Finland, particularly the Oulu region, is focused on developing the connections between the life sciences, nanotechnology, and information technology. Oulu Bioforum, Oulu Innovation, and other centers in Finland, supported by partners in the German cities of Halle and Leverkeusen, recently hosted “Bio Meets Nano and IT” to promote interdisciplinary and business collaboration between those involved in these three areas.
High-throughput approaches are a special interest in the Oulu region. Hans Söderlund, Ph.D., VTT Technical Research Center described the development of a high-throughput multiplexed system for analysis of transcriptional signatures that is based on advanced microfluidic technology.
“To measure total gene expression by conventional means is cumbersome and expensive,” he said. There are gene chips that can measure 40,000 genes and, at the other extreme, those that look at just a few. “We are interested in the space between 10 and 300 genes, looking at a large number of samples with high throughput.”
Transcript analysis with affinity capture (TRAC), a VTT technology, has been spun off to PlexPress TRAC involves exposure of RNA through cell lysis and then the addition of a capture probe that binds to streptavidin-coated magnetic beads. This way, data on 2,880 transcriptional levels (96 samples in a 30-plex experiment) is available in about four hours, Dr. Söderlund reported. Applications include cancer cells exposed to drug candidates, RNAi knockdown assays, and cell-cycle monitoring.
In a collaboration with the University of California, Berkeley, the company has transferred TRAC onto nanovolume chips for online analysis and is also trying to transfer the technology onto a printed format, reflecting VTT’s interest in getting wet chemistry onto chips to make low-cost biosensors. “We could, therefore, go up to high-throughput transcriptional profiling,” added Dr. Söderlund.
Olli-Pekka Kallioniemi, Ph.D., of the Institute for Molecular Medicine discussed the Institute’s medical systems biology approach, with the development of a high-throughput siRNA screen of cancer cells in 384-well plates. Scientists at the Institute are miniaturizing this to a functional cellular microarray where they will print siRNA from 20x384 well plates to see how the cells respond to the siRNAs.
“We can do the entire genome of siRNAs on a single microtiter-sized plate,” he said. The cells adhere to the spot and are transfected by the siRNA. The work has been applied to a prostate cancer cell line in a druggable genome screen. “This is pushing the limit of anything available today. We are now beginning to approach reasonable accuracy and reproducibility.”
In a collaboration with the University of Turku the team is looking at what genes are necessary for integrin signaling when cells invade. Live cell imaging of activated integrin siRNA hits in P13 cells can reveal what happens in cell morphology when this gene is knocked down.
“We use this to identify critical determinants of cell movements,” Dr. Kallioniemi said. “There are still lots of challenges, including the printing requirements for 40,000 siRNAs per experiment and managing up to 40,000 high-resolution images per experiment.” A further application is to improve the efficiency of hormonal therapies in prostate cancer by looking at the siRNAs that have an effect in androgen-deficient conditions.