A study led by Dr Janet Shipley from The Institute of Cancer Research (ICR) in London in collaboration with Dr Mauro Delorenzi from the SIB Swiss Institute of Bioinformatics in Lausanne has shown that a simple genetic test could help predict the aggressiveness of rhabdomyosarcoma tumours in children. The test, which should be introduced into clinical practice, would lead to changes in treatment for many patients, allowing some children to escape potentially long-term side-effects whilst giving others the intense treatments they need to increase their chances of survival. The results of the study are published online today in the Journal of Clinical Oncology.

Until now, the PAX3/FOXO1 fusion gene only served as a classification agent for tumour histology but never as a prognostic indicator. The research team found that children who have a tumour called rhabdomyosarcoma with this particular genetic fault have significantly poorer survival rates than other rhabdomyosarcoma patients. This fusion gene can thus be very useful in the prognosis of patient’s survival.

More than that, it can provide better information about how aggressively the tumour is likely to behave and help doctors to tailor treatment for each patient. So far, children diagnosed with rhabdomyosarcoma were treated with a combination of chemotherapy and surgery and sometimes radiotherapy. These treatments have helped improve survival rates, but they can also cause serious and long-term side-effects including the potential to develop another cancer later in life. But not all patients need such intense treatment. Dr Shipley says: “Our previous studies have raised issues with the current system of predicting patients’ risk, which is based on the appearance of patients’ tumours. Our new study finds that a simple genetic test should be incorporated into standard clinical practice as it significantly improves our ability to predict tumour aggressiveness. This fusion gene test could be used alongside other standard clinical measures to divide patients into one of four risk-groups, so that treatment can be tailored accordingly. Importantly, this will mean some patients who were previously categorised as high-risk could be able to avoid the side-effects associated with intense treatment, while others should receive the intense treatment they need to increase their chance of survival.”

The study required high level statistics expertise

To analyse the data for thousands of genes from 225 rhabdomyosarcoma samples, Dr Shipley called onto the expertise of the Bioinformatics Core Facility Group at the SIB Swiss Institute of Bioinformatics in Lausanne, which is led by Dr. Mauro Delorenzi. This group provides statistical and analysis support for either national and international academic and private teams. Dr. Edoardo Missiaglia and Dr. Pratyaksha Wirapati performed the analysis of the data provided in the frame of this study and constructed and evaluated systems to score the aggressiveness of the individual case of rhabdomyosarcoma. Their work allowed to identify a panel of 15 genes whose altered activity level could be used to predict how patients responded to treatment. However, it was also found that most of these gene changes are linked to the presence of the PAX3/FOXO1 fusion gene: the detection of which is much simpler and cheaper than that of altered gene activity levels. Dr Delorenzi says: “We showed that by making a good use of the information about the presence or absence of the fusion of the two gene PAX3 and FOXO1, alongside other standard clinical measures, we could create a risk scoring system that is very informative on the aggressiveness of a tumour; it is so good that the additional use of the complex gene activity information does not appear to help to further improve it.”

Using the new system, 31 per cent of patients in the study who would previously have been classified as intermediate risk would be reassigned to a lower risk group, while a further 29 per cent of intermediate-risk patients would be moved to a higher risk group. Combining the fusion gene test with two existing standard measures of risk for rhabdomyosarcomas – the patient’s age at diagnosis and the tumour’s stage of development – gave a simple but highly effective prognostic test.

The research team now intends to validate their findings using a larger European and independent data set. If confirmed, their method could be used in future clinical trials to assist clinicians in treatment decision. Dr Missiaglia adds: “In the same work we also show evidence that the gene activity information of 5 other genes might give important additional information in a subgroup, but since this is rare we do not yet have enough cases to be sure and this should be further tested on new data that are not yet available”.

Provided by Swiss Institute of Bioinformatics

The breakthrough has been described as a “potential Achilles’ heel” by lead research Professor Alan Clarke.

It comes from the work at the Cancer Research UK Centre in Cardiff into how genes and proteins are involved in the formation of cancer.

Prof Clarke said: “The interesting thing about cancer is that one of its primary features is to turn off a number of defensive mechanisms. As the cancer develops, these defensive mechanisms are got around, usually because the genes are switched off or deactivated.”

But deactivating DNMT1 also had a significant effect on other bodily functions, meaning it would not make a good target for cancer therapies.

MBD2 belongs to a family of proteins which turn off other genes and research carried out in Cardiff has found that deactivating it prevents colon tumours from developing.

“It’s fantastic and does it with virtually 100% efficiency,” Prof Clarke said. “And, taking out MBD2 isn’t that damaging to other tissues and systems – it appears to be tolerated reasonably well.

“Therefore, if we were to have a therapy targeting MBD2, any off-target effects would be limited.”

The research team has been examining the impact of MBD2 by creating mice which lack the gene. But many questions remain unanswered.

Prof Clarke said: “We have to show that if you don’t have MBD2 then the likelihood of getting a tumour is much reduced. And we don’t know if you take out MBD2 from a tumour whether it will disappear.

“We’ve been trying to develop a drug that specifically targets MBD2 but, unfortunately, attempts have not been successful because it’s a very difficult protein.

“We think that MBD2 deficiency suppresses tumorigenesis by failing to turn off a number of genes – some these will be important. We’re trying to delve down and find out which of the genes it regulates are important.

“We have a potential Achilles’ heel here to stop tumours forming and we’re also trying to find a drug target.

“We can imagine that this will be useful for patients who have had a tumour and have had therapy but who have a chance of relapsing. But we’re also testing the notion that regulating MBD2 will cause tumours to regress.”

Prof Clarke added: “The remarkable thing about the way we treat cancer is that we’re stuck with pretty much ancient technology.

“We mostly use poisons but although we have made progress with virtually all forms of cancer in terms of improving treatment, if we are going to make a huge step change it will have to come from a better understanding of the mechanisms that lead to cancer.

“That will come from a molecular understanding of cancer – if we really understand the molecular basis we can create drugs that make a big difference rather than small, incremental differences.”

The vaccine worked at shrinking similar mouse versions of breast and pancreatic tumors, but researchers from the University of Georgia and the Mayo Clinic said that it could be applied to other cancers, too, including colorectal and ovarian cancers and multiple myeloma.

Scientists have been working for decades to find a way to mobilize the immune system to be able to identify cancerous cells. The problem has always been that the immune system doesn’t recognize the cancerous cells as dangerous because they originated from the body in the first place, and therefore doesn’t attack them, researchers said.

But the new vaccine works by targeting the sugar coating of a protein called MUC1 located on the surfaces of the cancerous cells. The sugar coating differentiates the cancerous cells from normal, healthy cells. The mice were engineered so that their cancer cells overexpressed MUC1, just like human cancer cells do.

“This is the first time that a vaccine has been developed that trains the immune system to distinguish and kill cancer cells based on their different sugar structures on proteins such as MUC1,” study researcher Sandra Gendler, a professor at the Mayo Clinic, said in a statement. “We are especially excited about the fact that MUC1 was recently recognized by the National Cancer Institute as one of the three most important tumor proteins for vaccine development.”

The study will appear in the journal Proceedings of the National Academy of Sciences.

The vaccine has potential to be used on a wide variety of cancers because more than 70 percent of deadly cancers have the MUC1 protein, researchers said. AOL Lifestyle reported that researchers hope to try the vaccine in humans in the next couple of years.

And because MUC1 is overexpressed in 90 percent of people who were unresponsive to other therapies like Tamoxifen or Herceptin, the vaccine might in the future be a viable option for people whose cancers are difficult to treat, researchers added.

The experimental cancer vaccines in the works today are different from the preventive vaccines (like ones that ward off cervical cancer-causing HPV), which prevents cervical cancer.

The Daily Beast explains:

By “cancer vaccine,” scientists mean something that will stimulate the immune system to attack malignant cells.

Recently, researchers at the National Cancer Institute developed a promising vaccine that seems to stop the spread of metastatic breast and ovarian cancers in humans. The poxviral vaccine even seemed to be effective at completely ridding one person involved in the study of cancer, WebMD reported.

However, the vaccine wasn’t as overwhelmingly successful in the other 25 patients — for some of those people, the vaccine seemed to extend the amount of time before the cancer progressed by a few months, WebMD noted.

And earlier this year, University of Pennsylvania researchers announced a leukemia treatment that seems effective at obliterating leukemia cells, and was shown to completely rid patients of the cancer or at least significantly decrease their number of cancerous cells.

Epigenetic therapies against cancer have attracted considerable attention in recent years. But many of the drugs currently being studied as epigenetic anticancer therapies may have indiscriminate effects. A recent paper in Cancer Research from brain cancer researcher Erwin Van Meir’s laboratory highlights a different type of target within cancer cells that may be more selective. Postdoctoral fellow Dan Zhu is the first author of the paper.

Erwin Van Meir, PhD

The basic idea for epigenetic therapy is to focus on how cancer cells’ DNA is wrapped instead of the mutations in the DNA. Cancer cells often have aberrant patterns of methylation or chromatin modifications. Methylation is a punctuation-like modification of DNA that usually shuts genes off, and chromatin is the term describing DNA when it is clothed by proteins such as histones, a form of packaging that determines whether a gene is on or off.

In contrast to mutations that are hard-wired in the DNA, changes in cancer cells’ methylation or chromatin may be reversible with certain drug treatments. But a puzzle remains: if a drug wipes away methylation indiscriminately, that might turn on an oncogene just as much as it might restore a tumor suppressor gene.

The ability of an inhibitor of methylation to treat cancer may depend on cell type and context, explains chromatin/methylation expert and co-author Paula Vertino. She points out that one well-known methylation inhibitor, azacytidine (Vidaza), is a standard treatment for myelodysplastic syndrome, but the strategy of blanket-inhibition of methylation can’t be expected to work for all cancers. A similar challenge exists for agents that target histone acetylation in a global fashion.

Epigenetic therapies seek to modify how DNA is packaged in the cell.

Van Meir’s laboratory has been studying a tumor suppressor protein called BAI1 (brain angiogenesis inhibitor 1), which prevents tumor and blood vessel growth. BAI1 is produced by brain cells naturally, but is often silenced epigenetically in glioblastoma cells. His team found that azacytidine de-represses the BAI1 gene.

Methylation won’t turn a gene off without the help of a set of proteins that bind preferentially to methylated DNA. These proteins are what recognize the methylation state of a given gene and recruit repressive chromatin. Zhu and colleagues in Van Meir’s group found that one particular methyl-binding protein, MBD2, is overproduced in glioblastoma and is enriched on the BAI1 gene.

“Taken together, our results suggest that MBD2 overexpression during gliomagenesis may drive tumor growth by suppressing the anti-angiogenic activity of a key tumor suppressor. These findings have therapeutic implications since inhibiting MBD2 could offer a strategy to reactivate BAI1 and suppress glioma pathobiology,” the authors write.

By itself, MBD2 appears to be dispensable, since mice seem to be able to develop and survive without it. Not having it even seems to push back against tumor formation in the intestine, for example. Targeting MBD2 may represent an alternative way to steer away from cancer cells’ altered state.

Van Meir cautions: “We need to have a better understanding of all the genes that are turned on or off by silencing MBD2 in a given cancer before we can envision to use this approach for therapy.”

Vertino, Shaoman Yin and Steven Hunter, all at Emory, are co-authors on the paper. The work was supported by grants from the NIH and the Southeastern Brain Tumor Foundation and the Emory University Research Council.

Medical researchers have long known that cisplatin, a platinum compound used to fight tumors in nearly 70 percent of all human cancers, attaches to DNA. Its attachment to RNA had been assumed to be a fleeting thing, says UO chemist Victoria J. DeRose, who decided to take a closer look due to recent discoveries of critical RNA-based cell processes.

“We’re looking at RNA as a new drug target,” she said. “We think this is an important discovery because we know that RNA is very different in tumors than it is in regular healthy cells. We thought that the platinum would bind to RNA, but that the RNA would just degrade and the platinum would be shunted out of the cell. In fact, we found that the platinum was retained on the RNA and also bound quickly, being found on the RNA as fast as one hour after treatment.”

The National Institutes of Health-supported research is detailed in a paper placed online ahead of regular publication in ACS Chemical Biology, a journal of the American Chemical Society. Co-authors with DeRose, a member of the UO chemistry department and Institute of Molecular Biology, were UO doctoral students Alethia A. Hostetter and Maire F. Osborn.

The researchers applied cisplatin to rapidly dividing and RNA-rich yeast cells (Saccharomyces cerevisiae, a much-used eukaryotic model organism in biology). They then extracted the DNA and RNA from the treated cells and studied the density of platinum per nucleotide with mass spectrometry. Specific locations of the metal ions were further hunted down with detailed sequencing methods. They found that the platinum was two to three times denser on DNA but that there was a much higher whole-cell concentration on RNA. Moreover, the drug bound like glue to specific sections of RNA.

DeRose is now pursuing the ramifications of the findings. “Can this drug be made to be more or less reactive to specific RNAs?” she said. “Might we be able to go after these new targets and thereby reduce the drug’s toxicity?”

While cisplatin is effective in reducing tumor size, its use often is halted because of toxicity issues, including renal insufficiency, tinnitus, anemia, gastrointestinal problems and nerve damage.

The extensive roles of RNA have come under intense scrutiny since completion of the human genome opened new windows on DNA, life’s building blocks. It had been assumed that RNA was simply a messenger that coded for protein activity. New technologies, DeRose said, have shown that a vast amount of RNA performs an amazing level of different functions in gene expression, controlling it in specific ways during development or disease, particularly in cancer cells.

In this project, DeRose’s team only explored cisplatin’s binding on two forms of RNA: ribosomes, where the highest concentration of the drug was found; and messenger RNA. There are more areas to be looked at, said DeRose, whose group initially developed experience using and mapping platinum’s activity as a mimic for other metals in her research on RNA enzymes.

DeRose is now planning work with UO colleague Hui Zong, a biologist studying how cancer emerges, to extend the research into mouse cells to see if the findings in yeast RNA hold up. An additional collaboration with UO chemist Michael Haley involves the creation of new platinum-based drugs with “reaction handles” that will allow researchers to easily pull the experimental drugs out of cells, while still attached to their biological targets. New developments in ‘deep’ RNA sequencing, available through the UO’s Genomic Core Facilities, could then provide a much broader view of platinum’s preferred resting sites in the cell.

Mirna presented the data at the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics and the 2011 CPRIT Innovations in Cancer Prevention and Research conference.

According to the company, its researchers transfected liver cancer cells with the miRNA mimics and analyzed them four to eight days later for proliferation.

Cells were also transfected with an siRNA targeting kinesin family member 11, which lowers proliferation by 60 to 80 percent in hepatocellular carcinoma cell lines, in order to provide a comparison point for the anti-proliferative activity of the miRNAs.

Eight miRNAs demonstrated the highest “capacity to significantly inhibit the proliferation of multiple HCC cell lines,” the company said in a poster from the AACR-NCI-EORTC event. These included miR-34, which is the basis for Mirna’s lead drug candidate; miR-16; and let-7. The other miRNAs remain undisclosed.

The investigators then evaluated four undisclosed siRNA-delivery technologies in an orthotopic mouse model of human liver cancer using either a mimic of miR-34 or negative control.

Analysis by qRT-PCR revealed that the least effective delivery approach boosted levels of miR-34 in the mouse livers by around 40 copies per cell. The most effective — a lipid-based nanoparticle system — increased levels by more than 100,000 copies per cell and also delivered 10,000 copies of the miR-34 mimic per cell to spleen, lung, kidney, and pancreas one day after injection, Mirna said.

Lammers noted that Mirna expects to use this delivery system with its first drug candidate.

To assess the therapeutic effect of the miRNAs, mimics of miR-34, let-7, and two other undisclosed miRNAs were encapsulated in the nanoparticles of the best-performing delivery system and then frozen. Model mice were then given either one of the miRNA mimics, a negative control, or no treatment daily for three days and then every other day for 10 days.

“Four mice per treatment group were sacrificed on the thirteenth day after the initiation of treatment, while three animals per group were selected for five additional injections of formulated miRNA,” the company said. The mice were monitored for behavior and serum alpha fetoprotein levels, which were used to judge tumor growth.

Once AFP levels in the mice reached excessive levels or they stopped grooming themselves, the animals were sacrificed.

For the control mice, AFP levels increased exponentially during the two weeks following the start of the study. Levels in animals receiving the let-7 mimic were “significantly lower than the control groups,” but still higher than in mice receiving other miRNA mimics.

AFP levels in mice treated with miR-34 and two other unnamed miRNAs were unchanged during the treatment period, and most of them “actually had lower serum AFP levels after the treatment period than they had prior to the initiation of treatment,” Mirna noted.

“In effect, [this] meant there was a regression of the liver cancer,” an effect confirmed after the animals were sacrificed and analyzed, Lammers said.

Specifically, the team found no tumors in mice receiving one of the undisclosed miRNA mimics, and an immunohistochemical assay revealed that the “majority” of mice in the treatment groups contained no tumor cells at all.

Additional animals from the treatment groups received additional dosing for nine days. All four miRNAs “significantly increased the survival rates” of these animals, while those receiving mimics of two undisclosed miRNAs failed to develop tumors large enough to meet the moribund criteria set by the company during the study.

Despite the positive effects observed with the two undisclosed miRNAs, Mirna still intends to take its miR-34 mimic into the clinic first, Lammer said.

“We have done a lot of work on miR-34, and it is one of the most widely published microRNAs, as well,” he said. There is clearly a lot of interest” in it.

Notably, miR-34 has been linked to the tumor-suppressor protein p53. In 2007, for instance, two research groups separately reported that p53 directly targets members of the miR-34 family, suggesting the miRNA is a key component of the p53 network (GSN 6/7/2007).

At the same time, Mirna has built an intellectual property estate around the therapeutic use of miR-34. Earlier this year, the company announced that the US Patent and Trademark Office had allowed claims within an application describing methods of reducing cancer cell viability by introducing the miRNA into tumor cells (GSN 4/7/2011).

“Perhaps there is a luxury of riches we have because we have three phenomenal microRNAs that could all be very effective in liver cancer,” Lammers said. However, “we have to make choices in life,” especially as a small biotech with limited resources.

As part of its efforts to advance its miR-34 candidate, Mirna is in licensing talks with the owner of the drug-delivery technology it hopes to use with the drug, he said, although he declined to provide additional details.

The company has also identified oligo manufacturers and is preparing to conduct investigational new drug application-enabling toxicology work. Should everything remain on schedule, Mirna plans to file the IND by the end of 2012 and begin human testing early the next year.