Protein Acetylation in Age-Related Macular Degeneration: Mechanisms, Roles, and Therapeutic Perspectives

Abstract

Age-related macular degeneration (AMD) is a top cause of severe vision loss and blindness in older adults globally. This multifactorial disease arises from genetic, environmental, and age-related factors. Protein acetylation modification plays a key role in AMD progression through both epigenetic and non-epigenetic pathways. This review comprehensively discusses the multidimensional impacts of protein acetylation in AMD, particularly its dynamic regulation of angiogenesis, oxidative stress, inflammatory responses, and cellular senescence. Recent evidence shows that histone acetylation modification inhibits choroidal neovascularization (CNV) formation by regulating vascular endothelial growth factor (VEGF) and hypoxia-inducible factor (HIF-1α) expression, while upregulating the complement inhibitor clusterin to maintain Bruch's membrane integrity. Additionally, the NAD⁺-dependent deacetylase SIRT1 modulates the deacetylation of transcription factors such as PGC-1α, NF-κB, and FOXO3, enhancing mitochondrial antioxidant function and suppressing inflammatory cascades to disrupt the vicious cycle of oxidative stress and chronic inflammation. In terms of cellular senescence, histone hypoacetylation and hyperacetylation of non-histone proteins (e.g., p53, E2F1) jointly cause retinal pigment epithelial (RPE) cell-cycle arrest and autophagy imbalance, accelerating AMD progression. Genetic evidence further reveals subtype-specific expression changes and epigenetic regulatory mechanisms of histone deacetylases (HDACs), such as HDAC11 and HDAC1/3, in AMD. This article explores the clinical significance of these findings and proposes a novel combined therapeutic strategy. It involves synergistically targeting acetylation homeostasis with HDAC inhibitors (e.g., TSA, AN7) and SIRT1 activators while inhibiting abnormal angiogenesis, repairing metabolic disorders, and restoring autophagy function. This dual-targeting approach may overcome current anti-VEGF therapy limitations and open new precision management avenues for AMD.

Age-related macular degeneration (AMD) is a leading cause of severe vision impairment among the elderly in developed countries, with a projected global affected population of 288 million by 2040.^1,2 In its early stages, AMD may manifest as small drusen (diameter < 63 µm) or a few medium-sized drusen (diameter 63–124 µm) on the retina, with minimal damage to the retinal pigment epithelium (RPE).¹ In its intermediate stage, AMD is characterized by one or both eyes exhibiting extensive medium-sized drusen (diameter 63–124 µm) or one or more large drusen (diameter ≥ 125 µm) along with varying degrees of pigment epithelial damage.¹ According to the Age-Related Eye Disease Study (AREDS) group, the probability of this stage of AMD progressing to advanced AMD within 10 years is approximately 14%.³ Advanced AMD can be further classified into neovascular AMD and geographic atrophy (GA). The core pathogenesis of GA involves severe damage to the Bruch’s membrane, prominent inflammatory responses, and poor choroidal vascular perfusion, leading to the loss of function in the RPE layer. This results in widespread atrophy and loss of RPE and photoreceptor cells.¹ In neovascular AMD, various factors drive choroidal neovascularization (CNV) formation. These include angiogenic factors, such as vascular endothelial growth factor A (VEGF-A), fibroblast growth factor (FGF), and platelet-derived growth factor (PDGF); inflammatory factors (e.g., TNF-α, IL-1β); genetic factors, such as complement factor H (CFH) gene mutations; environmental factors; oxidative stress; and complement system activation.^2,4,5 Notably, hypoxia-induced VEGF-A upregulation, mediated by oxidative stress and complement activation, is a key driver of CNV in AMD.⁶ VEGF binds to its receptor VEGF receptor-2 (VEGFR-2), activating downstream pathways that promote the proliferation of vascular endothelial cells.⁷ This promotes the formation of immature CNV, which breaks through the Bruch’s membrane into the subretinal or sub-RPE space, leading to hemorrhage, leakage, fibrovascular pigment epithelial detachment (PED), and late-stage fibrous scarring.⁸ 

Protein post-translational modifications (PTMs) are critical steps in protein biosynthesis, where alterations in protein spatial structure or the addition of functional groups can significantly affect protein function.⁹ Acetylation, a type of PTM, can modify various proteins, including histones, p53, and tubulin.^10–12 Depending on the site of action, protein acetylation can be divided into three main types: N-terminal acetylation, histone acetylation, and C-terminal residue acetylation.¹³ These modifications are primarily mediated by different acetyltransferases that transfer acetyl groups to the N-termini of proteins, serine and threonine residues at the C-termini of proteins, and the α-amino group of histone lysine residues. Notably, N-terminal acetylation is irreversible, as no N-terminal deacetylases have been identified to date, unlike the reversible lysine acetylation and other dynamic post-translational modifications.^14,15 This irreversibility means that N-terminal acetylation has long-term impacts on protein stability, localization, and interactions, which is especially important in age-related pathologies.¹⁶ Collectively, N-terminal acetylation, histone acetylation, and C-terminal residue acetylation alter the biological functions of these proteins, affecting their stability, modulating cellular gene expression and cell cycle control, and participating in inflammatory responses.^17–22 These modifications play a significant role in the pathogenesis of various ocular diseases.²³ The core pathogenesis of AMD includes the formation of basal laminar deposits and drusen, abnormal lipid deposition in the RPE, complement system activation, inflammatory responses, CNV formation, and apoptosis.^6,24–26 Protein acetylation plays a significant role in the regulation of gene expression, oxidative stress, inflammation, and cellular senescence in AMD.^27–29 This review focuses on the role of protein acetylation in the pathogenesis of AMD, aiming to provide new insights for therapeutic targets in AMD. 

Protein Acetylation Modulates Three Key Mechanisms in AMD

Angiogenic Gene Expression and Regulation of Angiogenesis

CNV plays a critical role in the progression of AMD, and the expression and activity of VEGF are essential for CNV development.¹ VEGF stimulates the proliferation and migration of vascular endothelial cells, facilitating the development of neovascularization. The growth of these vessels leads to fluid accumulation and hemorrhage beneath the retina, as well as fibrosis, ultimately severely impairing the patient's vision.^2,6 Protein acetylation modification influences VEGF expression through various mechanisms, subsequently impacting the formation of CNV in AMD.³⁰ Histone acetylation, a key component of protein acetylation, significantly regulates angiogenic gene expression and inhibits neovascularization in AMD.^31–33 Histone acetylation predominantly occurs on four core histones: H2A, H2B, H3, and H4, with over 40 distinct lysine residues identified for acetylation.³⁴ This modification is facilitated by lysine acetyltransferases (KATs), which transfer acetyl groups to lysine residues, resulting in weakened interactions between histones and DNA. This makes DNA more accessible for transcription. Histone acetylation impacts a variety of cellular processes, including transcription, autophagy, mitosis, differentiation, and neural function.^35–37 

Research by Dahbash et al.³⁸ indicated that the histone deacetylase (HDAC) inhibitor AN7 can suppress Vegf gene expression by increasing the acetylation level of histone H3 in retinal endothelial cells. Additionally, systemic intraperitoneal injection of AN7 significantly reduces the area and vascular leakage of CNV in a laser-induced mouse model and protects the tight junction integrity of RPE cells under hypoxic conditions, aiding in the prevention of CNV development.³⁸ Research has also shown that HDAC inhibitors can counteract angiogenesis by reducing VEGF-induced phosphorylation of Akt and extracellular signal regulated kinase (ERK)1/2, as well as inhibiting the upregulation of the pro-angiogenic gene Angiopoietin-2 induced by VEGF in endothelial cells.^39,40 Trichostatin A (TSA), an HDAC inhibitor, can influence the formation of CNV by modulating the expression of VEGF and its receptors.⁴¹ Chan et al.⁴¹ demonstrated that TSA not only directly downregulates VEGF expression but also reduces the expression of HIF-1α, which indirectly affects VEGF production. HIF-1α is a transcription factor activated under hypoxic conditions that enhances the expression of various pro-angiogenic genes, including VEGF.⁴² When hypoxic, HIF-1α subunits bind with HIF-1β subunits and enter the nucleus, where they recognize the hypoxia response element (HRE) in the VEGF gene promoter to facilitate its transcription.⁴³ Acetylation can augment the transcriptional activity of HIF-1α, thereby increasing VEGF expression, an effect counteracted by TSA.⁴¹ Additionally, Chan et al.⁴¹ discovered that TSA reduces CNV occurrence by upregulating pigment epithelium-derived factor (PEDF, an anti-angiogenic factor), downregulating VEGFR-2 expression in human endothelial cells, and inhibiting epithelial–mesenchymal transition (EMT) in RPE cells. Furthermore, sirtuins, members of the histone deacetylase family, have inhibitors such as nicotinamide and sirtinol, which have been shown to reduce secretion of proangiogenic factors in RPE cells and inhibit proliferation of choroidal endothelial cells.^44,45 They are considered potential therapeutic approaches. 

Histone acetylation has been shown to alter the expression of clusterin, a secreted chaperone with multiple functions and a key protein found in drusen between the RPE and Bruch's membrane.^46,47 The specific role of clusterin in the pathogenesis of AMD remains largely unknown; however, studies suggest that it may have antiangiogenic properties.⁴⁸ As a complement inhibitor, clusterin can bind to the membrane attack complex and prevent cell lysis.³² Consequently, deficiency in clusterin may exacerbate inflammation and contribute to the exudative phase of AMD. Histone acetylation may upregulate clusterin expression. Research by Suuronen et al.⁴⁸ indicated that treatment with DNA methyltransferase (DNMT) inhibitors and HDAC inhibitors significantly increases the expression and secretion of clusterin mRNA and protein in ARPE-19 cells. Additionally, they observed that valproic acid (VPA), known to inhibit HDAC activity, significantly increased the expression and secretion of clusterin in RPE cells.⁴⁹ Therefore, modulating clusterin expression in RPE cells through histone acetylation may inhibit angiogenesis and inflammation during the pathogenesis of AMD. Beyond its role in upregulating clusterin to counteract angiogenesis, histone acetylation may further modulate vascular homeostasis through endothelial nitric oxide synthase (eNOS). eNOS is an enzyme specifically expressed in vascular endothelial cells and is responsible for catalyzing the production of nitric oxide (NO). NO, a vital signaling molecule, plays critical roles in the cardiovascular system, including regulating vascular tone, controlling endothelial cell proliferation and migration, and combating oxidative stress.⁵⁰ Research by Rossig et al.⁵¹ indicated that HDAC inhibitors can modulate eNOS expression by affecting mRNA stability and upregulating p53 protein levels, thereby inhibiting angiogenesis. 

Collectively, protein acetylation exerts a multifaceted regulatory role in AMD-associated angiogenesis by targeting both epigenetic and non-epigenetic pathways. Histone acetylation, mediated by KATs and antagonized by HDACs, dynamically controls the expression of pro-angiogenic genes such as VEGF and HIF-1α. HDAC inhibitors (e.g., AN7, TSA) not only suppress Vegf transcription by enhancing histone H3 acetylation but also disrupt HIF-1α-driven hypoxic signaling, thereby attenuating the occurrence of CNV. HDAC inhibitors can also upregulate clusterin—a complement inhibitor with antiangiogenic properties—by promoting acetylation-dependent transcriptional activation in RPE cells. Beyond canonical histone targets, acetylation modulates non-histone proteins critical for vascular homeostasis. For example, the acetylation status of eNOS influences NO bioavailability, thereby regulating vascular tone and endothelial cell proliferation. These findings highlight that protein acetylation integrates epigenetic regulation, hypoxic signaling, and vascular functional modulation to orchestrate angiogenesis in AMD. Targeting acetylation-related pathways (e.g., HDAC inhibitors) may synergize with existing anti-VEGF therapies to achieve broader therapeutic efficacy. 

The Regulatory Network of Oxidative Stress and Inflammation

Oxidative stress refers to an imbalance within the body between oxidation and antioxidant processes, with a shift toward increased oxidation. This results in elevated levels of free radicals or reactive oxygen species (ROS) that surpass the capacity of the antioxidant defense system to clear them, leading to tissue damage.⁵² In AMD, oxidative stress results from prolonged exposure to light and other environmental factors, causing RPE cells to produce excessive ROS. When these cells fail to effectively eliminate these harmful substances, oxidative damage occurs, affecting the function and structural integrity of RPE cells.⁵³ This damage is not limited to RPE cells but also extends to photoreceptors, Bruch's membrane, and choriocapillaris, triggering a cascade of reactions such as the abnormal deposition of extracellular matrix leading to drusen formation and complement system activation, playing a significant role in the pathogenesis of AMD.^4,54 On the other hand, oxidative stress can induce the production of inflammatory mediators within cells, such as TNF-α and interleukins. These mediators, in turn, can exacerbate oxidative stress, creating a vicious cycle. Consequently, there is a bidirectional interaction between oxidative stress and inflammatory responses, which can amplify each other and further intensify the pathological processes in AMD.⁵⁵ 

Macrophage polarization, a key cellular event in inflammation, regulates macrophage phenotype and function, influencing inflammation initiation, progression, and resolution.⁵⁶ In AMD, IL-4–induced M2 macrophages secrete profibrotic mediators such as TGF-β2, directly activating fibroblasts and exacerbating subretinal fibrosis.⁵⁷ Moreover, M2 polarization, regulated by pathways such as PI3K/Akt, plays a significant role in CNV formation in neovascular AMD.^57,58 HDAC inhibitors (e.g., panobinostat, TSA) can block M2 polarization through various mechanisms, including inhibiting the mitogen-activated protein kinase kinase (MEK)/peroxisome proliferator-activated receptor gamma (PPARγ)/retinoic acid (RA) pathway, oxidative phosphorylation, and retinol metabolism.⁵⁹ These inhibitors have shown efficacy in vitro and in vivo, suggesting that they may slow AMD progression by modulating macrophage polarization.⁵⁹ Targeting the epigenetic regulation of macrophage polarization could thus offer dual benefits in AMD therapy, inhibiting CNV in neovascular AMD and reducing subretinal fibrosis. 

In addition to influencing macrophage polarization, protein acetylation modulates antioxidant gene expression, mitochondrial function, and inflammatory mediator expression, playing a key role in AMD-related oxidative stress and inflammatory responses.^28,60,61 As a subtype of protein acetylation, histone acetylation modification influences gene expression in AMD and inhibits angiogenesis while also protecting retinal damage and suppressing inflammatory responses. Beyond regulating VEGF expression, as previously mentioned, TSA also plays a role in neuroprotection and reducing retinal inflammation. In a rat model of ocular ischemia, intraperitoneal injection of TSA (2.5 mg/kg) significantly increased the amplitude of electroretinogram (ERG) a- and b-waves in ischemic eyes.⁶² In vitro experiments revealed that TSA pretreatment significantly reduced TNF-α levels at 4 hours after retinal ischemia–reperfusion injury compared to controls. Additionally, TSA inhibited TNF-α− −induced secretion of metalloproteinases (MMP-1 and MMP-3), further mitigating retinal inflammation by suppressing these downstream inflammatory effectors.⁶² In terms of antioxidant gene regulation, HDAC inhibitors such as VPA enhance the antioxidant capacity of RPE cells and reduce oxidative damage in AMD by upregulating the expression of antioxidant enzyme genes, including superoxide dismutase (SOD1 and SOD2), catalase (CAT), and glutathione peroxidase (GPx4).⁶⁰ Furthermore, this study indicates that VPA not only induces the expression of antioxidant enzyme genes under normal conditions but also maintains their high-level expression under acute or chronic oxidative stress.⁶⁰ These mechanisms help elucidate why HDAC inhibitors can serve as a potential therapeutic approach for AMD. 

SIRT1, a member of the sirtuins family, is an NAD⁺-dependent protein deacetylase. It can deacetylate multiple transcription factors, including p53, nuclear factor kappa B (NF-κB), PPARγ and its coactivator 1-alpha (PGC-1α), FOXO, nuclear factor erythroid 2-related factor 2 (Nrf2), and E2F transcription factor 1 (E2F1), thereby activating the biological functions of these transcription factors.^61,63–65 Bromodomain and extraterminal (BET) proteins are crucial members of the bromodomain protein family. They interact with the p65 subunit of NF-κB at the acetylated lysine site at position 310 in the transcription activation region, thereby activating the expression of proinflammatory genes in RPE cells.⁶⁶ SIRT1, on the other hand, can deacetylate the p65 subunit of NF-κB directly, thus modulating its activity and reducing the expression of inflammation-related genes.⁶⁷ Deacetylation of PGC-1α reduces the production of ROS, thereby mitigating oxidative stress and preserving mitochondrial function in RPE cells.^68,69 Zhang et al.²⁸ observed decreased SIRT1 expression in RPE cells in AMD, leading to increased acetylation of PGC-1α. This acetylation diminishes mitochondrial biogenesis and triggers mitochondrial dysfunction, exacerbating oxidative stress in AMD. FOXO3, a member of the FOXO family of transcription factors, regulates gene expression in cells. Research by Wu et al.⁶⁵ indicated that, under oxidative stress in AMD, increased acetylation of FOXO3 enhances its binding to the CFH promoter region. This increased binding inhibits the interaction between signal transducer and activator of transcription 1 (STAT1) and the CFH promoter, suppressing CFH expression and exacerbating the pathological process of AMD. In contrast, the deacetylation activity of SIRT1 can diminish the recruitment of FOXO3 to the CFH regulatory region, ameliorating oxidative stress–induced suppression of CFH gene expression. Nrf2, a transcription factor in RPE cells activated under oxidative stress conditions, primarily induces the expression of antioxidant protective proteins, such as glutathione (GSH), superoxide dismutase (SOD), and catalase (CAT).⁶¹ Nrf2 not only regulates antioxidants but also has anti-inflammatory properties, suppressing the release of inflammatory cytokines such as TNF-α, IL-6, and IL-1β by inhibiting NF-κB and its cascade.⁷⁰ Research indicates that SIRT1 activation not only increases Nrf2 expression but also promotes its deacetylation, stabilizing nuclear translocation and enhancing transcriptional activity, which upregulates anti-inflammatory genes encoding SOD and GSH.⁶¹ The E2F1 transcription factor regulates DNA replication, damage repair, cell cycle, and apoptosis.⁷¹ Research indicates that E2F1 overexpression significantly increases glucose-6-phosphate dehydrogenase (G6PD) mRNA and protein levels in RPE cells, boosting signal transduction of the pentose phosphate pathway and enhancing cellular antioxidant capacity.^63,72,73 As a pivotal transcription factor, E2F1 directly modulates the expression of multiple DNA repair genes, such as ATM, BRCA1, Msh2, Msh6, PCNA, and RRM2, participating in DNA repair processes.^71,74,75 Additionally, Gong et al.⁶³ discovered that SIRT1 can enhance the antioxidant function of E2F1 in RPE cells through deacetylation. When SIRT1 is knocked down, increased acetylation of E2F1 leads to exacerbated DNA oxidative damage. In summary, SIRT1 may serve as a potential therapeutic approach for inhibiting oxidative stress and inflammation in AMD. 

In the pathogenesis of AMD, oxidative stress and chronic inflammation reinforce each other through pathological feedback loops, and protein acetylation serves as a master regulatory mechanism counteracting this vicious cycle. Mechanistically, HDAC inhibitors (e.g., TSA, VPA) mitigate oxidative damage by upregulating antioxidant enzymes (SOD1/2, CAT, GPx4) and suppress inflammatory cascades through inhibition of MMP-1/MMP-3 and downstream cytokines. Notably, these inhibitors (e.g., panobinostat, TSA) also intercept maladaptive immune responses by targeting macrophage polarization—a process critically implicated in both subretinal fibrosis and CNV. They inhibit the MEK/PPARγ/RA signaling pathway and retinol metabolism, reducing M2 macrophage polarization, thus suppressing the pathological processes of CNV and subretinal fibrosis. Concurrently, the NAD⁺-dependent deacetylase SIRT1 orchestrates mitochondrial biogenesis and antioxidant defenses via deacetylation of PGC-1α/Nrf2, and its modulation of NF-κB p65 deacetylation attenuates TNF-α/IL-6–driven retinal inflammation. Notably, FOXO3 acetylation dynamics critically regulate complement homeostasis: Hyperacetylation disrupts CFH expression to exacerbate complement-mediated inflammation, whereas SIRT1 restores CFH levels through targeted deacetylation. These findings collectively demonstrate that acetylation-driven crosstalk between antioxidant pathways and inflammatory signaling networks enables multidimensional intervention in the oxidative–inflammatory axis of AMD. Targeting dynamic acetylation regulation (e.g., SIRT1 activators, HDAC inhibitors) may synergistically mitigate oxidative damage and chronic inflammation, providing a dual therapeutic strategy for AMD treatment. 

Cellular Senescence and Autophagy Imbalance

Multiple pathophysiological factors converge to drive pathological senescence in RPE cells, encompassing upregulated senescence-associated genes, mitochondrial dysfunction, impaired DNA damage repair, and dysregulated autophagic flux, which collectively exacerbate the progression of AMD.^76,77 During aging, RPE cells experience a decline in proliferation and differentiation abilities, impairing their repair and regenerative functions and leading to further tissue damage.^78,79 This process also attracts choroidal endothelial cells (ECs) to migrate to the RPE, stimulating the formation of CNV and depriving photoreceptors of nutrients, thus causing their death, halting the cell cycle, and exacerbating the progression of GA.^80,81 

Protein acetylation plays a significant role in the aging of RPE cells, regulating the cell cycle, influencing DNA damage repair, and impacting mitochondrial function. Alterations in protein acetylation status can lead to a progressive decline in RPE cells function, culminating in cellular senescence.^63,82,83 Histone PTMs are significant occurrences during cellular senescence.⁸⁴ Histone acetylation is generally associated with gene activation, whereas histone deacetylation is linked to gene silencing. In the process of cellular senescence, increased activity of HDACs leads to elevated levels of histone deacetylation, which in turn suppresses the expression of genes related to cell proliferation and survival. This may result in cell-cycle arrest and a decline in cellular function, ultimately leading to cellular senescence.^85,86 Dubey et al.⁸² observed that, in aged mice, the acetylation profile of histones in the RPE/choroid complex exhibited an overall decrease in acetylation levels, including the loss of H3K14ac, H3K56ac, and H4K16ac marks. Concurrently, there was a significant reduction in the overall levels of histones H1, H2A, H2B, H3, and H4, suggesting that the decline in histone acetylation and the loss of histones are key characteristics of cellular senescence in RPE cells.⁸² 

Beyond its role in histone acetylation, the acetylation of p53 is linked to enhanced transcriptional activity, which in turn promotes cell-cycle arrest and cellular senescence. Research has shown that oxidative stress increases the acetylation of p53 at lysine 382, thereby upregulating genes associated with cell-cycle arrest and aging, such as p21^Waf1/Cip1.⁸⁷ Zhuge et al.⁸⁸ discovered that fullerenol (Fol) activates SIRT1, reducing acetylation of p53 and the expression of p21^Waf1/Cip1 in RPE cells, thus alleviating cellular senescence induced by oxidative stress in AMD. 

DNA damage repair mechanisms are vital for maintaining cellular functions and delaying cellular senescence. Defects in the DNA repair system increase cellular sensitivity to DNA damage, hastening cell aging.⁸⁹ In the DNA damage repair process of RPE cells, acetylation of E2F1 may exacerbate DNA damage and apoptosis. In contrast, SIRT1-mediated deacetylation of E2F1 helps preserve its activity in DNA repair, safeguarding RPE cells from oxidative stress damage and thus delaying cellular senescence.⁶³ 

Mitochondrial dysfunction induces the formation of lipid droplets and the accumulation of undigested material within cells, and it suppresses autophagy dynamics, further reducing mitochondrial oxidative and phosphorylation activities, thus accelerating cellular senescence.^90–92 Golestaneh et al.⁸³ found that the SIRT1/PGC-1α pathway is suppressed in induced pluripotent stem cells (iPSCs) derived from dermal fibroblasts of patients with dry AMD, which are differentiated into RPE cells in a disease model (AMD iPSC–RPE cells). This suppression leads to the inactivation of AMP-activated protein kinase (AMPK, an enzyme that plays a key role in cellular energy metabolism regulation and is involved in multiple aspects of cellular energy metabolism), affecting mitochondrial function, ultimately resulting in mitochondrial disintegration, increased oxidative stress, and cellular dysfunction. These changes collectively promote the aging of AMD iPSC–RPE cells.⁸³ 

Autophagy is a biological process in which cells degrade damaged, non-functional, or unnecessary cellular components, including organelles, through lysosomal degradation to maintain cellular homeostasis.⁹³ Autophagy plays a crucial role in maintaining RPE cell function, and its dysfunction may lead to drusen accumulation, promoting AMD progression.⁹⁴ Autophagy is also closely related to the oxidative stress response and DNA damage repair in RPE cells.⁷⁷ Differences in gene expression and functional abnormalities of key autophagy proteins can exacerbate the pathological process of AMD.⁹⁵ Hu et al.⁹⁶ observed that downregulation of CERKL (a gene associated with retinal degenerative diseases) in RPE cells significantly reduced SIRT1 protein levels, leading to increased acetylation of ATG5, ATG7, and LC3 (key autophagy-related proteins). Increased acetylation of these key proteins ultimately decreased RPE cell autophagy, exacerbated degenerative changes within cells, and promoted AMD progression. 

Protein acetylation orchestrates the crosstalk between cellular senescence and autophagic flux dysregulation in AMD through a multilayered regulatory axis. At the epigenomic level, age-dependent histone hypoacetylation (evidenced by diminished H3K14ac and H4K16ac signatures), coupled with global nucleosome depletion, epigenetically silences proliferative genes, committing RPE cells to irreversible senescence. Concurrent non-histone acetylation amplifies senescence signaling: Hyperacetylated p53 transcriptionally activates p21^Waf1/Cip1 to enforce cell-cycle arrest, and E2F1 impairs DNA repair capacity, potentiating oxidative genome instability. Mitochondrial dysfunction, a hallmark of AMD-associated senescence, is exacerbated through SIRT1/PGC-1α axis suppression, precipitating metabolic inflexibility and pathological lipid droplet biogenesis. Crucially, acetylation sabotage extends to autophagic flux—the guardian of RPE proteostasis. SIRT1 deficiency induces pathological hyperacetylation of core autophagy machinery (ATG5, ATG7, and LC3), impairing lysosomal acidification and exacerbating proteinopathic stress. These acetylation-driven perturbations coalesce into a self-reinforcing vicious cycle: Mitochondrial dysfunction and autophagic imbalance generate ROS and activate inflammatory mediators, which in turn accelerate epigenetic dysregulation and protein misfolding. Therapeutic targeting of acetylation homeostasis—particularly through SIRT1 allosteric activators (e.g., Fol) or isoform-selective HDAC inhibitors—may intercept this pathogenic circuitry via the tripartite mechanisms of restoring mitochondrial redox resilience, enhancing DNA damage tolerance, and reinstating autophagic clearance, thereby offering multimodal therapeutic leverage against AMD progression. 

Methodological Approaches and Experimental Models in AMD Acetylation Research

The investigation of protein acetylation in AMD relies on a combination of advanced methodologies and well-characterized experimental models. Here, we summarize the significant experimental methods and animal models covered in this article. 

Chromatin immunoprecipitation sequencing (ChIP-seq) has been employed to map histone acetylation dynamics at promoters of AMD-related genes (e.g., VEGF and CFH), revealing hypoxia-induced H3K27ac enrichment in retinal endothelial cells.^38,41 Building on these findings, HDAC inhibitors (e.g., TSA) have been validated in in vitro models, demonstrating dose-dependent suppression of VEGF and TNF-α in ARPE-19 cells under oxidative stress.^41,62 Furthermore, these compounds were further tested in laser-induced CNV mouse models, where AN7 significantly reduced CNV area through histone H3 hyperacetylation.³⁸ In addition, iPSC–RPE cells, generated from dry AMD patients, recapitulate the SIRT1/PGC-1α pathway suppression and autophagic defects, providing a platform for testing mitochondrial-targeted therapies.⁸³ Similarly, laser-induced CNV mice, a model for wet AMD pathology, enable evaluation of antiangiogenic therapies (e.g., TSA markedly reduces HIF-1α-driven VEGF expression).⁴¹ Building on these research approaches, we also look to future methods. For example, could combining CRISPR/Cas9-mediated gene editing (e.g., SIRT1-knockout RPE cells) with single-cell RNA sequencing (scRNA-seq) potentially resolve cell heterogeneity in acetylome regulation? This approach would enable more precise investigation of cell behavior and development of targeted therapies. 

Conclusions and Future Perspectives

Protein acetylation functions as a master regulatory switch in AMD pathogenesis, converging on three cardinal pathways through both epigenetic and non-epigenetic mechanisms. First, in angiogenesis, HDAC inhibitors (e.g., TSA, AN7) suppress hypoxia-driven VEGF expression via histone H3 hyperacetylation while simultaneously upregulating clusterin to stabilize Bruch's membrane integrity. The acetylation status of non-histone targets such as eNOS further fine tunes vascular tone and endothelial permeability, highlighting the pleiotropic role of acetylation in vascular homeostasis. Second, oxidative stress and inflammation are counterbalanced by SIRT1-mediated deacetylation: SIRT1 enhances mitochondrial biogenesis via PGC-1α activation, bolsters antioxidant defenses through Nrf2 nuclear translocation, and silences NF-κB–driven inflammatory cascades by deacetylating p65. Conversely, HDAC inhibitors amplify this protective axis by stabilizing antioxidant enzyme expression (SOD, CAT) and suppressing MMP-1/MMP-3–mediated tissue damage. Third, in cellular senescence, histone hypoacetylation (e.g., loss of H3K14ac, H4K16ac) couples with global nucleosome depletion to silence proliferative genes, and hyperacetylated p53 and E2F1 enforce cell-cycle arrest and impair DNA repair. Mitochondrial dysfunction, exacerbated by SIRT1/PGC-1α axis suppression, synergizes with autophagic failure—driven by ATG5/LC3 hyperacetylation—to fuel ROS accumulation and proteotoxic stress. Critically, these pathways intersect through acetylome-driven feedback loops: Oxidative stress amplifies histone deacetylase activity, which in turn aggravates mitochondrial collapse and inflammasome activation. Therapeutic targeting of this interconnected network—via SIRT1 activators to restore redox/autophagic balance or isoform-selective HDAC inhibitors to normalize epigenetic and vascular dysregulation—may offer a unified strategy to halt AMD progression. The main HDACs and HDAC inhibitors involved in altering protein acetylation in the three core pathogenic mechanisms of AMD are shown in the Figure. The Table lists the key HDAC subtypes, their PTMs, and their links to AMD. 

Figure.

 

The main HDACs and HDAC inhibitors involved in altering the protein acetylation status in the three core pathogenic mechanisms of AMD. Inhibiting CNV in AMD: HDAC inhibitors such as AN7 suppress Vegf gene expression by boosting histone H3 acetylation in retinal endothelial cells, thus inhibiting CNV. TSA, another HDAC inhibitor, indirectly affects VEGF production by reducing HIF-1α expression in RPE cells. VPA, also an HDAC inhibitor, enhances clusterin expression and secretion in RPE cells to inhibit CNV. Alleviating oxidative stress and inflammation in AMD: HDAC inhibitors (e.g., panobinostat, TSA) block M2 macrophage polarization via mechanisms such as inhibiting the MEK/PPARγ/RA pathway, oxidative phosphorylation, and retinol metabolism. This reduces profibrotic mediators (e.g., TGF-β2) secreted by M2 macrophages, alleviating subretinal fibrosis and inhibiting CNV formation. TSA also suppresses MMP-1 and MMP-3 secretion induced by TNF-α, further reducing retinal inflammation. HDAC inhibitors such as VPA upregulate antioxidant enzymes (e.g., SOD1, SOD2, CAT, GPx4) to reduce oxidative damage in AMD. SIRT1, an NAD⁺-dependent protein deacetylase, deacetylates the p65 subunit of NF-κB to reduce inflammatory gene expression in RPE cells. SIRT1-maintained PGC-1 deacetylation reduces ROS production, alleviating oxidative stress and maintaining mitochondrial function in RPE cells. The SIRT1 deacetylation also decreases FOXO3 recruitment to the CFH regulatory region, enhancing STAT1 interaction with the CFH promoter and improving CFH gene expression inhibition caused by oxidative stress, thus mitigating AMD progression. Additionally, SIRT1 activation increases Nrf2 expression and deacetylation, stabilizing its nuclear transport and enhancing transcriptional activity to upregulate anti-inflammatory genes such as SOD and GSH. SIRT1 also increases E2F1 deacetylation, improving DNA oxidative damage in RPE cells. Improving cellular senescence and autophagy imbalance in AMD: SIRT1 activation reduces p53 acetylation and p21^Waf1/Cip1 expression in RPE cells, alleviating cell-cycle arrest and senescence induced by oxidative stress in AMD. Increased SIRT1 levels enhance deacetylation of key autophagy proteins (ATG5, ATG7, LC3), boosting autophagy capacity in RPE cells and delaying AMD progression.

Table.

 

HDAC Subtypes, PTMs, and Their Roles in AMD Pathogenesis

 

Beyond these primary effects, protein acetylation modification also impacts the progression of AMD through several additional targets. As a stratified ECM complex located between the RPE and choroid, Bruch's membrane provides a supportive framework for RPE cells, creating an internal environment for nutrient transport, signal transduction, and metabolic waste removal.⁹⁷ Degeneration of Bruch's membrane also facilitates the formation of CNV by creating a physical pathway.⁹⁸ MMPs secreted by RPE cells can degrade the matrix components of Bruch's membrane, promoting CNV formation.⁹⁹ Changes in the activity of MMPs and their inhibitors (TIMPs) are closely related to the progression of CNV.¹⁰⁰ HDAC inhibitors, such as TSA and sodium butyrate (NaBy), can selectively inhibit the expression of certain MMPs and promote the expression of some TIMPs by modulating histone acetylation levels, offering potential therapeutic benefits in degenerative diseases.¹⁰⁰ Contrary to the importance of maintaining PGC-1α deacetylation for preserving mitochondrial function and reducing oxidative stress in RPE cells, the acetylation state of PGC-1α also sustains the expression of lipid metabolism-related genes in these cells.²⁷ SIRT1-mediated deacetylation of PGC-1α inhibits the downregulation of lipid metabolism-related genes in RPE cells, affecting fatty acid β-oxidation, cholesterol esterification, exogenous lipid uptake, cholesterol biosynthesis, and lipid peroxidation.²⁷ This contributes to lipid metabolic disorder and the accumulation of lipid droplets, ultimately promoting the development and progression of AMD.²⁷ This finding underscores the need for a nuanced understanding of how PGC-1α acetylation and deacetylation influence the pathogenesis of AMD. 

The potential expression changes of different HDAC subtypes in AMD need to be explored. Luu et al.¹⁰¹ found HDAC11 overexpression in early-stage light-induced retinal injury mouse models, concurrent with decreased H3K27ac levels. This finding suggests that HDAC11 overexpression promotes chromatin compaction, reduces euchromatin regions, and disrupts gene transcription and translation, driving photoreceptor apoptosis and retinal inflammation in AMD. Wang et al.¹⁰² used the assay for transposase-accessible chromatin using sequencing (ATAC-seq) to analyze chromatin accessibility in normal and AMD samples, identifying HDAC11 overexpression as a potential therapeutic target for AMD. Husain et al.¹⁰³ showed that, in the context of systemic inflammation, HDAC1 and HDAC3 upregulation may increase chemokine expression (e.g., Cxcl9), worsening NaIO₃-induced retinal degeneration in mice. MS-275 (entinostat) can target HDAC1 and HDAC3 overexpression to mitigate this process. These studies offer new insights into the roles of HDAC subtypes in AMD. Future research should explore the therapeutic potential of subtype-specific HDAC modulation. 

In summary, we speculate on the potential role of protein acetylation in optimizing AMD treatment protocols by targeting the identified acetylation sites and the three core mechanisms described in the text. First, the combination of HDAC inhibitors or SIRT1 activators with anti-VEGF drugs, which addresses both vascular abnormalities and metabolic repair, may improve therapeutic efficacy and reduce drug resistance. However, it should be noted that the response to HDAC inhibitors varies among different tissues and cells in the mammalian retina and remains controversial.¹⁰⁴ Moreover, certain HDAC inhibitor subtypes, such as VPA, may exhibit retinal toxicity.¹⁰⁴ These issues require further clinical trials based on acetylation regulatory mechanisms to confirm their safety and efficacy in humans. Second, although numerous studies indicate a general upregulation of HDACs in AMD,^101–103 driving pathogenesis, the specific expression differences among HDAC subtypes and their dependence on disease stages require close attention. For example, Anderson et al.¹⁰⁵ found that HDAC1, HDAC2, HDAC5, and HDAC6 expression was downregulated in the retina of AMD patients compared to healthy controls, as determined by mass spectrometry. This dynamic change may be linked to the epigenetic regulatory demands of different AMD stages. Therefore, there is a need to develop more selective HDAC inhibitors to meet the requirements of targeted therapy for different disease stages. Third, regarding the “double-edged sword” effect of acetylation (such as the contradictory role of PGC-1α in lipid metabolism and oxidative stress), temporal regulation (precise control of gene expression within a specific time window)¹⁰⁶ could reduce the impact on non-target proteins and avoid the side effects of continuous intervention. Finally, with the increasing popularity of gene-editing technologies, using CRISPR/Cas9 and other technologies to regulate the expression of specific acetylases or deacetylases and to intervene in multiple biological processes of target proteins in a step-by-step manner could achieve precise treatment for different pathogenic mechanisms of AMD. 

Acknowledgments

The authors thank Xiaoyan Dou, PhD, for her guidance and constructive suggestions on the writing of this review. 

Supported by grants from the Shenzhen Science and Technology Project (JCYJ20220818102603007), Basic Research Project of Shenzhen Natural Science Foundation (20240802235446001), and Shenzhen Municipal Medical Research Special Fund (A2402010). 

Disclosure: T. Luo, None; C. Li, None; L. Zhou, None; H. Sun, None; M.M. Yang, None