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Scientists find mutations linked to relapse in child cancer

Jo Carlowe

Monday, 4 February 2013

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After an intensive three-year hunt through the genome, researchers have pinpointed mutations that lead to drug resistance and relapse in childhood leukaemia.

The discovery, published online in Nature Genetics, suggests how scientists may be able to thwart a dangerous form of acute lymphoblastic leukaemia by detecting early emergence of chemotherapy-resistant leukaemia cells in patients and switching them to a different treatment strategy before the disease can fully reassert itself.

Medical researchers have suspected that the re-emergence of disease could be due to drug resistance, but previous efforts had not uncovered any definitive pathway.

Improved treatment has increased the overall cure rate to around 80% but the prognosis is poor for some 20% of patients who relapse.

"There has been no progress in curing children who relapse, in spite of giving them very high doses of chemotherapy and bone marrow transplants," said Dr. William L Carroll, of NYU Cancer Institute, USA, who lead the study.

For the new study, researchers at five U.S. institutions spent three years analysing multiple bone marrow samples from paediatric acute lymphoblastic leukemia (ALL) patients for more clues to the disease's progression.

The researchers analysed the entire transcriptome—or the full sequence of RNA —from 10 children with paediatric B lymphoblastic leukemia, the most common subtype of ALL.

For each patient, the team pieced together a complete sequence of RNA extracted from the bone marrow at three time points: at diagnosis, during remission, and upon relapse some months or years later. All told, the project required the researchers to sequence 100 billion letters of RNA. By comparing the before and after sequences, the team found that each patient had acquired between one and six mutations that changed the genetic code over the course of the disease. In some cases researchers were able to detect these mutations in a very small subset (0.01%) of the tissue samples at diagnosis so that these cells likely expanded because their drug resistant properties provided the leukaemia cells with a survival advantage.

In all, the team documented 20 relapse-specific mutations—none of which had previously been implicated in ALL recurrences. Two patients harboured a mutation in the same gene, NT5C2, which encodes a protein that normally regulates some building blocks used to construct DNA but also can degrade an important class of drugs called purine analogues used in ALL therapy.

When the researchers fully sequenced the NT5C2 gene in 61 other cases in which paediatric ALL patients had relapsed, they found five more mutations that altered the gene's coding region. Further experiments suggested that these NT5C2 mutations all increased the protein's enzymatic activity, making the cancer cells more resistant to a chemotherapy treatment designed to force the cells to kill themselves. All seven patients with NT5C2 mutations relapsed within three years of the initial diagnosis.

Armed with the new knowledge, Dr. Carroll says doctors may be better equipped to identify patients likely to relapse. "We plan to test the feasibility of screening patients during therapy using sophisticated sequencing technology to pick up low-level mutations in NT5C2 and other genes indicating that a mutant clone is growing," he says. His team is researching whether that advance warning could allow doctors to administer separate drugs to beat back the cancer cells, and is also working on a strategy to directly inhibit the mutant enzyme.

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