Genetic test can help identify brain tumors

A genetic test can help determine types of brain tumors which may help doctors pick the most effective form of treatment.

Scientists have developed a mathematical method for classifying forms of glioblastoma, an aggressive and deadly type of brain cancer, through variations in the way these tumor cells 'read' genes. Their system was capable of predicting the subclasses of glioblastoma tumors with 92 percent accuracy. With further testing, this system could enable physicians to accurately predict which forms of therapy would benefit their patients the most.

Their research was performed in collaboration with Donald M. O'Rourke, M.D., a neurosurgeon at the University of Pennsylvania Brain Tumor Center, who provided the glioblastoma samples necessary to validate the Wistar computer model. Their findings were published online in the journal Nucleic Acids Research.

"It has become increasingly obvious that understanding the molecular makeup of each patient tumor is the key to personalizing cancer treatments for individual patients," said Ramana Davuluri, Ph.D., Wistar's Tobin Kestenbaum Family Professor and associate director of Wistar's Center for Systems and Computational Biology. "We have developed a computational model that will allow us to predict a patient's exact variety of glioblastoma based on the transcript variants a given tumor produces."

"A gene can produce multiple variants, in the form of transcript variants and protein-isoforms. We found that when you use the gene expression information at variant/isoform-level, the statistical analyses recaptured the four known molecular subgroups but with a significant survival difference among the refined subgroups." said Davuluri. "Using patient data, we found that certain subgroups when combined with patient age, for example, could predict better outcomes using a given course of therapy."

"As more targeted therapies come into use, this is exactly the sort of information clinicians will need to provide the best hope of survival for their patients," Davuluri said. "In time, we think this could form the basis of a clinical test that will help oncologists decide a patient's course of treatment."

Glioblastomamultiforme is the most lethal of the malignant adult brain tumors, and accounts for over 50 percent of all cases of brain cancer. Even with aggressive combination therapies, the prognosis remains bleak, with median patient survival of 15 months after diagnosis. The disease is also molecularly heterogeneous, that is, composed of subtypes that are not genetically alike or produce the same array of proteins. Genetic data from the Cancer Genome Atlas (TCGA) consortium has led to the identification of four subtypes of glioblastoma, but Davuluri and his researchers sought to find a way to quickly identify which patient was which subtype.

In previous studies, Davuluri and his Wistar colleagues have established how changes in the way a cell reads its own DNA can create multiple variations of a single protein. These variant proteins are called isoforms, and they are produced as cells alter how they transcribe a given gene into RNA. Slight changes in how the cellular machine reads a gene can result in protein isoforms with subtle differences in enzymatic activity or longevity.

For example, their earlier research determined how human brains produce different isoforms of specific proteins throughout their lives. Developing fetal brains produce different isoforms of certain genes than adult brains. They also found that changes that trigger the production of the wrong isoform at the wrong time could lead to cancer.

In the Nucleic Acids Research study, the researchers combined assays of these protein isoforms with a computer model they call PIGExClass, or the Platform-independent Isoform-level Gene-EXpression based Classification-system. To categorize glioblastomas with PIGExClass, Davuluri and his colleagues first began with Cancer Genome Atlas data to develop a set of 121 isoform variants whose combination of differences could denote a specific subtype of the brain cancer. PIGExClass is, essentially, a software that ranks gene isoform data into sets based on a set of pre-determined values. The researchers found that, by using this classification system, they could predict the subtype of glioblastoma in the database with 92 percent accuracy.

"When we knew what combination of isoforms could create a specific signature for each type of glioblastoma, we could then create a simple laboratory assay that would look for these differences in patient samples," Davuluri said. "In this case the test would measure variations in the RNA abundance associated with these 121 isoforms that make up the signature."

With this new assay in hand, the researchers validated their research using 206 independent samples from the University of Pennsylvania Brain Tumor Tissue Bank. According to Davuluri, when you accounted for differences in the makeup of the pools of patients between TCGA and Penn, the accuracy of the assay remained the same.

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Common cause for brain tumors in children

A specific signaling pathway was found to be the common cause for many brain tumors in children.

An overactive signaling pathway is a common cause in cases of pilocytic astrocytoma, the most frequent type of brain cancer in children. This was discovered by a network of scientists coordinated by the German Cancer Research Center (as part of the International Cancer Genome Consortium, ICGC). In all 96 cases studied, the researchers found defects in genes involved in a particular pathway. Hence, drugs can be used to help affected children by blocking components of the signaling cascade.

The findings are published in the latest issue of the journal Nature Genetics.

Brain cancer is the primary cause of cancer mortality in children. Even in cases when the cancer is cured, young patients suffer from the stress of a treatment that can be harmful to the developing brain. In a search for new target structures that would create more gentle treatments, cancer researchers are systematically analyzing all alterations in the genetic material of these tumors. This is the mission of the PedBrain consortium, which was launched in 2010. Led by Professor Stefan Pfister from the German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ), the PedBrain researchers have now published the results of the first 96 genome analyses of pilocytic astrocytomas.

Pilocytic astrocytomas are the most common childhood brain tumors. These tumors usually grow very slowly. However, they are often difficult to access by surgery and cannot be completely removed, which means that they can recur. The disease may thus become chronic and have debilitating effects for affected children.

In previous work, teams of researchers led by Professor Dr. Stefan Pfister and Dr. David Jones had already discovered characteristic mutations in a major proportion of pilocytic astrocytomas. All of the changes involved a key cellular signaling pathway known as the MAPK signaling cascade. MAPK is an abbreviation for "mitogen-activated protein kinase." This signaling pathway comprises a cascade of phosphate group additions (phosphorylation) from one protein to the next -- a universal method used by cells to transfer messages to the nucleus. MAPK signaling regulates numerous basic biological processes such as embryonic development and differentiation and the growth and death of cells.

"A couple of years ago, we had already hypothesized that pilocytic astrocytomas generally arise from a defective activation of MAPK signaling," says David Jones, first author of the publication. "However, in about one fifth of the cases we had not initially discovered these mutations. In a whole-genome analysis of 96 tumors we have now discovered activating defects in three other genes involved in the MAPK signaling pathway that have not previously been described in astrocytoma."

"Aside from MAPK mutations, we do not find any other frequent mutations that could promote cancer growth in the tumors. This is a very clear indication that overactive MAPK signals are necessary for a pilocytic astrocytoma to develop," says study director Stefan Pfister. The disease thus is a prototype for rare cancers that are based on defects in a single biological signaling process.

In total, the genomes of pilocytic astrocytomas contain far fewer mutations than are found, for example, in medulloblastomas, a much more malignant pediatric brain tumor. This finding is in accordance with the more benign growth behavior of astrocytomas. The number of mutations increases with the age of the affected individuals.

About one half of pilocytic astrocytomas develop in the cerebellum, the other 50 percent in various other brain regions. Cerebellar astrocytomas are genetically even more homogenous than other cases of the disease: In 48 out of 49 cases that were studied, the researchers found fusions between the BRAF gene, a central component of the MAPK signaling pathway, and various other fusion partners.

"The most important conclusion from our results," says study director Stefan Pfister, "is that targeted agents for all pilocytic astrocytomas are potentially available to block an overactive MAPK signaling cascade at various points. We might thus in the future be able to also help children whose tumors are difficult to access by surgery."

The International Cancer Genome Consortium (ICGC), a network of scientists from currently 15 countries, aims to obtain a comprehensive description of genomic and epigenomic changes in all significant types of cancer. Germany takes part with the PedBrain Tumor Project to analyze pediatric brain tumors (medulloblastoma, which in Germany affects approximately 100 children each year; and pilocytic astrocytoma, which is diagnosed in approximately 200 children each year). Within the PedBrain Tumor Project, 300 samples of each tumor type will be analyzed, along with the same number of samples of healthy tissue from the same patients, to identify changes that are cancer-specific.

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Compulsive Eating Eased by Brain Surgery

A 10-year old girl who suffered compulsive eating caused by a benign brain tumor has the compulsive eating under control after brain surgery to remove the tumor.

Removal of a rare type of benign brain tumor helped bring a young girl's compulsive eating under control, doctors report.

The 10-year-old had what's known as a hypothalamic hamartoma -- a tumor in or around the brain's hypothalamus. One of the symptoms of this type of tumor is extremely early (precocious) puberty, as well as compulsive eating and excessive weight gain.

As reported online April 9 in the Journal of Neurosurgery: Pediatrics, by age 10 the girl already weighed 227 pounds and was gaining an average of five more pounds each month. Medication and counseling did nothing to curb her overeating.

Despite the fact that there was no record of it having been done before, neurosurgeons at the University of Texas-Houston and Children's Memorial Hermann Hospital in Houston decided to remove the girl's hypothalamic hamartoma in an effort to curb her overeating. The doctors called it a "last-ditch effort."

"The decision to proceed with this surgery was undertaken with great thought and after numerous discussions with the patient's family," Dr. David Sandberg, one of the study authors, said in a journal news release. "We were cautious about proceeding with a major operation in which the probability of success was completely unknown."

However, the surgery went well, the girl's appetite immediately lessened and she began eating smaller portions. Eighteen months after the surgery, her weight was still the same as it was before the operation. But it no longer increased, which was the goal of the surgery.

"The patient, her family, and treating physicians were all delighted with the outcome," Sandberg said.

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Researchers Make Living Model of Brain Tumor

Researchers have created a living 3-D model of a brain tumor and its surrounding blood vessels. In experiments, the scientists report that iron-oxide nanoparticles carrying the agent tumstatin were taken by blood vessels, meaning they should block blood vessel growth. The living-tissue model could be used to test the effectiveness of nanoparticles in fighting other diseases.

Brown University scientists have created the first three-dimensional living tissue model, complete with surrounding blood vessels, to analyze the effectiveness of therapeutics to combat brain tumors. The 3-D model gives medical researchers more and better information than Petri dish tissue cultures.

The researchers created a glioma, or brain tumor, and the network of blood vessels that surrounds it. In a series of experiments, the team showed that iron-oxide nanoparticles ferrying the chemical tumstatin penetrated the blood vessels that sustain the tumor with oxygen and nutrients. The iron-oxide nanoparticles are important, because they are readily taken up by endothelial cells and can be tracked by magnetic resonance imaging.

Previous experiments have shown that tumstatin was effective at blocking endothelial cell growth in gliomas. The tests by the Brown researchers took it to another level by confirming, in a 3-D, living environment, the iron-oxide nanoparticles' ability to reach blood vessels surrounding a glioma as well as tumstatin's ability to penetrate endothelial cells.

"The 3-D glioma model that we have developed offers a facile process to test diffusion and penetration into a glioma that is covered by a blood vessel-like coating of endothelial cells," said Don Ho, a graduate student in the lab of chemistry professor Shouheng Sun and the lead author of the paper in the journal Theranostics. "This assay would save time and money, while reducing tests in living organisms, to examine an agent's 3-D characteristics such as the ability for targeting and diffusion."

The tissue model concept comes from Jeffrey Morgan, a bioengineer at Brown and a corresponding author on the paper. Building on that work, Ho and others created an agarose hydrogel mold in which rat RG2-cell gliomas roughly 200 microns in diameter formed. The team used endothelial cells derived from cow respiratory vessels, which congregated around the tumor and created the blood vessel architecture. The advantage of a 3-D model rather than Petri-dish-type analyses is that the endothelial cells attach to the tumor, rather than being separated from the substrate. This means the researchers can study their formation and growth, as well as the action of anti-therapeutic agents, just as they would in a living organism.

"You want to see nanoparticles that diffuse through the endothelial cells, which is lost in 2-D because you just have diffusion into media," Ho said.

Read more: http://www.sciencedaily.com/releases/2012/02/120216134322

Genetic Breakthrough for Brain Cancer in Children

An international research team led by the Research Institute of the McGill University Health Centre (RI MUHC) has made a major genetic breakthrough that could change the way pediatric cancers are treated in the future. The researchers identified two genetic mutations responsible for up to 40 per cent of glioblastomas in children -- a fatal cancer of the brain that is unresponsive to chemo and radiotherapy treatment. The mutations were found to be involved in DNA regulation, which could explain the resistance to traditional treatments, and may have significant implications on the treatment of other cancers.

Using the knowledge and advanced technology of the team from the McGill University and Génome Québec Innovation Centre, the researchers identified two mutations in an important gene known as the histone H3.3. This gene, one of the guardians of our genetic heritage, is key in modulating the expression of our genes. "These mutations prevent the cells from differentiating normally and help protect the genetic information of the tumor, making it less sensitive to radiotherapy and chemotherapy," says Dr. Nada Jabado, hematologist-oncologist at The Montreal Children's Hospital of the McGill University Health Centre (MUHC) and principal investigator of the study.

"This research helps explain the ineffectiveness of conventional treatments against cancer in children and adolescents -- we've been failing to hit the right spot," says Dr. Jabado, who is also an Associate Professor of Pediatrics at McGill University. "It is clear now that glioblastoma in children is due to different molecular mechanisms than those in adults, and should not be treated in the same way. Importantly, we now know where to start focusing our efforts and treatments instead of working in the dark."

Inappropriate regulation of this gene has been observed in other cancers such as colon, pancreatic, lymphoma, leukemia and pancreatic neuroendocrine cancer, and future research could therefore reveal improved treatments for these diseases. "What is significant here is that for the first time in humans we have identified a mutation in one of the most important genes that regulates and protects our genetic information. This is the irrefutable proof that our genome, if modified, can lead to cancer and probably other diseases. What genomics has shown us today is only the beginning," says Dr. Jabado.

"Génome Québec is proud to have contributed to a project whose results will make a significant impact on the treatment of pediatric glioblastoma," underlines Marc Le Page, President and CEO of Génome Québec. "The outstanding contribution of experts in genomics and new sequencing technologies, made by the McGill University and Génome Québec Innovation Centre and as part of Dr. Jabado's project, is further proof that genomics has become essential for development and innovation in medical research. I wish to acknowledge the excellence of the teams involved in this study and the model of interdisciplinary collaboration that was implemented."

"Personalized medicine has amazing potential for many areas of health care, including infection, rare diseases and cancer. Researchers, like this team, play a vital role in translating discoveries into improved patient care," says Dr. Morag Park, Scientific Director of the CIHR Institute of Cancer Research. "Through research advancements like this, there is now greater emphasis on using genetic information to make medical decisions. We congratulate Dr. Jabado and her team on these results."

Brain tumours are the primary cause of death for children with cancer in Europe and North America. The diagnosis of glioblastoma in a child or adolescent remains a death sentence and about 200 children in Canada die every year of this cancer. Most children will die within the two years of their diagnosis regardless of treatment.

This work was supported by the Cole Foundation, and was funded in part by Genome Canada and the Canadian Institute for Health Research (CIHR) with co-funding from Genome BC, Génome Québec, CIHR-ICR (Institute for Cancer Research) and C17, through the Genome Canada/CIHR joint ATID Competition (project title: The Canadian Paediatric Cancer Genome Consortium: Translating next generation sequencing technologies into improved therapies for high-risk childhood cancer.

Read more: http://www.sciencedaily.com/releases/2012/01/120130102522

Cancer Sequencing Initiative Discovers Mutations Tied to Aggressive Childhood Brain Tumors

St. Jude Children's Research Hospital - Washington University Pediatric Cancer Genome Project provides first evidence linking cancer to mutations in genes involved in DNA organization

Researchers studying a rare, lethal childhood tumor of the brainstem discovered that nearly 80 percent of the tumors have mutations in genes not previously tied to cancer. Early evidence suggests the alterations play a unique role in other aggressive pediatric brain tumors as well.

The findings from the St. Jude Children's Research Hospital - Washington University Pediatric Cancer Genome Project (PCGP) offer important insight into a poorly understood tumor that kills more than 90 percent of patients within two years. The tumor, diffuse intrinsic pontine glioma (DIPG), is found almost exclusively in children and accounts for 10 to 15 percent of pediatric tumors of the brain and central nervous system.

"We are hopeful that identifying these mutations will lead us to new selective therapeutic targets, which are particularly important since this tumor cannot be treated surgically and still lacks effective therapies," said Suzanne Baker, Ph.D., co-leader of the St. Jude Neurobiology and Brain Tumor Program and a member of the St. Jude Department of Developmental Neurobiology. She is a corresponding author of the study published in the January 29 online edition of the scientific journal Nature Genetics.

DIPG is an extremely invasive tumor that occurs in the brainstem, which is at the base of the skull and controls such vital functions as breathing and heart rate. DIPG cannot be cured by surgery and is accurately diagnosed by non-invasive imaging. As a result, DIPG is rarely biopsied in the U.S. and little is known about it.

Cancer occurs when normal gene activity is disrupted, allowing for the unchecked cell growth and spread that makes cancer so lethal. In this study, investigators found 78 percent of the DIPG tumors had alterations in one of two genes that carry instructions for making proteins that play similar roles in packaging DNA inside cells. Both belong to the histone H3 family of proteins. DNA must be wrapped around histones so that it is compact enough to fit into the nucleus. The packaging of DNA by histones influences which genes are switched on or off, as well as the repair of mutations in DNA and the stability of DNA. Disruption of any of these processes can contribute to cancer.

Researchers said that the mutations seem unique to aggressive childhood brain tumors.

"It is amazing to see that this particular tumor type appears to be characterized by a molecular 'smoking gun' and that these mutations are unique to fast-growing pediatric cancers in the brain," said Richard K. Wilson, Ph.D., director of The Genome Institute at Washington University School of Medicine in St. Louis and one of the study's corresponding authors. "This is exactly the type of result one hopes to find when studying the genomes of cancer patients."

The results are the latest from the PCGP, an ambitious three-year effort to sequence the complete normal and cancer genomes of 600 children with some of the most poorly understood and aggressive pediatric cancers. The human genome includes the complete set of instructions needed to assemble and sustain human life. The goal is to identify differences that explain why cancer develops, spreads and kills. Researchers believe the findings will provide the foundation for new tools to diagnose, treat or prevent the disease.

For this study, researchers sequenced the complete normal and cancer genomes of seven patients with DIPG. "The mutations were found at such high frequency in the cancer genomes of those seven patients that we immediately checked for the same alterations in a larger group of DIPGs," Baker said. When researchers sequenced all 16 of the related genes that make closely related variants of histone H3 proteins in an additional 43 DIPGs, they found many of the tumors contained the same mistakes in only two of these genes.

Of the 50 DIPG tumors included in this study, 60 percent had a single alteration in the makeup of the H3F3A gene. When the mutated gene was translated into a protein, the point mutation led to the substitution of methionine for lysine as the 27th amino acid in this variant of histone H3 protein. Another 18 percent of the DIPG patients carried the same mistake in a different gene, HIST1H3B.

Researchers are now working to understand how mutations in H3F3A and HIST1H3B impact cell function and contribute to cancer. Earlier research provides some clues. The lysine that is mutated is normally targeted by enzymes that attach other molecules to histone H3, influencing how it interacts with other proteins that regulate gene expression, Baker said. Mutations in the enzymes that target histone H3 have been identified in other cancers, but this is the first report showing a specific alteration of histones in cancer.

Read more: http://www.marketwatch.com/story/cancer-sequencing-initiative-discovers-mutations-tied-to-aggressive-childhood-brain-tumors-2012-01-29

Biggest Ever Study Shows No Link Between Mobile Phone Use and Tumors

There is no link between long-term use of mobile phones and tumours of the brain or central nervous system, finds new research published online in the British Medical Journal.

In what is described as the largest study on the subject to date, Danish researchers found no evidence that the risk of brain tumours was raised among 358,403 mobile phone subscribers over an 18-year period.

The number of people using mobile phones is constantly rising with more than five billion subscriptions worldwide in 2010. This has led to concerns about potential adverse health effects, particularly tumours of the central nervous system.

Previous studies on a possible link between phone use and tumours have been inconclusive particularly on long-term use of mobile phones. Some of this earlier work took the form of case control studies involving small numbers of long-term users and were shown to be prone to error and bias. The International Agency for Research on Cancer (IARC) recently classified radio frequency electromagnetic fields, as emitted by mobile phones, as possibly carcinogenic to humans.

The only cohort study investigating mobile phone use and cancer to date is a Danish nationwide study comparing cancer risk of all 420,095 Danish mobile phone subscribers from 1982 until 1995, with the corresponding risk in the rest of the adult population with follow-up to 1996 and then 2002. This study found no evidence of any increased risk of brain or nervous system tumours or any cancer among mobile phone subscribers.

Read more: http://www.sciencedaily.com/releases/2011/10/111020191848

Research Points to Potential Therapy for Tumor-Associated Epilepsy

Glioma, one of the most deadly and common types of brain tumor, is often associated with seizures, but the origins of these seizures and effective treatments for them have been elusive. Now a team funded by the National Institutes of Health has found that human gliomas implanted in mice release excess levels of the brain chemical glutamate, overstimulating neurons near the tumor and triggering seizures.

The researchers also found that sulfasalazine, a drug on the market for treating certain inflammatory disorders, can reduce seizures in mice with glioma.

About 80 percent of people with glioma will experience at least one seizure during their illness, often as the first symptom. About one-third of patients will develop recurring seizures, known as tumor-associated epilepsy. Sen. Ted Kennedy, D-Mass., whose death was caused by a malignant glioma in August 2009, was diagnosed after having a seizure 15 months earlier.

"Seizures are a frequent symptom of glioma and are often poorly controlled by epilepsy medications," said Jane Fountain, Ph.D., a program director at NIH's National Institute of Neurological Disorders and Stroke (NINDS). "Understanding why the seizures occur and how to counteract them could help us substantially improve the quality of life for people with glioma."

Read more: http://www.sciencedaily.com/releases/2011/09/110911145157.htm