Reversing The Aging Clock With Epigenetic Reprogramming

By Deborah Borfitz 

January 13, 2021 | As aging researchers are aware, “birthday candles are not a good guide” to either human health or longevity. But there is an abundance of clues in the genome and, as suggested by studies in animals, some of age-related damage is reversible by removing or reprogramming problematic cells or blocking the activity of key proteins. 

As it turns out, DNA methylation—a frequently-used biomarker of biological age—is not just marking time like a clock on the wall but “actually controlling time within cells,” according to David Sinclair, an expert on aging at Harvard Medical School and cofounder of 4-year-old Life Biosciences. The revelation emerged from a study recently published in Nature (DOI: 10.1038/s41586-020-2975-4) where Harvard researchers showed, for the first time, that the pattern of DNA methylation in the genome can be safely reset to a younger age.

It was in fact a prerequisite to restoring youthful function and vision in old mice, says Sinclair, who has spent most of his adult life studying the epigenetic changes associated with aging. Up until a few years ago, he thought the process was unidirectional and that cells ultimately lost their identity and malfunctioned or became cancerous.

It “seemed crazy” to try to get proteins to return to the place they were in young cells, Sinclair says. Proteins move around in response to age-associated DNA damage and end up in the wrong places on the genome, causing the wrong genes to be turned on, but scientists did not know if proteins could go back, where the instructions were stored, or if they were being stored at all. 

As covered in his 2019 bestseller Lifespan, Sinclair now believes that aging is the result of the so-called epigenetic changes scrambling how the body reads genetic code. “We’re essentially looking for the polish to get the cell to read the genome correctly again,” he says, a process he likens to recovering music on a scratched CD.

Yamanaka Factors

Sinclair and his research associates have been focusing on the eye, in part because retinal tissues start aging soon after birth, he explains. While a damaged optic nerve can heal in a newborn, the injury is irreversible in a 1-year-old.

Yuancheng Lu, a former student of Sinclair’s, was also interested in the eye because his family has a vision-correction business and recognized sight loss as a “huge unmet need,” he continues. “We thought if we could take the age of those retinal cells back far enough, but not so far that they lose their identity, we might be able to see regrowth of the optic nerve if it was damaged.” 

Among the foundational work was a 2016 study in Cell (DOI: 10.1016/j.cell.2016.11.052) by Life Biosciences cofounder Juan Carlos Izpisua Belmonte (Salk Institute for Biological Studies) who partially erased cellular markers of aging in mice that aged prematurely, as well as in human cells, by turning on “Yamanaka factors” Oct4, Sox2, Klf4, and c-Myc (OSKM) highly expressed in embryonic stem cells. Short-term induction of OSKM ameliorated hallmarks of aging and modestly extended lifespan in the short-lived mice.

The lifespan gain was widely dismissed as “an artifact of shocking a mouse,” says Sinclair, since the mice died if the treatment continued for more than two days. Although the human health implications appeared unlikely, his Harvard team decided to try the approach using an adeno-associated virus as a vehicle to deliver the youth-restoring OSKM genes into the retinas of aging mice.

The technology kept killing the mice or causing them to get cancer until Lu decided to drop the c-Myc gene—an oncogene—in his experiments using human skin cells. “He looked at [damaged] cells that had been expressing OSK for three weeks and the nerves were growing back toward the brain to an unprecedented degree.” Moreover, the cells “got older by the damage and younger by the treatment.” 

As the broader team went on to show in the Nature paper, the trio of Yamanaka factors effectively made cells younger without causing them to lose their identity (i.e., turning back into induced pluripotent stem cells) or fueling tumor growth even after a year of continuous treatment of the entire body of a mouse. If anything, the mice had fewer tumors over the course of the study, says Sinclair.

Although the mice needed to be autopsied to definitively measure tumor burden, Sinclair says the study will be repeated to learn if the epigenetic reprogramming technique can increase lifespan.

Findings have implications beyond the treatment of age-related diseases specific to the eye, says Sinclair. Aging researchers have published studies showing other types of tissues, including muscle and kidney cells, can also be rejuvenated.

Clocked Results

In the latest study using mice, epigenetic reprogramming was found to have three beneficial effects on the eye: promotion of optic nerve regeneration, reversal of vision loss with a condition mimicking human glaucoma, and reversal of vision loss in aging animals without glaucoma. The latter finding, from Sinclair’s vantage point, is the most important one. “This is ultimately a story about finding a repository of youthful information in old cells that can reverse aging.”

Results of all three experiments are noteworthy and have been “commonly thought to be three separate processes,” says Sinclair. That is only because the fields of aging and acute and chronic disease are distinct disciplines that rarely talk to each other.

The Harvard team is pioneering a new way to tackle diseases of aging by addressing the underlying cause. This is the first time, as far as Sinclair is aware, where nerve damage was studied in old rather than young animals. “In the case of glaucoma and most diseases, aging is considered largely irrelevant, when of course we know glaucoma is a disease of aging.” 

A variety of aging clocks, including some the research team built themselves, have been deployed for studies because they are considered the most accurate predictor of biological age and future health, says Sinclair. As embryos, cells lay down different patterns of methylation to ensure they remember their purpose over the next 80 to 100 years. 

For unknown reasons, methyl groups get predictably added and subtracted from DNA bases across cell and tissue types and even species, Sinclair says. In 2013, UCLA’s Steve Horvath (another Life Biosciences cofounder) showed that machine learning could be used to pick out the “hot spots” and predict individual lifespan depending on how far above or below the DNA methylation line they sit (Genome Biology, DOI: 10.1186/gb-2013-14-10-r115).

A multitude of aging clocks have since been developed. “Eventually, we will need some standardization in the field, but there is nothing super-mysterious about aging clocks,” says Sinclair. “One of my grad students could probably get you one by the end of the day.”

Booming Field 

Aging research is a rapidly accelerating field and epigenetic reprogramming is poised to become a particularly active area of inquiry. “In terms of numbers, there are still only a dozen or so labs intensely working on this, but there are probably a hundred others I am aware of who are getting into it,” says Sinclair. 

Life Biosciences began with four labs, but new ones are now joining on an almost weekly basis, he adds. Collaborators have expanded work to the ear and other areas of the body beyond the eye, he adds. 

“We’re also reducing the cost of the DNA clock test by orders of magnitude so [biological age prediction] can be done on millions of people,” he continues. In the future, aging clocks are expected to be a routine test in physicians’ arsenal to guide patient care as well as to monitor response to cancer treatment.

Harvard University has already licensed two patents related to the technology used by the aging researchers to Life Biosciences, Sinclair says. The company has built a scientific team with a group of world-class advisors who developed gene therapy for the eye, which will be tested first for the treatment of glaucoma.

The role of chaperone-mediated autophagy in aging and age-related diseases is another promising area of research being pursued by Life Biosciences’ Ana Maria Cuervo, M.D, Ph.D., professor, and co-director of the Institute of Aging Studies at the Albert Einstein College of Medicine. Cuervo recently reported at a meeting that fasting-induced autophagy, the cell’s natural mechanism removes unnecessary or dysfunctional components, can greatly extend the lifespan of mice. She believes the triggering of this process might one day help treat diseases such as macular degeneration and Alzheimer’s.

The specialty of Manuel Serrano, Ph.D., the fourth company cofounder, is cellular senescence and reprogramming and how they relate to degenerative diseases of the lung, kidney, and heart. He is an internationally recognized scientist who has made significant contributions to cancer and aging research and works in the Institute for Research Biomedicine in Barcelona.