Single-cell multiomics reveals a gene regulatory circuit driving leukemia cell differentiation.

Cancer differentiation therapy aims to induce the maturation of neoplastic cells, but the mechanisms regulating cell fate decisions in oncogenic contexts remain unclear. In this study, we integrated single-cell chromatin accessibility and single-cell transcriptome analyses to explore the regulatory trajectories of a classical PML/RARα acute promyeloid leukemia (APL) cell line (NB4) post treatment by all-trans-retinoid acid (ATRA). Our findings indicated that ATRA activated specific PML/RARα-target enhancers to trigger a regulatory circuit composed of a positive feedforward gene regulatory circuit involving two transcription factors, SPI1 and CEBPE. This regulatory circuit was both necessary and sufficient to drive NB4 cells through an intermediate cell fate decision point to initiate terminal granulopoiesis. Moreover, ectopic expression of SPI1 and CEBPE promoted granulocytic differentiation in non-APL leukemia cell lines HL60 and K562. Our study sheds mechanistic insights into the differentiation trajectories induced by ATRA and illustrates a gene regulatory circuit that could be widely applied to promote differentiation of leukemia cells.