Daniel Yang, MD is an Assistant Professor of Medicine and a faculty member in the Institute for Stem Cell and Regenerative Medicine (ISCRM). One of the diseases the Yang Lab studies is hypertrophic cardiomyopathy (HCM), a genetic condition that impairs the heart’s ability to pump blood and can lead to heart failure or even sudden cardiac death.
Mutations (or variants) in myosin heavy chain 7 (MYH7) is one of the most common genetic causes of HCM. Knowing if a variant is disease-causing is helpful because doctors can screen family members of newly diagnosed patients for similar variants through a process called cascade screening. If a relative has a disease-causing variant, measures can be taken to manage the disease and potentially avoid life-threatening incidents.
However, there are at least 2,000 identified variants of MYH7, and the number is rising. Many of these abnormalities are classified as “variants of unknown significance” and they represent a challenge for patients and clinicians. Some variants may be benign. Some may be disease-causing (pathogenic). Oftentimes, it is unclear if a variant is pathogenic or benign given the lack of experimental and/or clinical data to help determine the biological effect of the variant on the heart. In fact, according to Dr. Yang, fifty to eighty percent of information gleaned from recommended genetic testing may not be useful due to the frequent finding of variants of unknown significance.
Dr. Yang, who sees HCM patients in his clinic, says this can leave entire families in a “genetic purgatory”. They have been told they or their loved ones have a variant that could be a concern, but they have no way of knowing for sure what that means for their future, especially if their heart looks healthy.
The ability to more accurately interpret the results of genetic testing would allow doctors to develop a care plan that makes most sense for an individual, sparing healthy people unnecessary interventions, and potentially protecting vulnerable patients from a catastrophic event. Unfortunately, because the usual method of studying one or two variants at a time in the lab is unable to keep pace with the rate of new variant discovery, thousands of MYH7 variants would be classified as variants of unknown significance.
Now a partnership between the Yang Lab and Dr. Lea Starita in the UW Department of Genome Sciences has received a five-year $4.3 million NIH grant to use an innovative gene editing technology to engineer hundreds or even thousands of mutations into stem cells at once and learn about them in parallel, creating a powerful tool for genetic studies.
The gene-editing technology at the center of this research is known as CRISPRa On-Target Editing Retrieval (CRaTER). The method, developed in the Yang Lab, significantly improves the efficiency of gene-editing in stem cells.
“Instead of painstakingly screening hundreds of stem cell colonies to find a correctly gene-edited clone, we can very efficiently sort for the correctly edited-cells in a high-throughput manner,” says Yang. “That’s enabled us to create stem cell libraries containing more than 300 variants.”
Yang explains that his lab performs the gene edits in induced pluripotent stem cells and then differentiates them to heart cells to determine the disease-causing potential of the variant in a method called deep mutational scanning. He credits Dr. Clayton Friedman, a postdoctoral researcher, for leading this part of the effort. In the grant-funded work, Dr. Starita and her team will help with the sequencing of the variant library and provide bioinformatic support for the deep mutational scan.
What would success look like over the life of the grant?
Yang offers a vision for the future. “With our genetic screen, our goal is to generate a variant effect map that will determine the risk of hypertrophic cardiomyopathy for every possible MYH7 variant, so that we can provide clinically actionable information for patients with MYH7 variants.” This information will help reassure patients with benign MYH7 variants and identify patients with pathogenic MYH7 variants who may be at risk for developing HCM.