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Zheng J, Liu Y, Liang Z, Wang YA, Yu W, Ding B, Wang H. A Rigorous Nuclear DNA-Excluding Mass Spectrometry Assay for Accurate Identification of 5-Methylcytosine in Mitochondrial DNA. Anal Chem 2025; 97:5914-5918. [PMID: 40079347 DOI: 10.1021/acs.analchem.4c06090] [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: 03/15/2025]
Abstract
5-Methylcytosine (5mC) functions as a well-characterized epigenetic DNA mark in nuclear DNA, but its presence in mitochondrial DNA (mtDNA) remains elusive. Here, we report a new and rigorous nuclear DNA (nDNA)-excluding mass spectrometry assay enabling the reliable and accurate identification of 5mC in mtDNA for the first time. First, circular mtDNA is enriched over 809-946-fold by combining alkaline lysis and linear DNA-specific RecBCD cutting; nDNA accounts for ∼12-19% of the DNA remaining after this step. Second, assisted by the restrictive endonucleases BbsI (for human mtDNA) and EcoRV (for mouse mtDNA), circular mtDNA was cut into only one or two linearized mtDNA fragments, while the residual nuclear DNA was efficiently degraded into shorter fragments; thus, the linearized mtDNA fragment(s) could be well isolated from the residual degraded nDNA via gel electrophoresis. Finally, the linearized mtDNA bands are excised and subjected to in-gel digestion followed by precise stable isotope-diluted LC-MS/MS analysis. With this sensitive and accurate method, we demonstrated that mtDNA is hypomethylated in a normal mouse cell line, which is rationally attributed to de novo methylation. Overall, we provide a powerful, gold-standard mass spectrometry assay for screening and identifying mtDNA 5mC in diverse scenarios.
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Affiliation(s)
- Jing Zheng
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yiran Liu
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Ziyu Liang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Ang Wang
- National Center for Nanoscience and Technology, Beijing 100190, China
| | - Wenqiang Yu
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Baoquan Ding
- National Center for Nanoscience and Technology, Beijing 100190, China
| | - Hailin Wang
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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2
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Arbeithuber B, Anthony K, Higgins B, Oppelt P, Shebl O, Tiemann-Boege I, Chiaromonte F, Ebner T, Makova KD. Mitochondrial DNA mutations in human oocytes undergo frequency-dependent selection but do not increase with age. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.09.627454. [PMID: 39713397 PMCID: PMC11661235 DOI: 10.1101/2024.12.09.627454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/24/2024]
Abstract
Mitochondria, cellular powerhouses, harbor DNA (mtDNA) inherited from the mothers. MtDNA mutations can cause diseases, yet whether they increase with age in human germline cells-oocytes-remains understudied. Here, using highly accurate duplex sequencing of full-length mtDNA, we detected de novo mutations in single oocytes, blood, and saliva in women between 20 and 42 years of age. We found that, with age, mutations increased in blood and saliva but not in oocytes. In oocytes, mutations with high allele frequencies (≥1%) were less prevalent in coding than non-coding regions, whereas mutations with low allele frequencies (<1%) were more uniformly distributed along mtDNA, suggesting frequency-dependent purifying selection. In somatic tissues, mutations caused elevated amino acid changes in protein-coding regions, suggesting positive or destructive selection. Thus, mtDNA in human oocytes is protected against accumulation of mutations having functional consequences and with aging. These findings are particularly timely as humans tend to reproduce later in life.
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Affiliation(s)
- Barbara Arbeithuber
- Department of Gynaecology, Obstetrics and Gynaecological Endocrinology, Experimental Gynaecology and Obstetrics, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Kate Anthony
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Bonnie Higgins
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Peter Oppelt
- Department of Gynaecology, Obstetrics and Gynaecological Endocrinology, Johannes Kepler University Linz, Kepler University Hospital, Altenberger Strasse 69, 4040 Linz and Krankenhausstrasse 26, 4020, Linz, Austria
| | - Omar Shebl
- Department of Gynaecology, Obstetrics and Gynaecological Endocrinology, Johannes Kepler University Linz, Kepler University Hospital, Altenberger Strasse 69, 4040 Linz and Krankenhausstrasse 26, 4020, Linz, Austria
| | - Irene Tiemann-Boege
- Institute of Biophysics, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
| | - Francesca Chiaromonte
- Center for Medical Genomics, Penn State University, University Park, PA 16802, USA
- Department of Statistics, The Pennsylvania State University, University Park, PA 16802 USA
- Sant’Anna School of Advanced Studies, Pisa, 56127 Italy
| | - Thomas Ebner
- Department of Gynaecology, Obstetrics and Gynaecological Endocrinology, Johannes Kepler University Linz, Kepler University Hospital, Altenberger Strasse 69, 4040 Linz and Krankenhausstrasse 26, 4020, Linz, Austria
| | - Kateryna D. Makova
- Department of Biology, Penn State University, University Park, PA 16802, USA
- Center for Medical Genomics, Penn State University, University Park, PA 16802, USA
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3
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Cinzori ME, Nicol M, Dewald AL, Goodrich JM, Zhou Z, Gardiner JC, Kerver JM, Dolinoy DC, Talge N, Strakovsky RS. Maternal mitochondrial DNA copy number and methylation as possible predictors of pregnancy outcomes in a Michigan pregnancy cohort. ENVIRONMENTAL EPIGENETICS 2024; 10:dvae021. [PMID: 39628676 PMCID: PMC11614404 DOI: 10.1093/eep/dvae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 08/26/2024] [Accepted: 10/28/2024] [Indexed: 12/06/2024]
Abstract
Little is understood about the roles of mitochondria in pregnancy-related adaptations. Therefore, we evaluated associations of maternal early-to-mid pregnancy mitochondrial DNA copy number (mtDNAcn) and mtDNA methylation with birth size and gestational length. Michigan women (n = 396) provided venous bloodspots at median 11 weeks gestation to quantify mtDNAcn marker NADH-ubiquinone oxidoreductase chain 1 (ND1) using real-time quantitative PCR and mtDNA methylation at several regions within four mitochondria-specific genes using pyrosequencing: MTTF (mitochondrially encoded tRNA phenylalanine), DLOOP (D-loop promoter region, heavy strand), CYTB (cytochrome b), and LDLR (D-loop promoter region, light strand). We abstracted gestational length and birthweight from birth certificates and calculated birthweight z-scores using published references. We used multivariable linear regression to evaluate associations of mtDNAcn and mtDNA methylation with birthweight and birthweight z-scores. Cox Proportional Hazards Models (PHMs) and quantile regression characterized associations of mitochondrial measures with gestational length. We also considered differences by fetal sex. Using linear regression and Cox PHMs, mtDNAcn was not associated with birth outcomes, whereas associations of mtDNA methylation with birth outcomes were inconsistent. However, using quantile regression, mtDNAcn was associated with shorter gestation in female newborns at the upper quantiles of gestational length, but with longer gestational length in males at the lower quantiles of gestational length. Maternal LDLR, DLOOP, and MTTF methylation was associated with longer gestational length in females at the upper quantiles and in males at lower gestational length quantiles. Maternal mtDNAcn and mtDNA methylation were associated with gestational length in babies born comparatively early or late, which could reflect adaptations in mitochondrial processes that regulate the length of gestation.
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Affiliation(s)
- Maria E Cinzori
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI 48824, United States
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI 48824, United States
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI 48824, United States
| | - Megan Nicol
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI 48824, United States
| | - Alisa L Dewald
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48109, United States
| | - Jaclyn M Goodrich
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48109, United States
| | - Zheng Zhou
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, United States
| | - Joseph C Gardiner
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI 48824, United States
| | - Jean M Kerver
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI 48824, United States
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48109, United States
| | - Nicole Talge
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI 48824, United States
| | - Rita S Strakovsky
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI 48824, United States
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI 48824, United States
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4
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Kalykaki M, Rubio-Tomás T, Tavernarakis N. The role of mitochondria in cytokine and chemokine signalling during ageing. Mech Ageing Dev 2024; 222:111993. [PMID: 39307464 DOI: 10.1016/j.mad.2024.111993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 09/15/2024] [Accepted: 09/17/2024] [Indexed: 09/28/2024]
Abstract
Ageing is accompanied by a persistent, low-level inflammation, termed "inflammageing", which contributes to the pathogenesis of age-related diseases. Mitochondria fulfil multiple roles in host immune responses, while mitochondrial dysfunction, a hallmark of ageing, has been shown to promote chronic inflammatory states by regulating the production of cytokines and chemokines. In this review, we aim to disentangle the molecular mechanisms underlying this process. We describe the role of mitochondrial signalling components such as mitochondrial DNA, mitochondrial RNA, N-formylated peptides, ROS, cardiolipin, cytochrome c, mitochondrial metabolites, potassium efflux and mitochondrial calcium in the age-related immune system activation. Furthermore, we discuss the effect of age-related decline in mitochondrial quality control mechanisms, including mitochondrial biogenesis, dynamics, mitophagy and UPRmt, in inflammatory states upon ageing. In addition, we focus on the dynamic relationship between mitochondrial dysfunction and cellular senescence and its role in regulating the secretion of pro-inflammatory molecules by senescent cells. Finally, we review the existing literature regarding mitochondrial dysfunction and inflammation in specific age-related pathological conditions, including neurodegenerative diseases (Alzheimer's and Parkinson's disease, and amyotrophic lateral sclerosis), osteoarthritis and sarcopenia.
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Affiliation(s)
- Maria Kalykaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Crete GR-70013, Greece
| | - Teresa Rubio-Tomás
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Crete GR-70013, Greece
| | - Nektarios Tavernarakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Crete GR-70013, Greece; Division of Basic Sciences, School of Medicine, University of Crete, Heraklion, Crete GR-71003, Greece.
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5
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Dong Q, Gong C, Jiang Q, Liu Y, Hu Y, Wang D, Liu H, Zheng T, Song C, Wang T, Ju R, Wang C, Song D, Liu Z, Liu Y, Lu Y, Fan J, Liu M, Gao T, An Z, Zhang J, Li P, Cao C, Liu X. Identification of differentially expressed tumour-related genes regulated by UHRF1-driven DNA methylation. Sci Rep 2024; 14:18371. [PMID: 39112494 PMCID: PMC11306747 DOI: 10.1038/s41598-024-69110-2] [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: 11/14/2023] [Accepted: 07/31/2024] [Indexed: 08/10/2024] Open
Abstract
Ubiquitin-like with PHD and RING finger domains 1 (UHRF1) is an epigenetic regulator that plays critical roles in tumours. However, the DNA methylation alteration patterns driven by UHRF1 and the related differentially expressed tumour-related genes remain unclear. In this study, a UHRF1-shRNA MCF-7 cell line was constructed, and whole-genome bisulfite sequencing and RNA sequencing were performed. The DNA methylation alteration landscape was elucidated, and DNA methylation-altered regions (DMRs) were found to be distributed in both gene bodies and adjacent regions. The DMRs were annotated and categorized into 488 hypermethylated/1696 hypomethylated promoters and 1149 hypermethylated/5501 hypomethylated gene bodies. Through an integrated analysis with the RNA sequencing data, 217 methylation-regulated upregulated genes and 288 downregulated genes were identified, and these genes were primarily enriched in nervous system development and cancer signalling pathways. Further analysis revealed 21 downregulated oncogenes and 15 upregulated TSGs. We also showed that UHRF1 silencing inhibited cell proliferation and migration and suppressed tumour growth in vivo. Our study suggested that UHRF1 and the oncogenes or TSGs it regulates might serve as biomarkers and targets for breast cancer treatment.
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Affiliation(s)
- Qincai Dong
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Chunxue Gong
- Institute of Health Sciences, Anhui University, Hefei, 230601, China
| | - Qian Jiang
- Institute of Health Sciences, Anhui University, Hefei, 230601, China
| | - Yue Liu
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Yong Hu
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Di Wang
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Hainan Liu
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Tong Zheng
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Caiwei Song
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Tingting Wang
- Institute of Health Sciences, Anhui University, Hefei, 230601, China
| | - Ruixia Ju
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Chen Wang
- Institute of Health Sciences, Anhui University, Hefei, 230601, China
| | - Dengcen Song
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Zijing Liu
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Yuting Liu
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Yuwei Lu
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Jinlian Fan
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Mengzi Liu
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Ting Gao
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Ziqian An
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Jiaxin Zhang
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Ping Li
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Cheng Cao
- Beijing Institute of Biotechnology, Beijing, 100850, China.
| | - Xuan Liu
- Beijing Institute of Biotechnology, Beijing, 100850, China.
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6
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Xiao M, Wei R, Yu J, Gao C, Yang F, Zhang L. CpG Island Definition and Methylation Mapping of the T2T-YAO Genome. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae009. [PMID: 39142816 PMCID: PMC12016031 DOI: 10.1093/gpbjnl/qzae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 08/16/2024]
Abstract
Precisely defining and mapping all cytosine (C) positions and their clusters, known as CpG islands (CGIs), as well as their methylation status, are pivotal for genome-wide epigenetic studies, especially when population-centric reference genomes are ready for timely application. Here, we first align the two high-quality reference genomes, T2T-YAO and T2T-CHM13, from different ethnic backgrounds in a base-by-base fashion and compute their genome-wide density-defined and position-defined CGIs. Second, by mapping some representative genome-wide methylation data from selected organs onto the two genomes, we find that there are about 4.7%-5.8% sequence divergency of variable categories depending on quality cutoffs. Genes among the divergent sequences are mostly associated with neurological functions. Moreover, CGIs associated with the divergent sequences are significantly different with respect to CpG density and observed CpG/expected CpG (O/E) ratio between the two genomes. Finally, we find that the T2T-YAO genome not only has a greater CpG coverage than that of the T2T-CHM13 genome when whole-genome bisulfite sequencing (WGBS) data from the European and American populations are mapped to each reference, but also shows more hyper-methylated CpG sites as compared to the T2T-CHM13 genome. Our study suggests that future genome-wide epigenetic studies of the Chinese populations rely on both acquisition of high-quality methylation data and subsequent precision CGI mapping based on the Chinese T2T reference.
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Affiliation(s)
- Ming Xiao
- College of Computer Science, Sichuan University, Chengdu 610065, China
| | - Rui Wei
- College of Computer Science, Sichuan University, Chengdu 610065, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chujie Gao
- College of Computer Science, Sichuan University, Chengdu 610065, China
| | - Fengyi Yang
- College of Computer Science, Sichuan University, Chengdu 610065, China
| | - Le Zhang
- College of Computer Science, Sichuan University, Chengdu 610065, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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7
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Cheng JC, Swarup N, Morselli M, Huang WL, Aziz M, Caggiano C, Kordi M, Patel A, Chia D, Kim Y, Li F, Wei F, Zaitlen N, Krysan K, Dubinett S, Pellegrini M, Wong DW. Single-stranded pre-methylated 5mC adapters uncover the methylation profile of plasma ultrashort Single-stranded cell-free DNA. Nucleic Acids Res 2024; 52:e50. [PMID: 38797520 PMCID: PMC11194076 DOI: 10.1093/nar/gkae276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 03/21/2024] [Accepted: 04/15/2024] [Indexed: 05/29/2024] Open
Abstract
Whole-genome bisulfite sequencing (BS-Seq) measures cytosine methylation changes at single-base resolution and can be used to profile cell-free DNA (cfDNA). In plasma, ultrashort single-stranded cfDNA (uscfDNA, ∼50 nt) has been identified together with 167 bp double-stranded mononucleosomal cell-free DNA (mncfDNA). However, the methylation profile of uscfDNA has not been described. Conventional BS-Seq workflows may not be helpful because bisulfite conversion degrades larger DNA into smaller fragments, leading to erroneous categorization as uscfDNA. We describe the '5mCAdpBS-Seq' workflow in which pre-methylated 5mC (5-methylcytosine) single-stranded adapters are ligated to heat-denatured cfDNA before bisulfite conversion. This method retains only DNA fragments that are unaltered by bisulfite treatment, resulting in less biased uscfDNA methylation analysis. Using 5mCAdpBS-Seq, uscfDNA had lower levels of DNA methylation (∼15%) compared to mncfDNA and was enriched in promoters and CpG islands. Hypomethylated uscfDNA fragments were enriched in upstream transcription start sites (TSSs), and the intensity of enrichment was correlated with expressed genes of hemopoietic cells. Using tissue-of-origin deconvolution, we inferred that uscfDNA is derived primarily from eosinophils, neutrophils, and monocytes. As proof-of-principle, we show that characteristics of the methylation profile of uscfDNA can distinguish non-small cell lung carcinoma from non-cancer samples. The 5mCAdpBS-Seq workflow is recommended for any cfDNA methylation-based investigations.
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Affiliation(s)
- Jordan C Cheng
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Neeti Swarup
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Marco Morselli
- Department of Molecular, Cell, and Developmental Biology, Life Sciences Division, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Wei-Lun Huang
- Center of Applied Nanomedicine, National Cheng Kung University, Tainan, Taiwan
| | - Mohammad Aziz
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Christa Caggiano
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Misagh Kordi
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Abhijit A Patel
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - David Chia
- Department of Pathology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yong Kim
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Feng Li
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Fang Wei
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Noah Zaitlen
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Kostyantyn Krysan
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Steve Dubinett
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, Life Sciences Division, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - David T W Wong
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
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8
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Pandey S, Anang V, Schumacher MM. Mitochondria driven innate immune signaling and inflammation in cancer growth, immune evasion, and therapeutic resistance. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2024; 386:223-247. [PMID: 38782500 DOI: 10.1016/bs.ircmb.2024.01.006] [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: 05/25/2024]
Abstract
Mitochondria play an important and multifaceted role in cellular function, catering to the cell's energy and biosynthetic requirements. They modulate apoptosis while responding to diverse extracellular and intracellular stresses including reactive oxygen species (ROS), nutrient and oxygen scarcity, endoplasmic reticulum stress, and signaling via surface death receptors. Integral components of mitochondria, such as mitochondrial DNA (mtDNA), mitochondrial RNA (mtRNA), Adenosine triphosphate (ATP), cardiolipin, and formyl peptides serve as major damage-associated molecular patterns (DAMPs). These molecules activate multiple innate immune pathways both in the cytosol [such as Retionoic Acid-Inducible Gene-1 (RIG-1) and Cyclic GMP-AMP Synthase (cGAS)] and on the cell surface [including Toll-like receptors (TLRs)]. This activation cascade leads to the release of various cytokines, chemokines, interferons, and other inflammatory molecules and oxidative species. The innate immune pathways further induce chronic inflammation in the tumor microenvironment which either promotes survival and proliferation or promotes epithelial to mesenchymal transition (EMT), metastasis and therapeutic resistance in the cancer cell's. Chronic activation of innate inflammatory pathways in tumors also drives immunosuppressive checkpoint expression in the cancer cells and boosts the influx of immune-suppressive populations like Myeloid-Derived Suppressor Cells (MDSCs) and Regulatory T cells (Tregs) in cancer. Thus, sensing of cellular stress by the mitochondria may lead to enhanced tumor growth. In addition to that, the tumor microenvironment also becomes a source of immunosuppressive cytokines. These cytokines exert a debilitating effect on the functioning of immune effector cells, and thus foster immune tolerance and facilitate immune evasion. Here we describe how alteration of the mitochondrial homeostasis and cellular stress drives innate inflammatory pathways in the tumor microenvironment.
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Affiliation(s)
- Sanjay Pandey
- Department of Radiation Oncology, Montefiore Medical Center, Bronx, NY, United States.
| | - Vandana Anang
- International Center for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Michelle M Schumacher
- Department of Radiation Oncology, Montefiore Medical Center, Bronx, NY, United States; Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, United States
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9
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Tsokkou S, Kavvadas D, Georgaki MN, Papadopoulou K, Papamitsou T, Karachrysafi S. Genetic and Epigenetic Factors Associated with Postpartum Psychosis: A 5-Year Systematic Review. J Clin Med 2024; 13:964. [PMID: 38398277 PMCID: PMC10888625 DOI: 10.3390/jcm13040964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/01/2024] [Accepted: 02/04/2024] [Indexed: 02/25/2024] Open
Abstract
Purpose: Postpartum psychosis (PPP) is a serious mental health illness affecting women post-parturition. Around 1 in 1000 women are affected by postpartum psychosis, and the symptoms usually appear within 2 weeks after birth. Postpartum mental disorders are classified into 3 main categories starting from the least to most severe types, including baby blues, postpartum depression, and postpartum psychosis. Materials and Methods: In this systematic review, genetic and epigenetic factors associated with postpartum psychosis are discussed. A PRISMA flow diagram was followed, and the following databases were used as main sources: PubMed, ScienceDirect, and Scopus. Additional information was retrieved from external sources and organizations. The time period for the articles extracted was 5 years. Results: Initially, a total of 2379 articled were found. After the stated criteria were applied, 58 articles were identified along with 20 articles from additional sources, which were then narrowed down to a final total of 29 articles. Conclusions: It can be concluded that there is an association between PPP and genetic and epigenetic risk factors. However, based on the data retrieved and examined, the association was found to be greater for genetic factors. Additionally, the presence of bipolar disorder and disruption of the circadian cycle played a crucial role in the development of PPP.
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Affiliation(s)
- Sophia Tsokkou
- Research Team “Histologistas”, Interinstitutional Postgraduate Program “Health and Environmental Factors”, Department of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (S.T.); (D.K.); (M.-N.G.); (K.P.); (T.P.)
- Laboratory of Histology-Embryology, Department of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Dimitrios Kavvadas
- Research Team “Histologistas”, Interinstitutional Postgraduate Program “Health and Environmental Factors”, Department of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (S.T.); (D.K.); (M.-N.G.); (K.P.); (T.P.)
- Laboratory of Histology-Embryology, Department of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Maria-Nefeli Georgaki
- Research Team “Histologistas”, Interinstitutional Postgraduate Program “Health and Environmental Factors”, Department of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (S.T.); (D.K.); (M.-N.G.); (K.P.); (T.P.)
- Environmental Engineering Laboratory, Department of Chemical Engineering, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Kyriaki Papadopoulou
- Research Team “Histologistas”, Interinstitutional Postgraduate Program “Health and Environmental Factors”, Department of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (S.T.); (D.K.); (M.-N.G.); (K.P.); (T.P.)
- Laboratory of Histology-Embryology, Department of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- A’ Neurosurgery University Clinic, Aristotle University of Thessaloniki, AHEPA General Hospital of Thessaloniki, 54636 Thessaloniki, Greece
| | - Theodora Papamitsou
- Research Team “Histologistas”, Interinstitutional Postgraduate Program “Health and Environmental Factors”, Department of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (S.T.); (D.K.); (M.-N.G.); (K.P.); (T.P.)
- Laboratory of Histology-Embryology, Department of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Sofia Karachrysafi
- Research Team “Histologistas”, Interinstitutional Postgraduate Program “Health and Environmental Factors”, Department of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (S.T.); (D.K.); (M.-N.G.); (K.P.); (T.P.)
- Laboratory of Histology-Embryology, Department of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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10
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Ceylan D, Arat-Çelik HE, Aksahin IC. Integrating mitoepigenetics into research in mood disorders: a state-of-the-art review. Front Physiol 2024; 15:1338544. [PMID: 38410811 PMCID: PMC10895490 DOI: 10.3389/fphys.2024.1338544] [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: 11/14/2023] [Accepted: 01/24/2024] [Indexed: 02/28/2024] Open
Abstract
Mood disorders, including major depressive disorder and bipolar disorder, are highly prevalent and stand among the leading causes of disability. Despite the largely elusive nature of the molecular mechanisms underpinning these disorders, two pivotal contributors-mitochondrial dysfunctions and epigenetic alterations-have emerged as significant players in their pathogenesis. This state-of-the-art review aims to present existing data on epigenetic alterations in the mitochondrial genome in mood disorders, laying the groundwork for future research into their pathogenesis. Associations between abnormalities in mitochondrial function and mood disorders have been observed, with evidence pointing to notable changes in mitochondrial DNA (mtDNA). These changes encompass variations in copy number and oxidative damage. However, information on additional epigenetic alterations in the mitochondrial genome remains limited. Recent studies have delved into alterations in mtDNA and regulations in the mitochondrial genome, giving rise to the burgeoning field of mitochondrial epigenetics. Mitochondrial epigenetics encompasses three main categories of modifications: mtDNA methylation/hydroxymethylation, modifications of mitochondrial nucleoids, and mitochondrial RNA alterations. The epigenetic modulation of mitochondrial nucleoids, lacking histones, may impact mtDNA function. Additionally, mitochondrial RNAs, including non-coding RNAs, present a complex landscape influencing interactions between the mitochondria and the nucleus. The exploration of mitochondrial epigenetics offers valuable perspectives on how these alterations impact neurodegenerative diseases, presenting an intriguing avenue for research on mood disorders. Investigations into post-translational modifications and the role of mitochondrial non-coding RNAs hold promise to unravel the dynamics of mitoepigenetics in mood disorders, providing crucial insights for future therapeutic interventions.
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Affiliation(s)
- Deniz Ceylan
- Department of Psychiatry, School of Medicine, Koç University, Istanbul, Türkiye
- Koç University Research Center for Translational Medicine (KUTTAM), Affective Laboratory, Istanbul, Türkiye
| | | | - Izel Cemre Aksahin
- Koç University Research Center for Translational Medicine (KUTTAM), Affective Laboratory, Istanbul, Türkiye
- Graduate School of Health Sciences, Koç University, Istanbul, Türkiye
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11
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Murphy MP, O'Neill LAJ. A break in mitochondrial endosymbiosis as a basis for inflammatory diseases. Nature 2024; 626:271-279. [PMID: 38326590 DOI: 10.1038/s41586-023-06866-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 11/14/2023] [Indexed: 02/09/2024]
Abstract
Mitochondria retain bacterial traits due to their endosymbiotic origin, but host cells do not recognize them as foreign because the organelles are sequestered. However, the regulated release of mitochondrial factors into the cytosol can trigger cell death, innate immunity and inflammation. This selective breakdown in the 2-billion-year-old endosymbiotic relationship enables mitochondria to act as intracellular signalling hubs. Mitochondrial signals include proteins, nucleic acids, phospholipids, metabolites and reactive oxygen species, which have many modes of release from mitochondria, and of decoding in the cytosol and nucleus. Because these mitochondrial signals probably contribute to the homeostatic role of inflammation, dysregulation of these processes may lead to autoimmune and inflammatory diseases. A potential reason for the increased incidence of these diseases may be changes in mitochondrial function and signalling in response to such recent phenomena as obesity, dietary changes and other environmental factors. Focusing on the mixed heritage of mitochondria therefore leads to predictions for future insights, research paths and therapeutic opportunities. Thus, whereas mitochondria can be considered 'the enemy within' the cell, evolution has used this strained relationship in intriguing ways, with increasing evidence pointing to the recent failure of endosymbiosis being critical for the pathogenesis of inflammatory diseases.
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Affiliation(s)
- Michael P Murphy
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
- Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Luke A J O'Neill
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland.
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12
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Mrowicka M, Mrowicki J, Majsterek I. Relationship between Biochemical Pathways and Non-Coding RNAs Involved in the Progression of Diabetic Retinopathy. J Clin Med 2024; 13:292. [PMID: 38202299 PMCID: PMC10779474 DOI: 10.3390/jcm13010292] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/22/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Diabetic retinopathy (DR) is a progressive blinding disease, which affects the vision and quality of life of patients, and it severely impacts the society. This complication, caused by abnormal glucose metabolism, leads to structural, functional, molecular, and biochemical abnormalities in the retina. Oxidative stress and inflammation also play pivotal roles in the pathogenic process of DR, leading to mitochondrial damage and a decrease in mitochondrial function. DR causes retinal degeneration in glial and neural cells, while the disappearance of pericytes in retinal blood vessels leads to alterations in vascular regulation and stability. Clinical changes include dilatation and blood flow changes in response to the decrease in retinal perfusion in retinal blood vessels, leading to vascular leakage, neovascularization, and neurodegeneration. The loss of vascular cells in the retina results in capillary occlusion and ischemia. Thus, DR is a highly complex disease with various biological factors, which contribute to its pathogenesis. The interplay between biochemical pathways and non-coding RNAs (ncRNAs) is essential for understanding the development and progression of DR. Abnormal expression of ncRNAs has been confirmed to promote the development of DR, suggesting that ncRNAs such as miRNAs, lncRNAs, and circRNAs have potential as diagnostic biomarkers and theranostic targets in DR. This review provides an overview of the interactions between abnormal biochemical pathways and dysregulated expression of ncRNAs under the influence of hyperglycemic environment in DR.
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Affiliation(s)
- Małgorzata Mrowicka
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, Mazowiecka 5, 92-215 Lodz, Poland; (J.M.); (I.M.)
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de Lima CB, Martin H, Pecora Milazzotto M, Sirard MA. Genome-wide methylation profile of mitochondrial DNA across bovine preimplantation development. Epigenetics 2023; 18:2241010. [PMID: 37523633 PMCID: PMC10392754 DOI: 10.1080/15592294.2023.2241010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/29/2023] [Accepted: 07/11/2023] [Indexed: 08/02/2023] Open
Abstract
This study characterized variations in the methylation profile of mitochondrial DNA (mtDNA) during initial bovine embryo development and correlated the presence of methylation with mtDNA transcription. Bovine oocytes were obtained from abattoir ovaries and submitted to in vitro culture procedures. Oocytes and embryos were collected at various stages (immature oocyte, IM; mature oocyte, MII; zygote, ZY; 4-cells, 4C; 16-cells, 16C and blastocysts, BL). Total DNA (including mtDNA) was used for Whole Genome Enzymatic Methyl Sequencing and for quantification of mtDNA copy number. Extracted RNA was used for quantification of mitochondrial transcripts using Droplet Digital PCR. We selected ND6, CYTB, tRNA-Phe and tRNA-Gln based on their location in the mitochondrial genome, functionality and/or previous literature associating these regions with cytosine methylation. The number of mtDNA copies per oocyte/embryo was found to be similar, while methylation levels in mtDNA varied among stages. Higher total methylation levels were found mainly at 4C and 16C. In specific gene regions, higher methylation levels were also observed at 4C and 16C (ND6, CYTB and tRNA-Phe), as well as an inverse correlation with the quantity of transcripts for these regions. This is a first description of epigenetic changes occurring in mtDNA during early embryonic development. Our results indicate that methylation might regulate the mtDNA transcription at a local level, particularly around the time of embryonic genome activation.
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Affiliation(s)
- Camila Bruna de Lima
- Centre de Recherche En Reproduction, Développement Et Santé Intergénérationnelle (CRDSI), Département des Sciences Animales, Université Laval, Québec, QC, Canada
- Universidade Federal Do ABC, Centro de Ciências Naturais E Humanas, Santo André, SP, Brazil
| | - Hélène Martin
- Centre de Recherche En Reproduction, Développement Et Santé Intergénérationnelle (CRDSI), Département des Sciences Animales, Université Laval, Québec, QC, Canada
| | - Marcella Pecora Milazzotto
- Centre de Recherche En Reproduction, Développement Et Santé Intergénérationnelle (CRDSI), Département des Sciences Animales, Université Laval, Québec, QC, Canada
- Universidade Federal Do ABC, Centro de Ciências Naturais E Humanas, Santo André, SP, Brazil
| | - Marc-André Sirard
- Centre de Recherche En Reproduction, Développement Et Santé Intergénérationnelle (CRDSI), Département des Sciences Animales, Université Laval, Québec, QC, Canada
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Naue J. Getting the chronological age out of DNA: using insights of age-dependent DNA methylation for forensic DNA applications. Genes Genomics 2023; 45:1239-1261. [PMID: 37253906 PMCID: PMC10504122 DOI: 10.1007/s13258-023-01392-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/15/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND DNA analysis for forensic investigations has a long tradition with important developments and optimizations since its first application. Traditionally, short tandem repeats analysis has been the most powerful method for the identification of individuals. However, in addition, epigenetic changes, i.e., DNA methylation, came into focus of forensic DNA research. Chronological age prediction is one promising application to allow for narrowing the pool of possible individuals who caused a trace, as well as to support the identification of unknown bodies and for age verification of living individuals. OBJECTIVE This review aims to provide an overview of the current knowledge, possibilities, and (current) limitations about DNA methylation-based chronological age prediction with emphasis on forensic application. METHODS The development, implementation and application of age prediction tools requires a deep understanding about the biological background, the analysis methods, the age-dependent DNA methylation markers, as well as the mathematical models for age prediction and their evaluation. Furthermore, additional influences can have an impact. Therefore, the literature was evaluated in respect to these diverse topics. CONCLUSION The numerous research efforts in recent years have led to a rapid change in our understanding of the application of DNA methylation for chronological age prediction, which is now on the way to implementation and validation. Knowledge of the various aspects leads to a better understanding and allows a more informed interpretation of DNAm quantification results, as well as the obtained results by the age prediction tools.
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Affiliation(s)
- Jana Naue
- Institute of Forensic Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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15
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Shao Z, Han Y, Zhou D. Optimized bisulfite sequencing analysis reveals the lack of 5-methylcytosine in mammalian mitochondrial DNA. BMC Genomics 2023; 24:439. [PMID: 37542258 PMCID: PMC10403921 DOI: 10.1186/s12864-023-09541-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 07/27/2023] [Indexed: 08/06/2023] Open
Abstract
BACKGROUND DNA methylation is one of the best characterized epigenetic modifications in the mammalian nuclear genome and is known to play a significant role in various biological processes. Nonetheless, the presence of 5-methylcytosine (5mC) in mitochondrial DNA remains controversial, as data ranging from the lack of 5mC to very extensive 5mC have been reported. RESULTS By conducting comprehensive bioinformatic analyses of both published and our own data, we reveal that previous observations of extensive and strand-biased mtDNA-5mC are likely artifacts due to a combination of factors including inefficient bisulfite conversion, extremely low sequencing reads in the L strand, and interference from nuclear mitochondrial DNA sequences (NUMTs). To reduce false positive mtDNA-5mC signals, we establish an optimized procedure for library preparation and data analysis of bisulfite sequencing. Leveraging our modified workflow, we demonstrate an even distribution of 5mC signals across the mtDNA and an average methylation level ranging from 0.19% to 0.67% in both cell lines and primary cells, which is indistinguishable from the background noise. CONCLUSIONS We have developed a framework for analyzing mtDNA-5mC through bisulfite sequencing, which enables us to present multiple lines of evidence for the lack of extensive 5mC in mammalian mtDNA. We assert that the data available to date do not support the reported presence of mtDNA-5mC.
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Affiliation(s)
- Zhenyu Shao
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Yang Han
- Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University & Chinese Academy of Medical Sciences (RU069), Shanghai, 200032, China
| | - Dan Zhou
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University & Chinese Academy of Medical Sciences (RU069), Shanghai, 201399, China.
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16
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Mongelli A, Mengozzi A, Geiger M, Gorica E, Mohammed SA, Paneni F, Ruschitzka F, Costantino S. Mitochondrial epigenetics in aging and cardiovascular diseases. Front Cardiovasc Med 2023; 10:1204483. [PMID: 37522089 PMCID: PMC10382027 DOI: 10.3389/fcvm.2023.1204483] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/29/2023] [Indexed: 08/01/2023] Open
Abstract
Mitochondria are cellular organelles which generate adenosine triphosphate (ATP) molecules for the maintenance of cellular energy through the oxidative phosphorylation. They also regulate a variety of cellular processes including apoptosis and metabolism. Of interest, the inner part of mitochondria-the mitochondrial matrix-contains a circular molecule of DNA (mtDNA) characterised by its own transcriptional machinery. As with genomic DNA, mtDNA may also undergo nucleotide mutations that have been shown to be responsible for mitochondrial dysfunction. During physiological aging, the mitochondrial membrane potential declines and associates with enhanced mitophagy to avoid the accumulation of damaged organelles. Moreover, if the dysfunctional mitochondria are not properly cleared, this could lead to cellular dysfunction and subsequent development of several comorbidities such as cardiovascular diseases (CVDs), diabetes, respiratory and cardiovascular diseases as well as inflammatory disorders and psychiatric diseases. As reported for genomic DNA, mtDNA is also amenable to chemical modifications, namely DNA methylation. Changes in mtDNA methylation have shown to be associated with altered transcriptional programs and mitochondrial dysfunction during aging. In addition, other epigenetic signals have been observed in mitochondria, in particular the interaction between mtDNA methylation and non-coding RNAs. Mitoepigenetic modifications are also involved in the pathogenesis of CVDs where oxygen chain disruption, mitochondrial fission, and ROS formation alter cardiac energy metabolism leading to hypertrophy, hypertension, heart failure and ischemia/reperfusion injury. In the present review, we summarize current evidence on the growing importance of epigenetic changes as modulator of mitochondrial function in aging. A better understanding of the mitochondrial epigenetic landscape may pave the way for personalized therapies to prevent age-related diseases.
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Affiliation(s)
- Alessia Mongelli
- Center for Translational and Experimental Cardiology (CTEC), Department of Cardiology, Zurich University Hospital and University of Zürich, Zurich, Switzerland
| | - Alessandro Mengozzi
- Center for Translational and Experimental Cardiology (CTEC), Department of Cardiology, Zurich University Hospital and University of Zürich, Zurich, Switzerland
| | - Martin Geiger
- Center for Translational and Experimental Cardiology (CTEC), Department of Cardiology, Zurich University Hospital and University of Zürich, Zurich, Switzerland
| | - Era Gorica
- Center for Translational and Experimental Cardiology (CTEC), Department of Cardiology, Zurich University Hospital and University of Zürich, Zurich, Switzerland
| | - Shafeeq Ahmed Mohammed
- Center for Translational and Experimental Cardiology (CTEC), Department of Cardiology, Zurich University Hospital and University of Zürich, Zurich, Switzerland
| | - Francesco Paneni
- Center for Translational and Experimental Cardiology (CTEC), Department of Cardiology, Zurich University Hospital and University of Zürich, Zurich, Switzerland
- Department of Cardiology, University Heart Center, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Frank Ruschitzka
- Center for Translational and Experimental Cardiology (CTEC), Department of Cardiology, Zurich University Hospital and University of Zürich, Zurich, Switzerland
- Department of Cardiology, University Heart Center, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sarah Costantino
- Center for Translational and Experimental Cardiology (CTEC), Department of Cardiology, Zurich University Hospital and University of Zürich, Zurich, Switzerland
- Department of Cardiology, University Heart Center, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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17
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Zhang W, Xiao D, Mao Q, Xia H. Role of neuroinflammation in neurodegeneration development. Signal Transduct Target Ther 2023; 8:267. [PMID: 37433768 PMCID: PMC10336149 DOI: 10.1038/s41392-023-01486-5] [Citation(s) in RCA: 446] [Impact Index Per Article: 223.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 03/22/2023] [Accepted: 05/07/2023] [Indexed: 07/13/2023] Open
Abstract
Studies in neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease and Amyotrophic lateral sclerosis, Huntington's disease, and so on, have suggested that inflammation is not only a result of neurodegeneration but also a crucial player in this process. Protein aggregates which are very common pathological phenomenon in neurodegeneration can induce neuroinflammation which further aggravates protein aggregation and neurodegeneration. Actually, inflammation even happens earlier than protein aggregation. Neuroinflammation induced by genetic variations in CNS cells or by peripheral immune cells may induce protein deposition in some susceptible population. Numerous signaling pathways and a range of CNS cells have been suggested to be involved in the pathogenesis of neurodegeneration, although they are still far from being completely understood. Due to the limited success of traditional treatment methods, blocking or enhancing inflammatory signaling pathways involved in neurodegeneration are considered to be promising strategies for the therapy of neurodegenerative diseases, and many of them have got exciting results in animal models or clinical trials. Some of them, although very few, have been approved by FDA for clinical usage. Here we comprehensively review the factors affecting neuroinflammation and the major inflammatory signaling pathways involved in the pathogenicity of neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, and Amyotrophic lateral sclerosis. We also summarize the current strategies, both in animal models and in the clinic, for the treatment of neurodegenerative diseases.
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Affiliation(s)
- Weifeng Zhang
- Laboratory of Gene Therapy, Department of Biochemistry, College of Life Sciences, Shaanxi Normal University, 199 South Chang'an Road, Xi'an, 710062, P.R. China
| | - Dan Xiao
- The State Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Air Force Medical University, No. 169 Changle West Road, Xi'an, 710032, P.R. China
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Air Force Medical University, No. 169 Changle West Road, Xi'an, 710032, China
| | - Qinwen Mao
- Department of Pathology, University of Utah, Huntsman Cancer Institute, 2000 Circle of Hope Drive, Salt Lake City, UT, 84112, USA
| | - Haibin Xia
- Laboratory of Gene Therapy, Department of Biochemistry, College of Life Sciences, Shaanxi Normal University, 199 South Chang'an Road, Xi'an, 710062, P.R. China.
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Ding B, Zhang X, Wan Z, Tian F, Ling J, Tan J, Peng X. Characterization of Mitochondrial DNA Methylation of Alzheimer's Disease in Plasma Cell-Free DNA. Diagnostics (Basel) 2023; 13:2351. [PMID: 37510095 PMCID: PMC10378411 DOI: 10.3390/diagnostics13142351] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/29/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Noninvasive diagnosis of Alzheimer's disease (AD) is important for patients. Significant differences in the methylation of mitochondrial DNA (mtDNA) were found in AD brain tissue. Cell-free DNA (cfDNA) is a noninvasive and economical diagnostic tool. We aimed to characterize mtDNA methylation alterations in the plasma cfDNA of 31 AD patients and 26 age- and sex-matched cognitively normal control subjects. We found that the mtDNA methylation patterns differed between AD patients and control subjects. The mtDNA was predominantly hypomethylated in the plasma cfDNA of AD patients. The hypomethylation sites or regions were mainly located in mt-rRNA, mt-tRNA, and D-Loop regions. The hypomethylation of the D-Loop region in plasma cfDNA of AD patients was consistent with that in previous studies. This study presents evidence that hypomethylation in the non-protein coding region of mtDNA may contribute to the pathogenesis of AD and potential application for the diagnosis of AD.
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Affiliation(s)
- Binrong Ding
- Department of Geriatrics, The Third Xiangya Hospital, Central South University, Changsha 410000, China
| | - Xuewei Zhang
- Health Management Center, Xiangya Hospital, Central South University, Changsha 410000, China
| | - Zhengqing Wan
- Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Feng Tian
- The 8 Ward, The Ninth Hospital of Changsha, Changsha 410000, China
| | - Jie Ling
- Medical Functional Experiment Center, School of Basic Medicine, Central South University, Changsha 410000, China
| | - Jieqiong Tan
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410000, China
- Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha 410000, China
- Hunan Key Laboratory of Molecular Precision Medicine, Changsha 410000, China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha 410000, China
| | - Xiaoqing Peng
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410000, China
- Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha 410000, China
- Hunan Key Laboratory of Molecular Precision Medicine, Changsha 410000, China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha 410000, China
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19
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Kaur N, Nayakoti S, Brock N, Halford NG. Uncovering plant epigenetics: new insights into cytosine methylation in rye genomes. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:3395-3398. [PMID: 37369102 DOI: 10.1093/jxb/erad144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
This article comments on:
Kalinka A, Starczak M, Gackowski D, Stępień E, Achrem M. 2023. Global DNA 5-hydroxymethylcytosine level and its chromosomal distribution in four rye species. Journal of Experimental Botany 74, 3488–3502.
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Affiliation(s)
- Navneet Kaur
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | | | - Natasha Brock
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
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Grady CI, Walsh LM, Heiss JD. Mitoepigenetics and gliomas: epigenetic alterations to mitochondrial DNA and nuclear DNA alter mtDNA expression and contribute to glioma pathogenicity. Front Neurol 2023; 14:1154753. [PMID: 37332990 PMCID: PMC10270738 DOI: 10.3389/fneur.2023.1154753] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/10/2023] [Indexed: 06/20/2023] Open
Abstract
Epigenetic mechanisms allow cells to fine-tune gene expression in response to environmental stimuli. For decades, it has been known that mitochondria have genetic material. Still, only recently have studies shown that epigenetic factors regulate mitochondrial DNA (mtDNA) gene expression. Mitochondria regulate cellular proliferation, apoptosis, and energy metabolism, all critical areas of dysfunction in gliomas. Methylation of mtDNA, alterations in mtDNA packaging via mitochondrial transcription factor A (TFAM), and regulation of mtDNA transcription via the micro-RNAs (mir 23-b) and long noncoding RNAs [RNA mitochondrial RNA processing (RMRP)] have all been identified as contributing to glioma pathogenicity. Developing new interventions interfering with these pathways may improve glioma therapy.
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Affiliation(s)
- Clare I. Grady
- Neurosurgery, MedStar Georgetown University Hospital, Washington, DC, United States
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health, Bethesda, MD, United States
| | - Lisa M. Walsh
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health, Bethesda, MD, United States
| | - John D. Heiss
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health, Bethesda, MD, United States
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21
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Mposhi A, Cortés-Mancera F, Heegsma J, de Meijer VE, van de Sluis B, Sydor S, Bechmann LP, Theys C, de Rijk P, De Pooter T, Vanden Berghe W, İnce İA, Faber KN, Rots MG. Mitochondrial DNA methylation in metabolic associated fatty liver disease. Front Nutr 2023; 10:964337. [PMID: 37305089 PMCID: PMC10249072 DOI: 10.3389/fnut.2023.964337] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 02/07/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction Hepatic lipid accumulation and mitochondrial dysfunction are hallmarks of metabolic associated fatty liver disease (MAFLD), yet molecular parameters underlying MAFLD progression are not well understood. Differential methylation within the mitochondrial DNA (mtDNA) has been suggested to be associated with dysfunctional mitochondria, also during progression to Metabolic Steatohepatitis (MeSH). This study further investigates whether mtDNA methylation is associated with hepatic lipid accumulation and MAFLD. Methods HepG2 cells were constructed to stably express mitochondria-targeted viral and prokaryotic cytosine DNA methyltransferases (mtM.CviPI or mtM.SssI for GpC or CpG methylation, respectively). A catalytically inactive variant (mtM.CviPI-Mut) was constructed as a control. Mouse and human patients' samples were also investigated. mtDNA methylation was assessed by pyro- or nanopore sequencing. Results and discussion Differentially induced mtDNA hypermethylation impaired mitochondrial gene expression and metabolic activity in HepG2-mtM.CviPI and HepG2-mtM.SssI cells and was associated with increased lipid accumulation, when compared to the controls. To test whether lipid accumulation causes mtDNA methylation, HepG2 cells were subjected to 1 or 2 weeks of fatty acid treatment, but no clear differences in mtDNA methylation were detected. In contrast, hepatic Nd6 mitochondrial gene body cytosine methylation and Nd6 gene expression were increased in mice fed a high-fat high cholesterol diet (HFC for 6 or 20 weeks), when compared to controls, while mtDNA content was unchanged. For patients with simple steatosis, a higher ND6 methylation was confirmed using Methylation Specific PCR, but no additional distinctive cytosines could be identified using pyrosequencing. This study warrants further investigation into a role for mtDNA methylation in promoting mitochondrial dysfunction and impaired lipid metabolism in MAFLD.
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Affiliation(s)
- Archibold Mposhi
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Fabian Cortés-Mancera
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Departamento de Ciencias Aplicadas, Instituto Tecnológico Metropolitano, Medellín, Colombia
| | - Janette Heegsma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Vincent E. de Meijer
- Department of Surgery, Division of Hepato-Pancreato-Biliary Surgery and Liver Transplantation, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Bart van de Sluis
- Section of Molecular Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Svenja Sydor
- Department of Internal Medicine, University Hospital Knappschaftskrankenhaus, Bochum, Germany
- Ruhr-University Bochum, Bochum, Germany
| | - Lars P. Bechmann
- Department of Internal Medicine, University Hospital Knappschaftskrankenhaus, Bochum, Germany
- Ruhr-University Bochum, Bochum, Germany
| | - Claudia Theys
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Peter de Rijk
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Neuromics Support Facility, VIB-UAntwerp Center for Molecular Neurology, University of Antwerp, Antwerp, Belgium
| | - Tim De Pooter
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Neuromics Support Facility, VIB-UAntwerp Center for Molecular Neurology, University of Antwerp, Antwerp, Belgium
| | - Wim Vanden Berghe
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - İkbal Agah İnce
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Medical Microbiology, School of Medicine, Acıbadem Mehmet Ali Aydınlar University, Istanbul, Türkiye
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Marianne G. Rots
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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22
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Low HC, Chilian WM, Ratnam W, Karupaiah T, Md Noh MF, Mansor F, Ng ZX, Pung YF. Changes in Mitochondrial Epigenome in Type 2 Diabetes Mellitus. Br J Biomed Sci 2023; 80:10884. [PMID: 36866104 PMCID: PMC9970885 DOI: 10.3389/bjbs.2023.10884] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 01/30/2023] [Indexed: 02/16/2023]
Abstract
Type 2 Diabetes Mellitus is a major chronic metabolic disorder in public health. Due to mitochondria's indispensable role in the body, its dysfunction has been implicated in the development and progression of multiple diseases, including Type 2 Diabetes mellitus. Thus, factors that can regulate mitochondrial function, like mtDNA methylation, are of significant interest in managing T2DM. In this paper, the overview of epigenetics and the mechanism of nuclear and mitochondrial DNA methylation were briefly discussed, followed by other mitochondrial epigenetics. Subsequently, the association between mtDNA methylation with T2DM and the challenges of mtDNA methylation studies were also reviewed. This review will aid in understanding the impact of mtDNA methylation on T2DM and future advancements in T2DM treatment.
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Affiliation(s)
- Hui Ching Low
- Division of Biomedical Science, Faculty of Science and Engineering, University of Nottingham Malaysia, Semenyih, Selangor, Malaysia
| | - William M. Chilian
- Integrative Medical Sciences, Northeast Ohio Medical University, Rootstown Township, OH, United States
| | - Wickneswari Ratnam
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Tilakavati Karupaiah
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor’s University Lakeside Campus, Subang Jaya, Selangor, Malaysia
| | - Mohd Fairulnizal Md Noh
- Nutrition, Metabolism and Cardiovascular Research Centre, Institute for Medical Research, National Institute of Health, Setia Alam, Shah Alam, Malaysia
| | - Fazliana Mansor
- Nutrition, Metabolism and Cardiovascular Research Centre, Institute for Medical Research, National Institute of Health, Setia Alam, Shah Alam, Malaysia
| | - Zhi Xiang Ng
- School of Biosciences, Faculty of Science and Engineering, University of Nottingham Malaysia, Semenyih, Selangor, Malaysia
| | - Yuh Fen Pung
- Division of Biomedical Science, Faculty of Science and Engineering, University of Nottingham Malaysia, Semenyih, Selangor, Malaysia,*Correspondence: Yuh Fen Pung,
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23
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High-fructose corn syrup intake increases hepatic mitochondrial DNA copy number and methylation in adolescent rats. Nutr Res 2023; 110:57-65. [PMID: 36682228 DOI: 10.1016/j.nutres.2022.12.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 12/14/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022]
Abstract
High-fructose corn syrup (HFCS) is consumed worldwide. However, it has been demonstrated that an increased intake of sweetened beverages, including those sweetened using fructose, is associated with the development of childhood obesity. It is unknown why the negative effects of fructose are stronger in young persons than in elderly individuals. In recent years, mitochondria have been identified as 1 of the targets of the negative effects of fructose; they possess their own genome called mitochondrial DNA (mtDNA), which encodes genes involved in metabolic functions. We hypothesized that HFCS intake affects mtDNA in the livers of rats, and that the intensity of these effects is age-dependent. The experimental period was divided into 3 parts: childhood and adolescence (postnatal day [PD] 21-60), young adulthood (PD61-100), and adulthood (PD101-140). Rats in the different age groups were assigned to receive either water (control group [CONT]) or a 20% HFCS solution (HFCS). The hepatic mtDNA copy number of the HFCS group was higher than that of the CONT group in childhood and adolescence. In addition, the mtDNA methylation level was increased in the HFCS group in the same experimental period. No significant differences were observed between the CONT and HFCS groups during the other experimental periods. We demonstrated that HFCS has the strongest effect on mtDNA during childhood and adolescence, suggesting a need to analyze the HFCS intake of young people.
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24
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Dragoni F, Garau J, Orcesi S, Varesio C, Bordoni M, Scarian E, Di Gerlando R, Fazzi E, Battini R, Gjurgjaj A, Rizzo B, Pansarasa O, Gagliardi S. Comparison between D-loop methylation and mtDNA copy number in patients with Aicardi-Goutières Syndrome. Front Endocrinol (Lausanne) 2023; 14:1152237. [PMID: 36998476 PMCID: PMC10043473 DOI: 10.3389/fendo.2023.1152237] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 02/28/2023] [Indexed: 03/16/2023] Open
Abstract
INTRODUCTION Aicardi-Goutières Syndrome (AGS) is a rare encephalopathy with early onset that can be transmitted in both dominant and recessive forms. Its phenotypic covers a wide range of neurological and extraneurological symptoms. Nine genes that are all involved in nucleic acids (NAs) metabolism or signaling have so far been linked to the AGS phenotype. Recently, a link between autoimmune or neurodegenerative conditions and mitochondrial dysfunctions has been found. As part of the intricate system of epigenetic control, the mtDNA goes through various alterations. The displacement (D-loop) region represents one of the most methylated sites in the mtDNA. The term "mitoepigenetics" has been introduced as a result of increasing data suggesting that epigenetic processes may play a critical role in the control of mtDNA transcription and replication. Since we showed that RNASEH2B and RNASEH2A-mutated Lymphoblastoid Cell Lines (LCLs) derived from AGS patients had mitochondrial alterations, highlighting changes in the mtDNA content, the main objective of this study was to examine any potential methylation changes in the D-loop regulatory region of mitochondria and their relationship to the mtDNA copy number in peripheral blood cells of AGS patients with mutations in various AGS genes and healthy controls. MATERIALS AND METHODS We collected blood samples from 25 AGS patients and we performed RT-qPCR to assess the mtDNA copy number and pyrosequencing to measure DNA methylation levels in the D-loop region. RESULTS Comparing AGS patients to healthy controls, D-loop methylation levels and mtDNA copy number increased significantly. We also observed that in AGS patients, the mtDNA copy number increased with age at sampling, but not the D-loop methylation levels, and there was no relationship between sex and mtDNA copy number. In addition, the D-loop methylation levels and mtDNA copy number in the AGS group showed a non-statistically significant positive relation. CONCLUSION These findings, which contradict the evidence for an inverse relationship between D-loop methylation levels and mtDNA copy number, show that AGS patients have higher D-loop methylation levels than healthy control subjects. Additional research is needed to identify the function of these features in the etiology and course of AGS.
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Affiliation(s)
- Francesca Dragoni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
- Molecular Biology and Transcriptomics Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Jessica Garau
- Neurogenetics Research Centre, IRCCS Mondino Foundation, Pavia, Italy
| | - Simona Orcesi
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Department of Child Neurology and Psychiatry, IRCCS Mondino Foundation, Pavia, Italy
| | - Costanza Varesio
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Department of Child Neurology and Psychiatry, IRCCS Mondino Foundation, Pavia, Italy
| | - Matteo Bordoni
- Cellular Model and Neuroepigenetics Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Eveljn Scarian
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Cellular Model and Neuroepigenetics Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Rosalinda Di Gerlando
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
- Molecular Biology and Transcriptomics Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Elisa Fazzi
- Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
- Unit of Child Neurology and Psychiatry, ASST Spedali Civili, Brescia, Italy
| | - Roberta Battini
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Pisa, Italy
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Altea Gjurgjaj
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Bartolo Rizzo
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Orietta Pansarasa
- Cellular Model and Neuroepigenetics Unit, IRCCS Mondino Foundation, Pavia, Italy
- *Correspondence: Orietta Pansarasa,
| | - Stella Gagliardi
- Molecular Biology and Transcriptomics Unit, IRCCS Mondino Foundation, Pavia, Italy
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25
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Wu Y, Zou H. Research Progress on Mitochondrial Dysfunction in Diabetic Retinopathy. Antioxidants (Basel) 2022; 11:2250. [PMID: 36421435 PMCID: PMC9686704 DOI: 10.3390/antiox11112250] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/07/2022] [Accepted: 11/12/2022] [Indexed: 09/07/2023] Open
Abstract
Diabetic Retinopathy (DR) is one of the most important microvascular complications of diabetes mellitus, which can lead to blindness in severe cases. Mitochondria are energy-producing organelles in eukaryotic cells, which participate in metabolism and signal transduction, and regulate cell growth, differentiation, aging, and death. Metabolic changes of retinal cells and epigenetic changes of mitochondria-related genes under high glucose can lead to mitochondrial dysfunction and induce mitochondrial pathway apoptosis. In addition, mitophagy and mitochondrial dynamics also change adaptively. These mechanisms may be related to the occurrence and progression of DR, and also provide valuable clues for the prevention and treatment of DR. This article reviews the mechanism of DR induced by mitochondrial dysfunction, and the prospects for related treatment.
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Affiliation(s)
- Yiwei Wu
- Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Haidong Zou
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
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26
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Marmolejo-Garza A, Medeiros-Furquim T, Rao R, Eggen BJL, Boddeke E, Dolga AM. Transcriptomic and epigenomic landscapes of Alzheimer's disease evidence mitochondrial-related pathways. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119326. [PMID: 35839870 DOI: 10.1016/j.bbamcr.2022.119326] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 02/06/2023]
Abstract
Alzheimers disease (AD) is the main cause of dementia and it is defined by cognitive decline coupled to extracellular deposit of amyloid-beta protein and intracellular hyperphosphorylation of tau protein. Historically, efforts to target such hallmarks have failed in numerous clinical trials. In addition to these hallmark-targeted approaches, several clinical trials focus on other AD pathological processes, such as inflammation, mitochondrial dysfunction, and oxidative stress. Mitochondria and mitochondrial-related mechanisms have become an attractive target for disease-modifying strategies, as mitochondrial dysfunction prior to clinical onset has been widely described in AD patients and AD animal models. Mitochondrial function relies on both the nuclear and mitochondrial genome. Findings from omics technologies have shed light on AD pathophysiology at different levels (e.g., epigenome, transcriptome and proteome). Most of these studies have focused on the nuclear-encoded components. The first part of this review provides an updated overview of the mechanisms that regulate mitochondrial gene expression and function. The second part of this review focuses on evidence of mitochondrial dysfunction in AD. We have focused on published findings and datasets that study AD. We analyzed published data and provide examples for mitochondrial-related pathways. These pathways are strikingly dysregulated in AD neurons and glia in sex-, cell- and disease stage-specific manners. Analysis of mitochondrial omics data highlights the involvement of mitochondria in AD, providing a rationale for further disease modeling and drug targeting.
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Affiliation(s)
- Alejandro Marmolejo-Garza
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, the Netherlands; Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, Faculty of Medical Sciences, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Tiago Medeiros-Furquim
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, the Netherlands; Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, Faculty of Medical Sciences, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ramya Rao
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, the Netherlands
| | - Bart J L Eggen
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, Faculty of Medical Sciences, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Erik Boddeke
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, Faculty of Medical Sciences, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen N, Denmark.
| | - Amalia M Dolga
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, the Netherlands.
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27
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Targeted Mitochondrial Epigenetics: A New Direction in Alzheimer’s Disease Treatment. Int J Mol Sci 2022; 23:ijms23179703. [PMID: 36077101 PMCID: PMC9456144 DOI: 10.3390/ijms23179703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/19/2022] [Accepted: 08/25/2022] [Indexed: 11/23/2022] Open
Abstract
Mitochondrial epigenetic alterations are closely related to Alzheimer’s disease (AD), which is described in this review. Reports of the alteration of mitochondrial DNA (mtDNA) methylation in AD demonstrate that the disruption of the dynamic balance of mtDNA methylation and demethylation leads to damage to the mitochondrial electron transport chain and the obstruction of mitochondrial biogenesis, which is the most studied mitochondrial epigenetic change. Mitochondrial noncoding RNA modifications and the post-translational modification of mitochondrial nucleoproteins have been observed in neurodegenerative diseases and related diseases that increase the risk of AD. Although there are still relatively few mitochondrial noncoding RNA modifications and mitochondrial nuclear protein post-translational modifications reported in AD, we have reason to believe that these mitochondrial epigenetic modifications also play an important role in the AD process. This review provides a new research direction for the AD mechanism, starting from mitochondrial epigenetics. Further, this review summarizes therapeutic approaches to targeted mitochondrial epigenetics, which is the first systematic summary of therapeutic approaches in the field, including folic acid supplementation, mitochondrial-targeting antioxidants, and targeted ubiquitin-specific proteases, providing a reference for therapeutic targets for AD.
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28
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Mitochondrial genome undergoes de novo DNA methylation that protects mtDNA against oxidative damage during the peri-implantation window. Proc Natl Acad Sci U S A 2022; 119:e2201168119. [PMID: 35858425 PMCID: PMC9335330 DOI: 10.1073/pnas.2201168119] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Mitochondrial remodeling during the peri-implantation stage is the hallmark event essential for normal embryogenesis. Among the changes, enhanced oxidative phosphorylation is critical for supporting high energy demands of postimplantation embryos, but increases mitochondrial oxidative stress, which in turn threatens mitochondrial DNA (mtDNA) stability. However, how mitochondria protect their own histone-lacking mtDNA, during this stage remains unclear. Concurrently, the mitochondrial genome gain DNA methylation by this stage. Its spatiotemporal coincidence with enhanced mitochondrial stress led us to ask if mtDNA methylation has a role in maintaining mitochondrial genome stability. Herein, we report that mitochondrial genome undergoes de novo mtDNA methylation that can protect mtDNA against enhanced oxidative damage during the peri-implantation window. Mitochondrial genome gains extensive mtDNA methylation during transition from blastocysts to postimplantation embryos, thus establishing relatively hypermethylated mtDNA from hypomethylated state in blastocysts. Mechanistic study revealed that DNA methyltransferase 3A (DNMT3A) and DNMT3B enter mitochondria during this process and bind to mtDNA, via their unique mitochondrial targeting sequences. Importantly, loss- and gain-of-function analyses indicated that DNMT3A and DNMT3B are responsible for catalyzing de novo mtDNA methylation, in a synergistic manner. Finally, we proved, in vivo and in vitro, that increased mtDNA methylation functions to protect mitochondrial genome against mtDNA damage induced by increased mitochondrial oxidative stress. Together, we reveal mtDNA methylation dynamics and its underlying mechanism during the critical developmental window. We also provide the functional link between mitochondrial epigenetic remodeling and metabolic changes, which reveals a role for nuclear-mitochondrial crosstalk in establishing mitoepigenetics and maintaining mitochondrial homeostasis.
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29
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Huang CH, Chang MC, Lai YC, Lin CY, Hsu CH, Tseng BY, Hsiao CK, Lu TP, Yu SL, Hsieh ST, Chen WJ. Mitochondrial DNA methylation profiling of the human prefrontal cortex and nucleus accumbens: correlations with aging and drug use. Clin Epigenetics 2022; 14:79. [PMID: 35752846 PMCID: PMC9233363 DOI: 10.1186/s13148-022-01300-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/20/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Despite the brain's high demand for energy, research on its epigenetics focuses on nuclear methylation, and much of the mitochondrial DNA methylation remains seldom investigated. With a focus on the nucleus accumbens (NAcc) and the prefrontal cortex (PFC), we aimed to identify the mitochondrial methylation signatures for (1) distinguishing the two brain areas, (2) correlating with aging, and (3) reflecting the influence of illicit drugs on the brain. RESULT We collected the brain tissue in the NAcc and the PFC from the deceased individuals without (n = 39) and with (n = 14) drug use and used whole-genome bisulfite sequencing to cover cytosine sites in the mitochondrial genome. We first detected differential methylations between the NAcc and the PFC in the nonusers group (P = 3.89 × 10-9). These function-related methylation differences diminished in the drug use group due to the selective alteration in the NAcc. Then, we found the correlation between the methylation levels and the chronological ages in the nonusers group (R2 = 0.34 in the NAcc and 0.37 in the PFC). The epigenetic clocks in illicit drug users, especially in the ketamine users, were accelerated in both brain regions by comparison with the nonusers. Finally, we summarized the effect of the illicit drugs on the methylation, which could significantly differentiate the drug users from the nonusers (AUC = 0.88 in the NAcc, AUC = 0.94 in the PFC). CONCLUSION The mitochondrial methylations were different between different brain areas, generally accumulated with aging, and sensitive to the effects of illicit drugs. We believed this is the first report to elucidate comprehensively the importance of mitochondrial DNA methylation in human brain.
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Affiliation(s)
- Chia-Hung Huang
- Forensic Biology Division, Institute of Forensic Medicine, Ministry of Justice, New Taipei City, Taiwan.,Forensic Pathology Division, Institute of Forensic Medicine, Ministry of Justice, New Taipei City, Taiwan.,Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Man-Chen Chang
- Forensic Biology Division, Institute of Forensic Medicine, Ministry of Justice, New Taipei City, Taiwan
| | - Yung-Chun Lai
- Forensic Biology Division, Institute of Forensic Medicine, Ministry of Justice, New Taipei City, Taiwan
| | - Chun-Yen Lin
- Forensic Biology Division, Institute of Forensic Medicine, Ministry of Justice, New Taipei City, Taiwan
| | - Cho-Hsien Hsu
- Forensic Pathology Division, Institute of Forensic Medicine, Ministry of Justice, New Taipei City, Taiwan
| | - Bo-Yuan Tseng
- Forensic Pathology Division, Institute of Forensic Medicine, Ministry of Justice, New Taipei City, Taiwan
| | - Chuhsing Kate Hsiao
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Tzu-Pin Lu
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Sung-Liang Yu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Sung-Tsang Hsieh
- Department of Anatomy and Cell Biology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Neurology, College of Medicine and National Taiwan University Hospital, National Taiwan University, Taipei, Taiwan
| | - Wei J Chen
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan. .,Department of Psychiatry, College of Medicine and National Taiwan University Hospital, National Taiwan University, Taipei, Taiwan. .,Center for Neuropsychiatric Research, National Health Research Institutes, Zhunan, Miaoli County, Taiwan.
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30
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Abstract
In the course of its short history, mitochondrial DNA (mtDNA) has made a long journey from obscurity to the forefront of research on major biological processes. mtDNA alterations have been found in all major disease groups, and their significance remains the subject of intense research. Despite remarkable progress, our understanding of the major aspects of mtDNA biology, such as its replication, damage, repair, transcription, maintenance, etc., is frustratingly limited. The path to better understanding mtDNA and its role in cells, however, remains torturous and not without errors, which sometimes leave a long trail of controversy behind them. This review aims to provide a brief summary of our current knowledge of mtDNA and highlight some of the controversies that require attention from the mitochondrial research community.
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Affiliation(s)
- Inna Shokolenko
- Department of Biomedical Sciences, Pat Capps Covey College of Allied Health Professions, University of South Alabama, Mobile, AL 36688, USA
| | - Mikhail Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA
- Correspondence:
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31
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Bordoni L, Malinowska AM, Petracci I, Szwengiel A, Gabbianelli R, Chmurzynska A. Diet, Trimethylamine Metabolism, and Mitochondrial DNA: An Observational Study. Mol Nutr Food Res 2022; 66:e2200003. [PMID: 35490412 DOI: 10.1002/mnfr.202200003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 04/14/2022] [Indexed: 12/11/2022]
Abstract
SCOPE Mitochondrial DNA copy number (mtDNAcn) and its methylation level in the D-loop area have been correlated with metabolic health and are suggested to vary in response to environmental stimuli, including diet. Circulating levels of trimethylamine-n-oxide (TMAO), which is an oxidative derivative of the trimethylamine (TMA) produced by the gut microbiome from dietary precursors, have been associated with chronic diseases and are suggested to have an impact on mitochondrial dynamics. This study is aimed to investigate the relationship between diet, TMA, TMAO, and mtDNAcn, as well as DNA methylation. METHODS AND RESULTS Two hundred subjects with extreme (healthy and unhealthy) dietary patterns are recruited. Dietary records are collected to assess their nutrient intake and diets' quality (Healthy Eating Index). Blood levels of TMA and TMAO, circulating levels of TMA precursors and their dietary intakes are measured. MtDNAcn, nuclear DNA methylation long interspersed nuclear element 1 (LINE-1), and strand-specific D-loop methylation levels are assessed. There is no association between dietary patterns and mtDNAcn. The TMAO/TMA ratio is negatively correlated with d-loop methylation levels but positively with mtDNAcn. CONCLUSIONS These findings suggest a potential association between TMA metabolism and mitochondrial dynamics (and mtDNA), indicating a new avenue for further research.
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Affiliation(s)
- Laura Bordoni
- Unit of Molecular Biology and Nutrigenomics, School of Pharmacy, University of Camerino, Camerino, 62032, MC, Italy
| | - Anna M Malinowska
- Department of Human Nutrition and Dietetics, Poznań University of Life Sciences, Poznań, 60-624, Poland
| | - Irene Petracci
- School of Advanced Studies, University of Camerino, Camerino, 62032, MC, Italy
| | - Artur Szwengiel
- Department of Food Technology of Plant Origin, Poznań University of Life Sciences, Poznań, 60-624, Poland
| | - Rosita Gabbianelli
- Unit of Molecular Biology and Nutrigenomics, School of Pharmacy, University of Camerino, Camerino, 62032, MC, Italy
| | - Agata Chmurzynska
- Department of Human Nutrition and Dietetics, Poznań University of Life Sciences, Poznań, 60-624, Poland
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32
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Arbeithuber B, Cremona MA, Hester J, Barrett A, Higgins B, Anthony K, Chiaromonte F, Diaz FJ, Makova KD. Advanced age increases frequencies of de novo mitochondrial mutations in macaque oocytes and somatic tissues. Proc Natl Acad Sci U S A 2022; 119:e2118740119. [PMID: 35394879 PMCID: PMC9169796 DOI: 10.1073/pnas.2118740119] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/25/2022] [Indexed: 12/18/2022] Open
Abstract
Mutations in mitochondrial DNA (mtDNA) contribute to multiple diseases. However, how new mtDNA mutations arise and accumulate with age remains understudied because of the high error rates of current sequencing technologies. Duplex sequencing reduces error rates by several orders of magnitude via independently tagging and analyzing each of the two template DNA strands. Here, using duplex sequencing, we obtained high-quality mtDNA sequences for somatic tissues (liver and skeletal muscle) and single oocytes of 30 unrelated rhesus macaques, from 1 to 23 y of age. Sequencing single oocytes minimized effects of natural selection on germline mutations. In total, we identified 17,637 tissue-specific de novo mutations. Their frequency increased ∼3.5-fold in liver and ∼2.8-fold in muscle over the ∼20 y assessed. Mutation frequency in oocytes increased ∼2.5-fold until the age of 9 y, but did not increase after that, suggesting that oocytes of older animals maintain the quality of their mtDNA. We found the light-strand origin of replication (OriL) to be a hotspot for mutation accumulation with aging in liver. Indeed, the 33-nucleotide-long OriL harbored 12 variant hotspots, 10 of which likely disrupt its hairpin structure and affect replication efficiency. Moreover, in somatic tissues, protein-coding variants were subject to positive selection (potentially mitigating toxic effects of mitochondrial activity), the strength of which increased with the number of macaques harboring variants. Our work illuminates the origins and accumulation of somatic and germline mtDNA mutations with aging in primates and has implications for delayed reproduction in modern human societies.
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Affiliation(s)
- Barbara Arbeithuber
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Experimental Gynaecology, Obstetrics and Gynaecological Endocrinology, Kepler University Hospital Linz, Johannes Kepler University Linz, 4020 Linz, Austria
| | - Marzia A. Cremona
- Department of Operations and Decision Systems, Université Laval, Québec, QC G1V0A6, Canada
- Population Health and Optimal Health Practices, CHU de Québec - Université Laval Research Center, Québec, QC G1V4G2, Canada
- Center for Medical Genomics, The Pennsylvania State University, University Park, PA 16802
| | - James Hester
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802
| | - Alison Barrett
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
| | - Bonnie Higgins
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
| | - Kate Anthony
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
| | - Francesca Chiaromonte
- Center for Medical Genomics, The Pennsylvania State University, University Park, PA 16802
- Department of Statistics, The Pennsylvania State University, University Park, PA 16802
- Institute of Economics and EMbeDS, Sant'Anna School of Advanced Studies, Pisa 56127, Italy
| | - Francisco J. Diaz
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802
| | - Kateryna D. Makova
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Center for Medical Genomics, The Pennsylvania State University, University Park, PA 16802
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Chen Q, Yu M, Tian Z, Cui Y, Deng D, Rong T, Liu Z, Song M, Li Z, Ma X, Lu H. Exogenous Glutathione Protects IPEC-J2 Cells against Oxidative Stress through a Mitochondrial Mechanism. Molecules 2022; 27:molecules27082416. [PMID: 35458611 PMCID: PMC9028222 DOI: 10.3390/molecules27082416] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/30/2022] [Accepted: 04/04/2022] [Indexed: 02/01/2023] Open
Abstract
The accumulation of reactive oxygen species (ROS) triggers oxidative stress in cells by oxidizing and modifying various cellular components, preventing them from performing their inherent functions, ultimately leading to apoptosis and autophagy. Glutathione (GSH) is a ubiquitous intracellular peptide with multiple functions. In this study, a hydrogen peroxide (H2O2)-induced oxidative damage model in IPEC-J2 cells was used to investigate the cellular protection mechanism of exogenous GSH against oxidative stress. The results showed that GSH supplement improved the cell viability reduced by H2O2-induced oxidative damage model in IPEC-J2 cells in a dose-dependent manner. Moreover, supplement with GSH also attenuated the H2O2-induced MMP loss, and effectively decreased the H2O2-induced mitochondrial dysfunction by increasing the content of mtDNA and upregulating the expression TFAM. Exogenous GSH treatment significantly decreased the ROS and MDA levels, improved SOD activity in H2O2-treated cells and reduced H2O2-induced early apoptosis in IPEC-J2 cells. This study showed that exogenous GSH can protect IPEC-J2 cells against apoptosis induced by oxidative stress through mitochondrial mechanisms.
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Affiliation(s)
- Qiuyu Chen
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China;
- State Key Laboratory of Livestockand Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (M.Y.); (Z.T.); (Y.C.); (D.D.); (T.R.); (Z.L.); (M.S.); (Z.L.)
| | - Miao Yu
- State Key Laboratory of Livestockand Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (M.Y.); (Z.T.); (Y.C.); (D.D.); (T.R.); (Z.L.); (M.S.); (Z.L.)
- Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China
- Guangdong Engineering Technology Research Center of Animal Meat Quality and Safety Control and Evaluation, Guangzhou 510640, China
| | - Zhimei Tian
- State Key Laboratory of Livestockand Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (M.Y.); (Z.T.); (Y.C.); (D.D.); (T.R.); (Z.L.); (M.S.); (Z.L.)
- Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China
- Guangdong Engineering Technology Research Center of Animal Meat Quality and Safety Control and Evaluation, Guangzhou 510640, China
| | - Yiyan Cui
- State Key Laboratory of Livestockand Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (M.Y.); (Z.T.); (Y.C.); (D.D.); (T.R.); (Z.L.); (M.S.); (Z.L.)
- Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China
- Guangdong Engineering Technology Research Center of Animal Meat Quality and Safety Control and Evaluation, Guangzhou 510640, China
| | - Dun Deng
- State Key Laboratory of Livestockand Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (M.Y.); (Z.T.); (Y.C.); (D.D.); (T.R.); (Z.L.); (M.S.); (Z.L.)
- Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China
- Guangdong Engineering Technology Research Center of Animal Meat Quality and Safety Control and Evaluation, Guangzhou 510640, China
| | - Ting Rong
- State Key Laboratory of Livestockand Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (M.Y.); (Z.T.); (Y.C.); (D.D.); (T.R.); (Z.L.); (M.S.); (Z.L.)
- Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China
- Guangdong Engineering Technology Research Center of Animal Meat Quality and Safety Control and Evaluation, Guangzhou 510640, China
- Qingyuan Longfa Pig Breeding Co., Ltd., Yingde 511500, China
| | - Zhichang Liu
- State Key Laboratory of Livestockand Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (M.Y.); (Z.T.); (Y.C.); (D.D.); (T.R.); (Z.L.); (M.S.); (Z.L.)
- Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China
- Guangdong Engineering Technology Research Center of Animal Meat Quality and Safety Control and Evaluation, Guangzhou 510640, China
| | - Min Song
- State Key Laboratory of Livestockand Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (M.Y.); (Z.T.); (Y.C.); (D.D.); (T.R.); (Z.L.); (M.S.); (Z.L.)
- Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China
- Guangdong Engineering Technology Research Center of Animal Meat Quality and Safety Control and Evaluation, Guangzhou 510640, China
| | - Zhenming Li
- State Key Laboratory of Livestockand Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (M.Y.); (Z.T.); (Y.C.); (D.D.); (T.R.); (Z.L.); (M.S.); (Z.L.)
- Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China
- Guangdong Engineering Technology Research Center of Animal Meat Quality and Safety Control and Evaluation, Guangzhou 510640, China
- Qingyuan Longfa Pig Breeding Co., Ltd., Yingde 511500, China
| | - Xianyong Ma
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China;
- State Key Laboratory of Livestockand Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (M.Y.); (Z.T.); (Y.C.); (D.D.); (T.R.); (Z.L.); (M.S.); (Z.L.)
- Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China
- Guangdong Engineering Technology Research Center of Animal Meat Quality and Safety Control and Evaluation, Guangzhou 510640, China
- Correspondence: (X.M.); (H.L.)
| | - Huijie Lu
- State Key Laboratory of Livestockand Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (M.Y.); (Z.T.); (Y.C.); (D.D.); (T.R.); (Z.L.); (M.S.); (Z.L.)
- Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China
- Guangdong Engineering Technology Research Center of Animal Meat Quality and Safety Control and Evaluation, Guangzhou 510640, China
- Correspondence: (X.M.); (H.L.)
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Mposhi A, Liang L, Mennega KP, Yildiz D, Kampert C, Hof IH, Jellema PG, de Koning TJ, Faber KN, Ruiters MHJ, Niezen-Koning KE, Rots MG. The Mitochondrial Epigenome: An Unexplored Avenue to Explain Unexplained Myopathies? Int J Mol Sci 2022; 23:ijms23042197. [PMID: 35216315 PMCID: PMC8879787 DOI: 10.3390/ijms23042197] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/01/2022] [Accepted: 02/07/2022] [Indexed: 02/01/2023] Open
Abstract
Mutations in either mitochondrial DNA (mtDNA) or nuclear genes that encode mitochondrial proteins may lead to dysfunctional mitochondria, giving rise to mitochondrial diseases. Some mitochondrial myopathies, however, present without a known underlying cause. Interestingly, methylation of mtDNA has been associated with various clinical pathologies. The present study set out to assess whether mtDNA methylation could explain impaired mitochondrial function in patients diagnosed with myopathy without known underlying genetic mutations. Enhanced mtDNA methylation was indicated by pyrosequencing for muscle biopsies of 14 myopathy patients compared to four healthy controls, at selected cytosines in the Cytochrome B (CYTB) gene, but not within the displacement loop (D-loop) region. The mtDNA methylation patterns of the four healthy muscle biopsies were highly consistent and showed intriguing tissue-specific differences at particular cytosines with control skin fibroblasts cultured in vitro. Within individual myopathy patients, the overall mtDNA methylation pattern correlated well between muscle and skin fibroblasts. Despite this correlation, a pilot analysis of four myopathy and five healthy fibroblast samples did not reveal a disease-associated difference in mtDNA methylation. We did, however, detect increased expression of solute carrier family 25A26 (SLC25A26), encoding the importer of S-adenosylmethionine, together with enhanced mtDNA copy numbers in myopathy fibroblasts compared to healthy controls. To confirm that pyrosequencing indeed reflected DNA methylation and not bisulfite accessibility, mass spectrometry was employed. Although no myopathy-related differences in total amount of methylated cytosines were detected at this stage, a significant contribution of contaminating nuclear DNA (nDNA) was revealed, and steps to improve enrichment for mtDNA are reported. In conclusion, in this explorative study we show that analyzing the mitochondrial genome beyond its sequence opens novel avenues to identify potential molecular biomarkers assisting in the diagnosis of unexplained myopathies.
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Affiliation(s)
- Archibold Mposhi
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (A.M.); (L.L.); (K.P.M.); (P.G.J.); (M.H.J.R.)
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands;
| | - Lin Liang
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (A.M.); (L.L.); (K.P.M.); (P.G.J.); (M.H.J.R.)
| | - Kevin P. Mennega
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (A.M.); (L.L.); (K.P.M.); (P.G.J.); (M.H.J.R.)
- Department of Laboratory Medicine, Laboratory of Metabolic Diseases, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (D.Y.); (C.K.); (I.H.H.); (K.E.N.-K.)
| | - Dilemin Yildiz
- Department of Laboratory Medicine, Laboratory of Metabolic Diseases, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (D.Y.); (C.K.); (I.H.H.); (K.E.N.-K.)
| | - Crista Kampert
- Department of Laboratory Medicine, Laboratory of Metabolic Diseases, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (D.Y.); (C.K.); (I.H.H.); (K.E.N.-K.)
| | - Ingrid H. Hof
- Department of Laboratory Medicine, Laboratory of Metabolic Diseases, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (D.Y.); (C.K.); (I.H.H.); (K.E.N.-K.)
| | - Pytrick G. Jellema
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (A.M.); (L.L.); (K.P.M.); (P.G.J.); (M.H.J.R.)
| | - Tom J. de Koning
- Department of Genetics, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands;
- Department of Clinical Sciences, Lund University, Lasarettgatan 40, 221 85 Lund, Sweden
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands;
| | - Marcel H. J. Ruiters
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (A.M.); (L.L.); (K.P.M.); (P.G.J.); (M.H.J.R.)
| | - Klary E. Niezen-Koning
- Department of Laboratory Medicine, Laboratory of Metabolic Diseases, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (D.Y.); (C.K.); (I.H.H.); (K.E.N.-K.)
| | - Marianne G. Rots
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (A.M.); (L.L.); (K.P.M.); (P.G.J.); (M.H.J.R.)
- Correspondence:
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Okada T, Sun X, McIlfatrick S, St. John JC. Low guanine content and biased nucleotide distribution in vertebrate mtDNA can cause overestimation of non-CpG methylation. NAR Genom Bioinform 2022; 4:lqab119. [PMID: 35047811 PMCID: PMC8759572 DOI: 10.1093/nargab/lqab119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/24/2021] [Accepted: 01/09/2022] [Indexed: 11/12/2022] Open
Abstract
Mitochondrial DNA (mtDNA) methylation in vertebrates has been hotly debated for over 40 years. Most contrasting results have been reported following bisulfite sequencing (BS-seq) analyses. We addressed whether BS-seq experimental and analysis conditions influenced the estimation of the levels of methylation in specific mtDNA sequences. We found false positive non-CpG methylation in the CHH context (fpCHH) using unmethylated Sus scrofa mtDNA BS-seq data. fpCHH methylation was detected on the top/plus strand of mtDNA within low guanine content regions. These top/plus strand sequences of fpCHH regions would become extremely AT-rich sequences after BS-conversion, whilst bottom/minus strand sequences remained almost unchanged. These unique sequences caused BS-seq aligners to falsely assign the origin of each strand in fpCHH regions, resulting in false methylation calls. fpCHH methylation detection was enhanced by short sequence reads, short library inserts, skewed top/bottom read ratios and non-directional read mapping modes. We confirmed no detectable CHH methylation in fpCHH regions by BS-amplicon sequencing. The fpCHH peaks were located in the D-loop, ATP6, ND2, ND4L, ND5 and ND6 regions and identified in our S. scrofa ovary and oocyte data and human BS-seq data sets. We conclude that non-CpG methylation could potentially be overestimated in specific sequence regions by BS-seq analysis.
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Placental mtDNA copy number and methylation in association with macrosomia in healthy pregnancy. Placenta 2021; 118:1-9. [PMID: 34972066 DOI: 10.1016/j.placenta.2021.12.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 11/20/2022]
Abstract
INTRODUCTION Fetal growth and development depend on metabolic energy from placental mitochondria. However, the impact of placental mitochondria on the occurrence of macrosomia remains unclear. We aimed to explore the association between macrosomia without gestational diabetes mellitus (non-GDM) and changes in placental mitochondrial DNA (mtDNA) copy number and methylation. METHODS Fifty-four newborns with macrosomia and 54 normal birthweight controls were enrolled in this study. Placental mtDNA copy number and mRNA expression of nuclear genes related to mitochondrial replication or ATP synthesis-related genes were measured by real-time quantitative polymerase chain reaction (qPCR). Methylation levels of the non-coding regulatory region D-loop and ATP synthesis-related genes were detected by targeted bisulfite sequencing. RESULTS Newborns with macrosomia had lower placental mtDNA copy number and higher methylation rates of the CpG15 site in the D-loop region (D-CpG15) and CpG6 site in the cytochrome C oxidase III (COX3) gene (COX3-CpG6) than normal birth weight newborns. After adjusting for potential covariates (gestational age, prepregnancy BMI, and infant sex), decreased placental mtDNA copy number (adjusted odds ratio [aOR] = 2.09, 95% confidence interval [CI] 1.03-4.25), elevated methylation rate of D-CpG15 (aOR = 2.06, 95% CI 1.03-4.09) and COX3-CpG6 (aOR = 2.13, 95% CI 1.08-4.20) remained significantly associated with a higher risk of macrosomia. DISCUSSION Reduced mtDNA copy number and increased methylation levels of specific loci at mtDNA would increase the risk of macrosomia. However, the detailed molecular mechanism needs further identification.
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Bicci I, Calabrese C, Golder ZJ, Gomez-Duran A, Chinnery P. Single-molecule mitochondrial DNA sequencing shows no evidence of CpG methylation in human cells and tissues. Nucleic Acids Res 2021; 49:12757-12768. [PMID: 34850165 PMCID: PMC8682748 DOI: 10.1093/nar/gkab1179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/29/2021] [Accepted: 11/18/2021] [Indexed: 01/11/2023] Open
Abstract
Methylation on CpG residues is one of the most important epigenetic modifications of nuclear DNA, regulating gene expression. Methylation of mitochondrial DNA (mtDNA) has been studied using whole genome bisulfite sequencing (WGBS), but recent evidence has uncovered technical issues which introduce a potential bias during methylation quantification. Here, we validate the technical concerns of WGBS, and develop and assess the accuracy of a new protocol for mtDNA nucleotide variant-specific methylation using single-molecule Oxford Nanopore Sequencing (ONS). Our approach circumvents confounders by enriching for full-length molecules over nuclear DNA. Variant calling analysis against showed that 99.5% of homoplasmic mtDNA variants can be reliably identified providing there is adequate sequencing depth. We show that some of the mtDNA methylation signal detected by ONS is due to sequence-specific false positives introduced by the technique. The residual signal was observed across several human primary and cancer cell lines and multiple human tissues, but was always below the error threshold modelled using negative controls. We conclude that there is no evidence for CpG methylation in human mtDNA, thus resolving previous controversies. Additionally, we developed a reliable protocol to study epigenetic modifications of mtDNA at single-molecule and single-base resolution, with potential applications beyond CpG methylation.
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Affiliation(s)
- Iacopo Bicci
- MRC-Mitochondrial Biology Unit, The Keith Peters Building, Cambridge CB2 0XY, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Claudia Calabrese
- MRC-Mitochondrial Biology Unit, The Keith Peters Building, Cambridge CB2 0XY, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Zoe J Golder
- MRC-Mitochondrial Biology Unit, The Keith Peters Building, Cambridge CB2 0XY, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Aurora Gomez-Duran
- MRC-Mitochondrial Biology Unit, The Keith Peters Building, Cambridge CB2 0XY, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
- Centro de Investigaciones Biológicas Margarita Salas. Spanish National Research Council, Madrid, Spain
| | - Patrick F Chinnery
- MRC-Mitochondrial Biology Unit, The Keith Peters Building, Cambridge CB2 0XY, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
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Jiang H, Yang X, Mi M, Wei X, Wu H, Xin Y, Jiao L, Sun S, Sun C. Development and performance evaluation of TaqMan real-time fluorescence quantitative methylation specific PCR for detecting methylation level of PER2. Mol Biol Rep 2021; 49:2097-2105. [PMID: 34854010 DOI: 10.1007/s11033-021-07027-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/26/2021] [Indexed: 12/01/2022]
Abstract
BACKGROUND PER2 gene methylation is closely related to the occurrence and progress of some cancers, but there is no method to quantitatively detect PER2 methylation in conventional laboratories. So, we established a TaqMan real-time fluorescence quantitative methylation specific PCR (TaqMan real-time FQ-MSP) assay and use it for quantitative detection of PER2 methylation in leukemia patients. METHODS According to the PER2 sequence searched by GenBank, a CpG sequence enrichment region of the PER2 gene promoter was selected, and the methylated and unmethylated target sequences were designed according to the law of bisulfite conversion of DNA to construct PER2 methylation positive and negative reference materials. Specific primers and probe were designed. The reference materials were continuously diluted into gradient samples by tenfold ratio to evaluate the analytical sensitivity, specificity, accuracy and reproducibility of the method, and the analytical sensitivity of TaqMan real-time FQ-MSP assay was compared with that of the conventional MSP assay. At the same time, the new-established TaqMan real-time FQ-MSP assay and the conventional MSP assay were used to detect the PER2 methylation level of 81 patients with leukemia, and the samples with inconsistent detection results of the two assays were sent to pyromethylation sequencing to evaluate the clinical detection performance. RESULTS The minimum detection limit of TaqMan real-time FQ-MSP assay for detecting PER2 methylation level established in this study was 6 copies/uL, and the coefficient of variation(CV) of intra-assay and inter-assay was less than 3%. Compared with the conventional MSP assay, it has higher analytical sensitivity. For the samples with inconsistent detection results, the results of pyrosequencing and TaqMan real-time FQ-MSP assay are consistent. CONCLUSION TaqMan real-time FQ-MSP assay of PER2 methylation established in this study has high detection performance and can be used for the detection of clinical samples.
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Affiliation(s)
- Huihui Jiang
- Qingdao University, Qingdao, 266000, Shandong, China
| | - Xin Yang
- Department of Laboratory Center, Yantai Yuhuangding Hospital Affiliated to Qingdao University, 20 Yuhuangding East Road, Yantai, 264000, Shandong, China
| | - Miaomiao Mi
- Department of Laboratory Center, Qilu Hospital of Shandong University, Jinan, 250000, Shandong, China
| | - Xiaonan Wei
- Department of Laboratory Center, Qingdao Women and Children's Hospital, Qingdao, 266000, Shandong, China
| | - Hongyuan Wu
- Qingdao University, Qingdao, 266000, Shandong, China
| | - Yu Xin
- Binzhou Medical University, Yantai, 264000, Shandong, China
| | - Liping Jiao
- Qingdao University, Qingdao, 266000, Shandong, China
| | - Shengjun Sun
- Department of Laboratory Center, Yantaishan Hospital, Yantai, 264000, Shandong, China
| | - Chengming Sun
- Department of Laboratory Center, Yantai Yuhuangding Hospital Affiliated to Qingdao University, 20 Yuhuangding East Road, Yantai, 264000, Shandong, China.
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Cao K, Feng Z, Gao F, Zang W, Liu J. Mitoepigenetics: An intriguing regulatory layer in aging and metabolic-related diseases. Free Radic Biol Med 2021; 177:337-346. [PMID: 34715295 DOI: 10.1016/j.freeradbiomed.2021.10.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/06/2021] [Accepted: 10/22/2021] [Indexed: 12/20/2022]
Abstract
As a key organelle in eukaryotic cells, mitochondria play a central role in maintaining normal cellular functions. Mitochondrial dysfunction is reported to be closely related with aging and various diseases. Epigenetic modifications in nuclear genome provide a substantial layer for the modulation of nuclear-encoded gene expression. However, whether mitochondria could also be subjected to such similar epigenetic alterations and the involved mechanisms remain largely obscure and controversial. Recently, accumulating evidence has suggested that mitochondrial epigenetics, also known as mitoepigenetics may serve as an intriguing regulatory layer in mitochondrial DNA (mtDNA)-encoded gene expression. Given the potential regulatory role of mitoepigenetics, mitochondrial dysfunction derived from mitoepigenetics-induced abnormal gene expression could also be closely associated with aging and disease development. In this review, we summarized the recent advances in mitoepigenetics, with a special focus on mtDNA methylation in aging and metabolic-related diseases as well as the new methods and technologies for the study of mitoepigenetics. Uncovering the regulatory role of mitoepigenetics will help to understand the underlying mechanisms of mitochondrial dysfunction and provide novel strategies for delaying aging and preventing metabolic-related diseases.
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Affiliation(s)
- Ke Cao
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Zhihui Feng
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China; Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Feng Gao
- School of Aerospace Medicine, Fourth Military Medical University, Xi'an, 710032, China
| | - Weijin Zang
- Department of Pharmacology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China
| | - Jiankang Liu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China; University of Health and Rehabilitation Sciences, Qingdao, 266071, China.
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Zhao H, Ma D, Xie J, Sanchez O, Huang F, Yuan C. Live-Cell Probe for In Situ Single-Cell Monitoring of Mitochondrial DNA Methylation. ACS Sens 2021; 6:3575-3586. [PMID: 34586782 DOI: 10.1021/acssensors.1c00731] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mitochondria, as the center of energy production, play an important role in cell homeostasis by regulating the cellular metabolism and mediating the cellular response to stress. Epigenetic changes such as DNA and histone methylation have been increasingly recognized to play a significant role in homeostasis and stress response. The cross-talking between the metabolome and the epigenome has attracted significant attention in recent years but with a major focus on how metabolism contributes to epigenomic changes. Few studies have focused on how epigenetic modifications may alter the mitochondrial composition and activity. In this work, we designed a novel probe targeting methylated CpGs of mitochondrial DNA (mtDNA). We demonstrated the capability of our probe to reveal the spatial distribution of methylated mtDNA and capture the mtDNA methylation changes at a single-cell level. We were also able to track single-cell mtDNA and nDNA methylation simultaneously and discovered the unsynchronized dynamics of the nucleus and mitochondria. Our tool offers a unique opportunity to understand the epigenetic regulation of mtDNA and its dynamic response to the microenvironment and cellular changes.
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Affiliation(s)
- Han Zhao
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Donghan Ma
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Junkai Xie
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Oscar Sanchez
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Fang Huang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue University Center for Cancer Research, West Lafayette, Indiana 47907, United States
| | - Chongli Yuan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue University Center for Cancer Research, West Lafayette, Indiana 47907, United States
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Lüth T, Wasner K, Klein C, Schaake S, Tse R, Pereira SL, Laß J, Sinkkonen L, Grünewald A, Trinh J. Nanopore Single-Molecule Sequencing for Mitochondrial DNA Methylation Analysis: Investigating Parkin-Associated Parkinsonism as a Proof of Concept. Front Aging Neurosci 2021; 13:713084. [PMID: 34650424 PMCID: PMC8506010 DOI: 10.3389/fnagi.2021.713084] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 09/01/2021] [Indexed: 01/08/2023] Open
Abstract
Objective: To establish a workflow for mitochondrial DNA (mtDNA) CpG methylation using Nanopore whole-genome sequencing and perform first pilot experiments on affected Parkin biallelic mutation carriers (Parkin-PD) and healthy controls. Background: Mitochondria, including mtDNA, are established key players in Parkinson's disease (PD) pathogenesis. Mutations in Parkin, essential for degradation of damaged mitochondria, cause early-onset PD. However, mtDNA methylation and its implication in PD is understudied. Herein, we establish a workflow using Nanopore sequencing to directly detect mtDNA CpG methylation and compare mtDNA methylation between Parkin-related PD and healthy individuals. Methods: To obtain mtDNA, whole-genome Nanopore sequencing was performed on blood-derived from five Parkin-PD and three control subjects. In addition, induced pluripotent stem cell (iPSC)-derived midbrain neurons from four of these patients with PD and the three control subjects were investigated. The workflow was validated, using methylated and unmethylated 897 bp synthetic DNA samples at different dilution ratios (0, 50, 100% methylation) and mtDNA without methylation. MtDNA CpG methylation frequency (MF) was detected using Nanopolish and Megalodon. Results: Across all blood-derived samples, we obtained a mean coverage of 250.3X (SD ± 80.5X) and across all neuron-derived samples 830X (SD ± 465X) of the mitochondrial genome. We detected overall low-level CpG methylation from the blood-derived DNA (mean MF ± SD = 0.029 ± 0.041) and neuron-derived DNA (mean MF ± SD = 0.019 ± 0.035). Validation of the workflow, using synthetic DNA samples showed that highly methylated DNA molecules were prone to lower Guppy Phred quality scores and thereby more likely to fail Guppy base-calling. CpG methylation in blood- and neuron-derived DNA was significantly lower in Parkin-PD compared to controls (Mann-Whitney U-test p < 0.05). Conclusion: Nanopore sequencing is a useful method to investigate mtDNA methylation architecture, including Guppy-failed reads is of importance when investigating highly methylated sites. We present a mtDNA methylation workflow and suggest methylation variability across different tissues and between Parkin-PD patients and controls as an initial model to investigate.
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Affiliation(s)
- Theresa Lüth
- Institute of Neurogenetics BMF, University of Lübeck and University Hospital Schleswig-Holstein Campus Lübeck, Lübeck, Germany
| | - Kobi Wasner
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Christine Klein
- Institute of Neurogenetics BMF, University of Lübeck and University Hospital Schleswig-Holstein Campus Lübeck, Lübeck, Germany
| | - Susen Schaake
- Institute of Neurogenetics BMF, University of Lübeck and University Hospital Schleswig-Holstein Campus Lübeck, Lübeck, Germany
| | - Ronnie Tse
- Institute of Neurogenetics BMF, University of Lübeck and University Hospital Schleswig-Holstein Campus Lübeck, Lübeck, Germany
| | - Sandro L. Pereira
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Joshua Laß
- Institute of Neurogenetics BMF, University of Lübeck and University Hospital Schleswig-Holstein Campus Lübeck, Lübeck, Germany
| | - Lasse Sinkkonen
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg
| | - Anne Grünewald
- Institute of Neurogenetics BMF, University of Lübeck and University Hospital Schleswig-Holstein Campus Lübeck, Lübeck, Germany
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Joanne Trinh
- Institute of Neurogenetics BMF, University of Lübeck and University Hospital Schleswig-Holstein Campus Lübeck, Lübeck, Germany
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42
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Chen Z, Rasheed M, Deng Y. The epigenetic mechanisms involved in mitochondrial dysfunction: Implication for Parkinson's disease. Brain Pathol 2021; 32:e13012. [PMID: 34414627 PMCID: PMC9048811 DOI: 10.1111/bpa.13012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 06/21/2021] [Accepted: 07/27/2021] [Indexed: 12/18/2022] Open
Abstract
Mitochondrial dysfunction is one of the crucial factors involved in PD’s pathogenicity, which emerges from a combination of genetic and environmental factors. These factors cause differential molecular expression in neurons, such as varied transcriptional regulation of genes, elevated oxidative stress, α‐synuclein aggregation and endogenous neurotoxins release, which induces epigenetic modifications and triggers energy crisis by damaging mitochondria of the dopaminergic neurons (DN). So far, these events establish a complicated relationship with underlying mechanisms of mitochondrial anomalies in PD, which has remained unclear for years and made PD diagnosis and treatment extremely difficult. Therefore, in this review, we endeavored to discuss the complex association of epigenetic modifications and other associated vital factors in mitochondrial dysfunction. We propose a hypothesis that describes a vicious cycle in which mitochondrial dysfunction and oxidative stress act as a hub for regulating DA neuron's fate in PD. Oxidative stress triggers the release of endogenous neurotoxins (CTIQs) that lead to mitochondrial dysfunction along with abnormal α‐synuclein aggregation and epigenetic modifications. These disturbances further intensify oxidative stress and mitochondrial damage, amplifying the synthesis of CTIQs and works vice versa. This vicious cycle may result in the degeneration of DN to hallmark Parkinsonism. Furthermore, we have also highlighted various endogenous compounds and epigenetic marks (neurotoxic and neuroprotective), which may help for devising future diagnostic biomarkers and target specific drugs using novel PD management strategies.
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Affiliation(s)
- Zixuan Chen
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Madiha Rasheed
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Yulin Deng
- School of Life Science, Beijing Institute of Technology, Beijing, China
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43
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Maresca A, Del Dotto V, Capristo M, Scimonelli E, Tagliavini F, Morandi L, Tropeano CV, Caporali L, Mohamed S, Roberti M, Scandiffio L, Zaffagnini M, Rossi J, Cappelletti M, Musiani F, Contin M, Riva R, Liguori R, Pizza F, La Morgia C, Antelmi E, Loguercio Polosa P, Mignot E, Zanna C, Plazzi G, Carelli V. DNMT1 mutations leading to neurodegeneration paradoxically reflect on mitochondrial metabolism. Hum Mol Genet 2021; 29:1864-1881. [PMID: 31984424 PMCID: PMC7372549 DOI: 10.1093/hmg/ddaa014] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 01/20/2020] [Indexed: 12/12/2022] Open
Abstract
ADCA-DN and HSN-IE are rare neurodegenerative syndromes caused by dominant mutations in the replication foci targeting sequence (RFTS) of the DNA methyltransferase 1 (DNMT1) gene. Both phenotypes resemble mitochondrial disorders, and mitochondrial dysfunction was first observed in ADCA-DN. To explore mitochondrial involvement, we studied the effects of DNMT1 mutations in fibroblasts from four ADCA-DN and two HSN-IE patients. We documented impaired activity of purified DNMT1 mutant proteins, which in fibroblasts results in increased DNMT1 amount. We demonstrated that DNMT1 is not localized within mitochondria, but it is associated with the mitochondrial outer membrane. Concordantly, mitochondrial DNA failed to show meaningful CpG methylation. Strikingly, we found activated mitobiogenesis and OXPHOS with significant increase of H2O2, sharply contrasting with a reduced ATP content. Metabolomics profiling of mutant cells highlighted purine, arginine/urea cycle and glutamate metabolisms as the most consistently altered pathways, similar to primary mitochondrial diseases. The most severe mutations showed activation of energy shortage AMPK-dependent sensing, leading to mTORC1 inhibition. We propose that DNMT1 RFTS mutations deregulate metabolism lowering ATP levels, as a result of increased purine catabolism and urea cycle pathways. This is associated with a paradoxical mitochondrial hyper-function and increased oxidative stress, possibly resulting in neurodegeneration in non-dividing cells.
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Affiliation(s)
- Alessandra Maresca
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna 40139, Italy
| | - Valentina Del Dotto
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40139, Italy
| | - Mariantonietta Capristo
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna 40139, Italy
| | - Emanuela Scimonelli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40139, Italy
| | - Francesca Tagliavini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna 40139, Italy
| | - Luca Morandi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40139, Italy
| | | | - Leonardo Caporali
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna 40139, Italy
| | - Susan Mohamed
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna 40139, Italy
| | - Marina Roberti
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari 70126, Italy
| | - Letizia Scandiffio
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari 70126, Italy
| | - Mirko Zaffagnini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Jacopo Rossi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Francesco Musiani
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Manuela Contin
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna 40139, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40139, Italy
| | - Roberto Riva
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna 40139, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40139, Italy
| | - Rocco Liguori
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna 40139, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40139, Italy
| | - Fabio Pizza
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna 40139, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40139, Italy
| | - Chiara La Morgia
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna 40139, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40139, Italy
| | - Elena Antelmi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40139, Italy
| | - Paola Loguercio Polosa
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari 70126, Italy
| | - Emmanuel Mignot
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94304, USA
| | - Claudia Zanna
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Giuseppe Plazzi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna 40139, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40139, Italy
| | - Valerio Carelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna 40139, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40139, Italy
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44
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Mitochondria-Induced Immune Response as a Trigger for Neurodegeneration: A Pathogen from Within. Int J Mol Sci 2021; 22:ijms22168523. [PMID: 34445229 PMCID: PMC8395232 DOI: 10.3390/ijms22168523] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 01/14/2023] Open
Abstract
Symbiosis between the mitochondrion and the ancestor of the eukaryotic cell allowed cellular complexity and supported life. Mitochondria have specialized in many key functions ensuring cell homeostasis and survival. Thus, proper communication between mitochondria and cell nucleus is paramount for cellular health. However, due to their archaebacterial origin, mitochondria possess a high immunogenic potential. Indeed, mitochondria have been identified as an intracellular source of molecules that can elicit cellular responses to pathogens. Compromised mitochondrial integrity leads to release of mitochondrial content into the cytosol, which triggers an unwanted cellular immune response. Mitochondrial nucleic acids (mtDNA and mtRNA) can interact with the same cytoplasmic sensors that are specialized in recognizing genetic material from pathogens. High-energy demanding cells, such as neurons, are highly affected by deficits in mitochondrial function. Notably, mitochondrial dysfunction, neurodegeneration, and chronic inflammation are concurrent events in many severe debilitating disorders. Interestingly in this context of pathology, increasing number of studies have detected immune-activating mtDNA and mtRNA that induce an aberrant production of pro-inflammatory cytokines and interferon effectors. Thus, this review provides new insights on mitochondria-driven inflammation as a potential therapeutic target for neurodegenerative and primary mitochondrial diseases.
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45
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Nedoluzhko A, Mjelle R, Renström M, Skjærven KH, Piferrer F, Fernandes JMO. The first mitochondrial 5-methylcytosine map in a non-model teleost (Oreochromis niloticus) reveals extensive strand-specific and non-CpG methylation. Genomics 2021; 113:3050-3057. [PMID: 34245830 DOI: 10.1016/j.ygeno.2021.07.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 06/16/2021] [Accepted: 07/05/2021] [Indexed: 12/26/2022]
Abstract
DNA methylation is one of the main epigenetic mechanisms that regulate gene expression in a manner that depends on the genomic context and varies considerably across taxa. This DNA modification was first found in nuclear genomes of eukaryote several decades ago and it has also been described in mitochondrial DNA. It has recently been shown that mitochondrial DNA is extensively methylated in mammals and other vertebrates. Our current knowledge of mitochondrial DNA methylation in fish is very limited, especially in non-model teleosts. In this study, using whole-genome bisulfite sequencing, we determined methylation patterns within non-CpG (CH) and CpG (CG) contexts in the mitochondrial genome of Nile tilapia, a non-model teleost of high economic importance. Our results demonstrate the presence of mitochondrial DNA methylation in this species predominantly within a non-CpG context, similarly to mammals. We found a strand-specific distribution of methylation, in which highly methylated cytosines were located on the minus strand. The D-loop region had the highest mean methylation level among all mitochondrial loci. Our data provide new insights into the potential role of epigenetic mechanisms in regulating metabolic flexibility of mitochondria in fish, with implications in various biological processes, such as growth and development.
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Affiliation(s)
- Artem Nedoluzhko
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Robin Mjelle
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway; Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Maria Renström
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | | | - Francesc Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
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46
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Kennedy E, Coulter E, Halliwell E, Profitos-Peleja N, Walsby E, Clark B, Phillips EH, Burley TA, Mitchell S, Devereux S, Fegan CD, Jones CI, Johnston R, Chevassut T, Schulz R, Seiffert M, Agathanggelou A, Oldreive C, Davies N, Stankovic T, Liloglou T, Pepper C, Pepper AGS. TLR9 expression in chronic lymphocytic leukemia identifies a promigratory subpopulation and novel therapeutic target. Blood 2021; 137:3064-3078. [PMID: 33512408 PMCID: PMC8176769 DOI: 10.1182/blood.2020005964] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) remains incurable despite B-cell receptor-targeted inhibitors revolutionizing treatment. This suggests that other signaling molecules are involved in disease escape mechanisms and resistance. Toll-like receptor 9 (TLR9) is a promising candidate that is activated by unmethylated cytosine guanine dinucleotide-DNA. Here, we show that plasma from patients with CLL contains significantly more unmethylated DNA than plasma from healthy control subjects (P < .0001) and that cell-free DNA levels correlate with the prognostic markers CD38, β2-microglobulin, and lymphocyte doubling time. Furthermore, elevated cell-free DNA was associated with shorter time to first treatment (hazard ratio, 4.0; P = .003). We also show that TLR9 expression was associated with in vitro CLL cell migration (P < .001), and intracellular endosomal TLR9 strongly correlated with aberrant surface expression (sTLR9; r = 0.9). In addition, lymph node-derived CLL cells exhibited increased sTLR9 (P = .016), and RNA-sequencing of paired sTLR9hi and sTLR9lo CLL cells revealed differential transcription of genes involved in TLR signaling, adhesion, motility, and inflammation in sTLR9hi cells. Mechanistically, a TLR9 agonist, ODN2006, promoted CLL cell migration (P < .001) that was mediated by p65 NF-κB and STAT3 transcription factor activation. Importantly, autologous plasma induced the same effects, which were reversed by a TLR9 antagonist. Furthermore, high TLR9 expression promoted engraftment and rapid disease progression in a NOD/Shi-scid/IL-2Rγnull mouse xenograft model. Finally, we showed that dual targeting of TLR9 and Bruton's tyrosine kinase (BTK) was strongly synergistic (median combination index, 0.2 at half maximal effective dose), which highlights the distinct role for TLR9 signaling in CLL and the potential for combined targeting of TLR9 and BTK as a more effective treatment strategy in this incurable disease.
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Affiliation(s)
- Emma Kennedy
- Department of Clinical and Experimental Medicine, Brighton and Sussex Medical School, Falmer, United Kingdom
| | - Eve Coulter
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
- Department of Haemato-Oncology, Division of Cancer Studies, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Emma Halliwell
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Nuria Profitos-Peleja
- Lymphoma Translational Group, Josep Carreras Leukaemia Research Institute, Badalona, Spain
| | - Elisabeth Walsby
- Cardiff CLL Research Group, Institute of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Barnaby Clark
- Molecular Pathology Laboratory, King's College Hospital, London, United Kingdom
| | - Elizabeth H Phillips
- Department of Haemato-Oncology, Division of Cancer Studies, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Thomas A Burley
- Department of Clinical and Experimental Medicine, Brighton and Sussex Medical School, Falmer, United Kingdom
| | - Simon Mitchell
- Department of Clinical and Experimental Medicine, Brighton and Sussex Medical School, Falmer, United Kingdom
| | - Stephen Devereux
- Department of Haemato-Oncology, Division of Cancer Studies, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Christopher D Fegan
- Cardiff CLL Research Group, Institute of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Christopher I Jones
- Department of Primary Care and Public Health, Brighton and Sussex Medical School, Falmer, United Kingdom
| | - Rosalynd Johnston
- Department of Haematology, Brighton and Sussex University Hospital Trust, Brighton, United Kingdom
| | - Tim Chevassut
- Department of Clinical and Experimental Medicine, Brighton and Sussex Medical School, Falmer, United Kingdom
- Department of Haematology, Brighton and Sussex University Hospital Trust, Brighton, United Kingdom
| | - Ralph Schulz
- German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | | | - Angelo Agathanggelou
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom; and
| | - Ceri Oldreive
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom; and
| | - Nicholas Davies
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom; and
| | - Tatjana Stankovic
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom; and
| | - Triantafillos Liloglou
- Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Chris Pepper
- Department of Clinical and Experimental Medicine, Brighton and Sussex Medical School, Falmer, United Kingdom
| | - Andrea G S Pepper
- Department of Clinical and Experimental Medicine, Brighton and Sussex Medical School, Falmer, United Kingdom
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47
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Cao K, Lv W, Wang X, Dong S, Liu X, Yang T, Xu J, Zeng M, Zou X, Zhao D, Ma Q, Lin M, Long J, Zang W, Gao F, Feng Z, Liu J. Hypermethylation of Hepatic Mitochondrial ND6 Provokes Systemic Insulin Resistance. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2004507. [PMID: 34141522 PMCID: PMC8188198 DOI: 10.1002/advs.202004507] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/18/2021] [Indexed: 05/10/2023]
Abstract
Mitochondrial epigenetics is rising as intriguing notion for its potential involvement in aging and diseases, while the details remain largely unexplored. Here it is shown that among the 13 mitochondrial DNA (mtDNA) encoded genes, NADH-dehydrogenase 6 (ND6) transcript is primarily decreased in obese and type 2 diabetes populations, which negatively correlates with its distinctive hypermethylation. Hepatic mtDNA sequencing in mice unveils that ND6 presents the highest methylation level, which dramatically increases under diabetic condition due to enhanced mitochondrial translocation of DNA methyltransferase 1 (DNMT1) promoted by free fatty acid through adenosine 5'-monophosphate (AMP)-activated protein kinase (AMPK) activation. Hepatic knockdown of ND6 or overexpression of Dnmt1 similarly impairs mitochondrial function and induces systemic insulin resistance both in vivo and in vitro. Genetic or chemical targeting hepatic DNMT1 shows significant benefits against insulin resistance associated metabolic disorders. These findings highlight the pivotal role of ND6 epigenetic network in regulating mitochondrial function and onset of insulin resistance, shedding light on potential preventive and therapeutic strategies of insulin resistance and related metabolic disorders from a perspective of mitochondrial epigenetics.
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Affiliation(s)
- Ke Cao
- Center for Mitochondrial Biology and MedicineThe Key Laboratory of Biomedical Information Engineering of Ministry of EducationSchool of Life Science and TechnologyXi'an Jiaotong UniversityXi'anShaanxi710049China
| | - Weiqiang Lv
- Center for Mitochondrial Biology and MedicineThe Key Laboratory of Biomedical Information Engineering of Ministry of EducationSchool of Life Science and TechnologyXi'an Jiaotong UniversityXi'anShaanxi710049China
| | - Xueqiang Wang
- Center for Mitochondrial Biology and MedicineThe Key Laboratory of Biomedical Information Engineering of Ministry of EducationSchool of Life Science and TechnologyXi'an Jiaotong UniversityXi'anShaanxi710049China
| | - Shanshan Dong
- Biomedical Informatics & Genomics CenterThe Key Laboratory of Biomedical Information Engineering of Ministry of EducationSchool of Life Science and TechnologyXi'an Jiaotong UniversityXi'anShannxi710049China
| | - Xuyun Liu
- Center for Mitochondrial Biology and MedicineThe Key Laboratory of Biomedical Information Engineering of Ministry of EducationSchool of Life Science and TechnologyXi'an Jiaotong UniversityXi'anShaanxi710049China
| | - Tielin Yang
- Biomedical Informatics & Genomics CenterThe Key Laboratory of Biomedical Information Engineering of Ministry of EducationSchool of Life Science and TechnologyXi'an Jiaotong UniversityXi'anShannxi710049China
| | - Jie Xu
- Center for Mitochondrial Biology and MedicineThe Key Laboratory of Biomedical Information Engineering of Ministry of EducationSchool of Life Science and TechnologyXi'an Jiaotong UniversityXi'anShaanxi710049China
| | - Mengqi Zeng
- Center for Mitochondrial Biology and MedicineThe Key Laboratory of Biomedical Information Engineering of Ministry of EducationSchool of Life Science and TechnologyXi'an Jiaotong UniversityXi'anShaanxi710049China
| | - Xuan Zou
- National & Local Joint Engineering Research Center of Biodiagnosis and BiotherapyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShannxi710004China
| | - Daina Zhao
- Center for Mitochondrial Biology and MedicineThe Key Laboratory of Biomedical Information Engineering of Ministry of EducationSchool of Life Science and TechnologyXi'an Jiaotong UniversityXi'anShaanxi710049China
| | - Qingqing Ma
- Guizhou Aerospace HospitalZunyiGuizhou563099China
| | - Mu Lin
- Guizhou Aerospace HospitalZunyiGuizhou563099China
| | - Jiangang Long
- Center for Mitochondrial Biology and MedicineThe Key Laboratory of Biomedical Information Engineering of Ministry of EducationSchool of Life Science and TechnologyXi'an Jiaotong UniversityXi'anShaanxi710049China
| | - Weijin Zang
- Department of PharmacologySchool of Basic Medical SciencesXi'an Jiaotong University Health Science CenterXi'anShaanxi710061China
| | - Feng Gao
- School of Aerospace MedicineFourth Military Medical UniversityXi'an710032China
| | - Zhihui Feng
- Center for Mitochondrial Biology and MedicineThe Key Laboratory of Biomedical Information Engineering of Ministry of EducationSchool of Life Science and TechnologyXi'an Jiaotong UniversityXi'anShaanxi710049China
- Frontier Institute of Science and TechnologyXi'an Jiaotong UniversityXi'anShaanxi710049China
| | - Jiankang Liu
- Center for Mitochondrial Biology and MedicineThe Key Laboratory of Biomedical Information Engineering of Ministry of EducationSchool of Life Science and TechnologyXi'an Jiaotong UniversityXi'anShaanxi710049China
- Frontier Institute of Science and TechnologyXi'an Jiaotong UniversityXi'anShaanxi710049China
- National & Local Joint Engineering Research Center of Biodiagnosis and BiotherapyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShannxi710004China
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Urban LA, Trinh A, Pearlman E, Siryaporn A, Downing TL. The impact of age-related hypomethylated DNA on immune signaling upon cellular demise. Trends Immunol 2021; 42:464-468. [PMID: 33994111 PMCID: PMC9650629 DOI: 10.1016/j.it.2021.04.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 11/21/2022]
Abstract
Aging is associated with decreased antigen-specific immunity and increased chronic inflammation. While DNA-sensing pathways might be involved, the molecular factors underlying these age-related aberrancies in immune signaling are unclear. Here, we consider the potential role of aging-induced hypomethylated DNA as a putative stimulant of age-associated inflammation.
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Affiliation(s)
- Lauren A Urban
- Department of Microbiology and Molecular Genetics, University of California-Irvine, Irvine, CA 92697, USA; The Edwards Lifesciences Center for Advanced Cardiovascular Technology, University of California-Irvine, Irvine, CA 92697, USA
| | - Annie Trinh
- Department of Microbiology and Molecular Genetics, University of California-Irvine, Irvine, CA 92697, USA; The Edwards Lifesciences Center for Advanced Cardiovascular Technology, University of California-Irvine, Irvine, CA 92697, USA
| | - Eric Pearlman
- Institute for Immunology, University of California-Irvine, Irvine, CA 92697, USA; Department of Ophthalmology, University of California-Irvine, Irvine, CA 92697, USA; Department of Physiology and Biophysics, University of California-Irvine, Irvine, CA 92697, USA
| | - Albert Siryaporn
- Department of Physics and Astronomy, University of California-Irvine, Irvine, CA 92697, USA; Department of Molecular Biology and Biochemistry, University of California-Irvine, Irvine, CA 92697, USA
| | - Timothy L Downing
- Department of Microbiology and Molecular Genetics, University of California-Irvine, Irvine, CA 92697, USA; The Edwards Lifesciences Center for Advanced Cardiovascular Technology, University of California-Irvine, Irvine, CA 92697, USA; Department of Biomedical Engineering, University of California-Irvine, Irvine, CA 92697, USA. @uci.edu
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König B, Koch AN, Bellanti JA. Studies of mitochondrial and nuclear DNA released from food allergen-activated neutrophils. Implications for non-IgE food allergy. Allergy Asthma Proc 2021; 42:e59-e70. [PMID: 33980341 DOI: 10.2500/aap.2021.42.210021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Background: Although adverse food reactions are commonly divided into immunoglobulin E (IgE) mediated food allergy (FA), and non-IgE FA, the current literature is providing support for the role of innate immune responses as an important component of non-IgE FA. Using a commercially available leukocyte activation (LA) assay, a recent quantitative study of total extracellular DNA released in cellular supernatants of human peripheral blood mononuclear cells exposed either to positive or negative tested foods demonstrated that leukocytes exposed to foods with positive LA test results showed higher DNA content than those exposed to foods with negative LA test results. In humans, the origin of DNA might be either the nucleus or the mitochondria. Analysis of emerging data from several laboratories, including our own, suggests that mitochondrial DNA induces inflammatory responses through induction of proinflammatory cytokines. Objective: This pilot study was designed primarily to convey the finding, and relevance of, mitochondrial DNA in the form of neutrophil extracellular traps (NET) as a new pathogenetic mechanism for innate immune-mediated non-IgE FA. Methods: The study population consisted of a total of six subjects, four in a major FA study group and two in a subgroup. Neutrophils were isolated and treated with food antigens that elicited positive and negative LA responses, and the released free DNA was analyzed for the cellular site of origin by using real-time polymerase chain reaction and for leukocyte calprotectin and S100 calcium-binding protein A12 (S100A12) proteins as markers of NETs. Results: We showed that cellular supernatants from neutrophils treated with foods that elicit positive LA responses can contain increased DNA levels of nuclear as well as mitochondrial origin. Supernatants from neutrophils treated with negative tested food (LA) responses did not induce the release of nuclear or mitochondrial DNA. Conclusion: Analysis of our data suggested that the induction of NETs that contain proinflammatory mitochondrial DNA may provide the critical link necessary for a better understanding of the pathogenesis of non-IgE-mediated FA. These discoveries may not only facilitate better diagnostic tests of FA but should also improve clinical management of allergic and other inflammatory diseases.
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Affiliation(s)
- Brigitte König
- From the Medical Microbiology and Virology, The University Clinic of Leipzig, Leipzig, Germany
| | | | - Joseph A. Bellanti
- Department of Pediatrics and Microbiology-Immunology, Georgetown University Medical Center, Washington, D.C., (USA); and
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Mitochondrial DNA Methylation and Human Diseases. Int J Mol Sci 2021; 22:ijms22094594. [PMID: 33925624 PMCID: PMC8123858 DOI: 10.3390/ijms22094594] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/23/2021] [Accepted: 04/25/2021] [Indexed: 12/12/2022] Open
Abstract
Epigenetic modifications of the nuclear genome, including DNA methylation, histone modifications and non-coding RNA post-transcriptional regulation, are increasingly being involved in the pathogenesis of several human diseases. Recent evidence suggests that also epigenetic modifications of the mitochondrial genome could contribute to the etiology of human diseases. In particular, altered methylation and hydroxymethylation levels of mitochondrial DNA (mtDNA) have been found in animal models and in human tissues from patients affected by cancer, obesity, diabetes and cardiovascular and neurodegenerative diseases. Moreover, environmental factors, as well as nuclear DNA genetic variants, have been found to impair mtDNA methylation patterns. Some authors failed to find DNA methylation marks in the mitochondrial genome, suggesting that it is unlikely that this epigenetic modification plays any role in the control of the mitochondrial function. On the other hand, several other studies successfully identified the presence of mtDNA methylation, particularly in the mitochondrial displacement loop (D-loop) region, relating it to changes in both mtDNA gene transcription and mitochondrial replication. Overall, investigations performed until now suggest that methylation and hydroxymethylation marks are present in the mtDNA genome, albeit at lower levels compared to those detectable in nuclear DNA, potentially contributing to the mitochondria impairment underlying several human diseases.
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