Hutch News

How cells put themselves to sleep

Discoveries about hibernating yeast could help us understand why some cancers resist chemo

Aug. 20, 2015
Illustration of dormant yeast cell

Under typical research conditions, baker’s yeast grows like gangbusters. But Fred Hutch researchers were interested in what happens to the fungus when they stop coddling it and recreate conditions closer to the cells’ natural, harsher home environment on grape skins and leaves. They found the cells behave very differently in these two life phases.

Illustration by Kim Carney / Fred Hutch News Service

Biologists, by definition, study life. But a group of molecular biologists at Fred Hutchinson Cancer Research Center have spent the past several years studying a physiological state that’s pretty much as un-lifelike as living systems get, a condition known as cellular quiescence.

Recently, these researchers have made new insights into what happens when yeast cells hunker down and enter that hibernation-esque phase of life. These findings, described in a study published Thursday in the journal Molecular Cell, could help reveal why some cancer cells survive even the harshest chemotherapies.

Under typical research conditions, baker’s yeast, the type most commonly used in basic science studies, grows like gangbusters. With a constant diet of simple glucose supplied by its scientist-caretakers, the single-celled fungus spawns daughter cells every 90 minutes, around the clock.

But Fred Hutch’s Drs. Toshio TsukiyamaLinda Breeden and Jeff McKnight are interested in what happens to the fungus when they stop coddling it and recreate conditions closer to the cells’ natural, harsher home environment on grape skins and leaves. How the cells behave in these two life phases — dividing or dormant — is very different, the researchers have seen.

Dr. Toshio Tsukiyama

Fred Hutch's Dr. Toshio Tsukiyama.

Photo by Scott Streble for Fred Hutch

When the biologists stop the constant food supply, the cells use up the remaining sugar over the course of several days, stop dividing and toughen up their cell walls, becoming slightly heavier as they prepare for what they perceive might be the long, sugar-free winter ahead. Once they enter this distinct inert state, “they’re like amazingly strong,” said Tsukiyama, who led the study along with Breeden and McKnight, and they can actually survive up to a month sitting in plain water.

The researcher was surprised at how different these dormant yeast were from the way the cells behave under typical research conditions.

“It’s the same yeast cells, but all of a sudden I feel like … someone caught this organism on the moon or Mars,” Tsukiyama said.

Interestingly, only young yeast cells can enter quiescence, and researchers don’t yet know why. A single yeast cell can divide about 25 times before it dies, but in general, only brand new, never-divided cells are able to hibernate.

“So if I’m a yeast, there’s no way I can enter quiescence,” joked the 52-year-old Tsukiyama.

How yeast are more like humans than we thought

Although these young, sleepy cells are weirdly fascinating in their own right, the researchers are interested in them primarily for what they can teach us about our own cells, or even about cancer.

“Tumor cells use quiescence … to protect themselves from stress, perhaps from chemotherapeutic agents,” said Dr. Robert Eisenman, a Fred Hutch biologist who studies how normal biological processes go awry in cancer cells. In other words, a small fraction of cancerous cells may keep themselves in dormant reserve, allowing them to escape killing by cancer treatments. Dormant cancer cells could be responsible for many cancer recurrences or even metastases.

Eisenman was not involved in the yeast quiescence study, but he and Tsukiyama are planning a future research project to determine whether the mechanisms of yeast dormancy hold true in healthy or cancerous human cells.

“Model organisms [like yeast], which themselves don’t get cancer but have the same kind of controls that higher organisms have, can really inform research in cancer with potential benefit,” Eisenman said.

This latest study was prompted by work started in Breeden’s laboratory. Her research team had been working with a technique that separates quiescent yeast cells from those that don’t enter dormancy and introduced that technique to Tsukiyama’s team.

To better understand what happens when yeast go quiet, the researchers examined yeast’s gene activity, also known as transcription, during dormancy. They weren’t the first to ask this question, but they were the first to study how genes turn on and off in purified quiescent cells.

As past research teams found, Tsukiyama and his colleagues saw that gene activity was reduced in quiescent cells — but much more dramatically than was previously thought. While actively dividing cells turn on between 70 and 80 percent of their genes, more than 95 percent of yeast’s 6,000 genes are shut off in dormancy, the researchers found.

“Transcription is massively different, on a level that nobody has ever seen before,” Tsukiyama said.

What this genetic shutdown means to science is that yeast quiescence is biologically distinct from its other stages of life, something that’s been debated among yeast biologists. But Tsukiyama hopes his group’s findings will lay that debate to rest and allow for more discoveries that could translate to human cells.

“I’m hoping that our paper will change people’s view that indeed [yeast] is a great model system,” he said. “As far as I know — of course, I’m biased — this is the strongest evidence so far that quiescence is a very different cell cycle stage.”

Clues to a cancer drug mystery

Tsukiyama’s team went on to identify the driver of the quiescence shutdown, a protein called Rpd3 that helps orchestrate changes to the way DNA is packaged inside the cell’s nucleus. What’s interesting about Rpd3, Tsukiyama said, is that it’s evolutionarily conserved from yeast to humans — often a marker of a protein’s importance — but researchers to date have been puzzled by the relatively minor role this protein seems to play in living cells.

When yeast living under typical laboratory conditions lack Rpd3, they’re more or less normal. But when Tsukiyama and his team tried to get those yeast cells to hibernate, most of them failed to go to sleep. Under the right conditions, 60 percent of healthy yeast cells will enter quiescence. But in the study, only about 10 percent of cells missing Rpd3 went dormant.

And that 10 percent didn’t look very happy about it, the researchers saw. They couldn’t survive nearly as long in dormancy as cells with Rpd3, and the researchers found that cells missing Rpd3 don’t undergo the same massive gene activity shutdown that healthy cells do.

That finding has an unexpected link to human health in that certain cancer drugs act by blocking the activity of proteins like Rpd3 in human cells. Those drugs, known as histone deacetylase inhibitors, are very effective against some types of cancer, especially leukemia — but nobody knows how these drugs work to kill cancer cells.

“If what we see in yeast is conserved in [human blood] cells, it can explain how these drugs work,” Tsukiyama said.

And that knowledge, Tsukiyama added, could help clinicians further refine existing histone deacetylase inhibitors to more precisely target cancer cells with fewer side effects.

But Tsukiyama is most excited about what he and his group have yet to uncover about quiescence. He suspects that there may be many more genes like Rpd3 – genes that should be important based on their evolutionary status, but don’t seem to do much under normal laboratory settings.

“There’s a good chance that by looking at the function of those genes in quiescence, maybe we can discover something that people have never seen before, because these are the growth conditions that yeast cells have evolved for,” he said.

“If what I think is right, quiescence is a gold mine.”

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Rachel Tompa is a staff writer at Fred Hutchinson Cancer Research Center. She joined Fred Hutch in 2009 as an editor working with infectious disease researchers and has since written about topics ranging from nanotechnology to global health. She has a Ph.D. in molecular biology from the University of California, San Francisco and a certificate in science writing from the University of California, Santa Cruz. Reach her at rtompa@fredhutch.org.

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