Protein arginine methyltransferases as regulators of cellular stress

Abstract

Arginine modification can be a “switch” to regulate DNA transcription and a post-translational modification via methylation of a variety of cellular targets involved in signal transduction, gene transcription, DNA repair, and mRNA alterations. This consequently can turn downstream biological effectors “on” and “off”. Arginine methylation is catalyzed by protein arginine methyltransferases (PRMTs 1–9) in both the nucleus and cytoplasm, and is thought to be involved in many disease processes. However, PRMTs have not been well-documented in the brain and their function as it relates to metabolism, circulation, functional learning and memory are understudied. In this review, we provide a comprehensive overview of PRMTs relevant to cellular stress, and future directions into PRMTs as therapeutic regulators in brain pathologies.

1. Introduction

Arginine methylation is a post-translational modification that has implications in the DNA damage response, gene expression regulation, and mRNA translation (Guccione and Richard, 2019). More specifically, post-translational modifications are alterations on amino acid side chains that modify the protein’s structure, stability, and function (Zhong et al., 2020). These modifications in histone proteins have a notable role in defining chromatin structure and gene expression regulation. The most common types of post-translational modifications are acetylation/methylation of lysine/arginine residues (Carr et al., 2015). Methylation of lysine in histones, via protein lysine methyltransferase (PKMTs), and arginine residues, by protein arginine methyltransferases (PRMTs,) are crucial to determine gene expression since methylation can lead to more condensed chromatin, which can prevent the access of transcription factors to their binding site (Hublitz et al., 2009; Jambhekar et al., 2019). While lysine methylation has a primary action of gene repression, arginine methylation can either activate or repress transcription. Although some of the PRMTs can be considered histone-specific, several PRMTs have been found to modify non-histone substrates (Yang and Bedford, 2013; Hamamoto et al., 2015). Methylation of non-histone proteins appears to be an indispensable post-translational modification, with a wide-range of roles in various cellular processes, including cell signaling, embryo development, cell cycle regulation, proliferation, survival, and differentiation (Carr et al., 2015; Hwang et al., 2021; Di Blasi et al., 2021). However, methylation of non-histone proteins is also implicated in cell stress response (Shi and Gibson, 2007), behavior (Godini et al., 2021), function (den Hoed et al., 2021), and cognitive disorders (Zhang et al., 2007).

PRMTs are a family of enzymes responsible for methylation of arginine residues in mammals (Bedford and Clarke, 2009). This methylation occurs by transferring methyl groups from S-adenosyl-L-methionine to target proteins, leading to changes in their stability, activity and localization (Angelopoulou et al., 2023). Humans have 9 PRMT isoforms, organized into 3 types depending on their methylation pattern. Type I PRMTs catalyze mono-methylation of the arginine residue forming mono-methyl arginine (MMA), and further methylating the same nitrogen atom again to form asymmetric dimethylarginine (ADMA). Type I PRMTs are composed by PRMT1, PRMT2, PRMT3, PRMT4, PRMT6, and PRMT8, with PRMT1 being the most expressed one. Type II PRMTs catalyze mono-methylation of the arginine residue and further methylate the other nitrogen atom of the arginine residue to form both MMA and symmetric dimethylarginine (SDMA). Type II PRMTs are composed by PRMT5 and PRMT9. Type III PRMTs (PRMT7) only methylate one nitrogen atom forming MMA (Guccione and Richard, 2019; Morales et al., 2016).

PRMTs are highly expressed in the central nervous system and recent studies suggest their involvement in development, differentiation, and maturation of neurons, oligodendrocytes, and astrocytes (Angelopoulou et al., 2023). Therefore, PRMTs play an important role in neuronal function and development, often associated with neurodegenerative disorders, such as Alzheimer’s (AD), Parkinson’s, and Huntington’s diseases, and other pathological scenarios including cancer, cardiovascular diseases, inflammation, and metabolic disorders (Angelopoulou et al., 2023; Jarrold and Davies, 2019; Couto et al., 2020; Srour et al., 2022; vanLieshout and Ljubicic, 2019). PRMT4 is overexpressed in 3xTg-AD mice to suggest compromised cerebral blood flow but restored upon PRMT4 inhibition (via TP-064) (Clemons et al., 2024). On the other hand, the accumulation of amyloid beta in AD can result in the inhibition of PRMT5 activity, leading to unregulated neuronal apoptosis (Angelopoulou et al., 2023). In this review, we aim to summarize the current knowledge of PRMTs, as modulators and response to neuronal stress evoked by various brain pathologies (i.e. AD, stroke) (Please see Table 1 and Fig. 1 for a summary of this review).

Table 1.

PRMTs and their relevant targets.

PRMT	Switch	Target	Effect/Pathway	Reference
PRMT1	down	Nrf2 (R437)	Reduced protection against oxidative stress	Liu et al. (2016)
	down	RelA (R30)	Increase expression of NF-κB target genes	Reintjes et al. (2016)
	up	p65	Coactivate NF-κB-mediated transcription at the HIV-1 LTR promoter and MIP2	Hassa et al. (2008)
	down	unknown	Increase accumulation of HIF-1α protein levels under hypoxic conditions	Lafleur et al. (2014)
	down	FOXO1	Reduce stress-induced apoptosis	Yamagata et al. (2008)
	down	STAT1 (R31)	Reduce transcription of interferon-mediated anti-proliferative gene expression	Mowen et al. (2001)
	down	E2F1	Reduce E2F1-dependent apoptosis	Zheng et al. (2013)
	down	unknown	Reduce dopaminergic neuronal cell death	Nho et al. (2020)
	down	MRE11	S-phase checkpoint defects	Boisvert et al. (2005b)
	down	p53BP1/MRE11	Decrease DNA repair capacity	Vadnais et al. (2018)
	down	FEN1 (R192)	Decrease cancer cell resistance to chemotherapy	He et al. (2020b)
	down	APE1	Increase DNA damage in the mitochondria and sensitizes cells to oxidative stress	Zhang et al. (2020)
	down	CIITA	Activates MHC through IFN-y and CIITA enhanceassome	Fan et al. (2017)
	down	NIP45	Impaired cytokine production by T helpers	Mowen et al. (2004)
PRMT2	up	unknown	Inhibit NF-κB-dependent gene expression and promotes cell death	Hassa et al. (2008)
	down	BRD4	Sensitizes cells to BET inhibitors and DNA damaging agents	Liu et al. (2022)
	up	unknown	Anti-depressant	Liu et al. (2024)
	up	Cobl	Induce neuronal morphogenesis	Hou et al. (2018)
	up	H3R8me2a	Co-activate oncogenic gene expression programs in Glioblastoma multiforme	Dong et al. (2018)
PRMT3	down	HIF1α	Inhibit angiogenesis in colorectal cancer	Zhang et al. (2021)
	down	HIF1α	Repressed Glycolysis pathway	Zhou et al. (2024)
PRMT4	down	Histone 3	Reduce arsenic-induced expression of ferritin gene	Huang et al. (2013)
	down	unknown	Reduce NF-κB-mediated transcription at the HIV-1 LTR promoter	Hassa et al. (2008)
	down	p300	Attenuate DNA damage response	Lee et al. (2011)
	down	Histone 3	Decrease expression of NF-κB-dependent genes	Miao et al. (2006)
PRMT5	down	unknown	Reduce oxidative stress and inflammation-induced cell death	Diao et al. (2019)
	down	p65 (R30)	Reduce expression of some NF-κB-regulated genes	Wei et al. (2013)
	down	unknown	Attenuate hypoxic induction of HIF-1α	Lim et al. (2012)
	down	FOXO1	Disturb development of muscle and regeneration	Kim et al. (2023)
	down	Smad7	Suppress cell proliferative activity	Cai et al. (2021)
	down	E2F1	Retore regulatory activity of the cell cycle and Induce apoptosis in cancer cells	Sloan et al. (2023)
	down	H4 (R3)	Cell-cycle arrest (apoptosis and loss of cell migratory activity	Yan et al. (2014)
	down	53BP1	Reduce 53BP1 levels and impairs NHEJ DNA repair	Hwang et al. (2020)
	down	Rad9	Increase susceptibility to DNA damage	He et al. (2011)
	down	RUVBL1	Reduce DSB repair activity	Clarke et al. (2017)
	down	TDP1	Increase cell replication, lethality and DNA damage	Rehman et al. (2018)
	down	KLF4	Suppress tumor progression and Induce tumor cell death	Zhou et al. (2019)
	down	no enzymatic function	Potentiates RAIL-mediated cytotoxicity	Tanaka et al. (2009)
	down	p65 (R30)	Suggested therapy for rheumatoid arthritis	Chen et al. (2017)
PRMT6	down	H3R2	Increase cellular senescence	Neault et al. (2012)
	unknown	Polymerase beta	Enhance polymerase β DNA binding and processivity	El-Andaloussi et al. (2006)
	up	GPS2	Increase expression of NF-κB target genes	Di Lorenzo et al. (2014)
PRMT7	down	unknown	Decrease hippocampal mitochondrial oxygen consumption rates	Acosta et al. (2023)
PRMT8	down	unknown	Increase inflammatory response and reduce mitochondrial reserve capacity under hypoxia	Couto et al. (2021)
PRMT9	down	SF3B2	Increase alternative splicing, aberrant synapse development and impaired learning and memory	Shen et al. (2024)

Fig. 1.

Schematic diagram showing PRMT’s involvement in key cellular processes of stress response.

2. Transcription factors

Transcription factors also undergo post-translational modifications, which alter their DNA-binding activity and modulate protein-protein interactions, subcellular localization, transcriptional activity, and protein stability (Kim et al., 2021). Moreover, transcription factors can act as a DNA methylation reader, capable of recognizing methyl-lysine and methyl-arginine regions of the histone, therefore modulating gene expression (Zhu et al., 2016). PRMTs can regulate the activity of several transcription factors such as FOXO1 (Forkhead box protein O1), by PRMT1, which prevents proteasomal degradation and favors nuclear localization (Yamagata et al., 2008). Cell stress response in neurodegeneration comprises several key transcription factors, such as the nuclear factor (erythroid 2)–related factor 2 (Nrf2) (Suzen et al., 2022), the nuclear factor-kappa B (NF-κB) (Kaltschmidt et al., 2022), heat shock factors (HSFs) (Gomez-Pastor et al., 2018) and proteins (HSP) (Beretta and Shala, 2022), hypoxia-inducible factors (HIFs) (Correia et al., 2013), forkhead box O (FOXO) (Du and Zheng, 2021), CCAAT/enhancer-binding proteins (C/EBPs) (Straccia et al., 2011), SRY-related HMG-box (SOX) (Stevanovic et al., 2023), homeobox (HOX) (Acquaah-Mensah et al., 2015), signal transducer and activator of transcription 1 (STAT1) (Wang et al., 2002), and E2F. All of these transcription factors are regulated through arginine methylation by PRMTs.

2.1. Nuclear factor erythroid 2-related factor 2 (NRF2)

Nrf2 is a transcription factor crucial for cellular defense against oxidative stress, as it activates cytoprotective gene expression (Gong and Yang, 2020; He et al., 2020a; Hammad et al., 2023) through binding of antioxidant response element (ARE), a regulatory sequence of DNA present in multiple genes of detoxification and antioxidant proteins (Chen and Kunsch, 2004). Nrf2 is the first transcription factor to bind to ARE and it was found that methylation by PRMT1 increased its’ transcriptional activity and DNA binding ability (Liu et al., 2016). Knocking down PRMT1 and PRMT4 blocks the binding of Nrf2 to the ARE of the ferritin gene in arsenic treated human cells interfering with cellular antioxidant response (Liu et al., 2016; Huang et al., 2013). Pyroptosis, a process of inflammation-induced cell death, via Nrf2/heme-oxygenase (HO-1) pathway is attenuated in ischemia/reperfusion model when PRMT5 is inhibited, all-the-while reducing oxidative stress. In confluence with the previous data, the protein levels of Nrf2 and HO-1 are also increased when PRMT5 is silenced (Diao et al., 2019; Zhang et al., 2022).

2.2. Nuclear factor kappa-B (NF-κB)

NF-κB is a family of inducible transcription factors that are involved in cellular stress, proliferation, synaptic plasticity, and learning/memory (Oeckinghaus and Ghosh, 2009; Snow and Albensi, 2016; Verma et al., 2023). RelA (p65) is one of the best-known NF-κB transcription factors relevant to AD. Expression and activation of p65 has been shown to up-regulate β-secretase cleavage and Aβ production, as observed in the brain of some sporadic AD patients (Snow and Albensi, 2016; Chen et al., 2012). One of the most prominent post-translational modifications of p65 is the methylation of arginine residues by PRMTs (Dai et al., 2022). Methylation of R30 (arginine 30) on p65, via PRMT5, occurs in response to interleukin IL-1b activation and it is essential for NF-κB-regulated genes that encode cytokines, chemokines, and growth factors (Wei et al., 2013). Reintjes et al. (2016) showed that PRMT1-mediated p65 methylation reduced overall expression of tumor necrosis factor alpha (TNF-α) (Reintjes et al., 2016). Interestedly, Hassa et al. (2008) showed that NF-κB-dependent transcription at the HIV-1 LTR (long terminal repeat) promoter in vitro is regulated by several PRMTs, where PRMT1, with PRMT4 as co-activator, strongly activated p65, but PRMT2 and PRMT5 function as repressors of NF-κB (Hassa et al., 2008). Thus, the regulation of NF-κB activity through arginine methylation is extremely complex and context-dependent.

2.3. Hypoxia-inducible factors (HIFs)

HIF is a transcription factor that triggers a cell survival program in conditions of oxygen deprivation, activating over 100 genes that encompass various cellular processes involved with hypoxia adaptation, such as anemia, tissue ischemia, angiogenesis, energy metabolism, cell proliferation, cell cycle control among others (Bouthelier and Aragones, 2020; Mitroshina and Vedunova, 2024). HIFs are heterodimeric transcription factors that have three isoforms of the α subunit (HIF-1α, HIF-2α, and HIF-3α). HIF-1α and HIF-2α are critical for the hypoxia response (Kenneth and Rocha, 2008), but HIF-1α is neuroprotective, thus regulating gene expression associated with cell death during neurodegeneration (Iyalomhe et al., 2017). HIF-1 is controlled by multiple post-translational modifications on different amino acid residues of its subunits. The asymmetric methylation of R282 (of HIF1a) by PRMT3 increases HIF-1α stability, which favors gene expression related to angiogenesis and the HIF1/VEGFA (vascular endothelial growth factor A) pathway, improving tissue vascularization (Zhang et al., 2021). Moreover, in a study with vascular calcification, the authors observed that depletion of PRMT3 regulated the glycolysis pathway by repressing the expression of β-glycerophosphate, Glucose transporter 1 (GLUT1), 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3), Pyruvate kinase M2 (PKM2) and lactate dehydrogenase A (LDHA) through HIF-1α (Zhou et al., 2024). In addition, PRMT1 can act as a repressor of HIF1/2α subunit; on the other hand, PRMT5 knockdown attenuated the hypoxic induction of HIF-1α, and the transcript levels of HIF-1-governed genes (i.e. VEGF, lysyl oxidase, and Phosphoinositide-dependent kinase 1), suggesting that PRMT5 is required for the HIF-1 signaling pathway (Lim et al., 2012; Lafleur et al., 2014).

2.4. Forkhead box protein (FOXO)

FOXO (part of the Forkhead family of transcription factors) protein target genes that encode metabolism and/or stress resistance mechanisms when cells are not generating enough energy or in the absence of insulin or insulin-like growth factors (Nemoto and Finkel, 2002; Oli et al., 2021). Several studies have suggested the potential involvement of FOXO in the progression of neurodegenerative diseases, such as AD, Parkinson’s, Huntington’s disease, amyloid lateral sclerosis, dementia and others (Maiese, 2016; Orea-Soufi et al., 2022). In AD patients FOXO3 is considered the largest inducer of cell death in response to Aβ mediated oxidative stress (Maiese, 2016). In fact, arginine methylation is one of the several post-translational modifications that regulate FOXO. PRMT1 can methylate the R248 and R250 residues within the FOXO motif blocking Akt (kinase protein)-mediated phosphorylation of FOXO1, changing the transcription factor’s activity. Reduced PRMT1 enhanced nuclear exclusion and proteasomal degradation of FOXO1 and decreased oxidative stress-induced apoptosis dependent of phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT) signaling pathway in HEK293 (Human Embryonic Kidney) cells, to suggest that FOXO1 methylation by PRMT1 activated expression of Bim gene (Bcl-2-interacting mediator), therefore, promotes apoptosis. Moreover, the knockdown of PRMT1 in human umbilical vein endothelial cells induced expression of endothelial nitric oxide synthase (eNOS) proteins which regulate vascular endothelial growth factor, to promote vascular homeostasis (Yamagata et al., 2008). PRMT5 is another methyltransferase enzyme that regulates FOXO1’s activity. In a PRMT5 knockout mouse embryonic myoblasts, Kim et al., 2023 showed that FOXO1 levels were increased and accumulated in the cytosol of the myoblasts leading to activation of autophagy and depletion of lipid droplets resulting in disturbed development of muscle and regeneration (Kim et al., 2023).

2.5. Signal transducer and activator of transcription 1 (STAT)

The STAT family comprises a group of cytoplasmic transcription factors that modulate cellular responses to a diverse array of extracellular signals, including cytokines and growth factors. STAT protein activation is primarily driven by tyrosine phosphorylation, predominantly mediated by Janus kinases (JAKs) (Awasthi et al., 2021). The JAK/STAT signaling pathway is a pivotal mechanism in determining gliogenic cell fate, influenced significantly by the overactivation of microglia and astrocytes. This pathway plays a crucial role in neuroinflammation observed in neurodegenerative diseases, by initiating innate immune responses, coordinating adaptive immune mechanisms, and regulating neuroinflammatory responses (Rusek et al., 2023). In tauopathies, tau accumulation activates STAT1, which results in the suppression of synaptic N-methyl-d-aspartate receptor (NMDAR) transcription. Acetylated STAT1 forms complexes with STAT3 in the cytoplasm, inhibiting its nuclear translocation and activation. This inhibition directly suppresses NMDAR expression, contributing to synaptic dysfunction and memory impairment (Hong et al., 2020). Mowen et al. (2001) showed that PRMT1 methylate R31 on STAT1, regulating the transcription of interferon-mediated anti-proliferative gene expression (Mowen et al., 2001). Also, PRMT5 can directly methylate SMAD7 (Mothers against decapentaplegic homolog 7); such protein modification ensures robust STAT3 activation via the Smad7-STAT3 axis, which is necessary for cell proliferation, while PRMT5 silencing or inhibition results in suppression of cell proliferation (Cai et al., 2021).

2.6. E2F

The E2F family comprises of nine transcription factors, all involved in cell cycle regulation during G1/S transition, and DNA synthesis; E2F1, E2F2, E2F3a are gene activators, while E2F3b, E2F4-8 are gene repressors (Chen et al., 2009). The role in promoting cell cycle progression or apoptosis will depend on the transcriptional activation of a subset of E2F target genes (Chu et al., 2007). In neurons, aberrant re-entry into the cell cycle is a pathological event that contributes to the progression and severity of neurodegenerative diseases. Although some studies have suggested that this phenomenon immediately leads to cell death and apoptosis (Frade and Ovejero-Benito, 2015), others have suggested a non-proliferative role of the cell-cycle proteins leading to cell senescence (Wu et al., 2024; Frank and Tsai, 2009; Nandakumar et al., 2021).

E2F1 plays contradictory roles, such as promote cell-cycle progression v. apoptosis (Cho et al., 2012). PRMT1 can methylate E2F1, induce apoptosis; while PRMT5-dependent methylation promoted cellular proliferation (Zheng et al., 2013). Inhibition of PRMT5 led to restored regulatory activity of the cell cycle through retinoblastoma tumor suppressor protein (p-RB)/E2F, and apoptosis (p53-dependent/p53-independent) (Sloan et al., 2023). PRMT5 is overexpressed in glioblastoma cells (patient-derived primary tumors and cell lines), where genetic attenuation of PRMT5 expression led to cell-cycle arrest, apoptosis, and loss of glial cell migratory activity (Yan et al., 2014).

3. DNA damage response

The DNA damage response involves multiple proteins and pathways aimed to avoid genome mutation and consequently cell degeneration or cancer. There are at least five major pathways involved in DNA damage repair in mammalian cells (Huang and Zhou, 2021): mismatch repair (MMR), that resolves single nucleotide mismatches generated during replication (Li, 2008); base excision repair (BER), that corrects covalent additions to DNA bases (Caldecott, 2020); nucleotide excision repair (NER), that clears bulky adducts and cross-linking lesions (Yang and Bedford, 2013); homologous recombination (HR) and non-homologous end joining (NHEJ), responsible for double-stranded breaks (Pannunzio et al., 2018). Posttranslational modifications are required for most of the DNA damage response proteins. PRMTs are essential in these processes, generating modified arginine residues such as mono-methylarginine (MMA), asymmetric dimethylarginine (ADMA) and/or symmetric dimethylarginine (SDMA).

3.1. Type I PRMTs

PRMT1 is responsible for almost 90 % of all arginine methylation and is the most studied and described PRMT that methylate arginine residues (Dhar et al., 2013; Easton et al., 2000). It has been observed in models of Parkinson’s Disease that PRMT1 regulates dopaminergic neuronal cell death through DNA damage repair system involving PARP1 (Poly (ADP-ribose) polymerase-1) – AIF (apoptosis-inducing factor) pathway. When SN4741 cells (a dopaminergic neuron model) are treated with 1-methyl-4-phenylpiridinium iodide (MPP+), which causes dopaminergic neuronal cell death, PRMT1 and histone 4R3 methylation is enhanced. Interestingly, MPP-induced dopaminergic neuronal cell death was reduced upon lower PRMT1 (via siRNA) levels to suggest that PRMT1 plays an important role in neuronal apoptotic pathways (Nho et al., 2020).

It is known that PRMT1 forms a complex with PARP1. Inhibition of PARP1 also reduced dopaminergic neuronal cell death provoked by MPP treatment while overexpression of PRMT1 leads to increased translocation of AIF to the nucleus, to suggest the importance of PRMT1 in apoptosis induced by DNA damage repair pathways via PARP1 and AIF (Nho et al., 2020). Although PARP1-AIF are not observed as being directly modified by PRMT1, many other proteins involved in the DNA damage response are substrates of PRMT1, such as MRE11 (Meiotic recombination 11), BRCA1 (Breast cancer type 1 susceptibility protein), 53BP1 (p53 binding protein 1), Pol β (polymerase beta), FEN1 (Flap endonuclease 1), APE1 (Apurinic/apyrimidinic endonuclease 1), and hnRNPUL1 (Heterogeneous Nuclear Ribonucleoprotein U Like 1).

MRE11 (Boisvert et al., 2005a; Boisvert et al., 2005b) is methylated by PRMT1 in the glycine arginine-rich (GAR) domain, which is required for exonuclease activity in the damaged DNA. MRE11 methylation interferes with the DNA damage checkpoint of the S-phase of the cell cycle (Boisvert et al., 2005a; Boisvert et al., 2005b). In mouse embryonic fibroblasts (MEFs), PRMT1 also methylates SAM68 (Src associated in mitosis, of 68 kDa), a protein involved in mRNA processing, transport, and translation (Bielli et al., 2011). PRMT1 is also essential for genome integrity and cell proliferation; loss of PRMT1 in MEFs leads to spontaneous DNA damage, delayed cell cycle progression, checkpoint defects, aneuploidy, and polyploidy. Additionally, the knockdown of PRMT1 in human osteosarcoma cells results in hypersensitivity to DNA damage along with a defect in the recruitment of the RAD51 (another protein involved in DNA damage repair) to the site of DNA damage (Yu et al., 2012). DNA damage repair proteins methylated by PRMT1 also affect 53BP1, playing a critical role in double-stranded break repair by promoting non-homologous end joining, while inhibiting homologous recombination (Yu et al., 2012; Vadnais et al., 2018). Furthermore, PRMT1 methylates DNA pol β and FEN1 at the arginine 137 and 192, respectively. This methylation interferes with the binding of proliferating cell nuclear antigen (PCNA) (Guo et al., 2010). PRMT1 also methylates APE1 at arginine 301 (R301), which is enhanced by oxidative situations, such as H2O2 and menadione (Zhang et al., 2020). This methylation does not affect its nuclease activity but enhances APE1 binding to the mitochondrial outer membrane translocase (TOM20), promoting APE1 translocation to the mitochondria. Deficiency in R301 methylation increases DNA damage in the mitochondria and sensitizes cells to oxidative stress (Zhang et al., 2020).

PRMT4 is essential in the DNA replication fork, as observed in MEF cells, which will use low-fidelity mechanisms of replication (i.e.: allow errors) of the DNA even under stress when the methyltransferase is silenced (via siRNA). The knockdown of PRMT4 leads to more single-stranded DNA gaps, while increased chromosomal breaks, fusion, and early separation of sister chromatids in mitotic cells. The results of co-immunoprecipitation studies suggest that PRMT4 binds to PARP1 to slow down the DNA replication fork (Genois et al., 2021).

PRMT6 also plays a role in DNA damage response by modifying histones H3R2, H3R17, H3R42, and H2AR29 either producing MMA or ADMA (Casadio et al., 2013; Waldmann et al., 2011; Guccione et al., 2007; Hyllus et al., 2007). PRMT6 methylation of H3R2 leads to the repression of tumor suppressor expression, such as p53 and p21 (Guccione et al., 2007; Neault et al., 2012). However, a H3R42me2a modification by PRMT6 stimulates the transcription of genes controlled by p53 (Casadio et al., 2013). In addition, PRMT6 methylates Polymerase β, to enhance its binding to DNA, processivity of polymerase and base excision repair activity (BER) (El-Andaloussi et al., 2006).

3.2. Type II PRMTs

PRMT5 methylates the GAR motif of 53BP1, to increase protein stability, which is essential for double-stranded break repair. The SDMA modification in 53BP1 by PRMT5 competes with the ADMA catalyzed by PRMT1 (Hwang et al., 2020). PRMT5 also symmetrically dimethylates four arginine residues (R19, R100, R104, and R192) of FEN1, which drives the base excision repair pathway (LP-BER). Cells expressing the methylation deficient FEN1 mutant (R192K or 4RK) display higher levels of γH2AX (a phosphorylated histone indicative of unrepaired DNA accumulation) compared to cells expressing FEN1 wild-type, which make these mutant cells more sensitive to oxidative stresses (Guo et al., 2010).

RAD9 is a component of the 9-1-1 complex involved in the DNA damage response and is methylated by PRMT5, a modification essential for the activation of checkpoint kinase 1 (CHK1) signaling, which regulates the S/M and G2/M cell cycle checkpoints (He et al., 2011; Lieberman et al., 2017). RUVBL1 (RuvB Like AAA ATPase 1) is an AAA+ ATPase involved in chromatin remodeling, transcription, and DNA repair. RUBVL1 was identified as a PRMT5 interacting partner and substrate symmetrically dimethylated on R205 (Clarke et al., 2017). Depletion of RUBVL1 impaired homologous recombinant-mediated double-stranded repair leading to increased γH2AX upon ionizing radiation exposure (Clarke et al., 2017). PRMT5 also methylates TDP1 (Tyrosyl-DNA Phosphodiesterase 1) at two arginine residues, and promotes TDP1 catalytic activity. TDP1 is an important DNA repair enzyme for the removal of trapped Top I (topoisomerase 1) cleavage complexes (TopIcc) that are generated by either DNA lesions (mismatches, abasic sites, nicks, and adducts) or Top I inhibitor (Camptothecin, CPT) during Top I-mediated cleavage–religation process. TopIcc may stall the progression of replication and transcription forks and generate DSBs. PRMT5 knock down leads to increased DNA damage in cells treated with CPT which implies that SDMA modification protects cells against DNA damage (Rehman et al., 2018).

4. Inflammation

Arginine methylation is an essential process of inflammatory regulation, mediated by the enzymatic actions of PRMT1, PRMT4, PRMT5, and PRMT6. These PRMTs act as inflammatory mediators by interacting with NF-κB (Srour et al., 2022; Kim et al., 2016). PRMT1’s methylation of NF-κB affects TNFα’s action in the inflammatory response. TNF-α is one of the primary proinflammatory cytokines that mediate systemic inflammation by stimulating the transcription of several genes involved in inflammation via NF-κB activation (i.e. A20, BCL-2, NLRP3, VCAM-1, ICAM-1, IL-1β, and IL-6) (Reintjes et al., 2016; Brasier, 2010; Liu et al., 2017). PRMT1 methylates the R30 site of the RelA/p65 subunit, prevent binding with the target DNA, and ultimately suppress gene expression responsive to TNF-α. PRMT1 acts as a negative regulator of inflammation through methylation of NF-κB. knockdown of PRMT1 also restores NF-κB targeted gene expression (NFKBIA, TNFα, and A20) in response to TNF-α (Reintjes et al., 2016).

Furthermore, PRMT1 has a role in the activation of major histocompatibility complex (MHC), it methylates CIITA (class II trans activator) leading to its degradation. CIITA associates with the DNA binding protein complexes to form the CIITA enhanceosome complex on the promoter of MHC class II genes to transactivate MHC class II genes. It is known that IFN-γ induce the expression of CIITA, and interestingly, downregulation of PRMT1 was observed in macrophage cells treated with IFN-γ. These findings suggest that PRMT1 reduce activation of MHC genes, which can reduce inflammatory response (Masternak et al., 2000; Meissner et al., 2012; Fan et al., 2017).

Likewise, PRMT1 is crucial for T helper’s cytokine production in an IL-4 and IFN-γ transcription activation manner. This process occurs by the arginine methylation of the N-terminal domain of the nuclear factor of activated T cells (NFAT)-interacting protein (NIP45) which act as a co-activator of NFAT and induce expression of IL-4 and IFN-y genes (Mowen et al., 2004).

PRMT4’s role in the inflammatory response is still not fully understood. PRMT4 can regulate ICAM-1 (Intercellular adhesion molecule-1), G-CSF (Granulocyte colony-stimulating factor), MCP-1 (Monocyte chemoattractant protein-1), and IP-10 (Interferon gamma-induced protein 10). The precise mechanism is unclear; however, a study by Miao et al. (2006) suggest that it is a co-activator through direct interaction with RelA/p65 in the presence of TNF-α (Miao et al., 2006). PRMT4 also methylates H3R17 histone in promoters involved in the inflammatory response, including TNF-α and IL-8 in monocytes (Miao et al., 2006). PRMT5 acts in the canonical NF-κB pathway, by binding with DR4 (Death receptor 4) protein and activating TNF-related apoptosis-inducing ligand (TRAIL) receptor, leading to multi-subunit IκB kinase (IKK) complex and NF-κB activation as well as triggering NF-κB target genes expression (Kim et al., 2016; Tanaka et al., 2020). Decreased PRMT5 activity causes an increase in TRAIL cytotoxicity, however without interfering with NF-κB signaling mediated by TNF-α action (Srour et al., 2022). PRMT5 also methylates the p65 subunit of NF-κB, regulating gene expression of several cytokines, chemokines, and growth factors NF-κB-dependent, such as IL-1α, IL-8, and TNF receptor-associated factor 1 (TRAF1). This methylation occurs at R30 and R35 with the methylation of R30 responsible for 85 % of NF-κB-dependent gene expression (Wei et al., 2013). Other studies suggest that PRMT5’s regulatory role on NF-κB pathways is caused by the IKK complex; inhibition of PRMT5 methylation led to reduced IKKβ and IKKα activation and RelA/p65 nuclear translocation. Lack of PRMT5 is also correlated with lower production of IL-6 and IL-8, as well as with inactivation of NF-κB, leading to cell proliferation and migration arrest (Chen et al., 2017).

PRMT6’s role in the regulation of inflammation is through direct interaction with NF-κB and G-protein pathway suppressor 2 (GPS2) (Di Lorenzo et al., 2014). A study with transgenic mice that overexpress PRMT6 showed that there is direct binding between PRMT6 and NF-κB (RelA/p65 subunit) that leads to increased expression of several NF-κB target genes, including IL-6, a process stimulated by TNF-α (Di Lorenzo et al., 2014). PRMT6 can have an indirect regulation of NF-κB through the methylation of coactivators, like p160/steroid receptor coactivator (SRC) proteins (Harrison et al., 2010). In addition to NF-κB methylation, PRMT6 also interacts with GPS2, a protein with several biological functions, including the mediation of mitogen-activated protein kinase (MAPK), RAS protein and JAK signaling pathways, all essential for the inflammatory response (Kim et al., 2016). PRMT6’s action on GPS2 occurs by the methylation of R323 and R312, a necessary process that prevents degradation and ensures GPS2 stability. Thus, PRMT6 can act as a regulator of inflammation (Huang et al., 2015). Other inflammatory markers/modulators also include PRMT8. PRMT8 knockout mouse model had higher levels of TNF-α and IbaI protein as compared to wildtype mice, while overexpression of PRMT8 significantly reduced levels of both Iba1 and TNF-α (Couto et al., 2021). IbaI is an intracellular calcium-binding protein specific to microglia and macrophages, and an important inflammatory marker for several diseases, such as traumatic brain injury, epilepsy and AD (Ohsawa et al., 2004; Novoa et al., 2022). In addition, after hypoxia, PRMT8−/− mice had a significant reduction in rolling leukocyte speed as compared with WT mice, which suggests increased inflammatory response due to leukocyte extravasation into the brain. These findings suggest that PRMT8 may also be involved in neuroinflammation (Couto et al., 2021).

5. Mitochondria

Mitochondria is an organelle present in all cells and has the essential role of generating ATP, the source of energy involved in cellular metabolism. This organelle, sometimes referred to as the lung of the cell, due to oxygen consumption, is also involved in the regulation of cell apoptotic pathways and has been shown to play important role in the pathogenesis of AD (Bhatia et al., 2022; McBride et al., 2006; Wang et al., 2009; Wang et al., 2008; Trimmer et al., 2000).

Evidence of PRMTs, more specifically PRMT8’s role in the homeostasis of mitochondria was observed in knockout mice (PRMT8−/−), when oxygen consumption rate of the hippocampus decreases. Mice lacking in PRMT8 had reduced hippocampal basal respiration and ATP production compared to wild-type mice and its mitochondrial reserved capacity was significantly lower under hypoxia when compared to wild-type mice under hypoxia. Oxygen consumption rates were similar to wild type mice when mice lacking PRMT8 were injected with a virus to overexpress PRMT8 (Couto et al., 2021). Finally, importance of PRMT8 in the mitochondria activity was suggested by increased RNA expression of the reactive oxygen species markers transthyretin (TTR) and solute carrier family 3 member 1 (Slc3a1) in knockout mice (PRMT8−/−), as well as a significant increase in phosphatidic acid, a regulator of mitochondrial function (Couto et al., 2021; Kameoka et al., 2018).

PRMT7 can also modulate the mitochondria. In a mouse model of mild traumatic brain injury (rm-TBI), PRMT7 protein levels were significantly lower 3 days after the TBI hits and hippocampal mitochondrial oxygen consumption rates (via Seahorse XFe24), especially ATP production, were altered when compared to sham mice, along with disrupted mitochondrial dynamics of fission and fusion proteins. When PRMT7 was overexpressed (via AAV) in the rmTBI mice, mitochondrial reserve capacity was significantly increased and ATP levels were similar to sham mice levels (Acosta et al., 2023). Altogether, the data suggest that PRMT7 and PRMT8 can modulate mitochondria respiration and cell viability, important in responding to cellular stress and a wide-variety of pathologies.

6. Future direction

It is important to consider various PRMT isoforms (PRMT1-9) in different situations of AD, brain injury, and/or other cellular stress pathologies. Modulation of various PRMT isoforms can be of therapeutic importance. Identifying specific pathologies v. PRMTs involved is currently the challenge.

Since PRMT5 is frequently upregulated in many types of cancers, much research has focused on finding modulators of this type II PRMT. In fact, different PRMT5 inhibitors have undergone clinical trials, such as GSK3326595, JNJ-64619178, PF-06939999, PRT811, AMG 193, which so far have inconclusive data or limited clinical efficacy with some adverse effect (Pfizer, n.d.; GlaxoSmithKline, n.d.; Therapeutics, n.d.; Janssen Research and Development L, n.d.; Amgen, n.d.). There is an additional ongoing clinical trial (phase I/II) for safety and tolerability in patients with advanced or metastatic solid tumors with MTAP (methylthioadenosine phosphorylase) deletion with a selective PRMT5 inhibitor (TNG908), which is estimated to be completed by September of 2025 (Tango Therapeutics I, n.d.).

PRMT4 inhibitors, such as TP-064 (Nakayama et al., 2018) and EZM302 (Drew et al., 2017), were developed and pre-clinically tested for multiple myeloma, where upregulation of PRMT4 was observed. Interestingly, in old female AD-mice model that have PRMT4 protein levels higher in the brain, treatment with TP-064 lead to improvement of brain blood flow (Clemons et al., 2024). So far, no clinical trials targeting PRMT4 are in progress.

Although PRMT1 is the most studied PRMT, the only 2 clinical trials so far were not specific, targeting instead, overall type 1. The inhibitors comprise of GSK3368715 (GlaxoSmithKline, n.d.), discontinued in 2022 due to high rate of thromboembolic events, and CST2190 (CytosinLab Therapeutics Co. L, n.d.), which was recently initiated, both for the treatment of solid tumors. There are a number of other inhibitors of PRMTs (Couto et al., 2020; Tong et al., 2024) with some isoform-specific and some type I, II and III specific. Additional challenges include the lack of agonists that can be PRMT isoform-specific to be able to modulate PRMT activity when it is downregulated in pathology. Considering the low success of clinical trials, more investigations need to be performed regarding these intriguing family of enzymes.

Data availability

No data was used for the research described in the article.