Nuclear phase separation directs HOX transcription in acute myeloid leukemia.

Abstract

Cancer requires transcriptional misregulation to preserve a stem cell-like state, as in acute myeloid leukemia (AML) through sustained activation of HOX genes. Most drivers of HOX in AML have established roles in transcriptional regulation in the nucleus. In contrast, the most common driver, mutant Nucleophosmin1 (NPM1c) is a cytoplasmic oncoprotein resulting from the de novo addition of a nuclear export sequence to the essential nucleolar RNA binding protein NPM1. Our lab and others have shown that NPM1c is necessary for HOX activation; however, the mechanism underlying nuclear activity by this predominantly cytoplasmic protein remains perplexing. We used high-resolution microscopy to investigate NPM1c's localization and role in HOX transcription. Unexpectedly, we observed a fraction (<10%) of NPM1c resides in unreported nuclear puncta or condensates with >100-fold higher enrichment than in the cytoplasm. Biophysical characterization reveals that NPM1c condensates are phase-separated. These condensates require a critical concentration of NPM1c to form and exhibit a concentration-dependent increase in size and number across multiple cell lines. Modulation of NPM1c concentration and subsequent condensate number dictated HOX mRNA levels and cell growth. These results are consistent with a role for NPM1c condensates in HOX misregulation. Further evaluation of a dozen truncations of NPM1c allowed us to unequivocally establish a link between NPM1c condensates, HOX activation, and preservation of the stem cell-like state. Moreover, we observed NUP98 and MLL—proteins found in leukemic oncofusions—enrich in NPM1c condensates, leading us to characterize the ability of numerous fusion oncoproteins to drive nuclear phase separation and activate HOX. Our results suggest that nuclear phase separation is a ubiquitous mechanism for HOX activation, providing a common therapeutic vulnerability across AML subtypes and possibly other cancers.