Report 2009 - Turku Centre for Biotechnology

Transcription

TURUN BIOTEKNIIKAN KESKUS
ÅBO BIOTEKNIKCENTRUM
TURKU CENTRE FOR BIOTECHNOLOGY
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Cell Signalling to Systems Biology Research
TURKU CENTRE
FOR BIOTECHNOLOGY
REPORT 2009
Tykistökatu 6 B
P.O.BOX 123
FI 20521 Turku, Finland
Tel: +358 2 333 8603, Fax 358 2 333 8000
Annual Report 2009
Turku Centre for Biotechnology
Published by:
P.O. Box 123, FI-20521 Turku, Finland
Tel. int. +358-2-333 8603, fax int. +358-2-333 8000
http://www.btk.fi
Editorial Board
Riitta Lahesmaa (Chair)
Tero Aittokallio
Eleanor Coffey
Garry Corthals
Michael Courtney
Konstantin Denessiouk
Attila Gyenesei
John Eriksson
Jyrki Heino
Johanna Ivaska
Panu Jaakkola
Marko Kallio
Olli Kallioniemi
Päivi Koskinen
Linnéa Linko
Tassos Papageorgiou
Lea Sistonen
Jukka Westermarck
Photographs:
KUV@TEHDAS Roni Lehti, Photograph archives of the Centre for Biotechnology.
Front cover image: Patrik Jones, back cover images:
(2nd from top) Tassos Papageorgiou, (bottom) Marko Kallio,
Photograph archives of the Centre for Biotechnology.
Graphic Design: Anne Asplund, Finepress Oy
Printed by: Finepress Oy, Turku
ISSN 1237-5217
CONTENTS
Board of Trustees...................................................................... 2
Chairman’s Foreword................................................................. 3
From the Director....................................................................... 4
Year 2009 in a Nutshell.............................................................. 6
PhD and MSc Theses................................................................ 9
Funding..................................................................................... 10
Personnel 2009......................................................................... 11
The Finnish DNA Microarray Centre........................................... 14
The Proteomics Facility.............................................................. 16
Cell Imaging Core (CIC) ............................................................ 19
Virus Vector Facility . ................................................................. 22
Protein Crystallography Core Facility.......................................... 24
Data Mining and Modeling Group.............................................. 25
Protein Kinase Regulation of Brain
Development and Disease......................................................... 29
Organisation of Neuronal Signaling Pathways............................ 33
Cytoskeletal and Survival Signaling............................................ 37
Cell Adhesion and Cancer......................................................... 42
Hypoxia in Cell Survival.............................................................. 45
Bioenergy Group....................................................................... 48
Kinetochore and Cancer Research Group.................................. 50
Canceromics Research Programme.......................................... 54
Signaling Pathways regulated by Oncogenic Pim Kinases......... 58
Molecular and Systems Immunology and Stem Cell Biology...... 61
Protein Crystallography.............................................................. 67
Bioinformatics Unit.................................................................... 72
Cell Fate
................................................................................ 76
Targeting Strategies for Gene Therapy....................................... 80
Transcriptional Regulation of Heat Shock Gene Expression....... 82
Cancer Cell Signaling................................................................. 86
Publications 2009...................................................................... 89
Life outside the Lab................................................................... 94
1
ORGANIZATION
Board of Trustees 2009
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,
Assistant Secretary
JAAKKOLA Minttu, Coordinator,
Turku Centre for Biotechnology and BioCity Turku
Members
ARO Eva-Mari, Academy Professor, the Academy of Finland,
University of Turku, Department of Biology
JALKANEN Sirpa, Professor, University of Turku,
MediCity Research Laboratory
JOHNSON Mark, Professor, Åbo Akademi University,
Department of Biochemistry and Pharmacy
KOUVONEN Ilkka, CEO, Turku Science Park Ltd
LAHTI Reijo, Professor, University of Turku,
Department of Biochemistry and Food Chemistry
LASSILA Olli, Professor, University of Turku,
Department of Medical Microbiology
PYRHÖNEN Seppo, Professor, University of Turku,
Department of Oncology
SAXÉN Henrik, Vice Rector, Research Professor,
Åbo Akademi University, Heat Engineering Laboratory
TÖRNQUIST Kid, Professor, Åbo Akademi University,
Department of Biology
Vice-members
ARO Hannu, Professor, University of Turku, Department of Surgery
HINKKANEN Ari, Professor of Cell and Molecular Biology,
Åbo Akademi University, Department of Biochemistry
HUPA Leena, Lecturer, Åbo Akademi University,
Åbo Akademi Process Chemistry
PIISPANEN Tero, Project Manager, Turku Science Park Ltd
SALAKOSKI Tapio, Professor, University of Turku,
Department of Information Technology
SISTONEN Lea, Academy Professor, the Academy of Finland SOUKKA Tero, Academy Research Fellow, Academy of Finland,
University of Turku, Department of Biotechnology
TOPPARI Jorma, Professor, University of Turku,
Department of Physiology
CHAIRMAN’S FOREWORD
During the past years the expenses of the top-of-line instruments and
the new research technologies have increased much faster than the
budgets of the Universities. It is a well-known fact that the financing
of the research infrastructure has become a major problem, not least
in Finland. The six Finnish biocenters established in August 2006 a
common organization, named as Biocenter Finland, to coordinate
the development of national infrastructure and core facilities in life
science area. Recently, the Finnish government decided to finance
Biocenter Finland activities during the period 2010-2015 by 45 M€.
The board of Biocenter Finland has already allocated most of its
budget for different biocenters, including BioCity Turku. This funding
allows Turku Centre for Biotechnology to renew its instrumentation
in genomics, proteomics and bioimaging. Some funding has also
been granted to bioinformatics, structural biology and virus vectors.
Biocenter Finland financing will also be used to support core facilities
in the Turku Center for Disease Modeling and the Turku PET centre. It
is fair to say that without the support from Biocenter Finland it would
have not anymore been possible to provide modern equipment
and technologies for Finnish life scientists. Despite this positive
development, the future of the research infrastructure remains to be
a major concern in all Finnish biocenters, since the present support
ends after year 2012. We should all work actively to secure the
continuation of national infrastructure funding also after that.
Turku Centre for Biotechnology has a long tradition in the building of
high quality core facilities that have had numerous users also outside
Turku. During the progression of the Biocenter Finland process the
Turku core facilities will get even more important national role. It has
been satisfying to realize that the organization and the administration
of the core facilities are more advanced in Turku than anywhere else
in Finland and that the working methods developed in Turku are
often announced as ideal models for other biocenters.
The beginning of the year 2010 brought remarkable changes in the
Finnish university administration and implementation of new full-cost
model in the research grants. For many scientists this has meant a
huge increase in the number of hours used in the administration of
the departments and the research projects. Similarly, the workload
of the persons, who are directly involved in the maintenance of the
departments has also dramatically increased. The complexity of the
financial systems and the lack of proper computer programs have
caused a lot of extra work and uncertainty. We can only hope that
during the years to come the scientists
will again be allowed to concentrate
on research instead of administrative
problems.
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
2
3
FROM THE DIRECTOR
Turku Centre of Biotechnology (CBT) was established in 1989 as
a joint independent department of University of Turku and Åbo
Akademi University. Today, it has evolved into a multidisciplinary
research and service unit successfully crossing the boundaries
of departments, faculties and even two universities! During the
past 20 years Turku University and Åbo Akademi University have
been centralizing demanding and expensive core facilities and
research services to CBT to enable the most cost efficient use of
the facilities for the local research community. CBT has developed
into an internationally recognized research environment and today
provides state-of the-art core facilities for altogether 80 BioCity
Turku research groups and six research programs featuring
altogether seven Academy of Finland Centers of Excellence.
In June 2009 CBT celebrated its 20th anniversary with a symposium
“From Cell Signaling to Medical Systems Biology” with participation
of world class scientists many of whom are closely linked to CBT.
The symposium dinner in Turku Castle was the highlight of the
festivities.
CBT has three key focus areas: 1) research, 2) education and
training, and 3) providing core facilities and state-of–the-art
technologies and research services in selected areas. The central
areas of research are cell signaling, regulation of gene and protein
expression and their interactions and systems biology. In 2009 we
published 54 papers and 7 Ph.D.s were completed. Our group
leaders were very active in organizing seminars, courses and
symposia. Two new international group leaders were recruited.
The Centre’s core facilities developed technology platforms and
services in a close interaction with researchers. A significant
investment has been made in developing the state-of-the-art
platforms in genomics and functional genomics, proteomics, cell
imaging and bioinformatics supporting the – omics technologies.
The animal core facility takes up a sizeable portion of basic resources
in serving researchers and Turku Centre for disease modelling.
A joint organization of the Finnish biocenters, Biocenter Finland,
was established in 2006 to facilitate national collaboration and
to coordinate development of research infrastructures in Finland.
In 2009, several of CBT group leaders worked intensively in
various Biocenter Finland infrastructure networks and prepared
for applications to develop infrastructures with funds Ministry of
Education allocated to Biocenter Finland for this purpose. An
international evaluation process resulted in substantial support to
develop infrastructures, many of them at CBT. Hence, in addition
to serving local needs, CBT now further develops and provides
national services in several areas within the Biocenter Finland
infrastructure network. Bioimaging and systems biology are the
central infrastructures in the research strategy of Biocity Turku,
and in the research strategy of both our universities. Vigorous
development of technology platforms, research core facilities,
and research infrastructures will continue, and support for both
instrumentation and personnel will be provided. This extended
collaborative network and available funding should provide us with
new efficient ways to further develop the research infrastructure in
Finland.
4
The universities prepared for going through a major change in the
beginning of 2010. This included definition of new strategies for
universities and Biocity Turku. Both the University of Turku and
Åbo Akademi University chose to profile themselves as a research
university, which is an excellent environment for CBT to build and
develop on its strengths in research and research infrastructure.
Moreover, molecular biosciences, CBT’s core competence is one
of the central strategic strong areas of research.
An important strategic goal of our universities is internationalization
and international competitiveness. The universities strive
towards strategic recruitment practice, to attract researchers
with international merit. This has always been a practice at CBT.
In fact, Finnish group leaders are a minority at our Centre. Our
host universities’ commitment in internationalization will hopefully
improve also availability of important administrative documents and
meetings in English so that our foreign researchers and personnel
can fully contribute to the development of our organizations.
The past year was very successful. Active participation to Biocenter
Finland infrastructure networks and numerous administrative
challenges and changes increased the workload of our researchers
as well as technical and administrative personnel. In spite of
that, scientific achievements include several special awards and
grants as well as papers published in top ranked journals by our
scientists.
It is my great pleasure to congratulate our scientists for their
excellent achievements and thank everyone involved - including
the CBT technical and administrative staff for their outstanding
contributions. My special thanks to Dr. Eleanor Coffey, our current
Vice Director, for taking the responsibility of directing and taking
care of several duties of our Centre in 2009 and enabling me to
carry out a sabbatical at Harvard Medical School. She took an
extraordinary and outstanding care of the Centre.
Thank you!
Riitta
Riitta Lahesmaa, M.D., Ph.D.,
Professor
Director
University of Turku and Åbo
Akademi University
5
YEAR 2009 IN A NUTSHELL
RESEARCH AND EDUCATION
2009
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54 scientific papers were published
Seven new Ph.D.´s graduated
CBT was awarded substantial funding (approximately 4
million €) from the Biocenter Finland infrastructure networks
Two new international group leaders were recruited
For undergraduate training, CBT again organized lecture
courses and practical demonstrations including a laboratory
course on “Functional Genomics” for Health Bioscience
and Biology students (4 study points) and on “Medical
Biotechnology” for Medical students (5 study points)
The 20th anniversary was celebrated with a symposium
“From Cell Signaling to Medical Systems Biology”
8 M.Sc. theses were completed
DEVELOPMENT OF INFRASTRUCTURE, RESEARCH
SERVICES AND CORE FACILITIES 2009
Finnish DNA Microarray Centre 2009
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The next-generation sequencing instrument: ABI SOLiD 3
was acquired and almost immediately upgraded to version
3Plus
FDMC’s website was renovated to improve the visibility of
the centre’s services
Several events were organized in collaboration with various
instrument manufacturers throughout the year to spread
information on available and emerging technologies related
to our services
FDMC personnel gave talks in many scientific events and
organized training courses to educate researchers on
various topics
Major efforts were carried out to further develop our
project consultation services to help customers design
their experiments. Also the centre’s bioinformatics team
continued developing bioinformatics data analysis
services
Proteomics and Mass spectrometry Laboratory 2009
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•
6
We became national coordinator of the new Proteomics
and Metabolomics network of Biocentre Finland and
secured BCF funding for personnel and instrumentation
We coordinated three Nordic Networks on proteomics and
mass spectrometry
Several courses were organised nationally and
internationally in collaboration with Nordforsk networks,
FinnProt and the local universities
QStar Elite: A second-hand Elite mass spectrometer was
purchased and configured to run in-line with Dionex 3000
LC system
Converted HCT Esquire (Ion trap, Bruker) for nanospray
LC-MS/MS
Cell Imaging Core 2009
•
•
•
•
•
CIC was awarded substantial funding for in vivo and high
resolution imaging from the Biocenter Finland Biological
Imaging network
CIC coordinated the Nordic Network on Imaging in Biology
and Medicine with participation from Finland, Sweden,
Norway, Russia, Denmark and Ireland. Network symposia
and training events were held in Finland, Sweden, Ireland
and Norway
The Leica TCS-SP5 Stimulated Emission Depletion (STED)
microscope for high resolution imaging were installed
Daniel Abankwa was recruited from the Institute for
Molecular Bioscience in Brisbane. He joined CBT as group
leader and head of CIC
CIC coordinated a plan to provide centralized, large scale
data storage to the imaging community in Turku. This will
be realized during 2010 in cooperation with Prof. Mark
Johnson at Åbo Akademi
Viral vector facility 2009
•
•
•
•
•
Lenti vector production was added to its service
repertoire
Funding was secured from the Biocenter Finland Viral
Gene Transfer infrastructure network to provide gene
transfer tools to researchers
Ketlin Adel was recruited as a new lab technician dedicated
to service provision
The Bio-safety level 2 lab was furnished with an inverted
fluorescence microscope
Jari Heikkilä, consultant on Lenti virus production, produced
an exciting study on the use of oncolytic alphavirus for
glioma treatment. This work was published in PLoS One
in January 2010
Bioinformatics Unit 2009
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The High-throughput bioinformatics group organized
a two-day Chipster microarray data analysis course in
collaboration with CSC
High-throughput screening of natural molecules was
established in conjunction with Prof. Pia Vuorela at Åbo
Akademi University
Increased collaboration between our unit and CSC in high
power computing and cloud computing
Participated in projects involving analysis of protein-protein
and protein-ligand interactions, computer-aided prediction
and intelligent molecular modeling and design; computerbased ligand docking and analysis; effects of molecular
recognition and mutations on protein function
Training of Ph.D. students in Bioinformatics and
Computational Biology within the National Graduate School
of Informational and Structural Biology. Contribution to
courses organized by CBT and Åbo Akademi University
Plans made to increase high-capacity storage infrastructure
for archiving services to support Structural Bioinformatics,
Structural Biology, Translational Area, Drug Discovery,
Chemical Informatics and Bioimaging
7
Protein crystallography facility 2009
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Continued participation in several courses (Medical
Biochemistry, TERBIO) and initiation of new ones (Protein
Crystallography and Structural Genomics’,’How to solve a
protein structure) with lectures and demonstrations in the
X-ray facility
Organised workshop ‘How to get the most from the protein
structures’
New collaborative projects initiated with other groups in
Finland and abroad
All major crystallographic programs were kept upgraded
to latest versions
Funding received from Biocenter Finland towards a new
X-ray generator
Quality Assurance Unit 2009
•
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•
Organized courses for the university on (1) quality assurance
and metrology and (2) how to assure the reliability of your
laboratory test results
Individual training for graduate and post-graduate
students
Carried out GLP inspections for the Central Animal
Laboratory
PhD and MSc Theses
2009
PhD Theses
Name
Supervisor
Anckar, Julius
Sistonen, Lea, Kaunisto, Aura
Eriksson, John Kochin, Vitaly
Eriksson, John
Mattila, Elina
Ivaska, Johanna
Mialon, Antoine
Westermarck, Jukka Pellinen, Teijo
Ivaska, Johanna
Åkerfelt, Malin
Sistonen, Lea
Site besides CBT
ÅA/ Dept. of Biology
UTU/ Dept. of Biology
VTT/ UTU/Department of Medical Biochemistry and Genetics
UTU/Department of
Medical Biochemistry and Genetics
VTT/ UTU/Department of Medical Biochemistry and Genetics
MSc Theses Name
Supervisor
Männistö, Katja
Koskinen, Päivi
Lindquist, Julia
Eriksson, John
Rautoma, Karoliina
Sistonen, Lea
Rosenberg, Susanna Eriksson, John
Sachin, Wakadkar
Papageorgiou, Tassos
Stykki, Heidi
Eriksson, John
Sun, Lihua
Coffey, Eleanor Site besides CBT
UTU/Dept. of Biology
University of Skövde,
Sweden
UTU/ Dept. of Biology
Tampere University of
Technology
CBT staff from left to right, front row: Virpi Korpiranta, Sarita Heinonen, Taina
Kalevo-Mattila, Hannele Vuori, second row: Marjo Hakkarainen, Riitta Lahesmaa,
Riina Plosila, Aila Jasmavaara, Susanna Pyökäri, Eva Hirvensalo, Sirkku Grönroos,
back row: Juha Strandén, Jouko Sandholm, Markku Saari, Pasi Viljakainen, Mikael
Wasberg, Satu Alanko, Perttu Terho, Petri Vahakoski, Mårten Hedman, Petri
Kouvonen, Arttu Heinonen.
8
9
FUNDING
PERSONNEL 2009
Sources of funding received
by Centre for Biotechnology in 2009 (9.4 Million €)
Academy of
Finland 15%
Tekes 3%
Others 12%
EU
13%
Services
20%
Universities 37%
Administration
LAHESMAA Riitta, Director, Professor,
Group Leader
GRÖNROOS Sirkku, Senior
Administrative Assistant
HEINO Ilona, Student
HIRVENSALO Eva, Clerical Official
JAAKKOLA Minttu, Coordinator
JASMAVAARA Aila, Clerical Official
PLOSILA Riina, Coordinator
BioCity Turku
HEINO Jyrki, Biocity Turku Scientific
Director, Professor
JAAKKOLA Minttu, Coordinator
Technical Staff
ANDERSEN Raija, Laboratory Technician
HEDMAN Mårten, Systems Manager
KORPIRANTA Virpi,
Instrument Maintenance
SARA Rolf, WASBERG Mikael,
Laboratory Manager
SOITAMO Ann-Christine, Student
STRANDÉN Juha, Laboratory Engineer
VAHAKOSKI Petri, Systems Manager
VILJAKAINEN Pasi, Senior Technician
VUORI Hannele, Instrument Maintenance
Data Mining and Modeling
AITTOKALLIO Tero, Group Leader,
Adjunct Professor
ELO Laura, Postdoctoral Fellow
GAO Bin, Undergraduate 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
NATRI Lari, Undergraduate Student
OKSER Sebastian, Graduate Student
PIIPPO Mirva, Undergraduate Student
SALMELA Pekka,
SALMI Jussi, Postdoctoral Fellow
TUIKKALA Johannes, Graduate Student
VÄHÄMAA Heidi, Graduate Student
Protein Kinase Function
in Brain Development and Disease
COFFEY, Eleanor, Group Leader,
Academy of Finland Research Fellow
BIALEK Agnieska,
DESHPANDE Prasannakumar,
Graduate Student
HEALY Mary-Ann, Undergraduate
HEIKILÄ. Hanna, Undergraduate Student
KOMULAINEN, Emilia, Graduate Student
MOHAMMAD Hasan, Graduate Student
MYSORE, Raghavendra,
Graduate Student
PADZIK, Artur, Graduate Student
Pyökäri Susanna, Laboratory Technician
SUN Lihua, Graduate Student
TUITTILA Minna,
Postdoctoral Researcher
10
WANG Yubao, Graduate student
ZDROJEWSKA, Justyna,
Graduate student
Proteomics and Mass Spectrometry
CORTHALS Garry, Group Leader,
Head of Proteomics
ANDERSÉN Raija, Laboratory Technician
CARREIRA DOS SANTOS Hugo Miguel
Baptista, Visiting Graduate Student
HEINONEN Arttu, Project Engineer
KANNASTE Olli, Undergraduate Student
KAUNISMAA Katri,
KOUVONEN Petri, Researcher
RALPH Eliza, Systems Administrator
ROKKA Anne, Postdoctoral Fellow
SUNI Veronika, Graduate Student
VEHMAS Anni, Undergraduate Student
NEES Susanne, Coordinator
SAEDI Firouz, Undergraduate student
Organisation of Neuronal
Signaling Pathways
COURTNEY Michael, Professor,
Group Leader
HO, Franz, Postdoctoral Researcher
LI, Lili, Graduate Student
LIU, Xiaonan, Graduate Student
LOPEZ RODRIGUES, Maykel,
Graduate Student
MARTINSSON, Peter,
PEVGONEN, Veera, Technicain
TUITTILA Minna,
VERGUN, Olga,
Postdoctroal Researcher
WANG, Xijun, Graduate Student
YADAV, Leena, Graduate Student
Protein Phosphorylation Group
ERIKSSON John, Group Leader,
Professor
ASAOKA Tomoko, Graduate Student
FERRARIS Saima, Graduate Student
HYDER Claire, Graduate Student
IMANISHI Susumu, Postdoctoral Fellow
KASTU Juha, Project Engineer
KAUNISTO Aura, Post-doctoral Fellow
KOCHIN Vitaly, Graduate Student
LAZARO, Glorianne, Exchange Student
LINDQVIST Julia, Graduate Student
ISONIEMI Kimmo, Graduate Student
PALLARI Hanna-Mari, Graduate Student
PEUHU Emilia, Graduate Student
REMES Mika, Graduate Student
SAARENTO Helena,
Research Associate
SÖDERSTRÖM Thomas,
Post-doctoral fellow
TORVALDSON Elin, Graduate student
Cell Imaging Core
COFFEY Eleanor, Academy of Finland
Research Fellow, Coordinator of the Cell
Imaging Unit
ERIKSSON John, Group Leader,
Professor
11
KORHONEN Jari, Project Engineer
SANDHOLM Jouko,
Research Engineer
TERHO Perttu, Project Engineer
Cell Adhesion and Cancer
IVASKA Johanna, Group Leader,
Professor
ARJONEN Antti,
HÖGNÄS Gunilla,
MARTTILA Heidi,
Laboratory Technician
MAI Anja, Graduate student
MATTILA Elina, Graduate student
NEVO Jonna, Graduate Student
PELLINEN Teijo, Graduate student
SIIVONEN Jenni,
TUOMI Saara, Graduate Student
VELTEL Stefan, Postdoctoral Fellow
VUORILUOTO Karoliina,
Graduate Student
Hypoxia Group
JAAKKOLA Panu, Group Leader,
Adjunct Professor,
Academy Research Fellow,
the Academy of Finland
HEIKKINEN Pekka, Graduate Student
HIMANEN Virpi,
HÖGEL Heidi, Graduate Student
JOKILEHTO Terhi, Graduate Student
KALEVO-MATTILA Taina,
KULJU Tuomas,
NUMMELA Marika, Graduate Student
PURSIHEIMO Juha-Pekka,
Postdoctoral Fellow
RANTANEN Krista, Graduate Student
RÄMÖ Olli, Undergraduate Student
VUORINEN Raisa,
Kinetochore and Cancer
Research Group
KALLIO Marko, Group Leader, Senior
Research Scientist, Adjunct Professor
AHONEN Leena, Postdoctoral Fellow
HALONEN Tuuli,
JAAKKOLA Kimmo,
Postdoctoral Fellow
KUKKONEN-MACCHI Anu,
Graduate Student
MÄKI-JOUPPILA Jenni,
Graduate Student
NARVI Elli, Postdoctoral Fellow
OETKEN-LINDHOLM Christina,
Postdoctoral Fellow
SALMELA Anna-Leena,
Graduate Student
TOIVONEN Pauliina,
WINSEL Sebastian,
Postdoctoral Fellow
VUORILUOTO Mariaana,
Graduate Student
12
Canceromics Reasearch 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
LAITERÄ Tiina, Undergraduate Student
MÄNNISTÖ Katja, 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 Group
LAHESMAA Riitta, Director,
Professor, Group Leader
AHLFORS Helena, Graduate Student
FILEN Sanna, Graduate Student
GUPTA Bhawna, Postdoctoral Fellow
HAKKARAINEN Marjo,
HEINONEN Mirkka, Graduate Student
HEINONEN Sarita, Laboratory Technician
JÄRVENPÄÄ Henna, Graduate Student
KORHONEN Juha, Graduate Student
KUMAR Sunil, Postdoctoral Fellow
KYLÄNIEMI Minna, Graduate Student
LAHTI Essi, Undergraduate Student
LUND Riikka, Postdoctoral Fellow
LÖNNBERG Tapio, Graduate Student
MOULDER Robert, Senior Scientist
NYSTRÖM Joel, Undergraduate Student
NÄRVÄ, Elisa, Undergraduate Student
RAHKONEN Nelly,
RASOOL Omid, Adjunct Professor,
Senior Scientist
SALONEN Verna, Graduate Student
TAHVANAINEN Johanna,
Graduate Student
TRIPATHI Subhash, Graduate Student
TUOMELA Soile, Graduate Student
Quality Assurance Unit
LINKO Linnéa, Group Leader,
Adjunct Professor
Computational Systems Biology
ORESIC Matej, Group Leader, Adjunct
Professor, Chief Research Scientist
KATAJAMAA Mikko, Graduate Student
LÖNNBERG Tapio, Graduate Student
Protein Crystallography
PAPAGEORGIOU Tassos, Group Leader,
Adjunct Professor
AGIUS Jeremie, Exchange Student
ANDERSSON Charlotta, Graduate
Student
CHOUHAN Bhanupratap Singh,
Undergraduate student
DHAVALA Prathusha, Undergraduate
Student
DUBREUIL Christine, Student
HAIKARAINEN Teemu,
Graduate Student
HAVUKAINEN Heli, Graduate Student
KAUKO Anni, Postdoctoral Fellow
ROUE Carole, Undergraduate Student
SAARINEN Susanna, Graduate Student
WECKSTRÖM Kristian, Senior Scientist
Bioinformatics Unit
DENESSIOUK Konstantin, Group Leader
(Structural Bioinformatics)
GYENESEI Attila, Group Leader
(High-throughput Bioinformatics)
CHOUHAN Bhanupratap Singh,
Graduate Student
JUNTTILA Sini, Graduate Student
LAIHO Asta, Project Engineer
KYTÖMÄKI Leena,
TAMMINEN Seppo,
Cell fate
SAHLGREN Cecilia, Group Leader,
Academy of Finland Research Fellow
MAMAEVA Veronika,
Postdoctoral Fellow
HIETAMÄKI Marika, Graduate Student
LANDOR Sebastian, Graduate Student
BATE-EYA Laurel Tabe,
Graduate Student
ANTFOLK Daniel,
ANTILA Christian,
GRANQVIST Cecilia,
NIEMI Rasmus, Undergraduate Student
SAARENTO, Helena,
Targeting Strategies for Gene
Therapy
SAVONTAUS Mikko, Group Leader,
Adjunct Professor
EEROLA Kim, Graduate Student
MATTILA Minttu,
TOIVONEN Raine, Graduate Student
Transcriptional Regulation of Heat
Shock
SISTONEN Lea, Group Leader,
Professor, Academy Professor until
July 2009
AALTO Anna, Undergraduate Student
AHLSKOG Johanna, Graduate Student
ANCKAR Julius, Postdoctoral Fellow
BERGMAN Heidi,
BJÖRK Johanna, Graduate Student
BLOM Malin, Undergraduate Student
BLOMSTER Henri, Graduate Student
BUDZYNSKI Marek, Graduate Student
CHITIKOVA Zhanna, Graduate Student
ELSING Alexandra, Graduate Student
HENRIKSSON Eva, Postdoctoral
Fellow
KARLBERG Henrica,
RAUTOMA Karoliina, Undergraduate
Student
SAARENTO Helena,
Research Associate
SANDQVIST Anton, Graduate Student
SIIMES Jenny, Undergraduate Student
VARTIAINEN Aki,
VIHERVAARA Anniina,
Graduate Student
ÅKERFELT Malin, Postdoctoral Fellow
Finnish DNA Microarray Centre
GYENESEI Attila, Group Leader
SARA Rolf, Technical Team Leader,
Laboratory Manager
Juha-Pekka Pursiheimo,
Senior Scientist
HEINONEN Tiia, Laboratory Technician
JUNNI Päivi, Laboratory Technician
NURMI Miina, Laboratory Technician
RISSANEN Oso, Laboratory Technician
SIPILÄ Anna, Undergraduate Student
VENHO Reija, Laboratory Technician
VIRTANEN Eveliina, Project Engineer
KYTÖMÄKI Leena,
Biotechnology Engineer
LAIHO Asta, Project Engineer
TAMMINEN Seppo,
JUNTTILA Sini, Project Engineer
Cancer Cell Signaling
WESTERMARCK Jukka,
Group Leader, Professor,
CÕME Christophe, Postdoctoral Fellow
HALONEN Tuuli, Graduate Student
KALEVO-MATTILA Taina,
KAUR Amanpreeet, Graduate student
LAINE Anni, Graduate Student
MANNERMAA Leni, Scientist
MIALON Antoine, Graduate Student
NIEMELÄ Minna, Graduate Student
OKKERI Juha, Postdoctoral fellow
POKHAREL Yuba, Postdoctoral fellow
VENTELÄ Sami, Postdoctoral Fellow
Biobanking and Biomolecular
Resources Research Infrastructure
(BBMRI)
VUORIO Eero, BBMRI Executive
Manager, Chancellor
SALMINEN-MANKONEN Heli,
Adjunct professor, Project manager
GRÖNROOS Sirkku, Project assistant
13
The Finnish DNA
Microarray Centre
http://fmsc.btk.fi
Head:
Attila Gyenesei, Ph.D., Senior Scientist, Group leader
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]
Personnel:
Tiia Heinonen, Päivi Junni, Leena Kytömäki, Asta Laiho, Miina Nurmi,
Oso Rissanen, Rolf Sara, Reija Venho, Eveliina Virtanen, JuhaPekka Pursiheimo, Riikka Lund, Sini Junttila, Seppo Tamminen,
Sarita Heinonen, Ritva Ala-Kulju, Anna Sipilä
General description:
The Finnish DNA Microarray Centre (FDMC) is an internationally
recognised Functional Genomics Core Facility that is part of 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, microarray based
services (gene expression analysis, exon-specific expression
analysis, miRNA analysis, ChIP-on-chip analysis, aCGH and SNP
genotyping), Real-Time PCR and traditional DNA sequencing. Our
service covers all 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.
FDMC hosts 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.
During 2009 the Centre acquired a high-throughput nextgeneration sequencing (NGS) instrument SOLiDTM 3Plus from
Applied Biosystems. The system supports a wide range of genetics
applications covering genomics, transcriptomics and epigenomics
and it is distinguished by its unmatched accuracy and capability of
generating more than 60 gigabases of map-able sequence data
per run. The combination of increased throughput, shorter run
times, and improved data analysis make the SOLiD technology
an ideal choice for research applications in any genetics project.
The system enables for example distinguishing strand specific
expression patterns, discovery of novel transcripts and splice
variations without the bias of microarrays, detecting SNPs at
low coverage with a low false positive rate, global assessment of
DNA-protein binding interactions and characterization of structural
rearrangements including balanced translocations.
The Microarray Centre offers a number of other genomic analysis
technologies for gene expression, SNP and genotyping studies
including a sequencing facility and real-time PCR service. Services
include BioRad Experion 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 and related
bioinformatics are held frequently to facilitate knowledge transfer within
the field, often this is done in collaboration with graduate schools.
Funding:
Ministry of Education and the Centre of Expertise of Southwest Finland
Users:
Finnish DNA Microarray Centre has customers from Finnish
universities, biocenters and research institutes in the field of
biosciences as well as local companies and foreign companies and
universities - altogether from more than 200 research groups.
Illumina Sentrix Bead Array© service was started with whole human
and mouse genome transcriptomic profiling and from the beginning
of 2007 rat arrays have also been offered for gene expression
studies. Illumina’s GoldenGate Assay protocol provides high-quality
and high-multiplex genotyping.
Affymetrix GeneChip© service has provided whole transcript
expression arrays for human, mouse and rat, and expression
arrays for a wide selection of organisms. Platform also provides
many arrays for SNP detection and copy number variation.
Agilent DNA technology service has provided whole genome
expression arrays, which are designed and validated for onecolor and two-color processing. From 2007 these have been also
available as multi-packs. Beside catalog arrays also custom arrays
have been processed. Also micro RNA arrays are available.
14
From left to right: Leena Kytömäki, Sini Junttila, Päivi Junni, Leni Mannermaa, Sanna
Vuorikoski, Attila Gyenesei, Riikka Lund, Juha-Pekka Pursiheimo, Eveliina Virtanen,
Reija Venho, Sarita Heinonen.
15
THE PROTEOMICS FACILITY
http://proteomics.btk.fi/
Head:
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.
Personnel:
Senior scientists: Dr. Anne Rokka, Ph.D.; Associate scientist:
Petri Kouvonen, M.Sc. (Ph.D. student); Laboratory Engineer: Arttu
Heinonen; Technician: Raija Andersen; Bioinformatician: Eliza
Ralph
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 facility aims to support life science research in need of
proteomics and MS services. Key questions revealed by proteomics
technologies are differences in protein abundance, measurement
of post translational modifications, defining protein complexes that
carry out specific functions and localisation of proteins in tissues.
To address these questions, the facility develops and innovates, in
collaboration with national research groups, new methodologies
in proteomics. Most services provided by the facility focus on
mass spectrometric strategies integrated with protein and peptide
enrichment workflows for large-scale quantitative analysis of
proteomes or detailed characterisation of single proteins, such
as their state of phosphorylation. In recent years the facility has
developed a wide basis of operation and expertise, which are:
Quantitative proteomics – several groups are independently
using labelling iTRAQ and more recently SILAC based
quantitation. In addition, several projects are providing a
framework for development of label-free quantitative analysis,
especially useful for clinical samples.
Post-translational modifications – several groups have
now published new tools in analysis of protein phosphorylation
and sumoylation.
Mass spectrometry imaging – MS imaging continues to
develop locally, with expansion of the activities taken up in
the new Master’s Degree Programme in Biomedical Imaging.
Biological mass spectrometry – numerous groups use the
Facility for additional analytical services that are not directly
related to proteomics, such as protein, peptide and small
molecule structure determination, mass determination and
peptide and protein purity analysis.
Protein separation – by liquid chromatography and a variety
of gel based methods such as 1-DE, 2-DE, peptide-IPG and
blue native gel electrophoresis.
Bioinformatics – identification, quantitation and validation
studies, reporting and software development.
16
From left to right: Anne Rokka, Arttu Heinonen, Petri Kouvonen, Eliza Ralph.
17
The core operations of the facility are in services and training in
proteomics to the local and national biosciences community.
In doing so the facility aims to cover diverse fields requiring the
analysis of proteins in cells, tissues, organisms and body fluids.
To achieve this, the facility is active in the following three activities:
Analytical services
The aim is to offer the best possible analytical proteomics services
to bioscience researchers in academia and industry, both locally
and nationally through Biocentre Finland coordinated activities.
Locally, a broad range of MS analyses are performed, whilst at the
national level the facility spearheads developments in two of its
services; MS-based quantitative proteomics and phosphorylation
determination.
Training
Our aim is to organise and coordinate of training events and
symposia focusing on Proteomics, mass spectrometry and
computational tools and procedures for the analysis of MS data.
Innovation
The facility develops tools and procedures in collaboration with
facility users and groups. Through activities linked to Biocenter
Finland services, two focus areas of development for the facility are
in quantitation and phosphorylation analysis.
The facility has excellent instrumentation for a wide range of MS
analyses, including four different mass spectrometers: an Ultraflex
II (MALDI-TOF/TOF), a QStar Pulsar and Elite (ESI-QqTOF) and a
Esquire HTC (ESI-ion trap MS). The ESI instruments are all in-line
coupled to nanoHPLC systems, and can also be used for direct
nanospray ESI. Additional nanoHPLC systems robotic microfraction
collectors enable real-time collection of peptide fractions, direct
on MALDI targets. A LIMS system and computational analysis
pipeline. The facility also hosts hotel services where visiting
scientists can use shared facility space for sample preparation and
analysis. In addition to analytical services, the facility organises
and participates in national collaborative programs and research
efforts with others throughout the Nordic region and worldwide.
The facility also participates actively in national and international
educational programs in Europe and abroad, such as Nordforsk,
EuPA and HUPO.
Funding:
Biocenter Finland, The Academy of Finland, TEKES, City of Turku,
Ministry of Education/Proteomics and the Centre of Expertise of
Southwest Finland, Turku University and Åbo Akademi University,
Bruker Daltonics, the Systems Biology Research Program.
Users:
Biocentre Finland universities, The University of Turku, Åbo
Akademi University, Turku Polytechnic. 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.
18
CELL IMAGING CORE (CIC)
http://[email protected]/
Coordinator and group leader:
Eleanor Coffey, Ph.D., Adjunct Professor in Cellular and Molecular
Biology, Turku Centre for Biotechnology, BioCity, 5th floor, Tykistökatu
6, FI-20521, Finland. Tel. +358-2-3338605, Fax. +358-2-3338000.
Technical Team:
Jouko Sandholm, M.Sc., Senior Researcher Microscopy, Email:
[email protected], Perttu Terho, B.Sc., Technical Engineer
Flow Cytometry, Email: [email protected]
Imaging Consultants:
Prof. Michael Courtney, Ph.D., Research Director, A.I.Virtanen
Institute, University of Kuopio, Finland. Email: [email protected]
Kaisa Heiskanen, Ph.D., Orion Pharma. Email: kaisa.heiskanen@
orionpharma.com
Steering Committee:
Prof. Olli Carpén, M.D., Ph.D., Prof. John Eriksson (chairman),
Ph.D., Prof. Jyrki Heino, M.D., Ph.D., Prof. Pekka Hänninen, Ph.D.,
Prof. Sirpa Jalkanen, M.D., Ph.D., Prof. Riitta Lahesmaa, M.D.,
Ph.D., Prof. Olli Lassila, M.D., Ph.D., Prof. Matti Poutanen, Ph.D.,
Prof. Lea Sistonen, Ph.D., Kid Törnquist, Ph.D.
The Cell Imaging Core (CIC) is a centralised facility that coordinates
biological imaging activities between the University of Turku,
Åbo Akademi University, VTT Technical Research Centre, Turku
Functional Genomics Centre, the National Centre for Disease
Models and the biophysics community, while providing services at
the national level. The mission of CIC is to provide state-of-theart cell imaging and cell sorting technologies and to make them
available to academic and industrial researchers.
The primary goal of CIC is to enhance the research and teaching
environment of BioCity Turku. To help meet these goals, the core unit
• 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
organising training courses and international workshops
As a result, CIC has grown in significance, the services provided
being instrumental to the publication of over 200 international
scientific articles in recent years, many of which are in the most
prestigious journals. Our staff include a coordinator and experienced
applications specialists who maintain the instruments, learn new
technologies and most importantly, provide personal training to
users. Our areas of technical expertise are confocal microscopy
19
University Medical School, Chicago), Irina Majoul (Royal Holloway,
London), Scott Brady (University of Illinois at Chicago), Gyorgy
Hajnoczky (Thomas Jefferson University, Philadelphia), Michael
Courtney (University of Kuopio), Teng Leong-Chew (Northwestern
University Medical School, Chicago), Stephen Ogg (Institute of
Medical Biology, Singapore), Kota Miura (EMBL, Heidelberg),
Martin Leahy (University of Limerick), Gregory McNerny (Univeristy
of California Davis). The CIC-initiated Nordic Network on Imaging
in Medicine and Biology adds to this list a range of additional
participants, principally from the Nordic area. Ongoing intimate
collaboration between these experts and the Cell Imaging Core
ensures continued transfer of advanced imaging skills from these
leading labs. To strengthen bioscience imaging in the Turku region,
CIC has expanded its web pages to include imaging technologies
and contacts across the campus. CIC maintains close contact
with imaging specialists locally and is a major player in the Turku
Bioimaging initiative, an active discussion forum established in
2007 to promote imaging in the Turku region.
From left to right: Jouko Sandholm, Eleanor Coffey, Perttu Terho, Markku Saari.
(including timelapse and spectral detection), widefield fast CCD
imaging, laser microdissection, high throughput cell sorting and
advanced flow cytometry software development.
To maintain the advanced, national level service provided so far,
we organise training programmes, service existing equipment,
sustain research on new imaging techniques, and implement the
latest technological advances demanded by the Finnish research
community. CIC has succeeded both as a service provider and as a
point of integration of emerging imaging technologies. Added value
is achieved by the present local expertise in the Turku area in the
fields of fluorescence-activated cell sorting, confocal microscopy,
fluorescence-based screening and robotic instrumentation,
imaging-based high-content screening, in vivo animal imaging, and
viral gene transfer, and by the presence of the National Centre for
Disease Models and the transgenic animal core facility.
CIC coordinates the Nordic Network on Imaging in Medicine and
Biology. This network gathers the leading units on cellular and
medical imaging in the Nordic region and was funded initially by the
Joint Committee of the Nordic Research Councils and currently by
Nordforsk, the funding agency of the Nordic Council of Ministers.
The network assembles 38 prominent research groups and aims to
improve interdisciplinary training and cooperation between diverse
imaging fields.
The following international leaders in the field have contributed
to advanced imaging education in Turku providing during their
visits practical as well as theoretical training: Jennifer LippincottSchwartz (NIH, USA), Stefan Hell (Max Planck Institute for
Biophysical Chemistry, Gottingen University, Germany), Rainer
Duden (Royal Holloway, London), Robert Goldman (Northwestern
20
21
VIRUS VECTOR FACILITY
http://virusvec.btk.fi
Coordinator:
Eleanor Coffey, Ph.D., Adjunct Professor in Cellular and Molecular
Biology, Turku Centre for Biotechnology, BioCity, 5th floor,
Tykistokatu 6, FI-20521, Finland. Tel. +358-2-3338605, Fax. +3582-33378000. Email: [email protected]
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.
Research, Development and Training:
Anna Cvrljevic, postdoctoral researcher (Westermarck lab), Turku
Centre for Biotechnology, BioCity 5th floor, Tykistökatu 6, FI-20521,
Finland. Email: [email protected]
Technical Team:
Marjo Hakkarainen, Laboratory Technician,
Susanna Pyökäri, Laboratory Technician,
Email: susanna.pyökä[email protected]
Ketlin Adel, Laboratory Technician, Email: [email protected]
The Virus Vector Facility produces viral vectors for local and national
research groups. During 2009, the Virus Vector Facility joined the
national infrastructure network on Viral Gene Transfer, funded by
Biocenter Finland. Our primary function is to facilitate the use of
viral vectors by national researchers. To meet these goals the virus
vector facility
•
Produces on demand adenoviruses and lentiviruses
expressing genes of interest, as a research service
•
provides a fully equipped bio-safety level-2 lab for
researchers wishing to produce their own vectors
(replication deficient viruses only)
•
supplies working protocols for production of adeno and
lenti vectors and trains researchers in the safe preparation
and handling of viral vectors
•
organises seminars and courses emphasizing practical
issues related to gene transfer technology
•
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 regular
customers from the universities of Turku, Oulu and Helsinki as well
as customers from biotech companies. In addition to customer
service, our infrastructure is used by 16 local research groups
producing adenoviruses, adeno-associated virus, retro- and lentivirus for their own research purposes. These viruses are typically
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. Another typical application is the use of
viral vectors for delivery of shRNA. Protocol optimization has been
completed for high efficiency gene silencing in primary cultured
neurons and T lymphocytes and more recently investigators are
using virally delivered miRNAs for gene knockdown studies.
22
From left to right: Susanna Pyökäri, Anna Cvrljevic, Jukka Westermarck,
Marjo Hakkarainen, Eleanor Coffey.
23
PROTEIN CRYSTALLOGRAPHY
CORE FACILITY
DATA MINING AND
MODELING GROUP
http://crystal.btk.fi
http://users.utu.fi/teanai/
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.
Principal investigators:
Tero Aittokallio, Ph.D., Docent in Biomathematics,
Department of Mathematics, University of Turku, FI-20014 Turku,
Finland. Tel. +358-2-3336030, Fax. +358-2-3336595.
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
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, Mar345
imaging plate detector, Osmic confocal mirrors, a Cryostream
Cooler (Oxford Cryosystems) and several computers running under
Unix or Linux operating systems for heavy duty calculations. The
Unit has several workstations to run variety of graphic software (O,
XtalView, Grasp, COOT, CCP4mg, PyMol), modeling and docking
programs (MODELLER, Hex, Discovery Studio), and various
crystallographic packages (HKL, 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 prepapations, we can offer full support and consultation on
protein purification strategies apart from the services in structure
determination and modeling. The Unit is able to undertake research
projects for academic groups and companies, either in the form of
collaborative efforts or as services. Protein Crystallography requires
a multi-disciplinary approach and we are especially interested
in bringing together expertise from various groups in order to
better understand the structure-function relationship of biological
macromolecules in key biological processes.
Funding:
Systems Biology research program, Biocenter Finland
24
Olli Nevalainen, Ph.D., Professor of Computer Science, Turku
Centre for Computer Science, Joukahaisenkatu 3-5 B, FI-20520
Turku, Finland. Tel. +358-2-3338631; Email: [email protected]
Biographies:
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 in the
Biomathematics Research Group.
Olli S. Nevalainen received his Ph.D. degree 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: Laura Elo, Ph.D., Jussi Salmi, Ph.D.,
Graduate students: Bin Gao, M.Sc., Jukka Hiissa, M.Sc., Ville
Koskinen, M.Sc., Rolf Linden, M.Sc., Sebastian Okser, M.Sc.,
Johannes Tuikkala, M.Sc., Heidi Vähämaa, M.Sc., Undergraduate
students: Aki Järvinen, Essi Laajala, Teemu Daniel Laajala, Lari
Natri, Mirva Piippo.
Description of the project:
The research group develops mathematical modeling methods and
implements computational analysis tools for mining data generated
by modern high-throughput biotechnologies. The large number of
components probed together with high technical and biological
variability can make it difficult to extract pertinent biological
information from the background noise. This has increased the
need for computational models and tools that can efficiently
integrate, visualize and analyze the experimental data so that the
most important questions can be addressed and the meaningful
interpretations can be made. The eventual aim is to model and
explain the observations as a dynamic interaction of key molecular
components and mechanisms controlling the underlying system.
Data mining protocols developed so far cover a wide range of highthroughput biotechnologies, such as gene and exon arrays (cDNA,
Affymetrix and Illumina platforms) for global gene expression
profiling, together with RNA interference (RNAi) and chromatin
immunoprecipitation (ChIP) studies (ChIP-chip and ChIP-seq) for
monitoring transcriptional regulation on a global scale, as well as
mass-spectrometry (MS)-based assays for large-scale proteomic
studies and comparative genomic hybridizations (CGH) for
detecting gene amplification or deletion events. One of the most
important computational challenges is to take full advantage of all
the accumulated data, both from own laboratory and from public
25
repositories, to obtain a more comprehensive view of the system
under study.
We are developing a data integration approach, which can
effectively correct for the technical variation characteristic to various
experimental platforms, and hence improve the comparability
of different experiments, identification of differentially expressed
genes and proteins, and inference of their interaction partners in
global cellular networks. Such integrative network-based modeling
approach can provide robust and unbiased means to reveal the
key molecular mechanisms behind the systems behavior and to
predict its response to various perturbations. In clinically-oriented
research, the modeling 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, Systems Biology research programme,
and the Graduate School in Computational Biology, Bioinformatics,
and Biometry (ComBi).
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:
Okser, S., Lehtimäki, T., Elo, L.L., Mononen, N., Peltonen, N.,
Kähönen, M., Juonala, M., Fan, Y.M., Hernesniemi, J.A., Laitinen,
T., Lyytikäinen, L.P., Rontu, R., Eklund, C., Hutri-Kähönen, N.,
Taittonen, L., Hurme, M., Viikari, J.S.A., Raitakari, O.T., and
Aittokallio, T. (2010).Genetic variants and their interactions in the
prediction of increased pre-clinical carotid atherosclerosis -- The
Cardiovascular Risk in Young Finns Study, PLoS Genetics (in
press).
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 (in press).
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,
Molecular & Cellular Proteomics (in press).
Lahti, L., Elo, L.L., Aittokallio, T., and Kaski, S. (2010) Probabilistic
analysis of probe reliability in differential gene expression studies with
short oligonucleotide arrays, IEEE Transactions on Computational
Biology and Bioinformatics (in press).
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, Photosynthesis Research (in press).
26
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.
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, Journal of Autoimmunity
35: 70-76.
Aittokallio, T. (2010) Dealing with missing values in large-scale
studies - microarray data imputation and beyond, Invited Review,
Briefings in Bioinformatics 11: 253-264.
Korolainen, M.A., Nyman, T.A., Aittokallio, T., and Pirttilä, T. (2010)
An update on clinical proteomics in Alzheimer’s research, Journal
of Neurochemistry 112: 1386-1414.
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 Biology 10: R77.
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.
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.
27
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Aittokallio, T. (2009) Optimized detection of differential expression in
global profiling experiments: case studies in clinical transcriptomic
and quantitative proteomic datasets. Briefings in Bioinformatics 10:
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Hiissa, J., Elo, L.L., Huhtinen, K., Perheentupa, A., Poutanen, M.
and Aittokallio, T. (2009) Resampling reveals sample-level differential
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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.
Clément-Ziza, M., Malabat, C., Weber, C., Moszer, I., Aittokallio, T.,
Letondal, C. and Rousseau, S. (2009) Genoscape: a Cytoscape
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Merisaari, H., Parkkola, R., Alhoniemi, E., Teräs, M., Lehtonen,
L., Haataja, L., Lapinleimu, H., Nevalainen, O.S. (2009) Gaussian
mixture model-based segmentation of MR images taken from
premature infant brains. J Neurosci Methods 182: 110-122.
PROTEIN KINASE REGULATION OF
BRAIN DEVELOPMENT AND DISEASE
http://www.btk.fi/index.php?id=1240
Principal investigator:
Eleanor Coffey, Ph.D., Academy of Finland 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.
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 was awarded a Wellcome Trust fellowship to carry
out postdoctoral research in Prof. Karl Åkerman’s laboratory from
1994-1997. In 1997 she founded the Neuronal Signaling group at
Åbo Akademi and in 2000 joined Turku Centre for Biotechnology
as a group leader in molecular and cellular biology. In addition to
running a research group, she directs the Cell Imaging Core at Turku
Centre for Biotechnology and coordinates the Nordic Network on
Imaging in Biology and Medicine. She currently holds an Academy
of Finland Research Fellow position.
Personnel:
Postdoctoral researcher: Minna Tuittila, Ph.D., Graduate
students: Artur Padzik, M.Sc., Justyna Zdrojewska, M.Sc., Emilia
Komulainen, M.Sc., Raghavendra Mysore, M.Sc., Yubao Wang,
M.Sc., Undergraduate and exchange students: Hanna Heikelä,
Lihua Sun, Agnieszka Bialek, Prasannakumar Deshpande.
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.
From left to right: Johannes Tuikkala, Heidi Vähämaa, Laura Elo, Rolf Linden, Jussi
Salmi, Olli Nevalainen, Ville Koskinen, and Tero Aittokallio.
28
A major challenge for signal transduction therapy is to selectively
target the pathological function of signaling 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 other targets under study, has highlighted
a critical role for JNK in maintaining microtubule homeostasis and
subsequently regulating axodendritic architecture. Identification of
the JNK phosphorylation site on kinesin-1 helped characterize a
role for JNK in regulation of fast axonal transport in neurons. We
combine biochemical, proteomic, cell biology and imaging methods
29
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 that we stumbled upon regarding JNK function
in the nervous system, was the compartmental segregation of
physiological verses pathological JNK function to 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 (the
type of neuronal death that occurs during brain development) and
in response to excitotoxic stimuli (the type of neuronal death that
occurs in epilepsy, stroke and contributes to neurodegenerative
disorders). Interestingly, although JNK is highly localised to the
cytoplasm in neurons, we have shown that cytosolic JNK does
not to contribute to these modes of neuronal death. Instead,
we find that cytosolic JNK regulates physiological processes
that maintain neuritic architecture and regulate migration. These
functions of JNK are in turn mediated via cytosol-localised targets,
independent of JNK-dependent transcriptional regulation. To
realise 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. By gaining information on how apoptotic
and physiological functions of signaling molecules are partitioned
within the cell allows selective targeting of inhibitors towards loci
where pro-apoptotic events take place. This work provides proof
of principal that subcellular targeting of inhibitor molecules provides
increased specificity with reduced physiological disturbance.
Funding:
EU 6th framework STREP “STRESSPROTECT”, EU 6th framework
ToK grant, “GAMIDI”, the Academy of Finland, Åbo Akademi
University, Turku University Biomedical Sciences Graduate School,
Finnish Graduate School in Neurosciences, Drug Discovery
Graduate School, Magnus Ehrnrooth’s Stiftelse, CIMO, Sitra and
the Torr Joe och Pentti Borgs Foundation.
Collaborators:
Michael Courtney (University of Kuopio), 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).
Neurochem Int.
J Immunol.
30
Mol Cell Biol.
Nat Neurosci.
Cellular
Signalling,
Cell Adhesion and Migration,
Journal of Biological Chemistry,
Molecular and Cellular Biology,
Dan Johansen, L., Naumanen, T., Knudsen, A., Westerlund, N.,
Gromova, I., Junttila, M., Nielsen, C., Bottzauw, T., Tolkovsky,
A., Westermarck, J., Coffey, E.T., Jäättelä, M., Kallunki, T. (2008)
IKAP localizes to membrane ruffles with filamin A and regulates
actin cytoskeleton organization and cell migration. Journal of Cell
Science, 121:854-64.
Westerlund, N., Zdrojewska, J., Courtney, M., Coffey, E. (2008)
SCG10 as a molecular effector of JNK1: Implications for the
therapeutic targeting of JNK in nerve regeneration. Expert Opinion
on Therapeutic Targets. 12:31-43. Review.
Semanova, M.M., Mäki-Hokkanen, A.M.J., Cao, C., Komarovski,
V., Forsberg, K.M., Koistinaho, M., Coffey, E.T., Courtney, M.J.
(2007) Rho mediates calcium-dependent activation of p38a and
subsequent excitotoxic cell death. Nature Neuroscience, 10(4):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.,
Runeberg-Roos, P., Saarma, M. (2004) PSPN/GFRalpha4 has a
significantly weaker capacity than GDNF/GFRalpha1 to recruit RET
to rafts, but promotes neuronal survival and neurite outgrowth.
FEBS Letters.569: 267-271.
31
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.
Biochem. Soc. Trans.
Courtney, M.J., Åkerman, K.E.O. and Coffey, E.T. (1997)
Neurotrophins protect cultured cerebellar granule cells against the
early phase of cell death by a two-component mechanism. Journal
of Neuroscience. 17: 4201-4211.
From left to right, front row: Hasan Mohammad, Emilia Komulainen, Justyna
Zdrojewska, Eleanor Coffey, back row: Raghavendra Mysore, Lihua Sun,
Prasannakumar Deshpande. Missing from the photo: Artur Padzik, Hanna Heikelä.
32
Organisation of Neuronal
Signaling Pathways
Michael Courtney, Ph.D., Research manager, Professor of Cell
Signaling. Contact information: Molecular Signaling Laboratory,
Department of Neurobiology, A.I. Virtanen Institute, University of
Kuopio, P.O. Box 1627, Neulaniementie 2, FIN-70211 Kuopio, Finland.
Biography:
Michael Courtney (b. 1967) graduated from University of Cambridge
in 1988 (B.A.), and the University of Dundee in 1991(Ph.D).
Postdoctoral fellowships from the Royal Society, Wellcome Trust,
Academy of Finland and Sigrid Jusélius Foundation supported his
quantitative imaging development and application activities from
1992 in Prof. Karl Åkerman’s laboratory in Åbo Akademi, Turku.
After group leader positions at BTK from 1998, he was appointed
from 2000 to a position at the A.I. Virtanen Institute, Kuopio and
from 2006 to BTK. He has been affiliated with the Cell Imaging Core
since its inception, and established and is running the Multimodal
Imaging Unit at Kuopio University. He was appointed to an Academy
of Finland Researcher post from 2003-2008, and Professor of Cell
Signaling at the University of Kuopio from 2008.
Personnel:
Post-doctoral researchers: Franz Ho Ph.D.Ph.D., Peter Martinsson
Ph.D., Minna Tuittila Ph.D., Olga Vergun Ph.D.
Graduate students: Dorota Kaminska M.Sc., Kaisa Kosonen B.Sc.,
Lili Li, B.Sc., Xiaonan Liu, M.Sc., Maykel Lopez-Rodriguez M.Sc.,
Leena Yadav M.Sc.
Undergraduate students: Tim Church, Soila Tossavainen
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 mammalian stress-activated MAPK pathway
have revealed the existence of a plethora of upstream regulators
competent to recruit this pathway. In particular, proteins with
putative scaffolding actions have been found. Such components
could in principle have a number of effects on the associated
upstream regulator, including (i) to potentiate their ability to activate
33
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 stresses recruit only select components
of these pathways. To achieve this, we currently focus on 3 areas:
i) The impact of post-synaptic density proteins on neuronal stressactivated protein kinase signaling 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. Recent publications
revealed protein complexes of the postsynaptic compartment as
upstream regulators of p38MAPK in neuronal stress responses
(Cao et al., 2005; Semenova et al., 2007). 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 on multiparameter
imaging that allows 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 live cell high High-Content
Analysis (HCA)), as well as TIR-FRET and TIR-FRAP techniques.
Total Internal Reflection methods exploit the spatially restricted
evanescent wave formed at the interface between media of different
refractive indices, thereby surpassing the classical diffraction limits.
These methods are ideally suited to measure signaling events and
protein turnover at protein complexes in the plasma-membrane
proximal zones of living cells. The live-cell HCA unit is nationally
unique and is now supported as a platform by two Biocenter
Finland networks as part of the national Biocenter infrastructure.
Funding:
The Academy of Finland, The EU 6th framework STREP
“STRESSPROTECT”, the EU 7th framework project “MEMOLOAD”,
The Sigrid Juselius Foundation, The University of Kuopio, The Drug
Discovery Graduate School, The Molecular Medicine Graduate
School.
Collaborators:
Eleanor Coffey and Tassos Papageorgiou (BTK, 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), Markus Rehm (Royal College Of Surgeons of
Ireland), Anita Truttman (CHUV, Lausanne University Hospital),
Mingjie Zhang (Hong Kong Institute of Science and Technology).
34
Waetzig, V., Wacker, U., Haeusgen, W., Björkblom, B., Courtney,
M.J., Coffey, E.T. and Herdegen, T. (2009) Concurrent protective
and destructive signaling of JNK2 in neuroblastoma cells. Cell
Signal. 21, 873-80
Hellwig, C.T., Kohler, B.F., Lehtivarjo A.-K., Dussmann, H., Courtney,
M.J., Prehn, J.H. and Rehm, M. (2008) Real-time analysis of TRAIL/
CHX-induced caspase activities during apoptosis initiation. J. Biol.
Chem. 283, 21676-85.
Björkblom, B., Vainio, J.C., Hongisto, V., Herdegen, T., Courtney,
M.J. and Coffey, E.T. (2008) All JNKs can kill but nuclear localization
is critical for neuronal death. J. Biol. Chem. 283, 19704-19713.
Hongisto, V., Vainio, J.C., Thompson, R., Courtney, M.J. and Coffey,
E.T. (2008) The Wnt pool of GSK-3β is critical for trophic deprivation
induced neuronal death. Mol. Cell. Biol. 28, 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 p38α and
subsequent excitotoxic cell death. Nat. Neurosci. 10, 436-443.
Tararuk, T., Östman N., Li, W., Björkblom, B., Padzik, A., Zdrojewska,
J., Hongisto, V., Herdegen, T., Konopka, W., Courtney M.J. and
Coffey, E.T. (2006) JNK1 phosphorylation of SCG10 determines
microtubule dynamics and axodendritic length. J. Cell Biol. 173,
265-277.
Björkblom, B., Östman, N., Hongisto, V., Komarovski, V., Filén, J.,
Nyman, T.A., Kallunki, T., Courtney, M.J. and Coffey, E.T. (2005)
Constitutively active cytoplasmic JNK1 is a dominant regulator of
dendritic architecture; role of MAP2 as an effector. J. Neurosci. 25,
6350-6361.
Cao, J., Viholainen, J.I., Dart, C., Warwick, H.K., Leyland, M.L.
and Courtney, M.J. (2005) The nNOS-PSD95 interface - a target
for inhibition of excitotoxic p38 stress-activated protein kinase
activation and cell death. J. Cell Biol. 168, 117-126.
Cao, J., Semenova, M.M., Solovyan, V.T., Han, J., Coffey, E.T and
Courtney, M.J. (2004) Distinct requirements for p38α and JNK
stress-activated protein kinases in different forms of apoptotic
neuronal death. J. Biol. Chem. 279, 35903-35913.
Solovyan, V.T., Bezvenyuk, Z., Salminen, A., Austin, C.A. and
Courtney M.J. (2002) The role of topoisomerase II beta in the
excision of DNA loop domains during apoptosis. J. Biol. Chem.
277, 21458-21467.
Coffey, E.T., Smiciene, G., Hongisto, V., Cao, J., Brecht, S.,
Herdegen, T. and Courtney, M.J. 2002) JNK2/3 is specifically
activated by stress, mediating c-Jun activation, in the presence of
constitutive JNK1 activity in cerebellar neurons. J. Neurosci. 22,
4335-4345.
35
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.
Courtney, M.J., Lambert, J.J. and Nicholls, D.G. (1990) The
interactions between plasma membrane depolarization and
glutamate receptor activation in the regulation of cytoplasmic free
calcium in cultured cerebellar granule cells. J. Neurosci. 10, 38733879.
Cytoskeletal and survival
signaling
Principal Investigator:
John E. Eriksson, Ph.D., Professor. Address: Dept. of Biology,
Åbo Akademi University, FI-20520 Turku, Finland.
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. +358–2–3338000.
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 Dr. Robert D. Goldman’s laboratory during 1990-1993
(Fogarty International Fellowship from the National Institutes of
Health 1991-1993). In November 1993 he joined the Centre for
Biotechnology as a senior research fellow in cell biology. In 1999 he
was appointed as Professor of Zoology at the Department of Biology,
University of Turku. In 2006 he was appointed as Professor of Cell
Biology at the Department of Biology, Åbo Akademi University and
became Head of Cell Biology at the department in 2007.
Description of the Project:
Reversible protein phosphorylation is a key determinant in many
fundamental cellular functions, such as survival, differentiation,
structural organization, and stress responses. We are especially
interested in phosphorylation-mediated signaling that maintains
normal cellular and structural homeostasis, and how disturbances
in the processing of this type of signaling are reflected as alterations
in cellular survival and organization. As model systems for signal
processing, we are studying apoptotic, stress-mediated, and
cytoskeletal signaling, and 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 have observed that growth signaling through the mitogenactivated kinase (MAPK) pathway has a dominant inhibiting
effect on apoptosis induced by death receptors (Fas, TRAIL,
and TNF receptors). We have shown that this mode of regulation
has ramifications both in regulating death receptor responses of
recently activated T-cells and in the resistance of certain tumor cell
lines to death receptor stimulation. We have determined that the
MAPK-mediated inhibition takes place by inhibiting the apoptotic
signaling from the death-inducing signaling complex (DISC) of
proteins assembled at the death receptor. We are determining the
molecular mechanisms of this inhibition and how the DISC proteins
and their interactions are regulated. Apoptosis is also affected by
stress-mediated signaling. We have observed that stress facilitates
death receptor-mediated apoptosis in a independently of heat
shock protein expression. The stress-mediated sensitization is
due to selective degradation of FLIP, a specific inhibitor of death
receptor signaling. Targeted FLIP degradation by ubiquitylation is
also responsible for the sensitization to TRAIL receptor-induced
apoptosis that we observed in differentiating 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 differentiation-related processes.
36
37
Intermediate filaments (IFs) are major cytoskeletal proteins
important for ultrastructural organization and protection against
various mechanical and other types of stresses. Recent studies
have provided evidence that IFs are also involved in regulation of
signaling. We have demonstrated that reversible phosphorylation is
the key mechanism behind the assembly dynamics of IF proteins.
Moreover, 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 elucidate 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) and Lea Sistonen (Turku Centre for Biotechnology).
The studies on IF-related signaling functions are carried out as a
collaboration with 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) and Bishr Omary (Stanford University, Palo Alto, USA).
Funding:
The Academy of Finland, TEKES, the European Union, the Finnish
Cancer Organizations, the Sigrid Jusélius Foundation, and the Åbo
Akademi Foundation.
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. 285:19324-9
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. Vimentin is a
functional partner of hormone sensitive lipase and facilitates
lipolysis. J. Proteome Res. 9:1786-1794.
38
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.
(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.16:1215-26.
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: 464-75.
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: 3944-53.
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.
39
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.
(2005) CD95 capping is ROCK-dependent and dispensable for
apoptosis. J. Cell Sci. 118: 2211-2223.
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.
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. (2005) Mol. Cell. 20: 33-44.
Eriksson, J.E., He, T., Trejo-Skalli, A.V., Härmälä-Brasken, A.S.,
Hellman, J., Chou, Y.H. and Goldman, R.D. (2004) Specific in vivo
phosphorylation sites determine the assembly dynamics of vimentin
intermediate filaments. J. Cell Sci. 117:919-32.
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.
Tran, S.E.F., Holmström, T.H., Ahonen, M., Kähäri, V-M. and
Eriksson J.E. (2001) MAPK/ERK overrides the apoptotic signaling
from Fas, TNF, and TRAIL receptors. J. Biol. Chem. 276: 1648416490.
Holmström, T.H., Schmitz, I., Söderström, T., Poukkula, M.,
Johnson, V.L., Krammer, P. H., Chow, S.C. and Eriksson, J.E.
(2000) MAPK/ERK signaling in activated T cells inhibits CD95/Fasmediated apoptosis downstream of DISC assembly. EMBO J. 19:
5418-5428.
40
From left to right, front row: Jenny Niinimäki, Petra Sonneborn, Emilia Peuhu, Tomoko
Asaoka, Gloriane Lazaro, Susumu Imanishi, second row: Hanna-Mari Pallari, Kimmo
Isoniemi, Juha Kastu, Claire Hyder, Erik Niemelä, Jenny Niinimäki, Vitaly Kochin,
John Eriksson.
41
Cell Adhesion and Cancer
Professor Johanna Ivaska, Ph.D.Ph.D., VTT Medical
Biotechnology, Itäinen Pitkäkatu 4C, FI-20520 Turku, Finland;
Phone: + 358 20 722 2807; FAX: + 358 20 722 2840,
email: [email protected]
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 2008-2012 in their
Cancer Signalosome project.
Personnel:
Post-docs: Elina Mattila, Ph.D.; Jeroe Pouwels, Ph.D.; Stefan Veltel,
Ph.D.; Ghaffar Muharram, Ph.D.. Graduate students: Jonna Nevo,
MSc; Karoliina Vuoriluoto, MSc; Anja Mai, MSc; Saara Tuomi, MSc;
Antti Arjonen, MSc; Reetta Virtakoivu, MSc; Gunilla Högnäs; MSc.
Technicians: Heidi Jalonen, Jenni Siivonen (both on maternity leave.
Substituted by Laura Lahtinen and Emilia Helminen).
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 behaviour
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 signalingsignaling pathways is well
established but incompletely understood. In normal cells permissive
signalingsignaling 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 signalingsignaling 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 propose to investigate spatially
regulated integrin membrane complexes. We aim to understand
adhesion regulated signaling and the biological function of integrin
membrane traffic in human malignancies.
42
From left to right, sitting: Ghaffar Muharram, Johanna Ivaska, Reetta Virtakoivu,
second row: Jeroen Pouwels, Jarkko Heiskanen, Saara Tuomi, Elina Mattila, Stefan
Veltel, Gunilla Högnäs, Laura Lahtinen, Jonna Nevo, Anja Mai, Emilia Helminen.
Tuomi, S., Mai, A., Nevo, J., Laine, JO, Vilkki, V., Öhman, TJ.,
Gahmberg, CG., Parker, PJ. and Ivaska, J. (2009) PKC Regulation
of an 5 Integrin–ZO-1 Complex Controls Lamellae Formation in
Migrating Cancer Cells. Science Signaling, 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.
Mattila E, Marttila H, Sahlberg N, Kohonen P, Tahtinen S, Halonen
P, Perala M, Ivaska J. (2010) Inhibition of receptor tyrosine kinase
signalling by small molecule agonist of T-cell protein tyrosine
phosphatase. BMC Cancer. 10(1):7.
Pellinen T., Tuomi, S., Arjonen, A., Wolf, M., Edgren, H., Meyer,
H., Grosse, R., Kitzing, T., Rantala, JK., Kallioniemi O., Fässler, R.,
Kallio, M., and Ivaska, J. (2008) Integrin traffic regulated by Rab21
is necessary for cytokinesis. Dev. Cell, 15:371-385.).
Mattila, E., Koskinen, K., Salmi, M. and Ivaska, J. (2008) Protein
tyrosine phosphatase TCPTP controls VEGFR-2 signalling. J. Cell
Sci. 121:3570-80.
Vuoriluoto, K., Jokinen, J., Salmivirta, M. Heino, J. and Ivaska, J.
(2008) Distinct syndecans function as integrin α2β1 co-receptors
in 2D and 3D collagen. Exp. Cell Res. 314:3369-81.
43
Pellinen T, Arjonen A, Vuoriluoto K, Kallio K, Fransen JA, Ivaska J.
Small GTPase Rab21 regulates cell adhesion and controls endosomal
traffic of beta1-integrins. J. Cell Biol. 2006 173:767-80.
Pellinen T. and Ivaska J. Integrin traffic, invited commentary (2006).
J Cell. Sci. 119:3723-31.
Mattila E., Pellinen, T., Nevo, J., Vuoriluoto, K. Arjonen, A. and
Ivaska, J (2005) Negative regulation of EGFR signalling via integrin
α1β1-mediated activation of protein tyrosine phosphatase TCPTP. Nat. Cell Biol. 7: 78-85.
Ivaska, J., Vuoriluoto, K., Huovinen, T., Izawa, I., Inagiki, K., and
Parker, PJ. (2005) PKCβ-mediated phosphorylation of vimentin
controls integrin recycling and motility. EMBO J. 24:3834-3845.
HYPOXIA IN CELL SURVIVAL
Panu Jaakkola, M.D., Ph.D., Senior fellow of The Academy of Finland.
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:
Post-doctoral scientist: Juha Pursiheimo, (Ph.D.)
Graduate students: Terhi Jokilehto, (M.Sc.), Pekka Heikkinen,
(M.Sc.), Heidi Högel, (M.Sc.), Krista Rantanen, (M.Sc.)
Technicians: Taina Kalevo-Mattila
Undergraduate students: Marika Nummela, Katri Piilonen,
Siri Tähtinen
Hypoxia (reduced O2 tension) is the main tissue damaging factor
in several ischemic diseases. In contrast to the normal tissue,
tumours use hypoxia as a growth-promoting factor. During ischemic
assaults such as strokes, hypoxia activates apoptosis and leads to
severe tissue damage. During cancer progression hypoxia causes
inhibition of apoptosis and enhances tumour aggressiveness and
metastasis. In keeping with this, it has been known for much of
the past century that hypoxia causes resistance cancer treatments
- both to chemotherapy and radiotherapy - and leads to poor
prognosis. The aim of the project is to reveal mechanisms by which
hypoxia regulates survival decisions in ischemic diseases and
cancer progression. Our group has undertaken two major avenues
to tackle the issue.
The reduced oxygen is sensed by a family of enzymes called the HIF
prolyl hydroxylases (PHD1-3). Under normoxia the hypoxia-inducible
factor (HIF) is hydroxylated by PHDs at critical proline residues. This
leads to ubiquitylation and proteosomal destruction of HIF. Under
hypoxic conditions the hydroxylation ceases and HIF is stabilised.
HIF then exerts its effects by activation of 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, differentiation of cancer cells as well
as 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-β (TGF-β) is one of the bestcharacterised 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-β 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
44
45
is an environmental factor in tumours that can convert the TGF-β
response into supporting tumorigenesis. Mechanistically, this
involves hypoxic dephosphorylation of a TGF-β effector Smad3.
Moreover, we have recently discovered that hypoxia converts
Smad7, an inhibitor of the TGF-β signaling, from an inhibitor into a
promoter of cell invasion.
Funding:
The Academy of Finland, Sigrid Juselius Foundation, Emil Aaltonen
Foundation
Collaborators:
Peter Ratcliffe and Chris Pugh (Oxford University, UK), Eric Metzen
(Luebeck University, Germany), Joachim Fandrey (Essen University,
Germany), Reidar Grenman (Turku University), Veli-Matti Kähäri
(Turku University), Heikki Minn (PET Centre, Turku University
Hospital)
Epstein, A.C.R., Gleadle, J.M., McNeill, L.A., Hewitson, K.S.,
O’Rourke, J., Mole, D.R., Mukherji, M., Metzen, E., Wilson, M.I.,
Dhanda, A., Tian, Y.-M., Masson, N., Hamilton, D.L., Jaakkola, P.,
Barstead, R., Hodgkin, J., Maxwell, P.H., Pugh, C.W., Schofield,
C.J., Ratcliffe, P.J. C.elegans EGL-9 and mammalian homologues
define a family of dioxygenases that regulate HIF through prolyl
hydroxylation. (2001) Cell 107; 43-54.
Pursiheimo, J., Taskén, K., Jalkanen, M. and Jaakkola, P.
Involvement of Protein Kinase A in FGF-2 Activated Transcription.
(2000) Proc. Natl. Acad. Sci. USA, 97(1): 168–173.
Cockman, M.E., Masson, N, Mole, D.R., Jaakkola, P, Chang, G.W., Clifford, S.C, Maher, E.R, Pugh, C.W., Ratcliffe, P.J., Maxwell,
P.H. Hypoxia inducible factor-alpha binding and ubiquitylation
by the von hippel-lindau tumor suppressor protein. (2000) J. Biol.
Chem. 275: 25733-25741.
Heikkinen P., Nummela M., Kähäri V.M. and Jaakkola P.M. (2010).
Hypoxia converts Smad7 from tumor suppressor into tumor
promoter. Cancer Res., In Press.
Heikkinen P.T., Nummela M., Leivonen S.K., Westermarck J.,
Hill C.S., Kähäri V.-M., Jaakkola P.M. (2010). Hypoxia activated
Smad3-specific dephosphorylation by PP2A. (2010). J Biol.Chem.,
285(6):3740-9. Epub 2009 Dec 1.
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(7):116978. Epub 2010 Feb 12.
Pursiheimo J., Rantanen K., Heikkinen P.T., Johansen T., Jaakkola
P.M. (2009). Hypoxia-activated autophagy accelerates degradation
of SQSTM1/p62. Oncogene, 28(3):334-344.
Rantanen K., Pursiheimo J., Högel H., Himanen V., Metzen E.,
Jaakkola P.M. (2008) Prolyl Hydroxylase PHD3 Activates Oxygendependent Protein Aggregation. Mol Biol Cell 19(5): 2231-40.
Jokilehto, T., Rantanen, K., Luukkaa, M., Grenman, R., Minn, H.,
Kronqvist, P., Jaakkola P.M. (2006). Overexpression and nuclear
translocation of HIF prolyl hydroxylase PHD2 in head and neck
squamous cell carcinoma associates with tumor aggressiveness.
Clin Cancer Res 12(4):1080-1087
Marxsen, J. H., Stengel, P., Doege, K., Heikkinen, P., Jokilehto,
T., Wagner, T., Jelkmann, W., Jaakkola, P., and Metzen, E. (2004)
Hypoxia-inducible factor-1 (HIF-1) promotes its degradation by
induction of HIF-alpha-prolyl-4-hydroxylases. Biochem J 381, 761767
Jaakkola, P., Mole, D. R., Tian, Y. M., Wilson, M.I., Gielbert, J.,
Gaskell, S.J., Kriegsheim, Av, Hebestreit, H.F., Mukherji, M.,
Schofield, C.J., Maxwell, P.H., Pugh, C.W., Ratcliffe, P.J. Targeting
of HIF-alpha to the von Hippel-Lindau ubiquitylation complex by
O2-regulated prolyl hydroxylation. (2001) Science 292; 468-72.
46
From left to right, front row: Panu Jaakkola, Krista Rantanen, Taina Kalevo-Mattila,
second row: Heidi Högel, Maiju Nuutila, Terhi Jokilehto, Marika Nummela.
47
Bioenergy Group
Patrik R. Jones, Ph.D., Group Leader, Turku collegium for Science
and Medicine, University of Turku, Centre for Biotechnology, Turku
BioCity, Tykistökatu 6A, 5krs, 20520, Turku. Tel.:+358-2-333-8094.
Email: [email protected].
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: Sanna Peltonen (Bioinformatics), Linda
Vuorijoki (Biochemistry)
Graduate student: Fernando Guerrero (funded by Center of
Excellence in Integrative Photosynthesis and Bioactive Compound
Research at Systems Biology Level)
To reduce greenhouse gas emissions and implement new
energy-production strategies that replace fossil fuels, alternative
fuel production methods are needed in the future. We target
fundamental and applied topics with the aim of contributing
towards the development of novel sustainable technologies for the
production of engine-ready fuels. The laboratory currently has two
main lines of research:
We study biochemical pathways of plant hydrocarbon biosynthesis
in order to generate components for metabolic engineering.
Photobiological model organisms are engineered in order to (a)
introduce biofuel-pathways that do not exist in nature and (b) to
modify host metabolism to favor those pathways.
Funding:
Varsinais-Suomi Cultural Foundation, Emil Aaltonen Foundation
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:H2Pathways. Microbial Biotechnology 1, 382-394.
Akhtar, K.M., and Jones P.R. (2008) Deletion of iscR stimulates
recombinant clostridial Fe-Fe hydrogenase activity and H2accumulation in Escherichia coli BL21(DE3). Applied Microbiology
and Biotechnology 78(5), 853-862.
Akhtar, K.M., and Jones P.R. (2008) Constructing a synthetic hydFhydE-hydG-hydA operon for engineering biohydrogen production.
Analytical Biochemistry 373(1), 170-172.
Park, M.-O., Mizutani, T., Jones. P.R. (2007) Glyceraldehyde3-phosphate:ferredoxin oxidoreductase from Methanococcus
maripaludis. Journal of Bacteriology 189(20), 7281-7289.
Jones, P.R. (2008) Improving fermentative biomass-derived H2production by engineering microbial metabolism. International
Journal of Hydrogen Energy 33, 5122-5130.
(1) Fundamental understanding for improving fermentative and
photobiological H2-production.
H2-pathways depend heavily
on O2-labile Fe-S clusters for electron transfer. We study Fe-S
cluster metabolism, with a particular focus on the repair of partially
damaged clusters, in order to enhance H2-pathways in general and
in order to contribute towards the development of O2-tolerant H2prodction strategies.
Both fermentative and photobiological H2-pathways will depend on
the use of NAD(P)H as a major electron-carrier, although NAD(P)
H is a thermodynamically unfavorable electron-donor for H2pathways. The aim is to contribute towards an understanding of
the mechanisms that are involved in the regulation of NADP(H)metabolism.
Both topics are studied with a combination of computational
and experimental sciences, with a focus on both individual
key-reactions and systems-level regulation of metabolism.
(2) Synthetic biology - metabolic pathway construction for synthesis
of novel hydrocarbon transport fuels.
48
From left to right. Fernando Guerrero, Sanna Peltonen, Linda Vuorijoki, Patrik Jones.
49
KINETOCHORE AND CANCER
RESEARCH GROUP
Marko Kallio, Ph.D. Docent, Senior Research Scientist and Team Leader,
VTT Medical Biotechnology, 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. Email:
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. 1996-1998 Dr. Kallio was in the laboratory of Prof. Gary
Gorbsky (Univ. Virginia, USA) as Post-doctoral Fellow and 19982000 in the laboratories of Prof. John Eriksson and Prof. Lea
Sistonen (Univ. Turku, Finland) as a Senior Post-doctoral Fellow.
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 Medical Biotechnology, a research institute affiliated with the
University of Turku.
Personnel:
Post-doctoral researchers:
Kimmo Jaakkola, M.D., Leena Laine, Ph.D., Elli Narvi, Ph.D.,
Christina Oetken-Lindholm, Ph.D., Sebastian Winsel, Ph.D.
Graduate students: Anu Kukkonen-Macchi, M.Sc., Jenni MäkiJouppila, M.Sc., Anna-Leena Salmela, M.Sc., Mariaana Vuoriluoto,
M.Sc.
Technicians: Pauliina Toivonen
Alumni: Tim Holmström, Ph.D., Jeroen Pouwels, Ph.D., Oana
Sicora, Ph.D., Asta Varis, Ph.D., Chang-Dong Zhang, Ph.D.
Description of the projects:
The Kinetochore and Cancer 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 have performed a number of high-throughput
screens (HTS) for small molecules, siRNAs and miRNAs with antimitotic activity. We are interested of conditions that suppress cell’s
viability as a consequence of premature inactivation of the spindle
assembly checkpoint, a conserved signaling pathway monitoring
fidelity of mitosis. Finally, we have launched a project to explore
the mechanisms of acquired resistance to microtubule-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.
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. In our research,
50
we have focused to study of the spindle assembly checkpoint (also
known as the mitotic or the kinetochore checkpoint) that monitors
interactions between the spindle microtubules and kinetochores, the
microtubule binding platforms of chromosomes. If mistakes occur
in the microtubule-kinetochore connections, the mitotic checkpoint
becomes active and prevents separation of sister chromatids until
errors in the chromosome alignment are corrected. Although
the main principles of the spindle assembly checkpoint are well
documented many molecular details remain to be explored. To this
end, we are investigating the function of Chromosome Passenger
Complex (CPC) and Ndc80 complex required for the spindle
assembly checkpoint signaling and ordered progression of mitosis.
We are especially interested of Aurora B, Incenp, and Hec1 proteins
that facilitate normal microtubule-chromosome associations. The
specific question we wish to answer is how members of CPC
proteins interact with each other and with mitotic co-factors, and
how they contribute to mitotic checkpoint signaling. The findings
are expected to catalyze cancer drug discovery by identification of
new possibilities for Hec1 and Aurora B inhibition.
In another set of projects, we are focusing on characterization of
the several anti-mitotic lead compounds, siRNAs and miRNAs
that we discovered during our recent HTSs. In particular, we are
working to validate the mechanism of action of three putative
anti-Hec1 compounds that effectively perturb normal mitosis and
trigger cancer cell killing in cell culture assays. Moreover, we aim
to determine the mechanism of action of the mitotic checkpoint
suppressing siRNAs and miRNAs using various cell-based and in
vitro assays.
Lastly, in a collaborative project with Prof. Kallioniemi we have
identified gene copy number and gene expression alterations in
parental lung and ovarian cancer cell lines and their microtubuledrug resistant variants. To directly link these genomic findings
with a drug efflux pump independent mechanisms of action of
microtubule-drug resistance, we are testing if re-expression of the
genes lost from the drug-resistant variant cell lines will re-sensitize
them to microtubule-drugs, and to silence the same genes alone or
in combinations in the parental lines to determine if their lost drives
development of microtubule-drug resistance. Other factors that we
have recently discovered to affect the sensitivity to microtubuledrugs are loss of certain tubulin isoforms that leads to abnormal
function of mitotic spindle and precocious inactivation of the mitotic
checkpoint causing formation of multinucleated progeny cells. We
expect to identify novel molecular mechanisms for the microtubuledrug insensitivity. These findings may have diagnostics value in the
development of individually optimized therapeutic regimens for
cancer patients and for design of new class of microtubule-drugs
that selectively target taxane-resistant tumours.
Funding:
VTT Technical Research Centre of Finland, The Academy of Finland,
Finnish Cancer Organisations, TuBS and DDGS Graduate Schools,
Bayer Schering Pharma
Collaborators:
Gary Gorbsky (OMRF, Oklahoma USA), Todd Stukenberg (Univ.
Virginia, USA), Olli Kallioniemi (FIMM),
51
Salmela AL, Pouwels J, Varis A, Kukkonen AM, Toivonen P, Halonen
PK, Perälä M, Kallioniemi O, Gorbsky GJ, Kallio MJ. (2009)
Carcinogenesis, 30:1032-1040.
Ahonen LJ, Kukkonen AM, Pouwels J, Bolton MA, Jingle CD,
Stukenberg PT, Kallio MJ. (2009).
segregation, overrides the spindle checkpoint, and perturbs
microtubule dynamics in mitosis. Curr. Biol. 12, 900-905.
Giodini A, Kallio MJ, Wall NR, Gorbsky GJ, Tognin S, Marchisio PC,
Symons M, Altieri DC. (2002) Regulation of microtubule stability
and mitotic progression by survivin. Cancer Res. 62, 2462-2467.
Chromosoma, 118:71-84.
Pellinen T, Tuomi S, Arjonen A, Wolf M, Edgren H, Meyer H, Grosse
R, Kitzing T, Rantala JK, Kallioniemi O, Fässler R, Kallio M, Ivaska
J. (2008).
Dev Cell, 15:371-385.
Vorozhko VV, Emanuele MJ, Kallio MJ, Stukenberg PT, Gorbsky GJ.
(2008) Multiple mechanisms of chromosome movement mediated
through the Ndc80 complex and dynein/dynactin. Chromosoma,
117:169-179.
(2007) Shugoshin 1 plays a central role in
kinetochore assembly and is required for kinetochore targeting of
Plk1. Cell Cycle. 6, 1579-1585.
Wang YY, Parvinen M, Toppari J, Kallio MJ. (2006) Inhibition of
Aurora kinases perturbs chromosome alignment and spindle
checkpoint signaling in rat spermatocytes. Exp Cell Res. 312,
3459-3470.
Ahonen LJ, Kallio MJ, Daum JR, Bolton M, Manke IA, Yaffe MB,
Stukenberg PT, Gorbsky GJ. (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.
Beardmore VA, Ahonen LJ, Gorbsky GJ, Kallio MJ. (2004) Survivin
dynamics increases at centromeres during G2/M phase transition
and is regulated by microtubule-attachment and Aurora B activity.
J Cell Sci. 117, 4033-4042. McCleland ML, Kallio MJ, Barrett-Wilt GA, Kestner CA, Shabanowitz
J, Hunt DF, Gorbsky GJ, Stukenberg PT. (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 ML, Gardner RD, Kallio MJ, Daum JR, Gorbsky GJ,
Burke DJ, Stukenberg PT. (2003) The highly conserved Ndc80
complex is required for kinetochore assembly, chromosome
congression, and spindle checkpoint activity. Genes Dev. 17, 101114. Kallio MJ, Beardmore VA, Weinstein J, Gorbsky GJ. (2002) Rapid
microtubule-independent dynamics of Cdc20 at kinetochores and
centrosomes in mammalian cells. J. Cell Biol. 158, 841-847.
Kallio MJ, McCleland ML, Stukenberg PT, Gorbsky GJ.
(2002) Inhibition of aurora B kinase blocks chromosome
52
From left to right, front row: Marko Kallio, second row: Jenni Mäki-Jouppila, Christina
Oetken-Lindholm, third row: Anu Kukkonen-Macchi, back row: Sebastian Winsel.
53
CANCEROMICS RESEARCH
PROGRAMME
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, Medical Biotechnology, VTT Technical Research Centre
of Finland and University of Turku. Laboratory address: Medical
Biotechnology, PharmaCity, Itäinen Pitkäkatu 4C, P.O. Box 106,
FI-20521 Turku, Finland.
Tel. +358-20-722 2800. Fax +358-20-722 2840.
Email: [email protected].
Biography:
Dr. Olli Kallioniemi (born 1960) 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, most recently
(1995-2002) as the Head of Translational Genomics Section at
the Cancer Genetics Branch, National Human Genome Research
Institute, at NIH, Bethesda, Maryland. Since 2003, he has been
Professor of Medical Biotechnology at the VTT Technical Research
Centre of Finland with a joint appointment at the University of Turku.
Academy of Finland Professorship 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 250 publications and editor or member
of the editorial board of six journals. Inventor of 15 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: Anna Aakula, M.Sc., Elmar Bucher, M.Sc., Mari
Björkman, M.Sc., Santosh Gupta, M.Sc., Kirsi Ketola, M.Sc.,
Pekka Kohonen, M.Sc. Paula Vainio, M.Sc., Sirkku Pollari, M.Sc.,
Coordinator: Riina Plosila, M.Sc.
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..
The aims of the various research programs are to:
1. Apply cancer genomics to identify key genes and pathways in
1.
breast and prostate cancer
2. Apply high-throughput RNA interference and chemical biology
2.
to identify living cells, with particular attention towards cancerspecific vulnerabilities and steroid-dependent signaling and
3. Translate the molecular discoveries towards drug discovery,
3.
clinical diagnostics and personalized medicine.
54
We are using advanced 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 biochip technologies, bioinformatics,
systems biology, translational cancer research and drug
development technologies, such as 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 Kuzneshov, Krister
Wennerberg (FIMM and Biomedicum Helsinki), Antti Poso, Tapio
Visakorpi, Jukka Westermarck and many others in other Universities
in Finland. We have over 100 collaborators in current EU projects
such as Epitron, Genica, APO-SYS, Prosper and Meta-Cancer
(FP7).
Funding:
The Academy of Finland, Tekes, Finnish Cancer Organizations and
Sigrid Juselius Foundation. Our biggest source of funding comes
from the EU framework projects, including Epitron, Genica, APOSYS, Prosper and Meta-Cancer (FP7).
Selected recent publications:
Rantala JK, Edgren H, Lehtinen L, Wolf M, Kleivi K, Moen Vollan HK,
Aaltola A-R, Laasola P, Kilpinen S, Saviranta P, Iljin K, Kallioniemi O.
Integrative Functional Genomics Analysis of Sustained Polyploidy
Phenotypes in Breast Cancer Cells Identifies an Oncogenic Profile
Role for GINS21,2. Neoplasia, in press, 2010
Gupta S, Iljin K, Sara H, Mpindi JP, Mirtti T, Vainio P, Rantala J,
Alanen K, Nees M, Kallioniemi O. FZD4 as a Mediator of ERG
Oncogene-Induced WNT Signaling and Epithelial-to-Mesenchymal
Transition in Human Prostate Cancer Cells. Cancer Res. 2010 Aug
16.
McBride DJ, Orpana AK, Sotiriou C, Joensuu H, Stephens PJ,
Mudie LJ, Hämäläinen E, Stebbings LA, Andersson LC, Flanagan
AM, Durbecq V, Ignatiadis M, Kallioniemi O, Heckman CA, Alitalo
K, Edgren H, Futreal PA, Stratton MR, Campbell PJ. Use of cancerspecific genomic rearrangements to quantify disease burden in
plasma from patients with solid tumors. Genes Chromosomes
Cancer. 2010 Aug 19.
International Cancer Genome Consortium. International network of
cancer genome projects. Nature, 464(7291):993-998, 2010.
Härmä V, Virtanen J, Mäkelä R, Happonen A, Mpindi JP, Knuuttila
M, Kohonen P, Lötjönen J, Kallioniemi O, Nees M. A comprehensive
panel of three-dimensional models for studies of prostate cancer
growth, invasion and drug responses. PLoS One, 5(5):e10431,
2010.
Pollari S, Käkönen SM, Edgren H, Wolf M, Kohonen P, Sara H,
Guise T, Nees M, Kallioniemi O. Enhanced serine production by
55
bone metastatic breast cancer cells stimulates osteoglastogenesis.
Breast Cancer Res Treat. 2010 Mar 30.
Nevo J, Mattila E, Pellinen T, Yamamoto DL, Sara H, Iljin K, Kallioniemi
O, Bono P, Heikkilä P, Joensuu H, Wärri A, Ivaska J. MammaryDerived Growth Inhibitor Alters Traffic of EGFR and Induces a Novel
Form of Cetuximab Resistance. Clin Cancer Res.,15(21):6570-81,
2009.
Main H, Lee KL, Yang H, Haapa-Paananen S, Edgren H, Jin
S, Sahlgren C, Kallioniemi O, Poellinger L, Lim B, Lendahl U.
Interactions between Notch- and hypoxia-induced transcriptomes
in embryonic stem cells. Exp Cell Res., 316(9):1610-1624, 2010.
Leivonen SK, Mäkelä R, Ostling P, Kohonen P, Haapa-Paananen
S, Kleivi K, Enerly E, Aakula A, Hellström K, Sahlberg N, Kristensen
VN, Børresen-Dale AL, Saviranta P, Perälä M, Kallioniemi O.
Protein lysate microarray analysis to identify microRNAs regulating
estrogen receptor signaling in breast cancer cell lines. Oncogene,
28(44):3926-3936, 2009.
Iljin K, Ketola K, Vainio P, Halonen P, Kohonen P, Fey V, Grafström
RC, Perälä M, Kallioniemi O. High-throughput 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(19):6070-6078, 2009.
Côme C, Laine A, Chanrion M, Edgren H, Mattila E, Liu X, Jonkers
J, Ivaska J, Isola J, Darbon JM, Kallioniemi O, Thézenas S,
Westermarck J. CIP2A is associated with human breast cancer
aggressivity. Clin Cancer Res., 15(16):5092-5100, 2009.
Varjosalo M, Björklund M, Cheng F, Syvänen H, Kivioja T, Kilpinen
S, Sun Z, Kallioniemi O, Stunnenberg HG, He, W-W, Ojala P, Taipale
J. Application of Active and Kinase-Deficient Kinome Collection
for Identification of Kinases Regulating Hedgehog Signaling. Cell,
133:537-548, 2008.
Pellinen T, Tuomi S, Arjonen A, Wolf M, Edgren H, Meyer H, Rantala
JK, Kallioniemi O, Fässler R, Kallio M and Ivaska J. Integrin traffic
regulated by Rab21 is necessary for cytokinesis. Dev. Cell.,
15(3):371-385, 2008.
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, Kallioniemi Olli. 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(9):R139, 2008.
Björkman M, Kristiina I, Halonen P, Henri S, Kaivanto E, Nees M,
Kallioniemi Olli. Defining the molecular action of HDAC inhibitors
and synergism with androgen deprivation in ERG-positive prostate
cancer. Int J Cancer, 123 (12):2774-2781, 2008.
Iljin K, Wolf M, Edgren H, Gupta S, Kilpinen S, Skotheim R, Peltola
M, Smit F, Verhaegh G, Schalken J, Nees M, Kallioniemi O. 2006.
TMPRSS2 fusions with oncogenic ETS factors in prostate cancer
involve unbalanced genomic rearrangements and are associated
with HDAC1 and epigenetic reprogramming. Cancer Res.,
66:10242-10246, 2006.
Edgren, H. & Kallioniemi, O. Integrated breast cancer genomics.
Cancer Cell, 10:453-454, 2006.
From left to right, sitting: Paula Vainio, Mari Björkman, Riina Plosila, Pekka Kohonen,
standing: Kirsi Ketola, Anna Aakula, Santosh Gupta, Olli Kallioniemi, Sirkku Pollari,
Elmar Bucher.
56
57
Signaling Pathways Regulated
by Oncogenic Pim Kinases
Päivi J. Koskinen, Ph.D., Senior Assistant, Adj. Prof. in Molecular and
Cell Biology. Laboratory address: Turku Centre for Biotechnology,
BioCity, Tykistökatu 6 B, P.O. Box 123, FIN-20521 Turku, Finland.
Tel. + 358-2-3338044, fax + 358-2-3338000.
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.
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 co-overexpress 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 collaborated with the group of Eleanor
Coffey (CBT) and 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 interference-based
approaches. In collaboration with the group of Garry Corthals
(CBT), we have developed sensitivity of the methodology to identify
phosphopeptides. In addition, we have been collaborating with two
groups of chemists (Jari Yli-Kauhaluoma, Viikki Biocenter, Helsinki
and Pascale Moreau, CNRS, France) to identify and validate Pim-
Personnel:
Postdoctoral researchers: Eeva Rainio, Ph.D.
Graduate students: Jouko Sandholm, M.Sc., Riitta Vahakoski, M.Sc.,
Niina Santio, M.Sc.
Undergraduate students: Sini Eerola, Heidi Ekman, Katja Männistö,
Sofia Pruikkonen, Juho Virtanen.
The studies of our research group focus on the signaling pathways
regulated by the oncogenic Pim family of serine/threonine-specific
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.
Most recently we have noticed that pim-1 overexpression 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. Most 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 cytokinedependent 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 phosphorylation-induced
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 kinases can
58
From left to right: Eeva Rainio, Päivi Koskinen, Heidi Ekman, Jouko Sandholm, Niina
Santio, Sofia Pruikkonen and Riitta Vahakoski.
59
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:
Academy of Finland, Turku University Foundation Drug Discovery
Graduate School.
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 of
the pro-apoptotic Bad protein by phosphorylating it on the Ser112
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.
60
MOLECULAR AND SYSTEMS
IMMUNOLOGY AND STEM CELL
BIOLOGY
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.
Biography:
Riitta Lahesmaa received her M.D. in 1984 and Ph.D. in 1987 from
the University of Turku, and was appointed Docent in Immunology
in 1990. She was a postdoctoral fellow at Stanford University
Medical Center with Professor Lawrence Steinman during the years
1990-1993 (NIH Fogarty Fellowship). In 1994 she moved to Syntex
Research Institute (later Roche Bioscience) in Palo Alto, California.
As a Principal Scientist she focused on lymphocyte signaling and
drug discovery with state-of-the-art functional genomics tools. In
1998 she was appointed Director of Turku Centre for Biotechnology.
In 2009 she carried out research in Professor Anjana Rao’s
laboratory in Immune Disease Institute, Harvard Medical School,
Boston. She also directs BioCity Turku Systems Biology Research
Program since 2000.
Personnel:
Senior scientists/ Post-doctoral researchers: Sanna Edelman,
Ph.D., Laura Elo-Uhlgren, Ph.D.; Bhawna Gupta, Ph.D.; Riikka
Lund, Ph.D.; Robert Moulder, Ph.D.; Juha-Pekka Pursiheimo,
Ph.D.; Sunil Raghav, Ph.D.; Omid Rasool, Ph.D.; Emaheswa
Reddy, Ph.D.; Johanna Tahvanainen, Ph.D.
Visiting Scientists: David Hawkins, Ph.D. (Ludwig Institute of
Cancer Research, San Diego, USA), Kanury Rao, Ph.D., (Director,
Immunology Group at ICGEB, New Delhi, India); Brigitta Stockinger,
Ph.D. (Principal Investigator, Division of Molecular Immunology,
NIMR, London, UK)
Graduate students: Helena Ahlfors, M.Sc.; Sanna Filen, M.Sc.
Henna Järvenpää, M.Sc.; Juha Korhonen, M.D.; Minna Kyläniemi,
M.Sc. Tapio Lönnberg, M.Sc.; Elisa Närvä, M.Sc.;Mirkka Heinonen,
M.Sc. Nelly Rahkonen, M.Sc.; Soile Tuomela, M.Sc. Subhash
Tripathi, M.Tech, M.Sc.
Technicians: Marjo Hakkarainen, Sarita Heinonen, Päivi Junni
Undergraduate students: Suvi Kantola, Kaarina Ranta, Marjo Linja,
Joel Nyström, Juuso Nästi, Verna Salonen
Description of the project :
Our research is focused on molecular systems immunology and
stem cell biology. We use holistic genome and proteome wide
methods and systems biology to reveal molecular mechanisms
of cell signaling, transcriptional and epigenetic programs that
determine cell differentiation and fate. These approaches are
exploited to understand molecular mechanisms of human immune
mediated diseases and certain types of cancer to provide novel
therapeutic means to modulate harmful cellular and immune
responses.
61
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. We have applied a holistic
approach to identify genes involved in human Th cell differentiation.
Detailed analysis of upstream T Cell Receptor (TCR)/key cytokine
receptor induced differentiation will increase our understanding
of these processes central for human health and disease
and provide novel insights into new therapeutic interventions.
STAT6 is known to be an essential upstream mediator of IL-4R
signaling and Th2 differentiation. Importantly, we identified for the
first time STAT6 target genes on a genome wide scale in human
CD4+ T cells - only small fraction of which were previously known
to be STAT-6 regulated. This study, published in Immunity, revealed
that in human surprisingly high proportion, up to 80% of IL-4 induced
response is STAT6 regulated revealing several new candidates
for therapeutic intervention (Elo L et al. 2010). Our studies on
IL-4 R signaling in lymphocytes also resulted in identification of
new IL4R/STAT-6 regulated proteins in human and mice as well
as mechanistic studies on their molecular functions (Aflakian N,
et al. 2009, Moulder R. et al. 2010, 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). Elucidating their functions further we
discovered that ATF3 and SATB1 are important regulators of human
Th cell differentiation. ATF3 promotes Th1 differentiation (Filen S. El
al. 2010) whereas SATB1 regulates multiple genes during early Th
cell differentiation (Ahlfors et al. 2010).
Human embryonic stem cells (hESC) have a unique capacity to
differentiate to any type of cell or tissue providing an enormous
potential for therapeutic applications. Our recent results based on
the use of high resolution microarray technology demonstrate that
it is essential to monitor stem cell lines carefully to minimize the
risk of malignancies in stem cell therapies. Our study published in
Nature Biotechnology and highlighted in Nature Methods revealed
that in prolonged culture human embryonic stem cells acquire
chromosomal abnormalities and changes in gene expression,
many of which are linked to cancer. (Närvä et al. 2010).
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. Current work aims
at further characterization and functional analysis of a panel of
selected factors in the maintenance of undifferentiated status of
hESC. Type 1 diabetes (T1D) is the most common metabolic-endocrine
disorder in children in western countries and the annual incidence
of T1D in Finland is record high. In almost all children, progression
to clinical T1D is associated with the presence of β cell specific
62
autoantibodies. Clinical T1D occurs when 80-90% of the β cells
have been destroyed. At this point T1D patient is dependent on
a daily insulin substitution for the rest of his/her life and there is
a high risk of developing acute and long-term complications.
Development of early diagnostics would enable early therapy and
possibly preventive treatments resulting in a significant reduction in
the health care costs.
Our objective is to study molecular mechanisms of T1D and
to discover molecular markers that indicate development of
autoimmunity and progression towards clinical T1D. Exploiting the
unique biobank of the Type 1 Diabetes Prediction and Prevention
Project in Finland (DIPP) we investigated transcriptomic profiles
of prospective whole-blood samples from children who have
developed T1D-associated autoantibodies and eventually clinical
T1D. Gene-level investigation of the data showed systematic
differential expression of 520 probesets. A network-based analysis
revealed then a highly significant down-regulated network of genes
involved in antigen presentation as well as T-cell receptor and insulin
signaling. (Elo et al. 2010). Further studies include analysis of larger
cohort of longitudinal samples using transciptomics, proteomics
and integrating the data with our previous metbolomics results
(Oresic et al. 2008).
Funding:
The Academy of Finland, The National Technology Agency of Finland
(TEKES), EU 6th framework “ESTOOLS”, JDRF, The Sigrid Jusélius
Foundation, The Finnish Cancer Organizations, Turku University
Hospital Fund, Graduate Schools (TuBS, DDGS, ISB), University
of Turku, Åbo Akademi University, European Research Council,
EU 7th framework “SYBILLA”, EU 7th framework “DIABIMMUNE”
EU 7th framework “NANOMMUNE”, EraSysBioPlus, European
Research Council
Collaborators:
Harri Lähdesmäki (Tampere University of Technology and Aalto
University, Reija Autio & Olli Yli-Harja (Tampere University of
Technology ), Tero Aittokallio & Olli Nevalainen (UTU), Peter
Andrews (University of Sheffield, UK) and the rest of EU FP6
ESTOOLS consortium (Altogether 20 partners), Outi Hovatta
(Karolinska Institute, Stockholm, Sweden), Matej Oresic (VTT
Technical Research Centre of Finland, Turku), Brigitta Stockinger
(NIMR, London, UK and visiting professor at CBT), Kanury V.S. Rao
(ICGEB, New Delhi, India and visiting professor at CBT), Anjana
Rao (Immune Disease Institute, Harvard Medical School, Boston,
MA, USA), Thomas Tushl (Rockefeller University, New York, NY,
USA), Christopher Burge (MIT, Cambridge, MA, USA), David
Goodlett (University of Washington, Seattle, WA, USA) , Matthias
Gstaiger & Ruedi Aebersol (ETZ, Zürich, Switzerland) and the rest
of EU FP7 SYBILLA partners (Altogether 14), Panu Jaakkola (Turku
Centre for Biotechnology), Olli Simell, Jorma Ilonen & Heikki Hyöty,
Juha Kere (Karolinska Institute, Stockholm, Sweden), Bing Ren
(Ludwig Institute for Cancer Research, University of California,
San Diego, USA), Mikael Knip (University of Helsinki) and the rest
of EU FP7 DIABIMMUNE partners (Altogether 12), Bengt Fadeel
(Karolinska Institute, Stockholm, Sweden ) and the rest of EU FP7
DIABIMMUNE partners (Altogether 14 partners).
Aflakian N, Ravichandran S, Sarwar Jamaal Md. S, Jarvenpää
H, Lahesmaa, R, Rao KVS. (2009) Integration of signals from the
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B-cell antigen receptor and the IL-4 receptor leads to a cooperative
shift in the cellular response axis. Mol Biosyst. 5:1661-71.
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. 116:1443-53.
Chen, Z., Lund, R., Aittokallio, T., Nevalainen, O. and Lahesmaa,
R. (2003) Identification of early, positively and negatively regulated
targets of STAT6 in IL-4 stimulated CD4+ T lymphocytes induced
to polarize to Th2 cells. J Immunol. 171: 3627-3635.
Cho SH, Goenka S, Henttinen T, Gudapati P, Reinikainen A,
Lahesmaa R, Boothby M. (2009) PARP-14, a member of the B
aggressive lymphoma (BAL) family, transduces survival signals in
primary B cells. Blood. 113:2416-25.
(2007) Systematic construction of gene coexpression networks
with applications to human T helper cell differentiation process.
Bioinformatics. 23: 2096-2103.
Elo LL#, Järvenpää H#, Tuomela S#, Raghav S#, Ahlfors H, Laurila
K, Gupta B, Lund RJ, Tahvanainen J, Hawkins RD, Orešic M,
Lähdesmäki H, Rasool O, Rao KVS*, Aittokallio T*, Lahesmaa
R. (2010) IL-4- and STAT6-mediated transcriptional regulation to
initiate Th2 program in human T cells. Immunity 32:852-62#, *
Equal contribution.
Elo LL*, Mykkänen J*, Nikula T, Järvenpää H, Aittokallio T, Hyöty H,
Ilonen J, Veijola R, Knip M, Simell O, Lahesmaa R. (2010) Genomewide gene expression profiling reveals early suppression of immune
response pathways in prediabetic children. *Equal contribution. J
Autoimmun. 35:70-6.
Filén JJ, Filén S, Moulder R, Tuomela S, Ahlfors H, West A,
Kouvonen P, Kantola S, Björkman M, Katajamaa M, Rasool O,
Nyman TA, Lahesmaa R. (2009)
Mol Cell Proteomics. 8:32-44.
Filén S, Ylikoski E, Tripathi S, West A, Björkman M, Nyström J,
Ahlfors H, Rao KVS, Coffey E, Rasool O, and Lahesmaa R. (2010)
ATF3 is a Positive Regulator of Human IFNG Gene Expression. J
Immunol. 184:4990-9.
From left to right, first row: Juha-Pekka Pursiheimo, Emaheswa Reddy, Riikka Lund,
Sarita Heinonen, Soile Tuomela, Sanna Edelman, second row: Omid Rasool, Emilia
Engström, Nelly Rahkonen, Johanna Tahvanainen, Riina Plosila, Marjo Hakkarainen,
Tapio Lönnberg, third row: Subhash Tripathi, Verna Salo, Riitta Lahesmaa.
Hämäläinen, H., Zhou, H., Chou, W., Hashizume, H., Heller, R. and
Lahesmaa R. (2001) Profiling Human Th1 and Th2 Differentiation
by High-density Oligonucleotide Arrays. Genome Biology 2 (7):
research0022.
Kumar D, Srikanth R, Ahlfors H, Lahesmaa R, Rao K, (2007)
Capturing cell-fate decisions from the molecular signatures of
a receptor-dependent signaling response. Molecular Systems
Biology. 3:150.
Lund, R., Aittokallio, T., Nevalainen, O. and Lahesmaa, R. (2003)
Identification of novel genes regulated by IL-12, IL-4 and TGFb
during the early polarization of CD4+ lymphocytes. J. Immunol.
171: 5328-5336.
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65
Lund, R., Chen, Z., Scheinin, J. and Lahesmaa, R. (2004) Early
target genes of IL-12/STAT4 signaling in T helper cells. J. Immunol.
172: 6775-6782.
Lund R*, Pykäläinen M*, Naumanen T, Dixon C, Chen Z, Ahlfors
H, Tuomela S, Tahvanainen J, Scheinin J, Henttinen T, Rasool O,
Lahesmaa R. (2007) Genome wide identification of Novel Genes
Involved in Early Th1 and Th2 Cell Differentiation J. Immunol.
178:3648-60.
Moulder R*, Lönnberg T*, Filén J-J, Elo L, Rainio E, Corthals G,
Oresic M, Nyman TA, Aittokallio T, Lahesmaa R (2010) (*equal
contribution). Quantitative Proteomics Analysis of the Nuclear
Fraction of Human CD4+ Cells in the Early Phases of IL-4 Induced
Th2 Differentiation. Mol Cell Proteomics. 9:1937-53.
Närvä E, Autio R, Rahkonen N, Kong L, Harrison N, Kitsberg
D, Borghese L, Itskovitz-Eldor J, Rasool O, Dvorak P, Hovatta
O, Otonkoski T, Tuuri T, Cui W, Brüstle O, Baker D, Maltby E,
Moore HD, Benvenisty N, Andrews PW, Yli-Harja O & Lahesmaa
R. (2010) High resolution genome wide DNA analysis on a large
panel of Human Embryonic Stem Cell lines reveals novel genomic
changes associated with culture and affecting gene expression.
Nat Biotechnol. 28:371-7.
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,
Equal contribution. J Exp Med. 205:2975-84.
*
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 KM,
Westermarck J, Rao KV, Lahesmaa R. (2008)
Blood. 113:1268-77.
Tuomela S, Rautajoki KJ, Moulder R, Nyman TA, Lahesmaa R.
(2009) Identification of novel Stat6 regulated proteins in IL-4-treated
mouse lymphocytes. Proteomics. 9:1087-98.
PROTEIN CRYSTALLOGRAPHY
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.
Biography:
Tassos Papageorgiou (b. 1962) 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
Undergraduate students: Simon Le Boulh, Pia Kinaret. Omid
Mohammadi, Bishwa Subedi, Kristian Wecström
Description of the projects:
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. The
crystal structures of Dps-like peroxide resistance protein (Dpr) from
the pathogenic bacterium Streptococcus suis in the iron-free, the
iron-bound and zinc-bound form have been recently determined. In
addition, EXAFS experiments performed at EMBL Hamburg have
provided detailed information of the geometry of the iron core and
showed a ferrihydrite-like structure. Based on our recent results,
a number of mutants have been generated to study the iron core
formation using X-ray crystallography, microcalorimetry, EXAFS,
magnetization and Mössbauer spectroscopy techniques. The
structure of Dpr from Streptococcus pyogenes was determined
in 2009 and structural studies on Helicobacter pylori neutrophilactivating protein (known as HP-NAP) were initiated to identify
potential ligand binding sites.
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 and biomedicine. Crystals of human GST-A1 have
been grown in our lab for use in structure-assisted drug design
efforts. In addition, the structure of a novel glutathione transferase
66
67
was determined by the SAD method using the anomalous signal
of Br. The overall fold and the geometry of the active site suggest a
new member of the glutathione transferase superfamily. Knock-out
and microarray experiments are currently in progress to provide
functional insights.
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.
In the theme of enzyme function and stability, we continued our
work on PhaZ7, an extracellular depolymerase involved in the
degradation of poly(R)-hydroxyalkanoates, a group of thermoplastic
polyesters considered as biodegradable substitutes for nondegradable plastics. The crystal structure of PhaZ7 depolymerase
at atomic (1.2) Å resolution in the presence of the serine protease
inhibitor PMSF was determined. A molecule of SO2 was found
covalently bound at the active site of the enzyme, suggesting a
preformed catalytic triad. Several mutants have been generated
by our collaborators and characterized. Crystal structure
determination is currently underway. The structure of Erwinia
carotovora asparaginase at 1.4 Å, the second highest resolution
for an L-asparaginase was determined. Asparaginases are widelyused enzymes in leukemia treatment for the last 30 years. However,
asparaginases from Erwinia chrysanthemi and E. coli cause severe
side-effects. Protein engineering efforts have been initiated for the
Erwinia carotovora enzyme based on its 3D-structure to produce
chimeric forms with reduced glutaminase activity (the main reason
of the side-effects) and high specificity for L-asparagine. 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.
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.
Wakadkar, S., Zhang,L.Q., Li, D.-C., Haikarainen, T., Dhavala,
P. & Papageorgiou, A.C. (2010). Expression, purification and
crystallization of Chetomium thermophilum Cu, Zn superoxide
dismutase. Acta Cryst F (in press).
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.
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.
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Axarli, I. Dhavala, P., Papageorgiou, A.C. & Labrou, N.E. (2009).
Crystallographic and functional characterization of the fluorodifeninducible glutathione transferase from Glycine max reveals an
active site topography suited for diphenylether herbicides and a
novel L-site. J. Mol. Biol. 385, 984-1002.
Axarli, I. Dhavala, P., Papageorgiou, A.C. & Labrou, N.E. (2009).
Crystal structrure of Glycine max glutathione transferase in complex
with glutathione: investigation of the induced-fit mechanism
operating by the tau class glutathione transferases. Biochem. J.
422, 247-256.
Mitsiki, E., Papageorgiou, A. C., Iyer, S., Thiyagarajan, N., Prior, S.
H., Sleep, D., Finnis, C. & Acharya, K. R. (2009). Structures of native
human thymidine phosphorylase and in complex with 5-iodouracil.
Biochem. Biophys. Res. Commun. 386, 666-670.
Dhavala, P. & Papageorgiou, A.C. (2009). The crystal structure
of Helicobacter pylori L-asparaginase at 1.4 Å resolution. Acta
Crystallogr. D 65, 1253-1261.
Havukainen, H., Haataja, S., Kauko, A., Pulliainen, A.T., Salminen,
A., Haikarainen, T., Finne, J. & Papageorgiou, A.C. (2008). Structural
basis of zinc- and terbium-mediated inhibition of ferroxidase activity
in Dps ferritin-like proteins. Protein Sci. 17, 1513-1521
Papageorgiou, A.C., Posypanova, G.A., Andersson, C.A., Sokolov,
N.N & Krasotkina, J. (2008) Structural and functional insights into
Erwinia carotovora L-asparaginase. FEBS J. 275, 4306-4316
Dhavala, P., Krasotkina, J., Dubreuil, C. & Papageorgiou, A.C.
(2008). Expression, purification and crystallization of Helicobacter
pylori L-asparaginase. Acta Crystallogr Sect F Struct Biol Cryst
Commun. 64, 740-742
Papageorgiou, A.C., Hermawan, S., Singh C.B. & Jendrossek,
D. (2008) Structural basis of poly(3-hydroxybutyrate) hydrolysis
by PhaZ7 depolymerase from Paucimonas lemoignei. J. Mol. Biol.
382, 1184-1194
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
69
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
Kauko, A., Pulliainen, A.T., Haataja, S., Meyer-Klaucke, W., Finne, J.
& Papageorgiou, A.C. (2006). Iron incorporation in Streptococcus
suis Dps-like peroxide resistance protein Dpr requires mobility in
the ferroxidase center and leads to the formation of a ferrihydritelike core. J. Mol. Biol. 364: 97-109
Papageorgiou, A.C., Saarinen, S., Ramirez-Bartutis, R., Kato, H.,
Uchiyama, T., Kirikae, T. & Miyoshi-Akiyama, T. (2006). Expression,
purification and crystallisation of Streptococcus dysgalactiaederived mitogen. Acta Crystallogr. F. 62: 242-244
Kapetaniou, E.G., Thanassoulas, A., Dubnovitsky, A.P., Nounesis,
G. & Papageorgiou, A.C. (2006). The effect of pH on the structure
and stability of Bacillus circulans ssp. alkalophilus phosphoserine
aminotransferase: Thermodynamic and crystallographic studies.
Proteins: Struct. Funct. Bioinform. 63: 742-753
Pulliainen, A.T., Kauko, A., Haataja, S., Papageorgiou, A.C. &
Finne, J. (2005). Dpr/Dps miniferritin: Insights into the mechanism
of iron incorporation and evidence for a central role in cellular iron
homeostasis in Streptococcus suis. Mol. Microbiol. 57, 10861100.
Kapetaniou, E.G, Braaz, R., Jendrossek, D. & Papageorgiou,
A.C. (2005). Crystallization and preliminary X-ray analysis of a
novel thermoalkalophilic depolymerase (PhaZ7) from Paucimonas
lemoignei. Acta Crystallogr. F 61: 479-481
Wikman, L.E.K., Krasotkina, J., Kuchumova, A., Sokolov, N.N.
& Papageorgiou, A.C. (2005). Crystallization and preliminary
crystallographic analysis of L-asparaginase from Erwinia carotovora.
Acta Crystallogr. F 61: 407-409
Dubnovitsky,. A.P., Ravelli, R.B.G., Popov, A.N. & Papageorgiou,
A.C. (2005). Strain relief at the active site of phosphoserine
aminotransferase induced by radiation damage. Protein Sci. 14:
1498-1507
From left to right, sitting: Bishwa Subedi, Teemu Haikarainen, back row: Tassos
Papageorgiou, Sachin Wakadkar, Prathusha Dhavala.
Mialon A., Sankinen, M., Söderström, H., Junttila, T.T., Holmström,
T., Koivusalo, R., Papageorgiou, A.C., Johnson, R.S., Hietanen, S.,
Elenius, K. & Westermarck, J. (2005). DNA topoisomerase I is a cofactor for c-Jun in the regulation of EGFR expression and cancer
cell proliferation. Mol. Cell. Biol. 25: 5040-5051
Dubnovitsky, A.P., Kapetaniou, E.G. & Papageorgiou, A.C.
(2005). Enzyme adaptation to alkaline pH: Atomic resolution (1.08
Å) structure of phosphoserine aminotransferase from Bacillus
alkalophilus. Protein Sci. 14: 97-110
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71
Bioinformatics unit
Group leader (Structural Bioinformatics):
Konstantin Denessiouk, Ph.D., Docent in Biochemistry.
Bioinformatics Group leader. Centre for Biotechnology,
Tykistökatu 6, BioCity 5th floor, Turku, 20520 Turku.
Personnel:
Bhanupratap Singh Chouhan.
Group leader (High-throughput Bioinformatics):
Attila Gyenesei, Ph.D., Senior Scientist, Group leader, 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: Sini Junttila, Asta Laiho, Leena Kytömäki, Seppo
Tamminen.
Description of the Project (2008-2009):
Tremendous amounts of data generated by high-throughput
technologies in genomics and transcriptomics like DNA microarray
and next-generation sequencing instruments that demand in-depth
analysis present unprecedented new challenges to data analyst and
biomedical researchers. The High-throughput bioinformatics (HTB)
group is engaged in the ongoing development of advanced analysis
tools and research on generating novel approaches for the analysis
of high-throughput data sets. Moreover, in close collaboration with
the Finnish Microarray and Sequencing Centre (FMSC) we provide
services in the analysis of DNA microarray and next generation
sequencing data produced within the Centre. Members of the
HTB group participate in the initial project meetings, held at the
beginning of each FMSC project, to assist the researchers with
designing the experiment to guarantee the optimal experimental
setup. Our bioinformatics services include data analysis of various
data types such that gene and exon-specific expression data, ChIPchip and ChIP-seq data, SNP genotyping data, etc. Additionally,
our group offers consultation and training for researchers to ensure
that they benefit from the computational tools used in the analysis
of biological data sets. Our aim is to educate and thereby enable
researchers to work on their own data, which allows them to take
the full benefit of their deep biological knowledge into consideration
during the data analysis. Various courses are organized by our team
each year to cover different aspects of data analysis.
The Bioinformatics Unit 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) computerbased analysis of protein-protein and protein-ligand interactions;
(b) computer-aided prediction and intelligent molecular modeling
and design; (c) computer-based ligand docking and analysis;
(d) quantum chemistry, molecular dynamics; and (d) analysis of
effects of molecular recognition and mutations on protein function.
During year 2009, in collaboration with Prof. Jyrki Heino, University
of Turku and Prof. Mark S. Johnson, Åbo Akademi University,
the collaboration has been started in in-depth structural analysis
72
of human integrin beta-propeller domains and identification of
structural features of integrins that distinguish human integrins
from the other protein superfamilies having the same fold. Several
matching sequences in bacteria that aligned surprisingly well with
the integrin alpha subunits were identified (Johnson et al., 2009;
Chouhan et al., 2010, ready to be submitted), giving a new insight
into existence and evolution of the integrin-like proteins in bacteria.
Additionally, our on-going research were focused on prediction of
effects of splice variation on protein function (in collaboration with
Prof. Riitta Lahesmaa, Turku Centre for Biotechnology), analysis of
effects of molecular recognition and mutations on protein function
in macromolecular receptor ErbB4 complexes (in collaboration with
Dr. Klaus Elenius, University of Turku).
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:
The Åbo Akademi University; The National Graduate School in
Informational and Structural Biology (ISB).
Collaborators:
Riitta Lahesmaa (Turku Centre for Biotechnology), Mark Johnson
(Åbo Akademi University), Dr. Klaus Elenius (University of Turku);
Prof. Jyrki Heino (University of Turku).
Chouhan B, Denesyuk A, Heino J, Johnson MS Denessiouk K.
(2010) Conservation of the human integrin-type beta-propeller
domain in bacteria. Ready to be submitted.
Kankare M, Salminen T, Laiho A, Vesala L, Hoikkala A. Changes
in gene expression linked with adult reproductive diapause in a
northern malt fly species: a candidate gene microarray study. BMC
Ecol. 2010 Feb 1;10:3.PMID: 20122138
Sirén A, Polvi A, Chahine L, Labuda M, Bourgoin S, Anttonen AK,
Kousi M, Hirvonen K, Simola KO, Andermann E, Laiho A, Soini J,
Koivikko M, Laaksonen R, Pandolfo M, Lehesjoki AE. Suggestive
evidence for a new locus for epilepsy with heterogeneous
phenotypes on chromosome 17q. Epilepsy Res. 2010 Jan;88(1):6575. Epub 2009 Nov 14.PMID: 19914042
Huvila J, Brandt A, Rojas CR, Pasanen S, Talve L, Hirsimäki P, Fey V,
Kytömäki L, Saukko P, Carpén O, Soini JT, Grénman S, Auranen A.
Gene Expression profiling og endometrial adenocarcinomas reveals
increased apolipoprotein E expression in poorly differentiated
tumors. Int J Gynecol Cancer. 2009 Oct;19(7):1226-31.
Oksala N, Levula M, Airla N, Pelto-Huikko M, Ortiz RM, Järvinen
O, Salenius JP, Ozsait B, Komurcu-Bayrak E, Erginel-Unaltuna
N, Huovila AP, Kytömäki L, Soini JT, Kähönen M, Karhunen PJ,
Laaksonen R, Lehtimäki T. ADAM-9, ADAM-15, and ADAM-17 are
upregulated in macrophages in advanced human atherosclerotic
plaques in aorta and carotid and femoral arteries--Tampere vascular
study. Ann Med. 2009;41(4):279-90.
Levula M, Airla N, Oksala N, Hernesniemi JA, Pelto-Huikko M,
Salenius JP, Zeitlin R, Järvinen O, Huovila AP, Nikkari ST, Jaakkola
73
O, Ilveskoski E, Mikkelsson J, Perola M, Laaksonen R, Kytömäki
L, Soini JT, Kahonen M, Parkkinen J, Karhunen PJ, Lehtimäki T.
ADAM8 and its single nucleotide polymorphism 2662 T/G are
associated with advanced atherosclerosis and fatal myocardial
infarction: Tampere vascular study. Ann Med. 2009 Jul 2:1-11.
Johnson MS, Lu N, Denessiouk K, Heino J, Gullberg D. (2009).
Integrins during evolution: Evolutionary trees and model organisms.
Biochim Biophys Acta. 1788: 779-789.
Fan YM, Karhunen PJ, Levula M, Ilveskoski E, Mikkelsson J,
Kajander OA, Järvinen O, Oksala N, Thusberg J, Vihinen M, Salenius
JP, Kytömäki L, Soini JT, Laaksonen R, Lehtimäki T. Expression
of sterol regulatory element-binding transcription factor (SREBF) 2
and SREBF cleavage-activating protein (SCAP) in human atheroma
and the association of their allelic variants with sudden cardiac
death. Thromb J. 2008 Dec 30;6:17.
Cloke B, Huhtinen K, Fusi L, Kajihara T, Yliheikkilä M, Ho KK,
Teklenburg G, Lavery S, Jones MC, Trew G, Kim JJ, Lam EW,
Cartwright JE, Poutanen M, Brosens JJ. The androgen and
progesterone receptors regulate distinct gene networks and
cellular functions in decidualizing endometrium.. Endocrinology.
2008 Sep;149(9):4462-74.
Akerfelt M, Henriksson E, Laiho A, Vihervaara A, Rautoma K, Kotaja
N, Sistonen L. Promoter ChIP-chip analysis in mouse testis reveals
Y chromosome occupancy by HSF2. Proc. Natl. Acad. Sci. U.S.A..
2008 Aug;105(32):11224-9
pathways due to SKI-1/S1P inhibition in HepG2 cells.. DNA Cell
Biol. 2007 Nov;26(11):765-72
Rodriguez A, Hilvo M, Kytömäki L, Fleming RE, Britton RS, Bacon
BR, Parkkila S. Effects of iron loading on muscle: genome-wide
mRNA expression profiling in the mouse. BMC Genomics. 2007
;8():379-0
De Windt A, Rai M, Kytömäki L, Thelen KM, Lutjohann D, Bernier L,
Davignon J, Soini J, Pandolfo M, Laaksonen R. Gene set enrichment
analyses revealed several affected pathways in Niemann-pick
disease type C fibroblasts.. DNA Cell Biol. 2007 Sep;26(9):665-71
Anckar J, Hietakangas V, Denessiouk K, Thiele DJ, Johnson
MS, Sistonen L. (2006). Inhibition of DNA binding by differential
sumoylation of heat shock factors. Mol Cell Biol. 26: 955-964.
Poukkula M, Kaunisto A, Hietakangas V, Denessiouk K, Katajamäki
T, Johnson MS, Sistonen L, Eriksson JE. (2005). Rapid turnover
of c-FLIPshort is determined by its unique C-terminal tail. J Biol
Chem. 280: 27345-27355.
Denessiouk KA, Johnson MS, Denesyuk AI. (2005). Novel CaNN
structural motif for protein recognition of phosphate ions. J Mol
Biol. 345: 611-629.
F.P. Pach, A. Gyenesei, and J. Abonyi. Visualization of fuzzy
association rules. Journal of Visual Languages and Computing,
Elsevier, in press, Available online, 2008.
F.P. Pach, A. Gyenesei, and J. Abonyi. MOSSFARM: Model structure
selection by fuzzy association rule mining. Journal of Intelligent and
Fuzzy Systems 19(6): 399-407, 2008.
F.P. Pach, A. Gyenesei, and J. Abonyi. Compact fuzzy association
rule based classifier. Expert Systems with Applications 34(4): 24062416, 2008.
Xhaard H, Backström V, Denessiouk K, Johnson MS. (2008).
Coordination of Na(+) by monoamine ligands in dopamine,
norepinephrine, and serotonin transporters. J Chem Inf Model. 48:
1423-1437.
Denessiouk KA, Denesyuk AI, Johnson MS. (2008). Negative
modulation of signal transduction via interleukin splice variation.
Proteins. 71: 751-770.
A. Gyenesei, U. Wagner, S. Barkow-Oesterreicher, E. Stolte, and
R. Schlapbach. Mining co-regulated gene profiles for the detection
of functional associations in gene expression data. Bioinformatics
23(15): 1927–1935, 2007.
De Windt A, Rai M, Bernier L, Thelen K, Soini J, Lefebvre C,
Chintawar S, Lavigne J, Saarinen L, Kytömäki L, Munzer JS,
Lujohann D, Pandolfo M, Davignon J, Seidah NG, Laaksonen R.
Gene set enrichment analysis reveals several globally affected
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75
Cell fate
Cecilia Sahlgren, Ph.D., Docent in Cell and Development Biology,
(Åbo Akademi University). Academy Research Fellow, Turku Centre
for Biotechnology, Åbo Akademi and Turku University, BioCity,
Tykistokatu 6B, FI-20521 Turku, Finland. Tel. +358-2-3338611,
Fax. +358-2-3338000. Email:
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 (attending the position
as professor of Biology) at 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:
Senior Scientist: Cecilia Sahlgren, Ph.D.
Post-doctoral researcher: Veronika Mamaeva
Graduate Students: Marika Hietamäki, M.Sc., Sebastian Landor,
M.Sc, Anders Mutvei, M.Sc (KI), Laurel Tabe Bate-Eya, M.Sci
Undergraduate Students: Daniel Antfolk, B.Sc, Christian Antila,
B.Sc, Cecilia Granqvist, B.Sc, Rasmus Niemi
Description of project:
Cell-cell communication in development and disease: Targeting the
Notch signaling pathway
The main focus of our research is directed at elucidating the basic
molecular principles of the signaling mechanisms that regulate 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. The main focus is 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 and function, ii) how Notch signaling
interlinks with other signaling 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) develop
technology platforms to regulate Notch signaling in targeted cell
populations and for bioimaging of cellular functions in vivo.
We have recently identified a Notch-hypoxia crosstalk of relevance
for tumor progression (Sahlgren et al., 2008), and are currently
participating in a project aimed at elucidating the Notch-hypoxia
transcriptome to gain insight in how such a crosstalk is manifested on
the transcriptome level and to obtain a molecular platform to better
understand the intersection between the two signaling cascades
in normal development and cancer (Main et al., 2010). We have
shown that Notch signaling converts hypoxia inherent to the tumor
microenvironment into epithelial mesenchymal transition (EMT)
76
required for the hypoxia-induced invasiveness of epithelial tumor
cells. The link between Notch and hypoxia in tumor progression
highlights the Notch pathway as an interesting therapeutic target
in cancer. The identified Hypoxia-Notch-EMT axis also emphasizes
the importance of understanding how Notch signaling becomes
derailed and how this is manifested in various aspects of tumor
progression. Half of the breast cancers have reduced levels of
Numb, a Notch antagonist, and Notch expression is associated
with poor prognosis. However, the specific role of Notch in breast
cancer is yet unclear. We have created 3D cellular models and
mouse models of breast cancer via orthotopic xenotransplantation
(OX) using breast cancer cells expressing different and tunable
levels of Notch activity to address these questions.
Interaction between key signaling mechanisms is important to
generate the diversity in signaling output required for proper control
of cellular differentiation and function. Notch crosstalks with other
major signaling pathways that modulate the signaling outcome. We
have contributed to working out the relationship between Notch
and the Notch antagonist, Numb (Chapman et al 2006) and to
establishing data on a PDGF-Notch signaling crosstalk of relevance
for vascular smooth muscle cell differentiation and function (Jin et al.,
2008). Current research focus includes interactions between Notch
receptors and ligands and the intermediate filament cytoskeleton,
and how these interactions determine trafficking, signaling activity
and Notch-driven stem cell functions. We aim to extend our
studies on Notch signaling crosstalk and implement proteomics
and mass-spec analysis to identify novel Notch binding proteins
and posttranslational modifications of Notch. A systematic attempt
to characterize how posttranslational modifications of Notch affect
signaling and to identify interacting proteins is likely to reveal novel
modes of regulation of Notch signaling.
The Notch pathway is highlighted as an interesting therapeutic
target, and developing strategies for local containment of Notch
inhibitors to the primary tumor would be a productive way towards
improving cancer therapy. Specific control over Notch activity is also
of interest for regulating stem cell differentiation and regenerative
therapy. We have recently described an approach to specifically
target cell populations with nanoparticles and this technology is
being further developed with the aim to specifically deliver Notch
inhibitors to tumor cells to prevent cancer progression (Rosenholm
et al 2009 a,b,c, Rosenholm et al., 2010). The developed technology
provides a system for efficient and tight dose control of Notch
signaling activity in a cell specific manner. In addition to the obvious
therapeutic value, such cell-specific action and tight dose control
of the Notch pathway should provide a useful tool for analyses of
the biological output of the pleiotropic and dose-dependent Notch
pathway. Further aims include developing the technology for a
precise control of Notch driven stem cells functions and for imaging
of stem cell functions and behaviour in vivo.
Funding:
The Academy of Finland, Åbo Akademi University (CoE in cell
stress and ageing), Turku Graduate School of Biomedical Sciences,
Magnus Ehrnrooth’s Stiftelse, Sigrid Jusélius Foundation, Finnish
Cancer Organizations, the Tor Joe och Pentti Borgs Foundation
(Åbo Akademi University).
Collaborators:
Prof. Milos Pekny (Sahlgrenska Academy at Göteborg University),
77
Prof. John Eriksson (Turku Centre for Biotechnology). Prof. Urban
Lendahl (Karolinska Institute), Prof. Lucio Miele (Loyola Medical
University, Chigaco), Ph.D Susumu Imanishi (Turku Centre for
Biotechnology), Prof. Lea Sistonen (Turku Centre for Biotechnology).
Dr.Tech Jessica Rosenholm (Laboratory for Physical Chemistry,
Åbo Akademi, Turku), Prof. Mika Linden (Dept of Chemistry, Ulm
University, Germany).
Sahlgren C and Lendahl U. (2006) Notch, stem cell control
and integration with other signaling mechanisms Regenerative
Medicine 1 (2):195-20
Selected Publications (#equal contribution):
Jessica M. Rosenholm, Emilia Peuhu, Laurel Tabe Bate-Eya, John
E. Eriksson, Cecilia Sahlgren#, Mika Lindén#. Cancer-Cell Specific
Induction of Apoptosis using Mesoporous Silica Nanoparticles as
Drug Delivery Vectors Small 2010 Jun 6;6(11):1234-41.# equal coauthor contribution
Aurelie de Thonel, Saima E. Ferraris, Hanna-Mari Pallari, Susumu
Y. Imanishi, Vitaly Kochin, Tomohisa Hosokawa, Shin-ichi Hisanga,
Cecilia Sahlgren, and John E. Eriksson. PKCζ regulates CDK5/p25
signaling during myogenesis in press (2010) MBC 21:1423-34
Heather Main*, Kian Leong Lee*, Henry Yang, Saija HaapaPaananen, Henrik Edgren, Shaobo Jin, Cecilia Sahlgren, Olli
Kallioniemi, Lorenz Poellinger, Bing Lim and Urban Lendahl.
Integration between Notch- and hypoxia-induced transcriptomes
in embryonic stem cells. (2010) Exp Cell Res. 316:1610-24
Jessica M Rosenholm, Dr., Emilia Peuhu, M.Sc., John Eriksson,
Prof. Dr., Cecilia Sahlgren, Dr. #, Mika Linden, Dr#. Targeted
Intracellular Delivery of Hydrophobic Agents using Mesoporous
Hybrid Silica Nanoparticles as Carrier Systems (2009) Nano Letters
9:3308-11 # equal co-author contribution
Jessica Rosenholm, Cecilia Sahlgren, Mika Lindén. Cancer cellspecific targeting of and targeted delivery by mesoporous silica
nanoparticles. (2010) Highlight to Journal of Material Chemistry
14:2707-2713
Jessica M Rosenholm, Dr., Annika Meinander, Dr., Emilia Peuhu,
M.Sc., Rasmus Niemi, Mr., John Eriksson, Prof. Dr., Cecilia
Sahlgren, Dr. #, Mika Linden, Dr#. Targeting of porous hybrid silica
nanoparticles to cancer cells. (2009) ACSNano 3:197-206 # equal
co-author contribution
Shaobo Jin, Emil M. Hansson, Saara Ihalainen, Cecilia Sahlgren,
Marc Baumann, Hannu Kalimo and Urban Lendahl. Notch signaling
regulates PDGF-receptorβ expression in vascular smooth muscle
cells. (2008) Circulation research 102:1483-91
Cecilia Granqvist, Rasmus Niemi, Veronika Mamaeva, Cecilia Sahlgren, Sebastian
Landor, Christian Antila, Daniel Antfolk. Missing from the picture: Marika Hietamäki.
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 105:6392-7.
Gavin Chapman#, Lining Liu#, Cecilia Sahlgren, Camilla Dahlqvist,
and Urban Lendahl. High levels of Notch signaling downregulate
Numb and Numblike. (2006) Journal of Cell Biology, 175(4):53540. # authors contributed equally
78
79
Targeting strategies for gene
therapy
Mikko Savontaus, M.D., Ph.D. Address: Turku Centre for
Biotechnology, Biocity, Tykistökatu 6B, P.O. Box 123, FI-20521
Turku, Finland. Tel. +358 2 333 8025, Fax +358 2 333 8000.
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 is
currently a senior scientist at the Turku Centre for Biotechnology
as well as a specialist in internal medicine at the Department of
Medicine at Turku University Hospital.
Personnel:
Graduate students: Raine Toivonen, M.Sc., Kim Eerola, M.Sc.
Undergraduate student: Minttu Mattila
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 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. In addition, we have used a similar strategy to target
tumor cells via the telomerase reverse transcriptase promoter. 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.
dilated cardiomyopathy. Ultrasound-guided injections are used
to analyze the efficacy and toxicity of our targeted vectors after
intramyocardial injection. Novel vectors with improved transcriptional
and transductional efficiency for target cells will be constructed by
combining hybrid serotype vectors with transcriptional targeting.
In addition, we are utilizing lentivirus technology for long-term
expression of therapeutic genes in the heart for heart failure and
hypertension. Our ultimate goal is to develop gene therapy vectors
for use in clinical trials by combining these approaches.
Funding:
Academy of Finland, Finnish Medical Foundation, Turku University
Hospital
Histochem Cell Biol. 133(3):349-57.
Toivonen, R., Suominen, E., Grenman, R. and Savontaus, M.
(2009) Retargeting Improves the Efficacy of a TelomeraseDependent Oncolytic Adenovirus for Head and Neck Cancer.
Oncology Reports 21: 165-171
Suominen, E., Toivonen, R., Grenman, R. and Savontaus, M. (2006)
Head and Neck Cancer Cells are efficiently infected by Ad5/35
Hybrid Virus. Journal of Gene Medicine 8:1223-1231.
Shinozaki, K., Suominen, E., Carrick, F., Sauter, B., Kähäri, V.-M.,
Lieber, A., Woo, S.L.C. and Savontaus, M. (2006). Efficient infection
of endothelial cells by a capsid-modified adenovirus. Gene Therapy
13:52-59.
Hutter, R., Valdiviezo, C., Sauter, B.V., Savontaus, M., Chereshnev,
I., Carrick, F.E., Bauriedel, G., Luderitz, B., Fallon, J.T., Fuster, V.
and Badimon, J.J. (2004) Caspase-3 and tissue factor expression
in lipid-rich plaque macrophages: evidence for apoptosis as
link between inflammation and atherothrombosis. Circulation
27;109(16):2001-8.
Ebert, O., Shinozaki, K., Huang, T.-G., Savontaus, M., GarciaSastre, A. and Woo S.L.C. (2003) VSV as oncolytic virus for
treatment of orthotopic hepatocellular carcinoma in immunecompetent rats. Cancer Research 63(13):3605-11.
Huang, T.-G., Savontaus, M., Shinozaki, K., Sauter, B. and Woo,
S.L.C. (2003) Telomerase dependent oncolytic adenovirus for
cancer treatment. Gene Therapy 10(15):1241-7.
Savontaus, M., Sauter, B.V., Huang, T.-G. and Woo, S.L.C. (2002)
Transcriptional Targeting of conditionally Replicating Adenovirus to
Dividing Endothelial Cells. Gene Therapy 9(14): 972-979
Currently the main focus of our group is in gene therapy for
cardiovascular disease. We are building on our previous findings
by analyzing the adenovirus receptor expression and vector
transduction efficiency in samples from patients with ischemic or
80
81
TRANSCRIPTIONAL REGULATION OF
HEAT SHOCK GENE EXPRESSION
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, FI-20521 Turku, Finland.
Tel. +358-2-333 8028, 215 3311; Fax +358-2-333 8000;
Email: [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:
Post-doctoral fellows: Julius Anckar, Ph.D., Eva Henriksson, Ph.D.,
Malin Åkerfelt, Ph.D.
Graduate students: Johanna Ahlskog, M.Sc., Johanna Björk,
M.Sc., Henri Blomster, M.Sc., Zhanna Chitikova, M.Sc., Alexandra
Elsing, M.Sc., Anton Sandqvist, M.Sc., Anniina Vihervaara, M.Sc.
Technician: Helena Saarento, M.Sc.
Undergraduate students: Anna Aalto, Heidi Bergman, Malin Blom,
Marek Budzynski, Henrica Karlberg, Karoliina Rautoma, Jenny
Siimes, Aki Vartiainen
The heat shock response is an evolutionarily well-conserved
cellular defence mechanism against protein-damaging stresses,
such as elevated temperatures or hyperthermia, 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. The mammalian HSF family consists of
four members HSF1-4. Although HSFs are best known as inducible
transcriptional regulators of genes encoding molecular chaperones
and other stress proteins, they are also important for normal
developmental processes and longevity pathways. The repertoire
of HSF targets has recently expanded well beyond the heat shock
genes, and the known functions governed by HSFs span from the
heat shock response to development, metabolism, lifespan and
disease, especially cancer and neurodegenerative disorders.
Our main interest is in elucidating 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 both the expression and activity of HSF1 and HSF2.
We have found that HSF1 is ubiquitously expressed and its activity
is primarily regulated by various post-translational modifications
82
(PTMs), such as acetylation, phosphorylation and sumoylation.
All these PTMs are induced by stress stimuli but their effects on
HSF1 vary. While examining the multi-site phosphorylation of
HSF1, we observed that in response to stress, HSF1 undergoes
phosphorylation-dependent sumoylation within a bipartite motif
which we found in many transcription factors and co-factors 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. Indeed, we have shown that 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 DNA-binding activity. Moreover, the duration of
HSF1 DNA-binding activity could be prolonged or diminished by
chemical compounds either activating or inhibiting the activity of
the longevity factor deacetylase SIRT1. These results suggest that
SIRT1-mediated deacetylation of HSF1 could maintain HSF1 in a
state competent for DNA-binding, thereby linking our research to
HSF1-mediated regulation of lifespan. Currently, our focus is on
a complex network of PTMs to decipher the post-translational
signature of HSF1.
Unlike HSF1, which is a stable protein evenly expressed in most
tissues and cell types, HSF2 shows a highly specific spatiotemporal
expression pattern during development, and we have demonstrated
that the amount of HSF2 is directly linked to its activity. Using
mouse spermatogenesis as a model system, we have 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 were able to show 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
have reported as novel HSF2 targets in the testis. Our original
finding that miR-18 regulates HSF2 activity in spermatogenesis
links miR-18 to HSF2-mediated physiological processes and opens
a whole new window of opportunities to elucidate the physiological
and stress-related functions of HSF2, either alone or in conjunction
with HSF1. Our studies on the formation of heterotrimers between
HSF1 and HSF2 and their impact on already established and newly
discovered targets genes should also shed light on the roles of HSFs
in protein-misfolding disorders, such as neurodegenerative diseases,
as well as in aging and cancer progression. So far, the studies have
mostly concentrated 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 either expression or
activity of these multi-faceted transcriptional regulators.
Funding:
The Academy of Finland, the Sigrid Jusélius Foundation, the
Finnish Cancer Organizations, and Åbo Akademi University (Centre
of Excellence in Cell Stress).
Collaborators:
Elisabeth Christians (University of Toulouse, France), Sampsa
Hautaniemi (University of Helsinki), Susumu Imanishi and John
83
Eriksson (Åbo Akademi University), Noora Kotaja and Jorma
Toppari (University of Turku), Pia Roos-Mattjus, Tiina Salminen,
Peter Slotte and Kid Törnquist (Åbo Akademi University), Valérie
Mezger (University of Paris Diderot, France), Jorma Palvimo
(University of Eastern Finland), Sandy Westerheide and Rick
Morimoto (Northwestern University, USA).
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, in press.
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.
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.
From left to right, standing: Lea Sistonen, Eva Henriksson, Johanna Björk, Jenny
Siimes, Malin Åkerfelt, Jenni Vasara, Alexsandra Elsing, Malin Blom, Aki Vartiainen,
sitting: Johanna Ahlskog, Anton Sandqvist, Mikael Puustinen, Marek Budzynski.
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 (epub. Dec 21, 2005).
*equal contribution
84
85
Cancer Cell Signaling
http: http://www.btk.fi/index.php?id=1279
Jukka Westermarck, M.D., Ph.D., Docent in Molecular Biology
(University of Turku). 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. Email: [email protected],
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 a
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 2011).
Personnel:
Seniors scientist: Jukka Westermarck, M.D., Ph.D.
Post-doctoral researchers: Christophe Come, Ph.D., Juha Okkeri,
Ph.D., Yuba Pokharel, Ph.D., Sami Ventelä, M.D., Ph.D.
Graduate students: Antoine Mialon, M.Sc., Minna Niemelä, M.Sc.,
Anni Laine, M.Sc., Tuuli Halonen, M.Sc., Amanpreet Kaur, M.Sc.,
Anchit Khanna, M.Sc. (IMT)
Technical personnel: Taina Kalevo-Mattila
Description of the project :
The goal of our research group is to identify novel signaling
mechanisms involved in malignant cell growth by isolating protein
complexes associated with proteins previously demonstrated to
have an important role in cancer progression. To identify protein
complexes, we use tandem affinity purification (TAP) and Streptag purification methods, both proven to be suitable for purification
of signaling protein complexes from mammalian cells in culture.
Identification of novel proteins involved in malignant growth may
also reveal novel possibilities for intervention in the therapy of
cancer and other hyperproliferative diseases.
Based on our recent work, we have identified several novel
interacting proteins for signaling proteins such as AP-1 transcription
factor c-Jun, MAPK kinase MEK1, and protein phosphatase PP2A.
Most of our future work will be focused on characterization of
PP2A interaction partner CIP2A, that we have demonstrated to
inhibit PP2A in human malignancies. As PP2A inhibition has been
recognized as a prerequisite for human cell transformation, it is
plausible that further understanding of the function of CIP2A will
reveal fundamental novel information about the basic mechanisms
of cancer progression. The overall goal of the proposed project
is to study the function and importance of CIP2A in cancer
progression by using combination of molecular biology, cell biology
and functional genetics methods. As our current results suggest
that targeting CIP2A could be beneficial in the treatment of cancer,
our goal is also to develop research models for evaluating the
suitability of CIP2A as a novel drug target for cancer therapies. In
addition, our aim is to purify new protein complexes related cancer
cell signaling.
86
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, Emil
Aaltonen Foundation, 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), Kirmo Wartiovaara (University of
Helsinki), Sampsa Hautaniemi (University of Helsinki), Ari Ristimäki
(University of Oulu), Jorma Toppari (University of Turku), Veli-Matti
Kähäri (Turku University Hospital), Reidar Grenman (Turku University
Hospital).
Kerosuo L, Fox H, Perälä N, Ahlqvist K, Suomalainen A, Westermarck
J, Sariola H, and Wartiovaara K; CIP2A increases self-renewal and
is linked to Myc in neural progenitor cells. Differentiation, in press,
2010
Heikkinen PT, Nummela M, Leivonen SK, Westermarck J, Hill CS,
Kähäri VM, and Jaakkola PM; Hypoxia activated Smad3-specific
dephosphorylation by PP2A. The Journal of Biological Chemistry,
285, 3740-3749, 2010.
Come C, Laine A, Chanrion M, Edgren H, Mattila E, Liu X, Jonkers
J, Ivaska J, Isola J, Darbon J-M, Kallioniemi O-P, and Thezenas S
and Westermarck J; CIP2A is associated with human breast cancer
aggressivity. Clinical Cancer Research, 15, 5092-5100, 2009.
Khanna A, Böckelman C, Hemmes A, Junttila MR, Wiksten J-P,
Lundin P, Junnila S, Murphy D, Evan GI, Haglund C, Westermarck
J*, and Ristimäki A*; c-Myc-dependent regulation and prognostic
role of CIP2A in gastric cancer. Journal of the National Cancer
Institute, 101, 793-805, 2009. *equal contribution
Puustinen P, Junttila MR, Vanhatupa S, Sablina AA, Hector ME,
Teittinen K, Raheem O, Ketola K, Lin S, Kast J, Haapasalo H, Hahn
WC, and Westermarck J; PME-1 Protects ERK Pathway activity
from Protein Phosphatase 2A-mediated Inactivation in human
malignant glioma. Cancer Research, 69, 2870-2877, 2009.
Wu J, Ovaska K, Vallenius T, Westermarck J, Mäkelä TP, and
Hautaniemi S; Protein-protein interaction portal for network level
analysis. Nature Methods, 6, 75-77, 2009
Westermarck J, Hahn WC; Multiple pathways regulated by the
tumor suppressor PP2A in transformation. Trends in Molecular
Medicine, 14,152-160, 2008.
Junttila MR, Li S-P, Westermarck J; Phosphatase-mediated crosstalk between MAPK signaling pathways in the regulation of cell
survival. The FASEB Journal, 22, 954-965, 2008.
Holmström TH, Mialon A, Kallio M, Nymalm Y, Mannermaa L, Holm
T, Johansson H, Black E, Gillespie DA, Salminen TA, Langel U,
Valdez BC, and Westermarck J; c-Jun supports ribosomal RNA
processing and nucleolar localization of a RNA helicase DDX21.
87
The Journal of Biological Chemistry, 283, 7046-7053, 2008.
Junttila, MR, Puustinen P, Niemelä M, Ahola R, Arnold H, Böttzauw
T, Ala-aho R, Nielsen C, Ivaska J, Taya Y, Lu SL, Li S, Chan EKL,
Wang X-J, Grenman R, Kast J, Kallunki T, Sears R, Kähäri V-M,
Westermarck J; CIP2A Inhibits PP2A in Human Malignancies. Cell,
130, 51–62, 2007.
Junttila MR, Ala-aho R, Jokilehto T, Peltonen J, Grenman R,
Jaakkola P, Westermarck J, and Kähäri V-M; p38alpha and p38delta
mitogen-activated protein kinase isoforms regulate invasion and
growth of head and neck squamous carcinoma cells. Oncogene,
26, 5267-5279, 2007.
Turku Centre for
Biotechnology
Ph.D. Theses 2009
1. Mialon, Antoine: Role and function of c-Jun protein complex in
cancer cell behavior. University of Turku, p. 120
2. Pellinen, Teijo: Beta1 integrin regulation. University of Turku,
p. 109
3. Mattila, Elina: Negative regulation of receptor tyrosine kinases
by T-cell protein tyrosine phosphatase. University of Turku, p.
126.
4. Anckar, Julius: Multisite post-translational regulation of heat
shock transcription factors. Åbo Akademi University, p. 162.
5. Kochin, Vitaly: Finding and characterizing protein phosphorylation
sites that determine cellular decisions and functions. Åbo
Akademi University, p. 185.
6. Kaunisto, Aura: Differential regulation of c-FLIP isoforms
through post-translation al modifications. University of Turku,
p.138.
7. Åkerfelt, Malin: Novel target genes for heat shock factors 1 and
2 in development. Åbo Akademi University, p. 166.
Publications 2009
1. Aflakian, N., Ravichandran, S., Sarwar Jamaal, Md. S.,
Järvenpää, 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.
2. Ahonen, L.J., Kukkonen, A.M., Pouwels, J., Bolton, M.A.,
Jingle, C.D., Stukenberg, P.T. & Kallio, M.J. 2009. Perturbation
of Incenp function impedes anaphase chromatid movements
and chromosomal passenger protein flux at centromeres.
Chromosoma, 118:71-84.
3. Axarli, I., Dhavala, P., Papageorgiou, A.C. & Labrou, N.E.
2009.
Biochem.
J., 422:247-256.
4. Axarli, I., Dhavala, P., Papageorgiou, A.C. & Labrou, N.E.
2009.
J. Mol. Biol., 385:984-1002.
5. Blomster, H.A., Hietakangas, V., Wu, J., Kouvonen, P.,
Hautaniemi, S. & Sistonen, L. 2009.
Mol.
Cell. Proteomics, 8:1382-1390.
6. Brandt, D.T., Baarlink, C., Kitzing, T.M., Kremmer, E., Ivaska,
J., Nollau, P. & Grosse, R. 2009.
Nat. Cell Biol., 11:557-568.
7. Cheng, F., Weidner-Glunde, M., Varjosalo, M., Rainio, E.M.,
Lehtonen, A., Schulz, T.F., Koskinen, P.J., Taipale, J. & Ojala,
P.M. 2009.
From left to right, front row: Jukka Westermarck, Tiina Laiterä, Anna Cvrljevic, Leni
Mannermaa, Christophe Côme, Yuba Raj Pokharel, Taina Kalevo-Mattila, Minna
Niemelä, Tuuli Halonen, Kowstan Eskandari, Amanpreet Kaur, second row: Juha
Okkeri, Anni Laine, Sami Ventelä, Otto Kauko.
88
PLoS Pathog., 5:e1000324.
8. 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
89
signals in primary B cells. Blood, 113:2416-2425.
9. Côme, C., Laine, A., Chanrion, M., Edgren, H., Mattila, E., Liu, X.,
Jonkers, J., Ivaska, J., Isola, J., Darbon, J.M., Kallioniemi, O.,
Thézenas, S. & Westermarck, J. 2009.
Clin. Cancer Res.,
15:5092-5100.
10.
11. Elo, L.L., Hiissa, J., Tuimala, J., Kallio, A., Korpelainen, E.
& 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.
12. 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.
13. Hackauf, B., Rudd, S., van der Voort, J.R., Miedaner, T. &
Wehling, P. 2009.
Theor.
Appl. Genet., 118:371-84.
14. Hiissa, J., Elo, L.L., Huhtinen, K., Perheentupa, A., Poutanen,
M. & Aittokallio, T. 2009. Resampling reveals sample-level
differential expression in clinical genome-wide studies. OMICS,
13:381-396.
15. Holmström, T.H., Rehnberg, J., Ahonen, L.J. & Kallio, M.J.
2009.
Mol. Oncol., 3:262-268.
16. Iljin, K., Ketola, K., Vainio, P., Halonen, P., Kohonen, P.
Clin. Cancer Res., 15:60706078.
17. Imanishi, S.Y., Kouvonen, P., Smått, J.H., Heikkilä, M., Peuhu,
E., Mikhailov, A., Ritala, M., Lindén, M., Corthals, G.L. &
Eriksson, J.E. 2009.
18.
19.
23.
24.
25.
26.
27.
28.
29.
30.
31.
2009. Neuropeptide Y polymorphism significantly magnifies
diabetes and cardiovascular disease risk in obesity: the Hoorn
Study. Eur. J. Clin. Nutr., 63:150-152.
BMC Res. Notes, 2:204.
20. Kaunisto, A., Kochin, V., Asaoka, T., Mikhailov, A., Poukkula,
M., Meinander, A. & Eriksson, J.E. 2009.
Cell Death Differ., 16:1215-1226.
21. Khanna, A., Böckelman, C., Hemmes, A., Junttila, M.R.,
Wiksten, J.P., Lundin, M., Junnila, S., Murphy, D.J., Evan,
90
22.
32.
33.
34.
91
35.
41.
42.
36.
37.
38.
43.
44.
39.
45.
40.
46.
47.
48.
49.
50.
51.
52.
53.
54.
.
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LIFE OUTSIDE THE LAB
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ÅBO BIOTEKNIKCENTRUM
TURKU CENTRE FOR BIOTECHNOLOGY
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Cell Signalling to Systems Biology Research
TURKU CENTRE
FOR BIOTECHNOLOGY
REPORT 2009
Tykistökatu 6 B
P.O.BOX 123
FI 20521 Turku, Finland
Tel: +358 2 333 8603, Fax 358 2 333 8000

Report 2009 - Turku Centre for Biotechnology

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