Background Myelodysplastic neoplasms (MDS) and acute myeloid leukemia (AML) exhibit a dynamic and diverse mutational landscape, especially during disease progression. Mutations in the splicing factors SF3B1 and U2AF1 drive overexpression of a highly active long isoform of interleukin-1 receptor-associated kinase 4 (IRAK4), triggering inflammation, oncogenesis and survival of cancer cells through activation of NFκB and other signaling pathways. NFκB target genes CCL4, IL1β and IER3 are highly expressed in patients with AML and MDS and associated with poor prognosis. Emavusertib is a potent oral inhibitor of IRAK4 and FLT3 with efficacy in pre-clinical leukemia models. Here, we describe our insights from RNA sequencing (RNA-seq) applied to clinical samples from the ongoing TakeAim Leukemia trial.

Methods In the Phase I/IIa of the TakeAim Leukemia trial (NCT04278768), patients with relapsed/refractory (R/R) AML or higher-risk MDS were treated with emavusertib. RNA-seq was performed on mononuclear cells from bone marrow, or peripheral blood, from 26 AML and 16 MDS patients, including 24 paired samples. The read depth ranged from 10.4–120 million reads and% reads aligned ranged from 67%-92%. Quality control was performed with FASTQC V0.11.8 and low-quality reads were removed using Trimgalore V0.6.3. Raw counts were normalized to total number of reads by calculating log2CPM (Counts Per Million).

Results MDS patients that responded to emavusertib had decreased gene expression levels of the NFκB target genes IL1β and IER3 (P≤0.05, respectively) compared to non-responders. A decrease in CCL4 expression was also observed (N.S.). Pathway analysis demonstrated significant downregulation of the Heme Metabolism, G2M Checkpoint, and E2F Targets pathways in on-treatment samples (FDR p-value <0.005 for all, normalized enrichment score= -3.39, -1.97 & -2.17, respectively). Notably E2F2 was decreased in on-treatment samples compared to baseline samples with a log2FC of ~1.3.

Conclusions RNA-seq pathway analysis indicates that inhibition of IRAK4 downregulates genes relevant to the development and pathophysiology of AML/MDS. Previous clinical research supports our findings describing IL1β and IE3 as important markers in the prognosis of AML/MDS. In addition, we observed that emavusertib downregulates pathways associated with heme metabolism, proliferation and cell cycle regulation (including E2F associated genes) that could translate into improved disease outcomes. Ongoing studies will attempt to identify treatment response biomarkers. Future research will examine the correlations of gene expression with mutational profiles, splicing factor mutations, emavusertib dose regimens, and use of proteomics technologies to assess targeted kinase phosphorylation levels (e.g. IRAK4, NFκB) and quantification of soluble markers.

Trial Registration Trial Registration NCT04278768

Ethics Approval The protocol and related documents were approved by the applicable regional review boards, ethics committees, or both, and all samples used in the analysis were from patients who provided written informed consent.