# Genetic–Epigenetic Interplay in Epilepsy: Pathways, Biomarkers, and Epigenome-Targeted Therapies

**Authors:** Andra-Giorgiana Zaruha, Patricia Codreanu, Mădălin-Codruț Coman, Monica Andreea Novac II, Simona Gabriela Duță-Ion, Ioana Ruxandra Jugănaru, Iulian Andrei Hotinceanu, Andra Dan, Livia Mălina Burtavel, Anca-Elena Eftenoiu, Diana Bârcă, Andreea Ionescu, Cerasela Paraschiv, Viorica-Elena Rădoi

PMC · DOI: 10.3390/epigenomes10010010 · Epigenomes · 2026-02-10

## TL;DR

This review explores how genetic and epigenetic factors interact in epilepsy, highlighting new therapeutic strategies targeting the epigenome.

## Contribution

The paper provides a comprehensive synthesis of genetic-epigenetic interactions in epilepsy and their therapeutic implications.

## Key findings

- Epigenetic mechanisms like DNA methylation and histone modifications interact with genetic factors in epilepsy.
- Environmental influences can modify gene expression through epigenetic dysregulation, contributing to epilepsy.
- Epigenome-targeted therapies, such as HDAC inhibitors and CRISPR/dCas9, show promise for precision treatment.

## Abstract

Epilepsy is a heterogeneous neurological disorder with a strong genetic basis, yet recent evidence underscores the critical role of epigenetic mechanisms in its pathogenesis. This review synthesizes current knowledge on how chromatin remodeling, histone modifications, DNA methylation, and transcriptional regulation intersect with classical channelopathies and signaling pathways. We emphasize how epigenetic dysregulation contributes to neuronal excitability and network plasticity, particularly through interactions with mTOR, PI3K-AKT, and GABAergic signaling cascades. The convergence of genetic mutations and epigenetic modifications creates a dynamic landscape in which environmental factors can modify gene expression and contribute to the development of epilepsy. Emerging therapeutic strategies—including epigenetic drugs (HDAC inhibitors, DNMT inhibitors), CRISPR/dCas9-based epigenome editing, and multi-omics approaches—offer promising avenues for precision medicine. This review provides a comprehensive synthesis of genetic and epigenetic mechanisms in epilepsy, examining how these layers interact to produce disease phenotypes and discussing the therapeutic implications of this multilayered regulation.

## Linked entities

- **Diseases:** epilepsy (MONDO:0005027)

## Full-text entities

- **Genes:** CDKN2A (cyclin dependent kinase inhibitor 2A) [NCBI Gene 1029] {aka ARF, CAI2, CDK4I, CDKN2, CMM2, INK4}, CHDH (choline dehydrogenase) [NCBI Gene 55349], GRIA2 (glutamate ionotropic receptor AMPA type subunit 2) [NCBI Gene 2891] {aka GLUR2, GLURB, GluA2, GluR-K2, HBGR2, NEDLIB}, KMT2D (lysine methyltransferase 2D) [NCBI Gene 8085] {aka AAD10, ALR, BCAHH, CAGL114, KABUK1, KMS}, HCN1 (hyperpolarization activated cyclic nucleotide gated potassium channel 1) [NCBI Gene 348980] {aka BCNG-1, BCNG1, DEE24, EIEE24, GEFSP10, HAC-2}, CDKN1A (cyclin dependent kinase inhibitor 1A) [NCBI Gene 1026] {aka CAP20, CDKN1, CIP1, MDA-6, P21, SDI1}, DNMT3A (DNA methyltransferase 3 alpha) [NCBI Gene 1788] {aka DNMT3A2, HESJAS, M.HsaIIIA, TBRS}, TET1 (tet methylcytosine dioxygenase 1) [NCBI Gene 80312] {aka CXXC6, LCX, bA119F7.1}, CHD6 (chromodomain helicase DNA binding protein 6) [NCBI Gene 84181] {aka CHD-6, CHD5, RIGB}, MIR132 (microRNA 132) [NCBI Gene 406921] {aka MIRN132, miRNA132, mir-132}, IL18 (interleukin 18) [NCBI Gene 3606] {aka IGIF, IL-18, IL-1g, IL1F4}, GABRA1 (gamma-aminobutyric acid type A receptor subunit alpha1) [NCBI Gene 2554] {aka DEE19, ECA4, EIEE19, EJM, EJM5}, MIR136 (microRNA 136) [NCBI Gene 406927] {aka MIRN136, miRNA136, mir-136}, SIRT1 (sirtuin 1) [NCBI Gene 23411] {aka SIR2, SIR2L1, SIR2alpha}, SMARCA2 (SWI/SNF related BAF chromatin remodeling complex subunit ATPase 2) [NCBI Gene 6595] {aka BAF190, BIS, BRM, NCBRS, SAMRCA2, SNF2}, EZH2 (enhancer of zeste 2 polycomb repressive complex 2 subunit) [NCBI Gene 2146] {aka ENX-1, ENX1, EZH2b, KMT6, KMT6A, WVS}, KCNT1 (potassium sodium-activated channel subfamily T member 1) [NCBI Gene 57582] {aka DEE14, EIEE14, ENFL5, KCa4.1, KNa1.1, SLACK}, CACNA1H (calcium voltage-gated channel subunit alpha1 H) [NCBI Gene 8912] {aka CACNA1HB, Cav3.2, ECA6, EIG6, HALD4}, MECP2 (methyl-CpG binding protein 2) [NCBI Gene 4204] {aka AUTSX3, MRX16, MRX79, MRXS13, MRXSL, PPMX}, Pvt1 (Pvt1 oncogene) [NCBI Gene 19296] {aka Ayu21-84Imeg, Gt(pU21)84Imeg, Mis-1, Mlvi-1, Pvt-1}, ADCY5 (adenylate cyclase 5) [NCBI Gene 111] {aka AC5, DSKOD, FDFM}, SLC12A5 (solute carrier family 12 member 5) [NCBI Gene 57468] {aka DEE34, EIEE34, EIG14, KCC2, hKCC2}, CACNA1E (calcium voltage-gated channel subunit alpha1 E) [NCBI Gene 777] {aka BII, CACH6, CACNL1A6, Cav2.3, DEE69, EIEE69}, ARX (aristaless related homeobox) [NCBI Gene 170302] {aka CT121, EIEE1, ISSX, MRX29, MRX32, MRX33}, PRKAB1 (protein kinase AMP-activated non-catalytic subunit beta 1) [NCBI Gene 5564] {aka AMPK, HAMPKb}, NRXN1 (neurexin 1) [NCBI Gene 9378] {aka Hs.22998, PTHSL2, SCZD17}, CHD7 (chromodomain helicase DNA binding protein 7) [NCBI Gene 55636] {aka CRG, HH5, IS3, KAL5}, BDNF (brain derived neurotrophic factor) [NCBI Gene 627] {aka ANON2, BULN2}, ALDH7A1 (aldehyde dehydrogenase 7 family member A1) [NCBI Gene 501] {aka ATQ1, EPD, EPEO4, PDE}, RHEB (Ras homolog, mTORC1 binding) [NCBI Gene 6009] {aka RHEB2}, SYN1 (synapsin I) [NCBI Gene 6853] {aka EPILX, EPILX1, MRX50, SYN1a, SYN1b, SYNI}, KCTD7 (potassium channel tetramerization domain containing 7) [NCBI Gene 154881] {aka CLN14, EPM3}, SRI (sorcin) [NCBI Gene 6717] {aka CP-22, CP22, SCN, V19}, ULK1 (unc-51 like autophagy activating kinase 1) [NCBI Gene 8408] {aka ATG1, ATG1A, UNC51, Unc51.1, hATG1}, CTNND1 (catenin delta 1) [NCBI Gene 1500] {aka BCDS2, CAS, CTNND, P120CAS, P120CTN, p120}, UBE3A (ubiquitin protein ligase E3A) [NCBI Gene 7337] {aka ANCR, AS, E6-AP, EPVE6AP, HPVE6A, PIX1}, REST (RE1 silencing transcription factor) [NCBI Gene 5978] {aka DFNA27, GINGF5, HGF5, NRSF, WT6, XBR}, GABRB3 (gamma-aminobutyric acid type A receptor subunit beta3) [NCBI Gene 2562] {aka DEE43, ECA5, EIEE43}, WDR26 (WD repeat domain 26) [NCBI Gene 80232] {aka CDW2, GID7, MIP2, SKDEAS}, SMARCA1 (SNF2 related chromatin remodeling ATPase 1) [NCBI Gene 6594] {aka ISWI, NURF140, SNF2L, SNF2L1, SNF2LB, SNF2LT}, ARID1B (AT-rich interaction domain 1B) [NCBI Gene 57492] {aka 6A3-5, BAF250B, BRIGHT, CSS1, DAN15, ELD/OSA1}, SCN1A (sodium voltage-gated channel alpha subunit 1) [NCBI Gene 6323] {aka DEE6, DEE6A, DEE6B, DRVT, EIEE6, FEB3}, Mir8114 (microRNA 8114) [NCBI Gene 102466257] {aka Gm27382, mmu-mir-8114}, CHORDC1 (cysteine and histidine rich domain containing 1) [NCBI Gene 26973] {aka CHP1}, Scn8a (sodium channel, voltage-gated, type VIII, alpha) [NCBI Gene 20273] {aka C630029C19Rik, NaCh6, Nav1.6, dmu, med, mnd-2}, TSC2 (TSC complex subunit 2) [NCBI Gene 7249] {aka LAM, PPP1R160, TSC4}, ZNF711 (ZFX family zinc finger ZNF711) [NCBI Gene 7552] {aka CMPX1, MRX65, MRX97, XLID97, ZNF4, ZNF5}, IL1B (interleukin 1 beta) [NCBI Gene 3553] {aka IL-1, IL1-BETA, IL1F2, IL1beta}, Mtor (mechanistic target of rapamycin kinase) [NCBI Gene 56717] {aka 2610315D21Rik, FRAP, FRAP2, Frap1, RAFT1, RAPT1}, GABRG2 (gamma-aminobutyric acid type A receptor subunit gamma2) [NCBI Gene 2566] {aka CAE2, DEE74, ECA2, EIEE74, FEB8, GEFSP3}, RAG1 (recombination activating 1) [NCBI Gene 5896] {aka RAG-1, RNF74}, Atg7 (autophagy related 7) [NCBI Gene 74244] {aka 1810013K23Rik, Agp7, Apg7l, Atg7l, Gm21553}, RELN (reelin) [NCBI Gene 5649] {aka ETL7, LIS2, PRO1598, RL}, Scn1a (sodium channel, voltage-gated, type I, alpha) [NCBI Gene 20265] {aka B230332M13, Nav1.1}, Dlx6os1 (distal-less homeobox 6, opposite strand 1) [NCBI Gene 320038] {aka A230055N17Rik, Dlx6as1, Evf-1, Evf-2, Evf1, Evf1/2}, AKT1 (AKT serine/threonine kinase 1) [NCBI Gene 207] {aka AKT, PKB, PKB-ALPHA, PRKBA, RAC, RAC-ALPHA}, ATRX (ATRX chromatin remodeler) [NCBI Gene 546] {aka JMS, MRX52, RAD54, RAD54L, XH2, XNP}, JUN (Jun proto-oncogene, AP-1 transcription factor subunit) [NCBI Gene 3725] {aka AP-1, AP1, c-Jun, cJUN, p39}, SIN3A (SIN3 transcription regulator family member A) [NCBI Gene 25942] {aka CHR15DELq24, DEL15Q24, WITKOS}, FOS (Fos proto-oncogene, AP-1 transcription factor subunit) [NCBI Gene 2353] {aka AP-1, C-FOS, p55}
- **Diseases:** fever (MESH:D005334), CHARGE syndrome (MESH:D058747), ATRX Syndrome (MESH:C538258), neurological disorder (MESH:D009461), LGS (MESH:D065768), metabolic disorders (MESH:D008659), convulsive (MESH:D012640), FCD (MESH:D000092222), X-linked epilepsies (MESH:C564516), status epilepticus (MESH:D013226), DEE (MESH:C562695), familial lateral temporal lobe epilepsy (MESH:C536956), structural (MESH:D020914), West Syndrome (MESH:D013036), neurologic diseases (MESH:D020271), focal epilepsies (MESH:D004828), Pitt-Hopkins syndrome (MESH:C537403), structural abnormalities in (MESH:C566527), structural anomalies (MESH:C536503), BFNE (MESH:D020936), drug-resistant epilepsy (MESH:D000069279), altered neuronal connectivity (MESH:D009372), Poison (MESH:D011041), Lobe Epilepsy (MESH:D004833), behavioral abnormalities (MESH:D001523), channelopathies (MESH:D053447), Neuroinflammation (MESH:D000090862), cortex (MESH:D000303), GLUT1 deficiency (MESH:C536830), idiopathic epilepsies (MESH:C562694), X-linked dominant disorders (MESH:D040181), Autosomal dominant epilepsies (MESH:C566739), infantile encephalopathy (MESH:C567924), febrile seizures (MESH:D003294), progressive myoclonic epilepsy type 3 (MESH:C567095), autism (MESH:D001321), injury to (MESH:D014947), inflammation (MESH:D007249), epileptic conditions (MESH:D020763), -coding RNA epilepsy (MESH:D012327), Lafora disease (MESH:D020192), transport (MESH:D007706), Nicolaides-Baraitser Syndrome (MESH:C536116), ADNFLE (MESH:C579932), Dravet Syndrome (MESH:D004831), abnormal brain development (MESH:D002658), neurological instability (MESH:D043171), Absence Epilepsy (MESH:D004832), Chronic epilepsy (MESH:D002908), cognitive deficits (MESH:D003072), movement disorders (MESH:D009069), Haploinsufficiency (MESH:C565160), KA (MESH:D011015), neonatal epileptic encephalopathy (MESH:D007232), neuronal damage (MESH:D009410), Unverricht-Lundborg disease (MESH:D020194), cortical developmental malformations (MESH:D054220), Hyperhomocysteinemia (MESH:D020138), pyridoxamine 5'-phosphate oxidase (PNPO) deficiency (MESH:C566449), periventricular nodular heterotopia (MESH:D054091)
- **Chemicals:** GABA (MESH:D005680), zebularine (MESH:C009131), chloride (MESH:D002712), 5-Methylcytosine (MESH:D044503), ezogabine (MESH:C101866), Miravirsen (MESH:C581159), TSA (MESH:C012589), memantine (MESH:D008559), Sirolimus (MESH:D020123), Ethosuximide (MESH:D005013), fat (MESH:D005223), Adenosine (MESH:D000241), N6-Methyladenosine (MESH:C010223), Pyridoxine (MESH:D011736), clobazam (MESH:D000078306), Vigabatrin (MESH:D020888), topiramate (MESH:D000077236), pyridoxal 5'-phosphate (MESH:D011732), levetiracetam (MESH:D000077287), calcium (MESH:D002118), fenfluramine (MESH:D005277), 5-aza-cytidine (MESH:D001374), inositol (MESH:D007294), cannabidiol (MESH:D002185), Sodium Butyrate (MESH:D020148), stiripentol (MESH:C021092), ATP (MESH:D000255), m6A (MESH:C005955), carbamazepine (MESH:D002220), KA (MESH:D007608), macrolide (MESH:D018942), amino acid (MESH:D000596), lamotrigine (MESH:D000077213), phenytoin (MESH:D010672), Quinidine (MESH:D011802), carbohydrate (MESH:D002241), Valproic Acid (MESH:D014635), Cl- (MESH:D002713), Curcumin (MESH:D003474), AntagomiR-134 (-), SAHA (MESH:D000077337), sodium (MESH:D012964), Everolimus (MESH:D000068338), pilocarpine (MESH:D010862), benzodiazepine (MESH:D001569), K+ (MESH:D011188)
- **Species:** Mus musculus (house mouse, species) [taxon 10090], Rattus norvegicus (brown rat, species) [taxon 10116], Homo sapiens (human, species) [taxon 9606]
- **Mutations:** p.Ser2215Phe

## Full text

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## Figures

4 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12921879/full.md

## References

106 references — full list in the complete paper: https://tomesphere.com/paper/PMC12921879/full.md

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Source: https://tomesphere.com/paper/PMC12921879