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Ugonabo O, Udoh UAS, Rajan PK, Reeves H, Arcand C, Nakafuku Y, Joshi T, Finley R, Pierre SV, Sanabria JR. The Current Status of the Liver Liquid Biopsy in MASH Related HCC: Overview and Future Directions. Biomolecules 2023; 13:1369. [PMID: 37759769 PMCID: PMC10526956 DOI: 10.3390/biom13091369] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/03/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Metabolic dysfunction-associated steatohepatitis (MASH) is one of the major risk factors for chronic liver disease and hepatocellular carcinoma (HCC). The incidence of MASH in Western countries continues to rise, driving HCC as the third cause of cancer-related death worldwide. HCC has become a major global health challenge, partly from the obesity epidemic promoting metabolic cellular disturbances but also from the paucity of biomarkers for its early detection. Over 50% of HCC cases are clinically present at a late stage, where curative measures are no longer beneficial. Currently, there is a paucity of both specific and sensitive biological markers for the early-stage detection of HCC. The search for biological markers in the diagnosis of early HCC in high-risk populations is intense. We described the potential role of surrogates for a liver biopsy in the screening and monitoring of patients at risk for nesting HCC.
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Affiliation(s)
- Onyinye Ugonabo
- Department of Medicine, Marshall University School of Medicine, Marshall University, Huntington, WV 25701, USA; (O.U.); (T.J.)
| | - Utibe-Abasi Sunday Udoh
- Marshall Institute for Interdisciplinary Research, Marshall University School of Medicine, Huntington, WV 25703, USA; (U.-A.S.U.); (P.K.R.); (Y.N.); (S.V.P.)
- Department of Surgery, Marshall University School of Medicine, Marshall University, Huntington, WV 25701, USA; (H.R.); (C.A.); (R.F.)
| | - Pradeep Kumar Rajan
- Marshall Institute for Interdisciplinary Research, Marshall University School of Medicine, Huntington, WV 25703, USA; (U.-A.S.U.); (P.K.R.); (Y.N.); (S.V.P.)
- Department of Surgery, Marshall University School of Medicine, Marshall University, Huntington, WV 25701, USA; (H.R.); (C.A.); (R.F.)
| | - Heather Reeves
- Department of Surgery, Marshall University School of Medicine, Marshall University, Huntington, WV 25701, USA; (H.R.); (C.A.); (R.F.)
| | - Christina Arcand
- Department of Surgery, Marshall University School of Medicine, Marshall University, Huntington, WV 25701, USA; (H.R.); (C.A.); (R.F.)
| | - Yuto Nakafuku
- Marshall Institute for Interdisciplinary Research, Marshall University School of Medicine, Huntington, WV 25703, USA; (U.-A.S.U.); (P.K.R.); (Y.N.); (S.V.P.)
- Department of Surgery, Marshall University School of Medicine, Marshall University, Huntington, WV 25701, USA; (H.R.); (C.A.); (R.F.)
| | - Tejas Joshi
- Department of Medicine, Marshall University School of Medicine, Marshall University, Huntington, WV 25701, USA; (O.U.); (T.J.)
| | - Rob Finley
- Department of Surgery, Marshall University School of Medicine, Marshall University, Huntington, WV 25701, USA; (H.R.); (C.A.); (R.F.)
| | - Sandrine V. Pierre
- Marshall Institute for Interdisciplinary Research, Marshall University School of Medicine, Huntington, WV 25703, USA; (U.-A.S.U.); (P.K.R.); (Y.N.); (S.V.P.)
| | - Juan Ramon Sanabria
- Marshall Institute for Interdisciplinary Research, Marshall University School of Medicine, Huntington, WV 25703, USA; (U.-A.S.U.); (P.K.R.); (Y.N.); (S.V.P.)
- Department of Surgery, Marshall University School of Medicine, Marshall University, Huntington, WV 25701, USA; (H.R.); (C.A.); (R.F.)
- Department of Nutrition and Metabolomic Core Facility, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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Sanclemente JL, Rivera-Velez SM, Horohov DW, Dasgupta N, Sanz MG. Plasma metabolome of healthy and Rhodococcus equi-infected foals over time. Equine Vet J 2023; 55:831-842. [PMID: 36273247 DOI: 10.1111/evj.13894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 09/25/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Foals that develop pulmonary ultrasonographic lesions on Rhodococcus equi (R. equi) endemic farms are treated with antibiotics because those at risk of developing clinical pneumonia (~20%) cannot be recognised early. Candidate biomarkers identified using metabolomics may aid targeted treatment strategies against R. equi. OBJECTIVES (1) To describe how foal ageing affects their plasma metabolome (birth to 8 weeks) and (2) to establish the effects that experimental infection with Rhodococcus equi (R. equi) has on foal metabolome. STUDY DESIGN Experimental study. METHODS Nine healthy newborn foals were experimentally infected with R. equi as described in a previous study. Foals were treated with oral antibiotics if they developed clinical pneumonia (n = 4, clinical group) or remained untreated if they showed no signs of disease (n = 5, subclinical group). A group of unchallenged foals (n = 4) was also included in the study. By the end of the study period (8 weeks), all foals were free of disease. This status was confirmed with transtracheal wash fluid evaluation and culture as well as thoracic ultrasonography. Plasma metabolomics was determined by GC-MS weekly for the study duration (8 weeks). RESULTS Foals' plasma metabolome was altered by ageing (birth to 8 weeks) and experimental infection with R. equi as demonstrated using multivariate statistical analysis. The intensities of 25 and 28 metabolites were altered by ageing and infection (p < 0.05) respectively. Furthermore, 20 metabolites changed by more than 2-fold between clinical and subclinical groups. MAIN LIMITATIONS The number of foals is limited. Foals were experimentally infected with R. equi. CONCLUSIONS Ageing and R. equi infection induced changes in the plasma metabolome of foals. These results provide an initial description of foal's plasma metabolome and serve as background for future identification of R. equi pneumonia biomarkers.
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Affiliation(s)
- Jorge L Sanclemente
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Sol M Rivera-Velez
- Molecular Determinants Core, Johns Hopkins All Children's Hospital, St Petersburg, Florida, USA
| | - David W Horohov
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Clinical Sciences, University of Kentucky, Lexington, Kentucky, USA
| | - Nairanjana Dasgupta
- Department of Mathematics and Statistics, College of Arts and Sciences, Washington State University, Pullman, Washington, USA
| | - Macarena G Sanz
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
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Young T, Gale SL, Ragg NLC, Sander SG, Burritt DJ, Benedict B, Le DV, Villas-Bôas SG, Alfaro AC. Metabolic Regulation of Copper Toxicity during Marine Mussel Embryogenesis. Metabolites 2023; 13:838. [PMID: 37512545 PMCID: PMC10385052 DOI: 10.3390/metabo13070838] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/19/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
The development of new tools for assessing the health of cultured shellfish larvae is crucial for aquaculture industries to develop and refine hatchery methodologies. We established a large-volume ecotoxicology/health stressor trial, exposing mussel (Perna canaliculus) embryos to copper in the presence of ethylenediaminetetraacetic acid (EDTA). GC/MS-based metabolomics was applied to identify potential biomarkers for monitoring embryonic/larval health and to characterise mechanisms of metal toxicity. Cellular viability, developmental abnormalities, larval behaviour, mortality, and a targeted analysis of proteins involved in the regulation of reactive oxygen species were simultaneously evaluated to provide a complementary framework for interpretative purposes and authenticate the metabolomics data. Trace metal analysis and speciation modelling verified EDTA as an effective copper chelator. Toxicity thresholds for P. canaliculus were low, with 10% developmental abnormalities in D-stage larvae being recorded upon exposure to 1.10 μg·L-1 bioavailable copper for 66 h. Sublethal levels of bioavailable copper (0.04 and 1.10 μg·L-1) caused coordinated fluctuations in metabolite profiles, which were dependent on development stage, treatment level, and exposure duration. Larvae appeared to successfully employ various mechanisms involving the biosynthesis of antioxidants and a restructuring of energy-related metabolism to alleviate the toxic effects of copper on cells and developing tissues. These results suggest that regulation of trace metal-induced toxicity is tightly linked with metabolism during the early ontogenic development of marine mussels. Lethal-level bioavailable copper (50.3 μg·L-1) caused severe metabolic dysregulation after 3 h of exposure, which worsened with time, substantially delayed embryonic development, induced critical oxidative damage, initiated the apoptotic pathway, and resulted in cell/organism death shortly after 18 h of exposure. Metabolite profiling is a useful approach to (1) assess the health status of marine invertebrate embryos and larvae, (2) detect early warning biomarkers for trace metal contamination, and (3) identify novel regulatory mechanisms of copper-induced toxicity.
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Affiliation(s)
- Tim Young
- Aquaculture Biotechnology Research Group, Department of Environmental Science, School of Science, Auckland University of Technology, Auckland 1010, New Zealand
- Centre for Biomedical and Chemical Sciences, School of Science, Auckland University of Technology, Auckland 1010, New Zealand
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | | | | | - Sylvia G. Sander
- Department of Chemistry, University of Otago, P.O. Box 56, Dunedin 9010, New Zealand
- Marine Mineral Resources Group, Research Division 4: Dynamics of the Ocean Floor, Magmatic and Hydrothermal Systems, GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstr. 1-3, 24148 Kiel, Germany
| | - David J. Burritt
- Department of Botany, University of Otago, 464 Great King St, Dunedin 9016, New Zealand
| | - Billy Benedict
- Department of Chemistry, University of Otago, P.O. Box 56, Dunedin 9010, New Zealand
| | - Dung V. Le
- Aquaculture Biotechnology Research Group, Department of Environmental Science, School of Science, Auckland University of Technology, Auckland 1010, New Zealand
- Faculty of Fisheries, Vietnam National University of Agriculture, Hanoi 000084, Vietnam
| | - Silas G. Villas-Bôas
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Andrea C. Alfaro
- Aquaculture Biotechnology Research Group, Department of Environmental Science, School of Science, Auckland University of Technology, Auckland 1010, New Zealand
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Fu J, Zhang Y, Liu J, Lian X, Tang J, Zhu F. Pharmacometabonomics: data processing and statistical analysis. Brief Bioinform 2021; 22:6236068. [PMID: 33866355 DOI: 10.1093/bib/bbab138] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/09/2021] [Accepted: 03/23/2021] [Indexed: 12/14/2022] Open
Abstract
Individual variations in drug efficacy, side effects and adverse drug reactions are still challenging that cannot be ignored in drug research and development. The aim of pharmacometabonomics is to better understand the pharmacokinetic properties of drugs and monitor the drug effects on specific metabolic pathways. Here, we systematically reviewed the recent technological advances in pharmacometabonomics for better understanding the pathophysiological mechanisms of diseases as well as the metabolic effects of drugs on bodies. First, the advantages and disadvantages of all mainstream analytical techniques were compared. Second, many data processing strategies including filtering, missing value imputation, quality control-based correction, transformation, normalization together with the methods implemented in each step were discussed. Third, various feature selection and feature extraction algorithms commonly applied in pharmacometabonomics were described. Finally, the databases that facilitate current pharmacometabonomics were collected and discussed. All in all, this review provided guidance for researchers engaged in pharmacometabonomics and metabolomics, and it would promote the wide application of metabolomics in drug research and personalized medicine.
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Affiliation(s)
- Jianbo Fu
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Ying Zhang
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Jin Liu
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Xichen Lian
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Jing Tang
- Department of Bioinformatics in Chongqing Medical University, China
| | - Feng Zhu
- College of Pharmaceutical Sciences in Zhejiang University, China
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5
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Rubio T, Felipo V, Tarazona S, Pastorelli R, Escudero-García D, Tosca J, Urios A, Conesa A, Montoliu C. Multi-omic analysis unveils biological pathways in peripheral immune system associated to minimal hepatic encephalopathy appearance in cirrhotic patients. Sci Rep 2021; 11:1907. [PMID: 33479266 PMCID: PMC7820002 DOI: 10.1038/s41598-020-80941-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/23/2020] [Indexed: 01/29/2023] Open
Abstract
Patients with liver cirrhosis may develop minimal hepatic encephalopathy (MHE) which affects their quality of life and life span. It has been proposed that a shift in peripheral inflammation triggers the appearance of MHE. However, the mechanisms involved in this immune system shift remain unknown. In this work we studied the broad molecular changes involved in the induction of MHE with the goal of identifying (1) altered genes and pathways in peripheral blood cells associated to the appearance of MHE, (2) serum metabolites and cytokines with modified levels in MHE patients and (3) MHE-regulated immune response processes related to changes in specific serum molecules. We adopted a multi-omic approach to profile the transcriptome, metabolome and a panel of cytokines of blood samples taken from cirrhotic patients with or without MHE. Transcriptomic analysis supports the hypothesis of alternations in the Th1/Th2 and Th17 lymphocytes cell populations as major drivers of MHE. Cluster analysis of serum molecules resulted in six groups of chemically similar compounds, suggesting that functional modules operate during the induction of MHE. Finally, the multi-omic integrative analysis suggested a relationship between cytokines CCL20, CX3CL1, CXCL13, IL-15, IL-22 and IL-6 with alteration in chemotaxis, as well as a link between long-chain unsaturated phospholipids and the increased fatty acid transport and prostaglandin production. We found altered immune pathways that may collectively contribute to the mild cognitive impairment phenotype in MHE. Our approach is able to combine extracellular and intracellular information, opening new insights to the understanding of the disease.
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Affiliation(s)
- Teresa Rubio
- Laboratory of Neurobiology, Centro Investigación Príncipe Felipe, Valencia, Spain
| | - Vicente Felipo
- Laboratory of Neurobiology, Centro Investigación Príncipe Felipe, Valencia, Spain
| | - Sonia Tarazona
- Departamento de Estadística e Investigación Operativa Aplicadas y Calidad, Universitat Politècnica de València, Valencia, Spain
| | - Roberta Pastorelli
- Protein and Metabolite Biomarkers Unit, Laboratory of Mass Spectrometry, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Desamparados Escudero-García
- Unidad de Digestivo, Hospital Clínico de Valencia, Departamento Medicina, Universidad de Valencia, Valencia, Spain
| | - Joan Tosca
- Unidad de Digestivo, Hospital Clínico de Valencia, Valencia, Spain
| | - Amparo Urios
- Laboratory of Neurobiology, Centro Investigación Príncipe Felipe, Valencia, Spain
- Neurological Impairment Laboratory, Fundación Investigación Hospital Clínico Universitario de Valencia, Instituto de Investigación Sanitaria-INCLIVA, Valencia, Spain
| | - Ana Conesa
- Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, Genetics Institute, University of Florida, Gainesville, USA.
| | - Carmina Montoliu
- Neurological Impairment Laboratory, Fundación Investigación Hospital Clínico Universitario de Valencia, Instituto de Investigación Sanitaria-INCLIVA, Valencia, Spain
- Departamento de Patología, Facultad de Medicina, Universidad de Valencia, Valencia, Spain
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6
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Quantitative proteomics to study aging in rabbit liver. Mech Ageing Dev 2020; 187:111227. [PMID: 32126221 DOI: 10.1016/j.mad.2020.111227] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 01/24/2020] [Accepted: 02/27/2020] [Indexed: 12/23/2022]
Abstract
Aging globally effects cellular and organismal metabolism across a range of mammalian species, including humans and rabbits. Rabbits (Oryctolagus cuniculus are an attractive model system of aging due to their genetic similarity with humans and their short lifespans. This model can be used to understand metabolic changes in aging especially in major organs such as liver where we detected pronounced variations in fat metabolism, mitochondrial dysfunction, and protein degradation. Such changes in the liver are consistent across several mammalian species however in rabbits the downstream effects of these changes have not yet been explored. We have applied proteomics to study changes in the liver proteins from young, middle, and old age rabbits using a multiplexing cPILOT strategy. This resulted in the identification of 2,586 liver proteins, among which 45 proteins had significant p < 0.05) changes with aging. Seven proteins were differentially-expressed at all ages and include fatty acid binding protein, aldehyde dehydrogenase, enoyl-CoA hydratase, 3-hydroxyacyl CoA dehydrogenase, apolipoprotein C3, peroxisomal sarcosine oxidase, adhesion G-protein coupled receptor, and glutamate ionotropic receptor kinate. Insights to how alterations in metabolism affect protein expression in liver have been gained and demonstrate the utility of rabbit as a model of aging.
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7
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Li B, Tang J, Yang Q, Cui X, Li S, Chen S, Cao Q, Xue W, Chen N, Zhu F. Performance Evaluation and Online Realization of Data-driven Normalization Methods Used in LC/MS based Untargeted Metabolomics Analysis. Sci Rep 2016; 6:38881. [PMID: 27958387 PMCID: PMC5153651 DOI: 10.1038/srep38881] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 11/15/2016] [Indexed: 02/06/2023] Open
Abstract
In untargeted metabolomics analysis, several factors (e.g., unwanted experimental & biological variations and technical errors) may hamper the identification of differential metabolic features, which requires the data-driven normalization approaches before feature selection. So far, ≥16 normalization methods have been widely applied for processing the LC/MS based metabolomics data. However, the performance and the sample size dependence of those methods have not yet been exhaustively compared and no online tool for comparatively and comprehensively evaluating the performance of all 16 normalization methods has been provided. In this study, a comprehensive comparison on these methods was conducted. As a result, 16 methods were categorized into three groups based on their normalization performances across various sample sizes. The VSN, the Log Transformation and the PQN were identified as methods of the best normalization performance, while the Contrast consistently underperformed across all sub-datasets of different benchmark data. Moreover, an interactive web tool comprehensively evaluating the performance of 16 methods specifically for normalizing LC/MS based metabolomics data was constructed and hosted at http://server.idrb.cqu.edu.cn/MetaPre/. In summary, this study could serve as a useful guidance to the selection of suitable normalization methods in analyzing the LC/MS based metabolomics data.
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Affiliation(s)
- Bo Li
- Innovative Drug Research and Bioinformatics Group, Innovative Drug Research Centre and School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Jing Tang
- Innovative Drug Research and Bioinformatics Group, Innovative Drug Research Centre and School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Qingxia Yang
- Innovative Drug Research and Bioinformatics Group, Innovative Drug Research Centre and School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Xuejiao Cui
- Innovative Drug Research and Bioinformatics Group, Innovative Drug Research Centre and School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Shuang Li
- Innovative Drug Research and Bioinformatics Group, Innovative Drug Research Centre and School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Sijie Chen
- College of Mathematics and Statistics, Chongqing University, Chongqing 401331, China
| | - Quanxing Cao
- Innovative Drug Research and Bioinformatics Group, Innovative Drug Research Centre and School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Weiwei Xue
- Innovative Drug Research and Bioinformatics Group, Innovative Drug Research Centre and School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Na Chen
- Innovative Drug Research and Bioinformatics Group, Innovative Drug Research Centre and School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Feng Zhu
- Innovative Drug Research and Bioinformatics Group, Innovative Drug Research Centre and School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
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Sanabria JR, Kombu RS, Zhang GF, Sandlers Y, Ai J, Ibarra RA, Abbas R, Goyal K, Brunengraber H. Glutathione species and metabolomic prints in subjects with liver disease as biological markers for the detection of hepatocellular carcinoma. HPB (Oxford) 2016; 18:979-990. [PMID: 28340971 PMCID: PMC5144552 DOI: 10.1016/j.hpb.2016.09.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 09/04/2016] [Accepted: 09/14/2016] [Indexed: 02/06/2023]
Abstract
BACKGROUND The incidence of liver disease is increasing in USA. Animal models had shown glutathione species in plasma reflects liver glutathione state and it could be a surrogate for the detection of hepatocellular carcinoma (HCC). METHODS The present study aimed to translate methods to the human and to explore the role of glutathione/metabolic prints in the progression of liver dysfunction and in the detection of HCC. Treated plasma from healthy subjects (n = 20), patients with liver disease (ESLD, n = 99) and patients after transplantation (LTx, n = 7) were analyzed by GC- or LC/MS. Glutathione labeling profile was measured by isotopomer analyzes of 2H2O enriched plasma. Principal Component Analyzes (PCA) were used to determined metabolic prints. RESULTS There was a significant difference in glutathione/metabolic profiles from patients with ESLD vs healthy subjects and patients after LTx. Similar significant differences were noted on patients with ESLD when stratified by the MELD score. PCA analyses showed myristic acid, citric acid, succinic acid, l-methionine, d-threitol, fumaric acid, pipecolic acid, isoleucine, hydroxy-butyrate and glycolic, steraric and hexanoic acids were discriminative metabolites for ESLD-HCC+ vs ESLD-HCC- subject status. CONCLUSIONS Glutathione species and metabolic prints defined liver disease severity and may serve as surrogate for the detection of HCC in patients with established cirrhosis.
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Affiliation(s)
- Juan R. Sanabria
- Department of Surgery, Case Western Reserve University School of Medicine, Cleveland, OH, USA,Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, OH, USA,Department of Preventive Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA,Department of Surgery and Research, Cancer Treatment Centers of America, Chicago, IL, USA,Department of Biostatistics, Cancer Treatment Centers of America, Chicago, IL, USA,Correspondence Juan R. Sanabria, Department of Surgery at Marshall University or Department of Proteomics and Metabolmics Core Facilities at Case Western Reserve University, Cleveland, OH, USA.Department of Surgery at Marshall University or Department of Proteomics and Metabolmics Core Facilities at Case Western Reserve UniversityClevelandOHUSA
| | - Rajan S. Kombu
- Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Guo-Fang Zhang
- Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Yana Sandlers
- Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Jizhou Ai
- Department of Surgery and Research, Cancer Treatment Centers of America, Chicago, IL, USA,Department of Biostatistics, Cancer Treatment Centers of America, Chicago, IL, USA
| | - Rafael A. Ibarra
- Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Rime Abbas
- Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Kush Goyal
- Department of Surgery, Case Western Reserve University School of Medicine, Cleveland, OH, USA,Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Henri Brunengraber
- Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, OH, USA,Department of Metabolomics and Proteomics Core Facilities, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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Dessì A, Murgia A, Agostino R, Pattumelli MG, Schirru A, Scano P, Fanos V, Caboni P. Exploring the Role of Different Neonatal Nutrition Regimens during the First Week of Life by Urinary GC-MS Metabolomics. Int J Mol Sci 2016; 17:265. [PMID: 26907266 PMCID: PMC4783994 DOI: 10.3390/ijms17020265] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/04/2016] [Accepted: 02/16/2016] [Indexed: 12/17/2022] Open
Abstract
In this study, a gas-chromatography mass spectrometry (GC-MS) metabolomics study was applied to examine urine metabolite profiles of different classes of neonates under different nutrition regimens. The study population included 35 neonates, exclusively either breastfed or formula milk fed, in a seven-day timeframe. Urine samples were collected from intrauterine growth restriction (IUGR), large for gestational age (LGA), and appropriate gestational age (AGA) neonates. At birth, IUGR and LGA neonates showed similarities in their urine metabolite profiles that differed from AGA. When neonates started milk feeding, their metabolite excretion profile was strongly characterized by the different diet regimens. After three days of formula milk nutrition, urine had higher levels of glucose, galactose, glycine and myo-inositol, while up-regulated aconitic acid, aminomalonic acid and adipic acid were found in breast milk fed neonates. At seven days, neonates fed with formula milk shared higher levels of pseudouridine with IUGR and LGA at birth. Breastfed neonates shared up-regulated pyroglutamic acid, citric acid, and homoserine, with AGA at birth. The role of most important metabolites is herein discussed.
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Affiliation(s)
- Angelica Dessì
- Neonatal Intensive Care Unit, Puericulture Institute and Neonatal Section, Azienda Ospedaliera Universitaria, University of Cagliari, 09042 Monserrato, Italy.
| | - Antonio Murgia
- Department of Life and Environmental Sciences, University of Cagliari, Via Ospedale 72, 09124 Cagliari, Italy.
| | - Rocco Agostino
- Neonatal Intensive Unit and Neonatal Pathology, "S. Giovanni Calibita" Hospital, Fatebenefratelli Isola Tiberina, 00186 Rome, Italy.
| | - Maria Grazia Pattumelli
- Neonatal Intensive Unit and Neonatal Pathology, "S. Giovanni Calibita" Hospital, Fatebenefratelli Isola Tiberina, 00186 Rome, Italy.
| | - Andrea Schirru
- Neonatal Intensive Care Unit, Puericulture Institute and Neonatal Section, Azienda Ospedaliera Universitaria, University of Cagliari, 09042 Monserrato, Italy.
| | - Paola Scano
- Department of Chemical and Geological Sciences, University of Cagliari, 09042 Monserrato, Italy.
| | - Vassilios Fanos
- Neonatal Intensive Care Unit, Puericulture Institute and Neonatal Section, Azienda Ospedaliera Universitaria, University of Cagliari, 09042 Monserrato, Italy.
| | - Pierluigi Caboni
- Department of Life and Environmental Sciences, University of Cagliari, Via Ospedale 72, 09124 Cagliari, Italy.
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Aravalli RN, Cressman ENK. Relevance of Rabbit VX2 Tumor Model for Studies on Human Hepatocellular Carcinoma: A MicroRNA-Based Study. J Clin Med 2015; 4:1989-97. [PMID: 26690234 PMCID: PMC4693154 DOI: 10.3390/jcm4121954] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 11/13/2015] [Accepted: 11/27/2015] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs are small (~22 nt), noncoding RNA molecules that have critical cellular functions in proliferation, differentiation, angiogenesis and apoptosis. miRNA expression profiling has been used to create signatures of solid tumors and, in many cases, it has been shown to correlate with the severity of the disease. The rabbit VX2 tumor model has been used widely to study a number of human cancers. Our objective in this study is to generate an miRNA signature of the VX2 tumor and to identify miRNAs that are highly expressed in this aggressive tumor. In this study, we performed miRNA profiling of the rabbit VX2 tumor using a microarray that has probes for 1292 unique miRNAs. Their expression in tumor samples was quantified and analyzed. We found that 35 miRNAs were significantly up-regulated in the VX2 tumor. Among these, 13 human miRNAs and eight members of the let-7 family were previously identified in cancers. In addition, we show that the expression of three miRNAs (miR-923, miR-1275, and miR-1308) is novel for the rabbit VX2 tumor, and their expression was not previously shown to be associated with any type of cancer. For the first time, we show the miRNA signature profile for a solid tumor in a rabbit model. miRNAs highly expressed in the VX2 tumor may serve as novel candidates for molecular biomarkers and as potential drug targets.
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Affiliation(s)
- Rajagopal N Aravalli
- Department of Radiology, University of Minnesota Medical School, Minneapolis, MN 55455, USA.
| | - Erik N K Cressman
- Department of Interventional Radiology, M.D. Anderson Cancer Center, Houston, TX 77030, USA.
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