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Sharma R, Bisht P, Kesharwani A, Murti K, Kumar N. Epigenetic modifications in Parkinson's disease: A critical review. Eur J Pharmacol 2024; 975:176641. [PMID: 38754537 DOI: 10.1016/j.ejphar.2024.176641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
Parkinson's Disease (PD) is a progressive neurodegenerative disorder expected to increase by over 50% by 2030 due to increasing life expectancy. The disease's hallmarks include slow movement, tremors, and postural instability. Impaired protein processing is a major factor in the pathophysiology of PD, leading to the buildup of aberrant protein aggregates, particularly misfolded α-synuclein, also known as Lewy bodies. These Lewy bodies lead to inflammation and further death of dopaminergic neurons, leading to imbalances in excitatory and inhibitory neurotransmitters, causing excessive uncontrollable movements called dyskinesias. It was previously suggested that a complex interplay involving hereditary and environmental variables causes the specific death of neurons in PD; however, the exact mechanism of the association involving the two primary modifiers is yet unknown. An increasing amount of research points to the involvement of epigenetics in the onset and course of several neurological conditions, such as PD. DNA methylation, post-modifications of histones, and non-coding RNAs are the primary examples of epigenetic alterations, that is defined as alterations to the expression of genes and functioning without modifications in DNA sequence. Epigenetic modifications play a significant role in the development of PD, with genes such as Parkin, PTEN-induced kinase 1 (PINK1), DJ1, Leucine-Rich Repeat Kinase 2 (LRRK2), and alpha-synuclein associated with the disease. The aberrant epigenetic changes implicated in the pathophysiology of PD and their impact on the design of novel therapeutic approaches are the primary focus of this review.
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Affiliation(s)
- Ravikant Sharma
- Research Unit of Biomedicine and Internal Medicine, Faculty of Medicine, University of Oulu, Aapistie 5, 90220, Oulu, Finland
| | - Priya Bisht
- Department of Pharmacology and Toxicology, National Institution of Pharmaceutical Education and Research, Hajipur, Vaishali, 844102, Bihar, India
| | - Anuradha Kesharwani
- Department of Pharmacology and Toxicology, National Institution of Pharmaceutical Education and Research, Hajipur, Vaishali, 844102, Bihar, India
| | - Krishna Murti
- Department of Pharmacy Practice, National Institution of Pharmaceutical Education and Research, Hajipur, Vaishali, 844102, Bihar, India
| | - Nitesh Kumar
- Department of Pharmacology and Toxicology, National Institution of Pharmaceutical Education and Research, Hajipur, Vaishali, 844102, Bihar, India.
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Lin SM, Huang HT, Fang PJ, Chang CF, Satange R, Chang CK, Chou SH, Neidle S, Hou MH. Structural basis of water-mediated cis Watson-Crick/Hoogsteen base-pair formation in non-CpG methylation. Nucleic Acids Res 2024:gkae594. [PMID: 38989613 DOI: 10.1093/nar/gkae594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/30/2024] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
Non-CpG methylation is associated with several cellular processes, especially neuronal development and cancer, while its effect on DNA structure remains unclear. We have determined the crystal structures of DNA duplexes containing -CGCCG- regions as CCG repeat motifs that comprise a non-CpG site with or without cytosine methylation. Crystal structure analyses have revealed that the mC:G base-pair can simultaneously form two alternative conformations arising from non-CpG methylation, including a unique water-mediated cis Watson-Crick/Hoogsteen, (w)cWH, and Watson-Crick (WC) geometries, with partial occupancies of 0.1 and 0.9, respectively. NMR studies showed that an alternative conformation of methylated mC:G base-pair at non-CpG step exhibits characteristics of cWH with a syn-guanosine conformation in solution. DNA duplexes complexed with the DNA binding drug echinomycin result in increased occupancy of the (w)cWH geometry in the methylated base-pair (from 0.1 to 0.3). Our structural results demonstrated that cytosine methylation at a non-CpG step leads to an anti→syntransition of its complementary guanosine residue toward the (w)cWH geometry as a partial population of WC, in both drug-bound and naked mC:G base pairs. This particular geometry is specific to non-CpG methylated dinucleotide sites in B-form DNA. Overall, the current study provides new insights into DNA conformation during epigenetic regulation.
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Affiliation(s)
- Shan-Meng Lin
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Hsiang-Ti Huang
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Pei-Ju Fang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Roshan Satange
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Chung-Ke Chang
- Taiwan Biobank, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Shan-Ho Chou
- Institute of Biochemistry, National Chung Hsing University, Taichung 402, Taiwan
| | - Stephen Neidle
- School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Ming-Hon Hou
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
- Doctoral Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
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3
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Bhargavan B, Chhunchha B, Kubo E, Singh DP. DNA methylation as an epigenetic mechanism in the regulation of LEDGF expression and biological response in aging and oxidative stress. Cell Death Discov 2024; 10:296. [PMID: 38909054 PMCID: PMC11193803 DOI: 10.1038/s41420-024-02076-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 06/15/2024] [Accepted: 06/18/2024] [Indexed: 06/24/2024] Open
Abstract
The physiological quantum of stress-inducible transcriptional protein, Lens Epithelium-Derived Growth Factor (LEDGF), is vital for the maintenance of cellular physiology. Erratic epigenetic reprogramming in response to oxidative stress or with advancing age is found to be a major cause in the gene silencing, leading to pathobiologies. Using aging human (h) eye lens/lens epithelial cells (LECs) coupled with redox-active Peroxiredoxin 6 (Prdx6)-deficient (Prdx6-/-) mLECs as model systems, herein, we showed that in aging/oxidative stress, the human LEDGF gene was regulated by unique methylation patterns of CGs nucleotides within and around the Sp1 binding site(s) of CpG island of the LEDGF promoter (-170 to -27nts). The process caused the repression of LEDGF and its target, Hsp27, resulting in reactive oxygen species (ROS) amplification and cellular insults. This phenomenon was opposed to the unmethylated promoter in LECs. Clinically, we observed that the loss of LEDGF in the Prdx6-/- mLECs or aging lenses/LECs, correlating with increased expression of DNMT1, DNMT3a, and DNMT3b along with the methyl CpG binding protein 2 (MeCP2). Upon oxidative stress, the expression of these molecules was increased with the dramatic reduction in LEDGF expression. While demethylating agent, 5-Aza deoxycytidine (5-AzaC) transposed the aberrant methylation status, and revived LEDGF and Hsp27 expression. Mechanistically, the chloramphenicol acetyltransferase (CAT) reporter gene driven by the LEDGF promoter (-170/ + 35) and ChIP assays uncovered that 5-AzaC acted on GC/Sp1 sites to release LEDGF transcription. The data argued, for the first time, that de novo methylation of CGs around and within Sp1 sites of the CpG island directly disrupted Sp1 activity, which ensued in LEDGF repression and its biological functions. The findings should improve our understanding of cellular insults-associated with aberrant DNMTs-mediated LEDGF's activity, and can offer strategies for therapeutic intervention to halt aging/oxidative stress-induced abnormalities.
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Affiliation(s)
- Biju Bhargavan
- Ophthalmology and Visual Sciences, University of Nebraska Medical Center, Omaha, NE, USA
| | - Bhavana Chhunchha
- Ophthalmology and Visual Sciences, University of Nebraska Medical Center, Omaha, NE, USA.
| | - Eri Kubo
- Department of Ophthalmology, Kanazawa Medical University, Ishikawa, 9200293, Japan
| | - Dhirendra P Singh
- Ophthalmology and Visual Sciences, University of Nebraska Medical Center, Omaha, NE, USA.
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Singh S, Kriti M, K.S. A, Sarma DK, Verma V, Nagpal R, Mohania D, Tiwari R, Kumar M. Deciphering the complex interplay of risk factors in type 2 diabetes mellitus: A comprehensive review. Metabol Open 2024; 22:100287. [PMID: 38818227 PMCID: PMC11137529 DOI: 10.1016/j.metop.2024.100287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/15/2024] [Accepted: 05/18/2024] [Indexed: 06/01/2024] Open
Abstract
The complex and multidimensional landscape of type 2 diabetes mellitus (T2D) is a major global concern. Despite several years of extensive research, the precise underlying causes of T2D remain elusive, but evidence suggests that it is influenced by a myriad of interconnected risk factors such as epigenetics, genetics, gut microbiome, environmental factors, organelle stress, and dietary habits. The number of factors influencing the pathogenesis is increasing day by day which worsens the scenario; meanwhile, the interconnections shoot up the frame. By gaining deeper insights into the contributing factors, we may pave the way for the development of personalized medicine, which could unlock more precise and impactful treatment pathways for individuals with T2D. This review summarizes the state of knowledge about T2D pathogenesis, focusing on the interplay between various risk factors and their implications for future therapeutic strategies. Understanding these factors could lead to tailored treatments targeting specific risk factors and inform prevention efforts on a population level, ultimately improving outcomes for individuals with T2D and reducing its burden globally.
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Affiliation(s)
- Samradhi Singh
- ICMR- National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhauri, Bhopal, 462030, Madhya Pradesh, India
| | - Mona Kriti
- ICMR- National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhauri, Bhopal, 462030, Madhya Pradesh, India
| | - Anamika K.S.
- Christ Deemed to Be University Bangalore, Karnataka, India
| | - Devojit Kumar Sarma
- ICMR- National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhauri, Bhopal, 462030, Madhya Pradesh, India
| | - Vinod Verma
- Stem Cell Research Centre, Department of Hematology, Sanjay Gandhi Post-Graduate Institute of Medical Sciences, Lucknow, 226014, Uttar Pradesh, India
| | - Ravinder Nagpal
- Department of Nutrition & Integrative Physiology, College of Health & Human Sciences, Florida State University, Tallahassee, FL, 32306, USA
| | - Dheeraj Mohania
- Dr. R. P. Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Rajnarayan Tiwari
- ICMR- National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhauri, Bhopal, 462030, Madhya Pradesh, India
| | - Manoj Kumar
- ICMR- National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhauri, Bhopal, 462030, Madhya Pradesh, India
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Sengupta P, Dutta S, Liew FF, Dhawan V, Das B, Mottola F, Slama P, Rocco L, Roychoudhury S. Environmental and Genetic Traffic in the Journey from Sperm to Offspring. Biomolecules 2023; 13:1759. [PMID: 38136630 PMCID: PMC10741607 DOI: 10.3390/biom13121759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/04/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023] Open
Abstract
Recent advancements in the understanding of how sperm develop into offspring have shown complex interactions between environmental influences and genetic factors. The past decade, marked by a research surge, has not only highlighted the profound impact of paternal contributions on fertility and reproductive outcomes but also revolutionized our comprehension by unveiling how parental factors sculpt traits in successive generations through mechanisms that extend beyond traditional inheritance patterns. Studies have shown that offspring are more susceptible to environmental factors, especially during critical phases of growth. While these factors are broadly detrimental to health, their effects are especially acute during these periods. Moving beyond the immutable nature of the genome, the epigenetic profile of cells emerges as a dynamic architecture. This flexibility renders it susceptible to environmental disruptions. The primary objective of this review is to shed light on the diverse processes through which environmental agents affect male reproductive capacity. Additionally, it explores the consequences of paternal environmental interactions, demonstrating how interactions can reverberate in the offspring. It encompasses direct genetic changes as well as a broad spectrum of epigenetic adaptations. By consolidating current empirically supported research, it offers an exhaustive perspective on the interwoven trajectories of the environment, genetics, and epigenetics in the elaborate transition from sperm to offspring.
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Affiliation(s)
- Pallav Sengupta
- Department of Biomedical Sciences, College of Medicine, Gulf Medical University, Ajman 4184, United Arab Emirates
| | - Sulagna Dutta
- School of Life Sciences, Manipal Academy of Higher Education (MAHE), Dubai 345050, United Arab Emirates
| | - Fong Fong Liew
- Department of Preclinical Sciences, Faculty of Dentistry, MAHSA University, Jenjarom 42610, Selangor, Malaysia
| | - Vidhu Dhawan
- Department of Anatomy, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | - Biprojit Das
- Department of Life Science and Bioinformatics, Assam University, Silchar 788011, India
| | - Filomena Mottola
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, 81100 Caserta, Italy
| | - Petr Slama
- Laboratory of Animal Immunology and Biotechnology, Department of Animal Morphology, Physiology and Genetics, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic
| | - Lucia Rocco
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, 81100 Caserta, Italy
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Lin CH, Li SC, Lin MH, Ho CJ, Lu YT, Lin Y, Lin PH, Tsai KW, Tsai MH. S100A6 participates in initiation of autoimmune encephalitis and is under epigenetic control. Brain Behav 2023; 13:e2897. [PMID: 36748983 PMCID: PMC10013942 DOI: 10.1002/brb3.2897] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 12/15/2022] [Accepted: 01/11/2023] [Indexed: 02/08/2023] Open
Abstract
INTRODUCTION Autoimmune encephalitis (AE) is caused by autoantibodies attacking neuronal cell surface antigens and/or synaptic antigens. We previously demonstrated that S100A6 was hypomethylated in patients with AE and that it promoted B lymphocyte infiltration through the simulated blood-brain barrier (BBB). In this study, we focused on the epigenetic regulation of S100A6, the process by which S100A6 affects B lymphocyte infiltration, and the therapeutic potential of S100A6 antibodies. METHODS We enrolled and collected serum from 10 patients with AE and 10 healthy control (HC) subjects. Promoter methylation and 5-azacytidine treatment assays were conducted to observe the methylation process of S100A6. The effect of S100A6 on B lymphocytes was analyzed using an adhesion assay and leukocyte transendothelial migration (LTEM) assay. A LTEM assay was also used to compare the effects of the serum of HCs, serum of AE patients, S100A6 recombinant protein, and S100A6 antibodies on B lymphocytes. RESULT The promoter methylation and 5-azacytidine treatment assays confirmed that S100A6 was regulated by DNA methylation. The adhesion study demonstrated that the addition of S100A6 enhanced adhesion between B lymphocytes and a BBB endothelial cell line in a concentration-dependent manner. The LTEM assay showed that the serum of AE patients, as well as S100A6, promoted B lymphocyte infiltration and that this effect could be attenuated by S100A6 antibodies. CONCLUSION We clarified that S100A6 was under epigenetic regulation in patients with AE and that it helped B lymphocytes to adhere to and infiltrate the BBB endothelial layer, which could be counteracted by S100A6 antibodies. Therefore, the methylation profile of S100A6 could be a marker of the activity of AE, and countering the effect of S100A6 may be a potential treatment target for AE.
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Affiliation(s)
- Chih-Hsiang Lin
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Sung-Chou Li
- Genomics and Proteomics Core Laboratory, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Ming-Hong Lin
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Research Center for Environmental Medicine, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chen-Jui Ho
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Yan-Ting Lu
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Yuyu Lin
- Genomics and Proteomics Core Laboratory, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Pei-Hsien Lin
- Genomics and Proteomics Core Laboratory, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Kuo-Wang Tsai
- Department of Research, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei, Taiwan
| | - Meng-Han Tsai
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Genomics and Proteomics Core Laboratory, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Medical School, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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Bingen JM, Clark LV, Band MR, Munzir I, Carrithers MD. Differential DNA methylation associated with multiple sclerosis and disease modifying treatments in an underrepresented minority population. Front Genet 2023; 13:1058817. [PMID: 36685876 PMCID: PMC9845287 DOI: 10.3389/fgene.2022.1058817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/28/2022] [Indexed: 01/06/2023] Open
Abstract
Black and Hispanic American patients frequently develop earlier onset of multiple sclerosis (MS) and a more severe disease course that can be resistant to disease modifying treatments. The objectives were to identify differential methylation of genomic DNA (gDNA) associated with disease susceptibility and treatment responses in a cohort of MS patients from underrepresented minority populations. Patients with MS and controls with non-inflammatory neurologic conditions were consented and enrolled under an IRB-approved protocol. Approximately 64% of donors identified as Black or African American and 30% as White, Hispanic-Latino. Infinium MethylationEPIC bead arrays were utilized to measure epigenome-wide gDNA methylation of whole blood. Data were analyzed in the presence and absence of adjustments for unknown covariates in the dataset, some of which corresponded to disease modifying treatments. Global patterns of differential methylation associated with MS were strongest for those probes that showed relative demethylation of loci with lower M values. Pathway analysis revealed unexpected associations with shigellosis and amoebiasis. Enrichment analysis revealed an over-representation of probes in enhancer regions and an under-representation in promoters. In the presence of adjustments for covariates that included disease modifying treatments, analysis revealed 10 differentially methylated regions (DMR's) with an FDR <1E-77. Five of these genes (ARID5B, BAZ2B, RABGAP1, SFRP2, WBP1L) are associated with cancer risk and cellular differentiation and have not been previously identified in MS studies. Hierarchical cluster and multi-dimensional scaling analysis of differential DNA methylation at 147 loci within those DMR's was sufficient to differentiate MS donors from controls. In the absence of corrections for disease modifying treatments, differential methylation in patients treated with dimethyl fumarate was associated with immune regulatory pathways that regulate cytokine and chemokine signaling, axon guidance, and adherens junctions. These results demonstrate possible associations of gastrointestinal pathogens and regulation of cellular differentiation with MS susceptibility in our patient cohort. This work further suggests that analyses can be performed in the presence and absence of corrections for immune therapies. Because of their high representation in our patient cohort, these results may be of specific relevance in the regulation of disease susceptibility and treatment responses in Black and Hispanic Americans.
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Affiliation(s)
- Jeremy M. Bingen
- Neurology, University of Illinois College of Medicine, Chicago, IL, United States,Physiology and Biophysics, University of Illinois College of Medicine, Chicago, IL, United States
| | - Lindsay V. Clark
- High Performance Biological Computing, and Roy J Carver Biotechnology Center, University of Illinois, Champaign, IL, United States
| | - Mark R. Band
- High Performance Biological Computing, and Roy J Carver Biotechnology Center, University of Illinois, Champaign, IL, United States
| | - Ilyas Munzir
- Neurology, University of Illinois College of Medicine, Chicago, IL, United States
| | - Michael D. Carrithers
- Neurology, University of Illinois College of Medicine, Chicago, IL, United States,Physiology and Biophysics, University of Illinois College of Medicine, Chicago, IL, United States,Neurology, Jesse Brown Veterans Administration Hospital, Chicago, IL, United States,*Correspondence: Michael D. Carrithers,
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Kiselev IS, Kulakova OG, Baturina OA, Kabilov MR, Boyko AN, Favorova OO. [A comparison of DNA methylation profiles of blood mononuclear cells in patients with multiple sclerosis in remission and relapse]. Zh Nevrol Psikhiatr Im S S Korsakova 2023; 123:60-64. [PMID: 37560835 DOI: 10.17116/jnevro202312307260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
OBJECTIVE To study the whole-genome DNA methylation profiles of peripheral blood mononuclear blood cells (PBMCs) of patients with relapsing-remitting multiple sclerosis (RRMS) in remission and relapse in order to assess the contribution of this epigenetic mechanism of gene expression regulation to the activity of the pathological process. MATERIAL AND METHODS Eight patients with RRMS in remission and 6 patients in relapse were included in the study. Methylation levels of DNA CpG sites in PBMCs were analyzed using Infinium HumanMethylation450 BeadChip DNA microarrays. RESULTS Seven differentially methylated positions (DMPs) were identified, of which 3 were hypermethylated (cg02981003, cg18486102, cg19533582) and 4 were hypomethylated (cg16814680, cg1964802, cg18584440, cg08291996) during RRMS relapse. Five DMPs are located in protein-coding genes (GPR123, FAIM2, BTNL2, ZNF8, ASAP2), one in microRNA gene (MIR548N), and one in an intergenic region. For all identified DMPs, we observed a change in DNA methylation levels of more than 20% (range 20.2-57.5%). Hierarchical clustering of DNA samples on the heatmap shows their clear aggregation into separate clusters corresponding to RRMS patients in the stages of relapse and remission. CONCLUSION For the first time it was shown that during relapse and remission of RRMS there are differences in the DNA methylation profile that allow discrimination between these clinical stages. These data indicate the involvement of the epigenetic mechanism of DNA methylation in the activation of the pathological process in RRMS.
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Affiliation(s)
- I S Kiselev
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - O G Kulakova
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - O A Baturina
- Institute of Chemical Biology and Fundamental Medicine - Genomics Core Facility, Novosibirsk, Russia
| | - M R Kabilov
- Institute of Chemical Biology and Fundamental Medicine - Genomics Core Facility, Novosibirsk, Russia
| | - A N Boyko
- Pirogov Russian National Research Medical University, Moscow, Russia
- Federal Center of Brain Research and Neurotechnologies of the Federal Medical Biological Agency, Moscow, Russia
| | - O O Favorova
- Pirogov Russian National Research Medical University, Moscow, Russia
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Kiselev I, Danilova L, Baulina N, Baturina O, Kabilov M, Boyko A, Kulakova O, Favorova O. Genome-wide DNA methylation profiling identifies epigenetic changes in CD4+ and CD14+ cells of multiple sclerosis patients. Mult Scler Relat Disord 2022; 60:103714. [PMID: 35245816 DOI: 10.1016/j.msard.2022.103714] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/29/2022] [Accepted: 02/24/2022] [Indexed: 10/19/2022]
Abstract
Multiple sclerosis (MS) is a chronic autoimmune and degenerative disease of the central nervous system, which develops in genetically predisposed individuals upon exposure to environmental influences. Environmental triggers of MS, such as viral infections or smoking, were demonstrated to affect DNA methylation, and thus to involve this important epigenetic mechanism in the development of pathological process. To identify MS-associated DNA methylation hallmarks, we performed genome-wide DNA methylation profiling of two cell populations (CD4+ T-lymphocytes and CD14+ monocytes), collected from the same treatment-naive relapsing-remitting MS patients and healthy subjects, using Illumina 450 K methylation arrays. We revealed significant changes in DNA methylation for both cell populations in MS. In CD4+ cells of MS patients the majority of differentially methylated positions (DMPs) were shown to be hypomethylated, while in CD14+ cells - hypermethylated. Differential methylation of HLA-DRB1 gene in CD4+ and CD14+ cells was associated with carriage of DRB1*15 allele independently from the disease status. Besides, about 20% of identified DMPs were shared between two cell populations and had the same direction of methylation changes; they may be involved in basic epigenetic processes occuring in MS. These findings suggest that the epigenetic mechanism of DNA methylation in immune cells contributes to MS; further studies are now required to validate these results and understand their functional significance.
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Affiliation(s)
- Ivan Kiselev
- Department of Molecular Biology and Medical Biotechnology, Pirogov Russian National Research Medical University, Ostrovityanova st. 1, Moscow 117997, Russian Federation
| | - Ludmila Danilova
- Vavilov Institute of General Genetics, Gubkin st. 3, Moscow 119991, Russian Federation; Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Natalia Baulina
- Department of Molecular Biology and Medical Biotechnology, Pirogov Russian National Research Medical University, Ostrovityanova st. 1, Moscow 117997, Russian Federation
| | - Olga Baturina
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russian Federation
| | - Marsel Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russian Federation
| | - Alexey Boyko
- Department of Molecular Biology and Medical Biotechnology, Pirogov Russian National Research Medical University, Ostrovityanova st. 1, Moscow 117997, Russian Federation
| | - Olga Kulakova
- Department of Molecular Biology and Medical Biotechnology, Pirogov Russian National Research Medical University, Ostrovityanova st. 1, Moscow 117997, Russian Federation
| | - Olga Favorova
- Department of Molecular Biology and Medical Biotechnology, Pirogov Russian National Research Medical University, Ostrovityanova st. 1, Moscow 117997, Russian Federation
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10
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Perdaens O, van Pesch V. Molecular Mechanisms of Immunosenescene and Inflammaging: Relevance to the Immunopathogenesis and Treatment of Multiple Sclerosis. Front Neurol 2022; 12:811518. [PMID: 35281989 PMCID: PMC8913495 DOI: 10.3389/fneur.2021.811518] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 12/27/2021] [Indexed: 12/18/2022] Open
Abstract
Aging is characterized, amongst other features, by a complex process of cellular senescence involving both innate and adaptive immunity, called immunosenescence and associated to inflammaging, a low-grade chronic inflammation. Both processes fuel each other and partially explain increasing incidence of cancers, infections, age-related autoimmunity, and vascular disease as well as a reduced response to vaccination. Multiple sclerosis (MS) is a lifelong disease, for which considerable progress in disease-modifying therapies (DMTs) and management has improved long-term survival. However, disability progression, increasing with age and disease duration, remains. Neurologists are now involved in caring for elderly MS patients, with increasing comorbidities. Aging of the immune system therefore has relevant implications for MS pathogenesis, response to DMTs and the risks mediated by these treatments. We propose to review current evidence regarding markers and molecular mechanisms of immunosenescence and their relevance to understanding MS pathogenesis. We will focus on age-related changes in the innate and adaptive immune system in MS and other auto-immune diseases, such as systemic lupus erythematosus and rheumatoid arthritis. The consequences of these immune changes on MS pathology, in interaction with the intrinsic aging process of central nervous system resident cells will be discussed. Finally, the impact of immunosenescence on disease evolution and on the safety and efficacy of current DMTs will be presented.
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Affiliation(s)
- Océane Perdaens
- Laboratory of Neurochemistry, Institute of Neuroscience, Université catholique de Louvain (UCLouvain), Brussels, Belgium
| | - Vincent van Pesch
- Laboratory of Neurochemistry, Institute of Neuroscience, Université catholique de Louvain (UCLouvain), Brussels, Belgium
- Department of Neurology, Cliniques universitaires Saint-Luc, Université catholique de Louvain (UCLouvain), Brussels, Belgium
- *Correspondence: Vincent van Pesch
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