Highlight HEALTH

A large-scale, multi-dimensional analysis of the genomic characteristics of glioblastoma, the most common primary brain tumor in adults, provides new insights into the roles of several genes and defines core biological pathways altered in tumor development [1]. The new Cancer Genome Atlas study, published in the September 4th advanced online edition of the journal Nature, also reveals a link between the DNA repair enzyme MGMT and a hypermutation phenotype, and has potential implications for the diagnosis and treatment of glioblastoma.

Glioblastoma is the most common and aggressive type of brain cancer. Patients newly diagnosed with glioblastoma have a median survival of approximately one year with generally poor response to therapy [2]. Gene expression profiling studies suggest multiple subtypes of glioblastoma that, when fully defined, may allow for more personalized therapeutic approaches [3-4].

The Cancer Genome Atlas (TCGA) is an integrated network of clinical sites, core resources and specialized genome characterization and genome sequencing centers that work together to accelerate our understanding of the molecular basis of cancer. The TCGA was launched in December 2005 as a pilot program to determine the feasibility of a large-scale effort to systematically explore genomic changes in all types of human cancer [5]. TCGA utilizes genome analysis technologies to catalog and discover major cancer causing genome alterations in large groups of human tumors through integrated multi-dimensional analyses. Glioblastoma is the first type of cancer to be studied in the TCGA pilot.

Investigators from seven cancer centers and research institutions across the U.S. integrated multiple types of data, including genetic mutations, gene expression, large-scale changes in chromosome number (amplification or deletion), epigenomics and clinical treatment. The scientists evaluated 206 biospecimens for DNA copy number, gene expression and DNA methylation (a chemical modification of DNA that reduces gene expression). Of these, 143 samples had matched normal peripheral blood DNA; 91 were selected for detection of somatic (meaning cells that differentiate into various tissues and organs, as opposed to germline cells (e.g. sperm and ova)) mutation in 601 selected genes. Eight genes were identified as significantly mutated, three of which were not previously reported for glioblastoma:

• Neurofibromatosis type 1 (NF1), the tumor suppressor responsible for the peripheral nerve disorder neurofibromatosis type 1.
• Avian erythroblastic leukemia viral oncogene homolog 2 (ERBB2), a gene that functions as a co-receptor for connective tissue-derived growth factors and is frequently amplified in breast cancer.
• Phosphatidylinositol 3-kinase, regulatory subunit 1 (PIK3R1), a gene that influences the activity of an enzyme called PI3 kinase, which regulates cell proliferation and survival.

Researchers then mapped the sequencing data with additional genome characterization information onto major biological pathways and identified a highly interconnected network of alterations. By copy number data alone, three critical biological signaling pathways were identified: the Receptor Tyrosine Kinase/Ras/Phosphatidylinositol 3-Kinase pathway (a.k.a. RTK/Ras/PI3K pathway), which controls cell proliferation, cell survival and RNA translation; the p53 signaling pathway, which controls senescence (aging) and apoptosis (cell death); and the Retinoblastoma (RB) signaling pathway, which controls cell cycle progression and cell division. In a given tumor sample, it was likely that there was at least one aberrant gene from each of the three pathways. In fact, 74% of the samples had mutations in all three pathways, suggesting that deregulation of the three pathways is a requirement for glioblastoma pathogenesis.

Oncologists already know glioblastomas that have a methylated MGMT gene (DNA methylation reduces gene expression) respond better to temozolomide, an alkylating chemotherapy drug that is the current standard of care for glioblastoma patients. By integrating methylation data, somatic mutation data and clinical treatment data, scientists identified a relationship between MGMT methylation and a hypermutator phenotype described previously [6]. In patients with MGMT methylation, temozolomide treatment introduces a strong selective pressure to mutate genes that are essential for DNA repair. Thus, patients who initially respond to temozolomide may evolve not only treatment resistance but also a hypermutator phenotype (since DNA repair genes have been mutated). Future selective therapies may therefore require targeting both DNA-repair-deficient cells and an alkylating agent.

National Institutes of Health (NIH) Director Elias A. Zerhouni, M.D. said [7]:

These impressive results from TCGA provide the most comprehensive view to date of the complicated genomic landscape of this deadly cancer. The more we learn about the molecular basis of glioblastoma, the more swiftly we can develop better ways of helping patients with this terrible disease. Clearly, it is time to move ahead and apply the power of large-scale, genomic research to many other types of cancer.

The power of this study lies in the statistically robust number of samples evaluated, allowing for the identification of molecular subtypes that may otherwise be undetectable. Additionally, multiple technologies were employed to identify genomic copy number alterations, which were used to validate the results from any one platform. These approaches highlight the power of comprehensive integrative analyses.

This is an excellent example of how current genome characterization technologies can systematically explore the universe of genomic changes involved in cancer. The TCGA is also studying lung and ovarian cancer.

References

1. The Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008 Sep 4. [Epub ahead of print] DOI: 10.1038/nature07385
   View abstract
2. Mischel and Cloughesy. Targeted molecular therapy of GBM. Brain Pathol. 2003 Jan;13(1):52-61.
   View abstract
3. Mischel et al. Molecular analysis of glioblastoma: pathway profiling and its implications for patient therapy. Cancer Biol Ther. 2003 May-Jun;2(3):242-7.
   View abstract
4. Liang et al. Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme. Proc Natl Acad Sci U S A. 2005 Apr 19;102(16):5814-9. Epub 2005 Apr 12.
   View abstract
5. NIH Launches Comprehensive Effort to Explore Cancer Genomics. National Cancer Institute Office of Media Relations press release. 2005 Dec 13.
6. Cahill et al. Loss of the mismatch repair protein MSH6 in human glioblastomas is associated with tumor progression during temozolomide treatment. Clin Cancer Res. 2007 Apr 1;13(7):2038-45.
   View abstract
7. The Cancer Genome Atlas Reports First Results of Comprehensive Study of Brain Tumors: Large-Scale Effort Identifies New Genetic Mutations, Core Pathways. National Cancer Institute Office of Media Relations press release. 2008 Sept 4.

The 2008 NF Conference was held last weekend (June 6 — 10) in Bonita Springs, Florida. The preeminent annual meeting provides a forum for basic and clinical neurofibromatosis (NF) investigators to present their research (pronounced noor-oh-fahy-broh-muh-toh-sis). The conference was attended by over 200 researchers from around the world

This year’s theme — Genes to Complications to Treatments — highlighted the progress being made in NF research and clinical care, as well as the research programs of the Children’s Tumor Foundation. Last year’s NF Conference focused on models, mechanisms and therapeutic targets.

The neurofibromatoses are familial cancer syndromes that predispose individuals to the development of a variety of benign and malignant tumors in the central and peripheral nervious systems. The disorders cause tumors to grow along various types of nerves and can also affect the development of bones and skin. Neurofibromatosis has been classified into three distinct types:

• Neurofibromatosis type 1 (NF1) occurs in 1:3,500 births and is caused by a mutation of the NF1 gene on chromosome 17q11.2. NF1 diagnostic criteria (two or more) include cafe-au-lait macules, freckling, optic glioma, Lisch nodules, bony abnormalities, a first-degree relative with NF1, two or more benign nerve sheath tumors (neurofibromas) of any type, or at least one plexiform neurofibroma [1-2].
  At least 95% of NF1 patients develop benign tumors called neurofibromas [3], which may be disfiguring or associated with pain and neurological defect. As there is no cure for neurofibromatosis, the only therapy is surgical removal of the tumor and associated nerve. Approximately 6 — 13% of NF1 patients will progress and develop a malignant peripheral nerve sheath tumor (MPNST), an aggressive sarcoma that has a high mortality rate (~ 50%) [4].

• Neurofibromatosis type 2 (NF2) occurs in 1:25,000 births and is caused by a mutation of the NF2 gene on chromosome 22q12. Ninety percent of NF2 patients develop bilateral vestibular schwannomas and/or spinal schwannomas. Enlarging schwannomas can compress adjacent structures, resulting in deafness or other neurologic deficits depending on their location. Surgical removal of these tumors is difficult, often resulting in patient morbidity. Although 95% of schwannomas occur sporadically, multiple schwannomas are the hallmark of inherited NF2 [5].

• Schwannomatosis occurs in 1:40,000 patients and, in contrast to NF2, develop multiple peripheral schwannomas, but not schwannomas of the vestibular nerve. Schwannomas in schwannomatosis patients are often associated with severe, intractable neuropathic pain and sometimes numbness, tingling and weakness. It was believed that a germline mutation in an unidentified gene predisposes patients to NF2 mutation [6]. Recently, the INI1 gene was identified as a possible schwannomatosis gene [7-8].

Both NF1 and NF2 are tumor suppressor genes.

The Children’s Tumor Foundation (CTF) is dedicated to ending neurofibromatosis through research. The CTF has funded NF research for over 25 years with the goal of identifying NF drug therapies and improving the lives of those living with the disorder. The Foundation also endeavors to increase public awareness of NF and provides resources for NF patients and their families.

For more information on NF, visit the Children’s Tumor Foundation and Neurofibromatosis Cafe.

CTF medical podcasts are also available.

References

1. Riccardi VM. The prenatal diagnosis of NF-1 and NF-2. J Dermatol. 1992 Nov;19(11):885-91.
   View abstract
2. Gutmann et al. The diagnostic evaluation and multidisciplinary management of neurofibromatosis 1 and neurofibromatosis 2. JAMA. 1997 Jul 2;278(1):51-7.
   View abstract
3. Rasmussen and Friedman. NF1 gene and neurofibromatosis 1. Am J Epidemiol. 2000 Jan 1;151(1):33-40.
   View abstract
4. Evans et al. Malignant peripheral nerve sheath tumours in neurofibromatosis 1. J Med Genet. 2002 May;39(5):311-4.
   View abstract
5. Evans et al. A genetic study of type 2 neurofibromatosis in the United Kingdom. I. Prevalence, mutation rate, fitness, and confirmation of maternal transmission effect on severity. J Med Genet. 1992 Dec;29(12):841-6.
   View abstract
6. Jacoby et al. Molecular analysis of the NF2 tumor-suppressor gene in schwannomatosis. Am J Hum Genet. 1997 Dec;61(6):1293-302.
   View abstract
7. Hulsebos et al. Germline mutation of INI1/SMARCB1 in familial schwannomatosis. Am J Hum Genet. 2007 Apr;80(4):805-10. Epub 2007 Feb 16.
   View abstract
8. Hadfield et al. Molecular characterisation of SMARCB1 and NF2 in familial and sporadic schwannomatosis. J Med Genet. 2008 Jun;45(6):332-9. Epub 2008 Feb 19.
   View abstract

Neurofibromatosis (NF) is a set of genetic disorders that can cause tumors to develop and grow along various types of nerves. The tumors may also affect the development of non-nervous system tissues such as skin and bone.

There are three types of NF tumors that result from mutation or loss of different tumor suppressor genes:

• Neurofibromatosis type 1 (NF1) is the most frequent inherited cause of brain and nerve tumors. One in every 3,000 children is born with NF1, making it also one of the most common inherited human diseases worldwide. Enlargement and deformation of bones may also occur. Approximately 50% of people with NF1 also have learning disabilities. NF1 is caused by a mutation or loss of the tumor suppressor gene NF1.

• Neurofibromatosis type 2 (NF2) is much rarer, occurring in one in 25,000 births. NF2 is characterized by the development of multiple tumors on the cranial and spinal nerves. The hallmark of NF2 is the formation of tumors that affect auditory nerves. Hearing loss beginning in the teens or early twenties is typically the first symptom of NF2. NF2 is caused by a mutation or loss of the tumor suppressor gene NF2.

• Schwannomatosis is even rarer than NF2, affecting one in 40,000 individuals. SImilar to NF1 and NF2, Schwannomatosis tumors can develop on cranial, spinal and/or peripheral nerves. Although patients with Schwannomatosis do not have learning disabilities, they experience chronic pain and occasionally numbness, tingling and weakness. The candidate Schwannomatosis tumor suppressor gene is named INI1.

The National Institutes of Health (NIH) is the primary source of federal funding for biomedical research. However, other agencies also support research initiatives. In 1996, Congress added Neurofibromatosis to the Congressionally Directed Medical Research Program (CDMRP-NFRP). This program has been responsible for many advances in NF research, including NF mouse models, learning disabilities and nerve signaling pathways. In 2005, the Neurofibromatosis Research Program (NFRP) established the NF Clinical Trials Consortium, which is comprised of 10 major hospitals nationwide. The Consortium was established, not for drug discovery, but as a pipeline to test drugs repurposed to treat NF, including rapamycin (a relatively new immunosuppressant drug) and lovastatin (a statin used for lowering cholesterol). The Consortium will initially focus on NF1 for proof of concept. Once established, it will have the option of expanding to encompass NF2 and Schwannomatosis studies.

NF research program funding in jeopardy

The U.S. House and Senate included an $8 million appropriation for the CDMRP-NFRP in the FY2008 Defense Bill. This is a decrease of $2 million from 2007 and is over a 66% decrease from the high-water mark of $25 million in FY2005. Recently, I wrote about Flat Funding of Biomedical Research and The Threat to America’s Health. Separate from the NIH, the CDMRP is another funding source that supports research initiatives. The drastic funding cuts in the CDMRP-NFRP, specific to NF studies, endanger the research investment made to date, particularly with the NF Clinical Trials Consortium described above.

The Children’s Tumor Foundation (CTF), a non-profit medical foundation dedicated to improving the health and well being of individuals and families affected by the neurofibromatoses, is the largest non-government funder of NF research in the world. In 1991, the CTF began a formal advocacy and lobbying program for federal funding of NF research. Recently, the CTF announced an advocacy campaign to increase federal funding of the CDMRP-NFRP [1]:

We are all aware of the budget pressures our country faces, and understand that the $25 million funded in 2005 is not realistic in the current environement. However, this small program has accomplished so much, and as we enter what we believe will be a period of rapidly increasing clinical trials, this is a particularly important time for continued support of this funding. We are asking all of you to contact your Congressman and Senators to seek their support. There is much discussion of earmark reform in Washington. It is important to note that this funding is not an earmark. It is not directed to any one institution, state or district. It is a long standing program that makes grants solely on a peer review basis. Further, this is not a partisan issue - this funding has benefited over the years from strong support from both Democrats and Republicans. The accomplishments and return on investment from the CDMRP are a shining example of what the federal government can achieve when legislators work with the scientific community and non-profit organizations.

Indeed, the CDMRP-NFRP is a small program. Congressional appropriations for NF from 1996 to 2008 totaled just $190.3 million. By comparison, CDMRP funding for breast cancer totaled $2222.7 million, for prostate cancer, $890 million [2]. Nevertheless, CDMRP funding for NF research in 2008 is critically important to address the needs of translational research (meaning to connect basic research to patient care), complications of NF with high morbidity and mortality, and refinement and standardization of imaging techniques and biomarkers for use in future clinical trials.

You can read more on the Children’s Tumor Foundation and Neurofibromatosis here at Highlight HEALTH. Additional non-profit organization resources are listed in the Highlight HEALTH Web Directory.

I’m actively involved in neuro-oncology, specifically NF research, and can attest to the importance of CDMRP-NFRP funding. I encourage you to take a moment and email your Senator and Representative and urge them to support increased Neurofibromatosis research funding through the CDMRP. You can find your legislators contact information by visiting the House and Senate websites. For the House website, simply enter your zip code in the box in the upper left corner; for the Senate website, select your state from the pulldown menu in the upper right corner. Use the contact information provided to email, fax or mail your request for support.

UPDATE: April 1st, 2008

Sample letters are now available (in MS Word format) for download, making it that much easier to email, fax or mail your Senator and Representative.

References

1. The Children’s Tumor Foundation: Advocacy. Accessed 2008 Mar 30.
2. Congressionally Directed Medical Research Programs: Funding History. Accessed 2008 Mar 30.