Ontogeny Dictates Oncogenic Potential, Lineage Hierarchy, and Therapy Response in Pediatric Leukemia [ChIP-Seq]

Pediatric cancers are increasingly linked to transformation events before birth, yet how ontogeny influences oncogenesis remains poorly understood. Using a humanized model of NUP98-NSD1-driven pediatric acute myeloid leukemia, particularly aggressive when accompanied by WT1 mutations, we investigated how the developmental stage of hematopoietic stem cells impacts leukemic transformation, disease progression and therapy response. Fetal-derived hematopoietic stem cells readily transform into leukemia, with WT1 mutations enhancing stemness and alter lineage hierarchy, while stem cells from later developmental stages progressively withstand transformation. Single-cell analyses revealed that fetal-origin versus postnatal leukemic stem cells exhibit greater quiescence and metabolic reliance on oxidative phosphorylation. Notably, therapeutic responses markedly differed between fetal- and postnatal-origin leukemias, even when driven by the same oncogenic mutations. In patients, onco-fetal transcriptional programs were associated with worse outcomes. We identified tailored combination therapies that specifically diminished aggressive fetal-origin leukemia, underscoring the need to consider ontogeny in treatment of pediatric cancers. NUP98-NSD1/WT1ko leukemic cells derived from the xenograft model were in vitro cultured and expanded in X-VIVO 10 medium, supplemented with 1% BSA and FLT3L, G-CSF, SCF, TPO and IL-6. Chromatin immunoprecipitation (ChIP) was performed using RPDM16 and H3K27ac antibodies. Following immunoprecipitation, DNA fragments were purified and assessed for quality control. High-quality DNA was used to prepare sequencing libraries, which were subsequently subjected to next-generation sequencing.