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

Oncogene. 2025 May;44(19):1350-1360. doi: 10.1038/s41388-025-03309-z. Epub 2025 Feb 22.

Abstract

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.

MeSH terms

  • CCAAT-Enhancer-Binding Proteins / genetics
  • Cell Differentiation* / drug effects
  • Cell Differentiation* / genetics
  • Cell Line, Tumor
  • Gene Expression Profiling
  • Gene Expression Regulation, Leukemic / drug effects
  • Gene Regulatory Networks*
  • HL-60 Cells
  • Humans
  • K562 Cells
  • Leukemia, Promyelocytic, Acute* / genetics
  • Leukemia, Promyelocytic, Acute* / pathology
  • Multiomics
  • Oncogene Proteins, Fusion / genetics
  • Proto-Oncogene Proteins
  • Single-Cell Analysis* / methods
  • Trans-Activators
  • Tretinoin / pharmacology

Substances

  • Tretinoin
  • proto-oncogene protein Spi-1
  • Oncogene Proteins, Fusion
  • CCAAT-Enhancer-Binding Proteins
  • Proto-Oncogene Proteins
  • Trans-Activators