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Unfolding a New Map of AMD
Roughly 18 million Americans are living with age-related macular degeneration (AMD), the most common cause of irreversible vision loss in the U.S. Unfortunately, for too many patients, the handful of available therapies are not effective.
AMD is, at least in part, driven by genetics. People can inherit genetic mutations that increase their risk of AMD. Yet for reasons science has yet to describe, not everyone who inherits a mutation—or risk allele—goes on to develop AMD. The key to solving this mystery is mapping the mechanism by which AMD risk alleles cause disease.
Kellogg physician-scientist and vitreoretinal surgeon Rajesh Rao, M.D., believes that map goes through unexpected and largely uncharted territory. Research to Prevent Blindness has awarded Dr. Rao a Catalyst Award for Innovative Research Approaches for AMD to explore it.
“Most genetic research looks for defects in the coding part of a gene’s DNA—the area containing instructions that turn DNA into protein,” explains Dr. Rao. “But mutations can also occur in non-coding part of a gene— the DNA tasked with regulatory housework.”
Dr. Rao is zeroing in on the non-coding genetic variant rs11200638, which, through mechanisms he hopes to help explain, is associated with a tenfold increase in a person’s risk of developing AMD.
“It’s the location of non-coding variants like rs11200638 that has thrown researchers off their trail,” he says. “rs11200638 is located in a non-coding, regulatory region known as a promoter. Classically, it is thought that variants in promoter regions influence their closest neighbor genes. But variants in promoters—and promoters themselves—are known to regulate genes thousands or millions of DNA bases away.”
“That leads us to hypothesize that rs11200638 could be regulating distant genes in AMD,” he continues. Located in the promoter of the gene HTRA1, rs11200638 can regulate previously unknown genes far away from its location, interacting with them through the phenomenon of genome folding.
“The body has trillions of cells and each contains perhaps six feet of DNA,” he explains. “The only way to contain all of that is to fold the strands of DNA. When picturing the genome folded, one can imagine how variants like rs11200638 might ‘contact’ faraway genes when folded in 3D space.”
Using retinal stem cell organoids, or living models of the retina, derived from patients carrying the high risk rs11200638 allele, Dr. Rao will attempt to correct the mutation, altering it to resemble the corresponding low risk allele common in people without AMD. Then, he will use 3D genome mapping tools such as MicroCapture C technology to see if long range contacts across the genome differ in retinal organoids derived from patients with the high risk rs11200638 variant compared to those of organoids in which the high-risk allele has been corrected to the low-risk allele, using gene editing techniques such as CRISPR-Cas9.
“This is one of the first studies, if not the first, to explore 3D genome folding as an AMD risk factor,” says Dr. Rao. “We hope it will help shed more light on the process by which a mutation in a non-coding region contributes to the disease, and ultimately yield new insights with therapeutic applications for AMD.”
