MicroRNA and cancer II

We haven't recently discussed the role of microRNA in cancer. Last time (February 2008) is here. There have been some relatively recent research announcements, so let's have a look.

If you want a refresher on the subject, here's a good introductory overview from Cancer Research UK: Micro RNAs and cancer. Although this piece is fairly elementary, it does have many good links to actual research papers.

Now let's jump into a few summaries of recent research.

What's Feeding Cancer Cells? (2/17/09)

Cancer cells grow and multiply rapidly, so they need lots of nutrients. Much is already known about how cancer cells use blood sugar, but other nutrients are also needed. One of these is the amino acid glutamine. This research found that the transcription factor Myc is able to enhance the expression of the enzyme glutaminase (GLS) in cellular mitochondria. GLS is the first enzyme that processes glutamine to produce energy in mitochondria. (Overexpression of Myc is frequently found in cancer – see here.)

The research found that depriving cancer cells of GLS slowed their growth significantly. It was suspected that Myc could directly up-regulate the GLS gene, but it was not that simple. Instead, it appears that Myc down-regulates genes for two types of microRNA: mi-R23a and mi-R23b. Since these mircoRNAs interfere with the GLS messenger RNA, the net effect of Myc is to enhance GLS production.

Research abstract: c-Myc suppression of miR-23a/b enhances mitochondrial glutaminase expression and glutamine metabolism

A new discovered mutation can hold the key to treat a large number of different cancers (2/17/09)

Since microRNA normally inhibits production of certain proteins, if the proteins affected promote cancer, the inhibitory miRNA will counteract this. This research examined cells of twelve different cancer types.

The basic finding was that mutations of the gene TARBP2 disrupts a pathway that produces anti-oncogenic microRNAs. Mutated TARBP2 diminishes TRBP protein expression, resulting in a defect in the processing of miRNAs. Specifically, the DICER1 protein, which is necessary for miRNA production, is adversely affected.

Research abstract: A TARBP2 mutation in human cancer impairs microRNA processing and DICER1 function

Micro RNA Plays A Key Role In Melanoma Metastasis (2/15/09)

Metastasis is the main process by which cancer becomes deadly, and it is especially problematic in melanoma. In order for cancer cells to metastasize (spread to another body location) they must become able to migrate and establish themselves in the new location. This research finds that the microRNA miR-182 assists in this process.

MiR-182 is frequently up-regulated in human melanoma, usually because melanoma cellular DNA contains extra copies of the miR-182 gene. This up-regulation was shown to assist metastasis. Conversely, down-regulation impedes invasion and triggers apoptosis. Over-expressed miR-182 is shown to repress the expression of two tumor suppressors, FOXO3 and MITF, which are both transcription factors. (For more on FOXO3, see here.)

Research abstract: Aberrant miR-182 expression promotes melanoma metastasis by repressing FOXO3 and microphthalmia-associated transcription factor

New Genes Involved In Acute Lymphoblastic Leukemia Play Fundamental Role In Prognosis Of The Disease (2/6/09)

This investigation found that 13 microRNAs were epigenetically regulated in an abnormal way in many patients with acute lymphoblastic leukaemia (ALL). This means that instead of having actual gene mutations, certain parts of the DNA were methylated in an unusual way, so that the underlying genes, which coded for microRNAs, were down-regulated. More precisely, certain histones of the cell's chromatin were methylated, so that genes located on the DNA wrapped around those histones would not be expressed. The genes involved coded for microRNAs that, evidently, are important for suppressing cancer. When approriate steps were taken to reverse abnormal epigenetic regulation of the affected genes, expression levels rose, confirming that the abnormal methylation patterns were responsible for down-regulation.

65% of 352 ALL patients had one or more methylation abnormalities affecting microRNA under investigation. There was a highly significant positive correlation between patient survival at 14 years after diagnosis and absence of such abnormalities. Consequently, tests for methylation problems with the appropriate microRNA genes should be good predictors of survival prospects.

Research abstract: Epigenetic regulation of microRNAs in acute lymphoblastic leukemia

Researchers Identify Another Potential Biomarker For Lung Cancer (1/13/09)

The research showed that smoking impacts bronchial airway gene expression. Various miRNAs were found that were differently expressed in bronchial airway epithelial cells, mostly down-regulated. Messenger RNAs were also identified, whose expression was inversely correlated to the miRNA expression (so that the corresponding genes appear to be down-regulated by the miRNA.)

MiR-218 was especially noteworthy. It is known to be strongly affected by smoking. The conclusion is that miR-218 levels modulate airway epithelial gene expression response to cigarette smoke, suggesting a role for miRNAs in regulating response to environmental toxins.

Research abstract: MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium

Molecule Linked To Muscle Maturation, Muscle Cancer (12/31/08)

The study clarified the role of MiR-29 in myogenesis (muscle cell formation) and found that its down-regulation is associated with rhabdomyosarcoma (RMS), a cancer caused by the proliferation of immature muscle cells. While miR-29 is required for maturation of myoblasts (immature muscle cells), it is also found to be mostly absent from RMS cells.

The study found, further, that the transcription factor NF-κB is responsible for down-regulating miR-29. (NF-κB is an old friend of ours. See here for a small part of the story about its role in inflammation. There's also much more to be said about the role of NF-κB in cancer, where it provides an important connection between inflammation and cancer.)

NF-κB acts to repress miR-29 through another transcription factor, YY1, and Polycomb-group proteins (which remodel chromatin to block transcription factors from DNA promoter sequences).

During myogenesis, NK-κB and YY1 are down-regulated, permitting expression of miR-29, which then further down-regulates YY1 and accelerates cell differentiation. However, in RMS the NF-κB–YY1 pathway remains active, silencing miR-29 and inhibiting differentiation. But reconstitution of miR-29 in RMS in mice inhibits tumor growth and stimulates differentiation,

Research abstract: NF-κB–YY1–miR-29 Regulatory Circuitry in Skeletal Myogenesis and Rhabdomyosarcoma

Harnessing MiRNA Natural Gene Repressors For Anticancer Therapy (12/1/08)

This research investigates the potential therapeutic use of miR-181a through its ability to repress expression of selected genes. If successful, this would provide a very clever kind of immunotherapy for cancer and possibly other diseases.

In immune system T cells miR-181a is highly expressed in developing T cells, but is markedly down-regulated in mature T cells. Mouse bone marrow cells were engineered to express desired therapeutic genes only when miR-181a is down-regulated. These cells were transplanted into mice and allowed to develop into mature T cells. The proteins repressed by miR-181a would therefore not be found in the immature cells, but would show up in the mature T cells. And so when the genes repressed by miR-181a corresponded to proteins that direct T cells to attack tumor cells expressing the protein hCD19, mice with the engineered bone marrow cells were able to reject tumors expressing hCD19.

Research article (open access): Harnessing endogenous miR-181a to segregate transgenic antigen receptor expression in developing versus post-thymic T cells in murine hematopoietic chimeras

Molecule Linked To Aggressive Cancer Growth And Spread Identified (11/13/08)

EZH2 is a polycomb group protein, which helps maintain transcriptional repression of genes over successive cell generations. It contributes to the epigenetic silencing of target genes and enables the survival and metastasis of cancer. The research indicates that miR-101 inhibits the expression and function of EZH2 in cancer cells.

The researchers found that miR-101 is significantly underexpressed in a variety of cancers, including prostate and breast cancer. In human prostate tumors miR-101 expression decreases as cancer progresses and expression of EZH2 increases. MiR-101 is coded for at two locations in cell DNA. One or both of those locations is found to be defective in 37.5% of localized prostate cancer cells and in 66.7% of metastatic cells. This suggests that that underexpression of miR-101 is responsible for overexpression of EZH2 and consequent cancer progression.

More: here (11/13/08)

Research abstract: Genomic Loss of microRNA-101 Leads to Overexpression of Histone Methyltransferase EZH2 in Cancer

Further reading:

MicroRNA—implications for cancer – excellent open access review article

Tags: cancer, microRNA

Induced pluripotent stem cells III

There is still some news from here that we need to look at. It has to do with reducing the risk of tumorigenicity by using a signaling protein Wnt3a – a member of the Wnt family of proteins – in place of the c-Myc transcription factor for inducing pluripotency in differentiated adult cells.

This press release gives the executive summary:

Embryonic-like Stem Cells Can Be Created Without Cancer-causing Gene (8/6/08)

Currently, IPS cells can be created by reprogramming adult cells through the use of viruses to transfer four genes (Oct4, Sox2, c-Myc and Klf4) into the cells' DNA. The activated genes then override the adult state and convert the cells to embryonic-like IPS cells.

However, this method poses significant risks for potential use in humans.

First, the viruses employed in the process, called retroviruses, are associated with cancer because they insert DNA anywhere in a cell's genome, thereby potentially triggering the expression of cancer-causing genes, or oncogenes. Second, c-Myc is a known oncogene whose overexpression can also cause cancer. For IPS cells to be employed to treat human diseases such as Parkinson's, researchers must find safe alternatives to reprogramming with retroviruses and oncogenes.

Earlier research has shown that c-Myc is not strictly required for the generation of IPS cells. However, its absence makes the reprogramming process time-consuming and highly inefficient.

To bypass these obstacles, the Whitehead researchers replaced c-Myc and its retrovirus with a naturally occurring signaling molecule called Wnt3a. When added to the fluid surrounding the cells being reprogrammed, Wnt3a promotes the conversion of adult cells into IPS cells.

What amounts to a crude form of gene therapy has been used to make IPS cells. The idea is to insert extra copies of genes for 4 different transcription factors into a cell's DNA in order to raise the expression level of those factors. The problem is that every insertion of a gene into a cell's DNA risks damage to some other random gene in the DNA. Wnt3a, on the other hand, is a signaling protein that normally affects cells only by attaching to receptors on the cell surface.

So what has been accomplished here is that the number of transcription factor genes that need to be inserted into the DNA is reduced from 4 to 3. In addition, the factor that is eliminated, c-Myc, has tumorigenicity risks of its own. Therefore, this research represents a small but useful improvement. However, it is probably only a first step.

More about the present research: here

We discussed earlier research aimed at eliminating use of c-Myc in making IPS cells here.

In fact, just a little bit earlier than the research discussed above, a team from Germany reported, on July 31 in Nature, making IPS cells by adding just two transcription factors. However, they didn't start with adult somatic cells, but with neural stem cells that already had higher expression levels of Sox2 and c-Myc. Given that, they needed to add only Oct4 and either Klf4 or more c-Myc. Here's the abstract:

Pluripotent stem cells induced from adult neural stem cells by reprogramming with two factors

Here we show that adult mouse neural stem cells express higher endogenous levels of Sox2 and c-Myc than embryonic stem cells, and that exogenous Oct4 together with either Klf4 or c-Myc is sufficient to generate iPS cells from neural stem cells. These two-factor iPS cells are similar to embryonic stem cells at the molecular level, contribute to development of the germ line, and form chimaeras. We propose that, in inducing pluripotency, the number of reprogramming factors can be reduced when using somatic cells that endogenously express appropriate levels of complementing factors.

Keep in mind that there's a further variable that's important here: the efficiency of the process, i. e. the yield of IPS cells obtained as a percentage of original cells at the beginning. It should be obvious that a fair amount of work still needs to be done to find a method of making IPS cells that's both efficient and produces cells that are potentially safe to use in therapeutic applications (as opposed to pure research).

OK, enough of that. Let's move on to something new.

One of the interesting questions about IPS cells is about exactly how close they are to actual embryonic stem cells, which are pluripotent by definition. The best way to measure the degree of closeness is by comparing gene expression levels between embryonic stem cells and IPS cells.

The next research has done exactly that. In fact, it studies gene expression levels for stem-like cells obtained from a wide variety of sources:

A new test distinguishes embryonic stem cells and those with equal therapeutic potential (8/24/08)

To distinguish adult stem cells from pluripotent cells, Loring’s team compared the gene activity of about 150 stem cell samples of various types, including reprogrammed cells, embryonic stem cells and neural stem cells. Out of this comparison popped 299 interacting genes that form what the researchers call a pluripotency network, or PluriNet. Measuring the activity of these genes could reliably distinguish the different kinds of stem cells, the team reports.

Here's the abstract for this research:

Regulatory networks define phenotypic classes of human stem cell lines

We report here the creation and analysis of a database of global gene expression profiles (which we call the 'stem cell matrix') that enables the classification of cultured human stem cells in the context of a wide variety of pluripotent, multipotent and differentiated cell types. Using an unsupervised clustering method to categorize a collection of ∼150 cell samples, we discovered that pluripotent stem cell lines group together, whereas other cell types, including brain-derived neural stem cell lines, are very diverse. Using further bioinformatic analysis we uncovered a protein–protein network (PluriNet) that is shared by the pluripotent cells (embryonic stem cells, embryonal carcinomas and induced pluripotent cells). Analysis of published data showed that the PluriNet seems to be a common characteristic of pluripotent cells, including mouse embryonic stem and induced pluripotent cells and human oocytes. Our results offer a new strategy for classifying stem cells and support the idea that pluripotency and self-renewal are under tight control by specific molecular networks.

Tags: stem cells, embryonic stem cells, induced pluripotent stem cells

Cancer stem cells II

Since we've just had a discussion of generalities about cancer stem cells (here), it seems like it would be fun to have a summary of research on CSCs that was presented at the recent meeting of the American Association for Cancer Research in San Diego, or reported since then. So here it is.

As general background, keep in mind that cell surface proteins CD44 and CD24 are considered to be markers of cancer stem cells in various (but not necessarily all) types of cancer. Also, certain cell signaling pathways are thought to be especially important in the activity of cancer stem cells. The list includes Wnt, Sonic hedgehog, Notch, and Bmi1.

Stem Cell-Like Cancer Cells Resistant To Standard Therapy, Responsive To Targeted Therapy (4/29/08)

Previous research had identified a subset of cells in breast tumors that have the ability to form colonies in culture and give rise to tumors in mouse models. Such cells are thought to be cancer stem cells. They express the cell surface glycoprotein CD44, but not CD24, and they appear to be resistant to standard chemotherapeutic agents. However, the drug lapatinib, which inhibits the HER2 pathway, seems to selectively kill these cells.

Getting To The Roots Of Breast Cancer (4/29/08)

This is another report on the research described in the previous item. It provides additional details on the research protocol.

Stem Cell Type Supposed To Be Crucial For Angiogenesis And Cancer Growth Does Not Exist? (4/22/08)

This study casts doubt on the existence of a certain type of bone-marrow derived stem cell that has been suspected of circulating in the blood and acting as a precursor to endothelial cells that make up blood vessel walls. Such cells, if they existed, would be an important target for inhibiting angiogenesis in tumors. The researchers showed, using advanced techniques with mouse models, that endothelial differentiation is not a typical function of bone-marrow derived stem cells.

Ovarian Cancer Stem Cells Identified, Characterized (4/17/08)

Researchers have identified, characterized and cloned ovarian cancer stem cells and have shown that these stem cells may be the source of ovarian cancer's recurrence and its resistance to chemotherapy. They isolated cells from samples of either peritoneal fluid or solid tumors. The cancer stem cells that were identified had traditional cancer stem cell markers including CD44 and MyD88 (which interacts with toll-like receptors to activate NF-κB).
The cells also showed a high capacity for repair and self-renewal. Such cells, when isolated, were capable of forming tumors 100 percent of the time. Within those tumors, 10 percent of the cells were CD44 positive, while 90 percent were CD44 negative, indicating that some cancer stem cells had undergone differentiation.

Stem Cells: The Role Of Cancer-initiating Cells In Diagnosis And Treatment (4/15/08)

This press release describes research presented at the AACR meeting related to stem cells and pancreatic, bladder, ovarian, and breast cancer, and glioma.

Research in pancreatic cancer found that in addition to CD44 and CD24, the enzyme aldehyde dehydrogenase was expressed in a small population of tumor cells. Cells expressing aldehyde dehydrogenase had greater growth capacity than those that didn't, and they were also associated with poorer overall survival.

In a study of breast cancer and glioma, surface markers were not found be sufficient as markers of stem cell activity. However, cells with low proteasome activity did have notably greater capacity for self-renewal and tumor production capacity. (Proteasomes are large protein complexes that degrade unneeded or damaged proteins.)

Researchers studying bladder transitional cell carcinomas found, in 40% of cases, CD44+ cells with other stem cell self-renewal patterns. In these cells, 85% had active Gli1, a part of the Hedgehog pathway, originally discovered in human glioblastoma. A relatively small percentage had active Bmi1, Stat3, or β-catenin (part of the Wnt pathway). None had active Oct4 or Nanog (pluripotent stem cells markers).

The research on ovarian cancer (noted above) involving CD44 and MyD88 markers is referenced again here.

Stem Cell Marker Controls Two Key Cancer Pathways (4/14/08)

Research into breast cancer stem cells has identified, for the first time, another gene that may be involved, Msi1. The investigators showed that Msi1 activated Wnt and Notch signaling. Other studies have shown that Msi1 is a marker of human adult stem cells in general because it has been found in human breast, colon, brain, skin, and other cells. Msi1 was found to affects mammary cells to influence whether they develop into muscle, milk duct linings, etc. Further, Msi1 was found to be expressed in particularly aggressive tumors.

Stem Cells And Cancer: Scientists Investigate A Fine Balancing Act (4/11/08)

This is a report of a general talk about how the mechanisms normally involved in balancing different functions of stem cells may also contribute to cancer. For example, research shows that Bmi1 is important for maintaining stocks of stem cells, and without it stocks of stem cells are depleted. But also Bmi1 is overactive in various cancers including brain tumors.

Secrets of cellular signaling shed light on new cancer stem cell therapies (4/10/08)

Researchers are beginning to study inhibition of signaling pathways that seem to be active in tumors fed by cancer stem cells. In this case, inhibition of the Notch pathway is being investigated as part of a treatment, together with chemotherapy, for metastatic breast cancer. An important question is whether cancer stem cells are sufficiently different from normal adult stem cells so that inhibition of Notch signaling is not harmful. Results of testing in mice indicate that Notch signals are not required for the maintenance of blood-forming stem cells in adult mice.

Stem cells and cancer: cancer pathways that also control the adult stem cell population (4/10/08)

Apc (adenomatosis polyposis coli) is a tumor-suppressing protein that controls β-catenin and hence affects Wnt signaling. When intestinal crypts are damaged and need to be regenerated, Wnt signaling directs stem cells to generate replacement cells. Apc normally turns off Wnt signaling of stem cells when it is no longer needed. The research here showed that if Apc is lost or damaged, Wnt signaling may continue and result in tumor formation

Cancer Stem Cells Created With New Technique (4/9/08)

One of the most important unresolved questions about cancer stem cells is how they originate to begin with. For instance, are they mutations of existing stem cells, or instead precancerous cells that have acquired stem-cell-like capabilities? The research here supports the latter scenario. Starting with normal skin cells, the researchers activated three genes associated with embryonic stem cells. The result closely resembled known cancer stem cells. And they also had more resemblance to normal embryonic stem cells than to normal adult stem cells. One of the genes was Myc, which has also been used to create pluripotent stem cells from skin cells. In addition to the scientific significance of this work, it should also facilitate study of cancer stem cells, which are otherwise hard to locate.

Module Map Links Embryonic Stem Cells And Cancer Stem Cells (4/9/08)

The researchers involved in the work described in the preceding report have additional related findings. They systematically compared gene expression patterns between embryonic stem cells and multiple types of human cancer cells. Gene expression patterns in diverse human epithelial cancers were much like patterns in embronic stem cells. Further, presence of these patterns in cancer cells strongly predicted metastasis and death. On the other hand, normal adult tissue stem cells had an opposite pattern, which was repressed in various human cancers compared to normal tissues. The researchers additionally demonstrated that c-Myc, but not other oncogenes, was sufficient to reactivate the ESC-like program in normal and cancer cells.

And here's some earlier research that features the Nanog and Bmi1 proteins:

To Evade Chemotherapy, Some Cancer Cells Mimic Stem Cells (9/19/07)

Anti-cancer treatments often effectively shrink the size of tumors, but some might have an opposite effect, actually expanding the small population of cancer stem cells believed to drive the disease, according to new findings.

"Our experiments suggest that some treatments could be producing more cancer stem cells that then are capable of metastasizing, because these cells are trying to find a way to survive the therapy," said one of the study's investigators, Vasyl Vasko.

When the researchers applied various anti-cancer drugs to experimental cancer cells, they found that surviving cells expressed more Nanog and Bmi1:

They selected a rare form of cancer, mesenchymal chondrosarcoma (MCS), which has not been well described and for which there is no effective treatment. The researchers first determined that Nanog and BMI1 stem cell markers were more highly expressed in metastatic tumors compared to primary tumors. ...

They then applied various therapies - from VEGF inhibitors such as Avastin to the proteasome inhibitor Velcade - in mice implanted with human MSC, and analyzed the effects on tumors. Some of the treatments seemed to work, because they led to a dramatic decrease in the size of the tumors, Dr. Vasko said. But analysis of stem cell expression before and after treatment revealed that even as some anti-cancer treatments shrank tumors, they increased expression of Nanog and BMI1. "These treatments were not enough to completely inhibit tumor growth, and the cancer stem cell markers were still present," Dr. Vasko said.

Tags: cancer, stem cells, cancer stem cells

Induced Pluripotent Stem Cells II

In this article from the April 4 Science, which I mentioned here, several research reports dealing with induced pluripotent stem cells were discussed. One of these I covered in the post I just noted.

Another just as important report apparently has not yet been formally published, but is (at least temporarily) available online since February 14 at Science Express:

Generation of Pluripotent Stem Cells from Adult Mouse Liver and Stomach Cells

Induced pluripotent stem (iPS) cells have been generated from mouse and human fibroblasts by the retroviral transduction of four transcription factors. However, the cell origins and molecular mechanisms of iPS cell induction remain elusive. This report describes the generation of iPS cells from adult mouse hepatocytes and gastric epithelial cells. These iPS cell clones appear to be equivalent to ES cells in gene expression and are competent to generate germ-line chimeras.

It's not surprising that this is significant research, as it's from the same team of Shinya Yamanaka that was the first to report successful creation of induced pluripotent stem cells. (See here.)

So what is this research about? Well, the investigators used the same four transcription factors (Oct3/4, Sox2, Klf4, and c-Myc) as employed in the majority of previous iPS studies. However, instead of applying the transcription factors to fibroblast cells, they were applied to two types of epithelial cells instead.

Fibroblasts are part of a body's connective tissue. They are involved in structure and support for other tissues and contain large amounts of the protein collagen. They do not divide for the most part, and so it is especially significant that it was possible to reprogram them into a stemcell-like state at all.

Epithelial cells, on the other hand, line the inner and outer surfaces of various body structures, including skin and the gastrointestinal tract. Such cells divide more frequently. They have to, in order to replace other cells of the same kind that are exposed to hostile environments. Epithelial cells also tend to be more adherent to other cells, because they more highly express an adherence protein called E-cadherin.

In some sense, then, epithelial cells are a little more like stem cells to begin with, so one might expect better results when attempting to reprogram them.

This expectation seems to have been met. One of the key differences the researchers found is that reprogrammed epithelial cells had less tendency to form cancerous tumors in mice into which they were included. Certainly not an inconsiderable advantage. This characteristic may be related to the finding that c-Myc seems to play a less essential role in reprogramming epithelial cells.

Specifically, reprogramming of epithelial cells was almost as efficient when c-Myc was not used as when it was included with the other three transcription factors. Yet it was not possible to accomplish reprogramming if any of the other three factors was omitted. In contrast, the efficiency of reprogramming fibroblasts dropped by 90% when c-Myc was omitted.

Another intriguing difference was that reprogrammed epithelial cells contained higher levels of expression of β-catenin than reprogrammed fibroblasts did. (You may recall – see here – that β-catenin is an important part of the Wnt signaling pathway.) In this regard, the reprogrammed epithelial cells are more like true embryonic stem cells than reprogrammed fibroblasts are. It's probably not a coincidence that expression of Nanog is stimulated by β-catenin, (see here), since Nanog is considered important for maintaining stem cell pluripotency.

A further advantage of the use of epithelial cells is that many fewer retroviral "integration sites" were needed to include the transcription factor genes into the cell genome, in comparison with fibroblasts. This is another way the risk of cancer is reduced.

Further reading:

• Stomach and liver cells reprogrammed – excellent 2/28/08 open access overview of the research from Nature Reports Stem Cells
  
  
• Epithelial cells made pluripotent – 2/14/08 blog post at The Scientist giving a good summary of the research findings
  
  
• Epithelial cells made pluripotent – blog post at Wisconsin Stem Cell Now on the preceding article, but noted mainly because it's by the owner of another interesting stem cell blog: Stem Cell Nation
  

Tags: stem cells, induced pluripotent stem cells

Induced pluripotent stem cells

It was one of the top science stories of 2007: number 2 on Science's list – reprogramming ordinary adult body cells (of mice and humans) to act like embryonic stem cells. (See here for summary.) As Science put it,

The riddle of Dolly the Sheep has puzzled biologists for more than a decade: What is it about the oocyte that rejuvenates the nucleus of a differentiated cell, prompting the genome to return to the embryonic state and form a new individual? This year, scientists came closer to solving that riddle. In a series of papers, researchers showed that by adding just a handful of genes to skin cells, they could reprogram those cells to look and act like embryonic stem (ES) cells.

The story really began in October 2006, when a team at Kyoto University in Japan, led by Shinya Yamanaka, announced that they had reprogrammed mouse skin cells into cells that closely resembled embryonic stem cells, based on certain characteristic genes that were expressed. The reprogramming was done by introducing genes for four important stem cell transcription factors (Oct4 (or sometimes the similar Oct3), Sox2, c-Myc, and Klf4) into the skin cells with the help of a genetically engineered retrovirus. (See here for more about Oct4.)

But the team could not at that time demonstrate that these reprogrammed cells would differentiate into a variety of adult cells after having been introduced into a mouse embryo which then developed into an adult mouse. Being able to do this would verify the pluripotency of the reprogrammed cells. (Pluripotency is the ability of a cell to develop into any type of fetal or adult cell. It is characteristic of embryonic stem cells.) The reprogrammed cells are called induced pluripotent stem (iPS) cells.

However, in June 2007 Yamanaka's team, along with two others, reported that they had been able to provide the missing demonstration of pluripotency. The second team that joined in reporting this accomplishment was led by Rudolf Jaenisch at MIT's Whitehead Institute for Biomedical Research. The third team was led jointly by Konrad Hochedlinger of the Harvard Stem Cell Institute and Kathrin Plath of the UCLA Institute for Stem Cell Biology and Medicine. (References: here, here, here, here, here, here, here, here, here.)

The crucial step, of course, was being able to reprogram adult human cells in the same way. For all anyone knew, this might be quite difficult. However, just five months later, in November 2007, Yamanaka's team, together with another led by James Thomson of the University of Wisconsin, announced that this objective had been accomplished. (References: here, here, here, here, here, here, here, here, here, here.)

Yamanaka's team used the same four transcription factors for the human cells as they used for the mouse cells. The cells they reprogrammed were adult human fibroblasts. Thomson's team also used Sox2 and Oct3/4, but instead of c-Myc and Klf4 they used other transcription factors: Nanog and Lin28. The cells they reprogrammed were fetal or newborn fibroblasts.

Very soon thereafter, the Japanese team announced that they could also dispense with c-Myc. That was good, because c-Myc is linked with cancer, as we discussed here. But the downside was that the process was much slower and less efficient. (References: here, here.)

In early December the Jaenisch tean from the Whitehead Institute collaborated with a team led by Tim Townes of the University of Alabama to show that their mouse iPS cells could treat a mouse model of sickle cell anemia. Specifically, they started with skin cells from sickle cell mice and made iPS cells. They also added a corrected hemoglobin gene, and then let the cells differentiate into blood-producing stem cells. When these cells were placed in mice whose defective blood stem cells had been killed, healthy red blood cells were eventually produced, alleviating the symptoms of sickle cell disease. (References: here, here, here, here, here, here, here.)

Of course, it's far too early to attempt such an experiment with humans. All concerns about the possiblity of cancer developing from the iPS cells would need to be cleared away. Then the procedure would need to be tested carefully using a lengthy series of clinical trials.

In late December, a team led by George Daley from Harvard Medical School and Children's Hospital in Boston announced thay they had also been able to convert ordinary human skin cells into embryonic-like stem cells. (See here.) The team had also programmed iPS cells from mesenchymal stem cells (adult stem cells found in bone marrow that can differentiate into fat, bone and cartilage).

Recently (mid-February), Kathrin Plath's team at UCLA has also announced success in reprogramming human skin cells, using the same techniques as previously reported. They have also verified that the induced pluripotent cells are very similar to embryonic stem cells:

Human Skin Cells Reprogrammed Into Embryonic Stem Cells (2/11/08)

The reprogrammed cells were not just functionally identical to embryonic stem cells. They also had identical biological structure, expressed the same genes and could be coaxed into giving rise to the same cell types as human embryonic stem cells.

As we've noted, there have been some potential problems with the work already mentioned. First, any process that activates c-Myc (directly or indirectly) runs risks of promoting cancerous tumors. Second, the processes have used retroviruses to introduce the necessary genetic material into cells to be reprogrammed. This also runs the risk of inducing cancer.

So Konrad Hochedlinger's team has come along with work in mice to reduce or remove these cancer-causing risks:

Discovery Could Help Reprogram Adult Cells To Embryonic Stem Cell-like State (2/15/08)

Harvard Stem Cell Institute (HSCI) and Massachusetts General Hospital (MGH) researchers have taken a major step toward eventually being able to reprogram adult cells to an embryonic stem cell-like state without the use of viruses or cancer-causing genes.

In a paper released online today by the journal Cell Stem Cell, Konrad Hochedlinger and colleagues report that they have discovered how long adult cells need to be exposed to reprogramming factors before they convert to an embryonic-like state, and have “defined the sequence of events that occur during reprogramming.”

This work on adult mouse skin cells should help researchers narrow the field of candidate chemicals and proteins that might be used to safely turn these processes on and off. This is particularly important because at this stage in the study of these induced pluripotent (iPS) cells, researchers are using cancer-causing genes to initiate the process, and are using retroviruses, which can activate cancer genes, to insert the genes into the target cells. As long as the work involves the use of either oncogenes or retroviruses, it would not be possible to use these converted cells in patients.

And hard on their heels, other teams are announcing similar findings:

Stem cell breakthrough may reduce cancer risk (2/27/08)

The main obstacle to using "reprogrammed" human stem cells – the danger that they might turn cancerous – has been solved, claims a US company.

PrimeGen, based in Irvine, California, says that its scientists have converted specialised adult human cells back to a seemingly embryonic state – using methods that are much less likely to trigger cancer than those deployed previously.

The company also claims to be able to produce reprogrammed cells faster and much more efficiently than other scientists.

More: here.

Additional reading:

• Redefining What is Embryonic Stem Cell: Nuclear Reprogramming and Epigenetic Remodeling of Fibroblasts – announcement of a talk on March 3, 2008 by Kathrin Plath, describing her reprogramming work.
  
• Reprogramming Battle: Egg Vs. Virus – an editorial with review of technical information, published online in Stem Cells, November 29, 2007
  
• Field Leaps Forward With New Stem Cell Advances – November 23, 2007 news article in Science about the first reported successes of reprogramming human skin cells into cells that act like embryonic stem cells
  
• Induced Pluripotent Stem Cell Lines Derived from Human Somatic Cells – research article in Science that is described in the preceding news article
  
• Teams Reprogram Differentiated Cells--Without Eggs – June 8, 2007 news article in Science about the reprogramming of mouse cells
  
• Reprogramming, Take Two – June 8, 2007 news article in Science about research on another approach to reprogramming, which achieved reprogramming of mouse somatic cells using zygotes whose nuclear DNA has been removed
  

Tags: stem cells, induced pluripotent stem cells

Wnt signaling

We've discussed Wnt signaling a couple of times before, here, and here.

Wnt refers to a family of proteins now numbering perhaps 20 or more, which have been found in a wide range of multicellular animals, from fruit flies, to fish, to mice and humans. Wnt proteins carry messages between cells, and are especially important in embryogenesis. They are known to play a large role in the control of stem cells and regeneration of body parts (in species where this occurs). In mammals, including humans, Wnt signaling, when it malfunctions, also seems to be involved in many types of cancer, degenerative diseases of aging, and other aging-related problems such as insulin resistance. It may be possible to ameliorate a number of these disease conditions once we have a better understanding of the details of Wnt signaling.

The "Wnt signaling pathway" refers to a sequence of proteins that, in the presence of earlier members of the pathway, change in behavior to affect proteins later in the pathway. The pathway begin when a Wnt protein (secreted by a nearby cell) binds to a cell surface protein, such as the whimsically-named Frizzled. Various other proteins in the pathway then interact, and eventually result in the build-up of a protein called β-catenin, which enters the cell nucleus, where it combines with various transcription factors to affect gene expression.

The name "Wnt" originates from the realization that two genes discovered earlier were homologous – the "wingless" gene in fruit flies (which, when mutated, yields flies without wings), and the Int genes found in mouse tumors.

Although Wnt genes and proteins have now been studied for nearly 20 years, the pace of discovery continues to increase. This is because of the large number of very interesting processes heavily influenced by Wnt signaling – from proliferation and differentiation of stem cells to embryonic development, regeneration of body parts, cancer, and degenerative diseases of aging.

The following summaries of research reports from just the past half year or so will give a buffet-style sample of Wnt-related investigations.

Carbohydrate Regulates Stem Cell Potency (2/1/08)

Embryonic stem cells are characterized by an ability to continually self-renew, but also to give rise to any adult cell type. Stem cell renewal is driven by several external signaling proteins and growth factors, including Wnt, FGF (fibroblast growth factor), and BMP (bone morphogenetic protein). In particular, Wnt signaling stimulates β-catenin to produce the transcription factor Nanog, which maintains pluripotency. However, the ability of these proteins to attach to stem cell surface proteins in order to induce a response seems to depend on the presence of a carbohydrate molecule called heparan sulfate (HS). Stem cells were found to reproduce less frequently but differentiate more frequently in proportion to experimental inhibition of HS production.

Beta-catenin Gradient Linked To Process Of Somite Formation (12/27/07)

In a developing vertebrate embryo somites are masses of a type of tissue (mesoderm) that will eventually develop into such adult tissue types as skeletal muscle and vertebrae. This research on mouse embryos demonstrates the importance of β-catenin as the principal mediator of the Wnt-signaling pathway, in the process of somite formation. In particular, there is a gradient in levels of β-catenin found in cells of the presomitic mesoderm (PSM), and this gradient is critical in regulating mesoderm maturation. This leads to the development of the characteristic vertebral column in embryos of vertebrate animals.

Certain Diseases, Birth Defects May Be Linked To Failure Of Protein Recycling System (12/20/07)

The Wnt signaling protein, like other proteins, is produced in the nuclei of certain cells, and it must be transported to the cell surface, so it can be secreted into the extracellular environment to regulate the growth of tissues during (and after) embryonic development. Another protein, called Wntless (Wls), acts as a cargo container for Wnt, and plays a key role in the transport process. Another protein, called Vps35, which makes up an important part of the "retromer complex", is responsible for moving empty Wls molecules (like freight cars) to where they are needed in the cell. But mutated Vps35 proteins can fail to perform their function, and consequently lead to the failure to transport Wnt out of the cell where it has been produced.

Grape Powder Blocks Genes Linked To Colon Cancer (11/14/07)

Previous research has found that the Wnt signaling pathway is linked to more than 85 percent of sporadic (i. e. not caused by a hereditary defect) colon cancers. Additionally, in vitro studies have shown that resveratrol is capable of blocking the Wnt pathway. The present research showed that in some colon cancer patients who consumed grape powder (which contains resveratrol and possibly other active ingredients), Wnt signaling in biopsied colon tissue was significantly reduced.

Odd protein interaction guides development of olfactory system (10/29/07)

The olfactory system of fruit flies has been shown to develop abnormally when the signaling protein Wnt5 is absent. However, if large amounts of Wnt5 but no Wnt5 receptors called "derailed" are present, development is even more abnormal. Specifically, structures called glomeruli in fruit fly antennal lobes (which are analogous to human olfactory bulbs) grow abnormally when Wnt5 is absent. But if Wnt5 is present in large amounts and there are no derailed receptors, malformed glomeruli develop in locations where they should not be.

Cilia: Small Organelles, Big Decisions (10/3/07)

Research into the development of zebra fish (a favorite of developmental biologists) has shown that organelles called cilia in the cells of developing embryos play a large role in the transduction of Wnt signaling proteins that guide the development process. By blocking the production of three proteins used by cilia, researchers were able to disrupt proper balances in the interpretation of Wnt signals, resulting in developmental defects.

New Insights into the Control of Stem Cells: Keeping the Right Balance (9/15/07)

The Wnt signaling pathway plays a crucial role in embryonic development, cell growth (proliferation), and maturation of cells into specialized cells (differentiation). It is also an important regulator of stem cells. An interaction between Wnt signaling and tyrosine kinases enables the proliferating cells to mature into specialized (differentiated) cells. Normally this interaction strikes a proper balance between proliferation and differentiation. Cancers, such as breast and colon cancer, result when the interaction gets unbalanced. In 90% of human cancers the tumor suppressor APC (adenomatous polypolis coli), one of the core components of the Wnt pathway, is deregulated. This results in excessive amounts of β-catenin, which triggers the onset of breast and colon cancer when it gets into the cell nucleus and affects gene expression.

Reactivating A Critical Gene Lost In Kidney Cancer Reduces Tumor Growth (8/15/07)

Studies of an important tumor-suppressor protein, sFRP-1 (secreted frizzled-related protein 1), in clear cell renal cell carcinoma, the most common type of kidney cancer, may reveal a means to defeat the cancer. sFRP-1 was found to control 13 tumor-promoting genes along the Wnt signaling pathway, which has been linked to a number of cancers, especially colon cancer. Several close relatives of sFRP-1 are also known to affect at least 20 Wnt-related proteins, and up-regulation of members of the sFRP-1 family may be an effective way to control cancers linked to Wnt signaling. In one experiment, increasing sFRP-1 expression in human renal cancer cells was effective, and Wnt regulated oncogenes, such as c-myc, were suppressed compared to untreated cells.

Why Aging Muscles Heal Poorly (8/9/07)

Stem cells normally found in muscle tissue are responsible for repair to muscles damaged by injury or age-related degeneration. But in aged muscle tissue, stem cells tend to produce scar-tissue cells called fibroblasts, instead of normal muscle cells (myoblasts). The overproduction of fibroblasts is a condition known as fibrosis. New research shows that it isn't the age of the muscle stem cells that is the problem, but rather the age of the cellular environment itself, including blood supply to the tissue. The malfunction appears to be a problem with Wnt signaling in the aged environment rather than with the actual stem cells. Muscle stem cells from young mice exhibited the same problems when exposed to an enviroment from older animals.

Related research found that Wnt signaling increased, with detrimental effect, due to age-related deficiency of a hormone called klotho. Klotho seems to inhibit Wnt signaling, and also has some control over insulin sensitivity. However, production of klotho seems to decline with age, possibly leading to age-related problems such as cancer, arterial disease, and insulin resistance.

Not A Relay Race, But A Team Game: New Model For Signal Transduction In Cells (6/27/07)

Details of the inner workings of the Wnt signal transduction process have remained incomplete, but are gradually coming into focus. Member of the Wnt family of proteins may dock with a variety of cell-surface proteins, including LRP6 (low density lipoprotein receptor-related protein 6) and members of the family of G protein-coupled receptors known as Frizzled. After the docking, a signaling cascade is triggered that transmits molecular messages via the cytoplasm to the nucleus. This research shows that the first step after docking involves large protein complexes formed from proteins already known to be part of the signaling pathway, such as phosphorylated LRP6, axin, and Dishevelled (Dvl).

Further reading:

The Wnt Homepage

Regeneration for Repair's Sake

The answer is blowing in the Wnt

Miller on Wnt and Klotho

A hazy shade of Wnt

Tags: Wnt, embryogenesis, stem cells, signal transduction, cancer, developmental biology, aging

MicroRNA and cancer

MicroRNAs are 18 to 25 nucleotide, noncoding RNA molecules that have been found to regulate a wide variety of cellular processes. Unusual levels of varions miRNAs have been shown to be diagnostic of pathology in a number of different cancers, such as chronic lymphocytic leukemia, lung cancer and pancreatic cancer.

The first microRNA was discovered in 1993, in C. elegans, but the term microRNA was not introduced until 2001. It took seven years for the second miRNA to be found, also in C. elegans, but many others then followed. Over 500 microRNAs have been identified in the human genome. Over a third of the human genome appears to be regulated by miRNAs orginally found is some mammal or another.

In some cases, changes to gene expression caused by miRNA seem to promote cancer. But in other cases, a miRNA may repress genes that promote cancer or its metastasis.

The p53 anti-cancer gene is affected by some miRNAs, but we will cover that in a separate note. Some miRNAs also seem to be related to cancer stem cells, which is a large topic that merits broader coverage. (See here, here.)

We've already looked at one example (here, and see below) where a gene associated with cancer can affect levels of some miRNAs. Unlike most other findings, this is a case where cancer-related pathology seems to affect miRNA expression levels, rather than the reverse.

One miRNA, in particular, stands out for the variety of genes it may affect. This miRNA is let-7, and it is known to be expressed in the later stages of animal development. Some estimates put the number of human genes affected by let-7 in the hundreds, though most of those may not be related to cancers. Ras is an important cancer-related protein that is suppressed by let-7 (See here, here.) (This report has more on let-7. See also here, here, here, here.)

The miRNA miR-21 has been associated with cancers of the colon, liver, and thyroid.

It's difficult to summarize the following research findings – they involve a variety of cancer types and many different miRNAs. Unusually high or low levels of some miRNAs seem to promote cancer in some cases, but suppress cancer in others. MiRNAs also work in a variety of different ways to affect gene expression and protein activity.

This diversity of effects due to miRNAs may well be the most interesting current finding to come out of research in this area.

Molecules may help predict survival in liver cancer (1/30/08)

In a long-term study of patients with liver cancer, it was found that those with the poorest survival history also had lower levels of 19 specific microRNAs in cancer cells compared to nearby noncancer cells than did patients with significantly better survival. This result is out of a total of 196 different microRNAs whose levels were measured.

Expression Patterns Of MicroRNAs Appear Altered In Colon Cancer, And Associated With Poor Outcomes (1/29/08)

In one cohort of 84 patients with colon cancer 37 different microRNAs were differently expressed in cancer cells compared with noncancer cells. 5 of these miRNAs could reliably discriminate between tumorous and nontumor tissue. The same 5 miRNAs had similar discriminatory powers in a different cohort of 113 patients. For the specific miRNA known as miR-21, high expression levels were associated with poor survival outcomes in both patient cohorts. (High levels of miR-21 are also associated with thyroid cancer, see here, and with liver cancer, see here.)

Two MicroRNAs Promote Spread Of Tumor Cells (1/28/08)

MicroRNAs have been shown in many studies to block translation of tumor suppressor genes. In this study, two specific miRNAs (out of 450 tested) have been shown to transform non-invasive human breast cancer cells into cells that rapidly metastasized in cell cultures and laboratory mice. One of the miRNAs, miR-373, was previously identified as a possible oncogene in testicular cancer. The other miRNA, miR-520c, hasn't previously been associated with cancer, but is similar to miR-373. Both miRNAs are found only in cancer cells. There is evidence that they downregulate the CD44 gene, and that in turn leads to metastasis of non-metastatic tumor cells. In human patients, metastatic cells are found to have higher levels of miR-373 and lower expression of CD44 than non-metastatic tumor cells.

Molecules Might Identify High-risk Acute-leukemia Patients (1/15/08)

In a study of leukemia cells from 122 patients with high- and intermediate-risk acute myeloid leukemia (AML) the same miRNAs could be found in both normal and leukemic cells, but there were differences in levels of various miRNAs present. Two specific miRNAs (miR-191 and miR-199a) were present at abnormally high levels that were clearly associated with patient survival. The same two miRNAs have been previously found to be associated with cancers of the lung, prostate, colon, stomach and breast. Another miRNA (miR-155) was associated with a gene mutation, and high levels of it have been reported in other cancers (see here, here) and to cause leukemia in mice.

Small Molecule Can Prevent Spread Of Breast Cancer, Study Suggests (1/9/08)

Three miRNAs have been found that prevent breast cancer metastasis by interfering with the expression of genes that give cancer cells the ability to proliferate and migrate. Researchers found lower levels of a few miRNAs (miR-335, miR-126 and miR-206) in metastatic cells compared to non-metastatic tumor cells. Testing in mice showed that raising levels of these miRNAs inhibited metastasis. Further analysis showed that miR-126 influences the proliferation rate of metastatic cells, while miR-335 and miR-206 influence the cancer cells' ability to migrate into lungs or bone. miR-335 was found to inhibit expression of SOX4 and TNC genes, which affect cell migration.

More: here, here

Virus Discovered Using Same Tools As Host Cell (12/17/07)

A microRNA expressed in the genome of the Kaposi's Sarcoma Associated Herpesvirus (KSHV) appears to be very similar in stucture and function to a miRNA associated with lymphoma – miR-155, mentioned above. KSHV itself causes a rare skin cancer that disproportionately affects HIV-infected individuals. Both miR-155 and the KSHV miRNA regulate the same genes, including several associated with B cell function and cell cycle regulation. Hence KSHV may promote B cell tumors by repressing one or more of these genes, as miR-155 seems to do.

Scientists Identify And Repress Breast Cancer Stem Cells In Mouse Tissue (12/17/07)

Since 2001 stem-like cells that appear to initiate cancer development have been discovered in breast, lung, brain and colon tissues, as well as in the blood. A microRNA (let-7) has now been found that can help to identify such cancer stem cells in breast cancer tissue of mice. Further tests indicate that let-7 can attack and eliminate these cancer progenitors.

MicroRNA Regulates Cancer Stem Cells: Could Lead To Treating Cancer As A Whole (12/13/07)

Another study involving the interaction of miRNA let-7 and cancer stem cells was conducted independently and published just before the one described above. In this study, researchers found a way to grow large quantities of tumor stem cells by growing human breast cancer cells in immunosuppressed mice. They found that these stem cells contained low amounts of several miRNAs, compared to more mature tumor cells or stem cells that had differentiated in culture. When let-7 was activated in these cells, they lost their ability to self-renew and began to differentiate. They also became less able to form tumors in mice or to metastasize. It appears that let-7 did this by switching off two cancer-related genes: the oncogene Ras, and HMG2A (see here, here).

Silencing Small But Mighty Cancer Inhibitors (12/10/07)

As discussed here, the important transcription factor Myc, which is overexpressed in many cancers, can also stop the production of at least 13 microRNAs. Some of these miRNAs have an inhibiting effect on cancer. In some cases re-introducing repressed miRNAs into Myc-containing cancer cells suppressed tumor growth in mice. So repression of miRNAs may be another pathway through which overexpression of Myc promotes cancer. The research involved lymphoma cells in mice, and showed that Myc repressed the miRNAs by directly attaching to the DNA at the miRNA genes.

Scientists discover new role for miRNA in leukemia (12/10/07)

A microRNA has been found to play a new role in the development of cancer, in this case chronic myeloid leukemia (CML). The miRNA is miR-328, and normally it is able to directly bind to a certain protein, inhibiting the activity of that protein. But if levels of miR-328 become abnormally low, the protein prevents white blood cells maturing as they should. The result is the build-up of immature white blood cells and entrance to what is called the "blast-crisis" phase of the disease.

Cellular Pathway Identified That Makes Prostate Cancer Fatal (11/27/07)

Expression levels of microRNAs were measured in samples of prostate cancer cells. Five different miRNAs were found to have unusual expression levels. One of these, miR-125b, was found at high levels in both androgen-dependent and the more dangerous androgen-independent prostate cancer cells.

Earlier research reports:

• MicroRNA Convicted Of Triggering Metastasis (9/26/07) – More: here – breast cancer, miR-10b
  
  
• Molecule Blocks Gene, Sheds Light On Liver Cancer (8/1/07) – liver cancer, miR-21
  
  
• New Genetic Marker Characterizes Aggressiveness Of Cancer Cells (6/25/07) – various cancers, let-7
  
  
• Tiny Genes May Increase Cancer Susceptibility, Scientists Find (5/23/07)
  
  
• Newly Identified Mechanism For Silencing Genes Points To Possible Anti-cancer Strategies (5/16/07)
  
  
• Pancreatic Cancer Markers Identified, May Predict Survival (5/1/07) – pancreatic cancer
  
  
• Biomarker Discovery Bodes Well For Better Cancer Diagnostics, Pharmacologist Says (5/1/07) – pancreatic cancer
  
  
• MicroRNAs Can Be Tumor Suppressors (4/25/07) – various cancers, let-7
  
  
• Leukemia Drug Turns Mini-molecules Up, Cancer Genes Down (3/2/07) – leukemia, miR-15b, miR-16-1, let-7
  
  
• MicroRNA Helps Prevent Tumors (2/22/07) – various cancers, let-7
  
  
• Micro Molecules Can Identify Pancreatic Cancer (1/10/07) – pancreatic cancer
  
  
• Pair Of MicroRNA Molecules Controls Major Oncogene In Most Common Leukemia (12/15/06) – leukemia, miR-29, miR-181 – more on miR-29 here
  
  
• MiRNA Fingerprint Identified In Platelet Formation (3/16/06) – leukemia
  
  
• Role Of MicroRNA Identified In Thyroid Cancer (12/23/05) – thyroid cancer, miR-21, miR-146, miR-181a, miR-221, miR-222
  
  
• Unusual RNAs Linked To Chronic Leukemia, May Help Treat It (9/18/05) – leukemia, miR-15, miR-16
  
  
• Yale Scientists Find MicroRNA Regulates Ras Cancer Gene (3/25/05) – lung cancer and others, let-7
  
  
• Small Molecule May Help Pinpoint Some Cancers (3/9/05) – lymphoma, miR-155
  

Tags: cancer, microRNA, cancer stem cell

Cancer and Myc

Myc is a gene that has been studied for over 20 years and is found to be overexpressed in many human cancers. The protein it codes for (which for simplicity we'll also refer to as Myc) is a transcription factor, like members of the FoxO family, which means it can enable or disable the expression of many other genes. How many? The estimate is about 15% of all human genes. Since there are at least 20,000 genes, the number regulated by Myc is 3000 or more. That's a lot of leverage.

Obviously, Myc is essential for cell function or it wouldn't have so much influence. The biological functions Myc affects include cell proliferation, cell growth, apopotosis, cell differentiation, and stem-cell self-renewal. It is possible for a single transcription factor to have such varied effects because other transcription factors (coactivators or corepressors) must also be present in order to activate or repress the expression of some specific other gene. That is, the expression of any particular gene depends on the presence (or absence) of a particular set of transcription factors.

Since Myc affects the functions mentioned above, it's hardly surprising to find that Myc is overexpressed in many cancers. In such cases, the difference between a normal cell and a cancer cell is the overexpression of Myc in the latter and possibly the abnormal presence of other coactivators or corepressors. The result in a cancer cell is excessive proliferation and/or avoidance of cell death by apoptosis.

Surely you've wondered why development of cancer therapies has taken so long. A large part of the reason is that so many genes involved in cancer interact with so many other genes that have essential functions. So it's not possible to interfere with the cancer-related genes without disrupting vital biological functions elsewhere in the body.

The expression of Myc itself is triggered by signals that are usually external to the cell and normally serve to stimulate cell growth and proliferation when needed, as in lymphocyte production, normal growth, or wound healing. Such signals are called mitogens, because they can initiate mitosis. Wnt, Shh, and EGF are mitogens that can lead to Myc expression.

It is probably almost impossible to hope to combat cancer by directly affecting Myc or its related mitogens, because all of these have essential normal functions themselves. Instead, anti-cancer research needs to examine how Myc may be overexpressed or complemented in harmful ways by other transcription factors.

One promising line of research involves cancer stem cells – cells that, like normal stem cells, can proliferate and differentiate into other cell types, and that also carry cancer-causing mutations. There is now thought to be a "signature" consisting of 11 genes that may be characteristic of cancer stem cells. One of these genes has an effect on Myc:

Scientists Uncover Role Of Cancer Stem Cell Marker: Controlling Gene Expression (1/18/08)

Scientists at Jefferson's Kimmel Cancer Center in Philadelphia have made an extraordinary advance in the understanding of the function of a gene previously shown to be part of an 11-gene "signature" that can predict which tumors will be aggressive and likely to spread. The gene, USP22, encodes an enzyme that appears to be crucial for controlling large scale changes in gene expression, one of the hallmarks of cancer cells. ...

In one example, they looked at the relationship between MYC and USP22. MYC, which is among the most commonly overexpressed genes in cancer, encodes a protein that controls the expression of thousands of other genes. The scientists showed that USP22 is a critical partner of MYC and that by depleting cells of USP22, they could prevent MYC from working properly, stopping it from inducing the invasive growth of cancer cells.

It turns out that Myc affects not only 3000 or so ordinary genes, but also a number of DNA sequences that code for microRNA – and some of these microRNAs play an important role in suppressing cancer. In fact, Myc can stop the production of at least 13 microRNAs:

Silencing Small But Mighty Cancer Inhibitors (12/12/07)

Researchers from Johns Hopkins and the University of Pennsylvania have uncovered another reason why one of the most commonly activated proteins in cancer is in fact so dangerous. As reported in Nature Genetics recently, the Myc protein can stop the production of at least 13 microRNAs, small pieces of nucleic acid that help control which genes are turned on and off.

Furthermore, additional observations showed that some of these microRNAs have an inhibiting effect on cancer, a striking result in itself:

[I]n several instances, re-introducing repressed miRNAs into Myc-containing cancer cells suppressed tumor growth in mice, raising the possibility that a sort-of gene therapy approach could be effective therapy for treating certain cancers.

Since the microRNAs repressed by Myc affect many other genes, there could be thousands of other genes indirectly affected by Myc:

"This study expands our understanding of how Myc acts as such a potent cancer-promoting protein," says Mendell. "We already knew that it can directly regulate thousands of genes. Through its repertoire of miRNAs, Myc likely influences the expression of thousands of additional genes. Activation of Myc therefore profoundly changes the program of genes that are expressed in cancer cells."

More: Researchers zero in on the tiniest members in the war on cancer (12/13/07)

Myc is actually a member of a family of genes, the Myc family. Most members of the family have similar functions. Separate members undoubtedly appeared in the course of evolution from the duplication of earlier members and later mutation. One member, called N-myc, plays a role in both normal development of the retina, as well as cancers of the retina (retinoblastoma).

Recent research has shown that N-myc seems to be responsible for the surprising fact that the retinas in all vertebrates have about the same thickness, regardless of the size of the entire animal or its eyes:

Eye Cancer Gene's Role In Retinal Development Defined (1/18/08)

"A series of complex developmental processes must be carefully orchestrated for the eye to form correctly," said Michael Dyer, Ph.D., associate member in the St. Jude Department of Developmental Neurobiology. "One important aspect of this coordination is that retinal thickness be the same, irrespective of eye size. For example, the mouse eye is about 5,000 times smaller than that of the elephant eye, but the retinal thickness in these two species is comparable."

Working with mice, the researchers found that a gene called N-myc coordinates the growth of the retina and other eye structures to ensure the retina has the proper thickness necessary to convert light from the lens into nerve impulses that the brain transforms into images.

Tags: cancer, Myc, microRNA