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Khan AM, Steffensen MA, Paskeviciute E, Abduljabar AB, Sørensen TL, Vorum H, Nissen MH, Honoré B. Neuroretinal degeneration in a mouse model of systemic chronic immune activation observed by proteomics. Front Immunol 2024; 15:1374617. [PMID: 38665911 PMCID: PMC11043527 DOI: 10.3389/fimmu.2024.1374617] [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: 01/22/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024] Open
Abstract
Blindness or vision loss due to neuroretinal and photoreceptor degeneration affects millions of individuals worldwide. In numerous neurodegenerative diseases, including age-related macular degeneration, dysregulated immune response-mediated retinal degeneration has been found to play a critical role in the disease pathogenesis. To better understand the pathogenic mechanisms underlying the retinal degeneration, we used a mouse model of systemic immune activation where we infected mice with lymphocytic choriomeningitis virus (LCMV) clone 13. Here, we evaluated the effects of LCMV infection and present a comprehensive discovery-based proteomic investigation using tandem mass tag (TMT) labeling and high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS). Changes in protein regulation in the posterior part of the eye, neuroretina, and RPE/choroid were compared to those in the spleen as a secondary lymphoid organ and to the kidney as a non-lymphoid but encapsulated organ at 1, 8, and 28 weeks of infection. Using bioinformatic tools, we found several proteins responsible for maintaining normal tissue homeostasis to be differentially regulated in the neuroretina and the RPE/choroid during the degenerative process. Additionally, in the organs we observed, several important protein pathways contributing to cellular homeostasis and tissue development were perturbed and associated with LCMV-mediated inflammation, promoting disease progression. Our findings suggest that the response to a systemic chronic infection differs between the neuroretina and the RPE/choroid, and the processes induced by chronic systemic infection in the RPE/choroid are not unlike those induced in non-immune-privileged organs such as the kidney and spleen. Overall, our data provide detailed insight into several molecular mechanisms of neuroretinal degeneration and highlight various novel protein pathways that further suggest that the posterior part of the eye is not an isolated immunological entity despite the existence of neuroretinal immune privilege.
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Affiliation(s)
| | | | - Egle Paskeviciute
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | | | - Torben Lykke Sørensen
- Department of Ophthalmology, Zealand University Hospital, Roskilde, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Vorum
- Department of Ophthalmology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Mogens Holst Nissen
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Bent Honoré
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
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Generation and identification of kokumi compounds and their validation by taste-receptor assay: An example with dry-cured lamb meat. Food Chem X 2022; 13:100218. [PMID: 35498975 PMCID: PMC9039938 DOI: 10.1016/j.fochx.2022.100218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/09/2022] [Accepted: 01/14/2022] [Indexed: 11/21/2022] Open
Abstract
Fifteen ɤ-glutamyl dipeptides (GGP) were identified in meat crust hydrolysate. In vitro cell based CaSR assay was applied to measure kokumi tastants functionality. Enriched extract of GGP following glutaminase treatment activated CaSR robustly. CaSR assay was used as an effective tool to screen kokumi tastants abundance in foods. Meat crusts can be a good source to generate kokumi tastants via enzymatic reactions.
Kokumi tastants are small γ-glutamyl peptides (GGP) that enhance flavour in foods. We sought to generate GGP from the meat crusts of dry-cured lamb, an underutilised protein resource, identify these using mass spectrometry, and validate their functional activity using a kokumi-calcium sensing receptor (CaSR) assay. The water-soluble extract (WSE) of meat crust was hydrolysed by protease A (PA) and treated with glutaminase (GA). Fifteen GGP were identified, with 14 being significantly increased in PA and GA groups compared to WSE, as were along with free amino acid levels. The GA extract activated CaSR with higher potency and efficacy than PA and WSE suggesting the generation of potent kokumi tastants. The in vitro receptor assay might be an expedient tool for screening kokumi tastants prior to conducting human sensory analysis. Collectively, our findings indicate that the meat crust can be a valuable source to generate kokumi tastants via a two-step enzymatic reaction.
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Fernandes J, Miranda RL, de Lemos ERS, Guterres A. MicroRNAs and Mammarenaviruses: Modulating Cellular Metabolism. Cells 2020; 9:E2525. [PMID: 33238430 PMCID: PMC7709035 DOI: 10.3390/cells9112525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/04/2020] [Accepted: 11/11/2020] [Indexed: 12/11/2022] Open
Abstract
Mammarenaviruses are a diverse genus of emerging viruses that include several causative agents of severe viral hemorrhagic fevers with high mortality in humans. Although these viruses share many similarities, important differences with regard to pathogenicity, type of immune response, and molecular mechanisms during virus infection are different between and within New World and Old World viral infections. Viruses rely exclusively on the host cellular machinery to translate their genome, and therefore to replicate and propagate. miRNAs are the crucial factor in diverse biological processes such as antiviral defense, oncogenesis, and cell development. The viral infection can exert a profound impact on the cellular miRNA expression profile, and numerous RNA viruses have been reported to interact directly with cellular miRNAs and/or to use these miRNAs to augment their replication potential. Our present study indicates that mammarenavirus infection induces metabolic reprogramming of host cells, probably manipulating cellular microRNAs. A number of metabolic pathways, including valine, leucine, and isoleucine biosynthesis, d-Glutamine and d-glutamate metabolism, thiamine metabolism, and pools of several amino acids were impacted by the predicted miRNAs that would no longer regulate these pathways. A deeper understanding of mechanisms by which mammarenaviruses handle these signaling pathways is critical for understanding the virus/host interactions and potential diagnostic and therapeutic targets, through the inhibition of specific pathologic metabolic pathways.
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Affiliation(s)
- Jorlan Fernandes
- Hantaviruses and Rickettsiosis Laboratory, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil;
| | - Renan Lyra Miranda
- Neurochemistry Interactions Laboratory, Universidade Federal Fluminense, Niterói 24020-150, Brazil;
| | - Elba Regina Sampaio de Lemos
- Hantaviruses and Rickettsiosis Laboratory, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil;
| | - Alexandro Guterres
- Hantaviruses and Rickettsiosis Laboratory, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil;
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Sitjà-Bobadilla A, Gil-Solsona R, Estensoro I, Piazzon MC, Martos-Sitcha JA, Picard-Sánchez A, Fuentes J, Sancho JV, Calduch-Giner JA, Hernández F, Pérez-Sánchez J. Disruption of gut integrity and permeability contributes to enteritis in a fish-parasite model: a story told from serum metabolomics. Parasit Vectors 2019; 12:486. [PMID: 31619276 PMCID: PMC6796429 DOI: 10.1186/s13071-019-3746-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/09/2019] [Indexed: 12/16/2022] Open
Abstract
Background In the animal production sector, enteritis is responsible for serious economic losses, and intestinal parasitism is a major stress factor leading to malnutrition and lowered performance and animal production efficiency. The effect of enteric parasites on the gut function of teleost fish, which represent the most ancient bony vertebrates, is far from being understood. The intestinal myxozoan parasite Enteromyxum leei dwells between gut epithelial cells and causes severe enteritis in gilthead sea bream (Sparus aurata), anorexia, cachexia, growth impairment, reduced marketability and increased mortality. Methods This study aimed to outline the gut failure in this fish-parasite model using a multifaceted approach and to find and validate non-lethal serum markers of gut barrier dysfunction. Intestinal integrity was studied in parasitized and non-parasitized fish by immunohistochemistry with specific markers for cellular adhesion (E-cadherin) and tight junctions (Tjp1 and Cldn3) and by functional studies of permeability (oral administration of FITC-dextran) and electrophysiology (Ussing chambers). Serum samples from parasitized and non-parasitized fish were analyzed using non-targeted metabolomics and some significantly altered metabolites were selected to be validated using commercial kits. Results The immunodetection of Tjp1 and Cldn3 was significantly lower in the intestine of parasitized fish, while no strong differences were found in E-cadherin. Parasitized fish showed a significant increase in paracellular uptake measured by FITC-dextran detection in serum. Electrophysiology showed a decrease in transepithelial resistance in infected animals, which showed a diarrheic profile. Serum metabolomics revealed 3702 ions, from which the differential expression of 20 identified compounds significantly separated control from infected groups in multivariate analyses. Of these compounds, serum inosine (decreased) and creatine (increased) were identified as relevant and validated with commercial kits. Conclusions The results demonstrate the disruption of tight junctions and the loss of gut barrier function, a metabolomic profile of absorption dysfunction and anorexia, which further outline the pathophysiological effects of E. leei.![]()
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Affiliation(s)
- Ariadna Sitjà-Bobadilla
- Fish Pathology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), 12595 Ribera de Cabanes, Castellón, Spain. .,Associated Unit of Marine Ecotoxicology (IATS-IUPA), Castellon, Spain.
| | - Rubén Gil-Solsona
- Research Institute for Pesticides and Water (IUPA), University Jaume I, Avda. Vicent Sos Baynat, s/n. Campus del Riu Sec, 12071, Castellón, Spain
| | - Itziar Estensoro
- Fish Pathology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), 12595 Ribera de Cabanes, Castellón, Spain
| | - M Carla Piazzon
- Fish Pathology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), 12595 Ribera de Cabanes, Castellón, Spain
| | - Juan Antonio Martos-Sitcha
- Nutrigenomics and Fish Endocrinology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), 12595 Ribera de Cabanes, Castellón, Spain.,Department of Biology, Faculty of Marine and Environmental Sciences, Instituto Universitario de Investigación Marina (INMAR), Campus Universitario de Puerto Real, University of Cádiz, 11510, Cádiz, Spain
| | - Amparo Picard-Sánchez
- Fish Pathology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), 12595 Ribera de Cabanes, Castellón, Spain
| | - Juan Fuentes
- Comparative Endocrinology and Integrative Biology, CCMar, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Juan Vicente Sancho
- Research Institute for Pesticides and Water (IUPA), University Jaume I, Avda. Vicent Sos Baynat, s/n. Campus del Riu Sec, 12071, Castellón, Spain
| | - Josep A Calduch-Giner
- Associated Unit of Marine Ecotoxicology (IATS-IUPA), Castellon, Spain.,Nutrigenomics and Fish Endocrinology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), 12595 Ribera de Cabanes, Castellón, Spain
| | - Félix Hernández
- Associated Unit of Marine Ecotoxicology (IATS-IUPA), Castellon, Spain.,Research Institute for Pesticides and Water (IUPA), University Jaume I, Avda. Vicent Sos Baynat, s/n. Campus del Riu Sec, 12071, Castellón, Spain
| | - Jaume Pérez-Sánchez
- Associated Unit of Marine Ecotoxicology (IATS-IUPA), Castellon, Spain.,Nutrigenomics and Fish Endocrinology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), 12595 Ribera de Cabanes, Castellón, Spain
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Fernández-Ochoa Á, Borrás-Linares I, Baños A, García-López JD, Guillamón E, Nuñez-Lechado C, Quirantes-Piné R, Segura-Carretero A. A fingerprinting metabolomic approach reveals deregulation of endogenous metabolites after the intake of a bioactive garlic supplement. J Funct Foods 2018. [DOI: 10.1016/j.jff.2018.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Antipurinergic therapy for autism-An in-depth review. Mitochondrion 2017; 43:1-15. [PMID: 29253638 DOI: 10.1016/j.mito.2017.12.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/11/2017] [Accepted: 12/14/2017] [Indexed: 12/13/2022]
Abstract
Are the symptoms of autism caused by a treatable metabolic syndrome that traces to the abnormal persistence of a normal, alternative functional state of mitochondria? A small clinical trial published in 2017 suggests this is possible. Based on a new unifying theory of pathogenesis for autism called the cell danger response (CDR) hypothesis, this study of 10 boys, ages 5-14years, showed that all 5 boys who received antipurinergic therapy (APT) with a single intravenous dose of suramin experienced improvements in all the core symptoms of autism that lasted for 5-8weeks. Language, social interaction, restricted interests, and repetitive movements all improved. Two children who were non-verbal spoke their first sentences. None of these improvements were observed in the placebo group. Larger and longer studies are needed to confirm this promising discovery. This review introduces the concept of M2 (anti-inflammatory) and M1 (pro-inflammatory) mitochondria that are polarized along a functional continuum according to cell stress. The pathophysiology of the CDR, the complementary functions of M1 and M2 mitochondria, relevant gene-environment interactions, and the metabolic underpinnings of behavior are discussed as foundation stones for understanding the improvements in ASD behaviors produced by antipurinergic therapy in this small clinical trial.
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Gale TV, Horton TM, Grant DS, Garry RF. Metabolomics analyses identify platelet activating factors and heme breakdown products as Lassa fever biomarkers. PLoS Negl Trop Dis 2017; 11:e0005943. [PMID: 28922385 PMCID: PMC5619842 DOI: 10.1371/journal.pntd.0005943] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 09/28/2017] [Accepted: 09/07/2017] [Indexed: 12/16/2022] Open
Abstract
Lassa fever afflicts tens of thousands of people in West Africa annually. The rapid progression of patients from febrile illness to fulminant syndrome and death provides incentive for development of clinical prognostic markers that can guide case management. The small molecule profile of serum from febrile patients triaged to the Viral Hemorrhagic Fever Ward at Kenema Government Hospital in Sierra Leone was assessed using untargeted Ultra High Performance Liquid Chromatography Mass Spectrometry. Physiological dysregulation resulting from Lassa virus (LASV) infection occurs at the small molecule level. Effects of LASV infection on pathways mediating blood coagulation, and lipid, amino acid, nucleic acid metabolism are manifest in changes in the levels of numerous metabolites in the circulation. Several compounds, including platelet activating factor (PAF), PAF-like molecules and products of heme breakdown emerged as candidates that may prove useful in diagnostic assays to inform better care of Lassa fever patients. Lassa fever afflicts tens of thousands of people in West Africa each year. The disease progresses rapidly, but there are no tests available to determine which patients are at high risk for dying. We measured the levels of small molecules in the blood of febrile patients with and without infection by LASV that presented to Kenema Government Hospital in Sierra Leone using Ultra High Performance Liquid Chromatography Mass Spectrometry (LCMS), which identifies compounds based on their precise mass. Computational analyses were used to identify compounds that differed in patients with an acute LASV infection, patients with evidence of prior exposure to LASV and patients with fever, but who did not have evidence of exposure to LASV. Several serum metabolites, including factors that are involved in blood clotting and breakdown products of heme, were identified that may prove useful in diagnostic assays that will inform better care of Lassa fever patients or development of therapeutic interventions.
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Affiliation(s)
- Trevor V. Gale
- Department of Microbiology and Immunology, Tulane University, New Orleans, Louisiana, United States of America
| | - Timothy M. Horton
- Department of Microbiology and Immunology, Tulane University, New Orleans, Louisiana, United States of America
| | - Donald S. Grant
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Robert F. Garry
- Department of Microbiology and Immunology, Tulane University, New Orleans, Louisiana, United States of America
- Zalgen Labs, LLC, Germantown, Maryland, United States of America
- Tulane Center of Excellence, Global Viral Network, New Orleans, Louisiana, United States of America
- * E-mail:
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Naviaux RK, Curtis B, Li K, Naviaux JC, Bright AT, Reiner GE, Westerfield M, Goh S, Alaynick WA, Wang L, Capparelli EV, Adams C, Sun J, Jain S, He F, Arellano DA, Mash LE, Chukoskie L, Lincoln A, Townsend J. Low-dose suramin in autism spectrum disorder: a small, phase I/II, randomized clinical trial. Ann Clin Transl Neurol 2017; 4:491-505. [PMID: 28695149 PMCID: PMC5497533 DOI: 10.1002/acn3.424] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 04/18/2017] [Accepted: 04/20/2017] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVE No drug is yet approved to treat the core symptoms of autism spectrum disorder (ASD). Low-dose suramin was effective in the maternal immune activation and Fragile X mouse models of ASD. The Suramin Autism Treatment-1 (SAT-1) trial was a double-blind, placebo-controlled, translational pilot study to examine the safety and activity of low-dose suramin in children with ASD. METHODS Ten male subjects with ASD, ages 5-14 years, were matched by age, IQ, and autism severity into five pairs, then randomized to receive a single, intravenous infusion of suramin (20 mg/kg) or saline. The primary outcomes were ADOS-2 comparison scores and Expressive One-Word Picture Vocabulary Test (EOWPVT). Secondary outcomes were the aberrant behavior checklist, autism treatment evaluation checklist, repetitive behavior questionnaire, and clinical global impression questionnaire. RESULTS Blood levels of suramin were 12 ± 1.5 μmol/L (mean ± SD) at 2 days and 1.5 ± 0.5 μmol/L after 6 weeks. The terminal half-life was 14.7 ± 0.7 days. A self-limited, asymptomatic rash was seen, but there were no serious adverse events. ADOS-2 comparison scores improved by -1.6 ± 0.55 points (n = 5; 95% CI = -2.3 to -0.9; Cohen's d = 2.9; P = 0.0028) in the suramin group and did not change in the placebo group. EOWPVT scores did not change. Secondary outcomes also showed improvements in language, social interaction, and decreased restricted or repetitive behaviors. INTERPRETATION The safety and activity of low-dose suramin showed promise as a novel approach to treatment of ASD in this small study.
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Affiliation(s)
- Robert K. Naviaux
- The Mitochondrial and Metabolic Disease CenterUniversity of CaliforniaSan Diego School of Medicine214 Dickinson St., Bldg CTF, Rm C102San Diego92103‐8467California
- Department of MedicineUniversity of CaliforniaSan Diego School of Medicine214 Dickinson St., Bldg CTF, Rm C102San Diego92103‐8467California
- Department of PediatricsUniversity of CaliforniaSan Diego School of Medicine214 Dickinson St., Bldg CTF, Rm C102San Diego92103‐8467California
- Department of PathologyUniversity of CaliforniaSan Diego School of Medicine214 Dickinson St., Bldg CTF, Rm C102San Diego92103‐8467California
| | - Brooke Curtis
- Alliant International University10455 Pomerado RoadSan DiegoCalifornia92131
| | - Kefeng Li
- The Mitochondrial and Metabolic Disease CenterUniversity of CaliforniaSan Diego School of Medicine214 Dickinson St., Bldg CTF, Rm C102San Diego92103‐8467California
- Department of MedicineUniversity of CaliforniaSan Diego School of Medicine214 Dickinson St., Bldg CTF, Rm C102San Diego92103‐8467California
| | - Jane C. Naviaux
- The Mitochondrial and Metabolic Disease CenterUniversity of CaliforniaSan Diego School of Medicine214 Dickinson St., Bldg CTF, Rm C102San Diego92103‐8467California
- Department of NeurosciencesUniversity of CaliforniaSan Diego School of Medicine9500 Gilman Drive.La JollaCA92093‐0662
| | - A. Taylor Bright
- The Mitochondrial and Metabolic Disease CenterUniversity of CaliforniaSan Diego School of Medicine214 Dickinson St., Bldg CTF, Rm C102San Diego92103‐8467California
- Department of MedicineUniversity of CaliforniaSan Diego School of Medicine214 Dickinson St., Bldg CTF, Rm C102San Diego92103‐8467California
| | - Gail E. Reiner
- The Mitochondrial and Metabolic Disease CenterUniversity of CaliforniaSan Diego School of Medicine214 Dickinson St., Bldg CTF, Rm C102San Diego92103‐8467California
- Department of NeurosciencesUniversity of CaliforniaSan Diego School of Medicine9500 Gilman Drive.La JollaCA92093‐0662
| | - Marissa Westerfield
- The Research in Autism and Development Laboratory (RAD Lab)University of California9500 Gilman DriveLa JollaCA92093‐0959
| | - Suzanne Goh
- Pediatric Neurology Therapeutics7090 Miratech DrSan DiegoCA92121
| | - William A. Alaynick
- The Mitochondrial and Metabolic Disease CenterUniversity of CaliforniaSan Diego School of Medicine214 Dickinson St., Bldg CTF, Rm C102San Diego92103‐8467California
- Department of MedicineUniversity of CaliforniaSan Diego School of Medicine214 Dickinson St., Bldg CTF, Rm C102San Diego92103‐8467California
| | - Lin Wang
- The Mitochondrial and Metabolic Disease CenterUniversity of CaliforniaSan Diego School of Medicine214 Dickinson St., Bldg CTF, Rm C102San Diego92103‐8467California
- Department of MedicineUniversity of CaliforniaSan Diego School of Medicine214 Dickinson St., Bldg CTF, Rm C102San Diego92103‐8467California
| | - Edmund V. Capparelli
- Department of Pediatricsand Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of CaliforniaSan Diego School of Medicine9500 Gilman DriveLa JollaCA92093‐0657
| | - Cynthia Adams
- Clinical and Translational Research Institute (CTRI)University of CaliforniaSan DiegoLa JollaCA92037
| | - Ji Sun
- Clinical and Translational Research Institute (CTRI)University of CaliforniaSan DiegoLa JollaCA92037
| | - Sonia Jain
- Department of Family Medicine and Public HealthUniversity of CaliforniaSan DiegoLa JollaCA92093
| | - Feng He
- Department of Family Medicine and Public HealthUniversity of CaliforniaSan DiegoLa JollaCA92093
| | - Deyna A. Arellano
- Clinical and Translational Research Institute (CTRI)University of CaliforniaSan DiegoLa JollaCA92037
| | - Lisa E. Mash
- The Research in Autism and Development Laboratory (RAD Lab)University of California9500 Gilman DriveLa JollaCA92093‐0959
- Department of PsychologySan Diego State University5500 Campanile DriveSan DiegoCA92182
| | - Leanne Chukoskie
- The Research in Autism and Development Laboratory (RAD Lab)University of California9500 Gilman DriveLa JollaCA92093‐0959
- Institute for Neural ComputationUniversity of California9500 Gilman DriveLa Jolla92093‐0523
| | - Alan Lincoln
- Alliant International University10455 Pomerado RoadSan DiegoCalifornia92131
| | - Jeanne Townsend
- Department of NeurosciencesUniversity of CaliforniaSan Diego School of Medicine9500 Gilman Drive.La JollaCA92093‐0662
- The Research in Autism and Development Laboratory (RAD Lab)University of California9500 Gilman DriveLa JollaCA92093‐0959
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Manchester M, Anand A. Metabolomics: Strategies to Define the Role of Metabolism in Virus Infection and Pathogenesis. Adv Virus Res 2017; 98:57-81. [PMID: 28433052 DOI: 10.1016/bs.aivir.2017.02.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Metabolomics is an analytical profiling technique for measuring and comparing large numbers of metabolites present in biological samples. Combining high-throughput analytical chemistry and multivariate data analysis, metabolomics offers a window on metabolic mechanisms. Because they intimately utilize and often rewire host metabolism, viruses are an excellent choice to study by metabolomics techniques. Studies of the effects of viruses on metabolism during replication in vitro and infection in animal models or human subjects have provided novel insights into these networks and provided new targets for therapy and biomarker development. Identifying the common metabolic pathways utilized by viruses has the potential to reveal those that can be targeted by broad-spectrum antiviral and vaccine approaches.
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Affiliation(s)
- Marianne Manchester
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland.
| | - Anisha Anand
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
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Webb TJ, Carey GB, East JE, Sun W, Bollino DR, Kimball AS, Brutkiewicz RR. Alterations in cellular metabolism modulate CD1d-mediated NKT-cell responses. Pathog Dis 2016; 74:ftw055. [PMID: 27297969 DOI: 10.1093/femspd/ftw055] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2016] [Indexed: 01/27/2023] Open
Abstract
Natural killer T (NKT) cells play a critical role in the host's innate immune response. CD1d-mediated presentation of glycolipid antigens to NKT cells has been established; however, the mechanisms by which NKT cells recognize infected or cancerous cells remain unclear. 5(')-AMP activated protein kinase (AMPK) is a master regulator of lipogenic pathways. We hypothesized that activation of AMPK during infection and malignancy could alter the repertoire of antigens presented by CD1d and serve as a danger signal to NKT cells. In this study, we examined the effect of alterations in metabolism on CD1d-mediated antigen presentation to NKT cells and found that an infection with lymphocytic choriomeningitis virus rapidly increased CD1d-mediated antigen presentation. Hypoxia inducible factors (HIF) enhance T-cell effector functions during infection, therefore antigen presenting cells pretreated with pharmacological agents that inhibit glycolysis, induce HIF and activate AMPK were assessed for their ability to induce NKT-cell responses. Pretreatment with 2-deoxyglucose, cobalt chloride, AICAR and metformin significantly enhanced CD1d-mediated NKT-cell activation. In addition, NKT cells preferentially respond to malignant B cells and B-cell lymphomas express HIF-1α. These data suggest that targeting cellular metabolism may serve as a novel means of inducing innate immune responses.
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Affiliation(s)
- Tonya J Webb
- Department of Microbiology and Immunology, University of Maryland School of Medicine and the Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD 21201, USA
| | - Gregory B Carey
- Department of Microbiology and Immunology, University of Maryland School of Medicine and the Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD 21201, USA
| | - James E East
- Department of Microbiology and Immunology, University of Maryland School of Medicine and the Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD 21201, USA
| | - Wenji Sun
- Department of Microbiology and Immunology, University of Maryland School of Medicine and the Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD 21201, USA
| | - Dominique R Bollino
- Department of Microbiology and Immunology, University of Maryland School of Medicine and the Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD 21201, USA
| | - Amy S Kimball
- Department of Microbiology and Immunology, University of Maryland School of Medicine and the Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD 21201, USA
| | - Randy R Brutkiewicz
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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Li S, Dunlop AL, Jones DP, Corwin EJ. High-Resolution Metabolomics: Review of the Field and Implications for Nursing Science and the Study of Preterm Birth. Biol Res Nurs 2016; 18:12-22. [PMID: 26183181 PMCID: PMC4684995 DOI: 10.1177/1099800415595463] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Most complex health conditions do not have a single etiology but rather develop from exposure to multiple risk factors that interact to influence individual susceptibility. In this review, we discuss the emerging field of metabolomics as a means by which metabolic pathways underlying a disease etiology can be exposed and specific metabolites can be identified and linked, ultimately providing biomarkers for early detection of disease onset and new strategies for intervention. We present the theoretical foundation of metabolomics research, the current methods employed in its conduct, and the overlap of metabolomics research with other "omic" approaches. As an exemplar, we discuss the potential of metabolomics research in the context of deciphering the complex interactions of the maternal-fetal exposures that underlie the risk of preterm birth, a condition that accounts for substantial portions of infant morbidity and mortality and whose etiology and pathophysiology remain incompletely defined. We conclude by providing strategies for including metabolomics research in future nursing studies for the advancement of nursing science.
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Affiliation(s)
- Shuzhao Li
- Department of Medicine, Emory University, Atlanta, GA, USA
| | - Anne L Dunlop
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA, USA
| | - Dean P Jones
- Department of Medicine, Emory University, Atlanta, GA, USA
| | - Elizabeth J Corwin
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA, USA
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12
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Burel JG, Apte SH, Doolan DL. Systems Approaches towards Molecular Profiling of Human Immunity. Trends Immunol 2016; 37:53-67. [DOI: 10.1016/j.it.2015.11.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 11/14/2015] [Accepted: 11/15/2015] [Indexed: 12/12/2022]
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13
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Krohne TU, Westenskow PD, Kurihara T, Friedlander DF, Lehmann M, Dorsey AL, Li W, Zhu S, Schultz A, Wang J, Siuzdak G, Ding S, Friedlander M. Generation of retinal pigment epithelial cells from small molecules and OCT4 reprogrammed human induced pluripotent stem cells. Stem Cells Transl Med 2014; 1:96-109. [PMID: 22532929 DOI: 10.5966/sctm.2011-0057] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Autologous retinal pigment epithelium (RPE) grafts derived from induced pluripotent stem cells (iPSCs) may be used to cure blinding diseases in which RPE dysfunction results in photoreceptor degeneration. Four-, two-, and one-factor-derived iPSCs (4F-, 2F-, and 1F-iPSCs, respectively) were differentiated into fully functional cuboidal pigmented cells in polarized monolayers that express RPE-specific markers. 1F-iPSCs-RPE (1F-iPS-RPE) strongly resembles primary human fetal RPE (hfRPE) based on proteomic and untargeted metabolomic analyses, and using novel in vivo imaging technology coupled with electroretinography, we demonstrated that 1F-iPS-RPE mediate anatomical and functional rescue of photoreceptors after transplantation in an animal model of RPE-mediated retinal degeneration. 1F-iPS0RPE cells were injected subretinally as a suspension and formed a monolayer dispersed between host RPE cells. Furthermore, 1F-iPS-RPE do not simply provide trophic support to rescue photoreceptors as previously speculated but actually phagocytose photoreceptor outer segments in vivo and maintain visual cycling. Thus, 1f-iPS-RPE grafts may be superior to conventional iPS-RPE for clinical use because 1F-IPS-RPE closely resemble hfRPE, mediate anatomical and functional photoreceptor rescue in vivo, and are generated using a reduced number of potentially oncogenic reprogramming factors.
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Affiliation(s)
- Tim U Krohne
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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14
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Li S, Nakaya HI, Kazmin DA, Oh JZ, Pulendran B. Systems biological approaches to measure and understand vaccine immunity in humans. Semin Immunol 2013; 25:209-18. [PMID: 23796714 DOI: 10.1016/j.smim.2013.05.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 05/09/2013] [Indexed: 02/01/2023]
Abstract
Recent studies have demonstrated the utility of using systems approaches to identify molecular signatures that can be used to predict vaccine immunity in humans. Such approaches are now being used extensively in vaccinology, and are beginning to yield novel insights about the molecular networks driving vaccine immunity. In this review, we present a broad review of the methodologies involved in these studies, and discuss the promise and challenges involved in this emerging field of "systems vaccinology."
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Affiliation(s)
- Shuzhao Li
- Emory Vaccine Center, Yerkes National Primate Research Center, 954 Gatewood Road, Atlanta, GA 30329, USA
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15
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Zhu ZJ, Schultz AW, Wang J, Johnson CH, Yannone SM, Patti GJ, Siuzdak G. Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database. Nat Protoc 2013. [PMID: 23391889 DOI: 10.1038/nprot,.2013.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Untargeted metabolomics provides a comprehensive platform for identifying metabolites whose levels are altered between two or more populations. By using liquid chromatography quadrupole time-of-flight mass spectrometry (LC-Q-TOF-MS), hundreds to thousands of peaks with a unique m/z ratio and retention time are routinely detected from most biological samples in an untargeted profiling experiment. Each peak, termed a metabolomic feature, can be characterized on the basis of its accurate mass, retention time and tandem mass spectral fragmentation pattern. Here a seven-step protocol is suggested for such a characterization by using the METLIN metabolite database. The protocol starts from untargeted metabolomic LC-Q-TOF-MS data that have been analyzed with the bioinformatics program XCMS, and it describes a strategy for selecting interesting features as well as performing subsequent targeted tandem MS. The seven steps described will require 2-4 h to complete per feature, depending on the compound.
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Affiliation(s)
- Zheng-Jiang Zhu
- Scripps Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, California, USA
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16
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Zhu ZJ, Schultz AW, Wang J, Johnson CH, Yannone SM, Patti GJ, Siuzdak G. Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database. Nat Protoc 2013; 8:451-60. [PMID: 23391889 DOI: 10.1038/nprot.2013.004] [Citation(s) in RCA: 306] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Untargeted metabolomics provides a comprehensive platform for identifying metabolites whose levels are altered between two or more populations. By using liquid chromatography quadrupole time-of-flight mass spectrometry (LC-Q-TOF-MS), hundreds to thousands of peaks with a unique m/z ratio and retention time are routinely detected from most biological samples in an untargeted profiling experiment. Each peak, termed a metabolomic feature, can be characterized on the basis of its accurate mass, retention time and tandem mass spectral fragmentation pattern. Here a seven-step protocol is suggested for such a characterization by using the METLIN metabolite database. The protocol starts from untargeted metabolomic LC-Q-TOF-MS data that have been analyzed with the bioinformatics program XCMS, and it describes a strategy for selecting interesting features as well as performing subsequent targeted tandem MS. The seven steps described will require 2-4 h to complete per feature, depending on the compound.
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Affiliation(s)
- Zheng-Jiang Zhu
- Scripps Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, California, USA
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18
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Droniou-Bonzom ME, Cannon PM. A systems biology starter kit for arenaviruses. Viruses 2012; 4:3625-46. [PMID: 23342371 PMCID: PMC3528283 DOI: 10.3390/v4123625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 11/28/2012] [Accepted: 12/05/2012] [Indexed: 12/05/2022] Open
Abstract
Systems biology approaches in virology aim to integrate viral and host biological networks, and thus model the infection process. The growing availability of high-throughput “-omics” techniques and datasets, as well as the ever-increasing sophistication of in silico modeling tools, has resulted in a corresponding rise in the complexity of the analyses that can be performed. The present study seeks to review and organize published evidence regarding virus-host interactions for the arenaviruses, from alterations in the host proteome during infection, to reported protein-protein interactions. In this way, we hope to provide an overview of the interplay between arenaviruses and the host cell, and lay the foundations for complementing current arenavirus research with a systems-level approach.
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Affiliation(s)
- Magali E Droniou-Bonzom
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, 2011 Zonal Avenue, Los Angeles, CA 90033, USA.
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19
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McNiven EMS, German JB, Slupsky CM. Analytical metabolomics: nutritional opportunities for personalized health. J Nutr Biochem 2012; 22:995-1002. [PMID: 21999844 DOI: 10.1016/j.jnutbio.2011.05.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 05/31/2011] [Indexed: 02/08/2023]
Abstract
Nutrition is the cornerstone of health; survival depends on acquiring essential nutrients, and dietary components can both prevent and promote disease. Metabolomics, the study of all small molecule metabolic products in a system, has been shown to provide a detailed snapshot of the body's processes at any particular point in time, opening up the possibility of monitoring health and disease, prevention and treatment. Metabolomics has the potential to fundamentally change clinical chemistry and, by extension, the fields of nutrition, toxicology and medicine. Technological advances, combined with new knowledge of the human genome and gut microbiome, have made and will continue to make possible earlier, more accurate, less invasive diagnoses, all while enhancing our understanding of the root causes of disease and leading to a generation of dietary recommendations that enable optimal health. This article reviews the recent contributions of metabolomics to the fields of nutrition, toxicology and medicine. It is expected that these fields will eventually blend together through development of new technologies in metabolomics and genomics into a new area of clinical chemistry: personalized medicine.
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20
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Issaq HJ, Fox SD, Chan KC, Veenstra TD. Global proteomics and metabolomics in cancer biomarker discovery. J Sep Sci 2011; 34:3484-92. [PMID: 22102289 DOI: 10.1002/jssc.201100528] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 10/06/2011] [Accepted: 10/06/2011] [Indexed: 12/15/2022]
Abstract
Chromatography and electrophoresis have been used for the last half-century to separate small and large molecules. Advances in MS instrumentation and techniques for sample introduction into the mass analyzer (i.e. matrix-assisted laser desorption/ionization and electrospray ionization), chromatography in all its formats and modes and two-dimensional gel electrophoresis, including two-dimensional difference gel electrophoresis, enabled the separation of complex biological mixtures, such as the proteome and the metabolome, in a biological sample. These advances have made it possible to identify compounds that can be used to discriminate between two samples taken from healthy and diseased individuals. The objective is to find proteins or metabolites that can be used as a clinical test for the early diagnosis, prognosis and monitoring of the disease and the outcome of therapy. In this manuscript, we present an overview of what has been achieved in the search for biomarkers, with emphasis on cancer, using separation science and MS.
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Affiliation(s)
- Haleem J Issaq
- Laboratory of Proteomics and Analytical Technologies, Advanced Technology Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702, USA.
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21
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A systems biology approach to nutritional immunology - focus on innate immunity. Mol Aspects Med 2011; 33:14-25. [PMID: 22061966 DOI: 10.1016/j.mam.2011.10.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 10/24/2011] [Accepted: 10/24/2011] [Indexed: 12/22/2022]
Abstract
Innate immunity and nutrient metabolism are complex biological systems that must work in concert to sustain and preserve life. The effector cells of the innate immune system rely on essential nutrients to generate energy, produce metabolic precursors for macromolecule biosynthesis and tune their responses to infectious agents. Thus disruptions to nutritional status have a substantial impact on immune competence and can result in increased susceptibility to infection in the case of nutrient deficiency, or chronic inflammation in the case of over-nutrition. The traditional, reductionist methods used in the study of nutritional immunology are incapable of exploring the extremely complex interactions between nutrient metabolism and innate immunity. Here, we review a relatively new analytical approach, systems biology, and highlight how it can be applied to nutritional immunology to provide a comprehensive view of the mechanisms behind nutritional regulation of the innate immune system.
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22
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Zamani Z, Arjmand M, Tafazzoli M, Gholizadeh A, Pourfallah F, Sadeghi S, Mirzazadeh R, Mirkhani F, Taheri S, Iravani A, Bayat P, Vahabi F. Early detection of immunization: a study based on an animal model using 1H nuclear magnetic resonance spectroscopy. Pak J Biol Sci 2011; 14:195-203. [PMID: 21870642 DOI: 10.3923/pjbs.2011.195.203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Vaccines require a period of at least three months for clinical trials, hence a method that can identify elicitation of immune response a few days after the first dose is a necessity. Evolutionary variable selections are modeling approaches for proper manipulation of available data which were used to set up an animal model for classification of time dependent 1HNMR metabolomic profiles and pattern recognition of fluctuations of metabolites in two groups of male rabbits. One group of rabbits was immunized with human red blood cells and the other used as control. Blood was obtained every 48 h from each rabbit for a period of six weeks and the serum monitored for antibodies and metabolites by 1HNMR spectra. Evaluation of data was carried out using orthogonal signal correction followed by principal component analysis and partial least square. A neural network was also set up to predict immunization profiles. A distinct separation in patterns of significant metabolites was obtained between the two groups, just a few days after the first and the second dose. These metabolites were used as targets of neural networks where each sample was used as test, validation and training and their quantitative influence predicted by regression. This model could be used for prediction of immunization in rabbits a few days after the first dose with 96% accuracy. Similar animals and human vaccine trials would assist greatly in reaching early conclusions in advance of the usual two month immunization schedule; resulting in an appreciable saving of cost and time.
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Affiliation(s)
- Z Zamani
- Department of Biochemistry, Pasteur Institute of Iran, Pasteur Avenue, Tehran, Iran
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23
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Tautenhahn R, Patti GJ, Kalisiak E, Miyamoto T, Schmidt M, Lo FY, McBee J, Baliga NS, Siuzdak G. metaXCMS: second-order analysis of untargeted metabolomics data. Anal Chem 2011; 83:696-700. [PMID: 21174458 PMCID: PMC3654666 DOI: 10.1021/ac102980g] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Mass spectrometry-based untargeted metabolomics often results in the observation of hundreds to thousands of features that are differentially regulated between sample classes. A major challenge in interpreting the data is distinguishing metabolites that are causally associated with the phenotype of interest from those that are unrelated but altered in downstream pathways as an effect. To facilitate this distinction, here we describe new software called metaXCMS for performing second-order ("meta") analysis of untargeted metabolomics data from multiple sample groups representing different models of the same phenotype. While the original version of XCMS was designed for the direct comparison of two sample groups, metaXCMS enables meta-analysis of an unlimited number of sample classes to facilitate prioritization of the data and increase the probability of identifying metabolites causally related to the phenotype of interest. metaXCMS is used to import XCMS results that are subsequently filtered, realigned, and ultimately compared to identify shared metabolites that are up- or down-regulated across all sample groups. We demonstrate the software's utility by identifying histamine as a metabolite that is commonly altered in three different models of pain. metaXCMS is freely available at http://metlin.scripps.edu/metaxcms/.
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24
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Baran R, Bowen BP, Bouskill NJ, Brodie EL, Yannone SM, Northen TR. Metabolite Identification in Synechococcus sp. PCC 7002 Using Untargeted Stable Isotope Assisted Metabolite Profiling. Anal Chem 2010; 82:9034-42. [DOI: 10.1021/ac1020112] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Richard Baran
- Life Sciences Division and Earth Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Benjamin P. Bowen
- Life Sciences Division and Earth Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Nicholas J. Bouskill
- Life Sciences Division and Earth Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Eoin L. Brodie
- Life Sciences Division and Earth Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Steven M. Yannone
- Life Sciences Division and Earth Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Trent R. Northen
- Life Sciences Division and Earth Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
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25
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Dunn WB, Broadhurst DI, Atherton HJ, Goodacre R, Griffin JL. Systems level studies of mammalian metabolomes: the roles of mass spectrometry and nuclear magnetic resonance spectroscopy. Chem Soc Rev 2010; 40:387-426. [PMID: 20717559 DOI: 10.1039/b906712b] [Citation(s) in RCA: 557] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The study of biological systems in a holistic manner (systems biology) is increasingly being viewed as a necessity to provide qualitative and quantitative descriptions of the emergent properties of the complete system. Systems biology performs studies focussed on the complex interactions of system components; emphasising the whole system rather than the individual parts. Many perturbations to mammalian systems (diet, disease, drugs) are multi-factorial and the study of small parts of the system is insufficient to understand the complete phenotypic changes induced. Metabolomics is one functional level tool being employed to investigate the complex interactions of metabolites with other metabolites (metabolism) but also the regulatory role metabolites provide through interaction with genes, transcripts and proteins (e.g. allosteric regulation). Technological developments are the driving force behind advances in scientific knowledge. Recent advances in the two analytical platforms of mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy have driven forward the discipline of metabolomics. In this critical review, an introduction to metabolites, metabolomes, metabolomics and the role of MS and NMR spectroscopy will be provided. The applications of metabolomics in mammalian systems biology for the study of the health-disease continuum, drug efficacy and toxicity and dietary effects on mammalian health will be reviewed. The current limitations and future goals of metabolomics in systems biology will also be discussed (374 references).
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Affiliation(s)
- Warwick B Dunn
- Manchester Centre for Integrative Systems Biology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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26
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Kafsack BF, Llinás M. Eating at the table of another: metabolomics of host-parasite interactions. Cell Host Microbe 2010; 7:90-9. [PMID: 20159614 PMCID: PMC2825149 DOI: 10.1016/j.chom.2010.01.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2009] [Revised: 01/27/2010] [Accepted: 01/28/2010] [Indexed: 01/07/2023]
Abstract
The application of metabolomics, the global analysis of metabolite levels, to the study of protozoan parasites has become an important tool for understanding the host-parasite relationship and holds promise for the development of direly needed therapeutics and improved diagnostics. Research advances over the past decade have opened the door for a systems biology approach to protozoan parasites with metabolomics, providing a crucial readout of metabolic activity. In this review, we highlight recent metabolomic approaches to protozoan parasites, including metabolite profiling, integration with genomics, transcription, and proteomic analysis, and the use of metabolic fingerprints for the diagnosis of parasitic infections.
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Affiliation(s)
- Björn F.C. Kafsack
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Manuel Llinás
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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27
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Tisoncik JR, Belisle SE, Diamond DL, Korth MJ, Katze MG. Is systems biology the key to preventing the next pandemic? Future Virol 2009; 4:553-561. [PMID: 20352075 DOI: 10.2217/fvl.09.53] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sporadic outbreaks of epizootics including SARS coronavirus and H5N1 avian influenza remind us of the potential for communicable diseases to quickly spread into worldwide epidemics. To confront emerging viral threats, nations have implemented strategies to prepare for pandemics and to control virus spread. Despite improved surveillance and quarantine measures, we find ourselves in the midst of a H1N1 influenza pandemic. Effective therapeutics and vaccines are essential to protect against current and future pandemics. The best route to effective therapeutics and vaccines is through a detailed and global view of virus-host interactions that can be achieved using a systems biology approach. Here, we provide our perspective on the role of systems biology in deepening our understanding of virus-host interactions and in improving drug and vaccine development. We offer examples from influenza virus research, as well as from research on other pandemics of our time - HIV/AIDS and HCV - to demonstrate that systems biology offers one possible key to stopping the cycle of viral pandemics.
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Affiliation(s)
- Jennifer R Tisoncik
- University of Washington, Department of Microbiology, Seattle, WA 98195-8070, USA, Tel.: +1 206 732 6120
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