Lifespan

I asked her to text me a photo of the mouse she was talking about. When the photo came over my phone, I couldn’t help but laugh.

“That’s not a sick mouse,” I replied. “That’s an old mouse.”

“David,” she said, “I think you’re mistaken. It says here that it’s the sister of these other mice in the cage, and they’re perfectly normal.”

Her confusion was understandable. At 16 months old, a regular lab mouse still has a thick coat of fur, a sturdy tail, a muscular figure, perky ears, and clear eyes. A tamoxifen-triggered ICE mouse at the same age has thinning, graying hair, a bent spine, paper-thin ears, and cloudy eyes.

Remember, we’d done nothing to change the genome. We’d simply broken the mice’s DNA in places where there aren’t any genes and forced the cell to paste, or “ligate,” them back together. Just to make sure, later we broke the DNA in other places, too, with the same results. Those breaks had induced a sirtuin response. When those fixers went to work, their absence from their normal duties and presence on other parts of the genome altered the ways in which lots of genes were being expressed at the wrong time.

THE MAKING OF THE ICE MOUSE TO TEST IF THE CAUSE OF AGING MIGHT BE INFORMATION LOSS. A gene from a slime mold that encodes an enzyme that cuts DNA at a specific place was inserted into a stem cell and injected into an embryo to generate the ICE mouse. Turning on the slime mold gene cut the DNA and distracted the sirtuins, causing the mouse to undergo aging.

Those findings were aligned to discoveries being made by Trey Ideker and Kang Zhang, at UC San Diego, and Steve Horvath, at UCLA. Steve’s name stuck, and today he’s the namesake of the Horvath Clock—an accurate way of estimating someone’s biological age by measuring thousands of epigenetic marks on the DNA, called methylation. We tend to think of aging as something that begins happening to us at midlife, because that’s when we start to see significant changes to our bodies. But Horvath’s clock begins ticking the moment we are born. Mice have an epigenetic clock, too. Were the ICE mice older than their siblings? Yes, they were—about 50 percent older.

We’d found life’s master clock winder.

In another manner of thinking, we’d scratched up the DVD of life about 50 percent faster than it normally gets scratched. The digital code that is, and was, the basic blueprint for our mice was the same as it had always been. But the analog machine built to read that code was able to pick up only bits and pieces of the data.

Here’s the vital takeaway: we could age mice without affecting any of the most commonly assumed causes of aging. We hadn’t made their cells mutate. We hadn’t touched their telomeres. We hadn’t messed with their mitochondria. We hadn’t directly exhausted their stem cells. Yet the ICE mice were suffering from a loss of body mass, mitochondria, and muscle strength and an increase in cataracts, arthritis, dementia, bone loss, and frailty.

All of the symptoms of aging—the conditions that push mice, like humans, farther toward the precipice of death—were being caused not by mutation but by the epigenetic changes that come as a result of DNA damage signals.

We hadn’t given the mice all of those ailments. We had given them aging.

And if you can give something, you can take it away.

FRUIT OF THE SAME TREE

Like the gnarled hands of giant zombies breaking free of the rocky soil, the ancient bristlecone pine trees of California’s White Mountains strike haunting silhouettes against the dewy morning sun.

The oldest of these trees have been here since before the pyramids of Egypt were built, before the construction of Stonehenge, and before the last of the woolly mammoths left our world. They have shared this planet with Moses, Jesus, Muhammad, and the first Buddha. Standing some two miles above sea level, adding fractions of a millimeter of growth to their twisted trunks each year, defying lightning storms and periodic droughts, they are the epitome of perseverance.

It’s easy to stand in wonder of these great and ancient things. It’s easy to be swept away by their might and majesty. It’s easy to simply stare at them in awe. But there’s another way to view these antediluvian patriarchs—a harder way, but a way in which we should seek to view every living thing on this planet: as our teachers.

Bristlecones are, after all, our eukaryotic cousins. About half of their genes are close relatives of ours.

Yet they do not age.

Oh, they add years to their lives—thousands upon thousands of them, marked by the nearly microscopic rings hidden in their dense heartwood, which also record in their size, shape, and chemical composition climate events long past, as when the eruption of Krakatoa sent a cloud of ash around the globe in 1883, leaving a fuzzy ring of growth in 1884 and 1885, barely a centimeter from the outer ring of bark that marks our current time.[76 - M. G. L. Baillie, A Slice Through Time: Dendrochronology and Precision Dating (London: Routledge, 1995).]

Yet even over the course of many thousands of years, their cells do not appear to have undergone any decline in function. Scientists call this “negligible senescence.” Indeed, when a team from the Institute of Forest Genetics went looking for signs of cellular aging—studying bristlecones from 23 to 4,713 years old—they came up empty-handed. Between young and old trees, their 2001 study found, there were no meaningful differences in the chemical transportation systems, in the rate of shoot growth, in the quality of the pollen they produced, in the size of their seeds, or in the way those seeds germinated.[77 - Along with bristlecones, Matthew LaPlante, my coauthor on Lifespan, looks at a wide variety of biology’s outliers that define the very edges of our understanding of plants and animals, from ghost sharks and elephants to beetles and microbacteria. M. D. LaPlante, Superlative: The Biology of Extremes (Dallas: BenBella Books, 2019).]

The researchers also looked for deleterious mutations—the sorts of which many scientists at the time expected to be a primary cause of aging. They found none.[78 - When researchers compared trees of a variety of ages to look for a steady incremental decline in annual shoot growth, they found “no statistically significant age-related differences.” R. M. Lanner, and K. F. Connor, “Does Bristlecone Pine Senesce?,” Experimental Gerontology 36, nos. 4–6 (April 2001): 675–85, https://www.sciencedirect.com/science/article/pii/S0531556500002345?via%3Dihub.] I expect that if they were to look for epigenetic changes, they would similarly come up empty-handed.

Bristlecones are outliers in the biological world, but they are not unique in their defiance of aging. The freshwater polyp known as Hydra vulgaris has also evolved to defy senescence. Under the right conditions, these tiny cnidarians have demonstrated a remarkable refusal to age. In the wild they might live for only a few months, subject to the powers of predation, disease, and desiccation. But in labs around the world they have been kept alive for upward of 40 years—with no signs that they’ll stop there—and indicators of health don’t differ significantly between the very young and the very old.

A couple of species of jellyfish can completely regenerate from adult body parts, earning them the nickname “immortal jellies.” Only the elegant moon jelly Aurelia aurita from the US West Coast and the centimeter-long Turritopsis dohrnii from the Mediterranean are currently known to regenerate, but I’m guessing the majority of jellies do. We just need to look. If you separate one of these amazing animals into single cells, the cells jostle around until they form clumps that then assemble back into a complete organism, like the T-1000 cyborg in Terminator 2, most likely resetting their aging clock.

Of course, we humans don’t want to be mashed into single cells to be immortal. What use is reassembling or spawning if you have no recollection of your present life? We may as well be reincarnated.

What matters is what these biological equivalents of F. Scott Fitzgerald’s backward-aging Benjamin Button teach us: that cellular age can be fully reset, something I’m convinced we will be able to do one day without losing our wisdom, our memories, or our souls.

Though it’s not immortal, the Greenland shark Somniosus microcephalus is still an impressive animal and far more closely related to us. About the size of a great white, it does not even reach sexual maturity until it is 150 years old. Researchers believe the Arctic Ocean could be home to Greenland sharks that were born before Columbus got lost in the New World. Radiocarbon dating estimated that one very large individual may have lived more than 510 years, at least up until it was caught by scientists so they could measure its age. Whether this shark’s cells undergo aging is an open scientific question; very few biologists had so much as looked at S. microcephalus until the past few years. At the very least, this longest-living vertebrate undergoes the process of aging very, very slowly.

Evolutionarily speaking, all of these life-forms are closer to us than yeast, and just think of what we’ve learned about human aging from that tiny fungus. But it is certainly forgivable to consider the distances between pine trees, hydrozoans, cartilaginous fish, and mammals like ourselves on the enormous tree of life and say, “No, these things are just too different.”

What, then, of another mammal? A warm-blooded, milk-producing, live-birth-giving cousin?

Back in 2007, aboriginal hunters in Alaska caught a bowhead whale that, when butchered, was found to have the head of an old harpoon embedded in its blubber. The weapon, historians would later determine, had been manufactured in the late 1800s, and they estimated the whale’s age at about 130. That discovery sparked a new scientific interest in Balaena mysticetus, and later research, employing an age-determining method that measures the levels of aspartic acid in the lens of a whale’s eye, estimated that one bowhead was 211 years old when it was killed by native whalers.

That bowheads have been selected for exceptional longevity among mammals should perhaps not be surprising. They have few predators and can afford to build a long-lived body and breed slowly. Most likely they maintain their survival program on high alert, repairing cells while maintaining a stable epigenome, thereby making sure the symphony of the cells plays on for centuries.

Can these long-lived species teach us how to live healthier and for longer?

In terms of their looks and habitats, pine trees, jellyfish, and whales are certainly very different from humans. But in other ways, we’re very similar. Consider the bowheads. Like us, they are complex, social, communicative, and conscious mammals. We share 12,787 known genes, including some interesting variants in a gene known as FOXO3. Also known as DAF-16, this gene was first identified as a longevity gene in roundworms by University of California at San Francisco researcher Cynthia Kenyon. She found it to be essential for defects in the insulin hormone pathway to double worm lifespan. Playing an integral role in the survival circuit, DAF-16 encodes a small transcription factor protein that latches onto the DNA sequence TTGTTTAC and works with sirtuins to increase cellular survival when times are tough.[79 - Investigating mutations in the gene Daf-2, researchers made a remarkable find: the largest reported lifespan extension of any living thing, namely twice as long. This relied on the involvement of two genes, Daf-2 and Daf-16, opening the door to new horizons of ways to understand how to prolong life. C. Kenyon, J. Chang, E. Gensch, et al., “A C. elegans Mutant That Lives Twice as Long as Wild Type,” Nature 366 (December 2, 1993): 461–64, https://www.nature.com/articles/366461a0; F. Wang, C.-H. Chan, K. Chen, et al., “Deacetylation of FOXO3 by SIRT1 or SIRT2 Leads to Skp2-Mediated FOXO3 Ubiquitination and Degradation,” Oncogene 31, no. 12 (March 22, 2012): 1546–57, https://www.nature.com/articles/onc2011347.]

In mammals, there are four DAF-16 genes, called FOXO1, FOXO3, FOXO4, and FOXO6. If you suspect that we scientists sometimes intentionally complicate matters, you’d be right, but not in this case. Genes in the same “gene family” have ended up with different names because they were named before DNA sequences were easily deciphered. It’s similar to the not uncommon situation in which people have their genome analyzed and learn they have a sibling on the other side of town.[80 - Why do genes often have a variety of names? The language of genetics is just like any other language; its words contain the echoes of history. Knowing the entire genome of a yeast cell, a nematode worm, or a human was the stuff of dreams less than a quarter century ago. Now, of course, I can sequence my own genome in a day on a USB drive–sized sequencer. When I was a student, genes would be given a name based on the characteristics of mutants we would generate with mutagenic chemicals. Typically, all we knew about a gene when we named it was its rough location on a particular chromosome. Only later were its distant cousins identified.]DAF-16 is an acronym for dauer larvae formation. In German, “dauer” means “long lasting,” and this is actually relevant to this story. Turns out, worms become dauer when they are starved or crowded, hunkering down until times improve. Mutations that activate DAF-16 extend lifespan by turning on the worm defense program even when times are good.

I first encountered FOXO/DAF-16 in yeast, where it is known as MSN2, which stands for “multicopy suppressor of SNF1 (AMPK) epigenetic regulator.” Like DAF-16, MSN2’s job in yeast is to turn on genes that push cells away from cell death and toward stress resistance.[81 - A. Brunet, L. B. Sweeney, J. F. Sturgill, et al., “Stress-Dependent Regulation of FOXO Transcription Factors by the SIRT1 Deacetylase,” Science 303, no. 5666 (March 24, 2004): 2011–15, https://www.ncbi.nlm.nih.gov/pubmed/14976264.] We discovered that when calories are restricted MSN2 extends yeast lifespan by turning up genes that recycle NAD, thereby giving the sirtuins a boost.[82 - O. Medvedik, D. W. Lamming, K. D. Kim, and D. A. Sinclair, “MSN2 and MSN4 Link Calorie Restriction and TOR to Sirtuin-Mediated Lifespan Extension in Saccharomyces cerevisiae,” PLOS Biology, October 2, 2007, http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0050261.]

Hidden within the sometimes byzantine way scientists talk about science are several repeating themes: low energy sensors (SNF1/AMPK), transcription factors (MSN2/DAF-16/FOXO), NAD and sirtuins, stress resistance, and longevity. This is no coincidence—these are all key parts of the ancient survival circuit.

But what about FOXO genes in humans? Certain variants called FOXO3 have been found in human communities in which people are known to enjoy both longer lifespans and healthspans, such as the people of China’s Red River Basin.[83 - The authors found convincing evidence linking FOXO3 and longevity in humans. L. Sun, C. Hu, C. Zheng, et al., “FOXO3 Variants Are Beneficial for Longevity in Southern Chinese Living in the Red River Basin: A Case-Control Study and Meta-analysis,” Nature Scientific Reports, April 27, 2015, https://www.nature.com/articles/srep09852.] These FOXO3 variants likely turn on the body’s defenses against diseases and aging, not just when times are tough but throughout life. If you’ve had your genome analyzed, you can check if you have any of the known variations of FOXO3 that are associated with a long life.[84 - H. Bae, A. Gurinovich, A. Malovini, et al., “Effects of FOXO3 Polymorphisms on Survival to Extreme Longevity in Four Centenarian Studies,” Journals of Gerontology, Series A: Biological Sciences and Medical Sciences 73, no. 11 (October 8, 2018): 1437–47, https://academic.oup.com/biomedgerontology/article/73/11/1439/3872296.] For example, having a C instead of a T variant at position rs2764264 is associated with longer life. Two of our children, Alex and Natalie, inherited two Cs at this position, one from Sandra and one from me, so all other genes being equal, and as long as they don’t live terribly negative lifestyles, they should have greater odds of reaching age 95 than I do, with my one C and one T, and substantially greater than someone with two Ts.

It’s worth pausing to consider how remarkable it is that we find essentially the same longevity genes in every organism on the planet: trees, yeast, worms, whales, and humans. All living creatures come from the same place in primordium that we do. When we look through a microscope, we’re all made of the same stuff. We all share the survival circuit, a protective cellular network that helps us when times are tough. This same network is our downfall. Severe types of damage, such as broken strands of DNA, cannot be avoided. They overwork the survival circuit and change cellular identity. We’re all subject to epigenetic noise that should, under the Information Theory of Aging, cause aging.

Yet different organisms age at very different rates. And sometimes, it appears, they do not age at all. What allows a whale to keep the survival circuit on without disrupting the epigenetic symphony? If the piano player’s skills are lost, how is it possible for a jellyfish to restore her ability?

These are the questions that have been guiding my thoughts as I have considered where our research is headed. What might seem like fanciful ideas, or concepts straight out of science fiction, are firmly rooted in research. Moreover, they are supported by the knowledge that some of our close relatives have figured out a workaround to aging.

And if they can, we can, too.

THE LANDSCAPE OF OUR LIVES

Before most people could even fathom the idea of mapping our genome, before we had the technology to map a cell’s entire epigenome and understand how it bundles DNA to turn genes on and off, the developmental biologist Conrad Waddington was already thinking deeper.

In 1957, the professor of genetics, from the University of Edinburgh, was trying to understand how an early embryo could possibly be transformed from a collection of undifferentiated cells—each one exactly like the next and with the exact same DNA—to the thousands of different cell types in the human body. Perhaps not coincidentally, Waddington’s ponderings came in the dawning years of the digital revolution, at the same time that Grace Hopper, the mother of computer programming, was laying the foundation for the first widely used computer language, COBOL. In essence, what Waddington was seeking to ascertain was how cells, all running on the same code, could possibly produce different programs.

There had to be something more than genetics at play: a program that controlled the code.

Waddington conceived of an “epigenetic landscape,” a three-dimensional relief map that represents the dynamic world in which our genes exist. More than half a century later, Waddington’s landscape remains a useful metaphor to understand why we age.

On the Waddington map, an embryonic stem cell is represented by a marble at the top of a mountain peak. During embryonic development, the marble rolls down the hill and comes to rest in one of hundreds of different valleys, each representing a different possible cell type in the body. This is called “differentiation.” The epigenome guides the marbles, but it also acts as gravity after the cells come to rest, ensuring that they don’t move back up the slope or hop over into another valley.

The final resting place is known as the cell’s “fate.” We used to think this was a one-way street, an irreversible path. But in biology there is no such thing as fate. In the last decade, we’ve learned that the marbles in the Waddington landscape aren’t fixed; they have a terrible tendency to move around over time.

At the molecular level, what’s really going on as the marble rolls down the slope is that different genes are being switched on and off, guided by transcription factors, sirtuins and other enzymes such as DNA methyltransferases (DNMTs) and histone methyltransferases (HMTs), which mark the DNA and its packing proteins with chemical tags that instruct the cell and its descendants to behave in a certain way.

What’s not generally appreciated, even in scientific circles, is how important the stability of this information is for our long-term health. You see, epigenetics was long the purview of scientists who study the very beginnings of life, not folks like me who are studying the other end of things.