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Maini Rekdal V, van der Luijt CRB, Chen Y, Kakumanu R, Baidoo EEK, Petzold CJ, Cruz-Morales P, Keasling JD. Edible mycelium bioengineered for enhanced nutritional value and sensory appeal using a modular synthetic biology toolkit. Nat Commun 2024; 15:2099. [PMID: 38485948 PMCID: PMC10940619 DOI: 10.1038/s41467-024-46314-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 02/21/2024] [Indexed: 03/18/2024] Open
Abstract
Filamentous fungi are critical in the transition to a more sustainable food system. While genetic modification of these organisms has promise for enhancing the nutritional value, sensory appeal, and scalability of fungal foods, genetic tools and demonstrated use cases for bioengineered food production by edible strains are lacking. Here, we develop a modular synthetic biology toolkit for Aspergillus oryzae, an edible fungus used in fermented foods, protein production, and meat alternatives. Our toolkit includes a CRISPR-Cas9 method for gene integration, neutral loci, and tunable promoters. We use these tools to elevate intracellular levels of the nutraceutical ergothioneine and the flavor-and color molecule heme in the edible biomass. The strain overproducing heme is red in color and is readily formulated into imitation meat patties with minimal processing. These findings highlight the promise of synthetic biology to enhance fungal foods and provide useful genetic tools for applications in food production and beyond.
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Affiliation(s)
- Vayu Maini Rekdal
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
- Miller Institute for Basic Research in Science, University of California, Berkeley, CA, 94720, USA
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
| | - Casper R B van der Luijt
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
- Department of Food Science, University of Copenhagen, 1958, Frederiksberg, Denmark
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA
| | - Yan Chen
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA
| | - Ramu Kakumanu
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA
| | - Edward E K Baidoo
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA
| | - Pablo Cruz-Morales
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Jay D Keasling
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA.
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA.
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.
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Akyol S, Ashrafi N, Yilmaz A, Turkoglu O, Graham SF. Metabolomics: An Emerging "Omics" Platform for Systems Biology and Its Implications for Huntington Disease Research. Metabolites 2023; 13:1203. [PMID: 38132886 PMCID: PMC10744751 DOI: 10.3390/metabo13121203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/29/2023] [Accepted: 12/02/2023] [Indexed: 12/23/2023] Open
Abstract
Huntington's disease (HD) is a progressive, fatal neurodegenerative disease characterized by motor, cognitive, and psychiatric symptoms. The precise mechanisms of HD progression are poorly understood; however, it is known that there is an expansion of the trinucleotide cytosine-adenine-guanine (CAG) repeat in the Huntingtin gene. Important new strategies are of paramount importance to identify early biomarkers with predictive value for intervening in disease progression at a stage when cellular dysfunction has not progressed irreversibly. Metabolomics is the study of global metabolite profiles in a system (cell, tissue, or organism) under certain conditions and is becoming an essential tool for the systemic characterization of metabolites to provide a snapshot of the functional and pathophysiological states of an organism and support disease diagnosis and biomarker discovery. This review briefly highlights the historical progress of metabolomic methodologies, followed by a more detailed review of the use of metabolomics in HD research to enable a greater understanding of the pathogenesis, its early prediction, and finally the main technical platforms in the field of metabolomics.
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Affiliation(s)
- Sumeyya Akyol
- NX Prenatal Inc., 4350 Brownsboro Road, Louisville KY 40207, USA;
| | - Nadia Ashrafi
- Department of Obstetrics and Gynecology, Oakland University-William Beaumont School of Medicine, 318 Meadow Brook Road, Rochester, MI 48309, USA; (N.A.); (A.Y.); (O.T.)
| | - Ali Yilmaz
- Department of Obstetrics and Gynecology, Oakland University-William Beaumont School of Medicine, 318 Meadow Brook Road, Rochester, MI 48309, USA; (N.A.); (A.Y.); (O.T.)
- Metabolomics Division, Beaumont Research Institute, 3811 W. 13 Mile Road, Royal Oak, MI 48073, USA
| | - Onur Turkoglu
- Department of Obstetrics and Gynecology, Oakland University-William Beaumont School of Medicine, 318 Meadow Brook Road, Rochester, MI 48309, USA; (N.A.); (A.Y.); (O.T.)
| | - Stewart F. Graham
- Department of Obstetrics and Gynecology, Oakland University-William Beaumont School of Medicine, 318 Meadow Brook Road, Rochester, MI 48309, USA; (N.A.); (A.Y.); (O.T.)
- Metabolomics Division, Beaumont Research Institute, 3811 W. 13 Mile Road, Royal Oak, MI 48073, USA
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Yu EA, Alemán JO, Hoover DR, Shi Q, Verano M, Anastos K, Tien PC, Sharma A, Kardashian A, Cohen MH, Golub ET, Michel KG, Gustafson DR, Glesby MJ. Plasma metabolomic analysis indicates flavonoids and sorbic acid are associated with incident diabetes: A nested case-control study among Women's Interagency HIV Study participants. PLoS One 2022; 17:e0271207. [PMID: 35802662 PMCID: PMC9269977 DOI: 10.1371/journal.pone.0271207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 06/26/2022] [Indexed: 02/02/2023] Open
Abstract
INTRODUCTION Lifestyle improvements are key modifiable risk factors for Type 2 diabetes mellitus (DM) however specific influences of biologically active dietary metabolites remain unclear. Our objective was to compare non-targeted plasma metabolomic profiles of women with versus without confirmed incident DM. We focused on three lipid classes (fatty acyls, prenol lipids, polyketides). MATERIALS AND METHODS Fifty DM cases and 100 individually matched control participants (80% with human immunodeficiency virus [HIV]) were enrolled in a case-control study nested within the Women's Interagency HIV Study. Stored blood samples (1-2 years prior to DM diagnosis among cases; at the corresponding timepoint among matched controls) were assayed in triplicate for metabolomics. Time-of-flight liquid chromatography mass spectrometry with dual electrospray ionization modes was utilized. We considered 743 metabolomic features in a two-stage feature selection approach with conditional logistic regression models that accounted for matching strata. RESULTS Seven features differed by DM case status (all false discovery rate-adjusted q<0.05). Three flavonoids (two flavanones, one isoflavone) were respectively associated with lower odds of DM (all q<0.05), and sorbic acid was associated with greater odds of DM (all q<0.05). CONCLUSION Flavonoids were associated with lower odds of incident DM while sorbic acid was associated with greater odds of incident DM.
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Affiliation(s)
- Elaine A. Yu
- Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - José O. Alemán
- Laboratory of Translational Obesity Research, New York University Grossman School of Medicine, New York, New York, United States of America
| | - Donald R. Hoover
- Department of Statistics and Biostatistics, Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Qiuhu Shi
- New York Medical College, Valhalla, New York, United States of America
| | - Michael Verano
- Laboratory of Translational Obesity Research, New York University Grossman School of Medicine, New York, New York, United States of America
| | - Kathryn Anastos
- Montefiore Medical Center, Bronx, New York, United States of America
| | - Phyllis C. Tien
- University of California, San Francisco, California, United States of America
- Department of Veterans Affairs Medical Center, San Francisco, California, United States of America
| | - Anjali Sharma
- Montefiore Medical Center, Bronx, New York, United States of America
| | - Ani Kardashian
- University of Southern California, Los Angeles, California, United States of America
| | - Mardge H. Cohen
- Cook County Health & Hospitals System and Rush University, Chicago, Illinois, United States of America
| | - Elizabeth T. Golub
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Katherine G. Michel
- Georgetown University School of Medicine, District of Columbia, United States of America
| | - Deborah R. Gustafson
- State University of New York Downstate Health Sciences University, New York, New York, United States of America
| | - Marshall J. Glesby
- Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, United States of America
- * E-mail:
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Adeniyi O, Baptista R, Bhowmick S, Cookson A, Nash RJ, Winters A, Shen J, Mur LAJ. Isolation and Characterisation of Quercitrin as a Potent Anti-Sickle Cell Anaemia Agent from Alchornea cordifolia. J Clin Med 2022; 11:jcm11082177. [PMID: 35456270 PMCID: PMC9024604 DOI: 10.3390/jcm11082177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/08/2022] [Accepted: 04/10/2022] [Indexed: 02/02/2023] Open
Abstract
Alchornea cordifolia Müll. Arg. (commonly known as Christmas Bush) has been used traditionally in Africa to treat sickle cell anaemia (a recessive disease, arising from the S haemoglobin (Hb) allele), but the active compounds are yet to be identified. Herein, we describe the use of sequential fractionation coupled with in vitro anti-sickling assays to purify the active component. Sickling was induced in HbSS genotype blood samples using sodium metabisulphite (Na2S2O5) or through incubation in 100% N2. Methanol extracts of A. cordifolia leaves and its sub-fractions showed >70% suppression of HbSS erythrocyte sickling. The purified compound demonstrated a 87.2 ± 2.39% significant anti-sickling activity and 93.1 ± 2.69% erythrocyte sickling-inhibition at 0.4 mg/mL. Nuclear magnetic resonance (NMR) spectra and high-resolution mass spectroscopy identified it as quercitrin (quercetin 3-rhamnoside). Purified quercitrin also inhibited the polymerisation of isolated HbS and stabilized sickle erythrocytes membranes. Metabolomic comparisons of blood samples using flow-infusion electrospray-high resolution mass spectrometry indicated that quercitrin could convert HbSS erythrocyte metabolomes to be like HbAA. Sickling was associated with changes in antioxidants, anaerobic bioenergy, and arachidonic acid metabolism, all of which were reversed by quercitrin. The findings described could inform efforts directed to the development of an anti-sickling drug or quality control assessments of A. cordifolia preparations.
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Affiliation(s)
- Olayemi Adeniyi
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3DA, UK; (O.A.); (R.B.); (S.B.); (A.C.); (A.W.)
- Biochemistry Unit, Department of Science Technology, The Federal Polytechnic, Ado-Ekiti 360231, Nigeria
| | - Rafael Baptista
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3DA, UK; (O.A.); (R.B.); (S.B.); (A.C.); (A.W.)
| | - Sumana Bhowmick
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3DA, UK; (O.A.); (R.B.); (S.B.); (A.C.); (A.W.)
| | - Alan Cookson
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3DA, UK; (O.A.); (R.B.); (S.B.); (A.C.); (A.W.)
| | - Robert J. Nash
- PhytoQuest Ltd., Plas Gogerddan, Aberystwyth SY23 3EB, UK;
| | - Ana Winters
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3DA, UK; (O.A.); (R.B.); (S.B.); (A.C.); (A.W.)
| | - Jianying Shen
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Correspondence: (J.S.); (L.A.J.M.)
| | - Luis A. J. Mur
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3DA, UK; (O.A.); (R.B.); (S.B.); (A.C.); (A.W.)
- Correspondence: (J.S.); (L.A.J.M.)
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5
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Tikunov AP, Tipton JD, Garrett TJ, Shinde SV, Kim HJ, Gerber DA, Herring LE, Graves LM, Macdonald JM. Green Chemistry Preservation and Extraction of Biospecimens for Multi-omic Analyses. Methods Mol Biol 2022; 2394:267-298. [PMID: 35094334 DOI: 10.1007/978-1-0716-1811-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The Environmental Protection Agency's definition of "Green Chemistry" is "the design of chemical products and processes that reduces or eliminates the use or generation of hazardous substances. Green chemistry applies across the life cycle of a chemical product, including its design, manufacture, use, and ultimate disposal." Conventional omic tissue extraction procedures use solvents that are toxic and carcinogenic, such as chloroform and methyl-tert-butyl ether for lipidomics, or caustic chaotropic solutions for genomics and transcriptomics, such as guanidine or urea. A common preservation solution for pathology is formaldehyde, which is a carcinogen. Use of acetonitrile as a universal biospecimen preservation and extraction solvent will reduce these hazardous wastes, because it is less toxic and more environmentally friendly than the conventional solvents used in biorepository and biospecimen research. A new extraction method never applied to multi-omic, system biology research, called cold-induced phase separation (CIPS), uses freezing point temperatures to induce a phase separation of acetonitrile-water mixtures. Also, the CO2 exposure during CIPS will acidify the water precipitating DNA out of aqueous phase. The resulting phase separation brings hydrophobic lipids to the top acetonitrile fraction that is easily decanted from the bottom aqueous fraction, especially when the water is frozen. This CIPS acetonitrile extract contains the lipidome (lipids), the bottom aqueous fraction is sampled to obtain the transcriptome (RNA) fraction, and the remaining water and pellet is extracted with 60% acetonitrile to isolate the metabolome (<1 kD polar molecules). Finally, steps 4 and 5 use a TRIzol™ liquid-liquid extraction SOP of the pellet to isolate the genome (DNA) and proteome (proteins). This chapter details the multi-omic sequential extraction SOP and potential problems associated with each of the 5 steps, with steps 2, 4, and 5 still requiring validation. The metabolomic and lipidomic extraction efficiencies using the CIPS SOP is compared to conventional solvent extraction SOPs and is analyzed by nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry (LC-MS), respectively. Acetonitrile biospecimen preservation combined with the CIPS multi-omic extraction SOP is green chemistry technology that will eliminate the generation of the hazardous substances associated with biospecimen processing and permits separation and safe disposal of acetonitrile avoiding environmental contamination.
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Affiliation(s)
- Andrey P Tikunov
- Departments of Biomedical Engineering, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Jeremiah D Tipton
- Departments of Biomedical Engineering, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, College of Medicine, Gainesville, FL, USA
| | - Timothy J Garrett
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, College of Medicine, Gainesville, FL, USA
| | - Sachi V Shinde
- Departments of Biomedical Engineering, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Hong Jin Kim
- Departments of Surgery, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - David A Gerber
- Departments of Surgery, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Laura E Herring
- Departments of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Lee M Graves
- Departments of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Jeffrey M Macdonald
- Departments of Biomedical Engineering, University of North Carolina School of Medicine, Chapel Hill, NC, USA.
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Narasimhan M, Khamkar V, Tilwani S, Dalal SN, Shetty D, Subramanian PG, Gupta S, Govekar R. Atypical activation of signaling downstream of inactivated Bcr-Abl mediates chemoresistance in chronic myeloid leukemia. J Cell Commun Signal 2021; 16:207-222. [PMID: 34596797 DOI: 10.1007/s12079-021-00647-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/20/2021] [Indexed: 11/28/2022] Open
Abstract
Chronic myeloid leukemia (CML) epitomises successful targeted therapy, where inhibition of tyrosine kinase activity of oncoprotein Bcr-Abl1 by imatinib, induces remission in 86% patients in initial chronic phase (CP). However, in acute phase of blast crisis, 80% patients show resistance, 40% among them despite inhibition of Bcr-Abl1 activity. This implies activation of either Bcr-Abl1- independent signalling pathways or restoration of signalling downstream of inactive Bcr-Abl1. In the present study, mass spectrometry and subsequent in silico pathway analysis of differentiators in resistant CML-CP cells identified key differentiators, 14-3-3ε and p38 MAPK, which belong to Bcr-Abl1 pathway. Their levels and activity respectively, indicated active Bcr-Abl1 pathway in CML-BC resistant cells, though Bcr-Abl1 is inhibited by imatinib. Further, contribution of these components to resistance was demonstrated by inhibition of Bcr-Abl1 down-stream signalling by knocking-out of 14-3-3ε and inhibition of p38 MAPK activity. The observations merit clinical validation to explore their translational potential.
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Affiliation(s)
- Mythreyi Narasimhan
- Rukmini Lab, ACTREC, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India.,Homi Bhabha National Institute, BARC Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Vaishnavi Khamkar
- Rukmini Lab, ACTREC, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India
| | - Sarika Tilwani
- Sorab Lab, ACTREC, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India.,Homi Bhabha National Institute, BARC Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Sorab N Dalal
- Sorab Lab, ACTREC, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India.,Homi Bhabha National Institute, BARC Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Dhanlaxmi Shetty
- Department of Cancer Cytogenetics, , ACTREC, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India
| | - P G Subramanian
- Hematopathology Lab, ACTREC, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India.,Homi Bhabha National Institute, BARC Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Sanjay Gupta
- Gupta Lab, ACTREC, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India.,Homi Bhabha National Institute, BARC Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Rukmini Govekar
- Rukmini Lab, ACTREC, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India. .,Homi Bhabha National Institute, BARC Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
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7
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Ch R, Rey G, Ray S, Jha PK, Driscoll PC, Dos Santos MS, Malik DM, Lach R, Weljie AM, MacRae JI, Valekunja UK, Reddy AB. Rhythmic glucose metabolism regulates the redox circadian clockwork in human red blood cells. Nat Commun 2021; 12:377. [PMID: 33452240 PMCID: PMC7810875 DOI: 10.1038/s41467-020-20479-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 12/01/2020] [Indexed: 02/07/2023] Open
Abstract
Circadian clocks coordinate mammalian behavior and physiology enabling organisms to anticipate 24-hour cycles. Transcription-translation feedback loops are thought to drive these clocks in most of mammalian cells. However, red blood cells (RBCs), which do not contain a nucleus, and cannot perform transcription or translation, nonetheless exhibit circadian redox rhythms. Here we show human RBCs display circadian regulation of glucose metabolism, which is required to sustain daily redox oscillations. We found daily rhythms of metabolite levels and flux through glycolysis and the pentose phosphate pathway (PPP). We show that inhibition of critical enzymes in either pathway abolished 24-hour rhythms in metabolic flux and redox oscillations, and determined that metabolic oscillations are necessary for redox rhythmicity. Furthermore, metabolic flux rhythms also occur in nucleated cells, and persist when the core transcriptional circadian clockwork is absent in Bmal1 knockouts. Thus, we propose that rhythmic glucose metabolism is an integral process in circadian rhythms.
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Affiliation(s)
- Ratnasekhar Ch
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
- School of Biological Sciences, Queen's University Belfast, Belfast, BT9 5DL, UK
| | - Guillaume Rey
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
- Unilabs Genetics Laboratory, 1003, Lausanne, Switzerland
| | - Sandipan Ray
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, PA, 19104, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502285, Telangana, India
| | - Pawan K Jha
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, PA, 19104, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Paul C Driscoll
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | | | - Dania M Malik
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, PA, 19104, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Radoslaw Lach
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
- Department of Oncology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Aalim M Weljie
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, PA, 19104, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - James I MacRae
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Utham K Valekunja
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, PA, 19104, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Akhilesh B Reddy
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, PA, 19104, USA.
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
- Chronobiology and Sleep institute (CSI), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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8
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Kawamura S, Otani M, Miyamoto T, Abe J, Ihara R, Inawaka K, Fantel AG. Different effects of an N-phenylimide herbicide on heme biosynthesis between human and rat erythroid cells. Reprod Toxicol 2021; 99:27-38. [PMID: 33249232 DOI: 10.1016/j.reprotox.2020.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/28/2020] [Accepted: 11/22/2020] [Indexed: 01/10/2023]
Abstract
Rat developmental toxicity including embryolethality and teratogenicity (mainly ventricular septal defects and wavy ribs) were produced by S-53482, an N-phenylimide herbicide that inhibits protoporphyrinogen oxidase (PPO) common to chlorophyll and heme biosynthesis. The sequence of key biological events in the mode of action has been elucidated as follows: inhibition of PPO interferes with normal heme synthesis, which causes loss of blood cells leading to fetal anemia, embryolethality and the development of malformations. In this study we investigated whether the rat is a relevant model for the assessment of the human hazard of the herbicide. To study effects on heme biosynthesis, human erythroleukemia, human cord blood, and rat erythroleukemia cells were treated with the herbicide during red cell differentiation. Protoporphyrin IX, a marker of PPO inhibition, and heme were determined. We investigated whether synchronous maturation of primitive erythropoiesis, which can contribute to massive losses of embryonic blood, occurs in rats. The population of primitive erythroblasts was observed on gestational days 11 through 14. Heme production was suppressed in rat erythroid cells. In contrast, heme reduction was not seen in both human erythroid cells when PPO was inhibited. Rats underwent synchronous maturation in primitive erythropoiesis. Our results combined with epidemiological findings that patients with deficient PPO are not anemic led us to conclude that human erythroblasts are resistant to the herbicide. It is suggested that the rat would be an inappropriate model for assessing the developmental toxicity of S-53482 in humans as rats are specifically sensitive to PPO inhibition by the herbicide.
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Affiliation(s)
- Satoshi Kawamura
- Environmental Health Science Laboratory, Sumitomo Chemical Co., Ltd., 1-98, Kasugade-naka 3-chome, Konohana-ku, Osaka, 554-8558, Japan.
| | - Mitsuhiro Otani
- Environmental Health Science Laboratory, Sumitomo Chemical Co., Ltd., 1-98, Kasugade-naka 3-chome, Konohana-ku, Osaka, 554-8558, Japan
| | - Taiki Miyamoto
- Environmental Health Science Laboratory, Sumitomo Chemical Co., Ltd., 1-98, Kasugade-naka 3-chome, Konohana-ku, Osaka, 554-8558, Japan
| | - Jun Abe
- Environmental Health Science Laboratory, Sumitomo Chemical Co., Ltd., 1-98, Kasugade-naka 3-chome, Konohana-ku, Osaka, 554-8558, Japan
| | - Ryo Ihara
- Environmental Health Science Laboratory, Sumitomo Chemical Co., Ltd., 1-98, Kasugade-naka 3-chome, Konohana-ku, Osaka, 554-8558, Japan
| | - Kunifumi Inawaka
- Environmental Health Science Laboratory, Sumitomo Chemical Co., Ltd., 1-98, Kasugade-naka 3-chome, Konohana-ku, Osaka, 554-8558, Japan
| | - Alan G Fantel
- Department of Pediatrics, University of Washington, 1959 NE Pacific St. Box 366320, Seattle, WA 98195-6320, USA
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Goncalves MD, Lu C, Tutnauer J, Hartman TE, Hwang SK, Murphy CJ, Pauli C, Morris R, Taylor S, Bosch K, Yang S, Wang Y, Van Riper J, Lekaye HC, Roper J, Kim Y, Chen Q, Gross SS, Rhee KY, Cantley LC, Yun J. High-fructose corn syrup enhances intestinal tumor growth in mice. Science 2019; 363:1345-1349. [PMID: 30898933 DOI: 10.1126/science.aat8515] [Citation(s) in RCA: 216] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 12/11/2018] [Accepted: 02/23/2019] [Indexed: 12/14/2022]
Abstract
Excessive consumption of beverages sweetened with high-fructose corn syrup (HFCS) is associated with obesity and with an increased risk of colorectal cancer. Whether HFCS contributes directly to tumorigenesis is unclear. We investigated the effects of daily oral administration of HFCS in adenomatous polyposis coli (APC) mutant mice, which are predisposed to develop intestinal tumors. The HFCS-treated mice showed a substantial increase in tumor size and tumor grade in the absence of obesity and metabolic syndrome. HFCS increased the concentrations of fructose and glucose in the intestinal lumen and serum, respectively, and the tumors transported both sugars. Within the tumors, fructose was converted to fructose-1-phosphate, leading to activation of glycolysis and increased synthesis of fatty acids that support tumor growth. These mouse studies support the hypothesis that the combination of dietary glucose and fructose, even at a moderate dose, can enhance tumorigenesis.
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Affiliation(s)
- Marcus D Goncalves
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA.,Division of Endocrinology, Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Changyuan Lu
- Department of Pharmacology, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10021, USA
| | - Jordan Tutnauer
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Travis E Hartman
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Seo-Kyoung Hwang
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Charles J Murphy
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA.,Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Chantal Pauli
- Institute for Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Roxanne Morris
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sam Taylor
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Kaitlyn Bosch
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sukjin Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yumei Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Justin Van Riper
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - H Carl Lekaye
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jatin Roper
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, NC 27708, USA
| | - Young Kim
- Department of Oral Pathology, School of Dentistry, Chonnam National University, Gwangju, Republic of Korea
| | - Qiuying Chen
- Department of Pharmacology, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10021, USA
| | - Steven S Gross
- Department of Pharmacology, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10021, USA
| | - Kyu Y Rhee
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Jihye Yun
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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10
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Wang Y, Kan Z, Wan X, McGinley JN, Thompson HJ. Differences in chemical composition predictive of in vitro biological activity among commercially important cultivars of genus Camellia. Food Chem 2019; 297:124950. [PMID: 31253304 DOI: 10.1016/j.foodchem.2019.06.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 05/24/2019] [Accepted: 06/05/2019] [Indexed: 12/22/2022]
Abstract
Leaves of plants from the genus Camellia (CAM) are used to make tea; however, there are limited data that compares chemical composition and biological activity of CAM cultivars used to make six tea types. Fourteen CAM cultivars were analyzed by HPLC and UPLC-Q-TOF-MS/MS and biological activity was assessed in a cell growth assay. Tea bioactives and cell growth inhibition varied 2-4 fold. EGCG was the dominant catechin that predicted the magnitude of growth inhibition. However, pure EGCG did not fully account for inhibitory activity suggesting that it may serve as a chemical marker for bioefficacy. As an unbiased characterization of differences in chemical composition among CAM, individual metabolomes were determined and used to generate principle components (PC). PC's from the metabolome were complementary to those from targeted analyses of tea bioactives and were predictive of growth inhibition. This study provides a frame work for identifying CAM cultivars with beneficial traits.
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Affiliation(s)
- Yijun Wang
- International Joint Laboratory on Tea Chemistry and Health Effects, State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, PR China
| | - Zhipeng Kan
- International Joint Laboratory on Tea Chemistry and Health Effects, State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, PR China
| | - Xiaochun Wan
- International Joint Laboratory on Tea Chemistry and Health Effects, State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, PR China
| | - John N McGinley
- Cancer Prevention Laboratory, Colorado State University, Fort Collins, CO, USA
| | - Henry J Thompson
- Cancer Prevention Laboratory, Colorado State University, Fort Collins, CO, USA.
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11
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Wang Y, Kan Z, Wang D, Zhang L, Wan X, McGinley JN, Thompson HJ. Differences in Chemical Composition among Commercially Important Cultivars of Genus Camellia. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:5457-5464. [PMID: 30577696 DOI: 10.1021/acs.jafc.8b06164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Leaves from plants of the genus Camellia are used to make beverages and food products; however, there is limited data that compares the chemical composition of the unprocessed leaves of cultivars traditionally used to make these products. Plucked, fresh leaves from 14 commercially important cultivars were analyzed by ultra-performance liquid chromatography-quadrupole time-of-flight tandem mass spectrometry. On the basis of assessment of 61 compounds that are known to be affected by postharvest tea processing methods, significant variation among unprocessed cultivar leaves was observed for compounds in five chemical classes: amino acids, catechins, flavonoids and flavone glycosides, phenolic acids, and alkaloids. These chemical differences were of sufficient magnitude to render two distinct chemically defined clusters of Camellia cultivars that did not reflect the traditional grouping of these cultivars based by species variant, tea type, or production region. Advanced statistical techniques identified candidate biomarkers for each chemical class to guide the development of comprehensive targeted analyses for constituents of biosynthetic pathways in which marked expression plasticity was observed. Targeted analyses of this type have the potential to identify Camellia species/cultivars that will facilitate the formulation of new beverages and designer foods with improved organoleptic characteristic and enhanced prebiotic or nutraceutical activity.
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Affiliation(s)
- Yijun Wang
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects , Anhui Agricultural University , Hefei , Anhui 230036 , People's Republic of China
| | - Zhipeng Kan
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects , Anhui Agricultural University , Hefei , Anhui 230036 , People's Republic of China
| | - Dongxu Wang
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects , Anhui Agricultural University , Hefei , Anhui 230036 , People's Republic of China
| | - Liang Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects , Anhui Agricultural University , Hefei , Anhui 230036 , People's Republic of China
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects , Anhui Agricultural University , Hefei , Anhui 230036 , People's Republic of China
| | - John N McGinley
- Cancer Prevention Laboratory , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Henry J Thompson
- Cancer Prevention Laboratory , Colorado State University , Fort Collins , Colorado 80523 , United States
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12
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Schrimpe-Rutledge AC, Codreanu SG, Sherrod SD, McLean JA. Untargeted Metabolomics Strategies-Challenges and Emerging Directions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1897-1905. [PMID: 27624161 PMCID: PMC5110944 DOI: 10.1007/s13361-016-1469-y] [Citation(s) in RCA: 685] [Impact Index Per Article: 85.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 07/27/2016] [Accepted: 07/29/2016] [Indexed: 05/05/2023]
Abstract
Metabolites are building blocks of cellular function. These species are involved in enzyme-catalyzed chemical reactions and are essential for cellular function. Upstream biological disruptions result in a series of metabolomic changes and, as such, the metabolome holds a wealth of information that is thought to be most predictive of phenotype. Uncovering this knowledge is a work in progress. The field of metabolomics is still maturing; the community has leveraged proteomics experience when applicable and developed a range of sample preparation and instrument methodology along with myriad data processing and analysis approaches. Research focuses have now shifted toward a fundamental understanding of the biology responsible for metabolomic changes. There are several types of metabolomics experiments including both targeted and untargeted analyses. While untargeted, hypothesis generating workflows exhibit many valuable attributes, challenges inherent to the approach remain. This Critical Insight comments on these challenges, focusing on the identification process of LC-MS-based untargeted metabolomics studies-specifically in mammalian systems. Biological interpretation of metabolomics data hinges on the ability to accurately identify metabolites. The range of confidence associated with identifications that is often overlooked is reviewed, and opportunities for advancing the metabolomics field are described. Graphical Abstract ᅟ.
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Affiliation(s)
- Alexandra C Schrimpe-Rutledge
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
- Center for Innovative Technology, Vanderbilt University, Nashville, TN, 37235, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 37235, USA
- Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN, 37235, USA
| | - Simona G Codreanu
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
- Center for Innovative Technology, Vanderbilt University, Nashville, TN, 37235, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 37235, USA
- Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN, 37235, USA
| | - Stacy D Sherrod
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
- Center for Innovative Technology, Vanderbilt University, Nashville, TN, 37235, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 37235, USA
- Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN, 37235, USA
| | - John A McLean
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA.
- Center for Innovative Technology, Vanderbilt University, Nashville, TN, 37235, USA.
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 37235, USA.
- Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN, 37235, USA.
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13
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Brandi J, Dando I, Pozza ED, Biondani G, Jenkins R, Elliott V, Park K, Fanelli G, Zolla L, Costello E, Scarpa A, Cecconi D, Palmieri M. Proteomic analysis of pancreatic cancer stem cells: Functional role of fatty acid synthesis and mevalonate pathways. J Proteomics 2016; 150:310-322. [PMID: 27746256 DOI: 10.1016/j.jprot.2016.10.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 10/09/2016] [Indexed: 12/28/2022]
Abstract
Recently, we have shown that the secretome of pancreatic cancer stem cells (CSCs) is characterized by proteins that participate in cancer differentiation, invasion, and metastasis. However, the differentially expressed intracellular proteins that lead to the specific characteristics of pancreatic CSCs have not yet been identified, and as a consequence the deranged metabolic pathways are yet to be elucidated. To identify the modulated proteins of pancreatic CSCs, iTRAQ-based proteomic analysis was performed to compare the proteome of Panc1 CSCs and Panc1 parental cells, identifying 230 modulated proteins. Pathway analysis revealed activation of glycolysis, the pentose phosphate pathway, the pyruvate-malate cycle, and lipid metabolism as well as downregulation of the Krebs cycle, the splicesome and non-homologous end joining. These findings were supported by metabolomics and immunoblotting analysis. It was also found that inhibition of fatty acid synthase by cerulenin and of mevalonate pathways by atorvastatin have a greater anti-proliferative effect on cancer stem cells than parental cells. Taken together, these results clarify some important aspects of the metabolic network signature of pancreatic cancer stem cells, shedding light on key and novel therapeutic targets and suggesting that fatty acid synthesis and mevalonate pathways play a key role in ensuring their viability. BIOLOGICAL SIGNIFICANCE To better understand the altered metabolic pathways of pancreatic cancer stem cells (CSCs), a comprehensive proteomic analysis and metabolite profiling investigation of Panc1 and Panc1 CSCs were carried out. The findings obtained indicate that Panc1 CSCs are characterized by upregulation of glycolysis, pentose phosphate pathway, pyruvate-malate cycle, and lipid metabolism and by downregulation of Krebs cycle, spliceosome and non-homologous end joining. Moreover, fatty acid synthesis and mevalonate pathways are shown to play a critical contribution to the survival of pancreatic cancer stem cells. This study is helpful for broadening the knowledge of pancreatic cancer stem cells and could accelerate the development of novel therapeutic strategies.
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Affiliation(s)
- Jessica Brandi
- University of Verona, Department of Biotechnology, Proteomics and Mass Spectrometry Laboratory, Verona 37134, Italy
| | - Ilaria Dando
- University of Verona, Department of Neuroscience, Biomedicine and Movement, Verona 37134, Italy
| | - Elisa Dalla Pozza
- University of Verona, Department of Neuroscience, Biomedicine and Movement, Verona 37134, Italy
| | - Giulia Biondani
- University of Verona, Department of Neuroscience, Biomedicine and Movement, Verona 37134, Italy
| | - Rosalind Jenkins
- University of Liverpool, MRC Centre for Drug Safety Science, Department of Molecular & Clinical Pharmacology, Liverpool L69 3GE, United Kingdom
| | - Victoria Elliott
- NIHR Liverpool Pancreas Biomedical Research Unit, Department of Molecular and Therapeutic Cancer Medicine, Royal Liverpool University Hospital, Liverpool L69 3GA, United Kingdom
| | - Kevin Park
- University of Liverpool, MRC Centre for Drug Safety Science, Department of Molecular & Clinical Pharmacology, Liverpool L69 3GE, United Kingdom
| | - Giuseppina Fanelli
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Lello Zolla
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Eithne Costello
- NIHR Liverpool Pancreas Biomedical Research Unit, Department of Molecular and Therapeutic Cancer Medicine, Royal Liverpool University Hospital, Liverpool L69 3GA, United Kingdom
| | - Aldo Scarpa
- University and Hospital Trust of Verona, Applied Research on Cancer Network (ARC-NET), Department of Pathology and Diagnostics, Verona 37134, Italy
| | - Daniela Cecconi
- University of Verona, Department of Biotechnology, Proteomics and Mass Spectrometry Laboratory, Verona 37134, Italy.
| | - Marta Palmieri
- University of Verona, Department of Neuroscience, Biomedicine and Movement, Verona 37134, Italy
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14
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Telu KH, Yan X, Wallace WE, Stein SE, Simón-Manso Y. Analysis of human plasma metabolites across different liquid chromatography/mass spectrometry platforms: Cross-platform transferable chemical signatures. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:581-93. [PMID: 26842580 PMCID: PMC5114847 DOI: 10.1002/rcm.7475] [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] [Indexed: 05/10/2023]
Abstract
RATIONALE The metabolite profiling of a NIST plasma Standard Reference Material (SRM 1950) on different liquid chromatography/mass spectrometry (LC/MS) platforms showed significant differences. Although these findings suggest caution when interpreting metabolomics results, the degree of overlap of both profiles allowed us to use tandem mass spectral libraries of recurrent spectra to evaluate to what extent these results are transferable across platforms and to develop cross-platform chemical signatures. METHODS Non-targeted global metabolite profiles of SRM 1950 were obtained on different LC/MS platforms using reversed-phase chromatography and different chromatographic scales (conventional HPLC, UHPLC and nanoLC). The data processing and the metabolite differential analysis were carried out using publically available (XCMS), proprietary (Mass Profiler Professional) and in-house software (NIST pipeline). RESULTS Repeatability and intermediate precision showed that the non-targeted SRM 1950 profiling was highly reproducible when working on the same platform (relative standard deviation (RSD) <2%); however, substantial differences were found in the LC/MS patterns originating on different platforms or even using different chromatographic scales (conventional HPLC, UHPLC and nanoLC) on the same platform. A substantial degree of overlap (common molecular features) was also found. A procedure to generate consistent chemical signatures using tandem mass spectral libraries of recurrent spectra is proposed. CONLUSIONS Different platforms rendered significantly different metabolite profiles, but the results were highly reproducible when working within one platform. Tandem mass spectral libraries of recurrent spectra are proposed to evaluate the degree of transferability of chemical signatures generated on different platforms. Chemical signatures based on our procedure are most likely cross-platform transferable.
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Affiliation(s)
| | | | | | | | - Yamil Simón-Manso
- Address reprint requests to: Yamil Simón-Manso, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA, Telephone: 301-975-8638, Fax: 301-975-2643,
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15
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Highly Active and Stable Large Catalase Isolated from a Hydrocarbon Degrading Aspergillus terreus MTCC 6324. Enzyme Res 2016; 2016:4379403. [PMID: 27057351 PMCID: PMC4807065 DOI: 10.1155/2016/4379403] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 12/11/2015] [Accepted: 12/20/2015] [Indexed: 11/17/2022] Open
Abstract
A hydrocarbon degrading Aspergillus terreus MTCC 6324 produces a high level of extremely active and stable cellular large catalase (CAT) during growth on n-hexadecane to combat the oxidative stress caused by the hydrocarbon degrading metabolic machinery inside the cell. A 160-fold purification with specific activity of around 66 × 105 U mg−1 protein was achieved. The native protein molecular mass was 368 ± 5 kDa with subunit molecular mass of nearly 90 kDa, which indicates that the native CAT protein is a homotetramer. The isoelectric pH (pI) of the purified CAT was 4.2. BLAST aligned peptide mass fragments of CAT protein showed its highest similarity with the catalase B protein from other fungal sources. CAT was active in a broad range of pH 4 to 12 and temperature 25°C to 90°C. The catalytic efficiency (Kcat/Km) of 4.7 × 108 M−1 s−1 within the studied substrate range and alkaline pH stability (half-life, t1/2 at pH 12~15 months) of CAT are considerably higher than most of the extensively studied catalases from different sources. The storage stability (t1/2) of CAT at physiological pH 7.5 and 4°C was nearly 30 months. The haem was identified as haem b by electrospray ionization tandem mass spectroscopy (ESI-MS/MS).
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16
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The strengths and weaknesses of NMR spectroscopy and mass spectrometry with particular focus on metabolomics research. Methods Mol Biol 2015; 1277:161-93. [PMID: 25677154 DOI: 10.1007/978-1-4939-2377-9_13] [Citation(s) in RCA: 313] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mass spectrometry (MS) and nuclear magnetic resonance (NMR) have evolved as the most common techniques in metabolomics studies, and each brings its own advantages and limitations. Unlike MS spectrometry, NMR spectroscopy is quantitative and does not require extra steps for sample preparation, such as separation or derivatization. Although the sensitivity of NMR spectroscopy has increased enormously and improvements continue to emerge steadily, this remains a weak point for NMR compared with MS. MS-based metabolomics provides an excellent approach that can offer a combined sensitivity and selectivity platform for metabolomics research. Moreover, different MS approaches such as different ionization techniques and mass analyzer technology can be used in order to increase the number of metabolites that can be detected. In this chapter, the advantages, limitations, strengths, and weaknesses of NMR and MS as tools applicable to metabolomics research are highlighted.
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17
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Madji Hounoum B, Blasco H, Nadal-Desbarats L, Diémé B, Montigny F, Andres CR, Emond P, Mavel S. Analytical methodology for metabolomics study of adherent mammalian cells using NMR, GC-MS and LC-HRMS. Anal Bioanal Chem 2015; 407:8861-72. [PMID: 26446897 DOI: 10.1007/s00216-015-9047-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 09/03/2015] [Accepted: 09/14/2015] [Indexed: 10/23/2022]
Abstract
We developed a methodology for the analysis of intracellular metabolites using nuclear magnetic resonance spectrometry (NMR), gas-chromatography coupled with mass spectrometry (GC-MS), and liquid chromatography coupled with high resolution mass spectrometry (LC-HRMS). The main steps for analysis of adherent cells in order to recover the widest possible range of intracellular compounds are blocking metabolic activity by quenching and extraction of intracellular metabolites. We explored three protocols to quench NSC-34 cell metabolism and four different extraction methods, analyzed by NMR. On the basis of the number of metabolites extracted and their relative standard deviation (RSD) analyzed by NMR, the most reproducible protocol [quenching by MeOH at -40 °C and extraction with CH2Cl2/MeOH/H2O (3:3:2)] was used to obtain intracellular media to be analyzed by GC-MS and LC-HRMS. GC-MS analysis was optimized by three oximation procedures followed by silylation derivatization and these were compared to silylation alone. Using reversed-phase liquid chromatography (C18), four different gradients for LC-MS were compared. The analytical protocols were determined to establish the reliability and suitability of sample treatments required to achieve the correct biological analysis of untargeted mammalian cell metabolomics.
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Affiliation(s)
- Blandine Madji Hounoum
- INSERM U930 "Imagerie et Cerveau", CHRU de Tours, Université François-Rabelais, 10 Bv Tonnellé, 37044, Tours, France
| | - Hélène Blasco
- INSERM U930 "Imagerie et Cerveau", CHRU de Tours, Université François-Rabelais, 10 Bv Tonnellé, 37044, Tours, France
| | - Lydie Nadal-Desbarats
- INSERM U930 "Imagerie et Cerveau", CHRU de Tours, Université François-Rabelais, 10 Bv Tonnellé, 37044, Tours, France
| | - Binta Diémé
- INSERM U930 "Imagerie et Cerveau", CHRU de Tours, Université François-Rabelais, 10 Bv Tonnellé, 37044, Tours, France
| | - Frédéric Montigny
- INSERM U930 "Imagerie et Cerveau", CHRU de Tours, Université François-Rabelais, 10 Bv Tonnellé, 37044, Tours, France
| | - Christian R Andres
- INSERM U930 "Imagerie et Cerveau", CHRU de Tours, Université François-Rabelais, 10 Bv Tonnellé, 37044, Tours, France
| | - Patrick Emond
- INSERM U930 "Imagerie et Cerveau", CHRU de Tours, Université François-Rabelais, 10 Bv Tonnellé, 37044, Tours, France
| | - Sylvie Mavel
- INSERM U930 "Imagerie et Cerveau", CHRU de Tours, Université François-Rabelais, 10 Bv Tonnellé, 37044, Tours, France.
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18
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Jové M, Maté I, Naudí A, Mota-Martorell N, Portero-Otín M, De la Fuente M, Pamplona R. Human Aging Is a Metabolome-related Matter of Gender. J Gerontol A Biol Sci Med Sci 2015; 71:578-85. [DOI: 10.1093/gerona/glv074] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/30/2015] [Indexed: 11/13/2022] Open
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19
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Arnold JM, Choi WT, Sreekumar A, Maletić-Savatić M. Analytical strategies for studying stem cell metabolism. ACTA ACUST UNITED AC 2015. [PMID: 26213533 DOI: 10.1007/s11515-015-1357-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Owing to their capacity for self-renewal and pluripotency, stem cells possess untold potential for revolutionizing the field of regenerative medicine through the development of novel therapeutic strategies for treating cancer, diabetes, cardiovascular and neurodegenerative diseases. Central to developing these strategies is improving our understanding of biological mechanisms responsible for governing stem cell fate and self-renewal. Increasing attention is being given to the significance of metabolism, through the production of energy and generation of small molecules, as a critical regulator of stem cell functioning. Rapid advances in the field of metabolomics now allow for in-depth profiling of stem cells both in vitro and in vivo, providing a systems perspective on key metabolic and molecular pathways which influence stem cell biology. Understanding the analytical platforms and techniques that are currently used to study stem cell metabolomics, as well as how new insights can be derived from this knowledge, will accelerate new research in the field and improve future efforts to expand our understanding of the interplay between metabolism and stem cell biology.
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Affiliation(s)
- James M Arnold
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - William T Choi
- Program in Developmental Biology and Medical Scientist Training Program, Baylor College of Medicine; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Arun Sreekumar
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mirjana Maletić-Savatić
- Program in Developmental Biology and Medical Scientist Training Program, Baylor College of Medicine; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA ; Departments of Pediatrics-Neurology and Neuroscience, and Program in Structural and Computational Biology and Molecular Biophysics Baylor College of Medicine, Houston, TX 77030, USA
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20
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Ser Z, Liu X, Tang NN, Locasale JW. Extraction parameters for metabolomics from cultured cells. Anal Biochem 2015; 475:22-8. [PMID: 25613493 DOI: 10.1016/j.ab.2015.01.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 11/11/2014] [Accepted: 01/05/2015] [Indexed: 11/18/2022]
Abstract
The successful extraction of metabolites is a critical step in metabolite profiling. By optimizing metabolite extraction, the range and quantitative capacity of metabolomics studies can be improved. We considered eight separate extraction protocols for the preparation of a metabolite extract from cultured mammalian cells. Parameters considered included temperature, pH, and cell washing before extraction. The effects on metabolite recovery were studied using a liquid chromatography high-resolution mass spectrometry (LC-HRMS) platform that measures metabolites of diverse chemical classes, including amino acids, lipids, and sugar derivatives. The temperature considered during the extraction or the presence of formic acid, a commonly used additive, was shown to have minimal effects on the measured ion intensities of metabolites. However, washing of samples before metabolite extraction, whether with water or phosphate-buffered saline, exhibited dramatic effects on measured intensities of both intracellular and extracellular metabolites. Together, these findings present a systematic assessment of extraction conditions for metabolite profiling.
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Affiliation(s)
- Zheng Ser
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Xiaojing Liu
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Ngoc Nu Tang
- Field of Genetics, Genomics, and Development, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jason W Locasale
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA; Field of Genetics, Genomics, and Development, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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Goldenberg NA, Everett AD, Graham D, Bernard TJ, Nowak-Göttl U. Proteomic and other mass spectrometry based “omics” biomarker discovery and validation in pediatric venous thromboembolism and arterial ischemic stroke: Current state, unmet needs, and future directions. Proteomics Clin Appl 2014; 8:828-36. [DOI: 10.1002/prca.201400062] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 10/06/2014] [Accepted: 11/03/2014] [Indexed: 01/02/2023]
Affiliation(s)
- Neil A. Goldenberg
- Clinical and Translational Research Organization; All Children's Research Institute; All Children's Hospital Johns Hopkins Medicine; St. Petersburg FL USA
- Johns Hopkins Medicine Pediatric Thrombosis Program; All Children's Hospital Johns Hopkins Medicine; St. Petersburg FL, USA and Johns Hopkins Bloomberg Children's Center, Baltimore, MD, USA
- Johns Hopkins Medicine Pediatric Stroke Program; All Children's Hospital Johns Hopkins Medicine; St. Petersburg FL USA and Johns Hopkins Children's Center, Baltimore, MD, USA
- Division of Hematology; Department of Pediatrics; Johns Hopkins University School of Medicine; Baltimore MD USA
| | - Allen D. Everett
- Division of Cardiology; Johns Hopkins University School of Medicine; Baltimore MD USA
- Pediatric Proteome Center; Department of Pediatrics; Johns Hopkins University School of Medicine; Baltimore MD USA
| | - David Graham
- Department of Molecular and Comparative Pathobiology; Johns Hopkins University; Baltimore MD USA
- Center for Resources in Integrative Biology; Johns Hopkins University School of Medicine; Baltimore MD USA
| | - Timothy J. Bernard
- Department of Pediatrics; Denver School of Medicine; University of Colorado; Aurora CO USA
- Pediatric Stroke Program; Children's Hospital Colorado; Aurora CO USA
| | - Ulrike Nowak-Göttl
- Department of Pediatrics; Universitätsklinikum Schleswig-Holstein; Kiel Germany
- Department of Medicine; Universitätsklinikum Schleswig-Holstein; Kiel Germany
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22
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Challenges of analyzing different classes of metabolites by a single analytical method. Bioanalysis 2014; 6:3393-416. [DOI: 10.4155/bio.14.236] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Complex biological samples include thousands of metabolites that range widely in both physiochemical properties and concentration. Simultaneously analyzing metabolites with different properties using a single analytical method is very challenging. The analytical process for metabolites comprises multiple steps including sampling, quenching, sample preparation, separation and detection. Each step can have a significant effect on the reliability and precision of ultimate analytic results. The aim of review is a discussion of considerations and challenges for the simultaneous analysis of metabolites using LC– and GC–MS systems. The review discusses available methodology for each analytical step, and presents the limitations and advantages of each method for the large-scale targeted metabolomics analysis of human and animal biological samples.
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23
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Bannur Z, Teh L, Hennesy T, Rosli W, Mohamad N, Nasir A, Ankathil R, Zakaria Z, Baba A, Salleh M. The differential metabolite profiles of acute lymphoblastic leukaemic patients treated with 6-mercaptopurine using untargeted metabolomics approach. Clin Biochem 2014; 47:427-31. [DOI: 10.1016/j.clinbiochem.2014.02.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 01/26/2014] [Accepted: 02/12/2014] [Indexed: 11/25/2022]
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Nunes de Paiva MJ, Menezes HC, de Lourdes Cardeal Z. Sampling and analysis of metabolomes in biological fluids. Analyst 2014; 139:3683-94. [DOI: 10.1039/c4an00583j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Metabolome analysis involves the study of small molecules that are involved in the metabolic responses that occur through patho-physiological changes caused by genetic stimuli or chemical agents.
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Affiliation(s)
- Maria José Nunes de Paiva
- Departamento de Química
- ICEx
- Universidade Federal de Minas Gerais
- 6627-31270901 Belo Horizonte, Brazil
- Universidade Federal de São João Del Rei
| | - Helvécio Costa Menezes
- Departamento de Química
- ICEx
- Universidade Federal de Minas Gerais
- 6627-31270901 Belo Horizonte, Brazil
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25
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Global LC/MS Metabolomics Profiling of Calcium Stressed and Immunosuppressant Drug Treated Saccharomyces cerevisiae. Metabolites 2013; 3:1102-17. [PMID: 24958268 PMCID: PMC3937837 DOI: 10.3390/metabo3041102] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 11/20/2013] [Accepted: 11/25/2013] [Indexed: 11/17/2022] Open
Abstract
Previous studies have shown that calcium stressed Saccharomyces cerevisiae, challenged with immunosuppressant drugs FK506 and Cyclosporin A, responds with comprehensive gene expression changes and attenuation of the generalized calcium stress response. Here, we describe a global metabolomics workflow for investigating the utility of tracking corresponding phenotypic changes. This was achieved by efficiently analyzing relative abundance differences between intracellular metabolite pools from wild-type and calcium stressed cultures, with and without prior immunosuppressant drugs exposure. We used pathway database content from WikiPathways and YeastCyc to facilitate the projection of our metabolomics profiling results onto biological pathways. A key challenge was to increase the coverage of the detected metabolites. This was achieved by applying both reverse phase (RP) and aqueous normal phase (ANP) chromatographic separations, as well as electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) sources for detection in both ion polarities. Unsupervised principle component analysis (PCA) and ANOVA results revealed differentiation between wild-type controls, calcium stressed and immunosuppressant/calcium challenged cells. Untargeted data mining resulted in 247 differentially expressed, annotated metabolites, across at least one pair of conditions. A separate, targeted data mining strategy identified 187 differential, annotated metabolites. All annotated metabolites were subsequently mapped onto curated pathways from YeastCyc and WikiPathways for interactive pathway analysis and visualization. Dozens of pathways showed differential responses to stress conditions based on one or more matches to the list of annotated metabolites or to metabolites that had been identified further by MS/MS. The purine salvage, pantothenate and sulfur amino acid pathways were flagged as being enriched, which is consistent with previously published literature for transcriptomics analysis. Thus, broad discovery-based data mining combined with targeted pathway projections can be an important asset for rapidly distilling, testing and evaluating a large amount of information for further investigation.
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26
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Kokubun T, D'Costa L. Direct and unbiased information recovery from liquid chromatography-mass spectrometry raw data for phenotype-differentiating metabolites based on screening window coefficient of ion currents. Anal Chem 2013; 85:8684-91. [PMID: 24004415 DOI: 10.1021/ac401545b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A reworking of a data mining strategy, in which statistical treatment of raw data from liquid chromatography-mass spectrometry (LC-MS) precedes recognition of chromatographic peaks, is presented. In this algorithm the tR-m/z plane of LC-MS data is divided into equal-sized segments of twelve seconds by one m/z unit each, and the total ion currents in corresponding segments as specified by the tR-m/z pair from multiple LC-MS runs are evaluated to generate mean ion currents (μ) and standard deviations (σ). The μ's and σ's of the segments, derived from contrasting classes of LC-MS data set (e.g., resistant-susceptible, case-control, etc.), are used to calculate the Z-factor (screening window coefficient) which is in turn used to rank the segments. Chromatographic peaks are recognized only where the ion currents are shown to differentiate the classes. The result-reporting format enables detection of positive as well as negative correlations between ion intensities and biological traits under study and thus points to the presence of potentially phenotype-discriminating metabolites. Examples of data analyses are presented, in which ions that may distinguish resistant and susceptible species of Aesculus to the leaf-miner Cameraria ohridella were detected.
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Affiliation(s)
- Tetsuo Kokubun
- Jodrell Laboratory, Royal Botanic Gardens, Kew , Richmond, Surrey TW9 3DS, United Kingdom
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27
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Liquid chromatography–mass spectrometry for metabolic footprinting of co-cultures of lactic and propionic acid bacteria. Anal Bioanal Chem 2013; 405:8151-70. [DOI: 10.1007/s00216-013-7269-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 07/18/2013] [Accepted: 07/22/2013] [Indexed: 12/28/2022]
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28
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Cuthbertson DJ, Johnson SR, Piljac-Žegarac J, Kappel J, Schäfer S, Wüst M, Ketchum REB, Croteau RB, Marques JV, Davin LB, Lewis NG, Rolf M, Kutchan TM, Soejarto DD, Lange BM. Accurate mass-time tag library for LC/MS-based metabolite profiling of medicinal plants. PHYTOCHEMISTRY 2013; 91:187-97. [PMID: 23597491 PMCID: PMC3697863 DOI: 10.1016/j.phytochem.2013.02.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 02/21/2013] [Accepted: 02/25/2013] [Indexed: 05/20/2023]
Abstract
We report the development and testing of an accurate mass-time (AMT) tag approach for the LC/MS-based identification of plant natural products (PNPs) in complex extracts. An AMT tag library was developed for approximately 500 PNPs with diverse chemical structures, detected in electrospray and atmospheric pressure chemical ionization modes (both positive and negative polarities). In addition, to enable peak annotations with high confidence, MS/MS spectra were acquired with three different fragmentation energies. The LC/MS and MS/MS data sets were integrated into online spectral search tools and repositories (Spektraris and MassBank), thus allowing users to interrogate their own data sets for the potential presence of PNPs. The utility of the AMT tag library approach is demonstrated by the detection and annotation of active principles in 27 different medicinal plant species with diverse chemical constituents.
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Affiliation(s)
- Daniel J. Cuthbertson
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
| | - Sean R. Johnson
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
| | - Jasenka Piljac-Žegarac
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
- Ruđer Bošković Institute, Bijenićka cesta 54, HR-10000 Zagreb, Croatia
| | - Julia Kappel
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
- Institute of Nutrition and Food Sciences, University of Bonn, Endenicher Allee 11-13, 53115 Bonn, Germany
| | - Sarah Schäfer
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
- Institute of Nutrition and Food Sciences, University of Bonn, Endenicher Allee 11-13, 53115 Bonn, Germany
| | - Matthias Wüst
- Institute of Nutrition and Food Sciences, University of Bonn, Endenicher Allee 11-13, 53115 Bonn, Germany
| | - Raymond E. B. Ketchum
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
| | - Rodney B. Croteau
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
| | - Joaquim V. Marques
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
| | - Laurence B. Davin
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
| | - Norman G. Lewis
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
| | - Megan Rolf
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO 63132, USA
| | - Toni M. Kutchan
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO 63132, USA
| | - D. Doel Soejarto
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St. (M/C 781), Chicago, IL 60612, USA
- Botany Department, Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605-2496, USA
| | - B. Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
- Corresponding author: Tel.: 509-335-3794; fax: 509-335-7643. (B.M. Lange)
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29
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Cannabinoids inhibit energetic metabolism and induce AMPK-dependent autophagy in pancreatic cancer cells. Cell Death Dis 2013; 4:e664. [PMID: 23764845 PMCID: PMC3698539 DOI: 10.1038/cddis.2013.151] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The anti-tumoral effects of cannabinoids have been described in different tumor systems, including pancreatic adenocarcinoma, but their mechanism of action remains unclear. We used cannabinoids specific for the CB1 (ACPA) and CB2 (GW) receptors and metabolomic analyses to unravel the potential pathways mediating cannabinoid-dependent inhibition of pancreatic cancer cell growth. Panc1 cells treated with cannabinoids show elevated AMPK activation induced by a ROS-dependent increase of AMP/ATP ratio. ROS promote nuclear translocation of GAPDH, which is further amplified by AMPK, thereby attenuating glycolysis. Furthermore, ROS determine the accumulation of NADH, suggestive of a blockage in the respiratory chain, which in turn inhibits the Krebs cycle. Concomitantly, inhibition of Akt/c-Myc pathway leads to decreased activity of both the pyruvate kinase isoform M2 (PKM2), further downregulating glycolysis, and glutamine uptake. Altogether, these alterations of pancreatic cancer cell metabolism mediated by cannabinoids result in a strong induction of autophagy and in the inhibition of cell growth.
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Forcisi S, Moritz F, Kanawati B, Tziotis D, Lehmann R, Schmitt-Kopplin P. Liquid chromatography–mass spectrometry in metabolomics research: Mass analyzers in ultra high pressure liquid chromatography coupling. J Chromatogr A 2013; 1292:51-65. [DOI: 10.1016/j.chroma.2013.04.017] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 03/29/2013] [Accepted: 04/10/2013] [Indexed: 12/27/2022]
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Kurlbaum M, Mülek M, Högger P. Facilitated uptake of a bioactive metabolite of maritime pine bark extract (pycnogenol) into human erythrocytes. PLoS One 2013; 8:e63197. [PMID: 23646194 PMCID: PMC3639945 DOI: 10.1371/journal.pone.0063197] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2012] [Accepted: 04/02/2013] [Indexed: 02/05/2023] Open
Abstract
Many plant secondary metabolites exhibit some degree of biological activity in humans. It is a common observation that individual plant-derived compounds in vivo are present in the nanomolar concentration range at which they usually fail to display measurable activity in vitro. While it is debatable that compounds detected in plasma are not the key effectors of bioactivity, an alternative hypothesis may take into consideration that measurable concentrations also reside in compartments other than plasma. We analysed the binding of constituents and the metabolite δ-(3,4-dihydroxy-phenyl)-γ-valerolactone (M1), that had been previously detected in plasma samples of human consumers of pine bark extract Pycnogenol, to human erythrocytes. We found that caffeic acid, taxifolin, and ferulic acid passively bind to red blood cells, but only the bioactive metabolite M1 revealed pronounced accumulation. The partitioning of M1 into erythrocytes was significantly diminished at higher concentrations of M1 and in the presence of glucose, suggesting a facilitated transport of M1 via GLUT-1 transporter. This concept was further supported by structural similarities between the natural substrate α-D-glucose and the S-isomer of M1. After cellular uptake, M1 underwent further metabolism by conjugation with glutathione. We present strong indication for a transporter-mediated accumulation of a flavonoid metabolite in human erythrocytes and subsequent formation of a novel glutathione adduct. The physiologic role of the adduct remains to be elucidated.
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Affiliation(s)
- Max Kurlbaum
- Universität Würzburg, Institut für Pharmazie und Lebensmittelchemie, Würzburg, Germany
| | - Melanie Mülek
- Universität Würzburg, Institut für Pharmazie und Lebensmittelchemie, Würzburg, Germany
| | - Petra Högger
- Universität Würzburg, Institut für Pharmazie und Lebensmittelchemie, Würzburg, Germany
- * E-mail:
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32
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Sana TR, Gordon DB, Fischer SM, Tichy SE, Kitagawa N, Lai C, Gosnell WL, Chang SP. Global mass spectrometry based metabolomics profiling of erythrocytes infected with Plasmodium falciparum. PLoS One 2013; 8:e60840. [PMID: 23593322 PMCID: PMC3621881 DOI: 10.1371/journal.pone.0060840] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 03/05/2013] [Indexed: 12/20/2022] Open
Abstract
Malaria is a global infectious disease that threatens the lives of millions of people. Transcriptomics, proteomics and functional genomics studies, as well as sequencing of the Plasmodium falciparum and Homo sapiens genomes, have shed new light on this host-parasite relationship. Recent advances in accurate mass measurement mass spectrometry, sophisticated data analysis software, and availability of biological pathway databases, have converged to facilitate our global, untargeted biochemical profiling study of in vitro P. falciparum-infected (IRBC) and uninfected (NRBC) erythrocytes. In order to expand the number of detectable metabolites, several key analytical steps in our workflows were optimized. Untargeted and targeted data mining resulted in detection of over one thousand features or chemical entities. Untargeted features were annotated via matching to the METLIN metabolite database. For targeted data mining, we queried the data using a compound database derived from a metabolic reconstruction of the P. falciparum genome. In total, over one hundred and fifty differential annotated metabolites were observed. To corroborate the representation of known biochemical pathways from our data, an inferential pathway analysis strategy was used to map annotated metabolites onto the BioCyc pathway collection. This hypothesis-generating approach resulted in over-representation of many metabolites onto several IRBC pathways, most prominently glycolysis. In addition, components of the “branched” TCA cycle, partial urea cycle, and nucleotide, amino acid, chorismate, sphingolipid and fatty acid metabolism were found to be altered in IRBCs. Interestingly, we detected and confirmed elevated levels for cyclic ADP ribose and phosphoribosyl AMP in IRBCs, a novel observation. These metabolites may play a role in regulating the release of intracellular Ca2+ during P. falciparum infection. Our results support a strategy of global metabolite profiling by untargeted data acquisition. Untargeted and targeted data mining workflows, when used together to perform pathway-inferred metabolomics, have the benefit of obviating MS/MS confirmation for every detected compound.
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Affiliation(s)
- Theodore R. Sana
- Life Sciences Group, Agilent Technologies, Santa Clara, California, United States of America
| | - D. Benjamin Gordon
- Life Sciences Group, Agilent Technologies, Santa Clara, California, United States of America
| | - Steven M. Fischer
- Life Sciences Group, Agilent Technologies, Santa Clara, California, United States of America
| | - Shane E. Tichy
- Life Sciences Group, Agilent Technologies, Santa Clara, California, United States of America
| | - Norton Kitagawa
- Life Sciences Group, Agilent Technologies, Santa Clara, California, United States of America
| | - Cindy Lai
- Life Sciences Group, Agilent Technologies, Santa Clara, California, United States of America
| | - William L. Gosnell
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Sandra P. Chang
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
- * E-mail:
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Li L, Li R, Zhou J, Zuniga A, Stanislaus AE, Wu Y, Huan T, Zheng J, Shi Y, Wishart DS, Lin G. MyCompoundID: Using an Evidence-Based Metabolome Library for Metabolite Identification. Anal Chem 2013; 85:3401-8. [DOI: 10.1021/ac400099b] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta,
Canada
| | - Ronghong Li
- Department
of Computing
Science, University of Alberta, Edmonton, Alberta, Canada
| | - Jianjun Zhou
- Department
of Computing
Science, University of Alberta, Edmonton, Alberta, Canada
| | - Azeret Zuniga
- Department of Chemistry, University of Alberta, Edmonton, Alberta,
Canada
| | | | - Yiman Wu
- Department of Chemistry, University of Alberta, Edmonton, Alberta,
Canada
| | - Tao Huan
- Department of Chemistry, University of Alberta, Edmonton, Alberta,
Canada
| | - Jiamin Zheng
- Department of Chemistry, University of Alberta, Edmonton, Alberta,
Canada
| | - Yi Shi
- Department
of Computing
Science, University of Alberta, Edmonton, Alberta, Canada
| | - David S. Wishart
- Department
of Computing
Science, University of Alberta, Edmonton, Alberta, Canada
- Department of Biological
Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Guohui Lin
- Department
of Computing
Science, University of Alberta, Edmonton, Alberta, Canada
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Marrocco C, D'Alessandro A, Girelli G, Zolla L. Proteomic analysis of platelets treated with gamma irradiation versus a commercial photochemical pathogen reduction technology. Transfusion 2013; 53:1808-20. [DOI: 10.1111/trf.12060] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 09/20/2012] [Accepted: 10/12/2012] [Indexed: 12/18/2022]
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Corominas-Faja B, Quirantes-Piné R, Oliveras-Ferraros C, Vazquez-Martin A, Cufí S, Martin-Castillo B, Micol V, Joven J, Segura-Carretero A, Menendez JA. Metabolomic fingerprint reveals that metformin impairs one-carbon metabolism in a manner similar to the antifolate class of chemotherapy drugs. Aging (Albany NY) 2012; 4:480-98. [PMID: 22837425 PMCID: PMC3433934 DOI: 10.18632/aging.100472] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Metabolomic fingerprint of breast cancer cells treated with the antidiabetic drug metformin revealed a significant accumulation of 5-formimino-tetrahydrofolate, one of the tetrahydrofolate forms carrying activated one-carbon units that are essential for the de novo synthesis of purines and pyrimidines. De novo synthesis of glutathione, a folate-dependent pathway interconnected with one-carbon metabolism was concomitantly depleted in response to metformin. End-product reversal studies demonstrated that thymidine alone leads to a significant but incomplete protection from metformin's cytostatic effects. The addition of the substrate hypoxanthine for the purine salvage pathway produces major rightward shifts in metformin's growth inhibition curves. Metformin treatment failed to activate the DNA repair protein ATM kinase and the metabolic tumor suppressor AMPK when thymidine and hypoxanthine were present in the extracellular milieu. Our current findings suggest for the first time that metformin can function as an antifolate chemotherapeutic agent that induces the ATM/AMPK tumor suppressor axis secondarily following the alteration of the carbon flow through the folate-related one-carbon metabolic pathways.
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Clinical metabolomics: the next stage of clinical biochemistry. BLOOD TRANSFUSION = TRASFUSIONE DEL SANGUE 2012; 10 Suppl 2:s19-24. [PMID: 22890264 DOI: 10.2450/2012.005s] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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38
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Metabolomic analysis of the effects of edible dry beans (Phaseolus vulgaris L.) on tissue lipid metabolism and carcinogenesis in rats. Br J Nutr 2012; 108 Suppl 1:S155-65. [PMID: 22916811 DOI: 10.1017/s0007114512000827] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Metabolite profiling using liquid chromatography-time-of-flight MS was undertaken to identify candidate metabolic processes that account for dry bean effects on disease risk with a specific focus on the development of breast cancer. Normal mammary gland and mammary carcinomas from previously reported experiments were evaluated. Principal component analysis (PCA) of mass spectral data revealed that tissue of both types from control-fed v. bean-fed rats could be distinguished by their metabolomic profiles. Candidate ion identification using MassTRIX analysis software revealed that alterations in eicosanoid, fatty acid, TAG and steroid metabolism partially accounted for the differences observed in both PCA. In addition, evidence was obtained consistent with the hypothesis that the varying inhibitory effects on mammary carcinogenesis of genetically distinct dry bean types were mirrored by differential patterns of lipid metabolites in mammary carcinoma. The use of MassTRIX provided links for metabolite profile enrichment with metabolic pathways in the Kyoto Encyclopedia of Genes and Genomes. Implicated pathways included a linkage between diacylglycerol and protein kinase C and eicosanoid metabolites and inducible cyclo-oxygenase-2 and/or eicosanoid degradation mediated via 15-PG dehydrogenase. These pathways have been reported to be misregulated during the development of cancer. The differences observed between control-fed and bean-fed rats in lipid metabolism require validation using targeted analytical methods and detailed analyses of how bean bioactive food components regulate genes that control lipid biosynthesis, interconversion and catabolism.
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39
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Murine macrophages response to iron. J Proteomics 2012; 76 Spec No.:10-27. [PMID: 22835775 DOI: 10.1016/j.jprot.2012.07.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2012] [Revised: 06/20/2012] [Accepted: 07/15/2012] [Indexed: 12/17/2022]
Abstract
Macrophages play a critical role at the crossroad between iron metabolism and immunity, being able to store and recycle iron derived from the phagocytosis of senescent erythrocytes. The way by which macrophages manage non-heme iron at physiological concentration is still not fully understood. We investigated protein changes in mouse bone marrow macrophages incubated with ferric ammonium citrate (FAC 10 μM iron). Differentially expressed spots were identified by nano RP-HPLC-ESI-MS/MS. Transcriptomic, metabolomics and western immunoblotting analyses complemented the proteomic approach. Pattern analysis was also used for identifying networks of proteins involved in iron homeostasis. FAC treatment resulted in higher abundance of several proteins including ferritins, cytoskeleton related proteins, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) at the membrane level, vimentin, arginase, galectin-3 and macrophage migration inhibitory factor (MIF). Interestingly, GAPDH has been recently proposed to act as an alternative transferrin receptor for iron acquisition through internalization of the GAPDH-transferrin complex into the early endosomes. FAC treatment also induced the up-regulation of oxidative stress-related proteins (PRDX), which was further confirmed at the metabolic level (increase in GSSG, 8-isoprostane and pentose phosphate pathway intermediates) through mass spectrometry-based targeted metabolomics approaches. This study represents an example of the potential usefulness of "integarated omics" in the field of iron biology, especially for the elucidation of the molecular mechanisms controlling iron homeostasis in normal and disease conditions. This article is part of a Special Issue entitled: Integrated omics.
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40
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D'Alessandro A, Rinalducci S, Marrocco C, Zolla V, Napolitano F, Zolla L. Love me tender: An Omics window on the bovine meat tenderness network. J Proteomics 2012; 75:4360-80. [DOI: 10.1016/j.jprot.2012.02.013] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 02/01/2012] [Accepted: 02/13/2012] [Indexed: 01/15/2023]
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41
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Chen Q, Park HC, Goligorsky MS, Chander P, Fischer SM, Gross SS. Untargeted plasma metabolite profiling reveals the broad systemic consequences of xanthine oxidoreductase inactivation in mice. PLoS One 2012; 7:e37149. [PMID: 22723833 PMCID: PMC3377762 DOI: 10.1371/journal.pone.0037149] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 04/13/2012] [Indexed: 02/07/2023] Open
Abstract
A major challenge in systems biology is integration of molecular findings for individual enzyme activities into a cohesive high-level understanding of cellular metabolism and physiology/pathophysiology. However, meaningful prediction for how a perturbed enzyme activity will globally impact metabolism in a cell, tissue or intact organisms is precluded by multiple unknowns, including in vivo enzymatic rates, subcellular distribution and pathway interactions. To address this challenge, metabolomics offers the potential to simultaneously survey changes in thousands of structurally diverse metabolites within complex biological matrices. The present study assessed the capability of untargeted plasma metabolite profiling to discover systemic changes arising from inactivation of xanthine oxidoreductase (XOR), an enzyme that catalyzes the final steps in purine degradation. Using LC-MS coupled with a multivariate statistical data analysis platform, we confidently surveyed >3,700 plasma metabolites (50-1,000 Da) for differential expression in XOR wildtype vs. mice with inactivated XOR, arising from gene deletion or pharmacological inhibition. Results confirmed the predicted derangements in purine metabolism, but also revealed unanticipated perturbations in metabolism of pyrimidines, nicotinamides, tryptophan, phospholipids, Krebs and urea cycles, and revealed kidney dysfunction biomarkers. Histochemical studies confirmed and characterized kidney failure in xor-nullizygous mice. These findings provide new insight into XOR functions and demonstrate the power of untargeted metabolite profiling for systemic discovery of direct and indirect consequences of gene mutations and drug treatments.
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Affiliation(s)
- Qiuying Chen
- Department of Pharmacology, Weill Cornell Medical College, New York, New York, United States of America
| | - Hyeong-Cheon Park
- Departments of Medicine, Pathology and Pharmacology, Renal Research Institute, New York Medical College, Valhalla, New York, United States of America
| | - Michael S. Goligorsky
- Departments of Medicine, Pathology and Pharmacology, Renal Research Institute, New York Medical College, Valhalla, New York, United States of America
| | - Praveen Chander
- Departments of Medicine, Pathology and Pharmacology, Renal Research Institute, New York Medical College, Valhalla, New York, United States of America
| | - Steven M. Fischer
- Metabolomics Laboratory, Agilent Technologies, Santa Clara, California, United States of America
| | - Steven S. Gross
- Department of Pharmacology, Weill Cornell Medical College, New York, New York, United States of America
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42
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Lakshmanan V, Rhee KY, Wang W, Yu Y, Khafizov K, Fiser A, Wu P, Ndir O, Mboup S, Ndiaye D, Daily JP. Metabolomic analysis of patient plasma yields evidence of plant-like α-linolenic acid metabolism in Plasmodium falciparum. J Infect Dis 2012; 206:238-48. [PMID: 22566569 DOI: 10.1093/infdis/jis339] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Metabolomics offers a powerful means to investigate human malaria parasite biology and host-parasite interactions at the biochemical level, and to discover novel therapeutic targets and biomarkers of infection. Here, we used an approach based on liquid chromatography and mass spectrometry to perform an untargeted metabolomic analysis of metabolite extracts from Plasmodium falciparum-infected and uninfected patient plasma samples, and from an enriched population of in vitro cultured P. falciparum-infected and uninfected erythrocytes. Statistical modeling robustly segregated infected and uninfected samples based on metabolite species with significantly different abundances. Metabolites of the α-linolenic acid (ALA) pathway, known to exist in plants but not known to exist in P. falciparum until now, were enriched in infected plasma and erythrocyte samples. In vitro labeling with (13)C-ALA showed evidence of plant-like ALA pathway intermediates in P. falciparum. Ortholog searches using ALA pathway enzyme sequences from 8 available plant genomes identified several genes in the P. falciparum genome that were predicted to potentially encode the corresponding enzymes in the hitherto unannotated P. falciparum pathway. These data suggest that our approach can be used to discover novel facets of host/malaria parasite biology in a high-throughput manner.
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Affiliation(s)
- Viswanathan Lakshmanan
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Yeshiva University, Bronx, New York, USA.
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43
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Paglia G, Magnúsdóttir M, Thorlacius S, Sigurjónsson OE, Guðmundsson S, Palsson BØ, Thiele I. Intracellular metabolite profiling of platelets: evaluation of extraction processes and chromatographic strategies. J Chromatogr B Analyt Technol Biomed Life Sci 2012; 898:111-20. [PMID: 22608809 DOI: 10.1016/j.jchromb.2012.04.026] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 04/12/2012] [Accepted: 04/22/2012] [Indexed: 01/14/2023]
Abstract
An extraction method for intracellular metabolite profiling should ideally be able to recover the broadest possible range of metabolites present in a sample. However, the development of such methods is hampered by the diversity of the physico-chemical properties of metabolites as well as by the specific characteristics of samples and cells. In this study, we report the optimization of an UPLC-MS method for the metabolite analysis of platelet samples. The optimal analytical protocol was determined by testing seven different extraction methods as well as by employing two different LC-MS methods, in which the metabolites were separated by using hydrophilic interaction liquid chromatography (HILIC) and reversed phase liquid chromatography (RPLC). The optimal conditions were selected using the coverage of the platelets' metabolome, the response of the identified metabolites, the reproducibility of the analytical method, and the time of the analysis as main evaluation criteria. Our results show that methanol-water (7:3) extraction coupled with HILIC-MS method provides the best compromise, allowing identification of 107 metabolites in a platelet cell extract sample, 91% of them with a RSD% lower than 20. A higher number of metabolites could be detected when analyzing the platelet samples with two different LC-MS methods or when using complementary extraction methods in parallel.
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Affiliation(s)
- Giuseppe Paglia
- Center for Systems Biology, University of Iceland, Sturlugata 8, Reykjavik, Iceland
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44
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D'Alessandro A, Marrocco C, Rinalducci S, Mirasole C, Failla S, Zolla L. Chianina beef tenderness investigated through integrated Omics. J Proteomics 2012; 75:4381-98. [PMID: 22510581 DOI: 10.1016/j.jprot.2012.03.052] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2012] [Revised: 03/12/2012] [Accepted: 03/27/2012] [Indexed: 12/25/2022]
Abstract
In the present study we performed an integrated proteomics, interactomics and metabolomics analysis of Longissimus dorsi tender and tough meat samples from Chianina beef cattle. Results were statistically handled as to obtain Pearson's correlation coefficients of the results from Omics investigation in relation to canonical tenderness-related parameters, including Warner Bratzler shear force, myofibrillar degradation (at 48 h and 10 days after slaughter), sarcomere length and total collagen content. As a result, we could observe that the tender meat group was characterized by higher levels of glycolytic enzymes, which were over-phosphorylated and produced accumulation of glycolytic intermediates. Oxidative stress promoted meat tenderness and elicited heat shock protein responses, which in turn triggered apoptosis-like cascades along with PARP fragmentation. Phosphorylation was found to be a key process in post mortem muscle conversion to meat, as it was shown not only to modulate glycolytic enzyme activities, but also mediate the stability of structural proteins at the Z-disk. On the other hand, phosphorylation of HSPs has been supposed to alter their functions through changing their affinity for target interactors. Analogies and breed-specific differences are highlighted throughout the text via a direct comparison of the present results against the ones obtained in a parallel study on Maremmana Longissimus dorsi. It emerges that, while the main cornerstones and the final outcome are maintained, post mortem metabolism in tender and tough meat yielding individuals is subtly modulated via specific higher levels of enzymes and amino acidic residue phosphorylation in a breed-specific fashion, and whether calcium homeostasis dysregulation was a key factor in Maremmana, higher early post mortem phosphocreatine levels in the Chianina tender group could favor a slower and prolonged glycolytic rate, prolonging the extent of the minimum hanging period necessary to obtain tender meat from this breed by a few days.
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Affiliation(s)
- Angelo D'Alessandro
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, snc, 01100 Viterbo, Italy
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45
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D'Alessandro A, Gevi F, Zolla L. Targeted mass spectrometry-based metabolomic profiling through multiple reaction monitoring of liver and other biological matrices. Methods Mol Biol 2012; 909:279-94. [PMID: 22903722 DOI: 10.1007/978-1-61779-959-4_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In a systemic viewpoint, relevant biological information on living systems can be grasped from the study of small, albeit pivotal molecules which constitute the fundamental bricks of metabolic pathways. This holds true for liver which plays, among its unique functions, a key role in metabolism. The nonbiased analysis of all this small-molecule complement in its entirety is known as metabolomics. However, no practical approach currently exists to investigate all metabolic species simultaneously without including a technical bias towards acidic or basic compounds, especially when performing mass spectrometry-based investigations. Technical aspects of rapid resolution reversed phase HPLC online with mass spectrometry are hereby described. Such an approach allows to discriminate and quantify a wide array of metabolites with extreme specificity and sensitivity, thus enabling to perform complex investigations even on extremely low quantities of biological material. The advantages also include the possibility to perform targeted investigations on a single (or a handful of) metabolite(s) simoultaneously through single (multiple) reaction monitoring, which further improves the dynamic range of concentrations to be monitored.Such an approach has already proven to represent a valid tool in the direct (on the liver) or indirect (on human red blood cell metabolism which is hereby presented as a representative model, but also on blood plasma or other biological fluids) assessment of metabolic poise modulation and pharmacokinetics for drug development.
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46
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Meat quality of the longissimus lumborum muscle of Casertana and Large White pigs: Metabolomics and proteomics intertwined. J Proteomics 2011; 75:610-27. [DOI: 10.1016/j.jprot.2011.08.024] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2011] [Revised: 08/04/2011] [Accepted: 08/28/2011] [Indexed: 01/06/2023]
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47
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Theodoridis GA, Gika HG, Want EJ, Wilson ID. Liquid chromatography-mass spectrometry based global metabolite profiling: a review. Anal Chim Acta 2011; 711:7-16. [PMID: 22152789 DOI: 10.1016/j.aca.2011.09.042] [Citation(s) in RCA: 328] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 09/18/2011] [Accepted: 09/29/2011] [Indexed: 12/12/2022]
Abstract
Untargeted, global metabolite profiling (often described as metabonomics or metabolomics) represents an expanding research topic and is, potentially, a major pillar for systems biology studies. To obtain holistic metabolic profiles from complex samples, such as biological fluids or tissue extracts, requires powerful, high resolution and information-rich analytical methods and for this spectroscopic technologies are generally used. Mass spectrometry, coupled to liquid chromatography (LC-MS), is increasingly being used for such investigations as a result of the significant advances in both technologies over the past decade. Here we try to critically review the topic of LC-MS-based global metabolic profiling and describe and compare the results offered by different analytical strategies and technologies. This review highlights the current challenges, limitations and opportunities of the current methodology.
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48
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Zhu J, Aja S, Kim EK, Park MJ, Ramamurthy S, Jia J, Hu X, Geng P, Ronnett GV. Physiological oxygen level is critical for modeling neuronal metabolism in vitro. J Neurosci Res 2011; 90:422-34. [PMID: 22002503 DOI: 10.1002/jnr.22765] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 06/29/2011] [Accepted: 07/16/2011] [Indexed: 11/09/2022]
Abstract
In vitro models are important tools for studying the mechanisms that govern neuronal responses to injury. Most neuronal culture methods employ nonphysiological conditions with regard to metabolic parameters. Standard neuronal cell culture is performed at ambient (21%) oxygen levels, whereas actual tissue oxygen levels in the mammalian brain range from 1% to 5%. In this study, we examined the consequences of oxygen level on the viability and metabolism of primary cultures of cortical neurons. Our results indicate that physiological oxygen level (5% O(2)) has a beneficial effect on cortical neuronal survival and mitochondrial function in vitro. Moreover, oxygen level affects metabolic fluxes: glucose uptake and glycolysis was enhanced at physiological oxygen level, whereas glucose oxidation and fatty acid oxidation were reduced. Adenosine monophosphate-activated protein kinase (AMPK) was more activated in 5% O(2) and appears to play a role in these metabolic effects. Inhibiting AMPK activity with compound C decreased glucose uptake, intracellular ATP level, and viability in neurons cultured in 5% O(2). These data indicate that oxygen level is an important parameter to consider when modeling neuronal responses to stress in vitro.
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Affiliation(s)
- Jing Zhu
- Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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49
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Theodoridis G, Gika HG, Wilson ID. Mass spectrometry-based holistic analytical approaches for metabolite profiling in systems biology studies. MASS SPECTROMETRY REVIEWS 2011; 30:884-906. [PMID: 21384411 DOI: 10.1002/mas.20306] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Metabonomics and metabolomics represent one of the three major platforms in systems biology. To perform metabolomics it is necessary to generate comprehensive "global" metabolite profiles from complex samples, for example, biological fluids or tissue extracts. Analytical technologies based on mass spectrometry (MS), and in particular on liquid chromatography-MS (LC-MS), have become a major tool providing a significant source of global metabolite profiling data. In the present review we describe and compare the utility of the different analytical strategies and technologies used for MS-based metabolomics with a particular focus on LC-MS. Both the advantages offered by the technology and also the challenges and limitations that need to be addressed for the successful application of LC-MS in metabolite analysis are described. Data treatment and approaches resulting in the detection and identification of biomarkers are considered. Special emphasis is given to validation issues, instrument stability, and QA/quality control (QC) procedures.
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Affiliation(s)
- Georgios Theodoridis
- Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
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50
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D'Alessandro A, D'Amici GM, Timperio AM, Merendino N, Zolla L. Docosohaexanoic acid-supplemented PACA44 cell lines and over-activation of Krebs cycle: An integrated proteomic, metabolomic and interactomic overview. J Proteomics 2011; 74:2138-58. [DOI: 10.1016/j.jprot.2011.06.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Revised: 05/17/2011] [Accepted: 06/06/2011] [Indexed: 10/18/2022]
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