Yale scientists develop advanced CRISPR tool to study complex genetic interactions

Advances in the gene-editing technology known as CRISPR-Cas9 over the past 15 years have yielded important new insights into the roles that specific genes play in many diseases. But to date this technology - which allows scientists to use a "guide" RNA to modify DNA sequences and evaluate the effects - is able to target, delete, replace, or modify only single gene sequences with a single guide RNA and has limited ability to assess multiple genetic changes simultaneously.

Now, however, Yale scientists have developed a series of sophisticated mouse models using CRISPR ("clustered regularly interspaced short palindromic repeats") technology that allows them to simultaneously assess genetic interactions on a host of immunological responses to multiple diseases, including cancer.

The findings were published March 20 in the journal Nature Biomedical Engineering.

Gene editing technologies allow scientists to use enzymes - in this case, Cas9 (CRISPR-associated protein 9) - as a sort of molecular scissors that can precisely cut or modify portions of DNA or RNA, revealing insights into the role these genes play in a variety of disorders.

The new tool, which is called CRISPR-Cas12a, can help researchers simultaneously assess the impact of multiple genetic changes involved in variety of immune system responses, the researchers say.

"We have created four new Cas12a mouse lines that will allow researchers to study complex genetic interactions and their effects involved in many disorders," said Sidi Chen, an associate professor of genetics and neurosurgery at Yale School of Medicine and a pioneer in the field of CRISPR technology. He is co-corresponding author of the new study.

With these powerful tool strains, Chen's lab was able to induce and track changes in a variety of immune system cells in response to gene editing, and to fine-tune sets of genes in different directions simultaneously. The lab also enabled the rapid generation of new disease and treatment models, such as genetic disease in the liver, lung cancer, and skin cancer.

This advance, he said, will offer a valuable tool to researchers creating new therapies for a host of pathologies, including cancer, metabolic disease, autoimmune disease, and neurological disorders.

Chen is a member of the Systems Biology Institute at Yale's West Campus and an affiliate of Yale Cancer Center, Yale Stem Cell Center, and Yale Center for Biomedical Data Science.

Matthew B. Dong and Xiaoyu Zhou, both of Yale's Department of Genetics, are co-corresponding authors. Kaiyuan Tang and Liqun Zhou are co-lead authors.

The research was funded by the National Institutes of Health and the U.S. Department of Defense.