Short Name: 

U. Turku

Name:

University of Turku

Lead: 

Prof. Olli Kallioniemi

Description:

The role in the project

U. Turku will perform the high-throughput miRNA functional screenings in order to identify prostate cancer specific miRNAs in WP2. It will also do the bioinformatic data analyses related to their own miRNA data and coordinate the data integration efforts related to the data produced by the participants as specified in WP2.

Expertise

Olli Kallioniemi group at U. Turku has expertise in high-throughput genomics and transcriptomics analysis of cancer, bioinformatic modelling, and in the functional, high-throughput screening with RNAi and drug libraries. These tools have facilitated the identification of critical genes in cancer and their role in tumour progression, such as AR, IGFBPs, S100P, ERG and HDACs in prostate cancer. These previously mentioned tools and others now under development are being applied to prostate and breast cancer research. The group is developing and applying high throughput genomics and transcriptomics analyses of cancer, bioinformatic modelling and the functional, high throughput analysis with RNAi and drugs using cell and lysate microarrays. The strategy is to integrate data from the aforementioned platforms in order to identify key drug targets and explore mechanisms of drug action and resistance. The group has wide bioinformatics resources including personnel with professional programming and web development experience, and in-house experience in database development. There are eight bioinformatics personnel with experience in developing new bioinformatics tools using the R statistical programming language. 

Facilities and research equipment

U. Turku has established a state-of-the-art cell-based High Throughput Screening (HTS) system, which is widely applicable to cancer research, functional target identification, and early-stage lead discovery. The HTS system includes robotic instrumentation (Hamilton Microlab STAR, Hamilton SWAP automation, Multidrop plate filler and Tecan plate washer), a Cytomat 6000 automated CO2 incubator, as well as PE-Envision plate reader, Acumen image cytometer and a FACS Array. Cell arrays and protein lysate arrays for multiple endpoints: U. Turku has set up a system, where cells are lysed in 384 -well plates after the RNAi treatment, and printed onto nitrocellulose slides. This makes it possible to generate dozens of copies of a microarray, representing all wells from a 10,000 -well HTS screen, and use specific antibodies to read the endpoints of the analysis.

Key personnel in the project and their role

1. Prof. Olli Kallioniemi, MD, PhD, Director of the Finnish Institute of Molecular Medicine (FIMM, an EMBL partnership organization. He is also the Director of the Centre of Excellence in Translational Genome scale Biology. Prof. Kallioniemi will be the responsible principal investigator for the project at the University of Turku

2. Dr. Merja Perälä, Ph.D. Senior scientist and team-leader of the High-throughput Screening team acts as a co-PI in this project.

3. Dr. Suvi-Katri Leivonen, PhD. Postdoctoral fellow, who will participate in miRNA functional HTS screenings.