Relationship Between Epigenetic Factors and Retrotransposons and the Etiopathogenesis of Neurodegenerative Diseases
- Authors: Mustafin R.N.1
-
Affiliations:
- Bashkir State Medical University
- Section: Reviews
- Submitted: 09.11.2024
- Accepted: 11.04.2025
- Published: 18.07.2025
- URL: https://kazanmedjournal.ru/kazanmedj/article/view/641725
- DOI: https://doi.org/10.17816/KMJ641725
- EDN: https://elibrary.ru/HHCXMZ
- ID: 641725
Cite item
Abstract
The pathogenesis of neurodegenerative diseases is associated with proteopathy and the abnormal aggregation of specific proteins, including amyloid-β and tau protein in Alzheimer's disease, α-synuclein in Parikinson disease, and TDP-43 and FUS in amyotrophic lateral sclerosis. Etiological factors may include viral infections because of the protective functions of the above proteins in relation to specific viruses. In turn, the latter may enhance the expression of retroelements. Another cause of neurodegenerative diseases is physiological aging, as it activates retroelements and is associated with proteopathy of antiviral proteins, which normally suppresses the expression of retroelements. It is assumed that the etiological factors of amyotrophic lateral sclerosis, Alzheimer disease, and Parkinson disease include the associated genetic polymorphisms, most of which localize within intronic and intergenic regions where retroelement genes are located. Thus, the etiological factors of neurodegenerative diseases include genetic predisposition to the excessive activation of retroelements, aging, and viral infections, thus causing pathogenic proteopathy and the aggregation of amyloid-β, tau protein, α-synuclein, TDP-43, and FUS. As a result, these proteins lose their ability to inhibit retroelements by causing their excessive activation and an inflammatory immune response to their transcripts. In turn, the expression products of polymorphic retroelements enhance the production of antiviral proteins and their proteopathy and aggregation. A vicious circle develops that promotes the progression of the condition; this circle may be broken by inhibitors of retroelements and specific microRNAs that may become the basis for targeted therapy for neurodegenerative diseases. As such, these processes do not induce nucleotide DNA sequence damage; rather, they indicate the epigenetic mechanisms of these diseases.
Keywords
About the authors
Rustam N. Mustafin
Bashkir State Medical University
Author for correspondence.
Email: ruji79@mail.ru
ORCID iD: 0000-0002-4091-382X
SPIN-code: 4810-2534
Scopus Author ID: 56603137500
ResearcherId: S-2194 -2018
Cand. Sci. (Biology), Assistant Professor, Depart. of Medical Genetics and Fundamental Medicine
Russian Federation, UfaReferences
- Niu H, Alvarez-Alvarez I, Guillen-Grima F, Aguinaga-Ontoso I. Prevalence and incidence of Alzheimer's disease in Europe: A meta-analysis. Neurologia. 2017;32(8):523–532. doi: 10.1016/j.nrl.2016.02.016 EDN: YEOSYV
- Xu L, Liu T, Liu L, et al. Global variation in prevalence and incidence of amyotrophic lateral sclerosis: a systematic review and meta-analysis. J Neurol. 2020;267:944–953. doi: 10.1007/s00415-019-09652-y EDN: RIWYUH
- Klokkaris A, Migdalska-Richards A. An Overview of Epigenetic Changes in the Parkinson's Disease Brain. Int J Mol Sci. 2024;25:6168. doi: 10.3390/ijms25116168 EDN: WSILNA
- Leblanc P, Vorberg IM. Viruses in neurodegenerative diseases: More than just suspects in crimes. PLoS Pathog. 2022;18:e1010670. doi: 10.1371/journal.ppat.1010670 EDN: FEXXYS
- Camacho-Soto A, Searles Nielsen S, Faust IM, et al. Incidence of amyotrophic lateral sclerosis in older adults. Muscle Nerve. 2022;66(3):289–296. doi: 10.1002/mus.27652 EDN: ZXKPYA
- Shelkovnikova TA, An H, Skelt L, et al. Antiviral Immune Response as a Trigger of FUS Proteinopathy in Amyotrophic Lateral Sclerosis. Cell Rep. 2019;29:4496–4508.e4. doi: 10.1016/j.celrep.2019.11.094 EDN: KCPYNC
- de Cecco M, Ito T, Petrashen AP, et al. L1 drives IFN in senescent cells and promotes age-associated inflammation. Nature. 2019;566(7742):73–78. doi: 10.1038/s41586-018-0784-9 EDN: ZXILUK
- Nurk S, Koren S, Rhie A, et al. The complete sequence of a human genome. Science. 2022;376(6588):44–53. doi: 10.1126/science.abj6987 EDN: WPZXKF
- Yong SY, Raben TG, Lello L, Hsu SDH. Genetic architecture of complex traits and disease risk predictors. Sci Rep. 2020;10:12055. doi: 10.1038/s41598-020-68881-8 EDN: AGBERY
- GNS HS, Marise VLP, Satish KS, et al. Untangling huge literature to disinter genetic underpinnings of Alzheimer's Disease: A systematic review and meta-analysis. Ageing Res Rev. 2021;71:101421. doi: 10.1016/j.arr.2021.101421 EDN: CHTGEU
- Kim JJ, Vitale D, Otani DV, et al. Multi-ancestry genome-wide association meta-analysis of Parkinson's disease. Nat Genet. 2024;56:27–36. doi: 10.1038/s41588-023-01584-8 EDN: SMXLJN
- Nakamura R, Misawa K, Tohnai G, et al. A multi-ethnic meta-analysis identifies novel genes, including ACSL5, associated with amyotrophic lateral sclerosis. Commun Biol. 2020;3:526. doi: 10.1038/s42003-020-01251-2 EDN: AOJGBW
- Savinova AV, Shnayder NA, Nasyrova RF. Genetics of familial amyotrophic lateral sclerosis. Bulletin of Siberian Medicine. 2021;20(3):193–202. doi: 10.20538/1682-0363-2021-3-193-202 EDN: WOSQWX
- Pereira GC, Sanchez L, Schaughency PM, et al. Properties of LINE-1 proteins and repeat element expression in the context of amyotrophic lateral sclerosis. Mob DNA. 2018;9:35. doi: 10.1186/s13100-018-0138-z EDN: ZPMHEO
- Grundman J, Spencer B, Sarsoza F, Rissman RA. Transcriptome analyses reveal tau isoform-driven changes in transposable element and gene expression. PLoS One. 2021;16:e0251611. doi: 10.1371/journal.pone.0251611 EDN: PPAGCI
- Gordevičius J, Goralski T, Bergsma A, et al. Human Endogenous Retrovirus Expression is Dynamically Regulated in Parkinson's Disease. bioRxiv. 2023. doi: 10.1101/2023.11.03.565438
- Liu S, Heumüller SE, Hossinger A, et al. Reactivated endogenous retroviruses promote protein aggregate spreading. Nat Commun. 2023;14:5034. doi: 10.1038/s41467-023-40632-z EDN: AUAJMG
- Mustafin RN. A hypothesis about interrelations of epigenetic factors and transposable elements in memory formation. Vavilov Journal of Genetic and Breeding. 2024;28(5):476–486. doi: 10.18699/vjgb-24-54 EDN: IJCHYH
- Sirotko I, Volobuev A, Romanchuk P. Genetics and Epigenetics of Alzheimer's Disease: new Cognitive Technologies and Neurocommunication. Bulletin of Science and Practice. 2021;7(2):89–111. doi: 10.33619/2414-2948/63/09 EDN: AJXFFL
- Iakovenko EV, Fedotova EYu, Illarioshkin SN. DNA methylation in Parkinson disease. Annals of clinical and experimental neurology. 2020;14(4):75–81. doi: 10.25692/ACEN.2020.4.10 EDN: PRPWSS
- Shpilyukova YuA, Fedotova EYu, Pogoda TV. Evaluation of methylation status of the 5'-promoter region of C9orf72 gene in Russian patients with neurodegenerative diseases. Neuromuscular Diseases. 2018;8(2):33–41. doi: 10.17650/2222-8721-2018-8-2-33-41 EDN: UUHPBQ
- Mustafin RN. The hypothesis of the origin of viruses from transposons. Molecular Genetics, Microbiolgy and Virology. 2018;36:182–190. doi: 10.17116/molgen201836041182 EDN: YWOYEX
- Eimer WA, Vijaya Kumar DK, Navalpur Shanmugam NK, et al. Alzheimer's Disease-Associated β-Amyloid Is Rapidly Seeded by Herpesviridae to Protect against Brain Infection. Neuron. 2018;99:56–63.e3. doi: 10.1016/j.neuron.2018.06.030
- Hategan A, Bianchet MA, Steiner J, et al. HIV Tat protein and amyloid-β peptide form multifibrillar structures that cause neurotoxicity. Nat Struct Mol Biol. 2017;24:379–386. doi: 10.1038/nsmb.3379 EDN: YXUIZJ
- Bortolotti D, Gentili V, Rotola A, et al. HHV-6A infection induces amyloid-beta expression and activation of microglial cells. Alzheimers Res Ther. 2019;11:104. doi: 10.1186/s13195-019-0552-6 EDN: ZDVDKK
- Rahmati M, Yon DK, Lee SW, et al. New-onset neurodegenerative diseases as long-term sequelae of SARS-CoV-2 infection: A systematic review and meta-analysis. J Med Virol. 2023;(7):e28909. doi: 10.1002/jmv.28909 EDN: TLKWSV
- Marreiros R, Muller-Schiffmann A, Trossbach SV, et al. Disruption of cellular proteostasis by H1N1 influenza A virus causes alpha-synuclein aggregation. Proc Natl Acad Sci USA. 2020;117:6741–6751. doi: 10.1073/pnas.1906466117 EDN: XGUWJW
- Santerre M, Arjona SP, Allen CN, et al. HIV-1 Vpr protein impairs lysosome clearance causing SNCA/alpha-synuclein accumulation in neurons. Autophagy. 2021;17:1768–1782. doi: 10.1080/15548627.2021.1915641 EDN: QHFFQP
- Iravanpour F, Farrokhi MR, Jafarinia M, Oliaee RT. The effect of SARS-CoV-2 on the development of Parkinson's disease: the role of α-synuclein. Hum Cell. 2024;37:1–8. doi: 10.1007/s13577-023-00988-2 EDN: DYWZLU
- Barbut D, Stolzenberg E, Zasloff M. Gastrointestinal Immunity and Alpha-Synuclein. J Parkinsons Dis. 2019;9:S313–S322. doi: 10.3233/JPD-191702
- Monogue B, Chen Y, Sparks H, et al. Alpha-synuclein supports type 1 interferon signalling in neurons and brain tissue. Brain. 2022;145:3622–3636. doi: 10.1093/brain/awac192 EDN: RYNWSQ
- Zhang L, Yang J, Li H, et al. Enterovirus D68 Infection Induces TDP-43 Cleavage, Aggregation, and Neurotoxicity. J Virol. 2023;97:e0042523. doi: 10.1128/jvi.00425-23 EDN: AOJEAV
- Yang J, Li Y, Wang S, et al. The SARS-CoV-2 main protease induces neurotoxic TDP-43 cleavage and aggregates. Signal Transduct Target Ther. 2023;8:109. doi: 10.1038/s41392-023-01386-8 EDN: TDHMLO
- Fung G, Shi J, Deng H, et al. Cytoplasmic translocation, aggregation, and cleavage of TDP-43 by enteroviral proteases modulate viral pathogenesis. Cell Death Differ. 2015;22:2087–2097. doi: 10.1038/cdd.2015.58 EDN: VGGLTV
- Cabrera-Rodríguez R, Pérez-Yanes S, Lorenzo-Sánchez I, et al. TDP-43 Controls HIV-1 Viral Production and Virus Infectiveness. Int J Mol Sci. 2023;24:7658. doi: 10.3390/ijms24087658 EDN: TJDFIS
- Guo C, Jeong HH, Hsieh YC, et al. Tau Activates Transposable Elements in Alzheimer's Disease. Cell Rep. 2018;23:2874–2880. doi: 10.1016/j.celrep.2018.05.004 EDN: FIULAK
- Tam OH, Rozhkov NV, Shaw R, et al. Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia. Cell Rep. 2019;29:1164–1177.e5. doi: 10.1016/j.celrep.2019.09.066
- Bello-Morales R, Andreu S, Ripa I, López-Guerrero JA. HSV-1 and Endogenous Retroviruses as Risk Factors in Demyelination. Int J Mol Sci. 2021;22:5738. doi: 10.3390/ijms22115738 EDN: QZNPEA
- Dopkins N, Fei T, Michael S, et al. Endogenous retroelement expression in the gut microenvironment of people living with HIV-1. EBioMedicine. 2024;103:105133. doi: 10.1016/j.ebiom.2024.105133 EDN: VYZZIA
- Cheng Y, Saville L, Gollen B, et al. Increased processing of SINE B2 ncRNAs unveils a novel type of transcriptome deregulation in amyloid beta neuropathology. Elife. 2020;9:e61265. doi: 10.7554/eLife.61265 EDN: PJRLQP
- Wang M, Wang L, Liu H, et al. Transcriptome Analyses Implicate Endogenous Retroviruses Involved in the Host Antiviral Immune System through the Interferon Pathway. Virol Sin. 2021;36:1315–1326. doi: 10.1007/s12250-021-00370-2 EDN: HGOGCJ
- Mustafin RN, Kazantseva AV, Kovas YuV, Khusnutdinova EK. Role of retroelements in the development of COVID-19 neurological consequences. Russian Open Medical Journal. 2022;11:313. doi: 10.15275/rusomj.2022.0313 EDN: IYUQMI
- Dechaumes A, Bertin A, Sane F, et al. Coxsackievirus-B4 Infection Can Induce the Expression of Human Endogenous Retrovirus W in Primary Cells. Microorganisms. 2020;8:1335. doi: 10.3390/microorganisms8091335 EDN: KAQXSC
- Li W, Jin Y, Prazak L, et al. Transposable elements in TDP-43-mediated neurodegenerative disorders. PLoS One. 2012;7:e44099. doi: 10.1371/journal.pone.0044099
- Liu EY, Russ J, Cali CP, et al. Loss of Nuclear TDP-43 Is Associated with Decondensation of LINE Retrotransposons. Cell Rep. 2019;27:1409–1421.e6. doi: 10.1016/j.celrep.2019.04.003
- Li TD, Murano K, Kitano T, et al. TDP-43 safeguards the embryo genome from L1 retrotransposition. Sci Adv. 2022;8:eabq3806. doi: 10.1126/sciadv.abq3806 EDN: EKKXHJ
- Sun W, Samimi H, Gamez M, et al. Pathogenic tau-induced piRNA depletion promotes neuronal death through transposable element dysregulation in neurodegenerative tauopathies. Nat Neurosci. 2018;21:1038–1048. doi: 10.1038/s41593-018-0194-1 EDN: SFHAMH
- Macciardi F, Giulia Bacalini M, Miramontes R, et al. A retrotransposon storm marks clinical phenoconversion to late-onset Alzheimer's disease. Geroscience. 2022;44:1525–1550. doi: 10.1007/s11357-022-00580-w EDN: KDVHMR
- Thomas R, Connolly KJ, Brekk OR, et al. Viral-like TLR3 induction of cytokine networks and α-synuclein are reduced by complement C3 blockade in mouse brain. Sci Rep. 2023;13:15164. doi: 10.1038/s41598-023-41240-z EDN: UUYGBS
- Hughes LS, Fröhlich A, Pfaff AL, et al. Exploring SVA Insertion Polymorphisms in Shaping Differential Gene Expressions in the Central Nervous System. Biomolecules. 2024;14:358. doi: 10.3390/biom14030358 EDN: CRPYSR
- Savage AL, Lopez AI, Iacoangeli A, et al. Frequency and methylation status of selected retrotransposition competent L1 loci in amyotrophic lateral sclerosis. Mol Brain. 2020;13:154. doi: 10.1186/s13041-020-00694-2 EDN: ZLMKWM
- Simula ER, Arru G, Zarbo IR, et al. TDP-43 and HERV-K Envelope-Specific Immunogenic Epitopes Are Recognized in ALS Patients. Viruses. 2021;13:2301. doi: 10.3390/v13112301 EDN: TEOHZY
- Li W, Lee MH, Henderson L, et al. Human endogenous retrovirus-K contributes to motor neuron disease. Sci Transl Med. 2015;7:307ra153. doi: 10.1126/scitranslmed.aac8201 EDN: VFAGUH
- Chang YH, Dubnau J. Endogenous retroviruses and TDP-43 proteinopathy form a sustaining feedback driving intercellular spread of Drosophila neurodegeneration. Nat Commun. 2023;14:966. doi: 10.1038/s41467-023-36649-z EDN: GOTHTY
- Mustafin RN, Khusnutdinova EK. Involvement of transposable elements in neurogenesis. Vavilov Journal of Genetics and Breeding. 2020;24:209–218. doi: 10.18699/VJ20.613 EDN: NNBKOK
- Dembny P, Newman AG, Singh M, et al. Human endogenous retrovirus HERV-K(HML-2) RNA causes neurodegeneration through Toll-like receptors. JCI Insight. 2020;5:e131093. doi: 10.1172/jci.insight.131093 EDN: CUXBJM
- Gazquez-Gutierrez A, Witteveldt J, R Heras S, Macias S. Sensing of transposable elements by the antiviral innate immune system. RNA. 2021;27:735–752. doi: 10.1261/rna.078721.121 EDN: EYHVVL
- Elbarbary RA, Maquat LE. Distinct mechanisms obviate the potentially toxic effects of inverted-repeat Alu elements on cellular RNA metabolism. Nat Struct Mol Biol. 2017;24:496–498. doi: 10.1038/nsmb.3416
- Larsen PA, Lutz MW, Hunnicutt KE, et al. The Alu neurodegeneration hypothesis: A primate-specific mechanism for neuronal transcription noise, mitochondrial dysfunction, and manifestation of neurodegenerative disease. Alzheimers Dement. 2017;13:828–838. doi: 10.1016/j.jalz.2017.01.017
- Gold J, Rowe DB, Kiernan MC, et al. Safety and tolerability of Triumeq in amyotrophic lateral sclerosis: the Lighthouse trial. Amyotroph Lateral Scler Frontotemporal Degener. 2019;20:595–604. doi: 10.1080/21678421.2019.1632899
- Li W, Pandya D, Pasternack N, et al. Retroviral Elements in Pathophysiology and as Therapeutic Targets for Amyotrophic Lateral Sclerosis. Neurotherapeutics. 2022;19:1085–1101. doi: 10.1007/s13311-022-01233-8 EDN: PVUASN
- Loyola AC, Zhang L, Shang R, et al. Identification of methotrexate as a heterochromatin-promoting drug. Sci Rep. 2019;9:11673. doi: 10.1038/s41598-019-48137-w
- Balmus G, Larrieu D, Barros AC, et al. Targeting of NAT10 enhances healthspan in a mouse model of human accelerated aging syndrome. Nat Commun. 2018;9:1700. doi: 10.1038/s41467-018-03770-3 EDN: TFLLBK
- Steiner JP, Bachani M, Malik N, et al. Human Endogenous Retrovirus K Envelope in Spinal Fluid of Amyotrophic Lateral Sclerosis Is Toxic. Ann Neurol. 2022;92:545–561. doi: 10.1002/ana.26452 EDN: BNMSVL
- Mustafin RN. The relationship of retroelements with microRNAs in memory formation. Opera Medica et Physiologica. 2023;10:87–102. doi: 10.24412/2500-2295-2023-4-87-102 EDN: WCGUBH
- Park EG, Ha H, Lee DH, et al. Genomic Analyses of Non-Coding RNAs Overlapping Transposable Elements and Its Implication to Human Diseases. Int J Mol Sci. 2022;23:8950. doi: 10.3390/ijms23168950 EDN: LOWPSN
Supplementary files
