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Jia K, Wang Y, Jiang L, Lai M, Liu W, Wang L, Liu H, Cao X, Li Y, Nie Z. Urine Metabolic Profiling for Rapid Lung Cancer Screening: A Strategy Combining Rh-Doped SrTiO 3-Assisted Laser Desorption/Ionization Mass Spectrometry and Machine Learning. ACS APPLIED MATERIALS & INTERFACES 2024; 16:12302-12309. [PMID: 38414269 DOI: 10.1021/acsami.3c19007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Lung cancer ranks among the cancers with the highest global incidence rates and mortality. Swift and extensive screening is crucial for the early-stage diagnosis of lung cancer. Laser desorption/ionization mass spectrometry (LDI-MS) possesses clear advantages over traditional analytical methods for large-scale analysis due to its unique features, such as simple sample processing, rapid speed, and high-throughput performance. As n-type semiconductors, titanate-based perovskite materials can generate charge carriers under ultraviolet light irradiation, providing the capability for use as an LDI-MS substrate. In this study, we employ Rh-doped SrTiO3 (STO/Rh)-assisted LDI-MS combined with machine learning to establish a method for urine-based lung cancer screening. We directly analyzed urine metabolites from lung cancer patients (LCs), pneumonia patients (PNs), and healthy controls (HCs) without employing any pretreatment. Through the integration of machine learning, LCs are successfully distinguished from HCs and PNs, achieving impressive area under the curve (AUC) values of 0.940 for LCs vs HCs and 0.864 for LCs vs PNs. Furthermore, we identified 10 metabolites with significantly altered levels in LCs, leading to the discovery of related pathways through metabolic enrichment analysis. These results suggest the potential of this method for rapidly distinguishing LCs in clinical applications and promoting precision medicine.
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Affiliation(s)
- Ke Jia
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yawei Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- School of Chemistry and Chemical Engineering, Jiangxi Province Engineering Research Center of Ecological Chemical Industry, Jiujiang University, Jiujiang, Jiangxi 332005, China
| | - Lixia Jiang
- Gannan Medical University, Ganzhou 341000, China
| | - Mi Lai
- Gannan Medical University, Ganzhou 341000, China
| | - Wenlan Liu
- Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| | - Liping Wang
- Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| | - Huihui Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaohua Cao
- School of Chemistry and Chemical Engineering, Jiangxi Province Engineering Research Center of Ecological Chemical Industry, Jiujiang University, Jiujiang, Jiangxi 332005, China
| | - Yuze Li
- State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering, College of Chemistry and Chemical Engineering, Ningxia University, Yinchuan 750021, China
| | - Zongxiu Nie
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Machigov EA, Igonina EV, Sviridova DA, Rubanovich AV, Abilev SK. The Genotoxic Effect of the Paraquat Radiomimetic on Escherichia coli Bacteria. BIOL BULL+ 2022. [DOI: 10.1134/s106235902212010x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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Petrella G, Montesano C, Lentini S, Ciufolini G, Vanni D, Speziale R, Salonia A, Montorsi F, Summa V, Vago R, Orsatti L, Monteagudo E, Cicero DO. Personalized Metabolic Profile by Synergic Use of NMR and HRMS. Molecules 2021; 26:4167. [PMID: 34299442 PMCID: PMC8304707 DOI: 10.3390/molecules26144167] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/01/2021] [Accepted: 07/07/2021] [Indexed: 12/25/2022] Open
Abstract
A new strategy that takes advantage of the synergism between NMR and UHPLC-HRMS yields accurate concentrations of a high number of compounds in biofluids to delineate a personalized metabolic profile (SYNHMET). Metabolite identification and quantification by this method result in a higher accuracy compared to the use of the two techniques separately, even in urine, one of the most challenging biofluids to characterize due to its complexity and variability. We quantified a total of 165 metabolites in the urine of healthy subjects, patients with chronic cystitis, and patients with bladder cancer, with a minimum number of missing values. This result was achieved without the use of analytical standards and calibration curves. A patient's personalized profile can be mapped out from the final dataset's concentrations by comparing them with known normal ranges. This detailed picture has potential applications in clinical practice to monitor a patient's health status and disease progression.
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Affiliation(s)
- Greta Petrella
- Department of Chemical Science and Technology, University of Rome “Tor Vergata”, 00133 Rome, Italy; (G.P.); (S.L.); (G.C.); (D.V.)
| | - Camilla Montesano
- Chemistry Department, University of Rome “Sapienza”, 00185 Rome, Italy;
| | - Sara Lentini
- Department of Chemical Science and Technology, University of Rome “Tor Vergata”, 00133 Rome, Italy; (G.P.); (S.L.); (G.C.); (D.V.)
| | - Giorgia Ciufolini
- Department of Chemical Science and Technology, University of Rome “Tor Vergata”, 00133 Rome, Italy; (G.P.); (S.L.); (G.C.); (D.V.)
| | - Domitilla Vanni
- Department of Chemical Science and Technology, University of Rome “Tor Vergata”, 00133 Rome, Italy; (G.P.); (S.L.); (G.C.); (D.V.)
| | - Roberto Speziale
- IRBM S.p.A., 00071 Pomezia, Italy; (R.S.); (V.S.); (L.O.); (E.M.)
| | - Andrea Salonia
- Urological Research Institute, IRCCS Ospedale San Raffaele, 20132 Milan, Italy; (A.S.); (F.M.); (R.V.)
- Division of Experimental Oncology, URI Urological Research Institute, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Francesco Montorsi
- Urological Research Institute, IRCCS Ospedale San Raffaele, 20132 Milan, Italy; (A.S.); (F.M.); (R.V.)
- Division of Experimental Oncology, URI Urological Research Institute, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Vincenzo Summa
- IRBM S.p.A., 00071 Pomezia, Italy; (R.S.); (V.S.); (L.O.); (E.M.)
| | - Riccardo Vago
- Urological Research Institute, IRCCS Ospedale San Raffaele, 20132 Milan, Italy; (A.S.); (F.M.); (R.V.)
- Division of Experimental Oncology, URI Urological Research Institute, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Laura Orsatti
- IRBM S.p.A., 00071 Pomezia, Italy; (R.S.); (V.S.); (L.O.); (E.M.)
| | - Edith Monteagudo
- IRBM S.p.A., 00071 Pomezia, Italy; (R.S.); (V.S.); (L.O.); (E.M.)
| | - Daniel Oscar Cicero
- Department of Chemical Science and Technology, University of Rome “Tor Vergata”, 00133 Rome, Italy; (G.P.); (S.L.); (G.C.); (D.V.)
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Huang M, Cai Q, Xu Y, Guo M, Zhu C, Li Y, Wu K, Zhou Z, Yang H. Paraquat affects the differentiation of neural stem cells and impairs the function of vascular endothelial cells: a study of molecular mechanism. ENVIRONMENTAL TOXICOLOGY 2019; 34:548-555. [PMID: 30698896 DOI: 10.1002/tox.22723] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 01/11/2019] [Accepted: 01/14/2019] [Indexed: 06/09/2023]
Abstract
OBJECTIVE To investigate the effect of paraquat (PQ) exposure on gene expression in neural stem cells as well as structures and functions of vascular endothelial cells. METHODS RNA-Seq was used to explore the differentially expressed genes in human umbilical cord blood-neural stem cells (HUCB-NSCs) at different stages (eg, proliferation, early and late differentiation) in the presence of PQ. The effects of PQ on human umbilical vein endothelial cells (HUVECs), including cell proliferation, apoptosis, cytokines secretion, and expression of tight junction proteins, were assessed with CCK-8, flow cytometry, ELISA, and western blot analysis, individually. RESULTS A total of 53 genes were up-regulated and 61 genes were down-regulated in PQ treated HUCB-NSCs, including seven genes associated with the differentiation of neural stem cells, for example, Gfap, S100B, Oct4, Gdf3, Sox1, Pax6, and Ngn1. PQ treatment significantly reduced the proliferation of HUVECs, inhibited cytokines secretion (VEGF, BFGF) and expressions of tight junction-associated protein (Claudin 1, Occludin, ZO-1), as well as induced significant apoptosis. CONCLUSION Our study suggests that PQ impairs the development of nervous system by regulating the expression of genes associated with neural stem cell differentiation, as well as the structure and function of vascular endothelial cells, which together lead to abnormality in the nervous system.
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Affiliation(s)
- Min Huang
- The Department of Occupational and Environmental Health, Lab of Molecular Toxicology, School of Public Health, Ningxia Medical University, Yinchuan, China
| | - Qian Cai
- The Department of Occupational and Environmental Health, Lab of Molecular Toxicology, School of Public Health, Ningxia Medical University, Yinchuan, China
| | - Yanlong Xu
- The Department of Occupational and Environmental Health, Lab of Molecular Toxicology, School of Public Health, Ningxia Medical University, Yinchuan, China
| | - Muzheng Guo
- The Department of Occupational and Environmental Health, Lab of Molecular Toxicology, School of Public Health, Ningxia Medical University, Yinchuan, China
| | - Chendi Zhu
- The Department of Occupational and Environmental Health, Lab of Molecular Toxicology, School of Public Health, Ningxia Medical University, Yinchuan, China
| | - Yinyin Li
- The Department of Occupational and Environmental Health, Lab of Molecular Toxicology, School of Public Health, Ningxia Medical University, Yinchuan, China
| | - Kexin Wu
- The Department of Occupational and Environmental Health, Lab of Molecular Toxicology, School of Public Health, Ningxia Medical University, Yinchuan, China
| | - Zhijun Zhou
- School of Public Health, MOE Key Laboratory for Public Health Safety, Key Lab of Health Technology Assessment of National Health Commission, Fudan University, Shanghai, China
| | - Huifang Yang
- The Department of Occupational and Environmental Health, Lab of Molecular Toxicology, School of Public Health, Ningxia Medical University, Yinchuan, China
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Evidence of bovine serum albumin-viologen herbicide binding interaction and associated structural modifications. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.03.058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Klawitter J, Klawitter J, Schmitz V, Shokati T, Epshtein E, Thurman JM, Christians U. Mycophenolate mofetil enhances the negative effects of sirolimus and tacrolimus on rat kidney cell metabolism. PLoS One 2014; 9:e86202. [PMID: 24497939 PMCID: PMC3907404 DOI: 10.1371/journal.pone.0086202] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 12/08/2013] [Indexed: 12/12/2022] Open
Abstract
Background and Purpose Mycophenolate mofetil (MMF) per se is not known to have negative effects on the kidney. MMF alone or in combination with sirolimus, can be the basis of calcineurin inhibitor (CNI)-free, kidney sparing drug protocols. However, long-term outcomes in patients on MMF/SRL seem to be inferior to those treated with regimens that include the CNI tacrolimus (TAC) due to an increased risk of allo-immune reactions. Interestingly, potential enhancement of the negative effects of SRL and TAC on the kidney by MMF has never been considered. Experimental Approach It was our aim to study the effects of TAC, SRL and MMF alone and evaluate their interactions when combined on the rat kidney. For this purpose we used a comprehensive molecular marker approach including measurements of urinary 8-isoprostane concentrations (oxidative stress marker) and changes of urinary metabolite patterns (1H-NMR spectroscopy) and comparing these markers to renal function (glomerular filtration rate (GFR)) and morphologic alterations (histology). Key Results While MMF alone did not impact GFR, its interaction with SRL and TAC led to a significant decrease of rats’ renal function. The decline went in parallel with a significant increase in urinary isoprostane concentrations and an enhancement of negative effects on urinary metabolite patterns. Conclusions In broad summary, the present study showed that MMF may enhance the negative effects of TAC on kidney function and may even display nephrotoxic properties when combined with SRL.
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Affiliation(s)
- Jelena Klawitter
- Department of Anesthesiology, University of Colorado, Aurora, Colorado, United States of America
- Division of Renal Diseases and Hypertension, University of Colorado, Aurora, Colorado, United States of America
- * E-mail:
| | - Jost Klawitter
- Department of Anesthesiology, University of Colorado, Aurora, Colorado, United States of America
| | - Volker Schmitz
- Department of Anesthesiology, University of Colorado, Aurora, Colorado, United States of America
- Department of General-, Visceral- and Transplantation Surgery, Charité, Campus Virchow, Berlin, Germany
| | - Touraj Shokati
- Department of Anesthesiology, University of Colorado, Aurora, Colorado, United States of America
| | - Ekaterina Epshtein
- Department of Anesthesiology, University of Colorado, Aurora, Colorado, United States of America
| | - Joshua M. Thurman
- Division of Renal Diseases and Hypertension, University of Colorado, Aurora, Colorado, United States of America
| | - Uwe Christians
- Department of Anesthesiology, University of Colorado, Aurora, Colorado, United States of America
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Everolimus and sirolimus in combination with cyclosporine have different effects on renal metabolism in the rat. PLoS One 2012; 7:e48063. [PMID: 23118926 PMCID: PMC3485290 DOI: 10.1371/journal.pone.0048063] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 09/19/2012] [Indexed: 01/05/2023] Open
Abstract
Enhancement of calcineurin inhibitor nephrotoxicity by sirolimus (SRL) is limiting the clinical use of this drug combination. We compared the dose-dependent effects of the structurally related everolimus (EVL) and sirolimus (SRL) alone, and in combination with cyclosporine (CsA), on the rat kidney. Lewis rats were treated by oral gavage for 28 days using a checkerboard dosing format (0, 3.0, 6.0 and 10.0 CsA and 0, 0.5, 1.5 and 3.0 mg/kg/day SRL or EVL, n = 4/dose combination). After 28 days, oxidative stress, energy charge, kidney histologies, glomerular filtration rates, and concentrations of the immunosuppressants were measured along with 1H-magnetic resonance spectroscopy (MRS) and gas chromatography- mass spectrometry profiles of cellular metabolites in urine. The combination of CsA with SRL led to higher urinary glucose concentrations and decreased levels of urinary Krebs cycle metabolites when compared to controls, suggesting that CsA+SRL negatively impacted proximal tubule metabolism. Unsupervised principal component analysis of MRS spectra distinguished unique urine metabolite patterns of rats treated with CsA+SRL from those treated with CsA+EVL and the controls. SRL, but not EVL blood concentrations were inversely correlated with urine Krebs cycle metabolite concentrations. Interestingly, the higher the EVL concentration, the closer urine metabolite patterns resembled those of controls, while in contrast, the combination of the highest doses of CsA+SRL showed the most significant differences in metabolite patterns. Surprisingly in this rat model, EVL and SRL in combination with CsA had different effects on kidney biochemistry, suggesting that further exploration of EVL in combination with low dose calcineurin inhibitors may be of potential benefit.
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Klawitter J, Klawitter J, Schmitz V, Brunner N, Crunk A, Corby K, Bendrick-Peart J, Leibfritz D, Edelstein CL, Thurman JM, Christians U. Low-salt diet and cyclosporine nephrotoxicity: changes in kidney cell metabolism. J Proteome Res 2012; 11:5135-44. [PMID: 23057591 DOI: 10.1021/pr300260e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cyclosporine (CsA) is a highly effective immunosuppressant used in patients after transplantation; however, its use is limited by nephrotoxicity. Salt depletion is known to enhance CsA-induced nephrotoxicity in the rat, but the underlying molecular mechanisms are not completely understood. The goal of our study was to identify the molecular effects of salt depletion alone and in combination with CsA on the kidney using a proteo-metabolomic strategy. Rats (n = 6) were assigned to four study groups: (1) normal controls, (2) low-salt fed controls, (3) 10 mg/kg/d CsA for 28 days on a normal diet, (4) 10 mg/kg/d CsA for 28 days on low-salt diet. Low-salt diet redirected kidney energy metabolism toward mitochondria as indicated by a higher energy charge than in normal-fed controls. Low-salt diet alone reduced phospho-AKT and phospho-STAT3 levels and changed the expression of ion transporters PDZK1 and CLIC1. CsA induced macro- and microvesicular tubular epithelial vacuolization and reduced energy charge, changes that were more significant in low-salt fed animals, probably because of their more pronounced dependence on mitochondria. Here, CsA increased phospho-JAK2 and phospho-STAT3 levels and reduced the phospho-IKKγ and p65 proteins, thus activating NF-κB signaling. Decreased expression of lactate transport regulator CD147 and phospho-AKT was also observed after CsA exposure in low-salt rats, indicating a decrease in glycolysis. In summary, our study suggests a key role for PDZK1, CD147, JAK/STAT, and AKT signaling in CsA-induced nephrotoxicity and proposes mechanistic explanations on why rats fed a low-salt diet have higher sensitivity to CsA.
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Affiliation(s)
- Jelena Klawitter
- Department of Anesthesiology, University of Colorado, Aurora, Colorado, USA.,Division of Renal Diseases and Hypertension, University of Colorado, Aurora, Colorado, USA
| | - Jost Klawitter
- Department of Anesthesiology, University of Colorado, Aurora, Colorado, USA
| | - Volker Schmitz
- Department of Anesthesiology, University of Colorado, Aurora, Colorado, USA.,Department of General-, Visceral- and Transplantation Surgery, Charité, Campus Virchow, Berlin, Germany
| | - Nina Brunner
- Department of Anesthesiology, University of Colorado, Aurora, Colorado, USA.,Department of General-, Visceral- and Transplantation Surgery, Charité, Campus Virchow, Berlin, Germany
| | - Amanda Crunk
- Department of Anesthesiology, University of Colorado, Aurora, Colorado, USA
| | - Kyler Corby
- Department of Anesthesiology, University of Colorado, Aurora, Colorado, USA
| | | | - Dieter Leibfritz
- Institute for Organic Chemistry, Universität Bremen, Bremen, Germany
| | - Charles L Edelstein
- Division of Renal Diseases and Hypertension, University of Colorado, Aurora, Colorado, USA
| | - Joshua M Thurman
- Division of Renal Diseases and Hypertension, University of Colorado, Aurora, Colorado, USA
| | - Uwe Christians
- Department of Anesthesiology, University of Colorado, Aurora, Colorado, USA
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Cho KI, Searle K, Webb M, Yi H, Ferreira PA. Ranbp2 haploinsufficiency mediates distinct cellular and biochemical phenotypes in brain and retinal dopaminergic and glia cells elicited by the Parkinsonian neurotoxin, 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). Cell Mol Life Sci 2012; 69:3511-27. [PMID: 22821000 PMCID: PMC3445802 DOI: 10.1007/s00018-012-1071-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 06/04/2012] [Accepted: 06/21/2012] [Indexed: 11/25/2022]
Abstract
Many components and pathways transducing multifaceted and deleterious effects of stress stimuli remain ill-defined. The Ran-binding protein 2 (RanBP2) interactome modulates the expression of a range of clinical and cell-context-dependent manifestations upon a variety of stressors. We examined the role of Ranbp2 haploinsufficiency on cellular and metabolic manifestations linked to tyrosine-hydroxylase (TH+) dopaminergic neurons and glial cells of the brain and retina upon acute challenge to 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), a parkinsonian neurotoxin, which models facets of Parkinson disease. MPTP led to stronger akinetic parkinsonism and slower recovery in Ranbp2+/− than wild-type mice without viability changes of brain TH+-neurons of either genotype, with the exception of transient nuclear atypia via changes in chromatin condensation of Ranbp2+/− TH+-neurons. Conversely, the number of wild-type retinal TH+-amacrine neurons compared to Ranbp2+/− underwent milder declines without apoptosis followed by stronger recoveries without neurogenesis. These phenotypes were accompanied by a stronger rise of EdU+-proliferative cells and non-proliferative gliosis of GFAP+-Müller cells in wild-type than Ranbp2+/− that outlasted the MPTP-insult. Finally, MPTP-treated wild-type and Ranbp2+/− mice present distinct metabolic footprints in the brain or selective regions thereof, such as striatum, that are supportive of RanBP2-mediated regulation of interdependent metabolic pathways of lysine, cholesterol, free-fatty acids, or their β-oxidation. These studies demonstrate contrasting gene-environment phenodeviances and roles of Ranbp2 between dopaminergic and glial cells of the brain and retina upon oxidative stress-elicited signaling and factors triggering a continuum of metabolic and cellular manifestations and proxies linked to oxidative stress, and chorioretinal and neurological disorders such as Parkinson.
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Affiliation(s)
- Kyoung-in Cho
- Department of Ophthalmology, Duke University Medical Center, DUEC 3802, 2351 Erwin Road, Durham, NC 27710 USA
| | - Kelly Searle
- Department of Ophthalmology, Duke University Medical Center, DUEC 3802, 2351 Erwin Road, Durham, NC 27710 USA
- Department of Epidemiology, The Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, 21205 MD
| | - Mason Webb
- Department of Ophthalmology, Duke University Medical Center, DUEC 3802, 2351 Erwin Road, Durham, NC 27710 USA
| | - Haiqing Yi
- Department of Ophthalmology, Duke University Medical Center, DUEC 3802, 2351 Erwin Road, Durham, NC 27710 USA
| | - Paulo A. Ferreira
- Department of Ophthalmology, Duke University Medical Center, DUEC 3802, 2351 Erwin Road, Durham, NC 27710 USA
- Department of Pathology, Duke University Medical Center, Durham, NC 27710 USA
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Wunnapuk K, Medley GA, Liu X, Grice JE, Jayasinghe S, Gawarammana I, Buckley NA, Roberts MS. Simple and sensitive liquid chromatography-tandem mass spectrometry methods for quantification of paraquat in plasma and urine: application to experimental and clinical toxicological studies. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:3047-52. [PMID: 21956020 DOI: 10.1016/j.jchromb.2011.09.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 09/02/2011] [Accepted: 09/04/2011] [Indexed: 11/30/2022]
Abstract
Simple, sensitive and specific liquid chromatography-tandem mass spectrometry (LC-MS/MS) methods have been developed and validated for quantification of paraquat (PQ) in plasma and urine. Plasma and urine sample preparation were carried out by one-step protein precipitation using cold acetonitrile (-20 to -10 °C). After centrifugation, an aliquot of 10 μL of supernatant was injected into a Kinetex™ hydrophilic interaction chromatography (HILIC) column with a KrudKatcher™ Ultra in-line filter. The chromatographic separation was achieved using the mobile phase mixture of 250 mM ammonium formate (with 0.8% aqueous formic acid) in water and acetonitrile at a flow rate of 0.3 mL/min. Detection was performed using an API2000 triple quadrupole tandem mass spectrometer in multiple reaction monitoring (MRM) mode via an electrospray ionization (ESI) source. The calibration curve was linear over the concentration range of 10-5000 ng/mL, with an LLOQ of 10 ng/mL. The inter- and intra-day precision (% R.S.D.) were <8.5% and 6.4% for plasma and urine, respectively with the accuracies (%) within the range of 95.1-102.8%. PQ in plasma and urine samples was stable when stored at -70 °C for three freeze-thaw cycles. The methods were successfully applied to determine PQ concentration in rat and human samples.
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Affiliation(s)
- Klintean Wunnapuk
- Therapeutics Research Centre, School of Medicine, University of Queensland, Brisbane, QLD, Australia
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MacLellan DL, Mataija D, Doucette A, Huang W, Langlois C, Trottier G, Burton IW, Walter JA, Karakach TK. Alterations in urinary metabolites due to unilateral ureteral obstruction in a rodent model. MOLECULAR BIOSYSTEMS 2011; 7:2181-8. [DOI: 10.1039/c1mb05080j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Muncey HJ, Jones R, De Iorio M, Ebbels TMD. MetAssimulo: simulation of realistic NMR metabolic profiles. BMC Bioinformatics 2010; 11:496. [PMID: 20925910 PMCID: PMC3224597 DOI: 10.1186/1471-2105-11-496] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Accepted: 10/06/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Probing the complex fusion of genetic and environmental interactions, metabolic profiling (or metabolomics/metabonomics), the study of small molecules involved in metabolic reactions, is a rapidly expanding 'omics' field. A major technique for capturing metabolite data is 1H-NMR spectroscopy and this yields highly complex profiles that require sophisticated statistical analysis methods. However, experimental data is difficult to control and expensive to obtain. Thus data simulation is a productive route to aid algorithm development. RESULTS MetAssimulo is a MATLAB-based package that has been developed to simulate 1H-NMR spectra of complex mixtures such as metabolic profiles. Drawing data from a metabolite standard spectral database in conjunction with concentration information input by the user or constructed automatically from the Human Metabolome Database, MetAssimulo is able to create realistic metabolic profiles containing large numbers of metabolites with a range of user-defined properties. Current features include the simulation of two groups ('case' and 'control') specified by means and standard deviations of concentrations for each metabolite. The software enables addition of spectral noise with a realistic autocorrelation structure at user controllable levels. A crucial feature of the algorithm is its ability to simulate both intra- and inter-metabolite correlations, the analysis of which is fundamental to many techniques in the field. Further, MetAssimulo is able to simulate shifts in NMR peak positions that result from matrix effects such as pH differences which are often observed in metabolic NMR spectra and pose serious challenges for statistical algorithms. CONCLUSIONS No other software is currently able to simulate NMR metabolic profiles with such complexity and flexibility. This paper describes the algorithm behind MetAssimulo and demonstrates how it can be used to simulate realistic NMR metabolic profiles with which to develop and test new data analysis techniques. MetAssimulo is freely available for academic use at http://cisbic.bioinformatics.ic.ac.uk/metassimulo/.
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Affiliation(s)
- Harriet J Muncey
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, UK
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Shariff MIF, Ladep NG, Cox IJ, Williams HRT, Okeke E, Malu A, Thillainayagam AV, Crossey MME, Khan SA, Thomas HC, Taylor-Robinson SD. Characterization of urinary biomarkers of hepatocellular carcinoma using magnetic resonance spectroscopy in a Nigerian population. J Proteome Res 2010; 9:1096-103. [PMID: 19968328 DOI: 10.1021/pr901058t] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hepatocellular carcinoma (HCC) is the commonest primary hepatic malignancy worldwide. Current serum diagnostic biomarkers, such as alpha-fetoprotein, are expensive and insensitive in early tumor diagnosis. Urinary biomarkers differentiating HCC from chronic liver disease would be practical and widely applicable. Using an 11.7T nuclear magnetic resonance system, urine was analyzed from three well-matched subject groups, collected at Jos University Teaching Hospital (JUTH), Nigeria. Multivariate factor analyses were performed using principal components analysis (PCA) and partial least-squares discriminant analysis (PLS-DA). All patients were of Nigerian descent: 18 hepatitis B surface antigen (HBsAg)-positive patients with HCC, 10 HBsAg positive patients with cirrhosis, and 15 HBsAg negative healthy Nigerian controls. HCC patients were distinguished from healthy controls, and from the cirrhosis cohort, with sensitivity/specificity of 100%/93% and 89.5%/88.9%, respectively. Metabolites that most strongly contributed to the multivariate models were creatinine, carnitine, creatine and acetone. Urinary (1)H MRS with multivariate statistical analysis was able to differentiate patients with HCC from normal subjects and patients with cirrhosis. Creatinine, carnitine, creatine and acetone were identified as the most influential metabolites. These findings have identified candidate urinary HCC biomarkers which have potential to be developed as simple urinary screening tests for the clinic.
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Affiliation(s)
- Mohamed I F Shariff
- Liver Unit, Department of Medicine, Imperial College London, QEQM Building, St. Mary's Hospital Campus, South Wharf Road, London W2 1NY, United Kingdom.
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16
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Klawitter J, Klawitter J, Kushner E, Jonscher K, Bendrick-Peart J, Leibfritz D, Christians U, Schmitz V. Association of immunosuppressant-induced protein changes in the rat kidney with changes in urine metabolite patterns: a proteo-metabonomic study. J Proteome Res 2010; 9:865-75. [PMID: 19994912 DOI: 10.1021/pr900761m] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The basic mechanisms underlying calcineurin inhibitor (CI) nephrotoxicity and its enhancement by sirolimus are still largely unknown. We investigated the effects of CIs alone and in combination with sirolimus on the renal proteome and correlated these effects with urine metabolite pattern changes. Thirty-six male Wistar rats were assigned to six treatment groups (n = 4/group for proteome analysis and n = 6/group for urine (1)H NMR metabolite pattern analysis): vehicle controls, sirolimus 1 mg/kg/day, cyclosporine 10 mg/kg/day, cyclosporine 10 mg/kg/day + sirolimus 1 mg/kg/day, tacrolimus 1 mg/kg/day, tacrolimus 1 mg/kg/day + sirolimus 1 mg/kg/day. After 28 days, 24 h-urine was collected for (1)H NMR-based metabolic analysis and kidneys were harvested for 2D-gel electrophoresis and histology. Cyclosporine affected the following groups of proteins: calcium homeostasis (regucalcin, calbindin), cytoskeleton (vimentin, caldesmon), response to hypoxia and mitochondrial function (prolyl 4-hydroxylase, proteasome, NADH dehydrogenase), and cell metabolism (kidney aminoacylase, pyruvate dehydrogenase, fructose-1,6-bis phosphate). Several of the changes in protein expression, confirmed by Western blot, were associated with and explained changes in metabolite concentrations in urine. Representative examples are an increase in kidney aminoacylase expression (decrease of hippurate concentrations in urine), up regulation of pyruvate dehydrogenase and fructose-1,6-bisphosphatase, (increased glucose metabolism), and down regulation of arginine/glycine-amidino transferase (most likely due to an increase in creatinine concentrations). Protein changes explained and qualified immunosuppressant-induced metabolite pattern changes in urine.
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Affiliation(s)
- Jost Klawitter
- Department of Anesthesiology, University of Colorado Denver, Aurora, CO 80045, USA.
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17
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Ishihara K, Katsutani N, Asai N, Inomata A, Uemura Y, Suganuma A, Sawada K, Yokoi T, Aoki T. Identification of urinary biomarkers useful for distinguishing a difference in mechanism of toxicity in rat model of cholestasis. Basic Clin Pharmacol Toxicol 2009; 105:156-66. [PMID: 19486331 DOI: 10.1111/j.1742-7843.2009.00410.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
This (1)H nuclear magnetic resonance metabonomics study was aimed to determine urinary biomarkers of cholestasis resulting from inhibition of biliary secretion of bile or obstruction of bile flow. To inhibit biliary secretion of bile, cyclosporine A was administered to male Sprague-Dawley rats. Obstruction of bile flow was induced by administration of 4,4'-methylene dianiline, alpha-naphthylisothiocyanate or bile duct ligation. Clinical pathological and histopathological examinations were performed to confirm cholestatic injury and (1)H nuclear magnetic resonance spectral data for urine samples were analysed to determine similarities and differences in profiles of metabolites using the Spotfire. In cyclosporine A-treated groups, serum total bilirubin and bile acid were significantly increased but no remarkable hepatic histopathological-changes were observed. In 4,4'-methylene dianiline-, alpha-naphthylisothiocyanate- and bile duct ligation-treated groups, serum alkaline phosphatase, gamma-glutamyltranspeptidase and total bilirubin levels increased significantly, and hepatic histopathological-changes were observed. On urinary (1)H nuclear magnetic resonance spectral analysis, area intensities derived from 0.66 to 1.90 ppm were decreased by cyclosporine A, whereas they were increased by other treatments. These metabolites were identified using the NMR suite as bile acids, branched-chain amino acids, n-butyrate, propionate, methyl malonate and valerate. These metabolites were further investigated by K-means clustering analysis. The cluster of these metabolites is considered to be altered by cholestasis. We conclude that bile acids, valine and methyl malonate have a possibility to be urinary cholestatic biomarkers, which distinguish a difference in mechanism of toxicity. (1)H nuclear magnetic resonance metabonomics thus appears to be useful for determining the mechanisms of toxicity and can be front-loaded in drug safety evaluation and biomarker discovery.
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Affiliation(s)
- Kenji Ishihara
- Tsukuba Research, Drug Safety Research Laboratories, Eisai Co, Ltd, Tsukuba, Japan.
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18
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Goldsmith P, Fenton H, Morris-Stiff G, Ahmad N, Fisher J, Prasad KR. Metabonomics: a useful tool for the future surgeon. J Surg Res 2009; 160:122-32. [PMID: 19592031 DOI: 10.1016/j.jss.2009.03.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2008] [Revised: 11/11/2008] [Accepted: 03/03/2009] [Indexed: 12/25/2022]
Abstract
BACKGROUND In the past decade or so, a range of technologies have emerged that have shown promise in increasing our understanding of disease processes and progression. These advances are referred to as the "omics" technologies; genomics, transcriptomics, and proteomics. More recently, another "omics" approach has come to the fore: metabonomics, and this technology has the potential for significant clinical impact. Metabonomics refers to the analysis of the metabolome, that is, the metabolic profile of a system. The advantage of studying the metabolome is that the end points of biological events are elucidated. RESULTS Although still in its infancy, the metabonomics approach has shown immense promise in areas as diverse as toxicology studies to the discovery of biomarkers of disease. It has also been applied to studies of both renal and hepatic transplants. Metabolome analysis may be conducted on a variety of biological fluids and tissue types and may utilize a number of different technology platforms, mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy being the most popular. In this review, we cover the background to the evolution of metabonomics and its applications with particular emphasis on clinical applications. CONCLUSIONS We conclude with the suggestion that metabonomics offers a platform for further biomarker development, drug development, and in the field of medicine.
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Affiliation(s)
- Paul Goldsmith
- Hepatopancreatobiliary and Transplant Unit, St. James's University Hospital, Leeds, United Kingdom.
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Klawitter J, Bendrick-Peart J, Rudolph B, Beckey V, Klawitter J, Haschke M, Rivard C, Chan L, Leibfritz D, Christians U, Schmitz V. Urine metabolites reflect time-dependent effects of cyclosporine and sirolimus on rat kidney function. Chem Res Toxicol 2009; 22:118-28. [PMID: 19099400 PMCID: PMC2646011 DOI: 10.1021/tx800253x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The clinical use of the immunosuppressant calcineurin inhibitor cyclosporine is limited by its nephrotoxicity. This is enhanced when combined with the immunosuppressive mTOR inhibitor sirolimus. Nephrotoxicity of both drugs is not yet fully understood. The goal was to gain more detailed mechanistic insights into the time-dependent effects of cyclosporine and sirolimus on the rat kidney by using a comprehensive approach including metabolic profiling in urine ((1)H NMR spectroscopy), kidney histology, kidney function parameters in plasma, measurement of glomerular filtration rates, the oxidative stress marker 15-F(2t)-isoprostane in urine, and immunosuppressant concentrations in blood and kidney. Male Wistar rats were treated with vehicle (controls), cyclosporine (10/25 mg/kg/day), and/or sirolimus (1 mg/kg/day) by oral gavage once daily for 6 and 28 days. Twenty-eight day treatment led to a decrease of glomerular filtration rates (cyclosporine, -59%; sirolimus, -25%). These were further decreased when both drugs were combined (-86%). Histology revealed tubular damage after treatment with cyclosporine, which was enhanced when sirolimus was added. No other part of the kidney was affected. (1)H NMR spectroscopy analysis of urine (day 6) revealed time-dependent changes of 2-oxoglutarate, citrate, and succinate concentrations. In combination with increased urine isoprostane concentrations, these changes indicated oxidative stress. After 28 days of cyclosporine treatment, urine metabonomics shifted to patterns typical for proximal tubular damage with reduction of Krebs cycle intermediates and trimethylamine-N-oxide concentrations, whereas acetate, lactate, trimethylamine, and glucose concentrations increased. Again, sirolimus enhanced these negative effects. Our results indicate that cyclosporine and/or sirolimus induce damage of the renal tubular system. This is reflected by urine metabolite patterns, which seem to be more sensitive than currently used clinical kidney function markers such as creatinine concentrations in serum. Metabolic profiling in urine may provide the basis for the development of toxicodynamic monitoring strategies for immunosuppressant nephrotoxicity.
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Affiliation(s)
- Jost Klawitter
- Departments of Anesthesiology and Nephrology, University of Colorado, Denver, Colorado, USA
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Psihogios NG, Gazi IF, Elisaf MS, Seferiadis KI, Bairaktari ET. Gender-related and age-related urinalysis of healthy subjects by NMR-based metabonomics. NMR IN BIOMEDICINE 2008; 21:195-207. [PMID: 17474139 DOI: 10.1002/nbm.1176] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
NMR-based metabonomic analysis is a well-established approach to characterizing healthy and diseased states. The aim of this study was to investigate inter-individual variability in the metabolic urinary profile of a healthy Greek population, not subjected to strict dietary limitations, by NMR-based metabonomics. The overall metabonomic urinalysis showed a homogeneous distribution among the population. The metabolic profile was examined in relation to gender and age, and reference intervals of major metabolites were determined. Multivariate data analysis led to the construction of two robust models that were able to predict the class membership of the subjects studied according to their gender and age. The most influential low molecular weight metabolites responsible for the differences in gender groups were citrate, creatinine, trimethylamine N-oxide, glycine, creatine and taurine, and for the differences in age groups they were citrate, creatinine, trimethylamine N-oxide and an unidentified metabolite (delta 3.78).
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Affiliation(s)
- Nikolaos G Psihogios
- Laboratory of Clinical Chemistry, Medical School, University of Ioannina, Ioannina, Greece
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Dinis-Oliveira RJ, Duarte JA, Sánchez-Navarro A, Remião F, Bastos ML, Carvalho F. Paraquat poisonings: mechanisms of lung toxicity, clinical features, and treatment. Crit Rev Toxicol 2008; 38:13-71. [PMID: 18161502 DOI: 10.1080/10408440701669959] [Citation(s) in RCA: 546] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Paraquat dichloride (methyl viologen; PQ) is an effective and widely used herbicide that has a proven safety record when appropriately applied to eliminate weeds. However, over the last decades, there have been numerous fatalities, mainly caused by accidental or voluntary ingestion. PQ poisoning is an extremely frustrating condition to manage clinically, due to the elevated morbidity and mortality observed so far and due to the lack of effective treatments to be used in humans. PQ mainly accumulates in the lung (pulmonary concentrations can be 6 to 10 times higher than those in the plasma), where it is retained even when blood levels start to decrease. The pulmonary effects can be explained by the participation of the polyamine transport system abundantly expressed in the membrane of alveolar cells type I, II, and Clara cells. Further downstream at the toxicodynamic level, the main molecular mechanism of PQ toxicity is based on redox cycling and intracellular oxidative stress generation. With this review we aimed to collect and describe the most pertinent and significant findings published in established scientific publications since the discovery of PQ, focusing on the most recent developments related to PQ lung toxicity and their relevance to the treatment of human poisonings. Considerable space is also dedicated to techniques for prognosis prediction, since these could allow development of rigorous clinical protocols that may produce comparable data for the evaluation of proposed therapies.
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Affiliation(s)
- R J Dinis-Oliveira
- REQUIMTE, Departamento de Toxicologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal.
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Bairaktari E, Seferiadis K, Liamis G, Psihogios N, Tsolas O, Elisaf M. Rhabdomyolysis-related Renal Tubular Damage Studied by Proton Nuclear Magnetic Resonance Spectroscopy of Urine. Clin Chem 2002. [DOI: 10.1093/clinchem/48.7.1106] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | | | - George Liamis
- Department of Internal Medicine, University Hospital, University of Ioannina, Medical School, 455 00 Ioannina, Greece
| | | | | | - Moses Elisaf
- Department of Internal Medicine, University Hospital, University of Ioannina, Medical School, 455 00 Ioannina, Greece
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Nicholson JK, Connelly J, Lindon JC, Holmes E. Metabonomics: a platform for studying drug toxicity and gene function. Nat Rev Drug Discov 2002; 1:153-61. [PMID: 12120097 DOI: 10.1038/nrd728] [Citation(s) in RCA: 1346] [Impact Index Per Article: 61.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The later that a molecule or molecular class is lost from the drug development pipeline, the higher the financial cost. Minimizing attrition is therefore one of the most important aims of a pharmaceutical discovery programme. Novel technologies that increase the probability of making the right choice early save resources, and promote safety, efficacy and profitability. Metabonomics is a systems approach for studying in vivo metabolic profiles, which promises to provide information on drug toxicity, disease processes and gene function at several stages in the discovery-and-development process.
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Affiliation(s)
- Jeremy K Nicholson
- Biological Chemistry Section, Biomedical Sciences Division, Faculty of Medicine, Imperial College of Science, Technology and Medicine, South Kensington, London SW7 2AZ, UK.
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