Wednesday, January 9, 2013

Haploid, Diploid, And Those You Should Avoid

Biological concepts – ploidy, polyploidy, aneuploidy, cancer, therapy-induced senescence

Do your genes or your environment make you
who you are. The cop out answer would seem to
be that it takes both. But it is definitely true.
Certainly, how you are raised affects your outlook.
But we have known for a few years now that your
genes are affected by your environment as well.
What happens to you determines how your genes
are expressed – it’s called epigenetics (epi = beyond).

We can argue about whether your genes or your upbringing is more important for making you who you are (nature vs. nurture), but no one is going to argue that your chromosomes aren’t important in the process.

Mom and Dad both contributed to your chromosome number, you got a copy of each chromosome from each parent, so you ended up with 2 copies of each, a state of being diploid (di = two, ploos = fold, and –oid = like). So what if you weren’t diploid, is it a good thing or a bad thing? You know there must be exceptions.
Let’s start with how offspring get their DNA. In sexual reproduction, the rule is that the female and male each contributes half the genetic material to the offspring. Humans, for example, have 23 different pairs chromosomes, one from each pair comes from the egg and one from the sperm.

The egg and sperm then each have just half of the full complement of chromosomes. Therefore, the egg and sperm are termed haploid (hap = single). Ploidy in general refers to the number of copies of whole sets of chromosomes in the nucleus. The haploid sperm meets the haploid egg, they date for a while, and then voila, a diploid zygote that turns into a teenager one day.

Mitosis is the replication of cells in which each new cell gets 2 copies of each chromosome, while meiosis is the process where in cells split and give one chromosome from each pair to a developing sperm or egg. Simple, yet it doesn’t always work perfectly. Meiosis may foul up and make eggs or sperm with a diploid number of chromosomes. If a diploid sperm meets a haploid egg, then the resulting zygote will have three copies of each chromosome – triploidy. Since all cells develop from this single zygotic cell, all the following mitoses will produce triploid cells.

Polyploid chromosomes can be anything over
the normal complement of two copies of each
chromosome. Remember that additional
individual chromosomes does not make a cell
polyploidy; polyploidy refers to additional SETS
of all the chromosomes.
In a similar unfortunate incidence, a newly formed diploid zygote may replicate its DNA twice before it splits, leading to a tetraploid (4n) embryo. It is rare, but it does occur. Triploid, tetraploid, and even higher numbers of chromosome sets are possible (hexaploid = 6n, dodecaploid = 20n), they are all called polyploidy (many fold).

Fully 10% of spontaneous abortions in humans are due to the presence of polyploid fetuses, usually triploid or tetraploid. There are regulatory patterns in effect in mammals that just can’t deal with additional copies of chromosomes and the genes they hold.

For every gene whose product performs a function, our cells make a certain amount of that protein, not too much or to little - just enough to do its job.  What if we then add two more copies of that gene by being tetraploid? This is called dosage imbalance, and it may cause double the amount of that protein to be made, or even more. This could severely affect that biochemical pathway.

If there is not a regulatory mechanism to account for the additional protein, the polyploid problem can be big enough to cause spontaneous abortion. Now imagine that the genes that produce regulatory proteins to control whole biochemical pathways are there in higher numbers – it isn’t hard to understand that this could wreak havoc with fetal development.

Females usually have two copies of the X chromosome, but only one functions in any given cell. This X inactivation is one type of dosage compensation and we will talk about it later in this series of posts. With additional X chromosomes, X inactivation controls may not be strong enough to limit the effect of X-linked genes. The problem could also occur in males with extra Y chromosomes, since there isn’t a Y inactivation pathway. Sex chromosomes account for sexual development of the fetus; polyploidy can lead to problems in development that are incompatible with survival.

The karyotype (spread of chromosomes) on the left is from
a normal cell. It has 23 paired chromomsome copies,
including the sex chromosomes at the bottom right. The
karyotype on the right is from a cancer cell. It has two
copies of a few chromosomes, three or four copies of others,
and even 2 Y chromosomes. Normal cell is diploid, while
the cancer cell is aneuploid. The more aneuploid the tumor
cells are, the poorer the outlook for the patient.
But this isn’t the only problem that polyploidy can cause in mammals. Almost every cancer cell shows changes in ploidy. In many cases, there are too many copies of some chromosomes, two copies of others, one copy of yet others. All of these are referred to as states of aneuploidy (an = not, and eu = good).

Current hypotheses state that aneuploidy in most cancers starts out as tetraploidy; a 4n condition resulting from inappropriate replication without mitosis (called endomitosis, more on this next week), or from the merging of two cancer cell nuclei to form one 4n cell.

The formation of tetraploid cancer cells has many ramifications, including messing up the cell's system for dividing up the chromosomes between the daughter cells during mitosis. If they don’t get divided equally, you could end up with some having too many copies of individual chromosomes, and some with too few copies – aneuploidy. So what induces tetraploidy in the cancer cells? We don’t really know, but is the source of a current argument in the cancer field.

Cancer cells can enter senescence due to a number
of stressors, like cancer drugs and radiation.
Additional stimuli include other kinds of stress,
including oxygen stress, DNA damage, and mitotic
problems. This was said to be the end of the story
until it was discovered that some cancer cells can
escape senescence and come back with a vengeance.
When cancer cells are exposed to chemotherapeutic drugs or radiation (as in treatment for cancer), they sometimes just go into a holding pattern. They don’t die, but they don’t replicate or grow either; they enter a therapy-induced cellular senescence (TCS). Treat the cancer early enough and you could put cancer on hold; maybe even give your immune system time to kill the offending cells.

Sounds good doesn’t it? Some groups are looking to use TCS in cancer therapy, but other groups are warning that TCS may be a harbinger of bad things to come. Some cancer cells can escape TCS and become very nasty.

A group in Seattle has done significant work in this area, first showing that it is a cell cycle regulating protein called cdc2/cdk1 that allows the cells to enter senescence. Their 2011 paper showed that this also promotes expression of proteins that stop the cell from undergoing apoptosis (killing itself). If the cells escape from TCS, they are now primed to resist all treatment efforts to make them undergo apoptosis. They may be super-cancer cells.

This same group published in 2012 that TCS also promotes polyploidy development in the cancer cells. Their data indicates that polyploid development increases the chance that the cancer cells will escape senescence and begin to proliferate again. Their longitudinal study also indicated that TCS induction led to poorer outcomes for a group of patients with a certain type of lung cancer. Maybe telling cancer cells to go to sleep isn’t such a good idea, they don’t wake up nicely.

So polyploidy in mammals is a big no-no! Cancer and abortion aren't harbingers a of a long-life. But there is an exception - I give you the red vizcacha rat (Tympnoctomys barrerae). A cute little rodent, T. barrerae lives exclusively in the desert region of west-central Argentina. He seems to survive just fine being tetraploid, having an amazing 4x = 2n = 102 chromosomes! He even has a cousin that is reputedly tetraploid as well.

The red vizcacha rat is also known as the plains
vizcacha rat. It is on the IUCN threatened list and
due to destruction of its habitat. It concentrates it
urine to an amazing degree, which allows it to save
its water – it lives in a desert for gosh sakes.

 The reigning hypothesis is that T. barrerae developed as a polyploid species because of a meiotic error in his close relative, the mountain vizcacha rat (Octomys mimax), who has a diploid number of chromosome set at 56. But we had better study he and his cousin quickly, as their habitats are being destroyed at an alarming rate. In only a few years, there may be no red or mountain vizcacha rats left in the wild. Wouldn’t be awful if we lost this exception and then found out that it could have helped us conquer cancer?

The math doesn’t suggest that T. barrerae resulted from a simple meiotic error in its cousin (56+56102), so a study was undertaken to investigate whether the large genome size of the red vizcacha rat could have developed purely from duplication of repeated sequences. Using techniques like self-genomic in situ hybridization and whole genome comparative genomic hybridization, T. barrerae (tetraploid) and O. mimax (diploid) were compared for similar sequences and repeats of the same sequences.

The results, published in 2012 in the journal Genome, indicate that despite some repetitive sequences around the centromeres of the chromosomes, it does not appear that the large genome is the result of sequence duplications. Comparative anaylsis with O. mimax also shows differences that do not suggest a mere doubling of the genome. Therefore, best evidence now says that T. barrerae evolved as a result of some hybridization of the mountain vizcacha rat and another species, with or without subsequent loss of some chromosomes pairs.

Having twice as much DNA in a cell nucleus most
often results in larger cells, and larger cells results
in larger organisms. But T. barrerae’s skull is not
appreciably larger than its diploid cousin, O. mimax.
This still leaves the question as to how this species overcomes the problems in embryonic and fetal development attributed to tetraploidy.  The unbalanced gene function in tetraploid cells has some how been overcome in fetal vizcacha rats. A study in 2008 showed that X-inactivation does indeed silence all but one copy of the X chromosome in the T. barrerae.

But even more stunning, experiments to look at the amount of protein made from certain crucial genes in T. barrerae show that it has the same amount of gene function as its diploid cousins. The rat has found some way to silence the extra copies of many of its genes. Scientists better keep looking at this exceptional animal.

Good thing we don’t have to worry about tetraploidy; it just makes life difficult. Thankfully, we don’t have any cells that are polyploid --- do we? We specialize in exceptions here, so you bet we do. And what’s more, we can’t live without them.

Suárez-Villota, E., Vargas, R., Marchant, C., Torres, J., Köhler, N., Núñez, J., de la Fuente, R., Page, J., Gallardo, M., & Jenkins, G. (2012). Distribution of repetitive DNAs and the hybrid origin of the red vizcacha rat (Octodontidae) Genome, 55 (2), 105-117 DOI: 10.1139/G11-084

Wang, Q., Wu, P., Dong, D., Ivanova, I., Chu, E., Zeliadt, S., Vesselle, H., & Wu, D. (2012). Polyploidy road to therapy-induced cellular senescence and escape International Journal of Cancer DOI: 10.1002/ijc.27810

For more information or classroom activities, see:

Diploid/haploid -

Polyploidy –

Therapy induced cell senescence –

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