One In Three Billion Found: Single Mutation In FOXL2 Gene May Cause Granulosa Cell Ovarian Cancer

“… Vancouver scientists from the Ovarian Cancer Research (OvCaRe) Program at BC Cancer Agency and Vancouver Coastal Health Research Institute have discovered that there appears to be a single spelling mistake in the genetic code of granulosa cell tumours, a rare and often untreatable form of ovarian cancer. This means that out of the three billion nucleotide pairs that make up the genetic code of the tumour, one – the same one in every tumour sample – is incorrect. The discovery, published online June 10th in the New England Journal of Medicine, marks the beginning of a new era of cancer genomics, where the complete genetic sequence of cancers can be unravelled and the mutations that cause them exposed. For women with granulosa cell tumours it represents the first specific diagnostic tool and clear path to develop much needed treatments for this cancer. …”

Found: One in Three Billion

The spelling mistake in the genetic code that causes a type of Ovarian Cancer

Eureka! Vancouver scientists from the Ovarian Cancer Research (OvCaRe) Program at BC Cancer Agency and Vancouver Coastal Health Research Institute have discovered that there appears to be a single spelling mistake in the genetic code of granulosa cell tumours, a rare and often untreatable form of ovarian cancer. This means that out of the three billion nucleotide pairs that make up the genetic code of the tumour, one – the same one in every tumour sample – is incorrect. The discovery, published online June 10th in the New England Journal of Medicine, marks the beginning of a new era of cancer genomics, where the complete genetic sequence of cancers can be unravelled and the mutations that cause them exposed. For women with granulosa cell tumours it represents the first specific diagnostic tool and clear path to develop much needed treatments for this cancer.

Dr. David Huntsman

David Huntsman, M.D. (Nfld.), Associate Professor, Department of Pathology & Laboratory Medicine, University of British Columbia; Genetic Pathologist, BC Cancer Agency

“This is really a two-fold discovery,” says Dr. David Huntsman, lead author and genetic pathologist at the BC Cancer Agency and Vancouver General Hospital and associate professor in the Department of Pathology and Laboratory Medicine at the University of British Columbia. “It clearly shows the power of the new generation of DNA sequencing technologies to impact clinical medicine, and for those of us in the area of ovarian cancer research and care, by identifying the singular mutation that causes granulosa cell tumours, we can now more easily identify them and develop news ways to treat them.”

In the past when scientists wanted to look at the sequence of a tumour, it was a laborious process, with each gene individually decoded into thousands of nucleotides and all data accumulated and sorted. Most studies could only look at one or at most a few of the 20,000 genes in the human genome whereas the new sequencing technologies allow scientists to look at everything at once. Through a collaboration between OvCaRe and the BC Cancer Agency’s Genome Sciences Centre, the research team used “next generation” sequencing machines that are able to decode billions of nucleotides at rapid speed and new computer techniques to quickly assemble the data. “This task would have been unfathomable in terms of both cost and complexity even two years ago,” says Dr. Marco Marra, Director of the BC Cancer Agency’s Genome Sciences Centre.

The OvCaRe team decoded four tumour samples of the relatively rare granulosa cell tumour, which affects five percent of ovarian cancer patients. Using the new sequencing technology and bioinformatics, they discovered a single nucleotide located in the FOXL2 gene was mutated in every sample. The research team further validated their work by examining a large number [95 samples] of additional tumour samples from across Canada and around the world, and are satisfied they have been able to validate that this mutation is present in almost all granulosa cell tumours and not in unrelated cancers. Most types of cancers, including ovarian cancers, have a broad range of genetic abnormalities. This finding shows that granulosa cell tumours have a characteristic single DNA spelling mistake that can serve as an easy to read identity tag for this cancer type.

“Although it has been suggested that hundreds of any cancer type would have to be sequenced at great depth to make clinically useful discoveries,” says Huntsman, “we had hypothesized that knowledge could be gained from much smaller studies if the cancers were carefully selected and represented clinically homogenous diseases. There are many rarer cancer types, like granulosa cell tumours that fit that bill and based upon our success in decoding granulosa cell tumours we are focusing on other rare tumours in what could be described as a guerrilla war on cancer. We hope that these studies will not only help future patients with rare tumours but will also teach us about more common ones as well.”

“This cancer is unique,” says Dr. Dianne Miller, gynecologic oncologist at BC Cancer Agency and Vancouver General Hospital. “For patients with this tumour type, it means they should all have the same response to the same treatment. And now that we have this pathway, we can look for existing cancer drugs that might work on this particular gene mutation to make the cancer disappear.”

The OvCaRe team was able to make this discovery because of the multidisciplinary nature of the group, which crosses two provincial health authorities and is made up of gynaecologists, pathologists, bioinformatics specialists, and oncologists. Further enhancing the team’s success is the centralization of patient treatment and record keeping.

“We are excited by this paper,” says Dr. Michael Birrer, professor, Department of Medicine, Harvard Medical School and director GYN/Medical Oncology, Medicine, Massachusetts General Hospital. “The ovarian cancer research and care community now has new biologic insights into this poorly understood tumour and a potential therapeutic target. More importantly, this tour de force study reveals the power of genomic approaches to cancer, particularly rare tumours.”

Ovarian cancer affects about one in 70 Canadian women. Approximately 2500 new cases are diagnosed each year and the five-year survival rate is only 30 per cent.

This study was supported by donors to VGH & UBC Hospital Foundation and the BC Cancer Foundation, and Genome BC for the development of Illumina sequencing at the BC Cancer Agency’s Genome Sciences Centre. OvCaRe and the BC Cancer Agency’s Genome Sciences Centre are also supported by the Michael Smith Foundation for Health Research.

Ovarian Cancer Research Program (OvCaRe) is a multidisciplinary research program involving clinicians and research scientists in gynaecology, pathology, and medical oncology. OvCaRe is a unique collaboration between the BC Cancer Agency, Vancouver Coastal Health Research Institute, and the University of British Columbia. Funding is provided through donations to VGH & UBC Hospital Foundation and the BC Cancer Foundation, who, in a joint partnership created a campaign to raise funds to make OvCaRe possible. The OvCaRe team is considered a leader in ovarian cancer research, breaking new ground in better identifying, understanding, and treating this disease. Earlier this year, the team discovered that ovarian cancer was not just one disease, but rather made up of several distinct subtypes.

Primary Sources:

Related N Engl J Med Editorial:  Shendure J, Stewart, CJ. Cancer Genomes on a Shoestring Budget. N Engl J Med 2009 0: NEJMe0903433 (Full Text).

Additional Reference:  Köbel M, Kalloger SE, Boyd N,et. al. Ovarian carcinoma subtypes are different diseases: implications for biomarker studies. PLoS Med. 2008 Dec 2;5(12):e232. PubMed PMID: 19053170; PubMed Central PMCID: PMC2592352.

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Stand Up To Cancer Funded Research Dream Team Takes Aim At Women’s Cancers

Stand Up To Cancer (SU2C), the Entertainment Industry Foundation’s charitable initiative supporting groundbreaking research aimed at getting new cancer treatments to patients in an accelerated timeframe, has reached a significant milestone, awarding the first round of three-year grants — that total $73.6 million — to five multi-disciplinary, multi-institutional research Dream Teams. … Each Dream Team’s project, funded for three years pending satisfactory achievement of stated milestones, is “translational” in nature, geared toward moving science from “bench to bedside” where it can benefit patients as quickly as possible. …

A Dream Team of leading cancer researchers will accelerate development of drugs to attack a mutated [PI3K] molecular pathway that fuels endometrial, breast and ovarian cancers, funded by a three-year $15 million grant awarded today by [SU2C] … Genetic aberrations in the network, known as the PI3K pathway, are found in half of all breast cancer patients, 60 percent of all cases of endometrial cancer and 20 percent of ovarian cancer patients. Other cancers that include a mutationally activated PI3K pathway include melanoma, colon and prostate cancers, brain tumors, and leukemia.

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Genetic Testing For Hereditary Breast and Ovarian Cancers Greatly Underutilized By High-Risk Women

A women’s lifetime breast cancer risk is approximately 13 percent, and her ovarian cancer risk is less than 2 percent.  But women with BRCA1 (BReast CAncer 1) or BRCA2 (BReast CAncer 2) gene mutations may be 3 to 7 times more likely to develop breast cancer, and 9 to 30 times more likely to develop ovarian cancer, respectively, than women who do not possess such mutations. A recent report, published online in the Journal of General Internal Medicine on May 20, 2009, states that genetic testing of high-risk women for hereditary breast and ovarian cancers is greatly underutilized.

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Infinity Announces Hedgehog Pathway Ovarian Cancer Preclinical Data; Results Indicate Significant Inhibition of Tumor Growth in Primary Ovarian Cancer

Infinity Pharmaceuticals, Inc. (Nasdaq:INFI), an innovative cancer drug discovery and development company, … announced the presentation of preclinical data from the natural product foundation of IPI-926, Infinity’s orally-available inhibitor of the Hedgehog pathway, demonstrating significant inhibition of tumor growth in a primary ovarian cancer model.

“CAMBRIDGE, Mass., Feb. 9, 2009 (GLOBE NEWSWIRE) — Infinity Pharmaceuticals, Inc. (Nasdaq:INFI), an innovative cancer drug discovery and development company, today announced the presentation of preclinical data from the natural product foundation of IPI-926, Infinity’s orally-available inhibitor of the Hedgehog pathway [see “Hedgehog Structure & Function,’ and ‘Hedgehog Inhibition’ Animations below under ‘Additional Resources’] demonstrating significant inhibition of tumor growth in a primary ovarian cancer model.

Data from the laboratory of Bo Rueda, Ph.D., Associate Professor, Department of Obstetrics, Gynecology and Reproductive Biology, Harvard Medical School and Associate Director, Vincent Center for Reproductive Biology, Massachusetts General Hospital, was introduced in an oral presentation entitled, Hedgehog inhibitor cyclopamine suppresses Gli1expression and inhibits serous ovarian cancer xenograft growth last week at the 40th Annual Meeting on Women’s Cancer of the Society of Gynecologic Oncologists. The data show that treatment with cyclopamine, the natural product foundation of IPI-926, in animals bearing grafts of primary ovarian cancer resulted in significant tumor growth inhibition compared to vehicle treated animals. Dr. Rueda’s models of ovarian cancer are derived from patient specimens that have not undergone prior tissue culture, and are believed to reflect the clinical presentation of ovarian cancer.

Infinity’s novel, oral, Hedgehog pathway inhibitor, IPI-926, is semi-synthetic derivative of the natural product cyclopamine with superior drug-like properties, including being 30 to 50 times more potent. In addition, IPI-926 has demonstrated significant anti-tumor activity and excellent pharmaceutical properties, including oral bioavailability, long plasma half-life and duration of action, and dose-dependent inhibition of tumor growth, in a number of preclinical models including pancreatic cancer, small cell lung cancer, and medulloblastoma.

IPI-926 is currently being evaluated in a Phase 1 trial in patients with advanced and/or metastatic solid tumors. The study is designed to evaluate the safety, tolerability and pharmacokinetics of IPI-926, and to determine a recommended dose and schedule for subsequent studies. Infinity will also evaluate potential anti-tumor activity of IPI-926 and examine pharmacodynamic markers of its biological activity.

Infinity anticipates publishing additional preclinical data with IPI-926 at the 2009 Annual Meeting of the American Association for Cancer Research (AACR) in April 2009.

About IPI-926

IPI-926 is a novel, proprietary inhibitor of the Hedgehog signaling pathway being evaluated in a Phase 1 clinical trial in patients with advanced solid tumors. IPI-926 is a derivative of the natural product cyclopamine that binds to and inhibits a key regulator of this pathway, the Smoothened receptor. The Hedgehog signaling pathway is normally active in regulating tissue and organ formation during embryonic development. However, abnormal activation of the Hedgehog pathway can lead to cancer and is believed to play a central role in allowing the proliferation and survival of several types of cancers, including pancreatic, prostate, lung, breast, and certain brain cancers. In preclinical models, IPI-926 has demonstrated significant anti-tumor activity and excellent pharmaceutical properties, including oral bioavailability, long plasma and tumor half-life, and dose-dependent inhibition of tumor growth, in a number of preclinical models.

About Infinity Pharmaceuticals, Inc.

Infinity is an innovative cancer drug discovery and development company seeking to discover, develop, and deliver to patients best-in-class medicines for the treatment of cancer and related conditions. Infinity combines proven scientific expertise with a passion for developing novel small molecule drugs that target emerging cancer pathways. Infinity’s two most advanced programs in Hsp90 inhibition and Hedgehog signaling pathway inhibition are evidence of its innovative approach to oncology drug discovery and development. For more information on Infinity, please refer to the company’s website at http://www.infi.com.

Forward-Looking Statements

This press release contains forward-looking statements within the meaning of The Private Securities Litigation Reform Act of 1995. These statements involve risks and uncertainties that could cause actual results to be materially different from historical results or from any future results expressed or implied by such forward-looking statements. Such forward-looking statements include statements regarding the utility of Hedgehog inhibitors, including IPI-926, in treating various types of cancer; future clinical trial activity of IPI-926; and the presentation of additional preclinical data on IPI-926. Such statements are subject to numerous factors, risks and uncertainties that may cause actual events or results to differ materially from the company’s current expectations. For example, there can be no guarantee that IPI-926 will successfully complete necessary preclinical and clinical development phases. In particular, management’s expectations could be affected by risks and uncertainties relating to: results of clinical trials and preclinical studies, including subsequent analysis of existing data and new data received from ongoing and future studies; the content and timing of decisions made by the U.S. Food and Drug Administration and other regulatory authorities, investigational review boards at clinical trial sites, and publication review bodies; Infinity’s ability to enroll patients in its clinical trials; decisions made by EORTC and other organizations evaluating data for presentation or publication; Infinity’s ability to obtain additional funding required to conduct its research, development and commercialization activities; unplanned cash requirements and expenditures; and Infinity’s ability to obtain, maintain and enforce patent and other intellectual property protection for any product candidates it is developing. These and other risks which may impact management’s expectations are described in greater detail under the caption “Risk Factors” included in Infinity’s registration statement on Form S-3 filed with the Securities and Exchange Commission on January 9, 2009. Further, any forward-looking statements contained in this press release speak only as of the date hereof, and Infinity expressly disclaims any obligation to update any forward-looking statements, whether as a result of new information, future events or otherwise.

CONTACT: Infinity Pharmaceuticals, Inc.
Monique Allaire
617-453-1105
Monique.Allaire@infi.com
http://www.infi.com”

Quoted Source Infinity Announces Hedgehog Pathway Preclinical Data in Ovarian Cancer – Data Demonstrate Significant Inhibition of Tumor Growth in Primary Ovarian Cancer, Press Release, Infinity Pharmaceuticals, Inc., Feb. 9, 2009.

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