Besides a healthy dose of good luck (Kunkel says it helps to not be killed in a war or a traffic accident), one key to longevity is a highly unusual combination of gene variants that protects against the customary diseases of old age. Several research teams are now in the process of uncovering these genes.

Kunkel, director of the Genomics Program at Children's Hospital in Boston, and his associates recently identified a genetic variant that is particularly prominent among sibling pairs in the New England Centenarian Study, perhaps the world's largest pool of centenarians. They are seeking additional genetic variants that might retard—or perhaps even prevent—many of the diseases that debilitate the old. "People with this rare combination of genes clearly age more slowly," Kunkel says. "When they reach 90, they don't look any older than 70."

Hundreds of centenarians around the world are now contributing their blood and medical histories to the search for these precious genes. They have become a key resource for researchers who hope that as these genes are revealed, their good effects may be reproduced in other people with the help of new drugs.

CLUSTERED IN FAMILIES
Kunkel was drawn to the hunt for longevity genes about six years ago, through a chance encounter with Thomas T. Perls, a Boston University Medical School geriatrician who had enrolled a large group of centenarians for his New England Centenarian Study. Kunkel's own research was focused on a deadly genetic disorder called Duchenne muscular dystrophy, which affects mostly boys. In 1986, he discovered a mutation that causes this muscle-wasting disease, and he is still working on a therapy for it (see Cures for Muscle Diseases?). But he could not resist the opportunity to also apply his knowledge of genetics to what he heard from Perls.

The two men were acquainted through Perls's wife, Leslie Smoot, who happened to be a postdoc in Kunkel's lab. When they met on a street in Cambridge, Massachusetts, in 1997 and started talking about their work, "Tom told me that many of the centenarians whose lineage he was examining were clustered in families," Kunkel recalls. "I realized that's just got to be genetics. We soon started a collaboration."

For his part, Perls remembers that at the beginning of his study he thought the centenarians had little in common except for their age. But he soon realized that many of them had an unusually large number of equally aged relatives. "We had a 108-year-old man who blew out his birthday candles next to his 102-year-old sister," Perls recalls. "They told us they had another sibling who was 103, and yet another who was only 99. Two other siblings—also centenarians—had passed away. Four siblings had died in childhood. So here was an incredible clustering, 5 or maybe 6 siblings out of 10! We've since found about 7 families like that." This implied that all these families carried especially protective genes. Shortly after the two scientists met, a new postdoc arrived in Kunkel's lab—Annibale A. Puca, a young Italian neurologist who wanted to work in genetics—and Kunkel suggested he take on this new project. "I warned him it was going to be a lot of work and high risk, but he said okay," Kunkel says, "and he spearheaded the whole program."

Puca and Perls rapidly expanded the group of centenarians, recruiting them through alumni associations, newspaper clippings, and state census lists. After taking samples of the centenarians' blood, the researchers extracted DNA from it and started looking for genetic markers—specific stretches of DNA that might occur more frequently among these extremely old men and women than among a group of younger people who were the study's controls. Most scientists believed that human longevity is far too complicated a trait to be influenced by only a few genes. There are so many independent mechanisms of aging that "the chance that only a few major genes control longevity in man is highly unlikely," wrote a self-styled "pessimist" on this issue, George M. Martin of the University of Washington in Seattle, in the journal Mechanisms of Ageing and Development in 2002. But Kunkel's lab took a different view. "In lower organisms, such as nematodes, fruit flies, and yeast, there are only a few genes that need to be altered to give a longer life span," Kunkel says. "My feeling was that there were only a few genes, perhaps four to six, in humans that would do the same."

The team proceeded to examine genetic markers for the entire genomes of 308 people, selected because they belonged to 137 sibships (sets of siblings) in which at least one member was over 98 and the others were over 90. "From early on, we saw a blip of a peak on chromosome 4," says Kunkel. "Eventually, in 2001, we found a linkage between one region of this chromosome and longevity."

SEARCH FOR A SNP
It was "phenomenal" to get a real linkage from such a slight hint in the original data, Kunkel declares. But that didn't mean further research would be easy. This stretch of DNA was so large—12 million DNA base pairs long—that it seemed it could contain as many as 200 genes. Furthermore, the researchers knew that within these genes they would have to look for variations in single bases of DNA—"single-nucleotide polymorphisms," or SNPs (pronounced "snips"). "SNPs really represent the difference between individuals," Kunkel explains. "Everybody's DNA is 99.9 percent identical—it's the SNPs that make us unique and allow certain people to live longer. Even though most of our DNA is alike, the 0.1 percent variation means that we have more than 10 million SNPs across the genome. And we're on the verge of being able to map them." For Kunkel, the critical question was "how would we find the one SNP in a single gene that might help a person to live much longer than average?"

The groundbreaking work of the Human Genome Project had not yet been completed at that time, and Kunkel realized that finding this particular SNP would be both expensive and time-consuming. It would also be quite different from zeroing in on a missing or severely garbled gene, as had been done for cystic fibrosis, muscular dystrophy, and other single-gene disorders. The widespread diseases of aging—heart disease, stroke, diabetes, cancer, and Alzheimer's disease—are much more complex and are triggered by subtle gene variations that produce only slightly altered proteins, Kunkel says. These proteins may either work a little better or be less active than those in the normal population, and several of them may work in concert. Searching for a single SNP would require doing thousands of genetic analyses on each of his subjects (now numbering 653) and comparing the results with the control group. "We estimated it would cost at least $5 million," Kunkel said. "It finally cost $8 million and took one-and-a-half years."

Ultimately, all that painstaking work paid off. The paper announcing the discovery of a SNP that contributes to longevity was published in the November 25, 2003, issue of the Proceedings of the National Academy of Sciences.

NOW FOR THE OTHERS
The long-sought SNP turned out to lie within the gene for microsomal transfer protein, or MTP, which had been known since the mid-1980s to be involved in cholesterol metabolism.

"It's quite clear that to live to be 100, you've got to maintain your cholesterol at a healthy level," says Kunkel. "It makes perfect sense. We know that increased LDL (the 'bad' cholesterol) and lowered HDL (the 'good' cholesterol) raise your cardiovascular risk and that cardiovascular diseases account for a large percentage of human mortality. So variations in the genes involved in cholesterol packaging will influence your life span. It's as if these centenarians had been on Lipitor [a cholesterol-lowering drug] from birth!"

This discovery might lead to drugs that are tailored to intervene in the cholesterol pathway. Because the MTP gene was already in the public domain, however, it could not be patented, much to the disappointment of the former Centagenetix Corporation (founded by Puca, Perls, and Kunkel and now a part of Elixir Pharmaceuticals of Cambridge, Massachusetts), which had bankrolled most of the study.

In any event, this SNP "cannot be the whole story," Kunkel declares. "There must be other gene variations that enable people to avoid age-related diseases. Some of our original families did not show linkages to chromosome 4." Nor did a group of centenarians who were tested in France.

Determined to find some of the other SNPs that produce longevity, Kunkel says he's going back to his sample and will redo the whole study. "We now have 310 sibships," he says. "Our genetic markers are much denser. I believe we can get 10 times the power in our next screen than we had in the first."

Moreover, the work can be done much more rapidly and inexpensively than last time, he notes, given the giant strides that have been made recently in human genetics. Not only has the entire human genome been sequenced, but many of the errors in the original draft have been corrected. Equally important, all the known genes in the genome are now available on a single Affymetrix DNA chip, allowing researchers to promptly identify which genes are activated and which are damped down in any given situation. In addition, as many as 10,000 different human SNPs have been placed on a single chip.

Similar tools have already turned up new gene variants in yeast, worms, and flies. But Kunkel will use the chips to analyze the DNA of humans. Once his lab gets started on the new longevity project, he believes, it will not take very long to get some definitive answers. He hopes these will lead to drugs that could mimic the protective effects of the centenarians' genes.

GOLD STANDARD
In fact, these studies foreshadow a far-reaching attack on all complex diseases—not just those of the aged but others, such as autism and hypertension. None of these ills could be tackled efficiently in the past. "The centenarians are the ideal control group for such research," Kunkel says. "To reach 100, you must have good alleles [versions of the genes] at all points. So if one wants to find the genes that are connected with hypertension, for instance, one can look across the genome for genes that are highly active in the hypertensive population but down-regulated in centenarians. Ultimately, that's what the centenarians' genes will be used for."

He believes that in the future, "every person who comes to our genetic clinic—or goes through any type of care system—with what appears to be a complex disease should be analyzed in detail. I mean that we should gather all the information we can about each patient's symptoms, the family history of these symptoms, any environmental insults the patient suffered, any learning disability—anything that would allow us to categorize the patient and [the patient's] family into subtypes of the disease which could be more related to one another and thus more likely to involve the same gene." To make this happen, Kunkel has just appointed a director of phenotyping (the Greek roots of this word mean "classifying phenomena into specific types") who will collect, categorize, and catalogue such patient information.

"We will also analyze the patients' genes but only in the context of the category of symptoms they exhibit," he says. "The samples we collect—under appropriate protocols—will be available to the national groups of patients and researchers that are organizing to find the underlying genetic bases of specific diseases." Eventually, he hopes, many complex disorders such as heart disease, diabetes, and autism will be broken down into more specific categories, which in turn may lead to more precise treatments or ways of preventing the disorder. Kunkel expects this process to accelerate in the near future as more patients' genes are compared with those of the gold standard for humans—the centenarians.

Download this story in Acrobat PDF format.
(requires Acrobat Reader)

Photos: Ed Kashi

Reprinted from the HHMI Bulletin,
Spring 2004, pages 12-17.
©2004 Howard Hughes Medical Institute