Nascent transcript and single-cell RNA-seq analysis defines the mechanism of action of the LSD1 inhibitor INCB059872 in myeloid leukemia

Gretchen Johnston, Haley E. Ramsey, Qi Liu, Jing Wang, Kristy R. Stengel, Shilpa Sampathi, Pankaj Acharya, Maria Arrate, Matthew C. Stubbs, Timothy Burn, Michael R. Savona, Scott W. Hiebert

Research output: Contribution to journalArticlepeer-review

4 Scopus citations

Abstract

Drugs targeting chromatin-modifying enzymes have entered clinical trials for myeloid malignancies, including INCB059872, a selective irreversible inhibitor of Lysine-Specific Demethylase 1 (LSD1). While initial studies of LSD1 inhibitors suggested these compounds may be used to induce differentiation of acute myeloid leukemia (AML), the mechanisms underlying this effect and dose-limiting toxicities are not well understood. Here, we used precision nuclear run-on sequencing (PRO-seq) and ChIP-seq in AML cell lines to probe for the earliest regulatory events associated with INCB059872 treatment. The changes in nascent transcription could be traced back to a loss of CoREST activity and activation of GFI1-regulated genes. INCB059872 is in phase I clinical trials, and we evaluated a pre-treatment bone marrow sample of a patient who showed a clinical response to INCB059872 while being treated with azacitidine. We used single-cell RNA-sequencing (scRNA-seq) to show that INCB059872 caused a shift in gene expression that was again associated with GFI1/GFI1B regulation. Finally, we treated mice with INCB059872 and performed scRNA-seq of lineage-negative bone marrow cells, which showed that INCB059872 triggered accumulation of megakaryocyte early progenitor cells with gene expression hallmarks of stem cells. Accumulation of these stem/progenitor cells may contribute to the thrombocytopenia observed in patients treated with LSD1 inhibitors.

Original languageEnglish (US)
Article number144758
JournalGene
Volume752
DOIs
StatePublished - Aug 20 2020
Externally publishedYes

Keywords

  • CoREST
  • GFI1
  • GFI1B
  • Histone acetylation
  • Histone demethylation
  • KDM1A
  • LSD1
  • Myeloid leukemia

ASJC Scopus subject areas

  • Genetics

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