 6(10): e26759. doi:10.1371/ journal.pone.0026759. IF – Quartile (JCR) 4.411 – Q1  Gazquez I, Moreno A, Aran I, Soto-Varela A, Santos S, Perez-Garrigues H, Lopez-Nevot A, Requena T, Lopez-Nevot MA, Lopez-Escamez JA*. MICA-STR A.4 is associated with slower hearing loss progression in patients with Meniere's disease. Otol Neurotol 2012; 33 (2):223-229. IF – Quartile (JCR)  Gazquez I, Requena Y, Espinosa JM, Batuecas A, Lopez-Escamez JA*. Genetic and clinical heterogeneity in Meniere's disease. Autoimmunity Rev 2012 (in press). IF - Quartile (JCR) 6,556 – Q1 HUMAN DNA VARIABILITY
Otology & Neurotology
 Role of neurotoxicity, genes regulating nitric oxide and cytokines in the PATENT APPLICATIONS
development of hearing loss in Meniere's disease (PI). ISCI I, Code: (Last 5 years)
PI100920. 2011-13.  Prevalence of autoimmune diseases and immunogenetic profile in A method to obtain useful data
Meniere's disease. (AI). PI: Angel Batuecas Caletrio. Consejeria de for diagnosis and prognosis of
Salud Castilla y León. Code: BIOSA-51-11. 2011-12.
sensorineural hearing loss.
Application number:  Identification of common and rare allelic variants at genomic level in Meniere's disease. Programme of professional development in Priority date: 14/12/2011 research. (PI). Fundación Progreso y Salud. Code: DP-0041-2011. Foreign applications: Pending CLINICAL TRIALS
 An 8mg of Acetyl-leucine oral suspension efficacy and tolerance in vestibular neuritis. A randomised double-blind placebo controlled proof- of-concept study (AI). Pierre-Fabre Medicament. 2011-12.  Effect of V0251 in acute vertigo. A randomised doublé-blind placebo controlled study. (PI). Pierre Fabre Medicament. Code: 2012-13. SCIENTIFIC INTEREST AREAS
Inner ear diseases are defined by hearing loss, tinnitus and/or imbalance. Common diseases causing hearing loss are multifactorial complex diseases and the interaction of genetic, epigenetic and environmental factors may determine the development of chronic otitis media, otosclerosis or age-related hearing loss. Similarly, vestibular disorders had a hereditary component that can be investigated by high throughtput genotyping and paral el massive sequencing. Recurrent vertigo is a common health problem caused by disorders of the vestibular system in the inner ear. The most common causes are benign paroxysmal positional vertigo, vestibular neuritis and Menière's disease. Among them, Menière´s disease if the most severe form of vertigo characterized by hearing loss, recurrent vertigo and tinnitus. Menière's disease occurs in young adults and it may affect both ears up to 40% of cases, causing a more severe hearing loss and chronic imbalance. The aim of our group is the discovery of genetic basis of Menière's disease and hearing loss progression. HUMAN DNA VARIABILITY
Otology & Neurotology
1.- Genomics of sporadic Meniere's disease.
Meniere´s disease is a chronic disorder of the inner ear causing vertigo, sensorineural hearing loss and tinnitus. The estimated prevalence of Meniere´s disease in Caucasians is 1–2 cases per 10000. The disease is multifactorial and the int eraction of several genes with the environment is probably involved. Th e goal of the proposed research is to elucidate novel genes and biochemical pathways associated with Meniere's disease, a chronic disorder of the inner ear causing vertigo, sensorineural hearing loss and tinnitus. Specifically, we plan to develop a ge nome-wide association study (GWAS) to determine the contribution of common allelic variants for the disease across a four-year period in a large multinational cohort of 2000 patients with sporadic Meniere's disease. Candidate SNPs will be validated in an independent cohort to define candidate genes. Bioinformatics analysis will explore gene/gene interactions an d define a network of genes and biochemical pathways. Functional in vitro studies will confirm the relevance the key of proteins in the pathophysiology of the disease. 2.- Identification of rare allelic variants in familial Meniere's disease by whole exome sequencing.
Meniere´s disease is a complex disorder where probably genetic and environmental factors determine its d evelopment. Although most patients with Meniere´s disease are sporadic, some of them present familial cases following an autosomal dominant mode of inheritance with incomplete penetrance. The frequency of familial disease is suggested to be between 4% and 20% and there have been numerous reports on familial Meniere´s disease, but the estimated pr oportion of which in Spain is stil unknown. Th e objectives of the familial study are: 1. To estimate the prevalence of familial MD in Spain in a large cohort of sporadic MD. 2. To investigate the contribution of rare allelic variants to develop familial MD by whole exome sequencing in 26 families with MD. 3. To analyze the relationship among rare allelic variants and endophenotypes in MD and to define familial specific 3. - Biomarkers for autoimmune inner ear disease.
Au toimmune inner ear disease (AIED) is a treatable cause of sensorineural hearing loss and it is important for patients,
physicians and audiologist professionals to recognize this entity properly for an early diagnosis and therapy. Despite of it, th ere is no biological marker for AIED and the diagnosis is based on clinical criteria. The importance of autoimmune phenomenon in the genesis of inner ear diseases is difficult to evaluate, because the clinical and biological evaluations for autoimmune deafness has not yet been well defined. The major goals of this project are to perform a genome-wide scan with 196,000 markers in >600 European Caucasian cases and 1500 controls as a first stage towards the identification of genes previously associated with other autoimmune disease. Replication in a large set of independent cases and controls in a second stage will identify candidate markers and genes asso ciated with autoimmune inner ear disease. HUMAN DNA VARIABILITY
Otology & Neurotology
4.- Mechanisms of hearing loss progression in Meniere's disease.
Glutamate NMDA receptors-mediated excitotoxicity and cochlear neurons apoptosis have a key role in hearing loss progression. The major goals of this project are to analyze polymorphism of cochlear neurotoxicity-related genes in Meniere's disease (SLC1A3, NOS1, NOS2, PPP3R1, NF-kB) and to monitor the levels of complement (c3, c4), circulating immunocomplexes, proinflamatory (IL-2, IL-17, INFg, TNF) and anti nflamatory (IL-4, IL-5, IL-10) cytokines. Functional studies will determine the relevance of neurotrophic factors in neuron survival and hearing preservation. Moreover, these molecules could be target to develop blocker drugs or gene therapies to reduce hearing loss progression. 5.- Development of human-based models for hearing loss using stem cells and patient-specific iPSCs.
Hearing loss progression results from nerve damage after endolymphatic hydrops. The transplantation of stem cells with the potential to produce functional differentiated cell types might be a promising therapeutic strategy for the treatment of hearing loss. We pursuit to develop a cell model of neuronal apoptosis by using iPSC obtained by transdifferentiation of human fibroblasts. Fibroblast can be reprogrammed to a pluripotent state with a combination of four transcription factors. First, we will use mRNA and several transcription factors to obtain iPSC by reprogramming fibroblasts. In a second phase, we will try to generate otic neurons from reprogrammed iPSC with the proneural genes Ascl1, Brn2 and MyT1L. HUMAN DNA VARIABILITY
Jose Luis Garcia-Perez, PhD
 International Scientist, Howard MAIN RESEARCH TOPICS
Hughes Medical Institute.  LINE-1 elements as epimutagens: impact on human health.  Member of the 7PM funded Network for human embryonic  Role of LINE-1 in Fanconi Anemia, Ataxia Telangiectasia, and DiGeorge stem cells, Eurosystem. syndrome: looking for therapeutic alternatives.


 The role of LINE-1 elements in the initiation and metastasis of: melanoma and ovarian cancers. Human Samples: melanoma and
ovarian cancer samples (cell lines
and DNA). Fanconi Anemia, Di George Syndrome and Ataxia  Morrish, T.*, García-Pérez, J.L.*, Stamato, T., Taccioli, G.E., Sekiguchi,
Telangiectasia samples (cell lines J. and Moran J.V. "Endonuclease independent LINE-1 retrotransposition at mammalian telomeres", Nature, 2007, 446: 208-212. * Both authors contributed equally to this work. Cell lines: hESCs and hiPSCs. A
panel of transformed cell lines
 Coufal, N.G., Garcia-Perez, J.L., Peng, G.E., Yeo G.W., Lovci, M.T.,
(HeLa, N-Tera2D1, etc). Morell, M., O´Shea, K.S., Moran, J.V., and Gage F.H. "L1 retrotransposition in human neural progenitor cells.", Nature, 2009, 460 (7259): 1127-1131.  García-Pérez, J.L.1 , Morell, M., Scheys, J.O., Kulpa, D.A., Morell, S.,
Carter, C.C., Hammer, G.D., Col ins, K.L., O'Shea, S., Menendez, P., and RESEARCH SUMMARY (last 4
Moran, J.V." Epigenetic silencing of engineered L1 retrotransposition events in human embryonic carcinoma cells", Nature 2010, 466(7307):769-73. 1, corresponding author. Published papers: 19; Impact
Factor=229.311 (JCR-2010); More than 300
citations (excluding self).
 Macia, A., Munoz-Lopez, M., Cortes, J.L., Hastings, R., Morell, S., Lucena- Aguilar, G., Marchal, J.A., Badge, R.M., and Garcia-Perez, J.L.
Grants: PI in 8 proposals, and co-IP in 3.
"Epigenetic control of retrotransposon expression in human embryonic Regional, National, European and International Calls. stem cells", Mol. Cell. Biol., 2011, 31(2): 300-16.
Invited Speaker in 14 International
 Coufal, N.G., Garcia-Perez, J.L., Peng, G.E., Marcheto, M.C.N., Muotri,
Research Centers. A.R., Mu, Y., Carson, C.T., Macia, A., Moran, J.V., and Gage F.H. "Ataxia-Telangiectasia Mutated modulates L1 retrotransposition in human neural stem cells", Proc Natl Acad Sci U S A. 2011 Dec 20;108(51):20382-7. Epub 2011 Dec 9. HUMAN DNA VARIABILITY
 Somatic Activity of LINE-1 Elements in Humans. Marie Curie (International Reintegration Grant, FP7-PEOPLE-
2007-4-3-IRG: SOMATIC LINE-1) and Marie Curie Actions, IntraEuropean Fellowship, EU.
 Biology of LINE-1 Elements. The Howard Hughes Medical Institute, USA.
 LINE-1 activity in Fanconi Anemia Patients, Health Ministry, Andalusia, Spain.
More than 40% of the human genome is composed of repeated DNA, and some types can be mobilized within the genome (e.g., Transposable Elements (TE)). As a result, the human genome is not static, and poses some degree of plasticity. Long Interspersed Element-1 (LINE-1 or L1) is the only autonomous retrotransposon (a class of TEs) in the human genome, with more than 600,000 copies per genome ( 17% of the genome). Furthermore, L1 is able to mobilize other non-autonomous TEs (Alu, SVA, U6) and cel ular mRNAs (giving rise to processed pseudogenes). Overall, L1 is responsible for a third of the human genome. Although most L1 elements in the genome are inactive, an average human genome contains 100 active L1 retrotransposons. Its mobility has resulted in a variety of human diseases, and its activity has shaped the human genome during evolution. L1 insertions within genes can alter their function, can modulate their expression at both splicing and poly-adenylation steps, and can provide regulatory sequences to genes. In addition, L1 insertions can be accompanied by genomic instability processes (deletions, translocations, etc), adding to the myriad of ways they shape our genome. Despite their abundance, little is known about their impact on human health. Our lab studies mobile DNA elements in humans, how they move and impact our genomes, and how the host regulates them. Pluripotent cells represent the best physiological model to study L1 biology, and due to our contributions my lab is uniquely positioned to study L1 biology and its regulation using an array of pluripotent cells (hESCs, iPSCs). We are currently using hESC/iPSC lines to infer the magnitude of the load of L1 retrotransposition in somatic tissues, using their differentiation potential. Notably, preliminary data from our and other groups indicate that the somatic activity of LINE-1s is a genetic driver for the origin and progression of most human cancers. In my lab, we are analyzing ongoing LINE-1 mobilization and the effect on the genome using human melanoma and ovarian primary/mestastasis pairs. Our long-term aim is to explore the possibility of developing chemical and biological tools to reduce the mobilization of LINE-1s in human cancers, with the ultimate goal of improving the treatment of this important human disease. A major finding in L1 biology is the description of epigenetic mechanisms that act to control L1 retrotransposition. My lab will conduct research to decipher the mechanism that acts to silence de novo L1 insertions in pluripotent cells, as it is a completely uncharacterized cellular pathway. In addition, my lab will conduct research aimed to determine the epimutagenic potential of de novo L1 insertions in an array of pluripotent cell types. The generation of "epimutations" by TE insertions is a new concept in human biology, and likely will change the way we think about the impact of TEs in genomes at the somatic and germ line level. Finally, data from my lab has demonstrated that L1 mobilization is de-regulated in Fanconi Anemia patients, Ataxia Telangiectasia patients, and Di George Syndrome patients. We are currently analyzing the impact of this de-regulation in these 3 human diseases, with the long term-aim of improving the treatment of these serious and incurable diseases. HUMAN DNA VARIABILITY
and Cell Therapy
Francisco Martin, PhD
 Development of safer and more efficient gene delivery tools for the treatment  Member of European Society of of immune-related diseases: Wiskott-Aldrich Syndrom and multiple sclerosis Gene and Cell Therapy  Generation of human cellular model to study genetic diseases  Member of Spanish Society of Gene and Cell Therapy  Generation of transgenic mesenchymal stem cells (MSCs) for the treatment of autoimmune diseases

 Generation of Al -In-One Doxycycline-responsive lentiviral vectors for conditional expression in Stem Cells. Human Samples: Umbilical cord,
MSCs, hESCs and hIPSC.

Available cell lines: hESCs, hiPSC
 Ikeda Y., Takeuchi Y., Martín F., Cosset F.L., Mitrophanous K., And Col ins
and proprietary transgenic K562WASKO M. Continous High-Titer HIV-1 Vector Production. Nature Biotechnology and hESCWASKO lines for modeling ; 21(5):569-72. IF. (2007)= 22.8

Animal models:
F Martín*, MG Toscano, C Frecha, M Santamaría, M Blumdel , A Thrasher
Collagen-induced arthritis (CIA); and Ignacio J. Molina. Lentiviral Vectors Transcriptionally Targeted To Experimental Autoimmune Hematopoietic Cells by WASP gene proximal promoter sequences. Gene Encephalomielitis (EAE). Therapy 2005; 12(8):715-23 I.F (2005).= 4.8;
 M Delgado, MG Toscano, K Benabdellah, M Cobo, F O' Valle, E Gonzalez- Rey, F Martin. Artritis Gene Therpay by In Vivo delivery of Lentiviral Vectors
Expressing Vasoactive Intestinal Peptide cDNA. Arthritis & Rheumatism.
2008;58:1026-1038 I.F (2009) 7.3
 Toscano M, Frecha C, Benabdellah, K, Trasher A.J., García Olivares E., RESEARCH ACTIVITY (Last five
Molina I, F Martin. Hematopoietic specific lentiviral vectors circunvent
potential toxicity problems caused by ectopic expression of Wiskott-Aldrich Syndrome protein. Human gene Therapy. 2008;179-197. I.F (2009) =
 Toscano MG, Benabdehal ah K, Frecha C, Cobo M, Muñoz P and Martin F.
Was cDNA sequences modulates transgene expression of Was promoter- driven LVs. Human Gene Therapy. 2009; 20:1279-1290 I.F. (2010)=
and Cell Therapy
 Toscano MG, Degado M, Kong W, Martin F and Doina Ganea.
Dendritic Cells Transduced With Lentiviral Vectors Expressing Vasoactive Intestinal Peptide (Vip) Differentiate Into Vip-Secreting PATENT APPLICATIONS (Last
Tolerogenic-Like DC. M olecular Therapy. 2010; 18(5):1035-1045
five years)
I.F. (2011)= 6.8
 Benabdel ah K, Cobo M, Muñoz P, Toscano MG and Martin F*. Vectores Lentivirales para la
identificación del linaje

Development of an all-in-one Lentiviral vector system based on the original TetR for the easy generation of Tet-ON cell lines. Plos One. 2011; e23734. I.F (2011)= 4.1
Application number: P201230449  P. Muñoz, M. Toscano, PJ Real, K. Benabdel ah, M. Cobo, C Bueno, V Priority date: 26/03/2012 Ramos-Mejía, P Menendez, P. Anderson, F. Martin. Specific Marking
Foreign applications: Pending of hESCs-derived hematopoieitc cells by WASP-promoter driven lentiviral vectors. Plos One. 2012; 7(6):e39091. I.F (2011)= 4.1
Highly inducible Tet-ON vector

 Cobo M, P Anderson P, Benabdellah K, MG Toscano M, Muñoz P, García-Perez A, Gutierrez I, Delgado M., Martin F*. Mesenchymal
Application number: EP11166754.9 stem cells expressing vasoactive intestinal peptide ameliorate Priority date: 19/05/2011 symptoms in a model of chronic multiple sclerosis. Cell Foreign applications: Transplantation. 2012; accepted I.F. (2011) = 6.2.
 Improvement of retroviral vectors for gene therapy applications. Science & Technology Ministry (Plan Nacional). Period: 2003-2006.  Development of safer and more efficient lentiviral vectors: applications for gene therapy of Wiskott-Aldrich Syndrome Fondo de Investigación Sanitaria (FIS). Instituto de Salud Carlos II . Period: 2007-2009.  Gene Therapy for Wiskott-Aldrich Syndrome: Development of a human cellular model for preclinic studies. Fondo de Investigación Sanitaria (FIS). Instituto de Salud Carlos III. Period: 2010-2012.  Gene-Cell Therapy for multiple sclerosis. Consejería de Innovación, Ciencia y Empresa (CICE). Junta de Andalucía. Period: 2010-2013  Gene-Cell Therapy of Wiskott-Aldrich Syndrome through gene editing. Consejería de Salud. Junta de Andalucía. Period: 2010-2012 HUMAN DNA VARIABILITY
and Cell Therapy
1.- Development of safer and more efficient gene therapy strategies for the treatment of primary
immunodeficiencies: Wiskott-Aldrich Sindrome.

We have developed physiologically regulated lentiviral vectors expressing WASP, the affected gene in Wiskott-Aldrich Syndrome. We have also developed several human cell models to study the role of WASP in cell biology and to study the safety and efficiency of GT strategies: 1- Using Zinc Finger Nucleases technology (ZFNs), we have developed he first human cell line WASKO to perform studies on the role of WASP on megakaryocytic development (K562WASKO) and the first human Embryonic Stem Cells WAS Ko. Parallel project w ith potential applications outside gene therapy field. We have generated a patent on the use
of W ASP gene as a marker for early hematopoietic progenitors and the use of WASP-promoter driven lentiviral
vectors for isolation/characterization of these populations. 2.- Cell-Gene therapy strategies for the treatment of autoimmune diseases.
The aim of this research line is to develop a new therapeutic strategy to tackle autoimmune diseases (in particular we have been focused in Multiple sclerosis). We have been focusing in improving the delivery of therapeutic genes to targeted tissues (inflamed CNS and lymphoid organs). We have combined the efficiency and transcriptional control of lentiviral vectors with the ability to migrate to inflammatory sites of mesenchymal stem cells (MSC). In this direction we are interested on improving the migratory potential of MSC to inflamed CNS and in the development of new doxycycline- regulated lentiviral vectors that stably and efficiently modulate gene expression in these MSCs and in its progeny. Parallel project with potential applications outside gene therapy field. We have patented recently the first
TetR-based doxycycline-responsive ALL-IN-ONE lentiviral vector able to modulate gene expression in primary
cells without the requirement of using transactivators (rtTA or tTA). The improved generation of this Tet-ON LVs achieved transgene regulation on bulk populations of all stem cells analyzed, including human Embryonic Stem Cells. This regulation is maintained over time and after differentiating the hESCs toward different cell types. GENOMIC ONCOLOGY AREA
 Genetic of monoclonal gammopathies: MGUS and MM.  Principal investigators:
 Genomic and pharmacogenomic of acute and chronic leukemias.
 Molecular basis of susceptibility to cancer-related infections: invasive fungal
Manuel Jurado Chacón, MD, PhD Juan Sainz Pérez, PhD  Biology of mesenchimal stem cells: their use for the treatment of graft-versus-  PhD. students:
 Genetic basis of immune-related disorders: rheumatoid arthritis. Carmen Belén Lupiañez Muñoz  Genetic of solid tumors: colorectal cancer. Luz María Canet Antequera Rafael Ríos Tamayo MOST RELEVANT PUBLICATIONS
 Sainz J, Lupiañez CB, Segura-Catena J, Vazquez L, Ríos R, Oyonarte S, Hemminki K, Försti A, Jurado M. Dectin-1 and DC-SIGN polymorphisms Juana Segura Catena associated with Invasive Pulmonary Aspergillosis infection. Plos One 2012; 7: Guest scientists: e32784 (1-10). PMID: 22384201. Impact factor: 4.411. Quartile: Q1 (biology; Emanuela Cosentino journal ranking: 12 of 86) Santiago Alvarado Jiménez  Martino A, Campa D, Jamroziak K, Reis RM, Sainz J, Buda G, García-Sanz R, Lesueur F, Marques H, Moreno V, Jurado J, Ríos R, Szemraj-Rogucka Z, Szemraj J, Tjønneland A, Overvad K, Juul Vangsted A, Vogel U, Mikala G, Kádár K, Szombath G, Varkonyi J, Orciuolo E, Dumontet C, Gemignani F, Rossi AM, Landi S, Petrini M, Houlston RS, Hemminki K, Canzian F. Impact of polymorphic variation at 7p15.3, 3p22.1 and 2p23.3 loci on risk of multiple myeloma. British Journal of Hematology 2012 (In press). PMID: Pending. Impact factor: 4.942. Quartile: Q1 (Hematology; journal ranking: 11 of 66)  Sainz J, Lupiañez CB, Romani L, Canet LM, Segura-Catena J, Soto-Pino MJ, RESEARCH ACTIVITY (2011-
Expósito-Ruiz M, Ferrer MA, García A, González-Utrilla A, Vallejo T, Oyonarte S, Hemminki K, Försti A, Cáliz R. Gender-associated differences of DC-SIGN, Dectin-2 and MCP-1 polymorphisms in the susceptibility to rheumatoid arthritis. Arthritis Research and Therapy 2012 (In press). PMID: Pending. Impact factor: 4.360. Quartil: Q2 (Rheumatology; journal ranking: 8 of 29)  Cáliz R, Ferrer MA, Saenz-López P, Fernández A, Marenco JL, Raya E, Moreno A, Sainz J, García-Sanchez A, Pérez MJ, Camacho I, González-Utrilla A, Velloso ML, Montero S, Velazquez MT, Coret V, Camacho M, Ureña I, Lopez-Nevot MA. FcgammaRII a 158 (F/V) polymorphism and response to rituximab treatment in rheumatoid arthritis. Rheumatology 2012 (In press). PMID: Pending. Impact factor: 4.171. Quartile: Q2 (Rheumatology; journal ranking: 9 of 29) GENOMIC ONCOLOGY

 Campa D, Martino A, Sainz J, Buda G, Jamroziak K, Weinhold N, Vieira Reis RM, García-Sanz R, Jurado M, Ríos R, Szemraj- ERA-NET Pathogenomics
Rogucka Z, Marques H, Lesuer F, Moreno V, Szemraj J, Orciuolo Trans-European cooperation and E, Gemignani F, Rossi AM, Dumontet C, Petrini M, Goldschmidt coordination of genome sequencing and H, Landi S, Canzian F. Comprehensive investigation of genetic functional genomics of human-pathogenic variation in the the 8q24 region and multiple myeloma risk in the IMMEnSE (International Multiple Myeloma rESEarch) Coordinator: Dr. Hermann Einsele consortium. British Journal of Hematology 2012; 157: 331-338. PMID: 22590720. Impact factor: 4.94 Quartile: Q1 (Hematology; journal ranking: 11 of 66) EHA, SEHH and PETHEMA
 Sainz J, Martino A, Buda G, Jamroziak K, Reis RM, García-Sanz R, Jurado M, Ríos R, Szemraj-Rogucka Z, Marques H, Lesueur F, Research networks focused on the Moreno V, Orciuolo E, Gemignani F, Landi S, Rossi AM, prevention, diagnosis and treatment of Dumontet C, Petrini M, Campa D, Canzian F. Genetics and hematological malignancies. molecular epidemiology of multiple myeloma: The rationale for the IMMEnSE consortium (Review). Int J Oncol. 2012 Mar; 40(3): 625-38. PMID: 22159523. Impact factor: 2.57. Quartile: Spanish Network Research of Infectious Q3 (Hematology; journal ranking: 86 of 185) Diseases (Red Española de Investigación  Sainz J, Rudolph A, Hein R, Hoffmeister M, Frank B, Brenner H, en Patología Infecciosa). Chang-Claude J, Hemminki K, Försti A. Effect of type-2 diabetes Coordinator: Jerónimo Pachón Díaz. Code: predisposing genetic variants on colorectal cancer risk. Journal RD 06/0008/0006. of Clinical Endocrinology and Metabolism 2012; 97: E845-E851. PMID: 22419714. Impact factor: 6.495. Quartile: Q1 (Endocrinology & Metabolism; journal ranking: 13 of 116) The Research Network for Inflammation  Campa D, Sainz J, Rudolph A, Pardini B, Naccarati A, Vodickova and Rheumatic Diseases (Red de L, Chang-Claude J, Brenner H, Novotny J, Försti A, Buch S, von investigación en Inflamación y Schönfels W, Hampe J, Schafmayer C, Völzke H, Hemminki K, Enfermedades Reumáticas). It integrates 8 Vodicka P, Barale R and Canzian F. A gene-wide investigation on basic and 8 clinical groups with important polymorphisms in the MDR1/ABCB1 trasporter and leadership role internationally on the susceptibility to colorectal cancer. Plos one. 2012; 7: e32784 identification and establishment of (1-7). PMID: 22396794. Impact factor: 4.411. Quartile: Q1 molecular bases and operating (biology; journal ranking: 12 of 86) mechanisms of inflammation. The characterization and establishment of clinical cohorts and cooperative databases (genetic groups), all of them oriented to the study of connective tissue disorders, spondyloarthritis, rheumatoid arthritis and osteoarthritis, among other rheumatic disease GENOMIC ONCOLOGY
IMMEnSE consortium aims to  Principal Investigator: Juan Sainz Pérez / Manuel Jurado Chacón (Genyo -
improve the understanding of Pfizer - University of Granada - Junta de Andalucía Centre for Genomics & genetic and pharmacogenetics of Oncological Research and Hematology department. University Hospital Virgen de las MM. The driving idea of the Nieves, Granada, Spain). Project title: Invasive aspergillosis: Biomarkers for
IMMEnSE consortium is to join prevention, diagnosis and treatment response. ASPBIOMICS consortium. Funding
together the efforts of different institution: ERA-NET Pathogenomics.
research groups with the constitution of a large bio- and  Principal Investigator: Juan Sainz Pérez (Genyo - Pfizer - University of Granada -
databank to al ow more powerful Junta de Andalucía Centre for Genomics & Oncological Research and Hematology and meaningful investigation able department. University Hospital Virgen de las Nieves, Granada, Spain). Project
to uncover the role played by title: Pharmacogenomics in the treatment of Invasive Pulmonary Aspergillosis in
genetic variants in MM genetics, as cancer patients. (Proyecto de Excelencia). Funding institution: Consejería de
successfully done for other Salud de la Junta de Andalucia, Spain.  Principal Investigator: Dr. Rafael Cáliz Cáliz (Virgen de las Nieves University
MCC Spain
Hospital, Granada). Project title: Resistance to DMARDs in rheumatoid arthritis
patients: the impact of g-170-MDR on the multidrug resistance. Funding
A population-based multicase- institution: Roche Pharma
control study which aims at analyzing the influence of  Principal Investigator: Manuel Jurado Chacón (Hematology department.
environmental factors and their University Hospital Virgen de las Nieves, Granada, Spain). Project title: Genomics
interaction with genetic factors in of Invasive Pulmonary Aspergillosis. Funding institution: Carlos III Institute (FIS,
common tumours (colorectal Fondo de Investigaciones Sanitarias), Granada, Spain. cancer, breast cancer, gastroesophageal cancer, prostate  Principal Investigator: Dr. Manuel Jurado Chacón (Hematology department.
cancer and chronic lymphocytic Virgen de las Nieves University Hospital, Granada, Spain). Project title: Genomics
leukaemia) or tumours with and invasive aspergillosis infection. Single nucleotide polymorphisms analysis to peculiar epidemiological predict susceptibility to invasive aspergillosis infection in cancer patients. Funding
characteristics in Spain. At
institution: Consejería de Salud de la Junta de Andalucia, Spain.
present, the MCC-Spain study includes 17 CIBERSP research groups. GENOMIC ONCOLOGY
1.- Genetics of monoclonal gammopathies: MGUS AND MM.
AspBIOmics aims to reach the following Multiple myeloma (MM) is a very heterogeneous hematologic malignancy that arises from a premalignant stage, the monoclonal gammopathy of  Development of a sensitive and undetermined significance (MGUS) or an intermediate stage called specific nucleic acid based detection smoldering myeloma (SMM). Despite recent progress in the understanding of its pathogenesis, further research is warranted, as the transformation  Development of a sensitive and from either MGUS or SMM to MM is still not preventable and the disease is specific antigen based detection not curable. MM occurs as consequence of the accumulation of numerous genetic alterations such as translocations involving immunoglobulin heavy  Discriminative role of antigens / chain (IgH) locus (11q13, 4p16, 16q23, 21q12, and 6p21), deletions at antibodies during IA infection  Identification of cytokines and long arm of chromosome 13, and multiple trisomies (chromosomes 3, 5, 9, chemokines correlated with 11, 15, 19 and 21) leading to a deregulation of many genes involved in cell development of IA proliferation, differentiation and migration (i.e., D-type cyclins, FGFR3 and  Responses of the innate immune MMSET among others). Several of these alterations can appear years cells to causes of IA infection before to the onset of MM, suggesting that additional genetic or epigenetic  Development of methods for the alterations must contribute to the development of the disease. In this detection of relevant biomarkers of IA regard, recent studies carried out by our group (and others) have shown  Molecular understanding of the that the presence of single nucleotide polymorphisms (SNPs) can resistance to antifungals used to potentially influence the development of the disease as well as its progression. Thus, the main purpose of our group is to determine the  Fitness of resistant strains in vivo genetic polymorphisms associated with MM and its progression as well as  Development of a method to survey to identify those SNPs that can also influence on drug disposition and resistant strains response. This research is conducted within the context of the IMMEnSE  Functional relevance of SNPs associated to IA (International Multiple Myeloma rESEarch) consortium.  Association of SNP, which are 2.- Genetics of hematological malignancies.
genetically and functionally relevant Most of the hematological malignancies are genetically characterized by  Collection and maintenance of recurrent aneuploidies and chromosomal translocations but these clinical specimens from haematological patients alterations do not account for the genetic basis of these diseases,  Collection of host, clinical and suggesting that additional genetic alterations may also confer susceptibility mycology data from all patients or resistance to a disease. Thereby, we aim to explore the possibility that according to the EORTC / MSG SNPs could be involved in susceptibility to malignant hemopathies and/or diagnostic criteria adverse drug reactions.  Global development of new diagnosti c methods for IA GENOMIC ONCOLOGY
IMMEnSE consortium members
Scientific groups agreeing to participate to Invasive pulmonary aspergillosis (IPA) is an opportunistic and fulminant infection caused by inhalation of Aspergillus spp. spores. The invasive stage of the disease is characterized by hyphal invasion and destruction of  Dr. Canzian, Dr. Campa, Dr. Martino, pulmonary tissue, which are most frequently observed in patients with pre- Genomic Epidemiology Group, existing infections or lung damage. Despite the use of new antifungal drugs German Cancer Research Center DKFZ, Heidelberg, Germany. and the development of more sophisticated methods of diagnosis, the  Dr. Gabriele Buda, Department of incidence of IPA continues to rise. Epidemiologic studies have Oncology, Transplants and Advanced demonstrated that hematological patients with similar clinical conditions Technologies, Section of Hematology, and extrinsic risk factors vary in their susceptibility to IPA, suggesting a possible genetic predisposition to develop the disease. Genetic factors  University, Via Roma 67, 56100, explain, at least in part, why some people resist infection more successful y than others, and gene disruptions can cause fatal vulnerability to specific Dr. Felipe de Arriba de la Fuente, Servicio de Hematología, Hospital pathogens. Indeed, single-nucleotide polymorphisms (SNPs) in the Morales Meseguer, Murcia, Spain promoter and coding regions of cytokine genes have been associated with  Dr. Ramón García Sanz, Servicio de changes in cytokine production or function and may therefore influence Hematología, Hospital de susceptibility to infections. Identification of patients who are more Salamanca, Univesidad de susceptible to infection could facilitate the implementation of effective Salamanca-Consejo Superior de prevention strategies
.In the context of an international consortium, Investigaciones Científicas, Salamanca, Spain. AspBIOmics, our group is focused on the identification of genetic variants  Dr. Krzystof Jamroziack, Department associated with IPA infection in order to design and implement risk-adapted of Hematology, Medical University of therapeutic strategies. On the other hand, although it is now well Lodz, Lodz, Poland. recognized that SNPs in genes modulating immune response are likely to  Dr. Rui Manuel Vieira Reis, Life and be determinants of host susceptibility to fungal infections, so far little is Health Sciences Research Institute known regarding the biological significance of these variants. For this (ICVS), School of Health Sciences, reason, we also aim to determine the biological consequences of genetic University of Minho, Braga, Portugal  Dr. Herlander Marques, Life and variations associated with IPA infection. Besides individual genetic Health Sciences Research Institute susceptibility of the host, with this consortium we also propose to develop (ICVS), School of Health Sciences, and evaluate a battery of in vitro assays for a comprehensive multimodality University of Minho, Braga, Portugal analysis including the detection of Aspergillus elements (RNA,  Dr. Niels Weinhold, Medizinische polysaccharides, proteins) and host factors including cytokine profiles. Klinik V, Universitaetsklinikum Existing diagnostic parameters will be included in the analysis to validate Heidelberg, Heidelberg, Germany the improvement of the methods under development over the existing Dr. Rajiv Kumar, Molecular Genetic Epidemiology Group, German Cancer ones. For a more detailed information regarding AspBIOmics consortium, Research Center, Heidelberg, visit our websit Dr. Enrico Orciuolo, Department of Oncology, Transplants and Advanced Technologies, Section of Hematology, Pisa University, Pisa, Italy GENOMIC ONCOLOGY
4.- Biology of mesenchimal stem cells: their use for the treatment of
IMMEnSE consortium members
gr aft-versus-host-disease
 Dr. Federica Gemignani, Department Allogeneic hematopoietic ste m cell transplantation (allo-HSCT) is a potentially of Biology, Section of Genetics, curative therapy for patients diagnosed with hematolgical malignancies. This University of Pisa, Pisa, Italy therapeutic approach has been associated with high toxicity levels caused by  Dr. Stefano Landi, Department of Biology, Section of Genetics, the development of either acute or chronic graft-versus-host-disease (GVHD), University of Pisa, Pisa, Italy which considerably increase morbidity and mortality rates. Within recent  Dr. Hartmut Goldschmidt, years, the incidence of GVHD has increased significantly among al o- Medizinische Klinik V, transplanted patients and, although its pathogenesis, clinical presentation, Universitaetsklinikum Heidelberg, long-term complications (malignancies, growth disorders and nutrition) and Heidelberg, Germany histology have been extensively studied, so far no optimal therapy has been  Dr. Mario Petrini, Department of Oncology, Transplants and Advanced 
 Due to their immunomodulatory properties, MSCs are considered to Technologies, Section of Hematology, be an attractive tool for the treatment of autoimmune diseases. MSCs reduce University, Pisa, Italy lymphocyte proliferation by interventions that specifically inhibit cell division  Dr. Charles Dumontet,INSERM and, at least in vitro, alloantigen-mediated cytotoxic T lymphocytes activation. U590, Laboratoire de Cytologie Recently it has also been suggested that infused mesenchymal stem cells Analytique, Faculte de Medecine (MSCs) might be an optional strategy for the treatmetn of GVHD as they are a Rockefeller, Universite Claude component of the marrow microenvironment that, along with other cellular Bernard Lyon I, Lyon, France.  DR. Anna María Rossi, Department of elements such as macrophages, fibroblasts, adipocytes, and osteoprogenitor Biology, Section of Genetics, and endothelial cells, contribute to the support of hematopoiesis and bone University of Pisa, Pisa, Italy homeostasis. Nonetheless, there are still many issues to be clarified to optimize their therapeutic use (number of infusions, dose of administred cells, IMMEnSE POPULATION
possible synergism with other therapies, their role in the process of relapse or in the occurrence of lethal infections). Based on these facts, our main 1673 multiple myleoma cases objective is to analyze the safety and feasibility of human MSCs infusion for 2964 healthy controls the treatment of chronic GVHD and to optimize and standardize processes to AspBIOmics consortium members
obtain and produce these cells as well as to evaluate the effect of MSCs infusion on T cell populations and cytokine production in patients treated with Scientific groups agreeing to participate to this novel therapy. 5.- Genetics of solid tumors
 Prof. Dr. Hermann Einsele Medizinische Klinik und Poliklinik II, In the context of both national and international research collaborations, our University of Würzburg, Germany group is trying to assess whether genetic factors either alone or by interaction  Dr. Juergen Löeffler Medizinische with environmental factors may play a role in determining the most common Klinik und Poliklinik II, University of Würzburg, Germany kind of cancers (colorectal, breast and prostate cancer). To this end, our  Prof. Dr. Axel A. Brakhage Molecular group is recruiting cases of different cancers and healthy controls to carry out and Applied Microbiology, Leibniz both candidate gene and genome-wide association (GWA) studies to reliably Institute for Natural Product identify genes associated with cancer. Research and Infection Biology, Hans-Knöl -Institue (HKI) and Microbiology and Molecular Biology, Friedrich-Schiller-University, Jena GENOMIC ONCOLOGY
6.- Genetic basis of autoimmune diseases: rheumatoid arthritis.
AspBIOmics consortium members
Rheumatoid arthritis (RA) is an autoimmune disease characterized by chronic inflammatory activity in the synovial joints often leading to progressive cartilage  Professor Jean Paul Latgé Institute and bone destruction. RA is three times more frequent in women than men and Pasteur, Paris, France emerging data suggest that women are more likely to present a worse course of  Dr. Cornelia Lass-Flörl, Division of the disease and to become severely disabled. Although different hypotheses Hygiene and Medical Microbiology, concerning sex-related differences in RA incidence and severity have been Medical University, Innsbruck generated, the hypothesis suggesting a sexual dimorphism in the intensity of  Dr. Agostinho Carvalho. Department immune responses remains as one of the most probable mechanisms in of Experimental Medicine and promoting and establishing a different synovial membrane inflammation and, Biochemical Sciences, University of subsequently, different levels of cartilage and bone erosion. Women have higher Perugia, Perugia, Italy immunoglobulin levels than men, they show stronger Th1-type cell-mediated  Dr. Alain Troesch. Global Executive Director – R&D Molecular Biology immune responses and they have higher absolute numbers of CD4+ lymphocytes bioMérieux, Centre Christophe and a more proactive cytokine profile, which likely contribute to their increased Mérieux, Grenoble, France autoimmune responses. Experimental studies in rodents have also shown  Dr. Javier Yugueros. R&D Molecular different immune responses between female and male animals and an equivalent Biology bioMérieux, Centre sexual dimorphism in the incidence of RA. The underlying reasons for this gender Christophe Mérieux, Grenoble, bias are still unknown, but studies in monozygotic twins have suggested that genetic factors may, at least in part, account for sex-related differences in the immune responses and, consequently, in the susceptibility to autoimmune AspBIOmics consortium
diseases. Genetic factors implicated in RA have been widely studied using both candidate genes and whole-genome screens but, so far, only a few studies have  Dr. Asta Försti. Molecular Genetic investigated the link between SNPs and the gender-associated differences in Epidemiology, German Cancer susceptibility to RA. Considering these facts, our research group is focused on the Research Center, Heidelberg, identification of genetic variants (tagging and potentially functional SNPs) within immune-related genes associated with the risk to develop RA. In addition, our  Dr. Kari Hemminki. Molecular group is studying whether gender and environmental factors interact to determine Genetic Epidemiology, German the risk of the disease.
Cancer Research Center, Heidelberg,  Dr. Lourdes Vazquez. Clinic Hospital of Salamanca (Salamanca, Spain)  Dr. Carlos Solano. General Hospital  Dr. Marisa Calabuig, Catalán Institute of Oncology (ICO, Barcelona, Spain)
1762 Acute leukemia and HSCT patients GENOMIC ONCOLOGY
Paul M. Lizardi, PhD
 DNA methylation biomarkers for cancer risk in head and neck cancer and cervical cancer  Professor, Department of Pathology. Yale University  DNA methylation biomarkers for cancer risk in colon cancer  Luminescent biosensors reporting loss of silencing of Line-1 retroelements in living cells  Genome-wide analysis of DNA methylation using third-generation, single-molecule sequencing platforms MOST RELEVANT PUBLICATIONS
 Lizardi PM. Next-generation sequencing-by-hybridization. Nature RESEARCH ACTIVITY (Last
Biotechnol. (2008) 26:649-650 five years)

 Brandsma JL, Sun Y, Lizardi PM, Tuck DP, Zelterman D, Haines GK 3rd, Martel M, Harigopal M, Schofield K, Neapolitano M. Distinct human papillomavirus type 16 methylomes in cervical cells at different stages of premalignancy. Virology. 389:100-7, 2009;  Szpakowski S, Sun X, Lage JM, Dyer A, Rubinstein J, Kowalski D, Sasaki C, Costa J, Lizardi PM. Loss of epigenetic silencing in tumors preferentially affects primate-specific retroelements. Gene. 448:151-67, 2009  Lizardi, PM. As we bring demethylating drugs to the clinic, we better know the DICE being cast. Comment. Oncogene. 2010 Oct 28;29(43):5772-4  Huang X, Narayanaswamy R, Fenn K, Szpakowski S, Sasaki C, Costa J, Blancafort P, Lizardi PM. Sequence-Specific Biosensors Report Drug-Induced Changes in Epigenetic Silencing in Living Cells. DNA Cell Biol. 2012 Feb 7 GENOMIC ONCOLOGY
Probes for Detection of DNA. NIH. 2008-2011 five years)
 Global DNA methylation profiles of head and neck cancers. NIH. 2005- HPV DNA methylation patterns
of diagnostic or prognostic
Genetic Analysis of Amplified Genomic DNA Archives. NIH. 2003-2007 significance in cervical cancer

1.- Biomarkers for risk of colorectal cancer based on DNA
Application number: methylation analysis of white cells from peripheral blood in
P201030217 Priority date: 16/02/2010 individuals with heritable genetic susceptibility
Foreign applications: NO This project aims to generate biomarkers for blood-based cancer risk tests. Long Hepitype distribution
2.- Luminescent biosensors reporting changes in the epigenetic
(LHD) longue distribution

status of chromatin in living cells.
This project is designed to eventually enable automated luciferase-based Application number: 61/332,376 screens for unwanted or nonspecific effects of epigenetics-modulatory drugs Priority date: 07/05/2010 3.- Analysis of allele-specific gene expression states in
Foreign applications: PCT/US2011/035803 heterogeneous cell populations using third-generation DNA
sequencing and DNA methylation information.
Rolling circle replication
reporter systems

This projects aims to generate new bioinformatics tools for advanced epigenetic analysis, at the whole genome level, of blood, solid tissues, or Application number: engineered tissues. 7,618,776 Priority date: 17/11/2009 Foreign applications: NO More information about these projects can be provided under
confidentiality basis

José A. Lorente, M.D., Ph.D.

 Unravel the molecular mechanisms leading chemoresistance in breast cancer.  Full Professor – Faculty of Medicine. Univ. of Granada  Development of in vitro 3D models for breast cancer molecular subtypes using  Chairman of the IFSA– primary breast cancer cells. International Forensic Strategic Alliance  Biology and clinical relevance of micrometastasis in solid tumors.  Chairman of the  Epithelial-Mesenchymal transition in breast cancer, lung cancer, colon cancer and prostate cancer. Professor of International Novel Technologies for CTCs isolation, detection and phenotypical characterization. Training Division of the FBI Novel Technologies for the molecular characterization of CTCs  Advisory Criminet and RECPC  Implication of cellular dormancy in metastatic process.
 Implication of CTCs in clinical drugs development.  Role of systemic and tumor oxidative stress in chemotherapy effectiveness and Human Samples: Breast cancer
breast cancer patient's outcome. tissue. Tumor biopsies of solid tumor, peripheral blood from breast MOST RELEVANT PUBLICATIONS
cancer, colon cancer, lung cancer patients.  Vera-Ramirez L, Ramirez-Tortosa MC, Lopez-Perez P, Granados-Principal S, Battino Available cell lines: primary
M, Quiles JL. Long-term effects of systemic cancer treatment on DNA oxidative breast cancer cell lines for cancer damage: the potential for targeted therapies. Cancer Lett 2012. In press. drug screening. Tumor Cells line isolated of the  Vera-Ramirez L, Sanchez-Rovira P, Ramirez-Tortosa MC, Ramirez-Tortosa CL, peripheral blood from small cell Granados-Principal S, Lorente JL, Quiles JL. Oxidative stress status in metastatic breast cancer patients receiving palliative chemotherapy and its impact on survival rates. Free Radical Res. 2012;46 (1):2-10  Vera-Ramirez L, RESUME OF GROUP ACTIVITY
chemotherapy-induced oxidative stress improve the survival rates of breast cancer (Last 5 years)
 Vera-Ramirez L, Sanchez-Rovira P, Ramirez-Tortosa CL, Quiles JL, Ramirez-Tortosa MC, Alvarez JC, Fernandez-Navarro M, Lorente JA. Gene-expression profiles, tumor microenvironment, and cancer stem cells in breast cancer: Latest advances towards an integrated approach. Cancer Treat Rev. 2010; 36(6):477-84.  R Rosel , MA Molina, MJ Serrano. EGFR mutations in circulating cell-free DNA. Lancet Oncology. 2012 (in Press). GENOMIC ONCOLOGY
 R Nadal, A Fernandez, P Sanchez-Rovira, M Salido, M Rodríguez, JL García-Puche, M Macià, JM Corominas, Ml Delgado-Rodriguez, L Gonzalez, J Albanell, M Fernández, F Solé, JA Lorente, MJ Serrano. Biomarkers Characterization of Circulating Tumour Cells in Breast Cancer Patients. Breast Cancer Research 2012, 14:R71. PATENT APPLICATIONS
 R. Nadal, A. Fernández M.Salido, J.A. Lorente, M. Rodríguez-Rivera, M. Delgado- (last 5 years)
Rodríguez, M. Macià, FG Ortega J.M. Corominas,JL García Puche, P. Sánchez-Rovira, F. Solé, María José Serrano. CD133 expression in circulating tumor cells from breast cancer patients: Potential role in breast cancer subtypes and resistance to isolation of circulating
chemotherapy.Int J Cancer. 2012 (in press). tumor cells
Application number: P201130821  Project: "Gene expression profile in response to chemotherapy and its relationship Priority date: 20/05/2011 with oxidative stress in breast cancer". Health Regional Ministry of Economy,
Foreign applications: No Innovation and Science of Andalusia, Spain. 2010-2013.
 Project: "Cell and microenvironment interactions: functional assays to develop novel biological therapies against chemoresistant breast tumors". Health Research
Fund. Ministry of Health, Spain. 2012-2015.

 Isolation and Genetic Characterization of Circulating Tumor Cells in patients with advanced colorectal cancer. Roche Pharma. 2011-2013  Isolation and Genomic analysis of Circulating tumor cells in non-small lung cancer patients. Pangaea Biotech. Period: 2012-
 Erlotinib program in NSCL cancer progression after a double platinum (and future maintenance monodrug): sequential determination CTCS and its correlation with
response to treatment and Overall Survival. Roche Pharma. 2012-2013
 AGTR1 as new predictive factor in ovarian cancer patients (2012-2013) PROJECT PROPOSAL
1.- Breast cancer chemoresistance is driven by tumor-microenvironment

Today, it is well known that the interactions between the stromal and epithelial compartments are key determinants of oncogenesis and disease progression. This conclusion has profound implications for cancer treatment and prognosis, since tumor microenvironment cells and associated molecules are now considered as potential therapeutic targets. In accordance with these novel concepts, our group has identified a subset of genes which is significantly and overexpressed after chemotherapy in breast showing different histopathological responses to chemotherapy. Interestingly these genes are functional y related with extracellular matrix remodeling, angiogenesis and developmental processes. Further functional validation using in vitro and in vivo models will confirm their therapeutic potential against chemoresistant and bad prognosis breast cancer. GENOMIC ONCOLOGY
2.- Generation of primary breast cancer cell lines to construct a 3D in vitro model.
Tumor-microenvironment interactions cannot be studied in a conventional 2D in vitro system, given that such interactions are dependent on spatial orientation of cells and extracellular materials, cell morphology, etc. 3D co-cultures of primary breast cancer cells and stromal fibroblasts offer a more realistic in vitro model. We are currently developing a 3D sub-model for each defined breast cancer molecular subtypes, from patients who registered good and bad histological responses to chemotherapy. The objective is to obtain an useful tool to perform functional validation assays of previous genomic data regarding chemoresistance. 3.- Impact of oxidative stress on breast cancer treatment. A variable significantly affecting patient's survival

Antineoplastic agents induce oxidative stress, leading to lipid, carbohydrate, protein and DNA damage and affecting cel structure and function. These adverse effects may fuel up the acquisition of new mutations and the development of treatment resistances and secondary malignancies. Despite the evident potential role of free radicals in cancer treatment failure and progression, studies exploring these interactions are extremely scarce. To gain further insights in this uncovered research topic, we analyzed the level of systemic oxidative damage and antioxidant markers in breast cancer patients receiving chemotherapy. We have shown that those patients showing increased plasma antioxidant total capacity and increased systemic DNA repair activity after chemotherapy also registered better survival rates. 4.- Genetic characterization of circulating tumor cells (CTCs) and the primary tumor in breast cancer patients
and colon cancer: identification of new prognostic markers.

The identification of new prognostic factors that allow us to discriminate and stratify patients for individualized treatment is one of the most important avenues of research in this field. Among these new markers, the presence of circulating tumor cells (CTCs) is considered indicative of hematogenous spread factor with considerable potential prognostic significance in metastasis formation. Recent studies show that these cells may have stem cell characteristics, which seem to play a crucial role in the initiation and progression of cancer as well as the ability to be resistant to chemotherapy treatments. The aim of this study is to determine the prognostic value of the presence of these cells in peripheral blood of breast cancer patients and colon cancer patients, genetic and phenotypic characterization, in addition to the primary tumor arising. 5. Molecular mechanisms of cell dormancy in breast cancer.
Clinical cancer dormancy is defined as an unusually long time between removal of the primary tumor and subsequent relapse in a patient who has been clinically disease-free Due to its small size and non-invasive nature, these dormant tumors are asymptomatic and, in many cases without being detected Elucidate the mechanisms regulating these processes will be instrumental in identifying new biomarkers of early cancer and may serve as a basis for the development of therapies based on tumor biology of this process. GENOMIC ONCOLOGY
6. Markers of response to treatment in lung cancer
The standard treatment of non-small cell lung cancer has undergone a dramatic change with the introduction of genetic data of expression of molecules involved in carcinogenesis. So now, cancer patients with advanced non-small cell lung, that overexpress EGFR mutation of T790, should be treated with inhibitors as TIK Genfitinib or Erlotinib, rather than the standard QT schemes. This has opened a new avenue for treating this serious disease and poor survival prognosis, advanced stages. However, despite the benefits of the treatments described there are a certain percentage of patients still present these mutations not respond to treatment with inhibitors of tyrosine kinase 7. Molecular characterization of CTCs in small cell lung cancer:
Small cell lung cancer (SCLC) makes up about 15 percent of all lung cancers Chemotherapy is of clear benefit in patients with small cell lung cancer. Without chemotherapy, the average survival is measured in weeks. Despite these favorable results, small cell lung cancer tends to recur or relapse within one to two years in the majority of patients, particularly those with extensive stage disease. We know that the CTCs may be useful biomarkers in the diagnosis and therapy lung cancer patients. The Molecular characterization of these CTCs in small cell lung cancer is necessary to understand the resistance mechanisms and dissemination that involved. The use and growth of Lung Cancer Cell Lines could be good tools to study these process trough molecular analyses. GENOMIC ONCOLOGY
Miguel Martin Hernandez, PhD
 Metabolic reprogramming in cancer. Rational targeting of cancer metabolism as a therapeutic strategy
Human Samples: solid tumors,
 Impact of aging, chronic or therapeutically-induced oxidative stress, and leukemia, MDS, PMF, hMSCs, genetic alterations on the hematopoietic niche and its role in MDS and hESCs and hIPSC.
Available cell lines: cancer cell
 Role of the mitochondria in normal hematopoiesis and leukemia. lines carrying extreme metabolic phenotypes, hMSCs, hESCs, hiPSC. MOST RELEVANT PUBLICATIONS

Animal models:
 Roldan, M., Menendez, P., Soria, B., Martin, M. Mitochondrial DNA
Oncogenic and antitumoral potential depletion in human embryonic stem cells resembles an extreme screenings by xenotransplants of metabolic phenotype of cancer cells. Submitted
human cells in NOD/SCI mouse models  Ramos-Mejia, V., Bueno, C., Roldan, M., Sanchez, L. Ligero, G., Mendenz, P., Martin, M. The adaptation of human embryonic stem cells to
different culture environments is accompanied by a mitochondrial
response. Stem Cells and Development 2012; 21: 1145-1155 (IF:
4.98, Q1)
 Sanchez, L.1, Gutierrez-Aranda, I.1, Ligero, G.1, Martin, M., Lucena-
Aguilar, G., Ayllon, V., Real, P.J., Ramos-Mejia, V., Bueno, C., Menendez, P. Maintenance of hESCs in media conditioned by human mesenchymal RESEARCH ACTIVITY (last five
stem cells obviates the requirement of exogenous bFGF supplementation. Tissue Eng. Part C 2012; 18: 387-396 (IF: 4.6, Q1)
Martin, M., Menendez, P. Biological impact of human embryonic stem
cells. Adv. Exp. Med. Biol. 2012; 741: 217-230 (IF: 1.38)
 Roldan, M., Macias, M., Garcia, R., Tinahones, F.J., Martin, M. Obesity
shortcircuits stemness gene network in human adipose multipotent stem cells. FASEB J. 2011; 25: 4111-4126 (IF: 6.5, Q1)
Martin, M., Cho, J., Cesare, A.J., Griffith, J.D., Attardi, G. Termination
factor-mediated DNA loop between termination and initiation sites drives
mitochondrial rRNA synthesis. Cell 2005; 123: 1227-1240 (IF: 32.4, Q1)
 Mitochondrial genetics and function in human stem cell biology: PATENT APPLICATIONS (the
development of novel protocols for cell differentiation with greater last five years)
potential for future therapies Andalusian Ministry of Health. Period:
Mesenteric stroma-derived
human multipotent stem cells
Alterations in stem and progenitor cell populations in patients with Application number: metabolic disorders. Andalusian Ministry of Health. Period: 2008-2010
P200991700000782 Priority date: 03/04/2009 Mitochondrial role in cell proliferation and differentiation during Foreign applications: NO embryogenesis by human embryonic stem cell models. Spanish
Ministry of Science. Period: 2007-2008.
1.- Metabolic Reprogramming as Cancer Targeting Therapies
Our research aims at understanding how nutrient metabolism contributes to  Cancer cell models with cancer development. Towards this goal, we are employing a extreme metabolic phenotypes multidisciplinary approach that includes metabolomics, biochemistry, for high throughput drug nanotechnology and mouse models, to elucidate molecular mechanisms that distinguish the metabolism of tumors from that of normal tissues. Our work is strongly oriented to define principles for rational targeting of cancer  In vitro and in vivo models for metabolism as a therapeutic strategy. In particular, we have already an testing and validation of novel optimized cellular platform for deep drug screening approaches to identify antitumoral compounds compounds which selectively kill cancer cell by blocking their metabolic  Metabolomic approaches in features. Four compounds have been already discovered with selective cell culture and tumor biopsies antitumor activity, and we are now studying their mechanism of action.  Metabolic nanosensors for 2.- Targeting the Hematopoietic Stem Cell Niche in MDS and PMF
clinical-bioimaging, sorting, Recent evidences strikingly support that alterations on the hematopoietic and tumor analysis niche are involved in the development of myelodisplastic syndrome (MDS) and primary myelofibrosis (PMF). The combination of risk factors such as aging, chronic or therapeutically-induced oxidative stress, and genetic alterations disturbing microenvironment homeostasis may induce a profound deregulation of the niche of utmost importance for disease development. We aim to decipher how aging, oxidative stress caused by factors such as iron overload, and metabolic alterations induced by genetic deregulation impact on the hematopoietic stem cell niche in MDS and PMF patients. To do this, we are currently recruiting and processing bone marrow (BM) biopsies from patients with MDS and PMF, in collaboration with our clinical partner Dr. Regina Garcia Delgado, from the Onco-hematology Service, University Hospital V. de la Victoria, Malaga. GENOMIC ONCOLOGY
Pedro Medi na, PhD
 MicroARNs and cancer.
 Member of the RNAREG
 SWI/SNF chromatin remodeling complex and their implication in cancer. consortium (Consolider Ingenio del Ministerio de Ciencia e Chromatin remodeling and Epigenetics.  Mouse models of cancer.  Member of the Royal Academy of Medicine of Galicia. 2012. MOST RELEVANT PUBLICATIONS
 Member of the Royal Academy of Medicine of Catalonia. 2012.  Medina PP, Nolde M and Slack FJ. OncomiR addiction in an in vivo
model of microRNA-induced pre-B cel lymphoma. Nature. 2010 8th Aug. Member of the Royal Academy of Medicine of Valencia. 2012.  Associate member of the The  Medina PP (*), Trang P (*) , Wiggins JF, Ruffino L, Kelnar K, Omotola M,
New York Academy of Sciences, Homer R, Brown D, Bader AG, Weidhaas JB and Slack FJ Regression of ID: 11044979, 2008. murine lung tumors by the let-7 microRNA. Oncogene 2009 Dec 7. (*)  Associate member of the USA Joint First author, PMID: 19966857 National Postdoctoral Association, ID: 202080915,  Medina PP, Castil o SD, Blanco S, Sanz-Garcia M, Largo C, Alvarez S,
Yokota J, Clevers HC, Cigudosa JC, Lazo PA, Sanchez-Cespedes M. The SRY-HMG box gene, SOX4, is a target of gene amplification at chromosome 6p in lung cancer. Human Molecular Genetics 2009 Apr 1;18(7):1343-52. PMID: 19153074.  Medina PP, Slack FJ. Blocking miRNAs in vivo. Nature Methods.
December. 2008. PMID: 19116612.  Medina PP, Slack FJ. miRNAs and Cancer, an overview. Cell Cycle. pedromedina 2008 Aug. PMID: 18719380.  Medina PP, Sanchez-Cespedes M. (2008) Involvement of the chromatin-
remodel ing factor BRG1/SMARCA4 in human cancer. Epigenetics 2008, April 2008. PMID: 18437052.  Medina PP, Romero O, Kohno T, Montuenga LM, Pio R, Yokota J. and
Sanchez-Cespedes M. (2007) Frequent Brg1/Smarca4-Inactivating Mutations In Human Lung Cancer. Human Mutation 2008 Apr 3;29(5):617-622. PMID: 18386774. GENOMIC ONCOLOGY
 Involvement of microRNAs in Lung Cancer. Entity: Hope Funds for BIOLOGICAL MATERIAL ACCESS

Cancer Research. HFCR­08­02­01. Length: 2008-2011. PI: Pedro, Human Samples: lung
Medina & Frank Slack. Yale University, New Haven, CT, USA.  Treating lymphoma by targeting microRNAs. Entity: Pardee Foundation. Available cell lines: lung cancer
Length: 2011-2012. PI: Frank Slack. Yale University, New Haven, CT, Animal models:
 SWI/SNF microRNAs and cancer (ref 334-11-223). ENTITY: Karolinska Transgenic, gene targeted mouse, Institute 750,000 Swedish Krhone (SEK). Length 2011-2016. PI: Pedro Immunodeficient mouse (SCID, nudes). Medina. (Gratefully declined).  SMARCA4 inactivation in the tumor Development (CEI B20F12/6). Campus of International Excel ence of BioHealth; Information Communications Technology (CEI-BioTic). PI: Pedro Medina •  International Leukemia Foundation Josep Carreras (FIJC 2011 F 11/01). PI: Pedro Medina.  Gene Expression Regulation and Cancer. Marie Curie Integration Grant: FP7-PEOPLE-2012 Proposal 321926. 7th Framework Programme for
Research. EUROPEAN COMMISSION. Between the top awardees
from Europe with 95.7/100 points..
 Programa Nacional de Proyectos de Investigación Fundamental no Orientada (SWI/SNF, microARNs and cancer) SAF2012-37252 (in RESEARCH LINE
1.- GENE EXPRESSION REGULATION increases the functional
versatility and adaptability of the cell by allowing it to express certain
proteins when needed. It is, therefore, one of the most important and complex processes of biology. Changes in the gene expression patterns are key in cancer cell transformation, through an increase in expression of genes that promote carcinogenesis (oncogenes) and/or a decrease in expression of genes that prevent it (tumour suppressor genes). MicroRNAs (miRNAs) and chromatin-structure both play important roles in this process and have been found to be critical in the development of human pathologies. Both of these regulatory elements, especially in the context of CANCER, have been the focus of my interest during my career. GENOMIC ONCOLOGY
The SWI/SNF complex is an ATP-dependent chromatin-remodelling complex that is known to regulate EPIGENETICALLY
the gene expression (Kwon, Imbalzano et al. 1994). Increasing evidence demonstrates that some components of the SWI/SNF complex ar e tumour suppressors and are involved in human cancer development. One subunit of this complex, SNF5, is inactivated in malignant rhabdoid tumours (MRTs) and heterozygous Snf5 knockout mice develop tumours that are histological ly similar to human MRTs (Roberts, Galusha et al. 2000; Roberts, Leroux et al. 2002). BRG1 (Medina and Sanchez-Cespedes 2008), the helicase/ATPase catalytic subunits of the SWI/SNF complex, is mutated in many different cancer cel lines (Wong, Shanahan et al. 2000; Medina, Romero et al. 2008). Additional y, germline BRG1 mutations linked to a Rhabdoid Tumour Predisposition Syndrome was reported in a family, strongly suggesting that is a bona fide tumour suppressor gene (Schneppenheim, Fruhwald et al.). Recently, it has been discovered that two other subunits of the chromatin-remodelling complex, BAF250 (ARID1A) and BAF180 (PBRM1) (Jones, Wang et al. ; Wiegand, Shah et al. ; Varela, Tarpey et al. 2011; Wilson and Roberts 2011), are frequently mutated in ovarian clear cell carcinoma and renal carcinoma, respectively. All these observations support an important role of the SWI/SNF complex in cancer, however its specific function is still unclear. 2.- MiRNAs are a recently discovered class of small RNA molecules that regulate gene expression at the post-transcriptional
level. Due to their small size and unusual nature, miRNAs were not discovered in humans until 2000. Today, over one
thousand miRNAs have been identified in the human genome. Aberrant biogenesis and/or expression of miRNAs have been
linked to human diseases including cancer (Medina and Slack 2008). During my training as a postdoc in this field I have
helped to reveal the critical role played by specific miRNAs in cancer. While most previous studies in the field used cell lines or
in vitro systems, we pioneered the functional study of the role of miRNAs using in vivo transgenic mouse models. We
demonstrated the therapeutic utility of let-7 microARN ectopic expression in vivo (Medina, Trang et al. 2010), and the
important of a single microARNs (miR-21) to the drive of tumor development (Medina, Nolde et al. 2010). In my recently
created group at the GenyO Center we will continue unveiling the role of the microRNAs in cancer with the hope to find novel
and useful cancer therapies.
Pablo Menéndez Buján, PhD, MBA
 Development of human-based models for acute leukemias using neonatal TEAM LEADER
or embryonic hematopoietic stem cells as well as patient-specific iPSCs.  Development of human sarcoma models based on the use of human  Member of The Spanish Stem mesenchymal stem cel s.
Cell Bank Steering Committee Generation of hematopoietic, mesenchymal and endothelial cells from hESCs and hIPSCs  Vocal of the Spanish  Role of the mitochondria in normal hematopoiesis and leukemia. Association of Gene and Cell  Coenzyme Q deficiency: understanding the genotype-phenotype association and metabolic dysfunction using patient-specific iPSC.
R. Rubio, I. Gutierrez, A. Saez, A. Labarga, P. Menendez*, R. Rodriguez.
"The differentiation stage of p53 and Rb-deficient Mesenchymal Stem lymphoma, umbilical cord, MSCs, Cells imposes the phenotype of in vivo sarcoma development". hESCs and hIPSC. Oncogene 2012 (in press). I.F: 7.8

Available cell lines: hESCs,
 MC. Chil ón, M. Gómez-Casares, C. López-Jorge, C. Rodriguez-Medina, A. hiPSC and proprietary transformed Molines, ME. Sarasquete, M. Alcoceba, C. Bueno, R. Montes, F. Ramos, MSC lines for cancer drug JN. Rodríguez, P. Giraldo, M. Ramírez, R. García-Delgado, JL. Fuster, M. González-Díaz and P. Menéndez*. Prognostic significance of FLT3
mutational status and expression levels in MLL-AF4 and MLL-germline Animal models:
Acute Lymphoblastic Leukemia. Leukemia (in press). I.F: 9.5
Sarcoma, leukemia and reconstitution hematopoietic  R. Rodriguez, R. Rubio, I. Gutierrez-Aranda, G. Melen, J. García-Castro & P. Menéndez*. "Expression of the FUS-CHOP fusion protein coupled to
p53 deficiency induces liposarcoma in fat-derived murine but not human
Mesenchymal Stem Cells" Stem Cells 2011; 29: 179-192. I.F: 7.8
 L. Sánchez, I. Gutierrez-Aranda, G. Ligero, R. Rubio, V. Ramos-Mejía, P. RESEACH ACTIVITY (Last five
Real, C. Bueno, M. Delgado, R. Rodríguez & P Menéndez*. "Enrichment
of hESC-derived multipotent mesenchymal stem cells with immunosuppressive and anti-inflammatory properties capable to protect
against experimental inflammatory bowel disease" Stem Cells
2011;29:251-262.I.F: 7.8.  R. Montes, V. Ayl ón, I. Gutiérrez, I. Prat, M.C. Hernández-Lamas, L. Ponce, G. te Kronnie, M. Greaves, C. Bueno*, P. Menéndez*. "Enforced
expression of MLL-AF4 fusion in cord blood CD34+ cells enhances the hematopoietic repopulating cell function and progenitor potential but is not sufficient for leukomogenesis". Blood 2011;117:4746-4758. I.F:
P. Menendez*, P. Catalina, R. Rodriguez, G. Melen, C. Bueno, M. Arriero, F.
García-Sánchez, A. Lassaleta, R. García-Sanz, J. García-Castro*. "Bone Marrow
Mesenchymal Stem Cel s from infant MLL-AF4+ leukemia harbour and express
the MLL-AF4 fusion gene". J. Exp. Med. 2009; 206: 3131-3141. I.F: 14.776
five years)
Coenzyme Q10 deficiency syndrome: understanding the genotype- phenotype association and metabolic dysfunction through generation of induced pluripotent stem cells (iPSC) from patient-specific uncorrected transformed Mesenchymal
and genetically-corrected cells. ERA-NET E-Rare-2 Call 2012 / EU
Stem Cells and animal model
for drug screening.
 Genomic analysis of mesenchymal stem cells to develop high Application number: throughput diagnostics for measuring the medicinal ingredient and tumourigenic contaminants in stem cell-based health products. Health
Priority date: 28/06/2012 Canada. Period: 2012-2014
Foreign applications: Pending  Infant MLL-AF4+ Acute Lymphoblastic Leukemia: towards the Procedure for the
elucidation of the cellular and molecular mechanisms underlying MLL- procurement of Mesenchymal
AF4 transformation in human stem cells. Spanish Association
Stem Cells for biomedical use.
Against Cancer. Period: 2012-2014.

Application number: P201030645 PROJECT PROPOSAL
Priority date: 30/04/2010 Foreign applications: 1.- Stem cell-based disease models for pro-B Acute Lymphoblastic
PCT/ES2011/070303 Leukemia with MLL-AF4 rearrangement
Mesenchymal Stem Cell-
Infant pro-B acute ALL harbouring the fusion oncogene MLL-AF4 is conditioned media for the
associated with very brief latency and dismal prognosis. Studies on identical differentiation of human
twins and retrospective screening of MLL-AF4 in neonatal blood spots have pluripotent Stem Cells.
revealed an in utero origin of MLL-AF4. However, Guthie cards do not allow an accurate quantification of the number and the phenotype of the MLL- Application number: AF4+ cells. This is important to understand MLL-AF4 B-lineage-specific affiliation and the relationship between MLL-AF4 frequency and MLL-AF4- Priority date: 08/04/2010 expressing cell phenotype with disease latency. Foreign applications: PCT/ES2011/070236 The absence of bona fide disease models reflects our poor understanding of the etiology, pathogenesis and cell-of-origin of this leukemia. Because of the mixed phenotype, hematopoietic stem/progenitor cells are likely targets for transformed Mesenchymal
transformation. To date, there is no a MLL-AF4 human-based disease Stem Cells for drug screening
model which faithfully reproduces the disease phenotype and latency. and toxicology
Human pluripotent stem cells (hESCs and hiPSCs) constitute a powerful tool for modelling different aspects of human disease that cannot otherwise Application number: be addressed by patient sample analyses. Differentiation of hESC/iPSC is a promising human-specific strategy to study the onset/emergence of Priority date: 16/02/2010 hematopoiesis. iPSC technology should allow modeling pre-symptomatic Foreign applications: NO abnormalities in patient-derived cells yielding valuable insights into disease mechanisms. Noticeably, MLL-AF4+ ALL manifests in utero, has a cel - GENOMIC ONCOLOGY
a) Recreate the MLL-AF4 rearrangement in hESCs using Zinc Finger
Nucleases-driven targeted genetic editing. MLL-AF4-carrying hESCs last five years)
will be explored to study the developmental impact of MLL-AF4 in Multipotent Stem Cell isolated
b) Generate iPSCs from MLL-AF4 blasts and CB units from newborns
from a human, genetically-
who developed pro-B ALL to study the developmental impact and modified and procedure
transformation capacity of MLL-AF4. c) Quantify and determine the phenotype of the MLL-AF4+ cells in
cryopreserved CB units from newborns who developed pro-B ALL. Application number: 2.-Clinical relevance of FLT3 activating mutations and FLT3
Priority date: 07/07/2009 transcriptional over-expression in infant Pro-B Acute
Foreign applications: NO Lymphoblastic Leukemia harbouring MLL-AF4 rearrangement
Use of Mesenchymal Stem
Infant acute lymphoblastic leukemia (ALL) is characterized by a pro-B Cells in the preparation of a
phenotype (CD10-), a very short latency (<12 months) and a dismal cellular composition for cell
prognosis (5-year event-free survival <20%). The t(4;11) encoding the MLL- therapies.
AF4 fusion oncogene is the genetic hallmark of this infant pro-B ALL. Different mouse and human models have revealed that MLL-AF4 itself is not Application number: sufficient for transformation suggesting the need of secondary cooperating oncogenic events. Gene expression studies based on clinical samples have Priority date: 02/04/2009 identified the tyrosin kinase receptor FLT3 to be over-expressed in MLL- Foreign applications: NO rearranged ALL, indicating that FLT3 gene may contribute to the Stem cell-specific promoter
pathogenesis of this dismal ALL. However, there is clinical controversy between international groups on whether this FLT3 over-expression is due Application number: to (i) activating mutations in the FLT3 kinase domain (i.e. ITD, D835Y and I836del) or (ii) simply due to the transcriptional activation of FLT3 in the Priority date: 04/04/2008 absence of such mutations. Foreign applications: PCT/ES2009/070091 The FLT3 mutational status have been widely studied in acute myeloid leukemia but it has not been yet addressed in cohorts of either pro-B ALL Procedure for the isolation of
MLL-AF4+ or other B-ALL subgroups such as TEL-AML1+, BCR-ABL+, E2A- the inner cell mass from
PBX1+ and hyperdiploid ALLs. mammalian blastocyst
In consequence, the clinical relevance of FLT3 expression and FLT3 Application number: activating mutations in the prognosis and evolution of these patients remains unknown. Here, we propose to enrol B-ALL pediatric patients Priority date: 01/06/2007 (MLL-AF4+; TEL-AML1+; BCR-ABL+; E2A-PBX1+ and hyperdiploid) for Foreign applications: analysis of the mutational status and expression level of FLT3 that will be PCT/ES2008/000377 correlated (Kaplan-Meyer curves and multivariate analysis) with critical clinical parameters including overall survival, disease-free survival, relapse rates and other mortality and morbidity-associated parameters. GENOMIC ONCOLOGY
Importantly, the information obtained from these clinical samples will be used to generate an experimental in vivo xenograft model in an attempt to recapitulate the latency and phenotype of the MLL-AF4+ pro-B ALL by lentiviral over-expression of both MLL-AF4 and wt FLT3 or mutated FLT3 (ITD, D835Y, I836del). This translational/clinical project will elucidate the role of FLT3 activating mutations in the pathogenesis, prognosis and evolution of pro-B ALL MLL-AF4+, eventually contributing to stratify patients based on FLT3 expression levels and mutational status. 3.- Mesenchymal Stem Cells as a target cell for understanding sarcomagenesis development.
Because of their unique properties, multipotent mesenchymal stromal cells (MSCs) represent one of the most promising adult stem cells being used worldwide in a wide array of clinical applications. Overall, compelling evidence supports the long-term safety of ex vivo expanded human MSCs which do not seem to transform spontaneously. However, experimental data reveal a link between MSCs and cancer and MSCs have been reported to inhibit or promote tumor growth depending on yet undefined conditions. Interestingly, solid evidence based on transgenic mice and genetic intervention of MSCs has placed these cells as the most likely cell of origin for certain sarcomas. This research area is being increasingly explored to develop accurate MSC-based models of sarcomagenesis which will be undoubtedly valuable in providing a better understanding about the etiology and pathogenesis of mesenchymal cancer, eventually leading to the development of more specific therapies directed against the sarcoma-initiating cell. Unfortunately, little is still known about the mechanisms underlying MSC transformation and further studies are required to develop bona fide sarcoma models based on human MSCs. Our lab has developed over the last 3 years MSC-based models for fibrosarcoma, leiomyosarcoma, osteosarcoma and liposarcoma. We have gained insights into the target cell for transformation and the oncogenic hits necessary for such transformation processes. These findings are important for the development of effective therapeutic approaches for sarcoma that can eliminate sarcoma tumors and their tumor-initiating cells. 4.- Coenzyme Q10 deficiency syndrome: understanding the genotype-phenotype association and metabolic
dysfunction through the generation of induced pluripotent stem cells (iPSCs) from patient-specific
uncorrected and genetically-corrected cells.

Coenzyme Q10 (CoQ10) is an electron carrier key in maintaining the homeostasis of the mitochondrial respiratory chain. Primary deficiency of CoQ10 is an autosomal recessive syndrome which originates from mutations in genes responsible for CoQ biosynthesis. CoQ10 deficiency leads to a disorder which manifests with encephalomyopathies, because the disruption of the energy metabolism affects tissues with high-energy demand such as cerebellum and skeletal muscle. Many COQ genes have been implicated in the primary CoQ10 deficiency, making the molecular diagnosis and clinical heterogeneity a chal enge. To date, there is not a clear genotype-phenotype association, and the only current treatment is CoQ10 supplementation which effectiveness remains poor. The generation of patient-specific induced pluripotent stem cells (iPSC) has emerged as a unique system to model human disease. We aim to generate and differentiate iPSC from CoQ-deficient patients, before and after correction of the genetic defect, to elucidate the pathogenesis and developmental mechanisms of primary CoQ10 deficiency. Our goals are:(i) study the lack of genotype-phenotype association by differentiating COQ-iPSC towards disease-affected tissues (motor neurons and skeletal muscle), and (ii) characterize the metabolic dysfunction of iPSC and the differentiated progeny to assess whether exogenous CoQ10 rescues metabolic homeostasis and influences differentiation of COQ-iPSC. We envision these studies will provide novel insights into the genotype-phenotype association and metabolic dysfunction in CoQ deficiency patients. GENOMIC ONCOLOGY
Carlos Rodríguez-Ma
nzaneque, PhD

 Characterization of the mechanism of action of extracellular
Principal Investigator of the Proteases and Extracellular metaloproteases by the identification and functional study of its
Matrix Group at GENyO biological substrates.
Member of The American Determination of tumor and stem cell plasticity by the modification of the Society for Matrix Biology extracellular microenvironment. Relevance for neo-vascularization

 Studies of functional genomics for the mechanisms of acquisition of
endothelial phenotypes by tumor cells.
Human Samples: Melanoma,
sarcoma, glioma, breast carcinoma. Available cell lines: From human
Tumor angiogenesis and vascular patterning: a and mouse tumours, mainly from mathematical model. PLoS One. 2011;6(5):e19989. melanoma, sarcoma, breast carcinoma and glioma. Primary cultures of pericytes and endothelial cells. Animal models:
Tumour angiogenesis is reduced in the Tc1 mouse model of Down's syndrome. Nature. 2010 Jun Xenografts at different locations, 10;465(7299):813-7 adamts1 knockout mouse colony. ADAMTS1 contributes to the acquisition of an endothelial-like phenotype in plastic tumor cells. Cancer Res. 2010 Jun 1;70(11):4676-86. RESEARCH ACTIVITY (last 5

syndecan-4 by ADAMTS1 provokes defects in adhesion. Int J Biochem Cell Biol. 2009 Apr;41(4):800-10. ADAMTS1 interacts with, cleaves, and modifies the extracellular location of the matrix inhibitor tissue factor pathway inhibitor-2. J Biol Chem. 2006 Jun 30;281(26):17827-37. GENOMIC ONCOLOGY
Identification of substrates of the extracellular protease ADAMTS1 by DIGE proteomic analysis. Proteomics. 2006 TECHNOLOGICAL TRANSFER
Apr;6 Suppl 1:S28-35. CAPACITIES

 Advanced techniques of 2D and Thrombospondin-1 suppresses spontaneous tumor growth and inhibits activation of matrix metalloproteinase-9 and mobilization of vascular endothelial growth factor. Proc Natl Acad Sci U  In vitro Modeling of S A. 2001 Oct 23;98(22):12485-90. MOST RELEVANT RESEARCH PROJECTS GRANTS
Animal models to study tumor progression and vasculature  Role of the extracellular protease ADAMTS1 for tumour plasticity and neo-vascularization phenomena. MICINN-Spain. Period: 2011-2013
 Experimental and theoretical study of the role of the extracellular microenvironment during mechanisms of neo-vascularization and
angiogenesis. CEIC-Andalucía, Spain. Period: 2011-2014.
1.- Characterization of the mechanism of action of ADAMTSs
metaloproteases by the identification and functional study of its
biological substrates.

Proteolysis in the tumor microenvironment occurs by the action of members of several families of proteases, including matrix metaloproteinases (MMPs), transmembrane ADAMs (a disintegrin and metalloprotease) and secreted ADAMTSs (a disintegrin and metalloprotease with thrombospondin motifs). The involvement of ADAMTS proteases during tumor progression has already been highlighted although its actions include apparently paradoxical actions such as the inhibition of angiogenesis, protection against tumor growth, and the induction of metastasis. These studies reveal the high complexity of the mechanism of action of extracellular proteases, and show the necessity to identify the specific substrates that are target of its activity in every tumor microenvironment. The first member of the family, ADAMTS1, represents a clear example of the mentioned complexity. While its anti-angiogenic properties have been confirmed, it has also been reported to have a relevant role for the aggressiveness and metastatic capacity of certain tumors. This research team keeps contributing in the description of some of these properties and, in parallel, they are involved in the identification of ADAMTS1 substrates. GENOMIC ONCOLOGY
2.- Determination of tumor and stem cell plasticity by the modification of the extracellular
During the last years the identification of cancer stem cells (CSCs) has been relevant for the understanding of trans-differentiation processes of tumor cells and to interpret their invasive and/or proliferative capacity. As a paradigm of tumor plasticity it has been described the phenomenon of vasculogenic mimicry (VM), defined by the ability of tumor cells t o form pseudo-vascular networks, enriched in extracellular matrix, and directly related with the acquisition of a gene signature similar to endothelial cells. This phenomenon was first characterized in highly malignant melanoma tumors, and more recently it also been found in cases of breast, ovarian, lung, and sarcoma tumors. The role of extracellular proteases in this kind of phenomena has been already suggested although the reported data is limited.In this context, there are major findings that reveal the role of physicochemical properties of the matrix for the specialization of stem cells. Mainly it has been characterized the relevance of changes in parameters such as the elasticity of extracellular matrix, and currently it is being studied the way that proteolisis of matrix components modulates these properties. It is r equired the comparison of differentiation processes to form endothelium from non-transformed stem cel s and from plastic tumor cells that carry aberrant signaling pathways. In addition it is needed a detailed analysis of the most intrinsic characteristics of the vascular niche. 3.- Studies of functional genomics for the mechanisms of acquisition of endothelial phenotypes by tumor
I n addition to the close relationship among extracellular proteases and its specific substrates, the characterization of tumor plasticity events in tumor cell lines and in human tumor specimens requires a detailed knowledge of the related gene expression profiles. The evaluation of these gene signatures, together with clinical parameters such as prognosis, drug resistance and metastasis appearance, will allow the identification of new molecules of interest to be evaluated from a functional perspective.


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