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Neuhofer CM, Prokisch H. Digenic Inheritance in Rare Disorders and Mitochondrial Disease-Crossing the Frontier to a More Comprehensive Understanding of Etiology. Int J Mol Sci 2024; 25:4602. [PMID: 38731822 PMCID: PMC11083678 DOI: 10.3390/ijms25094602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 05/13/2024] Open
Abstract
Our understanding of rare disease genetics has been shaped by a monogenic disease model. While the traditional monogenic disease model has been successful in identifying numerous disease-associated genes and significantly enlarged our knowledge in the field of human genetics, it has limitations in explaining phenomena like phenotypic variability and reduced penetrance. Widening the perspective beyond Mendelian inheritance has the potential to enable a better understanding of disease complexity in rare disorders. Digenic inheritance is the simplest instance of a non-Mendelian disorder, characterized by the functional interplay of variants in two disease-contributing genes. Known digenic disease causes show a range of pathomechanisms underlying digenic interplay, including direct and indirect gene product interactions as well as epigenetic modifications. This review aims to systematically explore the background of digenic inheritance in rare disorders, the approaches and challenges when investigating digenic inheritance, and the current evidence for digenic inheritance in mitochondrial disorders.
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Affiliation(s)
- Christiane M. Neuhofer
- Institute of Human Genetics, University Medical Center, Technical University of Munich, Trogerstr. 32, 81675 Munich, Germany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Centre Munich Neuherberg, Ingolstädter Landstraße 1, 85764 Oberschleißheim, Germany
- Institute of Human Genetics, Salzburger Landeskliniken, University Hospital of the Paracelsus Medical University, Müllner Hauptstraße 48, 5020 Salzburg, Austria
| | - Holger Prokisch
- Institute of Human Genetics, University Medical Center, Technical University of Munich, Trogerstr. 32, 81675 Munich, Germany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Centre Munich Neuherberg, Ingolstädter Landstraße 1, 85764 Oberschleißheim, Germany
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La Colla A, Cámara CA, Campisano S, Chisari AN. Mitochondrial dysfunction and epigenetics underlying the link between early-life nutrition and non-alcoholic fatty liver disease. Nutr Res Rev 2023; 36:281-294. [PMID: 35067233 DOI: 10.1017/s0954422422000038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Early-life malnutrition plays a critical role in foetal development and predisposes to metabolic diseases later in life, according to the concept of 'developmental programming'. Different types of early nutritional imbalance, including undernutrition, overnutrition and micronutrient deficiency, have been related to long-term metabolic disorders. Accumulating evidence has demonstrated that disturbances in nutrition during the period of preconception, pregnancy and primary infancy can affect mitochondrial function and epigenetic mechanisms. Moreover, even though multiple mechanisms underlying non-alcoholic fatty liver disease (NAFLD) have been described, in the past years, special attention has been given to mitochondrial dysfunction and epigenetic alterations. Mitochondria play a key role in cellular metabolic functions. Dysfunctional mitochondria contribute to oxidative stress, insulin resistance and inflammation. Epigenetic mechanisms have been related to alterations in genes involved in lipid metabolism, fibrogenesis, inflammation and tumorigenesis. In accordance, studies have reported that mitochondrial dysfunction and epigenetics linked to early-life nutrition can be important contributing factors in the pathogenesis of NAFLD. In this review, we summarise the current understanding of the interplay between mitochondrial dysfunction, epigenetics and nutrition during early life, which is relevant to developmental programming of NAFLD.
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Affiliation(s)
- Anabela La Colla
- Departamento de Química y Bioquímica, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, 7600 Mar del Plata, Argentina
| | - Carolina Anahí Cámara
- Departamento de Química y Bioquímica, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, 7600 Mar del Plata, Argentina
| | - Sabrina Campisano
- Departamento de Química y Bioquímica, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, 7600 Mar del Plata, Argentina
| | - Andrea Nancy Chisari
- Departamento de Química y Bioquímica, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, 7600 Mar del Plata, Argentina
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Boovarahan SR, Balu K, Prem P, Sivakumar B, Kurian GA. DNA hypomethylation by fisetin preserves mitochondria functional genes and contributes to the protection of I/R rat heart. Funct Integr Genomics 2023; 23:325. [PMID: 37880513 DOI: 10.1007/s10142-023-01257-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/15/2023] [Accepted: 10/16/2023] [Indexed: 10/27/2023]
Abstract
Myocardial I/R can alter the expression of different sets of cardiac genes that negatively influence the I/R outcome via epigenetic modifications. Fisetin is known to be cardioprotective against I/R, but its underlying epigenetic mode of action is not known and is addressed in the present study. Male Wistar rats were subjected to I/R by using the Langendorff perfusion system. Fisetin (20 mg/kg; i.p.) was administered before I/R induction, followed by the measurement of cardiac injury, hemodynamics, physiological indices, the differential expression of genes that regulate DNA methylation, and the function of mitochondria were performed. Fisetin administered I/R rat heart significantly reduced the global DNA hypermethylation and infarct size with an improved physiological recovery, measured via RPP (81%) and LVDP (82%) from the I/R control. Additionally, we noted decreased expression of the DNMT1 gene by 35% and increased expression of the TET1, TET2, and TET3 genes in fisetin-treated I/R rat hearts. Molecular docking analysis data reveals that the fisetin inhibits DNMT1 at the substrate binding site with minimum binding energy (- 8.2 kcal/mol) compared to the DNMT1 inhibitor, 5-azacytidine. Moreover, fisetin-treated I/R heart reversed the expression of the I/R-linked declined expression of bioenergetics genes (MT-ND1, MT-ND2, MT-ND4, MT-Cyt B, MT-COX1, MT-COX2, MT-ATP6), mitochondrial fission gene (Fis1), replication control genes PGC-1α, POLG, and TFAM to near-normal level. Based on the above findings, we demonstrated that fisetin possesses the ability to modulate the expression of different mitochondrial genes via influencing the global DNA methylation in cardiac tissue, which contributes significantly to the improved contractile function and thereby renders cardioprotection against I/R.
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Affiliation(s)
- Sri Rahavi Boovarahan
- Vascular Biology Lab, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, 613401, India
| | - Kirankumar Balu
- Vascular Biology Lab, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, 613401, India
| | - Priyanka Prem
- Vascular Biology Lab, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, 613401, India
| | - Bhavana Sivakumar
- Vascular Biology Lab, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, 613401, India
| | - Gino A Kurian
- Vascular Biology Lab, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, 613401, India.
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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: 0] [Impact Index Per Article: 0] [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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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: 2] [Impact Index Per Article: 2.0] [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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The potential role of environmental factors in modulating mitochondrial DNA epigenetic marks. VITAMINS AND HORMONES 2023; 122:107-145. [PMID: 36863791 DOI: 10.1016/bs.vh.2023.01.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Many studies implicate mitochondrial dysfunction in the development and progression of numerous chronic diseases. Mitochondria are responsible for most cellular energy production, and unlike other cytoplasmic organelles, mitochondria contain their own genome. Most research to date, through investigating mitochondrial DNA copy number, has focused on larger structural changes or alterations to the entire mitochondrial genome and their role in human disease. Using these methods, mitochondrial dysfunction has been linked to cancers, cardiovascular disease, and metabolic health. However, like the nuclear genome, the mitochondrial genome may experience epigenetic alterations, including DNA methylation that may partially explain some of the health effects of various exposures. Recently, there has been a movement to understand human health and disease within the context of the exposome, which aims to describe and quantify the entirety of all exposures people encounter throughout their lives. These include, among others, environmental pollutants, occupational exposures, heavy metals, and lifestyle and behavioral factors. In this chapter, we summarize the current research on mitochondria and human health, provide an overview of the current knowledge on mitochondrial epigenetics, and describe the experimental and epidemiologic studies that have investigated particular exposures and their relationships with mitochondrial epigenetic modifications. We conclude the chapter with suggestions for future directions in epidemiologic and experimental research that is needed to advance the growing field of mitochondrial epigenetics.
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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: 0] [Impact Index Per Article: 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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Burgstaller JP, Chiaratti MR. Mitochondrial Inheritance Following Nuclear Transfer: From Cloned Animals to Patients with Mitochondrial Disease. Methods Mol Biol 2023; 2647:83-104. [PMID: 37041330 DOI: 10.1007/978-1-0716-3064-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Mitochondria are indispensable power plants of eukaryotic cells that also act as a major biochemical hub. As such, mitochondrial dysfunction, which can originate from mutations in the mitochondrial genome (mtDNA), may impair organism fitness and lead to severe diseases in humans. MtDNA is a multi-copy, highly polymorphic genome that is uniparentally transmitted through the maternal line. Several mechanisms act in the germline to counteract heteroplasmy (i.e., coexistence of two or more mtDNA variants) and prevent expansion of mtDNA mutations. However, reproductive biotechnologies such as cloning by nuclear transfer can disrupt mtDNA inheritance, resulting in new genetic combinations that may be unstable and have physiological consequences. Here, we review the current understanding of mitochondrial inheritance, with emphasis on its pattern in animals and human embryos generated by nuclear transfer.
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Affiliation(s)
- Jörg P Burgstaller
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Marcos R Chiaratti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil.
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Liu H, Liu Y, Wang H, Zhao Q, Zhang T, Xie S, Liu Y, Tang Y, Peng Q, Pang W, Yao W, Zhou J. Geometric Constraints Regulate Energy Metabolism and Cellular Contractility in Vascular Smooth Muscle Cells by Coordinating Mitochondrial DNA Methylation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2203995. [PMID: 36106364 PMCID: PMC9661866 DOI: 10.1002/advs.202203995] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/24/2022] [Indexed: 06/15/2023]
Abstract
Vascular smooth muscle cells (SMCs) can adapt to changes in cellular geometric cues; however, the underlying mechanisms remain elusive. Using 2D micropatterned substrates to engineer cell geometry, it is found that in comparison with an elongated geometry, a square-shaped geometry causes the nuclear-to-cytoplasmic redistribution of DNA methyltransferase 1 (DNMT1), hypermethylation of mitochondrial DNA (mtDNA), repression of mtDNA gene transcription, and impairment of mitochondrial function. Using irregularly arranged versus circumferentially aligned vascular grafts to control cell geometry in 3D growth, it is demonstrated that cell geometry, mtDNA methylation, and vessel contractility are closely related. DNMT1 redistribution is found to be dependent on the phosphoinositide 3-kinase and protein kinase B (AKT) signaling pathways. Cell elongation activates cytosolic phospholipase A2, a nuclear mechanosensor that, when inhibited, hinders AKT phosphorylation, DNMT1 nuclear accumulation, and energy production. The findings of this study provide insights into the effects of cell geometry on SMC function and its potential implications in the optimization of vascular grafts.
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Affiliation(s)
- Han Liu
- Department of Physiology and PathophysiologySchool of Basic Medical Sciences; Hemorheology CenterSchool of Basic Medical SciencesPeking UniversityBeijing100191P. R. China
- Key Laboratory of Molecular Cardiovascular ScienceMinistry of EducationBeijing100191P. R. China
- National Health Commission Key Laboratory of Cardiovascular Molecular Biology and Regulatory PeptidesBeijing Key Laboratory of Cardiovascular Receptors ResearchPeking UniversityBeijing100191P. R. China
| | - Yuefeng Liu
- Department of Physiology and PathophysiologySchool of Basic Medical Sciences; Hemorheology CenterSchool of Basic Medical SciencesPeking UniversityBeijing100191P. R. China
- Key Laboratory of Molecular Cardiovascular ScienceMinistry of EducationBeijing100191P. R. China
- National Health Commission Key Laboratory of Cardiovascular Molecular Biology and Regulatory PeptidesBeijing Key Laboratory of Cardiovascular Receptors ResearchPeking UniversityBeijing100191P. R. China
| | - He Wang
- State Key Laboratory of Medicinal Chemical BiologyKey Laboratory of Bioactive MaterialsMinistry of EducationCollaborative Innovation Center of Chemical Science and Engineering (Tianjin)Nankai UniversityTianjin300071P. R. China
| | - Qiang Zhao
- State Key Laboratory of Medicinal Chemical BiologyKey Laboratory of Bioactive MaterialsMinistry of EducationCollaborative Innovation Center of Chemical Science and Engineering (Tianjin)Nankai UniversityTianjin300071P. R. China
| | - Tao Zhang
- Department of Vascular SurgeryPeking University People's HospitalBeijing100044P. R. China
| | - Si‐an Xie
- Department of Physiology and PathophysiologySchool of Basic Medical Sciences; Hemorheology CenterSchool of Basic Medical SciencesPeking UniversityBeijing100191P. R. China
- Key Laboratory of Molecular Cardiovascular ScienceMinistry of EducationBeijing100191P. R. China
- National Health Commission Key Laboratory of Cardiovascular Molecular Biology and Regulatory PeptidesBeijing Key Laboratory of Cardiovascular Receptors ResearchPeking UniversityBeijing100191P. R. China
| | - Yueqi Liu
- Department of Physiology and PathophysiologySchool of Basic Medical Sciences; Hemorheology CenterSchool of Basic Medical SciencesPeking UniversityBeijing100191P. R. China
- Key Laboratory of Molecular Cardiovascular ScienceMinistry of EducationBeijing100191P. R. China
- National Health Commission Key Laboratory of Cardiovascular Molecular Biology and Regulatory PeptidesBeijing Key Laboratory of Cardiovascular Receptors ResearchPeking UniversityBeijing100191P. R. China
| | - Yuanjun Tang
- Department of Physiology and PathophysiologySchool of Basic Medical Sciences; Hemorheology CenterSchool of Basic Medical SciencesPeking UniversityBeijing100191P. R. China
- Key Laboratory of Molecular Cardiovascular ScienceMinistry of EducationBeijing100191P. R. China
- National Health Commission Key Laboratory of Cardiovascular Molecular Biology and Regulatory PeptidesBeijing Key Laboratory of Cardiovascular Receptors ResearchPeking UniversityBeijing100191P. R. China
| | - Qin Peng
- Institute of Systems and Physical BiologyShenzhen Bay LaboratoryShenzhen518132P. R. China
| | - Wei Pang
- Department of Physiology and PathophysiologySchool of Basic Medical Sciences; Hemorheology CenterSchool of Basic Medical SciencesPeking UniversityBeijing100191P. R. China
| | - Weijuan Yao
- Department of Physiology and PathophysiologySchool of Basic Medical Sciences; Hemorheology CenterSchool of Basic Medical SciencesPeking UniversityBeijing100191P. R. China
| | - Jing Zhou
- Department of Physiology and PathophysiologySchool of Basic Medical Sciences; Hemorheology CenterSchool of Basic Medical SciencesPeking UniversityBeijing100191P. R. China
- Key Laboratory of Molecular Cardiovascular ScienceMinistry of EducationBeijing100191P. R. China
- National Health Commission Key Laboratory of Cardiovascular Molecular Biology and Regulatory PeptidesBeijing Key Laboratory of Cardiovascular Receptors ResearchPeking UniversityBeijing100191P. R. China
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The psychiatric risk gene BRD1 modulates mitochondrial bioenergetics by transcriptional regulation. Transl Psychiatry 2022; 12:319. [PMID: 35941107 PMCID: PMC9359996 DOI: 10.1038/s41398-022-02053-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 06/24/2022] [Accepted: 07/01/2022] [Indexed: 12/03/2022] Open
Abstract
Bromodomain containing 1 (BRD1) encodes an epigenetic regulator that controls the expression of genetic networks linked to mental illness. BRD1 is essential for normal brain development and its role in psychopathology has been demonstrated in genetic and preclinical studies. However, the neurobiology that bridges its molecular and neuropathological effects remains poorly explored. Here, using publicly available datasets, we find that BRD1 targets nuclear genes encoding mitochondrial proteins in cell lines and that modulation of BRD1 expression, irrespective of whether it is downregulation or upregulation of one or the other existing BRD1 isoforms (BRD1-L and BRD1-S), leads to distinct shifts in the expression profile of these genes. We further show that the expression of nuclear genes encoding mitochondrial proteins is negatively correlated with the expression of BRD1 mRNA during human brain development. In accordance, we identify the key gate-keeper of mitochondrial metabolism, Peroxisome proliferator-activated receptor (PPAR) among BRD1's co-transcription factors and provide evidence that BRD1 acts as a co-repressor of PPAR-mediated transcription. Lastly, when using quantitative PCR, mitochondria-targeted fluorescent probes, and the Seahorse XFe96 Analyzer, we demonstrate that modulation of BRD1 expression in cell lines alters mitochondrial physiology (mtDNA content and mitochondrial mass), metabolism (reducing power), and bioenergetics (among others, basal, maximal, and spare respiration) in an expression level- and isoform-dependent manner. Collectively, our data suggest that BRD1 is a transcriptional regulator of nuclear-encoded mitochondrial proteins and that disruption of BRD1's genomic actions alters mitochondrial functions. This may be the mechanism underlying the cellular and atrophic changes of neurons previously associated with BRD1 deficiency and suggests that mitochondrial dysfunction may be a possible link between genetic variation in BRD1 and psychopathology in humans.
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Investigating the role of DNMT1 gene expression on myocardial ischemia reperfusion injury in rat and associated changes in mitochondria. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148566. [PMID: 35489443 DOI: 10.1016/j.bbabio.2022.148566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 04/13/2022] [Accepted: 04/18/2022] [Indexed: 12/31/2022]
Abstract
Altered DNA methylation and mitochondrial dysfunction are the two key features of myocardial ischemia reperfusion injury (I/R), but their association with I/R remains unknown. In the present study, the relationship between DNA methyl transferase1 (DNMT1), the key methylation gene, and the mitochondrial quality control genes in rat heart during I/R was explored. We used the Langendorff rat heart model with 30 min of ischemia followed by 60 min of reperfusion and subsequent inhibition of DNMT1 with 5-azacytidine to evaluate the role of DNA methylation in I/R. Reperfusion significantly increased the expression of the DNMT1 gene, enzyme activity, and global DNA methylation levels, along with decreased mitochondrial copy, electron transport chain (ETC) activities, and ATP level. This was in agreement with the significant downregulation of 11 mitochondrial genes PGC-1α, TFAM, POLG, MFN1 and MFN2, FIS1, PARKIN, OPTN, ND1, ND4L, Cyt B and COX1 in I/R induced rat hearts. The expression pattern of the mitochondrial genes PGC-1α, TFAM, ND1 and Cyt B showed a significant negative correlation with DNMT1 expression. Rate pressure product, index of cardiac performance negatively correlated with DNMT1 expression (r = -0.8231, p = 0.0456). However, DNMT1 inhibited rat hearts via 5-azacytidine significantly improved the heart from I/R injury and reversed the I/R associated changes in the gene expression of TFAM, POLG, PGC-1α, ND1, COX1 and Cyt B, and improved the overall mtDNA copies, with a subsequent improvement in the ETC enzyme activity and ATP levels. To conclude, I/R augmented the DNMT1 activity with a subsequent increase in cardiac injury via downregulating the mitochondrial functional genes.
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12
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Chen K, Lu P, Beeraka NM, Sukocheva OA, Madhunapantula SV, Liu J, Sinelnikov MY, Nikolenko VN, Bulygin KV, Mikhaleva LM, Reshetov IV, Gu Y, Zhang J, Cao Y, Somasundaram SG, Kirkland CE, Fan R, Aliev G. Mitochondrial mutations and mitoepigenetics: Focus on regulation of oxidative stress-induced responses in breast cancers. Semin Cancer Biol 2022; 83:556-569. [PMID: 33035656 DOI: 10.1016/j.semcancer.2020.09.012] [Citation(s) in RCA: 113] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 02/08/2023]
Abstract
Epigenetic regulation of mitochondrial DNA (mtDNA) is an emerging and fast-developing field of research. Compared to regulation of nucler DNA, mechanisms of mtDNA epigenetic regulation (mitoepigenetics) remain less investigated. However, mitochondrial signaling directs various vital intracellular processes including aerobic respiration, apoptosis, cell proliferation and survival, nucleic acid synthesis, and oxidative stress. The later process and associated mismanagement of reactive oxygen species (ROS) cascade were associated with cancer progression. It has been demonstrated that cancer cells contain ROS/oxidative stress-mediated defects in mtDNA repair system and mitochondrial nucleoid protection. Furthermore, mtDNA is vulnerable to damage caused by somatic mutations, resulting in the dysfunction of the mitochondrial respiratory chain and energy production, which fosters further generation of ROS and promotes oncogenicity. Mitochondrial proteins are encoded by the collective mitochondrial genome that comprises both nuclear and mitochondrial genomes coupled by crosstalk. Recent reports determined the defects in the collective mitochondrial genome that are conducive to breast cancer initiation and progression. Mutational damage to mtDNA, as well as its overproliferation and deletions, were reported to alter the nuclear epigenetic landscape. Unbalanced mitoepigenetics and adverse regulation of oxidative phosphorylation (OXPHOS) can efficiently facilitate cancer cell survival. Accordingly, several mitochondria-targeting therapeutic agents (biguanides, OXPHOS inhibitors, vitamin-E analogues, and antibiotic bedaquiline) were suggested for future clinical trials in breast cancer patients. However, crosstalk mechanisms between altered mitoepigenetics and cancer-associated mtDNA mutations remain largely unclear. Hence, mtDNA mutations and epigenetic modifications could be considered as potential molecular markers for early diagnosis and targeted therapy of breast cancer. This review discusses the role of mitoepigenetic regulation in cancer cells and potential employment of mtDNA modifications as novel anti-cancer targets.
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Affiliation(s)
- Kuo Chen
- The First Affiliated Hospital of Zhengzhou University, 1 Jianshedong Street, Zhengzhou, 450052, China; Institue for Regenerative Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia
| | - Pengwei Lu
- The First Affiliated Hospital of Zhengzhou University, 1 Jianshedong Street, Zhengzhou, 450052, China
| | - Narasimha M Beeraka
- Center of Excellence in Regenerative Medicine and Molecular Biology (CEMR), Department of Biochemistry, JSS Academy of Higher Education and Research (JSS AHER), Mysuru, Karnataka, India
| | - Olga A Sukocheva
- Discipline of Health Sciences, College of Nursing and Health Sciences, Flinders University, Bedford Park, South Australia, 5042, Australia
| | - SubbaRao V Madhunapantula
- Center of Excellence in Regenerative Medicine and Molecular Biology (CEMR), Department of Biochemistry, JSS Academy of Higher Education and Research (JSS AHER), Mysuru, Karnataka, India
| | - Junqi Liu
- Cancer Center, The First Affiliated Hospital of Zhengzhou University, 1 Jianshedong Str., Zhengzhou, 450052, China
| | - Mikhail Y Sinelnikov
- Institue for Regenerative Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia
| | - Vladimir N Nikolenko
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia; Department of Normal and Topographic Anatomy, Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University (MSU), 31-5 Lomonosovsky Prospect, 117192, Moscow, Russia
| | - Kirill V Bulygin
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia; Department of Normal and Topographic Anatomy, Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University (MSU), 31-5 Lomonosovsky Prospect, 117192, Moscow, Russia
| | - Liudmila M Mikhaleva
- Research Institute of Human Morphology, 3 Tsyurupy Street, Moscow, 117418, Russian Federation
| | - Igor V Reshetov
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia
| | - Yuanting Gu
- The First Affiliated Hospital of Zhengzhou University, 1 Jianshedong Street, Zhengzhou, 450052, China
| | - Jin Zhang
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia
| | - Yu Cao
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia
| | - Siva G Somasundaram
- Department of Biological Sciences, Salem University, 223 West Main Street Salem, WV, 26426, USA
| | - Cecil E Kirkland
- Department of Biological Sciences, Salem University, 223 West Main Street Salem, WV, 26426, USA
| | - Ruitai Fan
- The First Affiliated Hospital of Zhengzhou University, 1 Jianshedong Street, Zhengzhou, 450052, China.
| | - Gjumrakch Aliev
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia; Research Institute of Human Morphology, 3 Tsyurupy Street, Moscow, 117418, Russian Federation; Institute of Physiologically Active Compounds of Russian Academy of Sciences, Severny pr. 1, Chernogolovka, Moscow Region, 142432, Russia; GALLY International Research Institute, 7733 Louis Pasteur Drive, #330, San Antonio, TX, 78229, USA
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Wagner A, Kosnacova H, Chovanec M, Jurkovicova D. Mitochondrial Genetic and Epigenetic Regulations in Cancer: Therapeutic Potential. Int J Mol Sci 2022; 23:ijms23147897. [PMID: 35887244 PMCID: PMC9321253 DOI: 10.3390/ijms23147897] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/12/2022] [Accepted: 07/14/2022] [Indexed: 02/01/2023] Open
Abstract
Mitochondria are dynamic organelles managing crucial processes of cellular metabolism and bioenergetics. Enabling rapid cellular adaptation to altered endogenous and exogenous environments, mitochondria play an important role in many pathophysiological states, including cancer. Being under the control of mitochondrial and nuclear DNA (mtDNA and nDNA), mitochondria adjust their activity and biogenesis to cell demands. In cancer, numerous mutations in mtDNA have been detected, which do not inactivate mitochondrial functions but rather alter energy metabolism to support cancer cell growth. Increasing evidence suggests that mtDNA mutations, mtDNA epigenetics and miRNA regulations dynamically modify signalling pathways in an altered microenvironment, resulting in cancer initiation and progression and aberrant therapy response. In this review, we discuss mitochondria as organelles importantly involved in tumorigenesis and anti-cancer therapy response. Tumour treatment unresponsiveness still represents a serious drawback in current drug therapies. Therefore, studying aspects related to genetic and epigenetic control of mitochondria can open a new field for understanding cancer therapy response. The urgency of finding new therapeutic regimens with better treatment outcomes underlines the targeting of mitochondria as a suitable candidate with new therapeutic potential. Understanding the role of mitochondria and their regulation in cancer development, progression and treatment is essential for the development of new safe and effective mitochondria-based therapeutic regimens.
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Affiliation(s)
- Alexandra Wagner
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (A.W.); (H.K.); (M.C.)
- Department of Simulation and Virtual Medical Education, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia
| | - Helena Kosnacova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (A.W.); (H.K.); (M.C.)
- Department of Simulation and Virtual Medical Education, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia
| | - Miroslav Chovanec
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (A.W.); (H.K.); (M.C.)
| | - Dana Jurkovicova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (A.W.); (H.K.); (M.C.)
- Correspondence:
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14
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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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15
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Lang M, Grünewald A, Pramstaller PP, Hicks AA, Pichler I. A genome on shaky ground: exploring the impact of mitochondrial DNA integrity on Parkinson's disease by highlighting the use of cybrid models. Cell Mol Life Sci 2022; 79:283. [PMID: 35513611 PMCID: PMC9072496 DOI: 10.1007/s00018-022-04304-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/01/2022] [Accepted: 04/12/2022] [Indexed: 11/29/2022]
Abstract
Mitochondria play important roles in the regulation of key cellular processes, including energy metabolism, oxidative stress response, and signaling towards cell death or survival, and are distinguished by carrying their own genome (mtDNA). Mitochondrial dysfunction has emerged as a prominent cellular mechanism involved in neurodegeneration, including Parkinson’s disease (PD), a neurodegenerative movement disorder, characterized by progressive loss of dopaminergic neurons and the occurrence of proteinaceous Lewy body inclusions. The contribution of mtDNA variants to PD pathogenesis has long been debated and is still not clearly answered. Cytoplasmic hybrid (cybrid) cell models provided evidence for a contribution of mtDNA variants to the PD phenotype. However, conclusive evidence of mtDNA mutations as genetic cause of PD is still lacking. Several models have shown a role of somatic, rather than inherited mtDNA variants in the impairment of mitochondrial function and neurodegeneration. Accordingly, several nuclear genes driving inherited forms of PD are linked to mtDNA quality control mechanisms, and idiopathic as well as familial PD tissues present increased mtDNA damage. In this review, we highlight the use of cybrids in this PD research field and summarize various aspects of how and to what extent mtDNA variants may contribute to the etiology of PD.
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Affiliation(s)
- Martin Lang
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy.
| | - Anne Grünewald
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg
| | - Peter P Pramstaller
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy.,Department of Neurology, University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Andrew A Hicks
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Irene Pichler
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy.
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16
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Guitton R, Dölle C, Alves G, Ole-Bjørn T, Nido GS, Tzoulis C. Ultra-deep whole genome bisulfite sequencing reveals a single methylation hotspot in human brain mitochondrial DNA. Epigenetics 2022; 17:906-921. [PMID: 35253628 PMCID: PMC9423827 DOI: 10.1080/15592294.2022.2045754] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
While DNA methylation is established as a major regulator of gene expression in the nucleus, the existence of mitochondrial DNA (mtDNA) methylation remains controversial. Here, we characterized the mtDNA methylation landscape in the prefrontal cortex of neurological healthy individuals (n=26) and patients with Parkinson’s disease (n=27), using a combination of whole-genome bisulphite sequencing (WGBS) and bisulphite-independent methods. Accurate mtDNA mapping from WGBS data required alignment to an mtDNA reference only, to avoid misalignment to nuclear mitochondrial pseudogenes. Once correctly aligned, WGBS data provided ultra-deep mtDNA coverage (16,723 ± 7,711) and revealed overall very low levels of cytosine methylation. The highest methylation levels (5.49 ± 0.97%) were found on CpG position m.545, located in the heavy-strand promoter 1 region. The m.545 methylation was validated using a combination of methylation-sensitive DNA digestion and quantitative PCR analysis. We detected no association between mtDNA methylation profile and Parkinson’s disease. Interestingly, m.545 methylation correlated with the levels of mtDNA transcripts, suggesting a putative role in regulating mtDNA gene expression. In addition, we propose a robust framework for methylation analysis of mtDNA from WGBS data, which is less prone to false-positive findings due to misalignment of nuclear mitochondrial pseudogene sequences.
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Affiliation(s)
- Romain Guitton
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Christian Dölle
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Guido Alves
- The Norwegian Centre for Movement Disorders and Department of Neurology, Stavanger University Hospital, Stavanger, Norway.,Department of Mathematics and Natural Sciences, University of Stavanger, University of Bergen, Stavanger, Norway
| | - Tysnes Ole-Bjørn
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Gonzalo S Nido
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Charalampos Tzoulis
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Medicine, University of Bergen, Bergen, Norway
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17
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Czegle I, Gray AL, Wang M, Liu Y, Wang J, Wappler-Guzzetta EA. Mitochondria and Their Relationship with Common Genetic Abnormalities in Hematologic Malignancies. Life (Basel) 2021; 11:1351. [PMID: 34947882 PMCID: PMC8707674 DOI: 10.3390/life11121351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 11/16/2022] Open
Abstract
Hematologic malignancies are known to be associated with numerous cytogenetic and molecular genetic changes. In addition to morphology, immunophenotype, cytochemistry and clinical characteristics, these genetic alterations are typically required to diagnose myeloid, lymphoid, and plasma cell neoplasms. According to the current World Health Organization (WHO) Classification of Tumors of Hematopoietic and Lymphoid Tissues, numerous genetic changes are highlighted, often defining a distinct subtype of a disease, or providing prognostic information. This review highlights how these molecular changes can alter mitochondrial bioenergetics, cell death pathways, mitochondrial dynamics and potentially be related to mitochondrial genetic changes. A better understanding of these processes emphasizes potential novel therapies.
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Affiliation(s)
- Ibolya Czegle
- Department of Internal Medicine and Haematology, Semmelweis University, H-1085 Budapest, Hungary;
| | - Austin L. Gray
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA; (A.L.G.); (Y.L.); (J.W.)
| | - Minjing Wang
- Independent Researcher, Diamond Bar, CA 91765, USA;
| | - Yan Liu
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA; (A.L.G.); (Y.L.); (J.W.)
| | - Jun Wang
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA; (A.L.G.); (Y.L.); (J.W.)
| | - Edina A. Wappler-Guzzetta
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA; (A.L.G.); (Y.L.); (J.W.)
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18
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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: 2] [Impact Index Per Article: 0.7] [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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19
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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: 0.7] [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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20
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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: 5.3] [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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21
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Zhou Z, Goodrich JM, Strakovsky RS. Mitochondrial Epigenetics and Environmental Health: Making a Case for Endocrine Disrupting Chemicals. Toxicol Sci 2021; 178:16-25. [PMID: 32777053 DOI: 10.1093/toxsci/kfaa129] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Recent studies implicate mitochondrial dysfunction in the development and progression of numerous chronic diseases, which may be partially due to modifications in mitochondrial DNA (mtDNA). There is also mounting evidence that epigenetic modifications to mtDNA may be an additional layer of regulation that controls mitochondrial biogenesis and function. Several environmental factors (eg, smoking, air pollution) have been associated with altered mtDNA methylation in a handful of mechanistic studies and in observational human studies. However, little is understood about other environmental contaminants that induce mtDNA epigenetic changes. Numerous environmental toxicants are classified as endocrine disrupting chemicals (EDCs). Beyond their actions on hormonal pathways, EDC exposure is associated with elevated oxidative stress, which may occur through or result in mitochondrial dysfunction. Although only a few studies have assessed the impacts of EDCs on mtDNA methylation, the current review provides reasons to consider mtDNA epigenetic disruption as a mechanism of action of EDCs and reviews potential limitations related to currently available evidence. First, there is sufficient evidence that EDCs (including bisphenols and phthalates) directly target mitochondrial function, and more direct evidence is needed to connect this to mtDNA methylation. Second, these and other EDCs are potent modulators of nuclear DNA epigenetics, including DNA methylation and histone modifications. Finally, EDCs have been shown to disrupt several modulators of mtDNA methylation, including DNA methyltransferases and the mitochondrial transcription factor A/nuclear respiratory factor 1 pathway. Taken together, these studies highlight the need for future research evaluating mtDNA epigenetic disruption by EDCs and to detail specific mechanisms responsible for such disruptions.
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Affiliation(s)
- Zheng Zhou
- Department of Animal Sciences, Michigan State University, East Lansing, Michigan 48824
| | - Jaclyn M Goodrich
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan 48109
| | - Rita S Strakovsky
- Department of Food Science and Human Nutrition.,Institute for Integrative Toxicology, Michigan State University, East Lansing, Michigan 48824
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22
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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: 21] [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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23
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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: 69] [Impact Index Per Article: 23.0] [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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24
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Goldsmith C, Rodríguez-Aguilera JR, El-Rifai I, Jarretier-Yuste A, Hervieu V, Raineteau O, Saintigny P, Chagoya de Sánchez V, Dante R, Ichim G, Hernandez-Vargas H. Low biological fluctuation of mitochondrial CpG and non-CpG methylation at the single-molecule level. Sci Rep 2021; 11:8032. [PMID: 33850190 PMCID: PMC8044111 DOI: 10.1038/s41598-021-87457-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/30/2021] [Indexed: 12/16/2022] Open
Abstract
Mammalian cytosine DNA methylation (5mC) is associated with the integrity of the genome and the transcriptional status of nuclear DNA. Due to technical limitations, it has been less clear if mitochondrial DNA (mtDNA) is methylated and whether 5mC has a regulatory role in this context. Here, we used bisulfite-independent single-molecule sequencing of native human and mouse DNA to study mitochondrial 5mC across different biological conditions. We first validated the ability of long-read nanopore sequencing to detect 5mC in CpG (5mCpG) and non-CpG (5mCpH) context in nuclear DNA at expected genomic locations (i.e. promoters, gene bodies, enhancers, and cell type-specific transcription factor binding sites). Next, using high coverage nanopore sequencing we found low levels of mtDNA CpG and CpH methylation (with several exceptions) and little variation across biological processes: differentiation, oxidative stress, and cancer. 5mCpG and 5mCpH were overall higher in tissues compared to cell lines, with small additional variation between cell lines of different origin. Despite general low levels, global and single-base differences were found in cancer tissues compared to their adjacent counterparts, in particular for 5mCpG. In conclusion, nanopore sequencing is a useful tool for the detection of modified DNA bases on mitochondria that avoid the biases introduced by bisulfite and PCR amplification. Enhanced nanopore basecalling models will provide further resolution on the small size effects detected here, as well as rule out the presence of other DNA modifications such as oxidized forms of 5mC.
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Affiliation(s)
- Chloe Goldsmith
- Department of Tumor Escape, Resistance and Immunity, TGF-Beta and Immuno-Regulation Team, Cancer Research Centre of Lyon (CRCL), INSERM U 1052, CNRS UMR 5286, UCBL1, Université de Lyon, Centre Léon Bérard, 28 rue Laennec, 69373, Lyon Cedex 08, France.
| | - Jesús Rafael Rodríguez-Aguilera
- Department of Cellular Biology and Development, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, 04510, Mexico City, Mexico
| | - Ines El-Rifai
- Department of Tumor Escape, Resistance and Immunity, TGF-Beta and Immuno-Regulation Team, Cancer Research Centre of Lyon (CRCL), INSERM U 1052, CNRS UMR 5286, UCBL1, Université de Lyon, Centre Léon Bérard, 28 rue Laennec, 69373, Lyon Cedex 08, France
| | - Adrien Jarretier-Yuste
- Department of Tumor Escape, Resistance and Immunity, TGF-Beta and Immuno-Regulation Team, Cancer Research Centre of Lyon (CRCL), INSERM U 1052, CNRS UMR 5286, UCBL1, Université de Lyon, Centre Léon Bérard, 28 rue Laennec, 69373, Lyon Cedex 08, France
| | - Valérie Hervieu
- Department of Surgical Pathology, Hospices Civils de Lyon, Groupement Hospitalier Est, Lyon, France
| | - Olivier Raineteau
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM, Stem Cell and Brain Research Institute U1208, Bron, France
| | - Pierre Saintigny
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, France
- Department of Translational Medicine, Centre Léon Bérard, Lyon, France
| | - Victoria Chagoya de Sánchez
- Department of Cellular Biology and Development, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, 04510, Mexico City, Mexico
| | - Robert Dante
- Dependence Receptors Cancer and Development Laboratory, Department of Signaling of Tumoral Escape. Cancer Research. Center of Lyon (CRCL), Inserm U 1052, CNRS UMR 5286, Université de Lyon, Centre Léon Bérard, 28 rue Laennec, 69373, Lyon Cedex 08, France
| | - Gabriel Ichim
- Cancer Cell Death Laboratory, Part of LabEx DEVweCAN, Université de Lyon, Lyon, France
- Cancer Research Centre of Lyon (CRCL), Inserm U 1052, CNRS UMR 5286, Université de Lyon, Centre Léon Bérard, 28 rue Laennec, 69373, Lyon Cedex 08, France
| | - Hector Hernandez-Vargas
- Department of Tumor Escape, Resistance and Immunity, TGF-Beta and Immuno-Regulation Team, Cancer Research Centre of Lyon (CRCL), INSERM U 1052, CNRS UMR 5286, UCBL1, Université de Lyon, Centre Léon Bérard, 28 rue Laennec, 69373, Lyon Cedex 08, France.
- Department of Translational Medicine, Centre Léon Bérard, Lyon, France.
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25
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Pérez-Muñoz AA, de Lourdes Muñoz M, García-Hernández N, Santander-Lucio H. A New Approach to Identify the Methylation Sites in the Control Region of Mitochondrial DNA. Curr Mol Med 2021; 21:151-164. [PMID: 32484108 DOI: 10.2174/1566524020666200528154005] [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: 12/28/2019] [Revised: 04/13/2020] [Accepted: 04/15/2020] [Indexed: 11/22/2022]
Abstract
Mitochondrial DNA (mtDNA) methylation has the potential to be used as a biomarker of human development or disease. However, mtDNA methylation procedures are costly and time-consuming. Therefore, we developed a new approach based on an RT-PCR assay for the base site identification of methylated cytosine in the control region of mtDNA through a simple, fast, specific, and low-cost strategy. Total DNA was purified, and methylation was determined by RT-PCR bisulfite sequencing. This procedure included the DNA purification, bisulfite treatment and RT-PCR amplification of the control region divided into three subregions with specific primers. Sequences obtained with and without the bisulfite treatment were compared to identify the methylated cytosine dinucleotides. Furthermore, the efficiency of C to U conversion of cytosines was assessed by including a negative control. Interestingly, mtDNA methylation was observed mainly within non-Cphosphate- G (non-CpG) dinucleotides and mostly in the regions containing regulatory elements, such as OH or CSBI, CSBII, and CSBIII. This new approach will promote the generation of new information regarding mtDNA methylation patterns in samples from patients with different pathologies or that are exposed to a toxic environment in diverse human populations.
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Affiliation(s)
- Ashael Alfredo Pérez-Muñoz
- Department of Genetics and Molecular Biology, Research and Advanced Studies Center of National Polytechnic Institute (CINVESTAV of IPN), Mexico City, Mexico
| | - María de Lourdes Muñoz
- Department of Genetics and Molecular Biology, Research and Advanced Studies Center of National Polytechnic Institute (CINVESTAV of IPN), Mexico City, Mexico
| | - Normand García-Hernández
- Unidad de Investigacion Medica en Genetica Humana, Unidad Medica de Alta Especialidad Hospital de Pediatria "Dr. Silvestre Frenk Freund", Centro Medico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Heriberto Santander-Lucio
- Department of Genetics and Molecular Biology, Research and Advanced Studies Center of National Polytechnic Institute (CINVESTAV of IPN), Mexico City, Mexico
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26
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F C Lopes A. Mitochondrial metabolism and DNA methylation: a review of the interaction between two genomes. Clin Epigenetics 2020; 12:182. [PMID: 33228792 PMCID: PMC7684747 DOI: 10.1186/s13148-020-00976-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/10/2020] [Indexed: 02/06/2023] Open
Abstract
Mitochondria are controlled by the coordination of two genomes: the mitochondrial and the nuclear DNA. As such, variations in nuclear gene expression as a consequence of mutations and epigenetic modifications can affect mitochondrial functionality. Conversely, the opposite could also be true. However, the relationship between mitochondrial dysfunction and epigenetics, such as nuclear DNA methylation, remains largely unexplored.
Mitochondria function as central metabolic hubs controlling some of the main substrates involved in nuclear DNA methylation, via the one carbon metabolism, the tricarboxylic acid cycle and the methionine pathway. Here, we review key findings and highlight new areas of focus, with the ultimate goal of getting one step closer to understanding the genomic effects of mitochondrial dysfunction on nuclear epigenetic landscapes.
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Affiliation(s)
- Amanda F C Lopes
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK. .,Medical Research Council - Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK.
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27
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Sanyal T, Paul M, Bhattacharjee S, Bhattacharjee P. Epigenetic alteration of mitochondrial biogenesis regulatory genes in arsenic exposed individuals (with and without skin lesions) and in skin cancer tissues: A case control study. CHEMOSPHERE 2020; 258:127305. [PMID: 32563914 DOI: 10.1016/j.chemosphere.2020.127305] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/28/2020] [Accepted: 06/01/2020] [Indexed: 05/22/2023]
Abstract
Chronic arsenic toxicity has become a global concern due to its adverse pathophysiological outcome and carcinogenic potential. It is already established that arsenic induced reactive oxygen species alters mitochondrial functionality. Major regulatory genes for mitochondrial biogenesis, i.e., PGC1α, Tfam, NRF1and NRF2 are located in the nucleus. As a result, mitochondria-nucleus crosstalk is crucial for proper mitochondrial function. This previous hypothesis led us to investigateinvolvement of epigenetic alteration behindenhanced mitochondrial biogenesis in chronic arsenic exposure. An extensive case-control study was conducted with 390 study participants (unexposed, exposed without skin lesion, exposed with skin lesion and exposed skin tumour) from highly arsenic exposed areas ofWest Bengal, India. Methylation specific PCRrevealed significant promoter hypomethylation oftwo key biogenesis regulatory genes, PGC1αandTfam in arsenic exposed individuals and also in skin tumour tissues. Linear regression analysis indicated significant negative correlation between urinary arsenic concentration and promoter methylation status. Increased expression of biogenesis regulatory genes wasobtained by quantitative real-time PCR analysis. Moreover, altered mitochondrial fusion-fission regulatory gene expression was also observed in skin tumour tissues. miR663, having tumour suppressor gene like function was known to be epigenetically regulated through mitochondrial retrograde signal. Promoter hypermethylation with significantly decreased expression of miR663 was found in skin cancer tissues compared to non-cancerous control tissue. In conclusion, results indicated crucial role of epigenetic alteration in arsenic induced mitochondrial biogenesis and arsenical skin carcinogenesis for the first time. However, further mechanistic studies are necessary for detailed understanding of mitochondria-nucleus crosstalk in arsenic perturbation.
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Affiliation(s)
- Tamalika Sanyal
- Department of Zoology, University of Calcutta, Kolkata, 700019, India; Department of Environmental Science, University of Calcutta, Kolkata, 700019, India
| | - Manabi Paul
- Department of Environmental Science, University of Calcutta, Kolkata, 700019, India
| | | | - Pritha Bhattacharjee
- Department of Environmental Science, University of Calcutta, Kolkata, 700019, India.
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28
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Doke M, Jeganathan V, McLaughlin JP, Samikkannu T. HIV-1 Tat and cocaine impact mitochondrial epigenetics: effects on DNA methylation. Epigenetics 2020; 16:980-999. [PMID: 33100130 PMCID: PMC8451453 DOI: 10.1080/15592294.2020.1834919] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
Human immunodeficiency virus (HIV) infection and the psychostimulant drug cocaine are known to induce epigenetic changes in DNA methylation that are linked with the severity of viral replication and disease progression, which impair neuronal functions. Increasing evidence suggests that changes in DNA methylation and hydroxymethylation occur in mitochondrial DNA (mtDNA) and represent mitochondrial genome epigenetic modifications (mitoepigenetic modifications). These modifications likely regulate both mtDNA replication and gene expression. However, mtDNA methylation has not been studied extensively in the contexts of cocaine abuse and HIV-1 infection. In the present study, epigenetic factors changed the levels of the DNA methyltransferases (DNMTs) DNMT1, DNMT3a, and DNMT3b, the Ten-eleven translocation (TET) enzymes 1, 2, and 3, and mitochondrial DNMTs (mtDNMTs) both in vitro and in vivo. These changes resulted in alterations in mtDNA methylation levels at CpG and non-CpG sites in human primary astrocytes as measured using targeted next-generation bisulphite sequencing (TNGBS). Moreover, mitochondrial methylation levels in the MT-RNR1, MT-ND5, MT-ND1, D-loop and MT-CYB regions of mtDNA were lower in the HIV-1 Tat and cocaine treatment groups than in the control group. In summary, the present findings suggest that mitoepigenetic modification in the human brain causes the mitochondrial dysfunction that gives rise to neuro-AIDS.
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Affiliation(s)
- Mayur Doke
- Department of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, Kingsville, TX, USA
| | - Venkatesh Jeganathan
- Department of Autoimmune and Musculoskeletal Disease, The Feinstein Institute for Medical Research, Manhasset, NY, USA
| | - Jay P McLaughlin
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Thangavel Samikkannu
- Department of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, Kingsville, TX, USA
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29
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Stewart JB, Chinnery PF. Extreme heterogeneity of human mitochondrial DNA from organelles to populations. Nat Rev Genet 2020; 22:106-118. [PMID: 32989265 DOI: 10.1038/s41576-020-00284-x] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2020] [Indexed: 02/06/2023]
Abstract
Contrary to the long-held view that most humans harbour only identical mitochondrial genomes, deep resequencing has uncovered unanticipated extreme genetic variation within mitochondrial DNA (mtDNA). Most, if not all, humans contain multiple mtDNA genotypes (heteroplasmy); specific patterns of variants accumulate in different tissues, including cancers, over time; and some variants are preferentially passed down or suppressed in the maternal germ line. These findings cast light on the origin and spread of mtDNA mutations at multiple scales, from the organelle to the human population, and challenge the conventional view that high percentages of a mutation are required before a new variant has functional consequences.
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Affiliation(s)
- James B Stewart
- Max Planck Institute for Biology of Ageing, Cologne, Germany.,Wellcome Centre for Mitochondrial Research, Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK. .,Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
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30
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Bunkar N, Sharma J, Chouksey A, Kumari R, Gupta PK, Tiwari R, Lodhi L, Srivastava RK, Bhargava A, Mishra PK. Clostridium perfringens phospholipase C impairs innate immune response by inducing integrated stress response and mitochondrial-induced epigenetic modifications. Cell Signal 2020; 75:109776. [PMID: 32916276 DOI: 10.1016/j.cellsig.2020.109776] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/27/2020] [Accepted: 09/06/2020] [Indexed: 10/23/2022]
Abstract
Clostridium perfringens, a rod-shaped, gram-positive, anaerobic, spore-forming bacterium is one of the most widely occurring bacterial pathogens, associated with a spectrum of diseases in humans. A major virulence factor during its infection is the enzyme phospholipase C encoded by the plc gene, known as Clostridium perfringens phospholipase C (CpPLC). The present study was designed to understand the role of CpPLC in inducing survival mechanisms and mitochondrial-induced epigenetic changes in a human lymphocyte cell culture model. Following exposure to CpPLC, a significant generation of mitochondrial reactive oxygen species was observed, which coincided with the changes in the expression of vital components of MAP/ERK/RTK signaling cascade that regulates the downstream cellular functions. These disturbances further led to alterations in the mitochondrial genome and functioning. This was supported by the observed upregulation in the expression of mitochondrial fission genes Drp1, Fis1, and Mff, and mitochondrial fusion genes MFN1, MFN2, and OPA1 following CpPLC exposure. CpPLC exposed cells showed upregulation of OMA1, DELE1, and HRI genes involved in the integrated stress response (ISR), which suggests that it may induce the ISR that provides a pro-survival mechanism to the host cell. CpPLC also initiated immune patho-physiologic mechanisms including mitochondrial-induced epigenetic modifications through a mitochondrial-ROS driven signaling pathway. Interestingly, epigenetic machinery not only play a pivotal role in lymphocyte homeostasis by contributing to cell-fate decisions but thought to be one of the mechanisms by which intracellular pathogens survive within the host cells. Importantly, the impairment of mtDNA repair among the CpPLC exposed cells, induced alterations within mtDNA methylation, and led to the deregulation of MT-CO1, MT-ND6, MT-ATPase 6, and MT-ATPase8 gene expression profiles that are important for mitochondrial bioenergetics and subsequent metabolic pathways. This was further confirmed by the changes in the activity of mitochondrial electron chain complexes (complex I, II, III, IV and V). The altered mtDNA methylation profile was also found to be closely associated with the varied expression of mitomiRs and their targets. CpPLC exposed cells showed up-regulation of miR24 expression and down-regulation of miR34a, miR150, and miR155, while the increased expression of mitomiR target genes i.e. of K-Ras, MYC, EGFR, and NF-kβ was also observed in these cells. Altogether, our findings provide novel insights into the derailment of redox signaling machinery in CpPLC treated lymphocytes and its role in the induction of survival mechanisms and mitochondrial-induced epigenetic modifications.
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Affiliation(s)
- Neha Bunkar
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Jahnavi Sharma
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Anju Chouksey
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Roshani Kumari
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Pushpendra Kumar Gupta
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Rajnarayan Tiwari
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Lalit Lodhi
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | | | - Arpit Bhargava
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Pradyumna Kumar Mishra
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India.
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31
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Sivalingam K, Samikkannu T. Neuroprotective Effect of Piracetam against Cocaine-Induced Neuro Epigenetic Modification of DNA Methylation in Astrocytes. Brain Sci 2020; 10:E611. [PMID: 32899583 PMCID: PMC7565945 DOI: 10.3390/brainsci10090611] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/29/2020] [Accepted: 09/03/2020] [Indexed: 01/27/2023] Open
Abstract
Cocaine abuse is known to alter mitochondrial biogenesis and induce epigenetic modification linked with neuronal dysfunction. Cocaine-induced epigenetic modification of DNA methylation and the mitochondrial genome may affect mitochondrial DNA (mtDNA) and nuclear DNA (nDNA), as epigenetic DNA methylation is key to maintaining genomic integrity in the central nervous system (CNS). However, the impact of cocaine-mediated epigenetic changes in astrocytes has not yet been elucidated. In this study, we explored the neuroprotective effect of piracetam against cocaine-induced epigenetic changes in DNA methylation in astrocytes. To study our hypothesis, we exposed human astrocytes to cocaine alone or in combination with the nootropic drug piracetam. We examined the expression of the DNA methyltransferases (DNMTs) DNMT-1, DNMT-3A, and DNMT-3B; global DNA methylation levels of 5-methycytosine (5-mC); and induction of ten-eleven translocation (TET) enzymes in astrocytes. In addition, we analyzed mtDNA methylation by targeted next-generation bisulfite sequencing. Our data provide evidence that cocaine impairs DNMT activity and thereby has impacts on mtDNA, which might contribute to the neurodegeneration observed in cocaine users. These effects might be at least partially prevented by piracetam, allowing neuronal function to be maintained.
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Affiliation(s)
| | - Thangavel Samikkannu
- Department of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, 1010 W Avenue B, Kingsville, TX 78363, USA;
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Hassanzadeh M, Mahernia S, Caprini G, Fossati G, Adib M, Moakedi F, Amanlou M. Epigenetic-based cancer therapeutics: new potential HDAC8 inhibitors. J Biomol Struct Dyn 2020; 40:297-311. [DOI: 10.1080/07391102.2020.1813203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Malihe Hassanzadeh
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Shabnam Mahernia
- Drug Design and Development Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
| | - Gianluca Caprini
- Centre for Research, Italfarmaco, S.p.A., Cinisello Balsamo, Italy
| | - Gianluca Fossati
- Centre for Research, Italfarmaco, S.p.A., Cinisello Balsamo, Italy
| | - Mehdi Adib
- School of Chemistry, College of Science, University of Tehran, Tehran, Iran
| | - Faezeh Moakedi
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Massoud Amanlou
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Drug Design and Development Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
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Milazzotto MP, de Lima CB, da Fonseca AM, dos Santos EC, Ispada J. Erasing gametes to write blastocysts: metabolism as the new player in epigenetic reprogramming. Anim Reprod 2020; 17:e20200015. [PMID: 33029209 PMCID: PMC7534565 DOI: 10.1590/1984-3143-ar2020-0015] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/23/2020] [Indexed: 12/13/2022] Open
Abstract
Understanding preimplantation embryonic development is crucial for the improvement of assisted reproductive technologies and animal production. To achieve this goal, it is important to consider that gametes and embryos are highly susceptible to environmental changes. Beyond the metabolic adaptation, the dynamic status imposed during follicular growth and early embryogenesis may create marks that will guide the molecular regulation during prenatal development, and consequently impact the offspring phenotype. In this context, metaboloepigenetics has gained attention, as it investigates the crosstalk between metabolism and molecular control, i.e., how substrates generated by metabolic pathways may also act as players of epigenetic modifications. In this review, we present the main metabolic and epigenetic events of pre-implantation development, and how these systems connect to open possibilities for targeted manipulation of reproductive technologies and animal production systems.
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Affiliation(s)
- Marcella Pecora Milazzotto
- Laboratório de Epigenética e Metabolismo Embrionário, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brasil
- Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Camila Bruna de Lima
- Laboratório de Epigenética e Metabolismo Embrionário, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brasil
- Département des Sciences Animales, Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle, Faculté des Sciences de l’Agriculture et de l’Alimentation, Université Laval, Quebec, Canada
| | - Aldcejam Martins da Fonseca
- Laboratório de Epigenética e Metabolismo Embrionário, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brasil
| | - Erika Cristina dos Santos
- Laboratório de Epigenética e Metabolismo Embrionário, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brasil
| | - Jessica Ispada
- Laboratório de Epigenética e Metabolismo Embrionário, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brasil
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Nguyen H, LaFramboise T. Complexities and pitfalls in analyzing and interpreting mitochondrial DNA content in human cancer. J Genet Genomics 2020; 47:349-359. [PMID: 33004308 DOI: 10.1016/j.jgg.2020.04.007] [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: 12/21/2019] [Revised: 04/01/2020] [Accepted: 04/20/2020] [Indexed: 11/29/2022]
Abstract
Mutations in the human mitochondrial genome have been observed in all types of human cancer, indicating that mutations might contribute to tumorigenesis, metastasis, recurrence, or drug response. This possibility is appealing because of the known shift from oxidative metabolism to glycolysis, known as the Warburg effect, that occurs in malignancy. Mitochondrial DNA (mtDNA) mutations could either be maternally inherited and predispose to cancer (germ line mutations) or occur sporadically in the mtDNA of specific tissues (tissue- or tumor-specific somatic mutations) and contribute to the tumor initiation and progression process. High-throughput sequencing technologies now enable comprehensive detection of mtDNA variation in tissues and bodily fluids, with the potential to be used as an early detection tool that may impact the treatment of cancer. Here, we discuss insights into the roles of mtDNA mutations in carcinogenesis, highlighting the complexities involved in the analysis and interpretation of mitochondrial genomic content, technical challenges in studying their contribution to pathogenesis, and the value of mtDNA mutations in developing early detection, diagnosis, prognosis, and therapeutic strategies for cancer.
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Affiliation(s)
- Hieu Nguyen
- Vinmec Research Institute of Stem Cell and Gene Technology (VRSIG), 458 Minh Khai, Vinh Tuy, Hai Ba Trung, Hanoi, Viet Nam; Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Thomas LaFramboise
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA.
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Bi H, Hojo K, Watanabe M, Yee C, Maski K, Saba S, Graff-Radford J, Machulda MM, St Louis EK, Humes IS, Flanagan EP, Nicolau S, Jones DT, Patterson MC, Kotagal S, Raz Y, Niu Z, Li J, Klein CJ. Expanded genetic insight and clinical experience of DNMT1-complex disorder. NEUROLOGY-GENETICS 2020; 6:e456. [PMID: 32754641 PMCID: PMC7357420 DOI: 10.1212/nxg.0000000000000456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/30/2020] [Indexed: 11/16/2022]
Abstract
Objective To report novel causal mutations, expanded clinical phenotypes, and clinical management of DNA methyltransferase 1 (DNMT1)-complex disorder. Methods Neurophysiologic testing, imaging, and genetic findings were summarized in clinical context for 5 cases with DNMT1-complex disorder. Results We identified 2 novel DNMT1 mutations (p.E510K and p.P1546A) by whole-exome sequencing (WES). Case 1 (p.E510K) presented with childhood ataxia, treatment-refractory seizures, and rapid cognitive decline in his 50s. Case 2 also had childhood onset and presented with seizures, language regression, hearing loss, narcolepsy with cataplexy symptoms, optic atrophy, sensory neuropathy, and hypogammaglobulinemia requiring IV immunoglobulin. Case 2 (p.P1546A) was identified with a de novo and the first mutation residing outside the targeting sequence domain. Case 3 (p.A570V) had paralytic asymmetric onset attacks triggered by emotionality and lasting sometimes for weeks. Neuropsychological testing showed executive dysfunction localizing to frontosubcortical and frontoparietal structures. He gradually developed left predominant brain atrophy. MRI showed T2 hyperintense lesions that enhanced on T1 postgadolinium images, and brain PET showed hypometabolism in atrophied regions. Case 4 (p.T497P) underwent left cochlear implant, resulting in significant hearing improvements at all tested frequencies (250–6,000 Hz). Case 5 (p.Y511H) had profound gait ataxia with posterior column atrophy of the spinal cord and abnormal evoked potentials primarily affecting the fasciculus gracilis. Conclusions Broader application of WES further expands genotype-phenotype correlations of DNMT1-complex disorder. Two mutations are identified with early childhood onsets. The expanded new phenotypes include asymmetric brain hemiatrophy with parenchymal gadolinium enhancement, spinal cord atrophy, prolonged cataplectic spells, and hypogammaglobulinemia. Hearing loss treatment by cochlear implantation is helpful and should be considered.
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Affiliation(s)
- Hongyan Bi
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Kaori Hojo
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Masashi Watanabe
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Christina Yee
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Kiran Maski
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Sadaf Saba
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Jonathan Graff-Radford
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Mary M Machulda
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Erik K St Louis
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Ilona Spitsyna Humes
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Eoin P Flanagan
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Stefan Nicolau
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - David T Jones
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Marc C Patterson
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Suresh Kotagal
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Yael Raz
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Zhiyv Niu
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Jun Li
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Christopher J Klein
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
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Zhu X, Xuan Z, Chen J, Li Z, Zheng S, Song P. How DNA methylation affects the Warburg effect. Int J Biol Sci 2020; 16:2029-2041. [PMID: 32549751 PMCID: PMC7294934 DOI: 10.7150/ijbs.45420] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 04/05/2020] [Indexed: 12/13/2022] Open
Abstract
Significant enhancement of the glycolysis pathway is a major feature of tumor cells, even in the presence of abundant oxygen; this enhancement is known as the Warburg effect, and also called aerobic glycolysis. The Warburg effect was discovered nearly a hundred years ago, but its specific mechanism remains difficult to explain. DNA methylation is considered to be a potential trigger for the Warburg effect, as the two processes have many overlapping links during tumorigenesis. Based on a widely recognized potential mechanism of the Warburg effect, we here summarized the relationship between DNA methylation and the Warburg effect with regard to cellular energy metabolism factors, such as glycolysis related enzymes, mitochondrial function, glycolysis bypass pathways, the tumor oxygen sensing pathway and abnormal methylation conditions. We believe that clarifying the relationship between these different mechanisms may further help us understand how DNA methylation works on tumorigenesis and provide new opportunities for cancer therapy.
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Affiliation(s)
- Xingxin Zhu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University.,NHC Key Laboratory of Combined Multi-organ Transplantation.,Key Laboratory of the diagnosis and treatment of organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019).,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou 310003, China
| | - Zefeng Xuan
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University.,NHC Key Laboratory of Combined Multi-organ Transplantation.,Key Laboratory of the diagnosis and treatment of organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019).,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou 310003, China
| | - Jun Chen
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University.,NHC Key Laboratory of Combined Multi-organ Transplantation.,Key Laboratory of the diagnosis and treatment of organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019).,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou 310003, China
| | - Zequn Li
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University.,NHC Key Laboratory of Combined Multi-organ Transplantation.,Key Laboratory of the diagnosis and treatment of organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019).,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou 310003, China
| | - Shusen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University.,NHC Key Laboratory of Combined Multi-organ Transplantation.,Key Laboratory of the diagnosis and treatment of organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019).,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou 310003, China
| | - Penghong Song
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University.,NHC Key Laboratory of Combined Multi-organ Transplantation.,Key Laboratory of the diagnosis and treatment of organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019).,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou 310003, China
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The Role of DNMT and HDACs in the Fetal Programming of Hypertension by Glucocorticoids. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:5751768. [PMID: 32318239 PMCID: PMC7149440 DOI: 10.1155/2020/5751768] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 03/07/2020] [Indexed: 12/13/2022]
Abstract
The causes of hypertension are complex and involve both genetic and environmental factors. Environment changes during fetal development have been linked to adult diseases including hypertension. Studies show that timed in utero exposure to the synthetic glucocorticoid (GC) dexamethasone (Dex) results in the development of hypertension in adult rats. Evidence suggests that in utero stress can alter patterns of gene expression, possibly a result of alterations in the topology of the genome by epigenetic markers such as DNA methyltransferases (DNMTs) and histone deacetylases (HDACs). The objective of this study was to determine the effects of epigenetic regulators in the fetal programming and the development of adult hypertension. Specifically, this research examined the effects of the HDAC inhibitor valproic acid (VPA) and the DNMT inhibitor 5-aza-2′-deoxycytidine (5aza2DC) on blood pressure (BP) and gene expression in prenatal Dex-programmed rats. Data suggest that both VPA and 5aza2DC attenuated the Dex-mediated development of hypertension and restored BP to control levels. Epigenetic DNMT inhibition (DNMTi) or HDAC inhibition (HDACi) also successfully attenuated elevations in the majority of altered catecholamine (CA) enzyme expression, phenylethanolamine N-methyltransferase (PNMT) protein, and elevated epinephrine (Epi) levels in males. Although females responded to HDACi similar to males, DNMTi drove increased glucocorticoid receptor (GR) and PNMT expression and elevations in circulating Epi in females despite showing normotensive BP.
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Mitochondrial dysfunction: An emerging link in the pathophysiology of polycystic ovary syndrome. Mitochondrion 2020; 52:24-39. [PMID: 32081727 DOI: 10.1016/j.mito.2020.02.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/31/2019] [Accepted: 02/12/2020] [Indexed: 12/19/2022]
Abstract
Polycystic ovary syndrome (PCOS) is a common endocrine disorder characterized by irregular menstrual cycles, hyperandrogenism and subfertility. Due to its complex manifestation, the pathogenic mechanism of PCOS is not well defined. Cumulative effect of altered genetic and epigenetic factors along with environmental factors may play a role in the manifestation of PCOS leading to systemic malfunction. With failure of genome-wide association study (GWAS) and other studies performed on nuclear genome to provide any clue for precise mechanism of PCOS pathogenesis, attention has been diverted to mitochondria. Mitochondrion plays an important role in cellular metabolic functions and is linked to Insulin Resistance (IR). Recently, increasing reports suggest that mitochondrial dysfunction may be a contributing factor in the pathogenesis of PCOS. Hence, in this review, we have discussed mitochondrial biology in brief and emphasizes on genetic and epigenetic aspects of mitochondrial dysfunction studied in PCOS women and PCOS-like animal models. We also highlight underlying mechanism behind mitochondrial dysfunction contributing to PCOS and its related complications such as obesity, diabetes, cardiovascular diseases, metabolic syndrome, non-alcoholic fatty liver disease (NAFLD) and cancer. Furthermore, contrasting remarks against involvement of mitochondrial dysfunction in PCOS pathophysiology have also been presented. This review enhances our understanding in relation to mitochondrial dysfunction in the etiology of PCOS and stimulates further research to explore a clear link between mitochondrial dysfunction and PCOS pathogenesis and progression. Understanding pathogenic mechanisms underlying PCOS will open new windows to develop promising therapeutic strategies against PCOS.
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Hypermethylation of mitochondrial DNA in vascular smooth muscle cells impairs cell contractility. Cell Death Dis 2020; 11:35. [PMID: 31959742 PMCID: PMC6971246 DOI: 10.1038/s41419-020-2240-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 01/08/2020] [Accepted: 01/08/2020] [Indexed: 01/26/2023]
Abstract
Vascular smooth muscle cell (SMC) from arterial stenotic-occlusive diseases is featured with deficiency in mitochondrial respiration and loss of cell contractility. However, the regulatory mechanism of mitochondrial genes and mitochondrial energy metabolism in SMC remains elusive. Here, we described that DNA methyltransferase 1 (DNMT1) translocated to the mitochondria and catalyzed D-loop methylation of mitochondrial DNA in vascular SMCs in response to platelet-derived growth factor-BB (PDGF-BB). Mitochondrial-specific expression of DNMT1 repressed mitochondrial gene expression, caused functional damage, and reduced SMC contractility. Hypermethylation of mitochondrial D-loop regions were detected in the intima-media layer of mouse carotid arteries subjected to either cessation of blood flow or mechanical endothelial injury, and also in vessel specimens from patients with carotid occlusive diseases. Likewise, the ligated mouse arteries exhibited an enhanced mitochondrial binding of DNMT1, repressed mitochondrial gene expression, defects in mitochondrial respiration, and impaired contractility. The impaired contractility of a ligated vessel could be restored by ex vivo transplantation of DNMT1-deleted mitochondria. In summary, we discovered the function of DNMT1-mediated mitochondrial D-loop methylation in the regulation of mitochondrial gene transcription. Methylation of mitochondrial D-loop in vascular SMCs contributes to impaired mitochondrial function and loss of contractile phenotype in vascular occlusive disease.
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Zylstra M, Bakhtazad A, Sabarinathan J. Photonic crystal slab edge directional coupler for deflection sensing. OPTICS EXPRESS 2019; 27:38509-38520. [PMID: 31878616 DOI: 10.1364/oe.27.038509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/03/2019] [Indexed: 06/10/2023]
Abstract
The design, fabrication, and transmission measurements of a photonic crystal slab edge directional coupler (PCDC) for submicron deflection sensing is presented. The dielectric modes between two structurally isolated photonic crystal edges allows for a directional coupler to be formed with low insertion loss and reduced coupling distances. The output transmission from the coupler can be related to the distance between neighbouring PC edges, thereby allowing it to be used as an intensity-based optomechanical sensor. PCDC sensors were fabricated by selectively etching the buried oxide (BOX) of surface micromachined silicon-on-insulator wafer. Based on transmission measurements, the sensitivity to horizontal separation between the edges of a fabricated PCDC of length 24.3 µm was evaluated to be 1.6 %/nm at 1495 nm. The transmission sensitivity to vertical separation between the PCDC edges of length 12.6 µm was calculated to be 0.25 %/nm, when the PCDC edges were initially displaced vertically by a distance of 300 nm. The PCDC sensors demonstrated here are compatible with broadband sources and do not depend on BOX thickness, reducing the probability of stiction.
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41
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Patil V, Cuenin C, Chung F, Aguilera JR, Fernandez-Jimenez N, Romero-Garmendia I, Bilbao JR, Cahais V, Rothwell J, Herceg Z. Human mitochondrial DNA is extensively methylated in a non-CpG context. Nucleic Acids Res 2019; 47:10072-10085. [PMID: 31665742 PMCID: PMC6821263 DOI: 10.1093/nar/gkz762] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/19/2019] [Accepted: 08/23/2019] [Indexed: 12/30/2022] Open
Abstract
Mitochondrial dysfunction plays critical roles in cancer development and related therapeutic response; however, exact molecular mechanisms remain unclear. Recently, alongside the discovery of mitochondrial-specific DNA methyltransferases, global and site-specific methylation of the mitochondrial genome has been described. Investigation of any functional consequences however remains unclear and debated due to insufficient evidence of the quantitative degree and frequency of mitochondrial DNA (mtDNA) methylation. This study uses WGBS to provide the first quantitative report of mtDNA methylation at single base pair resolution. The data show that mitochondrial genomes are extensively methylated predominantly at non-CpG sites. Importantly, these methylation patterns display notable differences between normal and cancer cells. Furthermore, knockdown of DNA methyltransferase enzymes resulted in a marked global reduction of mtDNA methylation levels, indicating these enzymes may be associated with the establishment and/or maintenance of mtDNA methylation. DNMT3B knockdown cells displayed a comparatively pronounced global reduction in mtDNA methylation with concomitant increases in gene expression, suggesting a potential functional link between methylation and gene expression. Together these results demonstrate reproducible, non-random methylation patterns of mtDNA and challenge the notion that mtDNA is lowly methylated. This study discusses key differences in methodology that suggest future investigations must allow for techniques that assess both CpG and non-CpG methylation.
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Affiliation(s)
- Vibha Patil
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon Cedex 08, France
| | - Cyrille Cuenin
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon Cedex 08, France
| | - Felicia Chung
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon Cedex 08, France
| | | | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country 48940, Spain
| | - Irati Romero-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country 48940, Spain
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country 48940, Spain
| | - Vincent Cahais
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon Cedex 08, France
| | - Joseph Rothwell
- Nutritional Epidemiology Group, International Agency for Research on Cancer (IARC), 69372 Lyon Cedex 08, France
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon Cedex 08, France
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Balzano F, Campesi I, Cruciani S, Garroni G, Bellu E, Dei Giudici S, Angius A, Oggiano A, Rallo V, Capobianco G, Dessole S, Ventura C, Montella A, Maioli M. Epigenetics, Stem Cells, and Autophagy: Exploring a Path Involving miRNA. Int J Mol Sci 2019; 20:ijms20205091. [PMID: 31615086 PMCID: PMC6834298 DOI: 10.3390/ijms20205091] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/07/2019] [Accepted: 10/10/2019] [Indexed: 02/07/2023] Open
Abstract
MiRNAs, a small family of non-coding RNA, are now emerging as regulators of stem cell pluripotency, differentiation, and autophagy, thus controlling stem cell behavior. Stem cells are undifferentiated elements capable to acquire specific phenotype under different kind of stimuli, being a main tool for regenerative medicine. Within this context, we have previously shown that stem cells isolated from Wharton jelly multipotent stem cells (WJ-MSCs) exhibit gender differences in the expression of the stemness related gene OCT4 and the epigenetic modulator gene DNA-Methyltransferase (DNMT1). Here, we further analyze this gender difference, evaluating adipogenic and osteogenic differentiation potential, autophagic process, and expression of miR-145, miR-148a, and miR-185 in WJ-MSCs derived from males and females. These miRNAs were selected since they are involved in OCT4 and DNMT1 gene expression, and in stem cell differentiation. Our results indicate a difference in the regulatory circuit involving miR-148a/DNMT1/OCT4 autophagy in male WJ-MSCs as compared to female cells. Moreover, no difference was detected in the expression of the two-differentiation regulating miRNA (miR-145 and miR-185). Taken together, our results highlight a different behavior of WJ-MSCs from males and females, disclosing the chance to better understand cellular processes as autophagy and stemness, usable for future clinical applications.
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Affiliation(s)
- Francesca Balzano
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy.
| | - Ilaria Campesi
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy.
| | - Sara Cruciani
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy.
| | - Giuseppe Garroni
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy.
| | - Emanuela Bellu
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy.
| | - Silvia Dei Giudici
- Istituto Zooprofilattico Sperimentale della Sardegna, Via Vienna 2, 07100 Sassari, Italy.
| | - Andrea Angius
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy.
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, 09042 Cagliari, Italy.
| | - Annalisa Oggiano
- Istituto Zooprofilattico Sperimentale della Sardegna, Via Vienna 2, 07100 Sassari, Italy.
| | - Vincenzo Rallo
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy.
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, 09042 Cagliari, Italy.
| | - Giampiero Capobianco
- Department of Medical, Surgical and experimental Sciences, Gynecologic and Obstetric Clinic, University of Sassari, 07100 Sassari, Italy.
| | - Salvatore Dessole
- Department of Medical, Surgical and experimental Sciences, Gynecologic and Obstetric Clinic, University of Sassari, 07100 Sassari, Italy.
| | - Carlo Ventura
- National Laboratory of Molecular Biology and Stem Cell Bioengineering of the National Institute of Biostructures and Biosystems (NIBB)-Eldor Lab, at the Innovation Accelerator, CNR, Via Piero Gobetti 101, 40129 Bologna, Italy.
| | - Andrea Montella
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy.
- Operative Unit of Clinical Genetics and Developmental Biology, Viale San Pietro 43/B, 07100 Sassari, Italy.
| | - Margherita Maioli
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy.
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, 09042 Cagliari, Italy.
- Center for developmental biology and reprogramming-CEDEBIOR, Department of Biomedical Sciences, University of Sassari Viale San Pietro 43/B, 07100 Sassari, Italy.
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Billard P, Poncet DA. Replication Stress at Telomeric and Mitochondrial DNA: Common Origins and Consequences on Ageing. Int J Mol Sci 2019; 20:ijms20194959. [PMID: 31597307 PMCID: PMC6801922 DOI: 10.3390/ijms20194959] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/04/2019] [Accepted: 10/05/2019] [Indexed: 12/12/2022] Open
Abstract
Senescence is defined as a stress-induced durable cell cycle arrest. We herein revisit the origin of two of these stresses, namely mitochondrial metabolic compromise, associated with reactive oxygen species (ROS) production, and replicative senescence, activated by extreme telomere shortening. We discuss how replication stress-induced DNA damage of telomeric DNA (telDNA) and mitochondrial DNA (mtDNA) can be considered a common origin of senescence in vitro, with consequences on ageing in vivo. Unexpectedly, mtDNA and telDNA share common features indicative of a high degree of replicative stress, such as G-quadruplexes, D-loops, RNA:DNA heteroduplexes, epigenetic marks, or supercoiling. To avoid these stresses, both compartments use similar enzymatic strategies involving, for instance, endonucleases, topoisomerases, helicases, or primases. Surprisingly, many of these replication helpers are active at both telDNA and mtDNA (e.g., RNAse H1, FEN1, DNA2, RecQ helicases, Top2α, Top2β, TOP3A, DNMT1/3a/3b, SIRT1). In addition, specialized telomeric proteins, such as TERT (telomerase reverse transcriptase) and TERC (telomerase RNA component), or TIN2 (shelterin complex), shuttle from telomeres to mitochondria, and, by doing so, modulate mitochondrial metabolism and the production of ROS, in a feedback manner. Hence, mitochondria and telomeres use common weapons and cooperate to resist/prevent replication stresses, otherwise producing common consequences, namely senescence and ageing.
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Affiliation(s)
- Pauline Billard
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, 69008 Lyon, France.
- Institut de Biopathologie moléculaire, Centre de Bio-Pathologie Est, Groupement hospitalier Est, Hospices Civils de Lyon, 69500 Bron, France.
| | - Delphine A Poncet
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, 69008 Lyon, France.
- Institut de Biopathologie moléculaire, Centre de Bio-Pathologie Est, Groupement hospitalier Est, Hospices Civils de Lyon, 69500 Bron, France.
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Sharma N, Pasala MS, Prakash A. Mitochondrial DNA: Epigenetics and environment. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2019; 60:668-682. [PMID: 31335990 PMCID: PMC6941438 DOI: 10.1002/em.22319] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/08/2019] [Accepted: 07/11/2019] [Indexed: 05/22/2023]
Abstract
Maintenance of the mitochondrial genome is essential for proper cellular function. For this purpose, mitochondrial DNA (mtDNA) needs to be faithfully replicated, transcribed, translated, and repaired in the face of constant onslaught from endogenous and environmental agents. Although only 13 polypeptides are encoded within mtDNA, the mitochondrial proteome comprises over 1500 proteins that are encoded by nuclear genes and translocated to the mitochondria for the purpose of maintaining mitochondrial function. Regulation of mtDNA and mitochondrial proteins by epigenetic changes and post-translational modifications facilitate crosstalk between the nucleus and the mitochondria and ultimately lead to the maintenance of cellular health and homeostasis. DNA methyl transferases have been identified in the mitochondria implicating that methylation occurs within this organelle; however, the extent to which mtDNA is methylated has been debated for many years. Mechanisms of demethylation within this organelle have also been postulated, but the exact mechanisms and their outcomes is still an active area of research. Mitochondrial dysfunction in the form of altered gene expression and ATP production, resulting from epigenetic changes, can lead to various conditions including aging-related neurodegenerative disorders, altered metabolism, changes in circadian rhythm, and cancer. Here, we provide an overview of the epigenetic regulation of mtDNA via methylation, long and short noncoding RNAs, and post-translational modifications of nucleoid proteins (as mitochondria lack histones). We also highlight the influence of xenobiotics such as airborne environmental pollutants, contamination from heavy metals, and therapeutic drugs on mtDNA methylation. Environ. Mol. Mutagen., 60:668-682, 2019. © 2019 Wiley Periodicals, Inc.
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Dou X, Boyd-Kirkup JD, McDermott J, Zhang X, Li F, Rong B, Zhang R, Miao B, Chen P, Cheng H, Xue J, Bennett D, Wong J, Lan F, Han JDJ. The strand-biased mitochondrial DNA methylome and its regulation by DNMT3A. Genome Res 2019; 29:1622-1634. [PMID: 31537639 PMCID: PMC6771398 DOI: 10.1101/gr.234021.117] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 08/23/2019] [Indexed: 01/19/2023]
Abstract
How individual genes are regulated from a mitochondrial polycistronic transcript to have variable expression remains an enigma. Here, through bisulfite sequencing and strand-specific mapping, we show mitochondrial genomes in humans and other animals are strongly biased to light (L)-strand non-CpG methylation with conserved peak loci preferentially located at gene-gene boundaries, which was also independently validated by MeDIP and FspEI digestion. Such mtDNA methylation patterns are conserved across different species and developmental stages but display dynamic local or global changes during development and aging. Knockout of DNMT3A alone perturbed mtDNA regional methylation patterns, but not global levels, and altered mitochondrial gene expression, copy number, and oxygen respiration. Overexpression of DNMT3A strongly increased mtDNA methylation and strand bias. Overall, methylation at gene bodies and boundaries was negatively associated with mitochondrial transcript abundance and also polycistronic transcript processing. Furthermore, HPLC-MS confirmed the methylation signals on mitochondria DNA. Together, these data provide high-resolution mtDNA methylation maps that revealed a strand-specific non-CpG methylation, its dynamic regulation, and its impact on the polycistronic mitochondrial transcript processing.
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Affiliation(s)
- Xiaoyang Dou
- Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jerome D Boyd-Kirkup
- Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Joseph McDermott
- Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiaoli Zhang
- Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing 100871, China
| | - Fang Li
- Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bowen Rong
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Epigenetics, Shanghai Ministry of Education, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Rui Zhang
- Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bisi Miao
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Epigenetics, Shanghai Ministry of Education, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Peilin Chen
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Hao Cheng
- Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jianhuang Xue
- The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - David Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois 60612, USA
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Fei Lan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Epigenetics, Shanghai Ministry of Education, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Jing-Dong J Han
- Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing 100871, China
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Sirard MA. Distribution and dynamics of mitochondrial DNA methylation in oocytes, embryos and granulosa cells. Sci Rep 2019; 9:11937. [PMID: 31417147 PMCID: PMC6695495 DOI: 10.1038/s41598-019-48422-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 07/30/2019] [Indexed: 11/16/2022] Open
Abstract
Comparison of mitochondrial DNA (mtDNA) methylation patterns in oocytes, blastocysts and ovarian granulosa cells indicates hitherto unsuspected dynamics. Oocytes and blastocysts recovered from cows subjected to ovarian stimulation and from non-stimulated abattoir ovaries were analyzed using bisulphite transformation of DNA followed by whole genome sequencing. The cow is a recognized as a good model for human oocyte and pre-implantation development. The number of mtDNA copies is high in oocytes (200,000-400,000) and early embryos, resulting in very high coverage (>3000x) and very low p values for each of 716 cytosine-based nucleosides. Methylation ratio was lowest in oocytes, following by blastocysts then granulosa cells and was not restricted to CG sites but was found also at CHG and CHH sites. The initial methylation pattern is conserved during the first week of life but not in somatic cells. RNA analysis of mitochondria encoded genes showed a significant inverse correlation between methylation and expression for almost all sequences. Methylation was more extensive in somatic tissues from mature animals than in immature pre-pubertal animals. Our findings suggest that mtDNA methylation might play a programming role during gametogenesis and would be subject to epigenetic regulation according to environment and/or maternal maturity.
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Affiliation(s)
- Marc-André Sirard
- Centre de recherche en reproduction, développement et santé intergénérationnelle (CRDSI) Département des Sciences Animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, Canada.
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Uysal F, Akkoyunlu G, Ozturk S. Decreased expression of DNA methyltransferases in the testes of patients with non-obstructive azoospermia leads to changes in global DNA methylation levels. Reprod Fertil Dev 2019; 31:1386-1394. [PMID: 31030726 DOI: 10.1071/rd18246] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 02/13/2019] [Indexed: 12/27/2022] Open
Abstract
DNA methylation plays key roles in epigenetic regulation during mammalian spermatogenesis. DNA methyltransferases (DNMTs) function in de novo and maintenance methylation processes by adding a methyl group to the fifth carbon atom of the cytosine residues within cytosine-phosphate-guanine (CpG) and non-CpG dinucleotide sites. Azoospermia is one of the main causes of male infertility, and is classified as obstructive (OA) or non-obstructive (NOA) azoospermia based on histopathological characteristics. The molecular background of NOA is still largely unknown. DNA methylation performed by DNMTs is implicated in the transcriptional regulation of spermatogenesis-related genes. The aim of the present study was to evaluate the cellular localisation and expression levels of the DNMT1, DNMT3A and DNMT3B proteins, as well as global DNA methylation profiles in testicular biopsy samples obtained from men with various types of NOA, including hypospermatogenesis (hyposperm), round spermatid (RS) arrest, spermatocyte (SC) arrest and Sertoli cell-only (SCO) syndrome. In the testicular biopsy samples, DNMT1 expression and global DNA methylation levels decreased gradually from the hyposperm to SCO groups (P P P <0.05). Although both DNMT1 and DNMT3A were localised in the cytoplasm and nucleus of the spermatogenic cells, staining for DNMT3B was more intensive in the nucleus of spermatogenic cells. In conclusion, the findings suggest that significant changes in DNMT expression and global DNA methylation levels in spermatogenic cells may contribute to development of male infertility in the NOA groups. Further studies are needed to determine the molecular biological effects of the altered DNMT expression and DNA methylation levels on development of male infertility.
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Affiliation(s)
- Fatma Uysal
- Department of Histology and Embryology, Akdeniz University School of Medicine, Campus, 07070, Antalya, Turkey; and Department of Histology and Embryology, Ankara University School of Medicine, 06100, Ankara, Turkey
| | - Gokhan Akkoyunlu
- Department of Histology and Embryology, Akdeniz University School of Medicine, Campus, 07070, Antalya, Turkey
| | - Saffet Ozturk
- Department of Histology and Embryology, Akdeniz University School of Medicine, Campus, 07070, Antalya, Turkey; and Corresponding author
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48
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Chocron ES, Munkácsy E, Pickering AM. Cause or casualty: The role of mitochondrial DNA in aging and age-associated disease. Biochim Biophys Acta Mol Basis Dis 2019; 1865:285-297. [PMID: 30419337 PMCID: PMC6310633 DOI: 10.1016/j.bbadis.2018.09.035] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/20/2018] [Accepted: 09/04/2018] [Indexed: 12/19/2022]
Abstract
The mitochondrial genome (mtDNA) represents a tiny fraction of the whole genome, comprising just 16.6 kilobases encoding 37 genes involved in oxidative phosphorylation and the mitochondrial translation machinery. Despite its small size, much interest has developed in recent years regarding the role of mtDNA as a determinant of both aging and age-associated diseases. A number of studies have presented compelling evidence for key roles of mtDNA in age-related pathology, although many are correlative rather than demonstrating cause. In this review we will evaluate the evidence supporting and opposing a role for mtDNA in age-associated functional declines and diseases. We provide an overview of mtDNA biology, damage and repair as well as the influence of mitochondrial haplogroups, epigenetics and maternal inheritance in aging and longevity.
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Affiliation(s)
- E Sandra Chocron
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78245-3207, USA
| | - Erin Munkácsy
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78245-3207, USA
| | - Andrew M Pickering
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78245-3207, USA; Department of Molecular Medicine, School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78245-3207, USA.
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49
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Morris MJ, Hesson LB, Poulos RC, Ward RL, Wong JWH, Youngson NA. Reduced nuclear DNA methylation and mitochondrial transcript changes in adenomas do not associate with mtDNA methylation. Biomark Res 2018; 6:37. [PMID: 30619609 PMCID: PMC6311003 DOI: 10.1186/s40364-018-0151-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 11/28/2018] [Indexed: 12/15/2022] Open
Abstract
Background Altered mitochondrial function and large-scale changes to DNA methylation patterns in the nuclear genome are both hallmarks of colorectal cancer (CRC). Mitochondria have multiple copies of a 16 kb circular genome that contains genes that are vital for their function. While DNA methylation is known to alter the nuclear genome in CRC, it is not clear whether it could have a similar influence in mtDNA; indeed, currently, the issue of whether mitochondrial genome (mtDNA) methylation occurs is controversial. Thus our goal here was to determine whether the methylation state of mtDNA is linked to mitochondrial gene transcription in colorectal adenomas, and to assess its suitability as a biomarker in CRC. Methods To investigate the relationship between DNA methylation and mitochondrial transcripts in adenomas, we performed RNA-sequencing and Whole Genome Bisulphite Sequencing (WGBS) of mtDNA-enriched DNA from normal mucosa and paired adenoma patient samples. Results Transcriptional profiling indicated that adenomas had reduced mitochondrial proton transport versus normal mucosa, consistent with altered mitochondrial function. The expression of 3 tRNAs that are transcribed from mtDNA were also decreased in adenoma. Overall methylation of CG dinucleotides in the nuclear genome was reduced in adenomas (68%) compared to normal mucosa (75%, P < 0.01). Methylation in mtDNA was low (1%) in both normal and adenoma tissue but we observed clusters of higher methylation at the ribosomal RNA genes. Levels of methylation within these regions did not differ between normal and adenoma tissue. Conclusions We provide evidence that low-level methylation of specific sites does exist in the mitochondrial genome but that it is not associated with mitochondrial gene transcription changes in adenomas. Furthermore, as no large scale changes to mtDNA methylation were observed it is unlikely to be a suitable biomarker for early-stage CRC. Electronic supplementary material The online version of this article (10.1186/s40364-018-0151-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- M J Morris
- 1Department of Pharmacology, School of Medical Sciences, UNSW Sydney, Sydney, NSW Australia
| | - L B Hesson
- 2Prince of Wales Clinical School and Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW Australia
| | - R C Poulos
- 2Prince of Wales Clinical School and Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW Australia.,3Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW Australia
| | - R L Ward
- 2Prince of Wales Clinical School and Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW Australia.,4Office of the Deputy Vice-Chancellor (Research), University of Queensland, QLD, Brisbane, Australia
| | - J W H Wong
- 2Prince of Wales Clinical School and Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW Australia.,5School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, Special Administrative Region of China
| | - N A Youngson
- 1Department of Pharmacology, School of Medical Sciences, UNSW Sydney, Sydney, NSW Australia
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50
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Ferreira LL, Cunha-Oliveira T, Veloso CD, Costa CF, Wallace KB, Oliveira PJ. Single nanomolar doxorubicin exposure triggers compensatory mitochondrial responses in H9c2 cardiomyoblasts. Food Chem Toxicol 2018; 124:450-461. [PMID: 30557669 DOI: 10.1016/j.fct.2018.12.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 12/08/2018] [Accepted: 12/13/2018] [Indexed: 12/31/2022]
Abstract
Dose-dependent and cumulative cardiotoxicity associated with doxorubicin (DOX) is the main limitation of anticancer therapy. Pediatric cancer survivors are particularly vulnerable, and no effective prevention measures are available. The aim of the present study was to investigate the persistent effects of nanomolar DOX concentrations and determine whether a pretreatment would induce mitochondrial adaptations in H9c2 cardiomyoblasts. H9c2 cells were incubated with DOX (10 and 25 nM) for 24 h, followed by 9 days of recovery in drug-free medium. We found that the sub-therapeutic DOX treatment induced persistent hypertrophy and dose-dependent cell cycle arrest in G2/M. Glycolytic activity, indirectly based on extracellular acidification rate, and basal respiration were significantly decreased in DOX-treated cells compared to controls, although both groups showed similar maximal respiration. Additionally, nanomolar DOX pretreatment resulted in upregulation of mitochondrial DNA transcripts accompanied by a decrease in DNA methyltransferase 1 (DNMT1) and global methylation levels. Finally, the pretreatment with DOX ameliorated H9c2 cells resistance against a subsequent exposure to DOX. These results suggest that nanomolar DOX pretreatment induced a beneficial and possibly epigenetic-based mitochondrial adaptation, raising the possibility that an early sub-therapeutic DOX treatment can be used as a preconditioning and protective approach during anticancer therapies.
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Affiliation(s)
- Luciana L Ferreira
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, UC Biotech Building, Biocant Park, 3060-197, Cantanhede, Portugal.
| | - Teresa Cunha-Oliveira
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, UC Biotech Building, Biocant Park, 3060-197, Cantanhede, Portugal.
| | - Caroline D Veloso
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, UC Biotech Building, Biocant Park, 3060-197, Cantanhede, Portugal.
| | - Cláudio F Costa
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, UC Biotech Building, Biocant Park, 3060-197, Cantanhede, Portugal.
| | - Kendall B Wallace
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, 55812, USA.
| | - Paulo J Oliveira
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, UC Biotech Building, Biocant Park, 3060-197, Cantanhede, Portugal.
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