Principal Investigator:
Olli Kallioniemi, M.D., Ph.D., Director, Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, 00140 University of Helsinki, Finland. Director of the Academy of Finland Centre of Excellence on Translational Genome-scale Biology (2006-2011), Medical Biotechnology,
VTT Technical Research Centre of Finland and University of Turku. Laboratory address: Medical Biotechnology, PharmaCity,
Itäinen Pitkäkatu 4C, FI-20521 Turku, Finland. Tel. +358-20-722 2800. Fax +358-20-722 2840. E-mail: [email protected].
Biography:
Dr. Olli Kallioniemi received his M.D. in 1984 and Ph.D. in 1988 at the University of Tampere in Finland. Olli Kallioniemi held several positions in the US over a 10-year period, such as Head of Translational Genomics Section at the Cancer Genetics Branch, National Human Genome Research Institute, at the NIH, Bethesda, Maryland during 1995-2002. In 2003, he was appointed as Professor of Medical Biotechnology at the VTT Technical Research Centre of Finland with a joint appointment at the University of Turku. Academy of Finland Professor in 2004-2007. In 2007, he was nominated as a director of the Institute for Molecular Medicine Finland (FIMM), a Nordic EMBL Partnership in Molecular Medicine. He continues to direct the ongoing projects in Turku until the end of 2011. He is an author of 263 publications and editor or member of the editorial board of six journals. Inventor of 18 issued patents, with a focus on technology development, such as Comparative Genomic Hybridization (CGH) in 1992, tissue microarrays in 1998 and cell-based RNAi microarrays in 2003. EACR young investigator award in 1994, Anders Jahre Prize in 1998, NIH Director’s lecture in 2000, Medal of the Swedish Medical Society in 2003, National Academy of Sciences (Finland) in 2005, EMBO Membership in 2006, and the Abbot-IFCC award in Molecular Diagnostics 2009. Personnel:
Ph.D-students and postdocs at the University of Turku: Anna Aakula, M.Sc., Santosh Gupta, M.Sc., Kirsi Ketola, M.Sc., Pekka Kohonen, Ph.D. Paula Vainio, M.D., Sirkku Pollari, M.Sc., Laboratory Technician: Pirjo Käpylä, Coordinator: Terhi Jokilehto, M.Sc.
Description of the Project:
The overall purpose of this research program is to develop and apply high-throughput technologies to understand mechanisms of progression of breast and prostate cancers as well as to identify mechanisms of drug response.
We use systems biology and chemical biology approaches to characterize the deregulation of cancer cell functions. The research is carried out in collaboration between the Institute for Molecular Medicine Finland (FIMM), the Medical Biotechnology Centre of the VTT Technical Research Centre of Finland and the Turku Centre for Biotechnology. Our group coordinates Academy of Finland Centre of Excellence in Translational Genome-Scale Cell Biology. We have developed and are applying biochip technologies, next-
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From left to right, first row: Paula Vainio, Mari Björkman, Riina Plosila, Pekka Kohonen, Back row: Kirsi Ketola, Anna Aakula, Santosh Gupta, Olli Kallioniemi, Sirkku Pollari, Elmar Bucher.
generation RNA sequencing, bioinformatics, systems biology, drug development technologies, cell microarrays, protein lysate microarrays, in silico profiling of gene expression in clinical samples and many others.
Collaborators:
Tomi Mäkelä, Lauri Aaltonen, Jussi Taipale, Päivi Ojala, Sampsa Hautaniemi, Heli Nevanlionna, Heikki Joensuu, Kari Alitalo, Jonathan Knowles, Emmy Verschuren, Sergey Kuznetshov, Samuli Ripatti, Krister Wennerberg (FIMM and Biomedicum Helsinki), Antti Poso, Samuel Kaski, Tapio Visakorpi, Jukka Westermarck and many others in other Universities in Finland. We have over 100 partners in EU-FP7 collaborative projects such as Epitron, Genica, APO-SYS, Prosper, Meta-Cancer and Systems Microscopy. Funding:
The Academy of Finland, Tekes, Finnish Cancer Organizations and Sigrid Juselius Foundation. Our biggest source of funding comes from the EU framework projects.
Selected recent publications:
Mpindi J.P., Sara H., Haapa-Paananen S., Kilpinen S., Pisto T., Bucher E., Ojala K., Iljin K., Vainio P., Björkman M., Gupta S., Kohonen P., Nees M. and Kallioniemi O. (2011) GTI: A Novel Algorithm for Identifying Outlier Gene Expression Profiles from Integrated Microarray Datasets. PLoS One 16: e17259.
Hanash S.M., Baik C.S. and Kallioniemi O. (2011) Emerging molecular biomarkers-blood-based strategies to detect and monitor cancer. Nat. Rev. Clin. Oncol. 8: 142-150.
Ostling P., Leivonen S.K., Aakula A., Kohonen P., Mäkelä R., Hagman Z., Edsjö A., Kangaspeska S., Edgren H., Nicorici D., Bjartell A., Ceder Y., Perälä M. and Kallioniemi O. (2011) Systematic Analysis of MicroRNAs Targeting the Androgen Receptor in Prostate Cancer Cells. Cancer Res. 71: 1956-1967.
Vainio P., Gupta S., Ketola K., Mirtti T., Mpindi J.P., Kohonen P., Fey V., Perälä M., Smit F., Verhaegh G., Schalken J., Alanen K.A., Kallioniemi O. and Iljin K. (2011) Arachidonic acid pathway members PLA2G7, HPGD, EPHX2, and CYP4F8 identified as putative novel therapeutic targets in prostate cancer. Am. J. Pathol. 178: 525-536. Edgren H., Murumagi A., Kangaspeska S., Nicorici D., Hongisto V., Kleivi K., Rye I.H., Nyberg S., Wolf M., Borresen-Dale A.L. and Kallioniemi O (2011) Identification of fusion genes in breast cancer by paired-end RNA-sequencing. Genome Biol.12: R6.
Kilpinen S., Ojala K., Kallioniemi O. (2010) Analysis of kinase gene expression patterns across 5681 human tissue samples reveals functional genomic taxonomy of the kinome. PLoS One. 5: e15068. Rantala J.K., Edgren H., Lehtinen L., Wolf M., Kleivi K., Vollan H.K., Aaltola A.R., Laasola P., Kilpinen S., Saviranta P., Iljin K. and Kallioniemi O. (2010) Integrative functional genomics analysis of sustained polyploidy phenotypes in breast cancer cells identifies an oncogenic profile for GINS2. Neoplasia 12: 877-888.
Gupta S., Iljin K., Sara H., Mpindi J.P., Mirtti T., Vainio P., Rantala J., Alanen K., Nees M. and Kallioniemi O. (2010) FZD4 as a mediator
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of ERG oncogene-induced WNT signaling and epithelial-to- mesenchymal transition in human prostate cancer cells. Cancer
Res. 70: 6735-45.
Härmä V., Virtanen J., Mäkelä R., Happonen A., Mpindi J.P., Knuuttila M., Kohonen P., Lötjönen J., Kallioniemi O. and Nees M. (2010) A comprehensive panel of three-dimensional models for studies of prostate cancer growth, invasion and drug responses.
PLoS One 5: e10431.
International Cancer Genome Consortium, Hudson T.J.,et al. (2010) International network of cancer genome projects. Nature 464: 993-998.
Pollari S., Käkönen S.M., Edgren H., Wolf M., Kohonen P., Sara H., Guise T., Nees M. and Kallioniemi O. (2011) Enhanced serine production by bone metastatic breast cancer cells stimulates osteoclastogenesis. Breast Cancer Res. Treat.125: 421-430. Leivonen S.K., Mäkelä R., Ostling P., Kohonen P., Haapa-Paananen S., Kleivi K., Enerly E., Aakula A., Hellström K., Sahlberg N., Kristensen V.N., Børresen-Dale A.L., Saviranta P., Perälä M. and Kallioniemi O. (2009) Protein lysate microarray analysis to identify microRNAs regulating estrogen receptor signaling in breast cancer cell lines. Oncogene, 28: 3926-3936.
Iljin K., Ketola K., Vainio P., Halonen P., Kohonen P., Fey V., Grafström R.C., Perälä M. and Kallioniemi O. (2009) 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: 6070-6078. Varjosalo M., Björklund M., Cheng F., Syvänen H., Kivioja T., Kilpinen S., Sun Z., Kallioniemi O., Stunnenberg H.G., He, W-W., Ojala P. and Taipale J. (2008) Application of Active and Kinase-Deficient Kinome Collection for Identification of Kinases Regulating Hedgehog Signaling. Cell 133: 537-548. Pellinen T., Tuomi S., Arjonen A., Wolf M., Edgren H., Meyer H., Rantala J.K., Kallioniemi O., Fässler R., Kallio M. and Ivaska J. (2008) Integrin traffic regulated by Rab21 is necessary for cytokinesis. Dev. Cell., 15: 371-385.
Kilpinen S., Autio R., Ojala K., Iljin K., Bucher E., Sara H., Pisto T., Saarela M., Skotheim R., Björkman M., Mpindi J. P., Haapa- Paananen S., Vainio P., Edgren H., Wolf M., Astola J., Nees M., Hautaniemi S. annd Kallioniemi O. (2008) Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues.
Genome Biol., 9: R139.