By Darrin S. Joy and Alicia Di Rado

The Department of Defense Prostate Cancer Research Program recently awarded a grant to City of Hope to support work on a new method to detect prostate cancer. The $479,000 award funds research to develop a more reliable assay used to screen for the disease.

Steven Smith, Ph.D., professor in the Division of Urology and Urologic Oncology, and members of his laboratory are collaborating with Naresh Menon, Ph.D., managing partner of ChromoLogic in Pasadena, Calif., on the novel method, which aims to harness the power of sensor chip technology. The team believes the new assay may circumvent shortcomings in existing methods and more accurately detect cancer.

Pathologists today confirm the presence of prostate cancer by inspecting a small sample of tissue, or biopsy, taken from the patient. They test for cancer by measuring the shape and density of the cells in the tissue specimen under the microscope.

About 75 percent of the tests are initially negative; and each year in the United States, nearly 25 percent of all prostate biopsies represent second or third attempts to diagnose cancer. Since the biopsies are painful and can be dangerous, physicians need a non-invasive test that can more accurately find the cancer or rule it out.

Some believe testing genes in fluid from the prostate for certain cancer-related flags — searching for telltale DNA methylation — offers an option.

Methylation is a chemical mark on DNA. It normally occurs in set patterns in cells. However, altered patterns of methylation on key genes often indicate cells are growing out of control, a hallmark of cancer.

“We’ve known since 1979 that alterations in DNA methylation are a general biomarker for cancer, but none of the available tests perform well in non-invasively obtained human specimens,” Smith said. That may soon change.

Smith’s team compared DNA methylation testing to other biomarkers for non-invasive testing, working together with City of Hope urologic oncologists Laura Crocitto, M.D., Kevin Chan, M.D., Mark Kawachi, M.D., and Timothy Wilson, M.D., Pauline and Martin Collins Family Chair in Urology, and collaborators at the Early Detection Research Network at the National Cancer Institute.

“We found that the currently available methylation tests do not perform as well as they should,” said Smith.

So, using technology they developed for methylation detection, the team improved testing with a set of prostate cancer biomarkers called the TMPRSS2:ERG fusions.

“They are clearly better than currently available tests and should be clinically useful,” he said. “Even so, we still want to improve the methylation tests, which is what this grant is about.”

Already, in today’s tests for methylation, physicians can obtain specimens of prostate secretion without having to remove tissue. Researchers then treat the DNA from the specimen with chemicals that alter unmethylated DNA but leave methylated DNA unchanged.

The mixture of chemicals and DNA is then bound to a matrix designed to clean the DNA of the processing chemicals. Once scientists recover the DNA from the matrix, they scan it for methylation sites on key genes.

“Cancer cells tend to have many more methylation sites on the genes we’re screening,” said Smith, “so the higher the amount of methylation, the more likely the sample is cancerous.”

But Smith and his team discovered that the process of preparing the sample DNA actually results in the loss of large amounts of DNA, which may affect test results — so they want to improve the method.

Because so much of the sample is lost, the amount of methylation detected may not accurately reflect the presence of cancer.

“Our results were a bit of a surprise since most of us thought that the DNA was being broken down by the chemicals. Instead we saw that it was lost during the purification step. The chip we plan to build in this proposal should get past that problem,” Smith explained.

Smith’s team aims to improve the technique’s reliability by reducing the loss of DNA. The team’s method — still in development — would dot tiny drops of DNA-filled fluid on a postage stamp-sized microfluidics chip — keeping more DNA for analysis and netting a potentially more accurate result.

“The detection technology ChromoLogic has developed is remarkable,” said Smith. “Our goal is to see if we can use it to set a new standard for prostate cancer detection in our collaboration with them.”

Prostate cancer is the most common cancer in men other than skin cancer. More than 28,600 men are expected to die from prostate cancer this year, according to the American Cancer Society, making prostate cancer is the second leading cause of cancer death in men behind lung cancer. Death rates from prostate cancer have fallen since the 1990s, as more men have gotten regular testing for early signs of the disease.