CC-90009, a novel cereblon E3 ligase modulator, targets acute myeloid leukemia blasts and leukemia stem cells

Blood. 2021 Feb 4;137(5):661-677. doi: 10.1182/blood.2020008676.

Abstract

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 coopts the CRL4CRBN to selectively target GSPT1 for ubiquitination and proteasomal degradation. Depletion of GSPT1 by CC-90009 rapidly induces acute myeloid leukemia (AML) apoptosis, reducing leukemia engraftment and leukemia stem cells (LSCs) 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 messenger RNA alternative splicing, leading to diminished response to CC-90009. The screen also revealed that the mTOR signaling and the integrated stress response 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 LSCs, whose elucidation gives insight into further assessment of CC-90009s clinical utility. These trials were registered at www.clinicaltrials.gov as #NCT02848001 and #NCT04336982).

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Acetamides / pharmacology*
  • Acetamides / therapeutic use
  • Adaptor Proteins, Signal Transducing / antagonists & inhibitors*
  • Animals
  • CRISPR-Cas Systems
  • Cell Line, Tumor
  • Humans
  • Isoindoles / pharmacology*
  • Isoindoles / therapeutic use
  • Leukemia, Myeloid, Acute / pathology*
  • Mice
  • Mice, Inbred NOD
  • Mice, SCID
  • Models, Molecular
  • Molecular Targeted Therapy*
  • Neoplasm Proteins / antagonists & inhibitors*
  • Neoplastic Stem Cells / drug effects*
  • Neoplastic Stem Cells / enzymology
  • Nuclear Factor 45 Protein / physiology
  • Nuclear Factor 90 Proteins / physiology
  • Peptide Termination Factors / metabolism
  • Piperidones / pharmacology*
  • Piperidones / therapeutic use
  • Proteasome Endopeptidase Complex / metabolism
  • Protein Conformation
  • Protein Processing, Post-Translational / drug effects
  • Proteolysis
  • Small Molecule Libraries
  • Stress, Physiological
  • TOR Serine-Threonine Kinases / physiology
  • U937 Cells
  • Ubiquitin-Protein Ligases / antagonists & inhibitors*
  • Ubiquitination / drug effects
  • Xenograft Model Antitumor Assays

Substances

  • Acetamides
  • Adaptor Proteins, Signal Transducing
  • CC-90009
  • CRBN protein, human
  • ILF2 protein, human
  • ILF3 protein, human
  • Isoindoles
  • Neoplasm Proteins
  • Nuclear Factor 45 Protein
  • Nuclear Factor 90 Proteins
  • Peptide Termination Factors
  • Piperidones
  • Small Molecule Libraries
  • peptide-chain-release factor 3
  • Ubiquitin-Protein Ligases
  • MTOR protein, human
  • TOR Serine-Threonine Kinases
  • Proteasome Endopeptidase Complex
  • CRL4 protein, human

Associated data

  • ClinicalTrials.gov/NCT04336982
  • ClinicalTrials.gov/NCT02848001