Cellular pathways influenced by protein arginine methylation: Implications for cancer

Abstract

Arginine methylation is an influential post-translational modification occurring on histones, RNA binding proteins, and many other cellular proteins, affecting their function by altering their protein-protein and protein-nucleic acid interactions. Recently, a wealth of information has been gathered, implicating protein arginine methyltransferases (PRMTs), enzymes that deposit arginine methylation, in transcription, pre-mRNA splicing, DNA damage signaling, and immune signaling with major implications for cancer therapy, especially immunotherapy. This review summarizes this recent progress and the current state of PRMT inhibitors, some in clinical trials, as promising drug targets for cancer.

Keywords: DNA damage signaling; PRMTs; S-adenosylmethionine; arginine methylation; epigenetics; immunotherapy; pre-mRNA splicing; small-molecule inhibitors; transcription.

Figure 1.. Classification of the types of methyl-arginines and protein arginine methyltransferases.

A. Type I and II PRMTs generate monomethyl-arginine (Rme1, MMA) from arginine as a first step, followed by asymmetrical dimethyl-arginine (Rme2a, aDMA; Type I, PRMT1, PRMT2, PRMT3, CARM1, PRMT6 and PRMT8) and symmetrical dimethyl-arginine (Rme2s, sDMA; Type II, PRMT5 and PRMT9) on the guanidino nitrogen atoms using S-adenosylmethionine (AdoMet) converting it to S-adenosylhomocysteine (AdoHcy). The Type III PRMT7 generates only Rme1 (MMA). The guanidinium moiety is shown as a triangle with its H-bonding and π-stacking properties. An arginine demethylase is not known. B. The known preference of arginine motifs for the PRMTs. PRMT7 has a preference for arginines within the RxR sequences; CARM1 prefers to methylate arginines with neighboring prolines, glycines, and methionines (PGM); PRMT1, PRMT3, PRMT5 and PRMT6 have preference for arginines with neighboring glycines within RGG/RG motifs.

Figure 2.. Arginine methylation as a regulator of transcriptional activity.

A. PRMT1 methylates H4R3me2a to facilitate p300-mediated acetylation on histones H3 and H4. H4R3me2a is recognized by TDRD3, which recruits methyl-USP9X and binds SMARCA4, which promotes H3 acetylation. PRMT1-MLL (mixed-lineage leukemia) fusion protein deposits H4R3me2a and recruits KDM4C for H3K9me3 demethylation. B. PRMT5 methylates H4R3me2s which inhibits the deposition of H4K5me3, H4Ac and H3Ac. H4R3me2s is recognized by PHF1 (PHD finger protein 1), which recruits CRL4B (Cullin4B-E3 ligase complex) and transcriptionally represses genes encoding tumor suppressors. PRMT7 methylates H4R17, which enhances H4R3me2a by PRMT5. C. PRMT5-catalyzed H3R2me2s is recognized by WDR5/MLL complex, which promotes H3K4me3. PRMT5-mediated H3R2me2s promotes transcription activation during anti-viral immunity and cancer progression. PRMT2-catalyzed H3R8me2a and CARM1-catalyzed H3R17me2a/H3R26me2a are also associated with transcriptional activation and cancer progression. PRMT6 methylates H3R2me2a and blocks H3K4-methylwriters including the WDR5/MLL complex and to facilitate AurB (Aurora kinase B)-mediated H3S10 phosphorylation.

Figure 3.. Protein arginine methyltransferases regulate the p53 and DNA damage response pathways.

A. PRMT5 methylates Sm proteins, SRSF1 (Serine and arginine rich splicing factor 1), and RBMX (RNA binding motif protein X-linked), to regulate MDM4 alternative splicing (AS) and p53 protein levels. SRSF1 and RBMX can coexist in a membraneless nuclear organelle and this is regulated by the methylation of RBMX by PRMT5. B. The MRE11-RAD50-NBS1 sensor complex at DSBs (double stranded breaks) activates the ATM (Ataxia telangiectasia mutated) kinase to phosphorylate the histone variant H2AX (γH2AX) and many other proteins to trigger DSB repair. PRMT1 methylation of MRE11 regulates its resection activities. The methylation of RNA binding protein hnRNPUL1 regulates interaction with NBS1. GFI1 is a transcription factor that enhances the PRMT1-mediated methylation of MRE11 in T cells and USP11 regulates the activity of PRMT1 by deubiquination. Circled ‘U’ denote ubiquitin. The methylation of the DSB repair proteins 53BP1, BRCA1, APE1 (apurinic/apyrimidinic endonuclease 1) is mediated by PRMT1, but the role of these methylation events remain unknown. Methylation of p14^ARF (alternative reading frame tumor suppressor product of the CDKN2A locus) allows its nucleolar export from NPM (nucleophosmin) to promoter apoptosis. C. DDX5 (DEAD-box helicase 5) is methylated by PRMT5 and this regulates association with XRN2 (5’−3’ exonuclease 2) for R-loop (RNA/DNA hybrid) resolution. DDX5 recruitment to DNA breaks is regulated by BRCA2 (Breast cancer gene 2). PRMT5 also methylates the RNA polymerase II C-terminal domain which lead to the recruitment of the helicase SETX (Senataxin) and XRN2 by SMN to resolve R-loops. CARM1 and PRMT1 methylates histones which attract the methyl-reader protein TDRD3 via its Tudor domain to recruit topoisomerase TOP3B (DNA topoisomerase III beta) to resolve R-loops. The resolution of R-loops prevents endogenous DNA damage and maintains genome stability. The RNA of the RNA/DNA hybrid of R-loops harbors m⁶A (N⁶-methyladenosine) and this event is regulated by PRMT1 methylation of the m⁶A methyltransferase (WTAP, METTL3, METTL14) component METTL14. D. PRMT5 methylates RUVBL1 (RuvB like AAA ATPase) activating TIP60α which acetylates H4K16 to block 53BP1 recruitment favoring HR (homologous recombination) over NHEJ (non-homologous end-joining). The alternative splicing (AS) of TIP60α is regulated by PRMT5 to promote HR. CARM1 methylation of the SWI/SNF complex subunit BAF155 at R1064 increases EZH2 (Enhancer of zeste 2 polycomb repressive complex 2 subunit) H3K27me3 methylation repressing NHEJ Shieldin component MAD2L2. The upregulation of NHEJ in HR-proficient high-grade serous ovarian cancers by EZH2 inhibition creates sensitivity to poly (ADP-ribose) polymerase inhibitors. PRMT5 also methylates FEN1, RAD9, TDP1, and KLF4 to maintain genomic stability.

Figure 4.. Arginine methylation negatively regulates the anti-viral response.

A. Methylation of IFI16 (interferon gamma inducible protein 16) and cGAS (Cyclic GMP-AMP synthase) by PRMT5 inhibits the cGAS/STING (Stimulator of Interferon genes) pathway. PRMT5 also negatively regulates the transcription of NLRC5 (NLR family CARD domain containing 5), a crucial transactivator of MHC (major histocompatibility complex) class genes. B. PRMT7 inhibits RIG-I-like receptors (retinoic acid-inducible gene-I-like receptors, RLRs), MDA5 (melanoma differentiation-associated gene 5), MAVS (mitochondrial antiviral signaling protein) and dsRNA ERV (Endogenous retrovirus) repetitive sequences to inhibit RIG-I signaling. PRMT3 and PRMT6 also inhibit this pathway preventing IRF-3 (Interferon regulatory factor 3) induced type I interferons.