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A number of clinically validated drugs have been developed by repurposing the CUL4-DDB1-CRBN-RBX1 (CRL4CRBN) E3 ubiquitin ligase complex with molecular glue degraders to eliminate disease-driving proteins. Here, we present the identification of a first-in-class GSPT1-selective cereblon E3 ligase modulator, CC-90009. Biochemical, structural and molecular characterization demonstrates that CC-90009 co-opts the CRL4CRBN to selectively target GSPT1 for ubiquitination and proteasomal degradation. Depletion of GSPT1 by CC-90009 rapidly induces AML apoptosis, reducing leukemia engraftment and leukemia stem cells (LSC) in large scale primary patient xenografting of 35 independent AML samples, including those with adverse risk features. Using a genome-wide CRISPR-Cas9 screen for effectors of CC-90009 response, we uncovered the ILF2 and ILF3 heterodimeric complex as a novel regulator of cereblon expression. Knockout of ILF2/ILF3 decreases the production of full-length cereblon protein via modulating CRBN mRNA alternative splicing, leading to diminished response to CC-90009. The screen also revealed that the mTOR signaling and the integrated stress response (ISR) specifically regulate the response to CC-90009 in contrast to other cereblon modulators. Hyperactivation of the mTOR pathway by inactivation of TSC1 and TSC2 protected against the growth inhibitory effect of CC-90009 by reducing CC-90009 induced binding of GSPT1 to cereblon and subsequent GSPT1 degradation. On the other hand, GSPT1 degradation promoted the activation of the GCN1/GCN2/ATF4 pathway and subsequent apoptosis in AML cells. Collectively, CC-90009 activity is mediated by multiple layers of signaling networks and pathways within AML blasts and LSC, whose elucidation gives insight into further assessment of CC-90009's clinical utility.

There is a growing body of evidence that the molecular properties of leukemia stem cells (LSCs) are associated with clinical outcomes in acute myeloid leukemia (AML), and LSCs have been linked to therapy failure and relapse. Thus, a better understanding of the molecular mechanisms that contribute to the persistence and regenerative potential of LSCs is expected to result in the development of more effective therapies. We therefore interrogated functionally validated data sets of LSC-specific genes together with their known protein interactors and selected 64 candidates for a competitive in vivo gain-of-function screen to identify genes that enhanced stemness in human cord blood hematopoietic stem and progenitor cells. A consistent effect observed for the top hits was the ability to restrain early repopulation kinetics while preserving regenerative potential. Overexpression (OE) of the most promising candidate, the orphan gene C3orf54/INKA1, in a patient-derived AML model (8227) promoted the retention of LSCs in a primitive state manifested by relative expansion of CD34+ cells, accumulation of cells in G0, and reduced output of differentiated progeny. Despite delayed early repopulation, at later times, INKA1-OE resulted in the expansion of self-renewing LSCs. In contrast, INKA1 silencing in primary AML reduced regenerative potential. Mechanistically, our multidimensional confocal analysis found that INKA1 regulates G0 exit by interfering with nuclear localization of its target PAK4, with concomitant reduction of global H4K16ac levels. These data identify INKA1 as a novel regulator of LSC latency and reveal a link between the regulation of stem cell kinetics and pool size during regeneration.

miRNA expression is deregulated in human acute myeloid leukemia (AML), however the impact of altered post-transcriptional programs on the genesis and maintenance of leukemia stem cells (LSC) remains undefined. In order to elucidate the functional role of miRNA in LSC and identify relevant miRNA candidates, we performed global miRNA profiling on sorted cell subpopulations from 16 AML patient and 3 umbilical cord blood samples (Eppert et al, Nature Medicine 2011). Supervised analysis guided by the ability of each sub-population to initiate leukemic engraftment after xenotransplantation into immune-deficient mice generated a unique miRNA signature. miR-126, a miRNA that we previously demonstrated to have a conserved role in maintaining hematopoietic stem cell (HSC) quiescence (Lechman et al. Cell Stem Cell, 2012), was more highly expressed in LSC-enriched fractions and chosen for further validation. To confirm that miR-126 is a bona fide LSC determinant, we utilized a bidirectional lentiviral reporter vector specific for miR-126 (Gentner et al. Science Translational Medicine, 2010) to sort cells from AML patient samples based on miR-126 bioactivity, and demonstrated that all in vivo leukemia-initiating capacity was confined to cells with elevated miR-126 bioactivity. Lentiviral enforced expression of miR-126 in primary AML patient samples significantly increased LSC frequency (3.5-52.3 fold) as assessed by limiting dilution transplantation assays, while diminishing cell cycle entry, differentiation marker expression (CD14,CD15) and colony forming potential. Sponge-mediated knockdown of miR-126 expression resulted in the opposite effects. These findings suggest that high levels of miR-126 bioactivity support self-renewal/maintenance of primitive AML cells at the cost of aberrant differentiation. Moreover, by preserving LSC quiescence miR-126 promoted chemotherapy resistance, in part through suppression of CDK3, a gatekeeper of G0 to G1 cell cycle transit. Enforced expression of CDK3 partially rescued the functional consequences of supra-physiological levels of miR-126 bioactivity, rendering previously resistant LSC susceptible to killing by AraC/Daunorubicin combination chemotherapy. Our human LSC miRNA signature, optimized by regression analysis on a cytogenetically normal AML patient cohort, was prognostic for survival in a large independent AML patient cohort (Ley et. al N Engl. J Med, 2013) further validating the clinical significance of miRNA as stem cell determinants. Furthermore, miRNA-126 alone was prognostic for survival in two independent cohorts of AML patients with normal cytogenetics. These data demonstrate a mechanistic role for miR-126 in governing intrinsic LSC properties and establish miR-126 as a critical biomarker for clinical outcome. Disclosures: Wang: Trillium Therapeutics/Stem Cell Therapeutics: Research Funding.

Acute myeloid leukemia (AML) is a hierarchical disease in which the bulk blast population is sustained by a minority population of leukemia stem cells (LSC). Evidence of functional heterogeneity in the LSC compartment, including variable responses to chemotherapy, underscores the importance of examining the entire stem cell compartment in studies of LSC biology. However, there are currently no phenotypic markers that can consistently segregate LSCs within the leukemic blast population. Although LSC activity is most often enriched in the CD34+CD38- cell fraction, LSCs are also frequently detected in other phenotypic fractions, and in some cases are absent from CD34+ fractions. Thus, LSC studies that focus only on CD34+CD38- blasts may miss biologically important clones that are present in other phenotypic cell fractions. To identify novel markers that will enable better enrichment of LSC activity, we examined gene expression data obtained from functionally validated LSC+ and LSC- cell fractions sorted from primary AML samples, and identified CD200 as a candidate cell surface marker for LSCs. In normal adult bone marrow and cord blood samples, CD200 is expressed on >95% of CD34+CD38- cells, and expression decreases on CD34+38+ cells, suggesting that CD200, similar to CD34, is a stem cell marker. Flow cytometric analysis of AML patient samples (n=57) demonstrated that CD200 expression was present on a greater proportion of CD45dim blasts compared to CD45high non-blast populations (69.2% vs 4.5%, p<0.0001) and was significantly higher on CD34+ compared to CD34- cells (RFI 51.7 vs 3.5, p<0.0001). Although CD200 expression correlated with CD34 expression in many cases, some samples with low to no CD34 expression had high CD200 expression on CD45dim blasts, suggesting that CD200 can be used to identify CD34- LSCs. To test whether CD200 can segregate LSC activity within the CD45dim blast population, we sorted 14 primary AML samples into cell fractions based on CD45 and CD200 expression followed by transplantation into cohorts of NSG mice. AML samples were prescreened for leukemic engraftment ability and were selected for sorting if: 1) CD45dim blasts comprised both CD200+ and CD200- cells or 2) the CD200+ fraction was <5% of bulk cells. In 7 of 14 patients, LSC activity was enriched within the CD200+ fraction (CD200+ LSCs). For example, in AML40, in which CD200+ cells constituted only 5% of the bulk, as few as 5000 CD200+ blasts generated a leukemic graft at a mean level of 20.6%, whereas up to 500,000 CD200- blasts generated no graft. Importantly, LSC activity in these samples could not be segregated by CD34/CD38 expression; in contrast, the CD200+ fraction encompassed all cell fractions with LSC activity regardless of CD34/CD38 phenotype. In 1 of 14 patients, LSC activity was present in both the CD200+ and CD200- fractions. In the remaining 6 patients, LSC activity was enriched in the CD200- fraction (CD200- LSCs). In these samples, <3% of the bulk population expressed CD200; in 5 of the 6 samples, CD200+ cells generated multi-lineage (CD19+ B plus CD19‒CD33+ myeloid) rather than leukemic grafts, consistent with the presence of pre-leukemic-HSCs (preL-HSCs) in this cell fraction. In 2 additional AML patient samples that generated multi-lineage rather than leukemic grafts following transplantation of bulk cells, we refined our sorting strategy and were able to separate CD200+ LSCs from CD200+ preL-HSCs as evidenced by mutational analysis of xenografts. High CD200 expression was significantly associated with shorter overall survival in univariate analysis in multiple independent AML cohorts, but was not significant in multivariate analysis due to association with NPM1 mutation. NPM1-mutated samples exhibited low CD200 expression on the bulk cells. Interestingly, 7 of the 9 AML patients with CD200+ LSCs had normal karyotype and NPM1 mutation. Our results demonstrate that a CD200-based sorting strategy can successfully enrich and/or segregate LSC activity, and separate LSCs from preL-HSCs in primary AML patient samples. This will now enable direct functional studies of the biological properties of these related but distinct stem cell populations. Furthermore, CD200 will be a valuable tool for the study of LSCs in the subset of NPM1-mutated AML. Disclosures No relevant conflicts of interest to declare.

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In the originally published version of this Letter, ref. 43 was erroneously provided twice. In the 'Estimation of relative cell-type-specific composition of AML samples' section in the Methods, the citation to ref. 43 after the GEO dataset GSE24759 is correct. However, in the 'Mice' section of the Methods, the citation to ref. 43 after 'TAMERE' should have been associated with a new reference1. The original Letter has been corrected online (with the new reference included as ref. 49).

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