Researchers have successfully merged two techniques for gene editing. This advancement allows them to rapidly explore the importance of various genetic mutations that contribute to both cancer development and its treatment.
Researchers at ETH Zurich have successfully merged two techniques for gene editing. This advancement allows them to rapidly explore the importance of various genetic mutations that contribute to both cancer development and treatment.
In recent years, scientists have developed numerous novel approaches utilizing CRISPR-Cas technology to accurately edit the genetic material of living organisms. One application of this technology is in cell therapy, where a patient’s immune cells can be specifically reengineered to combat cancer more effectively.
At ETH Zurich in Basel, researchers from the Department of Biosystems Science and Engineering have discovered another application for these innovative CRISPR-Cas techniques. Under the leadership of ETH Professor Randall Platt, the team is exploring how mutations in a cell’s genome influence its functionality. For instance, the DNA sequences in tumor cells are different from those in healthy cells. With their new method, the researchers can cultivate tens of thousands of cells with various gene variants in Petri dishes. They aim to determine which variants lead to cancer progression and which variants provide cancer cells with resistance to common treatments.
Combining Two Methods
While scientists previously had the capability to make individual modifications to cellular genomes, the project led by the ETH researchers was considerably more intricate. They altered one gene in two human cell lines in over 50,000 distinct ways, generating a vast array of cell variants for functional testing. To demonstrate their concept, they focused on the EGFR gene, which plays a crucial role in the development of several cancer types, including lung, brain, and breast cancer.
Platt and his team integrated two CRISPR-Cas techniques to create a large variety of EGFR gene variants. Both methods, developed in recent years by MIT and Harvard University researchers, come with their own strengths and weaknesses. One method, base editing, makes it straightforward to modify individual DNA components, known as bases, in a reliable manner. However, base editing’s capabilities are somewhat limited; typically, it can only swap the DNA base C with T or A with G.
Numerous Cells Altered
The second method employed by the researchers is prime editing, which is theoretically very powerful—similar to a word processor’s “search and replace” feature, it allows for precise alterations to specific genetic sequences. “This method lets us exchange any DNA base for another or insert or delete a specified number of bases from the genome,” Platt explains. “In essence, it provides extensive versatility.”
Nonetheless, prime editing has not proven to be consistently reliable, making it challenging to produce a wide pool of tens of thousands of modified cells for further analysis. However, Platt and his team have managed to achieve this.
Significance in Oncology
Having pools of cells with diverse gene variants is essential for research purposes. Oncologists are increasingly examining the genetic data of patients’ tumor cells at the base level, often gaining insights that guide them toward effective treatments for individual patients.
In recent years, researchers have compiled databases that include thousands of different genetic variants found in patients. For about half of these variants, comprehensive descriptions of their effects are available. For the other half, although they are documented in patients, their implications for cancer development or treatment remain unclear; these are termed “variants of uncertain significance.” Such findings provide little practical information for physicians when identified in a patient.
Researchers believe that oncology would greatly benefit from increased understanding of these variants. Consequently, they are aiming to generate laboratory cells with these gene variants for further functional analysis. Prior preparations have established a foundation for this endeavor. While base editing was an option, it was insufficient on its own. “Base editing only allowed the creation of about 10% of these variants,” clarifies Olivier Belli, a doctoral candidate in Platt’s lab and one of the study’s lead authors alongside master’s student Kyriaki Karava.
Discovery of New Relevant Variants
To systematically develop cells containing nearly all relevant variants of the EGFR gene, Platt and his team initially pinpointed the cancer-related areas within this gene. These regions contain mutations that either transform healthy cells into cancerous cells or alter a cancer cell’s sensitivity or resistance to drugs. Since base editing alone could not create all these variants, the researchers incorporated prime editing into their strategy.
The researchers eventually analyzed these modified cells. For a set of ten EGFR gene variants whose impacts on cancer progression were previously ambiguous, they were able to confirm their significance and describe it: some variants might influence cancer onset, while others may provide resistance to specific treatments. In the course of their research, the ETH scientists also uncovered a potentially new mechanism whereby an EGFR mutation can contribute to cancer. Additionally, they identified six novel gene variants that appear to be relevant to cancer but had not been documented previously.
The EGFR gene represents just one of several hundred human genes linked to cancer. This innovative research approach is now primed to unveil the significance of variants of uncertain significance across numerous other genes.
