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Etayo-Urtasun P, Sáez de Asteasu ML, Izquierdo M. Effects of Exercise on DNA Methylation: A Systematic Review of Randomized Controlled Trials. Sports Med 2024:10.1007/s40279-024-02033-0. [PMID: 38839665 DOI: 10.1007/s40279-024-02033-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2024] [Indexed: 06/07/2024]
Abstract
BACKGROUND Regular exercise reduces chronic disease risk and extends a healthy lifespan, but the underlying molecular mechanisms remain unclear. DNA methylation is implicated in this process, potentially altering gene expression without changing DNA sequence. However, previous findings appear partly contradictory. OBJECTIVE This review aimed to elucidate exercise effects on DNA methylation patterns. METHODS PubMed, Scopus and Web of Science databases were searched following PRISMA 2020 guidelines. All articles published up to November 2023 were considered for inclusion and assessed for eligibility using the PICOS (Population, Intervention, Comparison, Outcomes and Study) framework. Randomized controlled trials that assessed the impact of exercise interventions on DNA methylation in previously inactive adults were included. We evaluated the methodological quality of trials using the PEDro scale. RESULTS A total of 852 results were identified, of which 12 articles met the inclusion criteria. A total of 827 subjects were included in the studies. Intervention lengths varied from 6 weeks to 12 months. Most trials indicated that exercise interventions can significantly alter the DNA methylation of specific genes and global DNA methylation patterns. CONCLUSIONS The heterogeneity of results may arise from differences in participant demographics, intervention factors, measurement techniques, and the genomic contexts examined. Future research should analyze the influences of activity type, intensity, and duration, as well as the physical fitness outcomes on DNA methylation. Characterizing such dose-response relationships and identifying genes responsive to exercise are crucial for understanding the molecular mechanisms of exercise, unlocking its full potential for disease prevention and treatment.
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Affiliation(s)
| | - Mikel L Sáez de Asteasu
- Navarrabiomed, Pamplona, Spain
- Department of Health Sciences, Hospital Universitario de Navarra (HUN)-Universidad Pública de Navarra (UPNA), IdiSNA, Av. De Barañain s/n, 31008, Pamplona, Navarra, Spain
- CIBER of Frailty and Healthy Aging (CIBERFES), Instituto de Salud Carlos III, Madrid, Spain
| | - Mikel Izquierdo
- Navarrabiomed, Pamplona, Spain.
- Department of Health Sciences, Hospital Universitario de Navarra (HUN)-Universidad Pública de Navarra (UPNA), IdiSNA, Av. De Barañain s/n, 31008, Pamplona, Navarra, Spain.
- CIBER of Frailty and Healthy Aging (CIBERFES), Instituto de Salud Carlos III, Madrid, Spain.
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Venkatesan D, Muthukumar S, Iyer M, Babu HWS, Gopalakrishnan AV, Yadav MK, Vellingiri B. Heavy metals toxicity on epigenetic modifications in the pathogenesis of Alzheimer's disease (AD). J Biochem Mol Toxicol 2024; 38:e23741. [PMID: 38816991 DOI: 10.1002/jbt.23741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/09/2024] [Accepted: 05/09/2024] [Indexed: 06/01/2024]
Abstract
Alzheimer's disease (AD) is a progressive decline in cognitive ability and behavior which eventually disrupts daily activities. AD has no cure and the progression rate varies unlikely. Among various causative factors, heavy metals are reported to be a significant hazard in AD pathogenesis. Metal-induced neurodegeneration has been focused globally with thorough research to unravel the mechanistic insights in AD. Recently, heavy metals suggested to play an important role in epigenetic alterations which might provide evidential results on AD pathology. Epigenetic modifications are known to play towards novel therapeutic approaches in treating AD. Though many studies focus on epigenetics and heavy metal implications in AD, there is a lack of research on heavy metal influence on epigenetic toxicity in neurological disorders. The current review aims to elucidate the plausible role of cadmium (Cd), iron (Fe), arsenic (As), copper (Cu), and lithium (Li) metals on epigenetic factors and the increase in amyloid beta and tau phosphorylation in AD. Also, the review discusses the common methods of heavy metal detection to implicate in AD pathogenesis. Hence, from this review, we can extend the need for future research on identifying the mechanistic behavior of heavy metals on epigenetic toxicity and to develop diagnostic and therapeutic markers in AD.
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Affiliation(s)
- Dhivya Venkatesan
- Centre for Neuroscience, Department of Biotechnology, Karpagam Academy of Higher Education (Deemed to be University), Coimbatore, India
| | - Sindduja Muthukumar
- Human Cytogenetics and Stem Cell Laboratory, Department of Zoology, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Mahalaxmi Iyer
- Centre for Neuroscience, Department of Biotechnology, Karpagam Academy of Higher Education (Deemed to be University), Coimbatore, India
- Department of Microbiology, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Harysh Winster Suresh Babu
- Human Cytogenetics and Stem Cell Laboratory, Department of Zoology, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Abilash Valsala Gopalakrishnan
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Mukesh Kumar Yadav
- Department of Microbiology, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Balachandar Vellingiri
- Human Cytogenetics and Stem Cell Laboratory, Department of Zoology, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab, India
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Temgire P, Arthur R, Kumar P. Neuroinflammation and the role of epigenetic-based therapies for Huntington's disease management: the new paradigm. Inflammopharmacology 2024; 32:1791-1804. [PMID: 38653938 DOI: 10.1007/s10787-024-01477-0] [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: 06/20/2023] [Accepted: 04/09/2024] [Indexed: 04/25/2024]
Abstract
Huntington's disease (HD) is an inherited, autosomal, neurodegenerative ailment that affects the striatum of the brain. Despite its debilitating effect on its patients, there is no proven cure for HD management as of yet. Neuroinflammation, excitotoxicity, and environmental factors have been reported to influence the regulation of gene expression by modifying epigenetic mechanisms. Aside focusing on the etiology, changes in epigenetic mechanisms have become a crucial factor influencing the interaction between HTT protein and epigenetically transcribed genes involved in neuroinflammation and HD. This review presents relevant literature on epigenetics with special emphasis on neuroinflammation and HD. It summarizes pertinent research on the role of neuroinflammation and post-translational modifications of chromatin, including DNA methylation, histone modification, and miRNAs. To achieve this about 1500 articles were reviewed via databases like PubMed, ScienceDirect, Google Scholar, and Web of Science. They were reduced to 534 using MeSH words like 'epigenetics, neuroinflammation, and HD' coupled with Boolean operators. Results indicated that major contributing factors to the development of HD such as mitochondrial dysfunction, excitotoxicity, neuroinflammation, and apoptosis are affected by epigenetic alterations. However, the association between neuroinflammation-altered epigenetics and the reported transcriptional changes in HD is unknown. Also, the link between epigenetically dysregulated genomic regions and specific DNA sequences suggests the likelihood that transcription factors, chromatin-remodeling proteins, and enzymes that affect gene expression are all disrupted simultaneously. Hence, therapies that target pathogenic pathways in HD, including neuroinflammation, transcriptional dysregulation, triplet instability, vesicle trafficking dysfunction, and protein degradation, need to be developed.
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Affiliation(s)
- Pooja Temgire
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, 151401, Punjab, India
| | - Richmond Arthur
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, 151401, Punjab, India
| | - Puneet Kumar
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, 151401, Punjab, India.
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Ko YK, Chi S, Nam GH, Baek KW, Ahn K, Ahn Y, Kang J, Lee MS, Gim JA. Epigenome-wide Association Study for Tic Disorders in Children: A Preliminary Study in Korean Population. CLINICAL PSYCHOPHARMACOLOGY AND NEUROSCIENCE : THE OFFICIAL SCIENTIFIC JOURNAL OF THE KOREAN COLLEGE OF NEUROPSYCHOPHARMACOLOGY 2024; 22:295-305. [PMID: 38627076 PMCID: PMC11024688 DOI: 10.9758/cpn.23.1099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/24/2023] [Accepted: 11/24/2023] [Indexed: 04/20/2024]
Abstract
Objective : Tic disorders can affect the quality of life in both childhood and adolescence. Many factors are involved in the etiology of tic disorders, and the genetic and epigenetic factors of tic disorders are considered complex and heterogeneous. Methods : In this study, the differentially methylated regions (DMRs) between normal controls (n = 24; aged 6-15; 7 females) and patients with tic disorders (n = 16; aged 6-15; 5 females) were analyzed. We performed an epigenome-wide association study of tic disorders in Korean children. The tics were assessed using Yale Global Tic Severity Scale. The DNA methylation data consisted of 726,945 cytosine phosphate guanine (CpG) sites, assessed using the Illumina Infinium MethylationEPIC (850k) BeadChip. The DNA methylation data of the 40 participants were retrieved, and DMRs between the four groups based on sex and tic disorder were identified. From 28 male and 16 female samples, 37 and 38 DMRs were identified, respectively. We analyzed the enriched terms and visualized the network, heatmap, and upset plot. Results : In male, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed hypomethylated patterns in the ligand, receptor, and second signal transductors of the PI3K-Akt and MAPK signaling pathway (most cells were indicated as green color), and in female, the opposite patterns were revealed (most cells were indicated as red color). Five mental disorder-related enriched terms were identified in the network analysis. Conclusion : Here, we provide insights into the epigenetic mechanisms of tic disorders. Abnormal DNA methylation patterns are associated with mental disorder-related symptoms.
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Affiliation(s)
- Young Kyung Ko
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Internal Medicine, Korea University Guro Hospital, Seoul, Korea
| | - Suhyuk Chi
- Department of Psychiatry, Korea University Guro Hospital, Seoul, Korea
| | - Gyu-Hwi Nam
- PhileKorea Technology Co. Ltd., Daejeon, Korea
| | - Kyung-Wan Baek
- Department of Physical Education, Gyeongsang National University, Jinju, Korea
| | | | | | - June Kang
- Department of Brain and Cognitive Engineering, Korea University, Seoul, Korea
| | - Moon-Soo Lee
- Department of Psychiatry, Korea University Guro Hospital, Seoul, Korea
| | - Jeong-An Gim
- Department of Medical Science, Soonchunhyang University, Asan, Korea
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Jarosiewicz M, Krześlak A. Epigenetic implications of common brominated flame retardants (PBDEs and TBBPA): Understanding the health risks of BFRs exposure. CHEMOSPHERE 2024; 361:142488. [PMID: 38821124 DOI: 10.1016/j.chemosphere.2024.142488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/17/2024] [Accepted: 05/29/2024] [Indexed: 06/02/2024]
Abstract
Brominated flame retardants (BFRs) are synthetic chemicals incorporated into a wide variety of products, both for industrial applications and everyday use, with the primary aim of reducing their flammability or reducing the material burning rate. These compounds find widespread use in plastics, textiles, and electrical/electronic devices. However, BFRs can be released from products and, thus are determined in many environmental matrices such as soil, water and air.This review discuss the potential health implications of selected BFRs (PBDEs and TBBPA) exposure arising from their impact on the epigenetic mechanisms. Epigenetic modifications, such as DNA methylation and histone acetylation or methylation, as well as changes in miRNA pattern, play significant roles in gene expression and cell function and can be influenced by environmental factors.The studies indicate that PBDEs exposure can lead to global DNA hypomethylation, disrupting normal gene regulation and contributing to genomic instability. In animal models, PBDEs have been associated with adverse effects on neurodevelopment, including impairments in memory and learning. TBBPA exposure has also been linked to changes in DNA methylation patterns, alterations in histone posttranslational modifications and non-coding RNA expression. These epigenetic changes may contribute to health issues related to growth, development, and endocrine functions.The growing evidence of epigenetic modifications induced by BFRs exposure highlights the importance of understanding their potential risks to human health. Further investigations are needed to fully elucidate the long-term consequences of altered epigenetic marks and their impact on human health.
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Affiliation(s)
- Monika Jarosiewicz
- Department of Cytobiochemistry, Faculty of Biology and Environmental Protection, University of Lodz, 90-236, Lodz, Poland.
| | - Anna Krześlak
- Department of Cytobiochemistry, Faculty of Biology and Environmental Protection, University of Lodz, 90-236, Lodz, Poland
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Geens B, Goossens S, Li J, Van de Peer Y, Vanden Broeck J. Untangling the gordian knot: The intertwining interactions between developmental hormone signaling and epigenetic mechanisms in insects. Mol Cell Endocrinol 2024; 585:112178. [PMID: 38342134 DOI: 10.1016/j.mce.2024.112178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/30/2024] [Accepted: 02/04/2024] [Indexed: 02/13/2024]
Abstract
Hormones control developmental and physiological processes, often by regulating the expression of multiple genes simultaneously or sequentially. Crosstalk between hormones and epigenetics is pivotal to dynamically coordinate this process. Hormonal signals can guide the addition and removal of epigenetic marks, steering gene expression. Conversely, DNA methylation, histone modifications and non-coding RNAs can modulate regional chromatin structure and accessibility and regulate the expression of numerous (hormone-related) genes. Here, we provide a review of the interplay between the classical insect hormones, ecdysteroids and juvenile hormones, and epigenetics. We summarize the mode-of-action and roles of these hormones in post-embryonic development, and provide a general overview of epigenetic mechanisms. We then highlight recent advances on the interactions between these hormonal pathways and epigenetics, and their involvement in development. Furthermore, we give an overview of several 'omics techniques employed in the field. Finally, we discuss which questions remain unanswered and possible avenues for future research.
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Affiliation(s)
- Bart Geens
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59 box 2465, B-3000 Leuven, Belgium.
| | - Stijn Goossens
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59 box 2465, B-3000 Leuven, Belgium.
| | - Jia Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Jozef Vanden Broeck
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59 box 2465, B-3000 Leuven, Belgium.
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Broca-Brisson L, Disdier C, Harati R, Hamoudi R, Mabondzo A. Epigenetic alterations in creatine transporter deficiency: a new marker for dodecyl creatine ester therapeutic efficacy monitoring. Front Neurosci 2024; 18:1362497. [PMID: 38694899 PMCID: PMC11062253 DOI: 10.3389/fnins.2024.1362497] [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: 12/28/2023] [Accepted: 03/22/2024] [Indexed: 05/04/2024] Open
Abstract
Creatine transporter deficiency (CTD) is an X-linked disease caused by mutations in the Slc6a8 gene. The impaired creatine uptake in the brain leads to developmental delays with intellectual disability. We hypothesized that deficient creatine uptake in CTD cerebral cells impact methylation balance leading to alterations of genes and proteins expression by epigenetic mechanism. In this study, we determined the status of nucleic acid methylation in both Slc6a8 knockout mouse model and brain organoids derived from CTD patients' cells. We also investigated the effect of dodecyl creatine ester (DCE), a promising prodrug that increases brain creatine content in the mouse model of CTD. The level of nucleic acid methylation was significantly reduced compared to healthy controls in both in vivo and in vitro CTD models. This hypo-methylation tended to be regulated by DCE treatment in vivo. These results suggest that increased brain creatine after DCE treatment restores normal levels of DNA methylation, unveiling the potential of using DNA methylation as a marker to monitor the drug efficacy.
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Affiliation(s)
- Léa Broca-Brisson
- Département Médicaments et Technologies pour la Santé, CEA, INRAE, SPI, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Clémence Disdier
- Ceres Brain Therapeutics, ICM-Hôpital Pitié-Salpétrière, Paris, France
| | - Rania Harati
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Rifat Hamoudi
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Center of Excellence of Precision Medicine, Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirtes
- Division of Surgery and Interventional Science, University College London, London, United Kingdom
- ASPIRE Precision Medicine Research Institute Abu Dhabi, University of Sharjah, Sharjah, United Arab Emirates
- Center of Excellence of Precision Medicine, Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- BIMAI-Lab, Biomedically Informed Artificial Intelligence Laboratory, University of Sharjah, Sharjah, United Arab Emirates
| | - Aloïse Mabondzo
- Département Médicaments et Technologies pour la Santé, CEA, INRAE, SPI, Université Paris-Saclay, Gif-sur-Yvette, France
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Lossi L, Castagna C, Merighi A. An Overview of the Epigenetic Modifications in the Brain under Normal and Pathological Conditions. Int J Mol Sci 2024; 25:3881. [PMID: 38612690 PMCID: PMC11011998 DOI: 10.3390/ijms25073881] [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: 03/10/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Epigenetic changes are changes in gene expression that do not involve alterations to the DNA sequence. These changes lead to establishing a so-called epigenetic code that dictates which and when genes are activated, thus orchestrating gene regulation and playing a central role in development, health, and disease. The brain, being mostly formed by cells that do not undergo a renewal process throughout life, is highly prone to the risk of alterations leading to neuronal death and neurodegenerative disorders, mainly at a late age. Here, we review the main epigenetic modifications that have been described in the brain, with particular attention on those related to the onset of developmental anomalies or neurodegenerative conditions and/or occurring in old age. DNA methylation and several types of histone modifications (acetylation, methylation, phosphorylation, ubiquitination, sumoylation, lactylation, and crotonylation) are major players in these processes. They are directly or indirectly involved in the onset of neurodegeneration in Alzheimer's or Parkinson's disease. Therefore, this review briefly describes the roles of these epigenetic changes in the mechanisms of brain development, maturation, and aging and some of the most important factors dynamically regulating or contributing to these changes, such as oxidative stress, inflammation, and mitochondrial dysfunction.
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Affiliation(s)
| | | | - Adalberto Merighi
- Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco, Italy; (L.L.); (C.C.)
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Hu S, Feng L, Yang Z, Fan X, Gao H, Yang T. A recognition of exosomes as regulators of epigenetic mechanisms in central nervous system diseases. Front Mol Neurosci 2024; 17:1370449. [PMID: 38528957 PMCID: PMC10962328 DOI: 10.3389/fnmol.2024.1370449] [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: 01/14/2024] [Accepted: 02/28/2024] [Indexed: 03/27/2024] Open
Abstract
Exosomes, vesicular structures originating from cells, participate in the conveyance of proteins and nucleic acids. Presently, the centrality of epigenetic modifications in neurological disorders is widely acknowledged. Exosomes exert influence over various epigenetic phenomena, thereby modulating post-transcriptional regulatory processes contingent upon their constituent makeup. Consequently, the heightened attention directed toward exosomes as instigators of epigenetic alterations has burgeoned in recent years. Notably, exosomes serve as vehicles for delivering methyltransferases to recipient cells. More significantly, non-coding RNAs, particularly microRNAs (miRNAs), represent pivotal contents within exosomes, wielding the capacity to influence the expression of diverse factors within the cerebral milieu. The transfer of these exosomal contents amidst brain cells, encompassing neuronal cells and microglia, assumes a critical role in the genesis and progression of neurological disorders, also, this role is not limited to neurological disorders, it may deal with any human disease, such as cancer, and cardiovascular diseases. This review will concentrate on elucidating the regulation of exosome-induced epigenetic events and its subsequent ramifications for neurological diseases. A more profound comprehension of the involvement of exosome-mediated epigenetic regulation in neurological disorders contributes to a heightened awareness of the etiology and advancement of cerebral afflictions.
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Affiliation(s)
- Shunxin Hu
- Shandong First Medical University, Tai'an, China
| | - Lei Feng
- Jining First People's Hospital, Jining, China
| | | | - Xuechen Fan
- Jining First People's Hospital, Jining, China
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Breen C, Papale LA, Clark LR, Bergmann PE, Madrid A, Asthana S, Johnson SC, Keleş S, Alisch RS, Hogan KJ. Whole genome methylation sequencing in blood identifies extensive differential DNA methylation in late-onset dementia due to Alzheimer's disease. Alzheimers Dement 2024; 20:1050-1062. [PMID: 37856321 PMCID: PMC10916976 DOI: 10.1002/alz.13514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/17/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023]
Abstract
INTRODUCTION DNA microarray-based studies report differentially methylated positions (DMPs) in blood between late-onset dementia due to Alzheimer's disease (AD) and cognitively unimpaired individuals, but interrogate < 4% of the genome. METHODS We used whole genome methylation sequencing (WGMS) to quantify DNA methylation levels at 25,409,826 CpG loci in 281 blood samples from 108 AD and 173 cognitively unimpaired individuals. RESULTS WGMS identified 28,038 DMPs throughout the human methylome, including 2707 differentially methylated genes (e.g., SORCS3, GABA, and PICALM) encoding proteins in biological pathways relevant to AD such as synaptic membrane, cation channel complex, and glutamatergic synapse. One hundred seventy-three differentially methylated blood-specific enhancers interact with the promoters of 95 genes that are differentially expressed in blood from persons with and without AD. DISCUSSION WGMS identifies differentially methylated CpGs in known and newly detected genes and enhancers in blood from persons with and without AD. HIGHLIGHTS Whole genome DNA methylation levels were quantified in blood from persons with and without Alzheimer's disease (AD). Twenty-eight thousand thirty-eight differentially methylated positions (DMPs) were identified. Two thousand seven hundred seven genes comprise DMPs. Forty-eight of 75 independent genetic risk loci for AD have DMPs. One thousand five hundred sixty-eight blood-specific enhancers comprise DMPs, 173 of which interact with the promoters of 95 genes that are differentially expressed in blood from persons with and without AD.
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Affiliation(s)
- Coleman Breen
- Department of StatisticsUniversity of Wisconsin, Medical Sciences CenterMadisonWisconsinUSA
| | - Ligia A. Papale
- Department of Neurological SurgeryUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Lindsay R. Clark
- Wisconsin Alzheimer's Disease Research CenterUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
- Geriatric Research Education and Clinical CenterWilliam S. Middleton Memorial Veterans HospitalMadisonWisconsinUSA
| | - Phillip E. Bergmann
- Department of Neurological SurgeryUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Andy Madrid
- Department of Neurological SurgeryUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Sanjay Asthana
- Geriatric Research Education and Clinical CenterWilliam S. Middleton Memorial Veterans HospitalMadisonWisconsinUSA
- Wisconsin Alzheimer's InstituteUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Sterling C. Johnson
- Wisconsin Alzheimer's Disease Research CenterUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
- Geriatric Research Education and Clinical CenterWilliam S. Middleton Memorial Veterans HospitalMadisonWisconsinUSA
- Wisconsin Alzheimer's InstituteUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Sündüz Keleş
- Department of StatisticsUniversity of Wisconsin, Medical Sciences CenterMadisonWisconsinUSA
- Department of Biostatistics and Medical InformaticsUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Reid S. Alisch
- Department of Neurological SurgeryUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Kirk J. Hogan
- Wisconsin Alzheimer's InstituteUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
- Department of AnesthesiologyUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
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Balci-Ozyurt A, Yirün A, Cakır DA, Zeybek ND, Oral D, Sabuncuoğlu S, Erkekoğlu P. Evaluation of possible cytotoxic, genotoxic and epigenotoxic effects of titanium dioxide nanoparticles and possible protective effect of melatonin. Toxicol Mech Methods 2024; 34:109-121. [PMID: 37794599 DOI: 10.1080/15376516.2023.2259980] [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: 07/18/2023] [Accepted: 09/11/2023] [Indexed: 10/06/2023]
Abstract
Nanoparticles (NPs) are particles of matter that are between 1 to 100 nm in diameter. They are suggested to cause toxic effects in both humans and environment thorough different mechanisms. However, their toxicity profile may be different from the parent material. Titanium dioxide (TiO2) NPs are widely used in cosmetic, pharmaceutical and food industries. As a white pigment, the use of TiO2 is used in food coloring, industrial paints, clothing and UV filters has increased tremendously in recent years. Melatonin, on the other hand, is a well-known antioxidant and may prevent oxidative stress caused by a variety of different substances, including NPs. In the current study, we aimed to comparatively investigate the effects of normal-sized TiO2 (220 nm) and nano-sized TiO2 (21 nm) on cytopathology, cytotoxicity, oxidative damage (lipid peroxidation, protein oxidation and glutathione), genotoxicity (8-hydroxydeoxyguanosine), apoptosis (caspase 3, 8 and 9) and epigenetic alterations (global DNA methylation, H3 acetylation) on 3T3 fibroblast cells. In addition, the possible protective effects of melatonin, which is known to have strong antioxidant effects, against the toxicity of TiO2 were also evaluated. Study groups were: a. the control group; b. melatonin group; c. TiO2 group; d. nano-sized TiO2 group; e. TiO2 + melatonin group and f. nano-sized TiO2 + melatonin group. We observed that both normal-sized and nano-sized TiO2 NPs showed significant toxic effects. However, TiO2 NPs caused higher DNA damage and global DNA methylation compared to normal-sized TiO2 whereas normal-sized TiO2 led to lower H3 acetylation vs. TiO2 NPs. Melatonin showed partial protective effect against the toxicity caused by TiO2 NPs.
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Affiliation(s)
- Aylin Balci-Ozyurt
- Department of Pharmaceutical Toxicology, Hacettepe University Faculty of Pharmacy, Ankara, Turkey
- Department of Pharmaceutical Toxicology, Bahçeşehir University School of Pharmacy, İstanbul, Turkey
| | - Anıl Yirün
- Department of Pharmaceutical Toxicology, Hacettepe University Faculty of Pharmacy, Ankara, Turkey
- Department of Pharmaceutical Toxicology, Çukurova University Faculty of Pharmacy, Adana, Turkey
| | - Deniz Arca Cakır
- Department of Pharmaceutical Toxicology, Hacettepe University Faculty of Pharmacy, Ankara, Turkey
- Department of Vaccine Technology, Hacettepe University Vaccine Institute, Ankara, Turkey
| | - N Dilara Zeybek
- Department of Histology and Embryology, Hacettepe University, Faculty of Medicine, Ankara, Turkey
| | - Didem Oral
- Department of Pharmaceutical Toxicology, Hacettepe University Faculty of Pharmacy, Ankara, Turkey
- Department of Pharmaceutical Toxicology, Düzce University Faculty of Pharmacy, Düzce, Turkey
| | - Suna Sabuncuoğlu
- Department of Pharmaceutical Toxicology, Hacettepe University Faculty of Pharmacy, Ankara, Turkey
| | - Pınar Erkekoğlu
- Department of Pharmaceutical Toxicology, Hacettepe University Faculty of Pharmacy, Ankara, Turkey
- Department of Vaccine Technology, Hacettepe University Vaccine Institute, Ankara, Turkey
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Zhang H, Su Y, Zhao J, Song H, Zhou X. A ratiometric fluorescence assay for the detection of DNA methylation based on an alkaline phosphatase triggered in situ fluorogenic reaction. Analyst 2024; 149:507-514. [PMID: 38073500 DOI: 10.1039/d3an01854g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
The accurate and sensitive quantification of DNA methylation is significant for the early diagnosis of cancer. In this work, an alkaline phosphatase (ALP) triggered in situ fluorogenic reaction between ascorbic acid (AA) and 2,3-DAN was employed as a ratiometric fluorescent probe for the accurate and sensitive detection of DNA methylation with the assistance of ALP encapsulated liposomes. The quinoxaline derivative with a yellow fluorescence emission (I525) was generated from the reaction between AA and 2,3-DAN. Meanwhile, the consumption of 2,3-DAN declined its fluorescence intensity (I386). A ratiometric fluorescent probe (I525/I386) constructed by the above in situ fluorogenic reaction was applied for the accurate detection of DNA methylation. The methylated DNA was first captured by its complementary DNA in 96-well plates. Then, 5mC antibody (Ab) linked liposomes that were encapsulated with ALP recognized and combined with the methylation sites of the target DNA. After the liposomes were lysed by Triton X-100, the released ALP triggered the hydrolysis of ascorbic acid diphosphate (AAP) to form AA, participating in the fluorogenic reaction with 2,3-DAN to produce a quinoxaline derivative. Thus, the ratiometric fluorescence detection of DNA methylation was achieved using I525/I386 values. Using the ALP-enzyme catalyzed reaction and liposomes as signal amplifiers, a low detection limit of 82 fM was obtained for DNA methylation detection. Moreover, the accuracy of the assay could be improved using ratiometric fluorescent probes. We hope that the proposed assay will pave a new way for the accurate determination of low-abundance biomarkers.
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Affiliation(s)
- Hongding Zhang
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Xinyang Normal University, Xinyang 464000, PR China.
| | - Yinhui Su
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Xinyang Normal University, Xinyang 464000, PR China.
| | - Jiamiao Zhao
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Xinyang Normal University, Xinyang 464000, PR China.
| | - Huixi Song
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Xinyang Normal University, Xinyang 464000, PR China.
| | - Xiaohong Zhou
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Xinyang Normal University, Xinyang 464000, PR China.
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Akhouri V, Majumder S, Gaikwad AB. Targeting DNA methylation in diabetic kidney disease: A new perspective. Life Sci 2023; 335:122256. [PMID: 37949210 DOI: 10.1016/j.lfs.2023.122256] [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: 09/20/2023] [Revised: 10/30/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023]
Abstract
Diabetic kidney disease (DKD) is a leading diabetic complication causing significant mortality among people around the globe. People with poor glycemic control accompanied by hyperinsulinemia, dyslipidemia, hypertension, and obesity develop diabetic complications. These diabetic patients develop epigenetic changes and suffer from diabetic kidney complications even after subsequent glucose control, the phenomenon that is recognized as metabolic memory. DNA methylation is an essential epigenetic modification that contributes to the development and progression of several diabetic complications, including DKD. The aberrant DNA methylation pattern at CpGs sites within several genes, such as mTOR, RPTOR, IRS2, GRK5, SLC27A3, LCAT, and SLC1A5, associated with the accompanying risk factors exacerbate the DKD progression. Although drugs such as azacytidine and decitabine have been approved to target DNA methylation for diseases such as hematological malignancies, none have been approved for the treatment of DKD. More importantly, no DNA hypomethylation-targeting drugs have been approved for any disease conditions. Understanding the alteration in DNA methylation and its association with the disease risk factors is essential to target DKD effectively. This review has discussed the abnormal DNA methylation pattern and the kidney tissue-specific expression of critical genes involved in DKD onset and progression. Moreover, we also discuss the new possible therapeutic approach that can be exploited for treating DNA methylation aberrancy in a site-specific manner against DKD.
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Affiliation(s)
- Vivek Akhouri
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan 333031, India
| | - Syamantak Majumder
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan 333031, India
| | - Anil Bhanudas Gaikwad
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan 333031, India.
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14
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Vitorakis N, Piperi C. Insights into the Role of Histone Methylation in Brain Aging and Potential Therapeutic Interventions. Int J Mol Sci 2023; 24:17339. [PMID: 38139167 PMCID: PMC10744334 DOI: 10.3390/ijms242417339] [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: 11/11/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Epigenetic mechanisms play a primary role in the cellular damage associated with brain aging. Histone posttranslational modifications represent intrinsic molecular alterations essential for proper physiological functioning, while divergent expression and activity have been detected in several aspects of brain aging. Aberrant histone methylation has been involved in neural stem cell (NSC) quiescence, microglial deficits, inflammatory processes, memory impairment, cognitive decline, neurodegenerative diseases, and schizophrenia. Herein, we provide an overview of recent studies on epigenetic regulation of brain tissue aging, mainly focusing on the role of histone methylation in different cellular and functional aspects of the aging process. Emerging targeting strategies of histone methylation are further explored, including neuroprotective drugs, natural compounds, and lifestyle modifications with therapeutic potential towards the aging process of the brain.
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Affiliation(s)
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 M. Asias Street, 11527 Athens, Greece;
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15
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Yan L, Geng Q, Cao Z, Liu B, Li L, Lu P, Lin L, Wei L, Tan Y, He X, Li L, Zhao N, Lu C. Insights into DNMT1 and programmed cell death in diseases. Biomed Pharmacother 2023; 168:115753. [PMID: 37871559 DOI: 10.1016/j.biopha.2023.115753] [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: 08/07/2023] [Revised: 10/15/2023] [Accepted: 10/17/2023] [Indexed: 10/25/2023] Open
Abstract
DNMT1 (DNA methyltransferase 1) is the predominant member of the DNMT family and the most abundant DNMT in various cell types. It functions as a maintenance DNMT and is involved in various diseases, including cancer and nervous system diseases. Programmed cell death (PCD) is a fundamental mechanism that regulates cell proliferation and maintains the development and homeostasis of multicellular organisms. DNMT1 plays a regulatory role in various types of PCD, including apoptosis, autophagy, necroptosis, ferroptosis, and others. DNMT1 is closely associated with the development of various diseases by regulating key genes and pathways involved in PCD, including caspase 3/7 activities in apoptosis, Beclin 1, LC3, and some autophagy-related proteins in autophagy, glutathione peroxidase 4 (GPX4) and nuclear receptor coactivator 4 (NCOA4) in ferroptosis, and receptor-interacting protein kinase 1-receptor-interacting protein kinase 3-mixed lineage kinase domain-like protein (RIPK1-RIPK3-MLKL) in necroptosis. Our study summarizes the regulatory relationship between DNMT1 and different types of PCD in various diseases and discusses the potential of DNMT1 as a common regulatory hub in multiple types of PCD, offering a perspective for therapeutic approaches in disease.
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Affiliation(s)
- Lan Yan
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Qi Geng
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhiwen Cao
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Bin Liu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Li Li
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Peipei Lu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lin Lin
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lini Wei
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yong Tan
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaojuan He
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Li Li
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ning Zhao
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Cheng Lu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China.
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Zhang J, Wang Y, Zhang Y, Yao J. Genome-wide association study in Alzheimer's disease: a bibliometric and visualization analysis. Front Aging Neurosci 2023; 15:1290657. [PMID: 38094504 PMCID: PMC10716290 DOI: 10.3389/fnagi.2023.1290657] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/08/2023] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND Thousands of research studies concerning genome-wide association studies (GWAS) in Alzheimer's disease (AD) have been published in the last decades. However, a comprehensive understanding of the current research status and future development trends of GWAS in AD have not been clearly shown. In this study, we tried to gain a systematic overview of GWAS in AD by bibliometric and visualization analysis. METHODS The literature search terms are: ("genome-wide analysis" or "genome-wide association study" or "whole-genome analysis") AND ("Alzheimer's Disease" or "Alzheimer Disease"). Relevant publications were extracted from the Web of Science Core Collection (WoSCC) database. Collected data were further analyzed using VOSviewer, CiteSpace and R package Bibliometrix. The countries, institutions, authors and scholar collaborations were investigated. The co-citation analysis of publications was visualized. In addition, research hotspots and fronts were examined. RESULTS A total of 1,350 publications with 59,818 citations were identified. The number of publications and citations presented a significant rising trend since 2013. The United States was the leading country with an overwhelming number of publications (775) and citations (42,237). The University of Washington and Harvard University were the most prolific institutions with 101 publications each. Bennett DA was the most influential researcher with the highest local H-index. Neurobiology of Aging was the journal with the highest number of publications. Aβ, tau, immunity, microglia and DNA methylation were research hotspots. Disease and causal variants were research fronts. CONCLUSION The most frequently studied AD pathogenesis and research hotspots are (1) Aβ and tau, (2) immunity and microglia, with TREM2 as a potential immunotherapy target, and (3) DNA methylation. The research fronts are (1) looking for genetic similarities between AD and other neurological diseases and syndromes, and (2) searching for causal variants of AD. These hotspots suggest noteworthy directions for future studies on AD pathogenesis and genetics, in which basic research regarding immunity is promising for clinical conversion. The current under-researched directions are (1) GWAS in AD biomarkers based on large sample sizes, (2) studies of causal variants of AD, and (3) GWAS in AD based on non-European populations, which need to be strengthened in the future.
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Affiliation(s)
- Junyao Zhang
- Department of Anesthesiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yinuo Wang
- Department of Anesthesiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingying Zhang
- Department of Anesthesiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Junyan Yao
- Department of Anesthesiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Anesthesiology and Critical Care Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
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17
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Zhang H, Wu S, Xing Z, Wang HB. ALP-assisted chemical redox cycling signal amplification for ultrasensitive fluorescence detection of DNA methylation. Analyst 2023; 148:5753-5761. [PMID: 37842979 DOI: 10.1039/d3an01383a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Affinity assays allow direct detection of DNA methylation events without requiring a special sequence. However, the signal amplification of these methods heavily depends on nanocatalysts and bioenzymes, making them suffer from low sensitivity. In this work, alkaline phosphatase (ALP)-assisted chemical redox cycling was employed to amplify the sensitivity of fluorescence affinity assays for DNA methylation detection using Ru@SiO2@MnO2 nanocomposites as fluorescent probes. In the ALP-assisted chemical redox cycling reaction system, ALP hydrolyzed 2-phosphate-L-ascorbic acid trisodium salt (AAP) to produce AA, which could reduce MnO2 nanosheets to form Mn2+, making the fluorescence recovery of Ru@SiO2 nanoparticles possible. Meanwhile, AA was oxidized to dehydroascorbic acid (DHA), which was re-reduced by tris(2-carboxyethyl) phosphine (TCEP) to trigger a redox cycling reaction. The constantly generated AA could etch large amounts of MnO2 nanosheets and greatly recover Ru@SiO2 fluorescence, amplifying the signal of the fluorescence assay. Employing the proposed ALP-assisted chemical redox cycling signal amplification strategy, a sensitive affinity assay for DNA methylation detection was achieved using ALP encapsulated liposomes that were linked with the 5mC antibody (Ab) to bind with methylated sites. A detection limit down to 2.9 fM was obtained for DNA methylation detection and a DNA methylation level as low as 0.1% could be distinguished, which was superior to conventional affinity assays. Moreover, the affinity assays could detect DNA methylation more specifically and directly, implying their great potential for the analysis of tumor-specific genes in liquid biopsy.
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Affiliation(s)
- Hongding Zhang
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Xinyang Normal University, Xinyang 464000, PR China.
| | - Sifei Wu
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Xinyang Normal University, Xinyang 464000, PR China.
| | - Zhenhua Xing
- Xinyang Branch, Henan Boiler and Pressure Vessel Inspection Technology Research Institute, Xinyang 464000, PR China
| | - Hai-Bo Wang
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Xinyang Normal University, Xinyang 464000, PR China.
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18
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Park JW, Lee K, Kim EE, Kim SI, Park SH. Brain Tumor Classification by Methylation Profile. J Korean Med Sci 2023; 38:e356. [PMID: 37935168 PMCID: PMC10627723 DOI: 10.3346/jkms.2023.38.e356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 09/12/2023] [Indexed: 11/09/2023] Open
Abstract
The goal of the methylation classifier in brain tumor classification is to accurately classify tumors based on their methylation profiles. Accurate brain tumor diagnosis is the first step for healthcare professionals to predict tumor prognosis and establish personalized treatment plans for patients. The methylation classifier can be used to perform classification on tumor samples with diagnostic difficulties due to ambiguous histology or mismatch between histopathology and molecular signatures, i.e., not otherwise specified (NOS) cases or not elsewhere classified (NEC) cases, aiding in pathological decision-making. Here, the authors elucidate upon the application of a methylation classifier as a tool to mitigate the inherent complexities associated with the pathological evaluation of brain tumors, even when pathologists are experts in histopathological diagnosis and have access to enough molecular genetic information. Also, it should be emphasized that methylome cannot classify all types of brain tumors, and it often produces erroneous matches even with high matching scores, so, excessive trust is prohibited. The primary issue is the considerable difficulty in obtaining reference data regarding the methylation profile of each type of brain tumor. This challenge is further amplified when dealing with recently identified novel types or subtypes of brain tumors, as such data are not readily accessible through open databases or authors of publications. An additional obstacle arises from the fact that methylation classifiers are primarily research-based, leading to the unavailability of charging patients. It is important to note that the application of methylation classifiers may require specialized laboratory techniques and expertise in DNA methylation analysis.
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Affiliation(s)
- Jin Woo Park
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
- Department of Pathology, Yonsei University College of Medicine, Seoul, Korea
| | - Kwanghoon Lee
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Eric Eunshik Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Seong-Ik Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
- Institute of Neuroscience, Seoul National University College of Medicine, Seoul, Korea.
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19
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Tizabi Y, Bennani S, El Kouhen N, Getachew B, Aschner M. Interaction of Heavy Metal Lead with Gut Microbiota: Implications for Autism Spectrum Disorder. Biomolecules 2023; 13:1549. [PMID: 37892231 PMCID: PMC10605213 DOI: 10.3390/biom13101549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Autism Spectrum Disorder (ASD), a neurodevelopmental disorder characterized by persistent deficits in social interaction and communication, manifests in early childhood and is followed by restricted and stereotyped behaviors, interests, or activities in adolescence and adulthood (DSM-V). Although genetics and environmental factors have been implicated, the exact causes of ASD have yet to be fully characterized. New evidence suggests that dysbiosis or perturbation in gut microbiota (GM) and exposure to lead (Pb) may play important roles in ASD etiology. Pb is a toxic heavy metal that has been linked to a wide range of negative health outcomes, including anemia, encephalopathy, gastroenteric diseases, and, more importantly, cognitive and behavioral problems inherent to ASD. Pb exposure can disrupt GM, which is essential for maintaining overall health. GM, consisting of trillions of microorganisms, has been shown to play a crucial role in the development of various physiological and psychological functions. GM interacts with the brain in a bidirectional manner referred to as the "Gut-Brain Axis (GBA)". In this review, following a general overview of ASD and GM, the interaction of Pb with GM in the context of ASD is emphasized. The potential exploitation of this interaction for therapeutic purposes is also touched upon.
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Affiliation(s)
- Yousef Tizabi
- Department of Pharmacology, Howard University College of Medicine, Washington, DC 20059, USA
| | - Samia Bennani
- Faculty of Medicine and Pharmacy of Casablanca, Hassan II University, Casablanca 20100, Morocco
| | - Nacer El Kouhen
- Faculty of Medicine and Pharmacy of Casablanca, Hassan II University, Casablanca 20100, Morocco
| | - Bruk Getachew
- Department of Pharmacology, Howard University College of Medicine, Washington, DC 20059, USA
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA;
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20
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Yu J, Zhang Y, Xun Y, Tang H, Fu X, Zhang R, Zhu F, Zhang J. Methylation and expression quantitative trait loci rs1799971 in the OPRM1 gene and rs4654327 in the OPRD1 gene are associated with opioid use disorder. Neurosci Lett 2023; 814:137468. [PMID: 37660978 DOI: 10.1016/j.neulet.2023.137468] [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: 02/27/2023] [Revised: 08/26/2023] [Accepted: 08/30/2023] [Indexed: 09/05/2023]
Abstract
Opioid use disorder (OUD) is a chronic and relapsing brain disease that results in significant mortality worldwide. Genetic factors are estimated to contribute to 40%-60% of the liability, with polymorphisms of opioid receptor genes implicated in this disorder. However, the mechanisms underlying these associations are not yet fully understood. In the present study, we first examined the methylation levels in the promoter region of the OPRM1, OPRD1, and OPRK1 genes in 111 healthy controls (HCs) and 120 patients with OUD, and genotyped three tag SNPs in these genes. Correlations between these SNPs and the methylation levels of the CpG sites and expression levels of the genes were analyzed. After identifying the mQTLs and eQTLs, we determined the associations between the mQTLs/eQTLs and susceptibility to and characteristics of OUD in 930 HCs and 801 patients with OUD. Our results demonstrated that SNPs rs1799971 in the OPRM1 gene and rs4654327 in the OPRD1 gene were both mQTLs and eQTLs. We observed unique correlations between mQTLs and methylation levels of several CpG sites in the OUD group compared to the HC group. Interestingly, both the two mQTLs and eQTLs were associated with the susceptibility to OUD. In conclusion, we suppose that mQTLs and eQTLs in genes may underlie the associations between certain risk genetic polymorphisms and OUD. These mQTLs and eQTLs could potentially serve as promising biomarkers for better management of opioid misuse.
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Affiliation(s)
- Jiao Yu
- Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China; Shaanxi Provincial People's Hospital, Xi'an, Shaanxi 710061, China
| | - Yudan Zhang
- Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China; Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Yufeng Xun
- Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China; Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Hua Tang
- Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China; Xi'an International Medical Center Hospital, Xi'an, Shaanxi 710061, China
| | - Xiaoyu Fu
- Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China; Key Laboratory of National Health Commission for Forensic Science, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Rui Zhang
- Department of Psychiatry, Xi'an Mental Health Center, Xi'an, Shaanxi 710061, China
| | - Feng Zhu
- Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China; Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China.
| | - Jianbo Zhang
- Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China; Key Laboratory of National Health Commission for Forensic Science, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China.
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Raia T, Armeli F, Cavallaro RA, Ferraguti G, Businaro R, Lucarelli M, Fuso A. Perinatal S-Adenosylmethionine Supplementation Represses PSEN1 Expression by the Cellular Epigenetic Memory of CpG and Non-CpG Methylation in Adult TgCRD8 Mice. Int J Mol Sci 2023; 24:11675. [PMID: 37511434 PMCID: PMC10380323 DOI: 10.3390/ijms241411675] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/07/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
DNA methylation, the main epigenetic modification regulating gene expression, plays a role in the pathophysiology of neurodegeneration. Previous evidence indicates that 5'-flanking hypomethylation of PSEN1, a gene involved in the amyloidogenic pathway in Alzheimer's disease (AD), boosts the AD-like phenotype in transgenic TgCRND8 mice. Supplementation with S-adenosylmethionine (SAM), the methyl donor in the DNA methylation reactions, reverts the pathological phenotype. Several studies indicate that epigenetic signatures, driving the shift between normal and diseased aging, can be acquired during the first stages of life, even in utero, and manifest phenotypically later on in life. Therefore, we decided to test whether SAM supplementation during the perinatal period (i.e., supplementing the mothers from mating to weaning) could exert a protective role towards AD-like symptom manifestation. We therefore compared the effect of post-weaning vs. perinatal SAM treatment in TgCRND8 mice by assessing PSEN1 methylation and expression and the development of amyloid plaques. We found that short-term perinatal supplementation was as effective as the longer post-weaning supplementation in repressing PSEN1 expression and amyloid deposition in adult mice. These results highlight the importance of epigenetic memory and methyl donor availability during early life to promote healthy aging and stress the functional role of non-CpG methylation.
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Affiliation(s)
- Tiziana Raia
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Federica Armeli
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, 04100 Latina, Italy
| | | | - Giampiero Ferraguti
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Rita Businaro
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, 04100 Latina, Italy
| | - Marco Lucarelli
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy
- Pasteur Institute, Cenci Bolognetti Foundation, Sapienza University of Rome, 00161 Rome, Italy
| | - Andrea Fuso
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy
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22
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Vega-Benedetti AF, Loi E, Moi L, Zavattari P. DNA methylation alterations at RE1-silencing transcription factor binding sites and their flanking regions in cancer. Clin Epigenetics 2023; 15:98. [PMID: 37301955 PMCID: PMC10257853 DOI: 10.1186/s13148-023-01514-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND DNA methylation changes, frequent early events in cancer, can modulate the binding of transcription factors. RE1-silencing transcription factor (REST) plays a fundamental role in regulating the expression of neuronal genes, and in particular their silencing in non-neuronal tissues, by inducing chromatin modifications, including DNA methylation changes, not only in the proximity of its binding sites but also in the flanking regions. REST has been found aberrantly expressed in brain cancer and other cancer types. In this work, we investigated DNA methylation alterations at REST binding sites and their flanking regions in a brain cancer (pilocytic astrocytoma), two gastrointestinal tumours (colorectal cancer and biliary tract cancer) and a blood cancer (chronic lymphocytic leukemia). RESULTS Differential methylation analyses focused on REST binding sites and their flanking regions were conducted between tumour and normal samples from our experimental datasets analysed by Illumina microarrays and the identified alterations were validated using publicly available datasets. We discovered distinct DNA methylation patterns between pilocytic astrocytoma and the other cancer types in agreement with the opposite oncogenic and tumour suppressive role of REST in glioma and non-brain tumours. CONCLUSIONS Our results suggest that these DNA methylation alterations in cancer may be associated with REST dysfunction opening the enthusiastic possibility to develop novel therapeutic interventions based on the modulation of this master regulator in order to restore the aberrant methylation of its target regions into a normal status.
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Affiliation(s)
| | - Eleonora Loi
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, 09042, Cagliari, Italy
| | - Loredana Moi
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, 09042, Cagliari, Italy
| | - Patrizia Zavattari
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, 09042, Cagliari, Italy.
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23
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Zobdeh F, Eremenko II, Akan MA, Tarasov VV, Chubarev VN, Schiöth HB, Mwinyi J. The Epigenetics of Migraine. Int J Mol Sci 2023; 24:ijms24119127. [PMID: 37298078 DOI: 10.3390/ijms24119127] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/05/2023] [Accepted: 05/11/2023] [Indexed: 06/12/2023] Open
Abstract
Migraine is a complex neurological disorder and a major cause of disability. A wide range of different drug classes such as triptans, antidepressants, anticonvulsants, analgesics, and beta-blockers are used in acute and preventive migraine therapy. Despite a considerable progress in the development of novel and targeted therapeutic interventions during recent years, e.g., drugs that inhibit the calcitonin gene-related peptide (CGRP) pathway, therapy success rates are still unsatisfactory. The diversity of drug classes used in migraine therapy partly reflects the limited perception of migraine pathophysiology. Genetics seems to explain only to a minor extent the susceptibility and pathophysiological aspects of migraine. While the role of genetics in migraine has been extensively studied in the past, the interest in studying the role of gene regulatory mechanisms in migraine pathophysiology is recently evolving. A better understanding of the causes and consequences of migraine-associated epigenetic changes could help to better understand migraine risk, pathogenesis, development, course, diagnosis, and prognosis. Additionally, it could be a promising avenue to discover new therapeutic targets for migraine treatment and monitoring. In this review, we summarize the state of the art regarding epigenetic findings in relation to migraine pathogenesis and potential therapeutic targets, with a focus on DNA methylation, histone acetylation, and microRNA-dependent regulation. Several genes and their methylation patterns such as CALCA (migraine symptoms and age of migraine onset), RAMP1, NPTX2, and SH2D5 (migraine chronification) and microRNA molecules such as miR-34a-5p and miR-382-5p (treatment response) seem especially worthy of further study regarding their role in migraine pathogenesis, course, and therapy. Additionally, changes in genes including COMT, GIT2, ZNF234, and SOCS1 have been linked to migraine progression to medication overuse headache (MOH), and several microRNA molecules such as let-7a-5p, let-7b-5p, let-7f-5p, miR-155, miR-126, let-7g, hsa-miR-34a-5p, hsa-miR-375, miR-181a, let-7b, miR-22, and miR-155-5p have been implicated with migraine pathophysiology. Epigenetic changes could be a potential tool for a better understanding of migraine pathophysiology and the identification of new therapeutic possibilities. However, further studies with larger sample sizes are needed to verify these early findings and to be able to establish epigenetic targets as disease predictors or therapeutic targets.
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Affiliation(s)
- Farzin Zobdeh
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Husargatan 3, P.O. Box 593, 75124 Uppsala, Sweden
| | - Ivan I Eremenko
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Husargatan 3, P.O. Box 593, 75124 Uppsala, Sweden
- Advanced Molecular Technology, LLC, 354340 Moscow, Russia
| | - Mikail A Akan
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Husargatan 3, P.O. Box 593, 75124 Uppsala, Sweden
- Advanced Molecular Technology, LLC, 354340 Moscow, Russia
| | | | | | - Helgi B Schiöth
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Husargatan 3, P.O. Box 593, 75124 Uppsala, Sweden
| | - Jessica Mwinyi
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Husargatan 3, P.O. Box 593, 75124 Uppsala, Sweden
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Dynamic Regulation of DNA Methylation and Brain Functions. BIOLOGY 2023; 12:biology12020152. [PMID: 36829430 PMCID: PMC9952911 DOI: 10.3390/biology12020152] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/10/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023]
Abstract
DNA cytosine methylation is a principal epigenetic mechanism underlying transcription during development and aging. Growing evidence suggests that DNA methylation plays a critical role in brain function, including neurogenesis, neuronal differentiation, synaptogenesis, learning, and memory. However, the mechanisms underlying aberrant DNA methylation in neurodegenerative diseases remain unclear. In this review, we provide an overview of the contribution of 5-methycytosine (5mC) and 5-hydroxylcytosine (5hmC) to brain development and aging, with a focus on the roles of dynamic 5mC and 5hmC changes in the pathogenesis of neurodegenerative diseases, particularly Alzheimer's disease (AD), Parkinson's disease (PD), and Huntington's disease (HD). Identification of aberrant DNA methylation sites could provide potential candidates for epigenetic-based diagnostic and therapeutic strategies for neurodegenerative diseases.
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25
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Petrova EI, Galstyan SA, Telysheva EN, Ryzhova MV. [Total DNA methylation profile in assessing the MGMT gene promoter status in malignant gliomas]. ZHURNAL VOPROSY NEIROKHIRURGII IMENI N. N. BURDENKO 2023; 87:52-58. [PMID: 38054227 DOI: 10.17116/neiro20238706152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Methylation of the O-6-methylguanine-DNA methyltransferase (MGMT) gene promoter is currently the most important prognostic biomarker in therapy of IDH-wild-type glioblastoma. One can obtain information about this methylation from total DNA methylation profile. OBJECTIVE To analyze the DNA methylation signal intensity in the MGMT gene in samples of malignant gliomas and identify the most significant genomic positions for calculating the MGMT gene promoter status for further improvement of diagnostics and prediction of therapeutic options in patients with malignant gliomas. MATERIAL AND METHODS The study is based on 43 samples (frozen tissue or paraffin blocks) from patients with malignant gliomas. Tumor DNA samples were prepared using the Illumina Infinium MethylationEPIC BeadChip Kit and the Illumina Next-Seq 550 Sequencing System platform. DNA methylation profiles were analyzed using computational algorithms in the R language, specialized libraries minfi and mgmtstp27, as well as basic statistical functions in the Rstudio environment. RESULTS We established the MGMT gene promoter status in 43 samples of malignant gliomas considering total DNA methylation profile. In 24 samples (55%), the MGMT gene promoter was methylated. We compared methylation signal in certain CpG islands in groups with methylated and unmethylated MGMT gene promoters and identified the most significant positions for further improvement of data analysis algorithm. CONCLUSION These data demonstrate the possibilities and prospects for further improvement of algorithm for analysis of the MGMT gene promoter status based on total DNA methylation profile in patients with malignant gliomas as an alternative to methyl-specific PCR. Our results are consistent with data of other neuro-oncology researchers. Indeed, computational methods like MGMT-STP27 are quite powerful and can be used in scientific and clinical practice to assess prognosis and make decisions about chemotherapy with alkylating agents.
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Affiliation(s)
- E I Petrova
- Burdenko Neurosurgical Center, Moscow, Russia
| | | | | | - M V Ryzhova
- Burdenko Neurosurgical Center, Moscow, Russia
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