St. Jude researchers use DNA chips to determine how leukemia cells respond to different drugs

Finding is a significant step toward new insights for designing combination chemotherapy

Investigators at St. Jude Children’s Research Hospital have discovered numerous genes that alter their level of activity in characteristic patterns in response to specific chemotherapy treatments. The genes were identified in the leukemia cells of children undergoing chemotherapy for acute lymphoblastic leukemia (ALL).

The researchers say this finding is a significant step in the emerging field of pharmacogenomics—the study of a person’s entire set of genes in order to determine which ones control that individual’s response to drug therapy.

The goal of the St. Jude researchers is to understand how cancer cells respond or become resistant to specific treatments and use these new clues to take the guesswork out of designing combination drug treatments for deadly childhood leukemia, according to William E. Evans, Pharm.D., St. Jude scientific director.

“While this study’s findings occurred in children being treated specifically for ALL, these findings serve as a paradigm for a wide variety of cancers in children and adults,” Evans said.

Evans is senior author of a report on this study appearing in the April 21 online issue of Nature Genetics. ALL is a cancer of the white blood cells in which an excess number of immature and non-functional white blood cells overwhelm the body’s ability to make normal blood cells in the bone marrow. It is the most common type of cancer in children, with about 3,000 new cases each year.

“Custom designing therapy, based on patient’s leukemic-cell and normal-cell genetics, as well as the genetic changes with chemotherapy, will maximize the treatment effects while minimizing the risk of severe side effects,” said Ching-Hon Pui M.D., member of St. Jude Hematology Oncology Department and a collaborator on the research.

Evans and his colleagues used a technique called gene expression analysis to study the response to treatment of leukemia cells taken from children before and after their initial drug treatment for ALL. Specifically, the St. Jude researchers analyzed the levels of activity of more than 9,600 genes in the cancerous white blood cells of these children before and after treatment with methotrexate (MTX) and/or mercaptopurine (MP), two drugs commonly used to treat this cancer. The children received one of four treatment regimens: high-dose MTX; high-dose MTX plus MP; low-dose MTX plus MP; and MP alone.

Based on their observations of the activity of the 9,600 genes in response to treatment, the investigators identified 124 genes whose changes in expression differed depending on which treatment the child received.

Researchers observed marked differences depending on whether the drugs were given alone or in combination. The genes that altered their activity in response to chemotherapy included those involved in apoptosis (programmed cell death, or cell suicide), mismatch repair (repairing a form of DNA mutation caused by the insertion of the wrong building block into a new copy of a gene), the control of the cell cycle (growth, DNA duplication and division), and the response of cells to the stress of chemotherapy.

The response of these particular genes suggests that leukemia cells react to drug treatment in very specific ways, depending on the treatment, according to Dr. Evans. “This kind of information will give us important new clues to how these medications work, and what cancer cells do to try to protect themselves from these drugs,” he said.

Another important finding was the way that leukemia cells responded when these two drugs were given together, versus alone.

“We’ve long assumed that the effects of combination chemotherapy can’t be predicted just by trying to add up the effects of the different drugs used in the therapy,” Evans said. “But now we have real, detailed proof that combination therapy isn’t just the sum of its parts. And we can use these new insights to design more rational and effective ways to use these drugs.”

ALL occurs after pieces of DNA break off different chromosomes and switch locations, each piece of DNA moving to the other chromosome. This movement causes abnormal gene activity, including the activation of oncogenes (genes known to cause cancer). Previous studies at St. Jude showed that the prognosis for cure differs significantly among the various genetic subtypes of ALL. These differences make it possible to differentiate among the major subtypes of leukemic cells. The differentiation also helps researcher to identify some patients at high risk of failing treatment.

“Our previous studies of ALL focused on differences in gene expression in cancer cells before the patients were treated with chemotherapy,” Evans said. “In this latest study we identified for the first time the changes in gene expression caused by chemotherapy itself.”

The different patterns of gene responses evoked by MTX and MP were consistent with the fact that these two drugs kill cancer cells by different mechanisms. In addition, there are distinct differences between the way high-dose and low-dose MTX exert their effects.

“Based on these differences, it’s likely that other anti-cancer agents that kill cancer cells by significantly different mechanisms compared to MTX and MP, will also cause changes that are even more distinct than the ones we observed in this study,” Evans said. “This suggests that pharmacogenomics will continue to expand our understanding of genetic responses to therapy.”

Other authors of this paper include Meyling H. Cheok, (a student from the University of Bonn, Germany, working at St. Jude) and Wenjian Yang, Ching-Hon Pui, James R. Downing, Cheng Cheng, Clayton W. Naeve and Mary V. Relling, all of St. Jude.

The work was supported by the National Institutes of Health, a Cancer Center Support Grant from the US National Cancer Institute, the American Cancer Society, Dr. Hilmer Foundation, German Science Foundation and ALSAC.

St. Jude Children’s Research Hospital

St. Jude Children’s Research Hospital, in Memphis, Tennessee, was founded by the late entertainer Danny Thomas. The hospital is an internationally recognized biomedical research center dedicated to finding cures for catastrophic diseases of childhood. The hospital’s work is supported through funds raised by ALSAC. ALSAC covers all costs not covered by insurance for medical treatment rendered at St. Jude Children’s Research Hospital. Families without insurance are never asked to pay. For more information, please visit www.stjude.org.