As a Swiss army knife for DNA manipulation, CRISPR-Cas is "the holy grail"

CRISPR-Cas has undergone spectacular development over the past ten years. The gene editing method uses part of the bacterial defense mechanism against viruses. CRISPR-Cas allows scientists to edit specific genes in the DNA of organisms with unprecedented precision, speed and affordability. But new, even better technologies are already emerging. During the day LabNL becomes CRISPR-Cas, among others developments in DNA technologies, discussed by associate professor Raymond Staals from Wageningen University & Research.

By: Dimitri Reijerman

In the past, genetic modification techniques were labor-intensive and time-consuming. This made manipulation of DNA, the 'software of life', very expensive. Only specialized laboratories ventured into these techniques. That changed with the arrival of CRISPR-Cas around 2007-2008: genome research has become more accessible to scientists in all kinds of fields. This has led to an explosion of new discoveries and insights in the field of genetics and biology.

The Holy Grail

As a researcher at WUR, Staals was at the cradle of CRISPR-Cas. “CRISPR-Cas is the holy grail for genome editing. This is what we always wanted as researchers: a single protein that you can program to cut at a specific location in the DNA. It is also super cheap and efficient.”

Since then, Staals and his colleagues have been working almost daily on further developments within the various CRISPR-Cas technologies, in addition to related research. “About half of my CRISPR-Cas research is fundamental research with the central question: how do these systems work?” says the associate professor. “There are still many question marks, specifically about the so-called type III system. These systems are at least as interesting as the widely used Cas9. Especially in diagnostics, such as in the development of biosensors.”

“I currently have about ten PhD students in my research group, along with some postdocs, technicians and a lab manager. About 80 to 90 percent of our research focuses on CRISPR-Cas. I have been working on this since 2011, even before technology boomed. Fortunately, there is still more than enough for me to explore. We also do subsidized work for companies and work on metabolic engineering projects. We are also looking with interest at other bacterial defense systems. CRISPR-Cas is based on such an immune system, but there are many others.”

The collaboration between Staals and his fellow researchers has already borne fruit, the associate professor says: “The other half of our work is applied research to use genome editing. I also founded a spin-off company for this with a number of students, ScopeDX. This arose from a competition in which students tried to solve diagnostic problems. They wanted to continue with their findings. ScopeDX is now still a successful spin-off. That is very nice."

“The third major pillar is laboratory evolution,” says Staals. “We look at systems in nature, but you can make them better by allowing them to evolve in the lab. One of the bottlenecks when using CRISPR-Cas is that they usually cut the DNA in the right place, but sometimes accidentally cut in another place, so-called off targeting. Unfortunately, this happens regularly in practice. And especially in medical applications, you don't want off targeting. We want to be able to cut the DNA more precisely with the help of laboratory evolution.”

Applications in medicine

Despite the risks of off-targeting, CRISPR-Cas has become an indispensable part of medicine and the development of new medicines and therapies. Scientists believe that CRISPR-Cas will be able to correct genetic abnormalities responsible for hereditary diseases, such as sickle cell anemia, cystic fibrosis and cystic fibrosis.

According to Staals, many successes have been achieved over the past five years and the first patient has now been treated using DNA manipulation based on CRISPR-Cas. And in the coming years, these medical applications will gain momentum, the researcher thinks: “We will not only use Cas enzymes to cut DNA, but also let them serve as a means of transport. This way we can deliver other enzymes. This could have potential in treating certain types of cancers. And in the future I see other interesting methods to modify the DNA, such as prime editing and base editors. CRISPR-associated transposon homing is also promising.“

So there is a lot of optimism, although a lot of research into medical applications is taking place outside the Netherlands. “As pioneers in fundamental knowledge about CRISPR-Cas, the Netherlands, and certainly Wageningen, are among the world's best. We are still discovering new CRISPR-Cas systems and how they work,” says Staals. “However, this is not the case for applications of this technology. For that you have to look at Asia and the US. This also has to do with the fact that European regulations are holding us back somewhat. For example, CRISPR-Cas is still subject to GMO legislation in Europe. Still, I think that relaxing the regulations will happen in the long term.”

The future of CRISPR-Cas

In addition to possible relaxed EU regulations, Staals sees another important development that can greatly accelerate the research and application of CRISPR-Cas: artificial intelligence. “We already use AI. AlphaFold (an AI application that makes predictions about protein structures – ed.), just like CRISPR-Cas, has been a huge development in my field. During large-scale research, we get so much data thrown at us that it is no longer understandable to us, due to the order of magnitude. AI is actually very good at separating the wheat from the chaff and extracting useful information. And we can also ask AI what the best choices are for starting new experiments.”

As a Swiss army knife, we will hear a lot more about CRISPR-Cas. Because beyond medicine, the technology can be applied to many more areas, from agriculture and food production to cleaning up toxins in the environment (bioremediation) and combating the malaria mosquito, for example. However, a lot of (fundamental) research will still be needed to utilize the full potential of CRISPR-Cas and its successors, regardless of regulation and ethical issues.

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