Activation of targetable inflammatory immune signaling is seen in myelodysplastic syndromes with SF3B1 mutations

Abstract

Background:Mutations in the SF3B1 splicing factor are commonly seen in myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML), yet the specific oncogenic pathways activated by mis-splicing have not been fully elucidated. Inflammatory immune pathways have been shown to play roles in the pathogenesis of MDS, though the exact mechanisms of their activation in splicing mutant cases are not well understood.Methods:RNA-seq data from SF3B1 mutant samples was analyzed and functional roles of interleukin-1 receptor-associated kinase 4 (IRAK4) isoforms were determined. Efficacy of IRAK4 inhibition was evaluated in preclinical models of MDS/AML.Results:RNA-seq splicing analysis of SF3B1 mutant MDS samples revealed retention of full-length exon 6 of IRAK4, a critical downstream mediator that links the Myddosome to inflammatory NF-kB activation. Exon 6 retention leads to a longer isoform, encoding a protein (IRAK4-long) that contains the entire death domain and kinase domain, leading to maximal activation of NF-kB. Cells with wild-type SF3B1 contain smaller IRAK4 isoforms that are targeted for proteasomal degradation. Expression of IRAK4-long in SF3B1 mutant cells induces TRAF6 activation leading to K63-linked ubiquitination of CDK2, associated with a block in hematopoietic differentiation. Inhibition of IRAK4 with CA-4948, leads to reduction in NF-kB activation, inflammatory cytokine production, enhanced myeloid differentiation in vitro and reduced leukemic growth in xenograft models.Conclusions:SF3B1 mutation leads to expression of a therapeutically targetable, longer, oncogenic IRAK4 isoform in AML/MDS models.Funding:This work was supported by Cincinnati Children’s Hospital Research Foundation, Leukemia Lymphoma Society, and National Institute of Health (R35HL135787, RO1HL111103, RO1DK102759, RO1HL114582), Gabrielle’s Angel Foundation for Cancer Research, and Edward P. Evans Foundation grants to DTS. AV is supported by Edward P. Evans Foundation, National Institute of Health (R01HL150832, R01HL139487, R01CA275007), Leukemia and Lymphoma Society, Curis and a gift from the Jane and Myles P. Dempsey family. AP and JB are supported by Blood Cancer UK (grants 13042 and 19004). GC is supported by a training grant from NYSTEM. We acknowledge support of this research from The Einstein Training Program in Stem Cell Research from the Empire State Stem Cell Fund through New York State Department of Health Contract C34874GG. MS is supported by a National Institute of Health Research Training and Career Development Grant (F31HL132420).

The E592K variant of SF3B1 creates unique RNA missplicing and associates with high-risk MDS without ring sideroblasts

“…Other events that have been implicated in SF3B1-mutant MDS pathobiology include innate immune activation by missplicing of MAP3K7 and IRAK4, enhanced self-renewal by MECOM missplicing, impaired erythropoiesis by COASY missplicing, and hepcidin suppression by ERFE missplicing; all these genes were also canonically spliced in E592K cells (Supplementary Fig. 7) 3,4,[6][7][8] . A distinct E592K pathobiology is also suggested by its high co-occurrence with ASXL1/RUNX1/STAG2 mutations and mutual exclusivity with DNMT3A mutations, a starkly different pattern than that of other SF3B1 hotspots.…”

Emerging treatments for myelodysplastic syndromes: Biological rationales and clinical translation

“…The genetic inhibition of IRAK4-L expression induces differentiation of AML cells and decreases tumoral burden in in vivo experiments. 118 , 119 Therefore, IRAK4 inhibitors are promising therapeutic options to target the innate immune system. 120 Further preclinical studies also revealed that IRAK signaling is a mechanism of adaptive resistance in the setting of FLT3 -mutant AML.…”

What’s Next after Hypomethylating Agents Failure in Myeloid Neoplasms? A Rational Approach

“…Emavusertib (EMA) is a small molecule kinase inhibitor that blocks a serine/threonine kinase belonging to the interleukin one receptor-associated kinase four (IRAK4) family. Spliceosome mutations, such as SF3B1 and U2AF1 , induce the expression of IRAK4, leading to a targetable, longer, oncogenic IRAK4 isoform in MDS/AML [ 109 , 110 , 111 ]. Of note, IRAK4 signaling downstream of the IL-1 receptor or toll-like receptor family leads to increased NF-kB activity and promotes the dominance of MDS clones and a transition to AML [ 112 ].…”