PRMT5 methylome profiling uncovers a direct link to splicing regulation in acute myeloid leukemia

Abstract

Protein arginine methyltransferase 5 (PRMT5) has emerged as a promising cancer drug target, and three PRMT5 inhibitors are currently in clinical trials for multiple malignancies. In this study, we investigated the role of PRMT5 in human acute myeloid leukemia (AML). Using an enzymatic dead version of PRMT5 and a PRMT5-specific inhibitor, we demonstrated the requirement of the catalytic activity of PRMT5 for the survival of AML cells. We then identified PRMT5 substrates using multiplexed quantitative proteomics and investigated their role in the survival of AML cells. We found that the function of the splicing regulator SRSF1 relies on its methylation by PRMT5 and that loss of PRMT5 leads to changes in alternative splicing of multiple essential genes. This explains the requirement of PRMT5 for leukemia cell survival. We show that PRMT5 regulates Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:

Splicing Dysregulation as Oncogenic Driver and Passenger Factor in Brain Tumors

“…Approaches to more globally target splicing regulation by chemical inhibitors for the spliceosome machinery are also being evaluated in brain tumors. In this regard, a promising target is PRMT5, a type II methyltransferase that is responsible for depositing the majority of the symmetrical dimethylation marks on arginines (SDMA) and methylates several RNA binding proteins and spliceosomal proteins [133][134][135]. In MYC-driven tumors, PRMT5 enhances assembly of spliceosome components and MYC expression [136,137].…”

Transcriptomic and proteomic regulation through abundant, dynamic, and independent arginine methylation by Type I and Type II PRMTs

“…To characterize PRMT enzymes' substrate motifs, a variety of targeted enzymatic and computational approaches have been used (Wooderchak et al 2008;Gathiaka et al 2016;Gayatri et al 2016). Finally, others have tested the proteomic and transcriptomic consequences of inhibition of various PRMTs Eram et al 2016;Fong et al 2019;Musiani et al 2019;Radzisheuskaya et al 2019).…”

“…For instance, PTMScan-previously developed to immunoprecipitate post-translationally modified peptides after lysate protease cleavage (Stokes et al 2012)-was used in HEK293 cells to identify thousands of PRMT-regulated Rme1 sites (Larsen et al 2016) and to identify PRMT1 substrates in Toxoplasma (Yakubu et al 2017). Others have used PTMScan with SILAC to identify sites of all three methylarginine states, mostly found to be enriched in RNA-binding proteins and regulating splicing (Fong et al 2019;Musiani et al 2019;Radzisheuskaya et al 2019). Middle-down proteomics coupled with electron-transfer dissociation (ETD) was used to specifically identify arginine methylation in arginine-and serine-rich domains in RNA-binding proteins (Kundinger et al 2020).…”

PRMT5 function and targeting in cancer

“…Myc- or PRMT5-depletion resulted in aberrant splicing (either exon skipping or retained introns) of genes associated with cell cycle arrest or apoptosis [ 68 ]. Consistently, large-scale proteomic profiling of PRMT5 substrates identified factors related to RNA processing [ 13 , 57 ]. Among them, SRSF1, a serine/arginine rich protein functioning in alternative splicing, is directly methylated by PRMT5.…”

“…Notably, protein arginine methylation is commonly seen on splicing machinery components. Moreover, proteome-wide profiling revealed enrichment of arginine-methylated proteins implicated in control of RNA splicing, transport or degradation [ 13 , 14 , 56 , 57 ].…”