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A Look into the Hellish Cradles of Suns and Solar Systems

Wednesday, September 30, 2009

A Look into the Hellish Cradles of Suns and Solar Systems (8/19/09)
New images released today by ESO delve into the heart of a cosmic cloud, called RCW 38, crowded with budding stars and planetary systems. There, young stars bombard fledgling suns and planets with powerful winds and blazing light, helped in their task by short-lived, massive stars that explode as supernovae. In some cases, this onslaught cooks away the matter that may eventually form new solar systems. Scientists think that our own Solar System emerged from such an environment.

The dense star cluster RCW 38 glistens about 5500 light years away in the direction of the constellation Vela (the Sails). Like the Orion Nebula Cluster (ESO 12/01), RCW 38 is an “embedded cluster”, in that the nascent cloud of dust and gas still envelops its stars. Astronomers have determined that most stars, including the low mass, reddish ones that outnumber all others in the Universe, originate in these matter-rich locations. Accordingly, embedded clusters provide scientists with a living laboratory in which to explore the mechanisms of star and planetary formation.

Stellar cluster RCW 38 – click for 1280×1262 image

More: here, here

Induced pluripotent stem cells with one transcription factor

Friday, September 25, 2009

Just under three years ago, in October 2006, some important stem cell research was announced by a Japanese scientific team led by Shinya Yamanaka. The team showed how ordinary mouse skin cells could be transformed into cells that turned out to be pluripotent, just like embryonic stem cells (ESCs). The new cells were called induced pluripotent stem cells (iPSCs). Although "ground-breaking" is an over-used term, this research genuinely deserved the description.

Aside from the fact that it could be done at all, the surprising thing was that the transformation could be effected by adding transcribable genes for just four transcription factors to the skin cell DNA. Those genes were Oct4, Sox2, c-Myc, and Klf4. And now very recent research shows that, under the right conditions, just the addition of Oct4 alone can accomplish the same feat.

We discussed some of the early research here, with additional reports here, here, and here.

In the three years since the original announcement, research has extended and improved the process in a number of ways. The ultimate goal is to be able to produce pluripotent human stem cells that are in all important respects equivalent to embryonic stem cells, by a process that meets several important criteria:

  • Cells to be reprogrammed into a pluripotent state should be readily obtainable from human subjects (unlike embryonic cells or rare types of adult stem cells).
  • No permanent changes to cellular DNA should be made, only changes to gene expression.
  • The process should be relatively quick and efficient, so that reasonable number of pluripotent cells can be obtained for routine therapeutic or experimental uses.

Reprogramming of other cell types into pluripotent cells is important not just as a technical feat to prove it can be done. There are two other important objectives. The first is to develop human cell lines that model many types of pathology (cancer, Parkinson's disease, or whatever) to facilitate research into therapeutics for these diseases. The best way to develop such lines is first to obtain pluripotent cells with the appropriate pathology, derived from human subjects with the disease, which can't generally be done from embryonic sources. From there, several techniques can be used to produce appropriate cell cultures with the desired model pathology.

The second objective is longer-range but even more important: to manufacture cells, for patients with certain diseases, that can be used as therapeutic replacements for the patient's own malfunctioning tissue. This would be accomplished by obtaining pluripotent cells derived from the patient, correcting genetic problems in those cells, and then inducing the cells to differentiate into the required tissue type. Diseases that should be treatable in this way include Parkinson's disease, Type 1 diabetes, and heart disease. Starting with cells from the actual patient eliminates the problem of tissue incompatibility.

The criteria listed above that are imposed on the process are important for meeting both of these objectives.

In the three years since the original work was announced, dozens of research groups have set about testing improvements to the original procedures in order to progress towards the ultimate objectives. The improvements that have been made include:

  • adapting the procedures to work in species other than mice – including pigs and fruit flies, as well as humans
  • reducing the number of transcription factors that need to be introduced, or finding other suitable transcription factors
  • finding other cell types besides skin cells to start with, generally various types of non-pluripotent stem cells – which makes other improvements in the process easier to accomplish
  • changing the way that the transcription factors are introduced into the target cells, in order to avoid alteration of the original DNA (since such alterations may introduce risks of cancer or other cellular malfunction)
  • finding other proteins or small molecule compounds that can be added to enhance the efficiency and speed of the process

Quite a few important improvements have been announced within the past several months, along with other related news. The most interesting related news is a demonstration that iPSCs really are not only equivalent to ESCs in terms of gene expression, but are in fact equally pluripotent. This latter fact was convincingly demonstrated by cloning several generations of live, healthy mice from iPSCs. (We'll discuss that in a separate article, but here's an overview.)

What I want to discuss here is how the list of transcription factors (or their genes) that need to be added to a non-pluripotent cell has been reduced to just one: Oct4. The work was done by a mostly German team led by Hans Schöler of the Max Planck Institute for Molecular Biomedicine.

So how was this accomplished? Well, the trick is, you have to start with the right kind of cells. In this case the researchers used human fetal neural stem cells (HFNSCs). While such cells aren't pluripotent, they are "multipotent", which means they can normally differentiate into various other cell types.

Back in February the researchers in this study reported that reprogramming with just Oct4 could be done in mouse neural stem cells (see here, here, or here). But would this also work with human cells?

Yes. The latest report shows that HFNSCs can be reprogrammed to a pluripotent state using only Oct4 and Klf4, and (generally) even with Oct4 alone. How is this possible? It is known that mouse neural stem cells already express Sox2, c-Myc, and Klf4. As for the human case, the paper says, cautiously, that "The feasibility to reprogram directly NSCs by OCT4 alone might reflect their higher similarity in transcriptional profiles to ES cells than to other stem cells like haematopoietic stem cells or than to their differentiated counterparts."

And the main indication of this is that the process works: "One-factor human NiPS cells resemble human embryonic stem cells in global gene expression profiles, epigenetic status, as well as pluripotency in vitro and in vivo. These findings demonstrate that the transcription factor OCT4 is sufficient to reprogram human neural stem cells to pluripotency."

What this is saying is that there are several criteria for similarity to embryonic stem cells that the reprogrammed HFNSCs meet. At a molecular level the reprogrammed cells express the same genes and have the same epigenetic markers as ESCs. In addition, they can differentiate into many adult cell types both in vitro and in vivo (in the latter case, by forming teratomas (mixed masses of cell types) when implanted in mice).

There are still several drawbacks to this method for practical purposes, even of research. For one thing, human fetal neural stem cells are not exactly easily obtainable. And in addition, retroviruses were used (as in the original Yamanaka work) to introduce Oct4 into the cells. For therapeutic applications it would be absolutely necessary to use one of the other methods that have been explored and that do not disrupt the existing cell DNA or leave exogenous DNA in derived cells – since either alternative means the derived cells might revert to a more undifferentiated state. On top of all that, the process is still inefficient and slow.

Reprogramming methods that have been explored in other research include the introduction of genetic material in forms other than retroviruses, as well as direct delivery of the transcription factor proteins. The researchers in this study intend to investigate such possibilities, as well as use of other initial cell types: "Future studies will show if direct reprogramming is possible with small molecules or OCT4 recombinant protein alone. ... It will be interesting to extend this study to human NSCs derived from other sources, such as dental pulp, as well as to other stem-cell types."

Kim, J., Greber, B., Araúzo-Bravo, M., Meyer, J., Park, K., Zaehres, H., & Schöler, H. (2009). Direct reprogramming of human neural stem cells by OCT4 Nature DOI: 10.1038/nature08436

Further reading:

One step to human pluripotency (8/28/09) – blog post at The Scientist

Stem cells, down to one factor (8/28/09) – blog post at The Niche

Induced pluripotent stem cells, down to one factor (9/10/09) – excellent overview at Nature Reports Stem Cells

Direct reprogramming of human neural stem cells by OCT4 (8/28/09) – Nature research paper

One-gene method makes safer human stem cells (8/28/09) – New Scientist article

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Trigger-Happy Star Formation

Wednesday, September 23, 2009

Trigger-Happy Star Formation (8/12/09)
A new study from two of NASA's Great Observatories provides fresh insight into how some stars are born, along with a beautiful new image of a stellar nursery in our Galaxy. The research shows that radiation from massive stars may trigger the formation of many more stars than previously thought.

While astronomers have long understood that stars and planets form from the collapse of a cloud of gas, the question of the main causes of this process has remained open.

One option is that the cloud cools, gravity gets the upper hand, and the cloud falls in on itself. The other possibility is that a "trigger" from some external source -- like radiation from a massive star or a shock from a supernova -- initiates the collapse. Some previous studies have noted a combination of triggering mechanisms in effect.

By combining observations of Cepheus B from the Chandra X-ray Observatory and Spitzer Space Telescope, researchers have taken an important step in addressing this question. Cepheus B is a cloud of mainly cool molecular hydrogen located about 2,400 light years from the Earth. There are hundreds of very young stars inside and around the cloud -- ranging from a few millions years old outside the cloud to less than a million in the interior -- making it an important testing ground for star formation.

Cepheus B – press for 660×864 image

More: here, here, here, here, here

New anti-cancer role for p53

Tuesday, September 8, 2009

I suppose that just about everyone knows of the important role the p53 protein plays in protecting cells from becoming cancerous. The protein was identified 30 years ago and its gene (TP53) cloned soon thereafter. What's not so widely known is just how complex the operation of p53 in protecting against cancer really is. And very recent research shows the complexity is even more than previously thought.

However, the complexity is to be expected, because evolution doesn't "design" cellular mechanisms to work in a straightforward way. The mechanisms are simply the result of about a billion years of trial and error. Being pretty and elegant was not a criterion for success.

Nature is "hairy", knowing nothing of Occam's Razor, and caring even less. Simplicity is for wimps.

But one thing is clear: p53 plays a large role in preventing, or at least suppressing, the development of cancer. In many types of cancer, p53 is found to have mutations more than 50% of the time. Even if p53 isn't mutated, cancer cells generally have other p53 abnormalities, such as low levels of the protein or the presence of various factors that interfere with its activity.

Until the latest research, there have been two principal ways known in which p53 works against cancer, and several additional minor ways. The two main ways p53 has been known to act are binding to DNA as a transcription factor, and binding directly to certain proteins. And each of these mechanisms can lead to either of two main types of tumor suppression: apoptosis (cell death) and temporary or permanent suspension of the cell cycle, which is the process a cell goes through in order to divide and proliferate.

P53 is primarily a transcription factor. In this role it is found in a cell nucleus and binds to various specific DNA gene promoter regions, in order to direct transcription of the associated gene – the first step in production of proteins from a gene.

The proteins that are expressed as a result of this p53 activity can play a part in either apopotosis or cell cycle control (as well as other functions not directly related to cancer – see here, here, here). Which function is invoked depends on the type of signal that activates the p53. Among the possible conditions that may be signaled are detection of correctable or uncorrectable damage to DNA and detection of chromosome telomeres that are too short.

In addition to binding to DNA as a transcription factor, p53 is also capable of binding directly to other proteins in order to control their behavior. Mainly these proteins are involved with apoptosis, such as members of the Bcl2 family.

P53 itself is actually a family of proteins – there are at least 9 different RNA transcripts that can be derived from the TP53 gene. But one thing that each of these family members have in common is a segment, called the DNA binding domain. It is this part of the p53 that is capable of binding to either DNA or other proteins. (In general, a protein domain is a more-or-less self-sufficient component of a protein. Often the same domain appears in different members of a family of proteins.)

One indication of the importance of this p53 domain is the fact that point mutations (errors involving only a single nucleotide pair) in the part of TP53 that code for the binding domain are the only type of point mutations of p53 that are commonly found in tumors. Errors that affect portions of p53 outside of the binding domain are not associated with cancer.

There's one more thing to note about p53's role as a transcription factor. Namely, the RNA that is transcribed under the direction of p53 is not always messenger RNA (mRNA) that will eventually code for the production of a protein. P53 can also initiate the transcription of genes that code for microRNA (miRNA), which is a single-stranded RNA molecule that's normally only 21 to 23 nucleotides in length. Over 500 different types of miRNA have been found in human cells.

MicroRNA is never translated into a protein. Instead, miRNA molecules regulate the translation of messenger RNA for many different proteins (by binding with the mRNA to prevent translation). It has been known for some time that p53 acts as a transcription factor for the miRNA family known as miR-34. It has also been learned that among the proteins regulated by miR-34 are some found in pathways that lead to apoptosis or cell cycle arrest. The net effect is that miR-34 has tumor-suppressing properties, so this is another way that p53, as a transcription factor, helps suppress tumors.

Many other miRNA molecules, on the other hand, are found at high levels in cancer cells. Such miRNAs most likely inhibit expression of tumor suppressing genes, whose proteins might otherwise control cell proliferation or migration. We've discussed a number of miRNAs associated with cancer, mostly of the sort that promote cancer, here and here.

Nevertheless, there are miRNAs besides miR-34 that have anti-cancer effects. Three in particular are miR-16-1, miR-143, and miR-145. It has been observed that these miRNAs, and several others, are found at higher levels in cells where p53 has been activated as a result of DNA damage. (Normally, p53 formed in non-cancer cells is either quickly degraded or else inhibited by certain proteins, especially MDM2, so as not to unnecessarily promote apoptosis or cell cycle arrest. The presence of DNA damage results in the removal of these inhibitions on p53.)

It therefore appears that p53 is doing something to help produce a number of miRNAs, some of which are tumor suppressors. The curious thing, though, is that it can be shown that p53 is not a transcription factor for the genes that encode these miRNAs.

So what is it that p53 is doing instead to help produce these miRNAs? New research published in the July 23, 2009 issue of Nature answers this question – and it uncovers an entirely new mechanism through which p53 (and its binding domain, in particular) acts as a tumor suppressor. Here's the research abstract:

Modulation of microRNA processing by p53
MicroRNAs (miRNAs) have emerged as key post-transcriptional regulators of gene expression, involved in diverse physiological and pathological processes. Although miRNAs can function as both tumour suppressors and oncogenes in tumour development, a widespread downregulation of miRNAs is commonly observed in human cancers and promotes cellular transformation and tumorigenesis. This indicates an inherent significance of small RNAs in tumour suppression. However, the connection between tumour suppressor networks and miRNA biogenesis machineries has not been investigated in depth. Here we show that a central tumour suppressor, p53, enhances the post-transcriptional maturation of several miRNAs with growth-suppressive function, including miR-16-1, miR-143 and miR-145, in response to DNA damage. ... These findings suggest that transcription-independent modulation of miRNA biogenesis is intrinsically embedded in a tumour suppressive program governed by p53. Our study reveals a previously unrecognized function of p53 in miRNA processing, which may underlie key aspects of cancer biology.

To understand what's going on, it's necessary to explain a few things about how miRNAs are produced. It's not a simple 1-step process of transcribing an miRNA gene into the final short piece of RNA.

There are, instead, three steps. The first step is transcription, done just as is done for any other gene. The RNA produced in this step is many nucleotides long, and is called the "primary transcript" or pri-miRNA. This pri-miRNA is then cut into smaller pieces having a hairpin shape, called pre-miRNA. The pre-miRNA, in turn, is further processed to produce the final "mature" miRNA.

The intermediate step that converts pri-miRNA to pre-miRNA is performed by a protein complex known as the "microprocessor complex" (having nothing to do with computers, of course). One of the key proteins in this complex is an enzyme called Drosha. The final step, which is performed by another enzyme called Dicer, splits the pre-miRNA apart to yield the mature miRNA.

The main contribution of p53 in this process is to facilitate the action of Drosha. It seems that, although Drosha can do the job by itself (since miRNAs are needed even if p53 isn't active), p53 helps by binding (via its binding domain) with parts of the microprocessor complex. This is indicated by the observation that mutations in the binding domain disable p53 binding to the complex, resulting in lower levels of miRNA production.

So there you have it: an essentially novel way that p53 acts as a tumor suppressor, by facilitating production, non-transcriptionally, of tumor-suppressing miRNAs.

Suzuki, H., Yamagata, K., Sugimoto, K., Iwamoto, T., Kato, S., & Miyazono, K. (2009). Modulation of microRNA processing by p53 Nature, 460 (7254), 529-533 DOI: 10.1038/nature08199

Further reading:

Protein plays three cancer-fighting roles (7/22/09) – Science News article on the research

Link between p53 and miRNA – editor's summary in Nature of the research

Cancer: Three birds with one stone (7/23/09) – Nature news article on the research

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