Identification of cellular hierarchy in paediatric acute myeloid leukaemia: The Japan Children's Cancer Group trial ( JCCG AML ‐12)

RNA sequencing from 262 patients with paediatric acute myeloid leukaemia (AML) (JPLSG AML-12) was deconvoluted employing adult single-cell RNA-sequencing signatures and Zeng's method, which defined five cellular hierarchy subtypes: primitive, leukaemic stem/progenitor cell (LSPC)-Cycle, ProMono-like, granulocyte-monocyte progenitor (GMP)-like and intermediate. Principal component analysis revealed two main axes that distinguish paediatric from adult AML, with notable LSPC-Cycle and ProMono-like phenotype enrichment. LSPC-Cycle (>25% cycling stem-like cells) had proliferative and quiescent LSPCs, frequent French-American-British (FAB)-M7 and worst prognosis (overall survival odds ratio vs. GMP-like: 11.33). Morphology was related to the primitive (FAB-M0), GMP-like (M2/M4) and ProMono-like (M5) groups. Genomic patterns aligned with hierarchy: CBFA2T3::GLIS2, MYB::GATA1 and MECOM high expression in LSPC-Cycle; CBFB::MYH11, NUP98::NSD1 and NPM1 in the intermediate; and DEK::NUP214 and NUP98::KDM5A were concentrated in the primitive group. bZIP CEBPA and FLT3-ITD mutations clustered in the intermediate and primitive groups. Most of RUNX1::RUNX1T1 clustered in the intermediate group, whereas KMT2A::MLLT3 hierarchy differed with MECOM expression level. Paediatric AML comprised more primitive cells, rarely with mono-like/cDC-like dominance. LSPC-Cycle, FLT3-ITD and NUP98::KDM5A were considered independent prognostic factors in multivariate analysis. Findings indicate the prognostic relevance of cellular hierarchy and the importance of integrating hierarchy-specific molecular profiles for improved risk stratification and treatment formulation.