Preclinical Activity of the Clinical Stage Protein Arginine Methyltransferase 5 (PRMT5) Inhibitor PRT543 in Splicing Mutant Myelodysplastic Syndrome (MDS) and Acute Myeloid Leukemia (AML)

MDS and AML are generally incurable malignancies that need newer therapeutic options, as the disease-initiating stem cells are not eliminated by conventional therapies. Splicing factor mutations account for approximately 50% of mutations in MDS. Among those are SF3B1 and U2AF1 mutations, which are related to pathogenesis of disease by overactivation of oncogenic pathways, such as Interleukin-1 Receptor-Associated Kinase 4 (IRAK4) signaling. Via activation of IRAK4 and other pathways, spliceosome mutations can lead to a block in differentiation and malignant proliferation. PRMT5 is an enzyme involved in spliceosome complex formation and fidelity and is over-expressed in patients with MDS/AML. The inhibition of PRMT5 may contribute to stem/progenitor cell differentiation rather than aberrant proliferation in an undifferentiated immature state. The objective of this study is to determine the activity of a clinical stage PRMT5 inhibitor, PRT543, in subtypes of MDS/AML using cell lines and primary samples. In preclinical studies PRT543 showed broad antitumor activity in vitro and in vivo (Bhagwat AACR 2020) and is currently under investigation in a Phase I clinical trial in patients with myeloid malignancies.

We used a K562 cell line with CRISPR-introduced SF3B1 K700E mutation and isogenic control (K700K) in proliferation and myeloid differentiation assays with PRT543. The SF3B1 K700E mutant cells showed myeloid differentiation after treatment with the PRT543 PRMT5 inhibitor, as assessed by single cell colony assays and flow cytometry, while no substantial effects were observed in controls (K700K). We next evaluated PRMT5 expression in a large set of MDS CD34+ cells and observed substantial overexpression in SF3B1 mutant samples. Primary MDS/AML progenitors were cultured in methylcellulose colony forming unit (CFU) assays and treated with PRT543 at multiple concentrations versus vehicle controls. A majority of the SF3B1 patient samples showed a substantial increase in erythroid differentiation as assessed by colony formation and flow cytometry in the presence of 1nM and 5nM PRT543. In non-SF3B1 mutated patient samples, there was no clear difference in differentiation in the presence of PRT543.

We next evaluated whether PRMT5 inhibition led to inhibition of oncogenic IRAK4 pathways. Retention of exon 4 of IRAK4 occurs in splicing mutant MDS and leads to production of an active long IRAK4 isoform. As measured by RNA-seq, PRMT5 inhibition led to decreased retention of exon 4 in IRAK4 transcripts. This decrease in the IRAK4 long form in response to PRT543 treatment was confirmed by immunoblotting, demonstrating reduction of this oncogenic signaling pathway.

In summary, PRMT5 inhibition with PRT543 can release a differentiation block in MDS/AML, specifically in splicing mutant samples. PRMT5 inhibition decreases IRAK4-long isoform expression providing a potential mechanism for its activity in splicing factor mutant cases.