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Lu Q, Yu A, Pu J, Chen D, Zhong Y, Bai D, Yang L. Post-stroke cognitive impairment: exploring molecular mechanisms and omics biomarkers for early identification and intervention. Front Mol Neurosci 2024; 17:1375973. [PMID: 38845616 PMCID: PMC11153683 DOI: 10.3389/fnmol.2024.1375973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 05/08/2024] [Indexed: 06/09/2024] Open
Abstract
Post-stroke cognitive impairment (PSCI) is a major stroke consequence that has a severe impact on patients' quality of life and survival rate. For this reason, it is especially crucial to identify and intervene early in high-risk groups during the acute phase of stroke. Currently, there are no reliable and efficient techniques for the early diagnosis, appropriate evaluation, or prognostication of PSCI. Instead, plenty of biomarkers in stroke patients have progressively been linked to cognitive impairment in recent years. High-throughput omics techniques that generate large amounts of data and process it to a high quality have been used to screen and identify biomarkers of PSCI in order to investigate the molecular mechanisms of the disease. These techniques include metabolomics, which explores dynamic changes in the organism, gut microbiomics, which studies host-microbe interactions, genomics, which elucidates deeper disease mechanisms, transcriptomics and proteomics, which describe gene expression and regulation. We looked through electronic databases like PubMed, the Cochrane Library, Embase, Web of Science, and common databases for each omics to find biomarkers that might be connected to the pathophysiology of PSCI. As all, we found 34 studies: 14 in the field of metabolomics, 5 in the field of gut microbiomics, 5 in the field of genomics, 4 in the field of transcriptomics, and 7 in the field of proteomics. We discovered that neuroinflammation, oxidative stress, and atherosclerosis may be the primary causes of PSCI development, and that metabolomics may play a role in the molecular mechanisms of PSCI. In this study, we summarized the existing issues across omics technologies and discuss the latest discoveries of PSCI biomarkers in the context of omics, with the goal of investigating the molecular causes of post-stroke cognitive impairment. We also discuss the potential therapeutic utility of omics platforms for PSCI mechanisms, diagnosis, and intervention in order to promote the area's advancement towards precision PSCI treatment.
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Affiliation(s)
- Qiuyi Lu
- Department of Rehabilitation, The First Affiliated Hospital of Chongqing Medical University, Chonging, China
| | - Anqi Yu
- Department of Rehabilitation, The First Affiliated Hospital of Chongqing Medical University, Chonging, China
| | - Juncai Pu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chonging, China
| | - Dawei Chen
- Department of Rehabilitation, The First Affiliated Hospital of Chongqing Medical University, Chonging, China
| | - Yujie Zhong
- Department of Rehabilitation, The First Affiliated Hospital of Chongqing Medical University, Chonging, China
| | - Dingqun Bai
- Department of Rehabilitation, The First Affiliated Hospital of Chongqing Medical University, Chonging, China
| | - Lining Yang
- Department of Rehabilitation, The First Affiliated Hospital of Chongqing Medical University, Chonging, China
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2
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Tao Y, Yang Y, Zhu F, Wu M, Kong X, Wang P. Serum metabolome profiling, network pharmacology analysis, and experimental validation of Anoectochilus roxburghii in the treatment of carbon tetrachloride-induced liver injury. Biomed Chromatogr 2023; 37:e5706. [PMID: 37491783 DOI: 10.1002/bmc.5706] [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: 05/08/2023] [Revised: 06/29/2023] [Accepted: 07/05/2023] [Indexed: 07/27/2023]
Abstract
Anoectochilus roxburghii (Wall.) Lindl. (AR) has been traditionally used to treat inflammatory diseases, but the specific mechanism underlying its hepatoprotective effect remains unclear. Here, serum metabolomics and network pharmacology were employed to investigate the hepatoprotective mechanism of AR. Thirty male Sprague-Dawley rats were divided into six groups: normal, model, positive, high-dose AR, middle-dose AR, and low-dose AR. The positive group received therapeutic doses of silibinin, whereas the AR-treated groups received different doses of AR extract once daily. After 10 days of intragastric administration, the rats were intraperitoneally injected with a 50% CCl4 olive oil solution (2 mL/kg) to induce liver injury. Serum and liver samples were obtained, and GC-MS was utilized to monitor changes in serum metabolome. The levels of alkaline phosphatase, aspartate aminotransferase, alanine aminotransferase, and hydrooxproline in serum significantly increased in the model group. On the contrary, AR-treated group showed a significant decrease in the levels of alkaline phosphatase, aspartate aminotransferase, alanine aminotransferase, and hydrooxproline. Histopathological observation also revealed that the extent of liver injury was alleviated in the AR-treated group. Fifty differential metabolites were identified, suggesting that AR may prevent liver damage by modulating carbohydrate and amino acid metabolism.
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Affiliation(s)
- Yi Tao
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Ying Yang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Fei Zhu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Mei Wu
- Jinhua Academy of Agricultural Sciences, Jinhua, China
| | - Xiangjun Kong
- Jinhua Academy of Agricultural Sciences, Jinhua, China
| | - Ping Wang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
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3
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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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4
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Li W, Shao C, Zhou H, Du H, Chen H, Wan H, He Y. Multi-omics research strategies in ischemic stroke: A multidimensional perspective. Ageing Res Rev 2022; 81:101730. [PMID: 36087702 DOI: 10.1016/j.arr.2022.101730] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 08/23/2022] [Accepted: 09/03/2022] [Indexed: 01/31/2023]
Abstract
Ischemic stroke (IS) is a multifactorial and heterogeneous neurological disorder with high rate of death and long-term impairment. Despite years of studies, there are still no stroke biomarkers for clinical practice, and the molecular mechanisms of stroke remain largely unclear. The high-throughput omics approach provides new avenues for discovering biomarkers of IS and explaining its pathological mechanisms. However, single-omics approaches only provide a limited understanding of the biological pathways of diseases. The integration of multiple omics data means the simultaneous analysis of thousands of genes, RNAs, proteins and metabolites, revealing networks of interactions between multiple molecular levels. Integrated analysis of multi-omics approaches will provide helpful insights into stroke pathogenesis, therapeutic target identification and biomarker discovery. Here, we consider advances in genomics, transcriptomics, proteomics and metabolomics and outline their use in discovering the biomarkers and pathological mechanisms of IS. We then delineate strategies for achieving integration at the multi-omics level and discuss how integrative omics and systems biology can contribute to our understanding and management of IS.
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Affiliation(s)
- Wentao Li
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China.
| | - Chongyu Shao
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China.
| | - Huifen Zhou
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China.
| | - Haixia Du
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China.
| | - Haiyang Chen
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China.
| | - Haitong Wan
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China.
| | - Yu He
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China.
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Zhao HX, Li X, Liu JL, Guan GQ, Dan XG. Metabolomic profiling of bovine leucocytes transformed by Theileria annulata under BW720c treatment. Parasit Vectors 2022; 15:356. [PMID: 36199104 PMCID: PMC9533618 DOI: 10.1186/s13071-022-05450-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Background When Theileria annulata infects host cells, it undertakes unlimited proliferation as tumor cells. Although the transformed cells will recover their limited reproductive characteristics and enter the apoptosis process after treatment with buparvaquone (BW720c), the metabolites and metabolic pathways involved are not clear. Methods The transformed cells of T. annulata were used as experimental materials, and the buparvaquone treatment group and DMSO control group were used. Qualitative and quantitative analysis was undertaken of 36 cell samples based on the LC–QTOF platform in positive and negative ion modes. The metabolites of the cell samples after 72 h of drug treatment were analyzed, as were the different metabolites and metabolic pathways involved in the BW720c treatment. Finally, the differential metabolites and metabolic pathways in the transformed cells were found. Results A total of 1425 metabolites were detected in the negative ion mode and 1298 metabolites were detected in the positive ion mode. After drug treatment for 24 h, 48 h, and 72 h, there were 56, 162, and 243 differential metabolites in negative ion mode, and 35, 121, and 177 differential metabolites in positive ion mode, respectively. These differential metabolites are mainly concentrated on various essential amino acids. Conclusion BW720c treatment induces metabolic disturbances in T. annulata-infected cells by regulating the metabolism of leucine, arginine, and l-carnitine, and induces host cell apoptosis. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05450-0.
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Affiliation(s)
- Hong-Xi Zhao
- School of Agriculture, Ningxia University, Yinchuan, 750021, People's Republic of China.
| | - Xia Li
- School of Agriculture, Ningxia University, Yinchuan, 750021, People's Republic of China
| | - Jun-Long Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, 730046, People's Republic of China
| | - Gui-Quan Guan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, 730046, People's Republic of China
| | - Xin-Gang Dan
- School of Agriculture, Ningxia University, Yinchuan, 750021, People's Republic of China.
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6
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Bjerrum JT, Wang YL, Seidelin JB, Nielsen OH. IBD metabonomics predicts phenotype, disease course, and treatment response. EBioMedicine 2021; 71:103551. [PMID: 34419930 PMCID: PMC8379620 DOI: 10.1016/j.ebiom.2021.103551] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/22/2021] [Accepted: 08/09/2021] [Indexed: 02/07/2023] Open
Abstract
Metabonomics in inflammatory bowel disease (IBD) characterizes the effector molecules of biological systems and thus aims to describe the molecular phenotype, generate insight into the pathology, and predict disease course and response to treatment. Nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry (MS), and integrated NMR and MS platforms coupled with multivariate analyses have been applied to create such metabolic profiles. Recent advances have identified quiescent ulcerative colitis as a distinct molecular phenotype and demonstrated metabonomics as a promising clinical tool for predicting relapse and response to treatment with biologics as well as fecal microbiome transplantation, thus facilitating much needed precision medicine. However, understanding this complex research field and how it translates into clinical settings is a challenge. This review aims to describe the current workflow, analytical strategies, and associated bioinformatics, and translate current IBD metabonomic knowledge into new potential clinically applicable treatment strategies, and outline future key translational perspectives.
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Affiliation(s)
- Jacob T Bjerrum
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Borgmester Ib Juuls Vej 1 DK-2730, Denmark.
| | - Yulan L Wang
- Singapore Phenome Center, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Jakob B Seidelin
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Borgmester Ib Juuls Vej 1 DK-2730, Denmark
| | - Ole H Nielsen
- Faculty of Health and Medical Sciences, Institute of Clinical Medicine, University of Copenhagen, Denmark
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Sanclemente JL, Rivera-Velez SM, Dasgupta N, Horohov DW, Wood PL, Sanz MG. Plasma lipidome of healthy and Rhodococcus equi-infected foals over time. Equine Vet J 2021; 54:121-131. [PMID: 33445210 DOI: 10.1111/evj.13422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/22/2020] [Accepted: 01/03/2021] [Indexed: 01/08/2023]
Abstract
BACKGROUND Many foals that develop thoracic ultrasonographic lesions as a result of Rhodococcus equi infection heal on their own. However, most of these foals receive antimicrobials because foals at risk of developing clinical pneumonia cannot be identified. Untargeted lipidomics is useful to identify candidate biomarkers. OBJECTIVES (a) To describe the changes that occur in foal lipidomics as a result of ageing (birth to 8 weeks) and (b) To compare these results with those observed in foals after experimental infection with R. equi. STUDY DESIGN Experimental study. METHODS Healthy newborn foals (n = 9) were challenged with R. equi intratracheally the first week of life. Foals were treated with antimicrobials if they developed clinical pneumonia (n = 4, "clinical group") or were closely monitored if they showed no signs of disease (n = 5 "subclinical group"). An unchallenged group (n = 4) was also included. All foals were free of disease (transtracheal wash fluid evaluation and culture as well as thoracic ultrasonography) by 8 weeks of life. Plasma lipidomics was determined by LC-MS weekly for the study duration (8 weeks). RESULTS Both ageing and experimental infection altered the foal's plasma lipidome as demonstrated by multivariate statistical analysis. The intensities of 31 lipids were altered by ageing and 12 by infection (P < .05). Furthermore, nine lipids changed by more than twofold between clinical and subclinical groups. MAIN LIMITATIONS The number of foals is limited. Foals were experimentally challenged with R. equi. CONCLUSIONS Ageing and R. equi infection induced changes in the plasma lipidome of foals. These experimental results provide the background for future work in the discovery of earlier biomarkers of R. equi pneumonia. Early identification of foals at risk of developing clinical pneumonia is key in order to decrease antimicrobial use and development of antimicrobial resistance.
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Affiliation(s)
- Jorge L Sanclemente
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Sol Maiam Rivera-Velez
- Molecular Determinants Core, Johns Hopkins All Children's Hospital, Saint Petersburg, FL, USA
| | - Nairanjana Dasgupta
- Department of Mathematics and Statistics, College of Arts and Sciences, Washington State University, Pullman, WA, USA
| | - David W Horohov
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Clinical Sciences, University of Kentucky, Lexington, KY, USA
| | - Paul L Wood
- Metabolomics Unit, Department of Physiology and Pharmacology, College of Veterinary Medicine, Lincoln Memorial University, Harrogate, TN, USA
| | - Macarena G Sanz
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
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8
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Alkhalil A, Ball RL, Garg G, Day A, Carney BC, Kumar R, Hammamieh R, Moffatt LT, Shupp JW. Cutaneous Thermal Injury Modulates Blood and Skin Metabolomes Differently in a Murine Model. J Burn Care Res 2020; 42:727-742. [PMID: 33301570 PMCID: PMC8335952 DOI: 10.1093/jbcr/iraa209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
As the field of metabolomics develops further, investigations of how the metabolome is affected following thermal injury may be helpful to inform diagnostics and guide treatments. In this study, changes to the metabolome were tested and validated in a murine burn injury model. After a 30% total body surface scald injury or sham procedure sera and skin biopsies were collected at 1, 2, 6, or 24 hr. Burn-specific changes in the metabolome were detected compared to sham animals. The sera metabolome exhibited a more rapid response to burn injury than that of the skin and it peaked more proximal to injury (6 vs 24 hr). Progression of metabolic response in the skin was less synchronous and showed a higher overlap of the significantly modified metabolites (SMMs) among tested time-points. Top affected pathways identified by SMMs of skin included inositol phosphate metabolism, ascorbate and alderate metabolism, caffeine metabolism, and the pentose phosphate pathway. Future research is warranted in human and larger animal models to further elucidate the role of metabolomic perturbations and the pathophysiology following burn injury.
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Affiliation(s)
- Abdulnaser Alkhalil
- Firefighters' Burn and Surgical Research Laboratory, MedStar Health Research Institute, Washington, District of Columbia
| | - Robert L Ball
- Firefighters' Burn and Surgical Research Laboratory, MedStar Health Research Institute, Washington, District of Columbia.,The Burn Center, MedStar Washington Hospital Center, Washington, District of Columbia
| | - Gaurav Garg
- Firefighters' Burn and Surgical Research Laboratory, MedStar Health Research Institute, Washington, District of Columbia.,The Burn Center, MedStar Washington Hospital Center, Washington, District of Columbia
| | - Anna Day
- The Oak Ridge Institute for Science and Education, Fort Detrick, Maryland
| | - Bonnie C Carney
- Firefighters' Burn and Surgical Research Laboratory, MedStar Health Research Institute, Washington, District of Columbia.,Department of Biochemistry and Molecular Biology, Georgetown University School of Medicine, Washington, District of Columbia
| | - Raina Kumar
- Advanced Biomedical Computational Science, Frederick National Lab for Cancer Research, Maryland.,Integrative Systems Biology, US Army Center for Environmental Health, Center for Environmental Health, Fort Detrick, Maryland
| | - Rasha Hammamieh
- Integrative Systems Biology, US Army Center for Environmental Health, Center for Environmental Health, Fort Detrick, Maryland
| | - Lauren T Moffatt
- Firefighters' Burn and Surgical Research Laboratory, MedStar Health Research Institute, Washington, District of Columbia.,Department of Biochemistry and Molecular Biology, Georgetown University School of Medicine, Washington, District of Columbia
| | - Jeffrey W Shupp
- Firefighters' Burn and Surgical Research Laboratory, MedStar Health Research Institute, Washington, District of Columbia.,The Burn Center, MedStar Washington Hospital Center, Washington, District of Columbia.,Department of Surgery, Georgetown University School of Medicine, Washington, District of Columbia
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9
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Gao D, Niu M, Wei SZ, Zhang CE, Zhou YF, Yang ZW, Li L, Wang JB, Zhang HZ, Zhang L, Xiao XH. Identification of a Pharmacological Biomarker for the Bioassay-Based Quality Control of a Thirteen-Component TCM Formula (Lianhua Qingwen) Used in Treating Influenza A Virus (H1N1) Infection. Front Pharmacol 2020; 11:746. [PMID: 32523531 PMCID: PMC7261828 DOI: 10.3389/fphar.2020.00746] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 05/04/2020] [Indexed: 12/16/2022] Open
Abstract
As chemical analysis for quality control (QC) of traditional Chinese medicine (TCM) formula is difficult to guarantee the effectiveness, a bioassay method that combines QC with evaluation of therapeutic effects has been developed to assess the TCM quality. Here, we chose a thirteen-component TCM formula, Lianhua Qingwen capsule (LHQW), as a representative sample, to explore the pivotal biomarkers for a bioassay and to investigate close association between QC and pharmacological actions. Initially, our results showed that chemical fingerprinting could not effectively distinguish batches of LHQW. Pharmacological experiments indicated that LHQW could treat influenza A virus (H1N1) infection in the H1N1 mouse model, as claimed in clinical trials, by improving pathologic alterations and bodyweight loss, and decreasing virus replication, lung lesions and inflammation. Furthermore, by using serum metabolomics analysis, we identified two important metabolites, prostaglandin F2α and arachidonic acid, and their metabolic pathway, arachidonic acid metabolism, as vital indicators of LHQW in treatment of influenza. Subsequently, macrophages transcriptomics highlighted the prominent role of cyclooxygenase-2 (COX-2) as the major rate-limiting enzyme in the arachidonic acid metabolism pathway. Finally, COX-2 was validated by in vivo gene expression and in vitro enzymatic activity with 43 batches of LHQW as a viable pharmacological biomarker for the establishment of bioassay-based QC. Our study provides systematic methodology in the pharmacological biomarker exploration for establishing the bioassay-based QC of LHQW or other TCM formulas relating to their pharmacological activities and mechanism.
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Affiliation(s)
- Dan Gao
- Department of Pharmacy, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing Engineering Research Center for Nervous System Drugs, Beijing Institute for Brain Disorders, Key Laboratory for Neurodegenerative Diseases of Ministry of Education, Beijing, China.,Department of China Military Institute of Chinese Materia, the Fifth Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing, China
| | - Ming Niu
- Department of China Military Institute of Chinese Materia, the Fifth Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing, China
| | - Shi-Zhang Wei
- Department of China Military Institute of Chinese Materia, the Fifth Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing, China
| | - Cong-En Zhang
- Department of China Military Institute of Chinese Materia, the Fifth Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing, China
| | - Yong-Feng Zhou
- Department of China Military Institute of Chinese Materia, the Fifth Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing, China
| | - Zheng-Wei Yang
- Department of Pharmacy, the Sixth Medical Center, Chinese PLA (People's Liberation Army) General Hospital, Beijing, China
| | - Lin Li
- Department of Pharmacy, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing Engineering Research Center for Nervous System Drugs, Beijing Institute for Brain Disorders, Key Laboratory for Neurodegenerative Diseases of Ministry of Education, Beijing, China
| | - Jia-Bo Wang
- Department of China Military Institute of Chinese Materia, the Fifth Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing, China
| | - Hai-Zhu Zhang
- College of Pharmacy and Chemistry, Dali University, Dali, China
| | - Lan Zhang
- Department of Pharmacy, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing Engineering Research Center for Nervous System Drugs, Beijing Institute for Brain Disorders, Key Laboratory for Neurodegenerative Diseases of Ministry of Education, Beijing, China
| | - Xiao-He Xiao
- Department of China Military Institute of Chinese Materia, the Fifth Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing, China
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10
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Rivera-Velez SM, Broughton-Neiswanger LE, Suarez M, Piñeyro P, Navas J, Chen S, Hwang J, Villarino NF. Repeated administration of the NSAID meloxicam alters the plasma and urine lipidome. Sci Rep 2019; 9:4303. [PMID: 30867479 PMCID: PMC6416286 DOI: 10.1038/s41598-019-40686-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 02/21/2019] [Indexed: 12/31/2022] Open
Abstract
Non-steroidal anti-inflammatories (NSAIDs), such as meloxicam, are the mainstay for treating painful and inflammatory conditions in animals and humans; however, the repeated administration of NSAIDs can cause adverse effects, limiting the long-term administration of these drugs to some patients. The primary aim of this study was to determine the effects of repeated meloxicam administration on the feline plasma and urine lipidome. Cats (n = 12) were treated subcutaneously with either saline solution or 0.3 mg/kg body weight of meloxicam daily for up to 31 days. Plasma and urine lipidome were determined by LC-MS before the first treatment and at 4, 9 and 13 and 17 days after the first administration of meloxicam. The repeated administration of meloxicam altered the feline plasma and urine lipidome as demonstrated by multivariate statistical analysis. The intensities of 94 out of 195 plasma lipids were altered by the repeated administration of meloxicam to cats (p < 0.05). Furthermore, we identified 12 lipids in plasma and 10 lipids in urine that could serve as biomarker candidates for discriminating animals receiving NSAIDs from healthy controls. Expanding our understanding about the effects of NSAIDs in the body could lead to the discovery of mechanism(s) associated with intolerance to NSAIDs.
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Affiliation(s)
- Sol M Rivera-Velez
- Program in Individualized Medicine, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, 99164, WA, United States
| | - Liam E Broughton-Neiswanger
- Program in Individualized Medicine, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, 99164, WA, United States
| | - Martin Suarez
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, 99164, WA, United States
| | - Pablo Piñeyro
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, Ames, 1134, IA, United States
| | - Jinna Navas
- Program in Individualized Medicine, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, 99164, WA, United States
| | - Sandy Chen
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, 99164, WA, United States
| | - Julianne Hwang
- Program in Individualized Medicine, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, 99164, WA, United States
| | - Nicolas F Villarino
- Program in Individualized Medicine, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, 99164, WA, United States.
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11
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Cartlidge CR, U MRA, Alkhatib AMA, Taylor-Robinson SD. The utility of biomarkers in hepatocellular carcinoma: review of urine-based 1H-NMR studies - what the clinician needs to know. Int J Gen Med 2017; 10:431-442. [PMID: 29225478 PMCID: PMC5708191 DOI: 10.2147/ijgm.s150312] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the fifth most common malignancy, the third most common cause of cancer death, and the most common primary liver cancer. Overall, there is a need for more reliable biomarkers for HCC, as those currently available lack sensitivity and specificity. For example, the current gold-standard biomarker, serum alpha-fetoprotein, has a sensitivity of roughly only 70%. Cancer cells have different characteristic metabolic signatures in biofluids, compared to healthy cells; therefore, metabolite analysis in blood or urine should lead to the detection of suitable candidates for the detection of HCC. With the advent of metabonomics, this has increased the potential for new biomarker discovery. In this article, we look at approaches used to identify biomarkers of HCC using proton nuclear magnetic resonance (1H-NMR) spectroscopy of urine samples. The various multivariate statistical analysis techniques used are explained, and the process of biomarker identification is discussed, with a view to simplifying the knowledge base for the average clinician.
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Affiliation(s)
| | - M R Abellona U
- Department of Surgery and Cancer, Division of Computational and Systems Medicine, Faculty of Medicine, Imperial College London, London, UK
| | - Alzhraa M A Alkhatib
- Department of Surgery and Cancer, Division of Computational and Systems Medicine, Faculty of Medicine, Imperial College London, London, UK
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12
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Establishment and optimization of NMR-based cell metabonomics study protocols for neonatal Sprague-Dawley rat cardiomyocytes. Anal Biochem 2017; 517:50-52. [PMID: 27845029 DOI: 10.1016/j.ab.2016.11.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 11/10/2016] [Indexed: 11/23/2022]
Abstract
A quenching, harvesting, and extraction protocol was optimized for cardiomyocytes NMR metabonomics analysis in this study. Trypsin treatment and direct scraping cells in acetonitrile were compared for sample harvesting. The results showed trypsin treatment cause normalized concentration increasing of phosphocholine and metabolites leakage, since the trypsin-induced membrane broken and long term harvesting procedures. Then the intracellular metabolite extraction efficiency of methanol and acetonitrile were compared. As a result, washing twice with phosphate buffer, direct scraping cells and extracting with acetonitrile were chosen to prepare cardiomyocytes extracts samples for metabonomics studies. This optimized protocol is rapid, effective, and exhibits greater metabolite retention.
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13
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Abstract
Metabonomic techniques have considerable potential in the field of clinical diagnostics, typifying the application of a translational research paradigm. Care must be taken at all stages to apply appropriate methodology with accurate patient selection and profiling, and rigorous data acquisition and handling, to ensure clinical validity.An ever-increasing number of publications in a wide range of diseases and diverse patient groups suggest a variety of potential clinical uses; prospective studies in large validation cohorts are required to bring metabonomics into routine clinical practice. In this chapter, the utility of metabonomics as a diagnostic tool will be discussed.
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Affiliation(s)
- Lucy C Hicks
- Department of Medicine, Imperial College London, London, UK
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14
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Abstract
Without any prior knowledge, it can be an overwhelming task to get an overview of and insight into the field of metabonomics. This chapter introduces the concept of metabonomics, the most commonly applied techniques, and the inevitably indispensable multivariate statistical analyses in an easily digestible yet comprehensive manner.
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15
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Bjerrum JT, Wang Y, Hao F, Coskun M, Ludwig C, Günther U, Nielsen OH. Metabonomics of human fecal extracts characterize ulcerative colitis, Crohn's disease and healthy individuals. Metabolomics 2015; 11:122-133. [PMID: 25598765 PMCID: PMC4289537 DOI: 10.1007/s11306-014-0677-3] [Citation(s) in RCA: 175] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 05/14/2014] [Indexed: 12/12/2022]
Abstract
This study employs spectroscopy-based metabolic profiling of fecal extracts from healthy subjects and patients with active or inactive ulcerative colitis (UC) and Crohn's disease (CD) to substantiate the potential use of spectroscopy as a non-invasive diagnostic tool and to characterize the fecal metabolome in inflammatory bowel disease (IBD). Stool samples from 113 individuals (UC 48, CD 44, controls 21) were analyzed by 1H nuclear magnetic resonance (NMR) spectroscopy (Bruker 600 MHz, Bruker BioSpin, Rheinstetten, Germany). Data were analyzed with principal component analysis and orthogonal-projection to latent structure-discriminant analysis using SIMCA-P + 12 and MATLAB. Significant differences were found in the metabolic profiles making it possible to differentiate between active IBD and controls and between UC and CD. The metabolites holding differential power primarily belonged to a range of amino acids, microbiota-related short chain fatty acids, and lactate suggestive of an inflammation-driven malabsorption and dysbiosis of the normal bacterial ecology. However, removal of patients with intestinal surgery and anti-TNF-α antibody treatment eliminated the discriminative power regarding UC versus CD. This study consequently demonstrates that 1H NMR spectroscopy of fecal extracts is a potential non-invasive diagnostic tool and able to characterize the inflammation-driven changes in the metabolic profiles related to malabsorption and dysbiosis. Intestinal surgery and medication are to be accounted for in future studies, as it seems to be factors of importance in the discriminative process.
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Affiliation(s)
- Jacob Tveiten Bjerrum
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Yulan Wang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, The Chinese Academy of Sciences, Wuhan, People’s Republic of China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, People’s Republic of China
| | - Fuhua Hao
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, The Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Mehmet Coskun
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Christian Ludwig
- HWB-NMR, School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Ulrich Günther
- HWB-NMR, School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Ole Haagen Nielsen
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
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16
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Rantalainen M, Bjerrum JT, Olsen J, Nielsen OH, Wang Y. Integrative Transcriptomic and Metabonomic Molecular Profiling of Colonic Mucosal Biopsies Indicates a Unique Molecular Phenotype for Ulcerative Colitis. J Proteome Res 2014; 14:479-90. [DOI: 10.1021/pr500699h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Mattias Rantalainen
- Department
of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-17177 Stockholm, Sweden
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and
Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Jacob Tveiten Bjerrum
- Department
of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, DK-2200, Copenhagen, Denmark
- Department
of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, DK-2730 Herlev, Denmark
| | - Jørgen Olsen
- Department
of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Ole Haagen Nielsen
- Department
of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, DK-2730 Herlev, Denmark
| | - Yulan Wang
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and
Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
- Collaborative
Innovation Center for the Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310058, P. R. China
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17
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Geng L, Sun B, Gao B, Wang Z, Quan C, Wei F, Fang XD. MicroRNA-103 promotes colorectal cancer by targeting tumor suppressor DICER and PTEN. Int J Mol Sci 2014; 15:8458-72. [PMID: 24828205 PMCID: PMC4057742 DOI: 10.3390/ijms15058458] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Revised: 04/17/2014] [Accepted: 04/18/2014] [Indexed: 12/24/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of small, noncoding RNAs that act as key regulators in various physiological and pathological processes. However, the regulatory mechanisms for miRNAs in colorectal cancer remain largely unknown. Here, we found that miR-103 is up-regulated in colorectal cancer and its overexpression is closely associated with tumor proliferation and migration. In addition, repressing the expression of miR-103 apparently inhibits colorectal cancer cell proliferation and migration in vitro and HCT-116 xenograft tumor growth in vivo. Subsequent software analysis and dual-luciferase reporter assay identified two tumor suppressor genes DICER and PTEN as direct targets of miR-103, and up-regulation of DICER and PTEN obtained similar results to that occurred in the silencing of miR-103. In addition, restoration of DICER and PTEN can inhibit miR-103-induced colorectal cancer cell proliferation and migration. Our data collectively demonstrate that miR-103 is an oncogene miRNA that promotes colorectal cancer proliferation and migration through down-regulation of the tumor suppressor genes DICER and PTEN. Thus, miR-103 may represent a new potential diagnostic and therapeutic target for colorectal cancer treatment.
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Affiliation(s)
- Li Geng
- Department of General Surgery, the Second Hospital of Jilin University, Changchun 130041, Jilin, China.
| | - Bing Sun
- Department of Neurology, Changchun Central Hospital, Changchun 130041, Jilin, China.
| | - Bo Gao
- Department of General Surgery, the Second Hospital of Jilin University, Changchun 130041, Jilin, China.
| | - Zheng Wang
- Department of General Surgery, the Second Hospital of Jilin University, Changchun 130041, Jilin, China.
| | - Cheng Quan
- Department of General Surgery, the Second Hospital of Jilin University, Changchun 130041, Jilin, China.
| | - Feng Wei
- Department of Hepatobiliary and Pancreas Surgery, the First Hospital, Jilin University, Changchun 130021, Jilin, China.
| | - Xue-Dong Fang
- Department of General Surgery, the Second Hospital of Jilin University, Changchun 130041, Jilin, China.
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18
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Bjerrum JT, Rantalainen M, Wang Y, Olsen J, Nielsen OH. Integration of transcriptomics and metabonomics: improving diagnostics, biomarker identification and phenotyping in ulcerative colitis. Metabolomics 2013; 10:280-290. [PMID: 25221466 PMCID: PMC4161940 DOI: 10.1007/s11306-013-0580-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 08/10/2013] [Indexed: 12/18/2022]
Abstract
A systems biology approach to multi-faceted diseases has provided an opportunity to establish a holistic understanding of the processes at play. Thus, the current study merges transcriptomics and metabonomics data in order to improve diagnostics, biomarker identification and to explore the possibilities of a molecular phenotyping of ulcerative colitis (UC) patients. Biopsies were obtained from the descending colon of 43 UC patients (22 active UC and 21 quiescent UC) and 15 controls. Genome-wide gene expression analyses were performed using Affymetrix GeneChip Human Genome U133 Plus 2.0. Metabolic profiles were generated using 1H Nuclear magnetic resonance spectroscopy (Bruker 600 MHz, Bruker BioSpin, Rheinstetten, Germany). Data were analyzed with the use of orthogonal-projection to latent structure-discriminant analysis and a multivariate logistic regression model fitted by lasso. Prediction performance was evaluated using nested Monte Carlo cross-validation. The prediction performance of the merged data sets and that of relative small (<20 variables) multivariate biomarker panels suggest that it is possible to discriminate between active UC, quiescent UC, and controls; between patients with or without steroid dependency, as well as between early or late disease onset. Consequently, this study demonstrates that the novel approach of integrating metabonomics and transcriptomics combines the better of the two worlds, and provides us with clinical applicable candidate biomarker panels. These combined panels improve diagnostics and more importantly also the molecular phenotyping in UC and provide insight into the pathophysiological processes at play, making optimized and personalized medication a possibility.
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Affiliation(s)
- Jacob Tveiten Bjerrum
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Mattias Rantalainen
- Department of Statistics, Oxford University, Oxford, UK
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, The Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Yulan Wang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, The Chinese Academy of Sciences, Wuhan, People’s Republic of China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, People’s Republic of China
| | - Jørgen Olsen
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ole Haagen Nielsen
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
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19
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Dong F, Zhang L, Hao F, Tang H, Wang Y. Systemic responses of mice to dextran sulfate sodium-induced acute ulcerative colitis using 1H NMR spectroscopy. J Proteome Res 2013; 12:2958-66. [PMID: 23651354 DOI: 10.1021/pr4002383] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The interplay between genetic mutation and environmental factors is believed to contribute to the etiology of inflammatory bowel disease (IBD). While focused attention has been paid to the aforementioned research, time-specific and organ-specific metabolic changes associated with IBD are still lacking. Here, we induced acute ulcerative colitis in mice by providing water containing 3% dextran sulfate sodium (DSS) for 7 days and investigated the metabolic changes of plasma, urine, and a range of biological tissues by employing a (1)H nuclear magnetic resonance (NMR)-based metabonomics approach with complementary information on serum clinical chemistry and histopathology. We found that DSS-induced acute ulcerative colitis leads to significant elevations in the levels of amino acids in plasma and decreased levels in the membrane-related metabolites and a range of nucleotides, nucleobases, and nucleosides in the colon. In addition, acute-colitis-induced elevations in the levels of nucleotides in the liver were observed, accompanied by reduced levels of glucose. DSS-induced acute colitis also resulted in increased levels of oxidized glutathione and attenuated levels of taurine in the spleen. Furthermore, acute colitis resulted in depletion in the levels of gut microbial cometabolites in urine along with an increase in citric acid cycle intermediates. These findings suggest that DSS-induced acute colitis causes a disturbance of lipid and energy metabolism, damage to the colon and liver, a promoted antioxidative and anti-inflammatory response, and perturbed gut microbiotal communities. The information obtained here provided details of the time-dependent and holistic metabolic changes in the development of the DSS-induced acute ulcerative colitis, which could be useful in discovery of novel therapeutic targets for management of IBD.
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Affiliation(s)
- Fangcong Dong
- Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
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20
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Changes of lymph metabolites in a rat model of sepsis induced by cecal ligation and puncture. J Trauma Acute Care Surg 2012; 73:1545-52. [PMID: 23147180 DOI: 10.1097/ta.0b013e31826fc9e7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Sepsis is a clinical syndrome defined by a systemic response to infection and remains a prevalent clinical challenge. The underlying pathophysiology of sepsis is poorly understood. Using a metabolomic method, the present study observed changes in lymph composition during sepsis in a septic model in an attempt to find out new biomarkers for the early diagnosis and treatment of sepsis. METHODS Adult male Sprague-Dawley rats underwent cecal ligation and puncture. Blood samples were obtained via the lateral caudal vein, and lymph was obtained from the thoracic duct. Cytokines were measured in plasma and lymph samples by enzyme-linked immunosorbent assay at different time points after cecal ligation and puncture. Rat lymph samples were analyzed by high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry. Multivariate analysis was used to profile potential biomarkers in rat septic lymph samples. RESULTS Plasma and lymph tumor necrosis factor α, interleukin 1β, and interleukin 6 levels were elevated in septic group as compared with the control. Of the 10 characteristic metabolites identified in the septic model, six (palmitoyl-L-carnitine, creatinine, phenylalanine, isonicotinic acid, choline, and 5-azacytidine) were high, and four (1-O-Hexadecyl-2-lyso-glycero-3-phosphorylcholine, alanine, 4-amino-5-hydroxymethyl-2-methylpyrimidine, and asymmetric dimethylarginine) were low. CONCLUSION These biomarkers were mainly involved in energy metabolism and vascular tone and may prove beneficial to distinguish sepsis from other inflammatory conditions or predict outcomes.
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Patel NR, McPhail MJW, Shariff MIF, Keun HC, Taylor-Robinson SD. Biofluid metabonomics using (1)H NMR spectroscopy: the road to biomarker discovery in gastroenterology and hepatology. Expert Rev Gastroenterol Hepatol 2012; 6:239-51. [PMID: 22375528 DOI: 10.1586/egh.12.1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Metabolic profiling or 'metabonomics' is an investigatory method that allows metabolic changes associated with the presence of an underlying pathological process to be investigated. Various biofluids can be utilized in the process but urine, serum and fecal extract are most pertinent to the investigation of gastrointestinal and hepatological disease. Nuclear magnetic resonance spectroscopy-based metabonomic research has the potential to generate novel noninvasive diagnostic tests, based on biomarkers of disease, which are simple and cost effective yet retain high sensitivity and specificity characteristics. The process involves a number of key steps, including sample collection, data acquisition, chemometric techniques and, finally, validation. This technique-driven review aims to demystify the metabonomics pathway, while also illustrating the potential of this technique with recent examples of its application in hepato-gastroenterological disease.
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Affiliation(s)
- Neeral R Patel
- Liver Unit, Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, 10th Floor, QEQM Wing, St Mary's Hospital Campus, Imperial College London, South Wharf Street, London, W2 1NY, UK
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22
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Baur P, Martin FP, Gruber L, Bosco N, Brahmbhatt V, Collino S, Guy P, Montoliu I, Rozman J, Klingenspor M, Tavazzi I, Thorimbert A, Rezzi S, Kochhar S, Benyacoub J, Kollias G, Haller D. Metabolic phenotyping of the Crohn's disease-like IBD etiopathology in the TNF(ΔARE/WT) mouse model. J Proteome Res 2011; 10:5523-35. [PMID: 22029571 DOI: 10.1021/pr2007973] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The underlying biochemical consequences of inflammatory bowel disease (IBD) on the systemic and gastrointestinal metabolism have not yet been fully elucidated but could help to better understand the disease pathogenesis and to identify tissue-specific markers associated with the different disease stages. Here, we applied a metabonomic approach to monitor metabolic events associated with the gradual development of Crohn's disease (CD)-like ileitis in the TNF(ΔARE/WT) mouse model. Metabolic profiles of different intestinal compartments from the age of 4 up to 24 weeks were generated by combining proton nuclear magnetic resonance ((1)H NMR) spectroscopy and liquid chromatography-mass spectrometry (LC-MS). From 8 weeks onward, mice developed CD similar to the immune and tissue-related phenotype of human CD with ileal involvement, including ileal histological abnormalities, reduced fat mass and body weight, as well as hallmarks of malabsorption with higher energy wasting. The metabonomic approach highlighted shifts in the intestinal lipid metabolism concomitant to the histological onset of inflammation. Moreover, the advanced disease status was characterized by a significantly altered metabolism of cholesterol, triglycerides, phospholipids, plasmalogens, and sphingomyelins in the inflamed tissue (ileum) and the adjacent intestinal parts (proximal colon). These results describe different biological processes associated with the disease onset, including modifications of the general cell membrane composition, alteration of energy homeostasis, and finally the generation of inflammatory lipid mediators. Taken together, this provides novel insights into IBD-related alterations of specific lipid-dependant processes during inflammatory states.
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Affiliation(s)
- Pia Baur
- ZIEL-Research Center for Nutrition and Food Science, CDD-Center for Diet and Disease, Technische Universität München, Gregor-Mendel-Strasse 2, 85350 Freising-Weihenstephan, Germany
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23
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Ooi M, Nishiumi S, Yoshie T, Shiomi Y, Kohashi M, Fukunaga K, Nakamura S, Matsumoto T, Hatano N, Shinohara M, Irino Y, Takenawa T, Azuma T, Yoshida M. GC/MS-based profiling of amino acids and TCA cycle-related molecules in ulcerative colitis. Inflamm Res 2011; 60:831-40. [PMID: 21523508 DOI: 10.1007/s00011-011-0340-7] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 03/08/2011] [Accepted: 04/10/2011] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVE The roles that amino acids play in immunity and inflammation are well defined, and the relationship between inflammatory bowel disease (IBD) and certain amino acids has recently attracted attention. In this study, the levels of amino acids and trichloroacetic acid (TCA) cycle-related molecules in the colonic tissues and sera of patients with ulcerative colitis (UC) were profiled by gas chromatography/mass spectrometry (GC/MS), with the aim of evaluating whether the clinical state induced by UC leads to variations in the amino acid profile. MATERIALS AND METHODS Colonic biopsy samples from 22 UC patients were used, as well as serum samples from UC patients (n = 13), Crohn's disease (CD) patients (n = 21), and healthy volunteers (n = 17). RESULTS In the GC/MS-based profiling of amino acids and TCA cycle-related molecules, lower levels of 16 amino acids and 5 TCA cycle-related molecules were observed in the colonic lesion tissues of the UC patients, and the serum profiles of amino acids and TCA cycle-related molecules of the UC patients were different from those of the CD patients and healthy volunteers. CONCLUSIONS Our study raises the possibility that GC/MS-based profiling of amino acids and TCA cycle-related molecules is a useful early diagnostic tool for UC.
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Affiliation(s)
- Makoto Ooi
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1, Chuo-ku, Kusunoki-cho, Kobe, Hyogo, 650-0017, Japan
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24
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Ooi M, Nishiumi S, Yoshie T, Shiomi Y, Kohashi M, Fukunaga K, Nakamura S, Matsumoto T, Hatano N, Shinohara M, Irino Y, Takenawa T, Azuma T, Yoshida M. GC/MS-based profiling of amino acids and TCA cycle-related molecules in ulcerative colitis. Inflamm Res 2011. [PMID: 21523508 DOI: 10.1007/s00011-011-0340- 7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
OBJECTIVE The roles that amino acids play in immunity and inflammation are well defined, and the relationship between inflammatory bowel disease (IBD) and certain amino acids has recently attracted attention. In this study, the levels of amino acids and trichloroacetic acid (TCA) cycle-related molecules in the colonic tissues and sera of patients with ulcerative colitis (UC) were profiled by gas chromatography/mass spectrometry (GC/MS), with the aim of evaluating whether the clinical state induced by UC leads to variations in the amino acid profile. MATERIALS AND METHODS Colonic biopsy samples from 22 UC patients were used, as well as serum samples from UC patients (n = 13), Crohn's disease (CD) patients (n = 21), and healthy volunteers (n = 17). RESULTS In the GC/MS-based profiling of amino acids and TCA cycle-related molecules, lower levels of 16 amino acids and 5 TCA cycle-related molecules were observed in the colonic lesion tissues of the UC patients, and the serum profiles of amino acids and TCA cycle-related molecules of the UC patients were different from those of the CD patients and healthy volunteers. CONCLUSIONS Our study raises the possibility that GC/MS-based profiling of amino acids and TCA cycle-related molecules is a useful early diagnostic tool for UC.
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Affiliation(s)
- Makoto Ooi
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1, Chuo-ku, Kusunoki-cho, Kobe, Hyogo, 650-0017, Japan
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25
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Liu XR, Zheng XF, Ji SZ, Lv YH, Zheng DY, Xia ZF, Zhang WD. Metabolomic analysis of thermally injured and/or septic rats. Burns 2010; 36:992-8. [DOI: 10.1016/j.burns.2010.03.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Revised: 03/17/2010] [Accepted: 03/23/2010] [Indexed: 12/28/2022]
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26
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Hong YS, Ahn YT, Park JC, Lee JH, Lee H, Huh CS, Kim DH, Ryu DH, Hwang GS. 1H NMR-based metabonomic assessment of probiotic effects in a colitis mouse model. Arch Pharm Res 2010; 33:1091-101. [PMID: 20661720 DOI: 10.1007/s12272-010-0716-1] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Revised: 04/25/2010] [Accepted: 04/29/2010] [Indexed: 01/05/2023]
Abstract
Metabolic profiling of the fecal extracts of male mice was carried out to assess the effects of probiotics on colonic inflammation using (1)H NMR spectroscopy coupled with multivariate data analysis. The control group (n = 5) was administered phosphate buffered saline for 14 days. Acute colitis was induced with dextran sulfate sodium (DSS) for 7 days following administration of phosphate buffered saline for 7 days (DSS-treated group, n = 5). LAB + DSS-treated group (n = 5) was administered lactic acid bacteria (LAB) daily for 7 days followed by treatment with DSS for 7 days to investigate protective effect of LAB against DSS-inducible colitis. Histological damage, myeloperoxidase activity, and malondialdehyde content of colon tissue were reduced, whereas colon length increased in LAB + DSS-treated mice compared to those in DSS-treated mice. DSS treatment was associated with fecal excretion of amino acids, short chain fatty acids, and nucleotides, revealing significant decreases of threonine, alanine, glutamate, glutamine, aspartate, lysine, glycine, butyrate, uracil, and hypoxanthine together with increases of monosaccharides, glucose, and trimethylamine in the feces of mice with DSS-induced colitis. Increased levels of acetate, butyrate, and glutamine and decreased levels of trimethylamine were found in the feces of LAB + DSS-treated mice compared to DSS-treated mice alone. The increased short chain fatty acids levels in the feces of mice fed with LAB indicate that the probiotics have protective effects against DSS-induced colitis via modulation of the gut microbiota. This work highlights the possibility for alternative approach of metabonomics in feces for assessing the probiotic effect in an animal model of inflammatory bowel disease.
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Zhang S, Nagana Gowda GA, Ye T, Raftery D. Advances in NMR-based biofluid analysis and metabolite profiling. Analyst 2010; 135:1490-8. [PMID: 20379603 PMCID: PMC4720135 DOI: 10.1039/c000091d] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Significant improvements in NMR technology and methods have propelled NMR studies to play an important role in a rapidly expanding number of applications involving the profiling of metabolites in biofluids. This review discusses recent technical advances in NMR spectroscopy based metabolite profiling methods, data processing and analysis over the last three years.
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Affiliation(s)
- Shucha Zhang
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - G. A. Nagana Gowda
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Tao Ye
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Daniel Raftery
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
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Bjerrum JT, Hansen M, Olsen J, Nielsen OH. Genome-wide gene expression analysis of mucosal colonic biopsies and isolated colonocytes suggests a continuous inflammatory state in the lamina propria of patients with quiescent ulcerative colitis. Inflamm Bowel Dis 2010; 16:999-1007. [PMID: 19834973 DOI: 10.1002/ibd.21142] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Genome-wide gene expression (GWGE) profiles of mucosal colonic biopsies have suggested the existence of a continuous inflammatory state in quiescent ulcerative colitis (UC). The aim of this study was to use DNA microarray-based GWGE profiling of mucosal colonic biopsies and isolated colonocytes from UC patients and controls in order to identify the cell types responsible for the continuous inflammatory state. METHODS Adjacent mucosal colonic biopsies were obtained endoscopically from the descending colon in patients with active UC (n = 8), quiescent UC (n = 9), and with irritable bowel syndrome (controls, n = 10). After isolation of colonocytes and subsequent extraction of total RNA, GWGE data were acquired using Human Genome U133 Plus 2.0 GeneChip Array (Affymetrix, Santa Clara, CA). Data analysis was carried out by principal component analysis and projection to latent structure-discriminant analysis using the SIMCA-P 11 software (Umetrics, Umeå, Sweden). RESULTS A clear separation between active UC, quiescent UC, and control biopsies were found, whereas the model for the colonocytes was unable to distinguish between quiescent UC and controls. The differentiation between quiescent UC and control biopsies was governed by unique profiles containing gene expressions with significant fold changes. These primarily belonged to the family of homeostatic chemokines, revealing a plausible explanation for the abnormal regulated innate immune response seen in patients with UC. CONCLUSIONS This study has demonstrated the presence of a continuous inflammatory state in quiescent UC, which seems to reflect an altered gene expression profile of lamina propria cells.
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Affiliation(s)
- Jacob Tveiten Bjerrum
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Denmark
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Bjerrum JT, Nielsen OH, Hao F, Tang H, Nicholson JK, Wang Y, Olsen J. Metabonomics in ulcerative colitis: diagnostics, biomarker identification, and insight into the pathophysiology. J Proteome Res 2010; 9:954-62. [PMID: 19860486 DOI: 10.1021/pr9008223] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy and appropriate multivariate statistical analyses have been employed on mucosal colonic biopsies, colonocytes, lymphocytes, and urine from patients with ulcerative colitis (UC) and controls in order to explore the diagnostic possibilities, define new potential biomarkers, and generate a better understanding of the pathophysiology. Samples were collected from patients with active UC (n = 41), quiescent UC (n = 33), and from controls (n = 25) and analyzed by NMR spectroscopy. Data analysis was carried out by principal component analysis and orthogonal-projection to latent structure-discriminant analysis using the SIMCA P+11 software package (Umetrics, Umea, Sweden) and Matlab environment. Significant differences between controls and active UC were discovered in the metabolic profiles of biopsies and colonocytes. In the biopsies from patients with active UC higher levels of antioxidants and of a range of amino acids, but lower levels of lipid, glycerophosphocholine (GPC), myo-inositol, and betaine were found, whereas the colonocytes only displayed low levels of GPC, myo-inositol and choline. Interestingly, 20% of inactive UC patients had similar profiles to those who were in an active state. This study demonstrates the possibilities of metabonomics as a diagnostic tool in active and quiescent UC and provides new insight into pathophysiologic mechanisms.
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Affiliation(s)
- Jacob T Bjerrum
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Denmark.
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Rezzi S, Martin FP, Alonso C, Guilarte M, Vicario M, Ramos L, Martínez C, Lobo B, Saperas E, Malagelada JR, Santos J, Kochhar S. Metabotyping of Biofluids Reveals Stress-Based Differences in Gut Permeability in Healthy Individuals. J Proteome Res 2009; 8:4799-809. [DOI: 10.1021/pr900525w] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Serge Rezzi
- Bioanalytical Science Department, Metabonomics & Biomarkers Group, Nestlé Research Center, Lausanne, Switzerland, and Digestive Diseases Research Unit, Institut de Recerca, Department of Gastroenterology; Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Department of Medicine, Barcelona, Spain
| | - François-Pierre Martin
- Bioanalytical Science Department, Metabonomics & Biomarkers Group, Nestlé Research Center, Lausanne, Switzerland, and Digestive Diseases Research Unit, Institut de Recerca, Department of Gastroenterology; Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Department of Medicine, Barcelona, Spain
| | - Carmen Alonso
- Bioanalytical Science Department, Metabonomics & Biomarkers Group, Nestlé Research Center, Lausanne, Switzerland, and Digestive Diseases Research Unit, Institut de Recerca, Department of Gastroenterology; Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Department of Medicine, Barcelona, Spain
| | - Mar Guilarte
- Bioanalytical Science Department, Metabonomics & Biomarkers Group, Nestlé Research Center, Lausanne, Switzerland, and Digestive Diseases Research Unit, Institut de Recerca, Department of Gastroenterology; Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Department of Medicine, Barcelona, Spain
| | - María Vicario
- Bioanalytical Science Department, Metabonomics & Biomarkers Group, Nestlé Research Center, Lausanne, Switzerland, and Digestive Diseases Research Unit, Institut de Recerca, Department of Gastroenterology; Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Department of Medicine, Barcelona, Spain
| | - Laura Ramos
- Bioanalytical Science Department, Metabonomics & Biomarkers Group, Nestlé Research Center, Lausanne, Switzerland, and Digestive Diseases Research Unit, Institut de Recerca, Department of Gastroenterology; Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Department of Medicine, Barcelona, Spain
| | - Cristina Martínez
- Bioanalytical Science Department, Metabonomics & Biomarkers Group, Nestlé Research Center, Lausanne, Switzerland, and Digestive Diseases Research Unit, Institut de Recerca, Department of Gastroenterology; Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Department of Medicine, Barcelona, Spain
| | - Beatriz Lobo
- Bioanalytical Science Department, Metabonomics & Biomarkers Group, Nestlé Research Center, Lausanne, Switzerland, and Digestive Diseases Research Unit, Institut de Recerca, Department of Gastroenterology; Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Department of Medicine, Barcelona, Spain
| | - Esteban Saperas
- Bioanalytical Science Department, Metabonomics & Biomarkers Group, Nestlé Research Center, Lausanne, Switzerland, and Digestive Diseases Research Unit, Institut de Recerca, Department of Gastroenterology; Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Department of Medicine, Barcelona, Spain
| | - Juan Ramón Malagelada
- Bioanalytical Science Department, Metabonomics & Biomarkers Group, Nestlé Research Center, Lausanne, Switzerland, and Digestive Diseases Research Unit, Institut de Recerca, Department of Gastroenterology; Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Department of Medicine, Barcelona, Spain
| | - Javier Santos
- Bioanalytical Science Department, Metabonomics & Biomarkers Group, Nestlé Research Center, Lausanne, Switzerland, and Digestive Diseases Research Unit, Institut de Recerca, Department of Gastroenterology; Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Department of Medicine, Barcelona, Spain
| | - Sunil Kochhar
- Bioanalytical Science Department, Metabonomics & Biomarkers Group, Nestlé Research Center, Lausanne, Switzerland, and Digestive Diseases Research Unit, Institut de Recerca, Department of Gastroenterology; Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Department of Medicine, Barcelona, Spain
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