In a previous post, “How is Your Biologic Clock Ticking?”, we discussed the two types of biological clocks that govern our daily lives. There are the ones that are present in most cells, whose periodicity is about 12.2 hours. And, there is the one located in the brain that rides herd over them, forcing them to conform to a 12-hour period of wake/sleep, through the action of the hormone melatonin.
Scientists have long suspected that there must be another clock—one that determines not our daily life, but our overall longevity. Where would be a likely location for such a clock? The “obvious” answer would be in our DNA. After all, it is common knowledge that if you selected your parents wisely, you are almost guaranteed to live to the same ripe old age that they did. And, if you maintained a healthier lifestyle than they had, you may even be able to exceed it.
The boomer generation, the post-war wave of kids who grew up having it all (and demanding even more), expect to live the good life as long as biology would allow—and perhaps even more. Scientists, many of them boomers themselves, have been eager to oblige.
Telomeres – the chromosome stabilizers
TTAGGG. No, this is not a stuttering finger trying to print TAG nor is it a typo. This is a sequence of the nucleotides thymine, adenine, and guanine (or T, A, G, respectively). At both ends of each chromosome, this sequence repeats itself about 2500 times, forming caps that keep the structure of the chromosome stable. You can think of it as analogous to the metal cap at the end of a shoelace.
When cells divide, their chromosomes undergo duplication so that each daughter cell gets the full complement of genes of its mother cell. The only one catch? The telomeres don’t duplicate. This results in the telomeres getting shorter with each cell division. Eventually, when they get short to the point that the stability of the chromosome is compromised, cell division stops. This occurs in order to protect the organism from the metabolic and genetic chaos of unraveled chromosomes.
This explains why every cell can undergo only a certain number of divisions before entering a phase of senescence. With time, senescent cells accumulate mutations and lose most of its normal functions, eventually dying.
Since we are basically the sum of our cells, you can see how the process of telomere shortening translates into life-shortening. Stated differently, telomeres determine our longevity.
Indeed, certain diseases characteristic of aging, such as autoimmune diseases, are associated with truncated telomeres. Cancer incidence also rises with age. But here, the opposite thing happens. The telomeres don’t truncate; they actually elongate due to the activity of an enzyme called telomerase, thus keeping the cancer cell essentially immortal, which is the very essence of cancer.
The longevity clock
It appears almost inevitable that telomere length and its rate of shortening would predict longevity, right? Indeed, many studies looked into this tantalizing possibility. Just imagine. If we could control the enzyme that lengthens it, telomerase, we could prolong life, or, at the very least, avoid the diseases that make aging an unappealing prospect.
Like everything in nature, nothing is as it seems. There are always ‘confounding factors’, or as Donald Rumsfeld of Iraq war infamy might say, “the unknown unknowns.”
The evidence suggesting telomere length as a biomarker of aging in humans is equivocal. Indeed, the correlation between age and the length of telomeres is less than 0.5. More and more, researchers in the field developed a consensus that a single biomarker of aging doesn’t exist. If a biomarker exists at all, it must be multifactorial. That’s where things have stood since the discovery of the telomeres in 1978. [Historical note: Elizabeth Blackburn, Carol Greider, and Jack Szostak were awarded the 2009 Nobel Prize in Physiology or Medicine for the discovery of how chromosomes are protected by telomeres and the enzyme telomerase.]
The Gilgamesh project
An unusual article appeared in the April 8, 2014 issue of the usually dry, “just the facts, ma’am” journal Nature. It describes, in entertaining personal detail, the discovery of a marker of aging that really works. Here’s the story:
Three German teenagers, Steve Horvath, his identical twin Markus, and their friend Jörg Zimmermann formed ‘the Gilgamesh project’, which involved regular meetings where the three discussed mathematics, physics, and philosophy. The inspiration for the name, Horvath says, was the ancient Sumerian epic in which a king of Uruk searches for a plant that can restore youth. Fittingly, talks at their meetings often turned to ideas for how science might extend lifespan. Now, how more nerdy can you get?
The only one who remained faithful to the Gilgamesh project was Horvath. He supplemented his Ph.D in mathematics with a doctorate in biostatistics. In 2000, this led to a position in the genetics department at UCLA.
Now, an untenured assistant professor cannot undertake such a risky project as discovering a longevity clock, since failure rarely leads to tenure. But in 2006, after working and publishing on other projects, Horvath received tenure. It was now safe for him to embark on the Gilgamesh project again.
The astounding discovery
Horvath reasoned that environmental influences play a major role in the rate of our aging. These factors vary widely and can range from hormonal and dietary to stress, lifestyle, and even pollution.
They exert their influence through chemical and structural modifications made to the genome without altering the DNA sequence. The changes are made by adding a methyl group to the nucleotide sequence CpG (C and G are nucleic acid bases, cytosine, and guanine; the p stands for the phosphate group that connects them).
These methylation reactions are called epigenetic modifications. As cells age, the pattern of epigenetic alterations shifts, and some of the changes seem to mark time. To determine a person’s age, Horvath explored data for hundreds of far-flung positions on DNA from a sample of cells and noted how often those positions are methylated.
It sounds simple until you realize that a typical human genome contains more than 28 million CpG sites. How do you even begin to tackle such an improbable task?
As in many breakthroughs in science, lady luck came to the rescue. Horvath found success with a simple statistical model, which looked at how many cells in a drop of saliva have DNA methylated at just two particular CpG sites.
The index roughly paralleled participants’ ages with a correlation of 0.85, or 85%, and an average accuracy of about 5 years. As if this was not incredible enough—such an accurate prediction based on 2 CpG sites only—Horvath looked at even more sites and increased the predictive power of his method. But his manuscripts were rejected, because “they were too good to be true.”
By December 2012, his methylation database spanned 51 types of noncancerous tissue and cells, plus 20 kinds of cancer. The age estimator had grown to include 353 CpG sites. And the accuracy? An astounding 99.5% (or a correlation of 0.995). Bear in mind that, normally, biomarkers have a correlation of 0.6-0.7, and the telomere hypothesis had a correlation of less than 0.5.
The clock’s median error was 3.6 years, meaning that it could guess the age of half the donors to within 43 months for a broad selection of tissues. That accuracy improves to 2.7 years for saliva alone, 1.9 years for certain types of white blood cells, and 1.5 years for the brain cortex. The clock shows stem cells removed from embryos to be extremely young and the brains of centenarians to be about 100.
Why is it important?
Horvath’s method has many potential applications. Criminal investigators, for example, might find an epigenetic clock handy for establishing the age of a victim or an assailant by analyzing any biological residues left behind.
But the most interesting use of the clock will be to detect ‘age acceleration‘—discrepancies between a person’s epigenetic and chronological ages, either overall or in one particular part of their body.
Such discrepancies could be signs that something is awry. For instance, analyzing methylation data collected on more than 2,100 men and women aged 40 to 92 as part of the Framingham Heart Study, the researchers concluded that for every five-year increase in age acceleration, the risk of dying from any cause during the study jumped by 15%.
Researchers are also comparing the ages of different tissues from the same individual, in the hope of identifying more accurate, less invasive ways to diagnose disease or gauge the risk of future illness. Last year, Ideker and his collaborators reported that the epigenetic ages of breast, kidney, lung, and skin cancers were 40% older, on average, than the patients from which they were removed.
Distortions in epigenetic age seem to parallel other diseases more closely. Horvath says that recent work has found that people with HIV who have detectable viral loads appear older, epigenetically, than healthy people or those with HIV who have suppressed the virus.
Another study, not yet published, observes that some tissues show significant age acceleration in morbidly obese people. In the coming months, Horvath will be mining the vast Women’s Health Initiative database for more links. The database includes thousands of methylation profiles gathered as part of this 20-year, 160,000-person study spearheaded by the National Heart, Lung, and Blood Institute (NHLBI).
A tour de force
This tour de force was accomplished by analysis of ‘big data’, using statistical methods. The investigator is not even a trained biologist, rather he is a double Ph.D in math and statistics.
What has been accomplished goes beyond satisfying the curiosity of how long we are destined to live. It promises to develop into a platform that will rapidly decipher the mechanisms of diseases, their environmental causes, and their potential therapy. Three for the price of one. Amazing!