Epigenetic regulation of iron metabolism and ferroptosis in Parkinson’s disease: Identifying novel epigenetic targets

Abstract

Parkinson’s disease (PD) is a neurodegenerative disease, and emerging evidence has shown that iron deposition, ferroptosis and epigenetic modifications are implicated in the pathogenesis of PD. However, the interplay among these factors in PD has not been fully understood. In this review, we provide an overview of the current research progress on iron metabolism, ferroptosis and epigenetic alterations associated with PD. Furthermore, we present new frontiers concerning various epigenetic modifications related to iron metabolism and ferroptosis that might contribute to the pathology of PD. Notably, epigenetic modifications of iron metabolism and ferroptosis as both diagnostic and therapeutic targets in PD have been discussed. This opens new avenues for the regulation of iron homeostasis and ferroptosis in PD from epigenetic perspectives, and provides evidence for their potential implications in the diagnosis and treatment of PD.

Introduction

Parkinson’s disease (PD) is the second most common age-related neurodegenerative disease and was first described by James Parkinson [1]. Epidemiological data suggest that PD affects less than 1% of individuals aged 45 ~ 54 years, while it affects up to 5% of those over 85 years [2, 3]. Additionally, the prevalence of PD among males is approximately 1.5 times higher than that of females [4]. As one of the most common movement disorders, the number of patients suffering from PD is anticipated to increase dramatically to over 12 million by 2040 [5, 6], thereby imposing a long-term socioeconomic burden on the healthcare system and society.

The progressive degeneration of dopaminergic neurons in the substantia nigra pars compacta (SNpc) and the presence of Lewy bodies (LBs) composed of accumulated α-synuclein (α-syn) are considered typical pathological hallmarks of PD [7]. The main motor symptoms of PD include rigidity, resting tremors, and bradykinesia. Furthermore, studies have identified non-motor symptoms associated with PD, such as apathy, loneliness, anxiety, depression, psychosis, hallucinations, idiopathic REM sleep behavior disorder (iRBD) and cognitive dysfunction (like dementia) [8–13] These non-motor features can emerge years prior to a formal diagnostic motor manifestations of PD [11]. Due to the loss of dopaminergic neurons in PD patients, most current therapies focus on relieving of motor symptoms. Currently, the main effective treatments for PD are the dopamine precursor levodopa (L-DOPA) and surgical treatment, which can relieve motor symptoms by increasing dopaminergic neurotransmission or modulating motor circuits [14]. However, no treatment can halt or even slow the progression of PD. Therefore, developing new therapeutic strategies is crucial for the treatment of PD.

The etiology of PD is complex, and its pathogenesis has not been fully clarified [15–18]. Genetics and aging are considered the primary contributors to the pathogenesis of this disorder [19]. Additionally, gender [20, 21], traumatic brain injury, emotional stress and smoking are also supposed to be the potential risk factors for PD [22]. In terms of the pathological molecular mechanisms, researchers have focused on the aggregation of α-synuclein (α-syn) [23, 24], neuroinflammation [25], mitochondrial dysfunction [26], imbalance of the intestinal flora [27], oxidative stress (mainly iron) [28], dysfunction of metal ion metabolism [29], and epigenetic modifications [30]. In recent years, emerging evidence has implicated that iron deposits play a critical role in the pathogenesis of PD [31]; furthermore, ferroptosis is an iron-dependent form of programmed cell death identified in recent years. Several characteristic pathological changes associated with PD, such as glutathione (GSH) depletion, iron overload, abnormal lipid and mitochondrial metabolism, and increased ROS levels, are similar to those associated with ferroptosis [32]. This information provides an alternative explanation for the occurrence and progression of PD. Therefore, iron deposition and ferroptosis might be potential therapeutic targets for the treatment of PD.

Epigenetic modification is a reversible and heritable change in gene expression without alterations in the DNA sequence. Studies have shown that epigenetic modifications, including DNA methylation, histone modifications, and alterations in microRNA expression are also involved in PD [33]. Notably, the epigenetic regulation of iron metabolism and ferroptosis has also been reported [34]. Therefore, in this review, we briefly introduce recent updates on the involvement of iron metabolism, ferroptosis, and epigenetic alterations in PD. Additionally, we summarize current research progress on various epigenetic modifications related to iron metabolism and ferroptosis that might contribute to the pathology of PD. We propose that epigenetic modifications related to iron metabolism and ferroptosis might be potential therapeutic targets for both the diagnosis and treatment of PD.

Involvement of iron in PD

Iron, the most plentiful metal in the nervous system, plays a substantial role in the normal physiological activities of the brain by participating in various vital processes, including axon myelination, acetylcholine production, and the transmission of the respiratory chain [35, 36]. Transferrin receptor 1 (TFR1), divalent metal transporter 1 (DMT1), ferritin (FER), and ferroportin (FPN) collaborate to maintain intracellular iron homeostasis [37]. When the iron metabolism of cells is disrupted, accumulated intracellular Fe²⁺ reacts with H₂O₂ and undergoes a Fenton reaction to generate OH⋅ and other reactive oxygen species (ROS) that damage the phospholipid bilayer, proteins and nucleic acids. In PD patients, the accumulation of iron could cause a decrease in the number of dopaminergic neurons in the SNpc [38, 39]. Some studies have shown that iron is selectively deposited in the SN [40], before the appearance of motor signs [41]. Iron stimulates the aggregation of α-syn in cells, which can be increased by the presence of dopamine and H₂O_2, thereby promoting oxidative damage [42, 43]. Moreover, concentrations of iron can induce symptoms of PD in mice [44], such as rigidity and freezing of gait, as well as fluctuations in the density of dopamine receptors and the expression of the dopamine transporter (DAT) [45]. Importantly, deferoxamine (DFO), an effective iron chelator was found to alleviate behavioral deficits by down-regulating the expression of α-syn, TFR and DMT1 and protecting dopaminergic neurons in a 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced PD mouse model [46]. The iron chelator deferiprone (DFP) has also been shown to attenuate the death of dopaminergic neurons in PD mice [47]. Additionally, DFP and DFO have been shown to significantly improve the motor symptoms of PD patients (phase II clinical trials) [48, 49]. As research deepens, more and more evidence has suggested that iron accumulation plays a critical role in the etiology of PD [50].

Involvement of ferroptosis in PD

Ferroptosis is an iron-dependent form of programmed cell death identified in recent years [51, 52]. Briefly, when excessive amounts of cellular iron accumulate, redox reactions increase and the membrane integrity is damaged due to the lethal accumulation of lipid peroxides on cellular membranes, ultimately resulting in cell death. This form of regulated cell death is ferroptosis[53]. Cells undergoing ferroptosis generally exhibit increased oxidative stress and a diminished antioxidative capacity, which are often accompanied by abnormalities in mitochondrial structure [54]. These effects can be mitigated by either directly inhibiting lipid peroxidation or depleting iron [55]. Over the past decade, studies have elucidated the pathogenic mechanisms of ferroptosis in multiple diseases, including tumors [56], cardiovascular diseases [57], metabolic diseases [58], kidney injury [59], nervous system diseases [60–62] and other diseases [63]. Although the precise mechanisms underlying neuronal ferroptosis have not been fully elucidated, ferroptosis has been implicated in the degeneration of dopaminergic neurons in individuals with PD [64]. Several characteristic pathological changes associated with PD resemble those observed in ferroptosis, including GSH depletion, iron overload, abnormal lipid metabolism, altered mitochondrial function, and increased ROS levels [65]. This information provides an alternative explanation for both the onset and progression of PD.

A study revealed that the concentration of α-syn can be increased by ferroptosis in dopaminergic neurons and cause the degeneration of dopaminergic neurons in a Drosophila melanogaster model of PD. This process subsequently results in movement disorders and a reduced lifespan in Drosophila melanogaster [66]. Reduced GSH metabolism following oxidative stress in the SN is associated with mitochondrial dysfunction and constitutes a pivotal factor in the neuroinflammatory and neurodegenerative processes observed in patients with PD [67, 68]. An increase in GSH synthesis can attenuate the neurotoxicity of α-syn and protect neurons from lipid peroxidation and cell death induced by ferroptosis [66]. Studies have shown that MPP⁺-treated cells exhibit mitochondrial shrinkage, the downregulation of GPX4 and upregulation of DMT1 and TFR1 [69], which are classic features of ferroptosis. Similarly, a postmortem analysis of brains obtained from PD patients revealed limited binding activity of iron regulatory protein 1 (IRP1) but increased TFR1 expression in the SN. These changes lead to increased neuronal iron uptake and sensitize dopaminergic neurons to iron-induced oxidative damage [70, 71]. Apoptosis-inducing factor mitochondrial 2 (AIF-M2, FSP1) has been identified as a potent negative regulator of ferroptosis. It can catalyze CoQ10 in the cell membrane after myristoylation to restore its antioxidant effect and prevent cell death by reducing lipid peroxide levels [72] (Fig. 1). In contrast, acyl-CoA synthetase long chain family member 4 (ACSL4) is a key factor required for lipid peroxidation after GPX4 inactivation [73, 74]. Data have revealed the upregulation of ACSL4 along with a significant reduction in FSP1 in PD mice [75, 76]. In addition, knockdown of the ferritin heavy chain 1 gene (Fth1), known as a suppressor of ferroptosis [77], enhanced 6-OHDA-induced mitochondrial damage in PC-12 cells [78]. Conversely, the results of Fth1 overexpression were contradictory, indicating that Fth1 exerts cytoprotective effects in 6-OHDA-induced neurotoxicity and ferroptosis. These findings provide further evidence that ferroptosis is associated with the pathogenesis of PD.

Fig. 1. Schematic diagram illustrating the process of ferroptosis.

Several classical regulatory pathways for ferroptosis have been identified. ① Free PFUAs enter cells via CD36 and then are esterified into membrane PLs through the catalysis of ACSLs, LPCAT3, and LOXS, resulting in lethality after peroxidation. ②The GSH/GPX4 pathway is considered a canonical axis for controlling ferroptosis. System Xc- participates in cysteine import that is essential for GSH synthesis, which then affects the activity of glutathione peroxidases (GPXs) (mainly GPX4) to inhibit ferroptosis. Additionally, the FSP1-CoQ10-NAD(P)H pathway collaborates with GPX4 to inhibit phospholipid peroxidation and prevent ferroptosis. HSP90 and RSL3 can affect ferroptosis by inhibiting GPX4. ③ The regulation of iron metabolism. Fe³⁺ is taken up by the transferrin receptor on the membrane and then is converted to Fe²⁺ in endosomes and released from endosomes through DMT1. Intracellular free iron ions can cause the Fenton reaction and mediate mitochondrial damage. The NCOA4-mediated ferritinophagy pathway is also responsible for an increase in the intracellular iron level. Fe²⁺ is then exported via FPN1.④ Ferroptosis can be inhibited by the iron chelators DFO, DFP, DFS, Fer-1, etc. CD36 Cluster Differentiation 36, PUFA Polyunsaturated Fatty Acid, ACSL4 acyl-CoA synthetase long-chain family member 4, LPCAT Lysophosphatidylcholine Acyltransferase, PL Phospholipid, PL-OOH Phospholipid Hydroperoxide, MUFA Monounsaturated Fatty Acid, γ-GC Gamma-Glutamylcysteine, GSSG Oxidized Glutathione, GSR Glutathione Reductase, CoQ10 Coenzyme Q10, STEAP3 Six-Transmembrane Epithelial Antigen of the Prostate, DMT1 Divalent Metal Transporter 1, FPN1 Ferroportin 1, DFO Deferoxamine, DFP Deferiprone, DFS Desferasirox, Fer-1 Ferrostatin‐1.

The tumor suppressor gene TP53 can induce multiple pathological processes, such as mitochondrial dysfunction, ROS overload, abnormal protein aggregation and impaired autophagy, thus contributing to neurodegeneration [79–81]. Studies of PD patients and PD animal models have shown significant increases in both the level and activity of TP53. These changes are closely associated with the degeneration of dopaminergic neurons [82, 83]. Interestingly, TP53 also enhances ferroptosis by inhibiting the expression of the SLC7A11 gene, which is an important component of the cystine-glutamate antiporter system Xc-. System-Xc is one of the key antioxidant systems within cells and participates in the import of cysteine, which is essential for GSH synthesis [51, 84–86]. Similarly, lysophosphatidylcholine acyltransferase3 (LPCAT3) [87], mitochondrial voltage dependent anion channels (VDACs) [88], and lipoxygenases (LOXs), which predominantly catalyze the enzymatic peroxidation of esterified polyunsaturated FAs [89, 90] have all been found to induce ferroptosis and exhibit altered expression in individuals with PD [91].

Furthermore, ferroptosis in microglia can also affect PD. For example, in a human induced pluripotent stem cell (iPSC)-derived tri-culture system that contains microglia, neurons and astrocytes, microglia exhibit the strongest transcriptional response to iron dysregulation, and neurotoxic substances are released after microglia undergo ferroptosis, which can aggravate the process of PD [92]. In addition, susceptibility weighted imaging (SWI) of the brain revealed significant iron deposition in the SN of PD patients, accompanied by the infiltration of immune cells [93]. Studies employing machine learning methods, including LASSO regression and SVM models, have established novel hematological diagnostic models comprising 17 ferroptosis-related immune genes for PD. These findings show excellent diagnostic performance and accuracy in multiple PD patients, suggesting that ferroptosis plays an important role in the development of PD [93].

The above results revealed that the factors involved in ferroptosis including intracellular iron accumulation, increased lipid peroxidation, depleted GSH levels, decreased activity of system-Xc, and reduced CoQ10 levels are recognized as pathological hallmarks of PD. These findings further indicate a link between ferroptosis and PD. Importantly, some compounds have been found to exert their therapeutic effects by inhibiting ferroptosis in cellular or animal models of PD. For example, clausen amide [94], quercetin [62], clioquinol [95] and apoferritin [76] have shown potential to reduce MPTP‐induced dopaminergic neuronal injury and alleviate behavioral deficits in animals by inhibiting ferroptosis. Similarly, thonningianin A [96], hinokitiol [97], paeoniflorin [98], Ferrostatin‐1 [99] and α‐Lipoic acid [100] also function as ferroptosis inhibitors to increase cell viability and decrease ROS production in cell models of PD. These results suggest that targeting the ferroptotic pathway holds great potential for the development of therapeutic interventions for PD. However, the molecular mechanisms of ferroptosis, as well as drug toxicity and the ability to penetrate the blood-brain barrier (BBB), have limited the application of drugs targeting ferroptosis in the clinical treatment of PD. Notably, phase II clinical trials of the iron chelator DFP and the effects of DFO and desferasirox (DFS) on the treatment of PD patients indicate their potential as therapeutic interventions for PD by targeting ferroptosis [49, 101, 102].

Epigenetics in PD

In 1957, the developmental biologist Conrad H. Waddington first proposed the renowned concept of an epigenetic landscape (based on developmental biology and genetics) that is generally defined as “can produce heritable phenotypic changes without modifying the DNA sequence itself ” [103]. This definition means that identical genomes can produce different gene activity states that are long-lasting but potentially reversible. With the development of research, the content of epigenetics is constantly improving, including DNA methylation and hydroxymethylation, histone modifications (histone methylation, acetylation, ubiquitination, phosphorylation, glycosylation, etc.), and non-coding RNA changes (mainly microRNA) [104] (Fig. 2).

Fig. 2. Regulatory mechanism of epigenetics modifications.

DNA methylation and histone modification play crucial roles in regulating chromatin structure. DNA methylation and histone methylation make the chromatin structure more compact, causing transcriptional repression. On the other hand, histone acetylation promotes an open chromatin structure leading to transcriptional activation; changes in miRNA levels regulate gene expression by affecting mRNA transcription and thus participating in the regulation of cellular activity.

Recently, the role of epigenetics in various diseases has attracted extensive attention from researchers. Although the current research on epigenetics is still very limited, it has been demonstrated that epigenetics is associated with multiple physiological activities including cell development, differentiation, senescence, and metabolism, and is closely associated with various diseases, such as cancer [105], cardiovascular diseases [106, 107], metabolic diseases [108], and neurological diseases. In the nervous system, epigenetics can affect neurogenesis, the brain volume, synaptic plasticity, cognitive function, the stress response, etc., and plays important roles in the progression of neurodegenerative diseases, including Alzheimer’s disease (AD) [109], PD [33, 110], Huntington’s disease (HD) [111], and amyotrophic lateral sclerosis (ALS) [112, 113]. Epigenetic marks are promising candidates for understanding the etiology of PD because of their ability to mediate genetic and environmental possessions on phenotypes. In this section, we focus on various changes in epigenetic modifications in PD.

DNA methylation in PD

DNA methylation has been one of the most extensively studied epigenetic markers since its discovery following the determination of the DNA double-helix structure by Rollin Hotchkiss in 1948 [114]. The common detection methods are whole-genome bisulfite sequencing (WGBS), oxidative bisulfite sequencing (oxBS), nanopore sequencing (ONT), and single molecule real-time sequencing (SMRT); the strengths and limitations of these methods differ but chiefly depend on the sequencing sample and purpose [115]. DNA methylation is regulated mainly by DNA methyltransferases (DNMTs), including DNMT1, DNMT3A, and DNMT3B. Research has shown that mouse embryos with DNMT1 deactivation or DNMT3A/3B double knockout (KO) exhibit significant growth suppression, leading to lethality in early-gestation (Li et al., 1992, Okano et al., 1999). These DNMTs exhibit differential expression in different brain regions and are involved in age-dependent neurodevelopment [116, 117]. In terms of the modification sites, DNA methylation can be categorized into three types: 4-methylcytosine (4mC), 5-methylcytosine (5mC), and N6-methyladenine (6 mA). Among them, 5mC, the most prevalent form of methylation in eukaryotes, is also the most extensively studied DNA modification pattern. DNA methylation can mediate transcriptional repression and regulate cell division by influencing chromatin structure and dynamics [118]. A typical case of PD is that a reduced methylation level in the promoter region of the α-syn gene (SNCA) has been observed in the SN of PD patients [119, 120], which causes the overexpression of SNCA. This process, in turn, induces the abnormal aggregation of α-syn, which is a neuropathological hallmark of PD.

The ten-eleven translocation 1 (TET1) protein is a 5mC hydroxylase that can initiate the process of DNA demethylation by catalyzing the conversion of 5mC to 5hmC both in vivo and in vitro [121, 122]. It has been shown to be downregulated in PD patients, leading to a significant accumulation of α-syn [123]. The Tet1 gene is regulated by neuronal activity, can upregulate numerous memory-associated genes in nerve cells, and can impair memory under contextual fear conditions [124, 125], and 86 variants have been identified in the Tet1 gene in PD patients, suggesting that DNA methylation plays a crucial role in PD [126].

An epigenome-wide association study (EWAS) showed that DNA methylation in the peripheral blood mononuclear cells of PD patients was different from that of their brothers or twins without PD. Notably, PDE4D and GPR37 were hypermethylated, whereas MAPT and LY86 were significantly hypomethylated in PD patients. These findings indicate an association between alterations in DNA methylation and PD development [127]. Among them, the PDE4D gene encodes phosphodiesterase 4D (PDE4D), which belongs to the intracellular phosphodiesterase (PDEs) family. These results have shown that the α-syn-induced loss of synaptophysin can be prevented by inhibiting PDE4D activity [128], which is also associated with cognitive impairment [129]. GPR37 is an orphan G protein-coupled receptor (GPCR), also known as a parkin-associated endothelin-receptor-like receptor (Pael receptor), expressed in the hippocampus, SN and other brain regions. A recent study revealed the level of GPR37 was significantly increased in SN and cerebrospinal fluid (CSF) of patients with sporadic PD and PD mice. In contrast, significant differences in the expression of this gene have not been discovered in AD patients [130]. These findings suggest that inactivation of GPR37 exerts protective effects on dopaminergic neurons in individuals with PD. The hypermethylation of GPR37 may be an environmentally induced change that, in turn, is associated with PD. Lymphocyte antigen 86 (LY86), also known as myeloid differentiation protein 1 (MD-1), is a biomarker for inflammatory diseases, and relevant studies on its role in PD are still in the primary stage, indicating that it may be a potential focus in studies of the development of PD. MAPT, the gene encoding the microtubule-associated protein tau, is a susceptibility gene for idiopathic PD in Caucasian individuals [131]. Mutation of the MAPT gene can lead to various cognitive, behavioral and motor deficits in PD patients [132, 133].

Furthermore, PGC1-α, a major regulator of mitochondrial metabolism that contributes greatly to neuroprotection, has been shown to undergo hypermethylation at its promoter in the SN of PD patients [134]; the FOS gene (related to striatal dopamine levels), COX7B gene (affecting mitochondrial homeostasis), and RNF5 gene (associated with motor function) have all been found to exhibit altered methylation in individuals with PD [135]. Changes in the methylation levels of PARK7 (DJ-1) [136], NPAS2 [137], CYP2E1 [138] and NOS2 [139] have also been observed in PD. However, empirical evidence of the precise changes in the methylation of some crucial genes in PD patients or PD models has not yet been abundantly reported. This finding implies that further investigation is needed to determine whether or to what extent changes in DNA methylation are associated with PD. Further research is needed to understand how changes in DNA methylation contribute to the pathogenesis of PD.

Histone modifications in PD

In eukaryotes, an octamer of histones wraps around the outside of nuclear DNA (1.65 turns of approximately 146 bp), forming nucleosomes-the essential units of chromatin [140]. The exposed N-terminal amino acid residues of histones undergo covalent modifications such as methylation, acetylation, phosphorylation, ubiquitination, and SUMOylation by chromatin modifying enzymes, leading to dynamic histone post-translational modifications (HPTMs) [141, 142]. Crosstalk among these HPTMs plays a crucial role in the establishment of chromatin diversity, and distinct functional outcomes depend on their complex modification patterns. In recent decades, various approaches, such as chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq), cleavage under targets and tagmentation (CUT&Tag) and mass spectrometry (MS), have been developed to map epigenetic proteins across the genome. Recent studies have identified multiple histone modifications within individual cell profiles concurrently, such as scMulti-CUT&Tag [143], nano-CUT&Tag (nano-CT) [144], MulTI-Tag [145], nanobody-tethered transposition followed by sequencing (NTT-seq) [146], and ultrahigh-throughput CoTarget (uCoTarget, ultra-high throughput Combined TAgmenting enRichment for multiple epiGEneTic proteins in the same cells) [147]. Interestingly, a novel method nanoHiMe-seq has been described to profile histone modifications and DNA methylation simultaneously via ONT [148], although more practical proof is needed. The continuous improvement of these research methodologies is inextricably linked to their crucial roles in the life process. HPTMs can influence chromatin structure and function by modulating interactions between histones and DNA, as well as the interplay between histones to regulate development, cellular differentiation and responsiveness, the biological phenotype, and gene transcription, replication, and repair [149, 150]. Numerous studies have shown that HPTMs can be affected by external environmental factors and physiological states, thus contributing to various disease processes, such as immune system disorders [151], tumors [152], cardiovascular diseases [153], metabolic diseases [154], and neuropsychiatric disorders [155]. Although histone modifications have been poorly studied in PD, it is not arduous to comprehend from the existing results that histone modifications might play a critical role in PD [156]. Here, we briefly review the different histone modifications implicated in the development of PD, especially histone methylation and acetylation, which are extensively studied HPTMs.

Histone acetylation in PD

Histone acetyltransferases (HATs) regulate gene activation by adding acetyl groups to N-terminal lysine residues as well as the globular domains of histones [157, 158]. In humans, 18 different HDACs are classified into four classes. Class I enzymes include HDACs 1–3 and 8. Class II HDACs are grouped into two subclasses: Class IIa, comprising HDACs 4, 5, 7, and 9, and Class IIb, with HDACs 6 and 10 as members. Class III is also called SIRT1-7 and Class IV includes only HDAC11 [159]. Among them, Class I has been reported to attenuate the death of dopaminergic neurons in a PD cell model and a mouse model, exhibiting neuroprotective effects [160]. However, they seem to have the opposite functions in AD. The knockdown of HDAC2 or HDAC3 can ameliorate mitochondrial and endoplasmic reticulum (ER) dysfunction in an AD model [161]. Similarly, the overexpression and/or nuclear accumulation of Class IIa HDACs may be detrimental to dopaminergic neurons. For example, in iPSC-derived dopaminergic neurons from PD patients, HDAC4 expression is increased in the nucleus, which could upregulate some genes associated with PD-related cellular phenotypes, such as ER stress, autophagic and lysosomal perturbations, and increased α-synuclein release [162]. Nevertheless, the expression of HDAC4 is beneficial for restoring synaptic plasticity and alleviating cognitive impairment in AD mice [163]. Class IIb, such as HDAC6 has been found to exacerbate the pathological manifestations of AD, and HDAC6 inhibitors improve axonal transport and restore learning and memory in an AD model [164]. However, related research on Class IIb in PD is limited. Silence information regulator 1 (SIRT1) is an NAD-dependent deacetylase protein encoded by the SIRT1 gene (belonging to Class III), and the negative regulatory role of this protein in aging has been extensively reported [165]. Studies have found that in both PD models and PD patients, the level of SIRT1 is reduced in the frontal cortex, which may be associated with neuronal damage [166–168]. Resveratrol, a recognized natural SIRT1 activator, has been exploited to treat PD (as an epigenetic agent), and its phase I clinical trials have been completed in patients with AD; however, no clinical trials are evaluating the effects of resveratrol on PD [33, 169]. Similar neuroprotective effects of SIRT1 on several other neurodegenerative disorders have also been observed [170, 171].

In addition, studies have revealed that elevated nuclear α-syn in PD leads to decreased histone H3 acetylation, affecting gene transcription and resulting in cell death. A decrease in H3K9 acetylation along with an increase in H3K14 and H3K18 acetylation were observed in the motor cortex of PD brains [172]. A previous study demonstrated a significant increase in acetylation at histone H2B lysine 15 (H2BK15), H3K9/14, H3K27, H3K56, and H4K12 in PD [173]. In a PD cell model with mitochondrial dysfunction, H3K27, which is widely recognized as an enhancer- specific epigenetic marker, has also been shown to be significantly acetylated [174]. H3K27 genome-wide hyperacetylation has also been detected in PD brains [173]. In contrast, treatment with a histone deacetylase inhibitor (HDACI) has shown neuroprotective effects both on 6-OHDA-induced dopaminergic cells and MPTP-induced PD mouse model [175–177]. HDACIs significantly attenuate MPTP-induced adverse effects on motor and non-motor symptoms [178]. A recent study revealed that cinnamyl sulfonamide hydroxamate derivatives (NMJ-2 and NMJ-3, novel pan-HDACIs) significantly attenuated MPTP-induced oxidative stress, inflammation and decreased dopamine levels in the striatum, with aggravate motor and non-motor disorders in rats [178]. MC1568, a small molecule inhibitor of Class IIa HDACs, can protect dopaminergic neurons in the SN from 6-OHDA-induced neurodegeneration and microglial activation, decreasing the detrimental effects on movement in rats [156]. Contilisant+Tubastatin A, an inhibitor of HDAC6, has been found to reduce motor defects and ROS levels, and increase ATP production (an indicator of mitochondrial function) in Drosophila and human SH-SY5Y cell models via DJ-1 inactivation (PD model) [179]. These findings indicate that targeting HDACIs may be a rational therapeutic strategy for the development of disease-modifying therapies for PD, but clinical research on HDACIs in PD patients is still very superficial and further exploration is needed.

Histone methylation in PD

Unlike acetylation, histone methylation typically represses transcriptional activity by affecting chromatin structure. A study of α-syn protein pathy in a yeast model revealed a decrease in H3K36me2, which is a characterized histone marker involved in DNA repair [180]. Increased H3K9 methylation has been observed in α-syn transgenic flies and inducible neuroblastoma cells (SH-SY5Y) [181]. Additionally, significant H3K4 methylation at the SNCA promoter in the SN region has been reported in autopsy tissues from PD patients [182]. GSK-J4 (a histone demethylase inhibitor) was found to rescue the loss of dopaminergic neurons and motor defects in 6-OHDA-induced PD rats by increasing H3K4me3 levels [183]. Importantly, our recent results revealed increased methylation of H3K4 and H3K9 in 6-OHDA induced PC12 cells and the SN of a mouse PD model, suggesting that the altered methylation levels of histone H3 have significant research value in PD development. Although discoveries related to histone methylations in regulating the process of PD have been relatively limited, the available evidence suggests that these modifications represent a potential avenue for treating PD.

Histone ubiquitination in PD

Ubiquitination is the process by which ubiquitin is added to proteins through the action of three enzymes: ubiquitin activating enzyme (E1), ubiquitin coupling enzyme (E2) and ubiquitin ligase (E3) [184]. These modifications lead to proteasome-dependent degradation, which is involved in a variety of physiological and pathological processes, such as cell development, immune response, transcriptional regulation, and apoptosis [184]. It has been reported that histone ubiquitination can induce α-syn degradation in PD. For example, H2AK119 ubiquitination can promote proteasomal degradation to reduce α-syn protein aggregation, thereby preventing the development of PD [185].

MicroRNAs in PD

MicroRNAs (miRNAs) are a class of ncRNAs with a length of approximately 22 nucleotides that serve as endogenous regulators of gene expression. MiR-133b is expressed in midbrain dopaminergic neurons under physiological conditions, but its expression is significantly deficient in the midbrain [186], but increased in the plasma of PD patients [187]. The overexpression of miR-7, miR-153 and miR-155 has been recognized to regulate endogenous α-syn levels in the nervous system [188, 189]. The loss of miR-7 and the inhibition of miR-34b and miR-34c contribute to α-syn upregulation and accumulation as well as the loss of dopaminergic neurons in PD patients [190–192]. Moreover, upregulated miR-24, miR-34b and miR-148b, which are considered specific biological markers of PD, have been identified in individuals with PD [193]. The upregulation of hsa-miR-4639–5p and miR-137 have been identified in plasma and neurons by a dual-luciferase assay and a clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 (CRISPR-associated protein 9) system. These upregulated microRNAs can accelerate the neuronal death in PD patients, and the expression of hsa-miR4639-5p is regulated by HDAC11-mediated histone acetylation [194, 195]. MiR-30, miR-485, miR-29, and miR-26 are considered to be specific miRNAs related to PD pathogenesis and have the potential to become diagnostic biomarkers for PD patients [196]. An analysis revealed the significant differential expression of hsa-miR-221-3p, hsa-miR-105-5p, hsa-miR-214-3p and hsa-miR-29c-3p in the blood and plasma of PD patients [197, 198]. Furthermore, the abundance of hsa-miR-1260a in oral swabs correlated with disease severity, and olfactory function in PD patients, suggesting that hsa-miR-1260a could be a novel PD-specific miRNA associated with PD progression in the clinic [199]. The level of miR-30e-5p is significantly dependent on nuclear receptor related-1 (Nurr1), a potential susceptibility gene for PD. Studies of mouse models and patients have highlighted the involvement of the Nurr1-miR-30e-5p-NLRP3 (nucleotide-binding domain-like receptor protein 3) axis in inflammation-mediated neurodegeneration in patients with PD [200]. Compared with DNA methylation and HPTMs, the detection of miRNAs is more convenient, leading to miRNAs becoming more powerful candidates for the clinical diagnosis of PD. Although altered expression levels of miRNAs have been confirmed to be associated with the progression of PD, and the combined detection of multiple miRNAs can improve the reliability of the diagnosis in PD patients, more convincing evidence is needed to determine whether miRNAs can be applied as candidate biomarkers in clinical practice.

Epigenetic regulation of ferroptosis in PD

Recently, researchers have become interested in exploring how epigenetics regulate ferroptosis during PD [34], which provides a new avenue for investigating the associations among ferroptosis, epigenetics and PD. In the following sections, we discuss the epigenetic regulation of ferroptosis in PD and the possible mechanisms involved. We focused on the contributions of different epigenetic modifications involved in ferroptosis to PD to address the possible underlying regulatory mechanisms, as shown in Fig. 3.

Fig. 3. Epigenetic regulation of ferroptosis in PD and the possible mechanisms involved.

①DNA methylation regulates ferroptosis by inhibiting the expression of SLC7A11 and DPP4. Additionally, DPP4 can affect neuronal activity in individuals with PD by reducing BDNF levels. ② Erastine-induced H3K9ac and H3K27ac can promote ferroptosis by down-regulating GSH. This process can be reversed by NPD1, which has neuroprotective effect. ③ miR-494-3p enhances the process of ferroptosis and exacerbates PD by decreasing the level of REST, which can induce the expression of GSH and exert a neuroprotective effect. ④ miR-214 can induce lipid peroxidation, which is involved in ferroptosis by increasing ACSL4 expression, and is involved in PD by inducing the neurotoxicity of dopaminergic neurons. ⑤ HDAC9 can increase the Fe²⁺ content, initiating lipid peroxidation and aggravating ferroptosis, and induce the death of dopaminergic neurons and thus participate in PD. ⑥ miR-30-5p can increase the iron content by inhibiting the expression of FPN1, which can be regulated by H3K4me3 and H3K27me3, thus triggering lipid peroxidation and inducing ferroptosis. Additionally, miR-30-5p can also induce PD by damaging dopaminergic neurons. DPP4 Dipeptidyl Peptidase 4, BDNF Brain-Derived Neurotropic Factor, NPD1 Neuroprotectin D1, REST Repressor Element-1 Silencing Transcription Factor, FPN1 Ferroportin 1, SN Substantia Nigra.

Role of DNA methylation in regulating ferroptosis during PD

In mammals, DNA methylation is the most commonly investigated epigenetic mark. Methyl CpG binding protein 2 (MECP2) is expressed in the brainstem and thalamus and can interact with DNMTs, thus affecting gene expression and participating in neuronal development [201]. Studies have shown that inhibiting the expression of MECP2 can ameliorate MPTP-induced neurotoxicity in mice by activating NF-E2-related factor-2 (Nrf2) and brain-derived neurotropic factor (BDNF) [202]. Among them, BDNF can exert neuroprotective effects by promoting neuronal differentiation, regeneration and axon growth [203], thus reducing dyskinesia [204]. Interestingly, Mecp2 gene mutations correlate with abnormal iron overload in the caudate nucleus, SN and related gray matter [205], indicating connections among DNA methylation, imbalanced iron metabolism and PD.

Homocysteine (Hcy) is generated through the demethylation of arginine and is associated with neurotransmission, membrane integrity, macromolecular synthesis, and DNA methylation. Hcy can increase the expression of DNMT1, DNMT3a, and DNMT3b and increase the methylation of the Gpx4 gene, which significantly contributes to a reduction in GPX4 expression. This process exacerbates oxidative stress and promotes ferroptosis [206]. The upregulation of Hcy has been implicated in cognitive impairment in PD patients [207] through the regulation of Gpx4 methylation and accelerates the progression of PD [208]. Ferrostatin-1 (Fer-1) is the first discovered compound that can effectively protect cells from ferroptosis by suppressing lipid peroxidation. Fer-1 can inhibit the downregulation of the Gpx4 gene in 6-OHDA-induced PD cell models [209]. Furthermore, a recent study showed that Fer-1 dose-dependently inhibited Hcy-induced total DNA methylation, and ameliorated the decrease in cell viability, apoptosis, intracellular oxidative stress and ferroptosis induced by Hcy [210]. These results indicate that Hcy can aggravate ferroptosis in PD by inducing DNA methylation and that this process can be inhibited by Fer-1, suggesting that DNA methylation may be involved in the pathogenesis of ferroptosis in PD.

Very long-chain fatty acid protein 5 (ELOVL5) and fatty acid desaturase 1 (FADS1) are involved in the production of long-chain polyunsaturated fatty acids (PUFAs), which are vital factors involved in ferroptosis, in most cells. Hypermethylation of the promoter regions of ELOVL5 and FADS1 results in decreased expression of ELOVL5 and FADS1 and eventually leading to cell confrontation to ferroptosis [211]. Among these genes, the FADS gene is associated with bipolar disorder, which has neuropathological manifestations similar to those of PD (the axonal degeneration of monoaminergic neurons) [212, 213]. These findings may provide evidence for the potential associations among FADS gene methylation, ferroptosis and PD.

Furthermore, DNA methylation at specific CpG islands upstream of the transcriptional start site (TSS) in the FSP1 promoter negatively regulates the expression of FSP1, thus affecting ferroptosis [214]. Intriguingly, FSP1 may also be a possible target to protect against iron-dependent cell death in PD [215]. Similarly, an analysis of blood-based DNA methylome-wide associations in PD patients revealed that increased methylation levels of the SLC7A11 gene (encoding system Xc-) decrease the expression of system Xc- by inhibiting the transcription of this gene, resulting in reduced cystine absorption and GSH contents [216] and increasing the risk of PD (Fig. 3). SLC7A11 plays a crucial role in regulating system Xc-, which is directly linked to ferroptosis. These findings provide evidence that DNA methylation participates in the pathogenesis of PD by influencing ferroptosis. Moreover, dipeptidyl peptidase 4 (DPP4), also called CD26, is a glutathione suppressor that can promote lipid peroxidation and induce ferroptosis [217, 218]. Studies have shown that DPP4 inhibitors can block the death of dopaminergic neurons in PD patients by increasing BDNF expression (Fig. 3). Some studies have shown that the transcription of DPP4 is regulated by epigenetic mechanisms. For example, genotype-dependent methylation of the CpG island in the DPP4 promoter suppresses DPP4 gene expression [219]. H3K27me3 [220] and H3K9ac [221] in the DPP4 promoter can inhibit and promote DPP4 gene transcription, respectively. These findings link DNA methylation and ferroptosis to the progression of PD, suggesting potential combined treatment strategies for PD.

These results indicated that DNA methylation can influence the development of PD by aggravating ferroptosis, such as the methylation of the Gpx4, FSP1, and SLC7A11 genes. In addition, DNA methylation, such as the methylation of the FADS and DPP4 genes, can also serve as a connection between ferroptosis and PD. However, more investigations are needed to fully clarify the complex relationship between the DNA methylation of genes associated with ferroptosis and the development of PD. This analysis includes exploring the temporal dynamics of these methylation changes during disease progression and how they might affect ferroptosis during PD pathogenesis.

Histone modifications and ferroptosis during PD

As one of the intensively studied epigenetic codes, histone modifications influence the activity of dopaminergic neurons in PD through neuroinflammation and oxidative stress [222], which are associated with ferroptosis. Therefore, we explored how histone modifications influence PD through ferroptosis in detail.

Histone methylation and ferroptosis in PD

RSL3, a GPX4 inhibitor, can enhance the binding of Fe²⁺ to glutamate (E) and aspartate (D) residues in histone tails, affecting the structure of the histone octamer compound. In RSL3-induced ferroptotic cells, the repression of H3K37me3 induced by the histone lysine demethylase KDM6B decreased in a time-dependent manner. Loss of H3K79me3 has also been observed after subsequent treatment with RSL3. These changes play important roles in DNA fragmentation, cellular senescence and transcriptional activity [223], all of which are related to the pathogenesis of PD. RSL3 can enhance rotenone-induced neurotoxicity and damage of dopaminergic neurons [224], which can induce PD; however whether this process is mediated by exacerbating ferroptosis needs further exploration.

Lymphoid-specific helicase (LSH) is a member of the SNF2 family of chromatin remodeling ATPases [225]. Studies have shown that LSH can lead to the significant overexpression of fatty acid desaturase 2 (FADS2), a rate-limiting enzyme involved in ferroptosis. In the presence of LSH, the level of H3K4me3 (an active chromatin marker) at the FADS2 promoter increased significantly, whereas the level of H3K27me3 (a suppressive chromatin marker) decreased, thus suppressing ferroptosis by decreasing intracellular iron and lipid ROS accumulation [226]. However, FADS2 has been identified as one of the core genes overlapping between ferroptosis and PD [227], suggesting that ferroptosis, histone methylation and PD may be linked through this gene.

SET domain bifurcated histone lysine methyltransferase 1 (SETDB1) is a specific methyltransferase of H3K9 and is responsible for transcriptional repression via H3K9me in euchromatin genes, thus participating in various life processes, such as early embryonic development [228]. Knockdown of SETDB1 reduces H3K9me3 levels, accompanied by increase Fe²⁺ levels and a decrease in GPX4 and Nrf2 levels, leading to cellular lipid peroxidation and ferroptosis [229]. Notably, SETDB1 knockout significantly decreased repressive activities of zinc finger protein 746 (ZNF746) [230]. Overexpression of ZNF746 disrupts mitochondrial homeostasis and energy metabolism, facilitating the death of dopaminergic neurons in PD [231]. These findings suggest that SETDB1 may play a central role in the interplay between histone methylation, ferroptosis and PD.

Additionally, GSK-J4, a novel inhibitor of histone lysine demethylases (KDMs), increased the levels of H3K4me3 and H3K27me3 correspondingly. Treatment with GSK-J4 has been shown to increase TFR1 and FPN1 levels and decrease FER and free labile iron levels in 6-OHDA-treated SH-SY5Y cells [183]. Interestingly, GSK-J4 rescued the 6-OHDA-induced decreases in H3K4me3 and H3K27me3 levels in SH-SY5Y cells, where H3K4me3 is a crucial regulator of FPN1 expression [183]. In addition, GSK-J4 also increased cell viability, decreased 6-OHDA-induced apoptosis, and prevented 6-OHDA-induced motor defects in rats [183]. However, the associations among histone methylation, ferroptosis, and PD are not entirely clear. For example, protein arginine methyltransferase 1 (PRMT1), is the first protein arginine methyltransferase to be cloned and is most abundant in mammals [225, 232]. Studies have confirmed that both PRMT inhibitors and PRMT1 knockout can reduce the level of asymmetric dimethylation of histone H4 on arginine 3 (H4R3me2a) in ACSL1 promoter regions and even genome-wide, leading to the upregulated expression of ACSL1, a ferroptosis inducer that increases lipid peroxidation [233]. However, increased PRMT1 expression has been observed in the SNpc of MPTP-treated mice, indicating that PRMT1 might also be involved in the pathology of PD [234], which might be distinct from the mechanism related to ferroptosis. Although some findings have provided insights into the interplay between histone methylation, ferroptosis, and PD, further investigations are needed to elucidate the direct impact of histone methylation on PD through the regulation of ferroptosis.

Role of histone acetylation in regulating ferroptosis during PD

Histone deacetylases (HDACs) modulate transcription by removing acetyl groups from the amino acid residues (mainly lysine) of proteins such as histones or transcription factors [235]. Currently, 18 HDAC isoforms have been discovered in humans. Among them, HDAC9 is closely related to neuronal damage [236] (Fig. 3). In SH-SY5Y cells, HDAC9 can regulate the expression of the transcription factors HIF-1 and Sp1 by inducing their deacetylation, thereby increasing the expression of the pro-ferroptotic target gene Tfr1 and decreasing the expression of the anti-ferroptotic target gene Gpx4 simultaneously [237]. Both transcriptional changes contribute to the activation of ferroptosis, which can be prevented by HDAC9 silencing. Intriguingly, HDAC9 is expressed in the nigral dopaminergic neurons of adult PD mice. Inhibition of HDAC9 can promote the growth of neurite in SH-SY5Y cells and protect dopaminergic neurons from MPP⁺-induced neurotoxicity [238]. These effects may be related to the reduction in HDAC-induced ferroptosis. Elongation of very long-chain fatty acid-4 (ELOVL4) is a member of the elongation of very long-chain fatty acids (ELOVLs) family [239]. A recent study has found that elovanoids (ELVs) (synthesized from precursors produced by ELOVL4) and neuroprotectin D1 (NPD1) can reverse erastin-induced hyperacetylation of H3K27 and H3K9 and then inhibit ferroptosis by interfering with the downregulation of system Xc-, and decreasing cysteine uptake and GSH consumption [240]. Interestingly, ELVs and NPD1 can inhibit apoptosis and maintain the dendritic arbor of surviving dopaminergic neurons, which can limit neuroinflammatory signaling [241] and exert a neuroprotective effect on PD [242, 243] (Fig. 3).

Role of histone ubiquitination in regulating ferroptosis during PD

The classic tumor suppressor gene TP53 regulates cell proliferation, differentiation, metabolism, cell cycle arrest, apoptosis, and senescence [244–246]. Histone H2B monoubiquitinated at position 1 (H2Bub1) [247, 248] has been shown to be enriched at TP53 target genes [249, 250]. Recent studies have suggested that the induction of ferroptosis might represent an additional mechanism contributing to the oncosuppressive functions of TP53 [85]. Studies have shown that TP53 can promote ferroptosis by regulating SLC7A11 expression in cells, but delays ferroptosis in PD cells by binding to DPP4 and GPX4 [218, 251, 252]. The relationship between H2Bub1/TP53/ferroptosis may provide a novel avenue for treating PD. Additionally, the loss of the histone deubiquitinase MYSM1 could result in ferroptosis in hematopoietic stem cells (HSCs) by reducing protein synthesis rates [253], and whether this mechanism has a similar effect on PD may be worth exploring.

Role of histone phosphorylation in regulating ferroptosis during PD

Histone phosphorylation involves the transfer of a phosphate group to an amino acid residue of histone through the actions of protein kinases (PKs) and protein phosphatases (PPs), thus regulating transcriptional events and biological processes [254]. Autophagy is a conserved degradation pathway in which damaged organelles and macromolecules are degraded by lysosomes to meet metabolic needs and renew certain organelles under the regulation of autophagy-related genes [255], such as the Atg5 and Atg7 genes, which contribute to ferroptosis [256]. Nuclear receptor coactivator 4 (NCOA4) is a key regulator of the autophagic degradation of FER and thereby increases the level of free iron [257]. The phosphorylation of histone H3 on serine 10 (p-H3S10) can promote the transcription of the Ncoa4 gene [258], thereby suppressing FER heavy polypeptide 1 (FTH1) and GSH expression and inducing ferroptosis [259]. As an important promoter of ferroptosis [260], the protein expression of NCOA4 is increased in MPP⁺-induced SH-SY5Y cells, leading to the excessive lipid peroxidation and neuronal death [261]. Therefore, p-H3S10 may participate in PD by regulating the expression of NCOA4 in ferroptosis. Additionally, p-H3S10 is considered as a marker of primary neurogenesis and cellular responses, such as mitosis [262]. It can interact with other HPTMs, such as those involved in acetylation, to regulate gene transcription and is involved in the onset and deterioration of various diseases [263–265].

These findings highlight the importance of histone modifications in regulating ferroptosis during PD.

Roles of microRNAs in regulating ferroptosis during PD

MicroRNAs are the most extensively studied noncoding RNAs in epigenetics and play important roles in messenger RNA (mRNA) degradation and post-transcriptional regulation [266, 267]. In patients with PD, several microRNAs, including miR-30, miR-124, miR-29, miR-7, miR-485 and miR-26, are dysregulated [196]. Among them, miR-124 is enriched in the brain and is involved in a series of physiological and pathological changes in the nervous system [268]. The evidence suggests that miR-124 may participate in the progression of PD through multiple pathways, including regulating cell survival, mitochondrial metabolic disorders, and immune dysfunction in the nervous system. A clinical analysis indicates that decreased plasma levels of miR-124 may be recognized as a potential diagnostic biomarker for PD [268]. Moreover, the overexpression of miR-124-3p protects dopaminergic neurons in the SNpc and striatal fibers and counteracts motor behavior symptoms [269]. Interestingly, miR-124-3p can downregulate Fe²⁺ and lipid peroxidation responses, suggesting that miR-124-3p is a negative regulator of ferroptosis [270]; however, direct evidence for the neuroprotective effect of this regulatory mechanism in patients with PD is still lacking. MiR-30b-5p has been reported to exert inhibitory effects on cell proliferation and invasion [271]. The upregulation of miR-30-5p could cause Fe²⁺ accumulation by influencing the expression of FPN1 and then induce ferroptosis [272]. Furthermore, the serum miR-30-5p level is increased in PD patients and has the potential to be a biomarker for the early diagnosis and progression of PD [273]. Therefore, a potential research focus may be to determine whether increased serum level of miR-30-5p influences PD by inducing ferroptosis.

Repressor element-1 silencing transcription factor (REST), a neuroprotective molecule under physiological conditions, can activate neuronal proliferation and differentiation in the brain. REST is downregulated in neurological diseases such as depression and dementia, which cause neuronal death [274, 275]. The overexpression of REST significantly alleviates mitochondrial damage and increases the levels of TH, NSE, and GPX4 while decreasing ACSL4 levels in erastin-treated cells [276]. Researchers have discovered that miR-494-3p can bind to the Rest 3′-UTR, leading to a significant downregulation of REST, ROS production, mitochondrial injury, and ferroptosis and ultimately causing the death of neurons in MPTP-induced PD model mice. These processes are notably reversed by Fer-1 [276], suggesting that miR-494-3p may play a role in PD by inhibiting the expression of the Rest gene, which could induce ferroptosis. The suppression of miR-494-3p might represent a potential therapeutic approach for PD therapy, as shown in Fig. 3.

Notably, the level of miR-214 in the serum is increased in the early stage of PD (possibly due to a compensatory response) but tends to decrease with disease progression [277], indicating that miR-214 could serve as a potential biomarker for identifying PD at an early stage. Remarkably, miR-214 was also reported to increase the level of H3K27ac at the promoter regions of the ferroptosis driver genes ACSL4, SLC38A1 and PRKAA2, promoting the accumulation of RNA polymerase II (RNAP II) at these promoter regions and leading to transcriptional activation and subsequent induction of ferroptosis [278] (Fig. 3). These results support the relationship between miRNAs and ferroptosis in PD.

Diagnosis and therapy of PD

In recent years, the methods for diagnosing PD and treatment measures for PD have been constantly improved. Owing to the extremely complex genetic architecture of PD, the detection of risk genes for PD via genetic testing for mendelian forms, such as LRRK2 [279], GBA [280], SNCA [281], and several genes related to DNA methylation and ferroptosis, including Tet1, MAPT, PDE4D, GPR37, PARK7(DJ-1), FSP1, and SLC7A11, has become a relatively common testing approach in clinical practice. In addition, imaging techniques, such as structural magnetic resonance imaging (MRI), dopamine transporter-single photon emission computed tomography (DAT-SPECT), fluorodeoxyglucose positron emission tomography (FDG-PET), transcranial ultrasound, and radiotracer imaging of alpha-synuclein, have also been used in the diagnosis of PD [282]. Among them, structural MRI can be used to evaluate iron deposition in the SN [283]. Imaging techniques have high specificity and sensitivity for atypical parkinsonism, but they generally cannot distinguish the different subtypes of PD. Therefore, these methods must be used in combination with clinical symptoms and other clinical diagnostic criteria, such as the Movement Disorder Society Unified-Parkinson Disease Rating Scale (MDS-UPDRS) [284]. Interestingly, with the advancement of high-throughput sequencing and mass spectrometry, the concept and research methods of “omics” have been continuously improved. Recently developed spatial epigenomic, transcriptomic and proteomic methods, such as spatial, spatial CUT&Tag–RNA-seq, have been used to dissect epigenetic and transcriptional states in tissues, dynamically [285]. Different phenotypes can subsequently be observed by imaging an organ system [286], suggesting that imaging and epigenomics can be combined for the diagnosis of PD. Moreover, olfactory function has been extensively studied in PD patients using the UPSIT or Sniffin Stick test [287, 288]. Although the specificity of olfactory testing is low, its affordability and easy applicability make it a candidate for the initial clinical workup of screening for PD. In this review, several miRNAs, such as miR-124-3p, miR-30b-5p, miR-419-3p, and miR-214, which are also associated with ferroptosis, could also be identified as clinical biomarkers for the diagnosis of PD.

Currently, no treatment can achieve a cure for PD, but relevant clinical trials are exploring treatments. The common and effective drugs for PD are levodopa dopamine replacement agents, L-DOPA decarboxylase (DDC) inhibitors, dopamine agonists, monoamine oxidase B (MAO-B) inhibitors, and adenosine blockers [289]. Ferroptosis inhibitors (such as DFO, DFP and DFS) and epigenetic drugs (such as HDACIs, resveratrol, GSK-J4, SETDB1, and PRMT1) are considered potential therapeutic candidates, as mentioned above (Table 1). However, considering the toxic side effects, BBB permeability of drugs, the complex interactions between them, and the individual differences among patients, the clinical progress of single-ingredient drugs and compound-ingredient drugs for PD is extremely deliberate. Notably, numerous small molecules or compounds that are currently available can directly target and modulate proteins within ferroptosis-related pathways in patients with PD, including Fer-1, DFO and DFP. Given the heritability and reversibility of epigenetic modifications, drugs directly targeting epigenetics modifications have the potential to regulate pathological processes at the transcriptional level and allow altered genes with normal DNA sequences to experience functional recovery. Furthermore, the widespread use of epigenetics in the nervous system enhances the reliability of combining epigenetic treatments with conventional pharmacological approaches. Epigenetic drugs may increase chromatin accessibility for other therapeutic agents through chromatin decompaction, thereby significantly improving therapeutic efficacy with lower drug dosages. This property not only helps mitigate unwanted side effects but also aids in overcoming acquired drug resistance [290, 291]. Additionally, exercise, a nonpharmacological, holistic and patient-centered therapeutic intervention, has been widely applied to improve motor function in PD patients [292] through interventions, such as aqua‐based training, gait/balance/functional training, supervised slackline training, “Lee Silverman Voice training BIG” (LSVT BIG), and endurance training [293]. However, the effects of exercise, which requires individual modalities, volumes and intensities for different PD patients, are limited. The treatment of PD remains a challenge.

Table 1.

Candidate drugs and their main effects on iron metabolism, ferroptosis, epigenetics, and Parkinson’s disease.

Candidate drugs	Effect on iron metabolism /ferroptosis/epigenetics	Effect on Parkinson’s disease	References
Deferoxamine (DFO)	decreases the levels of TFR and DMT1; inhibits ferroptosis	alleviates behavioral deficits; decreases the expressions of α-syn; protects dopaminergic neurons	[46–49]
Deferiprone (DFP)	decreases iron deposition; inhibits ferroptosis	specially reduces the abnormal iron levels in the SN	[47–49]
Desferasirox (DFS)	decreases iron deposition; inhibits ferroptosis	reduces the aggregation of α-syn; ameliorates movement disorders	[101, 102]
Clausenamide	increases GSH peroxidase activity; alleviates erastin-induced ferroptosis	recovers MPTP-impaired gait performance; blocks lipid peroxidation in the midbrain	[94]
Quercetin	improves mitochondrial dysfunction; inhibits erastin- and RSL3-induced ferroptosis	attenuates MPP+-induced cell death; attenuates behavioral disorders; protects dopaminergic neurons	[62]
Clioquinol	decreases the iron content in the SN; suppresses oxidative stress both in vivo and in vitro	improves motor and non-motor deficits after MPTP intoxication	[95]
Apoferritin	decreases the iron content in the SN and regulates iron transporters; increases the expression of ACSL4 and decreases the expression of FSP1	rescues weight loss and improves motor deficits induced by MPTP; inhibits the MPTP-induced degeneration of dopaminergic neurons; decreases the number of Iba1-positive microglia in the SN of MPTP-induced mice	[76]
Thonningianin A	decreases iron accumulation, GSH levels, and lipid peroxidation	decreases the aggregation of α-syn	[96]
Hinokitiol	decreases ROS levels and lipid peroxidation; up-regulates the levels of SLC7A11, GPX4, TFR1 and FPN, and down-regulates the expression of FTH	rescues the deficits of locomotion and neurodevelopment	[97]
Paeoniflorin	reduces lipid ROS accumulation	protects against neuronal damage caused by MPP+	[98]
Ferrostatin‐1	suppresses the increases in GSH depletion, ROS levels, and iron contents; up-regulates the GPX4 protein expression.	decreases the aggregation of α-syn	[99]
α‐Lipoic acid	reduces the levels of iron, and ROS; increases the GSH level	increases the viability of MPP+ -induced PC12 cells	[100]
histone deacetylase inhibitor (HDACI)
Resveratrol	an activator of SIRT-1	inhibits microglial activation; decreases mitochondrial oxidative stress and apoptosis	[33, 169–171]
NMJ-2/NMJ-3 (cinnamyl sulfonamide hydroxamate derivatives)	inhibitors of histone deacetylases	improves motor function, cognition and depressive-like symptoms; decreases the levels of oxidative stress and inflammatory mediators in MPTP-treated rats	[178]
MC1568	an inhibitor of HDAC5	prevents microglial activation, decreased neurite length in, dopaminergic neurons, and 6-OHDA-induced nigrostriatal neurodegeneration	[156]
Contilisant+Tubastatin A	an inhibitor of HDAC6	reduces motor defects and ROS levels; improves mitochondrial function	[179]
histone demethylase inhibitor
GSK-J4	a potent inhibitor of KDM6A/B and KDM5B/C (the histone demethylase of H3K27me3/me2 and H3K4me3/me2); a possible iron chelator	decreases 6-OHDA-induced apoptosis in SH-SY5Y cells; rescues the motor deficits in SD rats; suppresses the 6-OHDA-induced increase in ROS production.	[183]
SETDB1	an activator of H3K9me; decreases the expression of GPX4 and increases the level of ferrous ion; enhances ferroptosis	may affect mitochondrial function by regulating ZNF746 expression and thus participates in the death of dopaminergic neurons in PD	[228–231]

Conclusion and perspectives

Evidence has gradually emerged regarding the involvement of epigenetics in PD. The imbalance of DNA methylation and miRNA levels have been reported to be effective early diagnostic biomarkers and potential therapeutic targets for PD. As described in our review, the methylation of the Gpx4, FSP1, and SLC7A11 genes may be involved in the process of PD through ferroptosis. The changes in miR-124, miR-30-5p, miR-494-3p and miR-214 could serve as connections between PD and ferroptosis. However, whether these factors induce ferroptosis first or exacerbate PD earlier remains unclear. The mechanisms of these factors in PD and ferroptosis must be explored. A further discussion of the roles of these mechanisms combined with ferroptosis in PD patients is needed.

Compared with changes in DNA methylation and miRNAs, the regulatory mechanisms of histone modifications in PD have been studied more extensively. For example, the increased H3K4me3 level in the FADS2 gene induced by LSH could upregulate the expression of FADS2, and then lead to ferroptosis in PD patients. SETDB1 knockdown could cause ferroptosis by decreasing H3K9me3 levels on the one hand and induce PD by leading to mitochondrial damage on the other hand. GSK-J4 could upregulate the expression of Fpn1 by increasing H3K4me3 levels and then inhibit ferroptosis in PD patients. The inhibition of PRMT could increase H4R3me2 levels in ACSL1 and then induce ferroptosis in PD. As the level of PRMT is decreased in PD mice, the different changes in PRMT may be worthy of exploration. HDAC9 can cause ferroptosis by increasing the expression of Tfr1 and Gpx4. When HDAC9 is inhibited, damage to DA neurons in PD are reduced, suggesting a potential relationship between histone acetylation, ferroptosis, and PD. Furthermore, some studies have shown that the ubiquitination and phosphorylation of histones play important roles in ferroptosis and PD, such as the H2Bub1/TP53/SLC7A11/ferroptosis/PD and p-H3S10/Ncoa4/FTH1/ferroptosis/PD pathways. An increase in H2Bub1 levels could upregulate the expression of the TP53 gene, which could influence ferroptosis in PD patients by adjusting the levels of SLC7A11, DPP4, and GPX4. Similarly, p-H3S10 could upregulate the expression of the Ncoa4 gene and then decrease FTH1expression, causing ferroptosis and accelerating the progression of PD.

Additionally, a novel epigenetic modification—histone lactylation has recently been reported in neurodegenerative diseases [294, 295] and is associated with ferroptosis [296]. In an AD transgenic mouse model (5×FAD), H4K12la increased microglial activation by influencing the positive loop of glycolysis/H4K12la/PKM2, thereby aggravating Aβ aggregation and leading to cognitive impairment in AD model mice [295]. As the substrate for lactation, lactate levels have been found to be abnormally increased in the CSF of patients with late-onset PD. The increased lactate level may lead to apoptosis by activating the AMPK/Akt/mTOR pathway. These changes can be attenuated by inhibiting the expression of hexokinase 2 (a key enzyme involved in glycolysis), thus decreasing lactate production [297]. Remarkably, H3K18la, a common site for H3 histone lactylation modification, has been found to reverse lactate-induced changes, and cause ferroptosis by reducing GPX4 expression [298]. These findings indicate that histone lactylation may be a potential avenue for exploring the connection between ferroptosis and PD. Currently, studies that directly link ferroptosis, epigenetics, and PD are limited. Further studies are needed to establish a causal relationship between ferroptosis and the progression of PD, as well as to determine whether the observed epigenetic changes are causal or consequential in relation to PD.

The development of gene editing has enabled the stable modifications of the human genome from the stem cell stage. In particular, rewriting the epigenetic landscape to control gene expression through CRISPR-Cas9 and other CRISPR systems is programmable, reversible, and does not require DNA breaks [299]. Recently, CRISPRoff, a programmable epigenetic memory writer, was shown to silence gene expression durably and specifically, and gene silencing can be reversed when DNA methylation is depleted [300]. Through the use of gene editing technology, an intervention for PD could be established by designing snRNAs that target PD susceptibility genes or key regulators of ferroptosis.

In conclusion, we have discussed the roles of different epigenetic changes including DNA methylation, histone modifications and miRNAs in the pathogenesis of PD through ferroptosis mechanisms. We have elaborated on the potential interplay between these epigenetic mechanisms and ferroptosis and propose that this interplay opens new possibilities for the exploration of new therapeutic strategies for PD. Although multiple studies have confirmed that epigenetics can impact the process of ferroptosis in various diseases, relatively few studies have linked ferroptosis, epigenetic modifications and PD. Thus, further studies are needed to elucidate their interplay in PD. Additionally, research is also required to develop new small-molecule epigenetic modulators that can also inhibit ferroptosis as possible preventative treatments for PD.

Competing interests

The authors declare no competing interests.