CRISPR-Cas – accurate DNA modification

All forms of life on earth contain genetic material. The information stored in that material determines the appearance and functioning of all organisms. In humans, for example, this information determines our eye and hair colour, and the DNA in plants determines characteristics such as the length and thickness of their roots. For centuries, humans have been trying to control and select those biological traits, for example by breeding animals and crossing plants. By directly modifying hereditary material, the technique CRISPR-Cas (CRISPR for short) makes that control and selection process much easier.

Currently, CRISPR-Cas is the focus of much attention. Five years ago, the European Court of Justice ruled that the technique falls under strict GMO legislation in the EU, but that may be about to change. The European Commission has made a new proposal in July 2023, which advises to have more flexibility in regulations. Due to the broad applicability of CRISPR-Cas, more flexibility in legislation and regulations may offer advantages, but it also leads to questions. Below, we have answered some of these questions about CRISPR-Cas.

What is CRISPR-Cas?

CRISPR-Cas is a recently developed technique that allows scientists to precisely modify the DNA of living organisms, and thus for instance change certain characteristics. The technique could, for example, make agricultural crops resistant to certain diseases. The CRISPR-Cas system works at the microscopic level: using a kind of template, it finds a specific piece of DNA in a cell and then removes, replaces or inserts a piece of DNA at this location. Exactly what the system does depends on how biologists 'set' the system.

In which organisms can we use CRISPR-Cas?

In principle, this microscopic toolkit can be used in all living organisms. CRISPR-Cas can not only alter the genetic material of plants, animals, bacteria and yeast, but also humans. There is also a method by which CRISPR-Cas cuts the RNA of viruses with the aim of disabling them. While CRISPR-Cas technology can be used in all living things, this does not mean that its use is always ethical.

Where did CRISPR-Cas originate?

The CRISPR-Cas technology was not made in a lab, but was discovered in nature. Bacteria use the system as a defence against viruses that are trying to infect them. The defence mechanism recognises the genetic material of such pathogens and then cuts it to eliminate the virus. Wageningen scientists, including John van der Oost, identified this defence system in bacteria. In 2012, researchers discovered that they could program the system itself so that it recognises and cuts not just pieces of virus, but any desired piece of genetic material.

Do we need to use CRISPR-Cas in agriculture?

In times of climate change, war, and a growing world population, we need to keep the earth liveable and produce sufficient food for everyone. The search for better crops has been going on for centuries and is known as plant breeding. Initially it was mainly about higher yields, but later on the emphasis shifted to include characteristics such as taste, nutritional value and shelf life. Today, we use plant breeding mainly to make crop plants resistant to drought, diseases and pests, for example. This can be done with conventional plant breeding methodes, but these often take many years and are labour-intensive, especially for crops that are genetically complex, such as wheat.

By combing knowledge about genes and their function with the CRISPR-Cas technique, plant breeders can work faster and more efficiently than with conventional methods. Within two to four years, breeders can then develop an improved variety, for example a tomato with additional nutrients or a drought-resistant type of wheat.

For arable farming and other forms of plant production to grow enough food in the short term and long term, proponents believe we should be able to use all available methods, including CRISPR-Cas. CRISPR-Cas should however not be seen as a panacea; we should continue to use existing plant breeding methods (such as mutating, hybridising and selecting) with innovative farming techniques such as precision agriculture and crop diversity. With all these techniques combined, we can respond more quickly to changing conditions, such as higher temperatures, longer periods of drought and increasingly brackish groundwater.

Which laws and regulations apply to CRISPR-Cas?

Like other modern techniques to modify DNA, CRISPR-Cas is subject to the European GMO directive, which was upheld by the European Court of Justice in 2018. This does not prohibit the use of this technique, but products treated with CRISPR-Cas do have to go through an additional authorisation process to ensure their safety. According to breeders, the high costs involved and time consuming procedures in this additional authorisation step are holding back the use of CRISPR-Cas.

In countries such as the United States, China and Argentina, CRISPR-Cas is not subject to GMO legislation. In 2019, the European Commission launched a lengthy process to investigate whether EU regulations on modern DNA modification techniques could also be more flexible for use in crops. By mid-2023, the Commission will make a proposal to update the GMO directive. Member States, including the Netherlands, will then have to vote on that proposal.

Until then, scientists are using CRISPR-Cas mainly in laboratories. In such contained and controlled spaces, the technique can be used without additional restrictions. For example, researchers can use CRISPR-Cas to remove or alter pieces of DNA (genes) in plants and bacteria to better understand their function.

What about the patents surrounding CRISPR-Cas?

"From the beginning of its development, many uses of CRISPR-Cas have been patented," says patent specialist Paul van Helvert. In the meantime, thousands of patents have been granted. Some of these describe a very specific protein or specific application of CRISPR-Cas, while others are much broader. "When the CRISPR-Cas technique was new, it was mainly universities and research institutes that held the patents," Van Helvert says. "Today, the majority of patents are held by companies."

If CRISPR-Cas soon becomes easier to use in Europe, there will be financial implications. Breeders and other users will then have to pay licence fees to use certain CRISPR-Cas techniques. To make some genetic changes, one patent will be enough, but for others breeders might need two or three different patents. This will increase their costs. "Then the focus will be on the trade-off between costs and development," says Van Helvert. If the technique saves a lot of time and quickly adds new characteristics to crops, the investment in a licence could pay off.

What concerns are there about the application of CRISPR-Cas?

Concerns about the application of CRISPR-Cas range from the safety of the technique to who actually has a particular interest in its application. Are they farmers, consumers and our nature that yearns for greening of agriculture, for instance, or do companies in particular stand to gain financially? In this interview, our CRISPR-Cas expert John van der Oost and interdisciplinary social scientist Phil Macnaghten address some of these concerns and questions.