The regulation of oxidative stress response by epigenetic modifications in acute respiratory distress syndrome

Abstract

Acute respiratory distress syndrome (ARDS), a life-threatening condition driven by diffuse alveolar-capillary injury and loss of redox homeostasis, still lacks effective targeted pharmacotherapies. Current management remains predominantly supportive, with lung-protective ventilation as the cornerstone of respiratory care. Although ARDS arises from diverse clinical insults, oxidative stress emerges as a shared pathogenic pathway across etiologies. Excessive reactive oxygen species (ROS) production not only directly injures epithelial and endothelial cells but also perpetuates inflammatory signaling. ROS generation and clearance are compartmentalized, governed by interconnected pathways that span multiple organelles and cellular processes, forming a dynamic redox network that becomes especially vulnerable during critical illness. Growing evidence implicates epigenetic mechanisms as key modulators of this redox-inflammation interface. In this review, we delineate how three pivotal epigenetic processes regulate oxidative stress in ARDS: DNA methylation, histone modifications, and non-coding RNAs. We also examine the crosstalk among these mechanisms and evaluate emerging interventions targeting these pathways, emphasizing both their therapeutic potential and the persistent challenges in clinical translation. Importantly, rather than viewing these mechanisms independently, this review integrates current evidence to highlight epigenetic regulation as a critical layer linking oxidative stress, inflammatory signaling, and cellular injury in ARDS. We further propose that effective therapeutic strategies may require stage-specific and cell-type-oriented modulation of epigenetic targets, rather than uniform systemic inhibition. By synthesizing these insights, this review aims to provide a conceptual framework that may help guide the development of more precise redox-targeted epigenetic interventions in ARDS.

Introduction

Acute respiratory distress syndrome (ARDS), often precipitated by infection, trauma, or aspiration, is a life-threatening clinical syndrome characterized by diffuse alveolar-capillary injury and severe hypoxemia.

In acute lung injury (ALI)/ARDS, oxidative stress reflects a mismatch between reactive oxygen species (ROS) production and endogenous antioxidant capacity under injurious stimuli. When ROS accumulate excessively, direct molecular injury follows: lipids, proteins, and nucleic acids are damaged, leading to structural disruption and functional impairment (1). Simultaneously, ROS can act as second messengers to sustain the activation of pro-inflammatory signaling pathways. A key mechanism underlying this process involves the persistent activation of nuclear factor-κB (NF-κB), which subsequently amplifies the inflammatory cascade (2). Delineating how oxidative stress is regulated may therefore help identify actionable therapeutic entry points in ALI/ARDS.

A further regulatory layer has come into focus: epigenetic control of gene expression. Without changing DNA sequence, DNA methylation, histone modifications, and non-coding RNAs dynamically modulate chromatin state and transcription (3). During ALI/ARDS progression, these epigenetic programs are implicated in reshaping oxidative stress-related transcriptional responses (4).

This review synthesizes current evidence on how these three epigenetic mechanisms regulate oxidative stress in ALI/ARDS, considers their potential crosstalk, and discusses translational opportunities for epigenetic-targeted strategies. Key challenges include achieving cell-type specificity, minimizing off-target effects, defining the optimal timing of intervention, and strengthening clinical validation.

The effect of oxidative stress on ARDS

Oxidative stress is markedly heightened during the onset and progression of ARDS. In response to injurious stimuli, inflammatory cells, particularly neutrophils and macrophages, are recruited to the lungs and undergo activation (5). At the same time, mitochondrial dysfunction in alveolar epithelial and vascular endothelial cells further increases ROS generation (6). When ROS production exceeds the capacity of key endogenous antioxidants, redox homeostasis is disrupted, culminating in a shift toward oxidative stress (7).

Excess ROS worsen lung injury through both direct oxidative damage and downstream inflammatory amplification. These mediators compromise the alveolar-capillary barrier, increase permeability, and contribute to pulmonary edema (5,8). In parallel, ROS can reinforce inflammatory signaling by engaging pathways such as NF-κB and MAPK and by promoting NLRP3 inflammasome activation, partly through redox-dependent modulation of upstream regulators that control NF-κB activation (9). Together, these processes may create a self-reinforcing loop in which inflammation and oxidative stress mutually potentiate each other (10,11).

Beyond these immediate signaling effects, increasing evidence suggests that oxidative stress may also exert longer-lasting influences on cellular behavior (12). Persistent ROS exposure has been reported to affect the activity of epigenetic modifiers, including DNA methyltransferases (DNMTs), histone deacetylases (HDACs), and ten-eleven translocation (TET) enzymes, thereby reshaping chromatin accessibility and transcriptional responsiveness (13). In this context, oxidative stress may not simply reflect ongoing injury but may contribute to stabilizing gene expression patterns that persist after the initial insult. This provides a potential explanation for how transient oxidative signals translate into more sustained cellular responses in ARDS.

Instead of being a bystander to inflammation, oxidative stress appears to contribute to barrier injury and physiological deterioration in ARDS, and its biomarkers often track with disease severity and outcomes. These observations support further development of redox-related biomarker panels for early risk stratification and as pharmacodynamic readouts in interventional trials (14). Translational progress will likely depend on clarifying dominant ROS sources and time windows in specific ARDS phenotypes, as well as standardizing sampling matrices, assays, and clinically meaningful cutoffs (15). Understanding how oxidative signals are translated into more durable changes in gene regulation, potentially through redox-sensitive effects on epigenetic regulators such as DNMTs (16), HDACs, or TET enzymes (17), may help explain the persistence of dysregulated inflammatory and oxidative responses in ARDS.

Epigenetic regulation of oxidative stress in ARDS

Epigenetic regulation has emerged as an important layer shaping oxidative stress responses in ARDS. Accordingly, this chapter is dedicated to three major epigenetic modalities: DNA methylation, histone modifications, and non-coding RNAs. It focuses on delineating how these mechanisms collectively modulate gene expression to influence redox homeostasis. Importantly, accumulating evidence indicates that epigenetic regulation of oxidative stress exhibits pronounced cell-type specificity and may exert distinct effects across different stages of disease progression, particularly in alveolar macrophages and epithelial cells, where redox-sensitive epigenetic programs can differentially shape inflammatory and repair responses (Figure 1).

Figure 1.

Epigenetic regulation of oxidative stress in ALI/ARDS. This schematic illustrates how DNA methylation, histone modifications, and non-coding RNAs form an interconnected epigenetic regulatory network that modulates oxidative stress-related signaling pathways in the injured lung during ALI/ARDS. DNA methylation-mediated transcriptional repression of antioxidant and cytoprotective genes, including FOXO1, SP-C, NRF2, and cyclin D1, contributes to impaired antioxidant defenses. Histone modifications, such as EZH2-mediated H3K27me3 and SETD7-associated H3K4me1, regulate the expression of redox-related genes through pathways involving PGC-1α, NF-κB, and FOXO1-ROCK1 signaling, thereby influencing ROS production and inflammatory responses. Non-coding RNAs, including microRNAs, long non-coding RNAs, and circular RNAs, further fine-tune oxidative stress responses by targeting key regulators such as SIRT1, BRD4, ACE2, and HIF-1α, ultimately affecting antioxidant enzyme activity and mitochondrial function. Dysregulation of these epigenetic mechanisms promotes excessive ROS accumulation and exacerbates pulmonary injury in ALI/ARDS. ACE2, angiotensin-converting enzyme 2; ALI, acute lung injury; ARDS, acute respiratory distress syndrome; BRD4, bromodomain-containing protein 4; EG, endothelial glycocalyx; EZH2, enhancer of zeste homolog 2; FOXO1, forkhead box O1; H3K27me3, histone H3 lysine 27 trimethylation; H3K4me1, histone H3 lysine 4 monomethylation; HIF-1α, hypoxia-inducible factor-1α; LPS, lipopolysaccharide; NF-κB, nuclear factor-κB; NRF2, nuclear factor erythroid 2-related factor 2; PGC-1α, peroxisome proliferator-activated receptor gamma coactivator-1α; ROCK1, Rho-associated protein kinase 1; ROS, reactive oxygen species; SETD7, SET domain-containing protein 7; SIRT1, sirtuin 1; SOD, superoxide dismutase; SP-C, surfactant protein C.

DNA methylation and oxidative stress in ARDS

During ARDS progression, changes in DNA methylation can modulate oxidative stress by reshaping the expression of key redox-related genes. In ALI/ARDS, this influence is most commonly discussed in two contexts: transcriptional silencing of antioxidant genes and delayed resolution of neutrophilic inflammation through impaired apoptosis. Emerging evidence further suggests that the functional consequences of these methylation changes may vary across different lung cell populations and stages of disease progression, indicating that DNA methylation-mediated redox regulation in ARDS is context dependent.

Transcriptional silencing of antioxidant genes

In ALI/ARDS, aberrant upregulation or persistent activation of DNA methyltransferase 1 (DNMT1) has been described as an upstream epigenetic event linked to the silencing of antioxidant programs. Mechanistically, DNMT1 can cooperate with Runt-related transcription factor 1 (RUNX1), promoting hypermethylation of the forkhead box O1 (FOXO1) promoter and repressing FOXO1 transcription. Lower FOXO1 levels weaken the transcriptional induction of downstream antioxidant targets, including manganese superoxide dismutase (SOD), which in turn diminishes antioxidant defense in lung tissue and may aggravate oxidative injury (18). Notably, the DNMT1-FOXO1 regulatory axis has been reported mainly in immune cells, particularly macrophages and neutrophils (19). In the early inflammatory phase of ARDS, when these cells constitute a major source of ROS, repression of FOXO1-dependent antioxidant programs may further exacerbate redox imbalance (20).

DNA methylation has also been implicated in repressing surfactant protein C (SP-C), a gene important for alveolar integrity and surfactant homeostasis. DNMT1 has been reported to associate with the SP-C promoter, increase promoter methylation, and suppress SP-C transcription. Reduced SP-C expression may disturb surfactant homeostasis and weaken the protective functions of the surfactant system, potentially creating conditions that favor ALI/ARDS initiation and progression (21). In contrast, methylation changes affecting SP-C have been reported mainly in alveolar epithelial cells, where reduced SP-C expression may impair epithelial barrier integrity and increase vulnerability to oxidative and mechanical stress during lung injury (22,23).

In mouse lung tissue, hypermethylation at specific CpG sites within the Nrf2 promoter has been associated with reduced Nrf2 expression. Correspondingly, expression of the downstream target glutathione peroxidase 4 (GPX4) decreases, which may contribute to ROS accumulation (24). These alterations have also been reported mainly in epithelial compartments, suggesting that epigenetic repression of the Nrf2-mediated antioxidant pathway may weaken intracellular antioxidant defense during both the acute inflammatory phase and subsequent stages of epithelial repair (25).

Overall, current evidence suggests that DNA methylation may influence different antioxidant pathways in distinct lung cell populations: mechanisms involving immune cells appear to amplify early oxidative bursts (26), whereas methylation changes in epithelial cells may contribute to more persistent redox imbalance during lung injury and repair (27).

Apoptosis resistance in neutrophils

DNA methylation may contribute to impaired neutrophil apoptosis by silencing genes involved in programmed cell death, such as cell cycle regulatory protein 1. As a consequence, activated neutrophils can be retained in the lung and continue to release injurious mediators, including ROS and neutrophil extracellular traps (NETs) (28). This persistence may intensify oxidative injury and reinforce inflammatory responses, creating a self-perpetuating cycle that sustains tissue damage. Such mechanisms are particularly relevant during the acute inflammatory phase of ARDS, when delayed neutrophil clearance can prolong oxidative and inflammatory injury within the alveolar microenvironment (29).

In summary, DNA methylation regulates oxidative stress in ALI/ARDS through the silencing of key protective genes, including FOXO1 and SP-C, as well as through effects on neutrophil senescence and programmed cell death. Through these pathways, antioxidant capacity may decline and inflammatory activity may be prolonged. Importantly, accumulating evidence suggests that these methylation-driven effects are not uniform across lung tissues but instead reflect differences between immune cells, epithelial cells, and potentially stromal populations.

In ALI/ARDS, aberrant DNA methylation may act as a relatively stable, upstream factor that contributes to redox dysregulation. Understanding these cell-type specific patterns may therefore be important for developing epigenetic-targeted interventions aimed at restoring oxidative balance during different stages of ARDS progression.

Histone modifications and oxidative stress in ARDS

Histone modifications constitute a core epigenetic mechanism involving covalent chemical alterations, primarily methylation and acetylation, on amino acid residues of histones. These marks modulate chromatin structure and transcription in a site-specific and context-dependent manner (30), with outcomes shaped by both the modification type and its extent. For example, histone acetylation is typically associated with chromatin relaxation and transcriptional activation (31), whereas histone methylation may be activating or repressive depending on the residue and methylation state.

Under physiological conditions, these modifications help maintain cellular homeostasis by fine-tuning gene expression. In pathological settings, disruption of this balance can distort transcriptional programs and contribute to ALI/ARDS initiation and progression. Similar to DNA methylation, the functional outcomes of histone modifications may differ among immune cells, epithelial cells, and stromal cells across different stages of lung injury (32).

Histone methylation and oxidative stress in ARDS

Histone methylation is controlled by histone methyltransferases (HMTs) and lysine demethylases (KDMs), which together maintain chromatin homeostasis. In ALI/ARDS, disruption of this balance has been linked to oxidative stress dysregulation and may exhibit cell-type specific regulatory patterns across different lung cell populations. Notably, enhancer of zeste homolog 2 (EZH2) catalyzes histone H3 lysine 27 trimethylation (H3K27me3). In ALI/ARDS, enhancer of zeste homolog 2 (EZH2) has been reported to suppress superoxide dismutase 1 (SOD1) transcription by increasing H3K27me3 enrichment at the SOD1 promoter. This repression can reduce ROS-scavenging capacity, potentially worsening pulmonary oxidative injury and contributing to downstream vascular remodeling, including pulmonary hypertension (33), a mechanism that may be particularly relevant in inflammatory or vascular-associated cells during the early inflammatory phase of lung injury (32).

On the other hand, SET domain containing 7 (SETD7), which catalyzes H3 lysine 4 monomethylation (H3K4me1) in human lung epithelial cells, has been shown to enhance NF-κB-dependent inflammatory signaling and may thereby promote oxidative injury (34). Evidence also suggests that SETD7 can downregulate peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α), a key regulator of mitochondrial biogenesis, in a methyltransferase-dependent manner. Reduced PGC-1α can decrease the transcription and expression of mitochondrial antioxidant enzymes, including SOD2 and catalase. As a result, mitochondrial ROS clearance may be impaired, with consequences that include compromised mitochondrial biogenesis and diminished antioxidant capacity (35). These alterations have been reported mainly in lung epithelial cells and may persist during both injury progression and epithelial repair stages.

Taken together, these observations highlight the context-dependent and multifaceted roles of histone methylation in oxidative stress regulation, suggesting that its regulatory effects may vary across distinct lung cell types and different stages of ARDS progression.

Histone acetylation and oxidative stress in ARDS

Histone acetylation is coordinated by histone acetyltransferases (HATs) and HDACs and serves as a major mechanism controlling chromatin accessibility and transcriptional activation (36). In ALI/ARDS, dysregulated acetylation has been implicated in oxidative stress, in part by shaping transcriptional programs that favor pro-inflammatory and pro-oxidant states. Increasing evidence indicates that the consequences of altered histone acetylation may differ among lung cell populations, including endothelial cells, epithelial cells, and infiltrating immune cells, and these effects may also vary across different stages of lung injury.

The dysregulated activity of class I/II HDACs, including prominent examples such as HDAC3, HDAC4, and HDAC5, has been implicated in promoting oxidative stress during ALI/ARDS. Beyond altering histone acetylation at gene promoters, these enzymes also deacetylate non-histone substrates and thereby influence multiple signaling pathways (37). Inflammatory stimuli such as lipopolysaccharide (LPS) have been reported to activate HDAC3/4/5 and to promote degradation of the endothelial glycocalyx. The glycocalyx, a key protective layer on the vascular endothelium, also provides an anchoring scaffold for extracellular superoxide dismutase 3 (SOD3). When the glycocalyx is disrupted, loss of SOD3 can follow, reducing local vascular ROS-scavenging capacity and potentially aggravating ALI/ARDS progression (38). These endothelial alterations may be particularly relevant during the early inflammatory phase of ARDS, when vascular barrier disruption and oxidative stress rapidly intensify (39).

HDAC3 has also been reported to promote oxidative stress through the FOXO1-ROCK1 signaling axis. Mechanistically, HDAC3 can suppress SOD activity. At the same time, it may enhance NADPH oxidase (NOX) activity, favoring ROS production. In conditional HDAC3 knockout mice, lung SOD activity is reported to recover, with concomitant reductions in NOX activity, thiobarbituric acid-reactive substances (TBARS; a lipid peroxidation marker), and overall ROS accumulation. Together, these results position HDAC3 as a bidirectional regulator of redox homeostasis, acting on both ROS generation and antioxidant defenses (37). Notably, these findings have been reported mainly in inflammatory and endothelial cell contexts, suggesting that HDAC3-dependent redox imbalance may be especially important during the early immune-dominant stage of lung injury (40).

HDAC6 has been reported to increase nitric oxide (NO) production in macrophages by activating the STAT1-interferon regulatory factor 1 (IRF1)-inducible nitric oxide synthase (iNOS) axis. Excess NO can react with ROS to form peroxynitrite, which may exacerbate lipid peroxidation and cellular injury. In parallel, HDAC5 has been reported to enhance NF-κB signaling by suppressing protein phosphatase 2A (PP2A). This shift may promote ROS release and NET formation in neutrophils. In turn, these events may amplify oxidative stress and aggravate lung tissue injury (41). Such mechanisms are likely most relevant during the early phase of lung injury, when neutrophil recruitment and activation are most pronounced (42).

Overall, histone modifications add a dynamic and context-dependent layer to oxidative stress regulation in ALI/ARDS. Aberrant HDAC activity and repressive histone methylation are consistently identified as key alterations across studies, pointing to histone-modifying enzymes as potential therapeutic targets. This prospect, however, is tempered by recognized challenges in achieving selectivity, optimal timing, and cell-type specificity. However, effective targeting of these pathways will likely require consideration of both cell-type specificity and the timing of intervention during different stages of disease progression.

Non-coding RNAs (ncRNAs) and oxidative stress in ARDS

ncRNAs, which do not encode proteins, have emerged as key components of epigenetic regulatory networks. By recruiting or sequestering chromatin-modifying complexes and by modulating mRNA stability and translation (43), ncRNAs influence gene expression at both transcriptional and post-transcriptional levels. Recent studies suggest that ncRNA-mediated regulation in ARDS is often dependent on the cellular context of the injured lung, particularly within epithelial, endothelial, and immune cell populations (44). In addition, the biological effects of ncRNAs may not be uniform throughout disease progression, as different regulatory patterns have been reported between the early inflammatory stage and later phases associated with tissue repair or fibrosis (45).

MicroRNA (miRNA) and oxidative stress in ARDS

miRNAs enable rapid post-transcriptional control by promoting target mRNA degradation or inhibiting translation. In ALI/ARDS models, miR-34a has been reported to be upregulated. miR-34a can directly target the mRNA of the antioxidant transcription factor FOXO3, reducing FOXO3 protein expression. Reduced FOXO3 activity impairs the induction of key antioxidant genes, such as those encoding SOD and glutathione peroxidases, resulting in diminished ROS clearance within lung epithelial cells. As a result, oxidative stress may worsen, accompanied by increased epithelial apoptosis and vascular injury (46). Notably, this regulatory axis has been primarily described in alveolar epithelial cells during the early inflammatory phase of ALI/ARDS, when epithelial oxidative damage and barrier disruption are prominent pathological features. miR-34a has also been reported to suppress the deacetylase SIRT1, which may reduce SIRT1-dependent deacetylation and activation of Nrf2. This shift is associated with lower SOD activity and reduced expression of heme oxygenase-1 (47). Such effects may further amplify oxidative injury during the acute stage of lung injury, when antioxidant defenses are critically required to counteract excessive ROS generation.

In addition, miR-1246 is reported to be elevated in LPS-induced ALI/ARDS models and may modulate oxidative stress by targeting angiotensin-converting enzyme 2 (ACE2). ACE2 is generally considered protective within the renin-angiotensin system and is linked to reduced ROS generation and preserved endothelial integrity. By suppressing ACE2, miR-1246 may weaken this protective axis, leading to increased intracellular ROS and enhanced endothelial apoptosis, thereby aggravating oxidative stress-related lung injury (48). This mechanism has been mainly observed in pulmonary endothelial cells, highlighting that miRNA-mediated oxidative regulation in ARDS can differ between epithelial and endothelial compartments of the lung.

Beyond epithelial and endothelial cells, emerging evidence suggests that certain miRNAs may also regulate oxidative stress responses in immune cells such as macrophages and neutrophils, particularly during the early inflammatory stage of ARDS, when immune-cell derived ROS significantly contribute to tissue injury.

Long non-coding RNAs (lncRNAs) and oxidative stress in ARDS

lncRNAs are transcripts longer than 200 nucleotides that regulate gene expression through diverse mechanisms. In ALI/ARDS, lncRNA Mir155hg has been described as a competing endogenous RNA (ceRNA) that sponges miR-450b-5p, thereby relieving miR-450b-5p-mediated repression of hypoxia-inducible factor-1α (HIF-1α). The resulting increase in HIF-1α can activate downstream transcriptional programs linked to oxidative stress and may amplify oxidative damage (49). This regulatory interaction has been reported mainly in inflammatory cells, particularly macrophages, suggesting that lncRNA-mediated modulation of oxidative pathways may contribute to immune-driven oxidative injury during the acute inflammatory phase of ARDS.

lncRNA Gadd7 has also been reported to bind lysine-specific demethylase 1 (LSD1) and recruit it to the promoter of Mitofusin 1 (Mfn1). LSD1 then demethylates repressive H3K9me2/me3 marks in this region, relieving repression and increasing Mfn1 transcription. Increased Mfn1 expression has been linked to excessive mitophagy, disrupted mitochondrial homeostasis, and heightened ROS production (50). Such mitochondrial regulatory effects may be particularly relevant in lung epithelial cells and fibroblasts, where mitochondrial dysfunction is increasingly recognized as a contributor to sustained oxidative stress and tissue remodeling in later stages of lung injury (51).

In addition, some lncRNAs have been implicated in fibroblast activation and extracellular matrix remodeling, processes that become more prominent during the repair or fibrotic phase of ARDS (52). Through modulation of oxidative stress and mitochondrial signaling, these lncRNAs may indirectly influence fibroproliferative responses and long-term lung remodeling (53).

Circular RNA (circRNA) and oxidative stress in ARDS

circRNAs are a class of non-coding RNAs with a covalently closed structure that confers resistance to degradation and often provides abundant miRNA-binding sites. In ALI/ARDS, circANKRD11 and circOSBPL2 have been reported to sponge miR-145-5p and miR-193a-5p, respectively. This derepression has been linked to increased expression of the pro-oxidant factor BRD4. Higher BRD4 activity may promote ROS generation and lipid peroxidation, thereby aggravating oxidative injury (54). These regulatory networks are thought to operate primarily in lung epithelial and endothelial cells during the acute phase of injury, when oxidative stress and inflammatory signaling are strongly activated.

In LPS-induced ALI, circPhkb expression has been reported to increase. By activating the TLR4/MyD88/NF-κB pathway, circPhkb may indirectly exacerbate oxidative stress-related alveolar macrophage apoptosis and promote pro-inflammatory cytokine release. The resulting inflammation may further increase ROS production, creating a feed-forward loop between inflammation and oxidative stress that worsens lung injury (55). This finding suggests that certain circRNAs may function predominantly in immune cells, particularly alveolar macrophages, where they amplify inflammation-driven oxidative damage during early disease stages.

Overall, ncRNAs often function as modulators that fine-tune oxidative stress-related pathways in ALI/ARDS. Although many candidates have been reported, only a subset has been validated consistently across models or cohorts, supporting a current view of ncRNAs primarily as regulatory mediators and potential biomarker leads.

Multilayered epigenetic regulatory network

Accumulating evidence indicates that oxidative stress in ALI /ARDS is not driven by a single signaling pathway but rather arises from multilayered regulatory networks (56). Among these, epigenetic mechanisms such as DNA methylation, histone modifications, and non-coding RNAs have emerged as key modulators of redox homeostasis (57). Importantly, these regulatory processes rarely act independently. Instead, they frequently interact with each other and form coordinated regulatory circuits that shape the transcriptional landscape of oxidative stress-related genes. Recent studies suggest that such interactions can be conceptualized as several representative epigenetic-oxidative stress regulatory modules, which contribute to persistent ROS production, mitochondrial dysfunction, and inflammatory amplification during the development of ALI/ARDS. Based on current evidence, these regulatory networks can be broadly categorized into three major modules (58).

Interaction between DNA methylation and histone modifications in the regulation of oxidative stress

The interaction between DNA methylation and histone modifications represents an important layer of epigenetic regulation that contributes to oxidative stress in ALI/ARDS. Rather than acting independently, these two regulatory systems often cooperate to influence chromatin structure and transcriptional activity under inflammatory and stress conditions. In particular, DNA methylation can facilitate the recruitment of histone-modifying enzymes to specific gene promoters. For example, DNA methyltransferases have been reported to interact with HDACs, leading to histone deacetylation and chromatin condensation (59). This coordinated epigenetic repression may limit the transcription of genes involved in antioxidant defense and redox homeostasis. As a result, the cellular capacity to neutralize ROS may be reduced, thereby contributing to oxidative injury during lung inflammation. Consistent with this concept, experimental studies have shown that HDACs are frequently upregulated in lung injury models and play an important role in the dysregulation of redox balance (59). Increased HDAC activity can suppress antioxidant signaling pathways and enhance inflammatory responses, ultimately promoting ROS accumulation in lung tissues. In contrast, pharmacological inhibition of specific HDAC isoforms has been shown to restore antioxidant responses, particularly through activation of the Nrf2/HO-1 signaling pathway, and alleviate lung injury in experimental models (60). In this context, DNA methylation may function together with histone deacetylation to establish a transcriptionally repressive chromatin environment that limits the expression of protective genes. Such coordinated epigenetic regulation may represent an important mechanism underlying persistent oxidative stress during the progression of ALI/ARDS. More recently, emerging evidence suggests that additional histone marks linked to cellular metabolism may further interact with this regulatory framework (61). For instance, histone lactylation has been associated with metabolic alterations and endothelial ferroptosis in LPS-induced ALI (62), highlighting a potential connection between metabolic reprogramming, epigenetic remodeling, and ROS generation.

Interaction between DNA methylation and non-coding RNAs in oxidative stress regulation

Another layer of epigenetic regulation involves the interaction between DNA methylation and ncRNAs (63). DNA methylation can regulate the transcription of these ncRNAs and thereby influence pathways related to oxidative stress and lung injury. Among the regulatory targets identified in ALI/ARDS, the Nrf2-Keap1 antioxidant pathway appears to be a central node linking DNA methylation-dependent ncRNA regulation to redox homeostasis (64). Alterations in DNA methylation may affect the expression of ncRNAs that regulate Nrf2 activity or its upstream inhibitor Keap1, ultimately influencing the transcription of antioxidant genes such as HO-1 and other cytoprotective factors. Disruption of this regulatory axis may weaken antioxidant defenses and promote ROS accumulation in injured lung tissues. In addition to Nrf2 signaling, several ncRNAs influenced by epigenetic regulation have been reported to target key modulators of oxidative stress and inflammation, including SIRT1 and HMGB1 (65). SIRT1 plays an important role in maintaining mitochondrial function and limiting oxidative damage, whereas HMGB1 is closely associated with inflammatory signaling and ROS amplification through activation of pathways such as NF-κB. Dysregulation of ncRNAs targeting these molecules may therefore contribute to the propagation of oxidative and inflammatory responses during the progression of ALI/ARDS. Recent studies have further highlighted the involvement of RNA epigenetic modifications, particularly N6-methyladenosine (m6A), in this regulatory network. Enzymes responsible for m6A modification, such as METTL3 and FTO, can influence the stability and translation of transcripts related to oxidative stress (66), mitochondrial function, and ferroptosis. Altered m6A regulation has been associated with enhanced ROS production and aggravated lung injury in experimental models of sepsis-induced ALI (67).

Taken together, these findings suggest that DNA methylation–dependent regulation of ncRNAs may form an important epigenetic module that connects antioxidant signaling, mitochondrial homeostasis, and inflammatory pathways, thereby contributing to oxidative stress amplification in ALI/ARDS.

Interaction between histone modifications and non-coding RNAs in oxidative stress regulation

In addition to DNA methylation, histone modifications contribute to oxidative stress regulation by controlling the transcription of specific non-coding RNAs. Among the most relevant regulators, HDACs, particularly SIRT1 and several HDAC family members, play a central role in maintaining redox balance. Under conditions of severe oxidative stress in ALI/ARDS, reduced SIRT1 activity can lead to increased histone acetylation at inflammatory and ncRNA-related loci, thereby promoting the expression of miRNAs such as miR-34a and miR-155 that enhance NF-κB signaling and ROS production (68). Histone methylation regulators also participate in this regulatory network. The histone methyltransferase EZH2 has been reported to modulate the transcription of lncRNAs involved in inflammatory and oxidative responses (68). Among these, lncRNA MALAT1 has received particular attention because it can influence endothelial dysfunction, mitochondrial signaling, and inflammatory activation during lung injury (69). Through these interactions, histone methylation and ncRNA expression jointly shape the activity of major oxidative stress pathways, including the Nrf2-associated antioxidant system. Importantly, oxidative stress itself can further remodel chromatin structure. Excessive ROS generation may alter the activity of histone-modifying enzymes, which subsequently changes the transcriptional profile of key ncRNAs involved in inflammation and cell injury. This creates a positive feedback loop in which oxidative stress promotes epigenetic alterations that further amplify inflammatory and oxidative signaling in lung tissues.

Recent studies also suggest that RNA epigenetic regulation intersects with histone-mediated chromatin control. The m6A methyltransferase METTL3, for example, can regulate the stability and translation of transcripts associated with inflammasome activation and oxidative stress in experimental models of sepsis-induced lung injury (66). These findings indicate that coordinated regulation among histone modifications, ncRNAs, and RNA methylation constitutes an important mechanism driving oxidative stress amplification in ALI/ARDS.

Epigenetic modifier-targeted therapeutic strategies and translational applications

The pathogenesis of ALI/ARDS is multifactorial. Current clinical management remains primarily supportive, focusing on lung-protective ventilation and treating underlying conditions, while specific pharmacologic interventions that directly target oxidative stress are still limited. As epigenetic research has advanced, DNA methylation, histone modifications, and non-coding RNAs have been increasingly implicated in regulating redox-related transcriptional programs. Therapeutic strategies that target epigenetic enzymes and RNA regulators derive from a clear mechanistic rationale, despite persistent barriers to clinical translation (Figure 2).

Figure 2.

Epigenetic and RNA-based strategies targeting oxidative stress in ALI/ARDS. This schematic summarizes representative epigenetic and RNA-based approaches that modulate oxidative stress-related pathways in ALI/ARDS. Pharmacological inhibition of DNMTs and histone-modifying enzymes alters redox-related transcriptional programs, whereas non-coding RNAs regulate key signaling molecules involved in oxidative stress and inflammation, including NRF2, SIRT1, CD2AP, and NF-κB. Through these converging regulatory mechanisms, epigenetic and RNA-targeted interventions are proposed to limit excessive ROS accumulation and attenuate inflammatory lung injury. ALI, acute lung injury; ARDS, acute respiratory distress syndrome; ATG5, autophagy-related gene 5; CD2AP, CD2-associated protein; DNMT, DNA methyltransferase; EZH2, enhancer of zeste homolog 2; GSH, glutathione; GSSG, glutathione disulfide; HA, hyaluronic acid; MDA, malondialdehyde; NF-κB, nuclear factor-κB; NOX, NADPH oxidase; NRF2, nuclear factor erythroid 2-related factor 2; ROS, reactive oxygen species; S-GAGs, sulfated glycosaminoglycans; SIRT1, sirtuin 1.

Intervention strategies targeting DNA methylation

Because DNA methylation is reversible, DNMT inhibition has been explored as a potential therapeutic approach. Decitabine is a widely studied DNMT inhibitor. Preclinical studies suggest that decitabine can attenuate lung injury in models of sepsis and ventilator-associated stress. In LPS-based models, pretreatment with decitabine or azacitidine has been reported to reduce serum myeloperoxidase (MPO) activity and malondialdehyde (MDA) levels. These changes are consistent with reduced oxidative burden and may help limit lipid peroxidation-related injury in pulmonary endothelial and alveolar epithelial compartments, thereby preserving lung structure and function. These agents have also been associated with lower circulating sulfated glycosaminoglycans and hyaluronic acid, suggesting attenuation of LPS-induced pulmonary endothelial glycocalyx shedding (70).

Beyond nucleoside analogs, several natural compounds have been reported to exhibit DNMT-inhibitory activity. Whether these observations hold true for ALI/ARDS, particularly under clinically relevant conditions of dosing and timing, remains unclear. While DNMT-targeted approaches demonstrate antioxidant effects in preclinical models, their clinical translation remains at an early stage, with key questions regarding safety, specificity, and therapeutic windows yet to be resolved.

Interventional strategies targeting histone modifications

Histone acetylation-deacetylation balance is closely tied to transcriptional programs that shape oxidative stress and inflammation in ALI/ARDS, making histone-modifying enzymes attractive, yet challenging, therapeutic targets. Preclinical studies have explored HDAC inhibition as one approach to rebalance these programs. For example, the HDAC3-selective inhibitor BRD3308 binds HDAC3 and suppresses its enzymatic activity, which is accompanied by increased H3K27 acetylation and activation of the autophagy-related gene 5 (Atg5) promoter. Upregulation of Atg5 may enhance autophagy-mediated clearance of excess ROS, dampen NLRP3-associated macrophage pyroptosis, and alleviate inflammatory injury and structural damage in experimental ALI/ARDS (71). In parallel, HDAC6 activity has been linked to heightened oxidative stress in macrophages, in part through increased NADPH oxidase signaling. Consistent with this mechanism, the HDAC6-selective inhibitor Tubastatin A has been reported to reduce NADPH oxidase activity and lower LPS-induced ROS production in macrophages (72).

Alterations in histone methylation can also shift the balance between antioxidant defenses and pro-inflammatory signaling. 3-Deazaneplanocin A (DZNep) promotes proteasomal degradation of the histone methyltransferase EZH2 and has been associated with macrophage polarization toward an M2-like phenotype, reduced ROS derived from M1 macrophages, and improved antioxidant capacity in lung tissue. Inhibiting other repressive methylation marks, such as those mediated by G9a/GLP, also exerts antioxidant effects. In experimental lung tissue, specific inhibitors like BIX01294 and UNC0642 reduce H3K9me2 levels, leading to increased expression of SOD2 at both the mRNA and protein levels (73).

Overall, pharmacological modulation of histone acetylation or methylation can, in preclinical settings, restore antioxidant gene expression, dampen inflammatory amplification, and improve lung injury phenotypes. Translational progress will therefore hinge on achieving greater target selectivity and defining effects that are both cell-type-specific and temporally restricted, considering the pleiotropic functions of HDACs and histone methyltransferases in immunity and tissue homeostasis.

Intervention strategies targeting noncoding RNAs

Therapeutic strategies targeting non-coding RNAs are broadly classified into three main categories: modulating miRNA activity with mimics or inhibitors; interfering with lncRNA function through knockdown or disruption of RNA-protein interactions; and employing circRNA-directed approaches, often by leveraging their role as competing endogenous RNAs.

miRNA-based strategies typically aim to suppress pro-oxidant miRNAs or restore antioxidant miRNAs. For instance, inhibition of miR-155 or miR-34a has been reported to relieve repression of SIRT1 and Nrf2, thereby strengthening antioxidant defenses (74,75). Conversely, increasing miR-140-5p levels has been linked to reduced NF-κB activation and attenuation of ROS-associated tissue injury (75). Proof-of-concept studies in mouse models support feasibility for miRNA targeting in ALI settings. One representative example is a miR-351-5p-specific antagomir, which counteracts LPS-induced miR-351-5p upregulation in lung tissue, releases suppression of the target gene AC6, restores cAMP production, and activates the downstream cAMP/PKA-AMPK axis. This signaling cascade has been associated with enhanced NRF2 protein expression and transcriptional activity, providing a mechanistic basis for more precise control of oxidative stress in LPS-induced ALI (76).

lncRNAs may regulate redox balance by scaffolding epigenetic complexes, acting as competing endogenous RNAs, or directly engaging chromatin modifiers. In preclinical models, silencing lncRNA MALAT1 has been associated with lower MDA levels and an increased GSH/GSSG ratio, consistent with reduced oxidative burden (77). Similarly, knockdown of lncRNA FOXD3-AS1 has been reported to block aberrant activation of the LSD1-MFN1 axis, improve mitochondrial function, and attenuate oxidative injury, suggesting that lncRNA-targeted interventions may converge on mitochondrial quality control and antioxidant capacity.

circRNAs can also modulate antioxidant pathways, most commonly by sequestering miRNAs and thereby derepressing redox-protective targets. Depending on the context, circRNAs may amplify oxidative injury or exert protective effects. In experimental ALI, circVMA21 has been shown to bind miR-497-5p, reduce its availability, and relieve repression of the target gene CD2AP. Upregulated CD2AP is then associated with suppression of NF-κB-driven inflammation alongside activation of Nrf2-dependent antioxidant programs, producing coordinated anti-inflammatory and antioxidative effects and alleviating lung inflammation, oxidative stress, and apoptosis.

Precision strategies for epigenetic therapy in ARDS

Lung-targeted delivery systems, combined with cell-type-specific promoters, represent a promising strategy to improve the specificity of epigenetic therapies in ARDS, where lung-specific inflammation and oxidative stress are central to disease progression. Inhalable nanoparticles, capable of encapsulating epigenetic drugs like DNMT or HDAC inhibitors, can directly target the lungs, maximizing local drug concentration while minimizing systemic exposure (78). Lipid-based nanoparticles or liposomes engineered to target alveolar epithelial cells and pulmonary endothelial cells via surface modifications enhance lung delivery (79). Beyond simply targeting the lungs, the combination with cell-type-specific promoters enhances therapeutic precision. For instance, SP-C, selectively expressed in alveolar type II epithelial cells (80), or CD68, specific to macrophages (81), can drive epigenetic modulators directly to relevant lung cells. Thus, the combination of targeted delivery and cell-specific activation maximizes therapeutic efficacy while preventing unnecessary off-target effects.

Timing of intervention is crucial because ARDS progresses through distinct stages with specific pathophysiological characteristics (82). During the early inflammatory phase, characterized by immune cell infiltration and ROS production, DNMT inhibition can mitigate inflammation and limit oxidative damage (83). Targeted delivery of DNMT inhibitors at this stage may prevent widespread tissue injury and attenuate the inflammatory response, which is essential to halt ARDS progression. However, as ARDS transitions into the repair phase, excessive DNMT inhibition can impair tissue regeneration by suppressing genes critical for repair processes (84). For instance, inhibition of DNMTs may hinder the activation of regenerative genes, essential for resolving inflammation and preventing fibrosis, which suggests the need for precise timing in therapeutic application. Similarly, HDAC inhibitors may show stage-dependent effects. In the early phase, HDAC inhibition may help reduce inflammatory markers and oxidative stress, but in the later stages, it may disrupt epithelial repair and contribute to fibrosis (85). The key to success lies in adjusting the timing to balance inflammation reduction and preserve repair capacity. Furthermore, m6A modifications, which regulate the stability and translation of RNA, may also have differential effects at various stages of ARDS (86). During the acute inflammatory phase, METTL3 and other m6A regulators may exacerbate inflammation by promoting pro-inflammatory mRNA stabilization (87). However, in the resolution phase, modulating m6A could be crucial to support cell survival and promote tissue repair, suggesting that targeting m6A pathways at the appropriate stage may enhance the resolution of inflammation while avoiding unnecessary immune suppression.

In conclusion, the combination of lung-targeted delivery systems and cell-specific promoters provides a precise and localized approach to epigenetic therapy for ARDS, while stage-specific regulation ensures that interventions are timely and effective. By optimizing the timing of these interventions, we can maximize therapeutic benefits and minimize adverse effects, offering a powerful strategy for treating oxidative stress and inflammation in the lungs.

Future perspectives

Epigenetic-targeted interventions have shown antioxidant and tissue-protective signals in preclinical ALI/ARDS models. Given the biological heterogeneity of ARDS, future therapeutic strategies may also need to consider subtype-oriented epigenetic interventions. Advances in single-cell multi-omics technologies are likely to accelerate this process. Integrating single-cell transcriptomics with epigenomic profiling, including chromatin accessibility and DNA methylation analyses, can help delineate the epigenetic reprogramming landscape across distinct lung cell populations during ARDS. Such approaches may reveal cell-specific regulatory circuits in alveolar epithelial cells, endothelial cells, macrophages, and neutrophils, thereby improving mechanistic understanding and helping to identify actionable therapeutic targets (88). With these advances, epigenetic modulation may become a testable, biomarker-guided adjunct for acute intervention, but rigorous clinical validation will be essential.

Conclusions

Oxidative stress is a central pathogenic feature of ALI and ARDS, contributing to inflammatory amplification and tissue damage across diverse clinical settings. Emerging evidence indicates that epigenetic mechanisms, including DNA methylation, histone modifications, and non-coding RNAs, play an important role in regulating redox-related gene expression and cellular stress responses in the injured lung. Dysregulation of these interconnected regulatory layers may sustain oxidative imbalance and exacerbate lung injury. A clearer understanding of epigenetic–redox interactions may help refine mechanistic insights into ARDS heterogeneity and inform future research aimed at identifying rational, targeted strategies for modulating oxidative stress in this challenging syndrome.

Supplementary

The article’s supplementary files as

Ethical Statement: The authors are accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.