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Patra SK, Szyf M. Epigenetic perspectives of COVID-19: Virus infection to disease progression and therapeutic control. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166527. [PMID: 36002132 PMCID: PMC9393109 DOI: 10.1016/j.bbadis.2022.166527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/05/2022] [Accepted: 08/18/2022] [Indexed: 11/20/2022]
Abstract
COVID-19 has caused numerous deaths as well as imposed social isolation and upheaval world-wide. Although, the genome and the composition of the virus, the entry process and replication mechanisms are well investigated from by several laboratories across the world, there are many unknown remaining questions. For example, what are the functions of membrane lipids during entry, packaging and exit of virus particles? Also, the metabolic aspects of the infected tissue cells are poorly understood. In the course of virus replication and formation of virus particles within the host cell, the enhanced metabolic activities of the host is directly proportional to viral loads. The epigenetic landscape of the host cells is also altered, particularly the expression/repression of genes associated with cellular metabolism as well as cellular processes that are antagonistic to the virus. Metabolic pathways are enzyme driven processes and the expression profile and mechanism of regulations of the respective genes encoding those enzymes during the course of pathogen invasion might be highly informative on the course of the disease. Recently, the metabolic profile of the patients' sera have been analysed from few patients. In view of this, and to gain further insights into the roles that epigenetic mechanisms might play in this scenario in regulation of metabolic pathways during the progression of COVID-19 are discussed and summarised in this contribution for ensuring best therapy.
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Affiliation(s)
- Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
| | - Moshe Szyf
- Department of Pharmacology & Therapeutics, McIntyre Medical Sciences Building, McGill University, Montreal, QC H3G 1Y6, Canada
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Lee DD, Park SJ, Zborek KL, Schwarz MA. A shift from glycolytic and fatty acid derivatives toward one-carbon metabolites in the developing lung during transitions of the early postnatal period. Am J Physiol Lung Cell Mol Physiol 2021; 320:L640-L659. [PMID: 33502935 DOI: 10.1152/ajplung.00417.2020] [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] [Indexed: 11/22/2022] Open
Abstract
During postnatal lung development, metabolic changes that coincide with stages of alveolar formation are poorly understood. Responding to developmental and environmental factors, metabolic changes can be rapidly and adaptively altered. The objective of the present study was to determine biological and technical determinants of metabolic changes during postnatal lung development. Over 118 metabolic features were identified by liquid chromatography with tandem mass spectrometry (LC-MS/MS, Sciex QTRAP 5500 Triple Quadrupole). Biological determinants of metabolic changes were the transition from the postnatal saccular to alveolar stages and exposure to 85% hyperoxia, an environmental insult. Technical determinants of metabolic identification were brevity and temperature of harvesting, both of which improved metabolic preservation within samples. Multivariate statistical analyses revealed the transition between stages of lung development as the period of major metabolic alteration. Of three distinctive groups that clustered by age, the saccular stage was identified by its enrichment of both glycolytic and fatty acid derivatives. The critical transition between stages of development were denoted by changes in amino acid derivatives. Of the amino acid derivatives that significantly changed, a majority were linked to metabolites of the one-carbon metabolic pathway. The enrichment of one-carbon metabolites was independent of age and environmental insult. Temperature was also found to significantly influence the metabolic levels within the postmortem sampled lung, which underscored the importance of methodology. Collectively, these data support not only distinctive stages of metabolic change but also highlight amino acid metabolism, in particular one-carbon metabolites as metabolic signatures of the early postnatal lung.
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Affiliation(s)
- Daniel D Lee
- Department of Pediatrics, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana.,Department of Anatomy, Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis, Indiana.,Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana
| | - Sang Jun Park
- Department of Preprofessional Studies, University of Notre Dame, South Bend, Indiana
| | - Kirsten L Zborek
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana
| | - Margaret A Schwarz
- Department of Pediatrics, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana.,Department of Anatomy, Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis, Indiana.,Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana
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Na JD, Choi YJ, Jun DS, Kim YC. Alleviation of paraquat-induced oxidative lung injury by betaineviaregulation of sulfur-containing amino acid metabolism despite the lack of betaine-homocysteine methyltransferase (BHMT) in the lung. Food Funct 2019; 10:1225-1234. [DOI: 10.1039/c8fo01457d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Betaine regulates sulfur-containing amino acid metabolism in the lung despite the lack of BHMT and increases pulmonary antioxidant capacity.
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Affiliation(s)
- Jong Deok Na
- College of Pharmacy
- Seoul National University
- Seoul 151-742
- Korea
| | - Yeo Jin Choi
- College of Pharmacy
- Seoul National University
- Seoul 151-742
- Korea
| | - Doo Sung Jun
- College of Pharmacy
- Seoul National University
- Seoul 151-742
- Korea
| | - Young Chul Kim
- College of Pharmacy
- Seoul National University
- Seoul 151-742
- Korea
- Research Institute of Pharmaceutical Sciences
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Targeting S-adenosylmethionine biosynthesis with a novel allosteric inhibitor of Mat2A. Nat Chem Biol 2017; 13:785-792. [PMID: 28553945 DOI: 10.1038/nchembio.2384] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 03/07/2017] [Indexed: 12/15/2022]
Abstract
S-Adenosyl-L-methionine (SAM) is an enzyme cofactor used in methyl transfer reactions and polyamine biosynthesis. The biosynthesis of SAM from ATP and L-methionine is performed by the methionine adenosyltransferase enzyme family (Mat; EC 2.5.1.6). Human methionine adenosyltransferase 2A (Mat2A), the extrahepatic isoform, is often deregulated in cancer. We identified a Mat2A inhibitor, PF-9366, that binds an allosteric site on Mat2A that overlaps with the binding site for the Mat2A regulator, Mat2B. Studies exploiting PF-9366 suggested a general mode of Mat2A allosteric regulation. Allosteric binding of PF-9366 or Mat2B altered the Mat2A active site, resulting in increased substrate affinity and decreased enzyme turnover. These data support a model whereby Mat2B functions as an inhibitor of Mat2A activity when methionine or SAM levels are high, yet functions as an activator of Mat2A when methionine or SAM levels are low. The ramification of Mat2A activity modulation in cancer cells is also described.
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Hao R, Du H, Guo L, Tian F, An N, Yang T, Wang C, Wang B, Zhou Z. Identification of dysregulated genes in rheumatoid arthritis based on bioinformatics analysis. PeerJ 2017; 5:e3078. [PMID: 28316886 PMCID: PMC5356478 DOI: 10.7717/peerj.3078] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 02/09/2017] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Rheumatoid arthritis (RA) is a chronic auto-inflammatory disorder of joints. The present study aimed to identify the key genes in RA for better understanding the underlying mechanisms of RA. METHODS The integrated analysis of expression profiling was conducted to identify differentially expressed genes (DEGs) in RA. Moreover, functional annotation, protein-protein interaction (PPI) network and transcription factor (TF) regulatory network construction were applied for exploring the potential biological roles of DEGs in RA. In addition, the expression level of identified candidate DEGs was preliminarily detected in peripheral blood cells of RA patients in the GSE17755 dataset. Quantitative real-time polymerase chain reaction (qRT-PCR) was conducted to validate the expression levels of identified DEGs in RA. RESULTS A total of 378 DEGs, including 202 up- and 176 down-regulated genes, were identified in synovial tissues of RA patients compared with healthy controls. DEGs were significantly enriched in axon guidance, RNA transport and MAPK signaling pathway. RBFOX2, LCK and SERBP1 were the hub proteins in the PPI network. In the TF-target gene network, RBFOX2, POU6F1, WIPF1 and PFKFB3 had the high connectivity with TFs. The expression status of 11 candidate DEGs was detected in GSE17755, the expression levels of MAT2A and NSA2 were significantly down-regulated and CD47 had the up-regulated tendency in peripheral blood cells of patients with RA compared with healthy individuals. qRT-PCR results of MAT2A, NSA2, CD47 were compatible with our bioinformatics analyses. DISCUSSION Our study might provide valuable information for exploring the pathogenesis mechanism of RA and identifying the potential biomarkers for RA diagnosis.
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Affiliation(s)
- Ruihu Hao
- Department of Orthopedics, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Haiwei Du
- Department of Bioinformatics, Beijing Medintell Biomed Co., Ltd, Beijing, China
| | - Lin Guo
- Department of Orthopedics, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Fengde Tian
- Department of Orthopedics, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Ning An
- Department of Orthopedics, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Tiejun Yang
- Department of Orthopedics, Affiliated Hospital of BeiHua University, Jilin, China
| | - Changcheng Wang
- Department of Orthopedics, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Bo Wang
- Department of Orthopedics, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Zihao Zhou
- Department of Orthopedics, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
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Yadetie F, Bjørneklett S, Garberg HK, Oveland E, Berven F, Goksøyr A, Karlsen OA. Quantitative analyses of the hepatic proteome of methylmercury-exposed Atlantic cod (Gadus morhua) suggest oxidative stress-mediated effects on cellular energy metabolism. BMC Genomics 2016; 17:554. [PMID: 27496535 PMCID: PMC4974784 DOI: 10.1186/s12864-016-2864-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 06/30/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Methylmecury (MeHg) is a widely distributed environmental pollutant with considerable risk to both human health and wildlife. To gain better insight into the underlying mechanisms of MeHg-mediated toxicity, we have used label-free quantitative mass spectrometry to analyze the liver proteome of Atlantic cod (Gadus morhua) exposed in vivo to MeHg (0, 0.5, 2 mg/kg body weight) for 2 weeks. RESULTS Out of a toltal of 1143 proteins quantified, 125 proteins were differentially regulated between MeHg-treated samples and controls. Using various bioinformatics tools, we performed gene ontology, pathway and network enrichment analysis, which indicated that proteins and pathways mainly related to energy metabolism, antioxidant defense, cytoskeleton remodeling, and protein synthesis were regulated in the hepatic proteome after MeHg exposure. Comparison with previous gene expression data strengthened these results, and further supported that MeHg predominantly affects many energy metabolism pathways, presumably through its strong induction of oxidative stress. Some enzymes known to have functionally important oxidation-sensitive cysteine residues in other animals are among the differentially regulated proteins, suggesting their modulations by MeHg-induced oxidative stress. Integrated analysis of the proteomics dataset combined with previous gene expression dataset showed a more pronounced effect of MeHg on amino acid, glucose and fatty acid metabolic pathways, and suggested possible interactions of the cellular energy metabolism and antioxidant defense pathways. CONCLUSIONS MeHg disrupts mainly redox homeostasis and energy generating metabolic pathways in cod liver. The energy pathways appear to be modulated through MeHg-induced oxidative stress, possibly mediated by oxidation sensitive enzymes.
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Affiliation(s)
- Fekadu Yadetie
- Department of Biology, University of Bergen, PO Box 7803, N-5020, Bergen, Norway
| | - Silje Bjørneklett
- Department of Biology, University of Bergen, PO Box 7803, N-5020, Bergen, Norway
| | - Hilde Kristin Garberg
- Department of Biomedicine, Proteomics Unit (PROBE) at the University of Bergen, Bergen, Norway
| | - Eystein Oveland
- Department of Biomedicine, Proteomics Unit (PROBE) at the University of Bergen, Bergen, Norway
| | - Frode Berven
- Department of Biomedicine, Proteomics Unit (PROBE) at the University of Bergen, Bergen, Norway
| | - Anders Goksøyr
- Department of Biology, University of Bergen, PO Box 7803, N-5020, Bergen, Norway
| | - Odd André Karlsen
- Department of Biology, University of Bergen, PO Box 7803, N-5020, Bergen, Norway.
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McDonagh B, Ogueta S, Lasarte G, Padilla CA, Bárcena JA. Shotgun redox proteomics identifies specifically modified cysteines in key metabolic enzymes under oxidative stress in Saccharomyces cerevisiae. J Proteomics 2009; 72:677-89. [PMID: 19367685 DOI: 10.1016/j.jprot.2009.01.023] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Post-translational redox modification of thiol groups can form the molecular basis of antioxidative protection and redox control. We have implemented a shotgun redox proteomic technique to identify the precise cysteines reversibly oxidised in key proteins. The method was applied to Saccharomyces cerevisiae subjected to peroxide treatment. Enrichment by covalent redox affinity chromatography allowed the isolation of a "redox subpeptidome" that was analysed by LC-MS/MS. Unique peptides containing specific reversibly oxidised cysteines were used to identify over 70 proteins in control and treated samples of which 27 were consistently present in all replicates. In most cases, the redox modification negatively affects their function and slows down their metabolic pathways. Integration of the data provides a snapshot consistent with a metabolic defensive strategy, regulating key enzymes by redox modification, redirecting energy toward ribulose-5-phosphate recycling for NADPH production and antioxidative defence.This generally applicable method has allowed us to discover new redox regulated proteins (DAHP and carbamoylphosphate synthases, Doa1p) and to precisely identify target cysteines in a number of known ones.
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Affiliation(s)
- Brian McDonagh
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales, Universidad de Córdoba, Cordoba, Spain
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