Proteomic Analysis Reveals IRAK4 As a Therapeutic Target in Chronic Lymphocytic Leukemia

Dimethylfumarate (DMF) and other electrophilic compounds are highly toxic to CLL cells in vitro and in xenograft animal models [Wu et al., 2010; Wu et al., 2016]. To study the mechanism of action, competitive isotopic tandem Orthogonal Proteolysis Activity Based Protein Profiling (isoTOP ABPP) - a chemical proteomic platform, which utilizes broad-spectrum cysteine reactive probes, - was applied to quantitatively map DMF protein targets in whole proteomes. Cells from 10 CLL patients were treated with 30 μM DMF for 4h followed by an isoTOP ABPP sample preparation and analysis workflow. Based on reproducible high isoTOP ABPP ratios across multiple biological replicates, cysteine 13 of interleukin-1 receptor-associated kinase 4 (IRAK4) was identified as a prominent target of DMF in CLL patient cells.

IRAK4 plays a critical role in Toll-like receptor (TLR) signal transduction. Engagement of IRAK4 with the signaling adaptor protein MyD88 in TLRs activates downstream NF-κB and type-I IFN pathways. Approximately 15-20% of CLL patients have dominant activating mutations of MyD88, and nearly all patients with the CLL-related disease Waldenstrom's Macroglobulinemia have such mutations. Hence, we sought to evaluate known inhibitors of IRAK4 kinase activity for their effect on CLL cells. Multiple IRAK4 inhibitors are currently in clinical development, primarily for the treatment of autoimmune conditions. We used PF06650833, a specific inhibitor of IRAK4, previously tested in phase 1 trials for patients with systemic lupus erythematosus, to evaluate its effect on CLL cells viability. In vitro , PF06650833 reduced CLL cell viability in a dose-dependent manner. Reduction in IRAK4 and IκBα protein levels were also observed in samples treated with at least 15 µM PF06650833 by Western blot analysis. In vivo studies provide a better opportunity to evaluate the effect of this drug in blocking microenvironment signaling. We utilized a murine xenograft model in which primary CLL cells are transplanted into the peritoneum of Rag2/gamma chain immunodeficient mice. Each mouse received a single intraperitoneal injection of 1-10 mg/kg PF06650833 one day after transplantation. Cells were recovered 6 days after the treatment and analyzed by flow cytometry, showing remarkable reduction in CLL survival in a dose-dependent manner.

In conclusion, unbiased proteomics analysis of a non-specific drug, DMF, identified IRAK4 as a target in cells from CLL patients. While the exact mode of action for DMF and PF06650833 might differ (disruption of higher IRAK4 complexes, inhibition of kinase dependent signaling or other), our results suggest that IRAK4 represents a potential druggable target in the management of patients with CLL.

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