Hutch News

DNA test exposes cancer risks

Microarray analysis helps scientists accurately measure cancer causing environmental exposures

April 1, 2004
 Dr. Johanna Lampe

From left, Dr. Johanna Lampe of Fred Hutchinson's Public Health Sciences Division is pictured with Drs. Sergey Stepaniants and Mao Mao, both of Rosetta Inpharmatics. The team collaborated to develop a molecular test to measure environmental exposures.

Photo by todd mcNaught

Scientists who study the causes of cancer soon may rely on molecular tests to measure a person's tobacco use, nutrient intake and exposure to potentially harmful chemicals. Rather than relying on individuals to self-report this information—as is standard practice for much of this research—scientists instead may be able to measure these exposures with accuracy in a drop of blood.

The study is the first to demonstrate that the approach, known as DNA microarray analysis, can distinguish successfully between smokers and nonsmokers. Based on this work, the researchers hope to adapt the method to measure a variety of exposures that are suspected to be risk factors for cancer and other diseases.

Dr. Johanna Lampe of the Public Health Sciences Division, who led the study along with Drs. Sergey Stepaniants and Mao Mao of Rosetta Inpharmatics, said that the method could be an enormously useful tool for epidemiologists, scientists who study the causes of disease.

An objective marker

"So often we must rely on people telling us what they ate or how many cigarettes they smoked," she said. "Having some kind of objective marker to measure these exposures is very important for studies that attempt to define risk factors for cancer. This method gives us a genetic profile that can be monitored and quantified."

The study appears in the March issue of Cancer Epidemiology, Biomarkers and Prevention. Others involved in the project are Dr. Jerry Radich of the Clinical Research Division; Dr. John Potter, PHS Division director and senior author of the paper; and Drs. Hongyue Dai, Peter Linsley and Stephen Friend of Rosetta, a subsidiary of Merck and Co., Inc.

The researchers used exposure to tobacco smoke as a test case for the technique's effectiveness because an individual's smoking status can be verified using a blood test that measures levels of cotinine, a substance produced when nicotine is metabolized.

"We set out to establish whether this approach had any utility at all," said Potter, who originally proposed to colleagues at Rosetta that arrays might be used in this way. "We reasoned that if we could not tell the difference between smokers and non-smokers using microarrays, we certainly would not be able to distinguish those who eat one serving of broccoli a week versus those who eat three. Now that we know this works in principle, we can explore its limits and its other possible applications. We are quite excited about testing further."

Microarray methods

Microarrays, or gene chips, allow researchers to analyze thousands of genes in a tissue sample simultaneously. The method provides a snapshot of which genes are switched on or off in response to a particular environmental exposure, such as tobacco smoke. To use microarrays, scientists must extract RNA, an intermediate molecule in the process of making proteins that provides a readout of genes that are active in a cell, from a blood or tissue sample. In this study, RNA was extracted from white blood cells known as leukocytes.

A signature pattern

The researchers obtained blood samples from 41 self-identified smokers and 44 self-identified nonsmokers, and measured cotinine levels to verify smoking status. Based on the microarray analysis, the investigators identified a signature pattern of 36 genes out of 21,000 genes whose activity levels differed between smokers and nonsmokers.

Although some of these genes were known to be influenced by tobacco smoke, many were not, a fact that Lampe said is another plus for the use of microarrays to measure exposures.

"The discovery of new genes that are regulated by cigarette smoke or other exposures provides us with the opportunity to generate some hypotheses about how certain environmental factors may lead to an increased risk of cancer," she said. "If we know what the genes are, we can begin to explore mechanisms."

'Now that we know this works in principle, we can explore its limits and its other possible applications. We are quite excited about testing further.'
Dr. John Potter, Public Health Sciences Division

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