Mutant NPM1 Hijacks Transcriptional Hubs to Maintain Pathogenic Gene Programs in Acute Myeloid Leukemia

Abstract

Nucleophosmin (NPM1) is a ubiquitously expressed nucleolar protein with a wide range of biological functions. In 30% of acute myeloid leukemia (AML), the terminal exon of NPM1 is often found mutated, resulting in the addition of a nuclear export signal and a shift of the protein to the cytoplasm (NPM1c). AMLs carrying this mutation have aberrant expression of the HOXA/B genes, whose overexpression lead to leukemogenic transformation. Here, for the first time, we comprehensively prove NPM1c binds to a subset of active gene promoters in NPM1c AMLs, including well-known leukemia-driving genes – HOXA/B cluster genes and MEIS1. NPM1c sustains the active transcription of key target genes by orchestrating a transcription hub and maintains the active chromatin landscape by inhibiting the activity of histone deacetylases (HDACs). Together, these findings reveal the neomorphic function of NPM1c as a transcriptional amplifier for leukemic gene expression and open up new paradigms for therapeutic intervention.

Mutant NPM1: Nuclear export and the mechanism of leukemogenesis

“…Regardless of this dissimilarity, which could be secondary to differences in the experimental procedures and bioinformatic analysis, both studies clearly show that NPM1c is recruited at HOX/MEIS and directly regulates the transcription of these critical targets. Indeed, NPM1c was found enriched at active chromatin sites, together with activating histone marks, MLL1 and RNA Polymerase II (Pol II) and specific degradation of NPM1c resulted in immediate halt of HOX/MEIS transcription (within 15 min) secondary to the loss of Pol II from these loci 13,14 . Furthermore, pharmacologic MLL‐Menin inhibition induced the loss of NPM1c from several of its chromatin targets, including MEIS1 , followed by their downregulation 13 …”

“…In addition to XPO1, Uckelmann et al 13 demonstrated that one of the two NPM1 acidic domains (~aa 120 to 150) is also necessary for an efficient NPM1c recruitment to chromatin. Wang et al 14 proposed that the generation of NPM1c phase separated nuclear condensates is critical for the recruitment of NPM1c to chromatin and to hijack the transcriptional machinery at its target loci. Whether NPM1c condensates are actually necessary for HOX/MEIS expression and whether the acidic domain is involved in the process of phase separation process itself remains to be clarified.…”

“…Using chromatin immunoprecipitation 13 and CUT&RUN techniques, 14 both studies demonstrate that NPM1c binds to chromatin. While Uckelmann et al 13 show that NPM1c is particularly enriched at a limited number of genes, all of which are highly dependent on NPM1c for their transcription, Wang et al 14 detected NPM1c at a much larger number of targets. Regardless of this dissimilarity, which could be secondary to differences in the experimental procedures and bioinformatic analysis, both studies clearly show that NPM1c is recruited at HOX/MEIS and directly regulates the transcription of these critical targets.…”

“…Wang et al 14 proposed that the generation of NPM1c phase separated nuclear condensates is critical for the recruitment of NPM1c to chromatin and to hijack the transcriptional machinery at its target loci.…”

Identification of a Micropeptide Linked to Cancer Stem Cell Regulation and Chemoresistance

“…Although homeobox gene deregulation is strongly linked with many human malignancies, IRX family has not yet been fully functionally explored (8,14,15). The IRX family includes six genes, IRX1, IRX2, and IRX4 (IRX cluster A) which are located in chromosome 5 and IRX3, IRX5, and IRX6 (IRX cluster B) which are located in chromosome 16 (13,16).…”