PRMT5 Inhibition Affects RNA Methylation and Is a Potential Therapeutic Target in BPDCN

Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare and clinically aggressive hematologic cancer that arises from malignant transformation of plasmacytoid dendritic cells (pDCs) and is predisposed to leukemic transformation. Apart from the recently approved therapy, Tagraxofusp-erzs, treatment options for BPDCN remain limited. A recurrent feature of BPDCN is dysregulated MYC expression, which is associated with dependence on Protein arginine methyltransferase 5 (PRMT5). PRMT5 catalyses symmetric dimethylation of arginine residues post translationally and is often overexpressed in hematological malignancies. It was recently reported that BPDCN patient samples were enriched for a PRMT5 gene signature. However, the role of elevated PRMT5 in BPDCN has not been studied. Moreover, how pharmacological inhibition of PRMT5 affects BPDCN remains unexplored. Here, we pursue the hypothesis that PRMT5 or PRMT5-regulated factors represent a potential therapeutic opportunity in BPDCN, a hematologic malignancy of unmet clinical need.

We report that elevated PRMT5 activity is critical for BPDCN. Compared to pDCs from healthy individuals, BPDCN cells expressed much higher levels of MYC and PRMT5. Functionally, in vitro growth of BPDCN cells treated with the PRMT5 inhibitor GSK3326595 (GSK595) was impaired in a dose-dependent manner, with net negative cell growth observed 6 days post-treatment. Similarly, bi-daily oral administration of GSK595 to CAL-1 xenografts significantly mitigated the growth of tumors, without any observed impact on body weight. In addition, the sensitivity of BPDCN cells to GSK595 was comparable to MOLM-13, which has been reported to be highly sensitive to PRMT5 inhibition. Correspondingly, this growth inhibition was associated with the induction of apoptosis. Thus, confirming the requirement for elevated PRMT5 levels in BPDCN.

We then transcriptionally profiled GSK595-treated BPDCN cells and identified differential splicing events (DSEs) across several splicing classes; of which intron retention (and to a lesser extent, exon skipping) events were substantially elevated. Interestingly, these upregulated intron retention events were over-represented for processes associated with RNA modification. Specifically, we found that splicing of several essential genes involved in RNA modification were dysregulated. Among these genes was Methyltransferase-like protein 3 (METTL3), an RNA methyltransferase writer which mediates m⁶A modification on mRNAs. In agreement, we show that PRMT5 inhibition decreased the expression of METTL3 along with its downstream targets – MYC & TAZ. We also show that the levels of m⁶A modification in GSK595-treated BPDCN cells decreased in a dose-dependent manner; thus, highlighting the reduced functional activity of METTL3 following PRMT5 inhibition. Taken together, our data implicates METTL3 and possibly other essential RNA modification genes as key downstream effectors of PRMT5 in BPDCN.

Collectively, our study highlights a novel link between PRMT5 and RNA modification in BPDCN. In addition, we show that elevated PRMT5 is important in BPDCN and its inhibition mitigates BPDCN progression. Therefore, PRMT5 inhibition is a potential therapeutic strategy for BPDCN.