Clonal Evolution of Pediatric Acute Myeloid Leukemia and Its Contribution to Disease Relapse

Relapse remains the leading cause of mortality in pediatric acute myeloid leukemia (AML), yet the genetic changes contributing to relapse remain incompletely defined. To address this gap, we performed whole-genome sequencing and targeted-capture sequencing on 39 diagnosis-relapse and 2 relapse-relapse pairs of pediatric AML. Mutational burden increased at relapse, largely reflecting spontaneous mutagenesis, whereas therapy-related signatures were rarely observed and only occasionally associated with pathogenic mutations. Although recurrently enriched mutations at relapse included those in FLT3, WT1, and TP53, relapse-fated subclones were frequently marked only by non-pathogenic or non-coding variants. Longitudinal deep sequencing in eight patients showed rapid depletion of major clones after induction therapy, whereas subclones often displayed variable chemosensitivity. Relapse-specific mutations emerged only late or remained undetectable during remission, suggesting that clonal selection of pre-existing clones is the predominant mechanism of relapse. Transcriptome analysis of paired RNA sequencing data revealed no differentially expressed genes, but gene set enrichment analysis and CIBERSORT deconvolution in each pair uncovered heterogeneous trajectories to relapse. Although relapse is often attributed to the emergence of stem-like phenotypes, our data demonstrate that transcriptional evolution is more diverse: some cases acquired stem-like features, whereas others showed partial differentiation, which was confirmed by re-analysis of a public single cell RNA sequence dataset. These changes were largely constrained by baseline differentiation states at diagnosis. Together, our data indicate that pediatric AML relapse arises through selection of pre-existing clones with diverse trajectories, underscoring the need to target both stem-like and differentiated populations to achieve durable cures.