Genome Accessibility and Modification Group

“Improving CRISPR-Cas9 efficiency for gene editing in human cells”

Gene therapy holds the possibility to revolutionize the way otherwise incurable genetic diseases are treated. In principle, it allows for the DNA within a cell to be changed. With the dawn of new gene editing technologies such as CRISPR-Cas9 (clustered, regularly interspaced, short palindromic repeats (CRISPR)-associated protein 9), repairing mutations within human cells has become reality. Our ability to program this bacterial defense mechanism with human target sequences, has unlocked unprecedented possibilities for gene therapy and personalized medicine.

While deleting a gene to impair its function within a cell is fairly easy now, the reversion of a detrimental mutation back to its normal state is much more difficult. This requires exchange of one sequence by another, which is only entirely precise when mediated by a process called homologous recombination or homology directed repair (HDR). While CRISPR-Cas9 has made gene editing by homologous recombination easier, its efficiency remains poor. This is a major limitation that must be overcome if genome editing technologies are to be used in medical treatments or commercial applications in biotechnology. The majority of research that focuses on improving CRISPR-Cas9 has tried to modify the components of the bacterial Cas9 system. Our approach, however, addresses this problem from a completely different perspective. We have shown that one can greatly increase repair by homologous recombination by making the cell’s genome more accessible to the editing machinery. Simply put, if reverting a mutation by gene editing is like breaking into a bank vault with a drill, then one way to speed up the process is to get a better drill. Instead, our method changes the composition of the vault from iron to wood. The underlying evidence for this project stems from our research in budding yeast, where we showed that making DNA more accessible enhances the rate of genome integrations. If true in mammalian cells, this research could become a fundamental aspect of genome editing, applicable not only to CRISPR-Cas9 but also to any gene editing technologies yet to come.

We are hosted at the CABMM and work in collaboration with our project partner and mentor SNF Prof. Matthias Altmeyer as well as our external project partner Prof. Susan M. Gasser (Director of the FMI, Basel). With the support of the Gebert Rüf Stiftung and the SNF/CTI BRIDGE proof of concept programme, we will expand our previous work from yeast to human cells by first showing that more accessible DNA increases the efficiency of CRISPR-Cas9 gene editing in somatic cells. Following this, we will test a number of small molecules for their ability to increase accessibility of DNA in the context of gene editing and enhance CRISPR-Cas9 editing efficiencies in human cells. Relying on our own research, our project partners and our support network of CRISPR-Cas9 experts, we will establish the data necessary to bridge from basic research to a tool that will enable the use of gene editing for biotech or medical applications.

 

Funding and Project Partners

This project is supported by the Gebert Rüf Foundation (GRS-017/17) and the SNSF/CTI BRIDGE programme (BRIDGE). We are hosted at the University of Zürich in the Department of Molecular Mechanisms of Disease (DMMD) and the Center for Applied Biotechnology and Molecular Medicine (CABMM). We work in collaboration with our project partner and mentor SNF Prof. Matthias Altmeyer as well as our external project partner Prof. Susan M. Gasser (Director of the FMI, Basel).

Prof. Dr. Matthias Altmeyer (matthias.altmeyer@dmmd.uzh.ch) / Project Partner and Mentor (University of Zürich, Zürich) / https://www.altmeyerlab.org

Prof. Dr. Susan M. Gasser (susan.gasser@fmi.ch) / Project Partner (Friedrich Miescher Institute for Biomedical Research, Basel) http://www.fmi.ch/gasser.s

Prof. Dr. Martin Jinek (jinek@bioc.uzh.ch) / External Specialist and Advisor (University of Zürich, Zürich) / https://www.bioc.uzh.ch/research/research-groups/jinek/

Prof. Dr. Jennifer A. Doudna (doudna@berkeley.edu) / External Specialist and Advisor (HHMI, Caribou Biosciences and UC Berkeley) / http://rna.berkeley.edu

 

Relevant Publications

Hauer, M.H., Seeber, A., Singh, V., Thierry, R., Sack, R., Amitai, A., Kryzhanovska, M., Eglinger, J., Holcman, D., Owen-Hughes, T. and Gasser, S.M. (2017). Histone degradation in response to DNA damage enhances chromatin dynamics and recombination rates. Nature Structural & Molecular Biology, doi: 10.1038/nsmb.3347.

PubMed

Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J.A., and Charpentier, E. (2012). A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity. Science 337, 816-821.

PubMed