The Academy: April 2007

%u25BA Wellcome Trust Sanger Institute Largest Cancer Genome Study Implicates More Mutations than Previously Thought

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he broadest survey yet of cancer genomes suggests that the number of mutated genes that drive development of the disease is greater than previously thought. Along with the driver mutations, each cell type carries many more passenger mutations that have no consequence on cancer formation. The study thus implies that the challenge lies in the ability to siftthrough mutations and decipher the drivers from the passengers.

“The human genome is a vast place and this, our first deep systematic exploration in cancer, has thrown up many surprises,” noted Mike Stratton, co-leader of the Cancer Genome Project at the Sanger Institute.

Scientists at the Wellcome Trust Sanger Institute report in Nature that they sequenced more than 250 million letters of DNA code, covering more than 500 genes and 200 cancers. The team identified possible driver mutations in 120 genes, most of which had not been seen before.

“It turns out that most mutations in cancers are passengers,” explained Dr. Andy Futreal, also co-leader of the Cancer Genome Project. “However, buried amongst them are much larger numbers of driver mutations than was previously anticipated. This suggests that many more genes contribute to cancer development than was thought.”

To distinguishing between the driver and passenger mutations, scientists will have to analyze much larger numbers of each cancer type. Faster DNA sequencing technologies will be important to achieve the scale of study needed.

The genes surveyed were of the kinase type, and Dr. Futreal said that one finding was that a group of kinases involved in the Fibroblast Growth Factor Receptor signaling pathway was hit much more than expected, particularly in colorectal cancers.

“This is a beautiful study,” commented Victor Velculescu, director of Cancer Genetics, from the Ludwig Center for Cancer Genetics and Therapeutics and Johns Hopkins University Kimmel Cancer Center. “It nicely shows the power of unbiased large-scale mutational analyses in human cancer and points to a large number of unappreciated protein kinases that appear to be important in tumorigenesis.”

The team also found that the mutations carry coded messages within them. The type of mutation varies between individual cancers, reflecting the processes that generated the mutations, some of which were active decades before the cancer showed itself. Although some patterns are understood, such as the signatures of damage from UV radiation or cancer-causing chemicals in tobacco, others still require decoding.

“The time is right to apply the powerful tools of genomics to obtain a comprehensive view of what goes wrong at the DNA level in cancer,” remarked Francis S. Collins, MD, PhD, director of the National Human Genome Research Institute at the NIH.

— Querida Anderson

%u25BA Memorial Sloan-Kettering Cancer Center Death Rates for Smokers Are Not Improved Although CT Screening Increases Early Diagnosis

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lthough CT screening found nearly three times as many lung cancers as predicted, researchers found no corresponding decrease in specifically detecting advanced lung cancers or in deaths from the disease.

The multicenter study was led by researchers at Memorial Sloan-Kettering Cancer Center, who published their findings in the March 7 issue of the Journal of the American Medical Association.

“Ours is the first study to ask whether detecting very small growths in the lung by CT is the same as intercepting cancers before they spread and become incurable,” explained Peter B. Bach, MD, MAPP, a lung physician and epidemiologist at Memorial Sloan-Kettering and the study’s first author. “We found an answer and it was no.”

The study enrolled 3,246 asymptomatic men and women with a median age of 60 who had smoked or still smoked for an average of 39 years. Starting in 1998, the patients had an initial CT scan and then at least three subsequent annual exams at either the Mayo Clinic in Minnesota, the H. Lee Moffitt Cancer Center & Research Institute in Florida or the Instituto Tumori in

Italy.

The researchers followed the volunteers to see how many had cancers detected by screening and how many had surgery to remove them. To ascertain rate of death from lung cancer, they used government records to follow the study participants for five years.

The team analyzed the effect of CT screening on the frequency of lung cancer cases, lung cancer resection, advanced lung cancer cases, and deaths from the disease. They compared their findings with what would have occurred in the absence of screening, according to a set of prediction models. Dr. Bach and Colin B. Begg, PhD, chair of the department of epidemiology and biostatistics at Memorial Sloan-Kettering, developed the statistical method for the study. The models were designed to apply to high-risk individuals, whose risk factor values fall within the following ranges: age 50 to 80 years, smoked for between 25 and 60 years, averaged between 10 and 60 cigarettes per day and if quit, had quit within the past 20 years.

The comparison found that CT screening increased detection three-fold and surgery 10-fold. The researchers diagnosed 144 cases of lung cancer, whereas 44.5 cases were expected. A total of 109 lung cancer surgeries were performed compared with the model prediction of 10.9. Overall, 96 of the cases detected were either stage I or stage II and 42 were advanced lung cancer. The model predicted 33.4 incidences of such later-stage disease. Hence, people with stage III or IV lung cancer were not much more likely to have their disease detected through the CT scanning format of this study than without screening altogether.

Similarly, while overall 38 deaths occurred due to lung cancer after the first year of screening, the model predicted a close 38.8 deaths. For the 67% of participants detected with early-stage lung cancer, only 12 died from non—small cell lung cancer during the study. Instead, the majority of individuals who died from the disease did not have their cancer detected when it was in an early stage and likely to be curable: 13 (34%) of those who died from lung cancer were initially diagnosed with stage III or stage IV non–small cell lung cancer, 7 (18%) were diagnosed with small cell lung cancer and 6 (16%) had no documented diagnosis of lung cancer prior to their death from lung cancer.

“With lung cancer the number one cause of cancer deaths in the United States, the medical profession continues to seek an effective and safeapproach to prevent deaths from this disease. According to our study, CT screening may not be it,” stated Dr. Bach.

— Querida Anderson

%u25BA University of Leicaster (UK) Rice Bran Reduces Intestinal Adenomas in Mice

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esearchers in the United Kingdom have found that a suitable daily dose of stabilized rice bran reduces precancerous adenomas in the stomach and large intestine of mice. The results, published online on January 9 in the British Journal of Cancer, confirm the dietary benefits of rice bran, which has been thought to have long-term health benefits and the potential to prevent diseases.

The study was led by Andreas Gescher, a professor in the department of cancer studies and molecular medicine at the University of Leicester in the UK. The stabilized rice bran used in the study was produced by El Dorado, CA-based NutraCea.

Gescher and his colleagues tested the effects of a diet containing 30% stabilized rice bran on mice with breast, prostate and intestinal cancer—a comparable diet in humans would contain about 200 grams of rice bran per day. They found that mice on the diet that included rice bran had an average reduction of 51% in the number of intestinal adenomas compared to mice on a control diet. Rice bran also decreased intestinal hemorrhage in the mice. In addition, the researchers found that when rice bran in the mice diet was reduced from 30% to 10%, the number of adenomas did not decrease significantly. Gescher said that the reduction of intestinal adenomas was dependent on the fiber content of the bran. Rice bran did not have any effect on the development of prostate or breast cancer.

According to NutraCea, the fiber content of their stabilized rice bran product is approximately 29%. Since the effects of the rice bran against adenomas depends on the fiber content, the company believes that their product Fiber Complex, which is the insoluble fraction of the rice bran and contains 43% fiber, would lead to even more significant effects.

— Prachi Patel-Predd

%u25BA Purdue University Holographic Images Show Tumor Response to Drugs

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urdue University physicists presented the first 3-D images showing the response of tumors to anticancer drugs at the American Physical Society meeting on March 6. The researchers have developed a new digital holographic imaging system to peek inside tumor cells.

The holographic imaging system comprises of a laser and a charged couple device chip—a microchip that captures images in digital cameras. Holography works by bouncing a light beam offan object and onto a recording medium such as a CCD chip and another light beam directly on the recording medium. This creates a pattern of bright and dark spots that change at the slightest movement of the object.

The Purdue researchers use the same principle, reflecting light offorganelles inside cancer cells that they grew in a laboratory. Organelles are specialized structures that play a key role in uncontrolled cell division and are a common target of anticancer drugs. Because organelles are typically in constant motion, they caused the bright and dark pattern to shimmer. But when the researchers added the anticancer drug colchicine to the cells, the drug limits the movement of organelles. “As the anticancer drug works, there is less motion inside the cell and the shimmer effect is reduced,” said David Nolte, a professor of physics at Purdue who led the research. “This can be seen right on the screen.”

The imaging system could have advantages in biological applications. It is sensitive to movements as small as half a micrometer. Besides, it can be used to visualize a large range of object sizes, from the sub-micrometer motion inside cells to larger, tens of micrometers sections of tumors.

“Biologists currently have to look at things on the cellular level through microscopes,” Nolte said. “With this technology, we now can detect things on the cellular level and the tissue scale at the same time.”

— Prachi Patel-Predd

%u25BA St. Jude Children's Research Hospital New Insight on Mutations Could Lead to Pediatric Leukemia Treatment

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reviously unsuspected genetic mutations that contribute to pediatric acute lymphoblastic leukemia (ALL) tumors could lead to novel methods for treating ALL, according to researchers at St. Jude Children’s Research Hospital in Memphis, TN. Acute lymphoblastic leukemia is the most common cancer in children, in which immature white blood cells rapidly multiply and become cancerous instead of developing into lymphocytes.

The research team used DNA microarray chips to investigate more than 350,000 single nucleotide polymorphisms—variations in a single nucleotide between two DNA sequences—in tumor samples from 242 pediatric patients with ALL. They found that 40% of patients had mutations in one of three genes that govern the normal differentiation and development of immature white blood cells into lymphocytes. In a paper published online in Nature on March 7, the researchers show that the PAX5 gene was most frequently mutated—it had variations in almost a third of the patients. Other genes, including EBF1 and Ikaros, which play important roles in the formation of lymphocytes, also had mutations.

The actual extent of mutations could be much higher, the researchers said.

“Although the identification of such a high frequency of mutations in this pathway was surprising, it is important to note that the approach used provides a lower limit of the true frequency of these mutations, since not every gene in this pathway could be accurately analyzed using this methodology,” said James Downing, scientific director and chair of the Pathology Department at St. Jude who led the work.

Understanding why progenitor white blood cells get stuck in their immature cancerous stage could lead to new therapies that eliminate the cells.

“If we could design a drug that bypasses the roadblock to differentiation, we could push these cells to become fully mature B lymphocytes,” Downing said. “And then the body would recognize them as defective B lymphocytes and destroy them.”

— Prachi Patel-Predd

%u25BA MESA Institute for Nanotechnology, University of Twente New "Caged" DNA System to Deliver Drugs

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esearchers at the MESA Institute for Nanotechnology of the University of Twente, Enschede, The Netherlands, have developed a new “caged” DNA system that combines DNA macromolecules with polymers containing iron, which represents a novel drug delivery system for gene therapy.

The walls of the cages are built step by step. DNA has a negative electrical charge, while the iron-containing polymer is positively charged. In addition, DNA is much more rigid than the polymer. When bound together by electrostatic forces, the polymer wraps around the DNA and forms a very stable couple with it.

The spherical cage can transport drugs and deliver them locally. The cage can be opened by allowing small molecules to function as “keys,” which oxidize the iron and break the bond between the DNA and the polymer. In the same way, it is possible to free DNA fragments from the cage, and apply them in gene therapy. Genes are inserted into cells and tissue to treat various inherited diseases.

Macroporous materials like the ones developed by the University of Twente researchers have a wide range of potential applications but are difficult to produce because of the size of their pores, which are typically larger than 50 nm.

The DNA-polymer combination is an example of “self-assembly,” in which molecules organize themselves. It is a powerful new method of creating the materials and an important step towards innovative applications. The research was led by Profs. Julius Vancso of the MESA Institute for Nanotechnology and Helmuth Möhwald of the Max-Planck-Institut für Kolloid- und Grenzflächenforschung in Gol, Germany, and is published in the February 26 issue of Angewantde Chieme International Edition.

Stated Prof. Vansco: “This is a powerful method to create the materials, and an important step towards innovative applications

for drug delivery.”

— John D. Zoidis, MD