New & Noteworthy

Cancer’s Chromosomal Chaos Explained (Partly)

June 01, 2012

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

Yeast, Place your Bets

May 25, 2012

Life is a balancing act.  An organism needs to grow and divide as fast as possible in its current environment.  But it also needs to be able to survive when the environment changes.

One way nature has come up with to deal with this balancing act is called bet hedging.  Basically some members in a population grow well in one set of circumstances and another set grows well in another.

Now this makes obvious sense when looking at members of a species that vary genetically.  Where it gets interesting is when bet hedging happens in a clonal population.

The idea is that even though they share the same DNA, there are epigenetic differences that cause subtle variations in gene expression levels between individuals.  These differences in gene expression patterns result in altered survival rates under different circumstances.

This phenomenon has been difficult to study because researchers need to focus on individuals and not populations.  Growth curves in liter flasks are of little use.

But now Levy and coworkers have come up with a new high throughput assay that allows them to look at how a few individuals are growing.  This has allowed them to quantitate how different individuals grow in a population and why the slower growers and/or the elderly are better able to survive stress.

The assay uses time-lapse bright-field microscopy to look at tens of thousands of microcolonies all at once.  What they find is a wide range of growth rates.  Somewhere between 1.3-10% of microcolonies grow at less than half the rate of the population as a whole (the number depends on the strain). 

The researchers identified multiple genes that impacted the range of growth rates within a population without necessarily affecting the overall growth rate.  In other words, this phenomenon isn’t simply due to chance–there are key genetic factors that help determine the amount of individual to individual variation in a population.

Levy and coworkers focused on Tsl1p, a component of the trimeric complex that synthesizes trehalose.  What they found was that those cells that made more Tsl1p divided less often and so grew more slowly.  Remember again, this is in a clonal population.

Trehalose is thought to help preserve proper protein folding under stress.  So the idea is that some subset of individuals is primed for stress but that in turn, this preparation makes them grow more slowly.  And this is just what the researchers found.

When they subjected colonies to heat stress, those that made lots of trehalose were more likely to survive.  But the survivors didn’t stay slow growing for long.  After multiple generations, the population returned to the original growth rate with the original individual to individual variation.  The phenotype was reversible.

Finally the researchers discovered that older yeast cells tended to make more trehalose and so survived stress better.  It may be that as a yeast cell gets older, it makes more Tsl1p which helps to set up the range of growth rates among individuals.  This may be one way individual to individual variation has evolved in yeast.

Bet hedging is obviously a great way to ensure the survival of a clonal population. Under ideal conditions, the fast growers can grow like mad, spreading themselves far and wide.  But when conditions become more hostile, a few slower, tougher individuals can survive to keep the population alive.

Video showing that slow growers survive heat shock and then revert to fast growers.

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

Categories: Research Spotlight

Tags: bet hedging, epigenetics, Saccharomyces cerevisiae, Tsl1, yeast

Sopping up Uranium with Yeast

March 23, 2012

Yeast may be good for more than making bread and beer or understanding how eukaryotes like humans work.  They may also be useful for cleaning up high volume, low concentration waste uranium (think uranium waste water).

The idea would be to add yeast to the contaminated area, have the yeast take the uranium up, put the yeast into radioactive waste and repeat with new yeast.  This would be a relatively cheap, simple way to detoxify this form of radioactive waste.

An obvious way to improve on this idea is to identify yeast strains that can accumulate more uranium than the wild type strain.  In a new study out in Geomicrobiology Journal, Sakamoto and coworkers have started down this path by identifying genes that allow yeast to grow in the presence of uranium and those involved in uranium accumulation.

They did this with two different screens using a set of 4,098 non-essential gene deletion strains.  In the first they identified 13 strains that grew more poorly than wild type at 0.5 mM uranium.  And in the second, they identified 17 strains that accumulated less uranium than wild type.

There was very little overlap between the two sets of strains suggesting different pathways (or sets of pathways) may be involved in accumulation and growth.  However, there were two deletion strains that showed up in both screens.  Both of the identified genes, PHO86 and PHO2, are involved in phosphate metabolism.

These genes definitely make sense.  A number of previous studies had hinted strongly that uranium accumulates on the surface of yeast in the form of insoluble uranium-phosphate complexes. 

The idea behind the importance of these genes is that yeast deals with higher uranium levels by scavenging more phosphate.  When genes involved in this process are knocked out, the yeast can’t get the extra phosphate it needs to form the insoluble uranium phosphate complexes.  Now it grows poorly and has less uranium on its surface. 

It will be interesting to see how the other genes are involved in uranium survival or accumulation.  Perhaps one day researchers will be able to turn yeast into a grade A uranium sponge.  Here’s hoping they can!

For those really interested, here is a list of the genes identified in each screen:

Uranium sensitive: PHO2, PHO84, PHO86, PHO87, VPS74, ENT5, CPR1, GLO2, OPI1, ATG15, PTC6, SLC1, and uncharacterized ORF, YPR116W.

Uranium accumulation: OPI1, PHO86, APL4, PEX10, VPS74, PHO2, SPT20, GAL11, SWP82, IVY1, FLO1, DIT2, RPL2A, and uncharacterized ORFs, YGL214W, YJR098C, YNL035C, and YPR116W.       

A nice lecture on bioremediation (using biology to clean up toxic waste)

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

Categories: Research Spotlight

Tags: bioremediation, nuclear waste, Saccharomyces cerevisiae, uranium, yeast

Multicellularity a Snap? Maybe so…

February 10, 2012

Some people might think that the transition from single-celled creatures to multi-cellular ones must have been tough.  After all, single celled organisms ruled the world for the first one or two billion years of life here on Earth. 

And yet, all multi-celled beasts didn’t evolve from the same ancestor.  Current theories are that multicellularity evolved dozens of times over the ages.  In fact, all of the transitional stages of multicellular life can be seen in the volvocine green algae species around today.  So maybe it isn’t so tricky after all.

Using a very clever screen in yeast, Ratcliff and coworkers have shown that they can get crude multicellular life to evolve in the lab.  Basically they only let the yeast that settled easily to the bottom of a shaking flask go on to reproduce.  Within 60 or so days, they had the beautiful, snowflake-like, multicellular beasts made up of multiple yeast cells shown in the image to the right.

Of course multicellular is more than having a bunch of cells stuck together.  Heck, yeast do that now in something called flocs.  No, to be multicellular, these yeast need to reproduce in a way that generates new multicellular yeast and to have specialized cells.  The snowflake yeast from this experiment did both.

These yeast did not reproduce by creating sperm and eggs that combine to generate progeny.  Instead they reproduced more like a lot of plants do.  They produced smaller versions of themselves which then went on to grow to “adulthood.”  Multicellular life gave birth to more multicellular life.

Cells within these snowflakes were also willing to die for the common good.  For example, the cell where the juvenile snowflake was attached would undergo apoptosis so the juvenile could be released.  No single-celled organism would willingly take that kind of hit for other cells.

So it looks like these researchers managed to evolve multicellular organisms from single-celled ones in just a few months.  Pretty amazing what can be learned from yeast!

Of course some care is needed here.  Yeast actually evolved from a multicellular ancestor so some sort of memory of multicellular life may still be lurking in its genes.  If true, this might make the transition from one to many simpler in yeast than in other single-celled organisms. 

This is why the researchers plan to try similar experiments with single celled organisms that have been single cells throughout their evolutionary life.  Then they’ll have an even better idea about how easy the “one to many cells” transition is.

Multicellular yeast having babies.

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

Categories: Research Spotlight

Tags: evolution, multicellular, Saccharomyces cerevisiae, yeast

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