1.Introduction
Epilepsy is a common neurological disorder in which excessive and
abnormal neuronal discharges can be observed and is characterized by
recurrent seizures(Chen et al., 2020). At present, antiepileptic drugs
(AEDs) are still the major methods of treatment for epilepsy in clinic
and about 1/3rd of patients with epilepsy are drug-resistant (DRE)(Moshé
et al., 2015). The epileptogenesis is usually involved in
neuropathological processes such as ion channel dysfunction, neuronal
injury, inflammatory response, synaptic plasticity, glial cell
proliferation and mossin fibrosis, whereby affecting neuronal function
in the brain(Gan et al., 2015). Owing to the neuropathological process
of epilepsy is complex and changeable, the pathogenesis of epilepsy is
not completely clear, which brings difficulties to the prevention and
treatment of epilepsy. In addition, an increasing number of epileptic
patients with potential genetic causes fully proves that the regulation
of genes may play a pathophysiological role in the epileptogenesis or
progression of epilepsy.
In gene regulation, epigenetics mainly regulates gene expression through
DNA methylation, histone modification and RNA methylation, so as to
change the genetic information of organisms, but does not change the
sequence of DNA nucleotides(Huang et al., 2021). At present, epigenetic
mechanisms have been proved to be necessary to maintain neuronal
function in the human brain(Hauser et al., 2018). A growing number of
studies have shown that epigenetic regulation including histone
modification, DNA methylation, ncRNAs and REST/NRSF, is also involved in
epilepsy(Henshall and Kobow, 2015; Citraro et al., 2017; Butler-Ryan and
Wood, 2021). In cultured hippocampal neurons of rats, it has been found
that the cellular memory of epileptogenesis may be related to epigenetic
regulation of epileptic target genes(Kiese et al., 2017). Importantly,
epigenetic regulation can influence susceptibility and severity of SE,
and in turn SE can also drive the changes of epigenetic markers that
influence the expression of epileptogenesis-associated genes(Henshall,
2018). In the CNS, DNA methylation has been demonstrated to be involved
in the expression of nerve cell-specific genes and is significantly
altered in the animal models of epilepsy and human epileptic tissues(Zhu
et al., 2012; Dębski et al., 2016). Meanwhile, improved cognitive
function and hyperexcitability phenotypes after status epilepticus (SE)
is also associated with altered DNA methylation(Henshall, 2018). In
addition, in animal models of
epilepsy and epileptic patients,
altered histone acetylation have been thought to be involved in
epileptogenesis and prolonged seizures also modify chromatin compaction
by histone acetylation (Citraro et al., 2017; Henshall, 2018). Different
brain-specific microRNAs have been observed to be abnormally expressed
in animal models of epilepsy and epileptic patients, particularly in
temporal lobe epilepsy (TLE)(Cattani et al., 2016). In addition, ncRNAs
including microRNAs and lncRNAs have been studied in epileptogenesis and
treatment of epilepsy and may play an antiepileptic role as a new
therapeutic strategy since they have highly selective targeting(Xiao et
al., 2018). MicroRNAs, as potential molecular biomarkers, can affect SE
by targeting epilepsy-related gene networks through post-transcriptional
mechanisms. Meanwhile, lncRNAs can also influence expression of some
genes which are involved in electrophysiological functions of neurons by
targeting microRNAs in epilepsy(Henshall, 2018). Thus, discovering new
therapeutic targets related to epigenetics and exploring the correlation
between epigenetics and epileptogenesis are crucial for the prevention
and treatment of epilepsy. Here, we discussed the role of epigenetic
mechanisms in the occurrence and treatment of
epilepsy.
2. Epigenetic modification inepilepsy
2.1DNA
methylation
DNA methylation, as an epigenetic modification, has been shown to be
involved in a variety of CNS disorders, including
epilepsy(Portales-Casamar et al., 2016). DNA methylation refers to the
formation of 5-methylcytosine (5mC) from cytosine under the catalytic
action of DNA methyltransferase, which occurs mainly in cytosine-guanine
dinucleotides (CpGs). In this process, DNA methyltransferases mainly
include DNMT1, DNMT3a and DNMT3b(Figure1 )(Heikkinen et al.,
2022). In the genome of normal cells, most CpG sequences are methylated
and the hypomethylated regions of DNA function are considered as
elements to regulate gene expression, such as promoters and
enhancers(Nishiyama and Nakanishi, 2021). Meanwhile, DNA methylation can
also promote the binding of various transcription factors(Nishiyama and
Nakanishi, 2021). Currently, two major regulatory mechanisms of DNA
methylation in modifying gene activity have been proposed. On the one
hand, DNA methylation can directly block the binding of transcription
factors, resulting in gene silencing. On the other hand, DNA methylation
can attract methyl-binding proteins, such as MBD1, MBD2, MBD3, MBD4 and
MeCP2, which recognize methylated cytosine, thereby indirectly leading
to the changes of gene expression(Heikkinen et al., 2022; Xie et al.,
2022). In addition, the methyl groups required for DNA methylation
depend mainly on the transmethylation of S-adenosine methionine (SAM) in
the methionine cycle of organisms, resulting in the formation of
S-adenosine homocysteine (SAH). Then, SAH is cleaved into adenosine and
homocysteine. Adenosine kinase (ADK) is a cytoplasmic enzyme that
catalyzes the conversion of adenosine to AMP. ADK activation represents
the main pathway of adenosine clearance, which can increase the DNA
methylation status of epigenome through the transmethylation pathway,
whereas experimental or therapeutic adenosine augmentation prevents the
reactions of DNA methylation(Williams-Karnesky et al., 2013). In
epilepsy, ADK also regulates intracellular adenosine to modulate
epileptogenesis by the epigenetic mechanism(Williams-Karnesky et al.,
2013; Xu et al., 2017). In addition, the ketogenic diet (KD), as an
important treatment for epilepsy, can enhance the production of
adenosine which is a metabolic feedback inhibitors of DNA
methylation(Lusardi et al., 2015; Longo et al., 2019). Relevant studies
have shown that DNA methylation contributes to neuron cell-specific gene
expression, which is significantly changed in the animal models of
epilepsy and epileptic patients(Zhu et al., 2012; Dębski et al., 2016).
In a word, nutrient metabolism and DNA methyltransferases may serve as a
potentially modifiable upstream mechanism regulating DNA methylation in
epileptogenesis.
In the KA-induced and pilocarpine-induced SE models, the similar
patterns of DNA hypermethylation have been demonstrated in the epileptic
hippocampal neurons (Murugan and Boison, 2020). Meanwhile, in the three
models of chronic epilepsy (pilocarpine injection, focal amygdala
stimulation and post-TBI), genome-wide changes in global DNA methylation
were also investigated (Dębski et al., 2016). This study has concluded
that changes in genomic DNA methylation provide the general pathological
mechanism of epileptogenesis(Dębski et al., 2016). It have been reported
that upregulated DNMT activity and associated changes of DNA methylation
in patients with TLE, including focal cortical dysplasia (FCD)(Dixit et
al., 2018). Moreover, FCD subtypes including FCDIa, FCDIIa and FCDIIb
may also be distinguished by DNA methylation profiles, which suggesting
that DNA methylation may serve as a biomarker for FCD(Kobow et al.,
2019). Recently, a study about human epilepsy has shown 224 genes with
differential DNA methylation persons in epilepsy patients and healthy
people(Wang et al., 2016b). In the epileptic samples, three genes
(TUBB2B, ATPGD1, HTR6 ) exhibited relative transcriptional
regulation by DNA methylation. TUBB2B and ATPGD1 showed
hypermethylation and reduced mRNA levels, while HTR6 showed
hypomethylation and increased mRNA levels(Wang et al., 2016b). These
findings suggest that some genes are differentially regulated by DNA
methylation in human epilepsy. Previous studies have shown that 27
hypomethylated genes and 119 hypermethylated genes are present in
hippocampal tissue from patients with DR-TLE compared with healthy
people(Miller-Delaney et al., 2015). Meanwhile, DNMT1 and DNMT3a are
highly expressed in the temporal neocortex of DR-TLE patients, which are
involved in DNA methylation(Zhu et al., 2012). The lower levels of
global DNA methylation and the lower expression of DNMT3a2 were found in
the hippocampus of TLE. Interestingly, compared with control and TLE
groups, the expression of DNMT3a1 and DNMT3a2 was more significant
reduced in the hippocampus of TLE with febrile seizures (FS) history(de
Nijs et al., 2019). Mesial temporal lobe epilepsy with hippocampal
sclerosis (mTLE-HS) is the most common focal epilepsy, which
characterized by strong drug resistance. In the intracortical KA-induced
mouse models of mTLE-HS, contralateral hippocampus (CLH) shows
substantial changes in gene expression and DNA methylation in glia and
neurons, in which some genes and pathways associated with antiepileptic
effects were upregulated(Berger et al., 2020). Although changes of gene
expression in CLH and ILH overlap to a large extent, changes of DNA
methylation were not overlapped(Berger et al., 2020). As the seizures
last longer, DNA methylation of many genomic sites is significantly
changed, and progression of epilepsy is also relevant to changes in DNA
methylation of inflammatory-related genes(Martins-Ferreira et al.,
2021). Therefore, seizures may be responsible for altered DNA
methylation of certain genes(Caramaschi et al., 2020). And changes of
DNA methylation may also contribute to the development of epilepsy.
At present, the regulation of synaptic function in epilepsy may also
have light with DNA methylation of related genes. Relevant studies have
shown that DNA methylation-dependent endocytosis may be involved in the
regulation of synaptic function in inhibitory cortical interneurons of
mice, which have potential significance in TLE(Pensold et al., 2020).
Moreover, synaptic NMDAR expression is also regulated by DNA
methylation. Related study has found that activated NMDAR-containing
GluN2A subunits control DNMT3a1 levels in neurons and drive degradation
of DNMT3a1 in a ubiquitin-like dependent manner, which may be associated
with synaptic plasticity and memory formation(Bayraktar et al., 2020).
At the same time, the upregulation of DNMT3b expression is also
regulated by NO produced by NMDAR activation in the hippocampus(de Sousa
Maciel et al., 2020). Moreover, glutamate dysfunction and cognitive
decline are also closely associated with changes in GRIN2Bpromoter methylation(Fachim et al., 2019). Overexpression of DNMT1 in ES
cells leads to epigenetic changes, which results in abnormal neuronal
differentiation with upregulated functional NMDARs(D’Aiuto et al.,
2011). SE can trigger early and late changes of BDEF andGRIN2B DNA methylation levels in the hippocampus(Ryley Parrish et
al., 2013). In the epileptic hippocampus, increased levels ofGRIN2B DNA methylation lead to decreased expression of GluN2B and
decreased levels of BDNF DNA methylation also result in increased
expression of BDNF. Meanwhile, inhibition of DNMT can decreaseGRIN2B mRNA expression and increase excitatory postsynaptic
potential in hippocampus of epileptic rats(Ryley Parrish et al., 2013).
The blocking of DNA methylation may play an important role in
epileptogenesis and treatment of epilepsy. Abnormal DNA methylation ofRASgrf1 is closely associated with epilepsy. RG108 as a DNMT
inhibitor, can block hypermethylation of the RASgrf1 promoter and
inhibited acute epileptic activity in the KA-induced epilepsy
models(Chen et al., 2017). The high-dose 5-Aza-2dC as a DNMT inhibitor,
significantly increase seizure threshold and attenuate seizures in
PTZ-kindled model of rats, which suggesting inhibited DNMT activity can
reduce epilepsy acquisition and seizure susceptibility(Williams-Karnesky
et al., 2013). Adenosine intervention can reverse DNA hypermethylation
in the epileptic brain, thereby inhibiting sprouting of mossy fibers in
the hippocampus and preventing the progression of epilepsy in a rat
model of TLE(Williams-Karnesky et al., 2013). Studies have shown that
methylation level of EPHX1 promoter is significantly correlated
with epilepsy that is resistant to carbamazepine (CBZ). EPHX1methylation may be a potential target of CBZ treatment and a potential
marker of DREs for CBZ (Lv et al., 2019). Elevated levels of matrix
metalloproteinase-9 (MMP-9) have been implicated in epileptogenesis of
humans and animals. Upregulated MMP-9 expression is primarily regulated
by deletion of MMP-9 gene proximal promoter including interweaved potent
silencing mechanisms-DNA methylation and polycomb repressive complex 2
(PRC2)-related repression(Zybura-Broda et al., 2016). In addition, DNA
demethylation has also been reported to depend on the gradual
dissociation of DNMT3a and DNMT3b, as well as the progressive binding of
DNA demethylation promoter Gadd45β to the MMP-9 proximal gene promoter
in vivo(Zybura-Broda et al., 2016). These studies identify MMP-9
expression is regulated by DNA methylation in human epilepsy.
In conclusion, DNA methylation is involved in the occurrence and
treatment of epilepsy. However, the regulatory mechanism of DNA
methylation in epilepsy is still not completely clear and needs further
exploration.