Engineering of RNA aptamers to selectively target tumor associated extracellular markers: Improved selection against complex targets and for selective cell uptake

• Applicant: Dr. Johannes Urban
• Subject Area: Cell Biology
• Term: from 2009 to 2011
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 106905252

The identification of tumor specific markers of pathology is a prerequisite to the development of therapeutic and diagnostic agents. However, to date only a few good tumor associated markers have been described and characterized mainly due to overlapping expression profiles in healthy tissue and limitations in the currently available laboratory techniques. Thus, we intend to establish a widely applicable protocol for the selective targeting of tumor tissue by using combinatorial RNA libraries. The hallmark of our system will be the stacked co-cultivation of monolayer tumor related and unrelated tissues separated by a permeable membrane. A single stranded RNA library containing 40 randomized bases (> 1014 species) will be applied to the (tumor unrelated) top layer leading to subtraction of RNA species that bind to ubiquitously expressed structures. RNA species passing the membrane and binding to the tumor related tissue are then selectively amplified by cDNA synthesis and in vitro transcription. Iterative rounds of this selection procedure will result in an enrichment of RNA species targeting specific tumor related markers. This approach will be applied not only to different cancer cell lines but also to VEGF (vascular endothelia growth factor) stimulated endothelial cells thereby mimicing tumor angiogenesis, as well as proteolytic degraded extracellular matrix intermediates as found in tumor surroundings. Moreover, in parallel we will perform selections for those RNAs that are able to internalize into the tumor cell. The outcome of this project will not only be an improved selection method for combinatorial RNA libraries to complex targets, but also lead to the identification of tumor specific markers that will be characterized in vivo for their use in tumor therapy and imaging.

• DFG Programme: Research Fellowships
• International Connection: USA
• Host: Professor Dr. Bruce A. Sullenger