Function of cardiovascular risk gene unraveled using genome editing of stem cells

Over the past decade we've learned that billions of people carry a mysterious specter in their DNA that strongly increases their risk for life threatening cardiovascular diseases, such as heart attacks, aneurysms or strokes, no matter what diet, exercise or medical regimen they follow.

Now, scientists have made a major breakthrough in unveiling this medical mystery by precisely cutting the DNA culprit from the genome, which prevents blood vessel cell abnormalities related to these devastating diseases.

Surprisingly they also find that this widely prevalent yet poorly understood DNA region may orchestrate a nefarious network of more than a third of all genes known to increase risk for coronary artery disease, opening the door to a new set of precision treatments aimed at cells of the blood vessel wall.

In a paper published in Cell, the researchers report that a large block of DNA, known as the 9p21.3 cardiovascular risk haplotype, causes abnormalities in vascular smooth muscular cells--the cells in blood vessel walls that normally allow them to expand and contract. These cells also can dysfunction and contribute to plaques that clog blood vessels, leading to heart attacks and stroke.

Although researchers knew the haplotype was tied to heightened disease risk, precisely what was happening in people's bodies remained a matter of speculation. One hurdle is that the disease risk haplotype is found only in humans, with poor similarity to regions in mice or other laboratory animals. Another challenge is that this region doesn't harbor any traditional protein coding genes, making it hard to predict what it might do.

"We call such regions 'gene deserts', and in the past they were neglected in research because people thought it was 'junk' DNA," says, co-author on the paper. "With rapid advances in genome sequencing and analysis, we are finding that these regions frequently play critical roles in the emergence of disease."

The team wanted to produce human blood vessel cells in a dish and then genetically interrogate them using genome editing. They collected blood from people who had either the high-risk or low-risk versions of the haplotype and reprogrammed them into induced pluripotent stem cells. At this stage the cells could be genetically tailored using specialized molecular scissors, called TALE nucleases, to remove the risk promoting or benign versions of this DNA from affected and unaffected donor cells. Next, they coaxed the edited stem cells into becoming vascular smooth muscle cells and studied them in detail using high-resolution gene profiling and bioengineering methods.

The team found that the cells of high-risk individuals showed an unusually broad set of abnormalities, with the risk cells affecting more than 3000 genes--nearly 10 percent of the total human gene catalog. Computer-based examinations of these genes suggested that the muscle cells might be deficient in key functions related to disease. When this was tested the team found that the mature high-risk VSMCs were weaklings compared to the low-risk cells, contracting with much less force and less able to cling to their surroundings than low-risk vascular muscle cells.

Next, the group asked whether these 3000 or so genes might help demystify the influence of around 100 other genes recently linked to coronary artery disease risk. Unexpectedly, the high-risk cells showed changes in more than a third of these (38), suggesting that the 9p21.3 haplotype somehow interacts with or even controls this network of genes.

Delving more deeply, the group identified a potential key master regulator (ANRIL), which itself is a member of an enigmatic class of genes that do not make proteins--instead generating genetic molecules called long non-coding RNAs. They noticed that risk cells had higher levels of several short forms of ANRIL. When they added these short ANRIL RNAs to healthy cells they developed key signatures of disease, indicating that these ANRIL RNAs may be master conductors of the switch between healthy and disease-promoting cell states in vascular muscle cells.

https://www.scripps.edu/news-and-events/press-room/2018/20181206baldwin-cell.html