TURKU CENTRE FOR BIOTECHNOLOGY – REPORT 2012
Transcription
TURKU CENTRE FOR BIOTECHNOLOGY – REPORT 2012
TURKU CENTRE FOR BIOTECHNOLOGY REPORT 2012 CONTENTS Organization.................................................................................2 Chairman’s Foreword ...................................................................3 From the Director .........................................................................4 Year 2012 in a Nutshell.................................................................5 Funding and Statistics .................................................................9 Publications 2012.......................................................................12 Personnel 2012..........................................................................19 Annual Report 2012 Turku Centre for Biotechnology Published by: Turku Centre for Biotechnology P.O. Box 123, FI-20521 Turku, Finland Tel. int. +358-2-333 8603, Fax int. +358-2-251 8808 http://www.btk.fi Editorial Board Riitta Lahesmaa (Chair) Daniel Abankwa Tero Aittokallio Eleanor Coffey Garry Corthals Michael Courtney Konstantin Denessiouk Laura Elo John Eriksson Attila Gyenesei David Hawkins Jyrki Heino Johanna Ivaska Panu Jaakkola Patrik R. Jones Marko Kallio Linnéa Linko Harri Lähdesmäki Matti Nykter Tassos Papageorgiou Cecilia Sahlgren Mikko Savontaus Lea Sistonen Juha Strandén Mikael Wasberg Jukka Westermarck Andrey Zavialov Photographs: KUV@TEHDAS Roni Lehti, Photograph archives of the Centre for Biotechnology. Cover images: Roni Lehti. Painosalama Oy, Turku 2013 ISSN 1237-5217 The Finnish Microarray and Sequencing Centre..........................23 Cell Imaging Core.......................................................................27 Proteomics Facility......................................................................29 Protein Crystallography Core Facility ..........................................32 Bioinformatics Core....................................................................34 Virus Vector Facility.....................................................................36 Mechanisms and Biosensors of Gtpases....................................38 Protein Kinase Regulation of Brain Development and Disease....42 Translational Proteomics.............................................................48 Organisation of Neuronal Signaling Pathways.............................51 Structural Bioinformatics.............................................................55 Data Mining and Modelling.........................................................57 Cytoskeletal and Survival Signaling.............................................61 Epigenomics...............................................................................67 Cell Adhesion and Cancer..........................................................69 Hypoxia in Cell Survival...............................................................72 Bioenergy Group........................................................................75 Mitosis and Drug Discovery........................................................77 Molecular Systems Immunology and Stem Cell Biology..............80 Computational Systems Biology.................................................86 Cell Culture Models for Tumor Cell Invasion and Epithelial Plasticity.88 Complex Biosystems Modeling...................................................91 Metabolome in Health and Disease.............................................93 Protein Crystallography...............................................................97 Cell Fate...................................................................................101 Targeting Strategies for Gene Therapy .....................................105 Regulation and Function of Heat Shock Transcription Factors..107 Cancer Cell Signaling ...............................................................112 Adenosine Deaminases............................................................116 Ph.D. Defences........................................................................119 Life Outside the Lab.................................................................120 ORGANIZATION CHAIRMAN’S FOREWORD Board of Trustees 2012 When looking back over the year 2012 it is easy to remember the inspiring 22nd Annual BioCity Symposium “Personal Genomics – From Technologies to Applications” in August as well as the many excellent Frontiers of Science seminars, most prominently the memorable lecture given by professor, Nobel laureate Martin Chalfie. The annual BioCity publication prize, the Elias Tillandz prize was shared by two papers, both published in the Nature series journals, which tells about the high impact of research performed in the Turku Centre for Biotechnology (CBT), and in the BioCity community in general. Chairman HEINO Jyrki, Professor, University of Turku, Department of Biochemistry and Food Chemistry, Scientific Director, BioCity Turku Vice-chairman ERIKSSON John, Professor, Åbo Akademi University, Department of Biosciences Secretary LAHESMAA Riitta, Professor, Director, Turku Centre for Biotechnology Assistant Secretary ALANKO Satu, Coordinator, Turku Centre for Biotechnology and BioCity Turku Members ARO Eva-Mari, Professor, University of Turku, Department of Biochemistry and Food Chemistry BUCHERT Johanna, Vice President, Strategic research, VTT HAAPALINNA Antti, Vice President, Research, R&D, Orion Corporation ORION PHARMA JALKANEN Sirpa, Professor, University of Turku, Department of Medical Microbiology and Immunology JOHNSON Mark, Professor, Åbo Akademi University, Department of Biosciences POUTANEN Matti, Professor, University of Turku, Institute of Biomedicine SAVILAHTI Harri, Professor, University of Turku, Department of Biology TERHO Perttu, Project Engineer, Turku Centre for Biotechnology TÖRNQUIST Kid, Professor, Åbo Akademi University, Department of Biosciences WILLFÖR Stefan, Professor, Åbo Akademi University, Department of Chemical Engineering Vice-members FARDIM Pedro, Professor, Åbo Akademi University, Department of Chemical Engineering HÄNNINEN Pekka, Professor, University of Turku, Institute of Biomedicine JAAKKOLA Ulla-Marjut, Director, Central Animal Laboratory,Turku Centre for Biotechnology LASSILA Olli, Professor, University of Turku, Department of Medical Microbiology and Immunology PETTERSSON Kim, Professor, University of Turku, Department of Biochemistry and Food Chemistry PRIMMER Craig, Professor, University of Turku, Department of Biology SLOTTE J. Peter, Professor, Åbo Akademi University, Department of Biosciences VUORELA Pia, Professor, Åbo Akademi University, Department of Biosciences 2 While Turku researchers have continued their excellent performances the turmoil in the Finnish universities has continued. Despite many uncertainties there have also been positive developments. Especially the continuation of the Biocenter Finland process is very good news for core facilities, their personnel and customers. The decision carried out by the rectors of the biocenter universities will hopefully guarantee that also in the future the modern technologies and top-of-the-line instruments are available for life science researchers in Finland. The processes aiming to connect the Finnish research infrastructure to European networks (ESFRI) has also moved forward together with the update of the Finnish research infrastructure road map. In the latter, Biocenter Finland successfully passed the first phase of the evaluation. Since 1995 most of the graduate students have participated in the activities of local or national graduate schools. In the life science area the schools have done excellent work in the training of Ph.D. candidates and they have been an important resource for the research field. The recent change in the national policy has led to the sad decision to terminate the present graduate schools. I want to take this opportunity to thank on the behalf of the entire BioCity Turku community, the directors and coordinators of the graduate schools, who have worked long hours for Ph.D. training and generated the exceptional spirit of the schools. Despite the change in the graduate school system your work has not been in vain. You have given an enormous contribution to life science in Finland that will be remembered by thankful students and supervisors. I also hope that the same persons who have actively developed the old graduate schools could continue their good work in the new system. The exceptional motivation for science and improvement of research technologies has made CBT one of the most import resources in the molecular life science area in Turku. There is no doubt that the staff of CBT will, also in the future, continue its excellent performance in research and provide essential core services for all researchers in Turku, as well as in other biocenters. Jyrki Heino, M.D., Ph.D., Professor of Biochemistry Scientific Director of the BioCity Turku and Chairman of the Board of the Turku Centre for Biotechnology 3 FROM THE DIRECTOR YEAR 2012 IN A NUTSHELL Our Centre had a very active year 2012. During the now finished three year budgeting period (2010-12) our Centre excelled in exceeding the goals set and agreed with our host universities. Altogether 32 PhDs and 193 publications were produced during 2010-12. Moreover, our investigators won several major research grants and awards. RESEARCH AND EDUCATION David Goodlett started at the Centre as a Finnish Distinguished Professor (FiDiPro) in biomarker discovery and cutting-edge proteomics technologies. Jane Zhi Chen was appointed an Academy Fellow, a highly competitive award by the Academy of Finland (AoF). Jukka Westermarck received a large grant from the Sigrid Jusélius Foundation. A new Centre of Excellence (CoE) in “Molecular Systems Immunology and Physiology” was kicked off. In this AoF CoE, Riitta Lahesmaa is responsible for molecular systems immunology, and the Centre’s affiliated group leaders Matej Oresic (VTT) and Harri Lähdesmäki (Aalto) play central roles in leading the CoE and directing the computational systems biology, respectively. Eleanor Coffey and Johanna Ivaska won the Tillandz prize for the best publications of Biocity Turku and Johanna Ivaska’s publication was further awarded the Medix prize. Our core facilities continued to be key players in the Biocenter Finland infrastructure network and, based on an evaluation by external international experts, were able to raise significant external funding to further develop the services. The Biocenter Finland networks have made an important impact in developing the Finnish research infrastructure and providing Finnish scientists access to state-of-the art technologies. Very important for the continuation of these activities was that in 2012 the Rectors of host universities of biocenters decided to partially continue Biocenter Finland funding, obtained in 2010-12 from the Ministry of Education. Our SAB composed of Dr. Doreen Cantrell (chair, University of Dundee, Scotland, UK), Dr. Martin Eilers (University of Marburg, Germany), Dr. Ron Germain (NIH, Bethesda, MD, US), Dr. Carlos Ibanez (Karolinska Institute, Stockholm, Sweden) and Dr. Tomas Mustelin (Medimmune, Gaithersburg, MD, US) visited the Centre in 2012. They were impressed with the breadth of the technologies on offer and complimented us on the cost efficiency with which the core facilities are run as well as on the scientific achievements. Our CBT ship has been sailing through storms and winds of change during the past three years. There have been multiple changes in the entire university structure, restructuring processes and introduction of new administrative systems. In spite of all this we have succeeded in exceeding our scientific and educational goals.I am grateful to all CBT scientists and personnel who have made significant contributions towards achieving our goals. I look forward to an exciting journey forward! Riitta Riitta Lahesmaa, M.D., Ph.D., Professor Director Turku Centre for Biotechnology University of Turku and Åbo Akademi University 4 DEVELOPMENT OF INFRASTRUCTURE, RESEARCH SERVICES AND CORE FACILITIES Finnish Microarray and Sequencing Centre · The Centre got substantial competitive funding through Biocenter Finland to continue developing and providing national services in the area of gene expression, its regulation and epigenetics. · The Centre has set up and now offers its new Epigenomics services for DNA methylation analysis (Enrichment based meDNA-seq, Whole Genome Bisulphite Sequencing, Reduced Representation Bisulphite Sequencing); and histone mark profiling (ChIP-seq) for analysis of chromatin status at gene enhancers, promoters and bodies. Acquisition of MiSeq Personal Sequencer from Ilumina to set up and provide services for RNA and smallRNA sequencing, targeted and small genome resequencing and metagenomics applications. · The bioinformatics team of the Centre has set up a new computer cluster to increase the computation power and storage capacity that the new next-generation sequencing instruments require. Data analysis pipeline has been developed for various next-generation sequencing applications including RNA-seq, Chip-seq, DNA methylation and target enrichment resequencing to detect small genetic variants. Proteomics and Mass spectrometry Laboratory · A one-week “Basic proteomics course” was organized · Avinash Jadav, Thaman Chand and Santhosh Thatikonda completed their Masters degree. · Tanya Lukash started in February as a visiting researcher · Mimi Nguyen was recruited as a senior scientist in June · New instruments: Q Exactive and TSQ Vantage are installed and in operation · Various new software and upgrades for quantitative proteomics installed and in operation · The LTQ Orbitrap Velos has been upgraded to LTQ Orbitrap Velos Pro. · SRM based targeted quantitative proteomics method was set up as a new service · Organised 6th Dubrovnik Mass Spectrometry in Biotechnology and Medicine Summer School organised · Organised Cancer Crosslinks Turku Seminar, 22 August 2012 · Organised Ourense Conference on Imaging Mass Spectrometry, Ourense, Spain, 3-5 September 2012 5 Cell Imaging Core · Pasi Kankaanpää started as coordinator of the Cell Imaging Core, and Ketlin Adel started as part-time technician for flow cytometry. · Several new instruments (e.g. Zeiss LSM780 confocal) were installed and several more were made available to users via CIC, thanks to new collaboration agreements. · CIC services were used by more than 300 people from more than 100 research groups, with 20% outside users. This resulted in more than 30 peer reviewed scientific publications. · CIC personnel conducted more than 100 hours of teaching on various national and international courses and workshops, and started the popular Lost in Imaging webinar series. · CIC continued its role as the key light microscopy unit of the Turku BioImaging umbrella organization, and had active roles in national and international organizations such as Finnish BioImaging and Euro-BioImaging. Protein crystallography facility · Participation in several courses (Medical Biochemistry, TERBIO, Protein Crystallography and Structural Genomics, Master’s degree program in Autonomous University of Barcelona) with lectures and demonstrations. Our course ‘Basic X-ray crystallography techniques: How to solve a protein structure’ was held in February-March. · The new X-ray generator run smoothly throughout the year. A vacuum problem was easily resolved. The Oxford cryosystem was repumped several times owing to vacuum problems and a future replacement with a newer model was put forward. · Organization committee of the annual meeting of the Finnish crystallographic and structural biology groups (FINNBOX) hosted in Turku (June 6th). · New projects at various stages were initiated in collaboration with other groups in Finland and abroad. · All major crystallographic programs were kept updated to latest versions. The molecular graphics and protein crystallization rooms moved to new locations, offering better functionalities. Viral vector facility · The viral vector facility produced 115 viral preps as a service and hosted 50 registered users of the BSL2 lab · The BSL2 lab was expanded in capacity for viral vector production and analysis. The lab infrastructure was enhanced and new laminar and incubator space enables higher user numbers. · Titrations and tests for replication competence were added to our services. · An aerosol filtration system was added to the cell sorter so that users with virally transduced cells can sort without risk. This particularly eases the production of stably transfected cell lines. Quality Assurance Unit · Organized courses for the university on (1) quality assurance and metrology and (2) how to assure the reliability of your laboratory test results · Individual training for graduate and post-graduate students · QA inspections for the Central Animal Laboratory and Forensic Medicine in GLP quality system · Internal audits of CBT · Linnéa Linko is a member in the Advisory Commission for Metrology and the chairman in its Education group as well as a member of The Eurachem Education and Training Working Group Bioinformatics Unit · Two new computational clusters were acquired, one dedicated to genome sequencing efforts (supporting BF Genomics), funded by the Center for Biotechnology (CBT), and a second cluster partly funded by Åbo Akademi · Workstations and software (modeling, computational chemistry, chemical structure databases, etc.) supporting BF Structural Biology and BF Translational Activities (DDCB) have been set up. · Structural bioinformatics projects (funded from research funds) and using BF-funded infrastructure supports researchers in Bergen (1 project), Heidelberg (2), Stockholm (1), Tampere (1) and Turku (10). · High-throughput bioinformatics group analyzed data for 26 Next Generation Sequencing projects and 13 microarray projects. 6 7 FUNDING AND STATISTICS PhD and MSc Theses PhD Theses (p. 119) Name Supervisor Site besides CBT Sirkku Pollari Olli Kallioniemi UTU/Department of Pharmacology, Drug Development and Therapeutics Elisa Närvä Riitta Lahesmaa UTU/Department of Medical Microbiology and Immunology Anna-Leena Salmela Marko Kallio UTU/Department of Biochemistry and Food Chemistry Krista Rantanen Panu Jaakkola UTU/Department of Medical Biochemistry and Genetics Minna Niemelä Jukka Westermarck UTU/Department of Medical Biochemistry and Genetics Juha Tapio Korhonen Riitta Lahesmaa, Mirja Puolakkainen UTU/Department of Medical Biochemistry and Genetics Tapio Lönnberg Riitta Lahesmaa, Matej UTU/Department of Medical Oresic Biochemistry and Genetics Sources of funding received by Center for Biotechnology in 2012 (12,4 Million €) Biocenter Finland 7% Services 18% Academy of Finland 18% EU 5% Others 9% TEKES 3% MSc Theses Name Supervisor Site besides CBT Heidi A. Bergman Alexandra Elsing, Lea Sistonen ÅA/Department of Biosciences Anna Aalto Johanna Ahlskog, Lea Sistonen ÅA/Department of Biosciences Jenni Vasara Jenny Joutsen, Lea Sistonen ÅA/Department of Biosciences Thatikonda Santhosh Kumar Cecilia Sahlgren, Garry ÅA/Department of Biosciences Corthals Ghimire Bishwa Raj Tapio Salakoski, Attila Gyenesei University of Turku/Department of Information Technology Pradeep Battula Tassos Papageorgiou University of Turku/Department of Information Technology Thaman Chand Garry Corthals, Jukka Teuhola University of Turku/Department of Information Technology Avinash Yadav Garry Corthals, Pentti Riikonen University of Turku/Department of Information Technology Lotta Oikari Zhi Jane Chen, Verna Salo, Riitta Lahesmaa University of Turku/Department of Biology Cecilia Granqvist Cecilia Sahlgren ÅA/Department of Biosciences Habib Baghiro Cecilia Sahlgren, Jessica Rosenholm ÅA/Department of Biosciences Adel Asghar Marko Kallio A.I.Virtanen Institute for Molecular sciences, Kuopio Noora Jaakola Garry Corthals, Jyrki Heino University of Turku/Department of Biochemistry and Food Chemistry 8 Universities 41% External funding 2006-2012 9 Citations in each year to CBT publications 10 From left to right: Jouko Sandholm, Petri Vahakoski, Hannele Vuori, Mårten Hedman, Virpi Korpiranta, Mikael Wasberg, Linnéa Linko, Sarita Heinonen, Markku Saari, Susanna Pyökäri, Juha Strandén, Päivi Junni, Pasi Viljakainen, Marjo Hakkarainen, Riitta Lahesmaa, Eva Hirvensalo, Sirkku Grönroos and Anne Lahdenperä. Number of graduates 2006-2012 11 PUBLICATIONS 2012 Ph.D. Theses 2012 1. Sirkku Pollari: Dissecting the molecular mechanisms of breast cancer bone metastasis for therapeutic targeting, University of Turku, p. 120 2. Elisa Närvä: Pluripotency and genetic stability of human pluripotent stem cells. University of Turku, 134 p. 3. Anna-Leena Salmela: The Spindle assembly checkpoint as a drug target - novel small-molecule inhibitors of aurora kinases. University of Turku, 159 p. 4. Krista Rantanen: The dual role of HIF hydroxylase PHD3 in cancer cell survival. University of Turku, 171 p. 5. Minna Niemelä: Identification and characterization of CIP2A as a novel oncogenic inhibitor of PP2A. University of Turku, 139 p. 6. Juha Tapio Korhonen: Bacterium - host cell interaction in Chlamydia pneumoniae infection: the bacterial invasion and intracellular growth. University of Turku, 107 p. 7. Tapio Lönnberg: System-wide approaches to uncover Th2 cell lineage commitment. University of Turku, 143 p. Publications 2012 1. Äijö T, Edelman S, Lönnberg T, Larjo A, Kallionpää H, Tuomela S, Engström E, Lahesmaa R and Lähdesmäki H, (2012) An integrative computational systems biology approach identifies lineage specific dynamic transcriptome signatures which drive the initiation of human T helper cell differentiation, BMC Genomics, 3:572. IF 4.1 2. Arjonen A, Alanko J, Veltel S, Ivaska J. (2012) Distinct Recycling of Active and Inactive β1 Integrins. Traffic. 2012 Jan 5. IF 4.9 3. Benatti C, Valensisi C, Blom JM, Alboni S, Montanari C, Ferrari F, Tagliafico E, Mendlewicz J, Brunello N, Tascedda F. J (2012) Transcriptional profiles underlying vulnerability and resilience in rats exposed to an acute unavoidable stress. J Neurosci Res. 90(11):2103-15. IF 2.7 4. Benson MJ, Aijö T, Chang X, Gagnon J, Pape UJ, Anantharaman V, Aravind L, Pursiheimo JP, Oberdoerffer S, Liu XS, Lahesmaa R, Lähdesmäki H, Rao A (2012) Heterogeneous nuclear ribonucleoprotein L-like (hnRNPLL) and elongation factor, RNA polymerase II, 2 (ELL2) are regulators of mRNA processing in plasma cells. Proc Natl Acad Sci U S A 109(40):16252-7. IF 9.7 5. Björkblom, B, Padzik, A., Mohammad, H., Westerlund, N., Komulainen, E., Hollos, P., Parviainen, L., Papageorgiou, A.C., Iljin, K., Kallioniemi, O., Kallajoki, M., Courtney, M.J., Mågård, M., James, P. & Coffey, E.T. (2012). JNK phosphorylation of MARCKSL1 determines actin stability 12 and migration in neurons and in cancer cells. Mol. Cell. Biol. 32: 3513-3526. IF 5.5 6. Björkman M, Östling P, Härmä V, Virtanen J, Mpindi JP, Rantala J, Mirtti T, Vesterinen T, Lundin M, Sankila A, Rannikko A, Kaivanto E, Kohonen P, Kallioniemi O, Nees M (2012) Systematic knockdown of epigenetic enzymes identifies a novel histone demethylase PHF8 overexpressed in prostate cancer with an impact on cell proliferation, migration and invasion. Oncogene. 31(29):3444-56. IF 6.4 7. Chouhan B., Denesyuk A., Heino J. Johnson MS and Denessiouk K. (2012) Evolutionary Origin of the alphaC Helix in Integrins. WASET 65: 546-549. 8. Chronopoulou EG, Papageorgiou AC, Markoglou A, Nikolaos E. Labrou NE (2012) Inhibition of human glutathione transferases by pesticides: Development of a simple analytical assay for the quantification of pesticides in water. Journal of Molecular Catalysis B: Enzymatic. 81:43–51. IF 2.7 9. Gómez-Gallego C, Collado MC, Ilo T, Jaakkola UM, Bernal MJ, Periago MJ, Salminen S, Ros G, Frias R (2012) Infant formula supplemented with polyamines alters the intestinal microbiota in neonatal BALB/cOlaHsd mice. J Nutr Biochem. 23(11):1508-13. IF 3.9 10.Elo LL, Kallio A, Laajala TD, Hawkins RD, Korpelainen E, Aittokallio T (2012) Optimized detection of transcription factor-binding sites in ChIP-seq experiments. Nucleic Acids Res. 40(1):e1. IF 8.0 11.Ferraris SE, Isoniemi K, Torvaldson E, Anckar J, Westermarck J, and Eriksson JE (2012) Nucleolar AATF regulates c-Jun-mediated apoptosis. Molecular Biology of the Cell, 23(21):4323-4332. IF 5.4 12.Frias R, Steiner JM, Williams DA, Sankari S, Westermarck E (2012) Urinary recovery of orally administered 51chromiumlabeled ethylenediamine tetra-acetic acid, lactulose, rhamnose, D-xylose, 3-O-methyl-D-glucose and sucrose in healthy adult male laboratory Beagles. American Journal of Veterinary Research. 73 (5): 654-658. IF 1.3 13.Frias R, Strube K, Ternes W, Collado MC, Spillmann T, Sankari S, Westermarck E (2012) Comparison of 51Cr-EDTA and iohexol as blood markers for intestinal permeability testing in Beagle dogs.Vet J. 192(1):123-5. IF 2.2 14.Gómez-Gallego C, Collado MC, Ilo T, Jaakkola UM, Bernal MJ, Periago MJ, Salminen S, Ros G, Frias R (2012) Infant formula supplemented with polyamines alters the intestinal microbiota in neonatal BALB/cOlaHsd mice. J Nutr Biochem. (11):1508-13. IF 3.9 15.Gyenesei A, Moody J, Laiho A, Semple CA, Haley CS, Wei WH (2012) BiForce Toolbox: powerful high-throughput computational analysis of gene-gene interactions in genomewide association studies. Nucleic Acids Res. 40(Web Server issue):W628-32. IF 8.0 13 16.Gyenesei A, Moody J, Semple CA, Haley CS, Wei WH (2012) High-throughput analysis of epistasis in genomewide association studies with BiForce. Bioinformatics. 28(15):1957-64. IF 5.5 17.Härmä V, Knuuttila M, Virtanen J, Mirtti T, Kohonen P, Kovanen P, Happonen A, Kaewphan S, Ahonen I, Kallioniemi O, Grafström R, Lötjönen J, Nees M (2012) Lysophosphatidic acid and sphingosine-1-phosphate promote morphogenesis and block invasion of prostate cancer cells in threedimensional organotypic models. Oncogene. 31(16):207589. IF 6.4 18.Ivaska J. (2012) Unanchoring integrins in focal adhesions. Nat. Cell. Biol.14:981-983 (Invited commentary). IF 19.5 19.Jonsdottir K, Zhang H, Jhagroe D, Skaland I, Slewa A, Björkblom B, Coffey ET, Gudlaugsson E, Smaaland R, Janssen EA, Baak JP (2012) The prognostic value of MARCKS-like 1 in lymph node-negative breast cancer. Breast Cancer Res Treat. 135(2):381-90. IF 5.2 20.Karaman DS, Diti Desai D, Senthilkumar R, Johansson EM, Råtts N, Odén M, Eriksson JE, Sahlgren C, Toivola DM and Rosenholm JM* (2012) Shape engineering vs organic modification of inorganic nanoparticles as a tool for enhancing cellular internalization. Nanoscale Res Lett. 7(1):358. IF 2.7 21.Köhnke M, Schmitt S, Ariotti N, Piggott AM, Parton RG, Lacey E, Capon RJ, Alexandrov K, Abankwa D (2012) Design and Application of In Vivo FRET Biosensors to Identify Protein Prenylation and Nanoclustering Inhibitors. Chem Biol. 19(7):866-74. IF 5.8 22.Korhonen JT, Puolakkainen M, Häivälä R, Penttilä T, Haveri A, Markkula E, Lahesmaa R (2012) Flotillin-1 (Reggie-2) contributes to Chlamydia pneumoniae growth and is associated with bacterial inclusion. Infect Immun. 80(3):1072-8. IF 4.2 23.Korhonen JT, Puolakkainen M, Haveri A, Tammiruusu A, Sarvas M, Lahesmaa R (2012) Chlamydia pneumoniae entry into epithelial cells by clathrin-independent endocytosis. Microb Pathog. 52(3):157-64. IF 2.1 24.Laiho A, Kiraly A, Gyenesei A. GeneFuncster: A Web Tool for Gene Functional Enrichment Analysis and Visualisation, D. Gilbert and M. Heiner (Eds.): CMSB 2012, LNCS 7605, pp. 382-385, 2012. Springer-Verlag Berlin Heidelberg 2012. 25.Lehtinen L, Vainio P, Wikman H, Reemts J, Hilvo M, Issa R, Pollari S, Brandt B, Oresic M, Pantel K, Kallioniemi O, Iljin K (2012) 15-Hydroxyprostaglandin dehydrogenase associates with poor prognosis in breast cancer, induces epithelialmesenchymal transition, and promotes cell migration in cultured breast cancer cells. J Pathol. 226(4):674-86. IF 6.3 26.Levula M, Oksala N, Airla N, Zeitlin R, Salenius JP, Järvinen O, Venermo M, Partio T, Saarinen J, Somppi T, Suominen V, Virkkunen J, Hautalahti J, Laaksonen R, Kähönen M, Mennander A, Kytömäki L, Soini JT, Parkkinen J, Pelto- 14 Huikko M, Lehtimäki T (2012) Genes involved in systemic and arterial bed dependent atherosclerosis--Tampere Vascular study. PLoS One. 7(4):e33787 IF 4.1 27.Lund RJ, Närvä E, Lahesmaa R (2012) Genetic and epigenetic stability of human pluripotent stem cells. Nat Rev Genet. 13(10):732-44. IF 38.1 28.Lund RJ, Nikula T, Rahkonen N, Närvä E, Baker D, Harrison N, Andrews P, Otonkoski T, Lahesmaa R (2012) Highthroughput karyotyping of human pluripotent stem cells. Stem Cell Res. 9(3):192-195. IF 5.2 29.Mamaeva V, Sahlgren C, Lindén M (2012) Mesoporous silica nanoparticles in medicine-Recent advances. Adv Drug Deliv Rev. pii: S0169-409X(12)00248-7. IF 11.5 30.Mathiasen DP, Egebjerg C, Andersen SH, Rafn B, Puustinen P, Khanna A, Daugaard M, Valo E, Tuomela S, Bøttzauw T, Nielsen CF, Willumsen BM, Hautaniemi S, Lahesmaa R, Westermarck J, Jäättelä M, and Kallunki T (2012) Identification of a c-Jun N-terminal kinase-2-dependent signal amplification cascade that regulates c-Myc levels in ras transformation. Oncogene, 31, 390-40. IF 6.4 31.McDonnell L, Andrén PE, Corthals GL. (2012) Preface. J Proteomics. 75(16):4881-2. IF 4.9 32.McDonnell LA, Heeren RM, Andrén PE, Stoeckli M, Corthals GL (2012) Going forward: Increasing the accessibility of imaging mass spectrometry. J Proteomics. 75(16):5113-21. IF 4.9 33.Närvä E, Rahkonen N, Emani MR, Lund R, Pursiheimo JP, Nästi J, Autio R, Rasool O, Denessiouk K, Lähdesmäki H, Rao A, Lahesmaa R (2012) RNA-binding protein L1TD1 interacts with LIN28 via RNA and is required for human embryonic stem cell self-renewal and cancer cell proliferation. Stem Cells. 30(3):452-60. IF 7.8 34.Niemelä M, Kauko O, Sihto H, Mpindi J-P, Nicorici D, Pernilä P, Kallioniemi O-P, Joensuu H, Hautaniemi S, and Westermarck J (2012) CIP2A signature reveals the MYC dependency of CIP2A-regulated phenotypes and its clinical association with breast cancer subtypes. Oncogene, 31(39):4266-4278. IF 6.9 35.Nilsson EM, Brokken LJ, Narvi E, Kallio MJ, Härkönen PL (2012) Identification of fibroblast growth factor-8b target genes associated with early and late cell cycle events in breast cancer cells. Mol Cell Endocrinol. 358(1):104-15. IF 4.2 36.Paatero I, Jokilammi A, Heikkinen PT, Iljin K, Kallioniemi OP, Jones FE, Jaakkola PM, Elenius K (2012) Interaction with ErbB4 promotes hypoxia-inducible factor-1α signaling. J Biol Chem. 287(13):9659-71. IF 4.8 37.Peet A, Kool P, Ilonen J, Knip M, Tillmann V; for the DIABIMMUNE Study Group. Collaborators (42) Koski K, Koski M, Härkönen T, Ryhänen S, Hämäläinen AM, Ormisson A, Ulich V, Kuzmicheva E, Mokurov S, Markova S, Pylova S, Isakova M, Shakurova E, Petrov V, Dorshakova 15 NV, Karapetyan T, Varlamova T, Kiviniemi M, Alnek K, Janson H, Uibo R, Salum T, von Mutius E, Weber J, Ahlfors H, Kallionpää H, Laajala E, Lahesmaa R, Lähdesmäki H, Moulder R, Nieminen J, Ruohtula T, Vaarala O, Honkanen H, Hyöty H, Kondrashova A, Oikarinen S, Harmsen HJ, De Goffau MC, Welling G, Alahuhta K, Virtanen SM (2012) Birth weight in newborn infants with different diabetes-associated HLA genotypes in three neighbouring countries: Finland, Estonia and Russian Karelia. Diabetes Metab Res Rev. 28(5):455-461. IF 3.4 38.Pellinen T, Rantala JK, Arjonen A, Mpindi JP, Kallioniemi O, Ivaska J (2012) A functional genetic screen reveals new regulators of β1-integrin activity. J Cell Sci. 125(Pt 3):64961. IF 6.1 39.Perdomo MF, Hosia W, Jejcic A, Corthals GL, Vahlne A (2012) Human serum protein enhances HIV-1 replication and up-regulates the transcription factor AP-1. Proc Natl Acad Sci U S A. 109(43):17639-44. IF 9.7 40.Pollari S, Käkönen RS, Mohammad KS, Rissanen JP, Halleen JM, Wärri A, Nissinen L, Pihlavisto M, Marjamäki A, Perälä M, Guise TA, Kallioniemi O, Käkönen SM (2012) Heparinlike polysaccharides reduce osteolytic bone destruction and tumor growth in a mouse model of breast cancer bone metastasis. Mol Cancer Res. 10(5):597-604. IF 4.4 41.Pollari S, Leivonen SK, Perälä M, Fey V, Käkönen SM, Kallioniemi O (2012) Identification of microRNAs inhibiting TGF-β-induced IL-11 production in bone metastatic breast cancer cells. PLoS One. 7(5):e37361. IF 4.1 42.Pouwels J, Nevo J, Pellinen T, Ylänne J, Ivaska J (2012) Negative regulators of integrin activity. J Cell Sci. 125(Pt 14):3271-80. IF 6.1 43.Rintanen N, Karjalainen M, Alanko J, Paavolainen L, Mäki A, Nissinen L, Lehkonen M, Kallio K, Cheng RH, Upla P, Ivaska J, Marjomäki V (2012) Calpains promote α2β1 integrin turnover in nonrecycling integrin pathway. Mol Biol Cell. 23(3):448-63. IF 4.9 44.Rissanen J, Moulder R, Lahesmaa R, Nevalainen OS (2012) Pre-processing of Orbitrap higher energy collisional dissociation tandem mass spectra to reduce erroneous iTRAQ ratios. Rapid Commun Mass Spectrom. 26(17):2099104. IF 2.8 45.Rosenholm JM, Mamaeva V, Sahlgren C, Lindén M (2012) Nanoparticles in targeted cancer therapy: mesoporous silica nanoparticles entering preclinical development stage. Nanomedicine (Lond). 7(1):111-20. IF 6.2 46.Salmela AL, Pouwels J, Kukkonen-Macchi A, Waris S, Toivonen P, Jaakkola K, Mäki-Jouppila J, Kallio L, Kallio MJ (2012) The flavonoid eupatorin inactivates the mitotic checkpoint leading to polyploidy and apoptosis. Exp Cell Res. 318(5):578-92. IF 3.6 47.Sandri C, Caccavari F, Valdembri D, Camillo C, Veltel S, Santambrogio M, Lanzetti L, Bussolino F, Ivaska J, Serini G 16 (2012) The R-Ras/RIN2/Rab5 complex controls endothelial cell adhesion and morphogenesis via active integrin endocytosis and Rac signaling. Cell Res. 22(10):1479-501. IF 8.2 48.Santos HM, Kouvonen P, Capelo JL, Corthals GL (2012) Isotopic labelling of peptides in tissues enhances mass spectrometric profiling. Rapid Commun Mass Spectrom. 26(3):254-62. IF 2.8 49.Sen Karaman D, Desai D, Senthilkumar R, Johansson EM, Råtts N, Odén M, Eriksson JE, Sahlgren C, Toivola DM, Rosenholm JM (2012) Shape engineering vs organic modification of inorganic nanoparticles as a tool for enhancing cellular internalization. Nanoscale Res Lett. 7(1):358. IF 2.7 50.Skopelitou K, Dhavala P, Papageorgiou AC, Labrou NE (2012) A glutathione transferase from Agrobacterium tumefaciens reveals a novel class of bacterial GST superfamily. PLoS One. 7(4):e34263. IF 4.1 51.Skopelitou K, Muleta AW, Pavli O, Skaracis GN, Flemetakis E, Papageorgiou AC, Labrou NE (2012) Overlapping protective roles for glutathione transferase gene family members in chemical and oxidative stress response in Agrobacterium tumefaciens. Funct Integr Genomics. 12(1):157-72. IF 2.8 52.Sundvall M, Korhonen A, Vaparanta K, Anckar J, Halkilahti K, Salah Z, Aqeilan RI, Palvimo JJ, Sistonen L, Elenius K (2012) Protein Inhibitor of Activated STAT3 (PIAS3) Protein Promotes SUMOylation and Nuclear Sequestration of the Intracellular Domain of ErbB4 Protein. J Biol Chem. 287(27):23216-26. IF 4.8 53.Teittinen KJ, Grönroos T, Parikka M, Junttila S, Uusimäki A, Laiho A, Korkeamäki H, Kurppa K, Turpeinen H, Pesu M, Gyenesei A, Rämet M, Lohi O (2012) SAP30L (Sin3Aassociated protein 30-like) is involved in regulation of cardiac development and hematopoiesis in zebrafish embryos. J Cell Biochem. 113(12):3843-52. IF 2.9 54.Tnimov Z, Guo Z, Gambin Y, Nguyen UT, Wu YW, Abankwa D, Stigter A, Collins BM, Waldmann H, Goody RS, Alexandrov K (2012) Quantitative Analysis of Prenylated RhoA Interaction with Its Chaperone, RhoGDI. J Biol Chem. 287(32):26549-62. IF 4.8 55.Toivonen R, Koskenvuo J, Merentie M, Söderström M, YläHerttuala S, Savontaus M. (2012) Intracardiac injection of a capsid-modified Ad5/35 results in decreased heart toxicity when compared to standard Ad5. Virol J. 9:296. IF 2.3 56.Tripathi P, Sahoo N, Ullah U, Kallionpää H, Suneja A, Lahesmaa R, Rao KV (2012) A novel mechanism for ERKdependent regulation of IL4 transcription during human Th2-cell differentiation. Immunol Cell Biol. 90(7):676-87. IF 3.7 57.Tuomela S, Salo V, Tripathi SK, Chen Z, Laurila K, Gupta B, Äijö T, Oikari L, Stockinger B, Lähdesmäki H, Lahesmaa R (2012) Identification of early gene expression changes during 17 human Th17 cell differentiation. Blood. 119(23):e151-60. IF 10.6 58.Ullah U, Tripathi P, Lahesmaa R, Rao KV (2012) Gene set enrichment analysis identifies LIF as a negative regulator of human Th2 cell differentiation. Sci Rep. 2:464. 59.Vainio P, Mpindi JP, Kohonen P, Fey V, Mirtti T, Alanen KA, Perälä M, Kallioniemi O, Iljin K (2012) High-Throughput Transcriptomic and RNAi Analysis Identifies AIM1, ERGIC1, TMED3 and TPX2 as Potential Drug Targets in Prostate Cancer. PLoS One. 7(6):e39801. IF 4.1 60.Ventelä S, Come C, Mäkelä J-A, Hobbs RM, Mannermaa L, Kallajoki M, Chan EK, Pandolfi PP, Toppari J, and Westermarck J (2012) CIP2A promotes proliferation of spermatogonial progenitor cells and spermatogenesis in mice. PLoS One, 7(3), e33209. IF 4.1 61.Ventelä S, Mäkelä J-A, Kulmala J, Westermarck J, and Toppari J (2012) Identification and regulation of a stagespecific stem cell niche enriched by Nanog positive spermatogonial stem cells in the mouse testis. Stem Cells, 30(5), 1008-1020. IF 7.8 62.Vesala L, Salminen TS, Laiho A, Hoikkala A, Kankare M (2012) Cold tolerance and cold-induced modulation of gene expression in two Drosophila virilis group species with different distributions. Insect Mol Biol. 21(1):107-18. IF 2.5 63.Virtakoivu R, Pellinen T, Rantala JK, Perälä M, Ivaska J (2012) Distinct roles of AKT isoforms in regulating β1-integrin activity, migration and invasion in prostate cancer. Mol Biol Cell. 23(17):3357-69. IF 4.9 64.Wei WH, Hemani G, Gyenesei A, Vitart V, Navarro P, Hayward C, Cabrera CP, Huffman JE, Knott SA, Hicks AA, Rudan I, Pramstaller PP, Wild SH, Wilson JF, Campbell H, Hastie ND, Wright AF, Haley CS (2012) Genome-wide analysis of epistasis in body mass index using multiple human populations. Eur J Hum Genet. 20(8):857-62. IF 4.4 65.Wilhelmsson U, Faiz M, de Pablo Y, Sjöqvist M, Andersson D, Widestrand A, Potokar M, Stenovec M, Smith PL, Shinjyo N, Pekny T, Zorec R, Ståhlberg A, Pekna M, Sahlgren C, Pekny M (2012) Astrocytes Negatively Regulate Neurogenesis through the Jagged1-Mediated Notch Pathway. Stem Cells. 30(10):2320-9. IF 7.8 66.Ylipaasto P, Smura T, Gopalacharyulu P, Paananen A, Seppänen-Laakso T, Kaijalainen S, Ahlfors H, Korsgren O, Lakey JR, Lahesmaa R, Piemonti L, Oresic M, Galama J, Roivainen M (2012) Enterovirus-induced gene expression profile is critical for human pancreatic islet destruction. Diabetologia. 55(12):3273-83. IF 6.8 18 PERSONNEL 2012 Administration LAHESMAA Riitta, Director, Professor, Group Leader ALANKO Satu, Coordinator GRÖNROOS Sirkku, Senior Administrative Assistant HIRVENSALO Eva, Clerical Official JASMAVAARA Aila, Clerical Official LAHDENPERÄ Anne, Coordinator SUVANTO Tuula, Project Secretary BioCity Turku HEINO Jyrki, Biocity Turku Scientific Director, Professor HEINO Ilona, Student ALANKO Satu, Coordinator Technical Staff HEDMAN Mårten, Systems Manager KORPIRANTA Virpi, Instrument Maintenance STRANDÉN Juha, Laboratory Engineer VAHAKOSKI Petri, Systems Manager VILJAKAINEN Pasi, Senior Technician VUORI Hannele, Instrument Maintenance WASBERG Mikael, Laboratory Manager Finnish Microarray and Sequencing Centre FEZAZI Bogata, Laboratory Technician GYENESEI Attila, Senior Scientist GHIMIRE Bishwa, Undergraduate Student HAWKINS David, Group Leader LUND Riikka, Senior Scientist PURSIHEIMO Juha-Pekka, Senior Scientist ALA Kulju Ritva, Student HEININEN-BROWN Mari, Undergraduate Student ISOJÄRVI Janne, Undergraduate Student JUNNI Päivi, Laboratory Technician JUNTTILA Sini, Project Engineer KAUKO Leni, Researcher KIRALY Andras, Graduate Student KYTÖMÄKI Leena, Project Engineer LAIHO Asta, Project Engineer RISSANEN Oso, Laboratory Technician SUNDSTRÖM Robin, Undergraduate Student VENHO Reija, Laboratory Technician VIRTANEN Eveliina, Project Engineer VUORIKOSKI Sanna, Researcher Cell Imaging Core KANKAANPÄÄ Pasi, Coordinator of the Cell Imaging Core COFFEY Eleanor, Academy of Finland Research Fellow, Head of the Cell Imaging Core ADEL Ketlin, Research Technician KORHONEN Jari, Project Engineer SANDHOLM Jouko, Research Engineer SAARI Markku, Project Engineer TERHO Perttu, Project Engineer Proteomics Facility CORTHALS Garry, Group Leader, Head of Proteomics HAAPANIEMI Pekka, Laboratory Technician HEINONEN Arttu, Project Engineer IMANISHI Susumu, Senior Scientist KOUVONEN Petri, Researcher MUTH-PAWLAK Dorotha, Senior Scientist ROKKA Anne, Senior Scientist Protein Crystallography Core PAPAGEORGIOU Tassos, Group Leader, Adjunct Professor HEDMAN Mårten, Systems Manager STRANDÉN Juha, Laboratory Engineer VAHAKOSKI Petri, Systems Manager VILJAKAINEN Pasi, Senior Technician Bioinformatics core DENESSIOUK Konstantin, Group Leader (Structural Bioinformatics) GYENESEI Attila, Senior Scientist (High-throughput Bioinformatics) CHOUHAN Bhanupratap Singh, Graduate Student GHIMIRE Bishwa, Undergraduate Student ISOJÄRVI Janne, Undergraduate Student JUNTTILA Sini, Graduate Student KYTÖMÄKI Leena, Project Engineer LAIHO Asta, Project Engineer Virus Vector facility COFFEY Eleanor, Group Leader, Coordinator ADEL Ketlin, Laboratory Technician Mechanisms and Biosensors of GTPases ABANKWA Daniel, Group Leader, Academy of Finland Research Fellow BLAZEVICS Olga, Postdoctoral Fellow GUZMAN Camilo, Postdoctoral Fellow LIGABUE Alessio, Postdoctoral Fellow MAI Anja, Postdoctoral Fellow KAJA NAJUMUDEEN Arafath, Graduate Student OETKEN-LINDHOLM Christina, Postdoctoral Fellow SILJAMÄKI Elina, Postdoctoral Fellow SOLMAN Maja, Graduate Student Protein Kinase Regulation of Brain Development and Disease COFFEY Eleanor, Group Leader, Academy of Finland Research Fellow ADUSUMALLI Ravi, Undergraduate Student DESHPANDE Prasannakumar, Graduate Student FLINKMAN Dani, Undergraduate Student FOUROTAN Behnoush, Undergraduate Student FREEMANTLE Erika, Postdoctoral researcher HOLLOS Patrik, Graduate Student 19 KOMULAINEN Emilia, Graduate Student MOHAMMAD Hasan, Graduate Student MYSORE Raghavendra, Graduate Student PADZIK Artur, Postdoctoral researcher NGUYEN Phuoc Hung, Graduate Student PYÖKÄRI Susanna, Laboratory technician ZDROJEWSKA Justyna, Graduate Student Translational Proteomics CORTHALS Garry, Group Leader, Head of Proteomics BULBUL Ahmed, Undergraduate Student CHAND Thaman, Graduate Student EEROLA Sini, Laboratory Technician HAAPANIEMI Pekka, Laboratory Technician HAKANEN Emmi, Laboratory Technician HEINONEN Arttu, Project Engineer IMANISHI Susumu, Senior Scientist JAAKKOLA Noora, Undergraduate Student KANNASTE Olli, Graduate Student KOTTAHACHCHI Darshana, Graduate Student KOUVONEN Petri, Senior Scientist (visiting ETH Zurich 2011-2013) KUMAR Santosh, Undergraduate Student LUKASH Tanya, Senior Scientist MUTH-PAWLAK Dorotha, Senior Scientist NEES Susanne, Coordinator NGUYEN Elizabeth, Postdoctoral Fellow ROKKA Anne, Senior Scientist SAEIDI Firouz, Undergraduate Student DE SANTOS Hugo, Graduate Student SUNI Veronika, Graduate Student THATIKONDA Santosh, Undergraduate Student VEHMAS Anni, Graduate Student YADAV Avinash, Graduate Student Organisation of Neuronal Signaling Pathways COURTNEY Michael, Affiliated Group Leader, Professor GASCOGNE Esther, Undergraduate Student HO Franz, Postdoctoral Researcher HOLME Andrea, Senior Scientist LI Lili, Graduate Student LIU Xiaonan, Graduate Student MARTINSSON Peter, Postdoctoral Researcher de MERA, Melero-Fernandez MIN Jungah, Senior Scientist RAI Surya, Undergarduate Student SEPPÄNEN Aila, Laboratory Technician VERGUN Olga, Postdoctroal Researcher WANG Xijun, Graduate Student 20 Structural Bioinformatics DENESSIOUK Konstantin, Docent, Group Leader CHOUHAN Bhanupratap Singh, Graduate Student HEININEN-BROWN Mari, Undergraduate Student Data Mining and Modeling ELO Laura, Group Leader, Adjunct Professor AITTOKALLIO Tero, Affiliated Group Leader, Adjunct Professor NEVALAINEN Olli, Affiliated Group Leader, Professor HEISKANEN Marja, Graduate Student JAAKKOLA Maria, Undergraduate Student KOSKINEN Anna, Undergraduate Student LINDEN Rolf, Graduate Student OKSER Sebastian, Graduate Student RANNIKKO Sami, Undergraduate Student SALMI Jussi, Postdoctoral Fellow SANTA Harri, Undergraduate Student SEYEDNASROLLAH Fatemehsadat, Undergraduate Student SUOMI Tomi, Graduate Student TUIKKALA Johannes, Graduate Student VÄHÄMAA Heidi, Graduate Student Cytoskeletal and Survival Signaling ERIKSSON John, Group Leader, Professor ASAOKA Tomoko, Graduate Student CHENG Fang, Post-doctoral fellow FERRARIS Saima, Graduate Student GULLMETS Josef, Graduate Student HYDER Claire, Graduate Student LINDQVIST Julia, Graduate Student LINDSTRÖM Michelle, Undergraduate Student MOHANASUNDARAM Ponnuswamy, Graduate Student NIEMELÄ Erik, Undergraduate Student ISONIEMI Kimmo, Graduate Student JOKO Alia, Graduate Student PAZIEWSKA Beata, Secretary PAUL Preethy, Post-doctoral fellow PYLVÄNÄINEN Joanna, Graduate Student RAJENDRAN Senthil Kumar, Postdoctoral Fellow SAARENTO Helena, Research Associate TORVALDSON Elin, Graduate student Molecular Systems Immunology and Stem Cell Biology LAHESMAA Riitta, Director, Professor, Group Leader BALA Kanchan, Postdoctoral fellow CHEN Zhi Jane, Senior Scientist EDELMAN Sanna, Postdoctoral fellow ELO-UHLGREN Laura, Adjunct Professor, Senior Scientist FEZAZI Bogata, Laboratory Technician GOODLETT David R., Visiting Professor HAKANEN Emmi, Undergraduate Student HAKKARAINEN Marjo, Laboratory Technician HEINONEN Mirkka, Graduate Student HEINONEN Sarita, Laboratory Technician HÄMÄLISTÖ Saara, Postdoctoral fellow JUNNI Päivi, Laboratory Technician KALLIONPÄÄ Henna, Graduate Student KANDURI Kartiek, Graduate Student KHAN MOHN Moin, Graduate Student KORHONEN Juha, Graduate Student KYLÄNIEMI Minna, Graduate Student LAAJALA Essi, Graduate Student LEHTIMÄKI Sari, Postdoctoral fellow LUND Riikka, Senior Scientist LÖNNBERG Tapio, Graduate Student MAURINEN Krista, Undergraduate Student MOULDER Robert, Senior Scientist MYLLYVIITA Johanna, Undergraduate Student NGYEN Elizabeth, Postdoctoral Fellow NÄRVÄ, Elisa, Graduate Student OIKARI Lotta, Undergraduate Student PIETILÄ Elina, Laboratory Technician RAHKONEN Nelly, Graduate Student RAJAMÄKI Anna, Undergraduate Student RAJAVUORI Anna, Undergraduate Student RAO Anjana, Visiting Professor RAO Kanury, Visiting Professor RASOOL Omid, Adjunct Professor, Senior Scientist REDDY Emaheswa, Postdoctoral fellow SALMI Jussi, Senior scientist SALO Verna, Graduate Student SARAPULOV Alexey, Graduate Student STOCKINGER Brigitta, Visiting Professor TAHVANAINEN Johanna, Postdoctoral fellow TRIPATHI Subhash, Graduate Student TUOMELA Soile, Graduate Student ULLAH Ubaid, Postdoctoral Fellow ÖLING Viveka, Postdoctoral Fellow Quality Assurance Unit LINKO Linnéa, Group Leader, Adjunct Professor Computational Systems Biology LÄHDESMÄKI Harri, Affiliated Group Leader, Professor ERKKILÄ Timo, Graduate Student INTOSALMI Jukka, Postdoctoral Fellow KANDURI Kartiek, Graduate Student KONG Lingjia, Graduate Student KÄHÄRÄ Juhani, Undergraduate Student LAAJALA Essi, Graduate Student LARJO Antti, Graduate Student LAURILA Kirsti, Postdoctoral fellow MALONZO Maia, Graduate Student MANNERSTRÖM Henrik, Graduate Student NOUSIAINEN Kari, Graduate Student OSMALA Maria, Graduate Student RAUTIO Sini, Undergraduate Student SOMANI Juhi, Undergraduate Student ÄIJÖ Tarmo, Graduate Student Cell Culture Models For Tumor Cell Invasion and Epithelial Platicity NEES Matthias, Affiliated Group Leader AHONEN Ilmari, Graduate student HÄRMÄ Ville, Postdoctoral fellow MISHRA Mrinal, Undergraduate Student SIMVARANAN Chamudeesvari, Undergraduate Student TOIVONEN Pauliina, Laboratory technician VIRTANEN Johannes, Laboratory technician ÅKERFELT Malin, Postdoctoral fellow Complex Biosystems Modeling NYKTER Matti, Affiliated Group Leader ANNALA Matti, Graduate Student GRANBERG Kirsi, Post-doctoral Fellow HÄYRYNEN Sergei, Undergraduate Student KALLIO Aleksi, Undergraduate Student KARTASALO Kimmo, Undergraduate Student KESSELI Juha, Post-doctoral Fellow KIVINEN Virpi, Graduate Student KYTÖLÄ Ville,Undergraduate Student LEPPÄNEN Simo-Pekka, Undergraduate Student LIUKSIALA Thomas, Undergraduate Student SARBU Septimia, Graduate Student SOININEN Tero, Undergraduate Student SORSA Liisa-Ida, Undergraduate Student SORSA Saija, Undergraduate Student WALTERING Kati, Post-doctoral Fellow YLIPÄÄ Antti, Graduate Student Metabolome In Health And Disease OREŠIČ Matej, Affiliated Group Leader BONDIA PONS Isabel, Research scientist HILVO Mika, Research scientist HYÖTYLÄINEN Tuulia, Team leader JÄNTTI Sirkku, Research scientist KIVILOMPOLO Maarit, Research scientist KOIVUNIEMI Artturi, Research scientist LAHTINEN Ulla, Laboratory technician LIETZEN Niina, Research scientist LINDFORS Erno, Research scientist MARINKOVIĆ Tijana, Research scientist MATTILA Ismo, Research scientist NYGREN Heli, Research scientist PEDDINTI Gopal, Research scientist PÖHÖ Päivi, Research scientist RUSKEEPÄÄ Anna-Liisa, Laboratory technician SYSI-AHO Marko, Team leader YETUKURI Laxman, Research scientist ZHAO Han, Laboratory technician ÖHRNBERG Leena, Laboratory technician Protein Crystallography PAPAGEORGIOU Tassos, Group Leader, Adjunct Professor BATTULA Pradeep, Undergraduate Student 21 FRIOUX Cleménce, Undergraduate Student MATTSSON Jesse, Undergraduate Student MULETA Abdi, Graduate Student OUDOT Anthony, Undergraduate Student PRIETO LOPEZ Carlos, Undergraduate Student SUBEDI Bishwa, Graduate Student Cell fate SAHLGREN Cecilia, Group Leader, Academy of Finland Research Fellow ANTFOLK Daniel, Undergraduate Student ANTILA Christian, Graduate Student LANDOR Sebastian, Graduate Student LERCHE Martina, Undergraduate Student MAMAEVA Veronika, Postdoctoral Fellow NIEMI Rasmus, Undergraduate Student NIINIMAKI Jenni, Undergraduate Student PRABHAKAR Neeraj, Graduate Student RÅTTS Natalie, Laboratory Technician SAARENTO, Helena, Laboratory Technician SARINKO Sara, Undergraduate Student SJÖQVIST Marika, Graduate Student Targeting Strategies for Gene Therapy SAVONTAUS Mikko, Affiliated Group Leader, Adjunct Professor EEROLA Kim, Graduate Student MATTILA Minttu, Graduate Student Regulation and Function of Heat Shock Transcription Factors SISTONEN Lea, Group Leader, Professor AHLSKOG Johanna, Postdoctoral Fellow ASPELIN Camilla, Graduate Student BERGMAN Heidi, Graduate Student BJÖRK Johanna, Postdoctoral Fellow BLOM Malin, Undergraduate Student BUDZYNSKI Marek, Graduate Student CRUL Tim, Visiting Scientist DA SILVA Alejandro, Undergraduate Student ELSING Alexandra, Graduate Student HENRIKSSON Eva, Senior Scientist HIMANEN Samu, Undergraduate Student JOUTSEN Jenny, Graduate Student LUNDSTEN Emine, Undergraduate Student LUSTIG Heidi, Undergraduate Student PUUSTINEN Mikael, Undergraduate Student ROOS-MATTJUS Pia, Senior Scientist SAARENTO Helena, Research Assistant SANDQVIST Anton, Postdoctoral Fellow TÓTH Noémi, Visiting Scientist VAINIO Petra, Graduate Student VASARA Jenni, Research Assistant VIHERVAARA Anniina, Graduate Student Cancer Cell Signaling WESTERMARCK Jukka, Group Leader, Professor ARSIOLA Tiina, Coordinator CVRLSEVIC Anna, Postdoctoral Fellow KALEVO-MATTILA Taina, Laboratory Technician KAUKO Otto, Graduate Student KAUR Amanpreet, Graduate Student LAINE Anni, Graduate Student NIEMELÄ Minna, Postdoctoral Fellow OKKERI Juha, Postdoctoral Fellow POKHAREL Yuba, Postdoctoral Fellow PUKONEN Inga, Laboratory Technician SITTIG Eleonora, Graduate Student XI Qiao, Graduate Student Adenosine Deaminases ZAVIALOV Andrey, Group Leader, Academy of Finland Research Fellow HASSAN KHAN Meraj, Graduate Student LIU Chengquian, Graduate Student MUKIIENKO Yuliia, Graduate Student RAI Balwant, Graduate Student SKALDIN Maksym, Graduate Student VERWIJMEREN Joyce, Undergraduate Student THE FINNISH MICROARRAY AND SEQUENCING CENTRE http://fmsc.btk.fi Contact information: Turku Centre for Biotechnology, BioCity, Tykistökatu 6A, P.O. Box 123, FIN-2050 Turku, Finland. Tel. +358-2-333 8041 Fax +358-2-251 8808. Email: [email protected] Heads/Coordinators Prof. Riitta Lahesmaa Dr. Attila Gyenesei (FMSC operation and services; bioinformatics) Dr. Riikka Lund (Next-generation sequencing, epigenomics and chromatin structure applications) Dr. Juha-Pekka Pursiheimo (Next-generation sequencing and personal sequencing applications) Affiliated group leaders: Bioinformatics: Dr. Reija Autio, Dr. Laura Elo-Uhlgren,, Prof. Harri Lähdesmäki, Prof. Matti Nykter. Next-generation sequencing: Prof. Jorma Palvimo Technical Team: Bishwa Ghimire, Bogata Fezazi, Päivi Junni, Sini Junttila, Leni Kauko, Leena Kytömäki, Asta Laiho, Oso Rissanen, Reija Venho, Eveliina Virtanen, Sanna Vuorikoski Steering Committee: Prof. Olli Carpén, Chair (University of Turku), Prof. Eva-Mari Aro (University of Turku), Prof. Klaus Elenius (University of Turku), Prof. Riitta Lahesmaa (University of Turku), Prof. Tarja Laitinen (University of Turku), Prof. Harri Lähdesmäki (University of Turku, Aalto University), Prof. Craig Primmer (University of Turku), Prof. Harri Savilahti (University of Turku), Prof. Lea Sistonen (Åbo Akademi University), Prof. Stina Syrjänen (University of Turku) Core facility description: The Finnish Microarray and Sequencing Centre (FMSC) is an internationally recognized Functional Genomics Core Facility that provides state-of-the-art research technologies and services in the areas of genomics, epigenomics, transcriptomics and bioinformatics for the Finnish and international scientific community. The main services include next-generation sequencing (NGS) and microarray based services mainly focusing on gene expression and its regulation as well as on epigenetics. We also provide quantitative Real-Time PCR and traditional DNA sequencing services. Our services cover all the steps from experimental planning and design to sample processing and bioinformatics data analysis. The Centre also regularly organizes courses, symposia and training for its users. Seminars and practical courses on microarrays, NGS and related bioinformatics are held frequently to facilitate knowledge transfer within the field. Since 2010 FMSC has had a key role within the Biocenter Finland national infrastructure program. According to the division of tasks within the Genome-wide Methods network, our Centre focuses 22 23 From left to right: Back row: Bogata Fezazi, Leni Kauko, Juha-Pekka Pursiheimo, Päivi Junni, Attila Gyenesei and Riikka Lund. Front row: Sanna Vuorikoski, Pasi Soidinsalo, Eveliina Virtanen, Asta Laiho, Sini Junttila, Cristina Valensisi, Reija Venho, Oso Rissanen and Kalyan Pasumarthy. on developing technologies in the areas of gene expression and its regulation; one of the key goals in the Centre is to develop and implement advanced techniques and provide services for epigenomic applications. Funding: Biocenter Finland University of Turku Åbo Akademi University Users: FMSC has provided genomics and transcriptomics services for over a decade, and thereby has gained a large customer base. FMSC processes annually thousands of microarray and NGS samples. In 2012 the Centre carried out 80 projects on NGS and microarray platforms from 51 research groups and analysed more than 2300 samples. The QPCR service ran > 2000 plates and was used by 116 research groups. The Centre’s Sanger sequencing service analysed > 4000 samples for 83 research projects. With our contribution, many papers were published during the last few years in high-quality journals (such as Nature Immunology, Immunity, Science). Publications with FMSC contributions and coauthors in 20102012 Publications 24 2012 FMSC contributions FMSC coauthors 2012 46 13 2011 36 2 2010 30 6 25 CELL IMAGING CORE http://www.btk.fi/cell-imaging/ Coordinator: Pasi Kankaanpää, M.Sc., Turku Centre for Biotechnology, BioCity, Tykistökatu 6B, FI-20520 Turku, Finland. Tel. +358 40 522 1090. Email: [email protected] Technical Team/Technical Team leaders: Jouko Sandholm, M.Sc., Senior Researcher Microscopy, Email: [email protected]; Markku Saari, M.Sc., Researcher Microscopy, Email: [email protected]; Jari Korhonen, M.Sc., Researcher Microscopy, Email: [email protected]; Perttu Terho, M.Sc., Technical Engineer Flow Cytometry, Email: perttu.terho@ btk.fi; Ketlin Adel, Researcher Flow Cytometry, Email: [email protected]. Steering Committee: Prof. Olli Carpén, M.D., Ph.D., University of Turku; Prof. John Eriksson (chairman), Ph.D., Åbo Akademi University; Prof. Jyrki Heino, M.D., Ph.D., University of Turku; Prof. Pekka Hänninen, Ph.D., University of Turku; Prof. Sirpa Jalkanen, M.D., Ph.D., University of Turku; Prof. Riitta Lahesmaa, M.D., Ph.D., University of Turku; Prof. Olli Lassila, M.D., Ph.D.; Prof. Matti Poutanen, Ph.D., University of Turku; Prof. Lea Sistonen, Ph.D., Åbo Akademi University; Kid Törnquist, Ph.D., Åbo Akademi University From left to right. Back row: Jouko Sandholm, Eleanor Coffey and Jari Korhonen. Front row: Markku Saari, Pasi Kankaanpää, Ketlin Adel and Perttu Terho. 26 Core facility description: The mission of the Cell Imaging Core (CIC) is to provide state-ofthe-art cell imaging and flow cytometry instruments and services to scientists and students mainly in the Turku area, but also elsewhere. Importantly, CIC is open to both academic and industrial researchers, and our goal is to have an open access policy that serves the national and international research community broadly. CIC services include a wide range of flow cytometry and cell sorting instruments and both basic and advanced light microscopes and other instruments. A total of more than 25 instruments are available, supporting a wide range of applications. Our services also include technical training to local and visiting researchers, consultation on experimental design and image acquisition, assistance in device maintenance, and providing ongoing education in theory and practice by organizing training courses and international workshops. We also constantly evaluate new methods and tools, implement relevant advances in hardware and software, and function as an organizing node in the cell imaging development of the Turku campus. Because reliably processing and quantifying data obtained with imaging devices has become as important as the data acquisition itself, CIC is also actively involved in the development of free software both for flow cytometry (Flowing Software, www.flowingsoftware. com) and microscopy (BioImageXD, www.bioimagexd.net). We also offer data analysis and visualization services and training and provide a high-end workstation for the post-processing needs of our customers. Other areas of expertise at CIC included STED super-resolution microscopy, live cell imaging, advanced confocal microscopy applications, FCS, laser-capture micro-dissection, high-throughput cell sorting and atomic force microscopy. 27 In 2012 CIC streamlined its economy, user policies, and quality control. We also acquired several new instruments, such as a Carl Zeiss LSM780 high-end confocal microscope, and a BioRad ChemiDoc gel imaging device. Importantly, we also established collaboration agreements with other major owners of light microscopes in BioCity, and now offer these instruments (e.g. Leica STED super-resolution, Leica Matrix high-throughput and Leica multi-photon confocal microscopes) as services through CIC. These collaboration agreements enable us to offer a wider range of services to our customers in a centralized manner, and they help the local light microscopy community to improve its economy and device maintenance. In 2012 CIC personnel taught on different courses and workshops in total more than 100 hours, among these a Turku BioImaging Summer School on image processing and a Turku Bionet workshop on how to prepare images for publication. CIC also introduced a new popular seminar series, Lost In Imaging, which focuses on practical and technical issues instead of scientific ones. Importantly, Lost in Imaging seminars are broadcast as webinars and recorded for later online viewing. In 2012 CIC services were used in approximately 33 peer reviewed, high quality scientific publications, among them the publication of the BioImageXD software in Nature Methods. CIC also continued to be the central representative of light microscopy and cell imaging in the Turku BioImaging organization, which has successfully brought all bioimaging in Turku under the same umbrella, the effects of which can be seen as increased funding and user numbers. Turku BioImaging has also improved our overall reputation and recognizability both nationally and internationally, and provides a positive atmosphere of collaboration under which bioimaging can be effectively developed. In 2012 CIC also actively continued to participate in the national Finnish BioImaging organization, and in the extensive Euro-BioImaging organization, which is currently under construction phase. Recent statistics show that CIC has grown to become the largest and most actively used light microscopic imaging facility in Finland. In 2012, our services (including collaboration instruments) were used by more than 300 people from more than 100 research groups, 20% of who came from outside our home universities. As the number of instruments continues to increase, and the activities in national and European organizations continue to become more prominent, we expect our usage numbers to continue to rise. This is a major challenge for CIC, requiring seamless collaboration with our customers, and secure funding for salaries for our personnel, including software and IT services. The cell imaging core is best contacted by our new designated email addresses and phone numbers for microscopy: microscopy@btk. fi, 044 - 923 1356, and for flow cytometry: [email protected], 044 - 923 1322. We warmly thank our users and collaborators for 2012 and look forward to future challenges together! Funding: The Academy of Finland, University of Turku, Åbo Akademi University, BioCity Turku Research Groups, Biocenter Finland, Health and Welfare Ministry 28 PROTEOMICS FACILITY http://www.btk.fi/proteomics Director: Garry Corthals, Ph.D. (2005). Address: Turku Centre for Biotechnology, BioCity, Tykistökatu 6, P.O. Box 123, FI-20521 Turku, Finland. Tel. +358-2-333 8889, Fax. +358-2-2158808. E-mail: [email protected] Personnel: Senior scientists: Anne Rokka, Ph.D.; Dorota Muth-Pawlak, Ph.D.; Susumu Imanishi, Ph.D.; Laboratory Engineer: Arttu Heinonen, M.Sc.; Technician: Pekka Haapaniemi, M.Sc. Steering Committee: Prof. Eva-Mari Aro (University of Turku), Dr. Eleanor Coffey (Åbo Akademi University), Prof. John Eriksson (Åbo Akademi University), Prof. Jyrki Heino (University of Turku), Prof. Riitta Lahesmaa (CBT), Prof. Matti Poutanen (University of Turku), Prof. Craig Primmer (University of Turku), Prof. Jukka Westermarck (CBT) and Prof. Johanna Ivaska (VTT & CBT) General description: The Turku Proteomics Facility is engaged in the development and application of proteomics and mass spectral methods in key areas of life science research. In doing so we have developed a wide basis of operation and expertise in Quantitative proteomics, Post-translational modification analysis, Imaging mass spectrometry, Biological mass spectrometry, Protein separation and Bioinformatics. The Mission of the Facility is to advance mass spectral methods and instrumentation to meet the needs in molecular biotechnology and medicine. Our goals are to identify new areas appropriate for mass spectrometry in biological sciences and to develop new approaches involving mass spectrometry, to apply cuttingedge mass spectrometry to tackle critical questions in biological sciences, and train students, postdoctoral fellows and practicing scientists in the use of mass spectrometry and encourage its wide and appropriate use. The facility receives funding locally through the University of Turku. National funding is provided for the facility to serve as a technology platform through financial support of Biocentre Finland. Nationally the facility spearheads mass spectrometric developments, training and application in quantitative analysis of proteins and proteomes, and analyses of PTMs. Analytical services: The facility offers access to advanced methods and sophisticated instrumentation that enable high-content protein and proteome measurements. Most services involve mass spectral methods integrated with services ranging from protein and peptide enrichment workflows for large-scale analysis of proteomes to detailed characterisation of single proteins. We aim to offer the best possible analytical proteomics services to bioscience researchers 29 in academia and industry, both locally and nationally through Biocentre Finland coordinated activities. A full representation of our services in 2012 were as follows: · Shotgun / discovery proteomics – ‘-omic-scale’ analysis of cells, tissues and fluids is available in all life sciences. Several integrated fractionation techniques have been developed to provide deep proteome coverage from exquisite sample amounts. · Quantitative proteomics – analysis of proteomes following isobaric or isotopic labelling with reagents such as iTRAQ and SILAC is offered. · Label-free quantitation – we have established a framework for label-free quantitative analysis, particularly useful for large-scale clinical studies. · Targeted quantitation – sensitive and selective qualitative or quantitative measurements of specific sets of proteins were introduced. · Post-translational modifications – a long standing history with phosphorylation analysis exists on campus, and we have expanded our ‘PTM tool set’ through newly developed methods by various closely affiliated groups, including sumoylation analysis. · Imaging mass spectrometry – imaging of tissues is offered as a collaborative service with the proteomics research group. · Biological mass spectrometry – various analytical measurements for protein, peptide and small molecule structure determination, mass determination and peptide and protein purity determination are offered. · Protein separation – numerous separation technologies including liquid chromatography and a variety of gel based methods such as 1-DE, 2-DE and peptide-IEF are available. · Bioinformatics – in all areas of proteomics bioinformatics services are offered including identification, quantitation and validation studies, and software development. Major mass spectrometry instrumentation: · For ESI-MS/MS – Q-Star Elite, LTQ Velos Orbitrap Pro with ETD, Q Exactive and TSQ Vantage · For MALDI-MS/MS – Ultrafelx II Funding: University of Turku Åbo Akademi University, Biocenter Finland, The Academy of Finland, City ofTurku, Ministry of Education, Centre of Expertise of Southwest Finland, ?, the Systems Biology Research Program and European Cooperation in Science and Technology (e-COST), Seventh Framework Programme (FP7). Users: The Turku Proteomics Facility assists costumers from national and international universities, research institutes and companies.in their scientific objectives. From left to right. Back row: Susumu Imanishi, Arttu Heinonen and Anne Rokka. Front row: Pekka Haapaniemi, Dorota Muth and Garry Corthals. 30 31 PROTEIN CRYSTALLOGRAPHY CORE FACILITY http://www.btk.fi/crystallography/ Head: Anastassios C. Papageorgiou, Ph.D., Adjunct Professor in Biochemistry and Structural Biology Turku Centre for Biotechnology, BioCity, Tykistökatu 6A, FI-20521 Turku, Finland. Tel. +358-2-3338012, Fax +358-2-3338000. E-mail: [email protected] structure-function relationship of biological macromolecules in key biological processes. Funding: Systems Biology research program, Biocenter Finland, University of Turku Users Main users include groups from UTU and ÅA as listed in http:// www.sci.utu.fi/projects/biokemia/bioxlabs/. Each group has at least three other collaborations. Technical Team: Technical support: Juha Strandén, Pasi Viljakainen. Computational support: Petri Vahakoski, Mårten Hedman Steering committee: Jyrki Heino, Professor, Department of Biochemistry and Food Chemistry, University of Turku; Reijo Lahti, Professor, Department of Biochemistry and Food Chemistry, University of Turku; Tiina Salminen, Senior lecturer, Department of Biochemistry, Åbo Akademi; BioXlabs-Turku Description of the Facility X-ray crystallography is a proven technique for detailed structurefunction studies of biological macromolecules. The Protein Crystallography Core Facility at CBT uses state-of-the-art equipment to determine the crystal structures of various proteins and their complexes. The Facility consists of an X-ray generator (Rigaku MicroMax 007 HF), Mar345 imaging plate detector, Varimax optics, a Cryostream Cooler (Oxford Cryosystems) and several computers running under Linux operating systems for heavy duty calculations. The Facility has several workstations to run a variety of molecular graphics software (COOT, CCP4mg, PyMol, Chimera, O, XtalView, Grasp), modeling and docking programs (MODELLER, Hex, Discovery Studio, ROSETTA), and various crystallographic packages (HKL, XDS, CNS, CCP4, SHELX, SOLVE, SHARP, PHENIX) for data processing, analysis, phasing and refinement. The Facility has long expertise in all steps of a crystal structure determination: protein purification, crystallization, data collection (both in-house and in synchrotron radiation sources), data processing, phase determination, refinement and detailed analysis of the final structure. Incubators at different temperatures (4° C, 16 °C and 23 °C) for crystallization set-ups and a number of various commercial screens for establishing initial crystallization conditions are available. In addition, we can provide homology modeling services and design of mutants for functional studies as well as ab initio predictions of protein structures. Since protein crystallography requires highly pure protein preparations, we can offer full support and consultation on protein purification strategies apart from the services in structure determination and modeling. The Facility is able to undertake research projects for academic groups and companies, either in the form of collaborative efforts or as services. Protein Crystallography requires a multi-disciplinary approach and we are especially interested in bringing together expertise from various groups in order to better understand the 32 The X-ray generator and imaging plate detector. Diffraction image recorded in the facility from a crystal grown by Anton Zavialov’s group. 33 BIOINFORMATICS CORE http://www.btk.fi/bioinformatics Contact information: Turku Centre for Biotechnology, BioCity, Tykistökatu 6A, P.O. Box 123, FIN-2050 Turku, Finland. Tel. +358-2-333 8041 Fax +358-2-251 8808. Email: [email protected] Heads/Coordinators Dr. Konstantin Denessiouk (Structural Bioinformatics) Dr. Attila Gyenesei (High-throughput Bioinformatics) · Computer-based ligand docking · Analysis and prediction of effects of molecular recognition and mutations on protein function Funding: Biocenter Finland University of Turku Åbo Akademi University Users: The Bioinformatics core has users from Finnish universities, biocenters and research institutes in the field of biosciences. Technical Team: Bhanupratap Singh Chouhan, Sini Junttila, Asta Laiho, Leena Kytömäki, Bishwa Ghimire, Janne Isojärvi Core facility description: The bioinformatics core at the Turku Centre for Biotechnology is divided into Structural Bioinformatics and High-throughput Bioinformatics facilities. The main goal of the Structural Bioinformatics Core is to apply methods and techniques of bioinformatics to study biological macromolecules, their interactions and function. We work in close collaboration with experimental groups and are able to provide structure-related analysis and prediction in different biological systems. The core works closely with the CSC Finnish IT Center for Science, the Finnish national supercomputing centre and the Structural Bioinformatics Laboratory at the Åbo Akademi University. High-throughput bioinformatics complements experimental genomics and transcriptomics by storing, analysing and integrating data and generating hypotheses to guide the design of new experiments to further elucidate gene function. The core provides services in the analysis of microarray and deep sequencing data. In addition to providing data analysis and data integration services we have robust methods for the design of experiments and novel microarrays for both diagnostics and biological marker selection. Our analysts are supported by robust super-computing facilities and state-of-the-art software. Team members are engaged in the ongoing development of advanced analysis tools and research on generating novel approaches for the analysis of high-throughput data sets. The main services of our core are: · Experimental design consultation · Data analysis of various microarray and deep sequencing data types · Data analysis education and training · Computer-based analysis of protein-protein and proteinligand interactions · Computer-aided prediction and intelligent molecular modeling and design 34 35 VIRUS VECTOR FACILITY http://virusvec.btk.fi/ Coordination Eleanor Coffey, Ph.D., Adjunct Professor in Cellular and Molecular Biology, Turku Center for Biotechnology, BioCity, 5th floor, Tykistokatu 6, FI-20521, Finland. Advisors and collaborators at Turku Center for Biotechnology: Jukka Westermarck, M.D., Ph.D., Professor, Mikko Savantaus, M.D., Ph.D. Technical Team Ketlin Adel, Laboratory Technician, Email: [email protected] The Virus Vector Facility produces viral vectors for local and national research groups. Since 2010, the Virus Vector Facility has participated in the national infrastructure network on Viral Gene Transfer, funded by the Biocenter Finland organisation. Our primary function is to facilitate the use of viral vectors by local researchers and researchers in other parts of Finland. To this end, the virus vector facility · propagates adenoviruses and produces lenti vectors expressing genes of interest, as a research service · maintains a fully equipped bio-safety level-2 lab where all equipment for viral production and safe sample monitoring are provided · supplies working protocols and consultation on production and safe handling of adeno and lenti vectors · coordinates a network of local experts from whom consultation on design of viral vectors can be sought The virus vector facility has a national user base with customers from the universities of Turku, Oulu and Helsinki as well as from biotech companies. In addition to customer service, our infrastructure is used by 50 local researchers producing adenoviruses, adenoassociated virus, retroviruses and lenti vectors for their research. These viruses are used to obtain high efficiency gene transfer in difficult to transfect cells such as primary cultures of T lymphocytes and neurons. They are also used in vivo in for transduction of cells in brain and for in vivo cancer studies. Use of viral gene transfer for gene knockdown including stable knockdown studies is also popular. To build on local expertise in gene transfer technologies, the Virus Vector Facility networks with experts in viral vector design. Thus a number of local experts on retroviruses and alpha-viruses are available for consultation on vector design, production and concentration. From left to right: Mikko Savontaus, Eleanor Coffey and Ketlin Adel. 36 37 MECHANISMS AND BIOSENSORS OF GTPASES Principle investigator: Daniel Abankwa, PhD, Docent (Adjunct Professor) at Åbo Akademi University, Academy of Finland Research Fellow. Tel. +358-2-3336969, Fax. +358-2-3338000. Email: [email protected] In the last three years, we have described an additional mechanism, which provides the missing structure-function link for small GTPase specificity. Using a combination of computational biology and ex vivo biophysical measurements, we have recently described a novel switch III. This is formed by the β2-β3 loop and helix α5, and is associated with the orientation of the G domain on the membrane. Thus the Ras orientation is stabilized by the HVR and helix α4 (Figure). We also showed that this orientation-switch is specific for different Ras isoforms, regulates GTPase signalling and combines with lateral segregation of Ras. Biography: Daniel Abankwa (b. 1972) graduated in Chemistry (Dipl. Chem.) from the Georg-August University in Göttingen in 1997 and received his PhD in Molecular Neurobiology from the Heinrich-Heine University Düsseldorf (2001). In 2002, he joined Prof. Horst Vogel at the EPFL in Lausanne as a Postdoc to become proficient in quantitative fluorescence techniques. In 2006, he went to the Institute for Molecular Biosciences in Brisbane, Australia with a Fellowship from the Swiss National Science Foundation. With Prof. John Hancock he worked as a senior postdoctoral fellow on Ras nanoclusters and discovered a novel orientation-switch III mechanism in Ras on the membrane. In 2008 he joined Prof. Kirill Alexandrov as a senior scientist/ junior group leader at the same institute, to work on Rab nanoclustering and a chemical screening project to identify lipid transferase inhibitors. In July 2011, Daniel joined the Turku Centre for Biotechnology. In June 2011 he became Docent at Åbo Akademi University and since September 2011 he is holding an Academy of Finland Research Fellowship. Research Questions: · We are interested in understanding the molecular and structural determinants of GTPase isoform specificity. · Building on our novel mechanistic insight, we are constructing specific biosensors to detect GTPase activity · Finally, we are applying our insight into the design of novel screening assays, which will allow the identification of novel isoform specific drugs. · What is the (path)physiological role of nanoclustering? Personnel: Postdocs: Olga Blazevics, Camilo Guzman, Alessio Ligabue, Anja Mai, Christina Oetken-Lindholm, Elina Siljamäki; Graduate students: Arafath Kaja Najumudeen, MSc; Maja Solman, MSc The novel orientation-switch III – the coding mechanism for small GTPase isoform specificity. Membrane anchored H-ras exists in two orientationconformers. Reorientation (blue curved arrow) was associated with a novel switch III region (red arrows) and is stabilized by membrane contacts of either the HVR (green; left) or helix α4 (blue; right). Description of the project Despite 30 years of intensive research, it is still not possible to block small GTPases, in particular Ras, specifically to treat cancer and other diseases. The major problem is to find a structural ‘pocket’ or mechanism that is characteristic for one out of the over 150 structurally highly related small GTPases. Crystal structures provided detailed insight into the soluble G domain, revealing that two parts of the molecule change their conformation upon GTP-mediated activation. These structural elements, switch I and II, are conserved in all GTPases and therefore not suitable for specific drug-targeting. However, in the last few years novel structural insight emerged that takes the organisation of Ras in the membrane into account. Funding: For almost two decades, the lipid modified C-terminal HyperVariable Region (HVR) of small GTPases was recognized as the primary structural determinant for isoform specificity. However, a mechanistic explanation as to how the HVR realizes this was missing. For Ras, we now have mechanistic insight how the HVR is actually involved in this. Distinct HVRs of H-, N- and K-ras4B guide the lateral segregation into distinct nanoscopic proteo-lipid domains (nanoclusters) in the plasma membrane. From these distinct nanoclusters, isoform specific signalling emerges. 38 The Academy of Finland, EU 7th framework (Marie-Curie grant), Cancer Society Finland, Biocenter Finland, Sigrid-Juselius Foundation Collaborators: Prof. Alemayehu Gorfe and Prof. John Hancock (UT Medical School, Houston, USA), Prof. Kirill Alexandrov (Institute for Molecular Bioscience, Brisbane, Australia), Dr. Christian Eggeling (Max-Planck Institute Göttingen, Germany), Prof. Johanna Ivaska (VTT, Turku Centre for Biotechnology), Dr. Harri Härmä (University of Turku), Prof. Dimitrios Stamou (University of Copenhagen, Denmark), Prof. Jukka Westermarck (Turku Centre for Biotechnology), Prof. Parton (Institute for Molecular Bioscience, Brisbane, Australia), Dr. Krishnaraj Rajalingam (University of Frankfurt, Germany), Prof. Mike Waters (Institute for Molecular Bioscience, Brisbane, Australia) Selected Publications: Köhnke M, Schmitt S, Ariotti N, Piggott AM, Parton RG, Lacey E, Capon RJ, Alexandrov K & Abankwa D (2012) Design and Application of In Vivo FRET Biosensors to Identify Protein Prenylation and Nanoclustering Inhibitors. Chemistry & Biology 19: 866–874 39 Sinha B, Köster D, Ruez R, Gonnord P, Bastiani M, Abankwa D, Stan RV, Butler-Browne G, Vedie B, Johannes L, Morone N, Parton RG, Raposo G, Sens P, Lamaze C & Nassoy P (2011) Cells respond to mechanical stress by rapid disassembly of caveolae. Cell 144: 402–413 Abankwa D, Gorfe AA, Inder K & Hancock JF (2010) Ras membrane orientation and nanodomain localization generate isoform diversity. Proceedings of the National Academy of Sciences 107: 1130–1135 Bastiani M, Liu L, Hill MM, Jedrychowski MP, Nixon SJ, Lo HP, Abankwa D, Luetterforst R, Fernandez-Rojo M, Breen MR, Gygi SP, Vinten J, Walser PJ, North KN, Hancock JF, Pilch PF & Parton RG (2009) MURC/Cavin-4 and cavin family members form tissue-specific caveolar complexes. J Cell Biol 185: 1259– 1273 Hill MM, Bastiani M, Luetterforst R, Kirkham M, Kirkham A, Nixon SJ, Walser PJ, Abankwa D, Oorschot VMJ, Martin S, Hancock JF & Parton RG (2008) PTRF-Cavin, a conserved cytoplasmic protein required for caveola formation and function. Cell 132: 113–124 Abankwa D, Hanzal-Bayer MF, Ariotti N, Plowman SJ, Gorfe AA, Parton RG, McCammon JA & Hancock JF (2008) A novel switch region regulates H-ras membrane orientation and signal output. EMBO J 27: 727–735 Abankwa D, Gorfe AA & Hancock JF (2008) Mechanisms of Ras membrane organization and signalling: Ras on a rocker. Cell Cycle 7: 2667–2673 Abankwa D, Gorfe AA & Hancock JF (2007) Ras nanoclusters: molecular structure and assembly. Semin Cell Dev Biol 18: 599– 607 From left to right. Back row: Maja Solman, Camillo Guzman, Elina Siljamäki, Cristina Oetken-Lindholm, Arafath Najumudeen, Alessio Ligabue and Olga Blaževitš. Front row: Daniel Abankwa and Anja Mai. 40 41 PROTEIN KINASE REGULATION OF BRAIN DEVELOPMENT AND DISEASE Principle investigator: Eleanor Coffey, Ph.D., Academy Research Fellow, Turku Centre for Biotechnology, Åbo Akademi and Turku University, BioCity, Tykistokatu 6B, FI-20521 Turku, Finland. Tel. +358-2-3338605, Fax. +358-2-3338000. Email: [email protected] Homepage: http://www.btk.fi/index.php?id=1240 Biography: Eleanor Coffey (b. 1967) graduated from Trinity College Dublin in 1990 and received her Ph.D. from the University of Dundee in 1994. She received a Wellcome Trust fellowship to carry out postdoctoral research in Prof. Karl Åkerman’s laboratory from 1994-1997. In 1997 she founded the Neuronal Signalling group at Åbo Akademi and in 2000 joined Turku Centre for Biotechnology as a group leader in molecular and cellular biology. In addition to running a research group, she directs the Cell Imaging Core at Turku Centre for Biotechnology and coordinates the nordic network on Imaging in Biology and Medicine. She was appointed to an Academy of Finland Research Fellow post from 2008 to 2013. Personnel: Postdoctoral researchers: Erika Freemantle, Ph.D., Artur Padzik, Ph.D. Graduate Students: Justyna Zdrojewska, M.Sc., Emilia Komulainen, M.Sc., Hasan Mohammed, M.Sc., Prasannakumar Deshpande, M.Sc., Patrik Hollos, B.Sc., Hung Phuoc, M.Sc., Raghavendra Mysore, M.Sc., Undergraduate student: Dani Flinkman, Behnoush Fourotan, Ravi Adusmalli. Technical staff: Susanna Pyökäri. Description of the project Neurodegenerative disorders such as Alzheimer’s and Parkinson’s disease as well as stroke are characterised by the irreversible loss of nerve cell function. These diseases for which no cure is known are among the most costly to society. The protein kinase JNK is recognised as a critical player in stroke and neurodegeneration. However exactly how this family of kinases mediates cell death in the brain remains largely unknown. Although targeting of JNK for drug-based therapy is already underway, our understanding of the physiological function of JNK in the brain is in its infancy. A major challenge for signal transduction therapy is to selectively target the pathological function of signalling molecules without interfering with important physiological roles. To achieve this, our lab established a proteomics-based screen to identify protein kinase substrates and thereby broaden our understanding of kinase function. While we have used this methodology to successfully identify both novel and known substrates for JNK, p38 and PIM kinases (collaboration with Päivi Koskinen), among others (collaboration Erwin Wagner), the main focus of our research 42 is to elucidate the molecular mechanism of JNK and JNK targets in the brain. Identification of novel JNK targets such as SCG10 and MAP2, as well as others under study, has highlighted a critical role for JNK in maintaining microtubule homeostasis and subsequently regulating axodendritic architecture and nerve cell movement. Identification of the JNK phosphorylation site on kinesin-1 helped characterize a role for JNK in regulation of fast axonal transport in neurons. We combine biochemical, proteomic, cell biology and imaging methods with neuronal and organotypic cultures as well as transgenic mice to validate kinase targets and elucidate their function. In collaboration with Laurent Nyguen, we have established methods to track radial migration of neurons in the developing telencephalon using 4D imaging. In addition, we are examining dendrite and spine morphology in JNK1-/- brains using lucifer yellow iontophoretic loading followed by quantitative 3D image analysis. An important finding from our lab is the compartmentalization of JNK function in neurons into physiological and pathological pools residing in the cytoplasm and nucleus respectively. By using compartment-targeted peptide inhibitors of JNK, we have shown that nuclear JNK activity is critical for neuronal death in response to trophic deprivation (neuronal death that occurs during brain development) and excitotoxic stimuli (neuronal death that occurs during epilepsy, stroke and is contributory in neurodegenerative disorders). To explore the therapeutic potential of compartmental targeted JNK inhibitors, we are collaborating with Peter Clarke (University of Lausanne). This study investigates the value of nuclear-targeted peptide inhibitors of JNK as protectants from brain damage that occurs following stroke. Interestingly, although JNK is highly localised to the cytoplasm in neurons, we find that cytosolic JNK does not to these particular death mechanisms in neurons of the central nervous system. Instead, JNK plays a critical role in corticogenesis, being required to control the duration of two critical steps during formation of the cortex, i.e. multipolar stage transition and radial migration. This function of JNK is mediated by SCG10 and is independent of nuclear JNK activity. An important new study in our lab is a proteomic screen for LRRK2 substrates. LRRK2 is a kinase that is the most frequently mutated protein in Parkinson’s disease, both familial and sporadic. Mutations in LRRK2 lead to a gain of function in kinase activity which is believed to underlie Parkinson’s pathology. Yet, substrates for LRRK2 have remained elusive and therefore the disease mechanism is unknown. In collaboration with European partners, we are searching for LRRK2 targets in brain using a shot-gun approach. We then examine the function of these targets in neurotoxicity and assess their potential as biomarkers for earlier detection of Parkinson’s. We hope that in the long run this will contribute helpful information for therapeutic treatment of Parkinson’s and in the shorter term, contribute tools that can be used for earlier clinical diagnosis. Funding: The Academy of Finland, Biocenter Finland, Turku University Biomedical Sciences Graduate School, CIMO, Magnus Ehrnrooth’s Stiftelse, Suomen Kultuuri Rahasto. 43 Collaborators: Michael Courtney (University of Kuopio), Peter James (University of Lund), Aoife Boyd (National University of Ireland Galway), Tuula Kallunki (Danish Cancer Society), Thomas Herdegen (University of Kiel), Peter Clarke (University of Lausanne), Erwin Wagner (Research Institute of Molecular Pathology), Scott Brady (Univeristy of Illinois at Chicago), Laurent Nguyen (University of Liege), Päivi Koskinen (University of Turku), Aideen Long (Trinity College, Dublin). Selected Publications: Björkblom B*, Padzik A*, Mohammad H, Westerlund N, Komulainen E, Hollos P, Parviainen L, Papageorgiou AC, Iljin K, Kallioniemi O, Kallajoki M, Courtney MJ, Mågård M, James P, Coffey ET. JNK Phosphorylation of MARCKSL1 Determines Actin Stability and Migration in Neurons and in Cancer Cells. Molecular and Cellular Biology. 2012 32(17):3513-26. *equal contribution. Jonsdottir K, Zhang H, Jhagroe D, Skaland I, Slewa A, Björkblom B, Coffey ET, Gudlaugsson E, Smaaland R, Janssen EA, Baak JP. The prognostic value of MARCKS-like 1 in lymph nodenegative breast cancer. Breast Cancer Research and Treatment. 2012 ;135(2):381-90. Mai, A., Veltel, S., Pellinen, T., Padzik, A., Coffey, E., Marjomäki, V., Ivaska, J. Competetive binding of Rab21 and p120RasGAP to integrins regulates receptor traffic and migration. Journal of Cell Biology. 194(2), 291-306, 2011. Westerlund N, Zdrojewska J, Padzik A, Komulainen E, Björkblom B, Rannikko E, Tararuk T, Garcia-Frigola C, Sandholm J, Nguyen L, Kallunki T, Courtney MJ, Coffey ET. Phosphorylation of SCG10/ stathmin-2 determines multipolar stage exit and neuronal migration rate. Nat Neurosci. 2011, 14(3):305-13. Mai A, Veltel S, Pellinen T, Padzik A, Coffey E, Marjomäki V, Ivaska J. Competitive binding of Rab21 and p120RasGAP to integrins regulates receptor traffic and migration. J Cell Biol. 2011 Jul 25;194(2):291-306. Matlawska-Wasowska K, Finn R, Mustel A, O’Byrne CP, Baird AW, Coffey ET, Boyd A. The Vibrio parahaemolyticus Type III Secretion Systems manipulate host cell MAPK for critical steps in pathogenesis. BMC Microbiol. 2010 Dec 30;10:329. Uusi-Oukari M, Kontturi LS, Coffey ET, Kallinen SA. (2010) AMPAR signaling mediating GABA(A)R delta subunit up-regulation in cultured mouse cerebellar granule cells. Neurochem Int. Filén S, Ylikoski E, Tripathi S, West A, Björkman M, Nyström J, Ahlfors H, Coffey E, Rao KV, Rasool O, Lahesmaa R. (2010) Activating transcription factor 3 is a positive regulator of human IFNG gene expression. J Immunol. 184:4990-4999. Podkowa M, Zhao X, Chow CW, Coffey ET, Davis RJ, Attisano L. (2010) Microtubule stabilization by bone morphogenetic protein receptor-mediated scaffolding of c-Jun N-terminal kinase promotes dendrite formation. Mol Cell Biol. 30:22412250. 44 Morfini, G., You, Y., Pollema, S., Kaminska, A., Pigino, G., Liu, K., Yoshioka, K., Björkblom, B., Coffey, E.T., Bagnato, C., Han, D., Huang, C., Banker, G. and Brady, S.T. (2009) Inhibition of fast axonal transport by pathogenic Huntingtin involves activation of JNK3 and phosphorylation of kinesin-1. Nature Neuroscience, 12:864-871. Waetzig, V, Wacker, U, Haeusgen, Björkblom,B, Courtney, M.J., Coffey, E.T. Herdegen, T. (2009) Concurrent protective and destructive signalling of JNK2 in neuroblastoma cells. Cellular Signalling, 21: 873-880. Naumanen, T., Johansen, L.D., Coffey, E.T., Kallunki, T. (2008) Loss of function of IKAP/ELP1: Could neuronal migration defect underlie familial disautonomia? Cell Adhesion and Migration, 2:236-239. Björkblom B, Vainio JC, Hongisto V, Herdegen T, Courtney MJ, Coffey ET. (2008) All JNKs can kill, but nuclear localization is critical for neuronal death. Journal of Biological Chemistry, 283:19704-13. Hongisto, V., Vainio, J.C., Thompson, R., Courtney, M.J., Coffey, E.T. (2008) The Wnt pool of GSK-3-beta is critical for trophic deprivation induced neuronal death. Molecular and Cellular Biology, 285:1515-27. Dan Johansen, L., Naumanen, T., Knudsen, A., Westerlund, N., Gromova, I., Junttila, M., Nielsen, C., Bottzauw, T., Tolkovsky, A., Westermarck, J., Coffey, E.T., Jäättelä, M., Kallunki, T. (2008) IKAP localizes to membrane ruffles with filamin A and regulates actin cytoskeleton organization and cell migration. Journal of Cell Science, 121:854-64. Westerlund, N., Zdrojewska, J., Courtney, M., Coffey, E. (2008) SCG10 as a molecular effector of JNK1: Implications for the therapeutic targeting of JNK in nerve regeneration. Expert Opinion on Therapeutic Targets. 12:31-43. Review. Semanova, M.M., Mäki-Hokkanen, A.M.J., Cao, C., Komarovski, V., Forsberg, K.M., Koistinaho, M., Coffey, E.T., Courtney, M.J. (2007) Rho mediates calcium-dependent activation of p38a and subsequent excitotoxic cell death. Nature Neuroscience, 10(4):436-443. Tararuk, R., Östman, N., Li, W., Björkblom, B., Padzik, A., Zdrojewska, J., Hongisto, V., Herdegen, T., Konopka, W., Courtney, M.J., Coffey, E.T. (2006) JNK1 phosphorylation of SCG10 determines microtubule dynamics and axodendritic length. Journal of Cell Biology. 173: 265-277. Björkblom, B., Östman, N., Hongisto, V., Komarovski, V., Filen, J., Nyman, T., Kallunki, T., Courtney, M., Coffey, E. (2005) Constitutively active cytoplasmic JNK1 is a dominant regulator of dendritic architecture; role of MAP2 as an effector. Journal of Neuroscience. 25: 6350-6361. Yang, J., Lindahl, M., Lindholm, P., Virtanen, H., Coffey, E., Runeberg-Roos, P., Saarma, M. (2004) PSPN/GFRalpha4 has a significantly weaker capacity than GDNF/GFRalpha1 to recruit RET to rafts, but promotes neuronal survival and neurite outgrowth. FEBS Letters.569: 267-271. 45 Cao, J., Semenova, M.M., Solovyan, V.T., Han, J., Coffey, E.T., Courtney, M.J. (2004) Distinct requirements for p38alpha and c-Jun N-terminal kinase stress-activated protein kinase s in different forms of apoptotic neuronal death. Journal of Biological Chemistry. 279: 35903-35913. Hongisto, V., Smeds, N., Brecht, S., Herdegen, T., Courtney, M.J., Coffey, E.T. (2003) Lithium blocks the c-Jun stress response and protects neurons via its action on glycogen synthase kinase 3. Molecular and Cellular Biology. 23: 6027-6036. Coffey, E.T., Smiciene, G., Hongisto, V., Cao, J., Brecht, S., Herdegen, T., Courtney, M.J. (2002) c-Jun N-terminal protein kinase (JNK) 2/3 is specifically activated by stress, mediating c-Jun activation, in the presence of constitutive JNK1 activity in cerebellar neurons. Journal of Neuroscience. 22: 43354345. Hietakangas, V., Elo, I., Rosenstrom, H., Coffey, E.T., Kyriakis, J.M., Eriksson, J.E., Sistonen, L. (2001) Activation of the MKK4-JNK pathway during erythroid differentiation of K562 cells is inhibited by the heat shock factor 2-beta isoform. FEBS Letters. 505: 168-172. Coffey, E.T., Hongisto, V., Dickens, M., Davis, R.J. and Courtney, M.J. (2000) Dual roles for c-Jun N-terminal kinase in developmental and stress responses in cerebellar granule neurons. Journal of Neuroscience. 20: 7602-7613. Courtney, M.J. and Coffey, E.T. (1999) The mechanisms of ARA-C induced apoptosis of differentiating cerebellar granule neurons. European Journal of Neuroscience. 11: 1073-1084. Coffey, E.T. and Courtney, M.J. (1997) Regulation of SAPKs in CNS neurons. Biochem Soc Trans. 25: S568. From top to bottom. Left side: Artur Padzik, Hung Phuoc, Eleanor Coffey, Susanna Pyökäri, Dani Flinkman and Hasan Mohammad. Right side: Prasannakumar Deshpande, Patrik Hollos, Justyna Zdrojewska and Erika Freemantle. 46 47 TRANSLATIONAL PROTEOMICS Principal investigator: Garry Corthals, Ph.D. Address: Turku Centre for Biotechnology, BioCity, Tykistökatu 6, FI-20521 Turku, Finland. Tel. +358-2-333 8889, Fax. +358-2-2158808. E-mail: [email protected] Biography: Garry Corthals received his PhD in 1997 and has since worked in the field of biomedical proteomics. He has held positions at the Medical School, University of Washington, Seattle, the Garvan Institute for Medical Research, Sydney, and Geneva University Hospital and Medical Faculty. He is now leads a research group in Translational Proteomics at the Turku Centre for Biotechnology that focuses on developing and applying proteomics methods to improve personalized therapies and to understand protein level changes related to diseases primarily through the use of mass spectrometry and bioinformatics. Amongst his publications and books is the first book that appeared on Biomedical Applications in Proteomics. Besides the research group Dr Corthals is the Director of the Turku Proteomics Facility, is Chair of the Finnish Proteomics and Metabolomics technology platform, the Nordic Quantitative Proteomics network of research schools, the Nordic Signals research network and the Nordic MS imaging network and Chairs the new Developments Committee of the European Proteomics Association (EuPA). His is also co-chair of the pan European Imaging MS network. Personnel: Senior scientists: Anne Rokka, PhD; Dorota Muth-Pawlak, PhD; Mimi Nguyen, PhD; Susumu Imanishi, PhD; Tanya Lukash, PhD; Petri Kouvonen, PhD (visiting ETH Zurich 2011-2013) Graduate students: Anni Vehmas, Olli Kannaste, Veronika Suni, Darshana Kottahachchi, Thaman Chand, Avinash Yadav Lab engineer: Arttu Heinonen Technician: Pekka Haapaniemi Undergraduate students: Santosh Thatikonda Coordinator: Susanne Nees Description of the project: Our group’s focus is to develop and apply powerful proteomics tools to be used in translational and systems biology based projects, where technological developments are driven by biological questions. Of particular interest to our group are endometriosis, epilepsy and prostate cancer, as well as several others biomedical projects including the development of methods for quantitative proteomics and phosphorylation analysis driven by our group or through collaborative research. The group of researchers involved in our work has a diverse set of skills, ranging from chemistry and biochemistry, to clinical backgrounds, to computational scientists and mathematicians, reflecting a multidisciplinary environment. All of our research essentially evolves around applications in mass spectrometry (MS), which, over the past two decades MS, has emerged as the 48 method of choice to discover, measure and characterize proteins and protein networks in biological systems. For the analysis of tissues we are interested in defining and measuring changes of proteins and peptides, which of these have an impact on their microenvironment, which enter body fluids such as the blood system, and ultimately which impact on disease progression or reflect a disease state. We therefore require methods that enable highly sensitive identification and quantitation of proteins in tissues and body fluids. Measurement of proteins in tissues and tissue-substructures is pursued analysis of minute amounts of cryosectioned tissues, that ultimately enable exquisite detailing of the molecular components of cellular substructures, adding important molecular detail for regions of interest. The quantitative aspect of these measurements focuses on measuring protein change in tissues. To this end we are investigating novel computational methods that enable quantitative measurements of proteins in tissues. We are also pursuing the use of MALDI imaging MS, which now allows the simultaneous analysis of the distributions of up to hundreds of peptides and proteins directly from a tissue section or tissue array. The technique uses the masses of the peptides and proteins to distinguish between different species and thus does not require any form of labeling. These profiles can be used to obtain biomolecular signatures associated with specific histological features, adding a further handle in our quest to distinguish different regions within a tissue and to differentiate and classify tissues. Another of interest for the group is the identification and quantitation of phosphopeptides and proteins. Again we have a two-tiered approach where we are developing both laboratory procedures as well as computational methods. Our recent observations have focused the on the use of planar surfaces that act as an enrichment and analytical platform for phosphopeptide analysis, paving the way for array based analyses. Our computational methods in phosphorylation analysis focus on increasing the speed and validation of phosphorylation analysis – nowadays seen as a bottleneck delaying true HTP phosphorylation analysis. Additionally we are developing several bioinformatics tools that allow the efficient investigation of proteomics workflows in the laboratory. Funding: The Academy of Finland, TEKES, Finnish Cancer Foundations, Nordforsk, the Systems Biology Research Program, Turku Centre for Computer Science Graduate Programme (TUCS), The National Graduate School in Informational and Structural Biology (ISB), the University of Turku, COST. Collaborators: Johanna Ivaska, Jukka Westermarck, Tiina Pakula (VTT), Laura Ruohonen (VTT), Laura Elo, Tuula Nyman, Marko Pesu Selected Publications: Koch S, Scifo E, Rokka A, Trippner P, Lindfors M, Korhonen R, Corthals G, Virtanen I, Lalowski M and Tyynelä J. (2013) 49 Cathepsin D deficiency induces cytoskeletal changes and affects cell migration pathways in the brain. Neurobiol Dis. 50:107-119 Perdomo MF, Hosia W, Jejcic A, Corthals GL and Vahlne A. (2012) Human serum protein enhances HIV-1 replication and upregulates the transcription factor AP-1. Proc Natl Acad Sci U S A. 109(43):17639-17644. McDonnell L, Andrén PE and Corthals GL. J Proteomics. (2012) Imaging mass spectrometry: a user’s guide to a new technique for biological and biomedical research. Preface. J Proteomics 75(16): 4881–4882. McDonnell LA, Heeren RM, Andrén PE, Stoeckli M and Corthals GL. (2012) Going forward: Increasing the accessibility of imaging mass spectrometry. J Proteomics. 75(16):5113-5121. Santos HM, Kouvonen P, Capelo JL and Corthals GL. (2012) Isotopic labelling of peptides in tissues enhances mass spectrometric profiling. Rapid Commun Mass Spectrom. 26(3):254-262. ORGANISATION OF NEURONAL SIGNALING PATHWAYS Principal investigator: Michael Courtney, Ph.D., Affiliated Group Leader at CBT, Professor of Cell Signaling at UEF. Contact information: Molecular Signaling Laboratory, Department of Neurobiology, A.I. Virtanen Institute, University of Eastern Finland, P.O. Box1627, Neulaniementie 2, FIN-70211 Kuopio, Finland. Tel. +358 40 355 3663. Email: [email protected] Homepage: www.uef.fi/aivi/neuro/signalling Facility page: www.uef.fi/aivi/muic Biography: Michael Courtney (b. 1967) graduated from University of Cambridge in 1988 (B.A.), and the University of Dundee in 1991 (Ph.D). Postdoctoral fellowships from the Royal Society, Wellcome Trust, Academy of Finland and Sigrid Jusélius Foundation supported his quantitative imaging development and application activities from 1992 in Prof. Karl Åkerman’s laboratory in Åbo Akademi, Turku. After group leader positions at BTK from 1998, he was appointed from 2000 to a position at the A.I. Virtanen Institute, Kuopio and from 2006 to BTK. He has been affiliated with the Cell Imaging Core in Turku since its inception, and established and is director of the Multimodal Imaging Unit at Kuopio University, now the University of Eastern Finland. He was appointed to an Academy of Finland Researcher post from 2003-2008, and Professor of Cell Signaling at the University of Eastern Finland from 2008. Personnel: Post-doctoral researchers and Senior Scientists: Peter Martinsson Ph.D., Melero-Fernandez de Mera Ph.D., Ph.D, Olga Vergun Ph.D.; Graduate students: Lili Li, M.Sc., Xijun Wang, M.Sc. Technician Aila Seppänen; From left to right. Back Row: Susumu Imanish, Olli Kannaste, Dorota Muth, Pekka Haapaniemi, Elizabeth Nguyen, Susanne Nees, Darshana Kottahachchi and Thaman Chand. Fron row: Arttu Heinonen, Garry Corthals, Anne Rokka and Tanya Lukash. 50 Description of the project: Neuronal cells possess a complex architecture consisting of multiple subcellular compartments. Disease states place cells under stressful conditions. The p38 and JNK stressactivated protein kinase pathways are widely accepted to play a significant role in cell death in and outside the nervous system, and drugs directly targeting stress activated protein kinases have been under development for many years. However, these pathways also contribute to development, differentiation, and even survival and proliferation. This suggests that direct stress-activated protein kinase inhibitors may be of only limited use. In order to exploit the pathways for the development of novel neuroprotective drugs, it will be necessary to elucidate the mechanisms that organise these pathways into pools with neurodegenerative or physiological functions within the complex structure of neuronal cells. Only then can the neurodegenerative activities of the pathways be selectively eliminated. It has been suggested that this may help reduce the neuronal death that contributes to neurodegenerative conditions such as Alzheimer’s 51 and Parkinson’s diseases, increasingly major causes of death, disability and socioeconomic impact in society. Previous studies of the mammalian stress-activated MAPK pathway have revealed the existence of a plethora of upstream regulators competent to recruit this pathway. In particular, proteins with putative scaffolding actions have been found. Such components could in principle have a number of effects on the associated upstream regulator, including (i) to potentiate their ability to activate the pathway, (ii) to restrict accessibility to activators, (iii) to channel the downstream consequence to select targets and (iv) to localise these properties to specific compartments within a cell. Our lab’s aim is to elucidate how neuronal cells compartmentalise the endogenous components of the stress-activated protein kinase pathway and how specific stimuli recruit only select components of these pathways. To achieve this, we focus mainly on 3 areas: i) Signalling between post-synaptic density proteins and neuronal stress-activated protein kinase pathways; ii) Small G-protein signaling pathways regulating stress-activated protein kinases in neurons; iii) Development and implementation of approaches to imaging of intracellular signaling pathways. The mechanisms which maintain selective responsiveness to upstream stimuli and restricted downstream consequences are anticipated to be a fruitful source of potential targets for future neuroprotective strategies. Thus we also utilise the information gleaned from studies of neuronal signaling mechanisms to develop and evaluate novel neuroprotective molecules in cooperation with collaborating partners from both the pharmaceutical industry and from academia. While pursuing these scientific goals, we also implement imaging methodologies. We adapt and establish the use of a wide range of FRET-based probes of cell signaling and multiparameter imaging methods, and are combining these with libraries of RNAi tools, expression plasmids and compounds. The probes allow spatiotemporal measurement of several pathways simultaneously in the same cells. We established facilities (physically located within Biocentre Kuopio, www.uef.fi/aivi/muic) to make available to all researchers facilities for live cell High-Content Analysis (HCA), High-Throughput Microscopy (HTM) and the associated liquid handling facilities, as well as TIR-FRET and TIR-FRAP techniques. · Total Internal Reflection methods exploit the spatially restricted evanescent wave formed at the interface between media of different refractive indices, thereby surpassing the classical diffraction limits. These methods are ideally suited to measure signaling events and protein turnover at protein complexes in the plasma-membrane proximal zones of living cells, such as the neuronal postsynaptic density. · The live-cell HCA unit is now interfaced with automated storage either at ambient, cooled or from humidified CO2regulated cell incubator as well as liquid handling facilities and is suitable for high-throughput imaging studies (up to ~1000 samples/hr, ~200000 sample capacity). A second imaging station with similar sample capacity, interfaced with pipetting robot and plate reader, is under further development. This nationally unique Biocentre Finland (BF) infrastructure platform is supported by two BF networks. Our 52 group continues to establish assays permitting application of HCA methods to primary cultured neurons, stem cells and in vivo models. More details can be found via the links at www.uef.fi/aivi/muic. Funding: The Academy of Finland, the photonics programme of the th Academy of Finland the EU 7 framework project “MEMOLOAD”, The University of Eastern Finland, The Doctoral Programme in Molecular Medicine. Collaborators: Eleanor Coffey and Tassos Papageorgiou (BTK, Åbo Akademi and University of Turku), Denise Manahan-Vaughan (University of Bochum), Mark Spaller (Brown University, Providence, RI), Antti Poso and Jari Koistinaho (University of Eastern Finland) and Anita Truttman (CHUV, Lausanne University Hospital). Selected Publications: Li L-L, Ginet V, Liu X, Vergun O, Tuittila M, Mathieu M, Bonny C, Puyal J, Truttmann AC, Courtney MJ. The nNOS-p38MAPK pathway is mediated by NOS1AP during neuronal death. J Neurosci, in press. Björkblom B, Padzik A, Mohammad H, Westerlund N, Komulainen E, Hollos P, Parviainen L, Papageorgiou AC, Iljin K, Kallioniemi O, Kallajoki M, Courtney MJ, Mågård M, James P, Coffey ET. c-Jun N-terminal kinase phosphorylation of MARCKSL1 determines actin stability and migration in neurons and in cancer cells. Mol Cell Biol. 2012 Sep;32(17):3513-26. D’Orsi B, Bonner H, Tuffy LP, Düssmann H, Woods I, Courtney MJ, Ward MW, Prehn JH (2012) Calpains Are Downstream Effectors of bax-Dependent Excitotoxic Apoptosis. J. Neurosci. 32:184758. Westerlund, N., Zdrojewska, J., Padzik, A. Komulainen, E., Björkblom, B., Rannikko E., Tararuk, T., Garcia-Frigola, C., Sandholm, J. Nguyen, L., Kallunki, T. Courtney, M.J., Coffey, E.T. (2011) Phosphorylation of SCG10/stathmin-2 determines multipolar stage exit and neuronal migration rate. Nat. Neurosci. 14:305-13. Yang H., Courtney, M.J., Martinsson, P., Manahan-Vaughan, D. (2011) LTD is enhanced, depotentiation is inhibited and LTP is unaffected by the application of a selective JNK inhibitor to the hippocampus of freely behaving rats. Eur. J. Neurosci.,33:1647-55. Waetzig, V., Wacker, U., Haeusgen, W., Björkblom, B., Courtney, M.J., Coffey, E.T. and Herdegen, T. (2009) Concurrent protective and destructive signaling of JNK2 in neuroblastoma cells. Cell Signal. 21, 873-80 Hellwig, C.T., Kohler, B.F., Lehtivarjo A.-K., Dussmann, H., Courtney, M.J., Prehn, J.H. and Rehm, M. (2008) Real-time analysis of TRAIL/ CHX-induced caspase activities during apoptosis initiation. J. Biol. Chem. 283, 21676-85. 53 Björkblom, B., Vainio, J.C., Hongisto, V., Herdegen, T., Courtney, M.J. and Coffey, E.T. (2008) All JNKs can kill but nuclear localization is critical for neuronal death. J. Biol. Chem. 283, 19704-19713. Hongisto, V., Vainio, J.C., Thompson, R., Courtney, M.J. and Coffey, E.T. (2008) The Wnt pool of GSK-3β is critical for trophic deprivation induced neuronal death. Mol. Cell. Biol. 28, 15151527. Westerlund, N., Zdrojewska, J., Courtney, M.J. and Coffey, E.T. (2008) SCG10 as a molecular effector of JNK1: Implications for the therapeutic targeting of JNK in nerve regeneration. Expert Opin. Ther. Targets, 12, 1-13. Semenova, M.M., Mäki-Hokkonen, A.M.J., Cao, J., Komarovski, V., Forsberg, K.M., Koistinaho, M. Coffey E.T. and Courtney, M.J. (2007) Rho mediates calcium-dependent activation of p38α and subsequent excitotoxic cell death. Nat. Neurosci. 10, 436-443. Tararuk, T., Östman N., Li, W., Björkblom, B., Padzik, A., Zdrojewska, J., Hongisto, V., Herdegen, T., Konopka, W., Courtney M.J. and Coffey, E.T. (2006) JNK1 phosphorylation of SCG10 determines microtubule dynamics and axodendritic length. J. Cell Biol. 173, 265-277. Björkblom, B., Östman, N., Hongisto, V., Komarovski, V., Filén, J., Nyman, T.A., Kallunki, T., Courtney, M.J. and Coffey, E.T. (2005) Constitutively active cytoplasmic JNK1 is a dominant regulator of dendritic architecture; role of MAP2 as an effector. J. Neurosci. 25, 6350-6361. Cao, J., Viholainen, J.I., Dart, C., Warwick, H.K., Leyland, M.L. and Courtney, M.J. (2005) The nNOS-PSD95 interface - a target for inhibition of excitotoxic p38 stress-activated protein kinase activation and cell death. J. Cell Biol. 168, 117-126. Cao, J., Semenova, M.M., Solovyan, V.T., Han, J., Coffey, E.T and Courtney, M.J. (2004) Distinct requirements for p38α and JNK stress-activated protein kinases in different forms of apoptotic neuronal death. J. Biol. Chem. 279, 35903-35913. Solovyan, V.T., Bezvenyuk, Z., Salminen, A., Austin, C.A. and Courtney M.J. (2002) The role of topoisomerase II beta in the excision of DNA loop domains during apoptosis. J. Biol. Chem. 277, 21458-21467. Coffey, E.T., Smiciene, G., Hongisto, V., Cao, J., Brecht, S., Herdegen, T. and Courtney, M.J. 2002) JNK2/3 is specifically activated by stress, mediating c-Jun activation, in the presence of constitutive JNK1 activity in cerebellar neurons. J. Neurosci. 22, 4335-4345. Coffey, E.T., Hongisto, V., Davis, R.J., Dickens, M. and Courtney, M.J. (2000) Dual Roles for c-Jun N-terminal kinase in developmental and stress responses in cerebellar granule neurons. J. Neurosci. 20, 7602-7613. Courtney, M.J., Åkerman, K.E.O. and Coffey, E.T. (1997) Neurotrophins protect cultured cerebellar granule neurons against the early phase of cell death by a two-component mechanism. J. Neurosci. 17, 4201-4211. 54 STRUCTURAL BIOINFORMATICS Principal Investigator: Konstantin Denessiouk, Ph.D., Docent in Biochemistry. Bioinformatics Group leader. Centre for Biotechnology, Tykistökatu 6, BioCity 5th floor, Turku, 20520 Turku. E-mail: [email protected] Personnel: Bhanupratap Singh Chouhan, MSc (Bioinformatics), Graduate Student; Mari Heininen-Brown, BSc (Bioinformatics), Undergraduate Student. Areas of Expertise: Our research involves studies of protein structure and function, protein ligand interactions and protein evolution by means of molecular modeling and computational biology. The group provides large spectrum of services in computational analysis of protein/nucleic acid sequences and structures. The Structural Bioinformatics group provides support for Structural Bioinformatics and Chemical Informatics (in conjunction with the Structural Bioinformatics Laboratory, lead by Prof. Mark S. Johnson at the Åbo Akademi University); and separately, support for projects and development of high-throughput screening (HTS) of natural molecules (in conjunction with Prof. Pia Vuorela, Department of Biosciences, Åbo Akademi University). The Structural Bioinformatics Group has its main expertise in: (a)computer-based analysis of protein-protein and proteinligand interactions (b)computer-aided prediction, molecular modeling and design (c) computer-based ligand docking and analysis (d)molecular dynamics (d) analysis of effects of molecular recognition and mutations on protein function Research Projects: In collaboration with laboratories of Prof. Mark S. Johnson (Åbo Akademi University) and Prof. Jyrki Heino (University of Turku) we continue our study on Structural Evolution of Integrins and Integrin Domains (Johnson et al., 2009; Chouhan et al., 2011). Within the project, we (1) identified several matching sequences in bacteria that aligned surprisingly well with portions of the integrin subunits (Johnson et al., 2009); and, separately, described a structurederived motif, which is specific only for the metazoan integrin domains, and searched for the metazoan integrin type β-propeller domains among all available sequences from bacteria and unicellular eukaryotic organisms (Chouhan et al., 2011). In collaboration with the laboratory of Prof. Riitta Lahesmaa (Turku Centre for Biotechnology, University of Turku and Åbo akademi University), we are characterizing a novel stem cell specific protein (Närvä et al., 2011). In collaboration with the laboratory of Dr. Klaus Elenius (University of Turku), we study effects of molecular recognition and mutations on protein function in macromolecular receptor ErbB4 complexes, 55 where we aim to construct the model of the ErbB4 dimer in its active form and structurally analyze possible effects of naturally occurring mutations on the ErbB4 conformational change and the protein function. Additionally, our on-going research is focused on molecular dynamics of S100 proteins in collaboration with Prof. S. Permyakov, Russian Academy of Sciences. Separately, the group guides individual training of MSc students, in collaboration with the Structural Bioinformatics Laboratory (Åbo Akademi University), and leads a Ph.D. student in Bioinformatics and Computational Biology within the National Graduate School of Informational and Structural Biology (Åbo Akademi University). Funding: Grants from the Sigrid Jusélius Foundation, and the Borg Foundation (Åbo Akademi University); Grant from the National Graduate School in Informational and Structural Biology (ISB). Collaborators: Prof. Riitta Lahesmaa (Turku Centre for Biotechnology), Prof. Mark S. Johnson (Åbo Akademi University), Dr. Klaus Elenius (University of Turku); Prof. Jyrki Heino (University of Turku); Prof. S. Permyakov, Russian Academy of Sciences. Selected Publications: Chouhan B., Denesyuk A.I., Heino J., Johnson M.S., Denessiouk K. (2012) Evolutionary origin of the αC helix in integrins. International Journal of Biological and Life Sciences. Submitted. Närvä E., Rahkonen N., Emani M.R., Lund R., Pursiheimo J.P., Nästi J., Autio R., Rasool O., Denessiouk K., Lähdesmäki H., Rao A., Lahesmaa R. (2011) RNA Binding Protein L1TD1 Interacts with LIN28 via RNA and is Required for Human Embryonic Stem Cell Self-Renewal and Cancer Cell Proliferation. Stem Cells 30: 452-460. Chouhan B., Denesyuk A., Heino J., Johnson M.S., Denessiouk K. (2011) Conservation of the human integrin-type beta-propeller domain in bacteria. PLoS One. 6: e25069. Johnson M.S., Lu N., Denessiouk K., Heino J., Gullberg D. (2009) Integrins during evolution: evolutionary trees and model organisms. Biochim. Biophys Acta 1788: 779-789. Xhaard H., Backström V., Denessiouk K., Johnson M.S. (2008) Coordination of Na(+) by monoamine ligands in dopamine, norepinephrine, and serotonin transporters. J. Chem. Inf. Model. 48: 1423-1437. Denessiouk K.A., Denesyuk A.I., Johnson M.S. (2008) Negative modulation of signal transduction via interleukin splice variation. Proteins 71: 751-770. Denessiouk K.A., Johnson M.S., Denesyuk A.I. (2005) Novel CalphaNN structural motif for protein recognition of phosphate ions. J. Mol. Biol. 345: 611-629. Denessiouk K.A., Johnson M.S. (2003) “Acceptor-donor-acceptor” motifs recognize the Watson-Crick, Hoogsteen and Sugar “donor-acceptor-donor” edges of adenine and adenosinecontaining ligands. J. Mol. Biol. 333: 1025-1043. 56 DATA MINING AND MODELLING Principal investigators: Laura Elo, Ph.D., Adjunct Professor in Biomathematics, Department of Mathematics and Statistics, University of Turku, FI-20014 Turku, Finland. Tel. +358-2-3336027, Fax. +358-2-2310311. E-mail: [email protected], homepage: http://users.utu.fi/laliel/ Tero Aittokallio, Ph.D., Adjunct Professor in Biomathematics, EMBL Group Leader, Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Finland. Tel. +358-50-3182426. E-mail: tero. [email protected]. Homepage: http://users.utu.fi/teanai/ Olli Nevalainen, Ph.D., Professor of Computer Science, Turku Centre for Computer Science, University of Turku, FI-20014 Turku, Finland. Tel. +358-2-3338631. E-mail: [email protected] Biographies: Laura Elo received her Ph.D. in Applied Mathematics from the University of Turku in 2007. In 2008 she received a Postdoctoral Fellowship from the Academy of Finland. Currently she is an Adjunct Professor in Biomathematics at the Department of Mathematics and Statistics, University of Turku. Tero Aittokallio received his Ph.D. in Applied Mathematics from the University of Turku in 2001. In 2006-2007, he was a postdoctoral research fellow in the Systems Biology Group at Institut Pasteur, Paris. Currently he is an EMBL Group Leader at FIMM. Olli Nevalainen received his Ph.D. in 1976. From 1972 to 1976, he was a lecturer with the Department of Computer Science, University of Turku. From 1976 to 1999, he was an Associate Professor, and since 1999 a Professor in the same department. Personnel: Post-doctoral researchers: Jussi Salmi, Ph.D. Graduate students: Marja Heiskanen, M.Sc., Teemu Daniel Laajala, M.Sc., Rolf Linden, M.Sc., Sebastian Okser, M.Sc., Tomi Suomi, M.Sc., Johannes Tuikkala, M.Sc., Heidi Vähämaa, M.Sc. Undergraduate students: Maria Jaakkola, Anna Koskinen, Sami Rannikko, Harri Santa, Fatemehsadat Seyednasrollah Description of the project: We develop mathematical modelling methods and implement computational data analysis tools for biological and biomedical 57 research. A specific focus is on mining and interpreting data generated by modern high-throughput biotechnologies, such as microarrays, deep sequencing, and mass-spectrometry-based proteomic assays. Rissanen, J., Moulder, R., Lahesmaa, R., Nevalainen, O.S. (2012) Pre-processing of Orbitrap higher energy collisional dissociation tandem mass spectra to reduce erroneous iTRAQ ratios. Rapid Commun. Mass Spectrom. 26: 2099-2104. The large number of molecular components together with high technical and biological variability can make it difficult to extract pertinent biological information from background noise. Therefore, computational models and tools are needed that can effectively integrate, analyse and visualise the experimental data so that meaningful interpretations can be made. A specific computational challenge is to take full advantage of all the accumulated data, both from own laboratory and from public repositories, to obtain a comprehensive view of the system under study. Elo, L.L. and Schwikowski, B. (2012) Mining proteomic data for biomedical research. Invited review in WIREs Data Mining Knowl. Discov. 2: 1-13. We have developed data integration and data-driven optimization approaches to improve the identification of reliable molecular markers and their interaction partners in global cellular networks. The eventual goal of the research is to model and explain the observations as dynamic interaction networks of the key molecular components and mechanisms controlling the underlying systems. An integrative network-based modelling approach can provide robust and unbiased means to reveal the key molecular mechanisms behind the systems behaviour and to predict its response to various perturbations. In clinicallyoriented research, the modelling approach has the potential to improve our understanding of the disease pathogenesis and help us to identify novel molecular markers for pharmaceutical or diagnostics applications. Funding: The Academy of Finland, Turku Systems Biology Research Programme, The Finnish Funding Agency for Technology and Innovation (Tekes), Finnish Doctoral Programme in Computational Sciences (FICS), and Turku Centre for Computer Science (TUCS). Collaborators: Riitta Lahesmaa (Turku Centre for Biotechnology), Tuula Nyman (University of Helsinki), Matej Orešic (VTT Biotechnology), Benno Schwikowski (Pasteur Institute, Paris), Mats Gyllenberg (University of Helsinki), Esa Uusipaikka (University of Turku), Samuel Kaski (Helsinki University of Technology), Timo Koski (Royal Institute of Technology, Stockholm), Eija Korpelainen (CSC – IT Center for Science), Jan Westerholm (Åbo Akademi University), Esa Tyystjärvi (University of Turku), and Mauno Vihinen (University of Tampere). Selected Publications: Elo, L.L., Kallio, A., Laajala, T.D., Hawkins, R.D., Korpelainen, E. and Aittokallio, T. (2012) Optimized detection of transcription factor binding sites in ChIP-seq experiments. Nucleic Acids Res. 40: e1. Laajala, T.D., Corander, J., Saarinen, N.M., Mäkelä, K., Savolainen, S., Suominen, M.I., Alhoniemi, E., Mäkelä, S.I., Poutanen, M. and Aittokallio, T. (2012) Improved statistical modeling of tumor growth and treatment effect in pre-clinical animal studies with highly heterogeneous responses in vivo. Clin. Cancer Res. 18: 4385-4396. 58 Pahikkala, T., Okser, S., Airola, A., Salakoski, T. and Aittokallio, T. (2012) Wrapper-based selection of genetic features in genomewide association studies through fast matrix operations. Algorithms Mol. Biol. 7: 11. Tuikkala, J., Vähämaa, H., Salmela, P., Nevalainen, O.S. and Aittokallio, T. (2012) A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization. BioData Min. 5 2. Nylund, C., Rappu, P., Pakula, E., Heino, A., Laato, L., Elo, L.L., Vihinen, P., Pyrhönen, S., Owen, G.R., Larjava, H., Kallajoki, M. and Heino, J. (2012) Melanoma-associated cancer-testis antigen 16 (CT16) regulates the expression of apoptotic and antiapoptotic genes and promotes cell survival. PLoS One 7: e45382. Heiskanen, M.A. and Aittokallio, T. (2012) Mining high-throughput screens for cancer drug targets - lessons from yeast chemicalgenomic profiling and synthetic lethality. Invited Focus Article in WIREs Data Mining Knowl. Discov. 2: 263-272. Tringham, M., Kurko, J., Tanner, L., Tuikkala, J., Nevalainen, O.S., Niinikoski, H., Näntö-Salonen, K., Hietala, M., Simell, O., Mykkänen, J. (2012) Exploring the transcriptomic variation caused by the Finnish founder mutation of lysinuric protein intolerance (LPI). Mol. Genet. Metab. 105: 408-415. Lindén, R. O., Eronen, V.P. and Aittokallio T. (2011) Quantitative maps of genetic interactions in yeast - Comparative evaluation and integrative analysis, BMC Syst. Biol. 5: 45. Lahti, L., Elo, L.L., Aittokallio, T. and Kaski, S. (2011) Probabilistic analysis of probe reliability in differential gene expression studies with short oligonucleotide arrays, IEEE/ACM Trans. Comput. Biol. Bioinform. 8: 217-225. Okser, S., Lehtimäki, T., Elo, L.L., Mononen, N., Peltonen, N., Kähönen, M., Juonala, M., Fan, Y.M., Hernesniemi, J.A., Laitinen, T., Lyytikäinen, L.P., Rontu, R., Eklund, C., Hutri-Kähönen, N., Taittonen, L., Hurme, M., Viikari, J.S.A., Raitakari, O.T. and Aittokallio, T. (2010). Genetic variants and their interactions in the prediction of increased pre-clinical carotid atherosclerosis -The Cardiovascular Risk in Young Finns Study, PLoS Genet. 6: e1001146. Moulder, R., Lönnberg, T., Elo, L.L., Filén, J.J., Rainio, E., Corthals, G., Orešic, M., Nyman, T.A., Aittokallio, T. and Lahesmaa, R. (2010) Quantitative proteomics analysis of the nuclear fraction of human CD4+ cells in the early phases of IL-4 induced Th2 differentiation, Mol. Cell Proteomics 9: 1937-1953. Elo, L.L., Mykkänen, J., Järvenpää, H., Nikula, T., Simell, S., Aittokallio, T., Hyöty, H., Ilonen, J., Veijola, J., Simell, T., Knip, M., 59 Simell, O. and Lahesmaa, R. (2010) Early suppression of immune response pathways characterizes children with pre-diabetes in genome-wide gene expression profiling, J. Autoimmun. 35: 7076. Eronen, V.P., Lindén, R.O., Lindroos, A., Kanerva, M. and Aittokallio T. (2010) Genome-wide scoring of positive and negative epistasis through decomposition of quantitative genetic interaction fitness matrices, PLoS ONE 5: e11611. Elo, L.L., Järvenpää, H., Tuomela, S., Raghav, S., Ahlfors, H., Laurila, K., Gupta, B., Lund, R.J., Tahvanainen, J., Hawkins, R.D., Orešic, M., Lähdesmäki, H., Rasool, O., Rao, K.V.S., Aittokallio, T. and Lahesmaa, R. (2010) Genome-wide profiling of interleukin-4 and STAT6 transcription factor regulation of human Th2 cell programming, Immunity 32: 852-862. Aittokallio, T. (2010) Dealing with missing values in large-scale studies - microarray data imputation and beyond, Invited Review, Brief. Bioinform. 11: 253-264. Laajala, T.D., Raghav, S., Tuomela, S., Lahesmaa, R., Aittokallio, T. and Elo, L.L. (2009) A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments. BMC Genomics 10:618. Hiissa, J., Elo, L.L., Huhtinen, K., Perheentupa, A., Poutanen, M. and Aittokallio, T. (2009) Resampling reveals sample-level differential expression in clinical genome-wide studies. OMICS 13: 381-396. Elo, L.L., Hiissa, J., Tuimala, J., Kallio, A., Korpelainen, E. and Aittokallio, T. (2009) Optimized detection of differential expression in global profiling experiments: case studies in clinical transcriptomic and quantitative proteomic datasets. Brief. Bioinform. 10: 547-555. Salmi, J., Nyman, T.A., Nevalainen, O.S. and Aittokallio, T. (2009) Filtering strategies for improving protein identification in highthroughput MS/MS studies. Proteomics 9: 848-860. Laajala, E., Aittokallio T., Lahesmaa, R. and Elo, L.L. (2009) Probelevel estimation improves the detection of differential splicing in Affymetrix exon array studies. Genome Biol. 10: R77. CYTOSKELETAL AND SURVIVAL SIGNALING Principal Investigator: John E. Eriksson, Ph.D., Professor. Address: Dept. of Biology, Åbo Akademi University, FI-20520 Turku, Finland. Tel. int. + 358–2–215 3313. Laboratory address: Turku Centre for Biotechnology, BioCity, Tykistökatu 6B, P.O. Box 123, FIN-20521 Turku, Finland. Tel. int. + 358–2–333 8036, Fax int. +358–2–333 8000. E-mail: [email protected] Biography: John E. Eriksson (b. 1957) received his Ph.D. at the Åbo Akademi University in 1990. He was a post-doctoral fellow at Northwestern University in the laboratory of Prof. Robert D. Goldman during 1990-1993 (Fogarty International Fellowship from the National Institutes of Health 1991-1993). In November 1993 he joined the Centre for Biotechnology as a Senior Research Fellow in Cell Biology. In 1999 he was appointed as Professor of Zoology at the Department of Biology, University of Turku. In 2006 he was appointed as Professor of Cell Biology at the Department of Biology, Åbo Akademi University and became Head of Cell Biology at the department in 2007. He is also the Chair of Turku BioImaging, Chair of the Biocenter Finland Imaging Infrastructure Network, and Chair of the Workpackage 12 (User access) in the Eurobioimaging ESFRI network. Personnel: Post-doctoral fellows: Fang Cheng, MD-Ph.D., Senthil Kumar, Ph.D., Hanna-Mari Pallari, Ph.D., Emilia Peuhu, Ph.D., Praseet Poduval, Ph.D. Graduate students: Tomoko Asaoka, MSc, Saima Ferraris, MSc, Claire Hyder, MSc, Kimmo Isoniemi, MSc, Julia Lindqvist, MSc, Ponnuswamy Mohanasundaram, MSc, Preethy Paul, MSc, Mika Remes, MSc, Elin Torvaldson, MSc Undegraduate students: Josef Gullmets, Jolanta Lundgren, Max Roberts, John Russell, Joanna Pylvänäinen. Laboratory Technician: Helena Saarento. Secretary: Beata Paziewska Description of the Project: Post-translational modifications (PTMs) modulate the activity of most eukaryotic proteins and are responsible for producing highly complex proteomes from relatively simple genomes. We use a selection of signaling networks that represent the core of our expertise to identify PTM targets and interactions when a cell is embarking upon fate-determining responses, such as activating transcriptional or post-translational defense and survival mechanisms or triggering death machineries. Our main models are apoptotic, stress-mediated, and cytoskeletal signaling and we are also interested in their interrelationship. By exploring the interactions between these completely different signaling modes, we hope to advance our understanding how critical intracellular signals are processed and integrated. We are especially interested in the interaction between death receptor, stress, and survival signaling. Early on, we observed that 60 61 growth signaling through the mitogen-activated kinase (MAPK/ERK) pathway has a dominant inhibiting effect on apoptosis induced by death receptors (Fas, TRAIL, and TNF receptors) and have shown that this mode of regulation has ramifications both in regulating death receptor responses of recently activated T-cells and in the resistance of certain tumor cell lines to death receptor stimulation. On the other hand death receptors are also able to activate survival signals, both MAPK/ERK and NF-kB and stress signaling facilitates death receptor-mediated apoptosis in a independently of heat shock protein expression. The survival of cells is, therefore, determined by a continuum between these signaling modalities. An example of a signaling hub protein that affects the survival in all of the above signaling modes is c-FLIP, which is a specific inhibitor of death receptor signaling. Targeted FLIP degradation by ubiquitylation is responsible for the sensitization to death receptor signals following heat stress and during differentiation erythroid cells. We have found a PKCalpha/beta-mediated signaling module that regulates the turnover FLIP by an isoform and phosphorylation site-specific mechanism. These findings help understanding the regulation of death receptor responses during stress, fever, or inflammation, as well as during cell growth and differentiation-related processes. Intermediate filaments (IFs) are major cytoskeletal proteins important for ultrastructural organization and protection against various mechanical and other types of stresses. We have established that intermediate filaments are important signaling determinants, a question that relates to how the organization of the cytoskeleton will affect different signaling modules. By employing the interactions of different IFs (keratin 8/18, vimentin, nestin) with their signaling partners as models, we have elucidated the relationship between the cytoskeletal structure and the signaling state of the cell, and how this relationship will affect cell differentiation, growth, and survival. We observed that IFs act as general scaffolds for signaling proteins, and have focused on the association of IFs with JNKs, Cdk5, PKC isoforms, 14-3-3, and surface adhesion molecules are all involved in key regulatory processes in the cell. Recently, we determined that vimentin is a regulator of lymphocyte adhesion and transcellular migration, showing that the vimentin IFs form a highly dynamic anchoring structure, which is involved in organizing the surface molecules crucial for the migration. Another topical highlight includes the discovery of nestin as regulator of Cdk5 signaling. We have shown that nestin forms a scaffold and rheostat for the Cdk5/p35 signaling complex and shown that this function is important both during the differentiation of muscle cells and in apoptosis of neuronal cells. Collaborators: The studies on apoptosis-related signaling are done in collaboration with Birgit Lane and David Lane (Institute of Medical Biology, A*Star, Singapore), Roger Johnson and Deirdre Meldrum (Biodesign Institute, Phoenix, USA), Henning Walczak (Imperial College, London, UK), and Lea Sistonen (Turku Centre for Biotechnology). The studies on IF-related signaling functions are carried out as a collaboration with Teng-Leong Chew and Robert Goldman (Northwestern Univ., Chicago, USA), Johanna Ivaska (Univ. of Turku), Sirpa Jalkanen (Univ. of Turku), Hannu Kalimo (Univ. of Turku), Andras Nagy (Univ. of Toronto, Canada), Kuo-Fen Lee (Salk Institute, CA, USA). 62 Funding: The Academy of Finland, TEKES, the European Union, the Finnish Cancer Organizations, the Sigrid Jusélius Foundation, and the Åbo Akademi Foundation. Selected Publications: Ferraris SE, Isoniemi K, Torvaldson E, Anckar J, Westermarck J, Eriksson JE. (2012) Nucleolar AATF regulates c-Jun-mediated apoptosis. Mol Biol Cell. 23(21):4323-32. Mohseni P., Sung H.K., Murphy A.J., Laliberte C.L., Pallari H-M., Henkelman M., Georgiou J., Xie G., Quaggin S.E., Thorner P.S., Eriksson J.E. & Nagy A. (2011). Nestin is not essential for development of the CNS but required for dispersion of acetylcholine receptor clusters at the area of neuromuscular junctions. J. Neurosci. 31: 11547-11552. Pallari H.M., Lindqvist J., Torvaldson E., Ferraris S.E., He T., Sahlgren C. & Eriksson J.E. (2011). Nestin as a regulator of Cdk5 in differentiating myoblasts. Mol. Biol. Cell 22: 1539-1549. Toivonen H.T., Meinander A., Asaoka T., Westerlund M., Pettersson F., Mikhailov A., Eriksson J.E. & Saxen H. (2011) Modeling reveals that dynamic regulation of c-FLIP levels determines cellto-cell distribution of CD95-mediated apoptosis. J. Biol. Chem. 286: 18375-18382. Yang J., Dominguez B., de Winter F., Gould T.W., Eriksson J.E. & Lee K.F. (2011). Nestin negatively regulates postsynaptic differentiation of the neuromuscular synapse. Nat. Neurosci. 14: 324-330. Asaoka T., Kaunisto A. & Eriksson J.E. (2011). Regulation of cell death by c-FLIP phosphorylation. Adv. Exp. Med. Biol. 691: 625-630. Peuhu E., Kaunisto A., Laihia J.K., Leino L. & Eriksson J.E. (2010). Molecular targets for the protodynamic action of cis-urocanic acid in human bladder carcinoma cells. BMC Cancer. 10: 521. Blom T., Bergelin N., Meinander A., Löf C., Slotte J.P., Eriksson J.E., Törnquist K. (2010). An autocrine sphingosine-1-phosphate signaling loop enhances NF-kappaB-activation and survival. BMC Cell Biol. 11: 45. Rosenholm J.M., Peuhu E., Bate-Eya L.T., Eriksson J.E., Sahlgren C. & Lindén M. (2010). Cancer-cell-specific induction of apoptosis using mesoporous silica nanoparticles as drug-delivery vectors. Small 6: 1234-1241. Blomster H.A., Imanishi S.Y., Siimes J., Kastu J., Morrice N.A., Eriksson J.E. & Sistonen L. (2010). In vivo identification of sumoylation sites by a signature tag and cysteine-targeted affinity purification. J. Biol. Chem. 285: 19324-19329. de Thonel A., Ferraris S.E., Pallari H.M., Imanishi S.Y., Kochin V., Hosokawa T., Hisanaga S., Sahlgren C. & Eriksson J.E. (2010). Protein kinase Czeta regulates Cdk5/p25 signaling during myogenesis. Mol. Biol. Cell 21: 1423-1434. Shen W.J., Patel S., Eriksson J.E., Kraemer F.B. (2010). Vimentin is a functional partner of hormone sensitive lipase and facilitates lipolysis. J. Proteome Res. 9: 1786-1794. Peuhu E., Rivero-Müller A., Stykki H., Torvaldson E., Holmbom T., Eklund P., Unkila M., Sjöholm R. & Eriksson J.E. (2010). 63 Inhibition of Akt signaling by the lignan matairesinol sensitizes prostate cancer cells to TRAIL-induced apoptosis. Oncogene 29: 898-908. Söderström, T.S., Nyberg, S., Nieminen, M.I. and Eriksson, J.E. (2005) CD95 capping is ROCK-dependent and dispensable for apoptosis. J. Cell Sci. 118: 2211-2223. Imanishi S.Y., Kouvonen P., Smått J.H., Heikkilä M., Peuhu E., Mikhailov A., Ritala M., Lindén M., Corthals G.L. & Eriksson J.E. (2009). Phosphopeptide enrichment with stable spatial coordination on a titanium dioxide coated glass slide. Rapid Commun. Mass Spectrom. 23: 3661-3667. Poukkula, M., Kaunisto, A., Hietakangas, V., Denessiouk, K., Katajamäki, T., Johnson, M.J., Sistonen, L. and Eriksson, J.E. (2005) Rapid turnover of c-FLIPshort is determined by its unique C-terminal tail. J. Biol. Chem. 280: 27345-27355. Rosenholm J.M., Peuhu E., Eriksson J.E., Sahlgren C. & Lindén M. (2009). Targeted intracellular delivery of hydrophobic agents using mesoporous hybrid silica nanoparticles as carrier systems. Nano Lett. 9: 3308-3311. Eriksson J.E., Dechat T., Grin B., Helfand B., Mendez M., Pallari H.M., Goldman R.D. (2009). Introducing intermediate filaments: from discovery to disease. J. Clin. Invest. 119: 1763-1771. Review. Rosenholm J., Meinander A. Peuhu E., Niemi R., Eriksson J.E., Sahlgren C. & Lindén M. (2009). Selective uptake of porous silica nanoparticles by cancer cells. Amer. Chem. Soc. 27: 197-206. Kaunisto A, Kochin V, Asaoka T, Mikhailov A, Poukkula M, Meinander A. & Eriksson JE. (2009). PKC-mediated phosphorylation regulates c-FLIP ubiquitylation and stability. Cell Death Differ.16: 1215-1226. Mikhailov A., Sokolovskaya A., Yegutkin G.G., Amdahl H., West A., Yagita H., Lahesmaa R., Thompson L.F., Jalkanen S., Blokhin D. & Eriksson J.E. (2008). CD73 participates in cellular multiresistance program and protects against TRAIL-induced apoptosis. J. Immunol. 181: 464-475. Meinander, A., Söderström, T.S., Kaunisto, A., Poukkula, M., Sistonen, L. and Eriksson, J.E. (2007) Fever-like hyperthermia controls T-lymphocyte persistence by inducing degradation of c-FLIPshort. J. Immunol. 178: 3944-3953. Imanishi S.Y., Kochin V., Ferraris S.E., deThonel A., Pallari H-M., Corthals G.L. & Eriksson J.E. (2007). Reference-facilitated phosphoproteomics: fast and reliable phosphopeptide validation by mikro-LC-ESI-Q-TOF MS/MS. Mol. Cell. Proteomics 6: 1380-1391. Goswami, A., Burikhanov, R., de Thonel, A., Fujita, N., Goswami, M., Zhao, Y., Eriksson, J.E., Tsuruo, T. and Rangnekar, V.M. (2005). Binding and phosphorylation of Par-4 by Akt is essential for cancer cell survival. Mol. Cell. 20: 33-44. Eriksson, J.E., He, T., Trejo-Skalli, A.V., Härmälä-Brasken, A.S., Hellman, J., Chou, Y.H. and Goldman, R.D. (2004) Specific in vivo phosphorylation sites determine the assembly dynamics of vimentin intermediate filaments. J. Cell Sci. 117: 919-932. Hietakangas, V., Poukkula, M., Heiskanen, K.M., Karvinen, J.T., Courtney, M.J., Sistonen, L. and Eriksson, J.E. (2003) Erythroid differentiation in K562 leukemia cells leads to sensitization to TRAIL-induced apoptosis by downregulation of FLIP. Mol. Cell. Biol. 23: 1278-1291. Hietakangas, V., Poukkula, M., Heiskanen, K.M., Karvinen, J.T., Sistonen, L. and Eriksson, J.E. (2003) Erythroid differentiation in K562 leukemia cells leads to sensitization to TRAIL-induced apoptosis by downregulation of FLIP. Mol. Cell. Biol. 23: 1278-1291. Sahlgren, C.M., Mikhailov, A., Vaittinen, S., Pallari, H.M., Kalimo, H., Pant, H.C. and Eriksson, J.E. (2003) Cdk5 regulates the organization of Nestin and its association with p35. Mol. Cell. Biol. 23: 5090-5106. Tran, S.E.F., Meinander, A., Holmström, T.H., Rivero-Muller, A., Heiskanen, K.M., Linnau, E.K., Courtney, M.J., Mosser, D.D., Sistonen, L. and Eriksson, J.E. (2003) Heat stress downregulates FLIP and sensitizes to Fas receptor-mediated apoptosis. Cell Death Differ. 10: 1137-1147. Nieminen, M., Henttinen, T., Merinen, M., Marttila-Ichihara, F., Eriksson, J.E. and Jalkanen S. (2006) Vimentin function in lymphocyte adhesion and transcellular migration. Nat. Cell Biol. 8: 156-162. Kochin, V., Imanishi S.Y. and Eriksson, J.E. (2006) Fast track to a phosphoprotein sketch – MALDI-TOF characterization of TLCbased tryptic phosphopeptide maps at femtomolar detection sensitivity. Proteomics 6: 5676-82. Sahlgren, C.M., Pallari, H-P., He, T., Chou, Y-H., Goldman, R.D. and Eriksson, J.E. (2006) An essential role of a nestin scaffold for regulation of Cdk5/p35 signaling in oxidant-induced death of neuronal progenitor cells. EMBO J. 25: 4808-4819. Imanishi, S.Y., Kochin, V. and Eriksson, J.E. (2006) Optimization of phosphopeptide elution conditions in immobilized Fe(III) affinity chromatography. Proteomics 7: 174-176. Pallari, H.M. and Eriksson, J.E. (2006) Intermediate filaments as signaling platforms. Science STKE. 19: pe53. Review. 64 From left to right. Back row: John Eriksson, Rajendran Senthil, Kimmo Isoniemi, Elin Torvaldsson, Claire Hyder, Helenta Saarento Julia Lindqvist, Erik Niemelä and Yves Nkizinkiko. Front row: Joanna Pylvänäinen, Alia Joko, Beata Padziewska, Fang Chen, Tomoko Asaoka, Josef Gulmets and Ponnuswamy Mohana Sundaram. 65 EPIGENOMICS Principal Investigator: David Hawkins, Ph.D., Turku Centre for Biotechnology, Biocity, 5th floor, Tykistökatu 6A, FI-20520, Finland. Tel. +358-2-3338094, Fax. +358-2-3338000. Email: [email protected]. Home page: http://www.btk.fi/research/research-groups/hawkins/ Personnel: Post-doctoral researchers: Kalyan Kumar Pasumarthy, Ph.D., Cristina Valensisi, Ph.D. Description of the project: Epigenomics includes histone tail modifications, DNA methylation and noncoding RNAs. These factors are closely linked to transcriptional regulation, and provide unique signatures of cellular identity. The epigenome exhibits remarkable cellular specificities and is likely critical in defining unique cell populations such stem cells. Using next-generation sequencing and computational technologies, we are investigating how the epigenome plays a role in pluri- and multipotency of stem cells. We are also investigating the transcriptional regulation and unique signatures of cellular differentiation. Funding: BioCenter Finland, Academy of Finland Collaborators: Riitta Lahesmaa, Turku Centre for Biotechnology Harri Lähdesmäki, Aalto University Riikka Lund, Turku Centre for Biotechnology Saara Laitinen, Finnish Red Cross Blood Service Selected Publications: Hon G., Hawkins, R.D., Caballero O.L., Lo C., Lister R., Pelizzola M., Valsesia A., Ye Z., Kuan S., Edsall L.E., Camargo A.A., Stevenson B.J., Ecker J.R., Bafna V., Strausberg R.L., Simpson A.J. And Ren B. (2012) Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res. 22: 246-258. Elo L.L., Kallio A., Laajala T.D., Hawkins R.D., Korpelainen E. and Aittokallio T. (2012) Optimized detection of transcription factor binding sites in ChIP-seq experiments. Nucl. Acids Res. 40: e1. Hawkins R.D†., Hon G.C†., Yang C., Antosiewicz J.E., Lee L.K., Ngo Q.M., Klugman S., Ching K.A., Edsall L.E., Kuan S., Yu P., Liu H., Zhang X., Green R.D., Lobanenkov V.V., Stewart R., Thomson J.A. and Ren B. (2011) Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency. Cell Research. 21: 1393-1409. †Equal contribution of work. From left to right: Cristina Valensisi and Kalyan Pasumarthy. 66 Alvarado D.M., Hawkins R.D., Bashiardes S., Veile R.A., Powder K.E., Speck J., Warchol M.E. and Lovett M. (2011) An RNAiBased Screen of Transcription Factor Gene Pathways During Sensory Regeneration in the Avian Inner Ear. J Neurosci. 31: 4535-4543. 67 Lister R†., Pelizzola M†., Kida Y.S., Hawkins R.D., Nery J.R., Hon G., Antosiewicz-Bourget J., O’Malley R., Castanon R., Klugman S., Downes M., Yu R., Stewart R., Ren B., Thomas J.A., Evans R.M. and Ecker JR. (2011) Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature. 471: 68-73. †Equal contribution of work. Egelhofer T.A†., Minoda A†., Klugman S., Kolasinska-Zwierz P., Alekseyenko A.A., Gadel S., Gorchakov A.A., Gu T., Kharchenko P.V., Kuan S., Latorre I., Linder-Basso D., Luu Y., Ngo Q., Rechtsteiner A., Riddle N.C., Schwartz Y.B., Vielle A., Elgin S.C.R., Kuroda M.I., Park P.J., Pirrotta V., Ren B., Ahringer J., Strome S., Karpen G^., Hawkins R.D^. and Lieb J.D^. (2011) Assessment of histone-modification antibody quality. Nat. Struct. Mol. Biol. 18: 91-93. †Equal contribution of work; ^Cocorresponding Authors. Harris R.A., Wang T., Coarfa C., Nagarajan R.P., Hong C., Downey S.L., Johnson B.E., Fouse S.D., Delaney A., Zhao Y., Olshen A., Ballinger T., Zhou X., Forsberg K.J., Gu J., Echipare L., O’Geen H., Lister R., Pelizzola M., Xi Y., Epstein C.B., Bernstein B.E., Hawkins R.D., Ren B., Chung W.Y., Gu H., Bock C., Gnirke A., Zhang M.Q., Haussler D., Ecker J.R., Li W., Farnham P.J., Waterland R.A., Meissner A., Marra M.A., Hirst M., Milosavljevic A. and Costello J.F. (2010) Comparison of sequencingbased methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat. Biotechnology. 28(10), 852-862. Elo L.L†.., Järvenpää H†., Tuomela S†., Raghav S†., Ahlfors H., Laurila K., Gupta B., Lund R,J., Tahvanainen J., Hawkins R,D., Oresic M., Lähdesmäki H., Rasool O., Rao K,V., Aittokallio T. and Lahesmaa R. (2010) Genome-wide profiling of interleukin-4 and STAT6 transcription factor regulation of human Th2 cell programming. Immunity. 32: 852-862. Hawkins R.D†., Hon G.C†. and Ren B. (2010) Next-Generation Genomics: An Integrative Approach. Nat. Rev. Genetics. 11: 476-486. Hawkins R.,D†., Hon G.C†., Lee L.K., Ngo Q., Lister R., Pelizzola M., Kuan S., Edsall L.E., Ye Z., Espinoza C., AntosiewiczBourget J., Agarwahl S., Shen L., Ruotti V., Wang W., Stewart R., Thomson J.A., Ecker J.R. and Ren B. (2010) Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell. 6: 279-491. Lister R†., Pelizzola M†., Dowen R.H., Hawkins R.D., Hon G.C., Tonti-Filippini J., Nery J.R., Lee L.K., Edsall L.E., AntosiewiczBourget J., Ruotti V., Elwell A., Hernandez A., Stewart R., Millar A.H., Thomson J.A., Ren B. and Ecker J.R. (2009) Human DNA methylomes at single-base resolution reveal widespread cellspecific epigenetic signatures. Nature. 462: 315-322. Heintzman N.D†., Hon G†., Hawkins R.D†., Kheradpour P., Ching K.A., Stuart R.K., Harp L.F., Ching C.W., Liu H., Zhang X., Green R.D., Crawford G.E., Kellis M. and Ren B. (2009) Histone modifications at human enhancers reflect global cell-typespecific gene expression. Nature. 459: 108-112. 68 CELL ADHESION AND CANCER Principal investigator: Johanna Ivaska, Professor, Ph.D., VTT Medical Biotechnology, Itäinen Pitkäkatu 4C, FI-20520 Turku, Finland; Phone: + 358 40 7203971; FAX: + 358 20 722 2840, email: [email protected] home page: http://www.btk.fi/research/research-groups/ivaska/ Biography: Johanna Ivaska (b. 1972) received her MSc in Biochemistry in 1995 and Ph.D. in 2000 from the University of Turku. In 2000 she received a Post-doctoral Fellowship from the Academy of Finland. In 2001 she received the EMBO Long Term Fellowship. She was a postdoctoral fellow at Cancer Research UK LIR in Prof. Peter Parker’s laboratory during 2000-2003. She returned to Finland in 2003 and joined VTT Medical Biotechnology and University of Turku Centre for Biotechnology as senior research fellow of the Academy of Finland and established her own research group. She was selected as a member of the EMBO Young Investigator program for 2007-2009. She was nominated professor of Molecular Cell Biology at University of Turku for 2008-2014 and her research group received ERC Starting Grant funding for 2008-2013 in their Cancer Signalosome project. Personnel: Post-doctoral researchers: Elina Mattila, Ph.D.; Jeroen Pouwels, Ph.D.; Emilia Peuhu, Ph.D.; Ghaffar Muharram, Ph.D. Graduate students: Antti Arjonen, M.Sc; Reetta Virtakoivu, M.Sc; Gunilla Högnäs; M.Sc., Riina Kaukonen, M.Sc., Jonna Alanko, M.Sc., Nicola De Franceschi, M.Sc., Habib Baghirov, M.Sc. Research assistant: Markku Saari, M.Sc (CIC, part-time). Technicians: Jenni Siivonen, Laura Lahtinen, Petra Laasola (VTT, part-time) Description of the project We investigate the relationship between cell adhesion and cancer. Cancer is a disease where cells grow out of control and invade, erode and destroy normal tissue. Invasive and metastatic behavior of malignant cells is the major cause of mortality in all cancer patients. Migration and cell proliferation are critically regulated by physical adhesion of cells to each other and to their non-cellular surroundings (i.e. extracellular matrix) mediated by a family of adhesion receptors called integrins. Adhesion dependency of signaling pathways is well established but incompletely understood. In normal cells permissive signaling from integrins are prerequisite for receptor tyrosine kinase (RTKs) induced proliferation. This regulation is lost upon transformation. In the past few years, we have performed genome-wide screens to identify integrin-binding intracellular proteins and regulators of integrin activity to gain novel insight into integrin signaling and traffic in cancer cells. Based on these findings we are currently actively investigating these topics: 1) regulation of integrin activity by SHARPIN in cell migration, development and cancer. 2) Co-operation between integrins and receptor-tyrosine kinases like Met. 3) Integrin endo/exocytic traffic in cancer cell invasion. 4) The functional role of vimentin and adhesion in EMT. With all these projects we aim to understand adhesion regulated signaling and the biological function of integrin membrane traffic in human malignancies. 69 Selected Publications: Arjonen, A., Alanko, J., Veltel, S., Ivaska, J. (2012) Distinct Recycling of Active and Inactive β1 Integrins. Traffic Jan 5 [Epub ahead of print]. Pellinen, T., Rantala, J.K., Arjonen, A., Mpindi, J-P., Kallioniemi, O. and Ivaska, J. (2012) A functional genetic screen reveals new regulators of β1-integrin activity. J Cell Sci. 125:649-661. Virtakoivu, R., Pellinen, T., Rantala, J.K., Perälä, M. and Ivaska, J. (2012) Distinct roles of AKT isoforms in regulating β1-integrin activity, migration and invasion in prostate cancer. Mol. Biol. Cell. 17:3357-3369. Högnäs, G., Tuomi, S., Veltel, S., Mattila, E., Murumägi, A., Edgren, H., Kallioniemi, O. and Ivaska, J. (2012) Cytokinesis failure due to derailed integrin traffic induces aneuploidy and oncogenic transformation in vitro and in vivo. Oncogene 31:3597-3606. Vuoriluoto, K., Haugen, H., Kiviluoto, S., Mpindi, J-P, Nevo, J., Gjerdrum, C., Lorens, J.B. and Ivaska, J. (2011) Vimentin regulates EMT induction and migration by governing Axl expression in breast cancer. Oncogene 30:1436-1448. Rantala, J.K., Pouwels, J., Pellinen, T., Veltel, S., Laasola, P., Potter, C., Duffy, T., Sundberg, J.P., Askari, J.A.-. Humphries, M., Kallioniemi, O., Parsons, M., Salmi, M. and Ivaska, J. (2011) Sharpin is an endogenous inhibitor of beta1-integrin activation. Nat. Cell Biol. 13:1315-1324. Mai, A., Veltel, S., Pellinen, T., Padzik, A., Coffey, E., Marjomäki, V. and Ivaska, J. (2011) Competitive binding of Rab21 and p120RasGAP to integrins regulates receptor trafficking in migrating cancer cells. J. Cell Biol. 194:291-306. Nevo, J., Mai, A., Tuomi, S., Pellinen, T., Pentikäinen, O.T., Heikkilä, P., Lundin, J., Joensuu, H., Bono, P. and Ivaska, J. (2010) Mammary derived growth inhibitor (MDGI) interacts with integrin α-subunits and suppresses integrin activity and invasion. Oncogene 29:6452-6463. From left to right: Jenni Siivonen, Antti Arjonen, Emilia Peuhu, Reetta Virtakoivu, Laura Lahtinen, Ghaffar Muharram, Markku Saari, Riina Kaukonen, Elina Mattila, Nicola De Franceschi, Jonna Alanko, Habib Baghirov, Pranshu Sahgal and Johanna Ivaska Tuomi, S., Mai, A., Nevo, J., Laine, JO, Vilkki, V., Öhman, TJ., Gahmberg, CG., Parker, PJ. and Ivaska, J. (2009) PKCε Regulation of an a5 Integrin-ZO-1 Complex Controls Lamellae Formation in Migrating Cancer Cells. Sci. Sign., 2 (77): ra32. Nevo, J., Mattila, E., Pellinen, T., Yamamoto, D.L., Sara, H., Iljin, K., Kallioniemi, O., Bono, P., Joensuu, H., Wärri, A. and Ivaska, J. (2009) Mammary Derived growth inhibitor facilitates escape from EGFR inhibitory therapy. Clin. Cancer Res. 15:6570-6578. Pellinen T., Tuomi, S., Arjonen, A., Wolf, M., Edgren, H., Meyer, H., Grosse, R., Kitzing, T., Rantala, JK., Kallioniemi O., Fässler, R., Kallio, M., and Ivaska, J. (2008) Integrin traffic regulated by Rab21 is necessary for cytokinesis. Dev. Cell, 15:371-385. Mattila, E., Koskinen, K., Salmi, M. and Ivaska, J. (2008) Protein tyrosine phosphatase TCPTP controls VEGFR-2 signalling. J. Cell Sci. 121:3570-80. Pellinen T, Arjonen A, Vuoriluoto K, Kallio K, Fransen JA, Ivaska J. (2006) Small GTPase Rab21 regulates cell adhesion and controls endosomal traffic of beta1-integrins. J. Cell Biol. 2006 173:767-80. Mattila E., Pellinen, T., Nevo, J., Vuoriluoto, K. Arjonen, A. and Ivaska, J (2005) Negative regulation of EGFR signalling via integrin α1β1mediated activation of protein tyrosine phosphatase TCPTP. Nat. Cell Biol. 7: 78-85. 70 71 HYPOXIA IN CELL SURVIVAL Principal investigator: Panu Jaakkola, M.D., Ph.D., Address: Turku Centre for Biotechnology, Biocity, Tykistökatu 6B, P.O. Box 123, FIN-20521, Turku, Finland, Tel. +358 2 3338566, Fax. +358 2 3338000, E-mail: [email protected] Biography: Panu Jaakkola (b. 1965) received his M.D. in 1992 and Ph.D. in 1998 at the University of Turku. In 1999 he received a Junior Fellowship from the Academy of Finland. He was a postdoctoral fellow at the University of Oxford in Prof. Peter Ratcliffe’s laboratory during 1999-2001. He joined the Turku Centre for Biotechnology in the fall 2001. In 2002-2007 he worked as a fellow of the Academy of Finland. Currently he is appointed as a senior research fellow by the medical faculty and is also a consultant at the department of medical oncology and radiation therapy at Turku university hospital. Personnel: Post-doctoral fellow: Krista Rantanen, (PhD) Graduate students: Heidi Högel, (M.Sc.), Petra Miikkulainen, (M.Sc.), Jonna Silen, (M.Sc.), Pekka Heikkinen, (M.Sc.), Technicians: Taina Kalevo-Mattila Description of the project: Hypoxia (reduced O2 tension) is the main tissue damaging factor in normal tissue. In contrast, tumours use hypoxia as a growthpromoting factor. During ischemic assaults such as strokes, hypoxia activates apoptosis and leads to severe tissue damage. During cancer progression hypoxia causes inhibition of apoptosis and enhances tumour aggressiveness and metastasis. In keeping with this, it has been known for much of the past century that hypoxia causes resistance cancer treatments -both to chemotherapy and radiotherapy -and leads to poor prognosis. The aim of the project is to reveal mechanisms by which hypoxia regulates survival decisions in ischemic diseases and cancer progression. Our group has undertaken two major avenues to tackle the issue. The reduced oxygen is sensed by a family of enzymes called the HIF prolyl hydroxylases (PHD1-3). Under normoxia the hypoxia-inducible factor (HIF) is hydroxylated by PHDs at critical proline residues. This leads to ubiquitylation and proteosomal destruction of HIF. Under hypoxic conditions the hydroxylation ceases and HIF is stabilised. HIF then exerts its effects by activation of some 200 genes. These have key functions in glucose homeostasis, angiogenesis, as well as cell survival and metastasis formation. Our studies have revealed novel and separate functions for two PHD isoforms (PHD2 and -3) in regulating cell growth, survival and regulation of apoptosis. For example, we have shown that the PHD3 isoform selectively regulates cell cycle progression under hypoxia. Moreover, we have demonstrated a strong interplay between the oxygen sensing and autophagy pathways for example through p62/SQSTM1. Besides studying several aspects of molecular and cellular biology of the hydroxylases, we study the clinical importance of these factors having a particular interest in renal clear cell and other carcinoma progression. Funding: The Academy of Finland, Sigrid Juselius Foundation, Finnish Cancer Unions. Turku University Hospital (EVO), Turku University Foundation 72 Collaborators: Peter Ratcliffe and Chris Pugh (Oxford University, UK), Eric Metzen (Luebeck University, Germany), Heikki Minn (PET Centre, Turku University Hospital) Selected Publications: Rantanen K., Pursiheimo J., Högel H., Miikkulainen P., Sundström J. and, Jaakkola P.M. (2012). p62/SQSTM1 regulates hypoxia response by attenuating normoxic PHD3 activity through aggregate sequestration and enhanced degradation. J Cell Sci. Jan 23. Högel H., Rantanen K., Jokilehto T., Grenman R. and, Jaakkola P.M. (2011). Prolyl hydroxylase PHD3 enhances the hypoxic survival and G1 to S transition of carcinoma cells. PloS One 6(11):e27112 Heikkinen P., Nummela M., Kähäri V.M. and Jaakkola P.M. (2010). Hypoxia converts Smad7 from tumor suppressor into tumor promoter. Cancer Res., 70(14):5984-93 Heikkinen P.T., Nummela M., Leivonen S.K., Westermarck J., Hill C.S., Kähäri V.-M., Jaakkola P.M. (2010). Hypoxia activated Smad3-specific dephosphorylation by PP2A. (2010). J Biol. Chem., 285(6):3740-9. Epub 2009 Dec 1. Pursiheimo J., Rantanen K., Heikkinen P.T., Johansen T., Jaakkola P.M. (2009). Hypoxia-activated autophagy accelerates degradation of SQSTM1/p62. Oncogene, 28(3):334-344. Rantanen K., Pursiheimo J., Högel H., Himanen V., Metzen E., Jaakkola P.M. (2008) Prolyl Hydroxylase PHD3 Activates Oxygendependent Protein Aggregation. Mol Biol Cell 19(5): 2231-40. Jokilehto, T., Rantanen, K., Luukkaa, M., Grenman, R., Minn, H., Kronqvist, P., Jaakkola P.M. (2006). Overexpression and nuclear translocation of HIF prolyl hydroxylase PHD2 in head and neck squamous cell carcinoma associates with tumor aggressiveness. Clin Cancer Res 12(4):1080-1087 Marxsen, J. H., Stengel, P., Doege, K., Heikkinen, P., Jokilehto, T., Wagner, T., Jelkmann, W., Jaakkola, P., and Metzen, E. (2004) Hypoxia-inducible factor-1 (HIF-1) promotes its degradation by induction of HIF-alpha-prolyl-4-hydroxylases. Biochem J 381, 761 Jaakkola, P., Mole, D. R., Tian, Y. M., Wilson, M.I., Gielbert, J., Gaskell, S.J., Kriegsheim, Av, Hebestreit, H.F., Mukherji, M., Schofield, C.J., Maxwell, P.H., Pugh, C.W., Ratcliffe, P.J. Targeting of HIF-alpha to the von Hippel-Lindau ubiquitylation complex by O2-regulated prolyl hydroxylation. (2001) Science 292; 468-72. Epstein, A.C.R., Gleadle, J.M., McNeill, L.A., Hewitson, K.S., O’Rourke, J., Mole, D.R., Mukherji, M., Metzen, E., Wilson, M.I., Dhanda, A., Tian, Y.-M., Masson, N., Hamilton, D.L., Jaakkola, P., Barstead, R., Hodgkin, J., Maxwell, P.H., Pugh, C.W., Schofield, C.J., Ratcliffe, P.J. C.elegans EGL-9 and mammalian homologues define a family of dioxygenases that regulate HIF through prolyl hydroxylation. (2001) Cell 107; 43-54. Pursiheimo, J., Taskén, K., Jalkanen, M. and Jaakkola, P. Involvement of Protein Kinase A in FGF-2 Activated Transcription. (2000) Proc. Natl. Acad. Sci. USA, 97(1): 168–173. Cockman, M.E., Masson, N, Mole, D.R., Jaakkola, P, Chang, G.W., Clifford, S.C, Maher, E.R, Pugh, C.W., Ratcliffe, P.J., Maxwell, P.H. Hypoxia inducible factor-alpha binding and ubiquitylation by the von hippel-lindau tumor suppressor protein. (2000) J. Biol. Chem. 275: 25733-25741. 73 From left to right: Back row: Anssi Rantasalo (guest), David Malatinszky, Pauli Kallio, Patrik Jones, Matts Nylund, Paulina Bartasun, Veronica Carbonell, Kati Thiel and Linda Vuorijoki. Front row: Tomas Zavrel (guest), Hariharan Dandapani, Kalim Akhtar, Andras Pasztor, Sanna Kreula and Jari Kämäräinen. 74 BIOENERGY GROUP Principle investigator: Patrik R. Jones, Ph.D., Affiliated Group Leader at CBT Department of Biochemistry and Food Chemistry, University of Turku, Tykistökatu 6B, 4krs, FI-20520 Turku, Finland, Tel.: +358-2-3337913, Email: [email protected], Homepage: http://www.btk.fi/index.php?id=114 Biography: Patrik R. Jones, born in Sweden 1968, is an Australian citizen that carried out his undergraduate studies in Uppsala University and University of Adelaide. He completed his PhD in Plant Biochemistry at University of Adelaide (P.B. Høj) and the Royal Veterinary & Agricultural University in Copenhagen (B. L. Møller). He did 2-year post-doc’s in the laboratory of Kazuki Saito (Chiba Univ.) and the Australian Wine Research Institute, followed by 3.5 years as P.I. at a 100% for-profit company in Japan where he developed synthetic model systems for evaluation of fermentative H2-production. In 2009, he moved to University of Turku as a member of the Collegium for Science and Medicine and Principal Investigator of the Bioenergy group. In 2010 he was awarded an ERC Starting Grant and the EU FP7 9-partner collaborative project DirectFuel (http://www.directfuel.eu/) as coordinator. In Turku, the aim is to develop photobiological systems for production of engine-ready transport fuels using sunlight, H2O and CO2 as substrate. Personnel: Seniors scientists: Kalim Akhtar, Ph.D., Matts Nylund, Ph.D. Postdoctoral researchers: Pauli Kallio, Ph.D., Fernando Guerrero, Ph.D. Graduate students: Veronica Carbonell, M.Sc., Jari Kämäräinen, M.Sc., Andras Pasztor, M.Sc., Francy El Souki, M.Sc., Linda Vuorijoki, M.Sc., Sanna Kreula, M.Sc. Technicians: Katie Thiel, M.Sc. Undergraduate students: Hariharan Dapandani, M.Sc. Description of the project Our research group is pursuing applied and fundamental projects with the aim to contribute towards the development of renewable fuel production using autotrophic and heterotrophic prokaryotes. Although the ultimate objective is to contribute towards application, the majority of our research is better described as fundamental. Even fuel pathway engineering operates far from practical reality, with a focus on understanding factors that influence pathway flux in model systems. Likewise, although our group currently is named ‘Bioenergy Group’ our research is best summarized as Engineering and Understanding Prokaryotic Metabolism. We are developing metabolic pathways for renewable fuel production and optimizing host metabolism to favor those pathways. We have selected fuels that potentially can be directly separated from the process: Short- to medium-chain alkanes and H2. The engineering is carried out in two prokaryotic model systems: Escherichia coli and Synechocystis sp. PCC6803. Also renewable fertilizer is targeted in recent projects. To aid the engineering, we are carrying out targeted prospecting for potential enzymes and also studying what factors influence 75 their functionality. In order to engineer prokaryotic metabolism we are studying how metabolism is regulated, in both E. coli and Synechocystis sp. PCC 6803. This includes the regulation of NADP(H) metabolism and the assembly and repair of iron-sulfur clusters. These studies are complemented by computational analysis of multi-level networks and stoichiometry. In collaboration with the group of Filip Ginter we are also developing the use of species-independent meta network analysis and methods to integrate distinct data-types. Funding: The Academy of Finland project PhotoBioH2, Nordic Energy Research AquaFEED project, EU FP7 collaborative projects DEMA and DirectFuel, EU FP7 Marie Curie training network PHOTO. COMM and ERC Starting project PhotoBioFuel. Collaborators: Within the DirectFuel consortium we have important collaborations ongoing with the groups of Ralf Steuer (Humboldt Univ. Berlin), Ladislav Nedbal (Global Change Research Centre, Czech Republic), Neil Marsh (Univ. Michigan), Wolfgang Hess (Univ. Freiburg) and Nigel Scrutton (Univ. Manchester). Without joint funding, locally in Turku, the groups of Ginter (UTU), Petre (ÅA) and Aitokallio (FIMM). Outside of Finland, we currently have active projects ongoing with the following collaborators without joint funding: Guy Hanke (Osnabruck Univ.), John Golbeck (Penn State), Toivo Kallas (UW Oshkosh), Sofie Van Landeghem (Ghent Univ.), Ron Milo (Weizmann Institute), Patrick Hallenbeck (Univ. Montreal) and Alison Smith (Univ. Cambridge). Selected Publications: Akhtar, M.K., Turner, N.J., Jones, P.R. (2012). Carboxylic acid reductase is a versatile enzyme for the conversion of fatty acids into fuels and chemical commodities. Proc. Natl. Acad. Sci. USA, doi: 10.1073/pnas.1216516110 Guerrero, F., Carbonell, V., Cossu, M., Correddu, D., Jones, P.R. (2012) Ethylene Synthesis and Regulated Expression of Recombinant Protein in Synechocystis sp. PCC 6803. PLOS One 7(11): e50470. doi:10.1371/journal.pone.0050470. Kämäräinen, J., Knoop, H., Stanford, N.J., Guerrero, F., Akhtar, M.K., Aro, E.M., Steuer, R., Jones, P.R. (2012) Physiological tolerance and stoichiometric potential of cyanobacteria for hydrocarbon fuel production. J. Biotechnol. 162, 67-74. Eser, B.E., Das, D., Jaehong, H., Jones, P.R., and Marsh, E.N.G. (2011) Oxygen-Independent Alkane Formation by Non-Heme Iron-Dependent Cyanobacterial Aldehyde Decarbonylase: Investigation of Kinetics and Requirement for an External Electron Donor. Biochem. 50, 10743Akhtar, M.K. and Jones, P.R. (2009) Construction of a synthetic YdbK-dependent pyruvate:H2 pathway in Escherichia coli BL21(DE3). Metabol. Eng. 11, 139-147. MITOSIS AND DRUG DISCOVERY Principal investigator: Marko Kallio, Ph.D. Docent, Principal Scientist and Team Leader, Affiliated Group Leader at CBT, VTT Biotechnology for Health and Wellbeing, Itäinen Pitkäkatu 4C, FI-20521, Turku,Finland and Turku Centre for Biotechnology, BioCity, Tykistökatu 6B, FI-20521 Turku, Finland. Tel. +358-(0)2-4788614, Fax +358(0)20-7222840, E-mail: [email protected] Biography: Marko Kallio (b. 1967) graduated in Genetics from University of Turku in 1992 and received his Ph.D. degree from Department of Human Genetics at University of Turku 1996. During his early career Dr. Kallio was in three laboratories; 1996-98 as a Post-doctoral fellow in the laboratory of Prof. Gary Gorbsky (Univ. Virginia, USA), 1998-2000 as a Senior Post-doctoral fellow in the laboratories of Prof. John Eriksson and Prof. Lea Sistonen (Univ. Turku, Finland) and 2000-2003 as an Assistant Research Professor at the University of Oklahoma HSC, USA. His research group received a Marie Curie Excellence grant for 2004-2008. In early 2004, Dr. Kallio moved back to Finland and has since been a Team leader at VTT Biotechnology for Health and Wellbeing, a research institute affiliated with the University of Turku. Personnel: Post-doctoral researchers: Leena Laine, Ph.D., Elli Narvi, Ph.D., Sebastian Winsel, Ph.D. Graduate students: Jenni Mäki-Jouppila, M.Sc., Anna-Leena Salmela, M.Sc., Mahesh Tambe, M.Sc. Under-graduate student: Sofia Pruikkonen Description of the projects: The Mitosis and Drug Discovery Team investigates mechanisms of cell division in somatic cells and in meiotic systems. Study of cell division errors may help to explain origin of genomic instability and can lead to discovery of novel therapeutic possibilities and diagnostics opportunities in the fight against cancer. We are especially interested of conditions that suppress cancer cell’s viability as a consequence of premature inactivation of the spindle assembly checkpoint (SAC), a conserved signalling pathway which monitors the fidelity of mitosis. In our main projects, we are working to validate the mechanism of action of our putative anti-Hec1 compounds and SAC targeting miRNAs that effectively perturb normal mitosis and trigger cancer cell killing in cell culture assays. Funding: VTT Technical Research Centre of Finland, Academy of Finland, TuBS and DDGS Graduate Schools, Bayer Schering Pharma AG Collaborators: Gary Gorbsky (OMRF, Oklahoma USA), Todd Stukenberg (Univ. Virginia, USA), Lauri Aaltonen (Biomedicum Helsinki), Lea Sistonen (Turku Centre for Biotechnology), Pirkko Härkönen (Univ. Turku). 76 77 Selected Publications: Salmela AL, Pouwels J, Mäki-Jouppila J, Kohonen P, Toivonen P, Kallio L, and Kallio M. (2012) Novel pyrimidine-2,4-diamine derivative suppresses the cell viability and spindle assembly checkpoint activity by targeting Aurora kinases. Carcinogenesis, in press. Nilsson EM, Brokken LJ, Narvi E, Kallio MJ, Härkönen PL. (2012) Identification of fibroblast growth factor-8b target genes associated with early and late cell cycle events in breast cancer cells. Mol Cell Endocrinol, 358: 104-15 Salmela AL, Pouwels J, Kukkonen-Macchi A, Waris S, Toivonen P, Jaakkola K, Mäki-Jouppila J, Kallio L, Kallio MJ. (2012) The flavonoid eupatorin inactivates the mitotic checkpoint leading to polyploidy and apoptosis. Exp Cell Res, 318: 578-92 Niittymäki I, Gylfe A, Laine L, Laakso M, Lehtonen HJ, Kondelin J, Tolvanen J, Nousiainen K, Pouwels J, Järvinen H, Nuorva K, Mecklin JP, Mäkinen M, Ristimäki A, Ørntoft TF, Hautaniemi S, Karhu A, Kallio MJ, Aaltonen LA. (2011) High frequency of TTK mutations in microsatellite-unstable colorectal cancer and evaluation of their effect on spindle assembly checkpoint. Carcinogenesis, 32: 305-11. Vuoriluoto M, Laine LJ, Saviranta P, Pouwels J, Kallio MJ. (2011) Spatio-temporal composition of the mitotic Chromosomal Passenger Complex detected using in situ proximity ligation assay. Mol Oncol, 5: 105-11. Kukkonen-Macchi A, Sicora O, Kaczynska K, Oetken-Lindholm C, Pouwels J, Laine L, and Kallio MJ. (2011) Loss of p38gamma MAPK induces pleiotropic mitotic defects and massive cell death. J Cell Sci, 124: 216-27. From left to right: Mahesh Tambe, Leena Laine, Jenni Mäki-Jouppila, Sofia Pruikkonen, Marko Kallio, Elli Narvi and Sebastian Winsel. 78 79 MOLECULAR SYSTEMS IMMUNOLOGY AND STEM CELL BIOLOGY Principle investigator: Riitta Lahesmaa, M.D., Ph.D., Professor, Turku Centre for Biotechnology, BioCity, Tykistökatu 6A, FI-20521 Turku, Finland. Tel. +358-2-333 8601, Fax. +358-2-333 8000. Email: [email protected], homepage: www.btk.fi Biography: Biography: Riitta Lahesmaa received her M.D. in 1984 and Ph.D. in 1987 from the University of Turku, and was appointed Docent in Immunology in 1990. She was a postdoctoral fellow at Stanford University Medical Center with Professor Lawrence Steinman during the years 1990-1993 (NIH Fogarty Fellowship). In 1994 she moved to Syntex Research Institute (later Roche Bioscience) in Palo Alto, California. As a Principal Scientist she focused on lymphocyte signaling and drug discovery with state-of-the-art functional genomics tools. In 1998 she was appointed Director of Turku Centre for Biotechnology. In 2009 she carried out research in Professor Anjana Rao’s laboratory in Immune Disease Institute, Harvard Medical School, Boston. She also directs BioCity Turku Research Program “Turku Centre for Systems Biology” since 2000. Personnel: Senior scientists: Jane Zhi Chen, Ph.D., Laura Elo-Uhlgren, Ph.D., Riikka Lund, Ph.D., Robert Moulder, Ph.D., Omid Rasool, Ph.D., Jussi Salmi, Ph.D. Post-doctoral researchers: Kanchan Bala, Sanna Edelman, Ph.D., Saara Hämälistö, Ph.D., Sari Lehtimäki, Ph.D., Elizabeth Ngyen, Ph.D., Emaheswa Reddy, Ph.D., Ubaid Ullah, Ph.D., Viveka Öling, Ph.D. Visiting Scientists: David R. Goodlett, Ph.D., Professor, Finnish Distinguished Professor, Kanury Rao, Ph.D., (Director, Immunology Group at ICGEB, New Delhi, India); Anjana Rao, Ph.D. Professor, La Jolla Institute for Allegy and Immunology, San Diego, CA, U.S., Brigitta Stockinger, Ph.D. (Principal Investigator, Division of Molecular Immunology, NIMR, London, UK) Graduate students: Henna Kallionpää, M.Sc., Kartiek Kanduri, M.Sc., Moin Khan, M.Sc., Minna Kyläniemi, M.Sc., Essi Laajala, M. Tech., Tapio Lönnberg, M.Sc., Elisa Närvä, M.Sc., Mirkka Heinonen, M.Sc., Nelly Rahkonen, M.Sc., Verna Salo, M.Sc., Alexey Sarapulov, M.Sc., Soile Tuomela, M.Sc., Subhash Tripathi, M.Tech, M.Sc. Technicians: Bogata Fezazi, Marjo Hakkarainen, Sarita Heinonen, Päivi Junni, Elina Pietilä Undergraduate students: Krista Maurinen, Johanna Myllyviita, Lotta Oikari, Anna Rajamäki Description of the project: Our research group belongs to the new “Centre of Excellence on Molecular Systems Immunology and Physiology” Academy of Finland selected for years 2012-17. In this CoE we are responsible for molecular systems immunology. In addition we focus on stem cell biology. We use holistic genome and proteome wide methods 80 and systems biology to reveal molecular mechanisms of cell signaling, transcriptional and epigenetic programs that determine cell differentiation and fate. These approaches are exploited to understand molecular mechanisms of human immune mediated diseases and certain types of cancer to provide novel therapeutic means to modulate harmful cellular and immune responses. T helper cell activation and differentiation to functionally distinct subsets. Selective activation of T helper (Th) cell subsets plays an important role in the pathogenesis of human allergy and inflammatory diseases. Dissecting pathways and regulatory networks leading to the development of Th1, Th2, Th17 or regulatory T cells (Treg) is essential to understand the pathogenesis of allergy and inflammatory diseases. Th2 cytokines lead to a series of inflammatory processes characteristic for asthma and other atopic diseases whereas Th1 and Th17 cells play a role in the pathogenesis of autoimmune diseases (e.g. type I diabetes). Treg cells have an important role in inhibiting all these T effector cell functions. Detailed analysis of upstream T cell Receptor (TCR)/key cytokine receptor induced differentiation will increase our understanding of these processes central for human health and disease and provide novel insights into new therapeutic interventions. STAT6 is known to be an essential upstream mediator of IL-4R signaling and Th2 differentiation. Importantly, we identified for the first time STAT6 target genes on a genome wide scale in human CD4+ T cells - only small fraction of which were previously known to be STAT6 regulated. This study, published in Immunity, revealed that in human surprisingly high proportion, up to 80% of IL-4 induced response is STAT6 regulated revealing several new candidates for therapeutic intevention (Elo L et al. 2010). This was the first study to identify any STAT targets in human lymphocytes on a genome wide scale (O’Shea et al. 2011). Our studies on IL-4 R signaling in lymphocytes also resulted in identification of new IL4R/STAT-6 regulated proteins in human and mice as well as mechanistic studies on their molecular functions (Aflakian N, et al. 2009, Moulder R. et al. 2010, Tripathi et al. 2011, Tuomela S. et al. 2009, Cho CH et al. 2009). We also identified for the first time on a genome wide scale genes engaged during the early stages of human Th17 cell specification (Tuomela et al. 2012). Our results have led to novel hypotheses on the key factors involved in human Th cell differentiation (Lund et al., 2007, Rautajoki et al. 2007, Ullah et al. 2012, Äijö et al. 2012). Elucidating their functions further we discovered that ATF3, PIM kinases and SATB1 are important regulators of human Th cell differentiation. ATF3 and PIM kinases promote Th1 differentiation (Filen S et al. 2010, Tahvanainen et al. 2012) whereas SATB1 regulates multiple genes during early Th cell differentiation (Ahlfors et al. 2010). Human embryonic stem cells (hESC) have a unique capacity to differentiate to any type of cell or tissue providing an enormous potential for therapeutic applications (Lund et al. 2012a). Our recent results based on the use of high resolution microarray technology demonstrate that it is essential to monitor stem cell lines carefully to minimize the risk of malignancies in stem cell therapies. Our study published in Nature Biotechnology and highlighted in Nature Methods revealed that in prolonged culture human embryonic stem cells acquire chromosomal abnormalities and changes in gene expression, many of which are linked to cancer. (Närvä et al. 2010). This was 81 followed up by a study published in Nature, where the number of copy number variations in both early and intermediate-stage human induced pluripotent stem (iPS) cells was compared with their respective parental, originating cells as well as embryonic stem cells. Again, the results suggested that the whole genome analysis should be included also as part of quality control of iPS cell lines to ensure that these cells remained genetically normal after the reprogramming process, before their use for studies and/or clinical applications. (Hussein S, et al. 2011). A novel high-througghput karyotyping assay was developed for this purpose (Lund et al. 2012b). Our goal is to elucidate the molecular mechanisms regulating self renewal and pluripotency of hESC and induced pluripotent stem cells (iPS). We have identified novel genes and signaling pathways characteristic for the pluripotent hESC and iPS cells based on a genome wide transcriptome analyses of hESC. This resulted in the discovery of a RNA binding protein L1TD1 selectively expressed in stem cells and required for hESC renewal (Närvä et al. 2012). Type 1 diabetes (T1D) is the most common metabolic-endocrine disorder in children in western countries and the annual incidence of T1D in Finland is record high. In almost all children, progression to clinical T1D is associated with the presence of β cell specific autoantibodies. Clinical T1D occurs when 80-90% of the β cells have been destroyed. At this point T1D patient is dependent on a daily insulin substitution for the rest of his/her life and there is a high risk of developing acute and long-term complications. Development of early diagnostics would enable early therapy and possibly preventive treatments resulting in a significant reduction in the health care costs. Our objective is to study molecular mechanisms of T1D and to discover molecular markers that indicate development of autoimmunity and progression towards clinical T1D. Exploiting the unique biobank of the Type 1 Diabetes Prediction and Prevention Project in Finland (DIPP) we investigated transcriptomic profiles of prospective whole-blood samples from children who have developed T1Dassociated autoantibodies and eventually clinical T1D. Gene-level investigation of the data showed systematic differential expression of 520 probesets. A network-based analysis revealed then a highly significant down-regulated network of genes involved in antigen presentation as well as T-cell receptor and insulin signaling. (Elo et al. 2010). Further studies include analysis of larger cohort of longitudinal samples using transciptomics, proteomics and integrating the data with our previous metbolomics results (Oresic et al. 2008). Funding: The Academy of Finland, The National Technology Agency of Finland (TEKES), JDRF, The Sigrid Jusélius Foundation, The Finnish Cancer Organizations, Turku University Hospital Fund, Graduate Schools (TuBS, ISB), University of Turku, Åbo Akademi University, European Research Council, EU 7th framework projects “SYBILLA”, “DIABIMMUNE”, “NANOMMUNE”, “PEVNET”, EraSysBioPlus, European Research Council. Collaborators: Ruedi Aebersold & Matthias Gstaiger (ETZ, Zürich, Swizrland) and the other 14 EU FP7 SYBILLA partners, Reija Autio (Tampere University of Technology ), Christopher Burge (MIT, Cambridge, MA, USA), 82 Sanjeev Galande (IISER, Pune, India), Heikki Hyöty (U. Tampere), Mikael Knip (U. Helsinki), Harri Lähdesmäki (Aalto University, CBT), David Goodlett (University of Washington, Seattle, WA, USA and a FiDiPro in CBT), Matej Oresic (VTT Technical Research Centre of Finland, Turku, CBT), Anjana Rao (La Jolla Institute for Allergy and Immunology, San Diego, CA, USA and visiting professor at CBT), Kanury V.S. Rao (ICGEB, New Delhi, India and visiting professor at CBT), Bing Ren (Ludwig Institute for Cancer Research, University of California, San Diego, USA), Olli Simell (U. Turku), Brigitta Stockinger (NIMR, London, UK and visiting professor at CBT), Thomas Tushl (Rockefeller University, New York, NY, USA) Selected Publications: Ahlfors H, Limaye A, Elo-Uhlgrén L, Notani D, Gottimukkala K, Burute M, Tuomela S, Rasool O, Galande S* & Lahesmaa R*. (2010) SATB1 dictates expression of multiple genes including IL-5 involved in human T helper cell differentiation. *Equal contribution. Blood 116:1443-1453. Benson MJ, Aijö T, Chang X, Gagnon J, Pape UJ, Anantharaman V, Aravind L, Pursiheimo JP, Oberdoerffer S, Liu XS, Lahesmaa R, Lähdesmäki H, Rao A. (2012) Heterogeneous nuclear ribonucleoprotein L-like (hnRNPLL) and elongation factor, RNA polymerase II, 2 (ELL2) are regulators of mRNA processing in plasma cells. Proc Natl Acad Sci U S A. 109: 16252-16257. Cho SH, Goenka S, Henttinen T, Gudapati P, Reinikainen A, Lahesmaa R, Boothby M. (2009) PARP-14, a member of the B aggressive lymphoma (BAL) family, transduces survival signals in primary B cells. Blood 113:2416-2425. Elo LL#, Järvenpää H#, Tuomela S#, Raghav S#, Ahlfors H, Laurila K, Gupta B, Lund RJ, Tahvanainen J, Hawkins RD, Orešič M, Lähdesmäki H, Rasool O, Rao KVS*, Aittokallio T*, Lahesmaa R. (2010) IL-4- and STAT6-mediated transcriptional regulation to initiate Th2 program in human T cells. Immunity, 32:852-862. #, * Equal contribution. Elo LL*, Mykkänen J*, Nikula T, Järvenpää H, Aittokallio T, Hyöty H, Ilonen J, Veijola R, Knip M, Simell O, Lahesmaa R. (2010) Genome-wide gene expression profiling reveals early suppression of immune response pathways in prediabetic children. *Equal contribution. J Autoimmun. 35:70-76. Filén JJ, Filén S, Moulder R, Tuomela S, Ahlfors H, West A, Kouvonen P, Kantola S, Björkman M, Katajamaa M, Rasool O, Nyman TA, Lahesmaa R. (2009) Quantitative Proteomics Reveals GIMAP Family Proteins 1 and 4 to Be Differentially Regulated during Human T Helper Cell Differentiation. Mol Cell Proteomics. 8:32-44. Filén S, Ylikoski E, Tripathi S, West A, Björkman M, Nyström J, Ahlfors H, Rao KVS, Coffey E, Rasool O, and Lahesmaa R. (2010) ATF3 is a Positive Regulator of Human IFNG Gene Expression. J Immunol. 184:4990-4999. Hussein S, Batada N, Vuoristo S, Autio R, Närvä E, Ng S, Hämäläinen R, Olsson C, Lundin K, Mikkola M, Trokovic R, Peitz M, Brüstle O, Alitalo K, Lahesmaa R, Nagy A #, Otonkoski T#. (2011). Increased mutation load is associated with reprogramming of human somatic cells. Nature 471:58-62. #.Equal contribution. Koh KP, Yabuuchi A, Rao S, Huang Y, Cunniff K, Nardone J, Laiho A, Tahiliani M, Sommer CA, Mostoslavsky G, Lahesmaa R, Orkin SH, Rodig SJ, Daley GQ, Rao A. (2011) Tet1 and tet2 regulate 83 84 20121015_0051.jpg From left to right: Riitta Lahesmaa, Ida Koho, Anne Lahdenperä, Essi Laajala, Saara Hämälistö, Viveka Öling, Elisa Närvä, Lotta Oikari, Robert Moulder, Jussi Salmi, Kartiek Kanduri, Santosh Boshale, Nelly Rahkonen, Omid Rasool, Päivi Junni, Sarita Heinonen, Moin Mohd Khan, Jane Chen Zhi, Subhash Tripathi, Marjo Hakkarainen, Minna Kyläniemi, Tapio Lönnberg and Mirkka Heinonen. 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells. Cell Stem Cell 8:200-13. Kumar D, Srikanth R, Ahlfors H, Lahesmaa R, Rao K. (2007) Capturing cell-fate decisions from the molecular signatures of a receptor-dependent signaling response. Molecular Systems Biology, 3:150. Lund RJ, Närvä E, Lahesmaa R. (2012) Genetic and epigenetic stability of human pluripotent stem cells. Nat Rev Genet. 13:732744. Review. Lund R*, Pykäläinen M*, Naumanen T, Dixon C, Chen Z, Ahlfors H, Tuomela S, Tahvanainen J, Scheinin J, Henttinen T, Rasool O, Lahesmaa R. (2007) Genome wide identification of Novel Genes Involved in Early Th1 and Th2 Cell Differentiation. J. Immunol 178:3648-3660. Närvä E, Autio R, Rahkonen N, Kong L, Harrison N, Kitsberg D, Borghese L, Itskovitz-Eldor J, Rasool O, Dvorak P, Hovatta O, Otonkoski T, Tuuri T, Cui W, Brüstle O, Baker D, Maltby E, Moore HD, Benvenisty N, Andrews PW, Yli-Harja O & Lahesmaa R. (2010) High resolution genome wide DNA analysis on a large panel of Human Embryonic Stem Cell lines reveals novel genomic changes associated with culture and affecting gene expression. Nat Biotechnol. 28:371-377. Närvä E, Rahkonen N, Emani MR, Lund R, Pursiheimo JP, Nästi J, Autio R, Rasool O, Denessiouk K, Lähdesmäki H, Rao A, Lahesmaa R. (2012) RNA Binding Protein L1TD1 Interacts with LIN28 via RNA and is Required for Human Embryonic Stem Cell Self-Renewal and Cancer Cell Proliferation. Stem Cells. 30:452-460. Oresic M, Simell S*, Sysi-Aho M*, Näntö-Salonen K*, SeppänenLaakso T*, Parikka V*, Katajamaa M*, Hekkala A, Mattila I, Keskinen P, Yetukuri L, Reinikainen A, Lähde J, Suortti T, Hakalax J, Simell T, Hyöty H, Veijola R, Ilonen J, Lahesmaa R, Knip M, Simell O. (2008) Dysregulation of lipid and amino acid metabolism precedes islet autoimmunity in children who later progress to type 1 diabetes. * Equal contribution. J Exp Med. 2008 205:2975-2984. O’Shea JJ, Lahesmaa R, Vahedi G, Laurence A, Kanno Y. (2011) Genomic views of STAT function in CD4(+) T helper cell differentiation. Nat Rev Immunol. 11:239-250. Tahvanainen J, Kallonen T, Lähteenmäki H, Heiskanen KM, Westermarck J, Rao KV, Lahesmaa R. (2009) PRELI is a mitochondrial regulator of human primary T helper cell apoptosis, STAT6 and Th2 cell differentiation. Blood, 113:1268-1277. Tahvanainen J, Kyläniemi MK, Kanduri K, Gupta B, Lähteenmäki H, Kallonen T, Rajavuori A, Rasool O, Koskinen PJ, Rao KV, Lähdesmäki H, Lahesmaa R. (2012) Proviral integration site for Moloney murine leukemia virus (PIM) kinases promote human T helper 1 cell differentiation. J Biol Chem. 2012 Dec 3. Tuomela S, Salo V, Tripathi SK, Chen Z, Laurila K, Gupta B, Äijö T, Oikari L, Stockinger B, Lähdesmäki H, Lahesmaa R. (2012) Identification of early gene expression changes during human Th17 cell differentiation. Blood. 119: e151-160. Aijö T, Edelman S, Lönnberg T, Larjo A, Kallionpää H, Tuomela S, Engström E, Lahesmaa R, Lähdesmäki H. (2012) An integrative computational systems biology approach identifies differentially regulated dynamic transcriptome signatures which drive the initiation of human T helper cell differentiation. BMC Genomics 13: 572. 85 COMPUTATIONAL SYSTEMS BIOLOGY Principal investigator: Harri Lähdesmäki, D.Sc. (Tech), Assistant Professor (tenure track), Academy Research Fellow, Affiliated Group Leader at CBT Contact information: Aalto University School of Science, Department of Information and Computer Science, PO Box 15400, FI-00076 Aalto, Finland. Tel. +358 9 47001, Fax. +358 9 470 23277, E-mail: [email protected], www-page: http://users.ics.tkk.fi/harrila/research/ Biography: Harri Lähdesmäki (b. 1977) graduated in bionformatics from Tampere University of Technology in 2005. Personnel: Post-doctoral researchers: Jukka Intosalmi, Kirsti Laurila Graduate students: Timo Erkkilä, Kartiek Kanduri, Lingjia Kong, Essi Laajala, Antti Larjo, Maia Malonzo, Henrik Mannerström, Kari Nousiainen, Maria Osmala, Tarmo Äijö Undergraduate students: Juhani Kähärä, Sini Rautio, Juhi Somani Description of the project: We use computational techniques to model and understand molecular regulatory mechanisms and their role in health and disease. We focus on developing statistical modeling and machine learning methods to understand transcriptional, posttranscriptional and epigenetic regulatory mechanisms, protein signaling pathways, and effects of mutations on regulatory mechanisms. We also develop methods for biological sequence analysis, combining heterogeneous biological information sources and analyzing high-throughput measurement data, such as deepsequencing and microarray measurements. Research projects are carried out in close collaboration with experimental groups, and we collaborate on molecular immunology, stem cell, cancer and type 1 diabetes systems biology research projects. Funding: Academy of Finland, EU FP7, EraSysBio+, Tekes, Aalto University, Emil Aaltonen Foundation, FICS and TISE graduate schools. Collaborators: Prof. Riitta Lahesmaa (University of Turku), Prof. Matej Orešič (VTT Technical Research Centre of Finland), Prof. Mikael Knip (University of Helsinki), Prof. Olli Simell (Hospital District of Southwest Finland) Benson MJ, Äijö T, Chang X, Gagnon J, Pape UJ, Anantharaman V, Aravind L, Pursiheimo J-P, Oberdoerffer S, Liu XS, Lahesmaa R, Lähdesmäki H and Rao A. (2012) Heterogeneous nuclear ribonucleoprotein L-like (hnRNPLL) and elongation factor, RNA polymerase II, 2 (ELL2) are regulators of mRNA processing in plasma cells. Proceedings of the National Academy of Sciences of the USA, in press Tuomela S, Salo V, Tripathi SK, Chen Z, Laurila K, Äijö T, Gupta B, Oikari L, Stockinger B, Lähdesmäki H and Lahesmaa R. (2012) Identification of early gene expression changes during human Th17 cell differentiation. Blood, Vol. 119, No. 23, pp. e151-160. Lehmusvaara S, Erkkilä T, Urbanucci A, Jalava S, Seppälä J, Kaipia A, Kujala P, Lähdesmäki H, Tammela TLJ and Visakorpi T. (2012) Goserelin and bicalutamide treatments alter the expression of microRNAs in prostate. The Prostate, in press. Lehmusvaara S, Erkkilä T, Urbanucci A, Waltering K, Seppälä J, Tuominen V, Isola J, Kujala P, Lähdesmäki H, Kaipia A, Tammela TLJ and Visakorpi T. (2012) Chemical castration and antiandrogens induce differential gene expression in prostate cancer. The Journal of Pathology, Vol. 227, No. 3, pp. 336--345. Urbanucci A, Sahu B, Seppälä J, Larjo A, Latonen LM, Waltering KK, Tammela TLJ, Vessella RL, Lähdesmäki H, Jänne OA and Visakorpi T. (2012) Overexpression of androgen receptor enhances the binding of the receptor to the chromatin in prostate cancer. Oncogene, Vol. 31, No. 17, pp. 2153-2163. Närvä E, Rahkonen N, Emani MR, Lund R, Pursiheimo J-P, Nästi J, Autio R, Rasool O, Denessiouk K, Lähdesmäki H, Rao A and Lahesmaa R. (2012) RNA binding protein L1TD1 interacts with LIN28 via RNA and is required for human embryonic stem cell self-renewal and cancer cell proliferation. Stem Cells, Vol. 30, No. 3, pp. 452-460. Annala, M., Laurila, K., Lähdesmäki, H., and Nykter, M., (2011) A linear model for transcription factor binding affinity prediction in protein binding microarrays, PLoS ONE, 6(5): e20059, 2011. Erkkilä T, Lehmusvaara S, Ruusuvuori P, Visakorpi T, Shmulevich I. and Lähdesmäki H. (2010) Probabilistic analysis of gene expression measurements from heterogeneous tissues, Bioinformatics, 26(20):2571-2577. Elo, L. L., Järvenpää, H., Tuomela, S., Raghav, S., Ahlfors, H., Laurila, K., Gupta, B., Lund, R. J., Tahvanainen, J., Hawkins, D., Oresic, M., Lähdesmäki, H., Rasool, O., Rao, K. V., Aittokallio, T. and Lahesmaa, R. (2010) Genome-wide Profiling of Interleukin-4 and STAT6 Transcription Factor Regulation of Human Th2 Cell Programming, Immunity, 32(6):727-862. Selected recent publications: Äijö T, Edelman S, Lönnberg T, Larjo A, Järvenpää H, Tuomela S, Engström E, Lahesmaa R and Lähdesmäki H. (2012) An integrative computational systems biology approach identifies lineage specific dynamic transcriptome signatures which drive the initiation of human T helper cell differentiation. BMC Genomics, 13:572. 86 87 CELL CULTURE MODELS FOR TUMOR CELL INVASION AND EPITHELIAL PLASTICITY Principle investigator: Matthias Nees, Ph.D., Docent for Genetics Affiliated Group Leader at CBT University of Turku, VTT Medical Biotechnology. Itäinen Pitkäkatu 4C, FI-20520 Turku, Finland Tel. +358-40-8314 839, Fax. +358-2 2840 Biography: Matthias Nees (b. 1966) graduated from the University of Heidelberg, Germany in 1993 for work in the field of head & neck cancers. He received his Ph.D. in 1997 from the German Cancer Research Center in Heidelberg, for work on Human Papillomaviruses (HPV). He did post-doctoral research at the National Institutes of Health (NCI, 1997-2001), and EMBL/Heidelberg University (2002 - 2005). He is currently a principal investigator and team leader at VTT Medical Biotechnology. Personnel: Post-doctoral researchers: Ville Härmä, Malin Åkerfelt Graduate students: Ilmari Ahonen Technicians: Pauliina Toivonen, Johannes Virtanen Undergraduate students: Mrinal Mishra, Chamudeesvari Simvaranan Description of the project: Over the past years, our group (located at VTT, Pharmacity) has systematically established a panel of organotypic, threedimensional cell- and tissue culture platforms for epithelial cancers (focus on breast, prostate and ovarian carcinomas). We have successfully utilized these models in both academic and custom research applications. Generally, all of our platforms aim to faithfully recapitulate the complex histology and texture, epithelial differentiation, extracellular matrix (ECM) and microenvironment (TME) of human cancer tissues, but also their often extreme heterogeneity and dynamic. These aspects are only poorly covered - if at all - by standard 2-dimensional or monolayer culture on plastic. Most importantly, our 3D platforms are thoroughly standardized and miniaturized, allowing reproducible experimentation on a previously unprecedented scale. Assays can be performed in 96- and 384-well plates, using plate-based high-content readers (IncuCyte, PE Envision, PE Operetta) for rapid experimental readout, or confocal spinning-disc microscopy for more detailed imaging. Imaging can be performed using a panel of methods, for example in real-time, live cell settings (using fluorochromes and reactive dyes), and subsequently analysed using end-point assays on fixed multicellular structures or spheroids. End-point assays are assisted by the use of suitable biomarkers and antibodies for multiplex immune fluorescence, pathway-specific molecule drugs, 3D siRNA transfection protocols, or specific reporter constructs (LiveAct; small GTPases, etc). In both approaches, 88 the functional readout is mainly based on morphometric nature and utilizes the phenotypic evaluation of spheroid structures by microscopy; as a consequence VTT has developed the AMIDA software package for automated image analyses that allows rapid segmentation of large numbers of confocal image stacks, together with statistical & machine learning solutions for the subsequent data normalization and interpretation. Thus, our approach strives to combine classic high-content screening efforts (batch segmentation and analysis of image content) with laboratory automation protocols (robotics) from high throughput screening. Morphological changes in the shape, size and morphology tumour organoid have been demonstrated by us and others to closely correlate with different stages of tumour histology and pathological grading. In particular, dynamic phenotypic changes (such as tumour cell invasion) are predictive for patient outcome. Scientifically, we mainly address the mechanisms and molecular pathways involved in the maintenance and loss of tissue organization (homeostasis) and epithelial differentiation, which is of surprisingly dynamic nature. Both the TME and ECM play decisive roles in the regulation of tumour spheroid morphology. Nevertheless, mature and well-differentiated structures are often of only metastable nature. The most aggressive tumour cells can undergo a spontaneous switch to invasive growth, demonstrating the remarkable plasticity of epithelial tumours. We have explored the functional role of proteases, G-protein coupled receptors and down-stream signalling pathways in this decision-making process, which could be a prerequisite for the formation of local or distant metastases. Morphological switches may also transform collective into single-cell patterns of invasion, or epithelial versus mesenchymal modes of motility. Also these can be specifically addressed with our models. Most recently, we have started to develop 3D co-culture platforms with stromal fibroblasts and cancer-associated (myo-)fibroblasts (CAFs). These recapitulate additional, very critical aspects of complex tumor biology (such as the role of the TME), and have been thoroughly standardized and miniaturized as well. As with simple 3D cultures, the goal here is to most faithfully recapitulate tumour heterogeneity and dynamic processes, and to provide tools for their experimental evaluation. Funding: The Academy of Finland (with Department of Biotechnology/India), VTT, University of Turku, EU Innovative Medicines Initiative (IMI), EU 7th framework, K. Albin Johansson Foundation Collaborators: List your key collaborators as follows: Lea Sistonen (Åbo Akademi), Pirkko Härkönen ( U. Turku), Olli Kallioniemi (FIMM), Varda Rotter (Weizmann Institute of Science, Rehovot/Israel), Markku Kallajoki (University Hospital Turku), Franz X. Bosch (Heidelberg University), Roland Grafström/Bengt Fadeel (Karolinska Institute) Selected Publications: Björkman M., Östling P., Härmä V., Virtanen J., Mpindi J.P., Rantala J., Mirtti T., Vesterinen T., Lundin M., Sankila A., Rannikko A., Kaivanto E., Kohonen P., Kallioniemi O., Nees M.: Systematic 89 knockdown of epigenetic enzymes identifies a novel histone demethylase PHF8 overexpressed in prostate cancer with an impact on cell proliferation, migration and invasion. Oncogene. 2012 Jul 19;31(29):3444-56. Härmä V., Knuuttila M., Virtanen J., Mirtti T., Kohonen P., Kovanen P., Happonen A., Kaewphan S., Ahonen I., Kallioniemi O., Grafström R., Lötjönen J., Nees M.: Lysophosphatidic acid and sphingosine-1-phosphate promote morphogenesis and block invasion of prostate cancer cells in three-dimensional organotypic models. Oncogene. 2012 Apr 19;31(16):2075-89. Härmä V., Virtanen J., Mäkelä R., Happonen A., Mpindi J.P., Knuuttila M., Kohonen P., Lötjönen J., Kallioniemi O., Nees M.: A comprehensive panel of three-dimensional models for studies of prostate cancer growth, invasion and drug responses. PLoS One. 2010 May 3;5(5):e10431. Björkman M., Rantala J., Nees M., Kallioniemi O.: Epigenetics of prostate cancer and the prospect of identification of novel drug targets by RNAi screening of epigenetic enzymes. Epigenomics. 2010 Oct;2(5):683-9. Rantala J.K., Mäkelä R., Aaltola A.R., Laasola P., Mpindi J.P., Nees M., Saviranta P., Kallioniemi O.: A cell spot microarray method for production of high density siRNA transfection microarrays. BMC Genomics. 2011 Mar 28;12:162. COMPLEX BIOSYSTEMS MODELING Principal investigator: Matti Nykter, D. Sc. (Tech), Professor,. Affiliated Group Leader at CBT, Institute of Biomedical Technology, University of Tampere Biokatu 8 (Finn-Medi 2), 33520 Tampere, Finland Tel. +358-40-8490651. Email: [email protected] Home page: http://www.uta.fi/ibt/institute/research/nykter/ Biography: Matti Nykter (b. 1978) received the degree of Master of Science (Engineering) with Distinction in information technology in 2002 and the degree of Doctor of Science (Technology) in signal processing in 2006 from Tampere University of Technology, Tampere, Finland. He has worked as a visiting researcher at The University of Texas M. D. Anderson Cancer Center in Houston, Texas, USA in 2004-2005, and as a post-doctoral research at the Institute for Systems Biology, Seattle, USA during 2007-2009. From 2010 till 2012 he was a group leader at the Department of Signal Processing at Tampere University of Technology. From beginning of 2013 he is a professor of bioinformatics at the Institute of Biomedical Technology, University of Tampere. His research interests are focused on development and application of computational methodologies to understand the mechanisms of gene regulation in context of disease related dysregulation Personnel: Post-doctoral researchers: Kati Waltering, PhD, Kirsi Granberg, PhD, Juha Kesseli, D.Sc. Graduate students: Antti Ylipää, Virpi Kivinen, Matti Annala, Septimia Sarbu Undergraduate students: Kimmo Kartasalo, Simo-Pekka Leppänen, Saija Sorsa, Thomas Liuksiala, Tero Soininen, Sergei Häyrynen, Ville Kytölä, Liisa-Ida Sorsa, Aleksi Kallio. Description of the project The Complex Biosystems Modeling laboratory uses systems biology methodology to study biology. Our research is rooted in high throughput measurement data from genomic and transcriptomic levels. We develop and apply computational tools and mathematical modelling to understand the biosystems. Research activities of our laboratory range from theoretical biology to experimental work. Theoretical work is focused on the fundamental principles of biological systems, such as the information processing and the effect of structural constrains to dynamics. Applied research is focused on cancer research as well as on immunology and cellular differentiation. Main research directions are currently related to cancer research. We are using deep sequencing the characterize the cancer genome of prostate cancer and glioma. We have identified novel oncogenic mechanisms that are currently ongoing functional validation. Another key project is related to understanding cell differentiation. We have integrated a collection of over three thousand gene arrays, measured from 166 normal cell types. Based on novel data integration and data analysis methodology, we are studying the gene networks that give raise to different cell types and 90 91 apply computational approach to uncover recipes for cell type reprogramming experiments. Funding: The Academy of Finland, Finnish Funding Agency for Technology and Innovation (Tekes), Tampere University of Technology, Tampere Doctoral Programme in Information Science and Engineering, Graduate School in Electronics, Telecommunications and Automation, Emil Aaltonen Foundation, Sigrid Juselius Foundation. Collaborators: Wei Zhang (University of Texas M.D. Anderson Cancer Center), Ilya Shmulevich (Institute for Systems Biology), Tapio Visakorpi (University of Tampere), Riitta Lahesmaa (Turku Centre for Biotechnology), Johanna Schleutker (University of Turku), Hannu Haapasalo (Tampere University Hospital), Harri Lähdesmäki (Aalto University), Merja Heinäniemi (University of Eastern Finland), Olli YliHarja (Tampere University of Technology). Selected Publications: Parker B.C., Annala M., Cogdell D., Granberg K., Sun Y., Ji P., Gumin J., Zheng H., Hu L., Li X., Yli-Harja O., Haapasalo H., Visakorpi T., Liu X., Liu C.-G., Sawaya R., Fuller G.N., Chen K., Lang F.L., Nykter M., and Zhang W. (2013) FGFR3-TACC3 fusion escapes miR-99a regulation and promotes tumorigenesis in glioblastoma. Journal of Clinical Investigations, 123(2). Moore L.M., Kivinen V., Liu Y., Annala M., Cogdell D., Liu X., Liu C.G., Sawaya R., Yli-Harja O., Shmulevich I., Fuller G.N., Zhang W., Nykter M. (2012) Transcriptome and Small RNA Deep Sequencing Reveals Deregulation of miRNA Biogenesis in Human Glioma. J Pathol (in press). Holmes K.M., Annala M., Chua C.Y., Dunlap S.M., Liu Y., Hugen N., Moore L.M., Cogdell D., Hu L., Nykter M., Hess K., Fuller G.N., Zhang W. (2012) Insulin-like growth factor-binding protein 2-driven glioma progression is prevented by blocking a clinically significant integrin, integrin-linked kinase, and NF-κB network. Proc Natl Acad Sci USA 109(9):3475-3480 Yang J., Ylipää A., Sun Y., Zheng H., Chen K., Nykter M., Trent J., Ratner N., Lev D.C. and Zhang W. (2011) Genomic and molecular characterization of malignant peripheral nerve sheath tumor identifies the IGF1R pathway as a primary target for treatment. Clin. Cancer Res . 17: 7563-7573. Annala M., Laurila K., Lähdesmäki H. and Nykter M. (2011) A linear model for transcription factor binding affinity prediction in protein binding microarrays. PLoS One . 6: e20059. Ylipää A., Hunt K.K., Yang J., Lazar A.J., Torres K.E., Lev D.C., Nykter M., Pollock R.E., Trent J. and Zhang W. (2011) Integrative genomic characterization and a genomic staging system for gastrointestinal stromal tumors. Cancer 117: 380-389. 92 METABOLOME IN HEALTH AND DISEASE Principal investigator: Matej Orešič, Ph.D., Prof., Affiliated Group Leader at CBT, VTT Technical Research Centre of Finland. Tietotie 2, P.O. Box 1000, FIN-02044 VTT, Espoo, Finland. E-mail: [email protected]. Home page: http://sysbio.vtt.fi/ Biography: Prof. Matej Orešič holds a PhD in biophysics from Cornell University. Since 2003 he leads the research in domains of quantitative biology and bioinformatics at VTT Technical Research Centre of Finland (Espoo, Finland), where he is a Research Professor in Systems Biology and Bioinformatics. Prof. Orešič is a director of the newly established Finnish Centre of Excellence in Molecular Systems Immunology and Physiology Research (2012-2017). He is also a cofounder and board member of Zora Biosciences, Oy. (Espoo, Finland) and current board member of the Metabolomics Society. His main research areas are metabolomics applications in biomedical research and computational systems biology. Recent investigations include studies of longitudinal metabolic profiles of children who progressed to type 1 diabetes, investigations of lipidomic profiles associated with acquired obesity and lipotoxicity induced insulin resistance and metabolomic studies of psychiatric disorders. Prof. Orešič has initiated the popular MZmine open source project, leading to popular software for metabolomics data processing. Prior to joining VTT, Prof. Orešič was a head of computational biology and modeling at Boston-based Beyond Genomics, Inc. and bioinformatician at LION Bioscience Research in Cambridge/MA. Personnel: Senior personnel: Tuulia Hyötyläinen, PhD, Team leader, Metabolomics (analytical chemistry, metabolite analytics), Marko Sysi-Aho, PhD, Team leader, Biosystems ModellingResearch scientists: sabel Bondia Pons, PhD (metabolomics, nutritional systems biology), Mika Hilvo, PhD (cancer metabolomics), Sirkku Jäntti, PhD (analytical chemistry), Maarit Kivilompolo, PhD (analytical chemistry), Artturi Koivuniemi, MSc (computational biophysics), Erno Lindfors, PhD (bioinformatics, network biology), Niina Lietzen, PhD (metabolomics), Tijana Marinković, PhD (computational systems biology, theoretical physics), Ismo Mattila, MSc (analytical chemistry), Heli Nygren, PhD (metabolite analytics), Gopal Peddinti, PhD (bioinformatics), Päivi Pöhö, MSc (analytical chemistry), Laxman Yetukuri, PhD (lipid bioinformatics) Technicians: Ulla Lahtinen (technician, analytical chemistry), AnnaLiisa Ruskeepää (technician, analytical chemistry), Han Zhao, MSc (information systems), Leena Öhrnberg (technician, analytical chemistry) Description of the project: Metabolome is sensitive to pathogenically relevant factors such as genetic variation, diet, development, age, immune system status or gut microbiota. Metabolomics has emerged as a powerful tool for the characterization of complex phenotypes as well as for the development of biomarkers for specific physiological responses. We are investigating: 93 1. how are the genetic and environmental factors imprinted in the metabolome 2. the mechanisms by which alterations of metabolome lead to (patho)physiological changes at the systems level 3.discovery and functional characterization of metabolic markers and targets for selected complex diseases. We are relying on metabolomics techniques to characterize the metabolome, combined with systems biology strategies to investigate, e.g., how changes in gene expression, gut microbial composition or immune/inflammatory status alter the metabolic phenotypes. Current biomedical interests include metabolic and autoimmune diseases. Funding: EU FP7, Juvenile Diabetes Research Foundation, Academy of Finland, NordForsk Collaborators: Prof. Mikael Knip (University of Helsinki), Prof. Olli Simell (Hospital District of Southwest Finland), Prof. Riitta Lahesmaa (University of Turku), Prof. Harri Lähdesmäki (Aalto University), Prof. Sami Kaski (Aalto University), Prof. Eytan Ruppin (Tel Aviv University), Antonio Vidal-Puig (University of Cambridge), Hannele Yki-Järvinen (University of Helsinki), Fredrik Bäckhed (Gothenburg University), Hilkka Soininen (University of Eastern Finland) Selected publications: Sayin S.I., Wahlström A., Felin J., Jäntti .S, Marschall H.U., Bamberg K., Angelin B., Hyötyläinen T., Orešič M., Bäckhed F. (2013) Gut microbiota regulates bile acid metabolism by reducing the levels of tauro-beta-muricholic acid, a naturally occurring FXR antagonist. Cell Metab 17(2):225-35. Orešič M., Seppänen-Laakso T., Sun D., Tang J., Therman S., Viehman R., Mustonen U., van Erp T. G. M., Hyötyläinen T., Thompson P., Toga A. W., Huttunen M. O., Suvisaari J., Kaprio J., Lönnqvist J. and Cannon T. D. (2012) Phospholipids and insulin resistance in psychosis: a lipidomics study of twin pairs discordant for schizophrenia, Genome Med. 4: e1. Orešič M., Hyötyläinen T., Herukka S.-K., Sysi-Aho M., Mattila I., Seppänan-Laakso T., Julkunen V., Gopalacharyulu P. V., Hallikainen M., Koikkalainen J., Kivipelto M., Helisalmi S., Lötjönen S. and Soininen H., (2011) Metabolome in progression to Alzheimer’s disease, Transl. Psychiatry 1: e57. Sysi-Aho M., Ermolov A., Gopalacharyulu P. V., Tripathi A., Seppänen-Laakso T., MaukonenJ, Mattila I., Ruohonen S. T., Vähätalo L., Yetukuri L., Härkönen T., Lindfors E., Nikkilä J., Ilonen J., Simell O., Saarela M., Knip M., Kaski S., Savontaus E. and Orešič M. (2011) Metabolic regulation in progression to autoimmune diabetes, PLoS Comp. Biol. 7: e1002257. Pietiläinen K., Róg T., Seppänen-Laakso T, Virtue S., Gopalacharyulu P., Tang J., Rodriguez-Cuenca S., Maciejewski A., Naukkarinen J., Rissanen A., Ruskeepää A.-L., Niemelä P., Velagapudi V., Castillo S., Nygren H., Hyötyläinen T., Kaprio J, Yki-Järvinen H, Vattulainen I., Vidal-Puig A. and Orešič M. (2011) Association of lipidome remodeling in the adipocyte membrane with acquired obesity in humans, PLoS Biol. 9: e1000623. Orešič M., Tang J., Seppänen-Laakso T., Mattila I., Saarni S. E., Saarni S. I., Lönnqvist J., Sysi-Aho M., Hyötyläinen T., Perälä J. and 94 Suvisaari J. (2011) Metabolome in schizophrenia and other psychotic disorders: a general population-based study, Genome Med. 3: e19. Hilvo M., Denkert C., Lehtinen L., Müller B., Brockmöller S., Seppänen-Laakso T., Budczies J, Bucher E., Yetukuri L., Castillo S., Berg E., Nygren H., Sysi-Aho M., Griffin J. L., Fiehn O., Loibl S., Richter-Ehrenstein C., Radke C., Hyötyläinen T., Kallioniemi O, Iljin K. and Orešič M. (2011) Novel theranostic opportunities offered by characterization of altered membrane lipid metabolism in breast cancer progression, Cancer Res. 71: 3236-3245. Pluskal T., Castillo S., Villar-Briones A and Orešič M. (2010) MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data, BMC Bioinformatics 11: 395. Westerbacka J., Kotronen A., Fielding B. A., Wahren J., Hodson L., Perttilä J., Seppänen-Laakso T., Suortti T., Arola J., Hultcrantz R., Castillo S., Olkkonen V. M., Frayn K. N., Orešič M. and Yki-Järvinen H. (2010) Splanchnic balance of free fatty acids, endocannabinoids and lipids in subjects with NAFLD, Gastroenterology 139: 1961-1971. Yetukuri L., Söderlund S., Koivuniemi A., Seppänen-Laakso T., Niemelä P. S., Hyvönen M., Taskinen M.-R., Vattulainen I., Jauhiainen M. and Orešič M. (2010) Composition and lipid spatial distribution of High Density Lipoprotein particles in subjects with low and high HDL-cholesterol, J. Lipid Res. 51: 2341-2351. Velagapudi V. R., Hezaveh R., Reigstad C. S., Gopalacharyulu P. V., Yetukuri L., Islam S., Felin J., Perkins R., Borén J., Orešič M., and Backhed F. (2010) The gut microbiota modulates host energy and lipid metabolism in mice, J. Lipid Res. 51: 1101-1112. Kotronen A., Velagapudi V. R., Yetukuri L., Westerbacka J., Bergholm R., Ekroos K., Makkonen J., Taskinen M.-R., Orešič M. and Yki-Järvinen H. (2009) Saturated fatty acids containing triacylglycerols are better markers of insulin resistance than total serum triacylglycerol concentrations, Diabetologia 52: 684-690. Gopalacharyulu P. V., Velagapudi V. R., Lindfors E., Halperin E. and Orešič M. (2009) Dynamic network topology changes in functional modules predict responses to oxidative stress in yeast, Mol. BioSyst. 5: 276-287. Orešič M., Simell S., Sysi-Aho M., Näntö-Salonen K., SeppänenLaakso T., Parikka V., Katajamaa M., Hekkala A., Mattila I., Keskinen P., Yetukuri L., Reinikainen A., Lähde J., Suortti T., Hakalax J., Simell T., Hyöty H., Veijola R., Ilonen J., Lahesmaa RKnip., M. and Simell O. (2008) Dysregulation of lipid and amino acid metabolism precedes islet autoimmunity in children who later progress to type 1 diabetes, J. Exp. Med. 205: 2975-2984. Nikkilä J., Sysi-Aho M., Ermolov A., Seppänen-Laakso T., Simell O., Kaski S., Orešič M. (2008) Gender dependent progression of systemic metabolic states in early childhood, Mol. Syst. Biol. 4: e197. Yetukuri L., Katajamaa M., Medina-Gomez G., Seppänen-Laakso T., Vidal Puig A. and Orešič M. (2007) Bioinformatics strategies for lipidomics analysis: characterization of obesity related hepatic steatosis, BMC Systems Biology 1: e12. Laaksonen R., Katajamaa M., Päivä H., Sysi-Aho M., Saarinen L., Junni P., Lütjohann D., Smet J., Van Coster R., SeppänenLaakso T., Lehtimäki T., Soini J. and Orešič M. (2006) A systems biology strategy reveals biological pathways and plasma biomarker candidates for potentially toxic statin induced changes in muscle, PLoS ONE 1: e97. 95 PROTEIN CRYSTALLOGRAPHY Principal investigator: Anastassios C. Papageorgiou, Ph.D., Adjunct Professor in Biochemistry and Structural Biology Turku Centre for Biotechnology, BioCity, Tykistökatu 6A, FI-20521 Turku, Finland. Tel. +358-2-3338012, Fax +358-2-3338000. E-mail: [email protected] Biography: Tassos Papageorgiou obtained his Ph.D. from the University of Athens in 1992. He was a postdoctoral fellow at the University of Oxford and University of Bath (UK). In May 2000, he joined the Centre for Biotechnology as senior scientist in protein crystallography. Personnel: Graduate students: Bishwa Subedi, Abdi Muleta Undergraduate students: Anthony Oudot, Jesse Mattsson, Carlos Prieto Lopez, Pradeep Battula, Cleménce Frioux Description of the project: We use X-crystallography, molecular biology, and biophysical techniques to study the structure and function of biological molecules. One of our major projects has been the Dps family of proteins that are widely spread among procaryotes and responsible for protection against oxidative stress due to their ability to oxidize and store iron. Although Dps proteins are structurally similar to ferritins, they form a spherical shell of 12 subunits instead of 24 and have a different ferroxidase center compared to that of ferritins. Based on our recent results, work on several new mutants continued in order to understand better the iron core formation using X-ray crystallography, microcalorimetry, EXAFS, magnetization measurements, and Mössbauer spectroscopy. From left to right. Tassos Papageorgiou, Pradeep Battula and Abdi Muleta. Work on newly identified bacterial adhesins continued during last year. With the increased resistance to antibiotics, adhesins have become an attractive therapeutic target in the fight against microbial diseases. Various constructs of two newly identified bacterial adhesins containing leucine-rich repeats were used for protein expression and purification. Small crystals were grown and are currently in optimization. In addition, biochemical data and docking calculations are in progress to study the precise binding mechanism to receptors found on the membrane of host cells. A third adhesin with galabiose-binding activity was expressed and purified. Small crystals were found in various conditions but instability and oligomerization problems have prompted us to look at alternative constructs and homologues. Studies on oxidative stress protection and detoxification mechanisms continued on human-rat chimeric glutathione transferases (GSTs) or mutants created through directed evolution approaches to produce new GSTs with altered specificity for new applications in biomedicine, environmental security, and agriculture. Crystals of human GST-A1 have been grown in our lab for use in structure-assisted drug design efforts. Docking calculations were carried out to study the binding of diphenylether herbicides in the active site. In addition, the structure of a novel 96 97 glutathione transferase was determined by the SAD method using the anomalous signal of bromide. The overall fold and the geometry of the active site suggest a new class, the eta class, of GSTs. Contrary to conventional GSTs that contain Ser or Tyr as catalytic residues, an arginine residue adjacent to the sulphur atom of the substrate analogue was found in the catalytic site. In the theme of enzyme function and stability, we continued our work on PhaZ7, an extracellular depolymerase involved in the degradation of poly(R)-hydroxyalkanoates (PHAs), a group of biodegradable thermoplastic polyesters considered as substitutes for non-degradable plastics. Several mutants were generated by our collaborators and characterized for their ability to bind PHAs. Crystal structure determination has revealed a large conformational change that may play a role in the enzyme’s function. Preliminary data following soaking with a tetramer analogue have shown binding and the structure is under refinement. Work on the Atu (acyclic terpene utilization) catabolic pathway found in P. Aeruginosa has continued using a combination of X-ray crystallography, biophysics, molecular biology, homology modelling, computational and bioinformatics tools. Atu enzymes are involved in the metabolisn of acyclic terpenes that possess a great potential in biotechnology, for example in the food, drink and pharmaceutical industry. Reprocessing of previously collected diffraction images gave a better data set extended to 2.35 Å. The structure is currently under rounds of refinement and extensive rebuilding. Recent reports implicating phosphoserine aminotransferase (PSAT), a vitamin B6 enzyme, in cancer and tuberculosis have led us to investigate closer the substrate binding mechanism of this enzyme for potential drug design efforts. Data of phosphoserinebound PSAT to 1.5 Å revealed local conformational changes that facilitate substrate binding through the formation of a tight phosphate-binding site. Funding: University of Turku, Biocenter Finland, Federation of European Microbiology Societies, EU FP7 (access to synchrotrons), Cultural Foundation of Southwestern Finland. Collaborators: Jukka Finne (University of Helsinki), Sauli Haataja (University of Turku), Vuokko Loimaranta (University of Turku), Dieter Jendrossek (University of Stuttgart), Nikos Labrou (Agricultural University of Athens), Li Duochuan (Shandong Agricultural University), Eleanor Coffey (ÅA), Selected publications: Battula, P., Dubnovitsky, A.P. and Papageorgiou, A.C. (2012). Structural basis of L-phosphoserine binding to phosphoserine aminotransferase. Acta Crystallogr. D (in press). MARCKSL1 determines actin stability and migration in neurons and in cancer cells. Mol. Cell. Biol. 32: 3513-3526. Skopelitou, K., Muleta, A.W., Pavli, O., Skaracis, G.N., Flemetakis, E., Papageorgiou, A.C. & Labrou, N.E. (2012) Overlapping protective roles for glutathione transferase gene family members in chemical and oxidative stress response in Agrobacterium tumefaciens. Funct. Integr. Genomics 12:157172. Skopelitou, K., Dhavala, P., Papageorgiou, A.C. & Labrou, N.E. (2012). A glutathione transferase from Agrobacterium tumefaciens reveals a novel class of bacterial GST superfamily. PLoS One 7(4): e34263. Chronopoulou, E.G., Papageorgiou, A.C., Markoglou, A. & Labrou, N.E. (2012). The inhibition of human glutathione transferases by xenobiotics: development of simple analytical assays for the quantification of pesticides in water. J. Mol. Catal. B 81: 43-51. Li, D.-C., Li, A.-N. & Papageorgiou, A.C. (2011) Cellulases from thermophilic fungi: Recent insights and biotechnological potential. Enzyme Res. Vol 2011, Article ID 308730 Haikarainen, T., Paturi, P., Lindén, J., Haataja, S., Meyer-Klaucke, W., Finne, J. & Papageorgiou, A.C. (2011). Magnetic properties and structural characterization of iron oxide nanoparticles formed by Streptococcus suis Dpr and four mutants. J. Biol. Inorg. Chem. 16: 799-807 Haikarainen, T., Thanassoulas, A., Stavros, P., Nounesis, G., Haataja, S. & Papageorgiou, A.C. (2011) Structural and thermodynamic characterization of metal ion binding in Streptococcus suis Dpr. J. Mol. Biol 405: 448-460. Wakadkar, S., Zhang,L.Q., Li, D.-C., Haikarainen, T., Dhavala, P. & Papageorgiou, A.C. (2011) Expression, purification and crystallization of Chetomium thermophilum Cu, Zn superoxide dismutase. Acta Cryst F 66: 648-655. Haikarainen, T., Tsou, C.C., Wu, J.J. & Papageorgiou, A.C. (2010) Structural characterization and biological implications of di-zinc binding in the ferroxidase center of Strepococcus pyogenes Dpr. Bichem. Biophys. Res. Comm. 398: 361-365. Haikarainen, T. & Papageorgiou, A.C. (2010) Dps-like proteins: Structural and functional insights into a versatile protein family. Cell. Mol. Life Sci. 67: 341-351. Axarli, I., Georgiadou, C., Dhavala, P., Papageorgiou, A.C. & Labrou, N. (2010) Investigation of the role of conserved residues Ser13, Asn48 and Pro49 in the catalytic mechanism of the tau class glutathione transferase from Glycine max. Bioch. Biophys. Acta 1804: 662-667. Papageorgiou, A.C. & Matsson, J. (2013) Protein analysis with X-ray crystallography. Methods Mol. Biol. (in press). Labrou, N., Papageorgiou, A.C. & Avramis, V.I. (2010) Structurefunction relationships and clinical applications of L-asparaginases. Curr. Med. Chem. 17: 2183-2195. Björkblom, B, Padzik, A., Mohammad, H., Westerlund, N., Komulainen, E., Hollos, P., Parviainen, L., Papageorgiou, A.C., Iljin, K., Kallioniemi, O., Kallajoki, M., Courtney, M.J., Mågård, M., James, P. & Coffey, E.T. (2012) JNK phosphorylation of Wakadkar, S., Hermawan, S., Jendrossek, D. & Papageorgiou, A.C. (2010) The crystal structure of PhaZ7 at atomic (1.2 Å) resolution reveals details of the active site and suggests a substrate-binding mode. Acta Cryst. F 66: 648-654. 98 99 Melissis, S.C., Papageorgiou, A.C., Labrou, N.E & Clonis, Y.D. (2010) Purification of moloney murine leukemia virus reverse transcriptase lacking RNase activity (M-MLVH-RT) on a 9-aminoethyladenine[1,6-diamine-hexane]-triazine selected from a combinatorial library of dNTP-mimetic ligands. J. Chromatogr. Sci. 48: 496-502. Haikarainen, T., Tsou, C.C., Wu, J.J. & Papageorgiou, A.C. (2010) Crystal structures of Streptococcus pyogenes Dpr reveal a dodecameric iron-binding protein with a ferroxidase site. J. Biol. Inorg. Chem. 15: 183-194. Axarli, I. Dhavala, P., Papageorgiou, A.C. & Labrou, N.E. (2009) Crystallographic and functional characterization of the fluorodifen inducible glutathione transferase from Glycine max reveals an active site topography suited for diphenylether herbicides and a novel L-site. J. Mol. Biol. 385: 984-1002. Axarli, I. Dhavala, P., Papageorgiou, A.C. & Labrou, N.E. (2009) Crystal structrure of Glycine max glutathione transferase in complex with glutathione: investigation of the induced-fit mechanism operating by the tau class glutathione transferases. Biochem. J. 422: 247-256. Mitsiki, E., Papageorgiou, A. C., Iyer, S., Thiyagarajan, N., Prior, S. H., Sleep, D., Finnis, C. & Acharya, K. R. (2009) Structures of native human thymidine phosphorylase and in complex with 5-iodouracil. Biochem. Biophys. Res. Commun. 386: 666-670. Dhavala, P. & Papageorgiou, A.C. (2009) The crystal structure of Helicobacter pylori L-asparaginase at 1.4 Å resolution. Acta Crystallogr. D 65: 1253-1261. Havukainen, H., Haataja, S., Kauko, A., Pulliainen, A.T., Salminen, A., Haikarainen, T., Finne, J. & Papageorgiou, A.C. (2008) Structural basis of zinc- and terbium-mediated inhibition of ferroxidase activity in Dps ferritin-like proteins. Protein Sci. 17: 1513-1521 Papageorgiou, A.C., Posypanova, G.A., Andersson, C.A., Sokolov, N.N & Krasotkina, J. (2008) Structural and functional insights into Erwinia carotovora L-asparaginase. FEBS J. 275: 4306-4316. Dhavala, P., Krasotkina, J., Dubreuil, C. & Papageorgiou, A.C. (2008) Expression, purification and crystallization of Helicobacter pylori L-asparaginase. Acta Crystallogr Sect F Struct Biol Cryst Commun. 64: 740-742 Papageorgiou, A.C., Hermawan, S., Singh C.B. & Jendrossek, D. (2008) Structural basis of poly(3-hydroxybutyrate) hydrolysis by PhaZ7 depolymerase from Paucimonas lemoignei. J. Mol. Biol. 382: 1184-1194 CELL FATE Principal investigator: Cecilia Sahlgren, PhD, Academy Research Fellow, Turku Centre for Biotechnology, BioCity, Tykistökatu 6B, FI-20521 Turku, Finland. Tel. 358-2-3338611, Fax. +358-2-251 8808 E-mail: [email protected] Biography: Cecilia Sahlgren received her Ph.D. from Turku Centre of Biotechnology, Åbo Akademi University December 2002. She was appointed research fellow at the Department of Biology at Åbo Akademi University from 2003-2005. 2005-2007 she was a postdoctoral fellow in Prof. Urban Lendahls lab at the Department of Cell and Molecular Biology at the Karolinska Institute. 2008 she was appointed senior research fellow Åbo Akademi University. In 2009 she founded the Cell fate group at the Turku Centre for Biotechnology. She currently holds an Academy of Finland Research Fellow position. Personnel: Post-doctoral researchers: Veronika Mamaeva, MD, PhD. Graduate students: Marika Sjöqvist, M.Sc, Neeraj Prabhakar, M.Sc. Sebastian Landor, M.Sc, Christian Antila, M.Sc, Laboratory Technician: Helena Saarento, Natalie Ratts. Undergraduate students: Daniel Antfolk, B.Sc, Jenni Niinimaki, B.Sc. Rasmus Niemi, B.Sc, Martina Lerche, B.Sc. Description of the project: We aim at understanding the basic molecular principles of signaling mechanisms regulating cell fate choices during stem cell differentiation, and how disturbances in these mechanisms link to cancer. Another important goal is to develop technology to specifically monitor and tune these signals at will in specific cell populations, in order to steer stem cell fate and curtail oncogenic activities. We are particularly interested in the role and regulation of the evolutionary conserved Notch signaling pathway, a key regulator of stem cell function and tumorigenesis. The main objectives of our research are to understand i) how the cellular microenvironment influences Notch signaling activities and how this impinges on cell identity, function and tumor progression, ii) how Notch signaling interlinks with other signaling and cellular mechanisms to fine tune and modulate the cellular response, iii) how intracellular temporal and spatial control of Notch signaling activities are achieved and to iv) develope technology platforms to regulate Notch signaling in targeted cell populations and tools for bioimaging of cellular functions in vivo. Funding: The Academy of Finland, Åbo Akademi University, Centre of Excellence in Cell Stress and Molecular Aging, EU 7th NotchIT, Turku Graduate school for Biomedical Sciences, Cancer Society of Finland, Sigrid Juselius Foundation. 100 101 Collaborators: Prof. Milos Pekny (Sahlgrenska Academy at Göteborg University), Prof. John Eriksson (Turku Centre for Biotechnology). Prof. Urban Lendahl (Karolinska Institute), Ph.D Susumu Imanishi (Turku Centre for Biotechnology), Prof. Lea Sistonen (Turku Centre for Bio- technology). Dr.Tech Jessica Rosenholm (Laboratory for Physical Chemistry, Åbo Akademi, Turku), Prof. Mika Linden (Dept of Chemistry, Ulm University, Germany), Professor Lucio Miele (The University of Mississippi Medical Centre), Professor Roberto Sequeiras (University of Oulu), Prof Carlijn Bouten, Dept of biomedical engineering, Eindhoven University of Technology, Ass. Professor Patricia Dankers, Dept for Chemcial Biology, Eindhoven University of Technology. Selected Publications: Jin, S., A.P. Mutvei, I.V. Chivukula, E.R. Andersson, D. Ramskold, R. Sandberg, K.L. Lee, P. Kronqvist, V. Mamaeva, P. Ostling, J.P. Mpindi, O. Kallioniemi, I. Screpanti, L. Poellinger, C. Sahlgren, and U. Lendahl. (2012) Non-canonical Notch signaling activates IL-6/JAK/STAT signaling in breast tumor cells and is controlled by p53 and IKKalpha/IKKbeta. Oncogene in press Karaman, D.S., D. Desai, R. Senthilkumar, E.M. Johansson, N. Ratts, M. Oden, J.E. Eriksson, C. Sahlgren, D.M. Toivola, and J.M. Rosenholm. (2012) Shape engineering vs organic modification of inorganic nanoparticles as a tool for enhancing cellular internalization. Nanoscale research letters. 7:358. Mamaeva, V., C. Sahlgren#, and M. Linden#. (2012) Mesoporous silica nanoparticles in medicine-Recent advances. Advanced drug delivery reviews in press (PubMed ahead of print). #shared corresponding authorship Rosenholm, J.M., V. Mamaeva, C. Sahlgren#, and M. Linden#. (2012) Nanoparticles in targeted cancer therapy: mesoporous silica nanoparticles entering preclinical development stage. Nanomedicine (Lond). 7:111-120. Wilhelmsson, U., M*. Faiz, Y. de Pablo*, M. Sjoqvist, D*. Andersson, A. Widestrand, M. Potokar, M. Stenovec, P.L. Smith, N. Shinjyo, T. Pekny, R. Zorec, A. Stahlberg, M. Pekna, C. Sahlgren, and M. Pekny. 2012. Astrocytes negatively regulate neurogenesis through the Jagged1-mediated Notch pathway. Stem Cells. 30:2320-2329. Rosenholm J.M., Mamaeva, V., Sahlgren C.# and Lindén, M.# (2011) Nanoparticles in targeted cancer therapy: Mesoporous silica nanoparticles entering preclinical developmentstage. Nanomedicine in press. #shared corresponding authorship Landor S., Mamaeva V., Mutvei A., Jin S., Busk M., Borra R., Grönroos T., Kronqvist P., Lendahl U. and Sahlgren C.. (2011) Hypo- and hyperactivated Notch signaling resets cellular metabolism in breast tumor cells by distinct mechanisms. / Proceedings of National Academy of Sciences of the United States of America,PNAS/108:18814-18819. Highlighted in Nature Chemical Biology: 2011 8: 20.Metabolism: A Warburg shakeup. Mamaeva V.,Rosenholm J.M., Tabe Bate-Eya L.,Bergman L., Peuhu E., Duchanoy A., Fortelius L.E., Landor S., Toivola D.M Lindén 102 M. and Sahlgren C. (2011) Mesoporous silica nanoparticles as drug delivery systems for targeted inhibition of Notch signaling in cancer. Molecular Therapy 19: 1538-1546. Rosenholm J.M, Sahlgren C.,# and Linden M.# (2011) Multifunctional mesoporous silica nanoparticles for combined therapeutic, diagnostic and targeted action in cancer treatment Current Drug Targets 12:1166-1186. #shared corresponding authorship Pallari H.M., Lindqvist J., Torvaldson E., Ferraris S.E., He T., Sahlgren C. and Eriksson J.E. (2011). Nestin as a regulator of Cdk5 in differentiating myoblasts. MolecularBiology of the Cel/. 22: 1539-1549. Das D., Lanner F., Main H., Andersson E.R., Bergmann O., Sahlgren C., Heldring N., Hermanson O., Hansson E.M. and Lendahl U. (2010) Notch induces cyclin-D1-dependent proliferation during a specific temporal window of neural differentiation in ES cells. DevelopmentalBiology 348: 153-166. Rosenholm J.M., Sahlgren C# ., Linden M.# (2010) Towards intelligent, targeted drug delivery systems using mesoporous silicananoparticles -- Opportunities & Challenges Nanoscale 2: 1870-1883. #shared corresponding authorship Rosenholm J.M., Peuhu E., Tabe Bate-Eya L., Eriksson J.E., Sahlgren C.,# and Lindén M.# (2010) Cancer-Cell Specific Induction of Apoptosis using Mesoporous Silica Nanoparticles as Drug Delivery Vectors, Small 6:1234-1241. #shared corresponding authorship de Thonel A., Ferraris S.E., Pallari H-M., Imanishi S.Y., Kochin V., Hosokawa T., Hisanga S., Sahlgren C. and Eriksson J.E. (2010). PKC??regulates CDK5/p25 signaling during myogenesis. Molecular Biology of the Cell 21: 1423-1434 Main H., Lee K.L., Yang H., Haapa-Paananen S., Edgren H., Jin S., Sahlgren C., Kallioniemi O., Poellinger L., Lim B. and Lendahl, U. (2010). Integration between Notch- and hypoxia-induced transcritpomes in embryonic stem cells. Experimental Cell Research 316: 1610-1624. Rosenholm J.M., Sahlgren C# ., Linden M.# (2010) Cancer cellspecific targeting of and targeted delivery by mesoporous silica nanoparticles. Highlight to Journal of Material Chemistry 14: 2707-2713. #shared corresponding authorship Rosenholm J.M., Peuhu E., Eriksson J.E., Sahlgren C# . and Linden M#.(2009) Targeted Intracellular Delivery of Hydrophobic Agents using Mesoporous Hybrid Silica Nanoparticles as Carrier Systems (2009) Nano Letters 9: 3308-3311.#shared corresponding authorship Rosenholm J.M., Meinander A., Peuhu E., Niemi R., Eriksson J.E., Sahlgren C# ., and Linden M# . (2009) Targeting of porous hybrid silica nanoparticles to cancer cells. ACSNano 3: 197-206. # shared corresponding authorship Jin S., Hansson E.M., Ihalainen S., Sahlgren C., Baumann M., Kalimo H., and Lendahl U. (2008) Notch signaling regulates PDGF-receptor expression in vascular smooth muscle cells. Circulation Research 102: 1483-91. 103 Sahlgren C., Gustafsson M., Jin S., Poellinger L. and Lendahl U.Notch signaling mediates hypoxia induced tumor cell migration and invasion. (2008) Proceedings of National Academy of Sciences of the United States of America, PNAS 105:6392-7. EDITORS’ CHOICE in Science Signaling: Sci. Signal. 1 (18), ec163. [DOI:10.1126/stke.118ec163]: Notching Up Tumor Progression Chapman G.,# Liu L.,# Sahlgren C., Dahlqvist C. and Lendahl, U. (2006) High levels of Notch signaling downregulate Numb and Numblike. Journal of Cell Biology, 175: 535-40. #authors contributed equally Sahlgren C.and Lendahl U. (2006) Notch, stem cell control and integration with other signaling mechanisms. Regenerative Medicine 1: 195-20 Sahlgren C., Pallari H.-M., He T., and Eriksson J.E. (2006) A nestin scaffold links Cdk5 signaling to oxidant-induced cell death. EMBO Journal 25: 4808-19. TARGETING STRATEGIES FOR GENE THERAPY Principal investigator: Mikko Savontaus, M.D., Ph.D., Affiliated Group Leader at CBT Address: Turku Centre for Biotechnology, Biocity, Tykistökatu 6B, P.O. Box 123, FIN-20521 Turku, Finland. Tel. +358 2 333 8025, Fax +358 2 333 8000. E-mail: [email protected] Biography: Mikko Savontaus (b. 1970) received his M.D. in 1996 and Ph.D. in 1997 from the University of Turku. He was a postdoctoral fellow at the Institute for Gene Therapy and Molecular Medicine at Mount Sinai School of Medicine in New York during 1999-2002. He did his training for internal medicine and cardiology at Turku University Hospital in 2003-2008. He is currently a group leader at the Turku Centre for Biotechnology as well as a cardiologist at the Department of Medicine at Turku University Hospital. Personnel: Graduate students: Minttu Mattila, M.Sc., Kim Eerola, M.Sc. Description of the project: Gene therapy is rapidly developing into a novel biomedical discipline that could have a major impact on health and healthcare in the 21st century. Traditionally gene therapy has been envisioned as a means to cure monogenic diseases with precisely defined genetic defects. However, recent clinical trials have demonstrated that gene therapy for complex multigenic disorders such as cardiovascular diseases and cancer are especially promising and may become a routine treatment modality in the near future. On the other hand, these trials have demonstrated that technical advances in gene therapy vector development are a key issue in developing clinically applicable gene therapy approaches. Our laboratory endeavors to tackle this problem of developing improved adenoviral gene therapy vectors for cardiovascular diseases and cancer by attempting to meet two objectives: 1. The expression of therapeutic genes must be tightly regulated (transcriptional targeting). 2. The tropism of the gene delivery vector must be restricted to the target tissue (transductional targeting). Such targeted vectors will increase efficacy and diminish the possibility of side effects by limiting transgene expression to the target cell population. In our previous work we have constructed conditionally replicating adenoviruses (CRADs) targeting tumor endothelial cells and have demonstrated that these vectors are able to specifically replicate in dividing endothelial cells and destroy tumor vasculature. We have also demonstrated that a hybrid Ad5/35 adenovirus, where the fiber gene of adenovirus serotype 5 has been replaced with the fiber from serotype 35, is highly efficient in infecting endothelial cells. From left to right: Jenni Niininmäki, Neeraj Prabhakar, Rasmus Niemi, Christian Antila, Daniel Antfolk, Veronika Mamaeva, Cecilia Sahlgren, Sebastian Landor and Hussein Shokry. 104 In our current projects we are building on these findings to develelop gene therapy for cardiovascular disease. We have analyzed adenovirus receptor expression and vector transduction efficiency in samples from patients with ischemic or dilated cardiomyopathy. 105 Novel vectors with improved transcriptional and transductional efficiency for target cells have been constructed by combining hybrid serotype vectors with transcriptional targeting. In addition, we are utilizing lentivirus technology for long-term expression of therapeutic genes for heart failure and hypertension. The effect of these vectors is currently studied in vivo using ultrasound-guided intramyocardial injection in mouse heart failure models. Our ultimate goal is to develop gene therapy vectors for use in clinical trials by combining these approaches. Funding: Finnish Medical Foundation, Turku University Hospital Selected publications: Toivonen R, Koskenvuo J, Merentie M, Söderström M, YläHerttuala S, Savontaus M (2012) Intracardiac injection of a capsid-modified Ad5/35 results in decreased heart toxicity when compared to standard Ad5. Virol J. 2012 9:296 Toivonen R, Mäyränpää MI, Kovanen PT, Savontaus M. (2010) Dilated cardiomyopathy alters the expression patterns of CAR and other adenoviral receptors in human heart. Histochem Cell Biol. 133(3):349-57. Toivonen, R., Suominen, E., Grenman, R. and Savontaus, M. (2009) Retargeting Improves the Efficacy of a Telomerase-Dependent Oncolytic Adenovirus for Head and Neck Cancer. Oncology Reports 21: 165-171 Suominen, E., Toivonen, R., Grenman, R. and Savontaus, M. (2006) Head and Neck Cancer Cells are efficiently infected by Ad5/35 Hybrid Virus. Journal of Gene Medicine 8:1223-1231. Shinozaki, K., Suominen, E., Carrick, F., Sauter, B., Kähäri, V.M., Lieber, A., Woo, S.L.C. and Savontaus, M. (2006). Efficient infection of endothelial cells by a capsid-modified adenovirus. Gene Therapy 13:52-59. Hutter, R., Valdiviezo, C., Sauter, B.V., Savontaus, M., Chereshnev, I., Carrick, F.E., Bauriedel, G., Luderitz, B., Fallon, J.T., Fuster, V. and Badimon, J.J. (2004) Caspase-3 and tissue factor expression in lipid-rich plaque macrophages: evidence for apoptosis as link between inflammation and atherothrombosis. Circulation 27;109(16):2001-8. Ebert, O., Shinozaki, K., Huang, T.-G., Savontaus, M., GarciaSastre, A. and Woo S.L.C. (2003) VSV as oncolytic virus for treatment of orthotopic hepatocellular carcinoma in immunecompetent rats. Cancer Research 63(13):3605-11. Huang, T.-G., Savontaus, M., Shinozaki, K., Sauter, B. and Woo, S.L.C. (2003) Telomerase dependent oncolytic adenovirus for cancer treatment. Gene Therapy 10(15):1241-7. Savontaus, M., Sauter, B.V., Huang, T.-G. and Woo, S.L.C. (2002) Transcriptional Targeting of conditionally Replicating Adenovirus to Dividing Endothelial Cells. Gene Therapy 9(14): 972-979 106 REGULATION AND FUNCTION OF HEAT SHOCK TRANSCRIPTION FACTORS Principal Investigator: Lea Sistonen, Ph.D., Professor of Cell and Molecular Biology, Department of Biosciences, Åbo Akademi University. Laboratory address: Centre for Biotechnology, BioCity, Tykistökatu 6, P.O.BOX 123, FIN-20521 Turku, Finland. Tel. +358-2-333 8028, 215 3311; E-mail: [email protected], [email protected] Biography: Lea Sistonen (b. 1959) completed her undergraduate studies at Åbo Akademi University in 1984 and received her Ph.D. from the University of Helsinki in 1990. She was a post-doctoral fellow at Northwestern University in Dr. Richard I. Morimoto’s laboratory in 1990-1993 (Fogarty International Fellowship 1991-1993). In November 1993 she joined the Centre for Biotechnology as a senior research fellow in molecular biology. In April 2000 she was appointed as Professor of Cell and Molecular Biology at Åbo Akademi University. During the 5-year period 2004-2009 she was Academy Professor, the Academy of Finland. Personnel: Senior scientists: Eva Henriksson, Ph.D., Pia Roos-Mattjus, Ph.D. Post-doctoral fellows: Johanna Ahlskog, Ph.D., Johanna Björk, Ph.D., Anton Sandqvist, Ph.D. Graduate students: Camilla Aspelin, M.Sc., Heidi Bergman, M.Sc., Marek Budzynski, M.Sc., Alexandra Elsing, M.Sc., Jenny Joutsen, M.Sc., Petra Vainio, M.Sc., Anniina Vihervaara, M.Sc. Research assistants: Helena Saarento, M.Sc., Jenni Vasara, M.Sc. Undergraduate students: Malin Blom, Alejandro Da Silva, Samu Himanen, Emine Lundsten, Heidi Lustig, Jens Luoto, Mikael Puustinen, Katri Thiele Visiting scientists: Tim Crul, Ph.D. and Noémi Tóth, Ph.D. (Biological Research Center, Szeged, Hungary) Description of the Project: The heat shock response is an evolutionarily well-conserved cellular defence mechanism against protein-damaging stresses, such as elevated temperatures, heavy metals, and viral and bacterial infections. The heat shock proteins (Hsps) function as molecular chaperones to protect cells by binding to partially denatured proteins, dissociating protein aggregates, and regulating the correct folding and intracellular translocation of newly synthesized polypeptides. Hsps are transcriptionally regulated by heat shock factors, HSFs (HSF1-4 in mammals). Although HSFs are best known as stress-inducible transcriptional regulators, they are also important for normal developmental processes. The repertoire of HSF targets has expanded well beyond the Hsps, and HSF functions span from the heat shock response to development, metabolism, lifespan and disease, especially cancer and neurodegenerative disorders. 107 We are interested in the molecular mechanisms by which the different members of the HSF family are regulated during normal development and under stressful conditions. In particular, we investigate the expression and activity of HSF1 and HSF2. We were the first to report that HSF2 forms a complex with HSF1 and regulates the heat shock response. Our studies on HSF1HSF2 heterotrimers and their impact on various target genes are designed to elucidate the roles of HSFs in protein-misfolding disorders, such as neurodegenerative diseases, as well as in aging and cancer progression. Most studies have focused on HSF1, but it is important to consider the existence of multiple HSFs and interactions between them, especially when searching for potential drugs to modify their expression and/or activity. We have found that HSF1 activity is primarily regulated by various post-translational modifications (PTMs), e.g. acetylation, phosphorylation and sumoylation. All these PTMs are induced by stress stimuli but their effects on HSF1 vary. Upon stress, HSF1 undergoes phosphorylation-dependent sumoylation within a bipartite motif, which we found in many transcriptional regulators and gave name PDSM (phosphorylation-dependent sumoylation motif). Stress-inducible hyperphosphorylation and sumoylation of HSF1 occur very rapidly, whereas acetylation of HSF1 increases gradually, indicating a role for acetylation in the attenuation phase of the HSF1 activity cycle. Our ultimate goal is to determine the PTM signatures for both HSF1 and HSF2. In contrast to HSF1, which is a stable protein and evenly expressed in most tissues and cell types, the amount of HSF2 varies and correlates with its activity. We have demonstrated that the ubiquitin E3 ligase APC/C (anaphase-promoting complex/ cyclosome) mediates ubiquitylation and degradation of HSF2 during the acute phase of the heat shock response. The stressrelated composition and role of APC/C are unknown and form our major future goal. We have expanded our studies to involve the stress effects on the cell cycle, adding a new dimension to the research field. To this end, our ChIP-sequencing studies, identifying HSF1 and HSF2 target sites in cycling and mitotic human cells under optimal growth conditions and upon acute heat stress, are of most importance. Our results highlight an orchestrated transcriptional response, mediated by both HSF1 and HSF2, that controls a multitude of cellular processes in stressed cycling cells. In mitosis, however, we found a limited capacity of HSF1 to interact with the condensed chromatin and induce transcription, whereas HSF2 is capable of binding to several targets, indicating a specific impact of HSF2 on transcription throughout the cell cycle progression. Using mouse spermatogenesis as a model system, we discovered an inverse correlation between the cell- and stage-specific wavelike expression patterns of HSF2 and a specific microRNA, miR18, which is a member of the Oncomir-1/miR-17~92 cluster. Intriguingly, miR-18 was found to repress the expression of HSF2 by directly targeting its 3’UTR. To investigate the in vivo function of miR-18, we developed a novel method T-GIST (Transfection of Germ cells in Intact Seminiferous Tubules) and showed that inhibition of miR-18 in intact mouse seminiferous tubules leads to increased HSF2 protein levels and altered expression of HSF2 target genes, including the Y-chromosomal multi-copy genes 108 that we previously had reported as novel HSF2 targets in the testis. Our original finding that miR-18 regulates HSF2 activity in spermatogenesis links miR-18 to HSF2-mediated physiological processes and opens a whole new window of opportunities to elucidate the physiological and stress-related functions of HSF2, either alone or in conjunction with HSF1. Funding: The Academy of Finland, the Sigrid Jusélius Foundation, the Finnish Cancer Organizations, Turku Doctoral Programme of Biomedical Sciences (TuBS), and Åbo Akademi University (Centre of Excellence in Cell Stress and Molecular Aging). Collaborators: Klaus Elenius, Susumu Imanishi, Noora Kotaja and Jorma Toppari (University of Turku), John Eriksson, Peter Slotte and Kid Törnquist (Åbo Akademi University), Marko Kallio and Matthias Nees (VTT Medical Biotechnology, Turku), Valérie Mezger (University of Paris Diderot, France), Rick Morimoto (Northwestern University, Evanston, IL, USA), Jorma Palvimo (University of Eastern Finland, Kuopio), Andrea Pichler (Max Planck Institute of Immunobiology, Freiburg, Germany), Laszlo Vigh (Biological Research Center, Szeged, Hungary). Selected Publications (2006-2012): Sundvall M.*, Korhonen A.*, Vaparanta K., Anckar J., Halkilahti K., Salah Z., Aqeilan R.I., Palvimo J.J., Sistonen L. and Elenius K. (2012) Protein inhibitor of activated STAT3 (PIAS3) promotes sumoylation and nuclear sequestration of the intracellular domain of ErbB4. J. Biol. Chem. 287: 23216-23226. Anckar J. and Sistonen L. (2011) Regulation of HSF1 function in the heat shock response: implications in aging and disease. Annu. Rev. Biochem. 80: 1089-1115. Ahlskog J.K., Björk J.K., Elsing A.N., Aspelin C., Kallio M., RoosMattjus P. and Sistonen L. (2010) Anaphase-promoting complex/ cyclosome participates in the acute response to proteindamaging stress. Mol. Cell. Biol. 30: 5608-5620. Åkerfelt M.*, Vihervaara A.*, Laiho A., Conter A., Christians E.C., Sistonen L. and Henriksson E. (2010) Heat shock transcription factor 1 localizes to sex chromatin during meiotic repression. J. Biol. Chem. 285: 34469-34476. Björk J.K.*, Sandqvist A.*, Elsing A.N., Kotaja N. and Sistonen L. (2010) miR-18, a member of OncomiR-1, targets heat shock transcription factor 2 in spermatogenesis. Development 137: 3177-3184. Åkerfelt M., Morimoto R.I. and Sistonen L. (2010) Heat shock factors: integrators of cell stress, development and lifespan. Nat. Rev. Mol. Cell Biol. 11: 545-555. Blomster H.A.*, Imanishi S.Y.*, Siimes J., Kastu J., Morrice N.A., Eriksson J.E. and Sistonen L. (2010) In vivo identification of sumoylation sites by a signature tag and cysteine-targeted affinity purification. J. Biol. Chem. 285: 19324-19329. Blomster H.A., Hietakangas V., Wu J., Kouvonen P., Hautaniemi S. and Sistonen L. (2009) Novel proteomics strategy brings 109 From left to right: Johanna Björk, Petra Vainio, Eva Henriksson, Heidi Bergman, Beata Paziewska, Emine Lundsten, Anniina Vihervaara, Helena Saarento, Camilla Aspelin, Samu Himanen, Lea Sistonen, Oskar Engberg, Jenny Joutsen, Sally Svartsjö, Alexandra Elsing, Pia Roos-Mattjus and Jenni Vasara. insight into the prevalence of SUMO-2 target sites. Mol. Cell. Proteomics 8: 1382-1390. Westerheide S.D.*, Anckar J.*, Stevens S.M.Jr., Sistonen L. and Morimoto R.I. (2009) Stress-inducible regulation of heat shock factor 1 by the deacetylase SIRT1. Science 323: 1063-1066. Sandqvist A., Björk J.K., Åkerfelt M., Chitikova Z., Grichine A., Vourc’h C., Jolly C., Salminen T.A., Nymalm Y. and Sistonen L. (2009) Heterotrimerization of heat-shock factors 1 and 2 provides a transcriptional switch in response to distinct stimuli. Mol. Biol. Cell 20: 1340-1347. Åkerfelt M.*, Henriksson E.*, Laiho A., Vihervaara A., Rautoma K., Kotaja N. and Sistonen L. (2008) Promoter ChIP-chip analysis in mouse testis reveals Y chromosome occupancy by HSF2. Proc. Natl. Acad. Sci. USA 105: 11224-11229. Östling P.*, Björk J.K.*, Roos-Mattjus P., Mezger V. and Sistonen L. (2007) HSF2 contributes to inducible expression of hsp genes through interplay with HSF1. J. Biol. Chem. 282: 7077-7086. Chang Y.*, Östling P.*, Åkerfelt M., Trouillet D., Rallu M., Gitton Y., El Fatimy R., Fardeau V., Le Crom S., Morange M., Sistonen L. and Mezger V. (2006) Role of heat shock factor 2 in cerebral cortex formation and as a regulator of p35 expression. Genes Dev. 20: 836-847. Anckar J.*, Hietakangas V.*, Denessiouk K., Thiele D.J., Johnson M.S. and Sistonen L. (2006) Inhibition of DNA binding by differential sumoylation of heat shock factors. Mol. Cell. Biol. 26: 955-964. Hietakangas V.*, Anckar J.*, Blomster H.A., Fujimoto M., Palvimo J.J., Nakai A. and Sistonen L. (2006) PDSM, a motif for phosphorylation-dependent SUMO modification. Proc. Natl. Acad. Sci. USA 103: 45-50. *equal contribution 110 111 CANCER CELL SIGNALING Principal investigator: Jukka Westermarck, M.D., Ph.D., Professor. Address: Turku Centre for Biotechnology, BioCity, Tykistökatu 6B, FIN-20251 Turku, Finland. Tel. +358-2-3338621, Fax +358-2-2158808. E-mail: [email protected]. Homepage: http://www.btk.fi/research/research-groups/westermarck/ Biography: Jukka Westermarck (b. 1969) received his M.D. in 1996 and Ph.D. in 1998 at the University of Turku. He was a postdoctoral fellow at European Molecular Biology Laboratory in Heidelberg, Germany, in Dr. Dirk Bohmann´s laboratory during 1999-2001. He was an Academy of Finland senior scientist during 20022007. Between 2006 -2009 he was appointed as a group leader at Institute of Medical Technology (IMT), University of Tampere, Finland. In 2008 he was appointed to a Research Professor position at the Finnish Cancer Institute, in 2009 to a Research Director position at Turku Centre for Biotechnology (leave of absence until 2014) and in 2011 to a part-time position as a Professor of Cancer Biology at Department of Pathology, University of Turku (until 2104). Personnel: Senior scientist: Jukka Westermarck, M.D., Ph.D. Post-doctoral researchers: Anna Cvrljevic, Ph.D., Juha Okkeri, Ph.D., Yuba Pokharel, Ph.D., Minna Niemelä, Ph.D. Graduate students: Otto Kauko, M.D., M.Sc., Amanpreet Kaur, M.Sc., Anni Laine, M.Sc., Xi Qiao, M.Sc., Eleonora Sittig, B.Sc. Technicians: Taina KalevoMattila, Lab.Tech., Inga Pukonen, B.Eng. Coordinator: Tiina Arsiola, Ph.D. Description of the project: The goal of our research group is to identify novel signaling mechanisms involved in malignant cell growth by isolating protein complexes associated with proteins previously demonstrated to have an important role in cancer progression. To identify protein complexes, we use tandem affinity purification (TAP) and Streptag purification methods, both proven to be suitable for purification of signaling protein complexes from mammalian cells in culture. Identification of novel proteins involved in malignant growth may also reveal novel possibilities for intervention in the therapy of cancer and other hyperproliferative diseases. Based on our recent work, we have identified several novel interacting proteins for signaling proteins such as AP-1 transcription factor c-Jun, MAPK kinase MEK1, and protein phosphatase PP2A. Most of our future work will be focused on characterization of PP2A interaction partner CIP2A, that we have demonstrated to inhibit PP2A in human malignancies. As PP2A inhibition has been recognized as a prerequisite for human cell transformation, it is plausible that further understanding of the function of CIP2A will reveal fundamental novel information about the basic mechanisms of cancer progression. The overall goal of the proposed project is to study the function and importance of CIP2A in cancer progression by using combination of molecular biology, cell biology 112 and functional genetics methods. As our current results suggest that targeting CIP2A could be beneficial in the treatment of cancer, our goal is also to develop research models for evaluating the suitability of CIP2A as a novel drug target for cancer therapies. In addition, our aim is to purify new protein complexes related cancer cell signaling. Funding: The Academy of Finland, Sigrid Juselius Foundation, Turku Graduate School of Biomedical Sciences, Cancer Research Foundation of Finland, Biocenter Finland, Foundation of the Finnish Cancer Institute. Collaborators: Rosalie Sears (Oregon Health and Science University), Owen Sansom (Beatson Institute for Cancer Research, Glasgow), Sampsa Hautaniemi (University of Helsinki), Ari Ristimäki and Caj Haglund (University of Helsinki), Olli-Pekka Kallioniemi (FIMM, Helsinki), Jorma Toppari (University of Turku), Veli-Matti Kähäri (Turku University Hospital), Heikki Joensuu (Helsinki University Hospital). Selected Publications: Laine, A., Sihto, H., Come, C., Zwolinska, A., Rosenfeldt, M., Khanna, A., Kähäri, V.-M., Evan, G.I., Junttila, M.R., Marine, J.-C., Ryan, K., Joensuu, H. and Westermarck, J. (2012). Senescence sensitivity of breast cancer cells is defined by positive feedback loop between CIP2A and E2F1. Cancer Discovery, in press. Niemelä, M., Kauko, O., Sihto, H., Mpindi, J.-P., Nicorici, D., Pernilä, P., Kallioniemi, O.-P., Joensuu, H., Hautaniemi, S. and Westermarck, J. (2012). CIP2A signature reveals the MYC dependency of CIP2A-regulated phenotypes and its clinical association with breast cancer subtypes. Oncogene 31: 42664278. Ventelä, S., Mäkelä, J.-A., Kulmala, J., Westermarck, J. and Toppari, J. (2012). Identification and regulation of a stage-specific stem cell niche enriched by Nanog positive spermatogonial stem cells in the mouse testis. STEM CELLS 30: 1008-1020. Ventelä, S., Come, C., Mäkelä, J.-A., Hobbs, R.M., Mannermaa, L., Kallajoki, M., Chan, E.K., Pandolfi, P.P., Toppari, J. and Westermarck, J. (2012). CIP2A promotes proliferation of spermatogonial progenitor cells and spermatogenesis in mice. PLoS ONE 7: e33209. Mathiasen, D.P., Egebjerg, C., Andersen, S.H., Rafn, B., Puustinen, P., Khanna, A., Daugaard, M., Valo, E., Tuomela, S., Bøttzauw, T., Nielsen, C.F., Willumsen, B.M., Hautaniemi, S., Lahesmaa, R., Westermarck, J., Jäättelä, M. and Kallunki, T. (2012). Identification of a c-Jun N-terminal kinase-2-dependent signal amplification cascade that regulates c-Myc levels in ras transformation. Oncogene 31: 390-401. Khanna, A., Okkeri, J., Bilgen, T., Tiirikka, T., Vihinen, V., Visakorpi, T. and Westermarck, J. (2011). ETS1 mediates MEK1/2dependent overexpression of cancerous inhibitor of protein phosphatase 2A (CIP2A) in human cancer cells. PLoS One 6: e17979. 113 Come, C., Laine, A., Chanrion, M., Edgren, H., Mattila, E., Liu, X., Jonkers, J., Ivaska, J., Isola, J., Darbon, J.-M., Kallioniemi, O.-P., Thezenas, S. and Westermarck, J. (2009). CIP2A is associated with human breast cancer aggressivity. Clin. Cancer Res. 15: 5092-5100. Khanna, A., Böckelman, C., Hemmes, A., Junttila, M.R., Wiksten, J.-P., Lundin, P., Junnila, S., Murphy, D., Evan, G.I., Haglund, C., Westermarck, J.* and Ristimäki, A.* (2009). c-Myc-dependent regulation and prognostic role of CIP2A in gastric cancer. J. Natl. Cancer Inst. 101: 793-805. *equal contribution Puustinen, P., Junttila, M.R., Vanhatupa, S., Sablina, A.A., Hector, M.E., Teittinen, K., Raheem, O., Ketola, K., Lin, S., Kast, J., Haapasalo, H., Hahn, W.C. and Westermarck, J. (2009). PME-1 protects extracellular signal-regulated pathway activity from protein phosphatase 2A-mediated inactivation in human malignant glioma. Cancer Res. 69: 2870-2877. Wu, J., Vallenius, T., Ovaska, K., Westermarck, J., Mäkelä, T.P. and Hautaniemi, S. (2009). Integrated network analysis platform for protein-protein interactions. Nat. Methods 6: 75-77. Westermarck, J. and Hahn, W.C. (2008). Multiple pathways regulated by the tumor suppressor PP2A in transformation. Trends Mol. Med. 14: 152-160. Junttila, M.R., Li, S.-P. and Westermarck, J. (2008). Phosphatasemediated crosstalk between MAPK signaling pathways in the regulation of cell survival. FASEB J. 22: 954-965. Junttila, M.R., Puustinen, P., Niemelä, M., Ahola, R., Arnold, H., Böttzauw, T., Ala-aho, R., Nielsen, C., Ivaska, J., Taya, Y., Lu, S.L., Li, S., Chan, E.K.L., Wang, X.-J., Grenman, R., Kast, J., Kallunki, T., Sears, R., Kähäri, V.-M. and Westermarck, J. (2007). CIP2A inhibits PP2A in human malignancies. Cell 130: 51–62. From top to bottom. Left row: Otto Kauko, Jukka Westermarck, Minna Niemelä and Juha Okkeri. Right row: Xi Qiao, Inga Pukonen, Anni Laine, Taina Kalevo-Mattila, Eleonora Sittig, Amanpreet Kaur and Tiina Arsiola 114 115 ADENOSINE DEAMINASES Principal investigator: Andrey Zavialov, Ph.D., Finnish Academy Research Fellow (group leader), Turku Centre for Biotechnology, University of Turku, Tykistokatu 6, FI-20520,Turku, Finland, Tel. +358403776216, Fax. +358-2-3338000, Email: [email protected] Biography: Andrey Zavialov (b. 1975) has obtained his M.S. in Biotechnology from Russian Chemical Technology University (Moscow) and a Ph.D. in Molecular Biology from Uppsala University (Sweden). Between 2005-2010 Dr Zavialov received his postdoctoral training in Immunology at Institute of Cellular and Molecular Pharmacology (France) and worked as a research scientist and an assistant research professor at A*-STAR’s Singapore Immunology Network (SIgN) and University of Hawaii at Manoa (U.S.A.). Dr. Zavialov is a recipient of the Harold M. Weintraub graduate student Award, EMBO and HFSP long-term fellowships. In 2011 he was selected as a Research Fellow of the Academy of Finland. Personnel: Graduate students: Maksym Skaldin (M.S.), Meraj Hassan Khan (M.S.), Chengquian Liu (M.S.), Yuliia Mukiienko (M.D.), Balwant Rai (M.D.) Undergraduate student: Joyce Verwijmeren Description of the project: Two distinct enzymes of adenosine deaminase, ADA1 and ADA2, have been found in humans. Inherited mutations in ADA1 result in severe combined immunodeficiency (SCID). This observation led to extensive studies of the structure and function of this enzyme that have revealed its important role in lymphocyte activation. In contrast, the physiological role of ADA2 is unknown. ADA2 activity in serum is increased in various diseases in which monocytes/ macrophages are activated. We have found that ADA2 is a heparin-binding protein. This allowed us to obtain highly purified enzyme and to study its biochemistry. ADA2 was identified as a member of a new class of adenosine deaminase related growth factors (ADGF), which are present in almost all organisms from flies to humans. Biochemical data suggest that ADA2 may be active at sites of inflammation during hypoxia and in areas of tumor growth where the adenosine concentration is significantly elevated and the extracellular pH is low. We showed that ADA2 is secreted by monocytes undergoing differentiation into macrophages or dendritic cells, and that activated T cells are likely the main target for ADA2. T cells bound the enzyme via A2A and A2B adenosine receptors expressed on their cell surface. It has been further demonstrated that ADA2 induces T cell proliferation independently of their activation with antigen, and that the resulting proliferating cells are CD4+ T-helper cells. Moreover, our recent results show that ADA2 binds to CD39+CD25+ T regulatory cells and induces proliferation of Th17- polarized T helper cells in the presence of Tregs, monocytes and ADA2. While this function is shared with ADA1, the unique role of ADA2 is to promote CD4+ T cell dependent 116 differentiation of monocytes into macrophages. The recently solved structure of ADA2 allows us to establish the role of unique ADA2 domains in the enzyme’s interaction with its specific receptor. The comparison of catalytic centres in the structure of ADA1 and ADA2 reveals differences in the binding pockets for the ADA inhibitor, deoxycoformycin. This opens the possibility of using structurebased drug design to find a specific inhibitor for ADA2, which could be chemically synthesize and tested in vitro. Our studies will explore the possibility that ADA2 is an immunomodulatory protein, which may directly or indirectly affect immune responses against intracellular pathogens or tumor cell proliferation. Our goal is to establish the physiological role of ADA2 in inflammation and tumor immunity and to explore its therapeutic potential. Funding: The Academy of Finland; CIMO Collaborators: Dr. Ivona Aksentijevich (NIH/NHGRI, U.S.A.), Dr. Urpo Lamminmäki (University or Turku), Dr. Tuomas Mirtti (University of Helsinki), Prof. Jose Parcel (Arnau de Vilanova University Hospital, Lleida, Spain), Dr. Anton Zavialov (University of Turku), Dr. Yuanan Lu (University of Hawaii, U.S.A.), Dr. Rafael Franco (University of Barcelona, Spain), Dr. Sergey Lavrenov ( Gauze Institute of new antibiotics, Moscow, Russia) Selected Publications: Zavialov, A. V., X. Yu, D. Spillmann, G. Lauvau and A.V. Zavialov.2010. Structural basis for the growth factor activity of human adenosine deaminase ADA2. J Biol Chem 285:12367-12377. Zavialov, A. V., E. Gracia, N. Glaichenhaus, R. Franco, and G. Lauvau. 2010. Human adenosine deaminase 2 induces differentiation of monocytes into macrophages and stimulates proliferation of T helper cells and macrophages. J Leukoc Biol 88:279-290. Gao, N., A. V. Zavialov, M. Ehrenberg, and J. Frank. 2007. Specific interaction between EF-G and RRF and its implication for GTPdependent ribosome splitting into subunits. J Mol Biol 374:13451358. Gao, H., Z. Zhou, U. Rawat, C. Huang, L. Bouakaz, C. Wang, Z. Cheng, Y. Liu, A. Zavialov, R. Gursky, S. Sanyal, M. Ehrenberg, J. Frank, and H. Song. 2007. RF3 induces ribosomal conformational changes responsible for dissociation of class I release factors. Cell 129:929-941. Rawat, U., H. Gao, A. Zavialov, R. Gursky, M. Ehrenberg, and J. Frank. 2006. Interactions of the Release Factor RF1 with the Ribosome as Revealed by Cryo-EM. J Mol Biol 357:1144-1153. Hauryliuk, V., A. Zavialov, L. Kisselev, and M. Ehrenberg. 2006. Class-1 release factor eRF1 promotes GTP binding by class-2 release factor eRF3. Biochimie 88:747-757. Zavialov, A. V., V. V. Hauryliuk, and M. Ehrenberg. 2005. Splitting of the posttermination ribosome into subunits by the concerted action of RRF and EF-G. Mol Cell 18:675-686. 117 Zavialov, A. V., V. V. Hauryliuk, and M. Ehrenberg. 2005. Guaninenucleotide exchange on ribosome-bound elongation factor G initiates the translocation of tRNAs. J Biol 4:9. Ph.D. DEFENCES Zavialov, A. V., and A. Engstrom. 2005. Human ADA2 belongs to a new family of growth factors with adenosine deaminase activity. Biochem J 391:51-57. Gao, N., A. V. Zavialov, W. Li, J. Sengupta, M. Valle, R. P. Gursky, M. Ehrenberg, and J. Frank. 2005. Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies. Mol Cell 18:663-674. Frank, J., J. Sengupta, H. Gao, W. Li, M. Valle, A. Zavialov, and M. Ehrenberg. 2005. The role of tRNA as a molecular spring in decoding, accommodation, and peptidyl transfer. FEBS Lett 579:959-962. Allen, G. S., A. Zavialov, R. Gursky, M. Ehrenberg, and J. Frank. 2005. The cryo-EM structure of a translation initiation complex from Escherichia coli. Cell 121:703-712. Zavialov, A. V., and M. Ehrenberg. 2003. Peptidyl-tRNA regulates the GTPase activity of translation factors. Cell 114:113-122. Valle, M., A. Zavialov, J. Sengupta, U. Rawat, M. Ehrenberg, and J. Frank. 2003. Locking and unlocking of ribosomal motions. Cell 114:123-134. Valle, M., A. Zavialov, W. Li, S. M. Stagg, J. Sengupta, R. C. Nielsen, P. Nissen, S. C. Harvey, M. Ehrenberg, and J. Frank. 2003. Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy. Nat Struct Biol 10:899-906. Rawat, U. B., A. V. Zavialov, J. Sengupta, M. Valle, R. A. Grassucci, J. Linde, B. Vestergaard, M. Ehrenberg, and J. Frank. 2003. A cryo-electron microscopic study of ribosome-bound termination factor RF2. Nature 421:87-90. Pedersen, K., A. V. Zavialov, M. Y. Pavlov, J. Elf, K. Gerdes, and M. Ehrenberg. 2003. The bacterial toxin RelE displays codonspecific cleavage of mRNAs in the ribosomal A site. Cell 112:131-140. Mora, L., A. Zavialov, M. Ehrenberg, and R. H. Buckingham. 2003. Stop codon recognition and interactions with peptide release factor RF3 of truncated and chimeric RF1 and RF2 from Escherichia coli. Mol Microbiol 50:1467-1476. Klaholz, B. P., T. Pape, A. V. Zavialov, A. G. Myasnikov, E. V. Orlova, B. Vestergaard, M. Ehrenberg, and M. van Heel. 2003. Structure of the Escherichia coli ribosomal termination complex with release factor 2. Nature 421:90-94. Zavialov, A. V., L. Mora, R. H. Buckingham, and M. Ehrenberg. 2002. Release of peptide promoted by the GGQ motif of class 1 release factors regulates the GTPase activity of RF3. Mol Cell 10:789-798. Zavialov, A. V., R. H. Buckingham, and M. Ehrenberg. 2001. A posttermination ribosomal complex is the guanine nucleotide exchange factor for peptide release factor RF3. Cell 107:115124. 118 119 LIFE OUTSIDE THE LAB 120 121 122 123 124 125 126 TURUN BIOTEKNIIKAN KESKUS ÅBO BIOTEKNIKCENTRUM TURKU CENTRE FOR BIOTECHNOLOGY TURUN BIOTEKNIIKAN KESKUS Tykistökatu 6 B P.O.BOX 123 FI 20521 Turku, Finland Tel: +358 2 333 8603, Fax +358 2 251 8808
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