SUMMARY
Acute myeloid leukemia (AML) progression and relapse is fueled by self-renewing leukemic stem cells (LSCs) whose molecular determinants have been difficult to discern from normal hematopoietic stem cells (HSCs) or to uncover in screening approaches focused on general AML cell properties. We have identified a unique set of RNA binding proteins (RBPs) that are enriched in human AML LSCs but repressed in HSCs. Using an in vivo two step CRISPR-Cas9-mediated screening approach to specifically score for cancer stem cell functionality, we found 32 RBPs essential for LSC propagation and self-renewal in MLL-AF9 translocated AML. Using knockdown or small molecule approaches we show that targeting key hit RBP ELAVL1 impaired LSC-driven in vivo leukemic reconstitution and selectively depleted primitive AML cells vs. normal hematopoietic stem and progenitors. Importantly, knockdown of Elavl1 spared HSCs while significantly reducing LSC numbers across genetically diverse leukemias. Integrative RNA-seq and eCLIP-seq profiling revealed hematopoietic differentiation, RNA splicing and mitochondrial metabolism as key features defining the leukemic ELAVL1-mRNA interactome with the mitochondrial import protein TOMM34 being a direct ELAVL1-stabilized target whose inhibition impairs AML propagation. Altogether, through the use of a stem cell-adapted in vivo CRISPR dropout screening strategy, this work demonstrates that a wide variety of post-transcriptionally acting RBPs are important regulators of LSC-survival and self-renewal and, as exemplified by ELAVL1, highlights their potential as therapeutic targets in AML.
Competing Interest Statement
The laboratory of K.H. receives some financial support from Twentyeight-Seven Therapeutics. This disclosure is not related to these studies. G.W.Y. is co-founder, member of the Board of Directors, on the Scientific Advisory Board, equity holder, and paid consultant for Eclipse BioInnovations. G.W.Y. is a visiting professor at the National University of Singapore. The interest of G.W.Y. interest have been reviewed and approved by the University of California San Diego in accordance with its conflict-of-interest policies.
Footnotes
Conflicts of interest disclosure KH’s lab receives some financial support from Twentyeight-Seven Therapeutics. This disclosure is not related to these studies. GWY is co-founder, member of the Board of Directors, equity holder, and paid consultant for Locana and Eclipse BioInnovations. GWY is co-founder of Enzerna and ProteoNA. GWY is a paid consultant for Ionis Pharmaceuticals and scientific advisory board member to Ribometrix and the Allen Institute of Immunology. The terms of this arrangement have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies. The authors declare no other competing financial interests.