151
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Effect of Oxylipins, Terpenoid Precursors and Wounding on Soft Corals' Secondary Metabolism as Analyzed via UPLC/MS and Chemometrics. Molecules 2017; 22:molecules22122195. [PMID: 29232862 PMCID: PMC6149794 DOI: 10.3390/molecules22122195] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 11/30/2017] [Accepted: 12/02/2017] [Indexed: 12/13/2022] Open
Abstract
The effect of three oxylipin analogues, a terpenoid intermediate and wounding on the secondary metabolism of the soft corals Sarcophyton glaucum and Lobophyton pauciflorum was assessed. Examined oxylipins included prostaglandin (PG-E1), methyl jasmonate (MeJA), and arachidonic acid (AA) in addition to the diterpene precursor geranylgeranylpyrophosphate (GGP). Post-elicitation, metabolites were extracted from coral heads and analyzed via UPLC-MS followed by multivariate data analyses. Both supervised and unsupervised data analyses were used for sample classification. Multivariate data analysis revealed clear segregation of PG-E1 and MeJA elicited S. glaucum at 24 and 48 h post elicitation from other elicitor samples and unelicited control group. PG-E1 was found more effective in upregulating S. glaucum terpene/sterol levels compared to MeJA. Metabolites showing upregulation in S. glaucum include campestene-triol and a cembranoid, detected at ca. 30- and 2-fold higher levels compared to unelicited corals. Such an elicitation effect was less notable in the other coral species L. pauciflorum, suggesting a differential oxylipin response in soft corals. Compared to MeJA and PG, no elicitation effect was observed for GGP, AA or wounding on the metabolism of either coral species.
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152
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Navas-Carrillo D, Rodriguez JM, Montoro-García S, Orenes-Piñero E. High-resolution proteomics and metabolomics in thyroid cancer: Deciphering novel biomarkers. Crit Rev Clin Lab Sci 2017; 54:446-457. [DOI: 10.1080/10408363.2017.1394266] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Diana Navas-Carrillo
- Department of Surgery, Hospital de la Vega Lorenzo Guirao, University of Murcia, Murcia, Spain
| | - José Manuel Rodriguez
- Department of Surgery, Hospital Universitario Virgen de la Arrixaca, University of Murcia, Murcia, Spain
| | | | - Esteban Orenes-Piñero
- Proteomic Unit, Instituto Murciano de Investigación Biosanitaria Virgen de la Arrixaca (IMIB-Arrixaca), Universidad de Murcia, Murcia, Spain
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153
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Giorgetti L, Giorgi G, Cherubini E, Gervasi PG, Della Croce CM, Longo V, Bellani L. Screening and identification of major phytochemical compounds in seeds, sprouts and leaves of Tuscan black kale Brassica oleracea (L.) ssp acephala (DC) var. sabellica L. Nat Prod Res 2017; 32:1617-1626. [DOI: 10.1080/14786419.2017.1392953] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Lucia Giorgetti
- Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Pisa, Italy
| | - Gianluca Giorgi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Edoardo Cherubini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Pier Giovanni Gervasi
- Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Pisa, Italy
| | - Clara Maria Della Croce
- Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Pisa, Italy
| | - Vincenzo Longo
- Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Pisa, Italy
| | - Lorenza Bellani
- Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Pisa, Italy
- Department of Life Sciences, University of Siena, Siena, Italy
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154
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Armitage EG, Ciborowski M. Applications of Metabolomics in Cancer Studies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 965:209-234. [PMID: 28132182 DOI: 10.1007/978-3-319-47656-8_9] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Since the start of metabolomics as a field of research, the number of studies related to cancer has grown to such an extent that cancer metabolomics now represents its own discipline. In this chapter, the applications of metabolomics in cancer studies are explored. Different approaches and analytical platforms can be employed for the analysis of samples depending on the goal of the study and the aspects of the cancer metabolome being investigated. Analyses have concerned a range of cancers including lung, colorectal, bladder, breast, gastric, oesophageal and thyroid, amongst others. Developments in these strategies and methodologies that have been applied are discussed, in addition to exemplifying the use of cancer metabolomics in the discovery of biomarkers and in the assessment of therapy (both pharmaceutical and nutraceutical). Finally, the application of cancer metabolomics in personalised medicine is presented.
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Affiliation(s)
- Emily Grace Armitage
- Centre for Metabolomics and Bioanalysis (CEMBIO), Faculty of Pharmacy, Universidad CEU San Pablo, Campus Monteprincipe, Madrid, Spain. .,Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow, UK. .,Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
| | - Michal Ciborowski
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
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155
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Andjelković U, Šrajer Gajdošik M, Gašo-Sokač D, Martinović T, Josić D. Foodomics and Food Safety: Where We Are. Food Technol Biotechnol 2017; 55:290-307. [PMID: 29089845 PMCID: PMC5654429 DOI: 10.17113/ftb.55.03.17.5044] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 05/31/2017] [Indexed: 12/21/2022] Open
Abstract
The power of foodomics as a discipline that is now broadly used for quality assurance of food products and adulteration identification, as well as for determining the safety of food, is presented. Concerning sample preparation and application, maintenance of highly sophisticated instruments for both high-performance and high-throughput techniques, and analysis and data interpretation, special attention has to be paid to the development of skilled analysts. The obtained data shall be integrated under a strong bioinformatics environment. Modern mass spectrometry is an extremely powerful analytical tool since it can provide direct qualitative and quantitative information about a molecule of interest from only a minute amount of sample. Quality of this information is influenced by the sample preparation procedure, the type of mass spectrometer used and the analyst's skills. Technical advances are bringing new instruments of increased sensitivity, resolution and speed to the market. Other methods presented here give additional information and can be used as complementary tools to mass spectrometry or for validation of obtained results. Genomics and transcriptomics, as well as affinity-based methods, still have a broad use in food analysis. Serious drawbacks of some of them, especially the affinity-based methods, are the cross-reactivity between similar molecules and the influence of complex food matrices. However, these techniques can be used for pre-screening in order to reduce the large number of samples. Great progress has been made in the application of bioinformatics in foodomics. These developments enabled processing of large amounts of generated data for both identification and quantification, and for corresponding modeling.
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Affiliation(s)
- Uroš Andjelković
- Department of Biotechnology, University of Rijeka, Radmile Matejčić 2, HR-51000 Rijeka, Croatia
- Department of Chemistry, Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, RS-11000 Belgrade, Serbia
| | - Martina Šrajer Gajdošik
- Department of Chemistry, J. J. Strossmayer University of Osijek, Cara Hadrijana 8/A, HR-31000 Osijek, Croatia
| | - Dajana Gašo-Sokač
- Faculty of Food Technology, J. J. Strossmayer University of Osijek, Franje Kuhača 20, HR-31000 Osijek, Croatia
| | - Tamara Martinović
- Department of Biotechnology, University of Rijeka, Radmile Matejčić 2, HR-51000 Rijeka, Croatia
| | - Djuro Josić
- Department of Biotechnology, University of Rijeka, Radmile Matejčić 2, HR-51000 Rijeka, Croatia
- Warren Alpert Medical School, Brown University, 222 Richmond St, Providence, RI 02903, USA
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156
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Gao P, Ji M, Fang X, Liu Y, Yu Z, Cao Y, Sun A, Zhao L, Zhang Y. Capillary electrophoresis - Mass spectrometry metabolomics analysis revealed enrichment of hypotaurine in rat glioma tissues. Anal Biochem 2017; 537:1-7. [PMID: 28847592 DOI: 10.1016/j.ab.2017.08.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 08/02/2017] [Accepted: 08/21/2017] [Indexed: 12/20/2022]
Abstract
Glioma is one of the most lethal brain malignancies with unknown etiologies. Many metabolomics analysis aiming at diverse kinds of samples had been performed. Due to the varied adopted analytical platforms, the reported disease-related metabolites were not consistent across different studies. Comparable metabolomics results are more likely to be acquired by analyzing the same sample types with identical analytical platform. For tumor researches, tissue samples metabolomics analysis own the unique advantage that it can gain more direct insight into disease-specific pathological molecules. In this light, a previous reported capillary electrophoresis - mass spectrometry human tissues metabolomics analysis method was employed to profile the metabolome of rat C6 cell implantation gliomas and the corresponding precancerous tissues. It was found that 9 metabolites increased in the glioma tissues. Of them, hypotaurine was the only metabolite that enriched in the malignant tissues as what had been reported in the relevant human tissues metabolomics analysis. Furthermore, hypotaurine was also proved to inhibit α-ketoglutarate-dependent dioxygenases (2-KDDs) through immunocytochemistry staining and in vitro enzymatic activity assays by using C6 cell cultures. This study reinforced the previous conclusion that hypotaurine acted as a competitive inhibitor of 2-KDDs and proved the value of metabolomics in oncology studies.
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Affiliation(s)
- Peng Gao
- Clinical Laboratory, Dalian Sixth People's Hospital, Dalian, 116031, China
| | - Min Ji
- Department of Interventional Therapy, Dalian Sixth People's Hospital, Dalian, 116031, China
| | - Xueyan Fang
- Department of Nursing, Dalian Sixth People's Hospital, Dalian, 116031, China
| | - Yingyang Liu
- Department of Nursing, Dalian Sixth People's Hospital, Dalian, 116031, China
| | - Zhigang Yu
- Clinical Technology Center, Dalian Medical University, Dalian, 116044, China
| | - Yunfeng Cao
- RSKT Biopharma Inc., Dalian, Dalian, 116023, China
| | - Aijun Sun
- Translational Medicine Center, Dalian Sixth People's Hospital, Dalian, 116031, China
| | - Liang Zhao
- Translational Medicine Center, Dalian Sixth People's Hospital, Dalian, 116031, China
| | - Yong Zhang
- Department of Surgery, Dalian Sixth People's Hospital, Dalian, 116031, China.
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157
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Bag S, Dutta D, Chaudhary A, Sing BC, Pal M, Ray AK, Banerjee R, Paul RR, Basak A, Das AK, Chatterjee J. Identification of α-enolase as a prognostic and diagnostic precancer biomarker in oral submucous fibrosis. J Clin Pathol 2017; 71:228-238. [PMID: 28821582 DOI: 10.1136/jclinpath-2017-204430] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/30/2017] [Accepted: 07/03/2017] [Indexed: 11/03/2022]
Abstract
AIMS Diagnostic ambiguities regarding the malignant potentiality of oral submucous fibrosis (OSF), an oral precancerous condition having dysplastic and non-dysplastic isoforms are the major failure for early intervention of oral squamous cell carcinoma (OSCC) patients. Our goal is to identify proteomic signatures from biopsies that can be used as precancer diagnostic marker for patient suffering from OSF. METHODS The high throughput techniques adopting de novo peptide sequencing (1D SDS-PAGE coupled nanoLC MALDI tandem mass spectrometry (MS/MS)-based peptide mass fingerprint), immunohistochemistry (IHC), Western blot (WB) and real-time PCR (RT-PCR) analysis are considered for such biomarker identification and multilevel validations. RESULTS Alpha-enolase is identified as an overexpressed protein in biopsies of oral submucous fibrosis with dysplasia (OSFWD) compared with oral submucous fibrosis without dysplasia (OSFWT) and normal oral mucosa (NOM). Total proteome analysis of an overexpressed protein band around 47 kDa of OSFWD identifies 334 peptides corresponding to 61 human proteins. Among them α-enolase is identified as a prime protein with highest number of peptides (44 out of 334 peptides) and sequence coverage (66.4%). Furthermore, RT-PCR, WB and IHC analysis also show mRNA and tissue level upregulation of α-enolase in OSFWD validating α-enolase as precancer marker. CONCLUSIONS This study for the first time identifies and validates α-enolase as a novel biomarker for early diagnosis of malignant potentiality of OSF. Hence, the identified protein marker, α-enolase can help in early therapeutic intervention of OSF patients leading to the reduction of patient's pain, treatment cost and enhancement of patient's quality of life.
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Affiliation(s)
- Swarnendu Bag
- Department of Biotechnology, National Institute of Technology Sikkim, South Sikkim, India
| | - Debabrata Dutta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Amrita Chaudhary
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Bidhan Chandra Sing
- Department of Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Mousumi Pal
- Department of Oral and Maxillofacial Pathology, Guru Nanak Institute of Dental Sciences and Research, Kolkata, India
| | - Ajoy Kumar Ray
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science and Technology, Shibpur, India
| | - Rita Banerjee
- Department of Science and Technology, New Delhi, India
| | - Ranjan Rashmi Paul
- Department of Oral and Maxillofacial Pathology, Guru Nanak Institute of Dental Sciences and Research, Kolkata, India
| | - Amit Basak
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Amit Kumar Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Jyotirmoy Chatterjee
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, India
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158
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Khamis MM, Adamko DJ, El-Aneed A. Development of a validated LC- MS/MS method for the quantification of 19 endogenous asthma/COPD potential urinary biomarkers. Anal Chim Acta 2017; 989:45-58. [PMID: 28915942 DOI: 10.1016/j.aca.2017.08.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 06/19/2017] [Accepted: 08/03/2017] [Indexed: 11/27/2022]
Abstract
Obstructive airways inflammatory diseases sometimes show overlapping symptoms that hinder their early and correct diagnosis. Current clinical tests are tedious and are of inadequate specificity in special population such as the elderly and children. Therefore, we are developing tandem mass spectrometric (MS/MS) methods for targeted analysis of urine biomarkers. Recently, proton-nuclear magnetic resonance (1H-NMR) analysis proposed 50 urinary metabolites as potential diagnostic biomarkers among asthma and chronic obstructive pulmonary disease (COPD) patients. Metabolites are divided into 3 groups based on chemical nature. For group 1 (amines and phenols, 19 urinary metabolites), we developed and validated a high performance liquid chromatographic (HPLC)-MS/MS method using differential isotope labeling (DIL) with dansyl chloride. Method development included the optimization of the derivatization reaction, the MS/MS conditions, and the chromatographic separation. Linearity varied from 2 to 4800 ng/mL and the use of 13C2-labeled derivatives allowed for the correction of matrix effects as well as the unambiguous confirmation of the identity of each metabolite in the presence of interfering isomers in urine. Despite the challenges associated with method validation, the method was fully validated as per the food and drug administration (FDA) and the European medicines agency (EMA) recommendations. Validation criteria included linearity, precision, accuracy, dilution integrity, selectivity, carryover, and stability. Challenges in selectivity experiments included the isotopic contributions of the analyte towards its internal standard (IS), that was addressed via the optimization of the IS concentration. In addition, incurred sample analysis was performed to ensure that results from patient samples are accurate and reliable. The method was robust and reproducible and is currently being applied in a cohort of asthma and COPD patient urine samples for biomarker discovery purposes.
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Affiliation(s)
- Mona M Khamis
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, SK, Canada
| | - Darryl J Adamko
- Department of Pediatrics, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Anas El-Aneed
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, SK, Canada.
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159
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Havelund JF, Heegaard NHH, Færgeman NJK, Gramsbergen JB. Biomarker Research in Parkinson's Disease Using Metabolite Profiling. Metabolites 2017; 7:E42. [PMID: 28800113 PMCID: PMC5618327 DOI: 10.3390/metabo7030042] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 01/08/2023] Open
Abstract
Biomarker research in Parkinson's disease (PD) has long been dominated by measuring dopamine metabolites or alpha-synuclein in cerebrospinal fluid. However, these markers do not allow early detection, precise prognosis or monitoring of disease progression. Moreover, PD is now considered a multifactorial disease, which requires a more precise diagnosis and personalized medication to obtain optimal outcome. In recent years, advanced metabolite profiling of body fluids like serum/plasma, CSF or urine, known as "metabolomics", has become a powerful and promising tool to identify novel biomarkers or "metabolic fingerprints" characteristic for PD at various stages of disease. In this review, we discuss metabolite profiling in clinical and experimental PD. We briefly review the use of different analytical platforms and methodologies and discuss the obtained results, the involved metabolic pathways, the potential as a biomarker and the significance of understanding the pathophysiology of PD. Many of the studies report alterations in alanine, branched-chain amino acids and fatty acid metabolism, all pointing to mitochondrial dysfunction in PD. Aromatic amino acids (phenylalanine, tyrosine, tryptophan) and purine metabolism (uric acid) are also altered in most metabolite profiling studies in PD.
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Affiliation(s)
- Jesper F Havelund
- Villum Centre for Bioanalytical Sciences, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark.
| | - Niels H H Heegaard
- Department of Autoimmunology and Biomarkers, Statens Serum Institute, DK-2300 Copenhagen, Denmark.
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, University of Southern Denmark, DK-5000 Odense, Denmark.
| | - Nils J K Færgeman
- Villum Centre for Bioanalytical Sciences, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark.
| | - Jan Bert Gramsbergen
- Institute of Molecular Medicine, University of Southern Denmark, DK-5000 Odense, Denmark.
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160
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Kumar R, Bohra A, Pandey AK, Pandey MK, Kumar A. Metabolomics for Plant Improvement: Status and Prospects. FRONTIERS IN PLANT SCIENCE 2017; 8:1302. [PMID: 28824660 PMCID: PMC5545584 DOI: 10.3389/fpls.2017.01302] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/11/2017] [Indexed: 05/12/2023]
Abstract
Post-genomics era has witnessed the development of cutting-edge technologies that have offered cost-efficient and high-throughput ways for molecular characterization of the function of a cell or organism. Large-scale metabolite profiling assays have allowed researchers to access the global data sets of metabolites and the corresponding metabolic pathways in an unprecedented way. Recent efforts in metabolomics have been directed to improve the quality along with a major focus on yield related traits. Importantly, an integration of metabolomics with other approaches such as quantitative genetics, transcriptomics and genetic modification has established its immense relevance to plant improvement. An effective combination of these modern approaches guides researchers to pinpoint the functional gene(s) and the characterization of massive metabolites, in order to prioritize the candidate genes for downstream analyses and ultimately, offering trait specific markers to improve commercially important traits. This in turn will improve the ability of a plant breeder by allowing him to make more informed decisions. Given this, the present review captures the significant leads gained in the past decade in the field of plant metabolomics accompanied by a brief discussion on the current contribution and the future scope of metabolomics to accelerate plant improvement.
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Affiliation(s)
- Rakesh Kumar
- Department of Plant Sciences, University of Hyderabad (UoH)Hyderabad, India
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Abhishek Bohra
- Crop Improvement Division, Indian Institute of Pulses Research (IIPR)Kanpur, India
| | - Arun K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Manish K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Anirudh Kumar
- Department of Botany, Indira Gandhi National Tribal University (IGNTU)Amarkantak, India
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161
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Pandey R, Caflisch L, Lodi A, Brenner AJ, Tiziani S. Metabolomic signature of brain cancer. Mol Carcinog 2017; 56:2355-2371. [PMID: 28618012 DOI: 10.1002/mc.22694] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 06/01/2017] [Accepted: 06/13/2017] [Indexed: 12/17/2022]
Abstract
Despite advances in surgery and adjuvant therapy, brain tumors represent one of the leading causes of cancer-related mortality and morbidity in both adults and children. Gliomas constitute about 60% of all cerebral tumors, showing varying degrees of malignancy. They are difficult to treat due to dismal prognosis and limited therapeutics. Metabolomics is the untargeted and targeted analyses of endogenous and exogenous small molecules, which charact erizes the phenotype of an individual. This emerging "omics" science provides functional readouts of cellular activity that contribute greatly to the understanding of cancer biology including brain tumor biology. Metabolites are highly informative as a direct signature of biochemical activity; therefore, metabolite profiling has become a promising approach for clinical diagnostics and prognostics. The metabolic alterations are well-recognized as one of the key hallmarks in monitoring disease progression, therapy, and revealing new molecular targets for effective therapeutic intervention. Taking advantage of the latest high-throughput analytical technologies, that is, nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS), metabolomics is now a promising field for precision medicine and drug discovery. In the present report, we review the application of metabolomics and in vivo metabolic profiling in the context of adult gliomas and paediatric brain tumors. Analytical platforms such as high-resolution (HR) NMR, in vivo magnetic resonance spectroscopic imaging and high- and low-resolution MS are discussed. Moreover, the relevance of metabolic studies in the development of new therapeutic strategies for treatment of gliomas are reviewed.
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Affiliation(s)
- Renu Pandey
- Department of Nutritional Sciences, The University of Texas at Austin, Austin, Texas
| | - Laura Caflisch
- Department of Hematology and Medical oncology, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Alessia Lodi
- Department of Nutritional Sciences, The University of Texas at Austin, Austin, Texas
| | - Andrew J Brenner
- Department of Hematology and Medical oncology, University of Texas Health Science Center at San Antonio, San Antonio, Texas.,Department of Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Stefano Tiziani
- Department of Nutritional Sciences, The University of Texas at Austin, Austin, Texas.,Dell Pediatric Research Institute, The University of Texas at Austin, Austin, Texas
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162
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Stryeck S, Birner-Gruenberger R, Madl T. Integrative metabolomics as emerging tool to study autophagy regulation. MICROBIAL CELL (GRAZ, AUSTRIA) 2017; 4:240-258. [PMID: 28845422 PMCID: PMC5568430 DOI: 10.15698/mic2017.08.584] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/01/2017] [Indexed: 12/15/2022]
Abstract
Recent technological developments in metabolomics research have enabled in-depth characterization of complex metabolite mixtures in a wide range of biological, biomedical, environmental, agricultural, and nutritional research fields. Nuclear magnetic resonance spectroscopy and mass spectrometry are the two main platforms for performing metabolomics studies. Given their broad applicability and the systemic insight into metabolism that can be obtained it is not surprising that metabolomics becomes increasingly popular in basic biological research. In this review, we provide an overview on key metabolites, recent studies, and future opportunities for metabolomics in studying autophagy regulation. Metabolites play a pivotal role in autophagy regulation and are therefore key targets for autophagy research. Given the recent success of metabolomics, it can be expected that metabolomics approaches will contribute significantly to deciphering the complex regulatory mechanisms involved in autophagy in the near future and promote understanding of autophagy and autophagy-related diseases in living cells and organisms.
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Affiliation(s)
- Sarah Stryeck
- Institute of Molecular Biology and Biochemistry, Center of Molecular Medicine, Medical University of Graz, 8010 Graz, Austria
| | - Ruth Birner-Gruenberger
- Research Unit for Functional Proteomics and Metabolic Pathways, Institute of Pathology, Medical University of Graz, 8010 Graz, Austria
| | - Tobias Madl
- Institute of Molecular Biology and Biochemistry, Center of Molecular Medicine, Medical University of Graz, 8010 Graz, Austria
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163
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Mirali M, Purves RW, Vandenberg A. Profiling the Phenolic Compounds of the Four Major Seed Coat Types and Their Relation to Color Genes in Lentil. JOURNAL OF NATURAL PRODUCTS 2017; 80:1310-1317. [PMID: 28448137 DOI: 10.1021/acs.jnatprod.6b00872] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Phenolic compounds can provide antioxidant health benefits for humans, and foods such as lentils can be valuable dietary sources of different subclasses of these secondary metabolites. This study used LC-MS analyses to compare the phenolic profiles of lentil genotypes with four seed coat background colors (green, gray, tan, and brown) and two cotyledon colors (red and yellow) grown at two locations. The mean area ratio per mg sample (MARS) values of various phenolic compounds in lentil seeds varied with the different seed coat colors conferred by specific genotypes. Seed coats of lentil genotypes with the homozygous recessive tgc allele (green and gray seed coats) had higher MARS values of flavan-3-ols, proanthocyanidins, and some flavonols. This suggests lentils featuring green and gray seed coats might be more promising as health-promoting foods.
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Affiliation(s)
- Mahla Mirali
- Plant Sciences Department, University of Saskatchewan , Saskatoon, SK, Canada S7N 5A8
| | - Randy W Purves
- Plant Sciences Department, University of Saskatchewan , Saskatoon, SK, Canada S7N 5A8
| | - Albert Vandenberg
- Plant Sciences Department, University of Saskatchewan , Saskatoon, SK, Canada S7N 5A8
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164
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Hamilton JS, Aguilar R, Petros RA, Verbeck GF. DAPNe with micro-capillary separatory chemistry-coupled to MALDI-MS for the analysis of polar and non-polar lipid metabolism in one cell. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:918-928. [PMID: 28251574 DOI: 10.1007/s13361-017-1623-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 01/27/2017] [Accepted: 01/31/2017] [Indexed: 06/06/2023]
Abstract
The cellular metabolome is considered to be a representation of cellular phenotype and cellular response to changes to internal or external events. Methods to expand the coverage of the expansive physiochemical properties that makeup the metabolome currently utilize multi-step extractions and chromatographic separations prior to chemical detection, leading to lengthy analysis times. In this study, a single-step procedure for the extraction and separation of a sample using a micro-capillary as a separatory funnel to achieve analyte partitioning within an organic/aqueous immiscible solvent system is described. The separated analytes are then spotted for MALDI-MS imaging and distribution ratios are calculated. Initially, the method is applied to standard mixtures for proof of partitioning. The extraction of an individual cell is non-reproducible; therefore, a broad chemical analysis of metabolites is necessary and will be illustrated with the one-cell analysis of a single Snu-5 gastric cancer cell taken from a cellular suspension. The method presented here shows a broad partitioning dynamic range as a single-step method for lipid analysis demonstrating a decrease in ion suppression often present in MALDI analysis of lipids. Graphical Abstract ᅟ.
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Affiliation(s)
- Jason S Hamilton
- Department of Chemistry, University of North Texas, Denton, TX, USA
| | - Roberto Aguilar
- Department of Chemistry, University of North Texas, Denton, TX, USA
| | - Robby A Petros
- Department of Chemistry, Texas Women's Univeristy, Denton, TX, USA
| | - Guido F Verbeck
- Department of Chemistry, University of North Texas, Denton, TX, USA.
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165
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Marshall DD, Powers R. Beyond the paradigm: Combining mass spectrometry and nuclear magnetic resonance for metabolomics. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 100:1-16. [PMID: 28552170 PMCID: PMC5448308 DOI: 10.1016/j.pnmrs.2017.01.001] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 01/04/2017] [Accepted: 01/08/2017] [Indexed: 05/02/2023]
Abstract
Metabolomics is undergoing tremendous growth and is being employed to solve a diversity of biological problems from environmental issues to the identification of biomarkers for human diseases. Nuclear magnetic resonance (NMR) and mass spectrometry (MS) are the analytical tools that are routinely, but separately, used to obtain metabolomics data sets due to their versatility, accessibility, and unique strengths. NMR requires minimal sample handling without the need for chromatography, is easily quantitative, and provides multiple means of metabolite identification, but is limited to detecting the most abundant metabolites (⩾1μM). Conversely, mass spectrometry has the ability to measure metabolites at very low concentrations (femtomolar to attomolar) and has a higher resolution (∼103-104) and dynamic range (∼103-104), but quantitation is a challenge and sample complexity may limit metabolite detection because of ion suppression. Consequently, liquid chromatography (LC) or gas chromatography (GC) is commonly employed in conjunction with MS, but this may lead to other sources of error. As a result, NMR and mass spectrometry are highly complementary, and combining the two techniques is likely to improve the overall quality of a study and enhance the coverage of the metabolome. While the majority of metabolomic studies use a single analytical source, there is a growing appreciation of the inherent value of combining NMR and MS for metabolomics. An overview of the current state of utilizing both NMR and MS for metabolomics will be presented.
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Affiliation(s)
- Darrell D Marshall
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States.
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166
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Ji Y, Rao J, Rong X, Lou S, Zheng Z, Lu Y. Metabolic characterization of human aqueous humor in relation to high myopia. Exp Eye Res 2017; 159:147-155. [PMID: 28322828 DOI: 10.1016/j.exer.2017.03.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 01/02/2017] [Accepted: 03/16/2017] [Indexed: 01/05/2023]
Abstract
High myopia is the common eye disorder worldwide, which may contribute to increase the risk of serious disorders including glaucoma and cataract. Although various studies including genomics, transcriptomics, and proteomics have been implicated to identify potential biomarkers (genes or proteins) for predicting high myopia and to reveal the underlying mechanism, the comprehensive metabolomics in relation to high myopia is very limited. In this study, we identified 242 metabolites in aqueous humor (AH) from a set of 40 cataract patients (including 20 with high myopia and 20 for controls), using a non-targeted metabolomic technology, gas chromatography coupled to time-of-flight mass spectrometer (GC/TOF MS). Further statistical analysis showed that 29 metabolites were significantly changed (Variable important for the projection, VIP ≥ 1 and p ≤ 0.05), between those two groups, while only 2 decreased metabolites were included. Moreover, for the first time, metabolite-metabolite correlations for AH were analyzed, which may dissect key regulatory elements or pathways involved in metabolism of amino acids, carbohydrates, and lipids. Accordingly, metabolic network was constructed based on those 29 changed metabolites in patients with high myopia. More than half of the changed metabolites were highly and positively associated, suggesting important roles of pathways involved in the metabolism of these metabolites in relation to high myopia. Altogether, this work not only provided potential biomarkers for the diagnosis and monitoring of high myopia formation, but also provided new insights into the underlying mechanisms.
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Affiliation(s)
- Yinghong Ji
- Department of Ophthalmology & Eye Institute, Eye & ENT Hospital of Fudan University, Key Laboratory of Myopia of State Health Ministry, and Key Laboratory of Visual Impairment and Restoration of Shanghai, No. 83 Fenyang Road, Shanghai, 200031, China
| | - Jun Rao
- Jiangxi Cancer Hospital, No. 519 East Beijing Road, Nanchang 330029, China
| | - Xianfang Rong
- Department of Ophthalmology & Eye Institute, Eye & ENT Hospital of Fudan University, Key Laboratory of Myopia of State Health Ministry, and Key Laboratory of Visual Impairment and Restoration of Shanghai, No. 83 Fenyang Road, Shanghai, 200031, China
| | - Shang Lou
- Jiangxi Cancer Hospital, No. 519 East Beijing Road, Nanchang 330029, China
| | - Zhi Zheng
- Jiangxi Cancer Hospital, No. 519 East Beijing Road, Nanchang 330029, China
| | - Yi Lu
- Department of Ophthalmology & Eye Institute, Eye & ENT Hospital of Fudan University, Key Laboratory of Myopia of State Health Ministry, and Key Laboratory of Visual Impairment and Restoration of Shanghai, No. 83 Fenyang Road, Shanghai, 200031, China.
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167
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Enche Ady CNA, Lim SM, Teh LK, Salleh MZ, Chin AV, Tan MP, Poi PJH, Kamaruzzaman SB, Abdul Majeed AB, Ramasamy K. Metabolomic-guided discovery of Alzheimer's disease biomarkers from body fluid. J Neurosci Res 2017; 95:2005-2024. [PMID: 28301062 DOI: 10.1002/jnr.24048] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 01/31/2017] [Accepted: 02/15/2017] [Indexed: 12/11/2022]
Abstract
The rapid increase in the older population has made age-related diseases like Alzheimer's disease (AD) a global concern. Given that there is still no cure for this neurodegenerative disease, the drastic growth in the number of susceptible individuals represents a major emerging threat to public health. The poor understanding of the mechanisms underlying AD is deemed the greatest stumbling block against progress in definitive diagnosis and management of this disease. There is a dire need for biomarkers that can facilitate early diagnosis, classification, prognosis, and treatment response. Efforts have been directed toward discovery of reliable and distinctive AD biomarkers but with very little success. With the recent emergence of high-throughput technology that is able to collect and catalogue vast datasets of small metabolites, metabolomics offers hope for a better understanding of AD and subsequent identification of biomarkers. This review article highlights the potential of using multiple metabolomics platforms as useful means in uncovering AD biomarkers from body fluids. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Che Nor Adlia Enche Ady
- Faculty of Pharmacy, University Teknologi MARA (UiTM), 42300 Bandar Puncak Alam, Selangor Darul Ehsan, Malaysia.,Collaborative Drug Discovery Research (CDDR) Group, Pharmaceutical and Life Sciences Community of Research, Universiti Teknologi MARA (UiTM), 40450 Shah Alam, Selangor Darul Ehsan, Malaysia
| | - Siong Meng Lim
- Faculty of Pharmacy, University Teknologi MARA (UiTM), 42300 Bandar Puncak Alam, Selangor Darul Ehsan, Malaysia.,Collaborative Drug Discovery Research (CDDR) Group, Pharmaceutical and Life Sciences Community of Research, Universiti Teknologi MARA (UiTM), 40450 Shah Alam, Selangor Darul Ehsan, Malaysia
| | - Lay Kek Teh
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM), 42300 Bandar Puncak Alam, Selangor Darul Ehsan, Malaysia
| | - Mohd Zaki Salleh
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM), 42300 Bandar Puncak Alam, Selangor Darul Ehsan, Malaysia
| | - Ai-Vyrn Chin
- Division of Geriatric Medicine, Department of Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Maw Pin Tan
- Division of Geriatric Medicine, Department of Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Philip Jun Hua Poi
- Division of Geriatric Medicine, Department of Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Shahrul Bahyah Kamaruzzaman
- Division of Geriatric Medicine, Department of Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Abu Bakar Abdul Majeed
- Faculty of Pharmacy, University Teknologi MARA (UiTM), 42300 Bandar Puncak Alam, Selangor Darul Ehsan, Malaysia.,Brain Degeneration and Therapeutics Group, Pharmaceutical and Life Sciences Community of Research, Universiti Teknologi MARA (UiTM), 40450 Shah Alam, Selangor Darul Ehsan, Malaysia
| | - Kalavathy Ramasamy
- Faculty of Pharmacy, University Teknologi MARA (UiTM), 42300 Bandar Puncak Alam, Selangor Darul Ehsan, Malaysia.,Collaborative Drug Discovery Research (CDDR) Group, Pharmaceutical and Life Sciences Community of Research, Universiti Teknologi MARA (UiTM), 40450 Shah Alam, Selangor Darul Ehsan, Malaysia
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168
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Arroyo-Manzanares N, Diana Di Mavungu J, Garrido-Jurado I, Arce L, Vanhaecke L, Quesada-Moraga E, De Saeger S. Analytical strategy for determination of known and unknown destruxins using hybrid quadrupole-Orbitrap high-resolution mass spectrometry. Anal Bioanal Chem 2017; 409:3347-3357. [PMID: 28280843 DOI: 10.1007/s00216-017-0276-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/16/2017] [Accepted: 02/22/2017] [Indexed: 12/15/2022]
Abstract
An analytical strategy based on a hybrid quadrupole-Orbitrap mass spectrometry was proposed for the simultaneous screening of known destruxins and characterization of potential members of this class of secondary metabolites, in order to evaluate the metabolite production of entomopathogenic fungi used as biocontrol agents. Initially, the fragmentation pathway of the known and commercially available destruxin A was established combining high resolution mass spectrometry (HRMS) and multiple stage MS data in order to obtain the strategy for the characterization of other destruxins for which reference standards were not available. Nineteen known destruxins including A, B, C, D, Ed, F, A1, B1, Ed1, A2, B2, D2, A3, DesmA, DesmB, DesmC, DesmB2, and two chloro-derivatives (Cl and E2 chlorohydrin) were unequivocally identified in Metarhizium brunneum using the proposed strategy. In addition, four unknown destruxins, namely C1, Ed2, G, and G1, were structurally elucidated and characterized for the first time in this fungal strain.
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Affiliation(s)
- Natalia Arroyo-Manzanares
- Faculty of Pharmaceutical Sciences, Laboratory of Food Analysis, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium. .,Department of Analytical Chemistry, University of Cordoba, Annex C3 Building, Campus of Rabanales, 14071, Cordoba, Spain.
| | - José Diana Di Mavungu
- Faculty of Pharmaceutical Sciences, Laboratory of Food Analysis, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
| | - Inmaculada Garrido-Jurado
- Department of Agricultural and Forestry Sciences, ETSIAM, University of Cordoba, Building C4, Campus of Rabanales, 14071, Cordoba, Spain
| | - Lourdes Arce
- Department of Analytical Chemistry, University of Cordoba, Annex C3 Building, Campus of Rabanales, 14071, Cordoba, Spain
| | - Lynn Vanhaecke
- Faculty of Veterinary Medicine, Department of Veterinary Public Health and Food Safety, Laboratory of Chemical Analysis, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Enrique Quesada-Moraga
- Department of Agricultural and Forestry Sciences, ETSIAM, University of Cordoba, Building C4, Campus of Rabanales, 14071, Cordoba, Spain
| | - Sarah De Saeger
- Faculty of Pharmaceutical Sciences, Laboratory of Food Analysis, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
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169
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Khamis MM, Adamko DJ, El-Aneed A. Mass spectrometric based approaches in urine metabolomics and biomarker discovery. MASS SPECTROMETRY REVIEWS 2017; 36:115-134. [PMID: 25881008 DOI: 10.1002/mas.21455] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 10/05/2014] [Accepted: 10/05/2014] [Indexed: 05/25/2023]
Abstract
Urine metabolomics has recently emerged as a prominent field for the discovery of non-invasive biomarkers that can detect subtle metabolic discrepancies in response to a specific disease or therapeutic intervention. Urine, compared to other biofluids, is characterized by its ease of collection, richness in metabolites and its ability to reflect imbalances of all biochemical pathways within the body. Following urine collection for metabolomic analysis, samples must be immediately frozen to quench any biogenic and/or non-biogenic chemical reactions. According to the aim of the experiment; sample preparation can vary from simple procedures such as filtration to more specific extraction protocols such as liquid-liquid extraction. Due to the lack of comprehensive studies on urine metabolome stability, higher storage temperatures (i.e. 4°C) and repetitive freeze-thaw cycles should be avoided. To date, among all analytical techniques, mass spectrometry (MS) provides the best sensitivity, selectivity and identification capabilities to analyze the majority of the metabolite composition in the urine. Combined with the qualitative and quantitative capabilities of MS, and due to the continuous improvements in its related technologies (i.e. ultra high-performance liquid chromatography [UPLC] and hydrophilic interaction liquid chromatography [HILIC]), liquid chromatography (LC)-MS is unequivocally the most utilized and the most informative analytical tool employed in urine metabolomics. Furthermore, differential isotope tagging techniques has provided a solution to ion suppression from urine matrix thus allowing for quantitative analysis. In addition to LC-MS, other MS-based technologies have been utilized in urine metabolomics. These include direct injection (infusion)-MS, capillary electrophoresis-MS and gas chromatography-MS. In this article, the current progresses of different MS-based techniques in exploring the urine metabolome as well as the recent findings in providing potentially diagnostic urinary biomarkers are discussed. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:115-134, 2017.
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Affiliation(s)
- Mona M Khamis
- College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, SK, S7N 5E5, Canada
- Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt
| | - Darryl J Adamko
- Department of Pediatrics, College of Medicine, University of Saskatchewan, 103 Hospital Drive, Saskatoon, SK, Canada
| | - Anas El-Aneed
- College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, SK, S7N 5E5, Canada
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170
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Shin JH, Ahn YG, Jung JH, Woo SH, Kim HH, Gorinstein S, Boo HO. Identification and Characterization of Diploid and Tetraploid in Platycodon grandiflorum. PLANT FOODS FOR HUMAN NUTRITION (DORDRECHT, NETHERLANDS) 2017; 72:13-19. [PMID: 28032246 DOI: 10.1007/s11130-016-0589-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Platycodon grandiflorum (PG), a species of herbaceous flowering perennial plant of the family Campanulaceae, has been used as a traditional oriental medicine for bronchitis, asthma, pulmonary tuberculosis, diabetes, hepatic fibrosis, bone disorders and many others similar diseases and as a food supplement. For the primary profiling of PG gas chromatography coupled with high resolution - time of flight mass spectrometry (GC/HR-TOF MS) was used as an analytical tool. A comparison of optimal extraction of metabolites was carried out with a number of solvents [hexane, methylene chloride, methanol, ethanol, methanol: ethanol (70:30, v:v)]. In extracts with methanol: ethanol (70:30 v:v) were detected higher amounts of metabolites than with other solvents. Principal component analysis (PCA) and partial least-squares discriminant analysis (PLS-DA) plots showed significant differences between the diploid and tetraploid metabolite profiles. Extracts of tetraploid showed higher amounts of amino acids, while extracts of diploid contained more organic acids and sugars. Graphical Abstract ᅟ.
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Affiliation(s)
- Jeoung-Hwa Shin
- Seoul Center, Korea Basic Science Institute, Anam-ro, Seongbuk-gu, Seoul, 02855, Republic of Korea
| | - Yun Gyong Ahn
- Western Seoul Center, Korea Basic Science Institute, Bugahyeon-ro, Seodaemun-gu, Seoul, 03760, South Korea
| | - Ju-Hee Jung
- Seoul Center, Korea Basic Science Institute, Anam-ro, Seongbuk-gu, Seoul, 02855, Republic of Korea
| | - Sun-Hee Woo
- Department of Crop Science, Chungbuk National University, Cheongju, 28644, South Korea
| | - Hag-Hyun Kim
- Faculty of Food Nutrition and Cookery, Woosong Information College, Daejeon, 34606, South Korea
| | - Shela Gorinstein
- Institute for Drug Research, School of Pharmacy, The Hebrew University, Hadassah Medical School, 91120, Jerusalem, Israel.
| | - Hee-Ock Boo
- PHYTO M&F Co. Ltd., BI Center, GIST, Gwangju, 61005, South Korea.
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171
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Menni C, Zierer J, Valdes AM, Spector TD. Mixing omics: combining genetics and metabolomics to study rheumatic diseases. Nat Rev Rheumatol 2017; 13:174-181. [PMID: 28148918 DOI: 10.1038/nrrheum.2017.5] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Metabolomics is an exciting field in systems biology that provides a direct readout of the biochemical activities taking place within an individual at a particular point in time. Metabolite levels are influenced by many factors, including disease status, environment, medications, diet and, importantly, genetics. Thanks to their dynamic nature, metabolites are useful for diagnosis and prognosis, as well as for predicting and monitoring the efficacy of treatments. At the same time, the strong links between an individual's metabolic and genetic profiles enable the investigation of pathways that underlie changes in metabolite levels. Thus, for the field of metabolomics to yield its full potential, researchers need to take into account the genetic factors underlying the production of metabolites, and the potential role of these metabolites in disease processes. In this Review, the methodological aspects related to metabolomic profiling and any potential links between metabolomics and the genetics of some of the most common rheumatic diseases are described. Links between metabolomics, genetics and emerging fields such as the gut microbiome and proteomics are also discussed.
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Affiliation(s)
- Cristina Menni
- The Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, Lambeth Palace Road, London, SE1 7EH, UK
| | - Jonas Zierer
- The Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, Lambeth Palace Road, London, SE1 7EH, UK
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Ana M Valdes
- The Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, Lambeth Palace Road, London, SE1 7EH, UK
- Academic Rheumatology, The University of Nottingham, Clinical Sciences Building, Nottingham City Hospital, Hucknall Road, Nottingham, NG5 1PB, UK
| | - Tim D Spector
- The Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, Lambeth Palace Road, London, SE1 7EH, UK
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172
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Viant MR, Kurland IJ, Jones MR, Dunn WB. How close are we to complete annotation of metabolomes? Curr Opin Chem Biol 2017; 36:64-69. [PMID: 28113135 PMCID: PMC5337156 DOI: 10.1016/j.cbpa.2017.01.001] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 12/28/2016] [Accepted: 01/02/2017] [Indexed: 01/04/2023]
Abstract
The metabolome describes the full complement of the tens to hundreds of thousands of low molecular weight metabolites present within a biological system. Identification of the metabolome is critical for discovering the maximum amount of biochemical knowledge from metabolomics datasets. Yet no exhaustive experimental characterisation of any organismal metabolome has been reported to date, dramatically contrasting with the genome sequencing of thousands of plants, animals and microbes. Here, we review the status of metabolome annotation and describe advances in the analytical methodologies being applied. In part through new international coordination, we conclude that we are now entering a new era of metabolome annotation.
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Affiliation(s)
- Mark R Viant
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| | - Irwin J Kurland
- Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Martin R Jones
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Warwick B Dunn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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173
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Yan D, Afifi L, Jeon C, Trivedi M, Chang HW, Lee K, Liao W. The metabolomics of psoriatic disease. PSORIASIS (AUCKLAND, N.Z.) 2017; 7:1-15. [PMID: 28824870 PMCID: PMC5562362 DOI: 10.2147/ptt.s118348] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Metabolomics is an emerging new "omics" field involving the systematic analysis of the metabolites in a biologic system. These metabolites provide a molecular snapshot of cellular activity and are thus important for understanding the functional changes in metabolic pathways that drive disease. Recently, metabolomics has been used to study the local and systemic metabolic changes in psoriasis and its cardiometabolic comorbidities. Such studies have revealed novel insights into disease pathogenesis and suggest new biochemical signatures that may be used as a marker of psoriatic disease. This review will discuss common strategies in metabolomics analysis, current findings in the metabolomics of psoriasis, and emerging trends in psoriatic metabolomics.
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Affiliation(s)
- Di Yan
- Department of Dermatology, University of California-San Francisco, San Francisco, CA, USA
| | - Ladan Afifi
- Department of Dermatology, University of California-San Francisco, San Francisco, CA, USA
| | - Caleb Jeon
- Department of Dermatology, University of California-San Francisco, San Francisco, CA, USA
| | - Megha Trivedi
- Department of Dermatology, University of California-San Francisco, San Francisco, CA, USA
| | - Hsin Wen Chang
- Department of Dermatology, University of California-San Francisco, San Francisco, CA, USA
| | - Kristina Lee
- Department of Dermatology, University of California-San Francisco, San Francisco, CA, USA
| | - Wilson Liao
- Department of Dermatology, University of California-San Francisco, San Francisco, CA, USA
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174
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Abstract
Traditional methods for the assessment of dietary intake are prone to error; in order to improve and enhance these methods increasing interest in the identification of dietary biomarkers has materialised. Metabolomics has emerged as a key tool in the area of dietary biomarker discovery and to date the use of metabolomics has identified a number of putative biomarkers. Applications to identify novel biomarkers of intake have in general taken three approaches: (1) specific acute intervention studies to identify specific biomarkers of intake; (2) searching for biomarkers in cohort studies by correlating to self-reported intake of a specific food/food group(s); (3) analysing dietary patterns in conjunction with metabolomic profiles to identify biomarkers and nutritypes. A number of analytical technologies are employed in metabolomics as currently there is no single technique capable of measuring the entire metabolome. These approaches each have their own advantages and disadvantages. The present review will provide an overview of current technologies and applications of metabolomics in the determination of new dietary biomarkers. In addition, it will address some of the current challenges in the field and future outlooks.
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175
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Gordon SM, Srinivasan L, Harris MC. Neonatal Meningitis: Overcoming Challenges in Diagnosis, Prognosis, and Treatment with Omics. Front Pediatr 2017; 5:139. [PMID: 28670576 PMCID: PMC5472684 DOI: 10.3389/fped.2017.00139] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 06/01/2017] [Indexed: 01/24/2023] Open
Abstract
Neonatal meningitis is a devastating condition. Prognosis has not improved in decades, despite the advent of improved antimicrobial therapy and heightened index of suspicion among clinicians caring for affected infants. One in ten infants die from meningitis, and up to half of survivors develop significant lifelong complications, including seizures, impaired hearing and vision, and delayed or arrested development of such basic skills as talking and walking. At present, it is not possible to predict which infants will suffer poor outcomes. Early treatment is critical to promote more favorable outcomes, though diagnosis of meningitis in infants is technically challenging, time-intensive, and invasive. Profound neuronal injury has long been described in the setting of neonatal meningitis, as has elevated levels of many pro- and anti-inflammatory cytokines. Mechanisms of the host immune response that drive clearance of the offending organism and underlie brain injury due to meningitis are not well understood, however. In this review, we will discuss challenges in diagnosis, prognosis, and treatment of neonatal meningitis. We will highlight transcriptomic, proteomic, and metabolomic data that contribute to suggested mechanisms of inflammation and brain injury in this setting with a view toward fruitful areas for future investigation.
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Affiliation(s)
- Scott M Gordon
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Lakshmi Srinivasan
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Mary Catherine Harris
- Division of Neonatology, Children's Hospital of Philadelphia, Perelman School of Medicine, Philadelphia, PA, United States
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176
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Duft RG, Castro A, Chacon-Mikahil MPT, Cavaglieri CR. Metabolomics and Exercise: possibilities and perspectives. MOTRIZ: REVISTA DE EDUCACAO FISICA 2017. [DOI: 10.1590/s1980-6574201700020010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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177
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Kew W, Goodall I, Clarke D, Uhrín D. Chemical Diversity and Complexity of Scotch Whisky as Revealed by High-Resolution Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:200-213. [PMID: 27752914 PMCID: PMC5174148 DOI: 10.1007/s13361-016-1513-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/16/2016] [Accepted: 09/18/2016] [Indexed: 05/25/2023]
Abstract
Scotch Whisky is an important product, both culturally and economically. Chemically, Scotch Whisky is a complex mixture, which comprises thousands of compounds, the nature of which are largely unknown. Here, we present a thorough overview of the chemistry of Scotch Whisky as observed by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Eighty-five whiskies, representing the majority of Scotch Whisky produced and sold, were analyzed by untargeted high-resolution mass spectrometry. Thousands of chemical formulae were assigned for each sample based on parts-per-billion mass accuracy of FT-ICR MS spectra. For the first time, isotopic fine structure analysis was used to confirm the assignment of high molecular weight CHOS species in Scotch Whisky. The assigned spectra were compared using a number of visualization techniques, including van Krevelen diagrams, double bond equivalence (DBE) plots, as well as heteroatomic compound class distributions. Additionally, multivariate analysis, including PCA and OPLS-DA, was used to interpret the data, with key compounds identified for discriminating between types of whisky (blend or malt) or maturation wood type. FT-ICR MS analysis of Scotch Whisky was shown to be of significant potential in further understanding of the complexity of mature spirit drinks and as a tool for investigating the chemistry of the maturation processes. Graphical Abstract ᅟ.
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Affiliation(s)
- Will Kew
- EaStCHEM, School of Chemistry, University of Edinburgh, Joseph Black Building, Edinburgh, EH9 3FJ, UK
| | - Ian Goodall
- The Scotch Whisky Research Institute, The Robertson Trust Building, Research Avenue North, Riccarton, Edinburgh, EH14 4AP, UK
| | - David Clarke
- EaStCHEM, School of Chemistry, University of Edinburgh, Joseph Black Building, Edinburgh, EH9 3FJ, UK.
| | - Dušan Uhrín
- EaStCHEM, School of Chemistry, University of Edinburgh, Joseph Black Building, Edinburgh, EH9 3FJ, UK.
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178
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Maslov D, Balashova E, Lokhov P, Archakov A. Pharmacometabonomics – the novel way to personalized drug therapy. ACTA ACUST UNITED AC 2017; 63:115-123. [DOI: 10.18097/pbmc20176302115] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The review is devoted to pharmacometabonomics - a new branch of science focused on personalization of drug therapy through the comprehensive analysis of metabolites of patient's biological fluids. It considers the history of pharmacometabonomic, positioning to other “-omic” sciences, and system approach, realized by this science, in determination of individual therapeutic dose of the drugs and also a technical implementation of pharmacometabonomic based on direct mass spectrometry of blood plasma metabolites. Special attention is paid to a comparative analysis of pharmacometabonomics and other main approaches to personalized therapy in the clinic, such as pharmacogenetics and therapeutic drug monitoring. Finally, prospects of pharmacometabonomics applications in clinical practice were also discussed.
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Affiliation(s)
- D.L. Maslov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - P.G. Lokhov
- Institute of Biomedical Chemistry, Moscow, Russia
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179
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The application of metabolomics for herbal medicine pharmacovigilance: a case study on ginseng. Essays Biochem 2016; 60:429-435. [PMID: 27980093 DOI: 10.1042/ebc20160030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/12/2016] [Accepted: 10/14/2016] [Indexed: 11/17/2022]
Abstract
Herbal medicines are growing in popularity, use and commercial value; however, there remain problems with the quality and consequently safety of these products. Adulterated, contaminated and fraudulent products are often found on the market, a risk compounded by the fact that these products are available to consumers with little or no medical advice. Current regulations and quality control methods are lacking in their ability to combat these serious problems. Metabolomics is a biochemical profiling tool that may help address these issues if applied to quality control of both raw ingredients and final products. Using the example of the popular herbal medicine, ginseng, this essay offers an overview of the potential use of metabolomics for quality control in herbal medicines and also highlights where more research is needed.
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180
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Nassar AF, Wu T, Nassar SF, Wisnewski AV. UPLC-MS for metabolomics: a giant step forward in support of pharmaceutical research. Drug Discov Today 2016; 22:463-470. [PMID: 27919805 DOI: 10.1016/j.drudis.2016.11.020] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 10/23/2016] [Accepted: 11/25/2016] [Indexed: 01/05/2023]
Abstract
Metabolomics is a relatively new and rapidly growing area of post-genomic biological research. As use of metabolomics technology grows throughout the spectrum of drug discovery and development, and its applications broaden, its impact is expanding dramatically. This review seeks to provide the reader with a brief history of the development of metabolomics, its significance and strategies for conducting metabolomics studies. The most widely used analytical tools for metabolomics: NMR, LC-MS and GC-MS, are discussed along with considerations for their use. Herein, we will show how metabolomics can assist in pharmaceutical research studies, such as pharmacology and toxicology, and discuss some examples of the importance of metabolomics analysis in research and development.
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Affiliation(s)
- Ala F Nassar
- School of Medicine, Department of Internal Medicine, Yale University, New Haven, CT, USA; Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, CT, USA.
| | - Terence Wu
- West Campus Analytical Core, Yale University, West Haven, CT, USA
| | - Samuel F Nassar
- Yale School of Medicine, Departments of Neurology and Immunobiology, New Haven, CT 06511, USA
| | - Adam V Wisnewski
- School of Medicine, Department of Internal Medicine, Yale University, New Haven, CT, USA
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181
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Weidt S, Haggarty J, Kean R, Cojocariu CI, Silcock PJ, Rajendran R, Ramage G, Burgess KEV. A novel targeted/untargeted GC-Orbitrap metabolomics methodology applied to Candida albicans and Staphylococcus aureus biofilms. Metabolomics 2016; 12:189. [PMID: 28003796 PMCID: PMC5097782 DOI: 10.1007/s11306-016-1134-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 10/18/2016] [Indexed: 10/26/2022]
Abstract
INTRODUCTION Combined infections from Candida albicans and Staphylococcus aureus are a leading cause of death in the developed world. Evidence suggests that Candida enhances the virulence of Staphylococcus-hyphae penetrate through tissue barriers, while S. aureus tightly associates with the hyphae to obtain entry to the host organism. Indeed, in a biofilm state, C. albicans enhances the antimicrobial resistance characteristics of S. aureus. The association of these microorganisms is also associated with significantly increased morbidity and mortality. Due to this tight association we hypothesised that metabolic effects were also in evidence. OBJECTIVES To explore the interaction, we used a novel GC-Orbitrap-based mass spectrometer, the Q Exactive GC, which combines the high peak capacity and chromatographic resolution of gas chromatography with the sub-ppm mass accuracy of an Orbitrap system. This allows the capability to leverage the widely available electron ionisation libraries for untargeted applications, along with expanding accurate mass libraries and targeted matches based around authentic standards. METHODS Optimised C. albicans and S. aureus mono- and co-cultured biofilms were analysed using the new instrument in addition to the fresh and spent bacterial growth media. RESULTS The targeted analysis experiment was based around 36 sugars and sugar phosphates, 22 amino acids and five organic acids. Untargeted analysis resulted in the detection of 465 features from fresh and spent medium and 405 from biofilm samples. Three significantly changing compounds that matched to high scoring library fragment patterns were chosen for validation. CONCLUSION Evaluation of the results demonstrates that the Q Exactive GC is suitable for metabolomics analysis using a targeted/untargeted methodology. Many of the results were as expected: e.g. rapid consumption of glucose and fructose from the medium regardless of the cell type. Modulation of sugar-phosphate levels also suggest that the pentose phosphate pathway could be enhanced in the cells from co-cultured biofilms. Untargeted metabolomics results suggested significant production of cell-wall biosynthesis components and the consumption of non-proteinaceous amino-acids.
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Affiliation(s)
- Stefan Weidt
- Polyomics, University of Glasgow, 211 Wolfson Wohl Translational Cancer Research Centre, Garscube Campus, Glasgow, G61 1QH UK
| | - Jennifer Haggarty
- Polyomics, University of Glasgow, 211 Wolfson Wohl Translational Cancer Research Centre, Garscube Campus, Glasgow, G61 1QH UK
| | - Ryan Kean
- Oral Sciences Research Group, Glasgow Dental School, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | | | | - Ranjith Rajendran
- Oral Sciences Research Group, Glasgow Dental School, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Gordon Ramage
- Oral Sciences Research Group, Glasgow Dental School, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Karl E. V. Burgess
- Polyomics, University of Glasgow, 211 Wolfson Wohl Translational Cancer Research Centre, Garscube Campus, Glasgow, G61 1QH UK
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182
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Jorge TF, Mata AT, António C. Mass spectrometry as a quantitative tool in plant metabolomics. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:20150370. [PMID: 27644967 PMCID: PMC5031636 DOI: 10.1098/rsta.2015.0370] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/16/2016] [Indexed: 05/03/2023]
Abstract
Metabolomics is a research field used to acquire comprehensive information on the composition of a metabolite pool to provide a functional screen of the cellular state. Studies of the plant metabolome include the analysis of a wide range of chemical species with very diverse physico-chemical properties, and therefore powerful analytical tools are required for the separation, characterization and quantification of this vast compound diversity present in plant matrices. In this review, challenges in the use of mass spectrometry (MS) as a quantitative tool in plant metabolomics experiments are discussed, and important criteria for the development and validation of MS-based analytical methods provided.This article is part of the themed issue 'Quantitative mass spectrometry'.
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Affiliation(s)
- Tiago F Jorge
- Plant Metabolomics Laboratory, ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Ana T Mata
- Plant Metabolomics Laboratory, ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Carla António
- Plant Metabolomics Laboratory, ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
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183
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Kapoore RV, Vaidyanathan S. Towards quantitative mass spectrometry-based metabolomics in microbial and mammalian systems. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2015.0363. [PMID: 27644979 PMCID: PMC5031630 DOI: 10.1098/rsta.2015.0363] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/27/2016] [Indexed: 05/03/2023]
Abstract
Metabolome analyses are a suite of analytical approaches that enable us to capture changes in the metabolome (small molecular weight components, typically less than 1500 Da) in biological systems. Mass spectrometry (MS) has been widely used for this purpose. The key challenge here is to be able to capture changes in a reproducible and reliant manner that is representative of the events that take place in vivo Typically, the analysis is carried out in vitro, by isolating the system and extracting the metabolome. MS-based approaches enable us to capture metabolomic changes with high sensitivity and resolution. When developing the technique for different biological systems, there are similarities in challenges and differences that are specific to the system under investigation. Here, we review some of the challenges in capturing quantitative changes in the metabolome with MS based approaches, primarily in microbial and mammalian systems.This article is part of the themed issue 'Quantitative mass spectrometry'.
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Affiliation(s)
- Rahul Vijay Kapoore
- Advanced Biomanufacturing Centre, ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK
| | - Seetharaman Vaidyanathan
- Advanced Biomanufacturing Centre, ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK
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184
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Mirali M, Purves RW, Stonehouse R, Song R, Bett K, Vandenberg A. Genetics and Biochemistry of Zero-Tannin Lentils. PLoS One 2016; 11:e0164624. [PMID: 27788158 PMCID: PMC5082924 DOI: 10.1371/journal.pone.0164624] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/28/2016] [Indexed: 12/13/2022] Open
Abstract
The zero-tannin trait in lentil is controlled by a single recessive gene (tan) that results in a phenotype characterized by green stems, white flowers, and thin, transparent, or translucent seed coats. Genes that result in zero-tannin characteristics are useful for studies of seed coat pigmentation and biochemical characters because they have altered pigmentation. In this study, one of the major groups of plant pigments, phenolic compounds, was compared among zero-tannin and normal phenotypes and genotypes of lentil. Biochemical data were obtained by liquid chromatography-mass spectrometry (LC-MS). Genomic sequencing was used to identify a candidate gene for the tan locus. Phenolic compound profiling revealed that myricetin, dihydromyricetin, flavan-3-ols, and proanthocyanidins are only detected in normal lentil phenotypes and not in zero-tannin types. The molecular analysis showed that the tan gene encodes a bHLH transcription factor, homologous to the A gene in pea. The results of this study suggest that tan as a bHLH transcription factor interacts with the regulatory genes in the biochemical pathway of phenolic compounds starting from flavonoid-3',5'-hydroxylase (F3'5'H) and dihydroflavonol reductase (DFR).
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Affiliation(s)
- Mahla Mirali
- Plant Sciences Department, University of Saskatchewan, Saskatoon, SK, Canada
| | - Randy W. Purves
- Plant Sciences Department, University of Saskatchewan, Saskatoon, SK, Canada
| | - Rob Stonehouse
- Plant Sciences Department, University of Saskatchewan, Saskatoon, SK, Canada
| | - Rui Song
- Plant Sciences Department, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kirstin Bett
- Plant Sciences Department, University of Saskatchewan, Saskatoon, SK, Canada
| | - Albert Vandenberg
- Plant Sciences Department, University of Saskatchewan, Saskatoon, SK, Canada
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185
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Muhamadali H, Xu Y, Morra R, Trivedi DK, Rattray NJW, Dixon N, Goodacre R. Metabolomic analysis of riboswitch containing E. coli recombinant expression system. MOLECULAR BIOSYSTEMS 2016; 12:350-61. [PMID: 26621574 DOI: 10.1039/c5mb00624d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In this study we have employed metabolomics approaches to understand the metabolic effects of producing enhanced green fluorescent protein (eGFP) as a recombinant protein in Escherichia coli cells. This metabolic burden analysis was performed against a number of recombinant expression systems and control strains and included: (i) standard transcriptional recombinant expression control system BL21(DE3) with the expression plasmid pET-eGFP, (ii) the recently developed dual transcriptional-translational recombinant expression control strain BL21(IL3), with pET-eGFP, (iii) BL21(DE3) with an empty expression plasmid pET, (iv) BL21(IL3) with an empty expression plasmid, and (v) BL21(DE3) without an expression plasmid; all strains were cultured under various induction conditions. The growth profiles of all strains together with the results gathered by the analysis of the Fourier transform infrared (FT-IR) spectroscopy data, identified IPTG-dependent induction as the dominant factor hampering cellular growth and metabolism, which was in general agreement with the findings of GC-MS analysis of cell extracts and media samples. In addition, the exposure of host cells to the synthetic inducer ligand, pyrimido[4,5-d] pyrimidine-2,4-diamine (PPDA), of the orthogonal riboswitch containing expression system (BL21(IL3)) did not display any detrimental effects, and its detected levels in all the samples were at similar levels, emphasising the inability of the cells to metabolise PPDA. The overall results obtained in this study suggested that although the BL21(DE3)-EGFP and BL21(IL3)-EGFP strains produced comparable levels of recombinant eGFP, the presence of the orthogonal riboswitch seemed to be moderating the metabolic burden of eGFP production in the cells enabling higher biomass yield, whilst providing a greater level of control over protein expression.
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Affiliation(s)
- Howbeer Muhamadali
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| | - Yun Xu
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| | - Rosa Morra
- Faculty of Life Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| | - Drupad K Trivedi
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| | - Nicholas J W Rattray
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| | - Neil Dixon
- Faculty of Life Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| | - Royston Goodacre
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
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186
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Rankin NJ, Preiss D, Welsh P, Sattar N. Applying metabolomics to cardiometabolic intervention studies and trials: past experiences and a roadmap for the future. Int J Epidemiol 2016; 45:1351-1371. [PMID: 27789671 PMCID: PMC5100629 DOI: 10.1093/ije/dyw271] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2016] [Indexed: 12/22/2022] Open
Abstract
Metabolomics and lipidomics are emerging methods for detailed phenotyping of small molecules in samples. It is hoped that such data will: (i) enhance baseline prediction of patient response to pharmacotherapies (beneficial or adverse); (ii) reveal changes in metabolites shortly after initiation of therapy that may predict patient response, including adverse effects, before routine biomarkers are altered; and( iii) give new insights into mechanisms of drug action, particularly where the results of a trial of a new agent were unexpected, and thus help future drug development. In these ways, metabolomics could enhance research findings from intervention studies. This narrative review provides an overview of metabolomics and lipidomics in early clinical intervention studies for investigation of mechanisms of drug action and prediction of drug response (both desired and undesired). We highlight early examples from drug intervention studies associated with cardiometabolic disease. Despite the strengths of such studies, particularly the use of state-of-the-art technologies and advanced statistical methods, currently published studies in the metabolomics arena are largely underpowered and should be considered as hypothesis-generating. In order for metabolomics to meaningfully improve stratified medicine approaches to patient treatment, there is a need for higher quality studies, with better exploitation of biobanks from randomized clinical trials i.e. with large sample size, adjudicated outcomes, standardized procedures, validation cohorts, comparison witth routine biochemistry and both active and control/placebo arms. On the basis of this review, and based on our research experience using clinically established biomarkers, we propose steps to more speedily advance this area of research towards potential clinical impact.
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Affiliation(s)
- Naomi J Rankin
- BHF Glasgow Cardiovascular Research Centre
- Glasgow Polyomics, University of Glasgow, Glasgow, UK
| | - David Preiss
- Clinical Trials Service Unit and Epidemiological Studies Unit, University of Oxford, Oxford, UK
| | - Paul Welsh
- BHF Glasgow Cardiovascular Research Centre
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187
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Jorge TF, Rodrigues JA, Caldana C, Schmidt R, van Dongen JT, Thomas-Oates J, António C. Mass spectrometry-based plant metabolomics: Metabolite responses to abiotic stress. MASS SPECTROMETRY REVIEWS 2016; 35:620-49. [PMID: 25589422 DOI: 10.1002/mas.21449] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 10/02/2014] [Accepted: 10/14/2014] [Indexed: 05/08/2023]
Abstract
Metabolomics is one omics approach that can be used to acquire comprehensive information on the composition of a metabolite pool to provide a functional screen of the cellular state. Studies of the plant metabolome include analysis of a wide range of chemical species with diverse physical properties, from ionic inorganic compounds to biochemically derived hydrophilic carbohydrates, organic and amino acids, and a range of hydrophobic lipid-related compounds. This complexitiy brings huge challenges to the analytical technologies employed in current plant metabolomics programs, and powerful analytical tools are required for the separation and characterization of this extremely high compound diversity present in biological sample matrices. The use of mass spectrometry (MS)-based analytical platforms to profile stress-responsive metabolites that allow some plants to adapt to adverse environmental conditions is fundamental in current plant biotechnology research programs for the understanding and development of stress-tolerant plants. In this review, we describe recent applications of metabolomics and emphasize its increasing application to study plant responses to environmental (stress-) factors, including drought, salt, low oxygen caused by waterlogging or flooding of the soil, temperature, light and oxidative stress (or a combination of them). Advances in understanding the global changes occurring in plant metabolism under specific abiotic stress conditions are fundamental to enhance plant fitness and increase stress tolerance. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 35:620-649, 2016.
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Affiliation(s)
- Tiago F Jorge
- Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier-Universidade Nova de Lisboa (ITQB-UNL), Avenida República, 2780-157, Oeiras, Portugal
| | - João A Rodrigues
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - Camila Caldana
- Max-Planck-partner group at the Brazilian Bioethanol Science and Technology Laboratory/CNPEM, 13083-970, Campinas-SP, Brazil
| | - Romy Schmidt
- Institute of Biology I, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Joost T van Dongen
- Institute of Biology I, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Jane Thomas-Oates
- Jane Thomas-Oates, Centre of Excellence in Mass Spectrometry, and Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Carla António
- Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier-Universidade Nova de Lisboa (ITQB-UNL), Avenida República, 2780-157, Oeiras, Portugal
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188
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Quantitative analysis of endogenous compounds. J Pharm Biomed Anal 2016; 128:426-437. [DOI: 10.1016/j.jpba.2016.06.017] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 06/08/2016] [Accepted: 06/09/2016] [Indexed: 01/19/2023]
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189
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Gómez-Canela C, Miller TH, Bury NR, Tauler R, Barron LP. Targeted metabolomics of Gammarus pulex following controlled exposures to selected pharmaceuticals in water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 562:777-788. [PMID: 27110989 PMCID: PMC4912218 DOI: 10.1016/j.scitotenv.2016.03.181] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 03/24/2016] [Accepted: 03/24/2016] [Indexed: 05/04/2023]
Abstract
The effects of pharmaceuticals and personal care products (PPCPs) on aquatic organisms represent a significant current concern. Herein, a targeted metabolomics approach using liquid chromatography-high resolution mass spectrometry (LC-HRMS) is presented to characterise concentration changes in 29 selected metabolites following exposures of aquatic invertebrates, Gammarus pulex, to pharmaceuticals. Method performance revealed excellent linearity (R(2)>0.99), precision (0.1-19%) and lower instrumental limits of detection (0.002-0.20ng) for all metabolites studied. Three pharmaceuticals were selected representing the low, middle and high range of measured acute measured toxicities (of a total of 26 compounds). Gammarids were exposed to both the no-observed-adverse-effect-level (NOAEL) and the lowest-observed-adverse-effect-level (LOAEL) of triclosan (0.1 and 0.3mgL(-1)), nimesulide (0.5 and 1.4mgL(-1)) and propranolol (100 and 153mgL(-1)) over 24h. Quantitative metabolite profiling was then performed. Significant changes in metabolite concentrations relative to controls are presented and display distinct clustered trends for each pharmaceutical. Approximately 37% (triclosan), 33% (nimesulide) and 46% (propranolol) of metabolites showed statistically significant time-related effects. Observed changes are also discussed with respect to internal concentrations of the three pharmaceuticals measured using a method based on pulverised liquid extraction, solid phase extraction and LC-MS/MS. Potential metabolic pathways that may be affected by such exposures are also discussed. This represents the first study focussing on quantitative, targeted metabolomics of this lower trophic level benthic invertebrate that may elucidate biomarkers for future risk assessment.
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Affiliation(s)
- Cristian Gómez-Canela
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034 Barcelona, Catalonia, Spain; Analytical & Environmental Sciences Division, Faculty of Life Sciences and Medicine, King's College London, 150 Stamford Street, London SE1 9NH, UK.
| | - Thomas H Miller
- Analytical & Environmental Sciences Division, Faculty of Life Sciences and Medicine, King's College London, 150 Stamford Street, London SE1 9NH, UK
| | - Nicolas R Bury
- Diabetes and Nutritional Sciences, Faculty of Life Sciences and Medicine, King's College London, 150 Stamford Street, London SE1 9NH, UK
| | - Romà Tauler
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034 Barcelona, Catalonia, Spain
| | - Leon P Barron
- Analytical & Environmental Sciences Division, Faculty of Life Sciences and Medicine, King's College London, 150 Stamford Street, London SE1 9NH, UK
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190
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Zhen S, Dong K, Deng X, Zhou J, Xu X, Han C, Zhang W, Xu Y, Wang Z, Yan Y. Dynamic metabolome profiling reveals significant metabolic changes during grain development of bread wheat (Triticum aestivum L.). JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2016; 96:3731-3740. [PMID: 26676564 DOI: 10.1002/jsfa.7561] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 11/27/2015] [Accepted: 12/03/2015] [Indexed: 05/29/2023]
Abstract
BACKGROUND Metabolites in wheat grains greatly influence nutritional values. Wheat provides proteins, minerals, B-group vitamins and dietary fiber to humans. These metabolites are important to human health. However, the metabolome of the grain during the development of bread wheat has not been studied so far. In this work the first dynamic metabolome of the developing grain of the elite Chinese bread wheat cultivar Zhongmai 175 was analyzed, using non-targeted gas chromatography/mass spectrometry (GC/MS) for metabolite profiling. RESULTS In total, 74 metabolites were identified over the grain developmental stages. Metabolite-metabolite correlation analysis revealed that the metabolism of amino acids, carbohydrates, organic acids, amines and lipids was interrelated. An integrated metabolic map revealed a distinct regulatory profile. The results provide information that can be used by metabolic engineers and molecular breeders to improve wheat grain quality. CONCLUSION The present metabolome approach identified dynamic changes in metabolite levels, and correlations among such levels, in developing seeds. The comprehensive metabolic map may be useful when breeding programs seek to improve grain quality. The work highlights the utility of GC/MS-based metabolomics, in conjunction with univariate and multivariate data analysis, when it is sought to understand metabolic changes in developing seeds. © 2015 Society of Chemical Industry.
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Affiliation(s)
- Shoumin Zhen
- College of Life Science, Capital Normal University, 100048, Beijing, China
| | - Kun Dong
- College of Life Science, Capital Normal University, 100048, Beijing, China
| | - Xiong Deng
- College of Life Science, Capital Normal University, 100048, Beijing, China
| | - Jiaxing Zhou
- College of Life Science, Capital Normal University, 100048, Beijing, China
| | - Xuexin Xu
- College of Agricultural and Biotechnology, China Agricultural University, 100091, Beijing, China
| | - Caixia Han
- College of Life Science, Capital Normal University, 100048, Beijing, China
| | - Wenying Zhang
- Hubei Collaborative Innovation Center for Grain Industry (HCICGI), Yangtze University, 434025, Jingzhou, China
| | - Yanhao Xu
- Hubei Collaborative Innovation Center for Grain Industry (HCICGI), Yangtze University, 434025, Jingzhou, China
| | - Zhimin Wang
- College of Agricultural and Biotechnology, China Agricultural University, 100091, Beijing, China
| | - Yueming Yan
- College of Life Science, Capital Normal University, 100048, Beijing, China
- Hubei Collaborative Innovation Center for Grain Industry (HCICGI), Yangtze University, 434025, Jingzhou, China
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191
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Tang H, Wang X, Xu L, Ran X, Li X, Chen L, Zhao X, Deng H, Liu X. Establishment of local searching methods for orbitrap-based high throughput metabolomics analysis. Talanta 2016; 156-157:163-171. [DOI: 10.1016/j.talanta.2016.04.051] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/21/2016] [Accepted: 04/24/2016] [Indexed: 01/28/2023]
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192
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Jiang M, Zhao X, Wang L, Xu L, Zhang Y, Li Z. Integrating candidate metabolites and biochemical factors to elucidate the action mechanism of Xue-sai-tong injection based on 1 H NMR metabolomics. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1026:87-96. [DOI: 10.1016/j.jchromb.2016.01.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 01/17/2016] [Accepted: 01/22/2016] [Indexed: 12/22/2022]
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193
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Marcinkiewicz-Siemion M, Ciborowski M, Kretowski A, Musial WJ, Kaminski KA. Metabolomics - A wide-open door to personalized treatment in chronic heart failure? Int J Cardiol 2016; 219:156-63. [PMID: 27323342 DOI: 10.1016/j.ijcard.2016.06.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 06/12/2016] [Indexed: 12/29/2022]
Abstract
Heart failure (HF) is a complex syndrome representing a final stage of various cardiovascular diseases. Despite significant improvement in the diagnosis and treatment (e.g. ACE-inhibitors, β-blockers, aldosterone antagonists, cardiac resynchronization therapy) of the disease, prognosis of optimally treated patients remains very serious and HF mortality is still unacceptably high. Therefore there is a strong need for further exploration of novel analytical methods, predictive and prognostic biomarkers and more personalized treatment. The metabolism of the failing heart being significantly impaired from its baseline state may be a future target not only for biomarker discovery but also for the pharmacologic intervention. However, an assessment of a particular, isolated metabolite or protein cannot be fully informative and makes a correct interpretation difficult. On the other hand, metabolites profile analysis may greatly assist investigator in an interpretation of the altered pathway dynamics, especially when combined with other lines of evidence (e.g. metabolites from the same pathway, transcriptomics, proteomics). Despite many prior studies on metabolism, the knowledge of peripheral and cardiac pathophysiological mechanisms responsible for the metabolic imbalance and progression of the disease is still insufficient. Metabolomics enabling comprehensive characterization of low molecular weight metabolites (e.g. lipids, sugars, organic acids, amino acids) that reflects the complete metabolic phenotype seems to be the key for further potential improvement in HF treatment (diet-based or biochemical-based). Will this -omics technique one day open a door to easy patients identification before they have a heart failure onset or its decompensation?
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Affiliation(s)
| | - M Ciborowski
- Clinical Research Centre, Medical University of Bialystok, Poland
| | - A Kretowski
- Clinical Research Centre, Medical University of Bialystok, Poland
| | - W J Musial
- Cardiology Department, University Hospital, Bialystok, Poland
| | - K A Kaminski
- Cardiology Department, University Hospital, Bialystok, Poland; Department of Population Medicine and Civilization Disease Prevention, Medical University of Bialystok, Poland.
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194
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Mirali M, Purves RW, Vandenberg A. Phenolic profiling of green lentil (Lens culinaris Medic.) seeds subjected to long-term storage. Eur Food Res Technol 2016. [DOI: 10.1007/s00217-016-2713-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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195
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Ghaste M, Mistrik R, Shulaev V. Applications of Fourier Transform Ion Cyclotron Resonance (FT-ICR) and Orbitrap Based High Resolution Mass Spectrometry in Metabolomics and Lipidomics. Int J Mol Sci 2016; 17:ijms17060816. [PMID: 27231903 PMCID: PMC4926350 DOI: 10.3390/ijms17060816] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/14/2016] [Accepted: 05/17/2016] [Indexed: 02/02/2023] Open
Abstract
Metabolomics, along with other "omics" approaches, is rapidly becoming one of the major approaches aimed at understanding the organization and dynamics of metabolic networks. Mass spectrometry is often a technique of choice for metabolomics studies due to its high sensitivity, reproducibility and wide dynamic range. High resolution mass spectrometry (HRMS) is a widely practiced technique in analytical and bioanalytical sciences. It offers exceptionally high resolution and the highest degree of structural confirmation. Many metabolomics studies have been conducted using HRMS over the past decade. In this review, we will explore the latest developments in Fourier transform mass spectrometry (FTMS) and Orbitrap based metabolomics technology, its advantages and drawbacks for using in metabolomics and lipidomics studies, and development of novel approaches for processing HRMS data.
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Affiliation(s)
- Manoj Ghaste
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, Denton, TX 76203, USA.
| | | | - Vladimir Shulaev
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, Denton, TX 76203, USA.
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196
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Aretz I, Meierhofer D. Advantages and Pitfalls of Mass Spectrometry Based Metabolome Profiling in Systems Biology. Int J Mol Sci 2016; 17:ijms17050632. [PMID: 27128910 PMCID: PMC4881458 DOI: 10.3390/ijms17050632] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 04/19/2016] [Accepted: 04/21/2016] [Indexed: 12/22/2022] Open
Abstract
Mass spectrometry-based metabolome profiling became the method of choice in systems biology approaches and aims to enhance biological understanding of complex biological systems. Genomics, transcriptomics, and proteomics are well established technologies and are commonly used by many scientists. In comparison, metabolomics is an emerging field and has not reached such high-throughput, routine and coverage than other omics technologies. Nevertheless, substantial improvements were achieved during the last years. Integrated data derived from multi-omics approaches will provide a deeper understanding of entire biological systems. Metabolome profiling is mainly hampered by its diversity, variation of metabolite concentration by several orders of magnitude and biological data interpretation. Thus, multiple approaches are required to cover most of the metabolites. No software tool is capable of comprehensively translating all the data into a biologically meaningful context yet. In this review, we discuss the advantages of metabolome profiling and main obstacles limiting progress in systems biology.
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Affiliation(s)
- Ina Aretz
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany.
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany.
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197
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Zhang T, Chen S, Syed I, Ståhlman M, Kolar MJ, Homan EA, Chu Q, Smith U, Borén J, Kahn BB, Saghatelian A. A LC-MS-based workflow for measurement of branched fatty acid esters of hydroxy fatty acids. Nat Protoc 2016; 11:747-63. [PMID: 26985573 PMCID: PMC4797065 DOI: 10.1038/nprot.2016.040] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Branched fatty acid esters of hydroxy fatty acids (FAHFAs) are a recently discovered class of endogenous mammalian lipids with antidiabetic and anti-inflammatory effects. We previously identified 16 different FAHFA families, such as branched palmitic acid esters of hydroxy stearic acids (PAHSAs); each family consists of multiple isomers in which the branched ester is at different positions (e.g., 5- and 9-PAHSA). We anticipate increased need for PAHSA measurements as markers of metabolic and inflammatory health. In this protocol, we provide a detailed description of the extraction of FAHFAs from human or mouse tissues, their enrichment by solid-phase extraction and subsequent analysis by LC-MS. For a sample size of 6-12, the time frame is 2-3 d.
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Affiliation(s)
- Tejia Zhang
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Shili Chen
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Ismail Syed
- Division of Endocrinology, Diabetes & Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Marcus Ståhlman
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden
| | | | - Edwin A. Homan
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Qian Chu
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Ulf Smith
- Lundberg Laboratory for Diabetes Research, Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Jan Borén
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Barbara B. Kahn
- Division of Endocrinology, Diabetes & Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
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198
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Zhang CE, Niu M, Li RY, Feng WW, Ma X, Dong Q, Ma ZJ, Li GQ, Meng YK, Wang Y, Yin P, He LZ, Li YM, Tan P, Zhao YL, Wang JB, Dong XP, Xiao XH. Untargeted Metabolomics Reveals Dose-Response Characteristics for Effect of Rhubarb in a Rat Model of Cholestasis. Front Pharmacol 2016; 7:85. [PMID: 27065293 PMCID: PMC4814850 DOI: 10.3389/fphar.2016.00085] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 03/16/2016] [Indexed: 12/25/2022] Open
Abstract
Cholestasis is a serious manifestation of liver diseases with limited therapies. Rhubarb, a widely used herbal medicine, has been frequently used at a relatively large dose for treating cholestasis. However, whether large doses are optimal and the therapeutic mechanism remain unclear. To explore these questions, the anti-cholestatic effect of five doses of rhubarb (0.21, 0.66, 2.10, 6.60, and 21.0 g/kg) in an alpha-naphthylisothiocyanate (ANIT)-induced rat model of cholestasis was examined by histopathology and serum biochemistry. A dose-dependent anti-cholestatic effect of rhubarb (0.21–6.6 g/kg) was observed, and an overdose of 21.0 g/kg showed a poor effect. LC-MS-based untargeted metabolomics together with pathway analysis were further applied to characterize the metabolic alterations induced by the different rhubarb doses. Altogether, 13 biomarkers were identified. The dose-response curve based on nine important biomarkers indicated that doses in the 0.42–6.61 g/kg range (EC20–EC80 range, corresponding to 4.00–62.95 g in the clinic) were effective for cholestasis treatment. The pathway analysis showed that bile acid metabolism and excretion, inflammation and amino acid metabolism were altered by rhubarb in a dose-dependent manner and might be involved in the dose-response relationship and therapeutic mechanism of rhubarb for cholestasis treatment.
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Affiliation(s)
- Cong-En Zhang
- College of Pharmacy, Chengdu University of Traditional Chinese MedicineChengdu, China; China Military Institute of Chinese Medicine, 302 Military HospitalBeijing, China
| | - Ming Niu
- China Military Institute of Chinese Medicine, 302 Military Hospital Beijing, China
| | - Rui-Yu Li
- College of Pharmacy, Chengdu University of Traditional Chinese MedicineChengdu, China; China Military Institute of Chinese Medicine, 302 Military HospitalBeijing, China
| | - Wu-Wen Feng
- College of Pharmacy, Chengdu University of Traditional Chinese MedicineChengdu, China; China Military Institute of Chinese Medicine, 302 Military HospitalBeijing, China
| | - Xiao Ma
- College of Pharmacy, Chengdu University of Traditional Chinese MedicineChengdu, China; China Military Institute of Chinese Medicine, 302 Military HospitalBeijing, China
| | - Qin Dong
- College of Pharmacy, Chengdu University of Traditional Chinese MedicineChengdu, China; China Military Institute of Chinese Medicine, 302 Military HospitalBeijing, China
| | - Zhi-Jie Ma
- China Military Institute of Chinese Medicine, 302 Military HospitalBeijing, China; Department of Pharmacy, Beijing Friendship Hospital, Capital Medical UniversityBeijing, China
| | - Guang-Quan Li
- College of Pharmacy, Chengdu University of Traditional Chinese MedicineChengdu, China; China Military Institute of Chinese Medicine, 302 Military HospitalBeijing, China
| | - Ya-Kun Meng
- China Military Institute of Chinese Medicine, 302 Military Hospital Beijing, China
| | - Ya Wang
- China Military Institute of Chinese Medicine, 302 Military Hospital Beijing, China
| | - Ping Yin
- China Military Institute of Chinese Medicine, 302 Military Hospital Beijing, China
| | - Lan-Zhi He
- China Military Institute of Chinese Medicine, 302 Military Hospital Beijing, China
| | - Yu-Meng Li
- China Military Institute of Chinese Medicine, 302 Military Hospital Beijing, China
| | - Peng Tan
- China Military Institute of Chinese Medicine, 302 Military Hospital Beijing, China
| | - Yan-Ling Zhao
- China Military Institute of Chinese Medicine, 302 Military Hospital Beijing, China
| | - Jia-Bo Wang
- China Military Institute of Chinese Medicine, 302 Military Hospital Beijing, China
| | - Xiao-Ping Dong
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine Chengdu, China
| | - Xiao-He Xiao
- China Military Institute of Chinese Medicine, 302 Military Hospital Beijing, China
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199
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Abstract
Plant-omics is rapidly becoming an important field of study in the scientific community due to the urgent need to address many of the most important questions facing humanity today with regard to agriculture, medicine, biofuels, environmental decontamination, ecological sustainability, etc. High-performance mass spectrometry is a dominant tool for interrogating the metabolomes, peptidomes, and proteomes of a diversity of plant species under various conditions, revealing key insights into the functions and mechanisms of plant biochemistry.
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Affiliation(s)
- Erin Gemperline
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Caitlin Keller
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States.,School of Pharmacy, University of Wisconsin-Madison , 777 Highland Avenue, Madison, Wisconsin 53705, United States
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200
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de Godoy MR, Hervera M, Swanson KS, Fahey GC. Innovations in Canine and Feline Nutrition: Technologies for Food and Nutrition Assessment. Annu Rev Anim Biosci 2016; 4:311-33. [DOI: 10.1146/annurev-animal-021815-111414] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Pet owners have increasing concerns about the nutrition of their pets, and they desire foods and treats that are safe, traceable, and of high nutritive value. To meet these high expectations, detailed chemical composition characterization of ingredients well beyond that provided by proximate analysis will be required, as will information about host physiology and metabolism. Use of faster and more precise analytical methodology and novel technologies that have the potential to improve pet food safety and quality will be implemented. In vitro and in vivo assays will continue to be used as screening tools to evaluate nutrient quality and adequacy in novel ingredients prior to their use in animal diets. The use of molecular and high-throughput technologies allows implementation of noninvasive studies in dogs and cats to investigate the impact of dietary interventions by using systems biology approaches. These approaches may further improve the health and longevity of pets.
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Affiliation(s)
- Maria R.C. de Godoy
- Department of Animal Sciences, University of Illinois, Urbana, Illinois 61801;, ,
| | | | - Kelly S. Swanson
- Department of Animal Sciences, University of Illinois, Urbana, Illinois 61801;, ,
| | - George C. Fahey
- Department of Animal Sciences, University of Illinois, Urbana, Illinois 61801;, ,
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