Integrated Genomic and Functional Analysis of Leukemia Stemness

Muhammad Yassin ⁴ Nasma Aqaqe ⁴ Abed Alkader Yassin ⁴ Nour Erhaid ⁴ Chen Katz-Even ⁴ Adi Zipin-Roitman ⁴ Eitan Kugler ³ Eric R. Lechman ² Olga I. Gan ² Amanda Mitchell ² John E. Dick ² Shai Izraeli ³ Michael Milyavsky ^1,4

¹Pathology, Sackler Faculty of Medicine, Tel Aviv University, Israel
²Department of Molecular Genetics, Princess Margaret Cancer Centre, Canada
³Department of Molecular Genetics, Sackler School of Medicine, Tel Aviv University, Israel

Acute leukemia is a rapidly progressing blood cancer with low survival rates. Unfavorable prognosis is attributed to insufficiently characterized subpopulations of Leukemia Stem Cells (LSC) that drive chemoresistance and leukemia relapse. Here we utilized a genetic reporter which assesses stemness to enrich and functionally characterize LSC. We observed heterogeneous activity of the ERG+85 enhancer-based fluorescent reporter in human leukemias. Cells with high reporter activity (tagBFP^High) exhibited elevated expression of stemness and chemoresistance genes and demonstrated increased clonogenicity and resistance to chemo- and radiotherapy as compared to their tagBFP^Neg counterparts. The tagBFP^High fraction was capable of regenerating the original cellular heterogeneity and demonstrated increased invasive ability. Moreover, the tagBFP^High fraction was enriched for leukemia initiating cells in a xenograft assay. We identified the ubiquitin hydrolase USP9X as a novel ERG transcriptional target that sustains ERG+85 positive cells by controlling ERG ubiquitination. Therapeutic targeting of USP9X led to preferential inhibition of the ERG-dependent leukemias.
Collectively, these results characterize human leukemia cell functional heterogeneity and suggest that targeting ERG via USP9X inhibition may be a potential treatment strategy in patients with leukemia.