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King WR, Acosta-Zaldívar M, Qi W, Cherico N, Cooke L, Köhler JR, Patton-Vogt J. Glycerophosphocholine provision rescues Candida albicans growth and signaling phenotypes associated with phosphate limitation. mSphere 2023; 8:e0023123. [PMID: 37843297 PMCID: PMC10732039 DOI: 10.1128/msphere.00231-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/30/2023] [Indexed: 10/17/2023] Open
Abstract
IMPORTANCE Candida albicans is the most commonly isolated species from patients suffering from invasive fungal disease. C. albicans is most commonly a commensal organism colonizing a variety of niches in the human host. The fungus must compete for resources with the host flora to acquire essential nutrients such as phosphate. Phosphate acquisition and homeostasis have been shown to play a key role in C. albicans virulence, with several genes involved in these processes being required for normal virulence and several being upregulated during infection. In addition to inorganic phosphate (Pi), C. albicans can utilize the lipid-derived metabolite glycerophosphocholine (GPC) as a phosphate source. As GPC is available within the human host, we examined the role of GPC in phosphate homeostasis in C. albicans. We find that GPC can substitute for Pi by many though not all criteria and is likely a relevant physiological phosphate source for C. albicans.
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Affiliation(s)
- William R. King
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Maikel Acosta-Zaldívar
- Department of Infectious Diseases, Boston Children’s Hospital/Harvard Medical School, Boston, Massachusetts, USA
| | - Wanjun Qi
- Department of Infectious Diseases, Boston Children’s Hospital/Harvard Medical School, Boston, Massachusetts, USA
| | - Nicholas Cherico
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Lauren Cooke
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Julia R. Köhler
- Department of Infectious Diseases, Boston Children’s Hospital/Harvard Medical School, Boston, Massachusetts, USA
| | - Jana Patton-Vogt
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
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Gut Microbial Metabolite-Mediated Regulation of the Intestinal Barrier in the Pathogenesis of Inflammatory Bowel Disease. Nutrients 2021; 13:nu13124259. [PMID: 34959809 PMCID: PMC8704337 DOI: 10.3390/nu13124259] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/20/2021] [Accepted: 11/25/2021] [Indexed: 12/14/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory disease. The disease has a multifactorial aetiology, involving genetic, microbial as well as environmental factors. The disease pathogenesis operates at the host-microbe interface in the gut. The intestinal epithelium plays a central role in IBD disease pathogenesis. Apart from being a physical barrier, the epithelium acts as a node that integrates environmental, dietary, and microbial cues to calibrate host immune response and maintain homeostasis in the gut. IBD patients display microbial dysbiosis in the gut, combined with an increased barrier permeability that contributes to disease pathogenesis. Metabolites produced by microbes in the gut are dynamic indicators of diet, host, and microbial interplay in the gut. Microbial metabolites are actively absorbed or diffused across the intestinal lining to affect the host response in the intestine as well as at systemic sites via the engagement of cognate receptors. In this review, we summarize insights from metabolomics studies, uncovering the dynamic changes in gut metabolite profiles in IBD and their importance as potential diagnostic and prognostic biomarkers of disease. We focus on gut microbial metabolites as key regulators of the intestinal barrier and their role in the pathogenesis of IBD.
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3
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Vonhof EV, Piotto M, Holmes E, Lindon JC, Nicholson JK, Li JV. Improved Spatial Resolution of Metabolites in Tissue Biopsies Using High-Resolution Magic-Angle-Spinning Slice Localization NMR Spectroscopy. Anal Chem 2020; 92:11516-11519. [PMID: 32815363 DOI: 10.1021/acs.analchem.0c02377] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
High-resolution magic-angle-spinning 1H NMR spectroscopy (HR-MAS NMR) is a well-established technique for assessing the biochemical composition of intact tissue samples. In this study, we utilized a method based on HR-MAS NMR spectroscopy with slice localization (SLS) to achieve spatial resolution of metabolites. The obtained 7 slice spectra from each of the model samples (i.e., chicken thigh muscle with skin and murine renal biopsy including medulla (M) and cortex (C)) showed distinct metabolite compositions. Furthermore, we analyzed previously acquired 1H HR-MAS NMR spectra of separated cortex and medulla samples using multivariate statistical methods. Concentrations of glycerophosphocholine (GPC) were found to be significantly higher in the renal medulla compared to the cortex. Using GPC as a biomarker, we identified the tissue slices that were predominantly the cortex or medulla. This study demonstrates that HR-MAS SLS combined with multivariate statistics has the potential for identifying tissue heterogeneity and detailed biochemical characterization of complex tissue samples.
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Affiliation(s)
- Elisabeth V Vonhof
- Section of Nutrition Research, Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Martial Piotto
- Bruker Biospin SAS, 34 Rue de l'Industrie, 67160 Wissembourg, France
| | - Elaine Holmes
- Section of Nutrition Research, Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington Campus, London SW7 2AZ, United Kingdom.,The Australian National Phenome Centre, Health Futures Institute, Murdoch University, Harry Perkins Building, 5 Robin Warren Drive, Murdoch, Western Australia 6150, Australia
| | - John C Lindon
- Section of Nutrition Research, Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Jeremy K Nicholson
- The Australian National Phenome Centre, Health Futures Institute, Murdoch University, Harry Perkins Building, 5 Robin Warren Drive, Murdoch, Western Australia 6150, Australia
| | - Jia V Li
- Section of Nutrition Research, Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington Campus, London SW7 2AZ, United Kingdom
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4
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Madhu B, Uribe-Lewis S, Bachman M, Murrell A, Griffiths JR. Apc Min/+ tumours and normal mouse small intestines show linear metabolite concentration and DNA cytosine hydroxymethylation gradients from pylorus to colon. Sci Rep 2020; 10:13616. [PMID: 32788746 PMCID: PMC7423954 DOI: 10.1038/s41598-020-70579-w] [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] [Received: 02/05/2020] [Accepted: 07/29/2020] [Indexed: 12/15/2022] Open
Abstract
Topographical variations of metabolite concentrations have been reported in the duodenum, jejunum and ileum of the small intestine, and in human intestinal tumours from those regions, but there are no published metabolite concentrations measurements correlated with linear position in the mouse small intestine or intestinal tumours. Since DNA methylation dynamics are influenced by metabolite concentrations, they too could show linear anatomical variation. We measured metabolites by HR-MAS 1H NMR spectroscopy and DNA cytosine modifications by LC/MS, in normal small intestines of C57BL/6J wild-type mice, and in normal and tumour samples from ApcMin/+ mice. Wild-type mouse intestines showed approximately linear, negative concentration gradations from the pylorus (i.e. the junction with the stomach) of alanine, choline compounds, creatine, leucine and valine. ApcMin/+ mouse tumours showed negative choline and valine gradients, but a positive glycine gradient. 5-Hydroxymethylcytosine showed a positive gradient in the tumours. The linear gradients we found along the length of the mouse small intestine and in tumours contrast with previous reports of discrete concentration changes in the duodenum, jejunum and ileum. To our knowledge, this is also the first report of a systematic measurement of global levels of DNA cytosine modification in wild-type and ApcMin/+ mouse small intestine.
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Affiliation(s)
- Basetti Madhu
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK.
| | - Santiago Uribe-Lewis
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Martin Bachman
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK.,Discovery Science and Technology, Medicines Discovery Catapult, Alderley Park, Macclesfield, SK10 4TG, UK
| | - Adele Murrell
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK.,Centre for Regenerative Medicine, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - John R Griffiths
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
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5
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Mendonça Machado N, Torrinhas RS, Sala P, Ishida RK, Guarda IFMS, Moura EGHD, Sakai P, Santo MA, Linetzky Waitzberg D. Type 2 Diabetes Metabolic Improvement After Roux-en-Y Gastric Bypass May Include a Compensatory Mechanism That Balances Fatty Acid β and ω Oxidation. JPEN J Parenter Enteral Nutr 2020; 44:1417-1427. [PMID: 32654184 DOI: 10.1002/jpen.1960] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 06/28/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND More than half of patients who undergo Roux-en-Y gastric bypass (RYGB) can experience type 2 diabetes (T2D) remission, but the systemic and gastrointestinal (GI) metabolic mechanisms of this improvement are still elusive. METHODS Paired samples collected before and 3 months after RYGB from 28 women with obesity and T2D were analyzed by metabolomics with gas chromatography coupled to mass spectrometry. Samples include plasma (n = 56) and biopsies of gastric pouch (n = 18), gastric remnant (n = 10), duodenum (n = 16), jejunum (n = 18), and ileum (n = 18), collected by double-balloon enteroscopy. RESULTS After RYGB, improvements in body composition and weight-related and glucose homeostasis parameters were observed. Plasma-enriched metabolic pathways included arginine and proline metabolism, urea and tricarboxylic acid (TCA) cycles, gluconeogenesis, malate-aspartate shuttle, and carnitine synthesis. In GI tissue, we observed alterations of ammonia recycling and carnitine synthesis in gastric pouch, phenylacetate metabolism and trehalose degradation in duodenum and jejunum, ketone bodies in jejunum, and lactose degradation in ileum. Intermediates molecules of the TCA cycle were enriched, particularly in plasma, jejunum, and ileum. Fluctuations of dicarboxylic acids (DCAs) were relevant in several metabolomic tests, and metabolite alterations included aminomalonate and fumaric, malic, oxalic, and succinic acids. The product/substrate relationship between these molecules and its pathways may reflect a compensatory mechanism to balance metabolism. CONCLUSIONS RYGB was associated with systemic and GI metabolic reprogramming. DCA alterations link ω and β fatty acid oxidation to homeostatic mechanisms, including TCA cycle improvement.
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Affiliation(s)
- Natasha Mendonça Machado
- Department of Gastroenterology, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Raquel Susana Torrinhas
- Department of Gastroenterology, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Priscila Sala
- Department of Gastroenterology, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Robson Kiyoshi Ishida
- Gastrointestinal Endoscopy Unit, Department of Gastroenterology, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ismael Francisco Mota Siqueira Guarda
- Gastrointestinal Endoscopy Unit, Department of Gastroenterology, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Eduardo Guimarães Hourneaux de Moura
- Gastrointestinal Endoscopy Unit, Department of Gastroenterology, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Paulo Sakai
- Gastrointestinal Endoscopy Unit, Department of Gastroenterology, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Marco Aurélio Santo
- Bariatric and Metabolic Surgery Unit, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Dan Linetzky Waitzberg
- Department of Gastroenterology, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
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Abstract
In a healthy colon, the microbiota produces a vast amount of metabolites that are essential to maintaining homeostasis in the colon microenvironment. In fact, these metabolites produced by the microbiota have been linked to diseases such as obesity, cardiovascular disease, and colorectal cancer. In this study, we used healthy nonhuman primate models to investigate the relationship between microbiota and tissue metabolites. We found that both microbiota and metabolites have location-specific signatures along the intestine. Most importantly, we found that metabolites from food sources correlate with multiple bacteria in different intestinal locations. Overall, this work presents a systems-level map of the association between the microbiota and the metabolites in healthy nonhuman primates, provides candidates for experimental validation, and suggests a possibility to regulate the gut microbiota through specific prebiotic combinations. The intestinal microbiota is highly metabolically active and plays an important role in many metabolic processes absent from the human host. Altered microbiota metabolism has been linked to diseases such as obesity, cardiovascular disease, and colorectal cancer. However, there is a gap in the current knowledge on how the microbiota interact with its host in terms of metabolic interactions. Here, we performed an integrated analysis between the mucosa-associated microbiota and the mucosa metabolome in healthy, nonhuman primates to investigate these relationships. The microbiota composition was distinct at each tissue location, with variation by host individual also observed. Microbiota-metabolome dynamics were primarily driven by interactions in the distal colon. These interactions were strongly correlated with dietary component, indicating a possibility to modulate microbiota-metabolomic interactions using prebiotic strategies. IMPORTANCE In a healthy colon, the microbiota produces a vast amount of metabolites that are essential to maintaining homeostasis in the colon microenvironment. In fact, these metabolites produced by the microbiota have been linked to diseases such as obesity, cardiovascular disease, and colorectal cancer. In this study, we used healthy nonhuman primate models to investigate the relationship between microbiota and tissue metabolites. We found that both microbiota and metabolites have location-specific signatures along the intestine. Most importantly, we found that metabolites from food sources correlate with multiple bacteria in different intestinal locations. Overall, this work presents a systems-level map of the association between the microbiota and the metabolites in healthy nonhuman primates, provides candidates for experimental validation, and suggests a possibility to regulate the gut microbiota through specific prebiotic combinations.
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Garza DR, Taddese R, Wirbel J, Zeller G, Boleij A, Huynen MA, Dutilh BE. Metabolic models predict bacterial passengers in colorectal cancer. Cancer Metab 2020; 8:3. [PMID: 32055399 PMCID: PMC7008539 DOI: 10.1186/s40170-020-0208-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 01/07/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a complex multifactorial disease. Increasing evidence suggests that the microbiome is involved in different stages of CRC initiation and progression. Beyond specific pro-oncogenic mechanisms found in pathogens, metagenomic studies indicate the existence of a microbiome signature, where particular bacterial taxa are enriched in the metagenomes of CRC patients. Here, we investigate to what extent the abundance of bacterial taxa in CRC metagenomes can be explained by the growth advantage resulting from the presence of specific CRC metabolites in the tumor microenvironment. METHODS We composed lists of metabolites and bacteria that are enriched on CRC samples by reviewing metabolomics experimental literature and integrating data from metagenomic case-control studies. We computationally evaluated the growth effect of CRC enriched metabolites on over 1500 genome-based metabolic models of human microbiome bacteria. We integrated the metabolomics data and the mechanistic models by using scores that quantify the response of bacterial biomass production to CRC-enriched metabolites and used these scores to rank bacteria as potential CRC passengers. RESULTS We found that metabolic networks of bacteria that are significantly enriched in CRC metagenomic samples either depend on metabolites that are more abundant in CRC samples or specifically benefit from these metabolites for biomass production. This suggests that metabolic alterations in the cancer environment are a major component shaping the CRC microbiome. CONCLUSION Here, we show with in sillico models that supplementing the intestinal environment with CRC metabolites specifically predicts the outgrowth of CRC-associated bacteria. We thus mechanistically explain why a range of CRC passenger bacteria are associated with CRC, enhancing our understanding of this disease. Our methods are applicable to other microbial communities, since it allows the systematic investigation of how shifts in the microbiome can be explained from changes in the metabolome.
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Affiliation(s)
- Daniel R. Garza
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Postbus 9101, 6500 HB Nijmegen, The Netherlands
| | - Rahwa Taddese
- Department of Pathology, Radboud University Medical Center, Postbus 9101, 6500 Nijmegen, HB Netherlands
| | - Jakob Wirbel
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Georg Zeller
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Annemarie Boleij
- Department of Pathology, Radboud University Medical Center, Postbus 9101, 6500 Nijmegen, HB Netherlands
| | - Martijn A. Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Postbus 9101, 6500 HB Nijmegen, The Netherlands
| | - Bas E. Dutilh
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Postbus 9101, 6500 HB Nijmegen, The Netherlands
- Theoretical Biology and Bioinformatics, Sience4Life, Utrecht University, Hugo R. Kruytgebouw, Room Z-509, Padualaan 8, Utrecht, The Netherlands
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8
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Nilsson Å, Duan RD. Pancreatic and mucosal enzymes in choline phospholipid digestion. Am J Physiol Gastrointest Liver Physiol 2019; 316:G425-G445. [PMID: 30576217 DOI: 10.1152/ajpgi.00320.2018] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The digestion of choline phospholipids is important for choline homeostasis, lipid signaling, postprandial lipid and energy metabolism, and interaction with intestinal bacteria. The digestion is mediated by the combined action of pancreatic and mucosal enzymes. In the proximal small intestine, hydrolysis of phosphatidylcholine (PC) to 1-lyso-PC and free fatty acid (FFA) by the pancreatic phospholipase A2 IB coincides with the digestion of the dietary triacylglycerols by lipases, but part of the PC digestion is extended and must be mediated by other enzymes as the jejunoileal brush-border phospholipase B/lipase and mucosal secreted phospholipase A2 X. Absorbed 1-lyso-PC is partitioned in the mucosal cells between degradation and reacylation into chyle PC. Reutilization of choline for hepatic bile PC synthesis, and the reacylation of 1-lyso-PC into chylomicron PC by the lyso-PC-acyl-CoA-acyltransferase 3 are important features of choline recycling and postprandial lipid metabolism. The role of mucosal enzymes is emphasized by sphingomyelin (SM) being sequentially hydrolyzed by brush-border alkaline sphingomyelinase (alk-SMase) and neutral ceramidase to sphingosine and FFA, which are well absorbed. Ceramide and sphingosine-1-phosphate are generated and are both metabolic intermediates and important lipid messengers. Alk-SMase has anti-inflammatory effects that counteract gut inflammation and tumorigenesis. These may be mediated by multiple mechanisms including generation of sphingolipid metabolites and suppression of autotaxin induction and lyso-phosphatidic acid formation. Here we summarize current knowledge on the roles of pancreatic and mucosal enzymes in PC and SM digestion, and its implications in intestinal and liver diseases, bacterial choline metabolism in the gut, and cholesterol absorption.
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Affiliation(s)
- Åke Nilsson
- Department of Clow-linical Sciences Lund, Division of Medicine, Gastroenterology, Lund University , Lund , Sweden
| | - Rui-Dong Duan
- Gastroenterology and Nutrition Laboratory, Department of Clinical Sciences, Lund University , Lund , Sweden
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9
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Le Gall G, Guttula K, Kellingray L, Tett AJ, Ten Hoopen R, Kemsley EK, Savva GM, Ibrahim A, Narbad A. Metabolite quantification of faecal extracts from colorectal cancer patients and healthy controls. Oncotarget 2018; 9:33278-33289. [PMID: 30279959 PMCID: PMC6161785 DOI: 10.18632/oncotarget.26022] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 08/10/2018] [Indexed: 12/19/2022] Open
Abstract
Colorectal cancer (CRC), a primary cause of morbidity and mortality worldwide is expected to rise in the coming years. A better understanding of the metabolic changes taking place during the disease progression is needed for effective improvements of screening strategies and treatments. In the present study, Nuclear Magnetic Resonance (NMR) metabolomics was used to quantify the absolute concentrations of metabolites in faecal extracts from two cohorts of CRC patients and healthy controls. The quantification of over 80 compounds revealed that patients with CRC had increased faecal concentrations of branched chain fatty acids (BCFA), isovalerate and isobutyrate plus valerate and phenylacetate but diminished concentrations of amino acids, sugars, methanol and bile acids (deoxycholate, lithodeoxycholate and cholate). These results suggest that alterations in microbial activity and composition could have triggered an increase in utilisation of host intestinal slough cells and mucins and led to an increase in BCFA, valerate and phenylacetate. Concurrently, a general reduction in the microbial metabolic function may have led to reduced levels of other components (amino acids, sugars and bile acids) normally produced under healthy conditions. This study provides a thorough listing of the most abundant compounds found in human faecal waters and presents a template for absolute quantification of metabolites. The production of BCFA and phenylacetate in colonic carcinogenesis warrants further investigations.
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Affiliation(s)
| | - Kiran Guttula
- Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Lee Kellingray
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Adrian J Tett
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Rogier Ten Hoopen
- Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - E Kate Kemsley
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - George M Savva
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Ashraf Ibrahim
- Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Arjan Narbad
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
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Lourenço M, De Sordi L, Debarbieux L. The Diversity of Bacterial Lifestyles Hampers Bacteriophage Tenacity. Viruses 2018; 10:v10060327. [PMID: 29914064 PMCID: PMC6024678 DOI: 10.3390/v10060327] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/08/2018] [Accepted: 06/11/2018] [Indexed: 12/26/2022] Open
Abstract
Phage therapy is based on a simple concept: the use of a virus (bacteriophage) that is capable of killing specific pathogenic bacteria to treat bacterial infections. Since the pioneering work of Félix d’Herelle, bacteriophages (phages) isolated in vitro have been shown to be of therapeutic value. Over decades of study, a large number of rather complex mechanisms that are used by phages to hijack bacterial resources and to produce their progeny have been deciphered. While these mechanisms have been identified and have been studied under optimal conditions in vitro, much less is known about the requirements for successful viral infections in relevant natural conditions. This is particularly true in the context of phage therapy. Here, we highlight the parameters affecting phage replication in both in vitro and in vivo environments, focusing, in particular, on the mammalian digestive tract. We propose avenues for increasing the knowledge-guided implementation of phages as therapeutic tools.
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Affiliation(s)
- Marta Lourenço
- Department of Microbiology, Institut Pasteur, F-75015 Paris, France.
- Collège Doctoral, Sorbonne Université, F-75005 Paris, France.
| | - Luisa De Sordi
- Department of Microbiology, Institut Pasteur, F-75015 Paris, France.
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11
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Dietz C, Ehret F, Palmas F, Vandergrift LA, Jiang Y, Schmitt V, Dufner V, Habbel P, Nowak J, Cheng LL. Applications of high-resolution magic angle spinning MRS in biomedical studies II-Human diseases. NMR IN BIOMEDICINE 2017; 30:10.1002/nbm.3784. [PMID: 28915318 PMCID: PMC5690552 DOI: 10.1002/nbm.3784] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/21/2017] [Accepted: 07/10/2017] [Indexed: 05/06/2023]
Abstract
High-resolution magic angle spinning (HRMAS) MRS is a powerful method for gaining insight into the physiological and pathological processes of cellular metabolism. Given its ability to obtain high-resolution spectra of non-liquid biological samples, while preserving tissue architecture for subsequent histopathological analysis, the technique has become invaluable for biochemical and biomedical studies. Using HRMAS MRS, alterations in measured metabolites, metabolic ratios, and metabolomic profiles present the possibility to improve identification and prognostication of various diseases and decipher the metabolomic impact of drug therapies. In this review, we evaluate HRMAS MRS results on human tissue specimens from malignancies and non-localized diseases reported in the literature since the inception of the technique in 1996. We present the diverse applications of the technique in understanding pathological processes of different anatomical origins, correlations with in vivo imaging, effectiveness of therapies, and progress in the HRMAS methodology.
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Affiliation(s)
- Christopher Dietz
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard-MIT Health Sciences & Technology, Charlestown, Massachusetts 02129, USA
- Faculty of Medicine, Julius Maximilian University of Würzburg, 97080 Würzburg, Germany
| | - Felix Ehret
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard-MIT Health Sciences & Technology, Charlestown, Massachusetts 02129, USA
- Faculty of Medicine, Julius Maximilian University of Würzburg, 97080 Würzburg, Germany
| | - Francesco Palmas
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard-MIT Health Sciences & Technology, Charlestown, Massachusetts 02129, USA
- Department of Chemical and Geological Sciences, University of Cagliari, Cagliari, Sardinia, 09042 Italy
| | - Lindsey A. Vandergrift
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard-MIT Health Sciences & Technology, Charlestown, Massachusetts 02129, USA
| | - Yanni Jiang
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard-MIT Health Sciences & Technology, Charlestown, Massachusetts 02129, USA
- Department of Radiology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210029 China
| | - Vanessa Schmitt
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard-MIT Health Sciences & Technology, Charlestown, Massachusetts 02129, USA
- Faculty of Medicine, Julius Maximilian University of Würzburg, 97080 Würzburg, Germany
| | - Vera Dufner
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard-MIT Health Sciences & Technology, Charlestown, Massachusetts 02129, USA
- Department of Hematology and Oncology, Charité Medical University of Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Piet Habbel
- Department of Hematology and Oncology, Charité Medical University of Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Johannes Nowak
- Department of Diagnostic and Interventional Radiology, University Hospital of Würzburg, 97080 Würzburg, Germany
| | - Leo L. Cheng
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard-MIT Health Sciences & Technology, Charlestown, Massachusetts 02129, USA
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12
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Kinross J, Mirnezami R, Alexander J, Brown R, Scott A, Galea D, Veselkov K, Goldin R, Darzi A, Nicholson J, Marchesi JR. A prospective analysis of mucosal microbiome-metabonome interactions in colorectal cancer using a combined MAS 1HNMR and metataxonomic strategy. Sci Rep 2017; 7:8979. [PMID: 28827587 PMCID: PMC5566496 DOI: 10.1038/s41598-017-08150-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 07/07/2017] [Indexed: 02/07/2023] Open
Abstract
Colon cancer induces a state of mucosal dysbiosis with associated niche specific changes in the gut microbiota. However, the key metabolic functions of these bacteria remain unclear. We performed a prospective observational study in patients undergoing elective surgery for colon cancer without mechanical bowel preparation (n = 18). Using 16 S rRNA gene sequencing we demonstrated that microbiota ecology appears to be cancer stage-specific and strongly associated with histological features of poor prognosis. Fusobacteria (p < 0.007) and ε- Proteobacteria (p < 0.01) were enriched on tumour when compared to adjacent normal mucosal tissue, and fusobacteria and β-Proteobacteria levels increased with advancing cancer stage (p = 0.014 and 0.002 respecitvely). Metabonomic analysis using 1H Magic Angle Spinning Nuclear Magnetic Resonsance (MAS-NMR) spectroscopy, demonstrated increased abundance of taurine, isoglutamine, choline, lactate, phenylalanine and tyrosine and decreased levels of lipids and triglycerides in tumour relative to adjacent healthy tissue. Network analysis revealed that bacteria associated with poor prognostic features were not responsible for the modification of the cancer mucosal metabonome. Thus the colon cancer mucosal microbiome evolves with cancer stage to meet the demands of cancer metabolism. Passenger microbiota may play a role in the maintenance of cancer mucosal metabolic homeostasis but these metabolic functions may not be stage specific.
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Affiliation(s)
- James Kinross
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Reza Mirnezami
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
| | - James Alexander
- Division of Digestive Diseases, Faculty of Medicine, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Richard Brown
- School of Biosciences, Cardiff University, Cardiff, UK
| | - Alasdair Scott
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Dieter Galea
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Kirill Veselkov
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Rob Goldin
- Centre for Pathology, Faculty of Medicine, Imperial College London, London, UK
| | - Ara Darzi
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Jeremy Nicholson
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Julian R Marchesi
- Division of Digestive Diseases, Faculty of Medicine, Department of Surgery and Cancer, Imperial College London, London, UK.
- School of Biosciences, Cardiff University, Cardiff, UK.
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13
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Xiao L, Cao W, Liu G, Fang T, Wu X, Jia G, Chen X, Zhao H, Wang J, Wu C, Cai J. Arginine, N-carbamylglutamate, and glutamine exert protective effects against oxidative stress in rat intestine. ACTA ACUST UNITED AC 2016; 2:242-248. [PMID: 29767095 PMCID: PMC5941035 DOI: 10.1016/j.aninu.2016.04.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/12/2016] [Accepted: 04/18/2016] [Indexed: 12/21/2022]
Abstract
The objective of the current study is to evaluate the effects of dietary supplementation with arginine (ARG), N-carbamylglutamate (NCG), and glutamine (GLN) on rat intestinal morphology and antioxidant status under oxidative stress. Rats were fed for 30 d with one of the following iso-nitrogenous diets: basal diet (BD), BD plus 1% ARG, BD plus 0.1% NCG, and BD plus 1% GLN. On day 28, half of the rats fed BD were intraperitoneally injected with 12 mg/kg body weight of diquat (DT; i.e., the DT group) and the other half was intraperitoneally injected with sterile solution (i.e., the control group). The other diet groups were intraperitoneally injected with 12 mg/kg body weight of DT (i.e., DT + 1% GLN [DT + GLN], DT + 1% ARG [DT + ARG], and DT + 0.1% NCG [DT + NCG]). Rat jejunum samples obtained at 48 h after DT injection were analyzed. Results showed that DT significantly decreased catalase (CAT) activity and glutathione (GSH) content by 58.25% and 56.57%, respectively, and elevated malondialdehyde (MDA) content and crypt depth (CD) by 19.39% and 22.13%, respectively, in the jejunum (P < 0.05, relative to the control group). Compared with the DT group, the DT + GLN group exhibited significantly improved villus height (VH), villus width (VW), villus surface area (VSA), CD and total antioxidant capacity (T-AOC) activity (P < 0.05); the DT + ARG group exhibited significantly increased the ratio of VH to CD (H:D) and T-AOC activity (P < 0.05); the DT + GLN, DT + ARG and DT + NCG groups exhibited significantly enhanced CAT activity and GSH content as well as decreased MDA content (P < 0.05). Moreover, VH, VW, VSA, CD and GSH content in the DT + GLN group were higher whereas MDA content was lower compared with the corresponding values observed in both the DT + ARG and the DT + NCG groups (P < 0.05). The H:D ratio in the DT + ARG group significantly increased compared with that in the DT + NCG and DT + GLN groups (P < 0.05). Collectively, this study suggested that dietary supplementation with 1% GLN, 0.1% NCG, and 1% ARG was effective in enhancing the antioxidant status and maintaining the morphological structure of rat jejunum under oxidative stress; of these supplements, 1% GLN exerted the greatest effects on mitigating oxidative stress.
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Affiliation(s)
- Liang Xiao
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China.,Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Chengdu 611130, China
| | - Wei Cao
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China.,Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Chengdu 611130, China
| | - Guangmang Liu
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China.,Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Chengdu 611130, China
| | - Tingting Fang
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China.,Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Chengdu 611130, China
| | - Xianjian Wu
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China.,Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Chengdu 611130, China
| | - Gang Jia
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China.,Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Chengdu 611130, China
| | - Xiaoling Chen
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China.,Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Chengdu 611130, China
| | - Hua Zhao
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China.,Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Chengdu 611130, China
| | - Jing Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Caimei Wu
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China.,Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Chengdu 611130, China
| | - Jingyi Cai
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China.,Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Chengdu 611130, China
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14
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Chen J, Xie P, Lin J, He J, Zeng C, Chen J. Effects of microcystin-LR on gut microflora in different gut regions of mice. J Toxicol Sci 2016; 40:485-94. [PMID: 26165645 DOI: 10.2131/jts.40.485] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
To reveal the toxicological effects of the hepatotoxic microcystin-leucine arginine (MC-LR) on gut microbial community composition in different gut regions, we conducted a subchronic exposure of BALB/c mice to MC-LR via intragastric administration. Denaturing gradient gel electrophoresis (DGGE) was employed to profile the shifts of microbes after MC-LR treatment in the jejuno-ileum, caecum and colon. DGGE profiles analysis showed that MC-LR increased the microbial species richness (number of microbial bands) in the caecum and colon as well as microbial diversity (Shannon-Wiener index) in the caecum. The cluster analysis of DGGE profiles indicated that the microbial structures in the caecum and colon shifted significantly after MC-LR treatment, while that in the jejuno-ileum did not. All the relatively decreased gut microbes belonged to Clostridia in the Firmicutes phylum, and most of them were Lachnospiraceae. The increased ones derived from a variety of microbes including species from Porphyromonadaceae and Prevotellaceae in the Bacteroidetes phylum, as well as Lachnospiraceae and Ruminococcaceae in the Firmicutes phylum, and among which, the increase of Barnesiella in Porphyromonadaceae was most remarkable. In conclusion, subchronic exposure to MC-LR could disturb the balance of gut microbes in mice, and its toxicological effects varied between the jejuno-ileum and the other two gut regions.
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Affiliation(s)
- Jing Chen
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, China
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15
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Cao W, Liu G, Fang T, Wu X, Jia G, Zhao H, Chen X, Wu C, Wang J, Cai J. Effects of spermine on the morphology, digestive enzyme activities, and antioxidant status of jejunum in suckling rats. RSC Adv 2015. [DOI: 10.1039/c5ra15793e] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Spermine is a ubiquitous cellular component that plays vital roles in the maintenance of nucleic acids, regulation of kinase activities, protein synthesis, control of ion channel activities and renewal of the gut epithelium.
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16
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Rothhardt JE, Kröger C, Broadley SP, Fuchs TM. The orphan regulator ReiD of Salmonella enterica is essential for myo-inositol utilization. Mol Microbiol 2014; 94:700-12. [PMID: 25213016 DOI: 10.1111/mmi.12788] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2014] [Indexed: 11/30/2022]
Abstract
In Salmonella enterica serovar Typhimurium (S. Typhimurium), the genomic island GEI4417/4436 is responsible for the utilization of myo-inositol (MI) as carbon and energy source. Here, we report the characterization of a novel, island-encoded positive autoregulator termed ReiD (STM4423) that is specific to certain S. enterica strains and Escherichia coli strain ED1a able to use MI. ReiD was essential for growth with this polyol and also contributed to S. Typhimurium proliferation in swine caecum content. Providing higher copy numbers of ReiD reduced the long lag phase of 2 days during growth of S. Typhimurium in MI medium by 50%. In a heterologous host, expression of ReiD activated the transcription from the promoter of iolE/iolG, whose products catalyse the initial two steps in MI degradation. Episomal expression of iolE/iolG1 rescued the otherwise zero growth phenotype of a reiD deletion mutant in MI medium. Gel mobility shift assays with purified ReiD demonstrated directed interaction of ReiD with its own promoter and that of iolE. The repressor IolR bound the reiD promoter, implying that reiD is part of the IolR regulon. Taken together, the regulator ReiD is a trigger to accelerate the switch from more easily accessible nutrients to MI utilization by S. Typhimurium.
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Affiliation(s)
- Johannes E Rothhardt
- Lehrstuhl für Mikrobielle Ökologie, Zentralinstitut für Ernährungs- und Lebensmittelforschung (ZIEL), Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
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17
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Pacholczyk-Sienicka B, Radek M, Radek A, Jankowski S. Characterization of metabolites determined by means of 1H HR MAS NMR in intervertebral disc degeneration. MAGNETIC RESONANCE MATERIALS IN PHYSICS BIOLOGY AND MEDICINE 2014; 28:173-83. [PMID: 25108703 PMCID: PMC4385564 DOI: 10.1007/s10334-014-0457-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Revised: 07/18/2014] [Accepted: 07/22/2014] [Indexed: 12/02/2022]
Abstract
Object The objective of this study is the identification of metabolites by means of 1H high resolution magic angle spinning nuclear magnetic resonance (1H HR MAS NMR) spectroscopy and the evaluation of their applicability in distinguishing between healthy and degenerated disc tissues.
Materials and methods Differences between the metabolic profiles of healthy and degenerated disc tissues were studied by means of 1H HR MAS NMR. Analysis was performed for 81 disc tissue samples (control samples n = 21, degenerated disc tissue samples n = 60). Twenty six metabolites (amino acids, carbohydrates, and alcohols) were identified and quantified. Results The results indicate that the metabolic profile of degenerated discs is characterized by the presence of 2-propanol and the absence of scyllo-inositol and taurine. The concentrations of 2-propanol and lactate increase with age. Conclusion PCA analysis of ex vivo 1H HR MAS NMR data revealed the occurrence of two groups: healthy and degenerative disc tissues. The effects of insufficient nutrient supply of discs, leading to their degeneration and back pain, are discussed. Electronic supplementary material The online version of this article (doi:10.1007/s10334-014-0457-0) contains supplementary material, which is available to authorized users.
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18
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Rapid diagnosis and staging of colorectal cancer via high-resolution magic angle spinning nuclear magnetic resonance (HR-MAS NMR) spectroscopy of intact tissue biopsies. Ann Surg 2014; 259:1138-49. [PMID: 23860197 DOI: 10.1097/sla.0b013e31829d5c45] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To develop novel metabolite-based models for diagnosis and staging in colorectal cancer (CRC) using high-resolution magic angle spinning nuclear magnetic resonance (HR-MAS NMR) spectroscopy. BACKGROUND Previous studies have demonstrated that cancer cells harbor unique metabolic characteristics relative to healthy counterparts. This study sought to characterize metabolic properties in CRC using HR-MAS NMR spectroscopy. METHODS Between November 2010 and January 2012, 44 consecutive patients with confirmed CRC were recruited to a prospective observational study. Fresh tissue samples were obtained from center of tumor and 5 cm from tumor margin from surgical resection specimens. Samples were run in duplicate where tissue volume permitted to compensate for anticipated sample heterogeneity. Samples were subjected to HR-MAS NMR spectroscopic profiling and acquired spectral data were imported into SIMCA and MATLAB statistical software packages for unsupervised and supervised multivariate analysis. RESULTS A total of 171 spectra were acquired (center of tumor, n = 88; 5 cm from tumor margin, n = 83). Cancer tissue contained significantly increased levels of lactate (P < 0.005), taurine (P < 0.005), and isoglutamine (P < 0.005) and decreased levels of lipids/triglycerides (P < 0.005) relative to healthy mucosa (R2Y = 0.94; Q2Y = 0.72; area under the curve, 0.98). Colon cancer samples (n = 49) contained higher levels of acetate (P < 0.005) and arginine (P < 0.005) and lower levels of lactate (P < 0.005) relative to rectal cancer samples (n = 39). In addition unique metabolic profiles were observed for tumors of differing T-stage. CONCLUSIONS HR-MAS NMR profiling demonstrates cancer-specific metabolic signatures in CRC and reveals metabolic differences between colonic and rectal cancers. In addition, this approach reveals that tumor metabolism undergoes modification during local tumor advancement, offering potential in future staging and therapeutic approaches.
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19
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An magnetic resonance-based plasma metabonomic investigation on abnormal Savda in different complicated diseases. J TRADIT CHIN MED 2014; 34:166-72. [PMID: 24783928 DOI: 10.1016/s0254-6272(14)60073-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
OBJECTIVE To provide potential evidence for the existence of abnormal Savda, we assessed host metabonomic responses and dynamic changes occurring in various diseases using 1H nuclear magnetic resonance (NMR)-based metabonomics. METHODS Plasma samples taken from patients with complicated diseases with abnormal Savda (n = 140, including 35 cases each of diabetes, asthma, breast cancer, and cervical carcinoma) and from healthy controls (n = 35) were analyzed by 1H NMR (600 MHz), and the spectral profiles were analyzed by multivariate analysis using orthogonal projection to latent structure with discriminant analysis. RESULTS Supervised modeling of the data provided very good discrimination between patients and healthy controls. Compared with the healthy controls, the patient groups with different disease conditions displayed similar metabolic changes, characterized by lower creatine, creatinine, lactate, and amino acid levels (including isoleucine, leucine, valine, alanine, and 1-methylhistidine) and higher lipid levels (very low-density lipoproteins and unsaturated lipids). Additionally, cancer patients (breast and cervical) showed decreased myo-inositol, a-glucose, and beta-glucose, and increased pyruvate and carnitine in plasma. CONCLUSION The data indicate that decreased oxidative defense, liver function abnormalities, amino acid deficiencies, and energy metabolism disorders are common characteristics of complicated diseases, which may be related to the formation of abnormal Savda.
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20
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Staib L, Fuchs TM. From food to cell: nutrient exploitation strategies of enteropathogens. MICROBIOLOGY-SGM 2014; 160:1020-1039. [PMID: 24705229 DOI: 10.1099/mic.0.078105-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Upon entering the human gastrointestinal tract, foodborne bacterial enteropathogens encounter, among numerous other stress conditions, nutrient competition with the host organism and the commensal microbiota. The main carbon, nitrogen and energy sources exploited by pathogens during proliferation in, and colonization of, the gut have, however, not been identified completely. In recent years, a huge body of literature has provided evidence that most enteropathogens are equipped with a large set of specific metabolic pathways to overcome nutritional limitations in vivo, thus increasing bacterial fitness during infection. These adaptations include the degradation of myo-inositol, ethanolamine cleaved from phospholipids, fucose derived from mucosal glycoconjugates, 1,2-propanediol as the fermentation product of fucose or rhamnose and several other metabolites not accessible for commensal bacteria or present in competition-free microenvironments. Interestingly, the data reviewed here point to common metabolic strategies of enteric pathogens allowing the exploitation of nutrient sources that not only are present in the gut lumen, the mucosa or epithelial cells, but also are abundant in food. An increased knowledge of the metabolic strategies developed by enteropathogens is therefore a key factor to better control foodborne diseases.
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Affiliation(s)
- Lena Staib
- ZIEL, Abteilung Mikrobiologie, and Lehrstuhl für Mikrobielle Ökologie, Fakultät für Grundlagen der Biowissenschaften, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, 85350 Freising, Germany
| | - Thilo M Fuchs
- ZIEL, Abteilung Mikrobiologie, and Lehrstuhl für Mikrobielle Ökologie, Fakultät für Grundlagen der Biowissenschaften, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, 85350 Freising, Germany
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21
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Reprint of: Musculoskeletal system in the old age and the demand for healthy ageing biomarkers. Mech Ageing Dev 2014; 136-137:94-100. [PMID: 24662191 DOI: 10.1016/j.mad.2014.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Population ageing has emerged as a major demographic trend worldwide due to improved health and longevity. This global ageing phenomenon will have a major impact on health-care systems worldwide due to increased morbidity and greater needs for hospitalization/institutionalization. As the ageing population increases worldwide, there is an increasing awareness not only of increased longevity but also of the importance of "healthy ageing" and "quality of life". Yet, the age related chronic inflammation is believed to be pathogenic with regards to its contribution to frailty and degenerative disorders. In particular, the frailty syndrome is increasingly being considered as a key risk indicator of adverse health outcomes. In addition, elderly may be also prone to be resistant to anabolic stimuli which is likely a key factor in the loss of skeletal muscle mass with ageing. Vital to understand these key biological processes is the development of biological markers, through system biology approaches, aiding at strategies for tailored therapeutic and personalized nutritional program. Overall aim is to prevent or attenuate decline of key physiological functions required to live an active, independent life. This review focus on core indicators of health and functions in older adults, where nutrition and tailored personalized programs could exhibit preventive roles, and where the aid of metabolomics technologies are increasingly displaying potential in revealing key molecular mechanisms/targets linked to specific ageing and/or healthy ageing processes.
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22
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Wu X, Li N, Li H, Tang H. An optimized method for NMR-based plant seed metabolomic analysis with maximized polar metabolite extraction efficiency, signal-to-noise ratio, and chemical shift consistency. Analyst 2014; 139:1769-78. [DOI: 10.1039/c3an02100a] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
An optimized method for NMR-based plant seed metabolomic analysis was established with extraction solvent, cell-breaking method and extract-to-buffer ratio.
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Affiliation(s)
- Xiangyu Wu
- 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
- University of Chinese Academy of Sciences
| | - Ning Li
- 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
- University of Chinese Academy of Sciences
| | - Hongde Li
- 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
- University of Chinese Academy of Sciences
| | - Huiru Tang
- 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
- University of Chinese Academy of Sciences
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23
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Li H, An Y, Zhang L, Lei H, Zhang L, Wang Y, Tang H. Combined NMR and GC–MS Analyses Revealed Dynamic Metabolic Changes Associated with the Carrageenan-Induced Rat Pleurisy. J Proteome Res 2013; 12:5520-34. [DOI: 10.1021/pr400440d] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Huihui Li
- 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, University of Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Yanpeng An
- 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, University of Chinese Academy of Sciences, Wuhan 430071, P. R. China
- State
Key Laboratory of Genetic Engineering, Biospectroscopy and Metabolomics,
School of Life Sciences, Fudan University, Shanghai 200433, P. R. China
| | - Lulu Zhang
- 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, University of Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Hehua Lei
- 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, University of Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Limin Zhang
- 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, University of Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - 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, University of Chinese Academy of Sciences, Wuhan 430071, P. R. China
- Collaborative
Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, P. R. China
| | - Huiru Tang
- 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, University of Chinese Academy of Sciences, Wuhan 430071, P. R. China
- State
Key Laboratory of Genetic Engineering, Biospectroscopy and Metabolomics,
School of Life Sciences, Fudan University, Shanghai 200433, P. R. China
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24
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Musculoskeletal system in the old age and the demand for healthy ageing biomarkers. Mech Ageing Dev 2013; 134:541-7. [DOI: 10.1016/j.mad.2013.11.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 10/24/2013] [Accepted: 11/11/2013] [Indexed: 12/19/2022]
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25
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Bishop AC, Ganguly S, Solis NV, Cooley BM, Jensen-Seaman MI, Filler SG, Mitchell AP, Patton-Vogt J. Glycerophosphocholine utilization by Candida albicans: role of the Git3 transporter in virulence. J Biol Chem 2013; 288:33939-33952. [PMID: 24114876 DOI: 10.1074/jbc.m113.505735] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Candida albicans contains four ORFs (GIT1,2,3,4) predicted to encode proteins involved in the transport of glycerophosphodiester metabolites. Previously, we reported that Git1, encoded by ORF 19.34, is responsible for the transport of intact glycerophosphoinositol but not glycerophosphocholine (GroPCho). Here, we report that a strain lacking both GIT3 (ORF 19.1979) and GIT4 (ORF 19.1980) is unable to transport [(3)H]GroPCho into the cell. In the absence of a GroPCho transporter, C. albicans can utilize GroPCho via a mechanism involving extracellular hydrolysis. Upon reintegration of either GIT3 or GIT4 into the genome, measurable uptake of [(3)H]GroPCho is observed. Transport assays and kinetic analyses indicate that Git3 has the greater transport velocity. We present evidence that GDE1 (ORF 19.3936) codes for an enzyme with glycerophosphodiesterase activity against GroPCho. Homozygous deletion of GDE1 results in a buildup of internal GroPCho that is restored to wild type levels by reintegration of GDE1 into the genome. The transcriptional regulator, Pho4, is shown to regulate the expression of GIT3, GIT4, and GDE1. Finally, Git3 is shown to be required for full virulence in a mouse model of disseminated candidiasis, and Git3 sequence orthologs are present in other pathogenic Candida species. In summary, we have characterized multiple aspects of GroPCho utilization by C. albicans and have demonstrated that GroPCho transport plays a key role in the growth of the organism in the host.
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Affiliation(s)
- Andrew C Bishop
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282
| | - Shantanu Ganguly
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Norma V Solis
- Division of Infectious Disease, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California 90502
| | - Benjamin M Cooley
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282
| | | | - Scott G Filler
- Division of Infectious Disease, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California 90502; David Geffen School of Medicine at UCLA, Los Angeles, California 90024
| | - Aaron P Mitchell
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Jana Patton-Vogt
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282.
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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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Metabolomics of colorectal cancer: past and current analytical platforms. Anal Bioanal Chem 2013; 405:5013-30. [PMID: 23494270 DOI: 10.1007/s00216-013-6777-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 01/18/2013] [Accepted: 01/22/2013] [Indexed: 02/07/2023]
Abstract
Metabolomics is coming of age as an important area of investigation which may help reveal answers to questions left unanswered or only partially understood from proteomic or genomic approaches. Increased knowledge of the relationship of genes and proteins to smaller biomolecules (metabolites) will advance our ability to diagnose, treat, and perhaps prevent cancer and other diseases that have eluded scientists for generations. Colorectal tumors are the second leading cause of cancer mortality in the USA, and the incidence is rising. Many patients present late, after the onset of symptoms, when the tumor has spread from the primary site. Once metastases have occurred, the prognosis is significantly worse. Understanding alterations in metabolic profiles that occur with tumor onset and progression could lead to better diagnostic tests as well as uncover new approaches to treat or even prevent colorectal cancer (CRC). In this review, we explore the various analytical technologies that have been applied in CRC metabolomics research and summarize all metabolites measured in CRC and integrate them into metabolic pathways. Early studies with nuclear magnetic resonance and gas-chromatographic mass spectrometry suggest that tumor cells are characterized by aerobic glycolysis, increased purine metabolism for DNA synthesis, and protein synthesis. Liquid chromatography, capillary electrophoresis, and ion mobility, each coupled with mass spectrometry, promise to advance the field and provide new insight into metabolic pathways used by cancer cells. Studies with improved technology are needed to identify better biomarkers and targets for treatment or prevention of CRC.
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Jiménez B, Mirnezami R, Kinross J, Cloarec O, Keun HC, Holmes E, Goldin RD, Ziprin P, Darzi A, Nicholson JK. 1H HR-MAS NMR spectroscopy of tumor-induced local metabolic "field-effects" enables colorectal cancer staging and prognostication. J Proteome Res 2013; 12:959-68. [PMID: 23240862 DOI: 10.1021/pr3010106] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Colorectal cancer (CRC) is a major cause of morbidity and mortality in developed countries. Despite operative advances and the widespread adoption of combined-modality treatment, the 5-year survival rarely exceeds 60%. Improving our understanding of the biological processes involved in CRC development and progression will help generate new diagnostic and prognostic approaches. Previous studies have identified altered metabolism as a common feature in carcinogenesis, and quantitative measurement of this altered activity (metabonomics/metabolomics) has the potential to generate novel metabolite-based biomarkers for CRC diagnosis, staging and prognostication. In the present study we applied high-resolution magic angle spinning nuclear magnetic resonance (HR-MAS NMR) spectroscopy to analyze metabolites in intact tumor samples (n = 83) and samples of adjacent mucosa (n = 87) obtained from 26 patients undergoing surgical resection for CRC. Orthogonal partial least-squares discriminant analysis (OPLS-DA) of metabolic profiles identified marked biochemical differences between cancer tissue and adjacent mucosa (R(2) = 0.72; Q(2) = 0.45; AUC = 0.91). Taurine, isoglutamine, choline, lactate, phenylalanine, tyrosine (increased concentrations in tumor tissue) together with lipids and triglycerides (decreased concentrations in tumor tissue) were the most discriminant metabolites between the two groups in the model. In addition, tumor tissue metabolic profiles were able to distinguish between tumors of different T- and N-stages according to TNM classification. Moreover, we found that tumor-adjacent mucosa (10 cm from the tumor margin) harbors unique metabolic field changes that distinguish tumors according to T- and N-stage with higher predictive capability than tumor tissue itself and are accurately predictive of 5-year survival (AUC = 0.88), offering a highly novel means of tumor classification and prognostication in CRC.
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Affiliation(s)
- Beatriz Jiménez
- Section of Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, SW7 2AZ London, United Kingdom
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Kuang H, Li Z, Peng C, Liu L, Xu L, Zhu Y, Wang L, Xu C. Metabonomics Approaches and the Potential Application in Foodsafety Evaluation. Crit Rev Food Sci Nutr 2012; 52:761-74. [DOI: 10.1080/10408398.2010.508345] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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30
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Martin FPJ, Collino S, Rezzi S, Kochhar S. Metabolomic applications to decipher gut microbial metabolic influence in health and disease. Front Physiol 2012; 3:113. [PMID: 22557976 PMCID: PMC3337463 DOI: 10.3389/fphys.2012.00113] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 04/05/2012] [Indexed: 12/22/2022] Open
Abstract
Dietary preferences and nutrients composition have been shown to influence human and gut microbial metabolism, which ultimately has specific effects on health and diseases’ risk. Increasingly, results from molecular biology and microbiology demonstrate the key role of the gut microbiota metabolic interface to the overall mammalian host’s health status. There is therefore raising interest in nutrition research to characterize the molecular foundations of the gut microbial–mammalian cross talk at both physiological and biochemical pathway levels. Tackling these challenges can be achieved through systems biology approaches, such as metabolomics, to underpin the highly complex metabolic exchanges between diverse biological compartments, including organs, systemic biofluids, and microbial symbionts. By the development of specific biomarkers for prediction of health and disease, metabolomics is increasingly used in clinical applications as regard to disease etiology, diagnostic stratification, and potentially mechanism of action of therapeutical and nutraceutical solutions. Surprisingly, an increasing number of metabolomics investigations in pre-clinical and clinical studies based on proton nuclear magnetic resonance (1H NMR) spectroscopy and mass spectrometry provided compelling evidence that system wide and organ-specific biochemical processes are under the influence of gut microbial metabolism. This review aims at describing recent applications of metabolomics in clinical fields where main objective is to discern the biochemical mechanisms under the influence of the gut microbiota, with insight into gastrointestinal health and diseases diagnostics and improvement of homeostasis metabolic regulation.
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Affiliation(s)
- François-Pierre J Martin
- Metabolomics and Biomarkers, Department of BioAnalytical Science, Nestlé Research Center, Nestec Ltd. Lausanne, Switzerland
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31
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Tian Y, Zhang L, Wang Y, Tang H. Age-related topographical metabolic signatures for the rat gastrointestinal contents. J Proteome Res 2011; 11:1397-411. [PMID: 22129435 DOI: 10.1021/pr2011507] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Symbiotic gut microbiota is essential for mammalian physiology and analyzing the metabolite compositions of gastrointestinal contents is vital for understanding the microbiome-host interactions. To understand the developmental dependence of the topographical metabolic signatures for the rat gastrointestinal contents, we systematically characterized the metabolite compositional variations of the contents in rat jejunum, ileum, cecum, and colon for two age-groups using (1)H NMR spectroscopy and multivariate analysis. Significant topographical metabolic variations were present for the jejunal, ileal, cecal, colonic contents, and feces, reflecting the absorption functions for each intestinal region and the gut microbiota therein. The concentrations of amino acids, lactate, creatine, choline, bile acids, uracil and urocanate decreased drastically from jejunal to ileal contents followed with steady decreases from cecal content to feces. Short-chain fatty acids (SCFAs) and arabinoxylan-related carbohydrates had highest levels in cecal content and feces, respectively. Such topographical metabolic signatures for the intestinal contents varied with animal age highlighted by the level changes for lactate, choline, taurine, amino acids, carbohydrates, keto-acids, and SCFAs. These findings provided essential information for the topographical metabolic variations in the gastrointestinal tract and demonstrated metabolic profiling as a useful approach for understanding host-microbiome interactions and functional status of the gastrointestinal regions.
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Affiliation(s)
- Yuan Tian
- 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 430071, PR China
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Heath P, Claus SP. Assessing hepatic metabolic changes during progressive colonization of germ-free mouse by 1H NMR spectroscopy. J Vis Exp 2011:3642. [PMID: 22215201 DOI: 10.3791/3642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
It is well known that gut bacteria contribute significantly to the host homeostasis, providing a range of benefits such as immune protection and vitamin synthesis. They also supply the host with a considerable amount of nutrients, making this ecosystem an essential metabolic organ. In the context of increasing evidence of the link between the gut flora and the metabolic syndrome, understanding the metabolic interaction between the host and its gut microbiota is becoming an important challenge of modern biology. Colonization (also referred to as normalization process) designates the establishment of micro-organisms in a former germ-free animal. While it is a natural process occurring at birth, it is also used in adult germ-free animals to control the gut floral ecosystem and further determine its impact on the host metabolism. A common procedure to control the colonization process is to use the gavage method with a single or a mixture of micro-organisms. This method results in a very quick colonization and presents the disadvantage of being extremely stressful. It is therefore useful to minimize the stress and to obtain a slower colonization process to observe gradually the impact of bacterial establishment on the host metabolism. In this manuscript, we describe a procedure to assess the modification of hepatic metabolism during a gradual colonization process using a non-destructive metabolic profiling technique. We propose to monitor gut microbial colonization by assessing the gut microbial metabolic activity reflected by the urinary excretion of microbial co-metabolites by (1)H NMR-based metabolic profiling. This allows an appreciation of the stability of gut microbial activity beyond the stable establishment of the gut microbial ecosystem usually assessed by monitoring fecal bacteria by DGGE (denaturing gradient gel electrophoresis). The colonization takes place in a conventional open environment and is initiated by a dirty litter soiled by conventional animals, which will serve as controls. Rodents being coprophagous animals, this ensures a homogenous colonization as previously described. Hepatic metabolic profiling is measured directly from an intact liver biopsy using (1)H High Resolution Magic Angle Spinning NMR spectroscopy. This semi-quantitative technique offers a quick way to assess, without damaging the cell structure, the major metabolites such as triglycerides, glucose and glycogen in order to further estimate the complex interaction between the colonization process and the hepatic metabolism. This method can also be applied to any tissue biopsy.
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Affiliation(s)
- Peter Heath
- School of Chemistry, Food and Pharmacy, The University of Reading
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Martin FPJ, Collino S, Rezzi S. 1H NMR-based metabonomic applications to decipher gut microbial metabolic influence on mammalian health. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2011; 49 Suppl 1:S47-S54. [PMID: 22290709 DOI: 10.1002/mrc.2810] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Recent advances in molecular biology and microbiology have increased awareness on the importance of the gut microbiota to the overall mammalian host's health status. There is therefore increasing interest in nutrition research to characterise the molecular foundations of the gut microbial mammalian crosstalk at both physiological and biochemical pathway levels. Tackling these challenges can be achieved through systems biology strategies based on the measurement of metabolites to assess the highly complex metabolic exchanges between diverse biological compartments, including organs, biofluids and microbial symbionts. By opening a direct biochemical window into the metabolome, metabonomics is uniquely suited for the identification of biomarkers providing better understanding of these complex metabolic processes. Recent applications of top-down system biology based on (1)H NMR spectroscopy coupled to advanced chemometric modelling approaches provided compelling evidence that system-wide and organ-specific changes in biochemical processes may be finely tuned by gut microbial activities. This review aims at describing current advances in NMR-based metabonomics where the main objective is to discern the molecular pathways and biochemical mechanisms under the influence of the gut microbiota. Furthermore, emphasis is given on nutritional approaches, where the quest for homeostatic balance is dependent not only on the host but also on the nutritional modulation of the gut microbiota-host metabolic interactions, using, for instance, probiotics and prebiotics.
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Affiliation(s)
- François-Pierre J Martin
- BioAnalytical Science, Metabonomics & Biomarkers, Nestlé Research Center, Lausanne, Switzerland.
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34
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Chen W, Zhou X, Huang D, Chen F, Du X. Metabolic Profiling of Human Colorectal Cancer Using High Resolution 1H Nuclear Magnetic Resonance Spectroscopy. CHINESE J CHEM 2011. [DOI: 10.1002/cjoc.201180423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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35
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Robust utilization of phospholipase-generated metabolites, glycerophosphodiesters, by Candida albicans: role of the CaGit1 permease. EUKARYOTIC CELL 2011; 10:1618-27. [PMID: 21984707 DOI: 10.1128/ec.05160-11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Glycerophosphodiesters are the products of phospholipase-mediated deacylation of phospholipids. In Saccharomyces cerevisiae, a single gene, GIT1, encodes a permease responsible for importing glycerophosphodiesters, such as glycerophosphoinositol and glycerophosphocholine, into the cell. In contrast, the Candida albicans genome contains four open reading frames (ORFs) with a high degree of similarity to S. cerevisiae GIT1 (ScGIT1) Here, we report that C. albicans utilizes glycerophosphoinositol (GroPIns) and glycerophosphocholine (GroPCho) as sources of phosphate at both mildly acidic and physiological pHs. Insertional mutagenesis of C. albicans GIT1 (CaGIT1) (orf19.34), the ORF most similar to ScGit1, abolished the ability of cells to use GroPIns as a phosphate source at acidic pH and to transport [(3)H]GroPIns at acidic and physiological pHs, while reintegration of a GIT1 allele into the genome restored those functions. Several lines of evidence, including the detection of internal [(3)H]GroPIns, indicated that GroPIns is transported intact through CaGit1. GroPIns transport was shown to conform to Michaelis-Menten kinetics, with an apparent K(m) of 28 ± 6 μM. Notably, uptake of label from [(3)H]GroPCho was found to be roughly 50-fold greater than uptake of label from [(3)H]GroPIns and roughly 500-fold greater than the equivalent activity in S. cerevisiae. Insertional mutagenesis of CaGIT1 had no effect on the utilization of GroPCho as a phosphate source or on the uptake of label from [(3)H]GroPCho. Growth under low-phosphate conditions was shown to increase label uptake from both [(3)H]GroPIns and [(3)H]GroPCho. Screening of a transcription factor deletion set identified CaPHO4 as required for the utilization of GroPIns, but not GroPCho, as a phosphate source.
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Azcárate-Peril MA, Sikes M, Bruno-Bárcena JM. The intestinal microbiota, gastrointestinal environment and colorectal cancer: a putative role for probiotics in prevention of colorectal cancer? Am J Physiol Gastrointest Liver Physiol 2011; 301:G401-24. [PMID: 21700901 PMCID: PMC3774253 DOI: 10.1152/ajpgi.00110.2011] [Citation(s) in RCA: 159] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Colorectal cancer (CRC) is the third most commonly diagnosed cancer in the United States, and, even though 5-15% of the total CRC cases can be attributed to individual genetic predisposition, environmental factors could be considered major factors in susceptibility to CRC. Lifestyle factors increasing the risks of CRC include elevated body mass index, obesity, and reduced physical activity. Additionally, a number of dietary elements have been associated with higher or lower incidence of CRC. In this context, it has been suggested that diets high in fruit and low in meat might have a protective effect, reducing the incidence of colorectal adenomas by modulating the composition of the normal nonpathogenic commensal microbiota. In addition, it has been demonstrated that changes in abundance of taxonomic groups have a profound impact on the gastrointestinal physiology, and an increasing number of studies are proposing that the microbiota mediates the generation of dietary factors triggering colon cancer. High-throughput sequencing and molecular taxonomic technologies are rapidly filling the knowledge gaps left by conventional microbiology techniques to obtain a comprehensive catalog of the human intestinal microbiota and their associated metabolic repertoire. The information provided by these studies will be essential to identify agents capable of modulating the massive amount of gut bacteria in safe noninvasive manners to prevent CRC. Probiotics, defined as "live microorganisms which, when administered in adequate amounts, confer a health benefit on the host" (219), are capable of transient modulation of the microbiota, and their beneficial effects include reinforcement of the natural defense mechanisms and protection against gastrointestinal disorders. Probiotics have been successfully used to manage infant diarrhea, food allergies, and inflammatory bowel disease; hence, the purpose of this review was to examine probiotic metabolic activities that may have an effect on the prevention of CRC by scavenging toxic compounds or preventing their generation in situ. Additionally, a brief consideration is given to safety evaluation and production methods in the context of probiotics efficacy.
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Affiliation(s)
- M. Andrea Azcárate-Peril
- 1Department of Cell and Molecular Physiology, University of North Carolina School of Medicine, Chapel Hill;
| | - Michael Sikes
- 2Department of Microbiology, North Carolina State University, Raleigh, North Carolina
| | - José M. Bruno-Bárcena
- 2Department of Microbiology, North Carolina State University, Raleigh, North Carolina
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37
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He Q, Ren P, Kong X, Xu W, Tang H, Yin Y, Wang Y. Intrauterine growth restriction alters the metabonome of the serum and jejunum in piglets. MOLECULAR BIOSYSTEMS 2011; 7:2147-55. [PMID: 21584308 DOI: 10.1039/c1mb05024a] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Intrauterine growth restriction (IUGR) is not only an underlying factor for stunted postnatal growth and newborn deaths, but also associated with disease prevalence, such as hypertension and diabetes, in both adult humans and animals. To investigate the metabolic status of IUGR, the differences in serum and jejunal tissue metabonome were examined in IUGR and normal weight 21 day old piglets. IUGR piglets had a significantly lower birth weight (785 ± 42 g vs. 1451 ± 124 g), weaned weight (3053 ± 375 g vs. 6489 ± 545 g) and average daily gain (108 ± 16 g vs. 240 ± 21 g) than normal weight piglets (p < 0.05). IUGR piglets also had a shorter villus height and smaller villus height to crypt depth ratio (p < 0.05) in jejunum. An NMR-based metabonomic study found that serum levels of glycoprotein, albumin and threonine were higher in IUGR than in normal weight piglets, while serum levels of HDL, lipids, unsaturated lipids, glycerophosphorylcholine, myo-inositol, citrate, glutamine and tyrosine were lower in IUGR piglets (p < 0.05). In addition, marked changes in jejunal metabolites, including elevated levels of lipids and unsaturated lipids, and decreased levels of valine, alanine, glutamine, glutamate, choline, glycerophosphorylcholine, trimethylamine-N-oxide, scyllo-inositol, lactate, creatine, glucose, galactose, phenylalanine, tyrosine, glutathione, inosine and taurine were observed in IUGR piglets (p < 0.05). These novel findings indicate that IUGR piglets have a distinctive metabolic status compared to normal weight piglets, including changes in lipogenesis, lipid oxidation, energy supply and utilization, amino acid and protein metabolism, and antioxidant ability; these changes could contribute to impaired growth and jejunal function.
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Affiliation(s)
- Qinghua He
- 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
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38
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Wang H, Tso VK, Slupsky CM, Fedorak RN. Metabolomics and detection of colorectal cancer in humans: a systematic review. Future Oncol 2011; 6:1395-406. [PMID: 20919825 DOI: 10.2217/fon.10.107] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Metabolomics represents one of the new omics sciences and capitalizes on the unique presence and concentration of small molecules in tissues and body fluids to construct a 'fingerprint' that can be unique to the individual and, within that individual, unique to environmental influences, including health and disease states. As such, metabolomics has the potential to serve an important role in diagnosis and management of human conditions. Colorectal cancer is a major public health concern. Current population-based screening methods are suboptimal and whether metabolomics could represent a new tool of screening is under investigation. The purpose of this systematic review is to summarize existing literature on metabolomics and colorectal cancer, in terms of diagnostic accuracies and distinguishing metabolites. Eight studies are included. A total of 12 metabolites (taurine, lactate, choline, inositol, glycine, phosphocholine, proline, phenylalanine, alanine, threonine, valine and leucine) were found to be more prevalent in colorectal cancer and glucose was found to be in higher proportion in control specimens using tissue metabolomics. Serum and urine metabolomics identified several other differential metabolites between controls and colorectal cancer patients. This article highlights the novelty of the field of metabolomics in colorectal oncology.
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Affiliation(s)
- Haili Wang
- University of Alberta, 130 University Campus, 112th St & 85th Avenue, Edmonton, AB, Canada
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39
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Martin FPJ, Montoliu I, Kochhar S, Rezzi S. Chemometric strategy for modeling metabolic biological space along the gastrointestinal tract and assessing microbial influences. Anal Chem 2010; 82:9803-11. [PMID: 21033673 DOI: 10.1021/ac102015n] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Over the past decade, the analysis of metabolic data with advanced chemometric techniques has offered the potential to explore functional relationships among biological compartments in relation to the structure and function of the intestine. However, the employed methodologies, generally based on regression modeling techniques, have given emphasis to region-specific metabolic patterns, while providing only limited insights into the spatiotemporal metabolic features of the complex gastrointestinal system. Hence, novel approaches are needed to analyze metabolic data to reconstruct the metabolic biological space associated with the evolving structures and functions of an organ such as the gastrointestinal tract. Here, we report the application of multivariate curve resolution (MCR) methodology to model metabolic relationships along the gastrointestinal compartments in relation to its structure and function using data from our previous metabonomic analysis. The method simultaneously summarizes metabolite occurrence and contribution to continuous metabolic signatures of the different biological compartments of the gut tract. This methodology sheds new light onto the complex web of metabolic interactions with gut symbionts that modulate host cell metabolism in surrounding gut tissues. In the future, such an approach will be key to provide new insights into the dynamic onset of metabolic deregulations involved in region-specific gastrointestinal disorders, such as Crohn's disease or ulcerative colitis.
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40
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Bathen TF, Sitter B, Sjøbakk TE, Tessem MB, Gribbestad IS. Magnetic resonance metabolomics of intact tissue: a biotechnological tool in cancer diagnostics and treatment evaluation. Cancer Res 2010; 70:6692-6. [PMID: 20699363 DOI: 10.1158/0008-5472.can-10-0437] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Personalized medicine is increasingly important in cancer treatment for its role in staging and its potential to improve stratification of patients. Different types of molecules, genes, proteins, and metabolites are being extensively explored as potential biomarkers. This review discusses the major findings and potential of tissue metabolites determined by high-resolution magic angle spinning magnetic resonance spectroscopy for cancer detection, characterization, and treatment monitoring.
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Affiliation(s)
- Tone F Bathen
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Trondheim, Norway.
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Tessem MB, Selnæs KM, Sjursen W, Tranø G, Giskeødegård GF, Bathen TF, Gribbestad IS, Hofsli E. Discrimination of Patients with Microsatellite Instability Colon Cancer using 1H HR MAS MR Spectroscopy and Chemometric Analysis. J Proteome Res 2010; 9:3664-70. [DOI: 10.1021/pr100176g] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- May-Britt Tessem
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology (NTNU), Trondheim, Norway, Department of Laboratory Medicine Children’s and Women’s Health, NTNU, Trondheim, Norway, Department of Pathology and Medical Genetics, St. Olavs University Hospital, Trondheim, Norway, Department of Surgery, Levanger Hospital, Sykehuset Innherred, Levanger, Norway, and Department of Oncology, St. Olavs University Hospital, Trondheim, Norway
| | - Kirsten M. Selnæs
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology (NTNU), Trondheim, Norway, Department of Laboratory Medicine Children’s and Women’s Health, NTNU, Trondheim, Norway, Department of Pathology and Medical Genetics, St. Olavs University Hospital, Trondheim, Norway, Department of Surgery, Levanger Hospital, Sykehuset Innherred, Levanger, Norway, and Department of Oncology, St. Olavs University Hospital, Trondheim, Norway
| | - Wenche Sjursen
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology (NTNU), Trondheim, Norway, Department of Laboratory Medicine Children’s and Women’s Health, NTNU, Trondheim, Norway, Department of Pathology and Medical Genetics, St. Olavs University Hospital, Trondheim, Norway, Department of Surgery, Levanger Hospital, Sykehuset Innherred, Levanger, Norway, and Department of Oncology, St. Olavs University Hospital, Trondheim, Norway
| | - Gerd Tranø
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology (NTNU), Trondheim, Norway, Department of Laboratory Medicine Children’s and Women’s Health, NTNU, Trondheim, Norway, Department of Pathology and Medical Genetics, St. Olavs University Hospital, Trondheim, Norway, Department of Surgery, Levanger Hospital, Sykehuset Innherred, Levanger, Norway, and Department of Oncology, St. Olavs University Hospital, Trondheim, Norway
| | - Guro F. Giskeødegård
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology (NTNU), Trondheim, Norway, Department of Laboratory Medicine Children’s and Women’s Health, NTNU, Trondheim, Norway, Department of Pathology and Medical Genetics, St. Olavs University Hospital, Trondheim, Norway, Department of Surgery, Levanger Hospital, Sykehuset Innherred, Levanger, Norway, and Department of Oncology, St. Olavs University Hospital, Trondheim, Norway
| | - Tone F. Bathen
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology (NTNU), Trondheim, Norway, Department of Laboratory Medicine Children’s and Women’s Health, NTNU, Trondheim, Norway, Department of Pathology and Medical Genetics, St. Olavs University Hospital, Trondheim, Norway, Department of Surgery, Levanger Hospital, Sykehuset Innherred, Levanger, Norway, and Department of Oncology, St. Olavs University Hospital, Trondheim, Norway
| | - Ingrid S. Gribbestad
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology (NTNU), Trondheim, Norway, Department of Laboratory Medicine Children’s and Women’s Health, NTNU, Trondheim, Norway, Department of Pathology and Medical Genetics, St. Olavs University Hospital, Trondheim, Norway, Department of Surgery, Levanger Hospital, Sykehuset Innherred, Levanger, Norway, and Department of Oncology, St. Olavs University Hospital, Trondheim, Norway
| | - Eva Hofsli
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology (NTNU), Trondheim, Norway, Department of Laboratory Medicine Children’s and Women’s Health, NTNU, Trondheim, Norway, Department of Pathology and Medical Genetics, St. Olavs University Hospital, Trondheim, Norway, Department of Surgery, Levanger Hospital, Sykehuset Innherred, Levanger, Norway, and Department of Oncology, St. Olavs University Hospital, Trondheim, Norway
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Beckonert O, Coen M, Keun HC, Wang Y, Ebbels TMD, Holmes E, Lindon JC, Nicholson JK. High-resolution magic-angle-spinning NMR spectroscopy for metabolic profiling of intact tissues. Nat Protoc 2010; 5:1019-32. [PMID: 20539278 DOI: 10.1038/nprot.2010.45] [Citation(s) in RCA: 302] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Metabolic profiling, metabolomic and metabonomic studies require robust study protocols for any large-scale comparisons and evaluations. Detailed methods for solution-state NMR spectroscopy have been summarized in an earlier protocol. This protocol details the analysis of intact tissue samples by means of high-resolution magic-angle-spinning (HR-MAS) NMR spectroscopy and we provide a detailed description of sample collection, preparation and analysis. Described here are (1)H NMR spectroscopic techniques such as the standard one-dimensional, relaxation-edited, diffusion-edited and two-dimensional J-resolved pulse experiments, as well as one-dimensional (31)P NMR spectroscopy. These are used to monitor different groups of metabolites, e.g., sugars, amino acids and osmolytes as well as larger molecules such as lipids, non-invasively. Through the use of NMR-based diffusion coefficient and relaxation times measurements, information on molecular compartmentation and mobility can be gleaned. The NMR methods are often combined with statistical analysis for further metabonomics analysis and biomarker identification. The standard acquisition time per sample is 8-10 min for a simple one-dimensional (1)H NMR spectrum, giving access to metabolite information while retaining tissue integrity and hence allowing direct comparison with histopathology and MRI/MRS findings or the evaluation together with biofluid metabolic-profiling data.
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Affiliation(s)
- Olaf Beckonert
- Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, South Kensington, London, UK
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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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44
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Saric J, Li JV, Wang Y, Keiser J, Veselkov K, Dirnhofer S, Yap IKS, Nicholson JK, Holmes E, Utzinger J. Panorganismal metabolic response modeling of an experimental Echinostoma caproni infection in the mouse. J Proteome Res 2009; 8:3899-911. [PMID: 19489577 PMCID: PMC2724024 DOI: 10.1021/pr900185s] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Indexed: 12/19/2022]
Abstract
Metabolic profiling of host tissues and biofluids during parasitic infections can reveal new biomarker information and aid the elucidation of mechanisms of disease. The multicompartmental metabolic effects of an experimental Echinostoma caproni infection have been characterized in 12 outbred female mice infected orally with 30 E. caproni metacercariae each, using a further 12 uninfected animals as a control group. Mice were killed 36 days postinfection and brain, intestine (colon, ileum, jejeunum), kidney, liver, and spleen were removed. Metabolic profiles of tissue samples were measured using high-resolution magic angle spinning (1)H NMR spectroscopy and biofluids measured by applying conventional (1)H NMR spectroscopy. Spectral data were analyzed via principal component analysis, partial least-squares-derived methods and hierarchical projection analyses. Infection-induced metabolic changes in the tissues were correlated with altered metabolite concentrations in the biofluids (urine, plasma, fecal water) using hierarchical modeling and correlation analyses. Metabolic descriptors of infection were identified in liver, renal cortex, intestinal tissues but not in spleen, brain or renal medulla. The main physiological change observed in the mouse was malabsorption in the small intestine, which was evidenced by decreased levels of various amino acids in the ileum, for example, alanine, taurine, glutamine, and branched chain amino acids. Furthermore, altered gut microbial activity or composition was reflected by increased levels of trimethylamine in the colon. Our modeling approach facilitated in-depth appraisal of the covariation of the metabolic profiles of different biological matrices and found that urine and plasma most closely reflected changes in ileal compartments. In conclusion, an E. caproni infection not only results in direct localized (ileum and jejenum) effects, but also causes remote metabolic changes (colon and several peripheral organs), and therefore describes the panorganismal metabolic response of the infection.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Jürg Utzinger
- Correspondence should be addressed to: Jürg Utzinger, Department of Public Health and Epidemiology, Swiss Tropical Institute, P.O. Box, CH-4002 Basel, Switzerland. Tel: +41 61 284-8129; fax: +41 61 284-8105; e-mail:
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45
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Backshall A, Alferez D, Teichert F, Wilson ID, Wilkinson RW, Goodlad RA, Keun HC. Detection of metabolic alterations in non-tumor gastrointestinal tissue of the Apc(Min/+) mouse by (1)H MAS NMR spectroscopy. J Proteome Res 2009; 8:1423-30. [PMID: 19159281 DOI: 10.1021/pr800793w] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this study, we have used metabolic profiling (metabolomics/metabonomics) via high resolution magic angle spinning (HRMAS) and solution state (1)H NMR spectroscopy to characterize small bowel and colon tissue from the Apc(Min/+) mouse model of early gastrointestinal (GI) tumorigenesis. Multivariate analysis indicated the presence of metabolic differences between the morphologically normal/non-tumor tissue from approximately 10 week-old Apc(Min/+) mice and their wild-type litter mates. The metabolic profile of isolated lamina propria and epithelial cells from the same groups could also be discriminated on the basis of genotype. Accounting for systematic variation in individual metabolite levels across different anatomical regions of the lower GI tract, the metabolic phenotype of Apc(Min/+) lamina propria tissue was defined by significant increases in the phosphocholine/glycerophosphocholine ratio (PC/GPC, +21%) and decreases in GPC (-25%) and the gut-microbial cometabolite dimethylamine (DMA, -40%) relative to wild type. In the whole tissue, elevated lactate (+15%) and myo-inositol (+19%) levels were detected. As the metabolic changes occurred in non-tumor tissue from animals of very low tumor burden (<2 polyps/animal), they are likely to represent the specific consequence of reduced Apc function and very early events in tumorigenesis. The observed increase in PC/GPC ratio has been previously reported with immortalisation and malignant transformation of cells and is consistent with the role of Apc as a tumor suppressor. Phospholipase A2, which hydrolyses phosphatidylcholine to Acyl-GPC, is a known modifier gene of the model phenotype (Mom1), and altered expression of choline phospholipid enzymes has been reported in gut tissue from Apc(Min/+) mice. These results indicate the presence of a metabolic phenotype associated with "field cancerization", highlighting potential biomarkers for monitoring disease progression, for early evaluation of response to chemoprevention, and for predicting the severity of the polyposis phenotype in the Apc(Min/+) model.
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Affiliation(s)
- Alexandra Backshall
- Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, London, United Kingdom
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46
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Martin FPJ, Wang Y, Yap IKS, Sprenger N, Lindon JC, Rezzi S, Kochhar S, Holmes E, Nicholson JK. Topographical Variation in Murine Intestinal Metabolic Profiles in Relation to Microbiome Speciation and Functional Ecological Activity. J Proteome Res 2009; 8:3464-74. [DOI: 10.1021/pr900099x] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Francois-Pierre J. Martin
- Nestlé Research Center, P. O. Box 44, Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland, Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, United Kingdom, and 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
| | - Yulan Wang
- Nestlé Research Center, P. O. Box 44, Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland, Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, United Kingdom, and 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
| | - Ivan K. S. Yap
- Nestlé Research Center, P. O. Box 44, Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland, Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, United Kingdom, and 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
| | - Norbert Sprenger
- Nestlé Research Center, P. O. Box 44, Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland, Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, United Kingdom, and 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
| | - John C. Lindon
- Nestlé Research Center, P. O. Box 44, Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland, Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, United Kingdom, and 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
| | - Serge Rezzi
- Nestlé Research Center, P. O. Box 44, Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland, Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, United Kingdom, and 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
| | - Sunil Kochhar
- Nestlé Research Center, P. O. Box 44, Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland, Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, United Kingdom, and 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
| | - Elaine Holmes
- Nestlé Research Center, P. O. Box 44, Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland, Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, United Kingdom, and 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
| | - Jeremy K. Nicholson
- Nestlé Research Center, P. O. Box 44, Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland, Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, United Kingdom, and 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
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47
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Duarte IF, Marques J, Ladeirinha AF, Rocha C, Lamego I, Calheiros R, Silva TM, Marques MPM, Melo JB, Carreira IM, Gil AM. Analytical Approaches toward Successful Human Cell Metabolome Studies by NMR Spectroscopy. Anal Chem 2009; 81:5023-32. [DOI: 10.1021/ac900545q] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Iola F. Duarte
- CICECO-Departmento de Química, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, Cytogenetics Laboratory and Center of Neurosciences and Cellular Biology, Faculty of Medicine, University of Coimbra, 3001-401 Coimbra, Portugal, and Research Unit “Molecular Physical-Chemistry”, University of Coimbra, Portugal
| | - Joana Marques
- CICECO-Departmento de Química, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, Cytogenetics Laboratory and Center of Neurosciences and Cellular Biology, Faculty of Medicine, University of Coimbra, 3001-401 Coimbra, Portugal, and Research Unit “Molecular Physical-Chemistry”, University of Coimbra, Portugal
| | - Ana F. Ladeirinha
- CICECO-Departmento de Química, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, Cytogenetics Laboratory and Center of Neurosciences and Cellular Biology, Faculty of Medicine, University of Coimbra, 3001-401 Coimbra, Portugal, and Research Unit “Molecular Physical-Chemistry”, University of Coimbra, Portugal
| | - Cláudia Rocha
- CICECO-Departmento de Química, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, Cytogenetics Laboratory and Center of Neurosciences and Cellular Biology, Faculty of Medicine, University of Coimbra, 3001-401 Coimbra, Portugal, and Research Unit “Molecular Physical-Chemistry”, University of Coimbra, Portugal
| | - Inês Lamego
- CICECO-Departmento de Química, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, Cytogenetics Laboratory and Center of Neurosciences and Cellular Biology, Faculty of Medicine, University of Coimbra, 3001-401 Coimbra, Portugal, and Research Unit “Molecular Physical-Chemistry”, University of Coimbra, Portugal
| | - Rita Calheiros
- CICECO-Departmento de Química, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, Cytogenetics Laboratory and Center of Neurosciences and Cellular Biology, Faculty of Medicine, University of Coimbra, 3001-401 Coimbra, Portugal, and Research Unit “Molecular Physical-Chemistry”, University of Coimbra, Portugal
| | - Tânia M. Silva
- CICECO-Departmento de Química, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, Cytogenetics Laboratory and Center of Neurosciences and Cellular Biology, Faculty of Medicine, University of Coimbra, 3001-401 Coimbra, Portugal, and Research Unit “Molecular Physical-Chemistry”, University of Coimbra, Portugal
| | - M. Paula M. Marques
- CICECO-Departmento de Química, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, Cytogenetics Laboratory and Center of Neurosciences and Cellular Biology, Faculty of Medicine, University of Coimbra, 3001-401 Coimbra, Portugal, and Research Unit “Molecular Physical-Chemistry”, University of Coimbra, Portugal
| | - Joana B. Melo
- CICECO-Departmento de Química, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, Cytogenetics Laboratory and Center of Neurosciences and Cellular Biology, Faculty of Medicine, University of Coimbra, 3001-401 Coimbra, Portugal, and Research Unit “Molecular Physical-Chemistry”, University of Coimbra, Portugal
| | - Isabel M. Carreira
- CICECO-Departmento de Química, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, Cytogenetics Laboratory and Center of Neurosciences and Cellular Biology, Faculty of Medicine, University of Coimbra, 3001-401 Coimbra, Portugal, and Research Unit “Molecular Physical-Chemistry”, University of Coimbra, Portugal
| | - Ana M. Gil
- CICECO-Departmento de Química, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, Cytogenetics Laboratory and Center of Neurosciences and Cellular Biology, Faculty of Medicine, University of Coimbra, 3001-401 Coimbra, Portugal, and Research Unit “Molecular Physical-Chemistry”, University of Coimbra, Portugal
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48
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Righi V, Durante C, Cocchi M, Calabrese C, Di Febo G, Lecce F, Pisi A, Tugnoli V, Mucci A, Schenetti L. Discrimination of Healthy and Neoplastic Human Colon Tissues by ex Vivo HR-MAS NMR Spectroscopy and Chemometric Analyses. J Proteome Res 2009; 8:1859-69. [DOI: 10.1021/pr801094b] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Valeria Righi
- Dipartimento di Biochimica “G. Moruzzi”, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna, Italy, Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi 183, 41100 Modena, Italy, Dipartimento di Medicina Interna e Gastroenterologia, Università di Bologna, Via G. Massarenti 9, 40138, Bologna, Italy, Dipartimento Emergenza/Urgenza, Chirurgia Generale e dei Trapianti, Università di Bologna, Via G. Massarenti 9, 40138 Bologna, Italy, and DiSTA, Università di Bologna, Viale Fanin
| | - Caterina Durante
- Dipartimento di Biochimica “G. Moruzzi”, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna, Italy, Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi 183, 41100 Modena, Italy, Dipartimento di Medicina Interna e Gastroenterologia, Università di Bologna, Via G. Massarenti 9, 40138, Bologna, Italy, Dipartimento Emergenza/Urgenza, Chirurgia Generale e dei Trapianti, Università di Bologna, Via G. Massarenti 9, 40138 Bologna, Italy, and DiSTA, Università di Bologna, Viale Fanin
| | - Marina Cocchi
- Dipartimento di Biochimica “G. Moruzzi”, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna, Italy, Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi 183, 41100 Modena, Italy, Dipartimento di Medicina Interna e Gastroenterologia, Università di Bologna, Via G. Massarenti 9, 40138, Bologna, Italy, Dipartimento Emergenza/Urgenza, Chirurgia Generale e dei Trapianti, Università di Bologna, Via G. Massarenti 9, 40138 Bologna, Italy, and DiSTA, Università di Bologna, Viale Fanin
| | - Carlo Calabrese
- Dipartimento di Biochimica “G. Moruzzi”, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna, Italy, Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi 183, 41100 Modena, Italy, Dipartimento di Medicina Interna e Gastroenterologia, Università di Bologna, Via G. Massarenti 9, 40138, Bologna, Italy, Dipartimento Emergenza/Urgenza, Chirurgia Generale e dei Trapianti, Università di Bologna, Via G. Massarenti 9, 40138 Bologna, Italy, and DiSTA, Università di Bologna, Viale Fanin
| | - Giulio Di Febo
- Dipartimento di Biochimica “G. Moruzzi”, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna, Italy, Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi 183, 41100 Modena, Italy, Dipartimento di Medicina Interna e Gastroenterologia, Università di Bologna, Via G. Massarenti 9, 40138, Bologna, Italy, Dipartimento Emergenza/Urgenza, Chirurgia Generale e dei Trapianti, Università di Bologna, Via G. Massarenti 9, 40138 Bologna, Italy, and DiSTA, Università di Bologna, Viale Fanin
| | - Ferdinando Lecce
- Dipartimento di Biochimica “G. Moruzzi”, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna, Italy, Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi 183, 41100 Modena, Italy, Dipartimento di Medicina Interna e Gastroenterologia, Università di Bologna, Via G. Massarenti 9, 40138, Bologna, Italy, Dipartimento Emergenza/Urgenza, Chirurgia Generale e dei Trapianti, Università di Bologna, Via G. Massarenti 9, 40138 Bologna, Italy, and DiSTA, Università di Bologna, Viale Fanin
| | - Annamaria Pisi
- Dipartimento di Biochimica “G. Moruzzi”, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna, Italy, Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi 183, 41100 Modena, Italy, Dipartimento di Medicina Interna e Gastroenterologia, Università di Bologna, Via G. Massarenti 9, 40138, Bologna, Italy, Dipartimento Emergenza/Urgenza, Chirurgia Generale e dei Trapianti, Università di Bologna, Via G. Massarenti 9, 40138 Bologna, Italy, and DiSTA, Università di Bologna, Viale Fanin
| | - Vitaliano Tugnoli
- Dipartimento di Biochimica “G. Moruzzi”, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna, Italy, Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi 183, 41100 Modena, Italy, Dipartimento di Medicina Interna e Gastroenterologia, Università di Bologna, Via G. Massarenti 9, 40138, Bologna, Italy, Dipartimento Emergenza/Urgenza, Chirurgia Generale e dei Trapianti, Università di Bologna, Via G. Massarenti 9, 40138 Bologna, Italy, and DiSTA, Università di Bologna, Viale Fanin
| | - Adele Mucci
- Dipartimento di Biochimica “G. Moruzzi”, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna, Italy, Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi 183, 41100 Modena, Italy, Dipartimento di Medicina Interna e Gastroenterologia, Università di Bologna, Via G. Massarenti 9, 40138, Bologna, Italy, Dipartimento Emergenza/Urgenza, Chirurgia Generale e dei Trapianti, Università di Bologna, Via G. Massarenti 9, 40138 Bologna, Italy, and DiSTA, Università di Bologna, Viale Fanin
| | - Luisa Schenetti
- Dipartimento di Biochimica “G. Moruzzi”, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna, Italy, Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi 183, 41100 Modena, Italy, Dipartimento di Medicina Interna e Gastroenterologia, Università di Bologna, Via G. Massarenti 9, 40138, Bologna, Italy, Dipartimento Emergenza/Urgenza, Chirurgia Generale e dei Trapianti, Università di Bologna, Via G. Massarenti 9, 40138 Bologna, Italy, and DiSTA, Università di Bologna, Viale Fanin
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49
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Chan ECY, Koh PK, Mal M, Cheah PY, Eu KW, Backshall A, Cavill R, Nicholson JK, Keun HC. Metabolic profiling of human colorectal cancer using high-resolution magic angle spinning nuclear magnetic resonance (HR-MAS NMR) spectroscopy and gas chromatography mass spectrometry (GC/MS). J Proteome Res 2009; 8:352-61. [PMID: 19063642 DOI: 10.1021/pr8006232] [Citation(s) in RCA: 340] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Current clinical strategy for staging and prognostication of colorectal cancer (CRC) relies mainly upon the TNM or Duke system. This clinicopathological stage is a crude prognostic guide because it reflects in part the delay in diagnosis in the case of an advanced cancer and gives little insight into the biological characteristics of the tumor. We hypothesized that global metabolic profiling (metabonomics/metabolomics) of colon mucosae would define metabolic signatures that not only discriminate malignant from normal mucosae, but also could distinguish the anatomical and clinicopathological characteristics of CRC. We applied both high-resolution magic angle spinning nuclear magnetic resonance (HR-MAS NMR) and gas chromatography mass spectrometry (GC/MS) to analyze metabolites in biopsied colorectal tumors and their matched normal mucosae obtained from 31 CRC patients. Orthogonal partial least-squares discriminant analysis (OPLS-DA) models generated from metabolic profiles obtained by both analytical approaches could robustly discriminate normal from malignant samples (Q(2) > 0.50, Receiver Operator Characteristic (ROC) AUC >0.95, using 7-fold cross validation). A total of 31 marker metabolites were identified using the two analytical platforms. The majority of these metabolites were associated with expected metabolic perturbations in CRC including elevated tissue hypoxia, glycolysis, nucleotide biosynthesis, lipid metabolism, inflammation and steroid metabolism. OPLS-DA models showed that the metabolite profiles obtained via HR-MAS NMR could further differentiate colon from rectal cancers (Q(2)> 0.60, ROC AUC = 1.00, using 7-fold cross validation). These data suggest that metabolic profiling of CRC mucosae could provide new phenotypic biomarkers for CRC management.
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Affiliation(s)
- Eric Chun Yong Chan
- Department of Pharmacy, Faculty of Science, National University of Singapore, 18 Science Drive 4, Singapore 117543, Singapore
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50
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Mal M, Koh PK, Cheah PY, Chan ECY. Development and validation of a gas chromatography/mass spectrometry method for the metabolic profiling of human colon tissue. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:487-494. [PMID: 19140133 DOI: 10.1002/rcm.3898] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In this study, a gas chromatography/mass spectrometry (GC/MS) method was developed and validated for the metabolic profiling of human colon tissue. Each colon tissue sample (20 mg) was ultra-sonicated with 1 mL of a mixture of chloroform/methanol/water in the ratio of 20:50:20 (v/v/v), followed by centrifugation, collection of supernatant, drying, removal of moisture using anhydrous toluene and finally derivatization using N-methyl-N-trifluoroacetamide (MSTFA) with 1% trimethylchlorosilane (TMCS). A volume of 1 microL of the derivatized mixture was injected into the GC/MS system. A total of 53 endogenous metabolites were separated and identified in the GC/MS chromatogram, all of which were selected to evaluate the sample stability and precision of the method. Of the identified endogenous metabolites 19 belonging to diverse chemical classes and covering a wide range of the GC retention times (Rt) were selected to investigate the quantitative linearity of the method. The developed GC/MS method demonstrated good reproducibility with intra- and inter-day precision within relative standard deviation (RSD) of +/-15%. The metabolic profiles of the intact tissue were determined to be stable (100 +/- 15%) for up to 90 days at -80 degrees C. Satisfactory results were also obtained in the case of other stability-indicating studies such as freeze/thaw cycle stability, bench-top stability and autosampler stability. The developed method showed a good linear response for each of the 19 analytes tested (r(2) > 0.99). Our GC/MS metabolic profiling method was successfully applied to discriminate biopsied colorectal cancer (CRC) tissue from their matched normal tissue obtained from six CRC patients using orthogonal partial least-squares discriminant analysis [two latent variables, R(2)Y = 0.977 and Q(2) (cumulative) = 0.877].
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Affiliation(s)
- Mainak Mal
- Department of Pharmacy, Faculty of Science, National University of Singapore, 18 Science Drive 4, Singapore 117543
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