12.11.2024 14:30
Research results, scientific publications
Researchers at ETH Zurich combined two methods for genetic modification. In this way, they can examine many genetic mutations at the same time to determine what significance the mutations have for the development and treatment of cancer.
Based on the Crispr/Cas technology, scientists have created a number of novel methods in recent years with which they can precisely change the genome of living beings. This can be used, for example, in cell therapy: a patient’s immune cells can be specifically reprogrammed so that they fight cancer better.
Researchers at the Department of Biosystems at ETH Zurich in Basel have now used these novel Crispr/Cas methods for another application: The researchers, led by ETH Professor Randall Platt, are using them to decipher how mutations in the genetic material affect the function of a cell . For example, the sequence of DNA building blocks in tumor cells differs from that in healthy cells. With the new approach, the researchers can create tens of thousands of cells with different gene variants in the Petri dish. This allows them to decipher which of the variants contribute to the development of cancer and which make the cancer cells resistant to common drugs.
Two methods combined
It has already been possible to make individual changes in the genetic makeup of cells. However, the ETH researchers’ project was much more complex: they changed a gene in two human cell lines in over 50,000 different ways and thus created a corresponding number of different cell variants. They then tested these cells for their function. As part of a proof of concept, they worked with the EGFR gene. It is central to the development of various types of cancer, including lung, brain and breast cancer.
In order for Platt and his team to create as many variants of this gene, they combined two Crispr/Cas methods. Researchers at MIT and Harvard University in the USA have developed these two methods in recent years. Both methods have advantages and disadvantages. With one, so-called base editing, individual building blocks of DNA can be changed very easily and reliably. However, the possibilities of base editing are limited: it can only replace the DNA building block C with the building block T or A with G.
Tens of thousands of cells changed
The second method used is prime editing. Theoretically, this method is very powerful: Similar to the “search and replace” function of a word processing program, individual gene sections can be specifically changed. “We can use it to replace any DNA building block with another one. Or, for example, we can insert three or ten building blocks into the genome or cut the same number out of it,” explains Platt. “In principle you can do whatever you want with it.”
But: Prime Editing does not work reliably. It is therefore difficult to use prime editing to create an entire pool of tens of thousands of differently modified cells that can then be used for screening. Platt and his team have now achieved this.
Important for cancer medicine
Cell pools with different gene variants are very important for research. Oncologists are increasingly analyzing the genetic information of tumor cells in patients, building block by building block. This information often gives them clues as to which medications might work for an individual patient.
In recent years, databases have emerged that contain thousands of different genetic variants from patients. The effects of around half of these variants are also well described. Of the other half, we know that they occur in patients, but we do not know whether and what influence they have on the development or treatment of cancer. Scientists speak here of “variants of unclear significance”. If a doctor finds such a variant in a patient, this information is of very little use to her.
Researchers are convinced that cancer medicine would benefit enormously if it received more information about these variants. They are therefore trying to produce cells with these gene variants in the laboratory. They can then examine these cells to determine their function. In recent years, researchers have been working towards this possibility. The base editing method was already available for this. The problem: Base editing alone is not enough. “You can only create about a tenth of these variants,” explains Olivier Belli, a doctoral student in Platt’s group and first author of the study together with master’s student Kyriaki Karava.
New relevant variants found
In order to systematically generate cells with virtually all possible relevant variants of the EGFR gene, Platt and his team first identified the cancer-relevant regions in this gene. These are those in which mutations cause a healthy cell to degenerate into a cancer cell, a cancer cell to become resistant to drugs or, conversely, to respond to the drugs. Because the researchers couldn’t create all of these gene variants using base editing, they added prime editing.
The researchers then examined these cells. They have now been able to demonstrate and describe such a significance for ten EGFR gene variants with a previously unclear influence on cancer: These variants play a role in the development of cancer or make it resistant to certain drugs. As part of this study, the ETH researchers also found a new mechanism for how cancer can arise as a result of a mutation in the EGFR gene. They also found six gene variants that appear to play a role in cancer but which have not yet been described – i.e. completely new, relevant gene variants.
The EGFR gene is just one of several hundred human genes linked to cancer. The new research approach is now ready to decipher the “variants of unclear significance” in all other genes.
Scientific contact person:
Randall Platt, ETH Zurich, [email protected]
Original publication:
Belli O, Karava K, Farouni R, Platt RJ: Multimodal scanning of genetic variants with base and prime editing. Nature Biotechnology, 12. November 2024, doi: 10.1038/s41587-024-02439-1
Further information:
