Finding that specific groups of genes are associated with resistance to particular drugs are important step in identifying new targets for anti-leukemia therapies

A relatively small number of genes are linked to either resistance or sensitivity to four major cancer drugs used to treat acute lymphoblastic leukemia (ALL), suggesting that these genes are key to treatment outcome. This study, by investigators from St. Jude Children's Research Hospital and Erasmus University Medical Center/Sophia Children's Hospital, Rotterdam, The Netherlands, is published in the Aug. 4, 2004 issue of the New England Journal of Medicine (NEJM).

The researchers identified four groups of genes, each of which had a characteristic pattern of expression in leukemia cells depending on whether they were sensitive or resistant to four widely used antileukemic agents. Investigators found that the expression pattern of these genes was significantly related to treatment outcome.

The study identified 123 previously unrecognized genes that are associated with resistance to cancer chemotherapy. Only three of these genes had been previously linked to drug resistance. These new genes represent potential targets for new agents that could be developed to overcome resistance to drugs currently used to treat ALL.

Despite the pioneering role of St. Jude in increasing the cure rate of childhood ALL from 4 percent to more than 80 percent during the past 40 years, the cause of failure in the remaining 20 percent of children is largely unknown, according to William E. Evans, Pharm.D., St. Jude scientific director. The current findings could help further reduce the number of failures. Evans is a senior author of the NEJM report.

"We've known for years that certain genetic changes in leukemic cells are associated with a high risk of treatment failure," Evans said. "But we also realized that many children who have an unfavorable genetic subtype of ALL are cured, and many patients whose genetic subtype was considered to be favorable weren't cured. The findings of this study are helping us understand why patients respond differently to treatment and point to new approaches to overcome these causes of disease relapse."

The researchers tested leukemic cells from 271 children newly diagnosed with ALL for sensitivity to four anti-cancer drugs: prednisolone, vincristine, L-asparaginase and daunorubicin. Using DNA microarray technology, the team determined the levels of expression of thousands of genes in each patient's leukemia cells, and then compared the level of expression (i.e., increased or decreased) of genes in cells that were resistant to each drug to the level of expression of genes in cells that were sensitive to the same drug.
The main study group included 173 children enrolled on the ALL-IX Dutch Childhood Oncology Group protocol at the Erasmus University/Sophia Children's Hospital, or on the German Cooperative Study Group for Childhood Acute Lymphoblastic Leukemia 92 and 97 protocols.

The study found a distinct group of genes that had a specific pattern of expression in leukemia cells according to their sensitivity or resistance to each of the four drugs. In addition, the study identified 123 genes linked to drug resistance and showed that the pattern of expression of these genes is significantly related to the risk of disease relapse.

The ability of these genes to forecast relapse was then validated in a completely independent group of 98 children who were treated with these same drugs, but on a different treatment protocol at St. Jude.

"The gene expression patterns linked to drug resistance were particularly important since they occurred in both the Rotterdam and the St. Jude patient populations, even though these two groups of children were treated with these drugs in different countries and on different protocols," said Rob Pieters, M.D., chair of Pediatric Oncology/Hematology at Erasmus University, and a senior author of the paper. "This is strong evidence of the link between these resistance genes and treatment outcome."

In addition, the researchers found that there is no universal cross-resistance gene that would block sensitivity to all four drugs. Rather, genes linked to resistance belonged to different functional categories (i.e., they did different tasks in the cell) and these differed for each medication.

"Learning the function of these genes gives us new insights into the causes of resistance to individual drugs used to treat children with ALL," said Monique den Boer, co-author of the study and head of the research laboratory of Pediatric Oncology/Hematology at the Erasmus University.

The study further supports the practice of combination anti-cancer drug therapy to treat ALL.

"The fact that resistance genes fall into groups that perform different functions in the cells demonstrates the importance of using combination therapy to treat cancer," said Ching-Hon Pui, M.D., director of the St. Jude Leukemia/Lymphoma division, the F.M. Kirby Clinical Research Professor for the American Cancer Society and a co-author of the paper.