Targeting epigenetic mechanisms in amyloid-β–mediated Alzheimer’s pathophysiology: unveiling therapeutic potential

Abstract

Alzheimer’s disease is a prominent chronic neurodegenerative condition characterized by a gradual decline in memory leading to dementia. Growing evidence suggests that Alzheimer’s disease is associated with accumulating various amyloid-β oligomers in the brain, influenced by complex genetic and environmental factors. The memory and cognitive deficits observed during the prodromal and mild cognitive impairment phases of Alzheimer’s disease are believed to primarily result from synaptic dysfunction. Throughout life, environmental factors can lead to enduring changes in gene expression and the emergence of brain disorders. These changes, known as epigenetic modifications, also play a crucial role in regulating the formation of synapses and their adaptability in response to neuronal activity. In this context, we highlight recent advances in understanding the roles played by key components of the epigenetic machinery, specifically DNA methylation, histone modification, and microRNAs, in the development of Alzheimer’s disease, synaptic function, and activity-dependent synaptic plasticity. Moreover, we explore various strategies, including enriched environments, exposure to non-invasive brain stimulation, and the use of pharmacological agents, aimed at improving synaptic function and enhancing long-term potentiation, a process integral to epigenetic mechanisms. Lastly, we deliberate on the development of effective epigenetic agents and safe therapeutic approaches for managing Alzheimer’s disease. We suggest that addressing Alzheimer’s disease may require distinct tailored epigenetic drugs targeting different disease stages or pathways rather than relying on a single drug.

Introduction

Alzheimer’s disease (AD) is the prevailing chronic neurodegenerative disorder, primarily known for its progressive memory decline and eventual development of dementia. Its key features include the accumulation of amyloid-β protein (Aβ) as extracellular plaques, the formation of tau-rich intracellular neurofibrillary tangles, the loss of synaptic connections, and the death of neurons, particularly in cerebral neocortex and hippocampus. Despite a century of research, the underlying biological mechanisms driving the development of AD remain elusive, and effective therapeutic strategies for its treatment are largely debatable. Memory and cognitive deficits observed in the prodromal and mild cognitive impairment (MCI) stages of AD are believed to primarily arise from synaptic dysfunction (Meftah and Gan, 2023). In AD, synaptic dysfunction is recognized as an early event, with subtle synaptic alterations detectable in individuals at the stage of subjective cognitive decline, which represents the earliest phase of AD (Enache et al., 2020). It is widely acknowledged that cognitive decline follows a biological continuum, with a significant portion of the disease process commencing before the appearance of noticeable neurocognitive symptoms, encompassing stages from subjective cognitive decline, MCI, and AD dementia (Jack et al., 2018). Remarkably, the impairment of cognition in the disease is more closely associated with synapse loss rather than the number of plaques and fibrillary tangles, degree of neuronal loss, or extent of gliosis (Meftah and Gan, 2023). Additionally, the synapse is where Aβ peptides are produced and serves as the focal point for toxic Aβ oligomers (Pelucchi et al., 2022). Importantly, multiple lines of evidence indicate that alterations in synaptic function and synapse degeneration occur during the earliest phases of AD, preceding the accumulation of misfolded protein aggregates and before neuronal loss (Meftah and Gan, 2023).

The phenomenon of synaptic plasticity, particularly long-term potentiation (LTP), is widely acknowledged as the neural mechanism underlying the processes of learning and memory. Extensive evidence has already established that soluble Aβ oligomers, rather than monomers or plaques, are the neurotoxic species of Aβ in the brain, leading to impairment of synaptic function, including the inhibition of LTP and facilitation of long-term depression (Li and Selkoe, 2020; Li and Stern, 2022). Importantly, alterations in synaptic function occur much earlier than changes in synaptic protein levels or synapse morphology induced by soluble Aβ oligomers. This temporal precedence can be attributed to the rapid physiological changes occurring within minutes when ion channels open or close, while protein synthesis involves the transfer of genetic information from DNA to mRNA through the process of transcription, which includes initiation, elongation, and termination. This genetic code is then used during translation, where amino acids are linked together in a specific order. Therefore, understanding synaptic dysfunction in the pathogenesis of AD would help in deciphering its etiology, enabling earlier diagnosis, and identifying therapeutic targets for treatment. Extensive evidence supports the notion that environmental influences can induce enduring alternations in gene expression, referred to as epigenetic modifications (Gauvrit et al., 2022). These modifications also hold a pivotal function in governing synaptic plasticity in response to neuronal activity (Maity et al., 2022). In this review, we delve into the intricate realm of recent discoveries that shed light on the specific epigenetic mechanisms through which Aβ oligomers exert their influence, leading to synaptic dysfunction. This exploration not only unravels the underlying processes but also elucidates the complex link between these mechanisms and the distinctive dementia phenotype witnessed in individuals suffering from AD. By meticulously dissecting these connections, we aim to provide a comprehensive understanding of the intricate interplay between Aβ oligomers and synaptic impairment, offering valuable insights into the pathogenesis of AD-related dementia.

Search Strategy

In this narrative review, all referenced studies were searched on PubMed, Science Direct and ClinicalTrials.gov using specific keywords, including Alzheimer’s disease, amyloid-beta, epigenetics, DNA methylation, hypomethylating agent, histone modification, histone deacetylation, HDAC inhibitor, inflammation, microglia, synaptogenesis, synaptic plasticity, long-term potentiation, cognition, enriched environment, transcranial magnetic stimulation, transcranial direct current stimulation, and therapy. The search was confined to articles published in English within the past two decades up to October 2023. We specifically included studies focused on the investigation of epigenetic modifications affecting synaptic function and the pathogenesis of AD.

Epigenetics Modification in Alzheimer’s Disease

Researchers are deeply intrigued by the extensive impact of epigenetic regulation on the formation of the nervous system and its intricate association with neurodegenerative conditions such as AD. Comprehensive investigations into epigenetic changes, spanning diverse populations, have revealed valuable insights into the underlying mechanisms of these diseases. These discoveries contribute to identifying potential biomarkers for early detection and illuminating promising targets for therapeutic intervention, ultimately paving the path for more effective approaches to addressing neurodegenerative disorders.

Importance of epigenetics in human diseases

Epigenetics encompasses inheritable modifications in gene activities that are induced by mechanisms unrelated to changes in DNA sequence. The epigenetic modifications are chemical alterations that impact gene expression without modifying the DNA sequence itself. Overall, epigenetic analyses involve investigating changes in DNA methylation, DNA–protein interactions, chromatin accessibility, histone modifications, and other related factors. The nucleus of eukaryotic cells contains tightly packaged chromatin, primarily composed of DNA and proteins. The fundamental unit of DNA packaging within the nucleus is the nucleosome, consisting of eight core histone proteins, H2A, H2B, H3, and H4, existing as a pair, along with the DNA molecule that coils around them. Nuclear chromatin plays a crucial role in regulating diverse cellular and biological processes. It achieves this by maintaining specific DNA loci in an “open” state, allowing accessibility to proteins involved in DNA replication, transcription, and DNA repair while other regions of DNA remain inaccessible. Epigenetics-mediated changes in DNA expression can impact both transcription and translation processes. Covalent modifications of DNA bases, such as methylation and modifications of histone proteins, can influence gene expression at the transcriptional level. On the other hand, non-coding RNAs, particularly microRNAs (miRNAs), a class of epigenetic modulators, play a role in regulating gene expression at the translational level (Lacal and Ventura, 2018).

Recently, there has been a significant focus on exploring the epigenetic changes associated with aging. Apart from the overall reduction in histone levels, as well as alternations in histone marks like acetylation and methylation (such as H3K27ac, H3K9ac, H3K56ac, H4K16ac, and H3K4me3) (Delgado-Morales et al., 2017; Nativio et al., 2020), age-related modifications in the epigenome also involve shifts in DNA hydroxymethylation and methylation patterns. These patterns primarily involve the presence of 5-methylcytosine or 5-hydroxymethylcytosine at cytosine-phosphate-guanine (CpG) dinucleotides (Kochmanski et al., 2018). In recent years, the study of epigenetics’ involvement in human diseases has gained substantial attention. It is now widely recognized that epigenetic modifications exert a profound influence on gene expression, and abnormalities in these modifications have been implicated in a range of disorders. This includes but is not limited to cancer, cardiovascular disease, neurological disorders, and notably, the COVID-19 syndrome (Farsetti et al., 2023). The investigation of epigenetic mechanisms holds great promise in deepening our understanding of disease development and potentially identifying new therapeutic targets.

Numerous epigenetic drugs, particularly those designed for cancer therapy, have undergone clinical trials. An illustration of this is guadecitabine, which belongs to the second generation of DNA methyltransferase inhibitors or hypomethylating agents. This class of drugs is pertinent because abnormal DNA methylation can cause various tumor suppressor genes to undergo promoter hypermethylation, leading to transcriptional silencing. In phase II clinical trial (NCT03179943), guadecitabine was tested in combination with atezolizumab (an anti-programmed cell death ligand 1) for patients with metastatic urothelial carcinoma unresponsive to initial immune checkpoint blockade therapy. The results indicated the success of the combination therapy in activating immune cells, mainly peripheral T and NK cells. This led to an enhanced infiltration of T cells into the tumor in a specific subgroup of patients. Correlative analysis indicated an absence of DNA demethylation in tumors following two treatment cycles (Jang et al., 2023). In another phase 1b NIBIT-M4 trial (NCT02608437) involving patients with advanced melanoma, the combination of guadecitabine with the anti-CTLA-4 antibody ipilimumab was shown to be safe, feasible, and well-tolerated. This combination therapy exhibited initial indications of both clinical and immunologic activity in metastatic melanoma patients. The 5-year follow-up data suggests that the integration of genetic immunoediting with the activation of adaptive immunity is a crucial requirement for achieving long-term clinical benefits through epigenetic immunomodulation in patients with advanced melanoma (Noviello et al., 2023). Moreover, histone deacetylase (HDAC) inhibitors have gained broader acceptance in clinical trials. For instance, a phase 3 trial involving a classical HDAC inhibitor, entinostat, combined with exemestane in hormone receptor-positive (HR⁺) advanced breast cancer patients demonstrated the general safety of the treatment. The trial reported manageable adverse events and a significant extension of progression-free survival compared to placebo plus exemestane (HR = 0.76, P = 0.046; Xu et al., 2023). Another clinical trial (NCT03291886) investigating the use of entinostat plus exemestane in advanced/recurrent breast cancer patients also revealed acceptable safety and prolonged progression-free survival (Iwata et al., 2023). Notably, a clinical trial (NCT03056495) has commenced to establish the maximal tolerable dose of vorinostat in AD patients. Furthermore, several clinical trials have employed miRNAs as biomarkers for diagnosing and monitoring the progression of various diseases. Hence, drugs targeting epigenetic modifications may offer a promising avenue for treating AD.

Epigenetic changes play a crucial role in the progression of AD

The primary factors contributing to the risk of developing AD include the process of aging, genetic factors, and epigenetic alterations. Alongside Aβ pathology, there is growing recognition of the association between AD and epigenetic abnormalities (Nativio et al., 2020; Sharma et al., 2020). Epigenetic mechanisms have the potential to regulate gene-environment interactions, thereby impacting susceptibility and influencing disease-related mechanisms (Sharma et al., 2020). It has been hypothesized that the interplay between epigenetic modifications and environmental factors plays a significant role in the development and progression of late-onset AD. These interactions, occurring across multiple genetic regions, are believed to contribute to an increased risk of developing late-onset AD (Gauvrit et al., 2022). Despite DNA-based polygenic scores capturing the minor effects of various single-nucleotide polymorphisms, the utilization of monozygotic twins in research has proven valuable for exploring non-genetic factors that play a role in the onset of AD. Polygenic scores for brain and cognitive traits do not explain the entire genetic variance seen in twin studies, which investigate shared environmental and genetic influences. Co-twin design studies confirm that the connection between biological markers (e.g., Aβ) and clinical markers (e.g., episodic memory impairment) in AD remains unaffected by genetic or environmental factors, suggesting the potential involvement of epigenetic modifications (Varjonen et al., 2023).

Alterations in DNA methylation have demonstrated connections with both aging and AD. Remarkable changes in DNA methylation have been detected in regulatory regions of AD neurons, exhibiting an accelerated state compared to typical aging processes (Li et al., 2019). Notably, AD individuals exhibit decreased global DNA methylation in brain regions commonly affected by AD, like the entorhinal cortex. Conversely, the frontal cortex, a site of synaptic loss in AD, displays higher DNA methylation levels in AD cases than in cognitively unimpaired individuals. Specific DNA methylation variations have been linked to early AD stages and susceptibility loci (De Jager et al., 2014). Utilizing large-scale DNA methylation arrays enable unbiased examination of site-specific methylation, revealing associations between genetic loci near AD risk genes (e.g., brain-derived neurotrophic factor [BDNF], BIN1, APOC1) and MCI/AD diagnosis (Vasanthakumar et al., 2020). Recently, an AD neuroimaging initiative study pinpoints the CpG site cg00386386, located in MED22, as linked to cognitive decline measured by the pre-Alzheimer’s cognitive composite (Li et al., 2021).

Blanco-Luquin et al. (2020) conducted a study involving 53 hippocampal post-mortem samples from AD patients. The research revealed a significant increase in DNA methylation levels in early AD samples compared to controls at CpG sites associated with ELOVL2, GIT1/TP53I13, HIST1H1A, and HIST1H3E/HIST1H3F genes. Notably, the methylation levels of ELOVL2 and HIST1H3E/HIST1H3F positively correlated with the deposition of p-tau protein in hippocampal samples. The ELOVL2 gene appears to play a central role in the innate immune defense system, while the protein encoded by GIT1 appears to have relevant effects on synapse formation and dendritic spine pruning in hippocampal neurons. Similarly, Jia et al. (2021) conducted a large epigenome-wide meta-analysis involving 3337 subjects. Utilizing MRI brain scans and genome-wide DNA methylation data, they identified differentially methylated CpG sites and genomic regions correlated with variation in hippocampal volume. These CpG sites were annotated to the brain-specific angiogenesis inhibitor 1-associated protein 2 (BAIAP2) gene (also known as IRSp53; cg26927218). BAIAP2 encodes a synaptic protein essential for learning and memory in the hippocampus. Additionally, a sex-specific meta-analysis, involving DNA methylation data from blood samples of 889 subjects aged 65 years and older, showed no overlap in significant DNA methylation differences between females and males (Silva et al., 2022). In females, the most significant CpG site, located near the promoter region of the PRRC2A gene, exhibited significant hypermethylation in AD subjects. In males, three out of the top 10 differentially methylated regions (DMRs) were mapped to promoter regions of the MCCC1, PM20D1, and KCTD11 genes. Notably, the MCCC1 gene is associated with mitochondrial homeostasis and has been implicated in sporadic Parkinson’s disease in multiple genome-wide association studies, while PM20D1 is associated with the response to Aβ accumulation in AD brains. These findings underscore the distinct sex-specific epigenetic architecture underlying AD.

In recent years, extensive epigenome studies on histone modifications in AD have yielded insights into their impact on disease initiation and progression (De Jager et al., 2014; Blanco-Luquin et al., 2020; Nativio et al., 2020; Chen et al., 2021). The dual nature of histone marks in AD has been revealed, with some lost and others gained, reflecting intricate dynamics (Nativio et al., 2020). A comprehensive multi-omics study examined AD patients’ temporal lobes vs. controls, showing enrichment of H3K27ac and H3K9ac marks, and reduced H3K122ac, linked to upregulated chromatin/transcription genes (CREBBP, EP300, TRRAP) encoding histone acetyltransferases (Nativio et al., 2020). In addition to identifying alterations in histone acetylation marks, Nativio et al. (2020) observed changes in several histone methylation marks in AD patients compared to elderly controls. The observed gains (H4K20me2, H3K4me2, H3K27me3, and H3K79me1) and losses (H3K79me2, H3K36me2, H4K20me3, H3K27me1, and H3K56me1) of marks were associated with both gene activation and repression. This underscores the potential dysregulation of histone methylation dynamics in AD (Nativio et al., 2020). Increased levels of the repressive histone modification H3K9me2 were observed in the prefrontal cortex of familial Alzheimer’s disease (FAD) mouse models, along with elevated expression of the histone acetyltransferases Ehmt1 and Ehmt2. Similar findings were noted in another AD mouse model and in the prefrontal cortex of AD patients, where EHMT1 expression was increased. Furthermore, the heightened H3K9me2 levels in the FAD mouse model correlated with decreased levels of α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) and N-methyl-D-aspartate (NMDA) glutamate receptor subunits. Treatment with EHMT1/2 inhibitors reversed the changes in H3K9me2 and glutamate receptor expression levels, providing additional evidence for epigenetic dysregulation in AD and suggesting a potential therapeutic strategy targeting histone methylation for AD treatment (Zheng et al., 2019). Iturria-Medina et al. (2022) used advanced machine learning to analyze multi-omics data from 1863 individuals’ brain tissue and blood, unveiling significant epigenetic (748 CpGs), gene expression (417 genes), protein (19 proteins), and metabolite (28 metabolites) changes in the three AD subtypes. These findings support personalized multi-omics AD taxonomy for tailored interventions.

MiRNAs, abundantly expressed in the central nervous system, show region- and age-specific patterns, including in the hippocampus and cortex of adult mice. MiRNAs play a crucial role in various neuronal compartments, including dendrites and synapto-dendritic areas, participating in the orchestration of events during neuronal activity. Within these locales, certain miRNAs like miR-9-3p, miR-17, miR-26, miR-29a-3p, miR-124, miR-132, miR-134, miR-137-5p, 138, miR-145, and miR-200c-3p are concentrated, actively regulating synaptic activity (Kaur et al., 2023). The complexity of AD pathogenesis encompasses diverse mechanisms like Aβ pathophysiology, tauopathy, synaptic dysfunction, and neuroinflammation, each associated with distinct miRNA abnormalities. For instance, in AD patients, cerebrospinal fluid levels of miR15a-5p, miR-16, miR-19b-3p, miR-103, miR-124-3p, miR125b-5p, miR130a-3p, miR140-5p, miR142-3p, miR146a, miR-328-3p, miR-340-5p, miR-361-5p, miR-223-3p, and miR-373-5p were reduced, while miR-let-7i-5p, miR10b-5p, miR-30a-5p, miR-100-5p, miR101-3p, miR106a, miR125b, miR132, miR143-3p, miR146a-5p, miR150-5p, miR-206, and miR-613 were elevated. These miRNAs are suggested as potential biomarkers for AD diagnosis due to their sensitivity and specificity (Kaur et al., 2023; Noor Eddin et al., 2023). A comprehensive understanding of AD-related neurobiological dysfunction relies on a consortium of pathological miRNAs, not a single one. Recent research with 826 AD patients and 658 controls reveals that miRNA clusters exhibit high sensitivity (0.89) and specificity (0.84) in AD diagnosis (Zhang et al., 2021). Furthermore, specific studies that utilize combinations of miRNAs have shown strong sensitivity and specificity in differentiating AD from other types of dementia (Martinez and Peplow, 2022). This suggests that a wide range of miRNAs may be involved in the pathophysiology of AD, potentially interconnected with the various aspects of its diverse mechanisms.

Aβ pathology and epigenetic dynamics

Evidence suggests that the accumulation of Aβ oligomers contributes significantly to AD development. Aβ is generated through the sequential proteolytic processing of the amyloid precursor protein (APP), wherein β-secretase (β-site APP-cleaving enzyme 1, BACE1) initiates cleavage, followed by subsequent cleavage by γ-secretase. Numerous environmental factors exert influence on genes associated with Aβ peptide production (BACE1, APP, PSEN2, and PSEN1), genes implicated in neurofibrillary tangle formation (GSK3β and MAPT), and genes contributing to the pathogenesis of late-onset AD (e.g. APOE). These influences may modify the aforementioned genes through various mechanisms, including (1) DNA methylation predominantly occurring on palindromic CpG sequences, which can form CpG islands. Notably, methylation at transcribed regions generally enhances transcriptional activity, while methylation at gene promoter regions typically reduces gene expression; (2) histone modifications, encompassing acetylation, phosphorylation, and methylation, on histone proteins. Such modifications play a crucial role in activating or deactivating diverse genes, constituting a pivotal regulatory mechanism for gene expression; (3) miRNAs, which bind to complementary sites on target mRNAs. In conjunction with components of the miRNA-induced silencing complexes, these miRNAs guide members of the Argonaute protein family to either degrade the bound mRNA or impede the initiation of its translation into protein products (He et al., 2020; Sharma et al., 2020). These epigenetic alterations in AD risk genes result in an elevation of Aβ production and Tau hyperphosphorylation.

Mastroeni et al. (2015) used human epigenetic PCR arrays, revealing parallels in epigenetic gene expression between Aβ-treated cells and AD brains. This model system allows for exploring disease-related biochemical changes. Specific DNA methylation shifts are linked to genes promoting apoptosis in response to Aβ₄₂ (Taher et al., 2014). Aβ₄₂ triggers abnormal histone acetylation patterns (Bie et al., 2014). Neuroinflammation-driven effects of Aβ₄₂ suppress H3 acetylation, DNA hypermethylation, and reduce neuroligin-1 expression, eventually impacting synaptic plasticity (Lithner et al., 2013). Aβ oligomer exposure elevates HDAC4 expression but not HDAC5 or HDAC1 in SH-SY5Y cells. Intriguingly, cytoplasmic HDAC4 guards neurons from exogenous Aβ oligomer neurotoxicity, while nuclear HDAC4 accumulation in Aβ-overexpressing cells contributes to disease progression (Chen et al., 2021). This aligns with HDAC4’s complex and dual role-neuroprotective in the cytoplasm, and neurotoxic in the nucleus (Sen et al., 2015). Aβ oligomer–induced epigenetic changes might involve Aβ₄₂ entering neuronal nuclei, binding to the Aβ interacting domain, engaging gene regulators, recruiting heterochromatin marks (H3K9Ac decrease, H3K9me3 increase) via specifically Aβ interacting domain binding. As a transcription factor, the binding of Aβ₄₂ to the Igf2 DMR2 (insulin-like growth factor 2–differentially methylated regions) and the Igf2 promoter results in increased DNA and histone methylation, ultimately reducing Igf2 expression. Notably, this effect is independent of the mechanisms involving H19 ICR (imprinting control region) DNA methylation (Fertan et al., 2023). Therefore, Aβ oligomers significantly contribute to AD development by inducing diverse epigenetic changes in neuronal cells (Figure 1). The dual role of Aβ₄₂ as a neuroprotective factor in the cytoplasm and a neurotoxic factor in the nucleus implies its unconventional role as a brain transcription factor and epigenetic regulator in AD, affecting genes independently of conventional mechanisms.

Figure 1.

Pathology of amyloid-beta and epigenetic fluctuations.

Epigenetic alterations, encompassing CpG site methylation, histone acetylation, and microRNA (miRNA), may enhance the susceptibility to Alzheimer’s disease. Such modifications impact key genes associated with Aβ peptide production (BACE1, APP, PSEN2, and PSEN1), neurofibrillary tangle formation (GSK3β and MAPT), and late-onset AD-related pathogenesis (e.g., APOE). The excessive Aβ production, binding to the Aβ interacting domain (AβID), engaging gene regulators, recruiting heterochromatin marks, or binding to other genes, instigating epigenetic alternations such as DNA methylation, histone modification, or miRNA changes. The excessive Aβ can also trigger neuroinflammation, leading to further epigenetic modification and culminating in synaptic dysfunction. Epigenetic modifications can potentially alter Aβ metabolism by a feedback mechanism. Created with BioRender.com. ApoE: Apolipoprotein E; APP: amyloid precursor protein; BACE1: β-site APP-cleaving enzyme 1; GSK3β: glycogen synthase kinase-3β; MAPT: microtubule-associated protein tau; PSEN: presenilin.

Epigenetics plays a role in inflammatory responses mediated by Aβ

The accumulation of Aβ protein precipitates the activation of microglia and astrocytes, a response concomitant with the release of inflammatory cytokines, including interleukin-1β (IL-1β), IL-6, IL-8, IL-12, IL-18, tumor necrosis factor-alpha, and transforming growth factor-beta (Leng and Edison, 2021). Recent investigations concentrating on microglial activation markers—specifically, monocyte chemotactic protein 1, chitinase-3-like protein 1, visinin-like protein-1, and glial fibrillary acidic protein—have observed their upregulation in the cerebrospinal fluids of individuals with AD (El Kadmiri et al., 2018). In the context of AD, microglia engage with Aβ oligomers and fibrils through various receptors, including scavenger receptors (SCARA-1, MARCO, SCARB-1, CD36, and RAGE), toll-like receptors (TLR2, TLR4, TLR6, and TLR9), G-protein coupled receptors (FPR2 and CMKLR1), α6β1 integrin, CD47, and triggering receptors expressed on myeloid cells 2 (Yu and Ye, 2015; Xu et al., 2022; Tamburini et al., 2023). Subsequent to initial recognition, microglial activation is facilitated through the nuclear factor kappa B (NF-κB) pathway (Combs et al., 2001). The persistent inflammation observed in AD results from the activation of NF-κB signaling, which prompts the release of cytokines and chemokines from microglia. NF-κB activation further initiates BACE1, facilitating the formation of Aβ fibrils. In turn, Aβ fibrils directly stimulate NF-κB, leading to the expression of APOE4 and mGluR5 (Sun et al., 2022). With the progression of aging in mammals, there is a gradual occurrence of hypomethylation in most tissues and hypermethylation in the promoter regions of genes. Furthermore, investigations have revealed alterations in DNA methylation in T-lymphocytes in response to aging, with a predominant presence of hypermethylated sites situated at CpG islands of silent genes and exhibiting enrichment for repressive histone marks (Van den Hove et al., 2014). The observed changes may stem from age-related processes, such as chronic antigen exposure, culminating in a proinflammatory phenotype.

The increase in microglial IL-1β levels with age is linked to DNA hypomethylation within the IL-1β promoter, suggesting a pivotal role for DNA methylation in the regulation of microglial inflammatory responses. Notably, the removal of DNA methylation is facilitated by ten-eleven translocation (TET) enzymes, dioxygenases responsible for catalyzing the oxidation of 5-methylcytosine into 5-hydroxymethylcytosine and other oxidative derivatives. Studies have shown that TETs not only fulfill diverse functions in the physiology of immune cells, including thymocytes, dendritic cells, T helper cells, and bone marrow-derived macrophages, but also exhibit a proinflammatory role in microglia (Carrillo-Jimenez et al., 2019). As an illustration, microglia associated with plaques in the hippocampus exhibited elevated TET2 expression in comparison to homeostatic microglia situated farther away from the plaques. Additionally, the ratio of Iba-1⁺ to TET2⁺ cells was notably high in individuals with AD and in the 5×FAD mouse model (Carrillo-Jimenez et al., 2019). In another investigation, TET2-knockdown 2×Tg-AD mice were employed to elucidate the impact of TET2 on inflammatory processes. The study demonstrated a heightened production of IL-1β, IL-6, and tumor necrosis factor-alpha in the TET2-knockdown AD hippocampus in comparison to both the control AD hippocampus and the TET2-knockdown WT hippocampus. This observation suggests an increased susceptibility of 2×Tg-AD mice to TET2-induced inflammatory reactions. Furthermore, an analysis of hippocampal RNA-sequencing data revealed that TET2-modulated genes in the early stage of 2×Tg-AD mice were significantly enriched in pathways associated with inflammatory responses (Li et al., 2020). Therefore, the interplay between Aβ, aging-related DNA methylation changes, and the involvement of TET enzymes, particularly TET2, underscores the intricate relationship between epigenetic modifications and neuroinflammation in the context of AD. These findings contribute to a deeper understanding of the molecular mechanisms underlying AD pathology and suggest potential avenues for therapeutic intervention targeting inflammatory processes associated with Aβ deposition.

Epigenetic Modification of Synaptic Function

Memory and cognitive deficits in the early stages of AD (prodromal and MCI) are rooted in synaptic dysfunction. Even in the initial stage (subjective cognitive decline), subtle synaptic changes become apparent, underscoring the importance of delving into the epigenetic foundation of synaptic function to gain insight into the pathophysiology of AD.

Epigenetic modifications contribute to synaptogenesis

It has been recognized that regulated synaptogenesis plays a fundamental role in organizing neural circuits during development and in facilitating learning and memory processes in the mature brain (Waites et al., 2005). Numerous electron microscopy studies have explored the morphology and density of dendritic spines in the rodent hippocampus following in training in memory-related tasks. Apparently, there was evidence of a transient rise in the number of excitatory synapses, noticeable within 2–6 hours after training but not after 24 hours (Scully et al., 2012). The function of transient synaptogenesis after training might be to group synaptic inputs along dendrites, leading to a more efficient excitation of the postsynaptic neuron (Borczyk et al., 2021).

Blocking DNA methyltransferases (DNMTs) activity has been shown to modify neuronal glutamatergic synaptic scaling and membrane excitability (Meadows et al., 2016). Post-mitotic neurons, contrary to the belief of stable epigenetics in differentiated cells, undergo dynamic DNA methylation changes. DNMTs, particularly DNMT1 and DNMT3a, play a key role in synapse formation by de novo DNA methylation of enhancer regions, with the gene Wwc1 affected by hyperDMRs (Kameda et al., 2021). Inhibiting DNMT activity reduces activity-induced excitatory synaptogenesis. DNMT3a/b deletion leads to hypomethylation of essential genes (Mapt, Kcna1, Camta, and Tiam1) in neurons, impeding their up-regulation during differentiation (Zocher et al., 2021). Activity-induced de novo DNA methylation holds similar significance to demethylation in shaping neuronal physiology. During adult neurogenesis, de novo DNMTs target neuronal gene enhancers and bodies, establishing neuron-specific methylomes and gene expressions. This aids newborn neuron maturation, enhancing hippocampal excitability and cognitive improvement (Zocher et al., 2021). Newly synthesized DNMTs govern maturation, dendritic outgrowth, and spine formation in hippocampal nascent neurons.

HDACs participate in chromatin remodeling and gene expression and play a role in the regulation of synaptogenesis and synaptic plasticity. Studies have demonstrated that inhibiting HDAC can improve synaptic function (Gräff et al., 2014). The discovery of a series of 3-amino-pyridine-2–urea compounds that selectively inhibit the HDAC–co-repressor of repressor element-1 silencing transcription factor complex has led to a noteworthy increase in dendritic spine density and synaptic proteins. Furthermore, these compounds successfully restore hippocampal LTP in 5×FAD mice (Fuller et al., 2019). Notwithstanding, Frankowski et al. (2021) observed a progressive decrease in HDAC2 levels during the differentiation of human induced pluripotent stem cells into neurons. By manipulating HDAC2 and Endophilin-B1 using lentiviral techniques, they discovered that knocking down HDAC2 or overexpressing a neuron-specific Endophilin-B1 isoform leads to mitochondrial elongation and enhanced protection against cytotoxic stress in human induced pluripotent stem cell-derived neurons. Therefore, the knockdown of HDAC2 affects explicitly genes involved in synaptogenesis (Frankowski et al., 2021).

Emerging evidence also highlights the role of non-coding RNAs in regulating the expression of multiple genes through epigenetic, transcriptional, or post-transcriptional mechanisms. Numerous miRNAs impact synaptogenesis. For example, miR-125b and miR-132 promote synaptogenesis: increased miR-125b expression lengthens neuron processes, while miR-132 expression leads to diverse spine shapes (Edbauer et al., 2010). Additionally, miR-199a, induced by methyl-CpG-binding protein 2, enhances excitatory synaptic density and transmission by inhibiting the mammalian target of the rapamycin signal pathway (Nakashima et al., 2021). Conversely, miR-134 suppresses synaptogenesis by targeting LimK1, reducing dendritic spine size (Schratt et al., 2006). miR-34a impairs synaptic function by targeting syntaxin-1A and synaptotagmin-1 mRNAs (Agostini et al., 2011). In dendrites, miR-138 limits dendritic spine size by inhibiting APT1, which controls synaptic proteins via palmitoylation (Siegel et al., 2009). Sun et al. (2019) showed that selectively deleting Dicer in postnatal astrocytes resulted in decreased MAPK/CREB signaling in neurons due to miR-324-5p targeting the C-C chemokine ligand 5–C-C chemokine receptor axis. This suggests that the altered astrocytic secretion milieu following miRNA dysfunction leads to lasting changes in astrocyte-neuron communication. Hence, synaptogenesis is also intertwined with epigenetic modifications.

Epigenetic agents regulate synaptic plasticity

Multiple studies, including ours, have shown that broad-spectrum HDAC inhibitors, such as trichostatin A (TSA) and sodium butyrate, have the ability to augment LTP in hippocampal slices and enhance memory consolidation in vivo, particularly in the context of fear conditioning (Vecsey et al., 2007; Gräff et al., 2014; Wei et al., 2020; Jin et al., 2023). The inhibition of HDACs has been shown to enhance the formation of LTP even with a “weak” sub-threshold stimulus (Maity et al., 2016; Jin et al., 2023). In particular, when the sub-threshold stimulus is paired with the application of an HDAC inhibitor, it results in the induction of a persistent LTP that shares similar molecular characteristics to those observed in multi-train LTP, including the involvement of PKA/CREB transcription (Vecsey et al., 2007). The CREB-binding protein possesses intrinsic histone acetyltransferase activity, and it has been observed that Cbp^+/– mice exhibit impairments in long-lasting LTP (L-LTP), while their “early” remained intact (Alarcón et al., 2004). The impaired L-LTP observed in Cbp^+/– mice was effectively restored through HDAC inhibition, indicating that the deficient L-LTP in these mice is attributed to reduced histone acetyltransferase activity. Supporting its specific involvement in long-lasting LTP, the administration of an HDAC inhibitor augmented the forskolin-induced expression of genes associated with memory formation (such as Nr4a1; Fass et al., 2003), suggesting a central role in the underlying mechanisms supporting L-LTP.

Among the Class-I HDACs, HDAC3 boasts the highest expression within the brain (Broide et al., 2007). A selective inhibitor of HDAC3, RGP966, has found utility in both in vitro and in vivo investigations concerning synaptic plasticity. Notably, studies have demonstrated that the acute administration of RGP966 to brain slices (Sartor et al., 2019) and its systemic application (Wei et al., 2020; Keiser et al., 2021) significantly increased hippocampal LTP during standard conditions or reinstated LTP in murine disease models. In ChIP-qRT-PCR experiments conducted on cells, RGP966 elicited an elevation in levels of H4K5ac and H4K8ac—both substrates of bromodomain-containing protein 4 (BRD4)—while leaving H3ac and acetylated tubulin unaffected. Specifically, RGP966 exhibited a propensity to heighten H4K5ac levels at the BDNF I promoter, with limited impact on the promotors of BDNF exon IV and IX. Notably, in BRD4-ChIP experiments, RGP966 bolstered the interaction between BRD4 and the promoters of BDNF exon I and IX, while evoking negligible alteration in the promoter of BDNF exon IV. The augmentation of BRD4 binding to the BDNF exon I and IX promoters, facilitated by RGP966, was counteracted upon co-administration of JQ1—an inhibitory agent targeting BRD4. Prominently, the amplification of hippocampal LTP induced by RGP966 encountered inhibition in the presence of JQ1, as evidenced by its effects being nullified (Sartor et al., 2019).

In our study, we demonstrated that HDAC3 is a target gene of miRNA132-3p. By either inhibiting HDAC3 by RGP966 or overexpressing miR-132 using a lentivirus expressing the mature miR-132 under the synapsin promoter (LV-miR-132), we observed a substantial enhancement of hippocampal LTP (Wei et al., 2020). Conversely, when miR-132 was knocked out in mice, it impeded synaptic transmission and plasticity (Remenyi et al., 2013). Similarly, miRNA-218 also plays a significant role in regulating presynaptic functions and learning-related behaviors. The miR-218 knockout mice exhibited deficits in presynaptic glutamate release in hippocampal neurons, leading to defective LTP and impaired learning and memory. Conversely, overexpressing miR-218 led to enhanced LTP compared to WT mice, potentially contributing to the improved learning and memory observed in these mice (Lu et al., 2021). The regulation of synaptic function by miR-218 involves targeting the 3′-untranslated region of complement component 3 mRNA, a key element of the immune system. Certain miRNAs, like miR-134-5p, exhibit a negative regulatory effect on hippocampal LTP. The depletion of miR-134-5p has been observed to restore LTP that was impaired by Aβ_1–42 oligomers (Baby et al., 2020). In AD rat brains, inhibiting miR-134-5p led to increased expression of plasticity-related proteins, such as CREB and BDNF, which are typically downregulated under AD conditions. Thus, several specific miRNAs have been identified as crucial regulators of synaptic plasticity and hippocampus-dependent memory.

Potential mechanism for the rapid enhancement of LTP by epigenetic agents

HDAC inhibitors, including TSA, sodium butyrate, RGP966, and CI-994, have demonstrated the ability to amplify hippocampal LTP or facilitate the induction of substantial LTP from initially weak sub-threshold stimuli in acute brain slices (Vecsey et al., 2007; Gräff et al., 2014; Sartor et al., 2019; Wei et al., 2020; Jin et al., 2023). The impact of HDAC inhibitors on synaptic function appears to occur through an unconventional epigenetic pathway, as the typical processes of transcription and translation do not manifest within such a short timeframe (within 30 minutes). Rather, these effects are likely directed towards non-histone proteins. Existing literature indicates that hydroxamates like TSA and SAHA (suberoylanilide hydroxamic acid) possess the ability to chelate several ions, including Zn²⁺, Ni²⁺, and Fe³⁺ (Griffith et al., 2011). Another study demonstrated that hydroxamate-based broad-spectrum HDAC inhibitors like SAHA and TSA, at moderate micromolar concentrations, can promptly inhibit L-type Ca²⁺ channels. It has been demonstrated that HDAC inhibitors can lead to an elevation in membrane resistance values, which represents a significant intrinsic parameter connected to the inhibition of voltage-dependent calcium channels (Urbano et al., 2018). These HDAC inhibitors impact certain Ca²⁺ signaling mechanisms, distinct from store-operated Ca²⁺ entry and intracellular Ca²⁺ release. These effects might involve receptor-operated Ca²⁺ entry or other alternative pathways (Zheng et al., 2017).

TSA also induces a rise in presynaptic release probability, aligning with improved synaptic function in developing neuronal cultures. This effect is evident in the heightened mEPSC frequency due to TSA, while amplitude remains unaffected (Rumbaugh et al., 2015). Furthermore, TSA and MC1568 exhibit the capacity to influence immediate early genes such as c-fos and c-jun within a short timeframe of 15–30 minutes. This phenomenon has been observed in various cell types (Khan and Davie, 2013). As a result, it is reasonable to infer that transcription processes are underway during the recording period. Therefore, applications of certain HDAC inhibitors could modulate Ca²⁺ channels, facilitate presynaptic release, and activate certain immediate early genes to boost synaptic function and enhance LTP.

Epigenetic Mechanisms Offer Cognitive Enhancement Strategies

Exploring the factors that promote favorable outcomes offers the promise of postponing or even averting diseases that are epigenetically regulated. This is especially significant because disturbances in the delicate epigenetic equilibrium, stemming from a combination of genetic variations, environmental factors, and lifestyle choices, are known to substantially contribute to the development of a wide range of illnesses. By gaining a deeper understanding of these influencing factors, we can better target interventions and strategies to mitigate the risk of epigenetically driven disease.

Enhanced synaptic function through behavioral epigenetic modifications

The environment plays a crucial role in postnatal neuronal development, with epigenetic modifications (DNA and histone) facilitating gene-environment interactions, through epigenetic mechanisms, environmental conditions have a substantial impact on cognitive performance in different neuropsychiatric diseases, exhibiting either positive or negative effects depending on the specific stimuli present (Fraga et al., 2021). In an enriched environment (EE), animals freely explore larger cages equipped with regularly rearranged toys, tunnels, and running wheels. This environment offers physical, cognitive, sensory, and social stimulation, which has been observed to have significant effects on synaptic plasticity and hippocampus-dependent learning and memory (Kempermann, 2019; Qu et al., 2022). Similar to the above-mentioned HDAC inhibitors, mice exposed to an EE exhibited significantly enhanced LTP compared to mice housed under standard housing (Li et al., 2013; Ohline and Abraham, 2019; Morè et al., 2023). Moreover, in EE mice, even “weak” stimulations that typically do not elicit significant LTP were capable of inducing a strong and enduring LTP response in the hippocampus. Subsequent studies conducted by us validated that the facilitation or enhancement of LTP in the EE was mediated by histone acetylation and its interaction with miR-132 (Wei et al., 2020; Jin et al., 2023).

It has been reported that an increase in miR-132 expression was observed in the mouse brain after exposure to EE training. Inducing the overexpression of miR-132 can replicate the effects of EE. These effects include enhancing LTP and mitigating synaptotoxic effects of Aβ oligomers (El Fatimy et al., 2018; Wei et al., 2020). Elevated production of miR-132 in the hippocampal neurons leads to an increase in dendritic spines and enhances synaptic transmission (Basu and Lamprecht, 2018). In contrast, deletion of gene encoding for miR-132 has demonstrated notable deficits in synaptic function (Remenyi et al., 2013; Stojanovic et al., 2020). The miRNA-132/212 cluster’s role in synaptic transmission and plasticity has been linked to various aspects, including glutamatergic synaptic transmission in LTP experiments (Remenyi et al., 2013), various other brain neuronal synaptic functions (Stojanovic et al., 2020; Bormann et al., 2021) and learning and memory processes involved CREB, methyl-CpG-binding protein 2, matrix metalloproteinase 9 signaling (Qi et al., 2018; Kuzniewska et al., 2022). Therefore, miR-132 serves as a critical post-transcriptional regulator in synaptic function, enabling fine-tuning of synaptic activity, plasticity, and connectivity.

The components of the NMDA receptor signaling pathway, such as calcium ion, PSD-95, CaMKII, PKA, MAPK, and CREB, have been definitively established as integral players in the processes of LTP and synaptic plasticity. Consistent with the signaling molecules involved, we and others have observed a notable upregulation in PSD-95, MAPK, and CREB expression following EE training (Li et al., 2013; Novaes et al., 2017). Likewise, upregulation of various molecules associated with synaptic function, including mitogen- and stress-activated protein kinase 1, tyrosine kinase receptor B, and synaptophysin, have demonstrated molecular events leading to improved synaptic activity following exposure to an EE (Morè et al., 2023). Thus, we propose that exposure to an EE has the potential to amplify synaptic efficacy and serve as a safeguard against the deterioration of synaptic function as the disease advances.

Our recent findings indicate that EE effectively enhances synaptic strength and mitigates AD-like phenotypes through the activation of β₂-adrenergic receptors (β₂-ARs) (Li et al., 2013). Activation of β₂-ARs exerts protective effects against synaptotoxic by enhancing histone acetylation (Jin et al., 2023). Stimulation of β₂-AR using specific agonists, formoterol and procaterol, notably enhances hippocampal LTP. Likewise, the enhancement of hippocampal LTP by pan-HDAC inhibitors (TSA and sodium butyrate) can be counteracted by the administration of a selective antagonist targeting β₂-AR, ICI 118551 or observed to be absent in mice lacking functional β₂-AR (β₂-AR knockout mice). Another study additionally discovered that β-AR–mediated synaptic plasticity resulted in a significant increase in H3 acetylation and transcription (Brandwein and Nguyen, 2019). Activation of β-adrenergic receptors (β-ARs) via convergent ERK and mammalian target of the rapamycin pathways trigger memory-enhancing gene transcription and synapse protein synthesis. This coordinated process generates local proteins for immediate synaptic strength and enables persistent potentiation by facilitating nucleus-level maintenance (Maity et al., 2022).

The well-documented effects of EE have been linked, in part, to elevated BDNF levels, particularly in the hippocampus (Cutuli et al., 2022). BDNF signaling promotes protein synthesis-dependent mechanisms to induce hippocampal LTP (Panja and Bramham, 2014). BDNF binds with high affinity to the tropomyosin-related kinase B receptor, exerting tropic effects on the central nervous system, promoting synaptic plasticity, neurite outgrowth, neuronal survival, and LTP (Kowiański et al., 2018). EE increases BDNF level, likely achieved by enhancing CREB activity, which binds to BDNF promoter-I and recruits the transcriptional coactivator CREB-binding protein, resulting in a sustained increase in BDNF expression (Esvald et al., 2020). In neuron-derived small extracellular vesicles (EVs), BDNF increased the expression of miR-218 and miR-132. These miRNAs are recognized for their roles in synaptogenesis and neuropsychiatric disorders. BDNF-induced EVs altered gene expression in treated neurons, targeting excitatory synapse formation. Essential for excitatory synapses, miR-218-5p, miR-132-5p, and miR-690, along with their EV-mediated delivery, were controlled by BNDF. BNDF sorted these miRNAs in neuronal small extracellular vesicles (sEVs), crucial for dendrite and synapse maturation. BNDF-EVs enhanced synaptic vesicle clustering, fostering synchronous neuronal activity and phenotypic spread (Antoniou et al., 2023).

It has been shown that BDNF can enhance the S-nitrosylation of HDAC2 and inhibit its deacetylase activity (Nott et al., 2008). Therefore, the impact of EE against AD-related synaptotoxicity may involve not only the β2-AR signaling pathway but also BDNF signaling. Interestingly, the observed increase in BDNF levels during exercise, such as in the case of EE, may be dependent on β2-AR activation (Han et al., 2019), suggesting that β2-AR activation can serve as an upstream regulator of BDNF. Regarding synaptic function, it has been demonstrated that activations of β2-AR and BDNF play a role in promoting hippocampal LTP and are associated with epigenetic modifications (Sharma et al., 2017; Jin et al., 2023).

Within the realm of EE, physical exercise promotes neuroplasticity and neurogenesis, thus enhancing the processes of learning and memory. These enhancements occur through mechanisms that stimulate the neurotrophic effects of BDNF within the hippocampus (Dong et al., 2022). Physical exercise also has the potential to induce significant cellular changes. Liu et al. (2020) showed that a 12-week physical exercise regimen in older individuals could epigenetically influence processes like myogenesis and adipogenesis through miRNA modulation. In another study, Yumi Noronha et al. (2023) identified 118 DMRs in response to a 14-week physical exercise program among post-menopausal women. Three of these genes, CALD1, RNF121, and MSI2, exhibited hypermethylation, while others displayed hypomethylation, impacting various biological functions. Hence, activities like exploring new environments and engaging in physical exercise stimulate the release of specific neurotransmitters or modulators in the brain. This, in turn, activates downstream signaling pathways and leads to advantageous biological effects via epigenetic mechanisms.

Enhanced synaptic function through physical epigenetic modifications

LTP has been widely studied in animals and in vitro hippocampal slices. There is a paucity of evidence regarding synaptic plasticity in humans due to the lack of non-invasive methods for assessing the phenomenon in vivo. Recently, non-invasive brain stimulation techniques, including transcranial magnetic stimulation (TMS), intermittent theta burst stimulation, and transcranial direct current stimulation, are gaining prominence as they can each induce LTP-like plasticity in the brain. TMS uses MRI-strength magnetic fields passing through the skull to induce focal electric currents in the target brain areas, modulating local neural activity with widespread effects in the cortex (Lefaucheur et al., 2014). Intermittent theta burst stimulation, a recent variation of TMS, administers bursts at a frequency of 5 Hz, mimicking the rhythmic patterns found in the hippocampus (Aoki et al., 2023). Additionally, transcranial direct current stimulation, an experimental neuromodulation approach, involves the application of low-intensity electrical currents to specific areas of the cortex. This method influences the spontaneous firing of neurons, with anodal stimulation increasing cortical excitability and cathodal stimulation decreasing it, potentially yielding lasting effects beyond the stimulation phase (Agboada et al., 2020).

Studies have revealed that both TMS and transcranial direct current stimulation induced LTP-like plasticity through mechanisms similar to those discovered in animals. These mechanisms include the involvement of NMDA receptors, AMPA receptors, and the BDNF-tropomyosin-related kinase B pathway (Stafford et al., 2018; Thomson et al., 2020). In awake mice, repetitive TMS targeting the frontal cortex has been demonstrated to induce specific epigenetic changes. These alternations involve dopamine D2 receptor-dependent persistent modifications in the protein levels of CDK5 and PSD-95, limited to the stimulated brain region. Notably, these modifications are linked to changes in histone acetylation within the gene promoter region. Significantly, the administration of an HDAC inhibitor (MS-275) effectively prevented these epigenetic events from taking place (Etiévant et al., 2015). The observed variability in TMS responses shows a direct correlation with epigenetic mechanisms (McGeary et al., 2022). This correlation makes epigenetic mechanisms a promising and innovative focal point for integrated approaches that combine neurostimulation and pharmacological interventions in individuals with psychiatric disorders. In a study by Capelli et al. (2017), it was found that low-frequency pulsed electromagnetic field stimulation in peripheral blood mononuclear cells of AD patients could trigger epigenetic regulation through miRNAs. This process appeared to contribute to the restoration of deregulated pathways associated with the pathological state. Nevertheless, more research is needed to delve into the intricate network of epigenetic signals and explore the potential risks of adverse effects.

Epigenetic Approaches for the Treatment of Alzheimer’s Disease

AD is characterized by cognitive decline and memory loss, leading researchers to explore various therapeutic strategies to restore or prevent cognitive dysfunction. Cognitive enhancement strategies encompass biochemical, physical, and behavioral interventions. One crucial aspect of AD-related synaptic dysregulation involves epigenetic changes, including DNA methylation, histone modification, and alterations in miRNA expression, which disrupt gene transcription, impair proteins, and lead to synaptic dysfunction. The prospect of reversing these epigenetic changes offers a promising avenue for AD therapy. Researchers have focused on targeting histone-modifying enzymes, such as HDACs, with inhibitors showing potential in animal models (Santana et al., 2023). Specifically, HDAC inhibitors like sodium butyrate, vorinostat, trichostatin A, and valproate have been found to enhance memory, improve cognition, and reduce Aβ levels in AD patients (Martínez-Iglesias et al., 2022). The emerging field of epigenetic-targeted therapies holds significant promise for the treatment of AD, offering hope for addressing the intricate synaptic dysregulation associated with this debilitating condition.

Despite targeting histone-modifying enzymes’ therapeutic promise for AD, clinical epigenetic drug application faces challenges due to side effects and complex regulation. Research into AD-related synaptic dysregulation’s epigenetic mechanisms is crucial to finding safe, specific drugs. HDAC inhibitors show potential in animals and clinical trials, but effectively utilizing their benefits and managing side effects remains a challenge in AD treatment pursuit. Instead of directly targeting epigenetic mechanisms, several drugs that aim to enhance synaptic function have shown promise. These drugs include BDNF, β2-AR agonists, and nootropics (Azman and Zakaria, 2022; Malík and Tlustoš, 2022). These compounds hold potential as therapeutic agents to improve synaptic plasticity and cognitive function. For example, Nosustrophine, a brain extract derived from porcine sources and produced using non-denaturing biotechnological methods, has been shown to regulate gene expression of AD-related PSEN2 and APOE, global 5-methylcytosine and de novo DNA methylation (DNMT3a), HDAC activity, HDAC3 expression, SIRT1 expression, acetylated histone H3 protein levels, as well as Aβ_1–42 levels (Martínez-Iglesias et al., 2022). Therefore, addressing multiple aspects of AD pathogenesis rather than focusing solely on one target of epigenetic modifications may offer enhanced effectiveness and reduced side effects in clinical treatment.

Conclusion and Perspective

Epigenetic modifications play a significant role in the multifaceted pathogenesis of AD, impacting various aspects of the condition. These aspects include Aβ production, tauopathy, neuroinflammation, reactive oxidative stress, and synaptic dysfunction, each with its own distinct epigenetic dysregulations. These epigenetic modifications encompass a wide range of processes, such as various histone modifications (acetylation, phosphorylation, methylation, ubiquitination, sumoylation), DNA methylation, hydroxymethylation, and the regulation of non-coding RNAs, including miRNAs (Figure 2).

Figure 2.

Epigenetic modifications in the development of Alzheimer’s disease and synaptic dysfunction.

Epigenetic dysregulations, such as alterations in histone modification, DNA methylation, and miRNA expression, intricately interact with multiple pathogenic factors of Alzheimer’s disease (including Aβ production, tauopathy, neuroinflammation, and reactive oxidative stress). These epigenetic dysregulations, along with the collective influence of Alzheimer’s pathogenic factors, contribute to the onset of synaptic dysfunction. Created with BioRender.com. Ac: Acetylation; Me: methylation.

Synaptic dysfunction emerges as an early hallmark of AD, occurring even before the onset of mild cognitive impairment. Research suggests that enhancing synaptic function through epigenetic mechanisms, such as augmenting LTP, can counteract Aβ-induced synaptic dysfunction and memory deficits. This underscores the potential for the development of drugs targeting epigenetic modifications as effective treatments for AD. Nevertheless, addressing a single aspect of AD pathogenesis with a single drug may not be sufficient. A more effective approach may involve using multiple epigenetic drugs tailored to address different pathogenic aspects, tailored to individual conditions.

Funding Statement

Funding: This work was supported by a grant from the Massachusetts Alzheimer’s Disease Research Center (5P50 AG 005134) (to SL).