contents - Turku Centre for Biotechnology
Transcription
contents - Turku Centre for Biotechnology
CONTENTS Organization.............................................................................. 2 Chairman’s Foreword................................................................. 3 From the Director....................................................................... 4 Year 2011 in a Nutshell.............................................................. 6 Funding and Statistics............................................................... 10 Publications 2011...................................................................... 13 Personnel 2011......................................................................... 19 Finnish Microarray and Sequencing Centre................................ 23 Cell Imaging Core...................................................................... 27 Proteomics Facility..................................................................... 31 Protein Crystallography Core Facility ........................................ 33 Bioinformatics Core................................................................... 34 Virus Vector Facility ................................................................... 37 Coordination of European Biobanking........................................ 38 Mechanisms and Biosensors of GTPases.................................. 40 Protein Kinase Regulation of Brain Development and Disease... 44 Translational Proteomics............................................................ 49 Organisation of Neuronal Signaling Pathways............................ 52 Structural Bioinformatics............................................................ 56 Data Mining and Modelling........................................................ 58 Cytoskeletal and Survival Signaling............................................ 63 Epigenomics.... .......................................................................... 69 Cell Adhesion and Cancer......................................................... 72 Hypoxia in Cell Survival.............................................................. 75 Bioenergy........ .......................................................................... 78 Mitosis and Drug Discovery Research........................................ 80 Canceromics Research Programme.......................................... 83 Signaling Pathways Regulated by Oncogenic Pim Kinases ..........87 Molecular Immunology and Systems Biology of Cell............................................................. 90 Computational Systems Biology................................................ 96 Complex Biosystems Modeling.................................................. 98 Protein Crystallography.............................................................. 100 Cell Fate.......... .......................................................................... 104 Targeting Strategies for Gene Therapy....................................... 107 Regulation and Function of Heat Shock Transcription Factors...... 109 Cancer Cell Signaling................................................................. 113 Adenosine Deaminases............................................................. 116 Ph.D. Theses 2011.................................................................... 119 Ph.D. Defences......................................................................... 120 Life outside the Lab................................................................... 122 1 ORGANIZATION CHAIRMAN’S FOREWORD Board of Trustees 2011 When assessing the present state of Finnish life science one cannot avoid very controversial feelings. Never in the history of this country have the quality of science and the resources for research been better, still there are increasing concerns about the future. The daily huge media interest on the economic crises in Europe has raised the anxiety to unprecedented and, hopefully, exaggerated levels. Nevertheless, budget cuts will also be inevitable in Finland. How much they will affect life science research remains to be seen. Despite the positive trends in the development of Finnish research infrastructure the future of this fundamental construction work is uncertain. Biocenter Finland has done excellent work in reorganizing national core services and promoting the division of labour between the Finnish biocentres. The job is not yet done and clearly worth of continuing. There are also great expectations related to the national research infrastructure roadmap and the potential Finnish participation in the European ESFRI processes. These important tasks have now been delegated to the new national research infrastructure policy committee that will be nominated later this spring by the Academy of Finland. Thus, many critical and far-reaching decisions will be made during the year 2012. Recent good news include the new strategy of TEKES. Previous criteria set for the various funding instruments were very difficult to fulfil by a typical life science or molecular medicine research project. The new policy of TEKES has not yet been tested in practice but there is a clear promise for a change to better. Presently, far too many interesting preliminary observations and innovative ideas become abandoned in the lack of suitable financing mechanisms. The total absence of proof-of-concept funding has led to unacceptable waste of potential innovations. This problem is far from being solved in Finland, but there is room for optimism that we are finally moving to right direction. 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 Biology 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 Looking at the recent achievements of the Turku Centre for Biotechnology it is delightful to notice that the uncertainties of the future have not discouraged the Turku scientists. Funding from the Biocenter Finland, the Academy of Finland (FIRI programme) and the University of Turku (strategic funding) have enabled the acquisition of up-to-date instruments. Based on that the core facilities have been able to establish novel technologies and offer new services. Recently also many outstanding young scientists have joined the Turku life science community. Importantly, many of the new recruits have moved to Turku from abroad. Turku Centre for Biotechnology has always been a forerunner in the internationalization of the Universities. One more reason to congratulate Turku Centre for Biotechnology is that the recent list of published papers is really impressive. Thus, even in the rapidly changing world, the Centre and its staff seem to have all critical elements needed for the continuing success also in the future. 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 In 2011 the City of Turku was the cultural capital of Europe, which is also reflected in this Annual Report. The annual BioCity Turku symposium was also flavored by this theme. In addition to culture, also science flourished in Turku. The researchers of Turku Centre of Biotechnology (CBT) organized a number of international meetings, workshops and seminars, including the Sigrid Juselius symposium on “Post-translational modification networks as survival determinants” and ESF epigenomics meeting “Epigenomics and Gene Regulatory Networks Controlling Cellular Responses” in Turku. CBT actively developed its strengths in research and core competence in research infrastructure in molecular biosciences. The Centre provided stateof the-art core facilities, education and training for BioCity Turku research groups and six research programs featuring altogether seven Academy of Finland Centers of Excellence. In 2011 research focused in cell signalling, regulation of gene and protein expression, and systems biology resulted in 61 papers, including articles published in top ranked journals such as Nature Neuroscience, Nature Cell Biology, PNAS and Nature. Altogether 11 Ph.D. students presented their dissertations, which is a great achievement. A new international group leader Andrey Zavialov became an Academy Fellow, a highly competitive award by the Academy of Finland (AoF), and started his research group at the Centre. Also, Daniel Abankwa became an Academy Fellow. Our group leaders succeeded well in obtaining national and international funding, including 11 grants from the AoF. Among these were the AoF FiRI grant to Daniel Abankwa to support development of cuttingedge cell imaging infrastructure. A new Centre of Excellence (CoE) in “Molecular Systems Immunology and Physiology” was selected by the AoF for 2012-17. In this AoF CoE Riitta Lahesmaa is responsible for molecular systems immunology, and CBTs affiliated group leaders Matej Oresic (VTT) and Harri Lähdesmäki (Aalto) play central roles in leading the CoE and directing the computational systems biology, respectively. Johanna Ivaska was awarded the distinguished Anders Jahre young investigator’s award and Jukka Westermarck received a highly competitive professorship of the Finnish Cancer Institute for a 2nd term. CBT nominated a new scientific advisory board, that is led by Dr. Doreen Cantrell (Dundee University, Scotland, UK) and has the following distinguished members: 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). We are looking forward to exciting discussions with this expert panel. The animal core facility continued to take up a sizeable portion of basic resources in serving researchers and Turku Centre for disease modeling. Substantial efforts were made to raise and assign resources to further develop the cutting-edge platforms in genomics, epigenomics and functional genomics, proteomics, cell imaging and bioinformatics. Funding from the host organisations and AoF was supplemented by competitive funding through the Biocenter Finland. Biocenter Finland was established in 2006 to facilitate national collaboration between the Finnish biocenters, and to coordinate development of research infrastructures in Finland. The Ministry of Education special funding for 2010-2012 has made it possible to significantly improve the research infrastructure in Finland. Several of CBT’s group leaders are actively engaged in these Biocenter Finland 4 infrastructure networks and were able to raise altogether 3 185 536 € through a competitive call. Accordingly, CBT now further develops and provides national services in a wide range of platforms within the Biocenter Finland infrastructure network. Bioimaging and systems biology infrastructures are at the core of the research strategy of both our universities and central infrastructures in the research strategy of BioCity Turku. The Biocenter Finland networks have made outstanding progress in developing the Finnish infrastucture for research and providing Finnish scientists access to the state-of-the-art technology. The key to this success has been the division of tasks between the biocenters and tight networking to share the knowledge and provide critical mass in this rapidly developing field. Most importantly, the additional resources have enabled Finnish biocenters to update their technology infrastructure and knowledge because funding has been provided not only for instruments, but also to hire and further train key personnel. One of the most important goals for 2012 is to secure the continuation of Biocenter Finland funding from the Ministry of Education. The results of the two years out of the period of three years are excellent and should speak for themselves. The international scientific advisory board who has evaluated the networks and the midterm results also clearly state this in their report. Our results during the first two years of this budget period (2010-12) have been outstanding and record breaking in many aspects. I wish to congratulate our scientists for their excellent accomplishments! I am deeply grateful to our administrative and technical personnel for your special commitment - without your contributions such results would not have been possible! Riitta Riitta Lahesmaa, M.D., Ph.D., Professor Director Turku Centre for Biotechnology University of Turku and Åbo Akademi University 5 YEAR 2011 IN A NUTSHELL RESEARCH AND EDUCATION 2011 • 61 scientific papers were published (p. 13) • 11 new Ph.D.´s graduated • Johanna Ivaska was granted Anders Jahre young investigator award • Jukka Westermarck’s professorship of the Finnish Cancer Institute was renewed (2012-14) • A new “Center of Excellence in Molecular Systems Immunology and Physiology” was chosen by the Academy of Finland for years 2012-17. The five CoE groups include Riitta Lahesmaa’s group and those led by two affiliated CBT group leaders, Harri Lähdesmäki and Matej Oresic. • Two new Academy Fellows, Daniel Abankwa and Andrey Zavialov were awarded by The Academy of Finland • David Goodlett was selected as a new Finnish Distinguished Professor by TEKES for years 2012-15 • CBT was awarded a substantial 1,034,812 € funding through Biocenter Finland • The Academy of Finland granted 873,810 € infrastructure funding (FIRI) to Daniel Abankwa and coapplicants Eleanor Coffey, Johanna Ivaska and Jukka Westermarck • For undergraduate training, CBT organized lecture courses and practical demonstrations including a laboratory course on “Functional Genomics” for Health Bioscience and Biology students (4 study points), “Medical Biotechnology” for Medical students (5 study points) and a lecture course (4 study points) on “Quality Systems” for Biochemistry and Health Bioscience students. • 12 M.Sc. theses were completed DEVELOPMENT OF INFRASTRUCTURE, RESEARCH SERVICES AND CORE FACILITIES 2011 Finnish Microarray and Sequencing Centre 2011 • The Centre got substantial competitive funding through Biocenter Finland to develop and provide national services in the area of gene expression, regulation of gene expression and epigenetics • Next-generation sequencing instrument: ABI SOLiD 4 was upgraded to SOLiD 5500 XL in August • Acquisition of the following instruments to expand our services: Affymetrix GeneTitan microarray system, Illumina HiSeq2000 next-generation sequencing platform and Diagenode SX-8G IP-Star automated system for epigenetics platform development • An ESF symposium “Epigenomics and Gene Regulatory Networks Controlling Cellular Responses” was organized in October with top speakers from US, Europe and Finland Altogether 38 publications, including papers in very high impact journals such as Nature, Nature Immunology, Immunity and Cell Stem Cell were published with contribution from the FMSC 6 Proteomics and Mass spectrometry Laboratory 2011 • Additional funding received to the Facility through Biocentre Finland for instrument purchases and laboratory personnel • Continued upgrades to important software for quantitative analysis • Development of new procedures for label-free quantitation and phosphorylation analysis • Two new mass spectrometers were ordered for PTM analysis and targeted quantitative proteomics • A 23% increase to 4300 hours of MS service operation • Several trainings courses were organised ranging from 3 day targeted courses on bioinformatics procedures including Scaffold, ProteinPilot, Mascot and MS courses for sample handling for iTRAQ analysis as well as week long courses on basic MS and Protein Phosphorylation 4th) Summer School in “Mass Spectrometry in Biotechnology and Medicine” in Dubrovnik • Dorota Muth was recruited in May to spearhead targeted quantitative MS • Pekka Haapaniemi (MSc) was recruited in November as a laboratory technician to assist in day to day running of the MS instruments • Firouz Saedi completed his Masters degree in bioinformatics and Avinash Jadav, Thaman Chand and Santhosh Thatikonda started their Masters degree. • Darshana Kottahachi started as a new Ph.D. student in quantitative MS. Cell Imaging Core 2011 • • • • • • • • • • • • • • • • • Throughout the year, a dozen microscopes and other instrumentation were tested by CIC staff locally and internationally to evaluate them for future purchase CIC staff helped in courses and gave lectures e.g. for Health Biosciences (TerBio) and BioImaging Masters students April 27-29: Zeiss on Campus and BioImageXD workshop Two big tender procedures were successfully concluded for microscope purchases Jouko Sandholm returns from research stay in the US Pasi Kankaanpää will replace Daniel Abankwa as the head of CIC CIC is a test site for the preparatory phase of the Euro-BioImaging initiative 8500 downloads of “Flowing Software”, flow cytometry analysis software developed by Perttu Terho at the Cell Imaging Core. http://www.flowingsoftware.com/ New CIC-instrumentation: Zeiss LSM780 confocal microscope with FCS capability Leica STED upgrade for STED-FCS, SymPhoTime software and analysis computer FLIM-FRET/ FRAP fast confocal unit from Lambert Instruments and VisiTech Evos fl cell culture fluorescence microscope Zeiss AxioVert 200M fluorescence microscope second hand purchase from Hormos Medical Oy BioTek Synergy H1 multimodal plate reader New powerful public image analysis computer and computers for CIC staff New computers for two flow cytometer New computer and Zen Software upgrade on LSM 510; hardware upgrades on LSM 510 7 • Various smaller upgrades, such as a new light source for a fluorescence microscope etc. • • • Viral vector facility 2011 • • • • • • The viral vector facility produced 115 viral preps as a service and hosted 50 registered users of the BSL2 lab The BSL2 lab was equipped with a Zeiss Axiovert 40 inverted fluorescence microscope with CCD camera for digital imaging of fluorescence reporters New infrastructure was purchased to expand the capacity of the BSL2 lab to accommodate the increase in user base. This was made possible because of additional funding from the Biocenter Finland organisation that was allocated during 2011 Bioinformatics Unit 2011 • • • • • • • • • • • • 8 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 IT support has integrated dedicated disks and software tools into the high-capacity server to support BF Biological Imaging. 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 23 Next Generation Sequences and 11 microarray projects (20 local; 13 domestic; 1 international). Protein crystallography facility 2011 Participation in several courses (Medical Biochemistry, TERBIO, Protein Crystallography and Structural Genomics’, ‘How to solve a protein structure’, Master’s degree program in Autonomous University of Barcelona) with lectures and demonstrations. New X-ray generator was installed. Training and demonstrations were arranged. BioXLabs-Turku (http://www.sci.utu.fi/projects/biokemia/ bioxlabs/) was launched with other crystallographic groups in Turku to facilitate training, share of resources, and exchange of information. Participation in the road show organized by Biocenter Finland Structural Biology Network. 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. New computers and 3D-monitors were purchased. Quality Assurance Unit 2011 Organized courses for the university on quality assurance and metrology and how to assure the reliability of laboratory test results Individual training for graduate and post-graduate students A M.Sc. thesis of Eeva Mäki was completed 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 PhD and MSc Theses PhD Theses (p. 119) Name Supervisor Björk Johanna Sistonen Lea Dhavala Prathusha Papageorgiou Tassos Gupta Santosh Kallioniemi Olli Haikarainen Teemu Papageorgiou Tassos Jokilehto Terhi Jaakkola Panu Ketola Kirsi Kallioniemi Olli Mai Anja Ivaska Johanna Nevo Jonna Ivaska Johanna Nikula Tuomas Lahesmaa Riitta Rantala Juha Kallioniemi Olli Vainio Paula Kallioniemi Olli Site besides CBT ÅA/Department of Biosciences UTU/Department of Medical Biochemistry and Genetics UTU/Department of Biochemistry and Food Chemistry UTU/Department of Biochemistry and Food Chemistry UTU/Department of Medical Biochemistry and Genetics UTU/Department of Biochemistry and Food Chemistry UTU/Department of Pharmacology, Drug Development and Therapeutics UTU/Department of Medical Biochemistry and Genetics UTU/Department of Medical Biochemistry and Genetics UTU/Department of Biochemistry and Food Chemistry UTU/Department of Pharmacology, Drug Development and Therapeutics MSc / M.D. Advanced Study Theses Name Supervisor Site besides CBT Fors Daniela Lea Sistonen ÅA/Department of Biosciences Laajala Essi Henna Kallionpää Aalto University/ and Harri Lähdesmäki School of Electrical Engineering Heikelä Hanna Eleanor Coffey University of Turku/ Department of Biology Hurme Miikka Eleanor Coffey University of Turku/ICT Lundgren Jolanta John Eriksson ÅA/Department of Biosciences Muleta Adbi Tassos Papageorgiou University of Turku/Department of Information Technology Mäki Eeva Linnéa Linko and University of Turku/Department Susanna Työppönen of Biochemistry and Food Chemistry Nuutila Maiju Heidi Högel and University of Turku/Department Panu M. Jaakkola of Biochemistry and Food Chemistry Rajavuori Anna Riitta Lahesmaa University of Turku/Medical Faculty Salo Verna Riitta Lahesmaa University of Turku/Health Biosciences Seijas Biel Hanser Jose Lea Sistonen ÅA/Department of Biosciences Subedi Bishwa Tassos Papageorgiou University of Turku/Department of Information Technology 9 FUNDING AND STATISTICS Number of graduates 2006-2011 Sources of funding received by Centre for Biotechnology in 2011 (12.3 Million €) Biocenter Finland EU Others, TEKES Services Academy of Finland ϮϬй Universities Publication impact factors 8 publications with IF > 10 30 publications with IF < 5 External funding 2006-2011 23 publications with IF 5-10 Citations per year 10 11 PUBLICATIONS 2011 1. Anckar J. and Sistonen L. Regulation of HSF1 function in the heat stress response: implications in aging and disease (2011) Annu. Rev. Biochem. 80: 1089-1115. Review. IF: 29.742. 2. 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. IF: 4.411. 3. Arjonen A., Kaukonen R. and Ivaska J. (2011) Filopodia and adhesion in cancer cell motility. Cell Adh. Migr. 5: 421430. 4. Asaoka T., Kaunisto A., Eriksson J.E. (2011) Regulation of cell death by c-FLIP phosphorylation. Adv. Exp. Med. Biol. 691: 625-630. IF: 1.379. 5. Björkman M., Ostling 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. and Nees M. (2011) 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. [Epub ahead of print]. IF: 7.414. 6. Böckelman C., Lassus H., Hemmes A., Leminen A., Westermarck J., Haglund C., Bützow R. and Ristimäki A. (2011) Prognostic role of CIP2A expression in serous ovarian cancer. Br. J. Cancer 105:989-995. IF: 4.831. 7. Chouhan B., Denesyuk A., Heino J., Johnson M.S. and Denessiouk K. (2011) Conservation of the Human IntegrinType Beta-Propeller Domain in Bacteria. PLos One 6: e25069. IF: 4.411. 8. Corthals G.L., Dunn M., James P., Gil C., Penque D., Albar J.P., Andrén P., Rabilloud T. and Marko-Varga G. (2011) The transition of the European Proteomics Association into the future. J. Proteomics. [Epub ahead of print]. IF: 5.074. From left to right: First row: Markku Saari, Riitta Lahesmaa, Hannele Vuori, Marjo Hakkarainen, Virpi Korpiranta, Elina Pietilä, Sarita Heinonen and Terhi Jokilehto Second row: Perttu Terho, Pasi Viljakainen, Petri Vahakoski, Mikael Wasberg, Juha Strandén, Mårten Hedman, Bogata Fezazi, Aila Jasmavaara, Susanna Pyökäri and Anne Rokka 9. Chrusciel M., Bodek G., Kirtiklis L., Lewczuk B., Hyder C.L., Blitek A., Kaczmarek M.M., Ziecik A.J., Andronowska A. (2011) Immortalization of swine umbilical vein endothelial cells (SUVECs) with the simian virus 40 large-T antigen. Mol. Reprod. Dev. 78: 597-610. IF: 2.395. 10.Edgren H., Murumagi A., Kangaspeska S., Nicorici D., Hongisto V., Kleivi K., Rye I.H., Nyberg S., Wolf M., Borresen-Dale A.L. and Kallioniemi O. (2011) Identification of fusion genes in breast cancer by paired-end RNAsequencing. Genome Biol. 12:R6. IF: 6.885. 11.Eriksson J.E. and Vandenabeele P. (2011) Workshop summary: cell death mechanisms controlled by the TNF family. Adv. Exp. Med. Biol. 691: 585-588. IF: 9.379. 12 13 12.Grouneva I., Rokka A. and Aro E.M. (2011) The thylakoid membrane proteome of two marine diatoms outlines both diatom-specific and species-specific features of the photosynthetic machinery. J. Proteome Res. 10: 53385353. IF: 5.460. 13.Haapa-Paananen S., Kiviluoto S., Waltari M., Puputti M., Mpindi J.P., Kohonen P., Tynninen O., Haapasalo H., Joensuu H., Perälä M. and Kallioniemi O. (2011) HES6 gene is selectively overexpressed in glioma and represents an important transcriptional regulator of glioma proliferation. Oncogene. [Epub ahead of print]. IF: 7.414. 14.Haikarainen T., Paturi P., Lindén J., Haataja S., MeyerKlaucke W., Finne J. and 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. IF: 3.287. 15.Haikarainen T., Thanassoulas A., Stavros P., Nounesis G., Haataja S. and Papageorgiou A.C. (2011) Structural and thermodynamic characterization of metal ion binding in Streptococcus suis Dpr. J. Mol. Biol. 405: 448-460. IF: 4.008. 16. Heinonen J., Taipaleenmäki H., Roering P., Takatalo M., Harkness L., Sandholm J., Uusitalo-Järvinen H., Kassem M., Kiviranta I., Laitala-Leinonen T. and Säämänen A.M. (2011) Snorc is a novel cartilage specific small membrane proteoglycan expressed in differentiating and articular chondrocytes. Osteoarthritis Cartilage 19: 1026-1035. IF: 3.953. 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. and Nees M. (2011) Lysophosphatidic acid and sphingosine-1phosphate promote morphogenesis and block invasion of prostate cancer cells in three-dimensional organotypic models. Oncogene. [Epub ahead of print]. IF: 7.414. 18. Hussein S.M., Batada N.N., Vuoristo S., Ching R.W., Autio R., Närvä E., Ng S., Sourour M., Hämäläinen R., Olsson C., Lundin K., Mikkola M., Trokovic R., Peitz M., Brüstle O., Bazett-Jones D.P., Alitalo K., Lahesmaa R., Nagy A. and Otonkoski T. (2011) Copy number variation and selection during reprogramming to pluripotency. Nature 471: 5862. IF: 36.104. 19.Hyder C.L., Isoniemi K.O., Torvaldson E.S. and Eriksson J.E. (2011) Insights into intermediate filament regulation from development to ageing. J. Cell Sci. 124: 1363-1372. IF: 6.290. 14 Cytokinesis failure due to derailed integrin traffic induces aneuploidy and oncogenic transformation in vitro and in vivo. Oncogene. [Epub ahead of print]. IF: 7.414. 22. Ivaska J. and Heino J. (2011) Cooperation between integrins and growth factor receptors in signaling and endocytosis. Annu. Rev. Cell Dev. Biol. 27: 291-320. IF: 14.078. 23. Ivaska J. (2011) Vimentin; Central hub in EMT induction? Small GTPases 2: 51-53. 24.Kakko T., Jaakkola U., Raitakari O.T. and Kallio J. (2011) Inflammatory effects of blood leukocytes: association with vascular function in neuropeptide Y proline 7-genotyped type 2 diabetes patients. Diab. Vasc. Dis. Res. 8: 221-228. IF: 2.468. 25.Khanna A., Okkeri J., Bilgen T., Tiirikka T., Vihinen M., Visakorpi T. and Westermarck J. (2011) ETS1 mediates MEK1/2-dependent overexpression of cancerous inhibitor of protein phosphatase 2A (CIP2A) in human cancer cells. PLoS One 6: e17979. IF: 4.411. 26. Koh K.P., Yabuuchi A., Rao S., Huang Y., Cunniff K., Nardone J., Laiho A., Tahiliani M., Sommer C.A., Mostoslavsky G., Lahesmaa R., Orkin S.H., Rodig S.J., Daley G.Q. and Rao A. (2011) Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells. Cell Stem Cell 8: 200-213. IF: 25.943. 27.Kouvonen P., Rainio E.M., Suni V., Koskinen P. and Corthals G.L. (2011) Enrichment and sequencing of phosphopeptides on indium tin oxide coated glass slides. Mol. Biosyst. 7: 1828-1837. IF: 3.825. 28.Kukkonen-Macchi A., Sicora O., Kaczynska K., OetkenLindholm C., Pouwels J., Laine L. and Kallio M.J. (2011) Loss of p38gamma MAPK induces pleiotropic mitotic defects and massive cell death. J. Cell Sci. 124: 216-227. IF: 6.290. 29. 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 Transactions on Computational Biology and Bioinformatics 8: 217-225. IF: 1.664. 30. Landor S.K., Mutvei A.P., Mamaeva V., Jin S., Busk M., Borra R., Grönroos T.J., Kronqvist P., Lendahl U. and Sahlgren C.M. (2011) Hypo- and hyperactivated Notch signaling induce a glycolytic switch through distinct mechanisms. Proc Natl Acad Sci U S A 108: 18814-18819. IF: 9.771. 20.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: e27112. IF: 4.411. 31.Legrain P., Aebersold R., Archakov A., Bairoch A., Bala K., Beretta L., Bergeron J., Borchers C., Corthals G.L., Costello C.E., Deutsch E.W., Domon B., Hancock W., He F., Hochstrasser D., Marko-Varga G., Salekdeh G.H., Sechi S., Snyder M., Srivastava S., Uhlen M., Hu C.H., Yamamoto T., Paik Y.K. and Omenn G.S. (2011) The human proteome project: Current state and future direction. Mol. Cell Proteomics. [Epub ahead of print]. IF: 8.354. 21.Högnäs, G., Tuomi, S., Veltel, S., Mattila, E., Murumägi, A., Edgren, H., Kallioniemi, O. and Ivaska, J. (2011) 32. Leivonen S.K., Rokka A., Ostling P., Kohonen P., Corthals G.L., Kallioniemi O. and Perälä M. (2011) Identification 15 of miR-193b targets in breast cancer cells and systems biological analysis of their functional impact. Mol. Cell Proteomics. 10: M110.005322. IF: 8.354. 33. Li, D.-C., Li., A.-N. & Papageorgiou, A.C. (2011). Cellulases from thermophilic fungi: Recent insights and biotechnological potential. Enzyme Res. 2011: 308730. 34. Lindén, R. O., Eronen, V.P. and Aittokallio T. (2011) Quantitative maps of genetic interactions in yeast Comparative evaluation and integrative analysis. BMC Systems Biology 5: 45. IF: 3.565. 44.Pollari S., Käkönen S.M., Edgren H., Wolf M., Kohonen P., Sara H., Guise T., Nees M., and Kallioniemi O. (2011) Enhanced serine production by bone metastatic breast cancer cells stimulates osteoclastogenesis. Breast Cancer Res. Treat. 125: 421-430. IF: 4.859. 35. 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 traffic and migration. J. Cell Biol. 194: 291-306. IF: 9.921. 45.Rantala J.K., Mäkelä R., Aaltola A.R., Laasola P., Mpindi J.P., Nees M., Saviranta P. and Kallioniemi O. (2011) A cell spot microarray method for production of high density siRNA transfection microarrays. BMC Genomics 12: 162. IF: 4.206. 36. Mamaeva V., Rosenholm J.M., Bate-Eya L.T., Bergman L., Peuhu E., Duchanoy A., Fortelius L.E., Landor S., Toivola D.M., Lindén M. and Sahlgren C. (2011) Mesoporous silica nanoparticles as drug delivery systems for targeted inhibition of Notch signaling in cancer. Mol. Ther. 19: 1538-1546. IF: 7.149. 46. Rantala J.K., Pouwels J., Pellinen T., Veltel S., Laasola P., Mattila E., Potter C.S., Duffy T., Sundberg J.P., Kallioniemi O., Askari J.A., Humphries M.J., Parsons M., Salmi M. and Ivaska J. (2011) SHARPIN is an endogenous inhibitor of b1-integrin activation. Nat. Cell Biol. 13: 1315-1324. IF: 19.407. 37.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-2dependent signal amplification cascade that regulates c-Myc levels in ras transformation. Oncogene 31: 390401. IF: 7.414. 47.Rodrigues A.J., Neves-Carvalho A., Teixeira-Castro A., Rokka A., Corthals G., Logarinho E. and Maciel P. (2011) Absence of ataxin-3 leads to enhanced stress response in C. elegans. PLoS One 6: e18512. IF: 4.411. 38.Mattila E. and Ivaska J. (2011) High-throughput methods in identification of protein tyrosine phosphatase inhibitors and activators. Anticancer Agents Med. Chem. 11: 141-150. Review. IF: 3.144. 39. 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. and 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. IF: 7.271. 40.O’Shea J.J., Lahesmaa R., Vahedi G., Laurence A. and Kanno Y. (2011) Genomic views of STAT function in CD4+ T helper cell differentiation. Nat. Rev. Immunol. 11: 239250. Review. IF: 35.196. 41. 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. Mol. Biol. Cell. 22: 1539-1549. IF: 5.861. 42.Petre I., Mizera A., Hyder C.L., Meinander A., Mikhailov A.., Morimoto R.I., Sistonen L., Eriksson J.E. and Back R.J. (2011) A simple mass-action model for the eukaryotic heat shock response and its mathematical validation. Natural Computing 10: 595-612. 16 43.Pihlaja R., Koistinaho J., Kauppinen R., Sandholm J., Tanila H. and Koistinaho M. Multiple cellular and molecular mechanisms Are involved in human Aβ clearance by transplanted adult astrocytes. Glia 59: 1643-1657. IF: 5.186. 48.Rosenholm J.M., Sahlgren C. and Lindén M. (2011) Multifunctional mesoporous silica nanoparticles for combined therapeutic, diagnostic and targeted action in cancer treatment. Curr. Drug Targets 12:1166-1186. IF: 3.061. 49.Toivonen H.T., Meinander A., Asaoka T., Westerlund M., Pettersson F., Mikhailov A., Eriksson J.E. and Saxén H. (2011) Modeling reveals that dynamic regulation of c-FLIP levels determines cell-to-cell distribution of CD95-mediated apoptosis. J. Biol. Chem. 286: 18375-82. IF: 5.328. 50.Tripathi P., Sahoo N., Ullah U., Kallionpää H., Suneja A., Lahesmaa R. and Rao K.V. (2011) A novel mechanism for ERK-dependent regulation of IL4 transcription during human Th2-cell differentiation. Immunol. Cell Biol. [Epub ahead of print]. IF: 3.741. 51.Tyurina Y.Y., Kisin E.R., Murray A., Tyurin V.A., Kapralova V.I., Sparvero L.J., Amoscato A.A., Samhan-Arias A.K., Swedin L., Lahesmaa R., Fadeel B., Shvedova A.A. and Kagan V.E. (2011) Global Phospholipidomics Analysis Reveals Selective Pulmonary Peroxidation Profiles upon Inhalation of Single-Walled Carbon Nanotubes. ACS Nano 5: 7342-7353. IF: 9.865. 52. Vainio P., Gupta S., Ketola K., Mirtti T., Mpindi J.P., Kohonen P., Fey V., Perälä M., Smit F., Verhaegh G., Schalken J., Alanen K.A., Kallioniemi O. and Iljin K. (2011) Arachidonic acid pathway members PLA2G7, HPGD, EPHX2, and CYP4F8 identified as putative novel therapeutic targets in prostate cancer. Am. J. Pathol. 178: 525-536. IF: 9.865. 17 53.Vainio P., Lehtinen L., Mirtti T., Hilvo M., Seppänen-Laakso T., Virtanen J., Sankila A., Nordling S., Lundin J., Rannikko A., Orešic M., Kallioniemi O. and Iljin K. (2011) Phospholipase PLA2G7, associated with aggressive prostate cancer, promotes prostate cancer cell migration and invasion and is inhibited by statins. Oncotarget 2: 1176-1190. 54.Vainio P., Wolf M., Edgren H., He T., Kohonen P., Mpindi J.P., Smit F., Verhaegh G., Schalken J., Perälä M., Iljin K. and Kallioniemi O. (2011) Integrative genomic, transcriptomic, and RNAi analysis indicates a potential oncogenic role for FAM110B in castration-resistant prostate cancer. Prostate. [Epub ahead of print]. IF: 3.377. 55.Vuoriluoto K., Haugen H., Kiviluoto S., Mpindi J.P., Nevo J., Gjerdrum C., Tiron C., Lorens J.B. and Ivaska J. (2011) Vimentin regulates EMT induction by Slug and oncogenic H-Ras and migration by governing Axl expression in breast cancer. Oncogene 30: 1436-1448. IF: 7.414. 56.Vuoriluoto K., Högnäs G., Meller P., Lehti K. and Ivaska J. (2011) Syndecan-1 and -4 differentially regulate oncogenic K-ras dependent cell invasion into collagen through a2b1 integrin and MT1-MMP. Matrix Biol. 30: 207-217. IF: 3.328. 57. Vuoriluoto M., Laine L.J., Saviranta P., Pouwels J. and Kallio M.J. (2011) Spatio-temporal composition of the mitotic Chromosomal Passenger Complex detected using in situ proximity ligation assay. Mol. Oncol. 5: 105-111. IF: 4.250. 58. Vähämaa H., Koskinen V.R., Hosia W., Moulder R., Nevalainen O, Lahesmaa R, Aittokallio T. and Salmi J. (2011) PolyAlign: A Versatile LC-MS Data Alignment Tool for Landmark-Selected and-Automated Use. Int. J. Proteomics 2011: 450290. 59.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. and Coffey E.T. (2011) Phosphorylation of SCG10/stathmin-2 determines multipolar stage exit and neuronal migration rate. Nat. Neurosci. 14: 305-313. IF: 14.191. 60. Yang J., Dominguez B., de Winter F., Gould T.W., Eriksson J.E. and Lee K.F. (2011) Nestin negatively regulates postsynaptic differentiation of the neuromuscular synapse. Nat. Neurosci. 14: 324-330. IF: 14.191. 61.Östling P., Leivonen S.K., Aakula A., Kohonen P., Mäkelä R., Hagman Z., Edsjö A., Kangaspeska S., Edgren H., Nicorici D., Bjartell A., Ceder Y., Perälä M. and Kallioniemi O. (2011) Systematic analysis of microRNAs targeting the androgen receptor in prostate cancer cells. Cancer Res. 71: 1956-1967. IF: 8.234. 18 PERSONNEL 2011 Administration LAHESMAA Riitta, Director, Professor, Group Leader ALANKO Satu, Coordinator GRÖNROOS Sirkku, Senior Administrative Assistant HIRVENSALO Eva, Clerical Official JASMAVAARA Aila, Clerical Official JOKILEHTO Terhi, Coordinator 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 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 Virus Vector facility WASBERG Mikael, Laboratory Manager COFFEY Eleanor, Group Leader, Coordinator ADEL Ketlin, Laboratory Technician Finnish Microarray and Sequencing Centre GYENESEI Attila, Senior Scientist 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 ABANKWA Daniel, Academy of Finland Research Fellow, Coordinator of the Cell Imaging Core COFFEY Eleanor, Academy of Finland Research Fellow, Head of the Cell Imaging Core ERIKSSON John, Group Leader, Professor 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, Postdoctoral Fellow KOUVONEN Petri, Researcher MUTH Dorotha, Senior Scientist NEES Susanne, Coordinator ROKKA Anne, Senior Scientist Biobanking and Biomolecular Resources Research Infrastructure (BBMRI) VUORIO Eero, Professor, BBMRI Executive Manager SALMINEN-MANKONEN Heli, Project manager, Adjunct professor GRÖNROOS Sirkku, Project assistant Mechanisms and Biosensors of GTPases ABANKWA Daniel, Group Leader, Academy of Finland Research Fellow GUZMAN Camilo, Postdoctoral Fellow KOUHI Reihaneh, Undergraduate Student LO Rebecca, Graduate Student NAJUMUDEEN Arafath, Graduate Student 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 HOLLOS Patrik, Undergraduate Student KOMULAINEN Emilia, Graduate Student MOHAMMAD Hasan, Graduate Student MYSORE Raghavendra, Graduate Student PADZIK Artur, Graduate Student ZDROJEWSKA Justyna, Graduate student Translational Proteomics CORTHALS Garry, Group Leader, Head of Proteomics BULBUL Ahmed, Undergraduate Student CHAND Thaman, Undergraduate Student EEROLA Sini, Laboratory Technician HAAPANIEMI Pekka, Laboratory Technician 19 HAKANEN Emmi, Laboratory Technician HEINONEN Arttu, Project Engineer IMANISHI Susumu, Postdoctoral Fellow JAAKKOLA Noora, Undergraduate Student KANNASTE Olli, Graduate Student KOTTAHACHCHI Darshana, Graduate Student KOUVONEN Petri, Researcher KUMAR Santosh, Undergraduate Student MUTH Dorotha, Senior Scientist NEES Susanne, Coordinator ROKKA Anne, Senior Scientist SAEIDI Firouz, Undergraduate Student DE SANTOS Hugo, Graduate Student SUNI Veronika, Graduate Student Organisation of Neuronal Signaling Pathways COURTNEY Michael, 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 MIN Jungah, Senior Scientist RAI Surya, Undergarduate Student SEPPÄNEN Aila, Laboratory Technician VERGUN Olga, Postdoctroal Researcher WANG Xijun, Graduate Student Structural Bioinformatics DENESSIOUK Konstantin, Docent, Group Leader CHOUHAN Bhanupratap Singh, Graduate Student HEININEN-BROWN Mari, Bioinformatician Data Mining and Modeling ELO Laura, Group Leader, Adjunct Professor AITTOKALLIO Tero, Group Leader, Adjunct Professor NEVALAINEN Olli, Group Leader, Professor ERONEN Ville- Pekka, Undergraduate Student GAO Bin, Undergraduate Student HEISKANEN Marja, Graduate Student HIISSA Jukka, Graduate Student JÄRVINEN Aki, Undergraduate Student KOSKINEN Ville, Undergraduate Student LAAJALA Essi, Undergraduate Student LAAJALA Teemu Daniel, Undergraduate Student LINDEN Rolf, Graduate Student OKSER Sebastian, Graduate Student SALMI Jussi, Postdoctoral Fellow SANTA Harri, 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, Undergraduate Student HYDER Claire, Graduate Student LINDQVIST Julia, Graduate Student LUNDGREN Jolanta, Undergraduate Student 20 MOHANASUNDARAM Ponnuswamy, Graduate Student ISONIEMI Kimmo, Graduate Student PALLARI Hanna-Mari, Post-doctoral fellow PAZIEWSKA Beata, Secretary PAUL Preethy, Undergraduate Student PEUHU Emilia, Graduate Student PRASEET Poduval, Postdoctoral Fellow PYLVÄNÄINEN Joanna, Undergraduate Student RAJENDRAN Senthil Kumar, Postdoctoral Fellow REMES Mika, Postdoctoral Fellow ROBERTS Maxwell, Undergraduate Student RUSSELL John, Undergraduate Student SAARENTO Helena, Research Associate TORVALDSON Elin, Graduate student Epigenomics HAWKINS David, Group Leader PASUMARTHY Kalyan, Postdoctoral Fellow VALENSISI Cristina, PostdoctoralFellow Cell Adhesion and Cancer IVASKA Johanna, Group Leader, Professor ALANKO Jonna, Graduate Student ARJONEN Antti, Graduate Student DE FRANCESCHI Nicola, Graduate Student HÖGNÄS Gunilla, Graduate Student KAUKONEN Riina, Graduate Student LAHTINEN Laura, Graduate Student MATTILA Elina, Postdoctoral Fellow MUHARRAM Ghaffar, Postdoctoral Fellow POUWELS Jeroen, Postdoctoral Fellow SAARI Markku, Coordinator SIIVONEN Jenni, Laboratory Technician TUOMI Saara, Postdoctoral Fellow VELTEL Stefan, Postdoctoral Fellow VIRTAKOIVU Reetta, Graduate Student Hypoxia in Cell Survival JAAKKOLA Panu, Group Leader, Adjunct Professor HEIKKINEN Pekka, Graduate Student HÖGEL Heidi, Graduate Student JOKILEHTO Terhi, Graduate Student KALEVO-MATTILA Taina, Laboratory Technician MIIKKULAINEN Petra, Laboratory Technician NUUTILA Maiju, Undergraduate Student RANTANEN Krista, Graduate Student Bioenergy JONES Patrik, Group Leader AKHTAR M. Kalim, Researcher CARBONELL Veronica, Graduate Student CORREDU Danilo, Undergraduate Student DAPANDANI Hariharan, Undergraduate Student EL SOUKI Francy, Graduate Student GUERRERO Fernando, Researcher KÄMÄRÄINEN Jari, Graduate Student OTANI Yumi, Coordinator PASZTOR Andras, Graduate Student PELTONEN Sanna, Graduate Student TALLIHÄRM Artur, Undergraduate Student VUORIJOKI Linda, Graduate Student WELDENGODGUAD Melak, Undergraduate Student Mitosis and Drug Discovery Research KALLIO Marko, Group Leader, Senior Research Scientist, Adjunct Professor ASGHAR Adel, Undergraduate Student JAAKKOLA Kimmo, Postdoctoral Fellow KUKKONEN-MACCHI Anu, Postdoctoral Fellow LAINE Leena, Postdoctoral Fellow MÄKI-JOUPPILA Jenni, Graduate Student NARVI Elli, Postdoctoral Fellow OETKEN-LINDHOLM Christina, Postdoctoral Fellow SALMELA Anna-Leena, Graduate Student TAMBE Mahesh, Graduate Student TOIVONEN Pauliina, Laboratory Technician WINSEL Sebastian, Postdoctoral Fellow Canceromics Research Programme KALLIONIEMI Olli, Group Leader, Director PLOSILA Riina, Coordinator AAKULA Anna, Graduate Student BUCHER Elmar, Graduate Student BJÖRKMAN Mari Graduate Student GUPTA Santosh, Graduate Student KETOLA Kirsi, Graduate Student KOHONEN Pekka, Graduate Student POLLARI Sirkku, Graduate Student VAINIO Paula, Graduate Student Signaling Pathways Regulated by Oncogenic Pim Kinases KOSKINEN Päivi, Group Leader, Adjunct Professor EEROLA Sini, Undergraduate Student EKMAN Heidi, Undergraduate Student RAINIO Eeva-Marja, Postdoctoral Fellow SANDHOLM Jouko, Graduate Student SANTIO Niina, Undergraduate Student VAHAKOSKI Riitta, Graduate Student VIRTANEN Juho, Undergraduate Student Molecular Immunology and Systems Biology of Cell Differentiation LAHESMAA Riitta, Director, Professor, Group Leader BALA Kanchan, Senior Scientist CHEN Zhi Jane, Senior Scientist EDELMAN Sanna, Postdoctoral Fellow ELO-UHLGREN Laura, Adjunct Professor, Senior Scientist FEZAZI Bogata, Laboratory Technician HAKANEN Emmi, Undergraduate Student HAKKARAINEN Marjo, Laboratory Technician HEINONEN Mirkka, Graduate Student HEINONEN Sarita, Laboratory Technician KALLIONPÄÄ Henna, Graduate Student KANDURI Kartiek, Graduate Student KHAN MOHN Moin, Graduate Student KORHONEN Juha, Graduae Student KYLÄNIEMI Minna, Graduate Student LAAJALA Essi, Undergraduate Student LUND Riikka, Senior Scientist LÖNNBERG Tapio, Graduate Student MAURINEN Krista, Undergraduate Student MOULDER Robert, Senior Scientist MYLLYVIITA Johanna, Undergraduate Student NÄRVÄ, Elisa, Graduate Student OIKARI Lotta, Undergraduate Student PIETILÄ Elina, Laboratory Technician RAHKONEN Nelly, Undergraduate Student RAJAVUORI Anna, Undergraduate Student RAO Anjana, Visiting Professor RAO Kanury, Visiting Professor RASOOL Omid, Adjunct Professor, Senior Scientist REDDY Emaheswa, Postdoctoral fellow SALO Verna, Graduate Student SARAPULOV Alexey, Graduate Student STOCKINGER Brigitta, Visiting Professor TAHVANAINEN Johanna, Postdoctoral fellow TRIPATHI Subhash, Graduate Student TUOMELA Soile, Graduate Student ÖLING Viveka, Postdoctoral Fellow Quality Assurance Unit LINKO Linnéa, Group Leader, Adjunct Professor Computational Systems Biology LÄHDESMÄKI Harri, Group Leader, Professor ALASOO Kaur, Undergraduate Student ERKKILÄ Timo, Graduate Student INTOSALMI Jukka, Post-doctoral Fellow KANDURI Kartiek, Graduate Student KONG Lingjia, Graduate Student KÄHÄRÄ Juhani, Undergraduate Student LARJO Antti, Graduate Student MALONZO Maia, Undergraduate Student MANNERSTRÖM Henrik, Graduate Student NOUSIAINEN Kari, Graduate Student OSMALA Maria, Graduate Student RAUTIO Sini, Undergraduate Student SEPPÄLÄ Janne, Undergraduate Student SOMANI Juhi, Undergraduate Student ÄIJÖ Tarmo, Graduate Student Complex Biosystems Modeling NYKTER Matti, Group Leader ANNALA Matti, Graduate Student GRANBERG Kirsi, Post-doctoral Fellow KARTASALO Kimmo, Undergraduate Student KESSELI Juha, Post-doctoral Fellow KIVINEN Virpi, Graduate Student LEPPÄNEN Simo-Pekka, Undergraduate Student LIUKSIALA Thomas, Undergraduate Student SARBU Septimia, Graduate Student SOININEN Tero, Undergraduate Student SORSA Saija, Undergraduate Student WALTERING Kati, Post-doctoral Fellow YLIPÄÄ Antti, Graduate Student Protein Crystallography PAPAGEORGIOU Tassos, Group Leader, Adjunct Professor BATTULA Pradeep, Undergraduate Student BRUNEAU Morgane, Undergraduate Student DHAVALA Prathusha, Graduate Student HERNANDEZ David, Undergraduate Student HAIKARAINEN Teemu, Graduate Student MATTSSON Jesse, Graduate Student MULETA Abdi, Undergraduate Student SIVARAMAN Chamundeeswari, Undergraduate Student SUBEDI Bishwa, Undergraduate Student 21 Cell fate SAHLGREN Cecilia, Group Leader, Academy of Finland Research Fellow ANTFOLK Daniel, Undergraduate Student ANTILA Christian, Undergraduate Student BAGHINOV Habib, Graduate Student BAGHIRO Habib, Undergraduate Student LANDOR Sebastian, Graduate Student MAMAEVA Veronika, Postdoctoral Fellow PRABHAKAR Neeraj, Undergraduate Student SAARENTO, Helena, Laboratory Technician SARINKO Sara, Undergraduate Student SJÖQVIST Marika, Graduate Student THATIKONDA Santosh Kumar, Graduate Student Targeting Strategies for Gene Therapy SAVONTAUS Mikko, Group Leader, Adjunct Professor EEROLA Kim, Graduate Student MATTILA Minttu, Undergraduate Student TOIVONEN Raine, Graduate Student Regulation and Function of Heat Shock Transcription Factors SISTONEN Lea, Group Leader, Professor AALTO, Anna, Undergraduate Student AHLSKOG Johanna, Postdoctoral Fellow BERGMAN Heidi, Undergraduate Student BJÖRK Johanna, Graduate Student BLOM Malin, Undergraduate Student BUDZYNSKI Marek, Graduate Student ELSING Alexandra, Graduate Student HENRIKSSON Eva, Postdoctoral Fellow HUDD Joachim, , Undergraduate Student JOUTSEN Jenny, Undergraduate Student LUNDSTEN Emine, Undergraduate Student PUUSTINEN Mikael, Undergraduate Student ROOS-MATTJUS Pia, Senior Scientist SAARENTO Helena, Research Associate SANDQVIST Anton, Postdoctoral Fellow SEIJAS BIEL Hanser Jose, Undergraduate Student VAINIO Petra, Graduate Student VASARA Jenni, Student VIHERVAARA Anniina, Graduate Student ÅKERFELT Malin, Postdoctoral Fellow Cancer Cell Signaling WESTERMARCK Jukka, Group Leader, Professor ANCHIT Khanna, Graduate Student CVRLSEVIC Anna, Postdoctoral Fellow HALONEN Tuuli, Graduate Student KALEVO-MATTILA Taina, Laboratory Technician KAUKO Otto, Graduate Student KAUR Amanpreet, Graduate Student LAINE Anni, Graduate Student NIEMELÄ Minna, Graduate Student OKKERI Juha, Postdoctoral Fellow POKHAREL Yuba, Postdoctoral Fellow PUKONEN Inga, Laboratory Technician SITTIG Eleonora, Laboratory Technician VENTELÄ Sami, Postdoctoral Fellow XI Qiao, Graduate Student Adenosine Deaminases ZAVIALOV Andrey, Group Leader, Academy of Finland Research Fellow REZA Salim, Graduate Student SKALDIN Maksym, Graduate Student FINNISH MICROARRAY AND SEQUENCING CENTRE http://fmsc.btk.fi Scientists in charge: Attila Gyenesei, Ph.D., Senior Scientist – FMSC services and operation, bioinformatics David Hawkins, Ph.D., Group Leader – Epigenetics and emerging technologies Riikka Lund, Ph.D., Senior Scientist – Epigenetics Juha-Pekka Pursiheimo, Ph.D., Senior Scientist – SOLID NGS Contact information: Turku Centre for Biotechnology, BioCity, Tykistökatu 6A, P.O. Box 123, FIN-2050 Turku, Finland. Tel. +358-2-333 8634 Fax +358-2-333 8000. Email: [email protected] http://fmsc.btk.fi Personnel: Päivi Junni, Sini Junttila, Andras Kiraly, Leena Kytömäki, Asta Laiho, Oso Rissanen, Reija Venho, Eveliina Virtanen, Sanna Vuorikoski, Leni Kauko, Ritva Ala-Kulju, Janne Isojärvi, Bishwa Ghimire, Robin Sundström. 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) General description: The Finnish Microarray and Sequencing Centre (FMSC), an internationally recognised Functional Genomics Core Facility belongs to the Turku Centre for Biotechnology. As a national core facility, we provide state-of-the-art research technologies and services in the areas of genomics, epigenomics, transcriptomics and bioinformatics for the Finnish as well as the international scientific community. Our services include next-generation sequencing and microarray based services mainly focusing on gene expression and regulation as well as epigenetics, Real-Time PCR and traditional DNA sequencing. Our service covers 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. FMSC hosts a high-throughput next-generation sequencing TM (NGS) instruments SOLiD 5500 XL from Life Technologies and HiSeq2000 from Illumina. The systems support a wide range of genetics applications covering genomics, transcriptomics and epigenomics and they have high accuracy and capability of generating more than 100 gigabases of mappable sequence data per run. The combination of increased throughput, shorter run times, and improved data analysis make both SOLiD and HiSeq technologies ideal choices for research applications in a wide range of projects. 22 23 Our Centre also provides services on commercial microarray platforms for genome-wide RNA expression profiling, SNP genotyping and comparative genomic hybridization needs. These platforms include Affymetrix GeneChip©, Illumina Sentrix Bead Array© and Agilent DNA technology services for all of which we have been granted the Certified Service Provider status. All platforms have dedicated scanners and software for array data analysis. Diverse aspects of the microarray techniques are continuously developed and tested. Additionally, Affymetrix GeneTitan microarray system was purchased to automate sample processing. The Microarray and Sequencing Centre also offers a number of other genomic analysis technologies for gene expression, SNP and genotyping studies including a sequencing facility and realtime PCR service. Services include BioRad Experion and Agilent Bioanalyzer runs for verifying the RNA quality. Bioinformatics data analysis and data mining are included in the data analysis service that is provided for microarray and nextgeneration sequencing customers. The data handling is done by our bioinformaticians, using both commercial and R/Bioconductor software tools. Seminars and practical courses on microarrays, next-generation sequencing and related bioinformatics are held frequently to facilitate knowledge transfer within the field, often this is done in collaboration with graduate schools. Major achievements in 2011: According to the division of tasks Turku node focuses on developing technologies in the areas of gene expression and its regulation. FMSC services according to the BF application: •· Sequencing of immunoprecipitated DNA/RNA (ChIP-seq, PAR-CLIP, ChIP-chip) •· RNA sequencing •· Gene expression microarrays Additionally, in response to the increasing demands in the epigenetic field one of the key goals in the Centre has been to develop advanced techniques and optimizing reagents and set up a service for Epigenomic applications.To achieve the goals the following was accomplished in 2011: •· 79 service projects were carried out in 2011. These included 50 microarray platform based projects and 29 next-generation sequencing projects (including ChIP-seq, FAIRE-seq, whole transcriptomics, small RNA, targeted resequencing, whole genome de-novo sequencing, methylation analysis, whole genome resequencing) •· PAR-CLIP technique has been set up. First sample sets were sequenced with SOLID 4 and analyzed by our affiliated group leader Prof Harri Lähdesmäki and his group. The technology development continues with a goal to provide PAR-CLIP through research collaboration from the second half of 2012. •· Chromatin Immunoprecipitation (ChIP) application has been set up in the Centre. This started with the optimization of the chromatin fragmentation to a size distribution optimal for genome-wide sequencing. In particular, the optimization was carried out also for challenging sample types. In the next phase a panel of good quality antibodies was selected for the ChIP application to enable genomewide profiling of the histone marks for active and inactive promoters and enhancers. The ChIP protocol was 24 optimized and the amount of starting material needed for ChIP was scaled down 25 times. Also the amount of antibodies and beads used for ChIP reactions were scaled down. We have successfully generated ChIP-Seq histone modification maps from Illumina sequencing. With the Biocentre Finland funding automated system for epigenetic sample preparation, SX-8G IP-Star® from Diagenode was purchased. The IP-Star robot enables epigenetic sample preparation in a standardized and quality controlled manner, which is crucial for the service. The internal quality control steps for monitoring the sample quality and sample preparation process were established. •· Reduced Representative Bisulfite Sequencing (RRBS) assay has been set up to for DNA methylation profiling. This technique enables global profiling of DNA methylation at the CpG islands and shores with single base pair resolution from a starting material as low as 500 ng of genomic DNA. In comparison to whole genome bisulfite sequencing, in RRBS enzymatic treatment is used to enrich the CpG-rich regions enabling cost efficient profiling of DNA methylome. We have established the entire pipeline from sample preparation and data acquisition to visualizing the results on UCSC browser. The Illumina TruSeq multiplexing/sample indexing library preparation kit has been optimized for compatability with low amounts of RRBS DNA to provide commercially, quality controlled reagents for library generation. Sequencing capacity and mapping efficiency (45-65%) are equivalent to or surpassing recently published results. Bisulfite conversion controls have been implemented to ensure accurate calling of methylation status. •· As the Helicos instrument, tested by the Centre in 2010, is not available for use, a HiSeq2000 instrument from Illumina was purchased (U. Turku funding) and installed in November 2011, in particular for epigenomic applications, as it supports both the RRBS and ChIP assay. Preparation of the ChIP samples for sequencing with SOLID platform was found to be challenging partly due to narrow chromatin fragment size distribution required for sequencing SOLID instrument. The RRBS and RNA-Seq applications have already been successfully run with the instrument. Currently, the work is carried out to set up the multiplexing of the ChIP samples for sequencing, which is currently not supported by commercial kits from Illumina. Multiplexing of the ChIP samples will significantly reduce the cost of ChIP-Seq analysis. In addition, the next focus areas are to explore possibilities and develop methods for analysis of challenging sample material, such as clinical sample material from FFPE tissues or with restricted starting amounts. •· The bioinformatics team of the Centre has set up a new computer cluster to increase the computation power and storage capacity the new next generation sequencing instrument requires. Development of data analysis pipeline for various next-generation sequencing applications including RNA-seq, Chip-seq and methylation analysis has been completed and applied to 23 NGS projects. 25 Funding: University of Turku Biocenter Finland Users: Finnish Microarray and Sequencing Centre has national and international customers from universities, biocenters and research institutes in the field of biosciences. CELL IMAGING CORE http://www.btk.fi/cell-imaging/ Coordinator and Group Leader: Daniel Abankwa, PhD, PI, Turku Centre for Biotechnology, BioCity, 5th floor, Tykistökatu 6B, FI-20520, Finland. Tel. +358-2-3336969, Fax. +358-2-3338000. Email: [email protected] Technical Team/Technical Team leaders: Perttu Terho, M.Sc., Technical Engineer Flow Cytometry, Email: [email protected], Markku Saari, M.Sc., Researcher Microscopy, Email: [email protected], Jari Korhonen, M.Sc., Researcher Microscopy, Email: [email protected], Jouko Sandholm, M.Sc., Senior Researcher Microscopy, 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 Core facility description: The mission of Cell Imaging Core (CIC) is to provide state-of-theart cell imaging and flow cytometry technologies and to make them available to scientists and students mainly coming from the University of Turku, Åbo Akademi University and VTT Technical Research Centre for Medical Biotechnology. Importantly, CIC is open to both academic and industrial researchers. One major goal of CIC is to enhance the research and teaching environment locally, nationally and internationally. Therefore, CIC · • provides numerous instruments (microscopes, flow cytometers etc.) for research and teaching use · • provides technical training to local and visiting researchers and to industries · • offers consultation on experimental design and image analysis · • evaluates new methods and fluorescence tools and communicates acquired knowledge to users · • implements advances in hardware and software relevant for biomedical sciences · • provides ongoing education in theory and practice by organizing training courses and international workshops From left to right: Asta Laiho, Attila Gyenesei, Juha-Pekka Pursiheimo, Reija Venho, Leni Mannermaa, Eveliina Virtanen, Leena Kytömäki, Sini Junttila, Riikka Lund, Päivi Junni, Cristina Valensisi and Kalyan Pasumarthy 26 Our staff includes a coordinator and experienced application specialists, who maintain the instruments, learn new technologies and most importantly, provide personal training to users. Our areas of technical expertise are STED superresolution microscopy, live cell imaging, F-techniques (FRET and FRAP imaging), confocal microscopy (including timelapse and spectral detection), highcontent imaging, widefield fast CCD imaging, laser-capture microdissection, high throughput cell sorting, flow cytometry FRET and advanced flow cytometry software development. The STED technique was developed by Stefan Hell in the group of Prof. Pekka Hänninen in the mid 1990s in Turku. Complementary to this 27 superresolution technology, we have two Atomic Force Microscopy (AFM) setups, which are coupled to a Zeiss LSM510 and the Leica STED microscope. Most of the instruments are provided in two facility areas of the CBT, while others are housed nearby within BioCity. Thanks to great funding success and local support in 2010/2011, we have significantly expanded our instrumentation to feature two new confocal microscopes with fluorescence lifetime imaging and fluorescence correlation spectroscopy capabilities (see list below). In addition, image analysis workstations that run the locally developed BioImageXD image analysis software have become available. We organize local and national training programs, service existing equipment, sustain research on new imaging techniques, and implement the latest technological advances demanded by the research community. A number of international leaders in the field of microscopic imaging have visited Turku for scientific presentations and lectures, such as Stefan Hell (MPI bpc Göttingen, Germany). Current information on events, services and pricing can be found on the facility webpages. CIC has succeeded both as a service provider and as a point of integration of emerging imaging technologies. In the Turku scientific community, added value is achieved by the first-class expertise in the fields of fluorescence-activated cell sorting, fluorescencebased screening, high-content screening, in vivo animal imaging, and viral gene transfer. CIC is nationally and internationally networked (e.g. through the Nordic Network on Imaging in Medicine and Biology). Importantly, CIC is one of the major contributors to Turku BioImaging, an umbrella organization, which aims at organizing and supporting bioimaging expertise in the Turku area. Through this activity, Turku BioImaging sites have become one of the first three test sites for the Euro-BioImaging initiative. Euro-BioImaging aims at providing access, service and training to state-of-the-art imaging technologies in Europe. To this end, a harmonized infrastructure deployment is planned in the next few years, which is meant to facilitate excellence in research. Funding: The Academy of Finland, University of Turku, Åbo Akademi University, BioCity Turku Research Groups, Biocenter Finland, Health and Welfare Ministry From left to right: Perttu Terho, Markku Saari, Daniel Abankwa, Jari Korhonen, Pasi Kankaanpää 28 29 PROTEOMICS FACILITY http://www.btk.fi/proteomics Coordinator and Group Leader: 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. +358-2-333 8000. E-mail: [email protected] Personnel: Senior scientists: Dr. Anne Rokka, Ph.D.; Dorota Muth, Ph.D.; Susumu Imanishi, Ph.D.; Project Engineer: Arttu Heinonen; Laboratory Technician: Pekka Haapaniemi; Researcher: Petri Kouvonen; Coordinator: Susanne Nees. 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, 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 MS methods and instrumentation to meet the needs in molecular biotechnology and medicine. Our goals are to identify new areas appropriate for MS in biological sciences and to develop new approaches involving MS, to apply cutting-edge MS to tackle critical questions in biological sciences, and train students, postdoctoral fellows and practicing scientists in the use of MS 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. From left to right: Garry Corthals, Anne Rokka, Arttu Heinonen, Susumu Imanishi and Dorota Muth 30 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 in academia and industry, both locally and nationally through Biocentre Finland coordinated activities. 31 A full representation of our services in 2011 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. · • Label-free quantitation – We have established a framework for label-free quantitative analysis, particularly useful for largescale clinical studies. · • 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 are offered. · • Protein separation – numerous separation technologies including liquid chromatography and a variety of gel based methods such as 1-DE, 2-DE, peptide-IPG and blue native gel electrophoresis. · • Bioinformatics – in all areas of proteomics bioinformatics services are offered including identification, quantitation and validation studies, reporting and software development. Major mass spectrometry instrumentation: For ESI-MS/MS – Q-Star Pulsar, Q-Star Elite and LTQ Velos Orbitrap with ETD For MALDI-MS/MS – Ultrafelx II ToF ToF system Funding: University of Turku and Åbo Akademi University, Biocenter Finland, The Academy of Finland, City of Turku, Ministry of Education, Centre of Expertise of Southwest Finland, Bruker Daltonics, the Systems Biology Research Program. Users: The University of Turku, Åbo Akademi University, Biocentre Finland universities, Turku Polytechnic, VTT - Molecular Biotechnology. CoE’s in: Translational Genome-Scale Biology; Evolutionary Genetics and Physiology; Integrative Photosynthesis and Bioactive Compound Research at Systems Biology Level; and Åbo Akademi CoE in Cell Stress. The Systems Biology Research Program, national research groups, Turku Hospitals, the Finnish Red Cross and the National Animal Research Centre. 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] 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 (O, XtalView, Grasp, COOT, CCP4mg, PyMol, Chimera), 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 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 multidisciplinary approach and we are especially interested in bringing together expertise from various groups in order to better understand the structure-function relationship of biological macromolecules in key biological processes. Funding: Systems Biology research program, Biocenter Finland, University of Turku 32 33 BIOINFORMATICS CORE Group leaders: 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] Attila Gyenesei, Ph.D., Turku Centre for Biotechnology, BioCity, Tykistökatu 6A, P.O. Box 123, FIN-2050 Turku, Finland. Tel. +3582-333 8634 Fax +358-2-333 8000. E-mail: [email protected] Personnel: Bhanupratap Singh Chouhan, Sini Junttila, Asta Laiho, Leena Kytömäki, Bishwa Ghimire, Janne Isojärvi Description of the Facility: 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. Genomics), funded by the Center for Biotechnology (CBT), and a second cluster partly funded by Åbo Akademi • · IT support has integrated dedicated disks and software tools into the high-capacity server to support BF Biological Imaging. • · 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 23 Next Generation Sequences and 11 microarray projects (20 local; 13 domestic; 1 international). 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). Biocenter Finland Infrastructure fund. Users: The Bioinformatics core has users from Finnish universities, biocenters and research institutes in the field of biosciences. 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 •· Computer-based ligand docking •· Analysis and prediction of effects of molecular recognition and mutations on protein function Major achievements in 2011: · • Two new computational clusters were acquired, one dedicated to genome sequencing efforts (supporting BF 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. and Anna Cvrljevic, 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 · • produces adenoviruses and lenti vectors expressing genes of interest, as a research service · • maintains a fully equipped bio-safety level-2 lab for researchers wishing to produce their own vectors · • supplies working protocols and technical advice on production and safe handling of adeno and lenti vectors From left to right: Ketlin Adel, Jukka Westermarck, Eleanor Coffey, Mikko Savontaus and Anna Cvrljevic · • 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 lentiviral 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 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. 36 37 COORDINATION OF EUROPEAN BIOBANKING www.bbmri.eu, www.bbmri.se/en/About-BBMRIse/BBMRI-Nordic Head: Eero Vuorio, Professor, Director, Biocenter Finland, P.O. Box 56, University of Helsinki, FI-00014 Helsinki, Finland Mobile phone +358-50-415 6595, E-mail: [email protected] Project Manager: Heli Salminen-Mankonen, Ph.D., Docent, University of Turku, Centre for Biotechnology, Tykistökatu 6, FI-20520 Turku, Finland, Tel: +358-2-333 8566, E-mail: [email protected] with data from clinical phenotyping and health-related registries. The new European legal entity (ERIC) developed by the European Commission to support the needs and operation of research infrastructures, foresees the establishment of operational sites (National Nodes) in different Member States under one legislation. The BBMRI Management Office in Turku has also played an active part in establishing the clinical biobanking network in Finland, and in organizing the collaboration of Nordic biobanks where many of the operational concepts and principles of BBMRI have been tested. Funding: The preparatory phase (1.2.2008-31.1.2011) of BBMRI has been financially supported by the European Commission (grant agreement 212111). Description of project: Human biological samples, such as blood, tissues or DNA, plus associated clinical and research data, as well as biomolecular research tools are key resources in unravelling genetic and environmental factors underlying diseases and influencing their outcome. Biological samples are used in high-throughput techniques which allow examination of changes in the genome, transcriptome, proteome, or metabolome. Insights derived from these are expected to assist with the development of new diagnostic, prognostic, and therapeutic tools. Consequently, biological resources are considered as the essential raw material for the advancement of biotechnology, human health and research and development in life sciences. This is the landscape where the pan-European Biobanking and Biomolecular Resources Research Infrastructure (BBMRI) is expected and prepared to integrate the existing quality controlled biobanks, biomolecular resources and enabling technologies into a novel pan-European biomedical research infrastructure, and to guide the way towards establishment of high quality de novo European biobanks adhering to the guidelines drafted by BBMRI. The European Commission has granted 5 Mio € funding (20082011) to the Preparatory Phase of BBMRI to conceptualise and secure funding for the construction of the European research infrastructure for biobanking and biomolecular resources. Management of BBMRI during the Preparatory Phase is divided between Universities of Turku and Graz. Eero Vuorio has served as a part-time Executive Manager and Heli Salminen as the Scientific Manager of BBMRI. This has been a sizeable task as BBMRI comprises 53 partners and nearly 250 associated organizations from 33 countries. The objectives addressed by the BBMRI consortium during the Preparatory Phase were to develop a plan to integrate existing quality controlled biobanks, biomolecular resources and enabling technologies into a novel pan-European biomedical research infrastructure (BBMRI-ERIC). BBMRI will not only provide a comprehensive source of information about existing biological sample collections and biomolecular resources, but will also provide an operational concept for a sustainable infrastructure, deliver standard operational procedures for future biobanking and codes of conduct for European biobanks. A particular challenge is the generation of an IT infrastructure capable of linking the existing biobank-derived genetic and molecular phenotyping data 38 39 MECHANISMS AND BIOSENSORS OF GTPASES Principal 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] 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 HeinrichHeine 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 on an Academy of Finland Research Fellowship. Personnel: Postdoc: Camilo Guzman; Graduate students: Arafath Kaja Najumudeen, MSc; Maja Solman, MSc, Rebecca Lo, MSc; Reihaneh Kouhi Esfahani, MSc. 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 GTPmediated 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. 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. vivo biophysical measurements, we have recently described a novel switch III. This is formed by the b2-b3 loop and helix a5, and is associated with the orientation of the G domain on the membrane. Thus the Ras orientation is stabilized by the HVR and helix a4 (Figure). We also showed that this orientation-switch is specific for different Ras isoforms, regulates GTPase signalling and combines with lateral segregation of Ras. 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 to identify novel isoform specific drugs. The novel orientation-switch III – the coding mechanism for small GTPase isoform specificity. Membrane anchored H-ras exists in two orientation-conformers. 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 a4 (blue; right). This mechanism also applies to other Ras isoforms (Figure 2). Funding: 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) 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 40 41 Selected Publications: Sinha, B., Koster, D., Ruez, R., Gonnord, P., Bastiani, M., Abankwa, D., Stan, R. V., Butler-Browne, G., Vedie, B., Johannes, L., Morone, N., Parton, R. G., Raposo, G., Sens, P., Lamaze, C., and Nassoy, P. (2011) Cells respond to mechanical stress by rapid disassembly of caveolae Cell 144, 402-413. Nguyen, U. T., Goodall, A., Alexandrov, K., and Abankwa, D. (2011) Isoprenoid Modifications. in Post-Translational Modifications in Health and Disease (Vidal, C. J. ed.), 1st Ed., Springer. pp 486 Crouthamel, M., Abankwa, D., Zhang, L., Dilizio, C., Manning, D. R., Hancock, J. F., and Wedegaertner, P. B. (2010) An N-terminal polybasic motif of G{alpha}q is required for signaling and influences membrane nanodomain distribution Mol. Pharmacol. 78: 767-777. Abankwa, D., Gorfe, A. A., Inder, K., and Hancock, J. F. (2010) Ras membrane orientation and nanodomain localization generate isoform diversity Proc. Natl. Acad. Sci. U S A 107, 1130-1135. Bastiani, M., Liu, L., Hill, M. M., Jedrychowski, M. P., Nixon, S. J., Lo, H. P., Abankwa, D., Luetterforst, R., Fernandez-Rojo, M., Breen, M. R., Gygi, S. P., Vinten, J., Walser, P. J., North, K. N., Hancock, J. F., Pilch, P. F., and Parton, R. G. (2009) MURC/ Cavin-4 and cavin family members form tissue-specific caveolar complexes J. Cell Biol. 185: 1259-1273. Hill, M. M., Bastiani, M., Luetterforst, R., Kirkham, M., Kirkham, A., Nixon, S. J., Walser, P., Abankwa, D., Oorschot, V. M., Martin, S., Hancock, J. F., and Parton, R. G. (2008) PTRF-Cavin, a conserved cytoplasmic protein required for caveola formation and function Cell 132: 113-124. Abankwa, D., Hanzal-Bayer, M., Ariotti, N., Plowman, S. J., Gorfe, A. A., Parton, R. G., McCammon, J. A., and Hancock, J. F. (2008) A novel switch region regulates H-ras membrane orientation and signal output Embo J. 27: 727-735. Abankwa, D., Gorfe, A. A., and Hancock, J. F. (2008) Mechanisms of Ras membrane organization and signalling: Ras on a rocker Cell Cycle 7: 2667-2673. Gorfe, A. A., Bayer, M.-H., Abankwa, D., Hancock, J. F., and McCammon, J. A. (2007) Structure and dynamics of the fulllength lipid-modified H-Ras protein in a 1,2-dimyristoylglycero-3phosphocholine bilayer J. Med. Chem. 50: 674-684. Abankwa, D., and Vogel, H. (2007) A FRET map of membrane anchors suggests distinct microdomains of heterotrimeric G proteins J. Cell Sci. 120: 2953-2962. From left to right: Camilo Guzman, Zuhair Iftikhar, Daniel Abankwa, Maja Solman and Arafath Najumudeen Abankwa, D., Gorfe, A. A., and Hancock, J. F. (2007) Ras nanoclusters: molecular structure and assembly Seminars in cell & developmental biology 18: 599-607. Perez, J. B., Segura, J. M., Abankwa, D., Piguet, J., Martinez, K. L., and Vogel, H. (2006) Monitoring the Diffusion of Single Heterotrimeric G Proteins in Supported Cell-membrane Sheets Reveals their Partitioning into Microdomains J. Mol. Biol. 363: 918930. 42 43 PROTEIN KINASE REGULATION OF BRAIN DEVELOPMENT AND DISEASE Principal 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/research/research-groups/coffeyeleanor-kinase-function-in-brain/ 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 is vice director of the Centre, and heads the Cell Imaging Core and Viral Vector Dacility. She was appointed to an Academy of Finland Research Fellow post from 2008 to 2013. Personnel: Graduate students: Artur Padzik, M.Sc., Justyna Zdrojewska, M.Sc., Emilia Komulainen, M.Sc., Raghu Mysore, M.Sc., Hasan Mohammed, M.Sc., Prasanna Deshpande, M.Sc. Undergraduate students: Dani Flinkman, Patrik Hollos, Ravi Adusumalli 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 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 44 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, Sitra. 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). 45 Selected Publications: 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: 305-313. From left to right: Raghavendra Mysore, Dani Flinkman, Artur Padzik, Eleanor Coffey, Justyna Zdrojewska, Emilia Komulainen, Hasan Mohammad and Prasannakumar Deshpande Mai A., Veltel S., Pellinen T., Padzik A., Coffey E., Marjomäki V., Ivaska J. (2011) Competitive binding of Rab21 and p120RasGAP to integrins regulates receptor traffic and migration. J. Cell Biol. 194: 291-306. Matlawska-Wasowska K., Finn R., Mustel A., O’Byrne C.P., Baird A.W., Coffey E.T., Boyd A. (2010) The Vibrio parahaemolyticus Type III Secretion Systems manipulate host cell MAPK for critical steps in pathogenesis. BMC Microbiol. 10: 329. Uusi-Oukari M., Kontturi L.S., Coffey E.T., Kallinen S.A. (2010) AMPAR signaling mediating GABA(A)R delta subunit up-regulation in cultured mouse cerebellar granule cells. Neurochem Int. 57: 136-42. Filén S., Ylikoski E., Tripathi S., West A., Björkman M., Nyström J., Ahlfors H., Coffey E., Rao K.V., 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 C.W., Coffey E.T., Davis R.J., 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: 2241-2250. 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 J.C., Hongisto V., Herdegen T., Courtney M.J., Coffey E.T. (2008) All JNKs can kill, but nuclear localization is critical for neuronal death. Journal of Biological Chemistry 283: 19704-19713. 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: 15151527. 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. 46 47 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: 436443. 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., RunebergRoos 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. 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: 4335-4345. 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. 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. +358-2-333 8000. E-mail: [email protected], Homepage: http://www.btk.fi/?id=109 Biography: Garry Corthals completed his Ph.D. in 1997 at Macquarie University in Sydney; and has since worked in the field of biomedical proteomics oriented mass spectrometry. After completing his post-doctoral studies with Ruedi Aebersold at the Department of Molecular Biotechnology, University of Washington, Seattle, he moved to the Garvan Institute for Medical Research in Sydney where he started a research group and was head of the Proteomics Facility. In 2001 he was recruited to Geneva University Hospital where his research continued to focus on technological aspects of biomedical mass spectrometry and to coordinate and develop the Mass spectrometry facility at Medical Faculty. Now at the Centre for Biotechnology his group focuses on translational aspects of proteomics based mass spectrometry. Additionally he is head of the Turku Proteomics Facility and coordinates the ProtMet.net, the Finnish Proteomics and Metabolomics infrastructure of Biocenter Finland. Further activities include the coordination of several Nordic networks including Nordic Quantitative Proteomics research schools, the Nordic Signals research network and the Nordic MS imaging network. He is chair of the new developments of the EuPA, serves on the HUPO education committee and the ASMS committee. He is also an editor of SciTopics Biochemistry, Genetics and Molecular Biology section. Personnel: Seniors scientists: Anne Rokka, Ph.D., Dorota Muth, Ph.D. Graduate students: Anni Vehmas, Olli Kannaste, Veronika Suni, Hugo de Santos, Darshana Kottahachchi Technical personnel: Arttu Heinonen, Sini Eerola, Emmi Hakanen, Pekka Haapaniemi Undergraduate students: Ahmed BulBul, Thaman Chand, Noora Jaakkola, Firouz Saeidi, Avinash Yadav, T. Santosh Kumar 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 method of choice to discover, measure and characterise 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 48 49 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. Leivonen S.K., Rokka A., Ostling P., Kohonen P., Corthals G.L., Kallioniemi O., Perälä M. (2011) Identification of miR-193b targets in breast cancer cells and systems biological analysis of their functional impact. Mol. Cell Proteomics 10: M110.005322. Rokka A., Aro E.M., Vener A.V. (2011) Thylakoid phosphoproteins: identification of phosphorylation sites. Methods Mol. Biol. 684: 171-186. Kouvonen P., Rainio E.M., Suni V., Koskinen P., Corthals G.L. (2011) Enrichment and sequencing of phosphopeptides on indium tin oxide coated glass slides. Mol. Biosyst. 7: 1828-1837. 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, Bruker Daltonics. Selected Publications: Santos H., Kouvonen P., Capelo J.L., Corthals G.L. (2012) Isotopic labelling of peptides in tissues enhances mass spectrometric profiling. Rapid Commun. Mass Spectrom. 26: 1–9 [in press] Grouneva I., Rokka A., Aro E.M. (2011) The thylakoid membrane proteome of two marine diatoms outlines both diatom-specific and species-specific features of the photosynthetic machinery. J. Proteome Res. 10: 5338-53. Corthals G.L., Dunn M., James P., Gil C., Penque D., Albar J.P., Andrén P., Rabilloud T., Marko-Varga G. (2011) The transition of the European Proteomics Association into the future. J. Proteomics 75: 18-22. Legrain P., Aebersold R., Archakov A., Bairoch A., Bala K., Beretta L., Bergeron J., Borchers C., Corthals G.L. et al. (2011) The human proteome project: Current state and future direction. Mol. Cell Proteomics 10: M111.009993. 50 From left to right: First row: Thaman Chand, Thatikonda Santhosh, Darshana Kottahachchi, Sini Eerola, Susumu Imanishi, Susanne Nees and Anne Rokka Second row: Firouz Saeidi, Arttu Heinonen, Dorota Muth, Garry Corthals, Olli Kannaste, Veronika Suni and Anni Vehmas 51 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 CBT from 1998, he was appointed from 2000 to a position at the A.I. Virtanen Institute, Kuopio and from 2006 to CBT. He has been affiliated with the Cell Imaging Core since its inception, and established and is running 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: Franz Ho Ph.D., Andrea Holme Ph.D., Peter Martinsson Ph.D., Jungah Min Ph.D., Ph.D, Olga Vergun Ph.D.; Graduate students: Lili Li, B.Sc., Xiaonan Liu, M.Sc., Xijun Wang, M.Sc., Laboratory Technician Aila Seppänen; Undergraduate students: Surya Rai, Esther Gascogne 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 stress-activated 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 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 52 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 have recently begun to combine these with targeted RNAi screens. 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 both live cell HighContent Analysis (HCA) and High-Throughput Microscopy (HTM) and also 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). This is a nationally unique Biocentre Finland (BF) infrastructure platform supported by two BF networks. Our group continues to establish assays permitting application of HCA methods to primary cultured neurons and recently, an in vivo model. More details can be found via the links at www.uef.fi/aivi/muic. Funding: The Academy of Finland, thThe EU 6th framework STREP “STRESSPROTECT”, the EU 7 framework project “MEMOLOAD”, The University of Eastern Finland, The Drug Discovery Graduate School, The Informational and Structural Biology Graduate School and The Doctoral Programme in Molecular Medicine. 53 Collaborators: Eleanor Coffey and Tassos Papageorgiou (CBT, Åbo Akademi and University of Turku), Christophe Bonny (University of Lausanne and Xigen Pharma AG), Denise Manahan-Vaughan (University of Bochum), Mark Spaller (Brown University, Providence, RI), Olli Pentikäinen (University of Jyväskylä), Antti Poso (University of Eastern Finland) and Anita Truttman (CHUV, Lausanne University Hospital). Selected Publications: D’Orsi B., Bonner H., Tuffy L.P., Düssmann H., Woods I., Courtney M.J., Ward M.W., Prehn J.H. (2012) Calpains Are Downstream Effectors of bax-Dependent Excitotoxic Apoptosis. J. Neurosci. 32: 1847-1858. 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: 305-313. Yang H., Courtney M.J., Martinsson P. and 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: 16471655. 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: 873-880. 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: 21676-21685. 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 p38a 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. 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-3b is critical for trophic deprivation induced neuronal death. Mol. Cell. Biol. 28: 1515-1527. 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 p38a 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. 54 55 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). 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 protein-ligand 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 b-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, 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. 56 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 aC 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: 452460. 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 “donoracceptor-donor” edges of adenine and adenosine-containing ligands. J. Mol. Biol. 333: 1025-1043. 57 DATA MINING AND MODELLING Principal investigators: Laura Elo, Ph.D., Affiliated Group Leader at CBT, Adjunct Professor in Biomathematics, Department of Mathematics, 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, Department of Mathematics, University of Turku, FI-20014 Turku, and FIMM-EMBL Group Leader, Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Finland. Tel. +358-50-3182426. E-mail: [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 the Biomathematics Research Group at the Department of Mathematics, 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 Academy Research Fellow at FIMM and Department of Mathematics, University of Turku. 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: Bin Gao, M.Sc., Marja Heiskanen, M.Sc., Jukka Hiissa, M.Sc., Ville Koskinen, M.Sc., Rolf Linden, M.Sc., Sebastian Okser, M.Sc., Tomi Suomi, M.Sc., Johannes Tuikkala, M.Sc., Heidi Vähämaa, M.Sc. Undergraduate students: Ville-Pekka Eronen, Aki Järvinen, Essi Laajala, Teemu Daniel Laajala, Harri Santa Description of the project: We develop mathematical modelling methods and implement computational data analysis tools for biological and biomedical 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. The large number of molecular components together with high technical and biological variability can make it difficult to extract pertinent biological information from the background noise. Therefore, computational models and tools are needed that can 58 efficiently integrate, visualise and analyse 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. 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 clinically-oriented 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. and Schwikowski B. (2012) Mining proteomic data for biomedical research. Invited review in WIREs Data Mining Knowl. Discov. 2: 1-13. 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. Lietzén N., Öhman T., Rintahaka J., Julkunen I., Aittokallio T., Matikainen S. and Nyman T.A. (2011) Quantitative subcellular proteome and secretome profiling of influenza A virus-infected human primary macrophages. PLoS Pathog. 7: e1001340. Vähämaa H., Koskinen V.R., Hosia W., Moulder R., Nevalainen O.S., Lahesmaa R., Aittokallio T. and Salmi J. (2011) PolyAlign - A versatile LC-MS data alignment tool for landmark-selected and automated use. Int. J. Proteomics 2011: 450290. Lindén R. O., Eronen V.P. and Aittokallio T. (2011) Quantitative maps of genetic interactions in yeast - Comparative evaluation and integrative analysis, BMC Systems Biology 5: 45. 59 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. Lietzén N., Natri L., Nevalainen O.S., Salmi J. and Nyman T.A. (2010) Compid: a new software tool to integrate and compare MS/ MS based protein identification results from Mascot and Paragon. J. Proteome Res. 9: 6795-800. 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 preclinical carotid atherosclerosis --The Cardiovascular Risk in Young Finns Study, PLoS Genet 6: e1001146. Ahlfors H., Limaye A., Elo L.L., Tuomela S., Burute M., Gottimukkala K.V., Notani D., Rasool O., Galande S. and Lahesmaa R. (2010) SATB1 dictates expression of multiple genes including IL-5 involved in human T helper cell differentiation. Blood 116: 1443-1453. 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. Codrea M.C., Hakala-Yatkin M., Kårlund-Marttila M., Nedbal L., Aittokallio T., Nevalainen O.S. and Tyystjärvi E. (2010) Mahalanobis distance screening of Arabidopsis mutants with chlorophyll fluorescence, Photosynth. Res. 205: 273-283. Talvinen K., Tuikkala J., Nykänen M., Nieminen A., Anttinen J., Nevalainen O.S., Hurme S., Kuopio T. and Kronqvist P. (2010) Altered expression of p120catenin predicts poor outcome in invasive breast cancer. J. Cancer. Res. Clin. Oncol. 136: 13771387. Elo L.L., Mykkänen J., Järvenpää H., Nikula T., Simell S., Aittokallio T., Hyöty H., Ilonen J., Veijola J., Simell T., Knip M., 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: 70-76. From left to right: Olli Nevalainen, Laura Elo, Marja Heiskanen, Sebastian Okser, Tero Aittokallio and Teemu Laajala 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. Piippo M., Lietzén N., Nevalainen O.S., Salmi J. and Nyman T.A. (2010) Pripper: prediction of caspase cleavage sites from whole proteomes. BMC Bioinformatics 11: 320. 60 61 Aittokallio T. (2010) Dealing with missing values in large-scale studies - microarray data imputation and beyond, Invited Review, Brief. Bioinform. 11: 253-264. Korolainen M.A., Nyman T.A., Aittokallio T. and Pirttilä T. (2010) An update on clinical proteomics in Alzheimer’s research, J. Neurochem 112: 1386-1414. 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. Clément-Ziza M., Malabat C., Weber C., Moszer I., Aittokallio T., Letondal C. and Rousseau S. (2009) Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks. Bioinformatics 25: 2617-2618. 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. Merisaari H., Parkkola R., Alhoniemi E., Teräs M., Lehtonen L., Haataja L., Lapinleimu H. and Nevalainen O.S. (2009) Gaussian mixture model-based segmentation of MR images taken from premature infant brains. J. Neurosci. Methods 182: 110-122. 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. Huhtinen K., Suvitie P., Hiissa J., Junnila J., Huvila J., Kujari H., Setälä M., Härkki P., Jalkanen J., Fraser J., Mäkinen J., Auranen A., Poutanen M. and Perheentupa A. (2009) Serum HE4 concentration differentiates malignant ovarian tumours from ovarian endometriotic cysts. Br J Cancer 100: 1315-1319. 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 19901993 (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 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 62 63 From left to right: First row: Josef Gulmets, Claire Hyder, Saima Ferraris, Rajendran Senthil, Tomoko Asaoka and Emilia Peuhu Second row: John Eriksson, John Russell, Kimmo Isoniemi, Erik Niemelä, Ponnuswamy Mohana Sundaram, Elin Torvaldsson, Julia Lindqvist, Helena Saarento and Beata Paziewska 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 differentiationrelated 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). Funding: The Academy of Finland, TEKES, the European Union, the Finnish Cancer Organizations, the Sigrid Jusélius Foundation, and the Åbo Akademi Foundation. 65 Selected Publications: 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 cell-to-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). Inhibition of Akt signaling by the lignan matairesinol sensitizes prostate cancer cells to TRAIL-induced apoptosis. Oncogene 29: 898-908. Imanishi S.Y., Kouvonen P., Smått J.H., Heikkilä M., Peuhu E., Mikhailov A., Ritala M., Lindén M., Corthals G.L. & Eriksson J.E. 66 (2009). Phosphopeptide enrichment with stable spatial coordination on a titanium dioxide coated glass slide. Rapid Commun. Mass Spectrom. 23: 3661-3667. 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: 13801391. 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. Söderström, T.S., Nyberg, S., Nieminen, M.I. and Eriksson, J.E. 67 (2005) CD95 capping is ROCK-dependent and dispensable for apoptosis. J. Cell Sci. 118: 2211-2223. EPIGENOMICS 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. 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/ 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. Personnel: Post-doctoral researchers: Kalyan Kumar Pasumarthy, Ph.D., Cristina Valensisi, Ph.D. 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: 12781291. 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. 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 multi-potency of stem cells. We are also investigating the transcriptional regulation and unique signatures of cellular differentiation. Funding: BioCenter Finland Collaborators: Riitta Lahesmaa, Turku Centre for Biotechnology Harri Lähdesmäki, Tampere University of Technology and 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. Alvarado D.M., Hawkins R.D., Bashiardes S., Veile R.A., Powder K.E., Speck J., Warchol M.E. and Lovett M. (2011) An RNAi-Based Screen of Transcription Factor Gene Pathways During Sensory Regeneration in the Avian Inner Ear. J. Neurosci. 31: 4535-4543. 68 69 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; ^Co-corresponding 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 sequencing-based 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: 476486. Hawkins R.,D†., Hon G.C†., Lee L.K., Ngo Q., Lister R., Pelizzola M., Kuan S., Edsall L.E., Ye Z., Espinoza C., Antosiewicz-Bourget 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. From left to right: Kalyan Pasumarthy, David Hawkins and Cristina Valensisi 70 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-type-specific gene expression. Nature 459: 108-112. 71 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, E-mail: [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 post-doctoral fellow at Cancer Research UK 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. integrin endo/exocytic traffic, a process critical for cell migration. Taken together, we aim to understand adhesion regulated signaling and the biological function of integrin membrane traffic in human malignancies. Selected Publications: 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. Högnäs, G., Tuomi, S., Veltel, S., Mattila, E., Murumägi, A., Edgren, H., Kallioniemi, O. and Ivaska, J. (2011) Cytokinesis failure due to derailed integrin traffic induces aneuploidy and oncogenic transformation in vitro and in vivo. Oncogene. e-pub 2011 Nov 28. Personnel: Post-doctoral researchers: Elina Mattila, Ph.D.; Jeroen Pouwels, Ph.D.; Stefan Veltel, Ph.D.; Ghaffar Muharram, Ph.D., Saara Tuomi, Ph.D., Emilia Peuhu, 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. Laboratory Technicians: Jenni Siivonen and Laura Lahtinen. 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 to gain novel insight into integrin signaling and traffic in cancer cells. Our results demonstrate that integrins can also convey negative regulation on RTKs via a mechanism that is often lost in epithelial carcinomas. Our aim is to extend our studies on identifying integrin binding proteins to understand the diverse and sometimes unexpected biological roles of integrins. In addition to defining cytoplasmic integrin triggered pathways, we are also actively investigating regulation of integrin activity and traffic by cytosolic proteins. Using high-throughput siRNA screening we have recently identified and important novel inhibitor of integrin activity called SHARPIN. In addition, we have extended these siRNA screens to identify previously unknown regulators of 72 From left to right: Antti Arjonen, Jeroen Pouwels, Stefan Veltel, Nicola De Franceschi, Gunilla Högnäs, Johanna Ivaska, Anja Mai, Jenni Siivonen, Laura Lahtinen, Riina Kaukonen, Jonna Alanko and Ghaffar Muharram 73 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. 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. Ivaska J. and Heino J (2011) Cooperation Between Integrins and Growth Factor Receptors in Signaling and Endocytosis. Annu. Rev. Cell Dev. Biol. Annu. Rev. Cell. Dev. Biol. 27: 291-320. Review. Arjonen A, Kaukonen R and Ivaska J. (2011) Filopodia and adhesion in cancer cell motility. Cell Adh Migr. 5:421-430. (Review) 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 a-subunits and suppresses integrin activity and invasion. Oncogene. 29: 6452-6463. Plantard, L. Arjonen, A., Lock, J.G., Nurani, G., Ivaska, J. and Strömblad S. (2010) PtdIns(3,4,5)P3 is a regulator of Myosin-X localization and filopodia formation. J. Cell Sci. 123: 3525-3534. Tuomi, S., Mai, A., Nevo, J., Laine, JO, Vilkki, V., Öhman, TJ., Gahmberg, CG., Parker, PJ. and Ivaska, J. (2009) PKCe 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. 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: 76780. Mattila E., Pellinen, T., Nevo, J., Vuoriluoto, K. Arjonen, A. and Ivaska, J (2005) Negative regulation of EGFR signalling via integrin a1b1-mediated activation of protein tyrosine phosphatase TCPTP. Nat. Cell Biol. 7: 78-85. 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 3338030, 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 he was appointed as a senior fellow of the Academy of Finland. Personnel: Graduate students: Terhi Jokilehto, (M.Sc.), Pekka Heikkinen, (M.Sc.), Heidi Högel, (M.Sc.), Krista Rantanen, (M.Sc.) Laboratory Technician: Taina Kalevo-Mattila Undergraduate students: Maiju Nuutila, Petra Miikkulainen Description of the project: Hypoxia (reduced O tension) is the main tissue damaging factor 2 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 hypoxiainducible 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 at least 80 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. Besides studying several aspects of molecular and cellular biology of the hydroxylases, we study the clinical importance of these factors. Transforming growth factor-b (TGF-b) is one of the best characterised tumour growth regulating factors. It restricts the growth of early stage tumours, but at later stages of tumour progression cancer cells begin to exploit it as a malignancy, invasion and metastasis promoting cytokine. This paradox of TGF-b was originally described in skin cancer models over ten years ago and since then the paradox has been recapitulated in several other cancer models. Our group has recently identified a putative mechanism by which this may occur. We have found that hypoxia is an environmental 74 75 factor in tumours that can convert the TGF-b response into supporting tumorigenesis. Mechanistically, this involves hypoxic dephosphorylation of a TGF-b effector Smad3. Moreover, we have recently discovered that hypoxia converts Smad7, an inhibitor of the TGF-b signaling, from an inhibitor into a promoter of cell invasion. 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. Funding: The Academy of Finland, Sigrid Juselius Foundation, Emil Aaltonen Foundation, Finnish Cancer Unions. Turku University Hospital Pursiheimo, J., Taskén, K., Jalkanen, M. and Jaakkola, P. (2000) Involvement of Protein Kinase A in FGF-2 Activated Transcription. Proc. Natl. Acad. Sci. USA 97: 168–173. Collaborators: Peter Ratcliffe and Chris Pugh (Oxford University, UK), Eric Metzen (Luebeck University, Germany), Reidar Grenman (Turku University), Veli-Matti Kähäri (Turku University), Heikki Minn (PET Centre, Turku University Hospital) 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. (2000) Hypoxia inducible factor-alpha binding and ubiquitylation by the von hippel-lindau tumor suppressor protein. J. Biol. Chem. 275: 25733-25741. Selected Publications: 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: 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: 5984-5993. 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: 3740-9. Jokilehto T., Högel H., Heikkinen, P., Rantanen K., Elenius, K., Sundström J., Jaakkola P.M. (2010). Retention of prolyl hydroxylase PHD2 in the cytoplasm prevents PHD2-induced anchorageindependent carcinoma cell growth. Exp. Cell Res. 316: 1169-1178. Pursiheimo J., Rantanen K., Heikkinen P.T., Johansen T., Jaakkola P.M. (2009). Hypoxia-activated autophagy accelerates degradation of SQSTM1/p62. Oncogene, 28: 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: 2231-2240. 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: 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: 761-767. 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. (2001) Targeting of HIF-alpha to the von Hippel-Lindau ubiquitylation complex by O2regulated prolyl hydroxylation. Science 292; 468-472. 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., From left to right: Heidi Högel and Krista Rantanen 76 77 BIOENERGY Principal Investigator: Patrik R. Jones, Ph.D., Affiliated Group Leader at CBT, University of Turku, Centre for Biotechnology, Turku BioCity, Tykistökatu 6B, 4krs, 20520, Turku. Tel.:+358-2-333-7913. E-mail: [email protected] Home page: http://www.btk.fi/research/affiliated-groups/jonespatrik-bioenergy-group/ Biography: Patrik Jones (b. 1968) completed his undergraduate degree in Agricultural Sciences (Oenology, Honours) at the University of Adelaide and obtained his Ph.D. (2001) from the University of Adelaide, Australia, and the Royal Veterinary and Agricultural University of Copenhagen, Denmark, on the topic of plant natural product metabolism. Before commencing his current position in Turku in 2008, he held a position as JSPS-funded post-doctoral fellow (2001-2002, plant natural product metabolism) at Chiba University, Japan; Research Chemist (2003-2004, wine chemistry and sensory perception) at the Australian Wine Research Institute in Adelaide, Australia; Research Director (2005-2008, microbial metabolic engineering and renewable fuel production) at Fujirebio Inc. (100% for-profit), Tokyo, Japan. Personnel: Undergraduate students: Danilo Corredu, Artur Tallihärm, Hariharan Dapandani, Melak Weldengodguad Graduate students: Sanna Peltonen, Linda Vuorijoki, Jari Kämäräinen, Veronica Carbonell, Andras Pasztor, Francy El Souki Researchers: Fernando Guerrero, M. Kalim Akhtar Coordinator: Yumi Otani Description of the project: We target the interface between fundamental and applied sciences by studying fundamental questions of applied importance. In most cases, we wish to answer or obtain insight about outstanding questions and issues which are important for current and theoretical biological energy conversion processes. The laboratory currently has two main lines of research: (1) Fermentative and photobiological H2-production. Topics include H2-pathway engineering, iron sulfur cluster metabolism and NADP(H)-homeostasis. The subjects are studied with a combination of computational and experimental methodologies, with a focus on key reactions and/or the entire metabolism of the cell (systems biology). (2) Synthesis of hydrocarbon transport fuels. We engineer a tiny fraction of the metabolism of model hosts in order to (a) introduce biofuel-pathways that do not exist in nature and (b) modify host metabolism to favor those pathways. The engineering is aided by computational flux balance analysis and development of engineering tools. Funding: European Research Council, EU FP7, Tekes, Academy of Finland, Nordic Energy Research Selected publications: Akhtar, M.K. and Jones, P.R. (2009) Construction of a synthetic YdbK-dependent pyruvate:H2 pathway in Escherichia coli BL21(DE3). Metabolic Engineering 11: 139-147. Veit, A., Akhtar, K.M., Mizutani, T., Jones P.R. (2008) Constructing and testing the thermodynamic limits of synthetic NAD(P)H:H2 Pathways. Microbial Biotechnology 1: 382-394. Akhtar, K.M., and Jones P.R. (2008) Deletion of iscR stimulates recombinant clostridial Fe-Fe hydrogenase activity and H2 accumulation in Escherichia coli BL21(DE3). Applied Microbiology and Biotechnology 78: 853-862. From left to right, first row: Patrik Jones, Fernando Guerrero, Danilo Correddu, second row: Linda Vuorijoki, Francy El Souki, Eva Fredriksson-Lidsele, Sanna Peltonen, Veronica Carbonell, Hariharan Dapandani, Melak Weldenegodguad, András Pásztor, Jari Kämäräinen 78 79 MITOSIS AND DRUG DISCOVERY RESEARCH Principal Investigator: Marko Kallio, Ph.D. Docent, Affiliated group leader at CBT, Principal Scientist and Team Leader, 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 with an honorary mention. In 1996-1998 Dr. Kallio was in the laboratory of Prof. Gary Gorbsky (Univ. Virginia, USA) as a Post-doctoral Fellow and in 1998-2000 in the laboratories of Prof. John Eriksson and Prof. Lea Sistonen (Univ. Turku, Finland) as a Senior Post-doctoral Fellow. In 2000-2003 Dr. Kallio worked as an Assistant Research Professor at University of Oklahoma HSC, USA. His research group received Marie Curie Excellence grant for 2004-2008. In early 2004, Dr. Kallio moved back to Finland and has since been a group leader at VTT Biotechnology for Health and Wellbeing, a research institute affiliated with the University of Turku. Personnel: Post-doctoral researchers: Anu Kukkonen-Macchi, Ph.D., 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. Undergraduate students: Adel Asghar Laboratory Technician: Pauliina Toivonen Alumni: Tim Holmström, Kimmo Jaakkola, M.D., Ph.D., Jeroen Pouwels, Ph.D., Oana Sicora, Ph.D., Christina Oetken-Lindholm, Ph.D., Asta Varis, Ph.D., Chang-Dong Zhang, Ph.D. Description of the projects: The Mitosis and Drug Discovery Team investigates mechanisms of cell division in somatic cells and in meiotic systems. Understanding cell division errors may help to explain origin of genomic instability and is expected to identify novel therapeutic possibilities for treatment of cancer. We are especially interested of conditions that suppress cancer cells’ viability as a consequence of premature inactivation of the spindle assembly checkpoint (SAC), a conserved signalling pathway monitoring fidelity of mitosis. To this end, we have performed a number of high-throughput screens (HTS) for anti-mitotic small molecules, siRNAs, and miRNAs. These activities have led to the identification of (i) novel pharmacophores targeting key mitotic proteins such as Hec1, Aurora B and Plk1, (ii) new mitotic gene functions and (iii) mitosis regulating miRNAs. Finally, we are investigating the mechanisms of acquired resistance to microtubule (mt)-drugs, a growing clinical problem in the treatment of cancer. Resistance to mt-drugs has links to malfunction of tubulin and mitotic checkpoint proteins but these mechanisms are poorly understood. 80 Errors during cell division may result in unequal distribution of DNA between the daughter cells. Gain or loss in the number of chromosomes of the genome is a known cause for miscarriages and birth defects in human, and a hallmark of cancer. Mitotic processes are also clinically relevant drug targets in cancer treatment as demonstrated by the great anti-cancer efficacy of microtubuletargeting drugs. In our main projects, we are working to validate the mechanism of action of putative anti-Hec1 compounds and several SAC targeting miRNAs that perturb normal mitosis and trigger cancer cell killing in cell culture assays. Moreover, we are characterizing the phenotypes of a handful of new mitosis targeting siRNAs that we have recently discovered. In our work we use various cell-based and biochemical assays in vitro as well as VTT biochip technologies. The results from these activities are expected to catalyze cancer drug discovery by identification of new possibilities for inhibition of Hec1, and SAC in general. Funding: VTT Technical Research Centre of Finland, The Academy of Finland, TuBS and DDGS Graduate Schools, Bayer HealthCare AG Collaborators: Gary Gorbsky (OMRF, Oklahoma USA), Todd Stukenberg (Univ. Virginia, USA), Olli Kallioniemi (FIMM). Lauri Aaltonen (Biomedicum Helsinki), Lea Sistonen (Turku Centre for Biotechnology). Selected Publications: Kukkonen-Macchi A., Sicora O., Kaczynska K., Oetken-Lindholm C., Pouwels J., Laine L., and Kallio M.J. (2011) Loss of p38gamma MAPK induces pleiotropic mitotic defects and massive cell death. J. Cell Sci., 124: 216-227. Niittymäki I., Gylfe A., Laine L., Laakso M., Lehtonen H.J., Kondelin J., Tolvanen J., Nousiainen K., Pouwels J., Järvinen H., Nuorva K., Mecklin J.P., Mäkinen M., Ristimäki A., Ørntoft T.F., Hautaniemi S., Karhu A., Kallio M.J., Aaltonen L.A. (2011) High frequency of TTK mutations in microsatellite-unstable colorectal cancer and evaluation of their effect on spindle assembly checkpoint. Carcinogenesis 32: 305-311. Vuoriluoto M., Laine L.J., Saviranta P., Pouwels J., Kallio M.J. (2011) Spatio-temporal composition of the mitotic Chromosomal Passenger Complex detected using in situ proximity ligation assay. Mol. Oncol. 5: 105-111. Salmela A.L., Pouwels J., Varis A., Kukkonen A.M., Toivonen P., Halonen P.K., Perälä M., Kallioniemi O., Gorbsky G.J., and Kallio M.J. (2009) Dietary flavonoid fisetin induces a forced exit from mitosis by targeting the mitotic spindle checkpoint. Carcinogenesis 30: 1032-1040. Pellinen T., Tuomi S., Arjonen A., Wolf M., Edgren H., Meyer H., Grosse R., Kilzing T., Rantala J.K., Kallioniemi O., Fässler R., Kallio M., and lvaska J. (2008). Integrin trafficking regulated by Rab21 is necessary for cytokinesis. Dev. Cell 15: 371-385. Pouwels J., Kukkonen A.M., Lan W., Daum J.R., Gorbsky G.J., Stukenberg T. and Kallio M.J. (2007) Shugoshin 1 plays a central role in kinetochore assembly and is required for kinetochore targeting of Plk1. Cell Cycle 6: 1579-1585. 81 Wang V.Y., Parvinen M., Toppari J., and Kallio M.J. (2006) Inhibition of Aurora kinases perturbs chromosome alignment and spindle checkpoint signaling in rat spermatocytes. Exp. CelI Res. 312: 3459-3470. Ahonen L.J., Kallio M.J., Daum J.R., Bolton M., Manke I.A., Yaffe M.B., Stukenberg P.T. and Gorbsky G.J. (2005) Polo-like kinase 1 creates the tension-sensing 3F3/2 phosphoepitope and modulates the association of spindle-checkpoint proteins at kinetochores. Curr Biol. 15: 1078-1089. McCleland M.L., Kallio M.J., Barrett-Wilt G.A., Kestner C.A., Shabanowitz J., Hunt D.F., Gorbsky G.J. and Stukenberg P.T. (2004) The vertebrate Ndc80 complex contains functional homologs of Spc24 and Spc25 and is required to establish and maintain kinetochore-microtubule attachment. Curr Biol. 14: 131-137. McCleland M.L., Gardner R.D., Kallio M.J., Daum J.R., Gorbsky G.J., Burke D.J. and Stukenberg P.T. (2003) The highly conserved Ndc80 complex is required for kinetochore assembly, chromosome congression, and spindle checkpoint activity. Genes. Dev. 17: 101-114. CANCEROMICS RESEARCH PROGRAMME Principal Investigator: Olli Kallioniemi, M.D., Ph.D., Director, Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, 00140 University of Helsinki, Finland. Director of the Academy of Finland Centre of Excellence on Translational Genome-scale Biology (2006-2011), Medical Biotechnology, VTT Technical Research Centre of Finland and University of Turku. Laboratory address: Medical Biotechnology, PharmaCity, Itäinen Pitkäkatu 4C, FI-20521 Turku, Finland. Tel. +358-20-722 2800. Fax +358-20-722 2840. E-mail: [email protected]. Biography: Dr. Olli Kallioniemi received his M.D. in 1984 and Ph.D. in 1988 at the University of Tampere in Finland. Olli Kallioniemi held several positions in the US over a 10-year period, such as Head of Translational Genomics Section at the Cancer Genetics Branch, National Human Genome Research Institute, at the NIH, Bethesda, Maryland during 1995-2002. In 2003, he was appointed as Professor of Medical Biotechnology at the VTT Technical Research Centre of Finland with a joint appointment at the University of Turku. Academy of Finland Professor in 2004-2007. In 2007, he was nominated as a director of the Institute for Molecular Medicine Finland (FIMM), a Nordic EMBL Partnership in Molecular Medicine. He continues to direct the ongoing projects in Turku until the end of 2011. He is an author of 263 publications and editor or member of the editorial board of six journals. Inventor of 18 issued patents, with a focus on technology development, such as Comparative Genomic Hybridization (CGH) in 1992, tissue microarrays in 1998 and cell-based RNAi microarrays in 2003. EACR young investigator award in 1994, Anders Jahre Prize in 1998, NIH Director’s lecture in 2000, Medal of the Swedish Medical Society in 2003, National Academy of Sciences (Finland) in 2005, EMBO Membership in 2006, and the Abbot-IFCC award in Molecular Diagnostics 2009. Personnel: Ph.D-students and postdocs at the University of Turku: Anna Aakula, M.Sc., Santosh Gupta, M.Sc., Kirsi Ketola, M.Sc., Pekka Kohonen, Ph.D. Paula Vainio, M.D., Sirkku Pollari, M.Sc., Laboratory Technician: Pirjo Käpylä, Coordinator: Terhi Jokilehto, M.Sc. From left to right: Pauliina Toivonen, Jenni Mäki-Jouppila, Leena Laine, Adel Ashgar, Anna-Leena Salmela, Elli Narvi, Mahesh Tambe, Lila Kallio and Sebastian Winsel. Standing: Marko Kallio Description of the Project: The overall purpose of this research program is to develop and apply high-throughput technologies to understand mechanisms of progression of breast and prostate cancers as well as to identify mechanisms of drug response. We use systems biology and chemical biology approaches to characterize the deregulation of cancer cell functions. The research is carried out in collaboration between the Institute for Molecular Medicine Finland (FIMM), the Medical Biotechnology Centre of the VTT Technical Research Centre of Finland and the Turku Centre for Biotechnology. Our group coordinates Academy of Finland Centre of Excellence in Translational Genome-Scale Cell Biology. We have developed and are applying biochip technologies, next- 82 83 generation RNA sequencing, bioinformatics, systems biology, drug development technologies, cell microarrays, protein lysate microarrays, in silico profiling of gene expression in clinical samples and many others. Collaborators: Tomi Mäkelä, Lauri Aaltonen, Jussi Taipale, Päivi Ojala, Sampsa Hautaniemi, Heli Nevanlionna, Heikki Joensuu, Kari Alitalo, Jonathan Knowles, Emmy Verschuren, Sergey Kuznetshov, Samuli Ripatti, Krister Wennerberg (FIMM and Biomedicum Helsinki), Antti Poso, Samuel Kaski, Tapio Visakorpi, Jukka Westermarck and many others in other Universities in Finland. We have over 100 partners in EU-FP7 collaborative projects such as Epitron, Genica, APO-SYS, Prosper, Meta-Cancer and Systems Microscopy. Funding: The Academy of Finland, Tekes, Finnish Cancer Organizations and Sigrid Juselius Foundation. Our biggest source of funding comes from the EU framework projects. Selected recent publications: Mpindi J.P., Sara H., Haapa-Paananen S., Kilpinen S., Pisto T., Bucher E., Ojala K., Iljin K., Vainio P., Björkman M., Gupta S., Kohonen P., Nees M. and Kallioniemi O. (2011) GTI: A Novel Algorithm for Identifying Outlier Gene Expression Profiles from Integrated Microarray Datasets. PLoS One 16: e17259. Hanash S.M., Baik C.S. and Kallioniemi O. (2011) Emerging molecular biomarkers-blood-based strategies to detect and monitor cancer. Nat. Rev. Clin. Oncol. 8: 142-150. Ostling P., Leivonen S.K., Aakula A., Kohonen P., Mäkelä R., Hagman Z., Edsjö A., Kangaspeska S., Edgren H., Nicorici D., Bjartell A., Ceder Y., Perälä M. and Kallioniemi O. (2011) Systematic Analysis of MicroRNAs Targeting the Androgen Receptor in Prostate Cancer Cells. Cancer Res. 71: 1956-1967. Vainio P., Gupta S., Ketola K., Mirtti T., Mpindi J.P., Kohonen P., Fey V., Perälä M., Smit F., Verhaegh G., Schalken J., Alanen K.A., Kallioniemi O. and Iljin K. (2011) Arachidonic acid pathway members PLA2G7, HPGD, EPHX2, and CYP4F8 identified as putative novel therapeutic targets in prostate cancer. Am. J. Pathol. 178: 525-536. Edgren H., Murumagi A., Kangaspeska S., Nicorici D., Hongisto V., Kleivi K., Rye I.H., Nyberg S., Wolf M., Borresen-Dale A.L. and Kallioniemi O (2011) Identification of fusion genes in breast cancer by paired-end RNA-sequencing. Genome Biol.12: R6. Kilpinen S., Ojala K., Kallioniemi O. (2010) Analysis of kinase gene expression patterns across 5681 human tissue samples reveals functional genomic taxonomy of the kinome. PLoS One. 5: e15068. Rantala J.K., Edgren H., Lehtinen L., Wolf M., Kleivi K., Vollan H.K., Aaltola A.R., Laasola P., Kilpinen S., Saviranta P., Iljin K. and Kallioniemi O. (2010) Integrative functional genomics analysis of sustained polyploidy phenotypes in breast cancer cells identifies an oncogenic profile for GINS2. Neoplasia 12: 877-888. From left to right, first row: Paula Vainio, Mari Björkman, Riina Plosila, Pekka Kohonen, Back row: Kirsi Ketola, Anna Aakula, Santosh Gupta, Olli Kallioniemi, Sirkku Pollari, Elmar Bucher. 84 Gupta S., Iljin K., Sara H., Mpindi J.P., Mirtti T., Vainio P., Rantala J., Alanen K., Nees M. and Kallioniemi O. (2010) FZD4 as a mediator 85 of ERG oncogene-induced WNT signaling and epithelial-tomesenchymal transition in human prostate cancer cells. Cancer Res. 70: 6735-45. Härmä V., Virtanen J., Mäkelä R., Happonen A., Mpindi J.P., Knuuttila M., Kohonen P., Lötjönen J., Kallioniemi O. and Nees M. (2010) A comprehensive panel of three-dimensional models for studies of prostate cancer growth, invasion and drug responses. PLoS One 5: e10431. International Cancer Genome Consortium, Hudson T.J.,et al. (2010) International network of cancer genome projects. Nature 464: 993-998. Pollari S., Käkönen S.M., Edgren H., Wolf M., Kohonen P., Sara H., Guise T., Nees M. and Kallioniemi O. (2011) Enhanced serine production by bone metastatic breast cancer cells stimulates osteoclastogenesis. Breast Cancer Res. Treat.125: 421-430. Leivonen S.K., Mäkelä R., Ostling P., Kohonen P., Haapa-Paananen S., Kleivi K., Enerly E., Aakula A., Hellström K., Sahlberg N., Kristensen V.N., Børresen-Dale A.L., Saviranta P., Perälä M. and Kallioniemi O. (2009) Protein lysate microarray analysis to identify microRNAs regulating estrogen receptor signaling in breast cancer cell lines. Oncogene, 28: 3926-3936. Iljin K., Ketola K., Vainio P., Halonen P., Kohonen P., Fey V., Grafström R.C., Perälä M. and Kallioniemi O. (2009) Highthroughput cell-based screening of 4910 known drugs and drug-like small molecules identifies disulfiram as an inhibitor of prostate cancer cell growth. Clin. Cancer Res., 15: 6070-6078. Varjosalo M., Björklund M., Cheng F., Syvänen H., Kivioja T., Kilpinen S., Sun Z., Kallioniemi O., Stunnenberg H.G., He, W-W., Ojala P. and Taipale J. (2008) Application of Active and Kinase-Deficient Kinome Collection for Identification of Kinases Regulating Hedgehog Signaling. Cell 133: 537-548. Pellinen T., Tuomi S., Arjonen A., Wolf M., Edgren H., Meyer H., Rantala J.K., Kallioniemi O., Fässler R., Kallio M. and Ivaska J. (2008) Integrin traffic regulated by Rab21 is necessary for cytokinesis. Dev. Cell., 15: 371-385. Kilpinen S., Autio R., Ojala K., Iljin K., Bucher E., Sara H., Pisto T., Saarela M., Skotheim R., Björkman M., Mpindi J. P., HaapaPaananen S., Vainio P., Edgren H., Wolf M., Astola J., Nees M., Hautaniemi S. annd Kallioniemi O. (2008) Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues. Genome Biol., 9: R139. 86 SIGNALING PATHWAYS REGULATED BY ONCOGENIC PIM KINASES Principal Investigator: Päivi J. Koskinen, Ph.D., Senior Assistant, Adjunct Professor in Molecular and Cell Biology. Current laboratory address: Section of Genetics and Physiology, Department of Biology, University of Turku, FIN-20014 University of Turku, Finland. Tel. + 358-2-3335936, Fax + 358-2-3336598. E-mail: [email protected] Biography: Päivi Koskinen (b. 1961) received her Ph.D. at the University of Helsinki in 1992. During years 1993-1996 she worked as a postdoctoral fellow in Dr. Robert Eisenman´s laboratory at the Fred Hutchinson Cancer Research Center in Seattle, USA. In 1996 she joined the Turku Centre for Biotechnology as a group leader and a research fellow of the Academy of Finland. Since 2006 she has been employed by the Department of Biology, University of Turku, where her group also moved during autumn 2011. Personnel: Co-supervisor: Eeva Rainio, Ph.D. Graduate students: Jouko Sandholm, M.Sc., Riitta Vahakoski, M.Sc., Niina Santio, M.Sc. Undergraduate students: Heidi Ekman, Juho Virtanen, Sini Eerola. Description of the Project: The studies of our research group focus on the signaling pathways regulated by the oncogenic Pim family of serine/threoninespecific protein kinases. We have shown that the three highly homologous members of this family are expressed in partially overlapping patterns, mainly in cells of the immune or the nervous system. In hematopoietic cells, pim expression can be induced by multiple cytokines and also by some hormones, suggesting a role for Pim kinases in signal transduction initiated by cytokine or hormone receptors. When overexpressed in lymphoid tissues of transgenic mice, pim genes promote lymphomagenesis, especially in cooperation with other oncogenes that either enhance cell proliferation (myc) or cell survival (bcl-2). We and others have observed that in human cancer patients, elevated levels of pim-1 mRNA and protein can be found in leukemias, lymphomas and solid tumors such as prostate cancer. Recently we have noticed that pim-1 overexpression also promotes radioresistance in patients suffering from squamocellular head and neck carcinomas. We have previously shown that Pim-1 stimulates activities of several cellular or viral transcription factors such as Myb, NFATc, EBNA2 as well as RUNX family members. More recently also LANA, the latency-associated nuclear antigen of Kaposi sarcoma-associated herpesvirus has been identified as a direct Pim substrate. We have also analysed expression of pim family genes during cytokine- dependent T helper cell differentiation. Furthermore, we have shown that Pim kinases promote cytokine-independent survival and inhibit apoptosis by several mechanisms, including upregulated expression of the anti-apoptotic Bcl-2 protein and phosphorylationinduced inactivation of the pro-apoptotic Bad protein. Altogether, our studies based on domestic or international collaborations have had a major impact to the understanding of Pim kinase activities in both normal and transformed cells and have explained why Pim 87 kinases can so efficiently co-operate with Myc family transcription factors in murine, and most likely also in human tumorigenesis. Even though Myc-overexpressing cells proliferate faster, they are more prone to apoptosis, so it is advantageous for them to cooverexpress also Pim kinases, which regulate the balance between anti- and proapoptotic factors and boost activities of transcription factors that are essential for production of cytokines and other survival factors. To further characterize the signaling pathways downstream of Pim kinases, we have used phosphoproteomics to reveal novel substrates for Pim kinases. These proteins have recently been confirmed as true Pim substrates and their functional validation is underway using both overexpression and RNA interferencebased approaches. Since we aim to identify the relevant phosphorylation target sites in the novel Pim substrates, we have participated in developing sensitivity of the methodology to identify phosphopeptides. In addition, we have been collaborating with three groups of chemists to identify and validate Pim-specific small molecule inhibitors, which appear to be great tools for our research, but may also have therapeutic value. Using these inhibitors, we have recently revealed a novel role for Pim kinases in stimulation of cancer cell migration and invasion. Funding: The Academy of Finland, TEKES, The Drug Discovery Graduate School. Key Collaborators: Jari Yli-Kauhaluoma (Viikki Biocenter, Helsinki), Pascale Moreau (CNRS, France), Asko Uri (University of Tartu, Estonia), Margarita Glazova (Sechenov Institute, St. Petersburg, Russia), Michael Nonet (Washington University, MO, USA), Päivi Ojala (Biomedicum Helsinki), Garry Corthals (CBT), Eleanor Coffey (CBT), Pirkko Härkönen (UTU), Sirpa Jalkanen (UTU). Selected Publications: Letribot, B., Akué-Gédu, R., Santio, N.M., El-Ghozzi, M., Avignant, D., Cisnetti, F., Koskinen, P.J., Gautier, A., Anizon, F. and Moreau, P. (2012) Use of Copper(I) Catalyzed Azide Alkyne Cycloaddition (CuAAC) for the preparation of conjugated pyrrolo[2,3-a]carbazole Pim kinase inhibitors. Eur. J. Med. Chem., in press. Sarek, G., Ma, L., Enbäck, J., Järviluoma, A., Haas, J. Gessain, A., Koskinen, P.J., Laakkonen, P. and Ojala, P.M. (2012) Kaposi’s sarcoma herpesvirus lytic replication compromises apoptotic response to p53 reactivation in virus-induced lymphomas. Oncogene, in press. Kouvonen, P., Rainio, E.M., Suni, V., Koskinen, P. and Corthals, G. (2011) Enrichment and sequencing of phosphopeptides using indium tin oxide coated glass slides. Mol. BioSyst. 7: 1828-1837. Santio, N.M., Vahakoski, R.L., Rainio, E.M., Sandholm, J.A., Virtanen, S.S., Prudhomme, M., Anizon, F., Moreau, P. and Koskinen, P.J. (2010) Pim-selective inhibitor DHPCC-9 reveals Pim kinases as potent stimulators of cancer cell migration and invasion. Mol. Cancer 19: 279. Kouvonen, P., Rainio, E.M., Suni, V., Koskinen, P. and Corthals, G.L. (2010) Data combination from multiple matrix-assisted 88 laser desorption/ionization (MALDI) matrices: opportunities and limitations for MALDI analysis. Rapid Commun. Mass Spectrom. 15: 3493-3495. Peltola, K.J., Hollmén, M., Maula, S.M., Rainio, E.M., Ristamäki, R., Luukkaa, M., Sandholm, J., Sundvall, M., Elenius, K., Koskinen, P.J., Grenman, R. and Jalkanen, S. (2009) Pim-1 kinase expression predicts radiation response in squamocellular carcinoma of head and neck and is under the control of epidermal growth factor receptor. Neoplasia 11: 629-636. Cheng, F., Weidner-Glunde, M., Varjosalo, M., Rainio, E.M., Lehtonen, A., Schulz, T.F., Koskinen, P.J., Taipale, J. and Ojala, P.M. (2009) KSHV reactivation from latency requires Pim-1 and Pim-3 kinases to inactivate the latency-associated nuclear antigen LANA. PLoS Pathogens, 5: e1000324. Aho, T.L.T., Peltola, K.J. and Koskinen, P.J. (2006) Pim-1 kinase phosphorylates RUNX family transcription factors and enhances their activity. BMC Cell Biol. 7: 1-9. Aho, T.L.T., Lund, R., Ylikoski, E., Matikainen, S., Lahesmaa, R. and Koskinen, P.J. (2005) Expression of human pim family genes is selectively upregulated by cytokines promoting Th1, but not Th2 cell differentiation. Immunol. 116: 82-88. Glazova, M., Aho, T.L.T., Palmetshofer, A., Murashov, A., Scheinin, M. and Koskinen, P.J. (2005). Pim-1 kinase enhances NFATc activity and neuroendocrine functions in PC12 cells. Mol. Brain Res. 138: 116-123. Rainio, E.M., Ahlfors, H., Carter, K., Ruuska, M., Matikainen, S., Kieff, E. and Koskinen, P.J. (2005) Pim kinases are upregulated by Epstein-Barr virus infection and enhance EBNA2 activity. Virol. 333: 201-206. Peltola, K.J., Paukku, K., Aho, T.L.T., Ruuska, M., Silvennoinen, O. and Koskinen, P.J. (2004). Pim-1 kinase inhibits Stat5-dependent transcription via its interactions with SOCS1 and SOCS3. Blood 103: 3744-3750. Aho, T.L.T., Sandholm, J., Peltola, K.J., Mankonen, H.P., Lilly, M. and Koskinen, P.J. (2004) Pim-1 kinase promotes inactivation 112 of the pro-apoptotic Bad protein by phosphorylating it on the Ser gatekeeper site. FEBS Lett. 571: 43-49. Yan, B., Zemskova, M., Kraft, A., Koskinen, P.J. and Lilly, M. (2003). The Pim-2 kinase phosphorylates Bad on serine-112 and reverses Bad-induced cell death. J. Biol. Chem. 278: 45358-45367. Rainio, E.M., Sandholm, J. and Koskinen, P.J. (2002). Transcriptional activity of NFATc1 is enhanced by the Pim-1 kinase. J. Immunol.168: 1524-1527. Eichmann, A., Yuan, L., Bréant, C., Alitalo, K. and Koskinen, P.J. (2000). Developmental expression of Pim kinases suggests functions also outside of the hematopoietic system. Oncogene 19: 1215-1224. 89 MOLECULAR IMMUNOLOGY AND SYSTEMS BIOLOGY OF CELL DIFFERENTIATION cell signaling, and transcriptional and epigenetic programs that determine cell differentiation and fate. We want to understand molecular mechanisms of human immune mediated diseases and certain types of cancer to enable development of novel therapeutic approaches to help patients suffering from these conditions. Principal 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] Home page: www.btk.fi 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. We were the first to identify STAT6 target genes on a genome wide scale in human CD4+ T cells - only a small fraction of which were previously known to be STAT-6 regulated. This study, published in Immunity, revealed that in human a surprisingly high proportion, up to 80%, of IL-4 induced response is STAT6 regulated. We identified several new candidates for therapeutic intevention (Elo L et al. 2010, O’Shea et a.. 2011). Our studies on IL-4 R signaling in lymphocytes resulted in identification of new IL4R/STAT-6 regulated proteins and their molecular functions in human and mice (Aflakian N, et al. 2009, Moulder R. et al. 2010, Tripathi et al. 2011, Tuomela S. et al. 2009, Cho CH et al. 2009). 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). We further discovered that ATF3 and SATB1 are important regulators of human Th cell differentiation. ATF3 promotes Th1 differentiation (Filen S et al. 2010) whereas SATB1 regulates multiple genes during early Th cell differentiation (Ahlfors et al. 2010). 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 Turku Centre for Systems Biology since 2000. Personnel: Senior scientists/ Post-doctoral researchers: Kanchan Bala, Jane Zhi Chen, Ph.D., Sanna Edelman, Ph.D., Laura Elo-Uhlgren, Ph.D.., Riikka Lund, Ph.D., Robert Moulder, Ph.D., Juha-Pekka Pursiheimo, Ph.D., Omid Rasool, Ph.D., Emaheswa Reddy, Ph.D., Jussi Salmi, Ph.D., Johanna Tahvanainen, Ph.D., Viveka Öling, Ph.D. Visiting Scientists: 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., Juha Korhonen, M.D., 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. Laboratory Technicians: Bogata Fezazi, Marjo Hakkarainen, Sarita Heinonen, Päivi Junni, Elina Pietilä Undergraduate students: Krista Maurinen, Johanna Myllyviita, Lotta Oikari, Anna Rajavuori Description of the project: Our research group is part of the “Centre of Excellence on Molecular Systems Immunology and Physiology” Academy of Finland nominated 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 and systems biology to identify and study molecular mechanisms of 90 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. Our recent results based on the use of high resolution microarray technology demonstrate the necessity of monitoring 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 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. The results suggest that whole genome analysis should be included as quality control of iPS cell lines to verify that the cells remain genetically normal after the reprogramming process, before use for studies and/or clinical applications. (Hussein S, et al. 2011). 91 From left to right: Bogata Fezazi, Alexey Sarapulov, Tapio Lönnberg, Khan Mohd Moin, Emani Maheswara Reddy, Robert Moulder, Kanduri Kartiek, Essi Laajala, Chen Zhi Jane, Sarita Heinonen, Juha-Pekka Pursiheimo, Iida Koho, Sanna Edelman, Terhi Jokilehto, Riitta Lahesmaa, Omid Rasool, Verna Salo, Marjo Hakkarainen, Henna Kallionpää, Minna Kyläniemi, Mirkka Heinonen, Lotta Oikari, Nelly Rahkonen, Johanna Myllyviita, Subhash Tripathi, Riikka Lund, Elisa Närvä and Elina Pietilä 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. 2011). 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 b cell specific autoantibodies. Clinical T1D occurs when 80-90% of the b cells have been destroyed. Today, a T1D patient is dependent on 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 significant health benefits. We are studying molecular mechanisms of T1D to discover molecular markers that would 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 showed systematic differential expression of 520 probesets. A network-based analysis revealed 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 transcriptomics, proteomics and integrating the data with our previous metabolomics data (Oresic et al. 2008). Funding: The Academy of Finland, The National Technology Agency of Finland (TEKES), EU 6th framework “ESTOOLS”, 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), Sanjeev Galande (IISER, Pune, India), Heikki Hyöty (U. Tampere), Mikael Knip (U. Helsinki), Harri Lähdesmäki (Aalto University), David Goodlett (University of Washington, Seattle, WA, USA and a FiDiPro in CBT) , Matej Oresic (VTT Technical Research Centre of Finland, Turku), 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) 92 93 Selected Publications: Aflakian N., Ravichandran S., Sarwar Jamaal Md. S., Jarvenpää H., Lahesmaa R., Rao K.V.S. (2009) Integration of signals from the B-cell antigen receptor and the IL-4 receptor leads to a cooperative shift in the cellular response axis. Mol. Biosyst. 5: 1661-1671. 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. Cho S.H., 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 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.*, 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 L.L.*, 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 J.J., Filén S., Moulder R., Tuomela S., Ahlfors H., West A., Kouvonen P., Kantola S., Björkman M., Katajamaa M., Rasool O., Nyman T.A., 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 K.V.S., 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 K.P., Yabuuchi A., Rao S., Huang Y., Cunniff K., Nardone J., Laiho A., Tahiliani M., Sommer C.A., Mostoslavsky G., Lahesmaa R., Orkin S.H., Rodig S.J., Daley G.Q., Rao A. (2011) Tet1 and tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells. Cell Stem Cell 8: 200-213. 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. Rasool O., Lahesmaa R. (2007) Genome wide identification of Novel Genes Involved in Early Th1 and Th2 Cell Differentiation . J. Immunol. 178: 3648-3660. Moulder R.*, Lönnberg T.*, Filén J-J., Elo L., Rainio E., Corthals G., Oresic M., Nyman T.A., Aittokallio T., Lahesmaa R. (*equal contribution) (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. 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 H.D., Benvenisty N., Andrews P.W., 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 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: 452460. 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. 205: 2975-84. O’Shea J.J., Lahesmaa R., Vahedi G., Laurence A., Kanno Y. (2011) Genomic views of STAT function in CD4(+) T helper cell differentiation. Nat. Rev. Immunol. 11: 239-50. Rautajoki, K., Marttila, E., Nyman, T., Lahesmaa, R. (2007) Interleukin-4 inhibits caspase-3 by regulating several proteins in the Fas pathway during initial stages of human T helper 2 cell differentiation. Mol. Cell Proteomics 6: 238-251. Tahvanainen J., Kallonen T., Lähteenmäki H., Heiskanen K.M., Westermarck J., Rao K.V., Lahesmaa R. (2009) PRELI is a mitochondrial regulator of human primary T helper cell apoptosis, STAT6 and Th2 cell differentiation. Blood 113: 1268-77. Tripathi P.*, Sahoo N.*, Ullah U.*, Järvenpää H., Suneja A., Lahesmaa R., Rao K.V.S. (2011) MAP kinase initiates digital regimes of signal sensing to control specificity and amplitude of human Th2 cell differentiation. Immunol. Cell Biol. doi: 10.1038/ icb.2011.87. [Epub ahead of print] *Equal contribution. Tuomela S., Rautajoki K.J., Moulder R., Nyman T.A., Lahesmaa R. (2009) Identification of novel Stat6 regulated proteins in IL-4treated mouse lymphocytes. Proteomics 9: 1087-98. Lund R.*, Pykäläinen M.*, Naumanen T., Dixon C., Chen Z., Ahlfors H., Tuomela S., Tahvanainen J., Scheinin J., Henttinen T., 94 95 COMPUTATIONAL SYSTEMS BIOLOGY 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: 2571-2577. Principal Investigator: Harri Lähdesmäki, D.Sc. (Tech), Prof. (pro term), 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. E-mail: [email protected] Home page: http://users.ics.tkk.fi/harrila/research/ 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: 727-862. Personnel: Post-doctoral researchers: Jukka Intosalmi Graduate students: Timo Erkkilä, Kartiek Kanduri, Lingjia Kong, Antti Larjo, Henrik Mannerström, Kari Nousiainen, Maria Osmala, Tarmo Äijö Undergraduate students: Kaur Alasoo, Juhani Kähärä, Maia Malonzo, Sini Rautio, Janne Seppälä, Juhi Somani Laurila K. and Lähdesmäki H. (2009) A protein-protein interaction guided method for competitive transcription factor binding improves target predictions, Nucleic Acids Research, 37: e146. 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. Laurila K. and Lähdesmäki H. (2009) Systematic analysis of disease-related regulatory mutation classes reveals distinct effects on transcription factor binding, In Silico Biology 9: 0018. Funding: Academy of Finland, EU FP7, EraSysBio+, Emil Aaltonen Foundation, FICS and TISE graduate schools. Äijö T. and Lähdesmäki H. (2009) Learning gene regulatory networks from gene expression measurements using nonparametric molecular kinetics. Bioinformatics 25: 2937-2944. Lähdesmäki H., Rust A. G. and Shmulevich I. (2008) Probabilistic inference of transcription factor binding from multiple data sources, PLoS ONE, 3: e1820. Lähdesmäki H. and Shmulevich I. (2008) Learning the structure of dynamic Bayesian networks from time series and steady state measurements. Machine Learning 71: 185-217. Ahdesmäki M., Lähdesmäki H., Gracey A., Shmulevich I. and Yli-Harja O. (2007) Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data, BMC Bioinformatics, 8: 233. Collaborators: Prof. Riitta Lahesmaa (University of Turku), Prof. Matej Orešic (VTT Technical Research Centre of Finland), Prof. Mikael Knip (University of Helsinki), Prof. Olli Simell (Hospital District of Southwest Finland) Selected publications: Närvä E., Rahkonen N., Emani M.R., Lund R., Pursiheimo J.-P., Nästi J., Autio R., Rasool O., Denessiouk K., Lähdesmäki H., Rao A. and Lahesmaa R., (in press) 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, in press. Urbanucci A., Sahu B., Seppälä J., Larjo A., Latonen L.M., Waltering K.K., Tammela T.L.J., Vessella R.L., Lähdesmäki H., Jänne O.A. and Visakorpi T., (in press) Overexpression of androgen receptor enhances the binding of the receptor to the chromatin in prostate cancer, Oncogene, in press. 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. 96 97 COMPLEX BIOSYSTEMS MODELING Principal investigator: Matti Nykter, D. Sc., Affiliated Group Leader at CBT, Department of Signal Processing, Tampere University of Technology, Korkeakoulunkatu 1, FI-33720 Tampere, Finland. Tel. +358-40-8490651. Email: [email protected] Home page: www.cs.tut.fi/~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 20042005, and as a post-doctoral research at the Institute for Systems Biology, Seattle, USA during 2007-2009. Since 2010, he has been a group leader at the Department of Signal Processing at Tampere University of Technology and affiliated group leader with Turku Centre for Biotechnology. His research interests are focused on development 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. 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. 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 (Luxemburg Center for Systems Biomedicine). Selected Publications: 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. Galas D. J., Nykter M., Carter G.W., Price N. D. and Shmulevich I. (2010) Biological information as set-based complexity, IEEE Transactions on Information Theory 56: 667-677. Litvak V., Ramsey S.A., Rust A.G., Zak D.E., Kennedy K.A., Lampano A.E., Nykter M., Shmulevich I. and Aderem A. (2009) Function of C/EBPdelta in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals. Nat. Immunol. 10: 437-43. Nykter M., Price N. D. , Aldana M., Ramsey S., Kauffman S. A., Hood L., Yli-Harja O., and Shmulevich I. (2008) Gene Expression Dynamics in the Macrophage Exhibit Criticality. PNAS 105: 18971900. 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 apply computational approach to uncover recipes for cell type reprogramming experiments. 98 99 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: Prathusha Dhavala, Teemu Haikarainen, Sachin Wakadkar, Bishwa Subedi, Abdi Muleta Undergraduate students: Morgane Bruneau, Jesse Mattsson, David Hernandez, Pradeep Battula 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, several mutants were generated to study the iron core formation using X-ray crystallography, microcalorimetry (with G. Nounesis, Athens), EXAFS (with Wolfram Meyer-Klaucke, EMBL-Hamburg), magnetization (with Petriina Paturi, Wihuri Laboratory, University of Turku) and Mössbauer spectroscopy (with Johan Linden, Åbo Akademi University) techniques. The magnetic properties of the iron core in the wild type protein and the mutants were studied and EXAFS experiments were performed at Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, USA. Studies on oxidative stress protection and detoxification mechanisms have been extended by determining high-resolution crystal structures of a tau family glutathione transferase (GST) from Glycine max in free form and in the presence of a substrate analogue. Importantly, the crystal structures revealed a novel site on the surface of the protein that may be utilised for storage and/ or transport of dangerous compounds for detoxification. Docking calculations were carried out to study the binding of diphenylether herbicides in the active site. Work is currently underway on chimeric GSTs or mutants created through directed evolution approaches to produce new GSTs with altered specificity for new applications in agriculture, biomedicine and environmental security. Crystals of human GST-A1 have been grown in our lab for use in structureassisted drug design efforts. In addition, the structure of a novel 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 (coined eta class) of the glutathione transferase superfamily. the degradation of poly(R)-hydroxyalkanoates (PHAs), a group of thermoplastic polyesters considered as biodegradable 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. Further analysis is currently underway and soaking with substrate analogues is in progress . Work on the Atu (acyclic terpene utilization) catabolic pathway found in P. Aeruginosa has been initiated 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. A preliminary structure of AtuE has been obtained to 2.5 Å resolution and is currently in the final stages of refinement. Funding: Academy of Finland, University of Turku, Biocenter Finland, Federation of European Microbiology Societies, EU FP7 (access to synchrotrons). Collaborators: Jukka Finne (University of Helsinki), Sauli Haataja (University of Turku), Dieter Jendrossek (University of Stuttgart), Nikos Labrou (Agricultural University of Athens), Li Duochuan (Shandong Agricultural University) Selected publications: 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 Skopelitou, K., Muleta, A.W, Pavli, O., Skaracis, G.N, Flemetakis, E., Papageorgiou, A.C. & Labrou, N.E. (2011). Overlapping protective roles for glutathione transferase gene family members in chemical and oxidative stress response in Agrobacterium tumefaciens. Funct. Integr. Genomics Sep 10. [Epub ahead of print] 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-zink binding in the ferroxidase center of Strepococcus pyogenes Dpr. Bichem. Biophys. Res. Comm. 398: 361-365. In the theme of enzyme function and stability, we continued our work on PhaZ7, an extracellular depolymerase involved in 100 101 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. Labrou, N., Papageorgiou, A.C. & Avramis, V.I. (2010) Structurefunction relationships and clinical applications of L-asparaginases. Curr. Med. Chem. 17: 2183-2195. 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. 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. 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 Saarinen S., Kato, H., Uchiyama, T., Miyoshi-Akiyama, T. & Papageorgiou, A.C. (2007) Crystal structure of Streptococcus dysgalactiae-derived mitogen reveals a zinc-binding site and alterations in TcR binding. J. Mol. Biol. 373: 1089-1097 Weckström, K. & Papageorgiou, A.C. (2007) Lower consolute boundaries of the nonionic surfactant C(8)E(5) in aqueous alkali halide solutions: An approach to reproduce the effects of alkali halides on the cloud-point temperature. J Colloid Interface Sci. 310: 151-162 Zhao, J., Hayashi, T., Saarinen, S., Papageorgiou, A.C., Kato, H., Imanishi, K., Kirikae, T., Abe, R., Uchiyama, T. & MiyoshiAkiyama, T. (2007) Cloning, expression and characterization of the superantigen streptococcal pyrogenic exotoxin-G from Streptococcus dysgalactiae. Inf. Immun. 75: 1721-1729 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. From left to right: Chamundeeswari Sivaraman, Bishwa Subedi, Abdi Muleta, Teemu Haikarainen and Tassos Papageorgiou 102 103 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. +358-2-3338000 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: Habib Baghinov, M.Sc, Marika Sjöqvist, M.Sc, Sebastian Landor, M.Sc, Christian Antila, M.Sc, Laboratory Technician: Helena Saarento Undergraduate students: Daniel Antfolk, B.Sc, Habib Baghiro, B.Sc. Neeraj Prabhakar, B.Sc, Santhosh Kumar, B.Sc, Sara Sarinko, 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 7thNotchIT, Turku Graduate school for Biomedical Sciences, Cancer Society of Finland, Sigrid Juselius Foundation. 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 104 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). Selected Publications: Rosenholm J.M., Mamaeva, V., Sahlgren C. # and Lindén, M.# (2011) Nanoparticles in targeted cancer therapy: Mesoporous silica nanoparticles entering preclinical development stage. 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) Hypoand 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: Nat. Chem. Biol. 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 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. Molecular Biology of the Cell. 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. Developmental Biology 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. #Sahlgren &Linden 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). PKCz 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. 105 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. TARGETING STRATEGIES FOR GENE THERAPY 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 Principal investigator: Mikko Savontaus, M.D., Ph.D. 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] 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 PDGFreceptorb expression in vascular smooth muscle cells. Circulation Research 102: 1483-91. 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. 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. Postdoctoral fellow: Raine Toivonen, Ph.D. 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. 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. Novel vectors with improved transcriptional and transductional From left to right: Sara Sarinko, Veronika Mamaeva, Neeraj Prabhakar Habib Baghiro, Santhosh Kumar, Sebastian Landor, Daniel Antfolk, Marika Sjöqvist, Cecilia Sahlgren and Christian Antila. 106 107 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., Mäyränpää M.I., Kovanen P.T. and Savontaus M. (2010) Dilated cardiomyopathy alters the expression patterns of CAR and other adenoviral receptors in human heart. Histochem Cell Biol. 133: 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: 2001-2008. Ebert O., Shinozaki K., Huang T.-G., Savontaus M., Garcia-Sastre A. and Woo S.L.C. (2003) VSV as oncolytic virus for treatment of orthotopic hepatocellular carcinoma in immune-competent rats. Cancer Research 63: 3605-3611. 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: 1241-1247. 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: 972-979. 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; Fax +358-2-333 8000. 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., Malin Åkerfelt, Ph.D. Graduate students: Marek Budzynski, M.Sc., Alexandra Elsing, M.Sc., Jenny Joutsen, M.Sc., Petra Vainio, M.Sc., Anniina Vihervaara, M.Sc. Laboratory Technician: Helena Saarento, M.Sc. Undergraduate students: Anna Aalto, Heidi Bergman, Malin Blom, Joachim Hudd, Emine Lundsten, Mikael Puustinen, Hanser Jose Seijas Biel, Jenni Vasara 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 stressinducible 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. Our main topic is 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 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 108 109 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. Among multiple lysine residues targeted by acetylation, K80 is located within the DNA-binding domain of HSF1 and its acetylation is required for reducing HSF1 DNAbinding activity. Importantly, the duration of HSF1 DNA-binding activity can be prolonged or diminished by chemical compounds either activating or inhibiting the activity of the NAD+-dependent deacetylase SIRT1. Our current focus is on a complex network of PTMs to decipher the post-translational signature of HSF1. In contrast to HSF1, which is a stable protein evenly expressed in most tissues and cell types, the amount of HSF2 varies and correlates with its activity. Recently, we reported the first evidence for the ubiquitin E3 ligase APC/C (anaphase-promoting complex/ cyclosome) mediating ubiquitination 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 will also determine the stress effects on the cell cycle, adding a new dimension to the research field. 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, miR-18, 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 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 HSF2mediated 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. 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. Our ongoing genome-wide ChIP-sequencing experiments to compare HSF1 and HSF2 occupancy in non-stressed and stressed cells for better understanding their actions in various chromatin environments, including cells arrested in mitosis, should give news insights on these multi-faceted transcriptional regulators. Funding: The Academy of Finland, the Sigrid Jusélius Foundation, the Finnish Cancer Organizations, Turku Doctoral Programme of Biomedical 110 Sciences (TuBS), and Åbo Akademi University (Centre of Excellence in Cell Stress and Molecular Aging). Collaborators: Susumu Imanishi, Noora Kotaja and Jorma Toppari (University of Turku), John Eriksson, Pia Roos-Mattjus, Peter Slotte and Kid Törnquist (Åbo Akademi University), Marko Kallio (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 (2006-2011): 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 protein-damaging 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 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. 111 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 CANCER CELL SIGNALING Principal Investigator: Jukka Westermarck, M.D., Ph.D., Professor. Address: Turku Centre for Biotechnology, BioCity, Tykistökatu 6 B, P.O. Box 123, FIN-20251 Turku, Finland. Tel. +358-2-333 8621, Fax +358-2-333 8000. E-mail: [email protected] Home page: http://www.btk.fi/research/research-groups/ westermarck-jukka-cancer-cell-signaling/ 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 2002-2007 and 20062009 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. 2009 he was appointed to Research director position at Turku Centre for Biotechnology (leave of absence until 2014). 2011 he was appointed to part-time position as Professor of cancer biology at Department of Pathology, University of Turku (until 2104). Personnel: Post-doctoral researchers: Anna Cvrljevic, Ph.D., Juha Okkeri, Ph.D., Yuba Pokharel, Ph.D., Sami Ventelä, M.D., Ph.D. Graduate students: Tuuli Halonen, M.Sc., Otto Kauko, M.Sc., Amanpreet Kaur, M.Sc., Anchit Khanna, M.Sc. (IMT), Anni Laine, M.Sc., Minna Niemelä, M.Sc., Qiao Xi, M.Sc., Eleonora Sittig, M.Sc. Laboratory Technicians: Taina Kalevo-Mattila, Inga Pukonen. 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. From left to right: First Row: Johanna Björk, Pia Roos-Mattjus, Jenni Vasara, Camilla Aspelin, Eva Henriksson, Anna Aalto, Emine Lundsten, Anniina Vihervaara, Heidi Bergman, Marek Budzynski and Beata Paziewska Second row: Lea Sistonen, Helena Saarento, Johanna Ahlskog, Noémi To´th, Tim Crul, Petra vainio, Jenny Joutsen, Alexandra Elsing and Anton Sanqvist 112 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 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 113 addition, our aim is to purify new protein complexes related cancer cell signaling. Funding: The Academy of Finland, Medical Research Fund of Tampere University Hospital, Turku Graduate School of Biomedical Sciences, Tampere Graduate School in Biomedicine and Biotechnology, Sigrid Juselius Foundation, Cancer Research Foundation of Finland, Association of International Cancer Research (UK). Collaborators: Tuula Kallunki (Danish Cancer Society), Rosalie Sears (Oregon Health and Science University), Owen Sansom (Beatson Institute for Cancer Research, Glasgow), Sampsa Hautaniemi (University of Helsinki), Ari Ristimäki (University of Oulu), Jorma Toppari (University of Turku), Veli-Matti Kähäri (Turku University Hospital), Heikki Joensuu (Helsinki University Hospital). Selected Publications: Niemelä M., Kauko O., Mpindi J.-P., Sihto H., Nicorici D., Kallioniemi O.-P., Joensuu H., Hautaniemi S. and Westermarck, J. (2011). CIP2A signature reveals MYC dependency of CIP2Aregulated phenotypes and its clinical association with breast cancer subtypes. Oncogene, in press. 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 cross talk 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. 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. (2011). Identification of a c-Jun N-terminal kinase 2 dependent signal amplification cascade that regulates c-Myc levels in Ras transformation. Oncogene, in press. Khanna A., Okkeri J., Bilgen T., Tiirikka T., Vihinen V., Visakorpi T. and Westermarck J. (2011). ETS1 mediates MEK1/2-dependent overexpression of cancerous inhibitor of protein phosphatase 2A (CIP2A) in human cancer cells. PLoS One 6: e17979. Ovaska K., Laakso M., Haapa-Paananen S., Louhimo R., Chen P., Aittomäki V., Valo E., Nunez-Fontarnau J., Rantanen V., Karinen S., Nousiainen K., Lahesmaa-Korpinen A.-M., Miettinen M., Saarinen L., Kohonen P., Wu J., Westermarck J. and Hautaniemi S. (2010). Large scale data intergration framework provides a comprehensive view on glioblastoma multiforme. Genome Med. 2: 65. Heikkinen P.T., Nummela M., Leivonen S.K., Westermarck J., Hill C.S., Kähäri V.M. and Jaakkola P.M. (2010). Hypoxia activated Smad3-specific dephosphorylation by PP2A. J. Biol. Chem. 285: 3740-3749. 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: 50925100. 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 114 From left to right: Juha Okkeri, Anni Laine, Taina Kalevo-Mattila, Anna Cvrljevic, Yuba Pokharel, Otto Kauko, Jukka Westermarck, Amanpreet Kaur and Eleonora Sittig 115 Adenosine Deaminases Principal investigator: Andrey Zavialov, Ph.D., Academy of Finland Research Fellow, Group leader, Turku Centre for Biotechnology, University of urku, 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.), Salim Reza (M.S.) 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 heparinbinding 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 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 116 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 Collaborators: 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., Yu X., Spillmann D., and Lauvau G. (2010) Structural basis for the growth factor activity of human adenosine deaminase ADA2. J. Biol. Chem. 285: 12367-12377. Zavialov, A. V., Gracia E., Glaichenhaus N., Franco R., and Lauvau G. (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., Zavialov A.V., Ehrenberg M., and Frank J. (2007). Specific interaction between EF-G and RRF and its implication for GTPdependent ribosome splitting into subunits. J. Mol. Biol. 374: 1345-1358. Gao, H., Zhou Z., Rawat U., Huang C., Bouakaz L., Wang C., Cheng Z., Liu Y., Zavialov A., Gursky R., Sanyal S., Ehrenberg M., Frank J. and Song H. (2007) RF3 induces ribosomal conformational changes responsible for dissociation of class I release factors. Cell 129: 929-941. Rawat, U., Gao H., Zavialov A., Gursky R., Ehrenberg M. and Frank J. (2006) Interactions of the Release Factor RF1 with the Ribosome as Revealed by Cryo-EM. J. Mol. Biol. 357: 1144-1153. Hauryliuk, V., Zavialov A., Kisselev L., and Ehrenberg M. (2006) Class-1 release factor eRF1 promotes GTP binding by class-2 release factor eRF3. Biochimie 88: 747-757. Zavialov, A. V., Hauryliuk V.V. and Ehrenberg M. (2005) Splitting of the posttermination ribosome into subunits by the concerted action of RRF and EF-G. Mol. Cell 18: 675-686. Zavialov, A. V., Hauryliuk V.V and Ehrenberg M. (2005) Guaninenucleotide exchange on ribosome-bound elongation factor G initiates the translocation of tRNAs. J. Biol. 4: 9. Zavialov, A. V., and Engstrom A. (2005) Human ADA2 belongs to a new family of growth factors with adenosine deaminase activity. Biochem J. 391: 51-57. Gao, N., Zavialov A.V., Li W., Sengupta J., Valle M., Gursky R.P., Ehrenberg M. and Frank J. (2005) Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies. Mol. Cell 18: 663-674. 117 Frank, J., Sengupta J., Gao H., Li W., Valle M., Zavialov A. and Ehrenberg M. (2005) The role of tRNA as a molecular spring in decoding, accommodation, and peptidyl transfer. FEBS Lett. 579: 959-962. Allen, G. S., Zavialov A., Gursky R., Ehrenberg M. and Frank J. (2005) The cryo-EM structure of a translation initiation complex from Escherichia coli. Cell 121: 703-712. Zavialov, A. V., and Ehrenberg M. (2003) Peptidyl-tRNA regulates the GTPase activity of translation factors. Cell 114: 113-122. Valle, M., Zavialov A., Sengupta J., Rawat U., Ehrenberg M. and Frank J. (2003) Locking and unlocking of ribosomal motions. Cell 114: 123-134. Valle, M., Zavialov A., Li W., Stagg S.M., Sengupta J., Nielsen R.C., Nissen P., Harvey S.C., Ehrenberg M. and Frank J. (2003) Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy. Nat. Struct. Biol. 10: 899-906. Rawat, U. B., Zavialov A.V., Sengupta J., Valle M., Grassucci R.A., Linde J., Vestergaard B., Ehrenberg M., and Frank J. (2003) A cryo-electron microscopic study of ribosome-bound termination factor RF2. Nature 421: 87-90. Pedersen, K., Zavialov A.V., Pavlov M.Y., Elf J., Gerdes K. and Ehrenberg M. (2003) The bacterial toxin RelE displays codon-specific cleavage of mRNAs in the ribosomal A site. Cell 112: 131-140. Mora, L., Zavialov A., Ehrenberg M and Buckingham R.H. (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., Pape T., Zavialov A.V., Myasnikov A.G., Orlova E.V., Vestergaard B., Ehrenberg M., and van Heel M. (2003) Structure of the Escherichia coli ribosomal termination complex with release factor 2. Nature 421: 90-94. Ph.D. THESES 2011 1. Björk, Johanna: Role and regulatory mechanisms of heat shock factor 2. Åbo Akademi University, 146 p. 2. Dhavala, Prathusha. Structural studies on Enzymes of Biotechnical and Biomedical Interest, University of Turku, 99 p. 3. Jokilehto, Terhi: The Cellular oxygen Sensor PHD2 in Cancer Growth. University of Turku, 133 p. 4. Nevo, Jonna: Novel Players in the Integrin Signaling Orchestra: TCPTP and MDGI University of Turku, 146 p. 5. Nikula, Tuomas: Transcriptional profiling of organspecific autoimmunity in human, University of Turku, 139 p. 6. Mai, Anja: In The Footsteps Of Migrating Cancer Cells, University of Turku, 145 p. 7. Haikarainen, Teemu: Dps-like Peroxide Resistance protein: Structural and functional studies on a versatile nanocontainer, University of Turku, 121 p. 8. Vainio, Paula: High-Throughput Screening for Novel prostate Cancer Drug Targets -Getting Personal, 74 p. 9. Ketola, Kirsi: Chemical Biology Screen for Prostate Cancer Therapeutics, University of Turku. 177 p. 10. Gupta, Santosh: Functional Study of Oncogenic Transcription Factor ERG and its Signaling in Prostate Cancer University of Turku, 40 p. 11. Rantala, Juha: A cell spot microarray method for highthroughput biology, University of Turku, 48 p. Zavialov, A. V., Mora L., Buckingham R.H. and Ehrenberg M. (2002) Release of peptide promoted by the GGQ motif of class 1 release factors regulates the GTPase activity of RF3. Mol. Cell 10: 789798. Zavialov, A. V., Buckingham R.H. and Ehrenberg M. (2001) A posttermination ribosomal complex is the guanine nucleotide exchange factor for peptide release factor RF3. Cell 107: 115-124. 118 119 Ph.D. DEFENCES 120 121 LIFE OUTSIDE THE LAB 122 123 124 125 126 127 128
Similar documents
Report 2009 - Turku Centre for Biotechnology
Canceromics Research Programme.......................................... 54 Signaling Pathways regulated by Oncogenic Pim Kinases......... 58 Molecular and Systems Immunology and Stem Cell Biolog...
More informationTURKU CENTRE FOR BIOTECHNOLOGY REPORT 2011
for molecular systems immunology, and CBTs affiliated group leaders Matej Oresic (VTT) and Harri Lähdesmäki (Aalto) play central roles in leading the CoE and directing the computational systems bio...
More informationReport 2010 - Turku Centre for Biotechnology
Cell Imaging Core (CIC)............................................................. 18 The Proteomics Facility . ........................................................... 21 Protein Crystallog...
More information