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Kumar A, Choudhary A, Munshi A. Epigenetic reprogramming of mtDNA and its etiology in mitochondrial diseases. J Physiol Biochem 2024:10.1007/s13105-024-01032-z. [PMID: 38865050 DOI: 10.1007/s13105-024-01032-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/04/2024] [Indexed: 06/13/2024]
Abstract
Mitochondrial functionality and its regulation are tightly controlled through a balanced crosstalk between the nuclear and mitochondrial DNA interactions. Epigenetic signatures like methylation, hydroxymethylation and miRNAs have been reported in mitochondria. In addition, epigenetic signatures encoded by nuclear DNA are also imported to mitochondria and regulate the gene expression dynamics of the mitochondrial genome. Alteration in the interplay of these epigenetic modifications results in the pathogenesis of various disorders like neurodegenerative, cardiovascular, metabolic disorders, cancer, aging and senescence. These modifications result in higher ROS production, increased mitochondrial copy number and disruption in the replication process. In addition, various miRNAs are associated with regulating and expressing important mitochondrial gene families like COX, OXPHOS, ND and DNMT. Epigenetic changes are reversible and therefore therapeutic interventions like changing the target modifications can be utilized to repair or prevent mitochondrial insufficiency by reversing the changed gene expression. Identifying these mitochondrial-specific epigenetic signatures has the potential for early diagnosis and treatment responses for many diseases caused by mitochondrial dysfunction. In the present review, different mitoepigenetic modifications have been discussed in association with the development of various diseases by focusing on alteration in gene expression and dysregulation of specific signaling pathways. However, this area is still in its infancy and future research is warranted to draw better conclusions.
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Affiliation(s)
- Anil Kumar
- Department of Human Genetics and Molecular Medicines, Central University of Punjab, Bathinda, India
| | - Anita Choudhary
- Department of Human Genetics and Molecular Medicines, Central University of Punjab, Bathinda, India
| | - Anjana Munshi
- Department of Human Genetics and Molecular Medicines, Central University of Punjab, Bathinda, India.
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2
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Ferreira T, Rodriguez S. Mitochondrial DNA: Inherent Complexities Relevant to Genetic Analyses. Genes (Basel) 2024; 15:617. [PMID: 38790246 PMCID: PMC11121663 DOI: 10.3390/genes15050617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Mitochondrial DNA (mtDNA) exhibits distinct characteristics distinguishing it from the nuclear genome, necessitating specific analytical methods in genetic studies. This comprehensive review explores the complex role of mtDNA in a variety of genetic studies, including genome-wide, epigenome-wide, and phenome-wide association studies, with a focus on its implications for human traits and diseases. Here, we discuss the structure and gene-encoding properties of mtDNA, along with the influence of environmental factors and epigenetic modifications on its function and variability. Particularly significant are the challenges posed by mtDNA's high mutation rate, heteroplasmy, and copy number variations, and their impact on disease susceptibility and population genetic analyses. The review also highlights recent advances in methodological approaches that enhance our understanding of mtDNA associations, advocating for refined genetic research techniques that accommodate its complexities. By providing a comprehensive overview of the intricacies of mtDNA, this paper underscores the need for an integrated approach to genetic studies that considers the unique properties of mitochondrial genetics. Our findings aim to inform future research and encourage the development of innovative methodologies to better interpret the broad implications of mtDNA in human health and disease.
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Affiliation(s)
- Tomas Ferreira
- Bristol Medical School, University of Bristol, Bristol BS8 1UD, UK
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge CB2 0SL, UK
| | - Santiago Rodriguez
- Bristol Medical School, University of Bristol, Bristol BS8 1UD, UK
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 1QU, UK
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3
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Caporossi D, Dimauro I. Exercise-induced redox modulation as a mediator of DNA methylation in health maintenance and disease prevention. Free Radic Biol Med 2024; 213:113-122. [PMID: 38242245 DOI: 10.1016/j.freeradbiomed.2024.01.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/09/2024] [Accepted: 01/15/2024] [Indexed: 01/21/2024]
Abstract
The evidence for physical activity (PA) as a major public health preventive approach and a potent medical therapy has increased exponentially in the last decades. The biomolecular mechanisms supporting the associations between PA and/or structured exercise training with health maintenance and disease prevention are not completely characterized. However, increasing evidence pointed out the role of epigenetic modifications in exercise adaptation and health-enhancing PA throughout life, DNA methylation being the most intensely studied epigenetic modification induced by acute and chronic exercise. The current data on the modulation of DNA methylation determined by physically active behavior or exercise interventions points out genes related to energy regulation, mitochondrial function, and biosynthesis, as well as muscle regeneration, calcium signaling pathways, and brain plasticity, all consistent with the known exercise-induced redox signaling and/or reactive oxygen species (ROS) unbalance. Thus, the main focus of this review is to discuss the role of ROS and redox-signaling on DNA methylation profile and its impact on exercise-induced health benefits in humans.
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Affiliation(s)
- Daniela Caporossi
- Unit of Biology and Genetics of Movement, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro De Bosis 15, Rome, 00135, Italy.
| | - Ivan Dimauro
- Unit of Biology and Genetics of Movement, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro De Bosis 15, Rome, 00135, Italy
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4
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García-Giménez JL, Cánovas-Cervera I, Pallardó FV. Oxidative stress and metabolism meet epigenetic modulation in physical exercise. Free Radic Biol Med 2024; 213:123-137. [PMID: 38199289 DOI: 10.1016/j.freeradbiomed.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/12/2024]
Abstract
Physical exercise is established as an important factor of health and generally is recommended for its positive effects on several tissues, organs, and systems. These positive effects come from metabolic adaptations that also include oxidative eustress, in which physical activity increases ROS production and antioxidant mechanisms, although this depends on the intensity of the exercise. Muscle metabolism through mechanisms such as aerobic and anaerobic glycolysis, tricarboxylic acid cycle, and oxidative lipid metabolism can produce metabolites and co-factors which directly impact the epigenetic machinery. In this review, we clearly reinforce the evidence that exercise regulates several epigenetic mechanisms and explain how these mechanisms can be regulated by metabolic products and co-factors produced during exercise. In fact, recent evidence has demonstrated the importance of epigenetics in the gene expression changes implicated in metabolic adaptation after exercise. Importantly, intermediates of the metabolism generated by continuous, acute, moderate, or strenuous exercise control the activity of epigenetic enzymes, therefore turning on or turning off the gene expression of specific programs which can lead to physiological adaptations after exercise.
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Affiliation(s)
- José Luis García-Giménez
- Faculty of Medicine and Dentistry, Department of Physiology, University of Valencia, Av/Blasco Ibañez, 15, Valencia, 46010, Spain; Biomedical Research Institute INCLIVA, Av/Menéndez Pelayo. 4acc, Valencia, 46010, Spain; CIBERER, The Centre for Biomedical Network Research on Rare Diseases, ISCIII, C. de Melchor Fernández Almagro, 3, 28029, Madrid, Spain.
| | - Irene Cánovas-Cervera
- Faculty of Medicine and Dentistry, Department of Physiology, University of Valencia, Av/Blasco Ibañez, 15, Valencia, 46010, Spain; Biomedical Research Institute INCLIVA, Av/Menéndez Pelayo. 4acc, Valencia, 46010, Spain.
| | - Federico V Pallardó
- Faculty of Medicine and Dentistry, Department of Physiology, University of Valencia, Av/Blasco Ibañez, 15, Valencia, 46010, Spain; Biomedical Research Institute INCLIVA, Av/Menéndez Pelayo. 4acc, Valencia, 46010, Spain; CIBERER, The Centre for Biomedical Network Research on Rare Diseases, ISCIII, C. de Melchor Fernández Almagro, 3, 28029, Madrid, Spain.
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5
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Hong J, Raza SHA, Ma H, Cao W, Chong Y, Wu J, Xi D, Deng W. Multiple omics analysis reveals the regulation of SIRT5 on mitochondrial function and lipid metabolism during the differentiation of bovine preadipocytes. Genomics 2024; 116:110773. [PMID: 38158141 DOI: 10.1016/j.ygeno.2023.110773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/30/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
Preadipocyte differentiation represents a critical stage in adipogenesis, with mitochondria playing an undeniable pivotal role. Given the intricate interplay between transcription and metabolic signaling during adipogenesis, the regulation of sirtuin 5 (SIRT5) on mitochondrial function and lipid metabolism was revealed via multiple omics analysis. The findings suggest that SIRT5 plays a crucial role in promoting mitochondrial biosynthesis and maintaining mitochondrial function during preadipocyte differentiation. Moreover, SIRT5 modulates the metabolic levels of numerous bioactive substances by extensively regulating genes expression associated with differentiation, energy metabolism, lipid synthesis, and mitochondrial function. Finally, SIRT5 was found to suppress triacylglycerols (TAG) accumulation while enhancing the proportion and diversity of unsaturated fatty acids, and providing conditions for the expansion and stability of membrane structure during mitochondrial biosynthesis through numerous gene regulations. Our findings provide a foundation for the identification of crucial functional genes, signaling pathways, and metabolic substances associated with adipose tissue differentiation and metabolism.
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Affiliation(s)
- Jieyun Hong
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Sayed Haidar Abbas Raza
- Guangdong Provincial Key Laboratory of Food Quality and Safety / Nation-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Hongming Ma
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Weina Cao
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Yuqing Chong
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Jiao Wu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Dongmei Xi
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Weidong Deng
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, Yunnan, China.
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6
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Meulders B, Marei WFA, Xhonneux I, Bols PEJ, Leroy JLMR. Effect of lipotoxicity on mitochondrial function and epigenetic programming during bovine in vitro embryo production. Sci Rep 2023; 13:21664. [PMID: 38066095 PMCID: PMC10709407 DOI: 10.1038/s41598-023-49184-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
Maternal metabolic disorders may cause lipotoxic effects on the developing oocyte. Understanding the timing at which this might disrupt embryo epigenetic programming and how this is linked with mitochondrial dysfunction is crucial for improving assisted reproductive treatments, but has not been investigated before. Therefore, we used a bovine in vitro model to investigate if pathophysiological palmitic acid (PA) concentrations during in vitro oocyte maturation and in vitro embryo culture alter embryo epigenetic patterns (DNA methylation (5mC) and histone acetylation/methylation (H3K9ac/H3K9me2)) compared to control (CONT) and solvent control (SCONT), at the zygote and morula stage. Secondly, we investigated if these epigenetic alterations are associated with mitochondrial dysfunction and changes in ATP production rate, or altered expression of epigenetic regulatory genes. Compared to SCONT, H3K9ac and H3K9me2 levels were increased in PA-derived zygotes. Also, 5mC and H3K9me2 levels were increased in PA-exposed morulae compared to SCONT. This was associated with complete inhibition of glycolytic ATP production in oocytes, increased mitochondrial membrane potential and complete inhibition of glycolytic ATP production in 4-cell embryos and reduced SOD2 expression in PA-exposed zygotes and morulae. For the first time, epigenetic alterations in metabolically compromised zygotes and morulae have been observed in parallel with mitochondrial dysfunction in the same study.
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Affiliation(s)
- Ben Meulders
- Laboratory of Veterinary Physiology and Biochemistry, Department of Veterinary Sciences, Gamete Research Centre, University of Antwerp, Wilrijk, Belgium.
| | - Waleed F A Marei
- Laboratory of Veterinary Physiology and Biochemistry, Department of Veterinary Sciences, Gamete Research Centre, University of Antwerp, Wilrijk, Belgium
- Department of Theriogenology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Inne Xhonneux
- Laboratory of Veterinary Physiology and Biochemistry, Department of Veterinary Sciences, Gamete Research Centre, University of Antwerp, Wilrijk, Belgium
| | - Peter E J Bols
- Laboratory of Veterinary Physiology and Biochemistry, Department of Veterinary Sciences, Gamete Research Centre, University of Antwerp, Wilrijk, Belgium
| | - Jo L M R Leroy
- Laboratory of Veterinary Physiology and Biochemistry, Department of Veterinary Sciences, Gamete Research Centre, University of Antwerp, Wilrijk, Belgium
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7
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Kaplánek R, Kejík Z, Hajduch J, Veselá K, Kučnirová K, Skaličková M, Venhauerová A, Hosnedlová B, Hromádka R, Dytrych P, Novotný P, Abramenko N, Antonyová V, Hoskovec D, Babula P, Masařík M, Martásek P, Jakubek M. TET protein inhibitors: Potential and limitations. Biomed Pharmacother 2023; 166:115324. [PMID: 37598475 DOI: 10.1016/j.biopha.2023.115324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/31/2023] [Accepted: 08/10/2023] [Indexed: 08/22/2023] Open
Abstract
TET proteins (methylcytosine dioxygenases) play an important role in the regulation of gene expression. Dysregulation of their activity is associated with many serious pathogenic states such as oncological diseases. Regulation of their activity by specific inhibitors could represent a promising therapeutic strategy. Therefore, this review describes various types of TET protein inhibitors in terms of their inhibitory mechanism and possible applicability. The potential and possible limitations of this approach are thoroughly discussed in the context of TET protein functionality in living systems. Furthermore, possible therapeutic strategies based on the inhibition of TET proteins are presented and evaluated, especially in the field of oncological diseases.
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Affiliation(s)
- Robert Kaplánek
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Zdeněk Kejík
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Jan Hajduch
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Kateřina Veselá
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Kateřina Kučnirová
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Markéta Skaličková
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Anna Venhauerová
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Božena Hosnedlová
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Róbert Hromádka
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Petr Dytrych
- 1st Department of Surgery-Department of Abdominal, Thoracic Surgery and Traumatology, First Faculty of Medicine, Charles University and General University Hospital, U Nemocnice 2, 121 08 Prague, Czech Republic
| | - Petr Novotný
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Nikita Abramenko
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Veronika Antonyová
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - David Hoskovec
- 1st Department of Surgery-Department of Abdominal, Thoracic Surgery and Traumatology, First Faculty of Medicine, Charles University and General University Hospital, U Nemocnice 2, 121 08 Prague, Czech Republic
| | - Petr Babula
- Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Michal Masařík
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Pavel Martásek
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic.
| | - Milan Jakubek
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic.
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8
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Todosenko N, Khaziakhmatova O, Malashchenko V, Yurova K, Bograya M, Beletskaya M, Vulf M, Gazatova N, Litvinova L. Mitochondrial Dysfunction Associated with mtDNA in Metabolic Syndrome and Obesity. Int J Mol Sci 2023; 24:12012. [PMID: 37569389 PMCID: PMC10418437 DOI: 10.3390/ijms241512012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/22/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Metabolic syndrome (MetS) is a precursor to the major health diseases associated with high mortality in industrialized countries: cardiovascular disease and diabetes. An important component of the pathogenesis of the metabolic syndrome is mitochondrial dysfunction, which is associated with tissue hypoxia, disruption of mitochondrial integrity, increased production of reactive oxygen species, and a decrease in ATP, leading to a chronic inflammatory state that affects tissues and organ systems. The mitochondrial AAA + protease Lon (Lonp1) has a broad spectrum of activities. In addition to its classical function (degradation of misfolded or damaged proteins), enzymatic activity (proteolysis, chaperone activity, mitochondrial DNA (mtDNA)binding) has been demonstrated. At the same time, the spectrum of Lonp1 activity extends to the regulation of cellular processes inside mitochondria, as well as outside mitochondria (nuclear localization). This mitochondrial protease with enzymatic activity may be a promising molecular target for the development of targeted therapy for MetS and its components. The aim of this review is to elucidate the role of mtDNA in the pathogenesis of metabolic syndrome and its components as a key component of mitochondrial dysfunction and to describe the promising and little-studied AAA + LonP1 protease as a potential target in metabolic disorders.
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Affiliation(s)
- Natalia Todosenko
- Center for Immunology and Cellular Biotechnology, Immanuel Kant Baltic Federal University, 236001 Kaliningrad, Russia; (N.T.); (O.K.); (V.M.); (K.Y.); (M.B.); (M.B.); (M.V.); (N.G.)
| | - Olga Khaziakhmatova
- Center for Immunology and Cellular Biotechnology, Immanuel Kant Baltic Federal University, 236001 Kaliningrad, Russia; (N.T.); (O.K.); (V.M.); (K.Y.); (M.B.); (M.B.); (M.V.); (N.G.)
| | - Vladimir Malashchenko
- Center for Immunology and Cellular Biotechnology, Immanuel Kant Baltic Federal University, 236001 Kaliningrad, Russia; (N.T.); (O.K.); (V.M.); (K.Y.); (M.B.); (M.B.); (M.V.); (N.G.)
| | - Kristina Yurova
- Center for Immunology and Cellular Biotechnology, Immanuel Kant Baltic Federal University, 236001 Kaliningrad, Russia; (N.T.); (O.K.); (V.M.); (K.Y.); (M.B.); (M.B.); (M.V.); (N.G.)
| | - Maria Bograya
- Center for Immunology and Cellular Biotechnology, Immanuel Kant Baltic Federal University, 236001 Kaliningrad, Russia; (N.T.); (O.K.); (V.M.); (K.Y.); (M.B.); (M.B.); (M.V.); (N.G.)
| | - Maria Beletskaya
- Center for Immunology and Cellular Biotechnology, Immanuel Kant Baltic Federal University, 236001 Kaliningrad, Russia; (N.T.); (O.K.); (V.M.); (K.Y.); (M.B.); (M.B.); (M.V.); (N.G.)
| | - Maria Vulf
- Center for Immunology and Cellular Biotechnology, Immanuel Kant Baltic Federal University, 236001 Kaliningrad, Russia; (N.T.); (O.K.); (V.M.); (K.Y.); (M.B.); (M.B.); (M.V.); (N.G.)
| | - Natalia Gazatova
- Center for Immunology and Cellular Biotechnology, Immanuel Kant Baltic Federal University, 236001 Kaliningrad, Russia; (N.T.); (O.K.); (V.M.); (K.Y.); (M.B.); (M.B.); (M.V.); (N.G.)
| | - Larisa Litvinova
- Center for Immunology and Cellular Biotechnology, Immanuel Kant Baltic Federal University, 236001 Kaliningrad, Russia; (N.T.); (O.K.); (V.M.); (K.Y.); (M.B.); (M.B.); (M.V.); (N.G.)
- Laboratory of Cellular and Microfluidic Technologies, Siberian State Medical University, 634050 Tomsk, Russia
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9
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Headley CA, Tsao PS. Building the case for mitochondrial transplantation as an anti-aging cardiovascular therapy. Front Cardiovasc Med 2023; 10:1141124. [PMID: 37229220 PMCID: PMC10203246 DOI: 10.3389/fcvm.2023.1141124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/11/2023] [Indexed: 05/27/2023] Open
Abstract
Mitochondrial dysfunction is a common denominator in both biological aging and cardiovascular disease (CVD) pathology. Understanding the protagonist role of mitochondria in the respective and independent progressions of CVD and biological aging will unravel the synergistic relationship between biological aging and CVD. Moreover, the successful development and implementation of therapies that can simultaneously benefit mitochondria of multiple cell types, will be transformational in curtailing pathologies and mortality in the elderly, including CVD. Several works have compared the status of mitochondria in vascular endothelial cells (ECs) and vascular smooth muscle cells (VSMCs) in CVD dependent context. However, fewer studies have cataloged the aging-associated changes in vascular mitochondria, independent of CVD. This mini review will focus on the present evidence related to mitochondrial dysfunction in vascular aging independent of CVD. Additionally, we discuss the feasibility of restoring mitochondrial function in the aged cardiovascular system through mitochondrial transfer.
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10
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Shukla P, Melkani GC. Mitochondrial epigenetic modifications and nuclear-mitochondrial communication: A new dimension towards understanding and attenuating the pathogenesis in women with PCOS. Rev Endocr Metab Disord 2023; 24:317-326. [PMID: 36705802 PMCID: PMC10150397 DOI: 10.1007/s11154-023-09789-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/16/2023] [Indexed: 01/28/2023]
Abstract
Mitochondrial DNA (mtDNA) epigenetic modifications have recently gained attention in a plethora of complex diseases, including polycystic ovary syndrome (PCOS), a common cause of infertility in women of reproductive age. Herein we discussed mtDNA epigenetic modifications and their impact on nuclear-mitochondrial interactions in general and the latest advances indicating the role of mtDNA methylation in the pathophysiology of PCOS. We highlighted epigenetic changes in nuclear-related mitochondrial genes, including nuclear transcription factors that regulate mitochondrial function and may be involved in the development of PCOS or its related traits. Additionally, therapies targeting mitochondrial epigenetics, including time-restricted eating (TRE), which has been shown to have beneficial effects by improving mitochondrial function and may be mediated by epigenetic modifications, have also been discussed. As PCOS has become a major metabolic disorder and a risk factor for obesity, cardiometabolic disorders, and diabetes, lifestyle/behavior intervention using TRE that reinforces feeding-fasting rhythms without reducing caloric intake may be a promising therapeutic strategy for attenuating the pathogenesis. Furthermore, future perspectives in the area of mitochondrial epigenetics are described.
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Affiliation(s)
- Pallavi Shukla
- Department of Molecular Endocrinology, Indian Council of Medical Research-National Institute for Research in Reproductive and Child Health (ICMR-NIRRCH), J.M. Street, Parel, Mumbai, 400012, India.
| | - Girish C Melkani
- Department of Pathology, Division of Molecular and Cellular Pathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, United States
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11
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Arya D, Balasinor N, Singh D. Varicocele associated male infertility: cellular and molecular perspectives of pathophysiology. Andrology 2022; 10:1463-1483. [PMID: 36040837 DOI: 10.1111/andr.13278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 08/18/2022] [Accepted: 08/18/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Varicocele is a common risk factor associated with reduced male fertility potential. The current understanding of varicocele pathophysiology does not completely explain the clinical manifestation of infertility. The present treatment options such as antioxidant supplementation and varicocelectomy only helps ∼35% of men to achieve spontaneous pregnancy. OBJECTIVE This review aims to summarize the available knowledge on cellular and molecular alterations implicated to varicocele associated male infertility and also highlights the new knowledge generated by 'Omics' technologies. MATERIALS AND METHODS PubMed, MEDLINE, Cochrane and Google Scholar databases are searched using different combinations of keywords (varicocele, infertile/fertile men with varicocele, cellular changes, molecular mechanisms, proteome, epigenome, transcriptome and metabolome). A total of 229 relevant human and animal studies published till 2021 were included in this review. RESULTS Current understanding advocates oxidative stress (OS) as a major contributory factor to the varicocele associated male infertility. Excessive OS causes alteration in testicular microenvironment and sperm DNA fragmentation which further contributes to infertility. Molecular and omics studies have identified several promising biomarkers such as AAMP, SPINT1, MKI67 (genetic markers), sperm quality and function related protein markers, global sperm DNA methylation level (epigenetic marker), Hspa2, Protamine, Gadd7, Dynlt1 and Beclin1 (mRNA markers), PRDX2, HSPA, APOA2, YKL40 (seminal protein markers), total choline and PHGDH (metabolic markers). DISCUSSION Mature spermatozoa harbours a plethora of molecular information in form of proteome, epigenome and transcriptome; which could provide very important clues regarding pathophysiology of varicocele associated infertility. Recent molecular and omics studies in infertile men with varicocele have identified several promising biomarkers. Upon further validation with larger and well-defined studies, some of these biomarkers could aid in varicocele management. CONCLUSION The present evidences suggest inclusion of OS and sperm DNA fragmentation tests could be useful to the diagnostic workup for men with varicocele. Furthermore, including precise molecular markers may assist in diagnostics and prognostics of varicocele associated male infertility. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Deepshikha Arya
- Department of Neuroendocrinology, ICMR- National Institute for Research in Reproductive and Child Health, Parel, Mumbai, 400012, India
| | - Nafisa Balasinor
- Department of Neuroendocrinology, ICMR- National Institute for Research in Reproductive and Child Health, Parel, Mumbai, 400012, India
| | - Dipty Singh
- Department of Neuroendocrinology, ICMR- National Institute for Research in Reproductive and Child Health, Parel, Mumbai, 400012, India
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12
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Sanyal T, Das A, Bhowmick P, Bhattacharjee P. Interplay between environmental exposure and mitochondrial DNA methylation in disease susceptibility and cancer: a comprehensive review. THE NUCLEUS 2022. [DOI: 10.1007/s13237-022-00392-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022] Open
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13
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Yadav T, Gau D, Roy P. Mitochondria-actin cytoskeleton crosstalk in cell migration. J Cell Physiol 2022; 237:2387-2403. [PMID: 35342955 PMCID: PMC9945482 DOI: 10.1002/jcp.30729] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 03/06/2022] [Accepted: 03/11/2022] [Indexed: 12/15/2022]
Abstract
Mitochondria perform diverse functions in the cell and their roles during processes such as cell survival, differentiation, and migration are increasingly being appreciated. Mitochondrial and actin cytoskeletal networks not only interact with each other, but this multifaceted interaction shapes their functional dynamics. The interrelation between mitochondria and the actin cytoskeleton extends far beyond the requirement of mitochondrial ATP generation to power actin dynamics, and impinges upon several major aspects of cellular physiology. Being situated at the hub of cell signaling pathways, mitochondrial function can alter the activity of actin regulatory proteins and therefore modulate the processes downstream of actin dynamics such as cellular migration. As we will discuss, this regulation is highly nuanced and operates at multiple levels allowing mitochondria to occupy a strategic position in the regulation of migration, as well as pathological events that rely on aberrant cell motility such as cancer metastasis. In this review, we summarize the crosstalk that exists between mitochondria and actin regulatory proteins, and further emphasize on how this interaction holds importance in cell migration in normal as well as dysregulated scenarios as in cancer.
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Affiliation(s)
- Tarun Yadav
- Biology, Indian Institute of Science Education and Research, Pune
| | - David Gau
- Bioengineering, University of Pittsburgh, USA
| | - Partha Roy
- Bioengineering, University of Pittsburgh, USA,Pathology, University of Pittsburgh, USA
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14
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Bordoni L, Malinowska AM, Petracci I, Szwengiel A, Gabbianelli R, Chmurzynska A. Diet, Trimethylamine Metabolism, and Mitochondrial DNA: An Observational Study. Mol Nutr Food Res 2022; 66:e2200003. [PMID: 35490412 DOI: 10.1002/mnfr.202200003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 04/14/2022] [Indexed: 12/11/2022]
Abstract
SCOPE Mitochondrial DNA copy number (mtDNAcn) and its methylation level in the D-loop area have been correlated with metabolic health and are suggested to vary in response to environmental stimuli, including diet. Circulating levels of trimethylamine-n-oxide (TMAO), which is an oxidative derivative of the trimethylamine (TMA) produced by the gut microbiome from dietary precursors, have been associated with chronic diseases and are suggested to have an impact on mitochondrial dynamics. This study is aimed to investigate the relationship between diet, TMA, TMAO, and mtDNAcn, as well as DNA methylation. METHODS AND RESULTS Two hundred subjects with extreme (healthy and unhealthy) dietary patterns are recruited. Dietary records are collected to assess their nutrient intake and diets' quality (Healthy Eating Index). Blood levels of TMA and TMAO, circulating levels of TMA precursors and their dietary intakes are measured. MtDNAcn, nuclear DNA methylation long interspersed nuclear element 1 (LINE-1), and strand-specific D-loop methylation levels are assessed. There is no association between dietary patterns and mtDNAcn. The TMAO/TMA ratio is negatively correlated with d-loop methylation levels but positively with mtDNAcn. CONCLUSIONS These findings suggest a potential association between TMA metabolism and mitochondrial dynamics (and mtDNA), indicating a new avenue for further research.
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Affiliation(s)
- Laura Bordoni
- Unit of Molecular Biology and Nutrigenomics, School of Pharmacy, University of Camerino, Camerino, 62032, MC, Italy
| | - Anna M Malinowska
- Department of Human Nutrition and Dietetics, Poznań University of Life Sciences, Poznań, 60-624, Poland
| | - Irene Petracci
- School of Advanced Studies, University of Camerino, Camerino, 62032, MC, Italy
| | - Artur Szwengiel
- Department of Food Technology of Plant Origin, Poznań University of Life Sciences, Poznań, 60-624, Poland
| | - Rosita Gabbianelli
- Unit of Molecular Biology and Nutrigenomics, School of Pharmacy, University of Camerino, Camerino, 62032, MC, Italy
| | - Agata Chmurzynska
- Department of Human Nutrition and Dietetics, Poznań University of Life Sciences, Poznań, 60-624, Poland
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15
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Walker BR, Moraes CT. Nuclear-Mitochondrial Interactions. Biomolecules 2022; 12:biom12030427. [PMID: 35327619 PMCID: PMC8946195 DOI: 10.3390/biom12030427] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/21/2022] [Accepted: 02/26/2022] [Indexed: 12/12/2022] Open
Abstract
Mitochondria, the cell’s major energy producers, also act as signaling hubs, interacting with other organelles both directly and indirectly. Despite having its own circular genome, the majority of mitochondrial proteins are encoded by nuclear DNA. To respond to changes in cell physiology, the mitochondria must send signals to the nucleus, which can, in turn, upregulate gene expression to alter metabolism or initiate a stress response. This is known as retrograde signaling. A variety of stimuli and pathways fall under the retrograde signaling umbrella. Mitochondrial dysfunction has already been shown to have severe implications for human health. Disruption of retrograde signaling, whether directly associated with mitochondrial dysfunction or cellular environmental changes, may also contribute to pathological deficits. In this review, we discuss known signaling pathways between the mitochondria and the nucleus, examine the possibility of direct contacts, and identify pathological consequences of an altered relationship.
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Affiliation(s)
- Brittni R. Walker
- Neuroscience Program, University of Miami Miller School of Medicine, 1420 NW 9th Avenue, Rm. 229, Miami, FL 33136, USA;
| | - Carlos T. Moraes
- Department of Neurology, University of Miami Miller School of Medicine, 1420 NW 9th Avenue, Rm. 229, Miami, FL 33136, USA
- Correspondence: ; Tel.: +1-305-243-5858
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16
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Mitochondrial DNA and Epigenetics: Investigating Interactions with the One-Carbon Metabolism in Obesity. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:9171684. [PMID: 35132354 PMCID: PMC8817841 DOI: 10.1155/2022/9171684] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 12/13/2022]
Abstract
Mitochondrial DNA copy number (mtDNAcn) has been proposed for use as a surrogate biomarker of mitochondrial health, and evidence suggests that mtDNA might be methylated. Intermediates of the one-carbon cycle (1CC), which is duplicated in the cytoplasm and mitochondria, have a major role in modulating the impact of diet on the epigenome. Moreover, epigenetic pathways and the redox system are linked by the metabolism of glutathione (GSH). In a cohort of 101 normal-weight and 97 overweight/obese subjects, we evaluated mtDNAcn and methylation levels in both mitochondrial and nuclear areas to test the association of these marks with body weight, metabolic profile, and availability of 1CC intermediates associated with diet. Body composition was associated with 1CC intermediate availability. Reduced levels of GSH were measured in the overweight/obese group (p = 1.3∗10−5). A high BMI was associated with lower LINE-1 (p = 0.004) and nominally lower methylenetetrahydrofolate reductase (MTHFR) gene methylation (p = 0.047). mtDNAcn was lower in overweight/obese subjects (p = 0.004) and independently correlated with MTHFR methylation levels (p = 0.005) but not to LINE-1 methylation levels (p = 0.086). DNA methylation has been detected in the light strand but not in the heavy strand of the mtDNA. Although mtDNA methylation in the light strand did not differ between overweight/obese and normal-weight subjects, it was nominally correlated with homocysteine levels (p = 0.035) and MTHFR methylation (p = 0.033). This evidence suggests that increased body weight might perturb mitochondrial-nuclear homeostasis affecting the availability of nutrients acting as intermediates of the one-carbon cycle.
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17
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Barbier-Torres L, Murray B, Yang JW, Wang J, Matsuda M, Robinson A, Binek A, Fan W, Fernández-Ramos D, Lopitz-Otsoa F, Luque-Urbano M, Millet O, Mavila N, Peng H, Ramani K, Gottlieb R, Sun Z, Liangpunsakul S, Seki E, Van Eyk JE, Mato JM, Lu SC. Depletion of mitochondrial methionine adenosyltransferase α1 triggers mitochondrial dysfunction in alcohol-associated liver disease. Nat Commun 2022; 13:557. [PMID: 35091576 PMCID: PMC8799735 DOI: 10.1038/s41467-022-28201-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/14/2022] [Indexed: 12/19/2022] Open
Abstract
MATα1 catalyzes the synthesis of S-adenosylmethionine, the principal biological methyl donor. Lower MATα1 activity and mitochondrial dysfunction occur in alcohol-associated liver disease. Besides cytosol and nucleus, MATα1 also targets the mitochondria of hepatocytes to regulate their function. Here, we show that mitochondrial MATα1 is selectively depleted in alcohol-associated liver disease through a mechanism that involves the isomerase PIN1 and the kinase CK2. Alcohol activates CK2, which phosphorylates MATα1 at Ser114 facilitating interaction with PIN1, thereby inhibiting its mitochondrial localization. Blocking PIN1-MATα1 interaction increased mitochondrial MATα1 levels and protected against alcohol-induced mitochondrial dysfunction and fat accumulation. Normally, MATα1 interacts with mitochondrial proteins involved in TCA cycle, oxidative phosphorylation, and fatty acid β-oxidation. Preserving mitochondrial MATα1 content correlates with higher methylation and expression of mitochondrial proteins. Our study demonstrates a role of CK2 and PIN1 in reducing mitochondrial MATα1 content leading to mitochondrial dysfunction in alcohol-associated liver disease.
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Affiliation(s)
- Lucía Barbier-Torres
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Ben Murray
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Jin Won Yang
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- College of Pharmacy, Woosuk University, Wanju, South Korea
| | - Jiaohong Wang
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Michitaka Matsuda
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Aaron Robinson
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Aleksandra Binek
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Wei Fan
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - David Fernández-Ramos
- Precision Medicine and Metabolism, CIC bioGUNE, BRTA, CIBERehd, Technology Park of Bizkaia, 48160, Derio, Bizkaia, Spain
| | - Fernando Lopitz-Otsoa
- Precision Medicine and Metabolism, CIC bioGUNE, BRTA, CIBERehd, Technology Park of Bizkaia, 48160, Derio, Bizkaia, Spain
| | - Maria Luque-Urbano
- Precision Medicine and Metabolism, CIC bioGUNE, BRTA, CIBERehd, Technology Park of Bizkaia, 48160, Derio, Bizkaia, Spain
| | - Oscar Millet
- Precision Medicine and Metabolism, CIC bioGUNE, BRTA, CIBERehd, Technology Park of Bizkaia, 48160, Derio, Bizkaia, Spain
| | - Nirmala Mavila
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Hui Peng
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Komal Ramani
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Roberta Gottlieb
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Zhaoli Sun
- Department of Surgery and Transplant Biology Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Suthat Liangpunsakul
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
- Roudebush Veterans Administration Medical Center, Indianapolis, IN, USA
| | - Ekihiro Seki
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Jennifer E Van Eyk
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Jose M Mato
- Precision Medicine and Metabolism, CIC bioGUNE, BRTA, CIBERehd, Technology Park of Bizkaia, 48160, Derio, Bizkaia, Spain
| | - Shelly C Lu
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
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18
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Abstract
Mitochondria are considered to be the powerhouse of the cell. Normal functioning of the mitochondria is not only essential for cellular energy production but also for several immunomodulatory processes. Macrophages operate in metabolic niches and rely on rapid adaptation to specific metabolic conditions such as hypoxia, nutrient limitations, or reactive oxygen species to neutralize pathogens. In this regard, the fast reprogramming of mitochondrial metabolism is indispensable to provide the cells with the necessary energy and intermediates to efficiently mount the inflammatory response. Moreover, mitochondria act as a physical scaffold for several proteins involved in immune signaling cascades and their dysfunction is immediately associated with a dampened immune response. In this review, we put special focus on mitochondrial function in macrophages and highlight how mitochondrial metabolism is involved in macrophage activation.
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Affiliation(s)
- Mohamed Zakaria Nassef
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Center of Systems Biology (BRICS), Technische Universität Braunschweig, Brunswick, Germany
| | - Jasmin E Hanke
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Center of Systems Biology (BRICS), Technische Universität Braunschweig, Brunswick, Germany
| | - Karsten Hiller
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Center of Systems Biology (BRICS), Technische Universität Braunschweig, Brunswick, Germany
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19
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Alikhani M, Touati E, Karimipoor M, Vosough M, Mohammadi M. Mitochondrial DNA Copy Number Variations in Gastrointestinal Tract Cancers: Potential Players. J Gastrointest Cancer 2021; 53:770-781. [PMID: 34486088 DOI: 10.1007/s12029-021-00707-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2021] [Indexed: 10/20/2022]
Abstract
Alterations of mitochondria have been linked to several cancers. Also, the mitochondrial DNA copy number (mtDNA-CN) is altered in various cancers, including gastrointestinal tract (GIT) cancers, and several research groups have investigated its potential as a cancer biomarker. However, the exact causes of mtDNA-CN variations are not yet revealed. This review discussed the conceivable players in this scheme, including reactive oxygen species (ROS), mtDNA genetic variations, DNA methylation, telomere length, autophagy, immune system activation, aging, and infections, and discussed their possible impact in the initiation and progression of cancer. By further exploring such mechanisms, mtDNA-CN variations may be effectively utilized as cancer biomarkers and provide grounds for developing novel cancer therapeutic agents.
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Affiliation(s)
- Mehdi Alikhani
- Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Eliette Touati
- Unit of Helicobacter Pathogenesis, Department of Microbiology, CNRS UMR2001, Institut Pasteur, 25-28 Rue du Dr Roux cedex 15, 75724, Paris, France
| | - Morteza Karimipoor
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Massoud Vosough
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Marjan Mohammadi
- Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
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20
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Bebbere D, Ulbrich SE, Giller K, Zakhartchenko V, Reichenbach HD, Reichenbach M, Verma PJ, Wolf E, Ledda S, Hiendleder S. Mitochondrial DNA Depletion in Granulosa Cell Derived Nuclear Transfer Tissues. Front Cell Dev Biol 2021; 9:664099. [PMID: 34124044 PMCID: PMC8194821 DOI: 10.3389/fcell.2021.664099] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/31/2021] [Indexed: 12/14/2022] Open
Abstract
Somatic cell nuclear transfer (SCNT) is a key technology with broad applications that range from production of cloned farm animals to derivation of patient-matched stem cells or production of humanized animal organs for xenotransplantation. However, effects of aberrant epigenetic reprogramming on gene expression compromise cell and organ phenotype, resulting in low success rate of SCNT. Standard SCNT procedures include enucleation of recipient oocytes before the nuclear donor cell is introduced. Enucleation removes not only the spindle apparatus and chromosomes of the oocyte but also the perinuclear, mitochondria rich, ooplasm. Here, we use a Bos taurus SCNT model with in vitro fertilized (IVF) and in vivo conceived controls to demonstrate a ∼50% reduction in mitochondrial DNA (mtDNA) in the liver and skeletal muscle, but not the brain, of SCNT fetuses at day 80 of gestation. In the muscle, we also observed significantly reduced transcript abundances of mtDNA-encoded subunits of the respiratory chain. Importantly, mtDNA content and mtDNA transcript abundances correlate with hepatomegaly and muscle hypertrophy of SCNT fetuses. Expression of selected nuclear-encoded genes pivotal for mtDNA replication was similar to controls, arguing against an indirect epigenetic nuclear reprogramming effect on mtDNA amount. We conclude that mtDNA depletion is a major signature of perturbations after SCNT. We further propose that mitochondrial perturbation in interaction with incomplete nuclear reprogramming drives abnormal epigenetic features and correlated phenotypes, a concept supported by previously reported effects of mtDNA depletion on the epigenome and the pleiotropic phenotypic effects of mtDNA depletion in humans. This provides a novel perspective on the reprogramming process and opens new avenues to improve SCNT protocols for healthy embryo and tissue development.
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Affiliation(s)
- Daniela Bebbere
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy.,Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Science, LMU Munich, Munich, Germany
| | - Susanne E Ulbrich
- ETH Zürich, Animal Physiology, Institute of Agricultural Sciences, Zurich, Switzerland
| | - Katrin Giller
- ETH Zürich, Animal Physiology, Institute of Agricultural Sciences, Zurich, Switzerland
| | - Valeri Zakhartchenko
- Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Science, LMU Munich, Munich, Germany
| | - Horst-Dieter Reichenbach
- Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Science, LMU Munich, Munich, Germany.,Bavarian State Research Center for Agriculture, Institute of Animal Breeding, Grub, Germany
| | - Myriam Reichenbach
- Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Science, LMU Munich, Munich, Germany.,Bayern-Genetik GmbH, Grub, Germany
| | - Paul J Verma
- Livestock Sciences, South Australian Research and Development Institute, Roseworthy, SA, Australia.,School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Eckhard Wolf
- Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Science, LMU Munich, Munich, Germany
| | - Sergio Ledda
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Stefan Hiendleder
- Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Science, LMU Munich, Munich, Germany.,School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia.,Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia.,Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
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21
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Breton S, Ghiselli F, Milani L. Mitochondrial Short-Term Plastic Responses and Long-Term Evolutionary Dynamics in Animal Species. Genome Biol Evol 2021; 13:6248094. [PMID: 33892508 PMCID: PMC8290114 DOI: 10.1093/gbe/evab084] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 04/13/2021] [Accepted: 04/20/2021] [Indexed: 12/15/2022] Open
Abstract
How do species respond or adapt to environmental changes? The answer to this depends partly on mitochondrial epigenetics and genetics, new players in promoting adaptation to both short- and long-term environmental changes. In this review, we explore how mitochondrial epigenetics and genetics mechanisms, such as mtDNA methylation, mtDNA-derived noncoding RNAs, micropeptides, mtDNA mutations, and adaptations, can contribute to animal plasticity and adaptation. We also briefly discuss the challenges in assessing mtDNA adaptive evolution. In sum, this review covers new advances in the field of mitochondrial genomics, many of which are still controversial, and discusses processes still somewhat obscure, and some of which are still quite speculative and require further robust experimentation.
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Affiliation(s)
- Sophie Breton
- Department of Biological Sciences, University of Montreal, Quebec, Canada
| | - Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Liliana Milani
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
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22
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Bressan P, Kramer P. Mental Health, Mitochondria, and the Battle of the Sexes. Biomedicines 2021; 9:biomedicines9020116. [PMID: 33530498 PMCID: PMC7911591 DOI: 10.3390/biomedicines9020116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 01/12/2023] Open
Abstract
This paper presents a broad perspective on how mental disease relates to the different evolutionary strategies of men and women and to growth, metabolism, and mitochondria—the enslaved bacteria in our cells that enable it all. Several mental disorders strike one sex more than the other; yet what truly matters, regardless of one’s sex, is how much one’s brain is “female” and how much it is “male”. This appears to be the result of an arms race between the parents over how many resources their child ought to extract from the mother, hence whether it should grow a lot or stay small and undemanding. An uneven battle alters the child’s risk of developing not only insulin resistance, diabetes, or cancer, but a mental disease as well. Maternal supremacy increases the odds of a psychosis-spectrum disorder; paternal supremacy, those of an autism-spectrum one. And a particularly lopsided struggle may invite one or the other of a series of syndromes that come in pairs, with diametrically opposite, excessively “male” or “female” characteristics. By providing the means for this tug of war, mitochondria take center stage in steadying or upsetting the precarious balance on which our mental health is built.
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23
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Sedley L. Advances in Nutritional Epigenetics-A Fresh Perspective for an Old Idea. Lessons Learned, Limitations, and Future Directions. Epigenet Insights 2020; 13:2516865720981924. [PMID: 33415317 PMCID: PMC7750768 DOI: 10.1177/2516865720981924] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/25/2020] [Indexed: 12/11/2022] Open
Abstract
Nutritional epigenetics is a rapidly expanding field of research, and the natural modulation of the genome is a non-invasive, sustainable, and personalized alternative to gene-editing for chronic disease management. Genetic differences and epigenetic inflexibility resulting in abnormal gene expression, differential or aberrant methylation patterns account for the vast majority of diseases. The expanding understanding of biological evolution and the environmental influence on epigenetics and natural selection requires relearning of once thought to be well-understood concepts. This research explores the potential for natural modulation by the less understood epigenetic modifications such as ubiquitination, nitrosylation, glycosylation, phosphorylation, and serotonylation concluding that the under-appreciated acetylation and mitochondrial dependant downstream epigenetic post-translational modifications may be the pinnacle of the epigenomic hierarchy, essential for optimal health, including sustainable cellular energy production. With an emphasis on lessons learned, this conceptional exploration provides a fresh perspective on methylation, demonstrating how increases in environmental methane drive an evolutionary down regulation of endogenous methyl groups synthesis and demonstrates how epigenetic mechanisms are cell-specific, making supplementation with methyl cofactors throughout differentiation unpredictable. Interference with the epigenomic hierarchy may result in epigenetic inflexibility, symptom relief and disease concomitantly and may be responsible for the increased incidence of neurological disease such as autism spectrum disorder.
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Affiliation(s)
- Lynda Sedley
- Bachelor of Health Science (Nutritional Medicine),
GC Biomedical Science (Genomics), The Research and Educational Institute of
Environmental and Nutritional Epigenetics, Queensland, Australia
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24
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Mitochondrial Dysfunction in Parkinson's Disease: Focus on Mitochondrial DNA. Biomedicines 2020; 8:biomedicines8120591. [PMID: 33321831 PMCID: PMC7763033 DOI: 10.3390/biomedicines8120591] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/05/2020] [Accepted: 12/08/2020] [Indexed: 12/14/2022] Open
Abstract
Mitochondria, the energy stations of the cell, are the only extranuclear organelles, containing their own (mitochondrial) DNA (mtDNA) and the protein synthesizing machinery. The location of mtDNA in close proximity to the oxidative phosphorylation system of the inner mitochondrial membrane, the main source of reactive oxygen species (ROS), is an important factor responsible for its much higher mutation rate than nuclear DNA. Being more vulnerable to damage than nuclear DNA, mtDNA accumulates mutations, crucial for the development of mitochondrial dysfunction playing a key role in the pathogenesis of various diseases. Good evidence exists that some mtDNA mutations are associated with increased risk of Parkinson’s disease (PD), the movement disorder resulted from the degenerative loss of dopaminergic neurons of substantia nigra. Although their direct impact on mitochondrial function/dysfunction needs further investigation, results of various studies performed using cells isolated from PD patients or their mitochondria (cybrids) suggest their functional importance. Studies involving mtDNA mutator mice also demonstrated the importance of mtDNA deletions, which could also originate from abnormalities induced by mutations in nuclear encoded proteins needed for mtDNA replication (e.g., polymerase γ). However, proteomic studies revealed only a few mitochondrial proteins encoded by mtDNA which were downregulated in various PD models. This suggests nuclear suppression of the mitochondrial defects, which obviously involve cross-talk between nuclear and mitochondrial genomes for maintenance of mitochondrial functioning.
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25
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Alhayaza R, Haque E, Karbasiafshar C, Sellke FW, Abid MR. The Relationship Between Reactive Oxygen Species and Endothelial Cell Metabolism. Front Chem 2020; 8:592688. [PMID: 33330380 PMCID: PMC7732658 DOI: 10.3389/fchem.2020.592688] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/12/2020] [Indexed: 12/12/2022] Open
Abstract
Cardiovascular disease (CVD) has been the leading cause of death for many decades, highlighting the importance of new research and treatments in the field. The role of hypoxia and subsequent free radical production [reactive oxygen species (ROS)] have become an area of particular interest in CVD. Interestingly, our laboratory and other laboratories have recently reported positive roles of subcellular ROS in modulating endothelial cell (EC) metabolism, proliferation, and angiogenesis. This bidirectional relationship between ROS and EC metabolism, as well as functional changes, continues to be an area of active research. Interestingly, ECs have been shown to rely on anaerobic processes for ATP generation, despite their direct access to oxygen. This paradox has proven to be beneficial as the major reliance on glycolysis produces ATP faster, preserves oxygen, and results in reduced ROS levels in contrast to oxidative phosphorylation. This review will address the relationship between ROS and carbohydrate, lipid, and nitrogen metabolism in ECs, and their effects on EC phenotype such as sprouting angiogenesis.
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Affiliation(s)
- Raid Alhayaza
- Alfaisal University School of Medicine, Riyadh, Saudi Arabia
| | - Emaan Haque
- Alfaisal University School of Medicine, Riyadh, Saudi Arabia
| | - Catherine Karbasiafshar
- Division of Cardiothoracic Surgery, Cardiovascular Research Center, Rhode Island Hospital, Brown University Alpert Medical School, Providence, RI, United States
| | - Frank W. Sellke
- Division of Cardiothoracic Surgery, Cardiovascular Research Center, Rhode Island Hospital, Brown University Alpert Medical School, Providence, RI, United States
| | - M. Ruhul Abid
- Division of Cardiothoracic Surgery, Cardiovascular Research Center, Rhode Island Hospital, Brown University Alpert Medical School, Providence, RI, United States
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26
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Bordoni L, Gabbianelli R. Mitochondrial DNA and Neurodegeneration: Any Role for Dietary Antioxidants? Antioxidants (Basel) 2020; 9:E764. [PMID: 32824558 PMCID: PMC7466149 DOI: 10.3390/antiox9080764] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/07/2020] [Accepted: 08/14/2020] [Indexed: 02/07/2023] Open
Abstract
The maintenance of the mitochondrial function is essential in preventing and counteracting neurodegeneration. In particular, mitochondria of neuronal cells play a pivotal role in sustaining the high energetic metabolism of these cells and are especially prone to oxidative damage. Since overproduction of reactive oxygen species (ROS) is involved in the pathogenesis of neurodegeneration, dietary antioxidants have been suggested to counteract the detrimental effects of ROS and to preserve the mitochondrial function, thus slowing the progression and limiting the extent of neuronal cell loss in neurodegenerative disorders. In addition to their role in the redox-system homeostasis, mitochondria are unique organelles in that they contain their own genome (mtDNA), which acts at the interface between environmental exposures and the molecular triggers of neurodegeneration. Indeed, it has been demonstrated that mtDNA (including both genetics and, from recent evidence, epigenetics) might play relevant roles in modulating the risk for neurodegenerative disorders. This mini-review describes the link between the mitochondrial genome and cellular oxidative status, with a particular focus on neurodegeneration; moreover, it provides an overview on potential beneficial effects of antioxidants in preserving mitochondrial functions through the protection of mtDNA.
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Affiliation(s)
- Laura Bordoni
- Unit of Molecular Biology, School of Pharmacy, University of Camerino, 62032 Camerino, Italy;
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The Role of Nutri(epi)genomics in Achieving the Body's Full Potential in Physical Activity. Antioxidants (Basel) 2020; 9:antiox9060498. [PMID: 32517297 PMCID: PMC7346155 DOI: 10.3390/antiox9060498] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022] Open
Abstract
Physical activity represents a powerful tool to achieve optimal health. The overall activation of several molecular pathways is associated with many beneficial effects, mainly converging towards a reduced systemic inflammation. Not surprisingly, regular activity can contribute to lowering the “epigenetic age”, acting as a modulator of risk toward several diseases and enhancing longevity. Behind this, there are complex molecular mechanisms induced by exercise, which modulate gene expression, also through epigenetic modifications. The exercise-induced epigenetic imprint can be transient or permanent and contributes to the muscle memory, which allows the skeletal muscle adaptation to environmental stimuli previously encountered. Nutrition, through key macro- and micronutrients with antioxidant properties, can play an important role in supporting skeletal muscle trophism and those molecular pathways triggering the beneficial effects of physical activity. Nutrients and antioxidant food components, reversibly altering the epigenetic imprint, have a big impact on the phenotype. This assigns a role of primary importance to nutri(epi)genomics, not only in optimizing physical performance, but also in promoting long term health. The crosstalk between physical activity and nutrition represents a major environmental pressure able to shape human genotypes and phenotypes, thus, choosing the right combination of lifestyle factors ensures health and longevity.
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28
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Aminuddin A, Ng PY, Leong CO, Chua EW. Mitochondrial DNA alterations may influence the cisplatin responsiveness of oral squamous cell carcinoma. Sci Rep 2020; 10:7885. [PMID: 32398775 PMCID: PMC7217862 DOI: 10.1038/s41598-020-64664-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 04/20/2020] [Indexed: 02/07/2023] Open
Abstract
Cisplatin is the first-line chemotherapeutic agent for the treatment of oral squamous cell carcinoma (OSCC). However, the intrinsic or acquired resistance against cisplatin remains a major obstacle to treatment efficacy in OSCC. Recently, mitochondrial DNA (mtDNA) alterations have been reported in a variety of cancers. However, the role of mtDNA alterations in OSCC has not been comprehensively studied. In this study, we evaluated the correlation between mtDNA alterations (mtDNA content, point mutations, large-scale deletions, and methylation status) and cisplatin sensitivity using two OSCC cell lines, namely SAS and H103, and stem cell-like tumour spheres derived from SAS. By microarray analysis, we found that the tumour spheres profited from aberrant lipid and glucose metabolism and became resistant to cisplatin. By qPCR analysis, we found that the cells with less mtDNA were less responsive to cisplatin (H103 and the tumour spheres). Based on the findings, we theorised that the metabolic changes in the tumour spheres probably resulted in mtDNA depletion, as the cells suppressed mitochondrial respiration and switched to an alternative mode of energy production, i.e. glycolysis. Then, to ascertain the origin of the variation in mtDNA content, we used MinION, a nanopore sequencer, to sequence the mitochondrial genomes of H103, SAS, and the tumour spheres. We found that the lower cisplatin sensitivity of H103 could have been caused by a constellation of genetic and epigenetic changes in its mitochondrial genome. Future work may look into how changes in mtDNA translate into an impact on cell function and therefore cisplatin response.
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MESH Headings
- Antineoplastic Agents/pharmacology
- Apoptosis/drug effects
- Apoptosis/genetics
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/pathology
- Cell Line, Tumor
- Cell Proliferation/drug effects
- Cell Proliferation/genetics
- Cell Survival/drug effects
- Cell Survival/genetics
- Cisplatin/pharmacology
- DNA, Mitochondrial/drug effects
- DNA, Mitochondrial/genetics
- DNA, Mitochondrial/metabolism
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Gene Expression Profiling/methods
- Gene Expression Regulation, Neoplastic/drug effects
- Humans
- Mitochondria/drug effects
- Mitochondria/genetics
- Mitochondria/metabolism
- Mouth Neoplasms/genetics
- Mouth Neoplasms/metabolism
- Mouth Neoplasms/pathology
- Neoplastic Stem Cells/drug effects
- Neoplastic Stem Cells/metabolism
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Affiliation(s)
- Amnani Aminuddin
- Drug and Herbal Research Centre, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, 50300, Kuala Lumpur, Malaysia
| | - Pei Yuen Ng
- Drug and Herbal Research Centre, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, 50300, Kuala Lumpur, Malaysia
| | - Chee-Onn Leong
- School of Pharmacy, International Medical University, Bukit Jalil, 57000, Kuala Lumpur, Malaysia
- Centre for Cancer and Stem Cell Research, Institute for Research, Development and Innovation, International Medical University, Bukit Jalil, 57000, Kuala Lumpur, Malaysia
| | - Eng Wee Chua
- Drug and Herbal Research Centre, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, 50300, Kuala Lumpur, Malaysia.
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29
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Hu X, Go YM, Jones DP. Omics Integration for Mitochondria Systems Biology. Antioxid Redox Signal 2020; 32:853-872. [PMID: 31891667 PMCID: PMC7074923 DOI: 10.1089/ars.2019.8006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 12/30/2019] [Indexed: 12/13/2022]
Abstract
Significance: Elucidation of the central importance of mitophagy in homeostasis of cells and organisms emphasizes that mitochondrial functions extend far beyond short-term needs for energy production. In mitochondria systems biology, the mitochondrial genome, proteome, and metabolome operate as a functional network in coordination of cell activities. Organization occurs through subnetworks that are interconnected by membrane potential, transport activities, allosteric and cooperative interactions, redox signaling mechanisms, rheostatic control by post-translational modifications, and metal ion homeostasis. These subnetworks enable use of varied energy precursors, defense against environmental stressors, and macromolecular rewiring to titrate energy production, biosynthesis, and detoxification according to cell-specific needs. Rewiring mechanisms, termed mitochondrial reprogramming, enhance fitness to respond to metabolic resources and challenges from the environment. Maladaptive responses can cause cell death. Maladaptive rewiring can cause disease. In cancer, adaptive rewiring can interfere with effective treatment. Recent Advances: Many recent advances have been facilitated by the development of new omics tools, which create opportunities to use data-driven analysis of omics data to address these complex adaptive and maladaptive mechanisms of mitochondrial reprogramming in human disease. Critical Issues: Application of omics integration to model systems reveals a critical role for metal ion homeostasis broadly impacting mitochondrial reprogramming. Importantly, data show that trans-omics associations are more robust and biologically relevant than single omics associations. Future Directions: Application of omics integration to mitophagy research creates new opportunities to link the complex, interactive functions of mitochondrial form and function in mitochondria systems biology.
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Affiliation(s)
- Xin Hu
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, Georgia
| | - Young-Mi Go
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, Georgia
| | - Dean P. Jones
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, Georgia
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30
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Dimauro I, Paronetto MP, Caporossi D. Exercise, redox homeostasis and the epigenetic landscape. Redox Biol 2020; 35:101477. [PMID: 32127290 PMCID: PMC7284912 DOI: 10.1016/j.redox.2020.101477] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/12/2020] [Accepted: 02/23/2020] [Indexed: 02/07/2023] Open
Abstract
Physical exercise represents one of the strongest physiological stimuli capable to induce functional and structural modifications in all biological systems. Indeed, beside the traditional genetic mechanisms, physical exercise can modulate gene expression through epigenetic modifications, namely DNA methylation, post-translational histone modification and non-coding RNA transcripts. Initially considered as merely damaging molecules, it is now well recognized that both reactive oxygen (ROS) and nitrogen species (RNS) produced under voluntary exercise play an important role as regulatory mediators in signaling processes. While robust scientific evidences highlight the role of exercise-associated redox modifications in modulating gene expression through the genetic machinery, the understanding of their specific impact on epigenomic profile is still at an early stage. This review will provide an overview of the role of ROS and RNS in modulating the epigenetic landscape in the context of exercise-related adaptations. Physical exercise can modulate gene expression through epigenetic modifications. Epigenetic regulation of ROS/RNS generating, sensing and neutralizing enzymes can impact the cellular levels of ROS and RNS. ROS might act as modulators of epigenetic machinery, interfering with DNA methylation, hPTMs and ncRNAs expression. Redox homeostasis might hold a relevant role in the epigenetic landscape modulating exercise-related adaptations.
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Affiliation(s)
- Ivan Dimauro
- Unit of Biology and Genetics of Movement, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro de Bosis 15, 00135, Rome, Italy
| | - Maria Paola Paronetto
- Unit of Biology and Genetics of Movement, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro de Bosis 15, 00135, Rome, Italy; Laboratory of Cellular and Molecular Neurobiology, IRCCS Fondazione Santa Lucia, Via Del Fosso di Fiorano, Rome, Italy
| | - Daniela Caporossi
- Unit of Biology and Genetics of Movement, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro de Bosis 15, 00135, Rome, Italy.
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31
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A Pilot Study on the Effects of l-Carnitine and Trimethylamine-N-Oxide on Platelet Mitochondrial DNA Methylation and CVD Biomarkers in Aged Women. Int J Mol Sci 2020; 21:ijms21031047. [PMID: 32033285 PMCID: PMC7037757 DOI: 10.3390/ijms21031047] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 01/31/2020] [Accepted: 02/03/2020] [Indexed: 12/24/2022] Open
Abstract
l-carnitine supplementation has been used for cardiovascular health protection for a long time. Recently, trimethylamine-N-oxide (TMAO), which is an end product of l-carnitine metabolism via the activity of microbiota, has been identified as a cardiovascular disease (CVD) biomarker. The aim of this study was to assess the effect of 6 months of l-carnitine supplementation in a group of aged women engaged in a regular physical training. Platelet mitochondrial DNA methylation, an emerging and innovative biomarker, lipid profile and TMAO levels have been measured. TMAO increased after l-carnitine supplementation (before 344.3 ± 129.8 ng/mL vs. after 2216.8 ± 1869.0 ng/mL; n = 9; paired t-test, p = 0.02). No significant effects on TMAO were exerted by training alone (n = 9) or by l-leucine supplementation (n = 12). TMAO levels after 6 months of l-carnitine supplementation were associated with higher low-density lipoprotein-cholesterol (LDL-c) (Spearman Rho = 0.518, p = 0.003) and total cholesterol (TC) (Spearman Rho = 0.407, p = 0.026) levels. l-carnitine supplementation increased D-loop methylation in platelets (+6.63%; paired t-test, p = 0.005). D-loop methylation was not directly correlated to the TMAO augmentation observed in the supplemented group, but its increase inversely correlated with TC (Pearson coefficient = −0.529, p = 0.029) and LDL-c (Pearson coefficient = −0.439, p = 0.048). This evidence supports the hypothesis that the correlation between l-carnitine, TMAO and atherosclerosis might be more complex than already postulated, and the alteration of mitochondrial DNA (mtDNA) methylation in platelets could be involved in the pathogenesis of this multifactorial disease.
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32
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Bordoni L, Smerilli V, Nasuti C, Gabbianelli R. Mitochondrial DNA methylation and copy number predict body composition in a young female population. J Transl Med 2019; 17:399. [PMID: 31779622 PMCID: PMC6883616 DOI: 10.1186/s12967-019-02150-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 11/19/2019] [Indexed: 12/15/2022] Open
Abstract
Background Since both genomic and environmental factors are involved in obesity etiology, several studies about the influence of adiposity on both nuclear DNA and mitochondrial DNA methylation patterns have been carried out. Nevertheless, few evidences exploring the usage of buccal swab samples to study mitochondrial DNA epigenetics can be found in literature. Methods In this study, mitochondrial DNA from buccal swabs collected from a young Caucasian population (n = 69) have been used to examine potential correlation between mitochondrial DNA copy number and methylation with body composition (BMI, WHtR and bioimpedance measurements). Results A negative correlation between mitochondrial DNA copy number and BMI was measured in females (p = 0.028), but not in males. The mean percentage of D-loop methylation is significantly higher in overweight than in lean female subjects (p = 0.003), and a specific CpG located in the D-loop shows per se an association with impaired body composition (p = 0.004). Body composition impairment is predicted by a combined variable including mtDNA copy number and the D-loop methylation (AUC = 0.785; p = 0.009). Conclusions This study corroborates the hypothesis that mitochondrial DNA carries relevant information about body composition. However, wider investigations able to validate the usage of mtDNA methylation from buccal swabs as a biomarker are warranted.
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Affiliation(s)
- Laura Bordoni
- Unit of Molecular Biology, School of Pharmacy, University of Camerino, Via Gentile III da Varano, 62032, Camerino, MC, Italy
| | - Vanessa Smerilli
- Unit of Molecular Biology, School of Pharmacy, University of Camerino, Via Gentile III da Varano, 62032, Camerino, MC, Italy
| | - Cinzia Nasuti
- Unit of Molecular Biology, School of Pharmacy, University of Camerino, Via Gentile III da Varano, 62032, Camerino, MC, Italy
| | - Rosita Gabbianelli
- Unit of Molecular Biology, School of Pharmacy, University of Camerino, Via Gentile III da Varano, 62032, Camerino, MC, Italy.
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33
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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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34
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Mitochondrial Retrograde Signalling and Metabolic Alterations in the Tumour Microenvironment. Cells 2019; 8:cells8030275. [PMID: 30909478 PMCID: PMC6468901 DOI: 10.3390/cells8030275] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/18/2019] [Accepted: 03/19/2019] [Indexed: 12/22/2022] Open
Abstract
This review explores the molecular mechanisms that may be responsible for mitochondrial retrograde signalling related metabolic reprogramming in cancer and host cells in the tumour microenvironment and provides a summary of recent updates with regard to the functional modulation of diverse cells in the tumour microenvironment.
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35
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Kahl KG, Stapel B, Frieling H. Link between depression and cardiovascular diseases due to epigenomics and proteomics: Focus on energy metabolism. Prog Neuropsychopharmacol Biol Psychiatry 2019; 89:146-157. [PMID: 30194950 DOI: 10.1016/j.pnpbp.2018.09.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/13/2018] [Accepted: 09/05/2018] [Indexed: 12/11/2022]
Abstract
Major depression is the most common mental disorder and a leading cause of years lived with disability. In addition to the burden attributed to depressive symptoms and reduced daily life functioning, people with major depression are at increased risk of premature mortality, particularly due to cardiovascular diseases. Several studies point to a bi-directional relation between major depression and cardiovascular diseases, thereby indicating that both diseases may share common pathophysiological pathways. These include lifestyle factors (e.g. physical activity, smoking behavior), dysfunctions of endocrine systems (e.g. hypothalamus-pituitary adrenal axis), and a dysbalance of pro- and anti-inflammatory factors. Furthermore, recent research point to the role of epigenomic and proteomic factors, that are reviewed here with a particular focus on the mitochondrial energy metabolism.
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Affiliation(s)
- Kai G Kahl
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Germany.
| | - Britta Stapel
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Germany
| | - Helge Frieling
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Germany
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36
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Liu L, He X, Zhao M, Yang S, Wang S, Yu X, Liu J, Zang W. Regulation of DNA methylation and 2-OG/TET signaling by choline alleviated cardiac hypertrophy in spontaneously hypertensive rats. J Mol Cell Cardiol 2019; 128:26-37. [PMID: 30660679 DOI: 10.1016/j.yjmcc.2019.01.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/24/2018] [Accepted: 01/14/2019] [Indexed: 12/17/2022]
Abstract
DNA methylation is a well-defined epigenetic modification that regulates gene transcription. However, the role of DNA methylation in the cardiac hypertrophy seen in hypertension is unclear. This study was performed to investigate genome-wide DNA methylation profiles in spontaneously hypertensive rats (SHRs) and Wistar-Kyoto rats (WKY), and the cardioprotective effect of choline. Eight-week-old male SHRs received intraperitoneal injections of choline (8 mg/kg/day) for 8 weeks. SHRs showed aberrant methylation distribution on chromosomes and genome regions, with decreased methylation levels at CHG and CHH sites. A total of 91,559 differentially methylated regions (DMRs) were detected between SHRs and WKY rats, of which 28,197 were demethylated and 63,362 were methylated. Choline treatment partly restored the DMRs in SHRs, which were related to 131 genes. Gene ontology analysis and Kyoto Encyclopedia of Genes and Genomes analysis of DMRs suggested that choline partly reversed the dysfunctions of biological processes, cellular components and molecular functions in SHRs. Moreover, the inhibition of 2-oxoglutarate accumulation by choline, thereby inhibiting excessive activation of ten-eleven translocation methylcytosine dioxygenase enzymes, may correlate with the beneficial effects of choline on methylation levels, cardiac hypertrophy and cardiac function of SHRs, as indicated by decreased heart rate and blood pressure, and increased ejection fraction and fractional shortening. This study provides the first genome-wide DNA methylation profile of the hypertrophic myocardium of SHRs and suggests a novel role for this epigenetic modification in hypertension. Choline treatment may represent a promising approach for modification of DNA methylation and optimization of the epigenetic profile for antihypertensive therapy.
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Affiliation(s)
- Longzhu Liu
- Department of Pharmacology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, PR China
| | - Xi He
- Department of Pharmacology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, PR China
| | - Ming Zhao
- Department of Pharmacology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, PR China
| | - Si Yang
- Department of Pharmacology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, PR China
| | - Shengpeng Wang
- Cardiovascular Research Center, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, PR China
| | - Xiaojiang Yu
- Department of Pharmacology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, PR China
| | - Jiankang Liu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Weijin Zang
- Department of Pharmacology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, PR China.
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Abstract
Marine organisms' persistence hinges on the capacity for acclimatization and adaptation to the myriad of interacting environmental stressors associated with global climate change. In this context, epigenetics-mechanisms that facilitate phenotypic variation through genotype-environment interactions-are of great interest ecologically and evolutionarily. Our comprehensive review of marine environmental epigenetics guides our recommendations of four key areas for future research: the dynamics of wash-in and wash-out of epigenetic effects, the mechanistic understanding of the interplay of different epigenetic marks and the interaction with the microbiome, the capacity for and mechanisms of transgenerational epigenetic inheritance, and the evolutionary implications of the interaction of genetic and epigenetic features. Emerging insights in marine environmental epigenetics can be applied to critical issues such as aquaculture, biomonitoring, and biological invasions, thereby improving our ability to explain and predict the responses of marine taxa to global climate change.
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Affiliation(s)
- Jose M Eirin-Lopez
- Environmental Epigenetics Laboratory, Center for Coastal Oceans Research, Institute for Water and Environment, Florida International University, North Miami, Florida 33181, USA;
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island 02881, USA;
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38
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Cianciulli A, Menga A, Ferdinando P, Iacobazzi V. FOXD3 acts as a repressor of the mitochondrial S-adenosylmethionine carrier (SLC25A26) gene expression in cancer cells. Biochimie 2018; 154:25-34. [DOI: 10.1016/j.biochi.2018.07.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 07/30/2018] [Indexed: 01/24/2023]
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Luyten LJ, Saenen ND, Janssen BG, Vrijens K, Plusquin M, Roels HA, Debacq-Chainiaux F, Nawrot TS. Air pollution and the fetal origin of disease: A systematic review of the molecular signatures of air pollution exposure in human placenta. ENVIRONMENTAL RESEARCH 2018; 166:310-323. [PMID: 29908461 DOI: 10.1016/j.envres.2018.03.025] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 03/13/2018] [Accepted: 03/14/2018] [Indexed: 05/24/2023]
Abstract
BACKGROUND Fetal development is a crucial window of susceptibility in which exposure-related alterations can be induced on the molecular level, leading to potential changes in metabolism and development. The placenta serves as a gatekeeper between mother and fetus, and is in contact with environmental stressors throughout pregnancy. This makes the placenta as a temporary organ an informative non-invasive matrix suitable to investigate omics-related aberrations in association with in utero exposures such as ambient air pollution. OBJECTIVES To summarize and discuss the current evidence and define the gaps of knowledge concerning human placental -omics markers in association with prenatal exposure to ambient air pollution. METHODS Two investigators independently searched the PubMed, ScienceDirect, and Scopus databases to identify all studies published until January 2017 with an emphasis on epidemiological research on prenatal exposure to ambient air pollution and the effect on placental -omics signatures. RESULTS From the initial 386 articles, 25 were retained following an a priori set inclusion and exclusion criteria. We identified eleven studies on the genome, two on the transcriptome, five on the epigenome, five on the proteome category, one study with both genomic and proteomic topics, and one study with both genomic and transcriptomic topics. Six studies discussed the triple relationship between exposure to air pollution during pregnancy, the associated placental -omics marker(s), and the potential effect on disease development later in life. So far, no metabolomic or exposomic data discussing associations between the placenta and prenatal exposure to air pollution have been published. CONCLUSIONS Integration of placental biomarkers in an environmental epidemiological context enables researchers to address fundamental questions essential in unraveling the fetal origin of disease and helps to better define the pregnancy exposome of air pollution.
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Affiliation(s)
- Leen J Luyten
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium; Unité de Recherche en Biologie Cellulaire (URBC) - Namur Research Institute for Life Sciences (Narilis), University of Namur, Belgium
| | - Nelly D Saenen
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Bram G Janssen
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Karen Vrijens
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Michelle Plusquin
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Harry A Roels
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium; Louvain Centre for Toxicology and Applied Pharmacology, Université catholique de Louvain, Brussels, Belgium
| | - Florence Debacq-Chainiaux
- Unité de Recherche en Biologie Cellulaire (URBC) - Namur Research Institute for Life Sciences (Narilis), University of Namur, Belgium
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium; Department of Public Health & Primary Care, Occupational and Environmental Medicine, Leuven University (KULeuven), Leuven, Belgium.
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Bai Y, Casas L, Scheers H, Janssen BG, Nemery B, Nawrot TS. Mitochondrial DNA content in blood and carbon load in airway macrophages. A panel study in elderly subjects. ENVIRONMENT INTERNATIONAL 2018; 119:47-53. [PMID: 29933237 DOI: 10.1016/j.envint.2018.06.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 04/20/2018] [Accepted: 06/04/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Mitochondria are sensitive to air pollutants due to their lack of repair capacity. Changes in mitochondrial DNA copy number (mtDNAcn) or content is a proxy of mitochondrial damage and has been associated with recent exposure to traffic-derived air pollutants, nitrogen dioxide (NO2) and black carbon (BC). Inhaled BC can be phagocytosed by airway macrophages (AMs), and its amount in AM reflects personal exposure to traffic-related air pollution. OBJECTIVES The present study investigated the relation between the internal marker AM BC and ambient NO2 concentration and examined the associations of mtDNAcn with NO2 and AM BC. METHODS A panel of 20 healthy retired participants (10 couples) living in Belgium underwent repeated assessments of health and air pollution exposure at 11 time points over one year. We increased exposure contrast temporarily by moving participants for 10 days to Milan, Italy (high exposure) and to Vindeln, Sweden (low exposure). Personal exposure to NO2 was measured during 5 consecutive days prior to each assessment time point. The amount of BC was assessed by image analysis in AMs retrieved from induced sputum collected at 7 time points. Blood mtDNAcn was determined by qPCR at each time point. Associations between AM BC and NO2, and of mtDNAcn with NO2 and AM BC were estimated using linear mixed effect models adjusted for covariates and potential confounders. RESULTS Mean concentrations of 5-day average NO2 were higher in Milan (64 μg/m3) and lower in Vindeln (4 μg/m3) than Belgium (26 μg/m3). Each 10 μg/m3 increment in NO2 exposure during the last 5 days was associated with 0.07 μm2 (95% CI: 0.001 to 0.012) increase in median area of AM BC. A 10 μg/m3 increase in NO2 was associated with 3.9% (95% CI: 2.2 to 5.5%) decrease in mtDNAcn. Consistently, each 1 μm2 increment in median area of AM BC was associated with 24.8% (95% CI: 6.8 to 39.3%) decrease in mtDNAcn. CONCLUSION In this quasi-experimental setting involving moving persons to places with high and low ambient air pollution, we found changes in AM BC according to ambient air pollution levels measured during the previous 5 days. Both higher ambient NO2 and the internal lung BC load, paralleled mitochondrial compromises as exemplified by lower mtDNA content.
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Affiliation(s)
- Yang Bai
- Center for Environment and Health, Department of Public Health and Primary Care, KU Leuven, Herestraat 49, 3000 Leuven, Belgium.
| | - Lidia Casas
- Center for Environment and Health, Department of Public Health and Primary Care, KU Leuven, Herestraat 49, 3000 Leuven, Belgium.
| | - Hans Scheers
- Center for Environment and Health, Department of Public Health and Primary Care, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Bram G Janssen
- Centre for Environmental Sciences, Hasselt University, Campus Diepenbeek, Agoralaan Gebouw D, 3590 Diepenbeek, Belgium.
| | - Benoit Nemery
- Center for Environment and Health, Department of Public Health and Primary Care, KU Leuven, Herestraat 49, 3000 Leuven, Belgium.
| | - Tim S Nawrot
- Center for Environment and Health, Department of Public Health and Primary Care, KU Leuven, Herestraat 49, 3000 Leuven, Belgium; Centre for Environmental Sciences, Hasselt University, Campus Diepenbeek, Agoralaan Gebouw D, 3590 Diepenbeek, Belgium.
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Su-Keene EJ, Bonilla MM, Padua MV, Zeh DW, Zeh JA. Simulated climate warming and mitochondrial haplogroup modulate testicular small non-coding RNA expression in the neotropical pseudoscorpion, Cordylochernes scorpioides. ENVIRONMENTAL EPIGENETICS 2018; 4:dvy027. [PMID: 30595847 PMCID: PMC6305488 DOI: 10.1093/eep/dvy027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 11/22/2018] [Accepted: 10/21/2018] [Indexed: 06/01/2023]
Abstract
Recent theory suggests that tropical terrestrial arthropods are at significant risk from climate warming. Metabolic rate in such ectothermic species increases exponentially with environmental temperature, and a small temperature increase in a hot environment can therefore have a greater physiological impact than a large temperature increase in a cool environment. In two recent studies of the neotropical pseudoscorpion, Cordylochernes scorpioides, simulated climate warming significantly decreased survival, body size and level of sexual dimorphism. However, these effects were minor compared with catastrophic consequences for male fertility and female fecundity, identifying reproduction as the life stage most vulnerable to climate warming. Here, we examine the effects of chronic high-temperature exposure on epigenetic regulation in C. scorpioides in the context of naturally occurring variation in mitochondrial DNA. Epigenetic mechanisms, including DNA methylation, histone modifications and small non-coding RNA (sncRNA) expression, are particularly sensitive to environmental factors such as temperature, which can induce changes in epigenetic states and phenotypes that may be heritable across generations. Our results indicate that exposure of male pseudoscorpions to elevated temperature significantly altered the expression of >60 sncRNAs in testicular tissue, specifically microRNAs and piwi-interacting RNAs. Mitochondrial haplogroup was also a significant factor influencing both sncRNAs and mitochondrial gene expression. These findings demonstrate that chronic heat stress causes changes in epigenetic profiles that may account for reproductive dysfunction in C. scorpioides males. Moreover, through its effects on epigenetic regulation, mitochondrial DNA polymorphism may provide the potential for an adaptive evolutionary response to climate warming.
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Affiliation(s)
- Eleanor J Su-Keene
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
- Department of Educational Leadership and Research Methodology, Florida Atlantic University, Boca Raton, FL, USA
| | - Melvin M Bonilla
- Graduate Program in Ecology, Evolution and Conservation Biology, University of Nevada, Reno, Reno, NV, USA
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, USA
| | - Michael V Padua
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
- University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - David W Zeh
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
- Graduate Program in Ecology, Evolution and Conservation Biology, University of Nevada, Reno, Reno, NV, USA
| | - Jeanne A Zeh
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
- Graduate Program in Ecology, Evolution and Conservation Biology, University of Nevada, Reno, Reno, NV, USA
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Hadj-Moussa H, Green SR, Storey KB. The Living Dead: Mitochondria and Metabolic Arrest. IUBMB Life 2018; 70:1260-1266. [PMID: 30230676 DOI: 10.1002/iub.1910] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 06/17/2018] [Accepted: 06/19/2018] [Indexed: 12/26/2022]
Abstract
Mitochondria are not just the powerhouses of the cell; these 'end of function' organelles are crucial components of cellular physiology and influence many central metabolic and signaling pathways that support complex multicellular life. Not surprisingly, these organelles play vital roles in adaptations for extreme survival strategies including hibernation and freeze tolerance, both of which are united by requirements for a strong reduction and reprioritization of metabolic processes. To facilitate metabolic rate depression, adaptations of all aspects of mitochondrial function are required, including; energetics, physiology, abundance, gene regulation, and enzymatic controls. This review discusses these factors with a focus on the stress-specific nature of mitochondrial genes and transcriptional regulators, and processes including apoptosis and chaperone protein responses. We also analyze the regulation of glutamate dehydrogenase and pyruvate dehydrogenase, central mitochondrial enzymes involved in coordinating the shifts in metabolic fuel use associated with extreme survival strategies. Finally, an emphasis is given to the novel mitochondrial research areas of microRNAs, peptides, epigenetics, and gaseous mediators and their potential roles in facilitating hypometabolism. © 2018 IUBMB Life, 70(12):1260-1266, 2018.
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Affiliation(s)
- Hanane Hadj-Moussa
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, ON, Canada
| | - Stuart R Green
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, ON, Canada
| | - Kenneth B Storey
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, ON, Canada
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43
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Abstract
Cytoplasmic components and their interactions with the nuclear genome may mediate patterns of phenotypic expression to form a joint inheritance system. However, proximate mechanisms underpinning these interactions remain elusive. To independently assess nuclear genetic and epigenetic cytoplasmic effects, we created a full-factorial design in which representative cytoplasms and nuclear backgrounds from each of two geographically disjunct populations of Drosophila melanogaster were matched together in all four possible combinations. To capture slowly-accumulating epimutations in addition to immediately occurring ones, these constructed populations were examined one year later. We found the K4 methylation of histone H3, H3K4me3, an epigenetic marker associated with transcription start-sites had diverged across different cytoplasms. The loci concerned mainly related to metabolism, mitochondrial function, and reproduction. We found little overlap (<8%) in sites that varied genetically and epigenetically, suggesting that epigenetic changes have diverged independently from any cis-regulatory sequence changes. These results are the first to show cytoplasm-specific effects on patterns of nuclear histone methylation. Our results highlight that experimental nuclear-cytoplasm mismatch may be used to provide a platform to identify epigenetic candidate loci to study the molecular mechanisms of cyto-nuclear interactions.
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Biró O, Hajas O, Nagy-Baló E, Soltész B, Csanádi Z, Nagy B. Relationship between cardiovascular diseases and circulating cell-free nucleic acids in human plasma. Biomark Med 2018; 12:891-905. [DOI: 10.2217/bmm-2017-0386] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cardiovascular diseases (CVDs) are the main cause of human morbidity and mortality worldwide. Early diagnosis could improve the efficiency of treatments. New biomarkers are needed for the identification of high-risk populations in order to make accurate diagnosis and therapy monitoring. Circulating cell-free nucleic acids (cf-NAs) offer a promising new noninvasive tool. These have a role in the regulation of normal physiological functions and in the development of pathological alterations. There is extended research on the clinical application and utilization of cell-free genomic DNA, mtDNA, mRNA, miRNA and long noncoding RNA in CVDs. These molecules could serve as components of new generation therapeutics. Our review focuses on the role of cf-NAs in the pathogenesis of CVDs and we are discussing also possible diagnostic applications and therapeutic implications.
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Affiliation(s)
- Orsolya Biró
- Department of Obstetrics & Gynecology, Semmelweis University, Budapest, Hungary
| | - Orsolya Hajas
- Institute of Cardiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Edina Nagy-Baló
- Institute of Cardiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Beáta Soltész
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Zoltán Csanádi
- Institute of Cardiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Bálint Nagy
- Department of Obstetrics & Gynecology, Semmelweis University, Budapest, Hungary
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Xie K, Sheppard A. Dietary Micronutrients Promote Neuronal Differentiation by Modulating the Mitochondrial‐Nuclear Dialogue. Bioessays 2018; 40:e1800051. [DOI: 10.1002/bies.201800051] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 04/30/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Kui Xie
- Liggins InstituteUniversity of AucklandGraftonAuckland 1023New Zealand
| | - Allan Sheppard
- Liggins InstituteUniversity of AucklandGraftonAuckland 1023New Zealand
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46
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Wiehe RS, Gole B, Chatre L, Walther P, Calzia E, Ricchetti M, Wiesmüller L. Endonuclease G promotes mitochondrial genome cleavage and replication. Oncotarget 2018; 9:18309-18326. [PMID: 29719607 PMCID: PMC5915074 DOI: 10.18632/oncotarget.24822] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/12/2018] [Indexed: 12/26/2022] Open
Abstract
Endonuclease G (EndoG) is a nuclear-encoded endonuclease, mostly localised in mitochondria. In the nucleus EndoG participates in site-specific cleavage during replication stress and genome-wide DNA degradation during apoptosis. However, the impact of EndoG on mitochondrial DNA (mtDNA) metabolism is poorly understood. Here, we investigated whether EndoG is involved in the regulation of mtDNA replication and removal of aberrant copies. We applied the single-cell mitochondrial Transcription and Replication Imaging Protocol (mTRIP) and PCR-based strategies on human cells after knockdown/knockout and re-expression of EndoG. Our analysis revealed that EndoG stimulates both mtDNA replication initiation and mtDNA depletion, the two events being interlinked and dependent on EndoG's nuclease activity. Stimulation of mtDNA replication by EndoG was independent of 7S DNA processing at the replication origin. Importantly, both mtDNA-directed activities of EndoG were promoted by oxidative stress. Inhibition of base excision repair (BER) that repairs oxidative stress-induced DNA damage unveiled a pronounced effect of EndoG on mtDNA removal, reminiscent of recently discovered links between EndoG and BER in the nucleus. Altogether with the downstream effects on mitochondrial transcription, protein expression, redox status and morphology, this study demonstrates that removal of damaged mtDNA by EndoG and compensatory replication play a critical role in mitochondria homeostasis.
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Affiliation(s)
| | - Boris Gole
- Department of Obstetrics and Gynecology, Ulm University, Ulm, 89075, Germany
- Present address: Centre for Human Molecular Genetics and Pharmacogenomics, Medical Faculty, University of Maribor, Maribor, SI-2000, Slovenia
| | - Laurent Chatre
- Department of Developmental and Stem Cell Biology, Institute Pasteur, Stem Cells and Development, 75724 Cedex 15, Paris, France
- Team Stability of Nuclear and Mitochondrial DNA, Unit of Stem Cells and Development, CNRS UMR 3738, 75724 Cedex 15, Paris, France
| | - Paul Walther
- Central Facility for Electron Microscopy, Ulm University, Ulm, 89081, Germany
| | - Enrico Calzia
- Institute of Anesthesiological Pathophysiology and Process Engineering, Ulm University Hospital, Ulm, 89081, Germany
| | - Miria Ricchetti
- Department of Developmental and Stem Cell Biology, Institute Pasteur, Stem Cells and Development, 75724 Cedex 15, Paris, France
- Team Stability of Nuclear and Mitochondrial DNA, Unit of Stem Cells and Development, CNRS UMR 3738, 75724 Cedex 15, Paris, France
| | - Lisa Wiesmüller
- Department of Obstetrics and Gynecology, Ulm University, Ulm, 89075, Germany
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Wone BWM, Yim WC, Schutz H, Meek TH, Garland T. Mitochondrial haplotypes are not associated with mice selectively bred for high voluntary wheel running. Mitochondrion 2018; 46:134-139. [PMID: 29626644 DOI: 10.1016/j.mito.2018.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 03/30/2018] [Accepted: 04/02/2018] [Indexed: 10/17/2022]
Abstract
Mitochondrial haplotypes have been associated with human and rodent phenotypes, including nonshivering thermogenesis capacity, learning capability, and disease risk. Although the mammalian mitochondrial D-loop is highly polymorphic, D-loops in laboratory mice are identical, and variation occurs elsewhere mainly between nucleotides 9820 and 9830. Part of this region codes for the tRNAArg gene and is associated with mitochondrial densities and number of mtDNA copies. We hypothesized that the capacity for high levels of voluntary wheel-running behavior would be associated with mitochondrial haplotype. Here, we analyzed the mtDNA polymorphic region in mice from each of four replicate lines selectively bred for 54 generations for high voluntary wheel running (HR) and from four control lines (Control) randomly bred for 54 generations. Sequencing the polymorphic region revealed a variable number of adenine repeats. Single nucleotide polymorphisms (SNPs) varied from 2 to 3 adenine insertions, resulting in three haplotypes. We found significant genetic differentiations between the HR and Control groups (Fst = 0.779, p ≤ 0.0001), as well as among the replicate lines of mice within groups (Fsc = 0.757, p ≤ 0.0001). Haplotypes, however, were not strongly associated with voluntary wheel running (revolutions run per day), nor with either body mass or litter size. This system provides a useful experimental model to dissect the physiological processes linking mitochondrial, genomic SNPs, epigenetics, or nuclear-mitochondrial cross-talk to exercise activity.
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Affiliation(s)
- Bernard W M Wone
- Department of Biochemistry & Molecular Biology, University of Nevada, Reno, NV 89557, USA; Department of Biology, University of South Dakota, Vermillion, SD 57069, USA.
| | - Won C Yim
- Department of Biochemistry & Molecular Biology, University of Nevada, Reno, NV 89557, USA
| | - Heidi Schutz
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA; Biology Department, Pacific Lutheran University, Tacoma, WA 98447, USA
| | - Thomas H Meek
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA; In Vivo Pharmacology Research Unit, Novo Nordisk, Seattle, WA 98109, USA
| | - Theodore Garland
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA.
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van der Harst P, de Windt LJ, Chambers JC. Translational Perspective on Epigenetics in Cardiovascular Disease. J Am Coll Cardiol 2017; 70:590-606. [PMID: 28750703 PMCID: PMC5543329 DOI: 10.1016/j.jacc.2017.05.067] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/30/2017] [Accepted: 05/31/2017] [Indexed: 12/19/2022]
Abstract
A plethora of environmental and behavioral factors interact, resulting in changes in gene expression and providing a basis for the development and progression of cardiovascular diseases. Heterogeneity in gene expression responses among cells and individuals involves epigenetic mechanisms. Advancing technology allowing genome-scale interrogation of epigenetic marks provides a rapidly expanding view of the complexity and diversity of the epigenome. In this review, the authors discuss the expanding landscape of epigenetic modifications and highlight their importance for future understanding of disease. The epigenome provides a mechanistic link between environmental exposures and gene expression profiles ultimately leading to disease. The authors discuss the current evidence for transgenerational epigenetic inheritance and summarize the data linking epigenetics to cardiovascular disease. Furthermore, the potential targets provided by the epigenome for the development of future diagnostics, preventive strategies, and therapy for cardiovascular disease are reviewed. Finally, the authors provide some suggestions for future directions.
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Affiliation(s)
- Pim van der Harst
- Departments of Cardiology and Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Durrer Center for Cardiovascular Research, Netherlands Heart Institute, Utrecht, the Netherlands.
| | - Leon J de Windt
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, the Netherlands
| | - John C Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom; Ealing Hospital NHS Trust, Middlesex, United Kingdom
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Clemente DBP, Casas M, Janssen BG, Lertxundi A, Santa-Marina L, Iñiguez C, Llop S, Sunyer J, Guxens M, Nawrot TS, Vrijheid M. Prenatal ambient air pollution exposure, infant growth and placental mitochondrial DNA content in the INMA birth cohort. ENVIRONMENTAL RESEARCH 2017; 157:96-102. [PMID: 28535425 DOI: 10.1016/j.envres.2017.05.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 05/12/2017] [Accepted: 05/14/2017] [Indexed: 05/06/2023]
Abstract
BACKGROUND The association between prenatal air pollution exposure and postnatal growth has hardly been explored. Mitochondrial DNA (mtDNA), as a marker of oxidative stress, and growth at birth can play an intermediate role in this association. OBJECTIVE In a subset of the Spanish birth cohort INMA we assessed first whether prenatal nitrogen dioxide (NO2) exposure is associated with infant growth. Secondly, we evaluated whether growth at birth (length and weight) could play a mediating role in this association. Finally, the mediation role of placental mitochondrial DNA content in this association was assessed. METHODS In 336 INMA children, relative placental mtDNA content was measured. Land-use regression models were used to estimate prenatal NO2 exposure. Infant growth (height and weight) was assessed at birth, at 6 months of age, and at 1 year of age. We used multiple linear regression models and performed mediation analyses. The proportion of mediation was calculated as the ratio of indirect effect to total effect. RESULTS Prenatal NO2 exposure was inversely associated with all infant growth parameters. A 10µg/m³ increment in prenatal NO2 exposure during trimester 1 of pregnancy was significantly inversely associated with height at 6 months of age (-6.6%; 95%CI: -11.4, -1.9) and weight at 1 year of age (-4.2%; 95%CI: -8.3, -0.1). These associations were mediated by birth length (31.7%; 95%CI: 34.5, 14.3) and weight (53.7%; 95%CI: 65.3, -0.3), respectively. Furthermore, 5.5% (95%CI: 10.0, -0.2) of the association between trimester 1 NO2 exposure and length at 6 months of age could be mediated by placental mtDNA content. CONCLUSIONS Our results suggest that impaired fetal growth caused by prenatal air pollution exposure can lead to impaired infant growth during the first year of life. Furthermore, molecular adaptations in placental mtDNA are associated with postnatal consequences of air pollution induced alterations in growth.
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Affiliation(s)
- Diana B P Clemente
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain; Center for Environmental Sciences, Hasselt University, Diepenbeek, Belgium; Universitat Pompeu Fabra, Barcelona, Spain; CIBER de Epidemiologia y Salud Pública (CIBERESP), Institute of Health Carlos III, Madrid, Spain.
| | - Maribel Casas
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain; CIBER de Epidemiologia y Salud Pública (CIBERESP), Institute of Health Carlos III, Madrid, Spain
| | - Bram G Janssen
- Center for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Aitana Lertxundi
- Universidad del País Vasco UPV-EUH, Spain; Health Research Institute, Biodonostia, San Sebastián, Spain
| | - Loreto Santa-Marina
- CIBER de Epidemiologia y Salud Pública (CIBERESP), Institute of Health Carlos III, Madrid, Spain; Health Research Institute, Biodonostia, San Sebastián, Spain; Public Health Division of Gipuzkoa, Basque Government, Spain
| | - Carmen Iñiguez
- CIBER de Epidemiologia y Salud Pública (CIBERESP), Institute of Health Carlos III, Madrid, Spain; Foundation for the Promotion of Health and Biomedical Research in the Valencian Region (FISABIO), Valencia, Spain; University of Valencia, Valencia, Spain
| | - Sabrina Llop
- CIBER de Epidemiologia y Salud Pública (CIBERESP), Institute of Health Carlos III, Madrid, Spain; University of Valencia, Valencia, Spain
| | - Jordi Sunyer
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain; CIBER de Epidemiologia y Salud Pública (CIBERESP), Institute of Health Carlos III, Madrid, Spain
| | - Mònica Guxens
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain; CIBER de Epidemiologia y Salud Pública (CIBERESP), Institute of Health Carlos III, Madrid, Spain; Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Centre - Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Tim S Nawrot
- Center for Environmental Sciences, Hasselt University, Diepenbeek, Belgium; Department of Public Health & Primary Care, Unit Environment & Health, Leuven University, Leuven, Belgium
| | - Martine Vrijheid
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain; CIBER de Epidemiologia y Salud Pública (CIBERESP), Institute of Health Carlos III, Madrid, Spain
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50
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Kang X, Hu L, Shen P, Li R, Liu D. SMRT Sequencing Revealed Mitogenome Characteristics and Mitogenome-Wide DNA Modification Pattern in Ophiocordyceps sinensis. Front Microbiol 2017; 8:1422. [PMID: 28798740 PMCID: PMC5529405 DOI: 10.3389/fmicb.2017.01422] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/13/2017] [Indexed: 11/24/2022] Open
Abstract
Single molecule, real-time (SMRT) sequencing was used to characterize mitochondrial (mt) genome of Ophiocordyceps sinensis and to analyze the mt genome-wide pattern of epigenetic DNA modification. The complete mt genome of O. sinensis, with a size of 157,539 bp, is the fourth largest Ascomycota mt genome sequenced to date. It contained 14 conserved protein-coding genes (PCGs), 1 intronic protein rps3, 27 tRNAs and 2 rRNA subunits, which are common characteristics of the known mt genomes in Hypocreales. A phylogenetic tree inferred from 14 PCGs in Pezizomycotina fungi supports O. sinensis as most closely related to Hirsutella rhossiliensis in Ophiocordycipitaceae. A total of 36 sequence sites in rps3 were under positive selection, with dN/dS >1 in the 20 compared fungi. Among them, 16 sites were statistically significant. In addition, the mt genome-wide base modification pattern of O. sinensis was determined in this study, especially DNA methylation. The methylations were located in coding and uncoding regions of mt PCGs in O. sinensis, and might be closely related to the expression of PCGs or the binding affinity of transcription factor A to mtDNA. Consequently, these methylations may affect the enzymatic activity of oxidative phosphorylation and then the mt respiratory rate; or they may influence mt biogenesis. Therefore, methylations in the mitogenome of O. sinensis might be a genetic feature to adapt to the cold and low PO2 environment at high altitude, where O. sinensis is endemic. This is the first report on epigenetic modifications in a fungal mt genome.
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Affiliation(s)
- Xincong Kang
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural UniversityChangsha, China
- Horticulture and Landscape College, Hunan Agricultural UniversityChangsha, China
- State Key Laboratory of Subhealth Intervention TechnologyChangsha, China
| | - Liqin Hu
- Horticulture and Landscape College, Hunan Agricultural UniversityChangsha, China
- State Key Laboratory of Subhealth Intervention TechnologyChangsha, China
| | - Pengyuan Shen
- Horticulture and Landscape College, Hunan Agricultural UniversityChangsha, China
- State Key Laboratory of Subhealth Intervention TechnologyChangsha, China
| | - Rui Li
- Nextomics BiosciencesWuhan, China
| | - Dongbo Liu
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural UniversityChangsha, China
- Horticulture and Landscape College, Hunan Agricultural UniversityChangsha, China
- State Key Laboratory of Subhealth Intervention TechnologyChangsha, China
- Hunan Co-Innovation Center for Utilization of Botanical Functional IngredientsChangsha, China
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