Sequencing of whole genomes has provided new perspectives into the blueprints of diverse organisms. Knowing the sequences, however, does not always tell us much about the function of the genes that regulate development and homeostasis. Our laboratory is using different strategies to dissect gene function relevant to human disease, such as cancer biology and stem cell research.
Functional genomic screens
RNA interference is a well established method for gene function analysis in cells and whole organisms. Our lab has developed innovative technology to perform large scale RNAi experiments in mammalian cells and in mice. We use endoribonuclease prepared siRNA (esiRNA) for the efficient and specific knock-down in genome wide screens to identify and characterize genes relevant to cancer biology and differentiation. We have recently extended this method and developed RNAi profiling in primary cancer cells, with the aim to implement functional data into personalized medicine. To achieve this goal our established expertise on RNAi profiling is translated to different tumor entities in collaboration with groups at the Faculty of Medicine Carl Gustav Carus of the TU Dresden. Furthermore, we have recently extended our esiRNA resources to long non-coding RNAs (lncRNAs) and have started to probe the functions of these new regulators.
CRISPR/Cas9 technology to inactivate cancer mutations
The genome scissor CRISPR/Cas9 opens up completely new possibilities for the area of cancer research. As programmable scissors this technology allows cleavage of DNA at predefined sites mutated in the genome of cancer cells without significantly targeting the healthy, wildtype alleles. Moreover, expression of Cas9 together with the cancer-specific guide (g)RNAs can be used to unmask mutations that drive cell growth and viability in cancer cell lines. As mutations that promote cancer growth can be identified with this technology, the scientific approach could significantly improve cancer diagnostics and potentially as a novel therapeutic approach.
Advanced genome engineering with designer recombinases
The need for fluent and precise genomic manipulation strategies has been exacerbated by the increasing pace of published genome sequences. Beyond the reading of complete genomes, the precise manipulation of the encoded information is becoming more important in modern molecular biology. Site-specific recombinases are prominent genetic engineering tools that allow the genetic manipulation of whole organisms. In order to expand the usefulness of these enzymes we are designing novel recombinases through directed molecular evolution in combination with rational design and test them for their usefulness in biology and medicine. A successful scientific example represents the development of the designer recombinase Brec1 that is capable of specifically removing the provirus from infected cells of most primary HIV-1 isolates found in humans. In future work, we will generate new designer recombinases to correct genetic alterations found in human diseases.
Future prospects and goals
- Improve esiRNA and CRISPR/Cas9 technology for functional genomic studies.
- Perform RNAi and CRISPR/Cas9 screens in a variety of stem cells to identify and characterize factors involved in self-renewal and differentiation.
- Perform phenotypic profiling of cancer cell lines and primary cancer material to identify and characterize candidate genes with therapeutic potential.
- Develop and apply tools that allow flexible and precise genomic manipulations.