{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,5]],"date-time":"2026-09-05T21:19:10Z","timestamp":1788643150988,"version":"build-2803163510"},"reference-count":72,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2026,5,18]],"date-time":"2026-05-18T00:00:00Z","timestamp":1779062400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100020598","name":"The Multiple Sclerosis Society of Western Australia","doi-asserted-by":"publisher","award":["032022"],"award-info":[{"award-number":["032022"]}],"id":[{"id":"10.13039\/501100020598","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000864","name":"Michael J. Fox Foundation","doi-asserted-by":"publisher","award":["18213"],"award-info":[{"award-number":["18213"]}],"id":[{"id":"10.13039\/100000864","id-type":"DOI","asserted-by":"publisher"}]},{"award":["18213"],"award-info":[{"award-number":["18213"]}],"id":[{"id":"https:\/\/ror.org\/03arq3225","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000864","name":"Shake It Up Australia","doi-asserted-by":"publisher","award":["18213"],"award-info":[{"award-number":["18213"]}],"id":[{"id":"10.13039\/100000864","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background\/Objectives: Parkinson\u2019s disease (PD) is associated with systemic molecular alterations that extend beyond the central nervous system, including changes in peripheral blood transcriptomic profiles. While prior studies have focused predominantly on coding-gene expression, the longitudinal behavior of the peripheral blood repeatome following clinical diagnosis remains poorly characterized. Here, we investigated temporal remodeling of repetitive-element transcription over 36 months post-diagnosis by integrating repeat subfamily- and locus-specific analyses. Methods: Repeatome expression was quantified using SalmonTE and DESeq2 in peripheral blood RNA-seq data from 1560 PD and control individuals at diagnostic baseline (BL) and four follow-up visits (6, 12, 24, and 36 months). Differential expression was assessed at the subfamily level, with additional locus-specific validation in a representative subset. Results: A total of 259 repeat subfamilies were differentially expressed (padj &lt; 0.05), of which 224 (86.5%) were already detected at baseline. Enrichment of differential expression was significantly higher at baseline than at later visits (odds ratio = 30.9, p &lt; 2.2 \u00d7 10\u221216), with limited additional divergence over time. Longitudinal analyses revealed non-linear trajectories in selected repeat families, including Alu and SVA subfamilies. Locus-specific analysis identified 237 significantly regulated elements, demonstrating heterogeneous, site-specific transcriptional changes, including clusters of differentially expressed loci and instances within PD-relevant genomic regions (e.g., SNCA and IKZF2). Conclusions: Peripheral blood repeatome expression differs between PD and control groups, with the dominant signal established at clinical diagnosis and modest longitudinal modulation thereafter. Integration of locus-level analysis indicates that subfamily level patterns arise from discrete genomic events rather than uniform regulation. These findings support a model of systemic, immune-associated transcriptomic remodeling in circulating blood cells and position the peripheral repeatome as a dynamic framework for biomarker discovery and future mechanistic investigation.<\/jats:p>","DOI":"10.3390\/genes17050577","type":"journal-article","created":{"date-parts":[[2026,5,20]],"date-time":"2026-05-20T15:45:34Z","timestamp":1779291934000},"page":"577","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Longitudinal Repeatome Remodeling in Peripheral Blood Following Parkinson\u2019s Disease Diagnosis"],"prefix":"10.3390","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9789-245X","authenticated-orcid":false,"given":"Jerzy K.","family":"Kulski","sequence":"first","affiliation":[{"name":"School of Biomedical Science, Discipline of Microbiology and Immunology, The University of Western Australia, Crawley, WA 6009, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6087-6643","authenticated-orcid":false,"given":"Sulev","family":"Koks","sequence":"additional","affiliation":[{"name":"Personalised Medicine Centre, Health Futures Institute, Murdoch University, Perth, WA 6150, Australia"},{"name":"Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,5,18]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1186\/s40035-019-0165-9","article-title":"The interplay of aging, genetics and environmental factors in the pathogenesis of Parkinson\u2019s disease","volume":"8","author":"Pang","year":"2019","journal-title":"Transl. Neurodegener."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1146\/annurev-pathol-011110-130242","article-title":"Parkinson\u2019s Disease: Genetics and Pathogenesis","volume":"6","author":"Shulman","year":"2011","journal-title":"Annu. Rev. Pathol. Mech. Dis."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1038\/s41582-020-0344-4","article-title":"Parkinson disease and the immune system\u2014Associations, mechanisms and therapeutics","volume":"16","author":"Tan","year":"2020","journal-title":"Nat. Rev. Neurol."},{"key":"ref_4","first-page":"504","article-title":"Parkinson\u2019s Disease and Its Management","volume":"40","author":"DeMaagd","year":"2015","journal-title":"Pharm. Ther."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1038\/s41419-023-05672-9","article-title":"Alpha-synuclein in Parkinson\u2019s disease and other synucleinopathies: From overt neurodegeneration back to early synaptic dysfunction","volume":"14","author":"Calabresi","year":"2023","journal-title":"Cell Death Dis."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"2179","DOI":"10.1007\/s12031-020-01776-5","article-title":"Tau in the Pathophysiology of Parkinson\u2019s Disease","volume":"71","author":"Pan","year":"2021","journal-title":"J. Mol. Neurosci."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"a009399","DOI":"10.1101\/cshperspect.a009399","article-title":"Alpha-Synuclein in Parkinson\u2019s disease","volume":"2","author":"Stefanis","year":"2012","journal-title":"Cold Spring Harb. Perspect. Med."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"104782","DOI":"10.1016\/j.nbd.2020.104782","article-title":"Genetics of Parkinson\u2019s disease: An introspection of its journey towards precision medicine","volume":"137","author":"Kim","year":"2020","journal-title":"Neurobiol. Dis."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.1016\/S1474-4422(19)30320-5","article-title":"Identification of novel risk loci, causal insights, and heritable risk for Parkinson\u2019s disease: A meta-analysis of genome-wide association studies","volume":"18","author":"Nalls","year":"2019","journal-title":"Lancet Neurol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1162","DOI":"10.1002\/ana.26923","article-title":"Alterations in Blood Methylome as Potential Epigenetic Biomarker in Sporadic Parkinson\u2019s Disease","volume":"95","author":"Bustos","year":"2024","journal-title":"Ann. Neurol."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Klokkaris, A., and Migdalska-Richards, A. (2024). An Overview of Epigenetic Changes in the Parkinson\u2019s Disease Brain. Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms25116168"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1177\/1535370220967325","article-title":"Transcriptomic profiles in Parkinson\u2019s disease","volume":"246","author":"Kurvits","year":"2021","journal-title":"Exp. Biol. Med."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1063","DOI":"10.12688\/f1000research.168556.1","article-title":"Single-cell RNA sequencing of cerebrospinal fluid reveals the expansion of innate lymphoid cells with upregulated transposable elements in multiple sclerosis","volume":"14","author":"Mosaddeghi","year":"2025","journal-title":"F1000Research"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Santiago, J.A., and Potashkin, J.A. (2015). Blood Biomarkers Associated with Cognitive Decline in Early Stage and Drug-Naive Parkinson\u2019s Disease Patients. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0142582"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"e698","DOI":"10.1212\/WNL.0000000000200699","article-title":"Genome-wide Association and Meta-analysis of Age at Onset in Parkinson Disease: Evidence from the COURAGE-PD Consortium","volume":"99","author":"Grover","year":"2022","journal-title":"Neurology"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1038\/s41531-021-00221-7","article-title":"A transcriptome-wide association study identifies susceptibility genes for Parkinson\u2019s disease","volume":"7","author":"Yao","year":"2021","journal-title":"NPJ Park. Dis."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1002\/mds.29257","article-title":"Blood Markers of Inflammation, Neurodegeneration, and Cardiovascular Risk in Early Parkinson\u2019s Disease","volume":"38","author":"Bartl","year":"2023","journal-title":"Mov. Disord."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1038\/s43587-021-00088-6","article-title":"RNA sequencing of whole blood reveals early alterations in immune cells and gene expression in Parkinson\u2019s disease","volume":"1","author":"Craig","year":"2021","journal-title":"Nat. Aging"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1038\/s41577-022-00684-6","article-title":"Inflammation and immune dysfunction in Parkinson disease","volume":"22","author":"Tansey","year":"2022","journal-title":"Nat. Rev. Immunol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1016\/j.brainresbull.2017.03.009","article-title":"Metabolic Dysfunction in Parkinson\u2019s Disease: Bioenergetics, Redox Homeostasis and Central Carbon Metabolism","volume":"133","author":"Anandhan","year":"2017","journal-title":"Brain Res. Bull."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1186\/s13024-025-00827-y","article-title":"Immune cell metabolic dysfunction in Parkinson\u2019s disease","volume":"20","author":"Mark","year":"2025","journal-title":"Mol. Neurodegener."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Sian-Hulsmann, J., Riederer, P., and Michel, T.M. (2024). Metabolic Dysfunction in Parkinson\u2019s Disease: Unraveling the Glucose-Lipid Connection. Biomedicines, 12.","DOI":"10.3390\/biomedicines12122841"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"101017","DOI":"10.1016\/j.bbih.2025.101017","article-title":"The contribution of type-I IFN-mediated neuroinflammation to Parkinson\u2019s disease progression","volume":"46","author":"Chen","year":"2025","journal-title":"Brain Behav. Immun.-Health"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"3622","DOI":"10.1093\/brain\/awac192","article-title":"Alpha-synuclein supports type 1 interferon signalling in neurons and brain tissue","volume":"145","author":"Monogue","year":"2022","journal-title":"Brain"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1460","DOI":"10.1002\/acn3.644","article-title":"The Parkinson\u2019s progression markers initiative (PPMI)\u2014Establishing a PD biomarker cohort","volume":"5","author":"Marek","year":"2018","journal-title":"Ann. Clin. Transl. Neurol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1038\/s43587-021-00042-6","article-title":"Deep sequencing of sncRNAs reveals hallmarks and regulatory modules of the transcriptome during Parkinson\u2019s disease progression","volume":"1","author":"Kern","year":"2021","journal-title":"Nat. Aging"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Koks, S. (2025). The Exon-Based Transcriptomic Analysis of Parkinson\u2019s Disease. Biomolecules, 15.","DOI":"10.3390\/biom15030440"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"11795735241286821","DOI":"10.1177\/11795735241286821","article-title":"Transcriptomics profiling of Parkinson\u2019s disease progression subtypes reveals distinctive patterns of gene expression","volume":"17","author":"Fabrizio","year":"2025","journal-title":"J. Cent. Nerv. Syst. Dis."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.ebiom.2018.04.004","article-title":"Tandem Repeats and Repeatomes: Delving Deeper into the\u2018Dark Matter\u2019 of Genomes","volume":"31","author":"Hannan","year":"2018","journal-title":"EBioMedicine"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1680","DOI":"10.1177\/15353702221117147","article-title":"Non-reference genome transposable elements (TEs) have a significant impact on the progression of the Parkinson\u2019s disease","volume":"247","author":"Pfaff","year":"2022","journal-title":"Exp. Biol. Med."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1007\/s12640-024-00688-1","article-title":"Transposable Elements: Emerging Therapeutic Targets in Neurodegenerative Diseases","volume":"42","author":"Singh","year":"2024","journal-title":"Neurotox. Res."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"13857","DOI":"10.1038\/s41598-023-41052-1","article-title":"Reference LINE-1 insertion polymorphisms correlate with Parkinson\u2019s disease progression and differential transcript expression in the PPMI cohort","volume":"13","author":"Pfaff","year":"2023","journal-title":"Sci. Rep."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"10932","DOI":"10.1038\/s41598-024-61753-5","article-title":"Deciphering the role of a SINE-VNTR-Alu retrotransposon polymorphism as a biomarker of Parkinson\u2019s disease progression","volume":"14","author":"Pfaff","year":"2024","journal-title":"Sci. Rep."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/s41531-021-00189-4","article-title":"Reference SVA insertion polymorphisms are associated with Parkinson\u2019s Disease progression and differential gene expression","volume":"7","author":"Pfaff","year":"2021","journal-title":"npj Park. Dis."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"4369","DOI":"10.1038\/s41598-019-40869-z","article-title":"Analysis of repetitive element expression in the blood and skin of patients with Parkinson\u2019s disease identifies differential expression of satellite elements","volume":"9","author":"Billingsley","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1780","DOI":"10.1177\/15353702231198078","article-title":"Longitudinal dysregulation of long non-coding RNAs in Parkinson\u2019s disease","volume":"248","author":"Cuttler","year":"2023","journal-title":"Exp. Biol. Med."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1038\/nrg.2016.139","article-title":"Regulatory activities of transposable elements: From conflicts to benefits","volume":"18","author":"Chuong","year":"2017","journal-title":"Nat. Rev. Genet."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1186\/s13100-025-00366-9","article-title":"Exploring transposable elements: New horizons in cancer diagnostics and therapeutics","volume":"16","author":"Chaaban","year":"2025","journal-title":"Mob. DNA"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/j.tig.2007.02.006","article-title":"Which transposable elements are active in the human genome?","volume":"23","author":"Mills","year":"2007","journal-title":"Trends Genet."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1186\/s13073-020-00740-7","article-title":"Widespread and tissue-specific expression of endogenous retroelements in human somatic tissues","volume":"12","author":"Larouche","year":"2020","journal-title":"Genome Med."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Chesnokova, E., Beletskiy, A., and Kolosov, P. (2022). The Role of Transposable Elements of the Human Genome in Neuronal Function Pathology. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms23105847"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"6731","DOI":"10.1007\/s11357-025-01765-9","article-title":"Epigenetic dysregulation of transposable elements in cognitive impairment and Alzheimer\u2019s disease","volume":"47","author":"Cavalier","year":"2025","journal-title":"Geroscience"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"RP96575","DOI":"10.7554\/eLife.96575","article-title":"Expression of most retrotransposons in human blood correlates with biological aging","volume":"13","author":"Tsai","year":"2024","journal-title":"eLife"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1038\/s41586-018-0784-9","article-title":"L1 drives IFN in senescent cells and promotes age-associated inflammation","volume":"566","author":"Ito","year":"2019","journal-title":"Nature"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"7621","DOI":"10.1016\/j.cell.2024.11.016","article-title":"Regulation of human interferon signaling by transposon exonization","volume":"187","author":"Pasquesi","year":"2024","journal-title":"Cell"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"11564","DOI":"10.1073\/pnas.0904477106","article-title":"The role of transposable elements in the regulation of IFN- 1 gene expression","volume":"106","author":"Thomson","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1016\/j.gde.2016.01.001","article-title":"How retrotransposons shape genome regulation","volume":"37","author":"Mita","year":"2016","journal-title":"Curr. Opin. Genet. Dev."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1007\/s10142-010-0168-1","article-title":"The transcript repeat element: The human Alu sequence as a component of gene networks influencing cancer","volume":"10","author":"Moolhuijzen","year":"2010","journal-title":"Funct. Integr. Genom."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1186\/s13100-025-00373-w","article-title":"Structural and transduction patterns of human-specific polymorphic SVA insertions","volume":"16","author":"Kirby","year":"2025","journal-title":"Mob. DNA"},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Camara, M.B., Sobeh, A.M., and Eichhorn, C.D. (2023). Progress in 7SK ribonucleoprotein structural biology. Front. Mol. Biosci., 10.","DOI":"10.3389\/fmolb.2023.1154622"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1038\/312171a0","article-title":"Alu sequences are processed 7SL RNA genes","volume":"112","author":"Ullu","year":"1984","journal-title":"Nature"},{"key":"ref_52","doi-asserted-by":"crossref","unstructured":"Wang, J., Samuels, D.C., Zhao, S., Xiang, Y., Zhao, Y.Y., and Guo, Y. (2017). Current Research on Non-Coding Ribonucleic Acid (RNA). Genes, 8.","DOI":"10.3390\/genes8120366"},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Dumetier, B., Sauter, C., Hajmirza, A., Pernon, B., Aucagne, R., Fournier, C., Row, C., Guidez, F., Rossi, C., and Lepage, C. (2022). Repeat Element Activation-Driven Inflammation: Role of NFkappaB and Implications in Normal Development and Cancer?. Biomedicines, 10.","DOI":"10.3390\/biomedicines10123101"},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Jeong, H.-H., Yalamanchili, H.K., Guo, C., Shulman, J.M., and Liu, Z. (2018). An ultra-fast and scalable quantification pipeline for transposable elements from next generation sequencing data. Pacific Symposium on Biocomputing 2018: Proceedings of the Pacific Symposium, World Scientific Publishing Co.","DOI":"10.1142\/9789813235533_0016"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/s13100-015-0041-9","article-title":"Repbase Update, a database of repetitive elements in eukaryotic genomes","volume":"6","author":"Bao","year":"2015","journal-title":"Mob. DNA"},{"key":"ref_56","unstructured":"(2025, October 05). RepeatMasker Open-4.0. Available online: http:\/\/www.repeatmasker.org."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/s13100-020-00230-y","article-title":"The Dfam community resource of transposable element families, sequence models, and genome annotations","volume":"12","author":"Storer","year":"2021","journal-title":"Mob. DNA"},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Saleh, A., Macia, A., and Muotri, A.R. (2019). Transposable Elements, Inflammation, and Neurological Disease. Front. Neurol., 10.","DOI":"10.3389\/fneur.2019.00894"},{"key":"ref_59","first-page":"2304","article-title":"Regulation of expression quantitative trait loci by SVA retrotransposons within the major histocompatibility complex","volume":"248","author":"Kulski","year":"2023","journal-title":"Exp. Biol. Med."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"1583","DOI":"10.36922\/gtm.1583","article-title":"Genome-wide analysis identifies non-reference transposable element polymorphisms associated with Parkinson\u2019s disease","volume":"2","author":"Wu","year":"2023","journal-title":"Glob. Transl. Med."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"87","DOI":"10.4161\/pri.4.2.11965","article-title":"Transcription of Alu DNA elements in blood cells of sporadic Creutzfeldt-Jakob disease (sCJD)","volume":"4","author":"Kiesel","year":"2010","journal-title":"Prion"},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Kulski, J.K., Pfaff, A.L., and Koks, S. (2024). SVA Regulation of Transposable Element Clustered Transcription within the Major Histocompatibility Complex Genomic Class II Region of the Parkinson\u2019s Progression Markers Initiative. Genes, 15.","DOI":"10.3390\/genes15091185"},{"key":"ref_63","doi-asserted-by":"crossref","unstructured":"Kulski, J.K., Pfaff, A.L., and Koks, S. (2025). The Transcription of Transposable Elements Differentially Regulated by SVAs in the Major Histocompatibility Complex Class IRegion of a Parkinson\u2019s Progression Markers Initiative Cohort. J. Mol. Pathol., 6.","DOI":"10.3390\/jmp6010001"},{"key":"ref_64","doi-asserted-by":"crossref","unstructured":"Kulski, J.K., Suzuki, S., Shiina, T., Pfaff, A.L., and Koks, S. (2024). Regulatory SVA retrotransposons and classical HLA genotyped-transcripts associated with Parkinson\u2019s disease. Front. Immunol., 15.","DOI":"10.3389\/fimmu.2024.1349030"},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"Pfaff, A.L., Bubb, V.J., Quinn, J.P., and Koks, S. (2020). An Increased Burden of Highly Active Retrotransposition Competent L1s Is Associated with Parkinson\u2019s Disease Risk and Progression in the PPMI Cohort. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21186562"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1146\/annurev-neuro-082823-020615","article-title":"The Role of Retrotransposons and Endogenous Retroviruses in Age-Dependent Neurodegenerative Disorders","volume":"47","author":"Frost","year":"2024","journal-title":"Annu. Rev. Neurosci."},{"key":"ref_67","first-page":"290","article-title":"The role of retroelements in Parkinson\u2019s disease development","volume":"29","author":"Mustafin","year":"2025","journal-title":"Vavilovskii Zhurnal Genet. Sel."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1038\/s41531-023-00626-6","article-title":"Immunological shifts during early-stage Parkinson\u2019s disease identified with DNA methylation data on longitudinally collected blood samples","volume":"10","author":"Pike","year":"2024","journal-title":"npj Park. Dis."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1038\/ng.368","article-title":"The regulated retrotransposon transcriptome of mammalian cells","volume":"41","author":"Faulkner","year":"2009","journal-title":"Nat. Genet."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"bbab417","DOI":"10.1093\/bib\/bbab417","article-title":"Locus-specific expression analysis of transposable elements","volume":"23","author":"Schwarz","year":"2022","journal-title":"Brief. Bioinform."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"101086","DOI":"10.1016\/j.crmeth.2025.101086","article-title":"A single-cell transposable element atlas of human cell identity","volume":"5","author":"Marston","year":"2025","journal-title":"Cell Rep. Methods"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1038\/s43587-024-00757-2","article-title":"Transposable element 5mC methylation state of blood cells predicts age and disease","volume":"5","author":"Morandini","year":"2025","journal-title":"Nat. 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