Scientists Develop Platform for Predicting Off-Target Effects of CRISPR Gene Editing Tool

Scientists Develop Platform for Predicting Off-Target Effects of CRISPR Gene Editing Tool

The use of the CRISPR gene editing tool has attracted considerable interest in recent years. CRISPR allows scientists to remove, add or alter genes with precision. However, even though the tool has been shown to be effective in vitro and in vivo in animal studies, there is potential for the tool to make off-target edits.

In order for the gene editing tool to be used to treat human diseases it must be safe, which means off-target effects must be minimized. If scientists can use the tool without causing collateral damage, CRISPR could be used to treat a wide range of genetic disorders and diseases.

If scientists can tell what the likely off-target effects will be, it will make it much easier to take steps to prevent unwanted gene edits. Scientists at the University of Texas have made significant steps toward improving the safety of the CRISPR gene editing tool by developing a platform that helps researchers predict potential off-target effects.

The University of Texas researchers developed a chip-hybridized association-mapping platform (CHAMP) that uses next generation sequencing chips for the parallel profiling of protein–nucleic acid interactions. The researchers used the platform to measure the interactions between proteins and approximately 107 unique DNA sequences simultaneously. The researchers used CHAMP to study DNA recognition by a type I-E CRISPR-Cas (Cascade) complex and Cas3 nuclease.

The study revealed that the cascade complex pays less attention to the third letter in a DNA sequence than to others. Stephen Jones, Ph.D., co-author of the paper, said, “If it were looking for the word ‘shirt’ and instead found the word ‘short,’ it might be fine with that.”

Armed with that knowledge, researchers could use computer modelling to predict the likely off target effects of the cascade complex by identifying which DNA segments a specific CRISPR molecule is likely to interact with. The platform could therefore be used to develop personalized gene therapies for patients while reducing the potential for unwanted gene edits.

The platform used chips that are already extensively used in genetic research along with a 3D printed mount to hold the chip under a microscope and software to analyze the results of the analysis. Since the design of the 3D mount and the software are both open source, the platform can be used by other researchers to conduct their own CRISPR analyses.

The researchers’ paper – Massively Parallel Biophysical Analysis of CRISPR-Cas Complexes on Next Generation Sequencing Chips was published in the journal Cell on June 29.


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