Whole-Genome Sequencing of 95 Japanese Patients with Pediatric Acute Myeloid Leukemia
Authors: Mimura Kaito , Shiba Norio , Okada Ai , Chiba Kenichi , Watanabe Kentaro , Deguchi Takao , Ohki Kentaro , Katayama Kotoe , Imoto Seiya , Saito Akiko M , Okamoto Yasuhiro , Adachi Souichi , Tomizawa Daisuke , Taga Takashi , Shiraishi Yuichi , Moritake Hiroshi , Kato Motohiro , Yoshida Kenichi 
Published: December 2024

Background

Pediatric acute myeloid leukemia (pAML) is one of the main causes of death in pediatric oncology. Most previous studies on the genetics of pAML are limited to exome or targeted sequencing, and the genome-wide mutational landscape of pAML is not well understood.

Methods

We performed whole-genome sequencing of the tumor and matched normal samples from 95 Japanese primary pAML patients enrolled in Japan Children's Cancer Group (JCCG) AML-12/AML-D16 studies. Tumor samples were collected from bone marrow and matched normal samples were collected from peripheral blood on remission. The median sequencing depth was 120x for tumor samples and 30x for matched normal samples. The super-computing resource was provided by Human Genome Center (the University of Tokyo).

Results

The landscape of somatic driver mutations in protein-coding regions generally agreed with previous reports. For non-coding drivers, unusual for hematological malignancies, the TERT promoter region was affected by 2 hotspot single-nucleotide variants (c.1-124C&gt;T and c.1-146C&gt;T; n=2, 2%).

Mutational signatures were extracted using SigProfiler (Islam et al. Cell Cenom. 2022). Clock-like signatures, namely SBS1 and SBS5, were ubiquitously detected in our cohort, and mutational burden was associated with age (p=8.059e-09 for SBS1, p=1.134e-06 for SBS5). In AMLs with RUNX1-RUNX1T1 and CBFB-MYH11, a reactive oxygen species (ROS)-related signature, SBS18, contributed to a significant number of somatic mutations, with association with age (p=0.02177). The frequencies of SBS18 mutations were similar between clonal and subclonal mutations, indicating that the mutational process mediated by ROS contributed to the entire process of clonal evolution of such AML subtypes.

Structural variation analysis identified recurrent drivers including translocations in RUNX1 (n=30, 32%) and KMT2A (n=17, 18%) gene loci, and tandem duplications in the long non-coding RNA CCDC26 region (n=5, 5%). Furthermore, RAG1/2-associated rearrangements in T-cell receptor loci (n=6, 6%) and immunoglobulin loci (n=4, 4%) were also detected. Whether a structural variation was associated with RAG1/2 was defined by the existence of a recombination signal sequence in proximity of the breakpoints. One patient had a complex rearrangement, chromoplexy, involving RAG1/2-associated deletion in TCRδ region and non-RAG1/2-associated RUNX1-RUNX1T1 translocation. This suggests that aberrant RAG1/2-associated double-strand breaks (DSBs) in the TCRδ region and DSBs in RUNX1 and RUNX1T1 regions (neither of which were associated with RAG1/2) may have coincided and simultaneously been repaired, illustrating the mutational events that may have occurred in the early pathogenesis of AML.

Conclusion

By whole-genome sequencing of Japanese pAML patients, novel mutational events throughout the genome including the non-coding regions were detected. Our data provides novel insights into the pathogenesis of pAML.