Stem cell biology

A novel method for detecting the cellular stemness state in normal and leukemic human hematopoietic cells can predict disease outcome and drug sensitivity

Abstract

Acute leukemia is an aggressive blood malignancy with low survival rates. A high expression of stem-like programs in leukemias predicts poor prognosis and is assumed to act in an aberrant fashion in the phenotypically heterogeneous leukemia stem cell (LSC) population. A lack of suitable genome engineering tools that can isolate LSCs based on their stemness precludes their comprehensive examination and full characterization. We hypothesized that tagging endogenous stemness-regulatory regions could generate a genome reporter for the putative leukemia stemness-state. Our analysis revealed that the ERG +85 enhancer region can serve as a marker for stemness-state and a fluorescent lentiviral reporter was developed that can accurately recapitulate the endogenous activity. Using our novel reporter, we revealed cellular heterogeneity in several leukemia cell lines and patient-derived samples. Alterations in reporter activity were associated with transcriptomic and functional changes that were closely related to the hematopoietic stem cell (HSC) identity. Notably, the differentiation potential was skewed towards the erythro-megakaryocytic lineage. Moreover, an ERG +85High fraction of AML cells could regenerate the original cellular heterogeneity and was enriched for LSCs. RNA-seq analysis coupled with in silico drug-screen analysis identified 4HPR as an effective inhibitor of ERG +85High leukemia growth. We propose that further utilization of our novel molecular tool will identify crucial determinants of LSCs, thus providing a rationale for their therapeutic targeting.

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Acknowledgements

The authors thank Dr. J. E. Pimanda (Prince of Wales Clinical School, Australia) for providing the PGL2-ERG+85 Luciferase vector. Nour Ershaid (Tel-Aviv University) for helping with FACS analysis. This work was partially supported by Israel Science Foundation (ISF 1512/14, to MM), Varda and Boaz Dotan Research Center in Hemato-Oncology (to MM and SI) and Israel Cancer Research Fund (RCDA 14-171 to MM). MY is a recipient of Israel Council for Higher Education PhD scholarship for minorities. NA is a recipient of a PhD scholarship from State of Israel Ministry of Science, Technology and Space. This work was performed in partial fulfillment of the requirements for a PhD degree of Muhammad Yassin, Nasma Aqaqe and Eitan Kugler, the Dr. Miriam and Sheldon G. Adelson Graduate School of Medicine, Sackler Faculty of Medicine, Tel Aviv University, Israel.

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Correspondence to Michael Milyavsky.

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BEB owns equity in Fulcrum Therapeutics, 1CellBio Inc, Nohla Therapeutics and HiFiBio Inc., and is an advisor for Fulcrum Therapeutics, HiFiBio Inc and Cell Signaling Technologies.The remaining authors declare that they have no conflict of interest.

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Yassin, M., Aqaqe, N., Yassin, A.A. et al. A novel method for detecting the cellular stemness state in normal and leukemic human hematopoietic cells can predict disease outcome and drug sensitivity. Leukemia 33, 2061–2077 (2019). https://doi.org/10.1038/s41375-019-0386-z

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