For the first biochip readouts, we concentrate on the quantification of cancer-relevant proteins on so-called reverse phase arrays. This is intended to increase the data gain from high throughput screens and to add readout options. The figure shows a first test chip for the detection and quantification of the p53 protein, which was spotted at a density allowing for positioning 12,000 samples on a chip with the size of a microscopic slide.
Unit 5: HT-Screens
NanoCAN's UNIT 5 bundles the efforts for discovering new drug targets and starting points for nucleic acid-based drugs. This mostly comprises systematic, hypothesis-generating high-throughput screens via a robotic platform. Medium-scale targeted functional genomics screens using complementary strategies and potentially providing some shortcuts are also performed, however. The subprojects within UNIT 5 are conducted by academic staff, of which one part also works interdisciplinary in the other units and the other part focuses on setting up the robotic screens to be available as core facility to the center. UNIT5 includes as subprojects:
The layout of the robotic platform was planned to allow for preparations of biological samples from the treated cells after the primary readout to convert the large scale experiments into a conserved array format for consecutive screens via other techniques. The robot station will be employed for high throughput screens, using, for example, genome-wide siRNA libraries, where a single screen in triplicate will comprise 60,000 individual cell experiments. In various settings, differential screens are employed to, e.g., uncover synthetic lethal relationships, which comprise scales of 120.000 single cell experiments per screen.
The subproject aims at a systematic functional genomics approach, analyzing a set of >100 candidate genes and miRNAs from available molecular profiles of metastatic breast cancers in order to identify new crucial regulators of metastasis formation and EMT. The data may not only provide valuable starting points for therapeutic strategies aiming at the suppression of metastatic spread and EMT, but also improve the understanding of the properties of cancer stem cells.
The goal of this project is to develop the tools and conditions for detecting CSC-markers in protein preparations of cells, which are arrayed on a chip format. The challenge associated with this is to find the appropriate balance between the accurate quantification of the CSC-markers in minute amounts of protein (corresponding the protein content of a single cell or less) and to achieve a sufficiently high throughput, so that the method can be used for future diagnostic approaches as well as for systematic large scale screens (see also: Unit 5).