Microbiologist John van der Oost of Wageningen University & Research (WUR) has received an ERC Proof of Concept grant to further develop a promising CRISPR-based approach to cancer treatment. With funding of €150,000, he and researcher Christian Südfeld will spend the next eighteen months working on a method to kill cancer cells from within, while sparing healthy cells as much as possible.

Tumour cells differ from healthy cells at multiple levels. They lack, for example, chemical markers on specific sites in the DNA that healthy cells do have: so-called methyl groups. These are small “tags” on the DNA that help determine which genes are active. In healthy cells, this pattern is relatively stable, but in tumour cells it becomes disrupted, causing the cell to spiral out of control. Wageningen researchers now aim to exploit this difference in methylation to target tumour cells using a new and targeted form of DNA editing.

The proposed therapy centres on a special variant of the well-known DNA-editing tool CRISPR-Cas9: ThermoCas9, originally discovered in a bacterium from a compost heap in Wageningen. This enzyme has a striking property: it distinguishes between DNA with and without methyl groups. “Because some tumour cells have far fewer methyl groups on their DNA than healthy cells, they form an ideal target for our ThermoCas9,” says John van der Oost, Emeritus Professor of Microbiology.

Targeting the Achilles’ heel
In laboratory experiments with human cells, the researchers have already shown that their CRISPR system damages DNA in cancer cells, but not in healthy cells. The next phase will focus on whether they can increase this damage to the point where tumour cells succumbs to it. “Sometimes a small amount of DNA damage leads to a scar that makes the genetic code unreadable,” Van der Oost explains. “If this happens in genes that are essential for the cell’s survival, it may lead to cell death. And the more of these essential genes we hit, the greater the chance that the tumour cell will die.”

Initially, the project focuses on liver cancer, a type of cancer that lends itself relatively well to experimental genetic therapies. In recent years, methods have been developed to deliver proteins and DNA — such as CRISPR components — to liver cells using nanoparticles. “The liver plays a key role in waste processing in our body,” Van der Oost says. “Nanoparticles in the bloodstream are naturally transported there for breakdown.” This means they easily reach their destination. “Before the liver actually breaks down the nanoparticles, CRISPR has time to do its job.”

Genetically messy
Clinical application of CRISPR-based cancer therapy is still a long way off. Moreover, the difference in methylation between healthy and cancerous cells is not a simple black-and-white story. Tumours are genetically messy. Some will still carry methyl groups at certain sites, while healthy cells may sometimes lack these chemical marks in parts of their DNA. As a result, the therapy is unlikely to hit every cancer cell and may also affect some healthy cells. “But existing treatments such as chemotherapy and radiotherapy also damage healthy cells,” Van der Oost notes.

In addition, the CRISPR system itself still needs refinement. ThermoCas9 is naturally active at high temperatures, around 60°C. Using a recently obtained 3D structure, artificial intelligence and laboratory evolution, the researchers aim to modify the enzyme so that it works optimally at body temperature.

About the ERC Proof of Concept
Postdoctoral researcher Christian Südfeld, who carried out much of the preparatory work, will spend the next eighteen months further optimising the system. The team also plans to establish collaborations with cancer specialists, potentially including researchers at the Netherlands Cancer Institute (NKI).

The ERC Proof of Concept is a prestigious top-up grant from the European Research Council for researchers who already hold an ERC grant. PoC funding is designed to bridge the gap between fundamental research and practical application. This year, thirteen researchers affiliated with Dutch knowledge institutions received this funding.