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Park S, Rehman MU, Ullah F, Tayara H, Chong KT. iCpG-Pos: an accurate computational approach for identification of CpG sites using positional features on single-cell whole genome sequence data. Bioinformatics 2023; 39:btad474. [PMID: 37555812 PMCID: PMC10444964 DOI: 10.1093/bioinformatics/btad474] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/11/2023] [Accepted: 08/08/2023] [Indexed: 08/10/2023] Open
Abstract
MOTIVATION The investigation of DNA methylation can shed light on the processes underlying human well-being and help determine overall human health. However, insufficient coverage makes it challenging to implement single-stranded DNA methylation sequencing technologies, highlighting the need for an efficient prediction model. Models are required to create an understanding of the underlying biological systems and to project single-cell (methylated) data accurately. RESULTS In this study, we developed positional features for predicting CpG sites. Positional characteristics of the sequence are derived using data from CpG regions and the separation between nearby CpG sites. Multiple optimized classifiers and different ensemble learning approaches are evaluated. The OPTUNA framework is used to optimize the algorithms. The CatBoost algorithm followed by the stacking algorithm outperformed existing DNA methylation identifiers. AVAILABILITY AND IMPLEMENTATION The data and methodologies used in this study are openly accessible to the research community. Researchers can access the positional features and algorithms used for predicting CpG site methylation patterns. To achieve superior performance, we employed the CatBoost algorithm followed by the stacking algorithm, which outperformed existing DNA methylation identifiers. The proposed iCpG-Pos approach utilizes only positional features, resulting in a substantial reduction in computational complexity compared to other known approaches for detecting CpG site methylation patterns. In conclusion, our study introduces a novel approach, iCpG-Pos, for predicting CpG site methylation patterns. By focusing on positional features, our model offers both accuracy and efficiency, making it a promising tool for advancing DNA methylation research and its applications in human health and well-being.
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Affiliation(s)
- Sehi Park
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
| | - Mobeen Ur Rehman
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
| | - Farman Ullah
- College of Information Technology in the United Arab Emirates University (UAEU), Abu Dhabi 15551, UAE
| | - Hilal Tayara
- School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, South Korea
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
- Advances Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, South Korea
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2
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The potential role of environmental factors in modulating mitochondrial DNA epigenetic marks. VITAMINS AND HORMONES 2023; 122:107-145. [PMID: 36863791 DOI: 10.1016/bs.vh.2023.01.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Many studies implicate mitochondrial dysfunction in the development and progression of numerous chronic diseases. Mitochondria are responsible for most cellular energy production, and unlike other cytoplasmic organelles, mitochondria contain their own genome. Most research to date, through investigating mitochondrial DNA copy number, has focused on larger structural changes or alterations to the entire mitochondrial genome and their role in human disease. Using these methods, mitochondrial dysfunction has been linked to cancers, cardiovascular disease, and metabolic health. However, like the nuclear genome, the mitochondrial genome may experience epigenetic alterations, including DNA methylation that may partially explain some of the health effects of various exposures. Recently, there has been a movement to understand human health and disease within the context of the exposome, which aims to describe and quantify the entirety of all exposures people encounter throughout their lives. These include, among others, environmental pollutants, occupational exposures, heavy metals, and lifestyle and behavioral factors. In this chapter, we summarize the current research on mitochondria and human health, provide an overview of the current knowledge on mitochondrial epigenetics, and describe the experimental and epidemiologic studies that have investigated particular exposures and their relationships with mitochondrial epigenetic modifications. We conclude the chapter with suggestions for future directions in epidemiologic and experimental research that is needed to advance the growing field of mitochondrial epigenetics.
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Mitochondrial DNA sequences and transcriptomic profiles for elucidating the genetic underpinnings of cisplatin responsiveness in oral squamous cell carcinoma. BMC Genom Data 2022; 23:47. [PMID: 35729497 PMCID: PMC9210765 DOI: 10.1186/s12863-022-01062-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 06/11/2022] [Indexed: 11/24/2022] Open
Abstract
Objectives Functional genetic variation plays an important role in predicting patients’ response to chemotherapeutic agents. A growing catalogue of mitochondrial DNA (mtDNA) alterations in various cancers point to their important roles in altering the drug responsiveness and survival of cancer cells. In this work, we report the mtDNA sequences, obtained using a nanopore sequencer that can directly sequence unamplified DNA, and the transcriptomes of oral squamous cell carcinoma (OSCC) cell lines with differing responses to cisplatin, to explore the interplay between mtDNA alterations, epigenetic regulation of gene expression, and cisplatin response in OSCC. Data description Two human OSCC cell lines, namely H103 and SAS, and drug-resistant stem-like cells derived from SAS were used in this work. To validate our hypothesis that cisplatin sensitivity is linked to mtDNA changes, we sequenced their mtDNA using a nanopore sequencer, MinION. We also obtained the whole transcriptomic profiles of the cells from a microarray analysis. The mtDNA mutational and whole transcriptomic profiles that we provide can be used alongside other similar datasets to facilitate the identification of new markers of cisplatin sensitivity, and therefore the development of effective therapies for OSCC.
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Guo L, Wang Y, Yang X, Wang T, Yin J, Zhao L, Lin Y, Dai Y, Hou S, Duan H. Aberrant mitochondrial DNA methylation and declined pulmonary function in a population with polycyclic aromatic hydrocarbon composition in particulate matter. ENVIRONMENTAL RESEARCH 2022; 214:113797. [PMID: 35779619 DOI: 10.1016/j.envres.2022.113797] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/12/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Air pollution exposure has been found to be associated with epigenetic modification of the mitochondrial genome, which could subsequently induce adverse health outcomes. However, very limited studies exist regarding the association between fine particulate matter (PM2.5) exposure and pulmonary function at the molecular level of mitochondrial epigenetic changes. This study aimed to investigate the association of platelet mitochondrial DNA (mtDNA) methylation with occupational PM2.5 exposure and pulmonary function. First, 768 participants were occupationally exposed to polycyclic aromatic hydrocarbon (PAH)-enriched PM2.5 in a coke-oven plant in East China. The levels of PM2.5, PAH components bound to PM2.5, and urinary PAH metabolites in the workplace environment were measured as an internal dose, respectively. mtDNA methylation was measured by bisulfite pyrosequencing of two genes of ATP synthase (MT-ATP6 and MT-ATP8). Mediation analysis was conducted to evaluate the role of mtDNA methylation in pulmonary alteration induced by PAH. A decreasing trend of platelet mtDNA methylation was observed with increase in PM2.5 exposure across all participants. As an important PAH metabolite in urine, 1-hydroxypyrene (1-OHP) was significantly negatively associated with FEV1/FVC (Forced Expiratory Volume in 1s/Forced Vital Capacity) ratio. The participants with high serum folate levels (≥10 nmol/L) showed positive association between MT-ATP6 methylation and FEV1/FVC ratio. Mediation analysis suggested that MT-ATP6 methylation mediated the significant association of urinary 1-OHP with FEV1/FVC. Our findings suggested the methylation of platelet mitochondrial gene MT-ATP6 and FEV1/FVC to be negatively associated with PM exposure. Platelet mtDNA methylation acted as an intermediary between PAH exposure and lung function decline. The mitochondrial epigenetic regulation in platelets, in response to PM exposure, might be involved in subsequent progress of abnormal pulmonary function.
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Affiliation(s)
- Liqiong Guo
- Wenzhou Safety (Emergency) Institute, Tianjin University, Wenzhou, China; Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin, China; Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin, China
| | - Yanhua Wang
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xueli Yang
- Department of Occupational & Environmental Health, School of Public Health, Tianjin Medical University, Tianjin, China
| | - Ting Wang
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jingjing Yin
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lei Zhao
- Wenzhou Safety (Emergency) Institute, Tianjin University, Wenzhou, China; Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin, China; Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin, China
| | - Yang Lin
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yufei Dai
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shike Hou
- Wenzhou Safety (Emergency) Institute, Tianjin University, Wenzhou, China; Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin, China; Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin, China.
| | - Huawei Duan
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China.
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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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Li J, Wang R, Shi W, Chen X, Yi J, Yang X, Jin S. Epigenetic regulation in radiation-induced pulmonary fibrosis. Int J Radiat Biol 2022; 99:384-395. [PMID: 35895014 DOI: 10.1080/09553002.2022.2089365] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
PURPOSE Radiation-induced pulmonary fibrosis (RIPF) is a common and serious adverse effect of radiotherapy for thoracic tumors, which occurs in the irreversible stage of radiation-induced lung injury (RILI) >6 months after irradiation. It is characterized by progressive and irreversible destruction of lung tissue and deterioration of lung function, which may impair quality of life and lead to respiratory failure and death. We hope this will draw attention to the involvement of epigenetics in the regulation of RIPF. CONCLUSIONS This review summarizes research progress on the role and mechanism of DNA methylation, noncoding RNA and RNA methylation in RIPF or RILI, and the possible role and mechanism of histone modification in RIPF. We have noticed that in tissue fibrosis, the epigenetic regulation mechanisms inside and outside the nucleus can influence each other. We speculate that RIPF may be regulated by an epigenetic regulatory network during its development, and believe that TGF-β, SNAIL, PTEN and EZH2 are four targets worthy of in-depth study.
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Affiliation(s)
- Jiale Li
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Rui Wang
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Wen Shi
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Xiaoyi Chen
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Junxuan Yi
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Xiangshan Yang
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Shunzi Jin
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
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7
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Zhou Z, Goodrich JM, Strakovsky RS. Mitochondrial Epigenetics and Environmental Health: Making a Case for Endocrine Disrupting Chemicals. Toxicol Sci 2021; 178:16-25. [PMID: 32777053 DOI: 10.1093/toxsci/kfaa129] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Recent studies implicate mitochondrial dysfunction in the development and progression of numerous chronic diseases, which may be partially due to modifications in mitochondrial DNA (mtDNA). There is also mounting evidence that epigenetic modifications to mtDNA may be an additional layer of regulation that controls mitochondrial biogenesis and function. Several environmental factors (eg, smoking, air pollution) have been associated with altered mtDNA methylation in a handful of mechanistic studies and in observational human studies. However, little is understood about other environmental contaminants that induce mtDNA epigenetic changes. Numerous environmental toxicants are classified as endocrine disrupting chemicals (EDCs). Beyond their actions on hormonal pathways, EDC exposure is associated with elevated oxidative stress, which may occur through or result in mitochondrial dysfunction. Although only a few studies have assessed the impacts of EDCs on mtDNA methylation, the current review provides reasons to consider mtDNA epigenetic disruption as a mechanism of action of EDCs and reviews potential limitations related to currently available evidence. First, there is sufficient evidence that EDCs (including bisphenols and phthalates) directly target mitochondrial function, and more direct evidence is needed to connect this to mtDNA methylation. Second, these and other EDCs are potent modulators of nuclear DNA epigenetics, including DNA methylation and histone modifications. Finally, EDCs have been shown to disrupt several modulators of mtDNA methylation, including DNA methyltransferases and the mitochondrial transcription factor A/nuclear respiratory factor 1 pathway. Taken together, these studies highlight the need for future research evaluating mtDNA epigenetic disruption by EDCs and to detail specific mechanisms responsible for such disruptions.
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Affiliation(s)
- Zheng Zhou
- Department of Animal Sciences, Michigan State University, East Lansing, Michigan 48824
| | - Jaclyn M Goodrich
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan 48109
| | - Rita S Strakovsky
- Department of Food Science and Human Nutrition.,Institute for Integrative Toxicology, Michigan State University, East Lansing, Michigan 48824
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Nedoluzhko A, Mjelle R, Renström M, Skjærven KH, Piferrer F, Fernandes JMO. The first mitochondrial 5-methylcytosine map in a non-model teleost (Oreochromis niloticus) reveals extensive strand-specific and non-CpG methylation. Genomics 2021; 113:3050-3057. [PMID: 34245830 DOI: 10.1016/j.ygeno.2021.07.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 06/16/2021] [Accepted: 07/05/2021] [Indexed: 12/26/2022]
Abstract
DNA methylation is one of the main epigenetic mechanisms that regulate gene expression in a manner that depends on the genomic context and varies considerably across taxa. This DNA modification was first found in nuclear genomes of eukaryote several decades ago and it has also been described in mitochondrial DNA. It has recently been shown that mitochondrial DNA is extensively methylated in mammals and other vertebrates. Our current knowledge of mitochondrial DNA methylation in fish is very limited, especially in non-model teleosts. In this study, using whole-genome bisulfite sequencing, we determined methylation patterns within non-CpG (CH) and CpG (CG) contexts in the mitochondrial genome of Nile tilapia, a non-model teleost of high economic importance. Our results demonstrate the presence of mitochondrial DNA methylation in this species predominantly within a non-CpG context, similarly to mammals. We found a strand-specific distribution of methylation, in which highly methylated cytosines were located on the minus strand. The D-loop region had the highest mean methylation level among all mitochondrial loci. Our data provide new insights into the potential role of epigenetic mechanisms in regulating metabolic flexibility of mitochondria in fish, with implications in various biological processes, such as growth and development.
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Affiliation(s)
- Artem Nedoluzhko
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Robin Mjelle
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway; Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Maria Renström
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | | | - Francesc Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
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Sharma J, Kumari R, Bhargava A, Tiwari R, Mishra PK. Mitochondrial-induced Epigenetic Modifications: From Biology to Clinical Translation. Curr Pharm Des 2021; 27:159-176. [PMID: 32851956 DOI: 10.2174/1381612826666200826165735] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/27/2020] [Indexed: 11/22/2022]
Abstract
Mitochondria are maternally inherited semi-autonomous organelles that play a central role in redox balance, energy metabolism, control of integrated stress responses, and cellular homeostasis. The molecular communication between mitochondria and the nucleus is intricate and bidirectional in nature. Though mitochondrial genome encodes for several key proteins involved in oxidative phosphorylation, several regulatory factors encoded by nuclear DNA are prominent contributors to mitochondrial biogenesis and function. The loss of synergy between this reciprocal control of anterograde (nuclear to mitochondrial) and retrograde (mitochondrial to nuclear) signaling, triggers epigenomic imbalance and affects mitochondrial function and global gene expressions. Recent expansions of our knowledge on mitochondrial epigenomics have offered novel perspectives for the study of several non-communicable diseases including cancer. As mitochondria are considered beacons for pharmacological interventions, new frontiers in targeted delivery approaches could provide opportunities for effective disease management and cure through reversible epigenetic reprogramming. This review focuses on recent progress in the area of mitochondrial-nuclear cross-talk and epigenetic regulation of mitochondrial DNA methylation, mitochondrial micro RNAs, and post-translational modification of mitochondrial nucleoid-associated proteins that hold major opportunities for targeted drug delivery and clinical translation.
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Affiliation(s)
- Jahnavi Sharma
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Roshani Kumari
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Arpit Bhargava
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Rajnarayan Tiwari
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Pradyumna K Mishra
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
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10
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Xie Z, Rahman I, Goniewicz ML, Li D. Perspectives on Epigenetics Alterations Associated with Smoking and Vaping. FUNCTION (OXFORD, ENGLAND) 2021; 2:zqab022. [PMID: 35330676 PMCID: PMC8788872 DOI: 10.1093/function/zqab022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/03/2021] [Accepted: 04/21/2021] [Indexed: 01/11/2023]
Abstract
Epigenetic alterations, including DNA methylation, microRNA, and long noncoding RNA, play important roles in the pathogenesis of numerous respiratory health conditions and diseases. Exposure to tobacco smoking has been found to be associated with epigenetic changes in the respiratory tract. Marketed as a less harmful alternative to combustible cigarettes, electronic cigarette (e-cigarette) has rapidly gained popularity in recent years, especially among youth and young adults. Accumulative evidence from both animal and human studies has shown that e-cigarette use (vaping) is also linked to similar respiratory health conditions as observed with cigarette smoking, including wheezing, asthma, and COPD. This review aims to provide an overview of current studies on associations of smoking and vaping with epigenetic alterations in respiratory cells and provide future research directions in epigenetic studies related to vaping.
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Affiliation(s)
- Zidian Xie
- Department of Clinical & Translational Research, University of Rochester Medical Center, Rochester, NY, USA
| | - Irfan Rahman
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Maciej L Goniewicz
- Department of Health Behavior, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, USA
| | - Dongmei Li
- Department of Clinical & Translational Research, University of Rochester Medical Center, Rochester, NY, USA,Address correspondence to D.L. (e-mail: )
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11
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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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12
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Doke M, Jeganathan V, McLaughlin JP, Samikkannu T. HIV-1 Tat and cocaine impact mitochondrial epigenetics: effects on DNA methylation. Epigenetics 2020; 16:980-999. [PMID: 33100130 PMCID: PMC8451453 DOI: 10.1080/15592294.2020.1834919] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
Human immunodeficiency virus (HIV) infection and the psychostimulant drug cocaine are known to induce epigenetic changes in DNA methylation that are linked with the severity of viral replication and disease progression, which impair neuronal functions. Increasing evidence suggests that changes in DNA methylation and hydroxymethylation occur in mitochondrial DNA (mtDNA) and represent mitochondrial genome epigenetic modifications (mitoepigenetic modifications). These modifications likely regulate both mtDNA replication and gene expression. However, mtDNA methylation has not been studied extensively in the contexts of cocaine abuse and HIV-1 infection. In the present study, epigenetic factors changed the levels of the DNA methyltransferases (DNMTs) DNMT1, DNMT3a, and DNMT3b, the Ten-eleven translocation (TET) enzymes 1, 2, and 3, and mitochondrial DNMTs (mtDNMTs) both in vitro and in vivo. These changes resulted in alterations in mtDNA methylation levels at CpG and non-CpG sites in human primary astrocytes as measured using targeted next-generation bisulphite sequencing (TNGBS). Moreover, mitochondrial methylation levels in the MT-RNR1, MT-ND5, MT-ND1, D-loop and MT-CYB regions of mtDNA were lower in the HIV-1 Tat and cocaine treatment groups than in the control group. In summary, the present findings suggest that mitoepigenetic modification in the human brain causes the mitochondrial dysfunction that gives rise to neuro-AIDS.
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Affiliation(s)
- Mayur Doke
- Department of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, Kingsville, TX, USA
| | - Venkatesh Jeganathan
- Department of Autoimmune and Musculoskeletal Disease, The Feinstein Institute for Medical Research, Manhasset, NY, USA
| | - Jay P McLaughlin
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Thangavel Samikkannu
- Department of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, Kingsville, TX, USA
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13
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Li Y, Zhang T, Zhang H, Wang X, Liu X, Huang Q, Li L. Clinical Significance of P16 Gene Methylation in Lung Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1255:133-142. [PMID: 32949396 DOI: 10.1007/978-981-15-4494-1_11] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Lung cancer is the leading cause of death from cancer in China. The lack of early screening technologies makes most patients to be diagnosed at advanced stages with a poor prognosis which often miss the best treatment opportunities. Thus, identifying biomarkers for minimally invasive detection and prognosis of early stage disease is urgently needed. Genetic and epigenetic alterations that promote tumorigenesis and metastasis exist in multiple cancers. These aberrant alterations usually represent early events in cancer progression suggesting their potential applications as a biomarker for cancer prediction. Studies have shown that DNA methylation is one of the key factors in progression of lung cancer. P16 promoter methylation is one of the most common epigenetic change plays a key role in lung cancer. In this review, we highlight the p16 gene methylation and its clinical significance in lung cancer.
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Affiliation(s)
- Yanjun Li
- Center for Clinical Single Cell Biomedicine, Henan Provincial People's Hospital, Zhengzhou, Henan, China.,Zhengzhou University People's Hospital, Zhengzhou, Henan, China.,Henan University People's Hospital, Zhengzhou, Henan, China
| | - Tingting Zhang
- Center for Clinical Single Cell Biomedicine, Henan Provincial People's Hospital, Zhengzhou, Henan, China.,Zhengzhou University People's Hospital, Zhengzhou, Henan, China.,Henan University People's Hospital, Zhengzhou, Henan, China
| | - Hui Zhang
- Center for Clinical Single Cell Biomedicine, Henan Provincial People's Hospital, Zhengzhou, Henan, China.,Zhengzhou University People's Hospital, Zhengzhou, Henan, China.,Henan University People's Hospital, Zhengzhou, Henan, China
| | - Xiangdong Wang
- Zhongshan Hospital, Fudan University, Shanghai, Shanghai, China
| | - Xiaozhuan Liu
- Center for Clinical Single Cell Biomedicine, Henan Provincial People's Hospital, Zhengzhou, Henan, China.,Zhengzhou University People's Hospital, Zhengzhou, Henan, China.,Henan University People's Hospital, Zhengzhou, Henan, China
| | - Qihong Huang
- Zhongshan Hospital, Fudan University, Shanghai, Shanghai, China
| | - Li Li
- Center for Clinical Single Cell Biomedicine, Henan Provincial People's Hospital, Zhengzhou, Henan, China. .,Zhengzhou University People's Hospital, Zhengzhou, Henan, China. .,Henan University People's Hospital, Zhengzhou, Henan, China. .,Department of Scientific Research and Discipline Construction, Henan Provincial People's Hospital, Zhengzhou, Henan, China.
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14
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Epigenetic Clock: DNA Methylation in Aging. Stem Cells Int 2020; 2020:1047896. [PMID: 32724310 PMCID: PMC7366189 DOI: 10.1155/2020/1047896] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 06/11/2020] [Accepted: 06/20/2020] [Indexed: 02/07/2023] Open
Abstract
Aging, which is accompanied by decreased organ function and increased disease incidence, limits human lifespan and has attracted investigators for thousands of years. In recent decades, with the rapid development of biology, scientists have shown that epigenetic modifications, especially DNA methylation, are key regulators involved in this process. Regular fluctuations in global DNA methylation levels have been shown to accurately estimate biological age and disease prognosis. In this review, we discuss recent findings regarding the relationship between variations in DNA methylation level patterns and aging. In addition, we introduce the known mechanisms by which DNA methylation regulators affect aging and related diseases. As more studies uncover the mechanisms by which DNA methylation regulates aging, antiaging interventions and treatments for related diseases may be developed that enable human life extension.
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15
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Wang W, Liu X, Wang X. How to breakthrough mitochondrial DNA methylation-associated networks. Cell Biol Toxicol 2020; 36:195-198. [PMID: 32514822 DOI: 10.1007/s10565-020-09539-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 06/02/2020] [Indexed: 12/21/2022]
Abstract
Mitochondrial DNA (mtDNA) plays an important role in regulating mitochondrial homeostasis, transcription, cell metabolism, and drug sensitivity. Patterns and regulations of mtDNA methylation vary among cell types, species, functions, and diseases. High-resolution mtDNA methylation maps of human and animal mitochondrial genomes addressed that the light (L)-strand non-CpG methylation of mtDNA varied among species, developing stages, and ages. Of DNA methyltransferases, DNMT3A was a critical enzyme in the dynamic regulation of mtDNA regional methylation patterns and strand bias. Altered mtDNA methylations may regulate dynamic occurrences of pathogenic mtDNA mutations. The number and sites of control regions, involved enzymes, and regulators during mtDNA methylation may vary among cell types and diseases. Specific regulatory and functional networks associated with mtDNA methylation mainly include mtDNA, regulatory factors, methyltransferases, nucleotides, mt-rRNAs, and other epigenetic modifications. Those carry out precise functions and regulations of mtDNA methylation-associated network, interactions with genome DNA and other signal pathways, and decisive roles in patient phenomes. A breakthrough in mtDNA methylation-associated networks will be a crucial milestone in the journey of understanding mitochondrial function at a higher level and discovering new mitochondria-based biomarkers and therapeutic targets.
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Affiliation(s)
- William Wang
- Zhongshan Hospital Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Fudan University, Shanghai, China.,Zhongshan Hospital Institute of Clinical Science, Jinshan Hospital Centre for Tumor Diagnosis and Therapy, Fudan University Shanghai Medical College, Shanghai, China
| | - Xiaoxia Liu
- Zhongshan Hospital Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Fudan University, Shanghai, China.,Zhongshan Hospital Institute of Clinical Science, Jinshan Hospital Centre for Tumor Diagnosis and Therapy, Fudan University Shanghai Medical College, Shanghai, China
| | - Xiangdong Wang
- Zhongshan Hospital Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Fudan University, Shanghai, China. .,Zhongshan Hospital Institute of Clinical Science, Jinshan Hospital Centre for Tumor Diagnosis and Therapy, Fudan University Shanghai Medical College, Shanghai, China.
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16
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Stoccoro A, Tannorella P, Migliore L, Coppedè F. Polymorphisms of genes required for methionine synthesis and DNA methylation influence mitochondrial DNA methylation. Epigenomics 2020; 12:1003-1012. [PMID: 32393056 DOI: 10.2217/epi-2020-0041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aim: Impaired methylation of the mitochondrial DNA and particularly in the regulatory displacement loop (D-loop) region, is increasingly observed in patients with neurodegenerative disorders. The present study aims to investigate if common polymorphisms of genes required for one-carbon metabolism (MTHFR, MTRR, MTR and RFC-1) and DNA methylation reactions (DNMT1, DNMT3A and DNMT3B) influence D-loop methylation levels. Materials & methods: D-loop methylation data were available from 133 late-onset Alzheimer's disease patients and 130 matched controls. Genotyping was performed with PCR-RFLP or high resolution melting techniques. Results: Both MTRR 66A > G and DNMT3A -448A > G polymorphisms were significantly associated with D-loop methylation levels. Conclusion: This exploratory study suggests that MTRR and DNMT3A polymorphisms influence mitochondrial DNA methylation; further research is required to better address this issue.
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Affiliation(s)
- Andrea Stoccoro
- Department of Translational Research & of New Surgical & Medical Technologies, University of Pisa, Via Roma 55, 56126, Pisa, Italy
| | - Pierpaola Tannorella
- Department of Translational Research & of New Surgical & Medical Technologies, University of Pisa, Via Roma 55, 56126, Pisa, Italy
- Current address: Unit of Genetics of Neurodegenerative & Metabolic Diseases, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Lucia Migliore
- Department of Translational Research & of New Surgical & Medical Technologies, University of Pisa, Via Roma 55, 56126, Pisa, Italy
| | - Fabio Coppedè
- Department of Translational Research & of New Surgical & Medical Technologies, University of Pisa, Via Roma 55, 56126, Pisa, Italy
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17
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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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18
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Dong Z, Pu L, Cui H. Mitoepigenetics and Its Emerging Roles in Cancer. Front Cell Dev Biol 2020; 8:4. [PMID: 32039210 PMCID: PMC6989428 DOI: 10.3389/fcell.2020.00004] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/08/2020] [Indexed: 12/11/2022] Open
Abstract
In human beings, there is a ∼16,569 bp circular mitochondrial DNA (mtDNA) encoding 22 tRNAs, 12S and 16S rRNAs, 13 polypeptides that constitute the central core of ETC/OxPhos complexes, and some non-coding RNAs. Recently, mtDNA has been shown to have some covalent modifications such as methylation or hydroxylmethylation, which play pivotal epigenetic roles in mtDNA replication and transcription. Post-translational modifications of proteins in mitochondrial nucleoids such as mitochondrial transcription factor A (TFAM) also emerge as essential epigenetic modulations in mtDNA replication and transcription. Post-transcriptional modifications of mitochondrial RNAs (mtRNAs) including mt-rRNAs, mt-tRNAs and mt-mRNAs are important epigenetic modulations. Besides, mtDNA or nuclear DNA (n-DNA)-derived non-coding RNAs also play important roles in the regulation of translation and function of mitochondrial genes. These evidences introduce a novel concept of mitoepigenetics that refers to the study of modulations in the mitochondria that alter heritable phenotype in mitochondria itself without changing the mtDNA sequence. Since mitochondrial dysfunction contributes to carcinogenesis and tumor development, mitoepigenetics is also essential for cancer. Understanding the mode of actions of mitoepigenetics in cancers may shade light on the clinical diagnosis and prevention of these diseases. In this review, we summarize the present study about modifications in mtDNA, mtRNA and nucleoids and modulations of mtDNA/nDNA-derived non-coding RNAs that affect mtDNA translation/function, and overview recent studies of mitoepigenetic alterations in cancer.
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Affiliation(s)
- Zhen Dong
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China.,Cancer Center, Medical Research Institute, Southwest University, Chongqing, China.,Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, China.,Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Chongqing, China
| | - Longjun Pu
- Umeå Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China.,Cancer Center, Medical Research Institute, Southwest University, Chongqing, China.,Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, China.,Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Chongqing, China
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19
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Stimulation of Na +/K +-ATPase with an Antibody against Its 4 th Extracellular Region Attenuates Angiotensin II-Induced H9c2 Cardiomyocyte Hypertrophy via an AMPK/SIRT3/PPAR γ Signaling Pathway. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:4616034. [PMID: 31636805 PMCID: PMC6766118 DOI: 10.1155/2019/4616034] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 07/09/2019] [Accepted: 08/02/2019] [Indexed: 02/06/2023]
Abstract
Activation of the renin-angiotensin system (RAS) contributes to the pathogenesis of cardiovascular diseases. Sodium potassium ATPase (NKA) expression and activity are often regulated by angiotensin II (Ang II). This study is aimed at investigating whether DR-Ab, an antibody against 4th extracellular region of NKA, can protect Ang II-induced cardiomyocyte hypertrophy. Our results showed that Ang II treatment significantly reduced NKA activity and membrane expression. Pretreatment with DR-Ab preserved cell size in Ang II-induced cardiomyopathy by stabilizing the plasma membrane expression of NKA and restoring its activity. DR-Ab reduced intracellular ROS generation through inhibition of NADPH oxidase activity and protection of mitochondrial functions in Ang II-treated H9c2 cardiomyocytes. Pharmacological manipulation and Western blotting analysis demonstrated the cardioprotective effects were mediated by the activation of the AMPK/Sirt-3/PPARγ signaling pathway. Taken together, our results suggest that dysfunction of NKA is an important mechanism for Ang II-induced cardiomyopathy and DR-Ab may be a novel and promising therapeutic approach to treat cardiomyocyte hypertrophy.
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20
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Sinton MC, Hay DC, Drake AJ. Metabolic control of gene transcription in non-alcoholic fatty liver disease: the role of the epigenome. Clin Epigenetics 2019; 11:104. [PMID: 31319896 PMCID: PMC6637519 DOI: 10.1186/s13148-019-0702-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/09/2019] [Indexed: 01/30/2023] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is estimated to affect 24% of the global adult population. NAFLD is a major risk factor for the development of cirrhosis and hepatocellular carcinoma, as well as being strongly associated with type 2 diabetes and cardiovascular disease. It has been proposed that up to 88% of obese adults have NAFLD, and with global obesity rates increasing, this disease is set to become even more prevalent. Despite intense research in this field, the molecular processes underlying the pathology of NAFLD remain poorly understood. Hepatic intracellular lipid accumulation may lead to dysregulated tricarboxylic acid (TCA) cycle activity and associated alterations in metabolite levels. The TCA cycle metabolites alpha-ketoglutarate, succinate and fumarate are allosteric regulators of the alpha-ketoglutarate-dependent dioxygenase family of enzymes. The enzymes within this family have multiple targets, including DNA and chromatin, and thus may be capable of modulating gene transcription in response to intracellular lipid accumulation through alteration of the epigenome. In this review, we discuss what is currently understood in the field and suggest areas for future research which may lead to the development of novel preventative or therapeutic interventions for NAFLD.
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Affiliation(s)
- Matthew C Sinton
- University/British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - David C Hay
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Amanda J Drake
- University/British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK.
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21
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Jiang L, Wang C, Tang J, Guo F. LightCpG: a multi-view CpG sites detection on single-cell whole genome sequence data. BMC Genomics 2019; 20:306. [PMID: 31014252 PMCID: PMC6480911 DOI: 10.1186/s12864-019-5654-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 03/27/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND DNA methylation plays an important role in multiple biological processes that are closely related to human health. The study of DNA methylation can provide an insight into the mechanism behind human health and can also have a positive effect on the assessment of human health status. However, the available sequencing technology is limited by incomplete CpG coverage. Therefore, it is crucial to discover an efficient and convenient method capable of distinguishing between the states of CpG sites. Previous studies focused on identifying methylation states of the CpG sites in single cell, which only evaluated sequence information or structural information. RESULTS In this paper, we propose a novel model, LightCpG, which combines the positional features with the sequence and structural features to provide information on the CpG sites at two stages. Next, we used the LightGBM model for training of the CpG site identification, and further utilized sample extraction and merged features to reduce the training time. Our results indicate that our method achieves outstanding performance in recognition of DNA methylation. The average AUC values of our method using the 25 human hepatocellular carcinoma cells (HCC) cell datasets and six human heptoplastoma-derived (HepG2) cell datasets were 0.9616 and 0.9213, respectively. Moreover, the average training times for our method on the HCC and HepG2 datasets were 8.3 and 5.06 s, respectively. Furthermore, the computational complexity of our model was much lower compared with other available methods that detect methylation states of the CpG sites. CONCLUSIONS In summary, LightCpG is an accurate model for identifying the DNA methylation status of CpG sites in single cells. Furthermore, three types of feature extraction methods and two strategies used in LightCpG are helpful for other prediction problems.
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Affiliation(s)
- Limin Jiang
- School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Chongqing Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Jijun Tang
- School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin, China
- Department of Computer Science and Engineering, University of South Carolina, Columbia, SC, USA
| | - Fei Guo
- School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin, China
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22
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Breton CV, Song AY, Xiao J, Kim SJ, Mehta HH, Wan J, Yen K, Sioutas C, Lurmann F, Xue S, Morgan TE, Zhang J, Cohen P. Effects of air pollution on mitochondrial function, mitochondrial DNA methylation, and mitochondrial peptide expression. Mitochondrion 2019; 46:22-29. [PMID: 30980914 DOI: 10.1016/j.mito.2019.04.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 02/25/2019] [Accepted: 04/01/2019] [Indexed: 12/30/2022]
Abstract
Mitochondrial DNA is sensitive to damage by exogenous reactive oxygen sources, including traffic-related air pollution (TRAP). Given the important role for mitochondria in human disease, we hypothesized that prenatal air pollution exposure may be associated with mitochondrial dysfunction and that mitochondrial-derived peptides (MDPs) might protect against these effects. In in vitro studies, 24-hour exposure to nanoparticulate matter (nPM) increased oxidation of mtDNA, decreased mitochondrial consumption rate (OCR), and decreased mtDNAcn in SH-SY5Y cells. Addition of MDPs rescued these effects to varying degrees. Liver tissue taken from C57Bl/6 males exposed for 10 weeks to nPM had lower OCR, lower mtDNAcn and higher MDP levels, similar to in vitro studies. In newborn cord blood, MDP levels were positively associated with prenatal TRAP exposures. Moreover, DNA methylation of two distinct regions of the D-Loop in the mitochondria genome was associated with levels of several MDPs. Our in vitro and in vivo data indicate that TRAP can directly affect mitochondrial respiratory function and mtDNAcn. Treatment of cells with MDPs can counteract TRAP induced-effects. Lastly, we present evidence that suggests MDPs may be regulated in part by mitochondrial DNA methylation in humans.
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Affiliation(s)
- Carrie V Breton
- Department of Preventive Medicine, Keck School of Medicine USC, 2001 N Soto St., Los Angeles, CA 90032, United States of America.
| | - Ashley Y Song
- Department of Preventive Medicine, Keck School of Medicine USC, 2001 N Soto St., Los Angeles, CA 90032, United States of America
| | - Jialin Xiao
- USC Leonard School of Gerontology, 3715 McClintock Ave, Los Angeles, CA 90089, United States of America
| | - Su-Jeong Kim
- USC Leonard School of Gerontology, 3715 McClintock Ave, Los Angeles, CA 90089, United States of America
| | - Hemal H Mehta
- USC Leonard School of Gerontology, 3715 McClintock Ave, Los Angeles, CA 90089, United States of America
| | - Junxiang Wan
- USC Leonard School of Gerontology, 3715 McClintock Ave, Los Angeles, CA 90089, United States of America
| | - Kelvin Yen
- USC Leonard School of Gerontology, 3715 McClintock Ave, Los Angeles, CA 90089, United States of America
| | - Constantinos Sioutas
- USC Viterbi School of Engineering, 3620 South Vermont Ave, Los Angeles, CA 90089, United States of America
| | - Fred Lurmann
- Sonoma Technology, 1450 N. McDowell Blvd., Suite 200, Petaluma, CA 94954, United States of America
| | - Shanyan Xue
- Department of Preventive Medicine, Keck School of Medicine USC, 2001 N Soto St., Los Angeles, CA 90032, United States of America
| | - Todd E Morgan
- USC Leonard School of Gerontology, 3715 McClintock Ave, Los Angeles, CA 90089, United States of America
| | - Junfeng Zhang
- Nicholas School of the Enviroment, Duke University, 308 Research Drive LSRC, Durham, NC 27708, United States of America
| | - Pinchas Cohen
- USC Leonard School of Gerontology, 3715 McClintock Ave, Los Angeles, CA 90089, United States of America
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23
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The role of mitochondria in cellular toxicity as a potential drug target. Cell Biol Toxicol 2018; 34:87-91. [PMID: 29511917 DOI: 10.1007/s10565-018-9425-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 02/13/2018] [Indexed: 12/13/2022]
Abstract
Mitochondrial malfunction is related to aging and to the onset of many diseases, such as obesity/diabetes, cancer, and cardiovascular and neurodegenerative diseases. The molecular principles of biological and toxicological processes the mitochondria can regulate should be disease-specific, cell type-specific, and drug targetable. Mitochondrial biology and toxicology is evolving and undergoing a revolution through fast-developing biotechnologies garnering increasing attention due to the importance of targeted therapies. Mitochondrial energy production and metabolism are conducted via post-mitochondrial signaling, and are controlled by extra-mitochondrial pathways. Mitochondrial biology and toxicology has a history spanning over 30 years and is one of the main scientific focuses at Cell Biology and Toxicology. It is our aim to pioneer innovations of mitochondrial biology and toxicology to improve the understanding, highlight the latest development, and find mitochondria-based targets for therapies. It is expected to know how drugs can initiate mitochondrial dysfunction, the role of nuclear messages in regulating mitochondrial DNA (MtDNA), and how mitochondria communicate between or with other cells. Further studies are crucial to discover how mitochondria control the process of immune response, autophagy/mitophagy, genome activation, and cell interaction. It is also needed to innovate how the transcription is started and terminated within mitochondria, the cytosolic proteins and other organelles interact with mitochondria, and MtDNA regulates the function of mitochondrial respiratory megacomplexes.
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24
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How Far Can Mitochondrial DNA Drive the Disease? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1038:1-8. [DOI: 10.1007/978-981-10-6674-0_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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