New & Noteworthy

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 Once it is withdrawn, he will die.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, cancer, synthetic lethal

Smoothing Over an Extra Chromosome

August 22, 2013

Let’s say you had a rock you had to move that was way too heavy for you to lift. You could either start lifting weights until you could move it yourself or get someone to help you. Most of us would start texting our friends pretty quick.

Jon Bon Jovi used scissors to go from fluffy to smooth. Yeast uses an extra chromosome XVI.

Turns out our friend S. cerevisiae can be the same way. Many strains of this yeast can exist as either a fluffy colony or a smooth one. In a new study, Tan and coworkers show that some of these strains switch between the two by gaining or losing one of their chromosomes. They’d rather “get” an extra chromosome than try to gain a mutation that activates the necessary gene(s).

In this study, the authors found a strain where around one in a thousand yeast switched between fluffy and smooth colonies. As the smooth colonies grew, they developed “blebs” – little bumps on the smooth colonies.  Turns out these were yeast that switched back to the fluffy morphology.  The authors set out to explore why this strain switches at such a high rate and why it would want to. 

A first look showed that when this yeast strain went from fluffy to smooth, it gained an extra copy of chromosome XVI.  When the new smoother yeast lost this extra chromosome, it reverted back to its fluffy look.  A harder look showed that an extra chromosome XVI wasn’t the only way to a smoother yeast.  Occasionally the fluffy to smooth change could be caused by an extra copy of chromosome III, X, or XV, and an extra copy of V caused a slightly smoother colony.

These results suggest a couple of different ways that an extra chromosome might be leading to a smooth colony.  One is that just having extra DNA around causes the change.  The other is that a variety of genes can cause the change when present in higher than normal doses.  The researchers show pretty convincingly that the second reason is probably the right mechanism.

First off they show that not all extra chromosomes are created equal.  Some lead to a very sickly yeast while others have no effect on fluffiness.  Just having extra DNA around is probably not the culprit.

The authors next set out to figure out exactly what was going on with chromosome XVI.  Through a series of deletion studies, they found a single gene responsible for the fluffy to smooth shift – DIG1.  Overexpression of this single gene caused fluffy colonies to turn smooth.  Presumably there are other genes on some of the other chromosomes that serve a similar function.

They next set out to determine why yeast would ever want to do this.  Turns out that, as you might expect, each phenotype has an advantage in a different situation.  On a solid surface the fluffy strain did better, while the smooth one did better in liquid media.  

The “extra chromosome option” is actually a great way for a sedentary beast like yeast to quickly deal with a new situation.  Gaining an extra chromosome is much simpler than gaining a new mutation that up-regulates a gene under certain situations.

Figuring out this mechanism of fluffy to smooth transitions isn’t just fun biology either.  It may also point us in new directions for treatments for a variety of diseases, including drug-resistant cancers and microbial infections. 

In many cases, these cells become resistant because their chromosome number has changed from what is considered the norm.  If we could find a way to force cells to maintain the correct number of chromosomes, we might be able to make them more susceptible to drugs.  As usual, yeast studies are much more than fluff…they smooth the way to the future.

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

Categories: Research Spotlight

Tags: aneuploidy, Saccharomyces cerevisiae