Periodic Reporting for period 1 - PROTEGE (Profile nucleases and Repurpose Off-Targets to Expand Gene Editing)
Berichtszeitraum: 2023-06-01 bis 2025-11-30
Programmable nucleases reside at the nexus of advanced gene editing and microbial defense. These nucleases degrade phage DNA but avoid genomic DNA to provide the microbe with adaptive immunity. The standard-bearer, CRISPR-Cas9, relies on a guide RNA (gRNA) – its program – to precisely cut a complimentary genetic sequence – its target –
for precision gene editing. These programmable nucleases deliver cure for genetic diseases like anemia, blindness, and cancer; quick disease model development; and diagnostics for viruses like SARS-CoV-2. Hunts across microbial genomes have exposed thousands of programmable nucleases. Each could be another valuable tool for genome engineers, but we know just too little about them to use them safely. Even Cas9 does not have guidetarget parity: It cuts partially matched ‘off-target’ genome sites, which can lead to dangerous side effects. Though we work hard to avoid off-targets, partial matching may have a bright side. What if we leverage it, using it to make gene editing more predictable? Using high-throughput biochemistry, we will Profile nucleases and Repurpose Off-Targets to Expand Gene Editing. The PROTÉGÉ research program will profile guide-target parity – specificity – across promising, newly discovered programmable nucleases. It will deliver a toolset for assessing this critical safety feature rapidly and broadly. Finally, we will test the hypothesis that purposefully misprogramming nucleases can direct specific repair outcomes. We intended to benefit Europe and the world community with safer and more diverse gene editing tools for achieving its Horizon Europe health, technology and environmental goals.
for precision gene editing. These programmable nucleases deliver cure for genetic diseases like anemia, blindness, and cancer; quick disease model development; and diagnostics for viruses like SARS-CoV-2. Hunts across microbial genomes have exposed thousands of programmable nucleases. Each could be another valuable tool for genome engineers, but we know just too little about them to use them safely. Even Cas9 does not have guidetarget parity: It cuts partially matched ‘off-target’ genome sites, which can lead to dangerous side effects. Though we work hard to avoid off-targets, partial matching may have a bright side. What if we leverage it, using it to make gene editing more predictable? Using high-throughput biochemistry, we will Profile nucleases and Repurpose Off-Targets to Expand Gene Editing. The PROTÉGÉ research program will profile guide-target parity – specificity – across promising, newly discovered programmable nucleases. It will deliver a toolset for assessing this critical safety feature rapidly and broadly. Finally, we will test the hypothesis that purposefully misprogramming nucleases can direct specific repair outcomes. We intended to benefit Europe and the world community with safer and more diverse gene editing tools for achieving its Horizon Europe health, technology and environmental goals.
As of 2025, we have profiled specificity across several promising programmable nucleases. We are actively developing and implementing our toolset for high-throughput profiling of newly discovered programmable nucleases. We continue to develop our strategy for directing specific repair outcomes. The results of our research have been presented by team members at over a dozen scientific meetings and public events.
This project's research is developing new genome editing tools, methods to accelerate their development, and ways to improve their safety and efficiency.