Abstract
Secondary mutational events in ETV6–RUNX1 -positive ALL bear hallmarks of off-target RAG activity.
Major Finding: Secondary mutational events in ETV6–RUNX1 -positive ALL bear hallmarks of off-target RAG activity.
Concept: Aberrant RAG recombinase activity specifically disrupts expression of B-cell maturation factors.
Impact: RAG-mediated recombination may drive structural variation in ETV6–RUNX1-positive ALL.
The ETV6–RUNX1 gene fusion is expressed in approximately 25% of childhood B-cell precursor acute lymphoblastic leukemias (ALL) and represents the most common genetic abnormality in pediatric ALL. The t(12;21) translocation that gives rise to ETV6–RUNX1 is acquired in utero, but the development of B-cell precursor ALL requires additional postnatal mutations. Papaemmanuil and colleagues performed whole-genome sequencing of 51 ETV6–RUNX1-positive diagnostic samples and found that the majority of intrachromosomal rearrangements were deletions, with many deletion breakpoints adjacent to recombination signal sequence (RSS) sites that are conserved targets for the recombination activating gene (RAG) endonucleases that mediate V(D)J recombination or adjacent to RSS-like motifs. These findings raise the possibility that RAG activity, which is elevated in ETV6–RUNX1-positive cells, may be targeting inappropriate regions in ALL. Clusters of deletion breakpoints proximal to RSS sites and RSS-like motifs often occurred within active gene promoter and enhancer regions, and specifically disrupted some of the most frequently altered genes in ALL, including those involved in B-cell differentiation. To distinguish driving events from passenger rearrangements simply clustering near transcribed genes, the authors integrated whole exome and genome data to identify genes also affected by rearrangement, point mutation, and/or copy number changes in ALL and uncovered recurring deletions or inactivating mutations in previously characterized ALL genes as well as in two previously unreported genes, ATF7IP and MGA. Although identifying RSS and RSS-like motifs near deletion breakpoints is not direct evidence of aberrant RAG activity in ALL, their functional relevance is plausible given their enrichment near rearrangements in ETV6–RUNX1 ALL and their absence among structural variations in breast, pancreatic, and prostate cancer. Together, these results suggest that RAG-mediated genomic rearrangement may be the predominant driver of B-cell precursor ALL initiated by the ETV6–RUNX1 fusion.