MIT’s CRISPR gene editing alternative inserts new DNA without cutting

The CRISPR gene editing system is such a powerful and revolutionary gene editing tool that it's already helping scientists create cancer vaccines and designer babies, turn humans into computers, perform in vivo human gene editing and cure inherited genetic diseases, and cure blindness and HIV to boot. It's also been voted one of the world's most lethal weapons by the UN, when combined with Gene Drives - something that has now prompted the search for something scientists are calling CRISPR Kryptonite in an attempt to stop unwanted gene editing from taking place, which, as I recently discussed can now happen, at a very limited scale, by simply inhaling a mRNA based aerosol mixture. All of which is the tip of the proverbial iceberg a CRISPR looks set to make its mark on human society in the coming decades and cure tens of thousands of genetic diseases that today are incurable.

The problem with CRISPR though is that sometimes cutting out DNA strands and pasting new ones in can have unwanted side effects, such as Cancer,  and while there's now a technology that lets us turn genes on and off at will without cutting it first that's still not a good enough solution for more advanced or complex gene editing requirements. Now researchers from MIT and Harvard University have developed a new CRISPR-based system that can insert new DNA sequences without needing to make cuts in a patients existing DNA, which should make the gene editing process much safer and more accurate.

Normally, the CRISPR tools are based on a bacterial self-defense system. When the bugs encounter predatory viruses called bacteriophages, they use enzymes like Cas9 to snip a piece of that virus's DNA and store it within themselves. That works a bit like a "Wanted" poster, letting the bacteria easily identify and fight the virus if they ever cross paths again.

In the last few years, scientists figured out how to use this technique to make cut-and-paste DNA edits in the cells of other organisms. Guide RNA sequences tell the enzymes where to cut, removing pieces of DNA from the cell and replacing them with new sections. That can be used to correct mutations that cause disease, or even prevent them entirely by snipping the offending sequences out of the genome of an embryo. Along with treating disease in humans, the method could be used in pest control or to make crops hardier and more nutritious.

As useful as CRISPR is so far, it's not without issues. Relying on the cell's natural repair mechanism means that sometimes errors occur, and other times off-target edits may appear in other parts of the genome. That's led researchers to develop other similar methods that may be a bit more gentle, silencing genes instead of cutting them out, or working more like a word processor's "search and replace" function.

The researchers on the new study set out to create a new system with a similarly light touch. Rather than using defensive enzymes like Cas9, the team investigated DNA sequences called Transposons. These are also called "Jumping Genes" thanks to their tendency to jump around in the genome, with some subtypes guided by proteins called transposases.

The team isolated the enzyme Cas12k from two species of cyanobacteria and manipulated them into jumping to set targets in the genome, then inserting new DNA sequences without having to cut anything. The new system was named CRISPR-Associated Transposase or CAST for short

"We dove deeply into this system in cyanobacteria, began taking CAST apart to understand all of its components, and discovered this novel biological function," says Jonathan Strecker, first author of the study. "CRISPR-based tools are often DNA-cutting tools, and they're very efficient at disrupting genes. In contrast, CAST is naturally set up to integrate genes. To our knowledge, it's the first system of this kind that has been characterised and manipulated."

The team tested the new system on E. coli, and were able to insert new DNA sequences up to 10 base pairs long into precise locations on the genome, and it worked 80 percent of the time, but the researchers say that could be improved with further research.

The CAST technique could be used for a few purposes. Genetic diseases could be healed by disabling the harmful mutation and inserting a new, healthy version instead. Or it could add a brand new, useful sequence without silencing any existing gene, effectively inserting a new ability, for example, the immune system's T cells could be targeted to make them more responsive to the presence of cancer.

"For any situation where people want to insert DNA, CAST could be a much more attractive approach," says Feng Zhang, senior author of the study and inventor of the CRISPR system. "This just underscores how diverse nature can be and how many unexpected features [of this technology] we have yet to find."

The research was published in the journal Science.

Source: MIT