Histone methylation of kidney disease: fact or fantasy?

Abstract

Histone methylation (HMT), the enzymatic addition of methyl groups to specific histone residues by histone methyltransferases, constitutes a key regulatory mechanism in gene expression and post-translational modulation. Although studies have explored HMT’s role in oncogenesis and other organ-specific disorders, HMT is now implicated in the pathogenesis of kidney diseases. A broad spectrum of experimental models, including both in vivo and in vitro systems, has demonstrated the involvement of HMT alterations in diverse renal pathologies such as acute kidney injury, renal fibrosis, diabetic nephropathy, lupus nephritis, polycystic kidney disease, kidney stones, renal cell carcinoma, and immunoglobulin A nephropathy. Targeted modulation of HMT has been associated with attenuated disease progression across these conditions. This review synthesizes current insights into HMT’s mechanistic roles in renal pathology and delineates its therapeutic potential as a strategic intervention in kidney disease management.

Introduction

In epigenetics, histone modification refers to the enzymatic alteration of histone residues via methylation, acetylation, phosphorylation, and ubiquitination. These chemical changes regulate a wide array of biological processes by modulating chromatin structure through histone–DNA interactions, resulting in either a relaxed or compact chromatin state. Histone methylation (HMT), involving the methylation of lysine or arginine residues on the N-terminal tails of histones H3 and H4, significantly influences chromatin dynamics and protein binding affinities through specific recognition by reader proteins [1,2]. The enzymatic activity of histone methyltransferases and demethylases, which respectively catalyze the addition and removal of methyl groups, controls the dynamic regulation of HMT [3].

Alterations in HMT patterns have been associated with cell lineage determination, physiological development, and the pathogenesis of numerous disorders, including malignancies and cardiovascular diseases. Abnormal HMT profiles contribute to the etiology of cardiovascular conditions such as dilated cardiomyopathy and atherosclerosis [4–6], while elevated HMT activity has been linked to multiple cancers, including lung, colorectal, gastric, breast, bladder, endometrial, and melanoma [7–9].

Mounting evidence implicates HMT in the pathogenesis of kidney diseases (KDs), including renal fibrosis (RF), diabetic nephropathy (DN), acute kidney injury (AKI), and lupus nephritis. This review synthesizes the prevailing modification patterns of HMT and the corresponding enzymatic regulators within KDs contexts. The methyltransferases responsible for H3K27 methylation-enhancer of zeste homologs EZH1 and EZH2 (Table 1) function as catalytic components of the polycomb repressive complex 2 (PRC2), mediating mono-, di-, and trimethylation at H3K27 [10,11]. EZH2 exerts transcriptional repression by catalyzing H3K27 methylation [12,13]. In contrast, Jumonji domain-containing (JMJD) proteins selectively demethylate H3K27me3. Among them, JMJD3 promotes gene activation by targeting regulatory regions for H3K27me3 removal [14]. Key enzymes catalyzing H3K4 methylation include members of the human mixed-lineage leukemia (MLL) family, set domain-containing proteins 7/9 (SET7/9), and SET and MYND domain protein 2 (SMYD2) [15,16]. SET7/9 and SMYD2 also modify H3K36 and several non-histone substrates [17]. Methylation of H3K9 is mediated by suppressor of variegation 3-9 homolog 1 (Suv39h1), Suv39h2, and euchromatic histone lysine methyltransferase 2 (G9a). While Suv39h1 and Suv39h2 induce H3K9 trimethylation, promoting transcriptional repression [18], G9a primarily generates mono- and di-methylated forms of H3K9 [19]. Disruptor of telomeric silencing 1-like (DOT1L), the sole methyltransferase for H3K79, catalyzes its di-methylation [2]. Arginine methylation is regulated by protein arginine methyltransferases (PRMTs) and corresponding demethylases. PRMTs exhibit distinct N-terminal domains and are classified into four types according to methyl group transfer patterns and arginine guanidino positioning. Type I PRMTs, including PRMT1, catalyze H4R3 methylation, a modification that enhances chromatin remodeling and transcription factor recruitment, thereby modulating transcriptional programs implicated in RF [20]. Lysine methyltransferase 5 A (KMT5A) is uniquely responsible for nucleosome-specific H4K20 methylation [21]. It is essential to clarify the connotation of ‘Fantasy’. HMT shows functional diversity in different disease stages and microenvironments of KDs. This heterogeneity does not imply that the research results are contradictory.

Table 1.

Common HMT modifications in KDs.

Modification sites	Modifying enzyme names	HMT	KD
H3K27	EZH1, EZH2 JMJD3	H3K27me3	Acute kidney injury, renal fibrosis, diabetic nephropathy, polycystic kidney disease, renal cell carcinoma, lupus nephritis, hyperuricemia nephropathy
H3K9	Suv39h1	H3K9me3	Diabetic nephropathy, renal cell carcinoma
	Suv39h2	H3K9me3	Renal fibrosis
	G9a	H3K9me1, H3K9me2, H3K9me3	Acute kidney injury, renal fibrosis, diabetic nephropathy, renal cell carcinoma
H3K4	MLL3	H3K4me3	Membranous nephropathy
	SMYD2	H3K4me2	Polycystic kidney disease
	MLL1	H3K4me1, H3K4me3	Acute kidney injury, renal fibrosis, diabetic nephropathy
	SET7/9	H3K4me1, H3K4me2, H3K4me3	Renal fibrosis, diabetic nephropathy
H3K79	Dot1L	H3K79me2	Acute kidney injury, renal fibrosis
H3K36	SMYD2	H3K36me3	Acute kidney injury, renal fibrosis, polycystic kidney disease
H4R3	PRMT1	H4R3me2a	Renal fibrosis
H4K20	KMT5A	H4K20me1	Diabetic nephropathy

Abbreviations: HMT, histone methylation; KDs, kidney diseases; EZH1, enhancer of zeste homologs 1; EZH2, enhancer of zeste homologs 2; Suv39h1, suppressor of variegation 3-9 homolog 1; JMJD3, Jumonji domain containing protein 3; Suv39h2, suppressor of variegation 3-9 homolog 2; G9a, euchromatic histone lysine methyltransferase 2; MLL1, myeloid/lymphoid or mixed-lineage leukemia 1; MLL3, myeloid/lymphoid or mixed-lineage leukemia 3; SET7/9, set domain-containing proteins 7/9; Dot1L, disruptor of telomeric silencing 1-like; SMYD2, SET and MYND domain containing protein 2; PRMT1, protein arginine methyltransferase 1; KMT5A, Lysine methyltransferase 5A.

Chronic kidney disease (CKD) constitutes a pressing public health issue. As reported by the Global Burden of Disease Study 2017, its global prevalence reached 9.1% in 2017, accompanied by a 41.5% rise in mortality since 1990, positioning CKD as a leading contributor to end-stage renal disease (ESRD) [22]. AKI, marked by high incidence, significant complication risk, and elevated mortality, imposes substantial healthcare costs and remains a pressing challenge [23]. DN, one of the most severe microvascular complications of diabetes, continues to increase among patients with both type 1 and type 2 diabetes, serving as the predominant cause of ESRD [24–26]. Polycystic kidney disease (PKD), the most common inherited renal disorder, affects roughly 1 in 1,000 individuals and is a major factor in ESRD progression [27]. Nephrolithiasis also contributes notably to the global renal disease burden, with prevalence rates of 8.8% in the United States and 6.4% in China. Its high recurrence rate considerably diminishes patients’ quality of life [28,29].

This review synthesizes current insights into the functional roles and underlying mechanisms of HMT in renal disease pathogenesis, identifying it as a promising target for therapeutic intervention in kidney disorders.

HMT and AKI

AKI, characterized by an abrupt reduction in renal function from diverse etiologies, represents a prevalent and severe condition in clinical practice. Its high incidence, potential for complications, elevated mortality, and substantial healthcare burden have positioned it as a major concern in public health discourse [23]. Various injurious stimuli—such as ischemia-reperfusion (IR), infection, and nephrotoxic insults—can trigger its onset [30]. The involvement of lysine methylation at critical histone sites, including H3K9, H3K27, H3K4, H3K79, and H3K36, has been associated with the molecular mechanisms underlying AKI (Figure 1).

Figure 1.

Injury mechanism of HMT modification in AKI. Abbreviations: HMT, histone methylation; AKI, acute kidney injury; Dot1L, disruptor of telomeric silencing 1-Like.PTEN, phosphatase and tensin homolog; EGFR, epidermal growth factor receptor; STAT3, signal transducer and activator of transcription 3; ERK1/2, extracellular signal-regulated kinase 1 and 2; ER stress, endoplasmic retlculum stress; EZH2, enhancer of zeste homolog 2; AhR, aryl hydrocarbon receptor. SA-β-gal, senescence-associated β-galactosidase, FoxO3a, forkhead box O3a; PGC-1α: peroxisome proliferator-activated receptor-gamma coactivator-1α; NF-κB, nuclear factor kappa B; Sirt1, sirtuin 1; Sirt3, sirtuin 3; RKIP, raf kinase inhibitor protein; ALK5, activin receptor-like kinase; Nox4, NADPH oxidase 4; FXR, farnesoid X receptor; Ces1, Carboxylesterase 1; ROS, reactive oxygen species; Nrf2, nuclear factor E2-related factor 2; G9a, euchromatic histone lysine methyltransferase 2; SMYD2, SET and MYND domain protein 2.

H3K9 methylation and G9a activation are essential mechanisms driving AKI onset and progression. In renal IR models, IR induces G9a expression at the Sirt1 promoter, elevating H3K9me2 levels and thereby repressing Sirt1 and Nrf2 transcription while enhancing the expression of MAPK family members [31,32]. G9a forms a transcriptional repression complex with chromobox homolog 1 (CBX1) at the Sirt1 promoter through H3K9me2 modification. This complex suppresses Sirt1 expression and modulating reactive oxygen species (ROS) production, ultimately aggravating renal tubular epithelial cell (RTEC) injury [32]. In both IR- and cisplatin-induced AKI models, G9a and H3K9me2 modification compete with farnesoid X receptor (FXR) for binding to the carboxylesterase 1 (Ces1) promoter, suppressing Ces1 transcription. This suppression leads to reduced expression of neutral triglyceride hydrolase and impaired fatty acid oxidation (FAO), promoting lipid accumulation and intensifying renal IR injury [33]. Pharmacological inhibition of H3K9 methylation via BIX01294, a G9a methyltransferase inhibitor, reverses Sirt1 methylation. This inhibition also restores antioxidant gene expression and reduces ROS generation [32]. G9a inhibition also enhances Nrf2 activity and suppresses MAPK signaling, attenuating RF [31]. In G9a-deficient mouse models, Ces1 expression increases, ameliorating lipotoxicity and preventing lipid buildup post-AKI. Both atorvastatin and the FXR agonist GW4064 confer renal protection by upregulating Ces1 and reprogramming lipid metabolism [33] (Figure 1).

EZH2 and H3K27me3 levels are markedly increased following renal IR injury. EZH2 binds to the phosphatase and tensin homolog (PTEN) promoter, repressing its transcription [34–36], while concurrently elevating epidermal growth factor receptor (EGFR) expression and activating the EGFR/ERK1/2/STAT3 signaling cascade. This cascade subsequently induces the expression of snail transcription factors and increases the level of H3pSer10. Through STAT6 and PI3K/AKT signaling, EZH2 also promotes M2 macrophage polarization, contributing to RF [35,36]. In hypoxia-reoxygenation (HR) cell models, EZH2 regulates Nox4 expression and transcription via the ALK5/Smad2/3 axis, thereby initiating pyroptosis in RTECs [37]. Moreover, EZH2 overexpression in this model activates p38 phosphorylation, triggers caspase-3, and elevates pro-inflammatory mediators, culminating in renal cell apoptosis [38]. In sepsis-induced AKI, EZH2 is enriched at the Sox9 promoter, repressing Sox9 and inhibiting Wnt/β-catenin signaling, leading to RTEC apoptosis [39]. Cisplatin exposure upregulates EZH2 and H3K27me3 in RTECs, suppressing Raf kinase inhibitor protein (RKIP) transcription, enhancing NF-κB p65 expression, and inducing apoptosis [40]. Cisplatin stimulation induces an indirect association between H3K27me3 and the aryl hydrocarbon receptor (AhR) promoter. This association elevates AhR expression, increasing senescence-associated β-galactosidase activity and gene expression to promote renal cell senescence [41]. For H3K27 methylation-targeted interventions, 3-deazaneplanocin A (3-DZNeP), a selective EZH2 inhibitor, disrupts EZH2 binding at the PTEN promoter. This disruption modulates PTEN transcription and suppresses epithelial-mesenchymal transition (EMT). This inhibition attenuates activation of the EGFR/ERK1/2/STAT3 cascade and reduces phosphorylation of STAT6, PI3K, and AKT, ultimately impairing M2 macrophage polarization and mitigating RF progression while preventing AKI-to-CKD transition [35]. In vitro, 3-DZNeP additionally impairs ALK5/Smad2/3 signaling and diminishes Nox4-mediated ROS generation, contributing to RF attenuation [37]. Renal protection is further enhanced through the relief of Sox9-mediated transcriptional repression, activation of Wnt/β-catenin signaling, and reduced RTEC apoptosis, accompanied by decreased macrophage infiltration in renal interstitial compartments [39]. Concurrently, 3-DZNeP inhibits NF-κB signaling, decreases pro-inflammatory cytokine production, suppresses p38 phosphorylation, and downregulates caspase-3 activity, collectively ameliorating renal IR injury [38,42]. Moreover, it attenuates cisplatin-induced RTEC apoptosis via E-cadherin-dependent pathways [43]. Another EZH2 inhibitor, ZLD1039, exhibits anti-inflammatory activity in cisplatin-treated renal tissue by suppressing H3K27me3, enhancing RKIP expression, and reducing NF-κB p65 activation [40]. BAY2416964, an AhR antagonist, indirectly downregulates EZH2 through AhR inhibition, thereby decreasing senescence-associated β-galactosidase activity and protecting against RTEC apoptosis and necrosis [41]. EED226, a potent PRC2 inhibitor, disrupts the EZH2–H3K27me3 interaction, inhibits phosphorylation of p53 and FOXO3a induced by cisplatin, and preserves mitochondrial protective factors such as Sirtuin3 and PGC1-α. It also suppresses inflammatory cell infiltration and limits macrophage recruitment [44] (Figure 1).

Studies examining H3K4 methylation and the role of MLL1 in AKI pathogenesis have revealed that in IR-induced AKI mouse models, enhanced recruitment of RNA polymerase II (Pol II) to the HMG CoA reductase (HMGCR) promoter drives upregulation of both HMGCR protein and mRNA, accompanied by elevated H3K4me3 at multiple transcription factor binding sites, thereby promoting cholesterol synthesis in renal tubules [45]. Concurrently, increased mRNA expression of Set1, BRG1, and H2A.Z was detected, paralleling elevated H3K4me3 and heightened levels of renal cortical cytokines, including transforming growth factor beta 1 (TGF-β1) and monocyte chemoattractant protein-1 (MCP-1), which collectively contributed to chronic inflammatory and fibrotic responses in renal tissue [46]. In urine samples from AKI patients, H3K4me3 enrichment at Pol II and HMGCR exon 1 significantly exceeded that observed in healthy individuals, showing a twofold increase [47]. Similar H3K4me3 elevations were identified across various AKI models, including maleate-induced nephrotoxicity, unilateral ureteral obstruction (UUO), and lipopolysaccharide (LPS) sensitization, with upregulated recruitment of inflammatory mediators such as tumor necrosis factor alpha (TNF-α) and MCP-1 implicated in LPS hyperresponsiveness [48]. In cisplatin-treated murine renal tubular cells, upregulation of MLL1, WDR5, and H3K4me3 was associated with increased p53 phosphorylation and suppressed E-cadherin expression, ultimately leading to RTEC apoptosis. Pharmacological inhibition of the MLL1/WDR5 complex via MM102 effectively suppressed the expression of MLL1, WDR5, and H3K4me3, reduced p53 phosphorylation, restored E-cadherin levels, and significantly improved renal function by mitigating tubular damage and apoptotic cell death [49].

Methylation of H3K79 and H3K36 plays a central role in the pathogenesis of AKI. Dot1L, the sole methyltransferase mediating H3K79 methylation, displays significantly elevated expression across multiple AKI models. Pharmacological inhibition of Dot1L by EPZ004777 suppresses the PI3K/AKT pathway, decreases ROS generation, and downregulates α-smooth muscle actin, vimentin, and fibronectin, collectively attenuating oxidative damage and ameliorating RF in vivo [37]. In IR-induced AKI mouse models, renal expression of SMYD2 and H3K36me3 is markedly increased, accompanied by elevated BAX and reduced BCL-2 levels, indicative of enhanced apoptotic activity. Administration of AZ505 effectively downregulates SMYD2 and H3K36me3, reduces the BAX/BCL-2 ratio, inhibits STAT3 and NF-κB phosphorylation, upregulates PTEN, and mitigates tubular epithelial cell damage and apoptosis [50] (Figure 1).

The histone demethylase JMJD3, which specifically targets H3K27me3, contributes to the survival and regeneration of RTECs following AKI. In murine models of I/R- and FA-induced AKI, upregulation of JMJD3 and H3K27me3 is observed in renal tissue. Inhibition of JMJD3 by GSKJ4 activates the TGF-β/Smad3 axis while concurrently suppressing renoprotective mediators such as Klotho and BMP-7, thereby aggravating epithelial injury, promoting apoptosis, and impeding cellular proliferation within renal tubules [51].

HMT and RF

CKD, characterized by sustained renal impairment, frequently advances to ESRD. Between 1990 and 2017, CKD-related mortality rose by 41.5%, with its global prevalence reaching approximately 9.1% in 2017 [22]. RF constitutes a predominant pathological hallmark and serves as a key prognostic indicator for both CKD and ESRD progression [52]. Although the molecular framework governing RF remains intricate, growing evidence highlights the regulatory influence of HMT activity in its pathogenesis [53]. Key HMT-targeted histone residues include H3K27, H3K9, H3K4, H3K79, H4R3, and H3K36 (Figure 2).

Figure 2.

Mechanism of HMT modification in RF injury. Abbreviations: HMT, histone methylation; RF, renal fibrosis; SUV39h2, suppressor of variegation 3-9 homolog 2; MLL1, mixed lineage leukemia protein 1; BDNF, plasma brain-derived neurotrophic factor; SET7/9, SET Domain-Containing Protein 7/9; PRMT1, protein arginine methyltransferase 1; TGFβ1, transforming growth factor β1; Acta2, alpha-actinin-2; G9a, euchromatic histone lysine methyltransferase 2; E2F, E2 promoter binding factor.

EZH2-mediated H3K27me3 exerts pro-fibrotic effects through mechanisms overlapping with those in AKI, including repression of PTEN and Smad7 to activate EGFR/ERK/STAT3 and TGF-β/Smad3 signaling [35,36,54–57]. Additionally, In RF, serum and uremic toxins induce dysregulated expression of ANRIL, an antisense non-coding RNA at the INK4 locus. ANRIL recruits EZH2 to the BDNF promoter, where increased H3K27me3 levels repress BDNF transcription, ultimately altering endothelial-related protein expression and disrupting mitochondrial dynamics, leading to endothelial dysfunction [58]. lncRNAs are key molecules in the pathophysiology of renal injury and can be used as biomarkers for the early diagnosis and prognosis of KDs [59]. Salvianolic acid B (SAB) reduces EZH2 and H3K27me3, enhances PTEN expression, and inhibits Akt phosphorylation, collectively suppressing fibronectin and α-SMA expression [57]. Emodin, a bioactive anthraquinone from rhubarb, downregulates EZH2 and H3K27me3, while restoring Smad7 expression in NRK-49F fibrotic cells and UUO kidneys. This intervention limits extracellular collagen deposition and interrupts Smad3- and CTGF-driven pro-fibrotic signaling, thereby mitigating tubulointerstitial fibrosis [55]. Gambogenic acid, a caged xanthone from Garcinia hanburyi Hook.f, promotes Sm-ad7 transcription and attenuates TGF-β/Smad3 signaling in injured kidneys, resulting in decreased α-SMA, fibronectin, and collagen expression in TCMK-1 tubular epithelial cells [56] (Figure 2).

Alterations in H3K9 methylation are implicated in the progression of RF. In UUO mouse models, TGF-β1 promotes G9a expression through Smad3 signaling, resulting in elevated H3K9me1 levels and increased expression of klotho, α-SMA, and fibronectin. Pharmacological inhibition of G9a by BIX01294 diminishes H3K9me1, downregulates klotho, and suppresses TGF-β1-induced α-SMA and fibronectin expression in renal fibroblasts. TGF-β1 also induces a redistribution of H3K9me3 within fibroblast nuclei in UUO kidneys, with pronounced expression in interstitial myofibroblasts and tubular epithelial cells [60,61]. In RF models, Suv39h2-mediated H3K9me3 downregulates Acta2 repressors in pericytes, thereby upregulating α-SMA and exacerbating RF. Treatment with chaetocin, an H3K9me3 inhibitor, restores Acta2 repressors in myofibroblasts and attenuates fibrotic progression [62]. Coordination between histone and DNA methyltransferases represents a recurrent regulatory axis in gene expression. In fibrotic human kidneys, UUO models, and TGF-β1-stimulated HK-2 cells, G9a and DNMT1 are concurrently upregulated, accompanied by increased H3K9me2 and 5-methylcytosine enrichment at the CDKN1A promoter. Administration of CM272, a reversible dual-target competitive inhibitor of G9a and DNMT1, or siRNA-mediated knockdown of both enzymes, suppresses E2F target gene expression, modulates CDKN1A methylation, alleviates cell cycle arrest, and significantly reduces fibrosis in both in vitro and in vivo settings [63] (Figure 2).

H3K4 methylation has emerged as a key epigenetic modification implicated in RF progression. In the UUO mouse model, TGF-β1 induces SET7/9 expression via the Smad3 signaling cascade, contributing to fibrogenesis. Sinefungin, a structural analog of S-adenosylmethionine (SAM), competitively binds SAM and inhibits the methyltransferase function of SET7/9. This inhibition leads to decreased expression of mesenchymal markers and extracellular matrix components, along with suppression of H3K4me1, collectively attenuating renal fibrotic remodeling [64]. MA-35, an indole-based compound, mitigates TGF-β1 signaling by blocking Smad3 phosphorylation, downregulating SET7/9, and reducing H3K4me1 enrichment at promoters of pro-fibrotic genes, thereby diminishing their transcriptional activation [65]. In models of IR-induced injury, H3K4me3 levels increase due to the upregulation of its methyltransferases, MLL1 and WDR5, which in turn enhances p16INK4a expression and accelerates RF development. Pharmacological inhibition of MLL1/WDR5 with MM102 or OICR-9429 reduces both H3K4me3 and p16INK4a expression, attenuating fibrotic and inflammatory responses in affected kidneys [66]. Additionally, UUO-induced renal injury elevates MLL1, menin, and H3K4me1 levels, upregulates TGF-β1, and suppresses E-cadherin, collectively promoting EMT and fibroblast activation. Disruption of the MLL1–menin interaction, either by MI-503 treatment or siRNA-mediated silencing of MLL1, reduces α-SMA, fibronectin, and Snail expression, downregulates TGF-β1, inhibits Smad3 and AKT phosphorylation, and restores E-cadherin levels, thereby mitigating RF pathogenesis [67] (Figure 2).

HMT-mediated modifications of H3K79, H3K36, and H4R3 play a significant role in the molecular pathology of RF. In UUO-induced RF mouse models, increased renal expression of DOT1L and elevated H3K79me2 levels correlate with PTEN suppression, Notch pathway activation, klotho downregulation, and TGF-β1 receptor signaling, which culminates in Smad3 activation and promotes both fibrogenesis and inflammation. In vitro, administration of EPZ5676-a selective DOT1L inhibitor-or DOT1L-targeting siRNA alleviates injury-induced epithelial G2/M arrest, reduces Snail, Twist, and Notch1 expression, and diminishes TGF-β1-induced expression of α-SMA, fibronectin, and type I collagen. Concurrently, Smad3 levels decline, while EMT and renal interstitial fibroblast activation are suppressed, collectively mitigating RF progression [68]. In parallel, UUO-induced RF models demonstrate upregulation of PRMT1 and H4R3Me2a, accompanied by increased expression of fibrotic markers including α-SMA, type I collagen, and fibronectin. PRMT1 inhibition via AMI-1 effectively downregulates both PRMT1 and H4R3Me2a, inhibits Smad3 phosphorylation, and reduces TGF-β1 levels. Simultaneously, Smad7 is upregulated, extracellular matrix accumulation is decreased, and fibroblast activation and proliferation are suppressed [69]. Additionally, SMYD2 and its associated H3K36me3 mark are upregulated in UUO-induced models. Pharmacologic blockade with the SMYD2 inhibitor Z505 or gene silencing via siRNA reduces Snail and Twist expression, mitigates G2/M arrest, and disrupts the activation of multiple fibrotic pathways including ERK1/2, AKT, STAT3, and NF-κB. These interventions lead to reduced inflammation and fibrosis attenuation [70] (Figure 2).

LSD1 (KDM1A), a histone demethylase targeting H3K4me1/2, drives RF progression by modulating chromatin states associated with fibrogenic gene expression. In the UUO murine model, LSD1 is markedly upregulated. Pharmacological inhibition with ORY1001 restores H3K4me1/2 levels, mitigates EMT, and reverses cell cycle arrest. This therapeutic strategy concurrently suppresses the TGF-β1/Smad3 and LSD1–14-3-3ζ–PKCα–Akt/STAT3 signaling axes, thereby attenuating fibroblast activation [71].

HMT and DN

DN, a prevalent complication in both type 1 and type 2 diabetes, represents one of the most severe forms of microvascular injury. It is typified by glomerular mesangial expansion, persistent inflammation, extracellular matrix accumulation, and cellular hypertrophy, and constitutes a major driver of ESRD progression [24]. With its rising incidence, DN has become the predominant cause of ESRD worldwide [25,26]. HMT play a central regulatory role in DN pathogenesis by controlling epigenetic programs that govern fibrotic remodeling, sustained inflammatory responses, and other pathological hallmarks [72,73]. Critical histone modification loci implicated in these mechanisms include H4K20, H3K4, H3K9, H3K27, and H3K79 (Figure 3).

Figure 3.

Mechanisms of HMT modifications in renal injury during DN. Abbreviations: HMT, histone methylation; DN, diabetic nephropathy; KMT5A, Lysine methyltransferase 5A; PTP1B,Protein tyrosine phosphatase 1B; IGFBP5, Insulin growth factor binding protein 5; EZH2, enhancer of zeste homolog 2; MLL1, mixed lineage leukemia protein 1; SET7/9, SET Domain-Containing Protein 7/9; SUV39h1, suppressor of variegation 3-9 homolog 1; PFN2, Profilin 2; EndMT, endothelial‑mesenchymal transformation; IGFBP5, Insulin growth factor binding protein 5; MCP-1, monocyte chemoattractant protein-1; SFRP-1, secreted frizzled-related protein 1; WT 1, Wilm’s tumor 1; Inc ZEB1-AS1, lncRNA zinc finger E-box binding homeobox1-anti-sense RNA 1; PI3K, phosphoinositide 3-kinase; JNK, c-Jun N-terminal kinase; SUV39h1, Suppressor of variegation 3–9 homolog 1; EMT, epithelial-mesenchymal transition; ECM, extracellular ma-trix.ER, endoplasmic reticulum.

H4K20 methylation is increasingly recognized as a key epigenetic determinant in DN pathogenesis. In glomerular endothelial (GEN) cells from both DN patients and rat models, expression of cAMP response element-binding protein (CREB) and KMT5A is markedly reduced. CREB and H4K20me1 are co-enriched at the promoter of protein tyrosine phosphatase 1B (PTP1B), whose upregulation in vascular endothelial cells modulates pro-inflammatory signaling pathways, thereby contributing to GEN injury and DN progression [74]. Hyperglycemic conditions induce upregulation of ETS proto-oncogene 1 (EST1) while suppressing KMT5A and H4K20me1 expression. Both H4K20me1 and EST1 bind to the PFN2 promoter, where coordinated regulation by KMT5A and EST1 governs PFN2 transcriptional dynamics. This regulatory cascade downregulates CD31 and increases vimentin, α-SMA, and S100A4 expression in human umbilical vein endothelial cells, collectively promoting EMT. Silencing PFN2 or EST1 reverses high-glucose-induced CD31 downregulation and attenuates the associated mesenchymal marker upregulation, thereby counteracting EMT driven by sh-KMT5A [75] (Figure 3).

H3K4 methylation has emerged as a significant epigenetic contributor to DN pathogenesis. In DN rats subjected to IR-induced kidney injury, both protein and mRNA levels of the H3K4Me2-specific methyltransferase SET7/9 were elevated, concurrently activating the NF-κB signaling cascade and enhancing inflammatory responses and renal impairment [76]. In monocytes, SET7/9 gene silencing via siRNA suppressed TNF-α-induced transcription of pro-inflammatory genes, reduced H3K4me deposition at their promoters, and diminished monocyte adhesion to endothelial and smooth muscle cells. This intervention also impaired NF-κB p65 recruitment to the regulatory regions of these genes under TNF-α stimulation [77]. In type 2 diabetic db/db mice, increased H3K4me2 levels at serine 10 facilitated chromatin decompaction and transcriptional activation, promoting glomerular cell proliferation and progression of glomerulosclerosis [78]. Under high-glucose conditions, TGF-β1-stimulated rat mesangial cells exhibited enhanced SET7/9 and H3K4me expression and promoter occupancy, which upregulated ECM-associated genes including connective tissue growth factor, collagen α1, and plasminogen activator inhibitor-1, thereby exacerbating diabetic RF. Targeted SET7/9 silencing attenuated both methylation levels and ECM gene expression, significantly mitigating TGF-β1-induced RF [73]. In glomeruli of type 1 diabetic rats and high-glucose-treated mesangial cells, elevated p21 expression coincided with decreased H3K9me2 and increased H3K4me1/3 levels, alongside enhanced SET7/9 recruitment to the p21 promoter. This epigenetic modulation contributed to mesangial expansion, inflammatory activation, extracellular matrix (ECM) accumulation, and cellular hypertrophy. Administration of TGF-β1-neutralizing antibodies reversed high-glucose-induced H3K4 methylation alterations and SET7/9 enrichment at the p21 locus [79]. In db/db mice, p53-primarily expressed in renal tubular cells-binds directly to lncRNA ZEB1-AS1, promoting H3K4me3 modification at the ZEB1 promoter. By repressing lncRNA ZEB1-AS1, p53 attenuates ZEB1 transcription, thereby limiting RF progression and ECM deposition in HK-2 cells. Pharmacological inhibition of p53 via PIF, or p53 gene deletion in proximal tubule cells, mitigated interstitial fibrosis in both db/db and STZ-induced DN models [80]. In DN mouse kidneys, Set7 deficiency modulated the phenotypic transition of GEN cells through transcriptional control of IGFBP5, which was linked to H3K4me1/2 enrichment. This regulation restored glomerular structure and reduced albuminuria. Additionally, Set7 inhibition by PFI-2 suppressed ROS generation, modulated IGFBP5 expression, and ameliorated renal injury and interstitial remodeling [81]. In db/db kidneys, X-box binding protein 1 (XBP1)-driven SET7/9 expression induced ER stress, enhancing MCP-1 transcription and inflammatory signaling. Silencing XBP1 using siRNAs or applying the ER chaperone betaine substantially reduced SET7/9, H3K4me1, and MCP-1 levels, alleviating ER stress and renal pathology [82] (Figure 3).

Epigenetic alterations involving H3K9, H3K27, and H3K79 methylation contribute to the initiation and progression of DN. In HK-2 cells exposed to high glucose, IL-6 and MCP-1 expression increases, whereas Suv39h1 and H3K9me3 levels decline. Overexpression of Suv39h1 attenuates inflammation and apoptosis, exerting protective effects in the diabetic milieu [83]. In MES 13 cells treated with high glucose or the Suv39h1 inhibitor chaetocin, reduced Suv39h1 expression is mediated via the PI3K and JNK pathways, resulting in decreased H3K9me3 enrichment at the p21WAF1 promoter and elevated fibronectin and p21WAF1 protein expression [18]. In Dot1lAC mice, Aqp5 upregulation correlates with diminished Dot1a and H3K79me2 occupancy at specific regions of the Aqp5 5′ flanking sequence. In DN patients, AQP5 colocalizes with AQP2 in the perinuclear compartment and is linked to impaired H3K79me2 deposition. Aberrant Aqp5 expression in Dot1l-deficient mice and DN patients may contribute to polyuria by disrupting Aqp2 membrane localization in renal Aqp2-expressing cells [84]. EZH2 enhances β-catenin signaling by increasing H3K27me3 accumulation at the β-catenin promoter, thereby promoting podocyte damage. Wilm’s tumor 1 suppresses the EZH2/β-catenin axis, resulting in β-catenin inactivation, reduced mesenchymal transition, preservation of podocyte structure, and mitigation of apoptosis and oxidative stress [85] (Figure 3).

HMT and other KDs

HMT contributes to the development of several renal pathologies, including lupus nephritis, PKD, nephrolithiasis, renal cell carcinoma (RCC), immunoglobulin A (IgA) nephropathy, and membranous nephropathy (MN) (Table 2).

Table 2.

Role of HMT modifications in other KDs.

KD	Modification sites	Modifying enzyme names	HMT	Mechanism of action	Models	Intervention methods	References
PKD	H3K27	EZH2	H3K27me3	Upregulation of STAT3	PKD1fl/fl mouse, PKD1fl/fl: Ezh2fl/fl mouse	GSK-126 EPZ-6438	[89]
PKD	H3K4	SMYD2	H3K4me2	Upregulation of TGF-β-Smad3-SMYD2	NRK-49F cell, SMYD2fl/fl mice	AZ505	[87]
PKD	H3K4	SMYD 2	H3K4me, H3K36me	Upregulation of STAT3, NF-κB, p65	PKD1-knockout mice	AZ505	[88]
RCC	H3K9	G9a	H3K9me2	Downregulation of SPINK5	Human RCC cell lines (786-O, SN12C, OSRC-2), xenograft tumor in nude mice	UNC0638	[92]
RCC	H3K27	EZH1	H3K27me3	Upregulation of VHL-defective ccRCC cells	VHL−/− ccRCC cell lines	JQ-EZ-05 GSK-126	[93]
Hyperuricemia nephropathy	H3K27	EZH2	H3K27me3	Downregulation of SLC7A11	A kidney stone rat model	GSK-126	[96]
Hyperuricemia nephropathy	H3K27	EZH2	H3K27me3	Upregulation of Mark and FoxO3a	Hyperoxaluria rat model	3-DZNeP	[94]
Hyperuricemia nephropathy	H3K27	EZH2	H3K27me3	Upregulation of Smad3, EGFR, ERK1/2	Hyperoxaluria rat model	3-DZNeP	[95]
MN	H3K4	MLL3	H3K4me3	Upregulation of cathepsin L	LPS induced proteinuria mice model	shRNA against MLL3	[101]
SLE	H3K27	JMJD3	H3K27me3	Upregulation of CD11a	CD4+ T cells in SLE patients	JMJD3 siRNA was transfected into SLE CD4+ T cells	[106]
SLE	H3K27	EZH2	H3K27me3	Upregulation of JAM-A	MRL/lpr mice	3-DZNeP	[105]

Abbreviations: HMT, histone methylation; KDs, kidney diseases; PKD, polycystic kidney disease; RCC, renal cell carcinoma; MN, membranous nephropathy; SLE, systemic lupus erythematosus; EZH1, enhancer of zeste homologs 1; EZH2, enhancer of zeste homologs 2; SMYD2, SET and MYND domain containing protein 2; G9a, euchromatic histone lysine methyltransferase 2; MLL3, myeloid/lymphoid or mixed-lineage leukemia 3; JMJD3, Jumonji domain containing protein 3; STAT3, signal transducer and activator of transcription 3; SPINK5, Serine Peptidase Inhibitor Kazal Type 5; SLC7A11, Solute Carrier Family 7, Member 11; ERK1/2, extracellular signal-regulated kinase 1 and 2; FoxO3a, forkhead box O3a; JAM-A, Junctional Adhesion Molecule A; NRK-49F, Normal Rat Kidney-49F; LPS, Lipopolysaccharide.

HMT and PKD

In autosomal dominant polycystic kidney disease (ADPKD)—the most prevalent hereditary kidney disorder and a major driver of ESKD—histone modifications play a regulatory role in gene expression and protein function, mediating the transcriptional activation or repression of disease-relevant pathways [27,86]. In both polycystin-1 (PKD1)-mutant mice and ADPKD patients, SMYD2 catalyzes H3K4 and H3K36 methylation, promoting activation of STAT3 and NF-κB (p65), which in turn enhances cystic epithelial cell proliferation and survival. SMYD2 and its associated histone marks are recruited to fibrotic gene promoters, initiating RF through canonical TGF-β–Smad3 signaling in NRK-49F fibroblasts. Pharmacological inhibition of SMYD2 using AZ505 or its genetic silencing suppresses TGF-β-induced fibrotic gene expression, disrupts renal fibroblast activation, and impairs stress fiber assembly [87,88]. Elevated EZH2 expression and H3K27me3 accumulation in PKD1-deficient cells, murine kidneys, and patient samples similarly activate STAT3, further driving cyst epithelial proliferation. Inhibition of EZH2 via GSK-126/EPZ-6438 or genetic ablation reduces cystogenesis in Madin-Darby canine kidney cells and retards cyst expansion in embryonic kidney models [89].

In renal epithelia with PKD1 mutations, mouse models, and human ADPKD tissues, both SMYD3 and H3K4me3 are markedly upregulated. SMYD3 promotes cyst growth and cell proliferation by activating the NF-κB/Stat3/Erk axis. Genetic deletion of SMYD3 mitigates cyst enlargement, reduces proliferative and inflammatory responses, and improves renal function [90].

HMT and RCC

RCC accounts for approximately 2–3% of adult malignancies [91], with its incidence increasing by about 2% over the past two decades. Epigenetic regulation significantly influences tumor initiation, progression, and therapeutic responsiveness. In a cohort of 80 RCC patients, including tumor and adjacent normal tissues, G9a expression was markedly elevated in both human RCC cell lines and clinical samples. By catalyzing H3K9me2 methylation, G9a represses the transcription of Serine Peptidase Inhibitor Kazal Type 5 (SPINK5), thereby enhancing RCC cell proliferation and promoting EMT. Pharmacological inhibition of G9a using UNC0638 or genetic ablation of G9a reduces H3K9me2 levels, restores SPINK5 expression, and elevates P53 levels, collectively suppressing renal carcinoma cell growth, motility, and invasiveness in vitro and in vivo [92]. In clear cell RCC, loss of the von Hippel-Lindau (pVHL) tumor suppressor constitutes a defining molecular event, with pVHL-deficient ccRCC cells exhibiting a pronounced reliance on the H3K27 methyltransferase EZH1 for survival. Inhibitors such as JQ-EZ-05 and GSK-126, targeting EZH1 and EZH2 respectively, significantly impair the proliferation and viability of VHL^−/− ccRCC cells [93].

HMT and hyperuricemia nephropathy

Kidney stones are characterized by high incidence and recurrence, with prevalence rates of 8.8% in the United States and 6.4% in China [28,29]. Beyond their acute presentation, they can progress to chronic renal failure. Calcium oxalate (CaOx) represents the most common stone type, and emerging evidence implicates epigenetic regulation in CaOx-induced renal injury.

In hyperoxaluria-induced rat models, renal expression of EZH2 and its associated H3K27me3 modification is markedly elevated [94–96]. This upregulation coincides with enhanced MAPK and FoxO3a signaling in RTECs, driving oxidative stress, inflammation, and CaOx crystal accumulation in vivo [94]. The downstream activation of Smad3, EGFR, and ERK1/2 contributes to tubular apoptosis and renal interstitial fibrosis [95]. In kidney stone patients, animal models, and oxalate-stimulated HK-2 cells, SOX4 transcriptionally regulates EZH2, increasing EZH2 and H3K27me3 expression. This elevation promotes ferroptosis by directly suppressing SLC7A11 transcription in HK-2 cells [96]. Pharmacological inhibition of EZH2 using 3-DZNeP or gene silencing via shRNA attenuates oxalate-induced tubular epithelial injury, likely through suppression of the JNK/FoxO3a axis [94]. In parallel, 3-DZNeP reduces uric acid-triggered renal fibroblast activation and limits Smad3, EGFR, and ERK1/2 phosphorylation. These effects are accompanied by reductions in serum uric acid and xanthine oxidase activity, along with inhibition of Smad3 and NF-κB pathways, collectively restraining renal fibroblast proliferation and EMT [95]. Additionally, both EZH2 knockout and pharmacologic blockade with GSK-126 alleviate oxalate-induced ROS accumulation and suppress CaOx crystal-driven ferroptosis [96].

In glyoxylic acid-induced CaOx nephrolithiasis models, SMYD2 directly interacts with and methylates PTEN, resulting in its transcriptional repression. This epigenetic modification triggers activation of the AKT/mTOR pathway and induces the expression of glycolysis-associated genes. Administration of AZ505 markedly decreases SMYD2 levels and downregulates glycolytic enzymes, concurrently reducing CaOx crystal accumulation and mitigating renal injury, inflammation, and fibrotic remodeling [97].

HMT and IgA nephropathy and MN

IgA nephropathy is the most widespread form of primary glomerulonephritis worldwide, characterized by IgA or IgA-containing immune complex deposition in the mesangial regions, leading to glomerular inflammation [98]. Analysis of peripheral blood mononuclear cells from 15 IgAN patients and 15 healthy controls demonstrated significantly elevated levels of FCRL4 and H3K4me3 in the IgAN cohort relative to controls [99].

MN constitutes a predominant cause of nephrotic syndrome in adults [100], with HMT playing a significant role in its molecular pathology. In both MN patients and LPS-induced mouse models, marked upregulation of H3K4me3 in podocytes has been reported, accompanied by increased expression of cathepsin L—a lysosomal cysteine protease-along with elevated synaptic protein levels and podocyte hypertrophy. Silencing of MLL3 via shRNA attenuated LPS-induced H3K4me3 and cathepsin L expression, restored synaptic protein levels, and ameliorated podocyte structural alterations [101].

HMT and lupus nephritis

Systemic lupus erythematosus (SLE), a prototypical systemic autoimmune condition, is characterized by diverse clinical manifestations-including rash, arthritis, lymphadenopathy, and multi-organ involvement-with frequent renal and cardiovascular complications. Its pathogenesis predominantly stems from dysregulated immune responses involving dendritic cells, T cells, and B cells, leading to sustained inflammatory mediator release and consequent tissue, vascular, and organ injury [102,103]. Recent studies have identified HMT as a significant regulatory layer in SLE pathophysiology.

The monoclonal antibody BT164, derived from lupus models, targets an epitope on the N-terminal tail of histone H3K27, specifically recognizing apoptosis-induced H3K27 trimethylation. This H3K27me3 modification serves as an autoantigen in both SLE patients and murine models [104]. Elevated EZH2 expression has been reported across multiple immune cell types in lupus, including whole blood, neutrophils, monocytes, B cells, and CD4+ T cells, where it correlates with increased JAM-A expression in the latter. In MRL/lpr mice, pharmacologic inhibition of EZH2 using 3-DZNeP attenuates lymphocyte hyperproliferation, reduces double-negative T cell populations, lowers circulating pro-inflammatory cytokine levels, and mitigates lupus-like symptoms [105].

JMJD3, a demethylase specific to H3K27me3, contributes to the reduction of H3K27me3 enrichment at the ITGAL (CD11a) promoter in CD4+ T cells from SLE patients. Increased JMJD3 occupancy at this site enhances CD11a transcription, driving hyperactivation of both T and B lymphocytes. Silencing JMJD3 via siRNA in SLE CD4+ T cells significantly lowered its expression and promoter binding, elevated H3K27me3 levels, and suppressed CD11a expression [106]. In monocytes from SLE patients exposed to interferon, reduced H3K27me3 levels were detected at ISG promoter regions. Pharmacological inhibition of KDM6A/B by GSK-J4 attenuated ISG expression in monocytes derived from SLE patients [107].

Challenge and future direction

Investigation into the theme ‘Histone Methylation of Kidney Disease: Fact or Fantasy’ has yielded substantial advances through diverse animal and cellular models. Current evidence decisively affirms the involvement of HMT in the pathogenesis of KD, substantiating its biological relevance as an established mechanism rather than a speculative concept.

In AKI, IR markedly induces the expression of multiple histone methyltransferases, including G9a (H3K9), EZH2 (H3K27), Mll1 (H3K4), Dot1l (H3K79), and SMYD2 (H3K36). This transcriptional upregulation enhances lysine methylation, thereby aggravating IR-related injury, promoting pro-inflammatory cytokine production, accelerating RTEC apoptosis, and contributing to RF. Investigations into RF have identified elevated expression of methyltransferases such as EZH2 (H3K27), G9a (H3K9), Mll1 (H3K4), SET7/9, DOT1L (H3K79), PRMT1 (H4R3), and SMYD2 (H3K36) in renal tissue, which correspond with enhanced HMT and activation of fibrotic pathways, advancing RF progression. In DN, hyperglycemia downregulates H4K20me1 and KMT5A, H3K9me3 and Suv39h1, while increasing H3K4me2 and SET7/9, as well as H3K27me3 and EZH2 levels, thereby elevating endothelial inflammatory mediators and contributing to endothelial injury and DN pathogenesis. In ADPKD, the overexpression of Smyd2 (H3K4 and H3K36) and EZH2 (H3K27) correlates with increased methylation activity, stimulating the proliferation of renal cyst epithelial cells. In RCC, heightened levels of G9a and H3K9me2 are associated with enhanced tumor cell proliferation. During kidney stone formation, increased EZH2 and H3K27me3 levels promote oxidative stress, inflammation, and CaOx crystal deposition in vivo. Elevated H3K4 methylation has also been observed in IgA nephropathy and MN. Additionally, in lupus nephritis, H3K27me3 serves as an autoantigen target in both human patients and murine models.

HMT alterations modulate gene expression and signaling cascades in KDs by reshaping chromatin structure and controlling transcriptional dynamics. Within key signaling networks, enzymes such as EZH2 (H3K27me3), G9a (H3K9me1/me2), SET7/9 (H3K4me1), and PRMT1 (H4R3me2a) activate the TGF-β/Smad3 axis through repression of tumor suppressors including PTEN and Smad7, leading to increased expression of pro-fibrotic genes. EZH2 downregulates PTEN via H3K27me3, initiating the EGFR/ERK/STAT3 cascade to enhance pro-inflammatory cytokine production and promote EMT. Concurrently, SET7/9 (H3K4me2) enhances NF-κB p65 binding at inflammatory gene promoters, intensifying NF-κB signaling and inflammatory activity. Through PTEN suppression, EZH2 also indirectly engages the Wnt/β-catenin pathway, aggravating podocyte damage. JMJD3 contributes to immune dysregulation by upregulating CD11a, thereby enhancing T and B cell activation. Dot1L (H3K79me2) and G9a (H3K9me2) drive cell proliferation and oxidative stress through either PTEN inhibition or PI3K/AKT pathway activation, respectively. At the transcriptional level, EZH2 (H3K27me3) epigenetically silences PTEN and SPINK5, while G9a (H3K9me2) also represses SPINK5 expression. MLL1 (H3K4me3) and SET7/9 (H3K4me1) transcriptionally activate TGF-β1, CTGF, and collagen genes, promoting ECM accumulation. G9a-mediated suppression of Sirt1 and Nrf2 weakens antioxidant defenses, whereas SET7/9 (H3K4me2) upregulates TNF-α and MCP-1, thereby intensifying inflammatory cell infiltration. Beyond mechanistic insights into KDs pathogenesis, early identification of HMT-related epigenetic changes and biomarkers is essential for timely diagnosis and intervention. Furthermore, targeting epigenetic regulators offers a compelling therapeutic strategy, as histone methyltransferase inhibitors may reverse aberrant histone marks and yield substantial clinical benefit.

HMT modifications in KDs exhibit functional divergence without implying inconsistency across studies or undermining translational relevance. Within a single disease context, a specific HMT mark may exert distinct regulatory effects. For instance, in IR models, EZH2-mediated H3K27me3 suppresses PTEN expression, thereby activating EGFR signaling and inducing EMT [35], whereas in septic conditions, EZH2 accumulation at the Sox9 promoter attenuates Wnt signaling and triggers apoptosis in renal tubular cells [39]. Such variation highlights the context-sensitive nature of H3K27me3 activity, shaped by differing microenvironmental cues such as hypoxia versus inflammation. Temporal dynamics also influence the functional role of HMT. In early-stage AKI, MLL1-mediated H3K4me3 facilitates cholesterol biosynthesis and pro-inflammatory mediator release through Pol II recruitment to the HMGCR promoter [45]. Conversely, during chronic fibrotic progression, SET7/9-induced H3K4me1 enhances TGF-β1 signaling, driving extracellular matrix accumulation [64]. These temporal variations highlight the potential of H3K4 methylation as a stage-specific indicator of disease evolution. Moreover, the same histone modification may exert diametrically opposed effects depending on disease context. In DN, Suv39h1-driven H3K9me3 is upregulated in high-glucose-exposed HK-2 cells, reducing inflammation and apoptosis, thereby exerting a cytoprotective influence. In contrast, during AKI, G9a-induced H3K9me2 suppresses Sirt1 transcription, aggravating oxidative stress in renal tubular epithelium [32]. These context-dependent outcomes reflect variations in H3K9 methyltransferase expression profiles and the disease-specific regulatory architecture of downstream targets.

HMT has emerged as a validated therapeutic target in KDs, with preclinical evidence demonstrating that pharmacologic modulation of HMT enzymes can reverse disease progression (Table 3). For instance, inhibition of G9a (e.g., via BIX01294) alleviates AKI by restoring Sirt1-mediated antioxidant defenses and suppressing MAPK-driven fibrosis [32,33]. EZH2 inhibitors (e.g., 3-DZNeP) mitigate both AKI and RF by reactivating tumor suppressors (e.g., PTEN, Smad7) and blocking pro-fibrotic signaling cascades (e.g., EGFR/STAT3, TGF-β/Smad3) [35,37,54]. These findings highlight HMT as a cross-disease therapeutic axis, with epigenetic modifiers potentially addressing the shared pathological pathways in KDs.

Table 3.

Summary of HMT inhibitors.

Inhibitor	Target point	Disease model
BIX01294	G9a	IR-AKI, cisplatin-AKI, UUO-RF
UNC0638	G9a	RCC
CM272	G9a	UUO-RF
3-DZNeP	EZH2	IR-AKI, cisplatin-AKI, sepsis-AKI, UUO-RF, TGF-β1-RF, hyperuricemia nephropathy, SLE
ZLD1039	EZH2	Cisplatin-AKI
BAY2416964	AhR, EZH2	Cisplatin-AKI
EED226	PRC2, EZH2	Cisplatin-AKI
GSK-126	EZH2	UUO-RF, RCC, PKD, hyperuricemia nephropathy
MM102	MLL1/WDR5 complex	IR-AKI, UUO-RF
EPZ004777	DOT1L	IR-AKI
AZ505	SMYD2	IR-AKI, UUO-RF, PKD
Chaetocin	Suv39h1, Suv39h2	UUO-RF, high glucose-DN
ORY1001	LSD1	UUO-RF
Sinefungin	SET7/9	UUO-RF
MA-35	SET7/9	UUO-RF
AMI-1	PRMT1	UUO-RF
EPZ5676	DOT1L	UUO-RF

Abbreviations: HMT, histone methylation; KDs, kidney diseases; AKI, acute kidney injury; IR, ischemia-reperfusion; UUO, unilateral ureteral obstruction; RF, renal fibrosis; DN, diabetic nephropathy; RCC, renal cell carcinoma; SLE, systemic lupus erythematosus; TGF-β1, transforming growth factor beta 1; EZH2, enhancer of zeste homologs 2; AhR, aryl hydrocarbon receptor; Suv39h1, suppressor of variegation 3-9 homolog 1; JMJD3, Jumonji domain containing protein 3; Suv39h2, suppressor of variegation 3-9 homolog 2; G9a, euchromatic histone lysine methyltransferase 2; MLL1, myeloid/lymphoid or mixed-lineage leukemia 1; SET7/9, set domain-containing proteins 7/9; Dot1L, disruptor of telomeric silencing 1-like; SMYD2, SET and MYND domain containing protein 2; PRMT1, protein arginine methyltransferase 1; PRC2, polycomb repressive complex 2.

While HMT-targeted therapies in nephrology remain in preclinical stages, cancer research provides critical translational insights. Approved EZH2 inhibitors such as Tazemetostat (for relapsed follicular lymphoma) and Valemetostat (for adult T-cell leukemia) have demonstrated safety and efficacy in clinical trials [108,109]. These agents suppress EZH2-mediated H3K27me3 to reactivate tumor suppressor genes, a mechanism analogous to their protective effects in preclinical KDs models. Notably, the next-generation EZH2 inhibitor SHR2554 (NCT06173999) is currently evaluated for peripheral T-cell lymphoma, with its anti-fibrotic and anti-inflammatory properties warranting exploration in RF and DN. Such cross-disciplinary applications underscore the translational promise of repurposing cancer-focused HMT inhibitors for kidney disorders.

HMT modifications exhibit stage-specific dynamics in KDs (e.g., early AKI-associated H3K4me3 at HMGCR [45] vs. chronic RF-related H3K4me1 at TGF-β1 [64]), positioning them as candidate biomarkers. Urinary H3K27me3 levels in AKI patients correlate with disease severity [40], while serum H4K20me1 may serve as a noninvasive marker for DN progression [74]. Integrating epigenetic profiles with clinical data could facilitate patient-tailoring of HMT inhibitors. For example, patients with high EZH2 activity may benefit from 3-DZNeP, while those with G9a-driven fibrosis may require BIX01294 [32,35]. Genome-wide CRISPR screens in renal cell lines have identified HMT enzymes (e.g., SMYD2, DOT1L) as regulators of fibrosis and apoptosis [70,87]. Expanding such screens to model complex KDs microenvironments (e.g., hyperglycemia, hypoxia) could uncover unrecognized epigenetic nodes, such as H3K36me3-mediated metabolic reprogramming in DN [50].

Despite the promising preclinical evidence supporting HMT as a therapeutic target in KDs, translating these findings into clinical applications remains fraught with challenges. A primary barrier lies in the specificity of HMT inhibitors: most currently developed agents lack absolute target selectivity, potentially causing off-target effects that may lead to systemic toxicity. For instance, EZH2 inhibitors not only repress renal fibrotic pathways but also disrupt hematopoiesis and immune surveillance in preclinical models, highlighting the need for more isoform-specific drug design.

Another critical obstacle is the permanence of epigenetic reprogramming. HMT modifications alter chromatin structure dynamically, but pharmacologic inhibition of methyltransferases may induce irreversible epigenetic changes, particularly in proliferative renal cells. This raises concerns about long-term safety, as persistent epigenetic shifts could predispose to oncogenic transformation or impaired renal regeneration. Integrating CRISPR-based screens to map HMT-driven epigenetic networks in renal cell subtypes may uncover tissue-specific targets, mitigating off-target effects.

Conclusion

This review delineates the mechanistic role of HMT in the pathogenesis of KDs and highlights the therapeutic relevance of targeting epigenetic modifications. HMT, therefore, represents an established determinant in renal pathology rather than a speculative concept. Future research should prioritize unraveling the interplay between HMT and other epigenetic regulators, including DNA methylation and non-coding RNA networks, advancing the development of selective HMT inhibitors, and identifying reliable epigenetic biomarkers to support both diagnostic precision and therapeutic innovation in KDs.

Funding Statement

This work was supported by the National Natural Science Foundation of China (82274307) and Research Funds of Center for Xin’an Medicine and Modernization of Traditional Chinese Medicine of IHM (2023CXMMTCM018).

Disclosure statement

The authors declare that there is no conflict of interest.