Paucity of Somatic Mutations in Aggressive Childhood Leukemia

In-depth DNA sequencing and RNA expression analysis shows that a particularly aggressive form of infant and childhood leukemia--mixed-lineage leukemia-rearranged gene (MLL-R) acute lymphoblastic leukemia (ALL)--is likely driven by a chromosomal translocation as this tumor type has among the lowest number of somatic mutations of any previously sequenced cancer type.

This type has a distinct MLL gene rearrangement and represents about 80% of all infant cases of ALL. It is sometimes diagnosed at birth and occurs within the first 12 months of life.

The genome-wide effort found that while 47% of the tumors sequenced harbored an activating mutation in the phosphoinositide 3-kinase-RAS pathway, these mutations were subclonal and were frequently lost following disease relapse.

The results are published  online in the March 2015 issue of Nature Genetics.  

As part of the St. Jude Children’s Research Hospital and Washington University Pediatric Cancer Genome Project, Anna K. Andersson, of the departments of pathology and computational biology at St. Jude in Memphis, and colleagues sequenced 65 MLL-R ALL infant tumors, 20 MLL-R tumors from older children, and matched bone marrow or peripheral blood samples at remission to identify other potential driver mutations to identify new therapeutic approaches. The sequencing effort is the most comprehensive on this relatively rare and aggressive form of childhood leukemia. While event-free survival is greater than 85% with current treatments, event-free survival remains in the range of 28% to 36% for MLL-R ALL.

The infant MLL-R ALL tumors had an average of 111 somatic mutations. Based on these observed number of mutations, the authors concluded that the somatic mutation rate of MLL-R ALL is about two-fold to 180-fold lower compared to all other adult and pediatric cancers except for pediatric low-grade glioma. Still, 81% of the identified missense mutations that were expressed were predicted to have a negative effect on the protein encoded by the gene.

"We frequently associate a cancer's aggressiveness with its mutation rate, but this work indicates that the two don't always go hand-in-hand," said study co-author Richard K. Wilson, PhD, director of The Genome Institute at Washington University School of Medicine in St. Louis, in a statement. "Still, our findings provide a new direction for developing more effective treatments for these very young patients."

About one-half of copy number alterations and structural variations per tumor could be attributed to the MLL-R--linked chromosomal rearrangement at 11q23. In the other half, the predominantly affected gene was Paired Box 5 (PAX5) which functions with MYC, and has previously been implicated in leukemia and ALL, cyclin-dependent kinase inhibitor 2A/2B (CDKN2A/CDKN2B) (which is associated with melanoma-pancreatic cancer syndrome), and DLEU1/DLEU2 noncoding RNA genes.

More than half of the MLL rearrangements were complex, involving more than two chromosomes. Two of the gene fusion partners with MLL identified were known as those with an established cancer-causing phenotype: KRAS and AFF1-RAD51B.

Besides KRAS, other PI3K-RAS pathway genes found mutated included NRAS, FLT3, NF1, PTPN11, and PIK3R1, all of which were expressed. Several of the activating mutations identified in PIK3R1 were novel, and one of the FLT3 mutations was the same as a previously identified mutation reported in a case of acute myeloid leukemia that had developed resistance to a kinase inhibitor. But, because most of these mutations were found in subclones of the tumor, the authors suggest that these may not be necessary to maintain the leukemia. In other words, targeting these mutations with drugs may not benefit patients.

Those infant patients, diagnosed within the first 12 months of life with an activating PI3K pathway mutation tended to be younger, and those with activating mutations in a major tumor clone tended to be younger suggesting that these activating mutations may decrease the latency of the disease. There was a trend towards a worse event-free and overall survival, and increased relapse for those patients with an activating pathway mutation, but the trend did reach statistical significance.

"These results show that to improve survival for patients with this aggressive leukemia we need to develop drugs that target the abnormal proteins produced by the MLL fusion gene, or that interact with the abnormal MLL fusion protein to shut down the cellular machinery that drives their tumors," said co-author James R. Downing, MD, of St. Jude Children’s Research Hospital, in a statement.  "That will not be easy, but this study found no obvious cooperating mutations to target."

Samples from older children with MLL-R ALL had more mutations compared to infants with MLL-R ALL, with half of the mutations in genes encoding epigenetic regulatory proteins which affect the activation of other genes. This suggests that there may be a distinct difference in the biology of MLL-R ALL in infants compared to older patients.