Lifespan. David Sinclair
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last that long. Instead, aging in yeast is measured by the number of times a mother cell divides to produce daughter cells. In most cases, a yeast cell gets to about 25 divisions before it dies. That, however, makes obtaining old yeast cells an exceptionally challenging task. Because by the time an average yeast cell expires, it is surrounded by 225, or 33 million, of its descendants.
It took a week of work, a lot of sleepless nights, and a whole lot of caffeinated beverages to collect enough regular old cells. The next day, when I developed the film to visualize the rDNA, what I saw astounded me.61
Just like the mutants, the normal old yeast cells were packed with ERCs.
That was a “Eureka!” moment. Not proof—a good scientist never has proof of anything—but the first substantial confirmation of a theory, the foundation upon which I and others would build more discoveries in the years to come.
The first testable prediction was if we put an ERC into very young yeast cells—and we devised a genetic trick to do that—the ERCs would multiply and distract the sirtuins, and the yeast cells would age prematurely, go sterile, and die young—and they did. We published that work in December 1997 in the scientific journal Cell, and the news broke around the world: “Scientists figured out a cause of aging.”
It was there and then that Matt Kaeberlein, a PhD student at the time, arrived at the lab. His first experiment was to insert an extra copy of SIR2 into the genome of yeast cells to see if it could stabilize the yeast genome and delay aging. When the extra SIR2 was added, ERCs were prevented, and he saw a 30 percent increase in the yeast cells’ lifespan, as we’d been hoping. Our hypothesis seemed to be standing up to scrutiny: the fundamental, upstream cause of sterility and aging in yeast was the inherent instability of the genome.
What emerged from those initial results in yeast, and another decade of pondering and probing mammalian cells, was a completely new way to understand aging, an information theory that would reconcile seemingly disparate factors of aging into one universal model of life and death. It looked like this:
Youth → broken DNA → genome instability → disruption of DNA packaging and gene regulation (the epigenome) → loss of cell identity → cellular senescence → disease → death.
The implications were profound: if we could intervene in any of these steps, we might help people live longer.
But what if we could intervene in all of them? Could we stop aging?
Theories must be tested and tested and tested some more—not just by one scientist but by many. And to that end, I was fortunate to have been put onto a research team that included some of the most brilliant and insightful scientists in the world.
There was Lenny Guarente, our indefatigable mentor. There was also Brian Kennedy, who started the yeast-aging project in Lenny’s lab and has since played a tremendously important role in understanding premature aging diseases and the impact of genes and molecules that increase health and longevity in model organisms. There were Monica Gotta and Susan Gasser at the University of Geneva, who are now some of the most influential researchers in the field of gene regulation; Shin-ichiro Imai, now a professor at Washington University, who discovered that sirtuins are NAD-utilizing enzymes and now does research into how the body controls sirtuins; Kevin Mills, who ran a lab in Maine, then became a cofounder of and chief scientific officer at Cyteir Therapeutics, which develops novel ways to fight cancer and autoimmune diseases; Nicanor Austriaco, who started the project with Brian, now teacher of biology and theology at Providence College, a great combo; Tod Smeal, chief scientific officer of cancer biology at the global pharmaceutical company Eli Lilly; David Lombard, who is now a researcher in the field of aging at the University of Michigan; Matt Kaeberlein, a professor at the University of Washington, who is testing molecules on dog longevity; David McNabb, whose lab at the University of Arkansas has made key and lifesaving discoveries about fungal pathogens; Bradley Johnson, an expert on human aging and cancer at the University of Pennsylvania; and Mala Murthy, a prominent neuroscientist now at Princeton.
Again and again I have been greatly privileged in the matter of those who work around me. And that was never truer than it was in Guarente’s lab at MIT. It was a dream team, and I often felt humbled by the people with whom I was surrounded.
When I began my career in this field, I dreamt of publishing just one study in a top-tier journal. During those years, our group was publishing one every few months.
We demonstrated that the redistribution of Sir2 to the nucleolus is a response to numerous DNA breakages, which happen as a result of ERCs multiplying and inserting back into the genome or joining together to form superlarge ERCs. When Sir2 moves to combat DNA instability, it causes sterility in old, bloated yeast cells. That was the first step of the survival circuit, though at the time we had no idea that it was as ancient and as essential to our very existence as it turned out to be.
We told the world that we could give yeast a Werner-like syndrome, causing exploded nucleoli.62 We described the ways in which mutants of SGS1, those we’d plagued with the yeast equivalent to the Werner syndrome mutation, accumulated ERCs more rapidly, leading to premature aging and a shortened lifespan.63 Crucially, by demonstrating that if you add an ERC to young cells they age prematurely, we had crucial evidence that ERCs don’t just happen during aging, they cause it. And by artificially breaking the DNA in the cell and watching the cellular response, we showed why sirtuins move—to help with DNA repair.64 That turned out to be the second step of the survival circuit.65 The DNA damage that gave rise to the ERCs was distracting Sir2 from the mating-type genes, causing them to become sterile, a hallmark of yeast aging.
It was epigenomic noise in its purest form.
It took another twenty years to learn if those findings in yeast were relevant to organisms more complex than yeast. We mammals have seven sirtuin genes that have evolved a variety of functions beyond what simple SIR2 can do. Three of them, SIRT1, SIRT6, and SIRT7, are critical to the control of the epigenome and DNA repair. The others, SIRT3, SIRT4, and SIRT5, reside in mitochondria, where they control energy metabolism, while SIRT2 buzzes around the cytoplasm, where it controls cell division and healthy egg production.
There had been many clues along the way. Brown University’s Stephen Helfand showed that adding extra copies of the dSir2 gene to fruit flies suppresses epigenetic noise and extends their lifespan. We found that SIRT1 in mammals moves from silent genes to help repair broken DNA in mouse and human cells.66 But the true extent to which the survival circuit is conserved between yeast and humans wasn’t fully known until 2017, when Eva Bober’s team at the Max Planck Institute for Heart and Lung Research in Bad Nauheim, Germany, reported that sirtuins stabilize human rDNA.67 Then, in 2018, Katrin Chua at Stanford University found that, by stabilizing human rDNA, sirtuins prevent cellular senescence—essentially the same antiaging function as we had found for sirtuins in yeast twenty years earlier.68
That was an astonishing revelation: over a billion years of separation between yeast and us, and, in essence, the circuit hadn’t changed.
By the time those findings appeared, though, it was clear to me that epigenomic noise was a likely catalyst of human aging. Two decades of research had already been leading us in that direction.69
In 1999, I moved from MIT across the river to Harvard Medical School, where I set up a new lab on aging. There I was hoping to answer a new question that had increasingly been occupying my thoughts.
I had noticed that yeast cells fed with lower amounts of sugar were not just living longer, but their rDNA was exceptionally compact—significantly delaying the inevitable ERC accumulation, catastrophic numbers of DNA breaks, nucleolar explosion, sterility, and death.
Why was that happening?
THE
It was a eureka moment—discovering why yeast cells age. Supercoiled circles of ribosomal DNA pinch off the yeast chromosome and accumulate as the yeast divide, distracting the Sir2 enzyme from its main role of controlling genes for sex and reproduction. David A. Sinclair and Leonard Guarente, “Extrachromosomal rDNA Circles—A Cause of Aging in Yeast,”
D. A. Sinclair, K. Mills, and L. Guarente, “Accelerated Aging and Nucleolar Fragmentation in Yeast SGS1 Mutants,”
Sinclair and Guarente, “Extrachromosomal rDNA Circles—A Cause of Aging in Yeast.”
K. D. Mills, D. A. Sinclair, and L. Guarente, “MEC1-Dependent Redistribution of the Sir3 Silencing Protein from Telomeres to DNA Double-Strand Breaks,”
Sinclair, Mills, and Guarente, “Accelerated Aging and Nucleolar Fragmentation in Yeast SGS1 Mutants.”
P. Oberdoerffer, S. Michan, M. McVay, et al., “SIRT1 Redistribution on Chromatin Promotes Genomic Stability but Alters Gene Expression During Aging,”
A. Ianni, S. Hoelper, M. Krueger, et al., “Sirt7 Stabilizes rDNA Heterochromatin Through Recruitment of DNMT1 and Sirt1,”
The authors show how SIRT7, in protecting against the instability of rDNA, also guards against the death of human cells. S. Paredes, M. Angulo-Ibanez, L. Tasselli, et al., “The Epigenetic Regulator SIRT7 Guards Against Mammalian Cellular Senescence Induced by Ribosomal DNA Instability,”
Oberdoerffer et al., “SIRT1 Redistribution on Chromatin Promotes Genomic Stability but Alters Gene Expression During Aging.”