Single-cell multiomic profiling reveals lineage plasticity in pediatric B-lineage Acute Lymphoblastic Leukemia during the early phase of treatment

The biological bases of transient myelomonocytic switch (mmSW) during induction therapy in B-cell precursor acute lymphoblastic leukemia (BCP-ALL) remains largely undefined. Here we integrated single-cell transcriptomic and surface marker profiling with genomic and DNA methylation analyses of pediatric BCP-ALLs, including matched diagnosis (Dx) and Day+15 samples from mmSW-positive (mmSWpos) and mmSW-negative cases. At Dx, mmSWpos leukemia samples were enriched for hematopoietic stem/progenitor-like cell subpopulations. Trajectory and entropy analyses identified a pre-existing “fate-uncertain” cell compartment co-expressing both lymphoid and myeloid programs. Longitudinal single-cell data showed that, in mmSWpos samples, this population undergoes complete transdifferentiation. mmSWpos are enriched for Ras pathway and chromatin regulation mutations and display a specific DNA hypermethylation pattern at Dx. These findings indicate that transient mmSW arises from intrinsic leukemic plasticity, in which immature transcriptomic and distinct epigenetic states at diagnosis enable lineage switching under the pressure of ALL treatment.