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Li J, Gui C, Yao H, Luo C, Song H, Lin H, Xu Q, Chen X, Huang Y, Luo J, Chen W. An Aging and Senescence-Related Gene Signature for Prognosis Prediction in Clear Cell Renal Cell Carcinoma. Front Genet 2022; 13:871088. [PMID: 35646056 PMCID: PMC9136295 DOI: 10.3389/fgene.2022.871088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/05/2022] [Indexed: 12/04/2022] Open
Abstract
Background: Clear cell renal cell carcinoma (ccRCC) is the most common solid lesion in the kidney. This study aims to establish an aging and senescence-related mRNA model for risk assessment and prognosis prediction in ccRCC patients. Methods: ccRCC data were obtained from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) datasets. By applying univariate Cox regression, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression, a new prognostic model based on aging and senescence-related genes (ASRGs) was established. Depending on the prognostic model, high- and low-risk groups were identified for further study. The reliability of the prediction was evaluated in the validation cohort. Pan-cancer analysis was conducted to explore the role of GNRH1 in tumors. Results: A novel prognostic model was established based on eight ASRGs. This model was an independent risk factor and significantly correlated with the prognosis and clinicopathological features of ccRCC patients. The high- and low-risk groups exhibited distinct modes in the principal component analysis and different patterns in immune infiltration. Moreover, the nomogram combining risk score and other clinical factors showed excellent predictive ability, with AUC values for predicting 1-, 3-, and 5-year overall survival in the TCGA cohort equal to 0.88, 0.82, and 0.81, respectively. Conclusion: The model and nomogram based on the eight ASRGs had a significant value for survival prediction and risk assessment for ccRCC patients, providing new insights into the roles of aging and senescence in ccRCC.
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Affiliation(s)
- Jiaying Li
- Department of Urology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Chengpeng Gui
- Department of Urology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Haohua Yao
- Department of Urology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Chenggong Luo
- Department of Urology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Hongde Song
- Department of Urology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Haishan Lin
- Department of Urology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Quanhui Xu
- Department of Urology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xu Chen
- Department of Urology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yong Huang
- Department of Urology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Junhang Luo
- Department of Urology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Junhang Luo, ; Wei Chen,
| | - Wei Chen
- Department of Urology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- *Correspondence: Junhang Luo, ; Wei Chen,
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2
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Geng H, Tsang M, Subbaraj L, Cleveland J, Chen L, Lu M, Sharma J, Vigneron DB, Kurhanewicz J, LaFontaine M, Luks T, Barshop BA, Gangoiti J, Villanueva-Meyer JE, Rubenstein JL. Tumor Metabolism and Neurocognition in CNS Lymphoma. Neuro Oncol 2021; 23:1668-1679. [PMID: 33625503 DOI: 10.1093/neuonc/noab045] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The mechanistic basis for neurocognitive deficits in CNS lymphoma and other brain tumors is incompletely understood. We tested the hypothesis that tumor metabolism impairs neurotransmitter pathways and neurocognitive function. METHODS We performed serial cerebrospinal fluid (CSF) metabolomic analyses using liquid chromatography-electrospray tandem mass spectrometry to evaluate changes in the tumor microenvironment in 14 patients with recurrent CNS lymphoma, focusing on 18 metabolites involved in neurotransmission and bioenergetics. These were paired with serial mini-mental state examinations (MMSE) and MRI studies for tumor volumetric analyses. Patients were analyzed in the setting of the phase I trial of lenalidomide/rituximab. Associations were assessed by Pearson and Spearman correlation coefficient. Generalized estimating equation (gee) models were also established, adjusting for within-subject repeated measures. RESULTS Of 18 metabolites, elevated CSF lactate correlated most strongly with lower MMSE score (p<8E-8, rho=-0.67). High lactate was associated with lower GABA, higher glutamate/GABA ratio and dopamine. Conversely, high succinate correlated with higher MMSE score. Serial analysis demonstrated a reproducible, time-dependent, reciprocal correlation between changes in lactate and GABA concentrations. While high lactate and low GABA correlated with tumor contrast enhancing volume, they correlated more significantly with lower MMSE scores than tumor volumes. CONCLUSIONS We provide evidence that lactate production and Warburg metabolism may impact neurotransmitter dysregulation and neurocognition in CNS lymphomas. We identify novel metabolomic biomarkers that may be applied in future studies of neurocognition in CNS lymphomas. Elucidation of mechanistic interactions between lymphoma metabolism, neurotransmitter imbalance and neurocognition may promote interventions that preserve cognitive function.
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Affiliation(s)
- Huimin Geng
- Laboratory Medicine, University of California, San Francisco (UCSF).,Helen Diller Family Comprehensive Cancer Center, UCSF
| | - Mazie Tsang
- Hematology/Oncology, UCSF.,Department of Medicine, UCSF
| | | | | | - Lingjing Chen
- Hematology/Oncology, UCSF.,Department of Medicine, UCSF
| | - Ming Lu
- Hematology/Oncology, UCSF.,Department of Medicine, UCSF
| | | | - Daniel B Vigneron
- Helen Diller Family Comprehensive Cancer Center, UCSF.,Radiology and Biomedical Imaging
| | - John Kurhanewicz
- Helen Diller Family Comprehensive Cancer Center, UCSF.,Radiology and Biomedical Imaging
| | | | | | - Bruce A Barshop
- Genetics and Pediatrics, University of California, San Diego
| | - Jon Gangoiti
- Genetics and Pediatrics, University of California, San Diego
| | | | - James L Rubenstein
- Helen Diller Family Comprehensive Cancer Center, UCSF.,Hematology/Oncology, UCSF
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3
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Houdelet C, Sinpoo C, Chantaphanwattana T, Voisin SN, Bocquet M, Chantawannakul P, Bulet P. Proteomics of Anatomical Sections of the Gut of Nosema-Infected Western Honeybee ( Apis mellifera) Reveals Different Early Responses to Nosema spp. Isolates. J Proteome Res 2020; 20:804-817. [PMID: 33305956 DOI: 10.1021/acs.jproteome.0c00658] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Honeybees play an important role in pollinating native plants and agricultural crops and produce valuable hive products. Within the last decade, honeybee colonies have been reported to be in decline, due to both biotic and abiotic stress factors including pathogens and pesticides. This study evaluated the impact of different isolates of Nosema spp. [Nosema apis spores (NA), Nosema ceranae from Apis mellifera from France (NF), N. ceranae from Apis cerana from Thailand (NC1), and N. ceranae from A. mellifera from Thailand (NC2)] on the different gut sections of newly emerged adult A. mellifera bees. With an attempt to decipher the early impact of Nosema spp. on the first barrier against Nosema infection, we used off-gel bottom-up proteomics on the different anatomical sections of the gut four days post inoculation. A total of 2185 identified proteins in the esophagus, 2095 in the crop, 1571 in the midgut, 2552 in the ileum, and 3173 in the rectum were obtained. Using label-free quantification, we observed that the response of the host varies according to the Nosema spp. (N. apis versus N. ceranae) and the geographical origin of Nosema. The proteins in the midgut of A. mellifera, orally inoculated with spores of N. ceranae isolated from France, were the most altered, when compared with controls, exhibiting 50 proteins down-regulated and 16 up-regulated. We thereby established the first mass-spectrometry-based proteomics of different anatomical sections of the gut tissue of Nosema-infected A. mellifera four days post inoculation, following infection by different isolates of Nosema spp. that provoked differential host responses. We reported an alteration of proteins involved in the metabolic pathways and specifically eight proteins of the oxidative phosphorylation pathway. More importantly, we propose that the collagen IV NC1 domain-containing protein may represent an early prognostic marker of the impact of Nosema spores on the A. mellifera health status. Data are available via ProteomeXchange with the identifier PXD021848.
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Affiliation(s)
- Camille Houdelet
- CR University Grenoble Alpes, Institute for Advanced Biosciences, Inserm U1209, CNRS UMR 5309, 38000 Grenoble, France.,Plateform BioPark Archamps, 260 Avenue Marie Curie, Archparc, 74166 Saint Julien-en Genevois, France
| | - Chainarong Sinpoo
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | | | - Sébastien N Voisin
- Plateform BioPark Archamps, 260 Avenue Marie Curie, Archparc, 74166 Saint Julien-en Genevois, France
| | | | - Panuwan Chantawannakul
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand.,Environmental Science Research Center (ESRC), Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Philippe Bulet
- CR University Grenoble Alpes, Institute for Advanced Biosciences, Inserm U1209, CNRS UMR 5309, 38000 Grenoble, France.,Plateform BioPark Archamps, 260 Avenue Marie Curie, Archparc, 74166 Saint Julien-en Genevois, France
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4
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Wone BWM, Pathak J, Davidowitz G. Flight duration and flight muscle ultrastructure of unfed hawk moths. ARTHROPOD STRUCTURE & DEVELOPMENT 2018; 47:457-464. [PMID: 29782921 DOI: 10.1016/j.asd.2018.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 05/17/2018] [Accepted: 05/17/2018] [Indexed: 06/08/2023]
Abstract
Flight muscle breakdown has been reported for many orders of insects, but the basis of this breakdown in insects with lifelong dependence on flight is less clear. Lepidopterans show such muscle changes across their lifespans, yet how this change affects the ability of these insects to complete their life cycles is not well documented. We investigated the changes in muscle function and ultrastructure of unfed aging adult hawk moths (Manduca sexta). Flight duration was examined in young, middle-aged, and advanced-aged unfed moths. After measurement of flight duration, the main flight muscle (dorsolongitudinal muscle) was collected and histologically prepared for transmission electron microscopy to compare several measurements of muscle ultrastructure among moths of different ages. Muscle function assays revealed significant positive correlations between muscle ultrastructure and flight distance that were greatest in middle-aged moths and least in young moths. In addition, changes in flight muscle ultrastructure were detected across treatment groups. The number of mitochondria in muscle cells peaked in middle-aged moths. Many wild M. sexta do not feed as adults; thus, understanding the changes in flight capacity and muscle ultrastructure in unfed moths provides a more complete understanding of the ecophysiology and resource allocation strategies of this species.
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Affiliation(s)
- Bernard W M Wone
- Department of Entomology, University of Arizona, Tucson, AZ, USA; Department of Biology, University of South Dakota, Vermillion, SD, USA.
| | - Jaika Pathak
- Department of Entomology, University of Arizona, Tucson, AZ, USA
| | - Goggy Davidowitz
- Department of Entomology, University of Arizona, Tucson, AZ, USA
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5
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The application of skin metabolomics in the context of transdermal drug delivery. Pharmacol Rep 2017; 69:252-259. [DOI: 10.1016/j.pharep.2016.10.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 09/17/2016] [Accepted: 10/12/2016] [Indexed: 01/09/2023]
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6
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Ingram T, Chakrabarti L. Proteomic profiling of mitochondria: what does it tell us about the ageing brain? Aging (Albany NY) 2016; 8:3161-3179. [PMID: 27992860 PMCID: PMC5270661 DOI: 10.18632/aging.101131] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 12/01/2016] [Indexed: 02/07/2023]
Abstract
Mitochondrial dysfunction is evident in numerous neurodegenerative and age-related disorders. It has also been linked to cellular ageing, however our current understanding of the mitochondrial changes that occur are unclear. Functional studies have made some progress reporting reduced respiration, dynamic structural modifications and loss of membrane potential, though there are conflicts within these findings. Proteomic analyses, together with functional studies, are required in order to profile the mitochondrial changes that occur with age and can contribute to unravelling the complexity of the ageing phenotype. The emergence of improved protein separation techniques, combined with mass spectrometry analyses has allowed the identification of age and cell-type specific mitochondrial changes in energy metabolism, antioxidants, fusion and fission machinery, chaperones, membrane proteins and biosynthesis pathways. Here, we identify and review recent data from the analyses of mitochondria from rodent brains. It is expected that knowledge gained from understanding age-related mitochondrial changes of the brain should lead to improved biomarkers of normal ageing and also age-related disease progression.
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Affiliation(s)
- Thomas Ingram
- SVMS, Faculty of Medicine, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Lisa Chakrabarti
- SVMS, Faculty of Medicine, University of Nottingham, Sutton Bonington, LE12 5RD, UK
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7
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Moon E, Park HM, Lee CH, Do SG, Park JM, Han NY, Do MH, Lee JH, Lee H, Kim SY. Dihydrolipoyl dehydrogenase as a potential UVB target in skin epidermis; using an integrated approach of label-free quantitative proteomics and targeted metabolite analysis. J Proteomics 2015; 117:70-85. [DOI: 10.1016/j.jprot.2014.12.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 12/06/2014] [Accepted: 12/12/2014] [Indexed: 12/23/2022]
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8
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Effects of diabetes on oxidative and nitrosative stress in kidney mitochondria from aged rats. J Bioenerg Biomembr 2014; 46:511-8. [PMID: 25425473 DOI: 10.1007/s10863-014-9594-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 11/19/2014] [Indexed: 12/17/2022]
Abstract
Diabetes mellitus (DM) is characterized by chronic hyperglycemia resulting from defects in the secretion and/or action of insulin. Diabetic nephropathy (DN) develops in diabetic patients and is characterized by a progressive deterioration of renal function. The mitochondrial electron transport chain (ETC) produces most of the reactive oxygen species (ROS) that are involved in diabetic nephropathy. Due to the high incidence of DM in the elderly, the aim of this study was to evaluate oxidative and nitrosative stress in kidney mitochondria from aged rats. We evaluated lipid peroxidation (LPO), nitric oxide (NO(•)) production, S-nitrosylation profiles, glutathione levels, and glutathione reductase and aconitase activities under streptozotocin (STZ)-induced experimental diabetes in kidney mitochondria from aged rats. The results showed an increase in LPO, NO(•) production, and S-nitrosylated proteins in rats with STZ-induced diabetes. A decrease in glutathione (GSH) levels and glutathione reductase (GR) and aconitase activities in the rats that received the STZ-induced diabetes treatment was also observed, when compared with the age-related controls. The data suggest that oxidative and nitrosative stresses promote mitochondrial oxidative dysfunction in the more advanced age rat kidney in STZ-induced diabetes.
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9
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Salminen A, Kauppinen A, Hiltunen M, Kaarniranta K. Krebs cycle intermediates regulate DNA and histone methylation: epigenetic impact on the aging process. Ageing Res Rev 2014; 16:45-65. [PMID: 24910305 DOI: 10.1016/j.arr.2014.05.004] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 05/20/2014] [Accepted: 05/29/2014] [Indexed: 02/01/2023]
Abstract
Many aging theories have proposed that mitochondria and energy metabolism have a major role in the aging process. There are recent studies indicating that Krebs cycle intermediates can shape the epigenetic landscape of chromatin by regulating DNA and histone methylation. A growing evidence indicates that epigenetics plays an important role in the regulation of healthspan but also is involved in the aging process. 2-Oxoglutarate (α-ketoglutarate) is a key metabolite in the Krebs cycle but it is also an obligatory substrate for 2-oxoglutarate-dependent dioxygenases (2-OGDO). The 2-OGDO enzyme family includes the major enzymes of DNA and histone demethylation, i.e. Ten-Eleven Translocation (TETs) and Jumonji C domain containing (JmjC) demethylases. In addition, 2-OGDO members can regulate collagen synthesis and hypoxic responses in a non-epigenetical manner. Interestingly, succinate and fumarate, also Krebs cycle intermediates, are potent inhibitors of 2-OGDO enzymes, i.e. the balance of Krebs cycle reactions can affect the level of DNA and histone methylation and thus control gene expression. We will review the epigenetic mechanisms through which Krebs cycle intermediates control the DNA and histone methylation. We propose that age-related disturbances in the Krebs cycle function induce stochastic epigenetic changes in chromatin structures which in turn promote the aging process.
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Affiliation(s)
- Antero Salminen
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland; Department of Neurology, Kuopio University Hospital, P.O. Box 1777, FIN-70211 Kuopio, Finland.
| | - Anu Kauppinen
- Department of Ophthalmology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland; Department of Ophthalmology, Kuopio University Hospital, P.O. Box 1777, FIN-70211 Kuopio, Finland
| | - Mikko Hiltunen
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland; Department of Neurology, Kuopio University Hospital, P.O. Box 1777, FIN-70211 Kuopio, Finland
| | - Kai Kaarniranta
- Department of Ophthalmology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland; Department of Ophthalmology, Kuopio University Hospital, P.O. Box 1777, FIN-70211 Kuopio, Finland
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10
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Cheng Z, Tsuda M, Kishita Y, Sato Y, Aigaki T. Impaired energy metabolism in a Drosophila model of mitochondrial aconitase deficiency. Biochem Biophys Res Commun 2013; 433:145-50. [PMID: 23438437 DOI: 10.1016/j.bbrc.2013.02.040] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 02/13/2013] [Indexed: 01/26/2023]
Abstract
Aconitase catalyzes the conversion of citrate to isocitrate in the tricarboxylic acid (TCA) cycle, and its deficiency in humans is associated with an infantile neurodegenerative disorder affecting mainly the cerebellum and retina. Here we investigated the effect of gene knockout and knockdown of the mitochondrial aconitase Acon in Drosophila. Acon-knockout flies were homozygous lethal, indicating that Acon is essential for viability. RNA interference-generated Acon-knockdown flies exhibited a variety of phenotypes, such as reduced locomotor activity, a shortened lifespan, and increased cell death in the developing brain. Metabolomic analysis revealed that acetyl-CoA, citrate/isocitrate, and cis-aconitate were significantly increased, while most metabolites of glycolysis and the TCA cycle were reduced. Reduced triacylglyceride and increased acetyl-CoA suggested that lipids were used as an energy source because of the impaired glycolysis and TCA cycle. The Acon-knockdown model should facilitate further understanding of the pathophysiology of m-aconitase deficiency in humans.
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Affiliation(s)
- Zhang Cheng
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-osawa, Hachioji, Tokyo 192-0397, Japan
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11
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Abstract
The main objective of this review is to examine the role of endogenous reactive oxygen/nitrogen species (ROS) in the aging process. Until relatively recently, ROS were considered to be potentially toxic by-products of aerobic metabolism, which, if not eliminated, may inflict structural damage on various macromolecules. Accrual of such damage over time was postulated to be responsible for the physiological deterioration in the postreproductive phase of life and eventually the death of the organism. This "structural damage-based oxidative stress" hypothesis has received support from the age-associated increases in the rate of ROS production and the steady-state amounts of oxidized macromolecules; however, there are increasing indications that structural damage alone is insufficient to satisfactorily explain the age-associated functional losses. The level of oxidative damage accrued during aging often does not match the magnitude of functional losses. Although experimental augmentation of antioxidant defenses tends to enhance resistance to induced oxidative stress, such manipulations are generally ineffective in the extension of life span of long-lived strains of animals. More recently, in a major conceptual shift, ROS have been found to be physiologically vital for signal transduction, gene regulation, and redox regulation, among others, implying that their complete elimination would be harmful. An alternative notion, advocated here, termed the "redox stress hypothesis," proposes that aging-associated functional losses are primarily caused by a progressive pro-oxidizing shift in the redox state of the cells, which leads to the overoxidation of redox-sensitive protein thiols and the consequent disruption of the redox-regulated signaling mechanisms.
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Affiliation(s)
- Rajindar S Sohal
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089, USA.
| | - William C Orr
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275, USA
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12
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Pichaud N, Chatelain EH, Ballard JWO, Tanguay R, Morrow G, Blier PU. Thermal sensitivity of mitochondrial metabolism in two distinct mitotypes of Drosophila simulans: evaluation of mitochondrial plasticity. J Exp Biol 2010; 213:1665-75. [DOI: 10.1242/jeb.040261] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
SUMMARY
The overall aim of this study was to (1) evaluate the adaptive value of mitochondrial DNA by comparing mitochondrial performance in populations possessing different haplotypes and distribution, and to (2) evaluate the sensitivity of different enzymes of the electron transport system (ETS) during temperature-induced changes. We measured the impact of temperature of mitochondrial respiration and several key enzymes of mitochondrial metabolism in two mitotypes (siII and siIII) of Drosophila simulans. The temperature dependencies of oxygen consumption for mitochondria isolated from flight muscle was assessed with complex I substrates (pyruvate + malate + proline) and with sn glycerol-3-phosphate (to reduce complex III via glycerophosphate dehydrogenase) in both coupled and uncoupled states. Activities of citrate synthase, cytochrome c oxidase (COX), catalase and aconitase, and the excess capacity of COX at high convergent pathway flux were also measured as a function of temperature. Overall, our results showed that functional differences between the two mitotypes are few. Results suggest that differences between the two mitotypes could hardly explain the temperature-specific differences measured in mitochondria performances. It suggests that some other factor(s) may be driving the maintenance of mitotypes. We also show that the different enzymes of the ETS have different thermal sensitivities. The catalytic capacities of these enzymes vary with temperature changes, and the corresponding involvement of the different steps on mitochondrial regulation probably varies with temperature. For example, the excess COX capacity is low, even non-existent, at high and intermediate temperatures (18°C, 24°C and 28°C) whereas it is quite high at a lower temperature (12°C), suggesting release of respiration control by COX at low temperature.
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Affiliation(s)
- Nicolas Pichaud
- Laboratoire de biologie intégrative, Département de Biologie, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, Québec, Canada, G5L 3A1
| | - Etienne Hébert Chatelain
- Laboratoire de biologie intégrative, Département de Biologie, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, Québec, Canada, G5L 3A1
| | - J. William O. Ballard
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney 2052, Australia
| | - Robert Tanguay
- Laboratoire de Génétique Cellulaire et développementale, Département de Médecine, Institut de Biologie intégrative et des systèmes, 1030 ave de la Médecine, Université Laval, Québec, Canada, G1V 0A6
| | - Geneviève Morrow
- Laboratoire de Génétique Cellulaire et développementale, Département de Médecine, Institut de Biologie intégrative et des systèmes, 1030 ave de la Médecine, Université Laval, Québec, Canada, G1V 0A6
| | - Pierre U. Blier
- Laboratoire de biologie intégrative, Département de Biologie, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, Québec, Canada, G5L 3A1
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13
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Rapid functional screening of Streptomyces coelicolor regulators by use of a pH indicator and application to the MarR-like regulator AbsC. Appl Environ Microbiol 2010; 76:3645-56. [PMID: 20382814 DOI: 10.1128/aem.02617-09] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
To elucidate the function of an unknown regulator in Streptomyces, differences in phenotype and antibiotic production between a deletion mutant and a wild-type strain (WT) were compared. These differences are easily hidden by complex media. To determine the specific nutrient conditions that reveal such differences, we used a multiwell method containing different nutrients along with bromothymol blue. We found several nutrients that provide key information on characterization conditions. By comparing the growth of wild-type and mutant strains on screened nutrients, we were able to measure growth, organic acid production, and antibiotic production for the elucidation of regulator function. As a result of this method, a member of the MarR-like regulator family, SCO5405 (AbsC), was newly characterized to control pyruvate dehydrogenase in Streptomyces coelicolor. Deletion of SCO5405 increased the pH of the culture broth due to decreased production of organic acids such as pyruvate and alpha-ketoglutarate and increased extracellular actinorhodin (ACT) production in minimal medium containing glucose and alanine (MMGA). This method could therefore be a high-throughput method for the characterization of unknown regulators.
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14
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Vance JT, Williams JB, Elekonich MM, Roberts SP. The effects of age and behavioral development on honey bee (Apis mellifera) flight performance. ACTA ACUST UNITED AC 2009; 212:2604-11. [PMID: 19648405 DOI: 10.1242/jeb.028100] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A critical but seldom-studied component of life history theory is how behavior and age affect whole-organism performance. To address this issue we compared the flight performance of honey bees (whose behavioral development and age can be assessed independently via simple manipulations of colony demographics) between distinct behavioral castes (in-hive nurse bees vs out-of-hive foragers) and across lifespan. Variable-density gases and high-speed video were used to determine the maximum hovering flight capacity and wing kinematics of age-matched nurse bees and foragers sampled from a single-cohort colony over a period of 34 days. The transition from hive work to foraging was accompanied by a 42% decrease in body mass and a proportional increase in flight capacity (defined as the minimum gas density allowing hovering flight). The lower flight capacity of hive bees was primarily due to the fact that in air they were functioning at a near-maximal wing angular velocity due to their high body masses. Foragers were lighter and when hovering in air required a much lower wing angular velocity, which they were able to increase by 32% during maximal flight performance. Flight performance of hive bees was independent of age, but in foragers the maximal wingbeat frequency and maximal average angular velocity were lowest in precocious (7-14 day old) foragers, highest in normal-aged (15-28 day old) foragers and intermediate in foragers older than 29 days. This pattern coincides with previously described age-dependent biochemical and metabolic properties of honey bee flight muscle.
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Affiliation(s)
- Jason T Vance
- School of Life Sciences, University of Nevada, 4505 S. Maryland Parkway, Las Vegas, NV 89154, USA
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15
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Nguyen TTA, Michaud D, Cloutier C. A proteomic analysis of the aphid Macrosiphum euphorbiae under heat and radiation stress. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2009; 39:20-30. [PMID: 19000926 DOI: 10.1016/j.ibmb.2008.09.014] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Revised: 09/16/2008] [Accepted: 09/18/2008] [Indexed: 05/15/2023]
Abstract
Temperature and solar radiation can be important sources of abiotic stress for small herbivorous insects living in close association with plants. We examined the effects of daily fluctuations of heat and UV radiation on the proteome and performance of winged and wingless morphs of the aphid Macrosiphum euphorbiae. A daily regime of 4h of heat stress at 35 degrees C had more negative effects on the aphid's fitness than a similar period of UV-B stress (11.6kJm(-2) per day), and these effects were most pronounced on wingless aphids. Aphid proteomes as detected on 2-D gels revealed approximately 470 protein spots, with the fluctuating heat stress leading to many more changes than exposure to UV-B. The reduced performance of aphids under heat stress correlated with lower abundance of several enzymes in central pathways of energy metabolism, including the TCA cycle and the respiratory chain. Several exoskeletal proteins were induced or their abundance was increased under high temperature stress, suggesting that cuticle barrier enhancement at molting in response to heat stress is an aphid adaptation to stressful thermal conditions. The proteome of winged aphids was more broadly modulated under stress than that of wingless aphids. Greater homeostatic capabilities as revealed at the proteomic level could explain the higher tolerance of the alate aphid morph to environmental stress and its more stable performance and fitness.
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Affiliation(s)
- Thi Thuy An Nguyen
- Département de biologie, Pavillon Vachon, Université Laval, Québec, Québec, Canada
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16
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Dubessay P, Garreau-Balandier I, Jarrousse AS, Fleuriet A, Sion B, Debise R, Alziari S. Aging impact on biochemical activities and gene expression of Drosophila melanogaster mitochondria. Biochimie 2007; 89:988-1001. [PMID: 17524546 DOI: 10.1016/j.biochi.2007.03.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2007] [Accepted: 03/19/2007] [Indexed: 11/21/2022]
Abstract
The consequences of aging are characterized by a decline in the main cellular functions, including those of the mitochondria. Although these consequences have been much studied, efforts have often focused solely on a few parameters used to assess the "state" of mitochondrial function during aging. We performed comparative measurements of several parameters in young (a few days) and old (8 and 12 weeks) adult male Drosophila melanogaster: respiratory complex activities, mitochondrial respiration, ATP synthesis, lipid composition of the inner membrane, concentrations of respiratory complex subunits, expression of genes (nuclear and mitochondrial) coding for mitochondrial proteins. Our results show that, in the mitochondria of "old" flies, the activities of three respiratory complexes (I, III, IV) are greatly diminished, ATP synthesis is decreased, and the lipid composition of the inner membrane (fatty acids, cardiolipin) is modified. However, the respiration rate and subunit concentrations measured by Western blot are unaffected. Although cellular mitochondrial DNA (mtDNA) content remains constant, there is a decrease in concentrations of nuclear and mitochondrial transcripts apparently coordinated. The expression of nuclear genes encoding the transcription factors TFAM, TFB1, TFB2, and DmTTF, which are essential for the maintenance and expression of mtDNA are also decreased. The decrease in nuclear and mitochondrial transcript concentrations may be one of the principal effects of aging on mitochondria, and could explain observed decreases in mitochondrial efficiency.
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Affiliation(s)
- Pascal Dubessay
- Equipe Génome Mitochondrial, UMR CNRS 6547, Université Blaise Pascal-Clermont II, 63177 Aubière, France
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17
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Llorens JV, Navarro JA, Martínez-Sebastián MJ, Baylies MK, Schneuwly S, Botella JA, Moltó MD. Causative role of oxidative stress in a Drosophila model of Friedreich ataxia. FASEB J 2007; 21:333-44. [PMID: 17167074 DOI: 10.1096/fj.05-5709com] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Friedreich ataxia (FA), the most common form of hereditary ataxia, is caused by a deficit in the mitochondrial protein frataxin. While several hypotheses have been suggested, frataxin function is not well understood. Oxidative stress has been suggested to play a role in the pathophysiology of FA, but this view has been recently questioned, and its link to frataxin is unclear. Here, we report the use of RNA interference (RNAi) to suppress the Drosophila frataxin gene (fh) expression. This model system parallels the situation in FA patients, namely a moderate systemic reduction of frataxin levels compatible with normal embryonic development. Under these conditions, fh-RNAi flies showed a shortened life span, reduced climbing abilities, and enhanced sensitivity to oxidative stress. Under hyperoxia, fh-RNAi flies also showed a dramatic reduction of aconitase activity that seriously impairs the mitochondrial respiration while the activities of succinate dehydrogenase, respiratory complex I and II, and indirectly complex III and IV are normal. Remarkably, frataxin overexpression also induced the oxidative-mediated inactivation of mitochondrial aconitase. This work demonstrates, for the first time, the essential function of frataxin in protecting aconitase from oxidative stress-dependent inactivation in a multicellular organism. Moreover our data support an important role of oxidative stress in the progression of FA and suggest a tissue-dependent sensitivity to frataxin imbalance. We propose that in FA, the oxidative mediated inactivation of aconitase, which occurs normally during the aging process, is enhanced due to the lack of frataxin.
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Affiliation(s)
- José V Llorens
- Departament de Genètica, Universitat de València, Carrer Doctor Moliner 50, 46100-Burjassot, Valencia, Spain
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18
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Chakravarti B, Chakravarti DN. Oxidative modification of proteins: age-related changes. Gerontology 2006; 53:128-39. [PMID: 17164550 DOI: 10.1159/000097865] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Aging is a complex biological phenomenon which involves progressive loss of different physiological functions of various tissues of living organisms. It is the inevitable fate of life and is a major risk factor for death and different pathological disorders. Based on a wide variety of studies performed in humans as well as in various animal models and microbial systems, reactive oxygen species (ROS) are believed to play a key role in the aging process. The production of ROS is influenced by cellular metabolic activities as well as environmental factors. ROS can react with all major biological macromolecules such as carbohydrates, nucleic acids, lipids, and proteins. Since, in general, proteins are the key molecules that play the ultimate role in various structural and functional aspects of living organisms, this review will focus on the age-related oxidative modifications of proteins as well as on mechanism for removal or repair of the oxidized proteins. The topics covered include protein oxidation as a marker of oxidative stress, experimental evidence indicating the role of ROS in protein oxidation, protein carbonyl content, enzymatic degradation of oxidized proteins, and effects of caloric restriction on protein oxidation in the context of aging. Finally, we will discuss different strategies which have been or can be undertaken to slow down the oxidative damage of proteins and the aging process.
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Affiliation(s)
- Bulbul Chakravarti
- Keck Graduate Institute of Applied Life Sciences, Claremont, California, USA.
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19
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Martin I, Grotewiel MS. Oxidative damage and age-related functional declines. Mech Ageing Dev 2006; 127:411-23. [PMID: 16527333 DOI: 10.1016/j.mad.2006.01.008] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2006] [Indexed: 12/31/2022]
Abstract
Most organisms experience progressive declines in physiological function as they age. Since this senescence of function is thought to underlie the decrease in quality of life in addition to the increase in susceptibility to disease and death associated with aging, identifying the mechanisms involved would be highly beneficial. One of the leading mechanistic theories for aging is the oxidative damage hypothesis. A number of studies in a variety of species support a strong link between oxidative damage and life span determination. The role of oxidative damage in functional senescence has also been investigated, albeit not as comprehensively. Here, we review these investigations. Several studies show that the age-related loss of a number of functions is associated with an accrual of oxidative damage in the tissues mediating those functions. Additionally, treatments that increase the accumulation of oxidative damage with age frequently exacerbate functional losses. Moreover, treatments that reduce the accumulation of oxidative damage often attenuate or delay the loss of function associated with aging. These data provide the foundation for a link between oxidative damage and functional senescence, thereby supporting the oxidative damage hypothesis of aging within the context of age-related functional decline.
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Affiliation(s)
- Ian Martin
- Department of Human Genetics and Neuroscience Program, Virginia Commonwealth University School of Medicine, Richmond, 23298, USA
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20
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Hunzinger C, Wozny W, Schwall GP, Poznanović S, Stegmann W, Zengerling H, Schoepf R, Groebe K, Cahill MA, Osiewacz HD, Jägemann N, Bloch M, Dencher NA, Krause F, Schrattenholz A. Comparative Profiling of the Mammalian Mitochondrial Proteome: Multiple Aconitase-2 Isoforms IncludingN-formylkynurenine Modifications as Part of a Protein Biomarker Signature for Reactive Oxidative Species. J Proteome Res 2006; 5:625-33. [PMID: 16512678 DOI: 10.1021/pr050377+] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The activity of mitochondria induces, as a byproduct, a variety of post-translational modifications in associated proteins, which have functional downstream consequences for processes such as apoptosis, autophagy, and plasticity; e.g., reactive oxygen species (ROS), which induce N-formyl-kynurenine from oxidized tryptophans in certain mitochondrial proteins which are localized in close spatial proximity to their source. This type of fast molecular changes has profound influence on cell death and survival with implications in a number of pathologies. The quantitative and differential analysis of bovine heart mitochondria by four 2D-PAGE methods, including 2D-PAGE with high-resolution IEF as first dimension, revealed that due to limited resolution, those methods employing blue native-, tricine-urea-, and 16-BAC-PAGE as the first dimension are less applicable for the differential quantitative analysis of redundant protein spots which might give insight into post-translational modifications that are relevant in age- and stress-related changes. Moreover, 2D-PAGE with high resolution IEF was able to resolve a surprisingly large number of membrane proteins from mitochondrial preparations. For aconitase-2, an enzyme playing an important role in mitochondrial aging, a more thorough molecular analysis of all separable isoforms was performed, leading to the identification of two particular N-formylkynurenine modifications. Next to protein redundancy, native protein-protein interactions, with the potential of relating certain post-translational modification patterns to distinct oligomeric states, e.g., oxidative phosphorylation super complexes, might provide novel and (patho-) physiologically relevant information. Among proteins identified, 14 new proteins (GenBank entries), previously not associated with mitochondria, were found.
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Yarian CS, Toroser D, Sohal RS. Aconitase is the main functional target of aging in the citric acid cycle of kidney mitochondria from mice. Mech Ageing Dev 2005; 127:79-84. [PMID: 16289253 PMCID: PMC2835517 DOI: 10.1016/j.mad.2005.09.028] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2005] [Accepted: 09/30/2005] [Indexed: 11/28/2022]
Abstract
The activities of the citric acid cycle enzymes were determined in mitochondria isolated from kidneys of relatively young, middle age, and old mice. Aconitase exhibited the most significant decrease in activity with age. The activity of alpha-ketoglutarate dehydrogenase exhibited a modest decrease in activity, while NADP(+)-isocitrate dehydrogenase (NADP(+)-ICD) activity increased moderately with age. Activities of citrate synthase, NAD(+)-isocitrate dehydrogenase (NAD(+)-ICD), succinyl-CoA synthetase (SCS), succinate dehydrogenase (SD), fumarase (FUM), and malate dehydrogenase (MD) were not affected. The molar ratio of the intra-mitochondrial redox indicator, NADPH:NADP(+), was higher in young compared to old animals, while the NADH:NAD(+) molar ratio remained unchanged. It is suggested that an age-related decrease in aconitase activity along with relatively subtle alterations in activities of some other citric acid cycle enzymes are likely to contribute to a decline in the overall efficiency of mitochondrial bioenergetics. The biological consequences of such alterations include age-related fluctuations in the citric acid cycle intermediates, which are precursors of protein synthesis, activators of fatty acid synthesis, and can also act as ligands for orphan G-protein coupled receptors.
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Affiliation(s)
| | | | - Rajindar S. Sohal
- Corresponding author. Tel.: +1 323 442 1860; fax: +1 323 224 7473. (R.S. Sohal)
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