New CRISPR technology can determine whether genetic mutations are pathogenic or benign

Breaking new ground 25. dec 2022 3 min Associate Professor Claus Storgaard Sørensen, Associate Professor Morten Frödin Written by Kristian Sjøgren

Doctors have had great difficulty in identifying the significance of mutations among people with diseases such as cancer. Researchers have solved this problem with newly developed CRISPR technology that makes determining the effects of mutations and the optimal treatment much easier.

Advances in genetic technology have enabled researchers to sequence the DNA of a person with cancer and thereby identify mutations that may influence the development of the disease.

Nevertheless, determining whether or not a mutation causes cancer has proved difficult or impossible for researchers and doctors. They therefore cannot determine whether a specific treatment developed to counteract the effect of a specific mutation actually works.

These problems are now being solved with the development of a new technological platform to determine how individual mutations affect cells. Using the same technology, researchers can also rapidly determine whether a specific drug kills cancer cells with a mutation determined to be pathogenic.

“Our method is clinically useful because we can rapidly investigate whether a mutation is pathogenic or benign. We have already created a company to perform genomic analysis of potential pathogenic mutations for drug developers, who want to find new targets for drugs and determine whether their existing drugs work well on specific mutations,” explains a researcher involved in developing the method, Claus Storgaard Sørensen, Associate Professor, Biotech Research and Innovation Centre, University of Copenhagen.

The research has recently been published in Nature Genetics, the world-leading journal in the field, in collaboration with Morten Frödin, Associate Professor, Biotech Research & Innovation Centre, University of Copenhagen.

Genes can mutate in thousands of ways

Researchers from the University of Copenhagen collaborated with doctors and researchers at Rigshospitalet, who face the problem that they can identify how their patients’ DNA has mutated but cannot determine which individual mutations are important.

For example, a single mutation in one of the BRCA genes (BRCA1 and BRCA2) can lead to the development of breast cancer and ovarian cancer.

“The problem is that a BRCA gene can mutate in thousands of ways. Some of these mutations can cause cancer, whereas others are benign, having no impact on cancer. However, whether a given mutation promotes the disease is not known for the vast majority of mutations. A person with such a mutation has a problem. The current methods need a very long time to estimate whether a given mutation caused the cancer and whether the existing drugs are effective. Neither the patients nor the doctors can wait that long,” says Morten Frödin.

Studied the effects of every mutation

The researchers invented a new CRISPR technology to solve this problem by simultaneously inserting the potentially pathogenic genetic mutation from a patient and a mutation that is known to be benign into cells in the laboratory. The researchers then observe how the cells with the patient’s genetic mutation develop compared with the cells with the benign control mutation.

The researchers furthermore compare the changes with a series of additional controls consisting of mutations with varying degrees of pathogenicity. They can do all this in mixtures of mutations of uncertain significance and control benign mutations and still get a robust and rapid response.

The researchers can thereby determine how a specific person’s mutation affects the development of the cells and the development of disease characteristics. The cells may grow more rapidly or more slowly, or they may no longer function optimally. They may also lose the ability to repair the DNA, which typically characterises cancer.

By analysing all the genetic mutations from the patient, the researchers have reduced the total analysis time from many months to just 7–14 days.

Finally, the researchers can monitor cells that are affected by specific mutations and can determine what happens to these cells when the researchers expose them to drugs that are already on the market.

For BRCA mutations among women with breast cancer, the researchers can use their method to identify which mutations caused a specific woman’s breast cancer and which drugs are effective against these mutations.

“The technology is a breakthrough compared with the previous methods. We can now very precisely and rapidly translate mutations in the DNA into specific changes in the cells, and this has enormous therapeutic value,” explains Morten Frödin.

Can be used for many diseases with a genetic origin

The researchers have also shown that their method is not just a future vision but can be implemented today and used clinically. Currently, the researchers are using the technology on mutations from women with breast cancer.

Claus Storgaard Sørensen says that although the first successes and collaborations have been achieved in cancer, the technology can also be used for many other diseases of genetic origin.

“We have recently developed this technology for mutations that cause atherosclerosis and life-threatening cardiovascular disease. Identifying the mutations that are pathogenic can result in treatment that can provide normal life expectancy,” Morten Frödin continues.

“We have been contacted by many clinical geneticists who work with such diseases as restricted growth, mental impairment and musculoskeletal disorders. They know many mutations that are associated with the various diseases but do not know which mutations are significant and which are not. We can determine this, and this can help to identify new drug targets and improve treatment and genetic counselling,” concludes Claus Storgaard Sørensen.

Multiparametric and accurate functional analysis of genetic sequence variants using CRISPR-Select” has been published in Nature Genetics. In 2019, the Novo Nordisk Foundation awarded a grant to Claus Storgaard Sørensen for the project Novel Compound-based Sensitisation Approach to Radiation Therapy.

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