New & Noteworthy

Too Much of a Good Thing Can Be Hazardous to Your Health

July 02, 2018

When someone says they can “read you like a book”, they probably aren’t saying that they know your entire genome sequence. (…or for you Westworld fans, you certainly hope they aren’t saying they’ve got access to the Delos Incorporated “library”!).


Can someone read you (or your genome) like an open book?

But in fact everyone’s genome CAN be thought of as a book, sort of like a giant cookbook. Within your genome are many “recipes” for gene products — DNA sequences that each give instructions on how, when, and where to make a protein or RNA molecule. The recipes of the genome are used to “cook up” a person!

When a parent cell divides and creates another cell, it makes a copy of its genome “cookbook” and passes it down to the new cell. It’s extremely important to make sure that there aren’t any errors in the newly copied text, as mistakes in recipes for crucial enzymes can have disastrous results for the cell. Indeed, our cells (as well as yeast cells, and in fact, all organisms) have enzymes that are dedicated to scrupulously inspecting the new copies of our genome cookbooks that are made during cell division, and then helping to correct any errors.


No typos here!

A certain class of these enzymes are known as DNA mismatch repair (MMR) proteins. These enzymes carefully proofread the newly made copy of the genome, and if something doesn’t match the original version, they will help fix the error.

You might think that having more of these MMR proteins would be a good thing, because there would be more thorough checking and repairing of the new copy of the genome. But the situation isn’t so simple, especially when it comes to human cancer.

Previous studies show that some cancers and cancer predisposition syndromes have less of the MMR proteins. This makes sense because cancers almost always arise due to genome mutations, and it is known that if a cell has less of the error-checking MMR proteins, there are more genome mutations. However, other studies report a puzzling discrepancy: in some cancers, there are in fact MORE of the MMR proteins rather than less!

In their recent GENETICS study, Chakraborty and coworkers decided to investigate this discrepancy further. They analyzed data from two databases of human cancer genome information, The Cancer Genome Atlas (TCGA) and the cBioPortal for Cancer Genomics, specifically looking at how much the genes encoding MMR proteins were turned on or off in cancer.

They observed that many types of human cancer cells make more of two particular MMR proteins: MSH2 and MSH6. It turns out (as it often does!) that our good buddy Saccharomyces cerevisiae has MMR proteins very similar to the human ones, also encoded by genes called MSH2 and MSH6. So Chakraborty and coworkers made yeast cells that overexpress the yeast genes MSH2 and MSH6 and used the awesome power of yeast genetics (and genomics) (#APOYG!) to investigate whether this might lead to cellular and genome changes like those seen in human cancers.

Using various yeast genetic assays to measure rates of genome alterations such as homologous recombination, mutations, and loss of large chromosome regions, Chakraborty et al. observed increased rates for all of these measures of genome instability in cells when both MSH2 and MSH6 were overexpressed, but not for overexpression of either one alone (or of other MMR proteins). So even though there are more of the “good guy” MMR proteins in these cells, this actually ends up making the genome of the cell MORE likely to get damaging mutations of the same types seen in cancer cells.

So why is too much of a good thing such a bad thing in this case? The authors hypothesize that both Msh2p and Msh6p act together as a joined pair to go to the spot where the chromosomal DNA is actively being copied (“replicated”). When they are both overexpressed, too many of the Msh2p-Msh6p pairs can go to the replication spot and actually interfere with the copying process.


Medieval scribe and author Jean Miélot at his desk, late 15th century (from Wikimedia Commons)

It’s as if you were a medieval scribe carefully copying an illuminated manuscript of a genome cookbook, and instead of one supervisor occasionally checking your work, there are a bunch of people constantly looking over your shoulder and maybe even bumping into your arm, causing you to make mistakes in your writing. They may even make you drop the book you’re copying, scattering pages so that you might leave some out or put them back in the wrong order, seriously messing up your work!

Here’s hoping our cells don’t overdo it with their MMR proteins, so that they can be careful with their cookbook copying job and do it “write”!

by Barbara Dunn, Ph.D. and Kevin MacPherson, M.S.

Categories: Research Spotlight

Tags: MSH6 , DNA replication , DNA mismatch repair , MSH2 , cancer

Yeast Reveals a Vicious Circle Between Sugar and Cancer

November 10, 2017

The housing crisis that started in 2006 is a classic example of a vicious circle. As prices went down, some people couldn’t afford their mortgages and so were foreclosed upon. These foreclosed houses entered the market and caused prices to drop further which caused more foreclosures and so on. Only a Herculean effort by the government and the Federal Reserve was able to break this cycle.


A vicious circle between foreclosed homes and home prices popped the housing bubble starting in 2006. A similar vicious circle between glucose fermentation and cancer cell aggressiveness makes for particularly nasty cancers. (Wikimedia Commons)

Vicious circles can happen in biology too.

In a new study in Nature Communications, Peeters and coworkers have used our friend Saccharomyces cerevisiae to uncover one of these in cancer cells. And it turns out that this yeast is the perfect model organism for this study. (Funny how often that is true…)

Both S. cerevisiae and cancer tend to utilize their sugar through fermentation instead of respiration. This process in yeast is obviously great news for beer and wine drinkers. However, it is not such great news for people with cancer.

In the Warburg effect (named after the scientist who discovered it), the more aggressive a cancer is, the more sugar it ferments. This new study suggests that the consumption of sugar via fermentation and the aggressiveness of the cancer are related in a vicious circle.

Fermentation creates the byproduct fructose-1,6-bisphosphate (Fru1,6bisP) which, according to this study, activates the oncogene Ras which causes the cell to grow faster. As it grows faster, it ferments sugar faster creating more Fru1,6bisP which activates more Ras and so on. The cancer cells grow out of control until doctors apply some Herculean treatment to put a stop to it.

While yeast and cancer cells have a lot in common, wild type yeast isn’t quite up to cancer’s standards when it comes to cancer’s unbridled intake of glucose into the glycolysis pathway. These authors turned yeast a bit more cancer-like in this regard by deleting the TPS1 gene. Tps1p is a yeast hexokinase that tightly regulates yeast’s glucose intake into glycolysis.

Yeast cells without TPS1 deal poorly with glucose and need to be grown in galactose. When Peeters and coworkers added glucose to tps1Δ cells that had been previously grown in galactose, the cells activated Ras, a potent oncogene. This activation caused the cell to undergo apoptosis as assayed by cytochrome c release from the mitochondria, exposure of phosphadityl serine on the plasma membrane and generation of reactive oxygen species.

Deletion of hexokinase 2 eliminated this activation of Ras and suppressed the apoptosis. This suggests that perhaps some buildup of an intermediate metabolite in the glycolytic pathway might be to blame for the Ras activation.

The authors tested this hypothesis by removing the cell wall of wild type yeast cells and adding glycolysis metabolites to the resulting spheroplasts. They found that one metabolite, Fru1,6bisP, activated Ras. Supporting this finding, they found that deletion of both PFK1 and PFK2, two genes that encode phosphofructokinase 1, the enzyme responsible for making Fru1,6bisP, eliminated Ras activation in tps1Δ cells. Together, these data support the idea that Fru1,6bisP is the culprit behind Ras activation in yeast.


Vicious circles like the one behind the Warburg effect are everywhere! (Twisted Doodles)

All well and good, but what about human cancer cells? Is something similar going on there? You have probably guessed that the answer is yes.

The authors first depleted the level of Fru1,6bisP in two different cell lines by starving them of glucose for 48 hours. They then added back glucose, which has been shown to increase the levels of Fru1,6bisP in cells, and measured the activation level of Ras and two of its downstream targets, MEK and ERK. All three were transiently activated in both HEK293T and Hela Kyoto cell lines. Looks like Fru1,6bisP activates Ras in cancer cells as well.

So this might explain the Warburg effect that I mentioned earlier. The more glucose a cancer cell uses during fermentation, the more Fru1,6bisP it generates. And the more Fru1,6bisP that is made, the more Ras gets activated prompting the cell to grow faster. Which of course results in more glucose getting fermented and so on.

I don’t have time to go into the work these authors did to try to uncover the mechanism by which Fru1,6bisP activates Ras, but suffice it to say that it does not appear to be a direct interaction with Ras. Instead, it appears to work at least partially by disrupting the interaction between Ras and one of its guanine nucleotide exchange factors, Cdc25p (or Sos1 in humans).

And the story is not yet complete. There is still a lot of work to do in pinning down the specifics of this vicious circle. Yeast will undoubtedly be instrumental in helping us work through the rest of the details.

by Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight

Tags: cancer , Warburg Effect , PFK1 , PFK2 , TPS1 , fermentation

Knock out YME1, Luke

April 20, 2017

Death Star Explosion & Millenium Falcon

Instead of an exhaust port, one of a mitochondrion’s fatal flaws may be the YME1 gene. Image from Manoel Lemos, flickr.

In the original Star Wars, Luke destroys the Death Star with a precise strike of proton torpedoes down a small thermal exhaust port. For him it was as easy as bullseyeing “womp rats in my T-16 back home.”

Luke and the rest of the Rebel Alliance learned of this engineered fatal flaw from Jyn and her friends in the prequel Rogue One. With this information the Rebel Alliance was able to keep the rebellion alive long enough to finally bring down the Empire by the end of Return of the Jedi.

It turns out that our friend Saccharomyces cerevisiae has taught us about a fatal flaw in mitochondria. Like proton torpedoes in an exhaust port, when the gene YME1 is inactivated, mitochondria become unstable. But instead of bits of Death Star raining down on nearby planets, mitochondrial DNA (mtDNA) is released into the cytoplasm.

Sometimes this mtDNA can end up in the nucleus and find its way into nuclear DNA. And if the conclusions of a new study in Genome Medicine by Srinivasainagendra and coworkers turns out to be right, this numtogenesis (as the authors call this process) can have profound consequences when it happens in people. Their data suggests that it might lead to cancer or possibly cause cancers to spread.

These researchers searched through whole genomes of colon adenocarcinoma patients and found that these cancer cells had 4.2-fold more mtDNA insertions compared to noncancerous cells from the same patient. They also found that patients with more of these insertions tended to do worse (although the sample sizes were too small to say this definitively).

Why is this happening in the cancer cells? What has caused the mitochondria to give up their DNA?

Srinivasainagendra and coworkers turned to previous work that had been done on the YME1 gene in the yeast S. cerevisiae to find one possible reason. YME1 had been shown to be an important suppressor mtDNA migration to the nucleus. Perhaps this was true in mammalian cells as well.

A search through the genomes of cancers suggested that this seemed to be the case. Around 16% of the colorectal tumors they looked at had a mutated YME1L1 gene, the human homologue of YME1. And mutated YME1L1 genes were found in other tumors as well.

If only destroying gene function was as fun.

They used CRISPR/Cas9 to directly test the effects of knocking out YME1L1 in the breast cancer cell line MCF-7. The knock out cells had a 4-fold increase in the amount mtDNA in the nuclear fraction compared to cells that still had working YME1L1.

As a final experiment, they used a yeast strain, yme1-1, in which YME1 function was inactivated, to show that the human homologue, YME1L1, could suppress the migration of mtDNA to the nucleus.

This yme1-1 strain has a TRP1 gene encoded in the mtDNA instead of the nucleus. Since the gene cannot be read by the mitochondrial transcription machinery, the only way this yeast strain can survive in the absence of tryptophan is if the TRP1 gene moves from the mitochondrion to the nucleus. 

In their experiment, with vector alone, they got around 1000 TRP+ colonies with yme1-1. When they added back yeast YME1, this number dropped to less than 50 compared to the 100 or so they got when they added the human homologue, YME1L1. So YME1L1 can suppress mtDNA migration to the nucleus.  

Given that YME1L1 was mutated in just a subset of the cancers, it is unlikely that it is the only player in the mtDNA these authors found in the nuclei of cancer cells. But it does look like it is one way this can happen.

And it would have been very hard to fish out the human gene without the critical work that had been done in yeast previously. Yeast shows us the way again. #APOYG

by Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight

Tags: nuMt , nuMtogenesis , cancer , YME1L1 , MCF-7 , mtDNA , YME1 , colon cancer , CRISPR/Cas9

Feed a Cold, Starve a Cancer?

March 02, 2017

Unlike a fever, starving some cancers is actually a good treatment. And our friend yeast may be able to help. Image from

You may have heard the old wives’ tale of feed a cold, starve a fever. Turns out that this isn’t particularly good advice (although some studies do suggest that with a fever, you shouldn’t force-feed yourself). It also turns out to have probably originated in the 19th century and not from Chaucer in the 14th as many websites claim.

But while starving a fever is probably never a good idea, starving a cancer can be. Not by following the medical myth that since cancers use a lot of sugar, you can starve them by cutting down on sugar in your diet. Instead you can starve some cancers by denying them the amino acid asparagine (Asn).

On their way to becoming cancerous, acute lymphoblastic leukemia (ALL) cells lose their ability to make Asn. This means that unlike the cells around it, they need to pull Asn from the blood to make their proteins and to survive.

Doctors exploit this weakness by injecting L-asparaginase amidohydralase (L-ASNase) into patients which starves the cancer cell by depleting Asn levels in the blood. The cells around the cancer cells are fine because they can still make Asn.

Right now doctors use L-ASNase from two different bacterial sources: Escherichia coli and Erwinia chrysanthemi. But if a recent study by Costa and coworkers in Scientific Reports holds up, they might want to think about switching to using the Saccharomyces cerevisiae L-ASNase encoded by the ASP1 gene.

An older study had suggested that the yeast enzyme might be too weak to be useful. This new study finds that this is not the case.

The difference between the older study and this one was the purification protocol. The older study purified the native enzyme through multiple chromatography steps while this study used a single affinity chromatography step. The purified yeast and E. coli versions have comparable activity in this study.

They are also comparable in terms of being able to work with very low concentrations of Asn. This is important as Asn levels are very low in the blood.

What makes the yeast enzyme potentially better is that it is much worse at hydrolyzing a second amino acid, glutamine, than are the bacterial versions. This higher specificity for Asn is important because one of the major side effects of the current treatment is neurotoxicity caused by decreased levels of glutamine in the blood. Since the yeast version hydrolyzes glutamine at a lower rate, they predict patients may not suffer as badly from this side effect with the yeast version.

Of course this is all for naught if the yeast enzyme can’t kill cancer cells! Or if it kills cells indiscriminately.

The S. cerevisiae version was nearly as good as the E.coli version in tissue culture. After 72 hours of incubation, both versions had little effect on normal cells (HUVEC), and both were cytotoxic to the L-ASNase-sensitive cell line MOLT-4 with the E. coli version killing 95% of MOLT-4 cells and the yeast version killing 85% of them.


Move over dog, yeast is humanity’s best friend now. Image from pixabay.

Taken together these results suggest that the S. cerevisiae version may be an alternative to the bacterial versions. It may be able to kill cancer cells with fewer side effects.

But the yeast version is not the only alternative in town. Another group is engineering the E. coli version to lessen its propensity for hydrolyzing glutamine. Either way it looks like certain leukemia patients may be getting an effective cancer treatment with fewer side effects.

Beer, wine, bread, chocolate, and now maybe a treatment for a nasty form of leukemia. Yeast may be humanity’s best friend. #APOYG!

by Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight Yeast and Human Disease

Tags: Recombinant protein therapy , Acute lymphocytic leukemia , Proteins , cancer

Too Much of a Good Thing

November 09, 2016

Just like too much salt can ruin a cookie, so too can too many copies of a gene ruin a cell.Image from Wikimedia Commons.

Like a ruined cookie with too much salt, a cell can go haywire when it has too many copies of certain genes. And of course, cells can deal perfectly well with too many copies of other genes. Just like adding too many chocolate chips to your cookies might make an even better cookie!

Finding out which genes are like salt and which ones are like chocolate chips is of more than just general biological interest. It might help us to explain why cancer happens and to possibly find better treatments.

As you probably know, cancer cells are pretty messed up genetically. Their DNA is littered with mutations, rearrangements and somatic copy number amplifications (SCNAs).

A big reason for this genetic jumble is early DNA changes that increase the rate of mutations in a cell. This “mutator” trait makes a cell more likely to stumble on the mutations it needs to grow out of control or refuse to die.

In their new study in GENETICS, Ang and coworkers set out to find genes that can cause a mutator phenotype when they are part of a SCNA. In other words, which genes lead to an increased mutation rate when expressed at a higher level.

This is important because there are so many SCNAs in a typical cancer cell that it can be hard to figure out which ones matter and which ones don’t (or to put it into cancer parlance, to tell the drivers from the passengers). And despite all of the CRISPR hoopla and other mammalian resources, it would still be a very long process to find “dosage mutator” genes in cell culture and/or living animals.

Which is why Ang and coworkers used our favorite workhorse, the yeast Saccharomyces cerevisiae, to find genes that may cause an increased mutation rate when overexpressed.

The assay is conceptually simple. Yeast that have a functioning CAN1 gene do not survive in the presence of the drug canavanine. So these researchers looked for cells that did better in the presence canavanine when overexpressing a single gene. Presumably, they are surviving because that extra gene resulted in the CAN1 gene being mutated more often because of an increased mutation rate.

They found 37 genes that fit the bill, 18 of which that were involved in biological pathways known to affect genome stability. Combining this with previous studies that looked at gene deletions, this brings the grand total of suspected yeast mutator genes to 210.

Most of these 210 were identified because of mutations that made them stop working which can make figuring out why they cause the mutator phenotype relatively simple. For example, if a mutation kills a gene responsible for fixing DNA mistakes, then you are going to get more DNA mistakes in that cell. It is a little trickier to understand how extra copies of a gene might cause an increased mutation rate.

Ang and coworkers focused on trying to figure out the mechanism behind their top 5 dosage mutator genes: PIF1, MPH1, UBP12, RRM3, and DNA2. Since 4/5 of these code for helicases, they first checked to see if just being a helicase is enough to be a dosage mutator gene. It isn’t.

They retested 48 DNA helicases in their assay and found that none of them caused an increased mutation rate when mutated. There is more to a dosage mutator than being a helicase!

In the next set of experiments, they wanted to determine if the five strains, each overexpressing one of these five genes, had a higher mutation rate by the same mechanism. They tested this by determining the sensitivity of these 5 strains to 3 different DNA damaging agents. The idea is that if they share the same mechanism, they should have the same sensitivity profiles to each of these agents. They did not.

For example, overexpressing MPH1 resulted in a higher sensitivity to all three agents while overexpressing UBP12 only increased sensitivity to two of them. So each strain probably has an increased mutation rate for a different reason.

They next wanted to see if the increased mutation rate was due to a loss or gain of function. They did this by comparing the profiles of strains either deleted for or overexpressing the dosage mutator genes. The idea is that if overexpression leads to a loss of function, then deleting and overexpressing the genes should have the same profile. The three they could test like this did not.

The authors conclude from this that the increased mutation rate for MPH1, UBP12, and RRM3 is most likely due to the gain of an inappropriate function as opposed to a loss of function. In a final set of experiments, Ang and coworkers focused on what that new function might be in their strongest mutant, MPH1.


Finding out which genes are like salt and which are like chocolate chips can help us to explain why cancer happens and to possibly find better treatments. Image from flickr.

First they showed that of the three activities associated with Mph1p, only DNA binding and not its ATPase or helicase activities were important for it causing an increased mutation rate when overexpressed. From this they reasoned that perhaps Mph1p was displacing some other important DNA binding protein and that it was this displacement that was causing the increased mutation rate.

Through a set of experiments we don’t have time to go into here, they provided evidence that Mph1p was outcompeting the flap endonuclease Rad27p for DNA binding. This makes some sense as previous work had shown that deleting RAD27 causes mutation rates to go way up. So too much Mph1p keeps Rad27p from getting to where it needs to be with the end result being an increased mutation rate.

All this MPH1 work may have important implications in some human cancers. Nonsense or missense mutations in FANCM, the human homolog of MPH1, are known to make people more likely to get cancer. And there are examples of cancers where FANCM is overexpressed. Perhaps that overexpression results in an increased mutation rate in these cancers.

Yet again yeast is giving researchers new targets for, and new ways to think about, human disease. Thanks, yeast, for finding all of these mutator genes for us to investigate further! #APOYG!

by Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight Yeast and Human Disease

Tags: cancer , overexpression , mutator , MPH1 , genome-wide , forward mutation

Lessons from Yeast: Poisoning Cancer

April 06, 2016

Certain genes on an extra chromosome can be like poison. Other genes can be the antidote. Image from BedlamSupplyCo on Etsy.

In the book Dune, the mentat Thufir Hawat is captured by the evil Harkonnens and given a residual poison. He can only stay alive by getting a constant dose of the antidote. Once it is withdrawn, he will die.

A new study in the journal GENETICS by Dodgson and coworkers shows that the same sort of thing can happen to yeast that carry an extra chromosome. In this case, certain genes on the extra chromosome turn out to be like the residual poison. And a second gene turns out to be the antidote.

Once that second gene is deleted, the yeast cell dies. It has been deprived of its antidote.

This synthetic lethal phenotype isn’t just a cool finding in yeast either. Cancer cells invariably have extra and missing chromosomes. If scientists could find similar “antidote genes” in specific types of cancers and target them, then the cancer cell would die. And this would happen without damaging the other cells of the body that have a typical number of chromosomes.

The first thing these researchers did was to make separate yeast strains each with an extra chromosome I, V, VIII, IX, XI, XII, or XVI. The next step was to see what happens when every gene was deleted individually, one at a time, from each strain.

As expected, these yeast did pretty well when a gene on the extra chromosome was deleted. So, for example, a strain with an extra chromosome I tolerated a gene deleted from chromosome I. This makes sense as this just brings that gene back to its normal copy number.

But this was not the case with chromosomes VIII and XI. Here deleting genes on the extra chromosome often had a negative effect. This suggested that the screen probably had a high number of false positives and these researchers later confirmed this.

Likely reasons for the high number of false positives include the strain with the extra chromosome being W303 and the deletion strain being S288C, errors in the deletion collection itself, and what they refer to as neighboring gene effects. Basically this last one is the effect that deleting a gene has on nearby genes.

Once Dodgson and coworkers corrected for these problems, they found two broad sets of phenotypes – general and chromosome specific.

The general ones were the ones shared by most or all of the strains. These were deletions that affected the yeast no matter which chromosome they had an extra copy of.

For the most part, these genes were enriched for the Gene Ontology (GO) term vesicle-mediated transport, indicating that they have something to do with the transportation of substances in membrane-bounded vesicles. For example, deletion of MNN10, HOC1, and MNN11, genes all involved in protein transport and membrane-related processes, had a negative effect on many of the yeast strains with an extra chromosome. Consistent with this, brefeldin A, a drug that targets protein trafficking, negatively affected most of the strains.

Another gene that affected many of these strains when deleted was TPS1. This gene encodes a subunit of trehalose-6-phosphate synthase, a key enzyme for making trehalose, a molecule that helps yeast deal with stress. Perhaps not surprisingly, having an extra chromosome is stressful!

cancer cells

Cancer cells invariably have extra and missing chromosomes. Image from pixabay.

In addition to the genes that affect many strains with an extra chromosome, there were also genes that were chromosome specific. The best characterized of these was the EDE1 gene in the strain with an extra chromosome IX. Deleting EDE1 in this strain increased its doubling time by more than 80 minutes while only causing an increase of 5 minutes in the doubling time of wild type yeast. This was a severe phenotype in their assay.

They next tried to find which gene on chromosome IX might be responsible for the severe effect of deleting EDE1. Since EDE1 is known to be involved in endocytosis, they looked for genes involved in the same process. And they found one – PRK1.

The strain with a deleted EDE1 gene and an extra chromosome IX was rescued by deleting one copy of the PRK1 gene. The extra PRK1 gene was the poison and the EDE1 gene was the antidote.

If a similar pair could be found in cancers that often have the same set of extra chromosomes, then perhaps scientists could develop drugs that target an antidote gene. Now the cancer cells would die and the “normal” cells would be fine. Thanks again, yeast, for pointing us toward new ways to treat human disease.

by Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight Yeast and Human Disease

Tags: aneuploidy , synthetic lethal , cancer

Those Yeast Got Talent

March 11, 2015

Thriving in a yeast culture is a lot like becoming a finalist on American Idol—you need some minor advantage to hang around and then a big finish to dominate. Image by Michael Tanne via Wikimedia Commons

The winners of American Idol go through quite a selection process. They start out as one of tens of thousands of people who audition, and survive each cut until they are finally crowned.

At the first cuts, those with any sort of advantage are kept in the pool and the others dropped. As the cuts continue, contestants not only need to have had that stronger initial advantage (or a bit of luck), but they also need to have picked up some new skills from all of those off- and on-air performances.

Some of these contestants start with a lot of raw talent but then progress only a little, while others are able to hone their weaker initial talent with lots of practice. Once their numbers are winnowed down to a handful, it gets close to being anyone’s game because the remaining contestants are so talented.

A new study by Levy and coworkers paints a similar sort of picture for evolving populations of yeast. Very early on a whole lot of yeast stumble upon weak, beneficial mutations that keep them going in the population. These are the yeast that make the initial cut in the hurly-burly world of the Erlenmeyer flask.

At later times a few yeast end up with strongly beneficial mutations that allow them to start to dominate. These are the pool of yeast that are the finalists of the flask.

Of course a big difference (among many) between American Idol and the yeast in this experiment is that the pool of contestants in the flask hangs around—they are not thrown off the show. This means that some cell that didn’t do too well early on can suddenly gain a strongly beneficial mutation and begin to dominate. Until, of course, that cell is usurped by another more talented yeast, in which case that finalist will fade away unless it can adapt.

And this study isn’t just a fascinating dissection of evolutionary population dynamics either. It might also have implications for treating bacterial infections and even cancer.

Bacteria and cancer cells live in large populations with each cell trying to outcompete the others. By understanding the set of mutations that allow some cells to succeed against the others and become more harmful, researchers may be able to come up with new ways to treat these devastating diseases.

One of the trickiest parts of this experiment was figuring out how to follow lots of yeast lineages all at once in a growing culture. Levy and coworkers accomplished this by adding 500,000 unique DNA barcodes to a yeast population and using high-throughput DNA sequencing to follow the lineages in real time.

They set up two replicate cultures and followed them for around 168 generations. In both cultures the researchers saw that while most of the lineages became much less common, around 5% happened upon a beneficial mutation that allowed them to increase in number by generation 112.

In other words, around 25,000 lineages ended up with beneficial mutations that let them make the first cut in both cultures. This translates to a beneficial mutation rate of around 1 X 10-6 per cell per generation and means that around 0.04% of the yeast genome (around 5000 base pairs) can change in a way that confers a growth advantage.

But of course not all mutations are the same. Weakly beneficial mutations are very common, which means both cultures have plenty of these early on. This is why the replicate cultures behave so similarly up to around generation 80.

Eventually, though, a few yeast stumble upon stronger, more beneficial mutations. Since these are rarer and harder to get, each replicate culture gets them at different generations. This is why the cultures begin to diverge as the 100 or so of the strongest beneficial mutations begin to dominate.

The experiment did not go on for long enough to see many double mutations. In other words, it was very rare in this experiment to see a yeast lineage succeed because it had developed additive beneficial mutations. This is because there simply wasn’t enough time for a yeast cell to get a beneficial mutation and establish itself and then have one of its lineage gain and establish a second beneficial mutation. There was no Jennifer Hudson who came in 7th but then went on to win a Grammy and an Oscar.

When a cancerous tumor is developing, however, there is plenty of time for multiple “beneficial” mutations to be established. These mutations are only beneficial for the tumor; they are devastating for the person with cancer. This is why it is so critically important to understand not only which mutations are implicated in cancer, but also the dynamics of how they accumulate in the cancer cell population during progression of the disease. Talented yeast in the hands of talented researchers are helping us figure this out.

by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight

Tags: evolution , Saccharomyces cerevisiae , cancer

Using Yeast to Find Better Cancer Treatments

October 24, 2013

Current cancer treatments are a lot like trying to destroy a particular red plate by letting a bull loose in a china shop.  Yes, the plate is eventually smashed, but the collateral damage is pretty severe.

Yeast may help us find ways to treat cancers without all that collateral damage.

Ideally we would want something a bit more discriminating than an enraged bull.  We might want an assassin that can fire a single bullet that destroys that red plate. 

One way to identify the assassin that can selectively find and destroy cancer cells is by taking advantage of the idea of synthetic lethal mutations.  “Synthetic lethal” is a genetic term that sounds a lot more complicated than it really is.  Basically the idea is that mutating certain pairs of genes kills a cell, although mutating each gene by itself has little or no effect.

A synthetic lethal strategy seems tailor made for cancer treatments.  After all, a big part of what happens when a cell becomes cancerous is that it undergoes a series of mutations.  If scientists can find and target these mutated genes’ synthetically lethal partners, then the cancer cell will die but normal cells will not.

This is just what Deshpande and coworkers set out to do in a new study in the journal Cancer Research.  They first scanned a previous screen that looked at 5.4 million pairwise interactions in the yeast S. cerevisiae to find the best synthetic lethal pairs. They found 116,000 pairs that significantly affected cell growth only if both genes in the pair were mutated.

A deeper look into the data revealed that 24,000 of these pairs had human orthologs for both genes. In 500 of these pairs, at least one of the partner genes had been shown to be mutated in certain cancers. Using a strict set of criteria (such as the strength and reproducibility of the synthetic lethal effect, and the presence of clear one-to-one orthology between yeast and human), the authors narrowed these 500 down to 21 pairs that they decided to study in mammalian cell lines.

When the authors knocked down the expression of both genes in these 21 gene pairs in a mammalian cell line, they found six that significantly affected growth.  They focused the rest of the work on the strongest two pairs, SMARCB1/PMSA4 and ASPSCR1/PSMC2.  These mammalian gene pairs correspond to the yeast orthologs SNF5/PRE9 and UBX4/RPT1, respectively.

The authors identified two separate cancer cell lines that harbored mutated versions of the SMARCB1 gene.  When this gene’s synthetic lethal partner, PMSA4, was downregulated in these cancer lines, the growth of each cell line was severely compromised. The same was not true for a cell line that had a wild type version of SMARCB1—this cell line was not affected by downregulating PMSA4.  The authors used a synthetic lethal screen in yeast to identify a new cancer target which when downregulated selectively killed the cancer without killing “normal” cells.

This proof of principle set of experiments shows how the humble yeast may one day speed up the process of finding cancer treatments without all those nasty side effects (like vomiting, hair loss, anemia and so on).  Yeast screens can first be used to identify target genes and then perhaps also to find small molecules that affect the activity of those gene products.  Yeast may one day tame the raging bull in a china shop that is current cancer treatments.

by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight Yeast and Human Disease

Tags: Saccharomyces cerevisiae , synthetic lethal , cancer

Alternative Ways to Increase a Cell’s Shelf Life

June 05, 2013

Like milk or eggs, most cells with linear chromosomes have a shelf life. Each time these cells divide, they lose a little off the end of their chromosomes. Eventually, too much is lost and the cells crap out. Or, to use a more scientific term, they become senescent.

expiration date

Cells have lots of ways to keep their telomeres long and extend their “cell-by” dates.

But this is not the fate of every cell. Some cells, like those that go on to become sperm or eggs, use a reverse transcriptase called telomerase to extend their telomeres as part of their normal life cycle. And they aren’t the only ones. Around 85% of cancers hijack the telomerase and use it for their own nefarious ends.

The other 15% of cancers use a variety of different mechanisms to keep their telomeres from getting too short (Cesare and Reddel, 2010). All these different ways are lumped together in a single category called alternative lengthening of telomeres or ALT. The telomeres are lengthened in these cells by recombination with other telomeres, either those on other chromosomes or those that exist as shed, extrachromasomal bits. 

While telomere extension may keep cells alive, it can sometimes be a double-edged sword. A double stranded DNA break is usually recognized as DNA damage. However, if the break happens near a telomere seed (a sequence that looks like a telomere), then the DNA damage response can be suppressed and the end can be extended into a new telomere, in a process called chromosome healing. But now the cell could be in trouble, with new, partial chromosomes being created and getting pulled this way and that.

In a new study out in GENETICS, Lai and Heierhorst decided to investigate whether chromosome healing happens in yeast cells that have stayed alive because of ALT.  What they found was that chromosome healing at telomere seeds was suppressed in these post-senescence survivors.

They created these ALT dependent, post-senescence survivors from an est2 mutant strain that lacked the catalytic subunit of telomerase.  Without telomerase, the only way for these cells to survive is by using ALT. 

In the first experiment, they looked at whether the post-senescence survivors could create a new telomere by chromosome healing.  The authors used a galactose inducible HO endonuclease to create a double stranded break near an 81 base pair sequence known to be a telomere seed sequence in wild type. 

Broken DNA usually signals cells to pause the cell cycle until the damage is repaired. This is known as the DNA damage checkpoint. During chromosome healing in wild type, this checkpoint is suppressed so the chromosome break isn’t recognized as DNA damage.

In the post-senescence survivors, even after 21 hours there was no evidence of a telomere forming.  They didn’t suppress the DNA damage checkpoint either.

Lai and Heierhorst determined that these ALT-dependent cells could still repair a different break that was not near a telomere seed sequence. They just couldn’t repair the break at the telomere seed. And this wasn’t because the DNA damage checkpoint was active. When they prevented the checkpoint by using a rad53 mutant, the telomere still wasn’t repaired.

Instead, the post-senescence survivors eventually repaired the break by some other mechanism, generating lots of differing products in the process. When they repaired breaks at sites that were not telomere seeds, they were able to use homologous recombination. But homologous recombination was suppressed at the telomere seed site.

Since ALT is used in cancer cells, and happens most often in some of the least-curable types of cancer, whatever we can learn about the process in yeast is valuable. It may give us clues on how to change the expiration date of those cancer cells to “ASAP”.

by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight Yeast and Human Disease

Tags: DNA damage checkpoint , Saccharomyces cerevisiae , cancer , telomere

Breaking Up is Hard to Do

May 01, 2013

When a cell goes cancerous, its chromosomes get seriously messed up. Pieces get deleted, duplicated, mixed and matched. One of the worst things that can happen, in terms of a cell keeping its chromosomes together, is that a chromosome ends up with two centromeres.

Tug of War

When a chromosome gets pulled in two directions, it tears. No one wins that tug-of-war.

A centromere is the part of a chromosome that gets attached to the spindle so it can be moved to the right place during cell division. When there are two centromeres, both get attached and something has to give if the chromosome is pulled in two different directions. Often this means that the DNA of the chromosome breaks between the two centromeres.

This isn’t as simple as the rope breaking during a tug-of-war, though. A chromosome can withstand around 480 piconewtons of force before breaking, but the force exerted by the spindle that breaks the chromosome between the centromeres is just one piconewton or less. Clearly something else is going on to create those breaks!

In a new study out in GENETICS, Song and coworkers looked more closely at what happens when a dicentric chromosome breaks. They used a diploid strain of S. cerevisiae to show that where the DNA breaks is not random. In their experiments, the break tended to happen within 10 kilobases (kb) of the “foreign” centromere.

They used a previously described system where a conditional centromere was placed 50 kb from the normal centromere on chromosome III. This conditional centromere is only turned on in the absence of galactose. They then mated this strain to an unrelated one, resulting in a diploid with a high degree of heterozygosity. In other words, the chromosomes from each strain were different at lots of different places.

Song and coworkers streaked diploids from isolated colonies to a plate lacking galactose and then investigated how the yeast managed to resolve its double centromere issue. Two key ways that the yeast could eliminate the additional centromere involve crossing over between sister chromatids or break-induced repair. They focused on these as it is relatively easy to identify the DNA breakpoint. Because the two chromosomes in each pair are so different, they just needed to look for a loss of heterozygosity. In other words, where did the chromosomes become the same?

When they looked through 27 colonies, they found that the breaks weren’t randomly spread between the centromeres. Surprisingly, about half of them happened very near the conditional centromere. To make sure that there wasn’t something special about these sequences, they looked at two different strains with the conditional centromere located in different places on chromosome V instead of III. They obtained similar results.

Since the force exerted by the spindle isn’t enough to break the chromosome, there must be enzymes involved in creating the DNA breaks. But why do they prefer the region near the conditional centromere? One possibility is that the DNA there is stretched and is more open to enzymes. As the chromosome is being pulled apart, an enzyme gets into this region and manages to cut the DNA.

Although we don’t have time to go into it here, the paper also has a lot to say about the variety of ways that a diploid cell resolves its extra centromere in a way that allows it to survive. And that will inform the study of chromosome dynamics in all kinds of cells.

by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight

Tags: DNA repair , Saccharomyces cerevisiae , cancer

Hate the CIN, Love the CINner

March 21, 2013

At first our favorite small eukaryote, S. cerevisiae, might not seem like a great model for cancer studies. After all, budding yeast can’t tell us anything about some of the pathways that go wrong in cancer, like growth factor signaling. And it clearly can’t help explain what happens in specific tissues of the human body. But in other ways, it actually turns out to be a great model.

We don’t need to forgive yeast for its CINs – we can be glad that it’s a CINner!

For example, all the details of cell cycle control were originally worked out in yeast.  And now a whole new batch of genes has been found that influence a phenomenon, chromosome instability (CIN), that is important in both yeast and cancer cells.

As the name implies, chromosomes are unstable in cells suffering from CIN. Big chunks of DNA are lost, or break off and fuse to different chromosomes, turning the genome into an aneuploid mess. And this mess has consequences.

CIN can cause new mutations or make old ones have a stronger effect.  Eventually these mutations can affect genes that are important for keeping a cell’s growth in line.  Once these are compromised, a tumor cell is born. 

Since CIN is pretty common in yeast, we might be able to better understand it in cancer cells by studying it in yeast. The Hieter lab at the University of British Columbia has come up with a powerful screen to get yeast to confess why it CINs. 

A previous study from the group set the stage by finding a large group of mutants that have CIN phenotypes, implying that those genes are involved in keeping chromosome structure stable. In a new paper in G3: Genes, Genomes, Genetics, van Pel et al. uncovered the network of interactions among the genes in this set, using synthetic genetic array (SGA) technology. And they confirmed that the human homologs of some of these genes interact in the same way as in yeast, making them potential targets for cancer therapies.

The idea behind SGA studies is that if two proteins are involved in the same process, then a strain carrying mutations in both of their genes will be much worse off than a strain carrying either single mutation. In the worst case, the double mutant will be dead. This is known as a synthetic lethal interaction.

Yeast is a great model for doing these sorts of studies on a very large scale.  We can construct networks showing how lots of different genes interact, and most importantly, find the genes that are central to many interactions.   These “hubs” are likely to be the key players in those processes.

The researchers looked specifically for interactions between genes that are involved with CIN in yeast and are also similar to human cancer-related genes. They came up with various interaction hubs that will be interesting research subjects for a long time to come. In this study, they focused on one of these: genes involved with the DNA replication fork.

One of these in particular, CTF4, is a hub for both physical and genetic interactions. Unfortunately, Ctf4p doesn’t look like a good target for chemotherapy. It’s thought to act as a scaffold, and lacks any known activity that could potentially be inhibited by a drug. However, the interaction network around CTF4 that van Pel et al. uncovered suggests another way to target this hub. If a gene that interacts with CTF4 itself has a synthetic lethal interaction with another gene, and we could re-create the synthetic lethal phenotype in a cancer cell, we might be able to knock out the whole process. And that is just what they found in human cells.

First the authors identified a couple of human genes that were predicted from the yeast screen to be close to human CTF4 in the interaction network and to have a synthetic lethal interaction with each other. They then lowered the expression of one using small interfering RNA (siRNA), and reduced the activity of the other with a known inhibitor. Neither treatment alone had much effect, but combining them significantly reduced cell viability.

Since cancer cells frequently carry mutations in CIN genes, it should be possible to create a synthetic lethal interaction, guided by the yeast interaction network, where one partner is mutated in cancer cells (equivalent to using siRNA in this study) and the other partner is inhibited with a drug. Since it relies on a cancer-specific mutation, this approach has the potential to selectively target cancer cells while not disturbing normal cells, the ultimate goal for chemotherapy.

by Maria Costanzo, Ph.D., Senior Biocurator, SGD

Categories: Research Spotlight Yeast and Human Disease

Tags: yeast model for human disease , DNA replication , Saccharomyces cerevisiae , cancer

Cancerous Avalanche

March 05, 2013

Cancer often gets going with chromosome instability.  Basically a cell gets a mutation that causes its chromosomes to mutate at a higher rate.  Now it and any cells that come from it build mutations faster and faster until they hit on the right combination to make the cell cancerous.  An accelerating avalanche of mutations has led to cancer.


A mutation causing chromosomal instability can start an avalanche that leads to cancer.

There are plenty of obvious candidates for the genes that start these avalanches: genes like those involved in segregating chromosomes and repairing DNA, for example.  But there are undoubtedly sleeper genes that no one has really thought of.  In a new study out in GENETICS, Minaker and coworkers have used the yeast S. cerevisiae to identify three of these genes — GPN1 (previously named NPA3), GPN2, and GPN3.

A mutation in any one of these genes leads to chromosomal problems.  For example, mutations in GPN1 and GPN2 cause defects in sister chromatid cohesion and mutations in GPN3 confer a visible chromosome transmission defect.  All of the mutants also show increased sensitivity to hydroxyurea and ultraviolet light, two potent mutagens.  And if two of the genes are mutated at once, these defects become more severe.  Clearly, mutating GPN1, GPN2, and/or GPN3 leads to an increased risk for even more mutations!

What makes this surprising is what these genes actually do in a cell.  They are responsible for getting RNA polymerase II (RNAPII) and RNA polymerase III (RNAPIII) into the nucleus and assembled properly.  This was known before for GPN1, but here the authors show that in gpn2 and gpn3 mutants, RNAPII and RNAPIII subunits also fail to get into the nucleus. Genetic and physical interactions between all three GPN proteins suggest that they work together in overlapping ways to get enough RNAPII and RNAPIII chugging away in the nucleus.

So it looks like having too little RNAPII and RNAPIII in the nucleus causes chromosome instability. This is consistent with previous work that shows that mutations in many of the RNAPII subunits have similar effects.  Still, these genes would not be the first ones most scientists would look at when trying to find causes of chromosomal instability. Score another point for unbiased screens in yeast leading to a better understanding of human disease.

by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight Yeast and Human Disease

Tags: chromosome instability , Saccharomyces cerevisiae , RNA polymerase II , RNA polymerase III , cancer

Cancer’s Chromosomal Chaos Explained (Partly)

June 01, 2012

Because they have the wrong number of chromosomes, cancers can sample many different genetic combinations.

One reason cancer is so tricky to treat has to do with its adaptability.  It can quickly try out new genetic combinations until it hits upon one that can survive whatever treatment a doctor is currently throwing at it.  The result is return of the cancer after remission.

One way cancer is able to change its genetics so rapidly has to do with chromosome instability.  The number of chromosomes in a cancer cell is much less stable than in a normal cell.  This allows the cancer cell to constantly explore a wide range of chromosomal combinations.

It is still an open question how this dynamic instability happens.  The gene-centric theory suggests that mutations in key genes are the main driving force.  The chromosome-centric model says that having the wrong number of chromosomes is the critical component.

Distinguishing between these two models using cancer cells has proven difficult because these cells always have mutated genes.  There is simply no way to look at just chromosome numbers in this system.  This is where yeast can help.

In a recent paper published in PLoS Genetics, Zhu and coworkers used yeast to explore whether altered chromosome number was sufficient to explain chromosome instability.  They found that chromosome numbers alone can explain some but not all of chromosomal instability.

The authors created various chromosomal combinations in yeast by sporulating isogenic triploid yeast cells.  These cells had different numbers of genetically identical chromosomes.  They then explored the stability of each chromosome number combination using both FACS and qPCR.

What they found was that chromosome number certainly impacted chromosomal stability.  Chromosome number became less and less stable as the chromosome number veered further and further from the haploid state.  Of course, once the cells became diploid, stability returned. 

The authors explain this with the idea that there is only so much cellular machinery to move chromosomes to the proper place during mitosis.  As more and more chromosomes are added to the cell, the machinery becomes increasingly taxed, resulting in more and more errors. 

But once the diploid state is reached, all the genes are present to make twice as much mitotic machinery.  Now stable chromosome segregation can happen.

This was the broad pattern Zhu and coworkers observed but it certainly wasn’t the whole story.  The authors found islands of stability in the chromosomal chaos. 

For example, very often when there were equal numbers of chromosome VII (ChrVII) and chromosome X (ChrX), the chromosome number was more stable than predicted.   They explored this further and found evidence that suggested that at least part of this was due to the MAD1 gene on ChrVII and the MAD2 gene on ChrX. 

Stable chromosome numbers required that these genes be present in a 1:1 ratio.  Once the ratio strayed from one, chromosomal instability increased.  But these genes don’t explain everything.  There were unstable combinations where the MAD1/MAD2 ratio was correct.  As might be expected, there are other gene combinations that can lead to instability as well.

So incorrect chromosome number alone can explain the chromosomal instability seen in cancer cells.  But genes clearly play a role too, as evidenced by the islands of stability and the MAD1 gene and MAD2 genes.  As usual, reality is probably a combination of the two models. 

So it looks like chromosome number does play an important role in chromosomal instability.  Too many chromosomes may overtax the mitotic machinery so that chromosomes end up mis-segregated.

by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight Yeast and Human Disease

Tags: genetics , cancer , yeast , chromosomal instability , Saccharomyces cerevisiae , chromosome