The role of N6-methyladenosine (m⁶A) RNA methylation modification in kidney diseases: from mechanism to therapeutic potential

Writers: the catalysts of m⁶A methylation

A particular class of methyltransferase enzymes, known as writers, is in charge of the m⁶A methylation process. These writers assemble into a sophisticated m⁶A methyltransferase complex (MTC), which functions as a pivotal hub in the intricate network of epigenetic regulation. Methyltransferase-like 3 (METTL3), methyltransferase-like 14 (METTL14) and Wilms tumor 1-associated protein (WTAP) are the key components that form the core of the MTC. This enzymatic complex governs the site-specific methylation of structurally diverse RNA substrates through its catalytic activity, establishing a crucial layer of post-transcriptional gene regulation. The regulation of this modification process not only safeguards cellular homeostasis but also ensures the fidelity of genetic information flow from transcription to protein synthesis. Disruption of these regulatory mechanisms precipitates multifaceted pathophysiological manifestations by distorting RNA-protein interactions and compromising translational accuracy. Notably, METTL3-alternatively designated as MT-A70-acts as the catalytic subunit critical to this process, and the first-identified key writer protein (Sorci et al., 2018). It binds to S-adenosylmethionine (SAM) and transfers a methyl group from SAM to the sixth nitrogen atom of adenosine, thereby catalyzing m⁶A methylation (Bokar et al., 1997; Schwartz et al., 2013; Jiang et al., 2021). Recent investigations have pinpointed further regulatory components situated in the MTC. These encompass viral-like m⁶A methyltransferase proteins, RNA-binding motif proteins, zinc finger CCCH-type proteins, as well as Cbl proto-oncogene-like protein 1. Such elements exert an influence on the activity of METTL3 (Wang et al., 2020; Zhu et al., 2021; Su et al., 2022).

As one of the core components, METTL14 bears a strong resemblance to METTL3 in terms of its genetic makeup, yet it doesn’t have the ability to catalyze reactions on its own. What it does instead is to enhance the methylation activity of METTL3, and the two join together to form a heterodimer, with METTL14 playing an irreplaceable role in the entire catalytic process (Liu et al., 2014; Wang et al., 2014a). WTAP, the third core component, lacks intrinsic methyltransferase activity but critically amplifies the catalytic efficiency of the METTL3-METTL14 heterodimer, positioning it as indispensable for methylation regulation (Sorci et al., 2018). At first, WTAP was found to be a splicing factor for the Wilms Tumor 1 (WT1) protein. It performs a crucial function in regulating the mammalian cell cycle and is of significant importance throughout the initial phases of embryonic development (Shi, Wei & He, 2019). WT1, a transcription factor specific to podocytes, is crucial for kidney growth and function (Lee, Kim & Kim, 2014; Zhang, Fu & Zhou, 2019).

Other proteins implicated in m⁶A modification include NSUN2, a component of the SETD family, which has recently been linked to RNA methylation (Li & Huang, 2024). Similarly, NSUN6 (METTL16), due to its structural similarity to METTL3 and METTL14, is hypothesized to drive m⁶A modifications on targeted RNA molecules (Guarnacci et al., 2024). Additionally, DNMT3A and DNMT3B, traditionally associated with DNA methylation, have shown potential RNA methylation activity, indicating a more extensive involvement in RNA modification (Zhang et al., 2021; Chen et al., 2024c). Histone methyltransferases such as H3K36, SETD6, and SETD7 are also under investigation for their potential roles in RNA methylation.

The YTH domain protein family, known as “readers” of m⁶A modifications, influences RNA splicing, stability, and immunogenicity, contributing to immune regulation and antitumor immunity (Ma et al., 2024a). ZC3H13, a zinc finger protein interacting with the m⁶A methylation complex, has an important function in m⁶A modification (Lin et al., 2022). RNA-binding proteins like RBM15/RBM15B may also participate in m⁶A modification through their interaction with the MTC (Cao et al., 2024; Ma et al., 2024b). Lastly, heterogeneous nuclear ribonucleoprotein A2B1 (HNRNPA2B1), another RNA-binding protein, is a subject of ongoing research for its potential involvement in m⁶A modification (Li et al., 2023b).

Erasers: the demethylases of m⁶A

The process of m⁶A demethylation entails stripping away methyl groups from adenosine components within RNA molecules. This stands apart from the methylation function carried out by writer enzymes. Enzymes responsible for this function are termed erasers, with fat mass and obesity-associated protein (FTO) (Huang et al., 2021) and AlkB Homologue 5 (ALKBH5) (Bokar et al., 1997) being the most well-characterized members of this group. FTO and ALKBH5 both belong to the AlkB family, which is a group of DNA repair enzymes (Zaccara, Ries & Jaffrey, 2019; Gao et al., 2024).

FTO, widely expressed in lipid-rich tissues and the brain, contributes to regulating the alternative splicing of RUNX1T1, a key factor in lipid metabolism, and is involved in the 3′ end processing of mRNA in 293T cells (Wang et al., 2024a). Predominantly localized in the nucleus, FTO exhibits a unique C-terminal folding mechanism that enhances its mRNA demethylation activity, thereby having a considerable impact on gene expression (Jia et al., 2011). The second-identified demethylase, ALKBH5, features an A-rich motif at its N-terminus, and such a motif facilitates its presence in nuclear speckles (Martinez De La Cruz et al., 2021; Qu et al., 2022). Both FTO and ALKBH5 contain an ALKB domain in their central regions, which includes two active sites that bind Fe(II), α-ketoglutarate (α-KG), and the RNA substrate. Through its demethylation activity, ALKBH5 influences mRNA stability, splicing, and translation, as well as participates in mRNA nuclear export and processing (Liu et al., 2023).

Readers: the effectors of m⁶A methylation

The fact that m⁶A can pinpoint binding sites between RNA and methylated proteins serves as evidence for its role in modified transcripts, including mRNA (Carroll, Narayan & Rottman, 1990; Song et al., 2024). In the process of m⁶A recognition, reader proteins specifically engage with m⁶A-modified RNA, coordinating the recruitment of RNA-binding proteins to their designated targets and influencing the secondary structure of mRNA (Narayan et al., 1994; Jiang et al., 2021). The YTH domain protein family, which includes YTHDF1, YTHDF2, YTHDF3, YTHDC1, and YTHDC2, is made up of the three main subtypes of m⁶A-binding proteins. It’s worth noting that YTHDF1, YTHDF2, YTHDF3, and YTHDC2 are mainly found in the cytoplasm (Xu et al., 2024). YTHDF2 is primarily involved in regulating RNA decay, YTHDF1 and YTHDF3 govern the translational effectiveness of their target mRNAs (Wang et al., 2015; Shi et al., 2017).

YTH domain proteins are not the only ones capable of recognizing m⁶A modifications. Additional proteins capable of binding m⁶A, such as HNRNPA2B1, have also been identified (Siculella et al., 2023), heterogeneous nuclear ribonucleoprotein C, fragile X messenger ribonucleoprotein 1, and IGF2BP (Ramesh-Kumar & Guil, 2022), also play significant roles in this process.

Recent studies have identified Fragile X-related protein 1(FXR1) as a novel m⁶A reader that extends the diversity of m⁶A-mediated regulatory mechanisms. Unlike canonical readers that contain YTH or KH domains, FXR1 interacts with m⁶A-modified RNA transcripts through an unconventional RNA-binding domain. This interaction enhances the stability and translation of target mRNAs involved in cell cycle regulation, inflammation, and stress responses (Khan et al., 2024a, 2024b, 2025). Importantly, FXR1 has been shown to function in both physiological contexts, such as muscle development and pathological conditions including tumorigenesis and immune regulation, suggesting its potential relevance in kidney diseases as well.

Erasers, which actively reverse m⁶A methylation, exemplify its dynamic and reversible regulatory nature. Readers, in turn, interpret the methylation marks to regulate RNA translation and degradation, thereby fine-tuning gene expression (Lv et al., 2021; Liang et al., 2022). Dysregulation of m⁶A readers, such as YTHDF1-3 and YTHDC1-2, can disrupt this balance, contributing to pathological conditions, including kidney diseases (Zhang et al., 2023).

The m⁶A methylome and its associated proteins are dynamically regulated, underscoring their vital role in maintaining cellular homeostasis. The potential problems that can result from their improper regulation in disease states are also highlighted. The functional coordination of m⁶A-associated enzymes and proteins is central to disease mechanisms in the kidney, modulating processes such as cellular proliferation, fibrosis, and inflammation. Dysregulation of specific Writers or Erasers, whether through overexpression or downregulation, can lead to abnormal m⁶A methylation patterns, potentially disrupting normal renal function and exacerbating disease progression (Li et al., 2022). For instance, the m⁶A reader YTHDF2 has been shown to contribute to renal fibrosis by stabilizing the mRNA of pro-fibrotic genes (Zhao & Yang, 2024).

Investigating the precise mechanisms by which these enzymes and proteins influence kidney pathophysiology, such as their role in modulating inflammatory responses in diabetic kidney disease (Lan et al., 2022), could reveal new diagnostic biomarkers and therapeutic targets. Similar observations have been previously put forward regarding cancer progression (Qin et al., 2024). Table 1 provides a succinct summary of the functions executed by key enzymes and proteins within the m⁶A methylation process and their involvement in the pathogenesis of renal diseases.

Acute kidney injury

This section primarily draws on preclinical data from animal models and in vitro experiments to explore the role of m⁶A modification in acute kidney injury. While these studies provide valuable mechanistic insights, further clinical validation is needed to confirm their applicability in human disease.

AKI is a medical condition characterized by a swift and significant decline in the kidneys’ ability to effectively filter waste and maintain fluid balance, marking a crucial disruption in renal function, often leading to CKD and, in severe cases, end-stage renal disease (ESRD) (Ronco, Bellomo & Kellum, 2019). A complete understanding of the molecular mechanisms underlying AKI, particularly during its initial phases, is critical for advancing targeted therapeutic strategies. Emerging research points to the participation of m⁶A modification in the process of acute kidney injury pathogenesis (Mao et al., 2023). Mechanistically, m⁶A modification participates in AKI pathogenesis through three key etiologies: nephrotoxic drugs (Mao et al., 2023), sepsis (Poston & Koyner, 2019), and ischemia/reperfusion (I/R) injury (Chen et al., 2023).

Clinically, drug-induced kidney injury is responsible for nearly 25% of AKI cases, predominantly due to damage to renal tubular epithelial cells, resulting in acute tubular necrosis (Perazella & Rosner, 2022). Mechanistically, cisplatin a common nephrotoxic agent, accumulates in renal tubular cells and triggers multiple intracellular stress responses, such as DNA damage, oxidative stress, mitochondrial dysfunction, and endoplasmic reticulum stress (Tang et al., 2023). In models of cisplatin-induced AKI, an increase in the total RNA m⁶A methylation content within kidney tissues has been detected, along with variations in the expression of key regulatory factors, such as METTL3, METTL14, WTAP, FTO, and ALKBH5 (Li et al., 2021). Further studies by Zhou et al. (2019) revealed that cisplatin enhances m⁶A methylation by suppressing FTO while upregulating METTL3/14, leading to p53 activation and subsequent Bax/Bcl-2/Caspase3-mediated apoptosis. Therapeutically, these findings suggest that targeting METTL3 or FTO could mitigate cisplatin nephrotoxicity. A key factor leading to AKI is ischemia-reperfusion injury (IRI), with ischemic and septic acute tubular necrosis being major contributors. These conditions are associated with a high mortality rate of 78.⁶% among hospitalized and intensive care unit patients (Menon, Symons & Selewski, 2023). Animal-based experimental studies have demonstrated that IRI involves a mechanistic interplay between ALKBH5 and CCL28 mRNA stability. Alkbh5 knockout mice exhibit reduced renal damage post-IRI due to increased CCL28 m⁶A levels, which modulate the Treg/inflammatory cell axis (Chen et al., 2023). These findings indicate that targeting the ALKBH5/CCL28/Treg axis may offer a promising therapeutic approach for the treatment of AKI. Translational studies indicate that hydralazine, a demethylating agent, prevents IRI-related fibrosis in mice (Tampe et al., 2017), highlighting ALKBH5 inhibition as a potential therapeutic strategy. Emerging research also implicates the YAP/TEAD1 pathway in protecting tubular epithelial cells from necroptosis and inflammation in cisplatin-induced AKI. In a recent study, TEAD1 overexpression preserved mitochondrial integrity and suppressed RIPK3/MLKL-mediated necroptosis in proximal tubular cells, leading to reduced inflammatory cytokine release (Tran et al., 2025). Although m⁶A levels were not directly measured, these findings raise the possibility that TEAD1–YAP signaling may intersect with the METTL3/METTL14 m⁶A machinery to coordinate mitochondrial and inflammatory gene expression in AKI. Sepsis-associated acute kidney injury (SA-AKI) represents a significant clinical challenge, as it is among the most prevalent and severe complications affecting patients with sepsis. Around 35% to 50% of patients with sepsis develop AKI, and the mortality rate for these patients can reach as high as 35% (Peerapornratana et al., 2019). m⁶A RNA methylation has been closely linked to SA-AKI pathogenesis. In vitro studies have identified seven key genes (Hmox1, Spp1, Socs3, Mapk14, Lcn2, Cxcl1, and Cxcl12) that play critical roles in SA-AKI-related signaling pathways (Liu et al., 2022). Notably, the mmu-miR-7212-5p-Hmox1 signaling mechanism is implicated in ferroptosis and underpins the pathophysiological characteristics of SA-AKI. In addition, it has been discovered that insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) can upregulate the expression of macrophage migration inhibitory factor (MIF) by enhancing E2F transcription factor 1 (E2F1) through m⁶A modification, which subsequently leads to podocyte apoptosis in SA-AKI (Mao et al., 2023).

The comprehensive results underscore the pivotal significance of m⁶A methylation and its associated regulatory elements, including METTL3, METTL14, FTO, and ALKBH5, in deciphering the initiation of AKI and in devising innovative therapeutic strategies. While research has demonstrated the detrimental effects of cisplatin and meclofenamic acid on kidney injury, the exact fundamental processes still need to be completely clarified. Therefore, a deeper exploration of m⁶A methylation’s role in AKI, particularly in drug-induced kidney injury, is essential for pinpointing potential therapeutic targets and pushing forward treatment approaches.

Chronic kidney disease

This section integrates preclinical research with limited clinical data to examine the role of m⁶A modification in chronic kidney disease. Although animal models and in vitro experiments have uncovered key molecular mechanisms, clinical evidence remains scarce.

CKD stands as a significant global health concern. It is estimated that approximately 10 percent of the adult population worldwide grapples with this condition. Moreover, the impact of CKD is far-reaching, with an annual death toll of 1.2 million individuals and a substantial burden of 28 million disability–adjusted life years (DALYs) (GBD Chronic Kidney Disease Collaboration, 2020). Clinically, the occurrence of CKD exhibits a strong positive correlation with advancing age (Cockwell & Fisher, 2020). Pathologically, CKD is characterized as a multifactorial process involving structural remodeling and progressive functional decline of the kidneys (Kalantar-Zadeh et al., 2021). Its progression is governed by a complex molecular network, with current research primarily focusing on key pathological mechanisms such as immune-mediated inflammation, oxidative stress, fibrosis, apoptosis, and metabolic dysregulation.

Mechanistically, emerging epigenetic studies reveal that m⁶A modification dynamically regulates CKD progression. Transcriptomic studies utilizing the unilateral ureteral obstruction (UUO) model have proven that m⁶A modification is widely distributed in renal tissues and closely associated with disease progression (Sun et al., 2023). Of particular interest, renal tissues in the UUO model exhibit a global reduction in m⁶A levels, accompanied by downregulation of methyltransferases METTL3/14 and upregulation of the demethylase FTO (Liu et al., 2023c). This m⁶A loss is enriched in pathological pathways like epithelial-mesenchymal transition and fibrosis, as confirmed by GO/KEGG analyses (Yue et al., 2018). Therapeutically, interventions like genistein alleviate fibrosis by activating ALKBH5 to reduce m⁶A levels highlighting the clinical potential of m⁶A modulation.

Further mechanistic insights that YTHDF1 protein has been found to be significantly upregulated in multiple renal fibrosis models, including UUO, folic acid-induced, and ischemia-reperfusion injury models, with its pro-fibrotic effects potentially mediated through the regulation of the YAP signaling pathway. Clinically, YTHDF1 overexpression in human fibrotic kidneys correlates with YAP levels, while CKD patients exhibit reduced leukocyte m⁶A and elevated FTO (Liu et al., 2023c). Beyond YTHDF1 and the YAP pathway, m⁶A-dependent regulation of PTEN has been implicated in renal fibrosis. Myeloid-specific PTEN deficiency aggravates tubular inflammation and collagen deposition in UUO mice, while METTL14-mediated m⁶A on PTEN mRNA enhances its stability and dampens PI3K/Akt-driven fibrotic signaling (An et al., 2022). Similar METTL14–PTEN crosstalk has been demonstrated in gastric cancer models, underscoring its translational potential in CKD (Yao et al., 2021). These findings suggest two therapeutic paradigms: 1. global inhibition of m⁶A modification may confer renal protection, and 2. differential regulation of specific methyltransferases (e.g., METTL14) may reverse renal dysfunction.

Diabetic kidney disease

This section is based on preclinical studies and a growing body of clinical evidence. Research in animal models and human cohorts has shown altered m⁶A marks in diabetic nephropathy patients, highlighting the potential of m⁶A regulators as biomarkers.

Renal fibrosis is a common pathological manifestation in DKD patients, impacting roughly half of individuals diagnosed with type 2 diabetes, and affecting about one-third of those living with type 1 diabetes, ultimately leading to the progression of CKD. Mechanistically, total flavonoids of Abelmoschus manihot (TFA) alter METTL3-associated m⁶A dynamics, activate the NLRP3 inflammasome, and modulate PTEN/PI3K/Akt signaling. In this way, TFA can significantly reduce podocyte injury and death under high glucose (HG) circumstances (Liu et al., 2021b). This discovery offers fresh perspectives on the intricate mechanisms that underlie podocyte injury triggered by DKD. Clinically, METTL3 overexpression in DKD patients’ podocytes correlates with kidney damage, while its genetic deletion reduces inflammation/apoptosis in experimental models (Chen et al., 2024b). Translational studies show that silencing the METTL3 gene via the AAV9 vector alleviates proteinuria and pathological tissue damage in streptozotocin (STZ)-induced diabetic mice and db/db mice (Wu et al., 2024), highlighting therapeutic potential. Concurrently, METTL3-driven m⁶A hypermethylation exacerbates podocyte injury through the TIMP2/Notch axis (mechanistic basis); clinically, this pathway may be pharmacologically targeted by METTL3 inhibitors currently in preclinical development (Jiang et al., 2022).

During the progression of DN, endoplasmic reticulum stress (ERS) is vital in causing apoptosis of renal tubular epithelial cells. It has been highlighted by recent studies that the lncRNA taurine-upregulated gene 1 (TUG1), with its initial connection to retinal development, is a participant in the pathogenesis of DKD (Ageeli Hakami, 2024). Mechanistic insights further identify METTL14’s dual roles. On one hand, METTL14 has been shown to regulate m⁶A and modify TUG1, thereby activating the MAPK/ERK signaling pathway, which promotes the death of renal tubular epithelial cells and exacerbates ERS, accelerating the progression of DKD (Zheng et al., 2023). On the other hand, under high-glucose conditions, METTL14 expression and m⁶A methylation levels decrease. Additionally, METTL14-mediated PTEN inhibits the activation of the PI3K/Akt pathway, leading to the upregulation of HDAC5 in renal tubular cells under hyperglycemic conditions, followed by epithelial-to-mesenchymal transition (EMT) (Xu et al., 2021). Interestingly, METTL14 expression is upregulated in renal tissues of diabetic nephropathy patients and in human renal glomerular endothelial cells (HRGECs) exposed to high-glucose conditions, suggesting its critical role in exacerbating renal inflammatory responses and oxidative stress (Fu et al., 2024). Overexpressing METTL14 in HRGECs amplifies reactive oxygen species (ROS), TNF-α, and IL-6 production, triggering enhanced cellular apoptosis. Conversely, METTL14 silencing attenuates these inflammatory mediators and apoptotic responses (Yang et al., 2024a). Additionally, METTL14 influences the expression of α-klotho through m⁶A modification, deteriorating kidney function, and inflammatory responses in db/db mice. Clinically, METTL14-mediated α-klotho suppression worsens DKD, though α-klotho partially compensates, suggesting combination therapies. Under hyperglycemic conditions, overexpression of WTAP markedly amplifies NLRP3 inflammasome activation, driving the secretion of pro-inflammatory cytokines such as IL-1β and IL-18, which aggravates renal injury (Huang et al., 2024). The insights gleaned from the study underscore the crucial role played by m⁶A modification, orchestrated by WTAP, in cellular signaling pathways. This suggests its significant therapeutic potential in the context of DN. Notably, WTAP deficiency in pancreatic β-cells induces metabolic disturbances, as evidenced by hyperglycemia and impaired insulin secretion in β-cell-specific WTAP knockout (Wtap-betaKO) mice. Mechanistic studies reveal that WTAP loss reduces m⁶A modification levels, impairing the expression of transcription factors and genes essential for insulin production (Li et al., 2023a). This dual regulatory function-linking WTAP to both renal pathology and β-cell dysfunction-emphasizes its systemic impact on diabetes progression. In parallel, histone deacetylase 5 (HDAC5) has been implicated in DN pathogenesis. Xu et al. (2021) demonstrated that HDAC5 expression was upregulated in both diabetic and UUO models. Furthermore, suppression of HDAC5 mitigates the progression of hyperglycemia-driven EMT within renal tubular cells. HDAC5 modulates transforming growth factor β1 (TGF-β1) activity via the PI3K/Akt pathway, thereby promoting renal fibrosis under high-glucose conditions. These findings position HDAC5 as a viable target for mitigating fibrotic damage in DN.

Collectively, m⁶A regulators (METTL3, METTL14, WTAP) orchestrate DKD progression through NLRP3 activation, oxidative stress, and fibrosis. Clinical correlations in patient tissues and therapeutic efficacy in preclinical models (e.g., TFA, AAV9-METTL3 silencing) validate their translational relevance. Targeting these hubs may disrupt pathogenic networks while addressing compensatory mechanisms like α-klotho restoration.

Renal cell carcinoma

This section relies on preclinical data and clinical observations. Studies in animal models and human renal cancer tissues have identified significant alterations in m⁶A regulators, which may serve as prognostic biomarkers.

Emerging studies demonstrate that m⁶A RNA modification, orchestrated by diverse regulators, critically influences RCC pathogenesis by modulating oncogenic or tumor-suppressive pathways. Mechanistically, METTL3 overexpression in advanced RCC is driven by HIF-1α in hypoxia, facilitating m⁶A-dependent PLOD2 upregulation to drive tumor proliferation and metastasis (Chen et al., 2024a). This positions METTL3 inhibition as a potential therapeutic strategy.

Conversely, METTL14 downregulation reduces m⁶A modification of BPTF mRNA, enhancing its stability to promote glycolysis and metabolic reprogramming (Zhang et al., 2021). While METTL14 deficiency activates the ATP-P2RX⁶-Ca2+-ERK1/2-MMP9 axis through P2RX⁶ mRNA stabilization, accelerating invasion (Gong et al., 2019). Clinically, these molecular alterations correlate with poor prognosis in RCC patients, with TCGA/GEO datasets confirming distinct m⁶A regulatory signatures between tumor and normal tissues that predict progression trajectories (Ying et al., 2021; Wang et al., 2024c).

WTAP, another methyltransferase complex component, modifies m⁶A patterns on lncRNAs to influence RCC progression. Further mechanistic insights reveal WTAP-mediated m⁶A enrichment on TEX41 lncRNA triggers YTHDF2-dependent degradation, altering SUZ12-associated histone methylation and HDAC1 expression (Zhou et al., 2024). Therapeutically, experimental manipulation using dCas13b-M3M14 fusion proteins to overexpress m⁶A-modified MUC15 and HRG suppresses RCC metastasis (Gan et al., 2021), suggesting targeted epitranscriptome editing as a viable strategy. Prognostically, the miR-501-3p-CDK2 axis amplifies WTAP expression, stabilizing S1PR3 mRNA via IGF2BP to activate PI3K/Akt signaling, correlating with reduced survival (Ying et al., 2021; He et al., 2021). While demethylases like FTO and ALKBH5 show dysregulation, their controversial roles necessitate further validation as clinical biomarkers (Strick et al., 2020; Guimarães-Teixeira et al., 2021). Collectively, these findings position METTL3 inhibition and m⁶A-targeted editing as promising clinical interventions against RCC progression.

Lupus nephritis

This section incorporates clinical data from human cohorts, including elevated METTL3 expression in LN biopsy tissues and PBMCs from systemic lupus patients, supporting the relevance of m⁶A dysregulation in this disease.

LN, a notable complication associated with systemic lupus erythematosus (SLE), comes into being as a result of immune system dysregulation and persistent inflammatory processes. At the core of its pathogenesis lies the formation of endogenous immune complexes. Such complexes set in motion complement cascades and launch inflammatory pathways, ultimately leading to the damage of renal parenchymal cells. Emerging research emphasizes the interplay between immune cell infiltration and environmentally triggered epigenetic alterations in LN progression (Yu et al., 2022; Li et al., 2024). Mechanistically, m⁶A RNA methylation heterogeneity defines two subtypes (1/2) with distinct expression patterns of regulators including METTL3, WTAP, YTHDC2, YTHDF1, FMR1, and FTO (Zhao et al., 2021b). These subtypes exhibit divergent immune microenvironment profiles and pathway activation. Clinically, seven m⁶A-related markers correlate strongly with renal dysfunction, offering prognostic value and guiding subtype-specific immunotherapy.

Further mechanistic insights reveal the role of m⁶A readers in cytokine signaling modulation. For instance, IMP2, an m⁶A-binding protein, governs autoimmune inflammation by post-transcriptionally regulating C/EBPβ and C/EBPδ stability in response to IL-17 and TNFα (Bechara et al., 2021). Therapeutically, this regulatory axis influences cytokine-driven renal injury, positioning IMP2 as a promising intervention target for LN. Similarly, targeting the IGF2BP2/m⁶A-epigenetic axis has been shown to mitigate autoimmune antibody-induced glomerular damage by stabilizing transcription factors critical for inflammatory signaling, and addresses clinical challenges like poor drug specificity and limited efficacy of conventional treatments (Slivka et al., 2019). Collectively, these advances position m⁶A regulators as precision therapeutic targets against LN.

Obstructive nephropathy

This section is based on preclinical studies and clinical observations. Animal models and human tissue samples have shown that m⁶A regulatory factors drive fibrotic progression in obstructive nephropathy.

Ureteral obstruction disrupts renal physiology through hemodynamic disturbances, impaired glomerular filtration, and metabolic dysregulation, culminating in structural pathologies such as renal fibrosis. The UUO model serves as a standard experimental tool for investigating tubulointerstitial fibrosis, enabling multi-level exploration of fibrotic mechanisms spanning molecular, genomic, and cellular domains (Nørregaard et al., 2023). Mechanistically, m⁶A regulatory factors critically drive fibrotic progression in obstructive nephropathy (ON) (Liu et al., 2021a; Jung et al., 2024). The up-regulation and activation of METTL3 and other pivotal methyltransferases are critical for regulating the expression of fibrosis-related genes and propelling the progression of fibrotic pathogenesis. Fibrosis-associated miRNAs, including miR-145 and miR-21, exhibit dynamic interactions with m⁶A modifications to regulate key signaling pathways. Notably, METTL3-dependent induction of miR-21 activates the miR-199a-3p/Par4 axis, amplifying fibrotic cascades (Yi et al., 2024). TGF-β stimulation of HK-2 cells elevates METTL3 levels and subsequent m⁶A modifications, upregulating C/EBP transcription factors. METTL3 inhibition attenuates C/EBPβ and C/EBPδ expression, confirming m⁶A-dependent regulation of these transcriptional regulators. Functional studies demonstrate that C/EBPβ and C/EBPδ mediate TGF-β-driven EMT and fibrotic remodeling (Jung et al., 2024). Clinically, these molecular pathways present intervention opportunities, as evidenced by ALKBH5’s role in UUO models, where its reduced expression correlates with elevated m⁶A levels and exacerbated fibrosis. Therapeutically, genistein administration restores ALKBH5 expression, mitigating m⁶A hypermethylation and fibrosis (Ning et al., 2020), paralleling outcomes from genetic ALKBH5 manipulation studies.

Further mechanistic insights reveal that FTO promotes fibrogenesis by modulating pro-fibrotic gene methylation, with FTO silencing shown to alleviate UUO- and TGF-β1-induced inflammation, apoptosis, and impaired autophagy (Zhang et al., 2022; Yang et al., 2023). At the molecular level, transcriptomic profiling identifies RUNX1 as a key downstream effector, where FTO stabilizes RUNX1 mRNA via demethylation to activate the PI3K/AKT pathway and propagate fibrotic signaling (Wang et al., 2024a) Clinically, this FTO-RUNX1 axis offers a promising therapeutic target, as pharmacological FTO inhibition reverses pathological RUNX1 upregulation in experimental models. Collectively, these findings position METTL3, ALKBH5 and FTO as mechanistically validated targets with translational potential for mitigating obstruction-induced renal fibrosis (Wang et al., 2024a).

Other kidney diseases

This section includes preclinical data and clinical observations. Studies in animal models and human cohorts have identified specific m⁶A regulators associated with various renal pathologies, such as alcohol-induced nephropathy and autosomal dominant polycystic kidney disease.

Emerging evidence highlights the regulatory significance of m⁶A methylation across diverse renal pathologies through distinct mechanistic pathways with clear clinical implications. In alcohol-induced nephropathy, suppressed FTO expression elevates m⁶A modification of PPAR-α mRNA via YTHDF2-mediated recognition, activating NLRP3 inflammasomes and NFκB signaling to exacerbate inflammatory renal injury (Yu et al., 2021). Clinically, this pathway identifies FTO/YTHDF2 as potential therapeutic targets for alcohol-related kidney damage. Parallel investigations in autosomal dominant polycystic kidney disease (ADPKD) reveal METTL3 upregulation correlating with cystogenesis, where mechanistically elevated methionine and SAM levels enhance METTL3 activity, promoting m⁶A-dependent stabilization of c-Myc and Avpr2 transcripts to facilitate cyst growth through c-Myc-driven proliferation and cAMP pathway activation (Ramalingam et al., 2021). Therapeutically, transgenic METTL3 deletion attenuates cyst expansion in murine models, while dietary methionine restriction demonstrates clinical potential by disrupting these metabolic-epigenetic interactions. In focal segmental glomerulosclerosis (FSGS), mechanistically dysregulated m⁶A dynamics contribute to glomerular dysfunction through METTL14-mediated m⁶A modifications that suppress Sirt1 expression-a nephroprotective deacetylase-in both murine models and human podocytes (Lu et al., 2021). Clinically, this METTL14/Sirt1 axis exacerbates proteinuria and glomerulosclerosis, positioning METTL14 modulation as a therapeutic strategy.

Collectively, these disease-specific regulatory networks highlight distinct mechanistic pathways: alcohol-associated injury involves FTO/YTHDF2-mediated inflammatory activation, ADPKD centers on METTL3-driven metabolic-epigenetic crosstalk, and FSGS links to METTL14-dependent Sirt1 downregulation. Such insights advance renal disease etiology understanding while clinically validating m⁶A modifiers as therapeutic targets across nephropathies.

Integrated signaling networks across renal pathologies

Epitranscriptomic regulation by m⁶A methylation interfaces with conserved signaling pathways that transcend traditional disease classifications (Fig. 3). This integrative analysis reveals four principal regulatory networks central to renal pathophysiology (Table 3), with implications for targeted therapeutic interventions.

Clinical evidence and translational insights

Translational efforts are increasingly incorporating human data on m⁶A regulators in kidney disease, like in LN, METTL3 expression was found to be markedly elevated. One study reported significantly higher METTL3 and ALKBH5 levels in PBMCs from systemic lupus patients, and robust METTL3 immunostaining in LN biopsy tissues, notably in infiltrating immune cells and tubules (Liu et al., 2024). Similarly, transcriptome analyses of human kidney biopsy cohorts have revealed dysregulated m⁶A machinery. In IgA nephropathy, for instance, nine m⁶A regulators (readers/erasers such as YTHDF2 and IGF2BP3) were significantly downregulated in patient glomeruli compared to controls (Wang et al., 2024b). In DKD, emerging evidence shows altered m⁶A marks in patients: diabetic nephropathy patients exhibit reduced global m⁶A levels in urine and blood, alongside decreased FTO expression (Li & Mu, 2024). Notably, a logistic regression model combining glomerular YTHDC1, METTL3 and ALKBH5 expression distinguished early vs advanced DKD, and retained predictive accuracy when applied to patients’ PBMC samples (2025). These clinical findings support the relevance of m⁶A dysregulation in human kidney disease and hint at biomarker potential.

Beyond glomerulonephritis, m⁶A regulators have been linked to CKD and renal cancers. In clear-cell renal cell carcinoma (ccRCC), multiple m⁶A enzymes- including the writer METTL3 and demethylase ALKBH-are significantly overexpressed in tumor tissue vs normal kidney (Chen et al., 2020). In the same study, a two-gene signature (METTL3 and METTL14) was constructed by LASSO regression to stratify ccRCC patient survival, achieving good prognostic performance (Chen et al., 2020). Other CKD forms also show altered m⁶A profiles: for instance, patient samples from ADPKD demonstrate upregulation of METTL3 in cystic kidneys. Collectively, these patient-based studies illustrate that many m⁶A alterations observed in model systems likewise occur in human disease, bolstering their translational significance.

To date, however, interventional m⁶A-targeted therapies in nephrology remain unrealized. A recent review emphasizes that “currently there is no drug related to RNA methylation modification that is on clinical trial for kidney diseases” (Luan, Kopp & Zhou, 2022). No ClinicalTrials.gov entries specifically address m⁶A modulation in renal patients (as of mid-2025). This gap underscores the nascent stage of clinical translation in this field: mechanistic insights abound, but rigorous human validation and trials are just beginning.

To bridge mechanism and medicine, multi-center prospective studies are needed to evaluate m⁶A regulators as biomarkers and targets. Cohorts of CKD patients (e.g., diabetic nephropathy, glomerulonephritis, polycystic kidney disease) should be followed longitudinally with systematic collection of biospecimens (blood, urine, biopsy). Quantitative assays for m⁶A levels and regulator expression (e.g., LC-MS for m⁶A/A ratio, RT-qPCR or ELISA for METTL3/FTO/ALKBH5) should be standardized and correlated with clinical outcomes (eGFR decline, proteinuria, histology). Multi-omics integration (combining m⁶A methylome, transcriptome, proteome) in patient samples could uncover disease-driving networks and refine therapeutic targets. On the interventional front, preclinical testing of m⁶A modulators in kidney disease models is warranted. Ultimately, early-phase trials- for instance, repurposing epigenetic drugs or novel RNA methylation inhibitors in selected patient subsets- could establish proof-of-concept. Taken together, these approaches would help translate m⁶A biology into clinically actionable strategies in nephrology.

Patient-based analyses have begun to tie m⁶A to renal outcomes. For example, Zhao et al. (2021b) identified an LN-specific m⁶A signature (METTL3, WTAP, YTHDC2, YTHDF1, FMR1) that cleanly separated lupus nephritis biopsies from healthy kidney tissue. Chen et al. (2020) showed METTL3 and ALKBH5 upregulation in ccRCC tumors and derived a METTL3/METTL14 prognostic score. In DKD, Shi et al. (2017) found urinary m⁶A levels fall with disease progression, and constructed a glomerular/PBMC model including METTL3 and ALKBH5 to diagnose early DKD (Li, Xu & Li, 2025). Such clinical reports, though still limited, illustrate the bridge between m⁶A mechanistic work and human disease.

Limitations of current strategies

Despite promise, significant challenges remain. Many reported inhibitors are not highly specific for a single m⁶A enzyme. For instance, IOX1 inhibits many 2-OG dioxygenases (not just ALKBH5), raising off-target risk (Fang et al., 2025). Furthermore, compounds identified by virtual screens often lack selectivity or have unknown in vivo behavior. Natural products like genistein can have broad biological effects beyond m⁶A modulation, and their pharmacokinetic profiles in patients are poorly characterized (Ning et al., 2020). Moreover, virtually all data so far come from cell lines or animal models; human validation is lacking. m⁶A-based biomarkers and therapeutic hypotheses must be tested in large, well-controlled patient cohorts. The idea of using m⁶A profiles to guide, say, immunotherapy or targeted drug choice in kidney disease is attractive but remains speculative without clinical evidence. In short, issues of target specificity, off-target toxicity, pharmacodynamics, and population variability have not been resolved (Tang et al., 2024).

Future directions (toward clinical translation)

To bridge these gaps, research should pursue several avenues. First, the development of highly selective m⁶A modulators is crucial. Advances in AI-driven design can help: for example, leveraging predicted structures of METTL3, FTO, ALKBH5, etc., to design molecules with optimized specificity and drug-like properties. High-throughput screening (virtual and biochemical) should continue to identify and refine lead compounds, with follow-up in vivo testing of ADME/toxicity. Second, the clinical relevance of m⁶A markers must be validated. Large-scale studies should assess whether m⁶A enzyme levels or global m⁶A patterns in blood or biopsy correlate with disease stage, progression, or response to therapy. Third, combination strategies should be explored: it may be that partial modulation of m⁶A synergizes with existing treatments (e.g. RAAS inhibitors, immunosuppressants, SGLT2 inhibitors) to improve outcomes. Finally, continued integration of AI tools—such as predictive models of m⁶A target networks and patient stratification algorithms—will be important. By systematically addressing specificity, safety, and efficacy, these steps can move m⁶A-targeted approaches from bench toward bedside in renal disease.