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Uthailak N, Adisakwattana P, Chienwichai P, Tipthara P, Tarning J, Thawornkuno C, Thiangtrongjit T, Reamtong O. Metabolite profiling of Trichinella spiralis adult worms and muscle larvae identifies their excretory and secretory products. Front Cell Infect Microbiol 2023; 13:1306567. [PMID: 38145042 PMCID: PMC10749202 DOI: 10.3389/fcimb.2023.1306567] [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: 10/04/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023] Open
Abstract
Human trichinellosis is a parasitic infection caused by roundworms belonging to the genus Trichinella, especially Trichinella spiralis. Early and accurate clinical diagnoses of trichinellosis are required for efficacious prognosis and treatment. Current drug therapies are limited by antiparasitic resistance, poor absorption, and an inability to kill the encapsulating muscle-stage larvae. Therefore, reliable biomarkers and drug targets for novel diagnostic approaches and anthelmintic drugs are required. In this study, metabolite profiles of T. spiralis adult worms and muscle larvae were obtained using mass spectrometry-based metabolomics. In addition, metabolite-based biomarkers of T. spiralis excretory-secretory products and their related metabolic pathways were characterized. The metabolic profiling identified major, related metabolic pathways involving adenosine monophosphate (AMP)-dependent synthetase/ligase and glycolysis/gluconeogenesis in T. spiralis adult worms and muscle larvae, respectively. These pathways are potential drug targets for the treatment of the intestinal and muscular phases of infection. The metabolome of larva excretory-secretory products was characterized, with amino acid permease and carbohydrate kinase being identified as key metabolic pathways. Among six metabolites, decanoyl-l-carnitine and 2,3-dinor-6-keto prostaglandin F1α-d9 were identified as potential metabolite-based biomarkers that might be related to the host inflammatory processes. In summary, this study compared the relationships between the metabolic profiles of two T. spiralis growth stages. Importantly, the main metabolites and metabolic pathways identified may aid the development of novel clinical diagnostics and therapeutics for human trichinellosis and other related helminthic infections.
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Affiliation(s)
- Naphatsamon Uthailak
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Poom Adisakwattana
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Peerut Chienwichai
- Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Phornpimon Tipthara
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Joel Tarning
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Charin Thawornkuno
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Tipparat Thiangtrongjit
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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Ndlovu IS, Silas E, Tshilwane SI, Chaisi M, Vosloo A, Mukaratirwa S. Preliminary insights on the metabolomics of Trichinella zimbabwensis infection in Sprague Dawley rats using GCxGC-TOF-MS (untargeted approach). Front Mol Biosci 2023; 10:1128542. [PMID: 36876045 PMCID: PMC9983363 DOI: 10.3389/fmolb.2023.1128542] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 02/08/2023] [Indexed: 02/19/2023] Open
Abstract
Trichinella infections have been documented globally and have been detected in wild and/or domestic animals except Antarctica. There is paucity of information in the metabolic responses of hosts during Trichinella infections and biomarkers for infection that can be used in the diagnosis of the disease. The current study aimed to apply a non-targeted metabolomic approach to identify Trichinella zimbabwensis biomarkers including metabolic response from sera of infected Sprague-Dawley rats. Fifty-four male Sprague-Dawley rats were randomly assigned into T. zimbabwensis infected group (n = 36) and the non-infected control (n = 18). Results from the study showed that the metabolic signature of T. zimbabwensis infection consists of enriched methyl histidine metabolism, disturbance of the liver urea cycle, impeded TCA cycle, and upregulation of gluconeogenesis metabolism. The observed disturbance in the metabolic pathways was attributed to the effects caused by the parasite during its migration to the muscles resulting in downregulation of amino acids intermediates in the Trichinella-infected animals, and therefore affecting energy production and degradation of biomolecules. It was concluded that T. zimbabwensis infection caused an upregulation of amino acids; pipecolic acid, histidine, and urea, and upregulation of glucose and meso-Erythritol. Moreover, T. zimbabwensis infection caused upregulation of the fatty acids, retinoic acid, and acetic acid. These findings highlight the potential of metabolomics as a novel approach for fundamental investigations of host-pathogen interactions as well as for disease progression and prognosis.
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Affiliation(s)
- I S Ndlovu
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa
| | - Ekuyikeno Silas
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa
| | - S I Tshilwane
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - M Chaisi
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa.,Foundational Biodiversity Science, South African National Biodiversity Institute, Pretoria, South Africa
| | - A Vosloo
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa
| | - S Mukaratirwa
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa.,One Health Center for Zoonoses and Tropical Veterinary Medicine, School of Veterinary Medicine, Ross University, Basseterre, Saint Kitts and Nevis
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Chienwichai P, Nogrado K, Tipthara P, Tarning J, Limpanont Y, Chusongsang P, Chusongsang Y, Tanasarnprasert K, Adisakwattana P, Reamtong O. Untargeted serum metabolomic profiling for early detection of Schistosoma mekongi infection in mouse model. Front Cell Infect Microbiol 2022; 12:910177. [PMID: 36061860 PMCID: PMC9433908 DOI: 10.3389/fcimb.2022.910177] [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: 04/01/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Mekong schistosomiasis is a parasitic disease caused by blood flukes in the Lao People’s Democratic Republic and in Cambodia. The standard method for diagnosis of schistosomiasis is detection of parasite eggs from patient samples. However, this method is not sufficient to detect asymptomatic patients, low egg numbers, or early infection. Therefore, diagnostic methods with higher sensitivity at the early stage of the disease are needed to fill this gap. The aim of this study was to identify potential biomarkers of early schistosomiasis using an untargeted metabolomics approach. Serum of uninfected and S. mekongi-infected mice was collected at 2, 4, and 8 weeks post-infection. Samples were extracted for metabolites and analyzed with a liquid chromatography-tandem mass spectrometer. Metabolites were annotated with the MS-DIAL platform and analyzed with Metaboanalyst bioinformatic tools. Multivariate analysis distinguished between metabolites from the different experimental conditions. Biomarker screening was performed using three methods: correlation coefficient analysis; feature important detection with a random forest algorithm; and receiver operating characteristic (ROC) curve analysis. Three compounds were identified as potential biomarkers at the early stage of the disease: heptadecanoyl ethanolamide; picrotin; and theophylline. The levels of these three compounds changed significantly during early-stage infection, and therefore these molecules may be promising schistosomiasis markers. These findings may help to improve early diagnosis of schistosomiasis, thus reducing the burden on patients and limiting spread of the disease in endemic areas.
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Affiliation(s)
- Peerut Chienwichai
- Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Kathyleen Nogrado
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Phornpimon Tipthara
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Joel Tarning
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Yanin Limpanont
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Phiraphol Chusongsang
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Yupa Chusongsang
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Kanthi Tanasarnprasert
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Poom Adisakwattana
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- *Correspondence: Onrapak Reamtong,
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Yengo BN, Shintouo CM, Hotterbeekx A, Yaah NE, Shey RA, Quanico J, Baggerman G, Ayong L, Vanhamme L, Njemini R, Souopgui J, Colebunders R, Ghogomu SM. Immunoinformatics Design and Assessment of a Multiepitope Antigen (OvMCBL02) for Onchocerciasis Diagnosis and Monitoring. Diagnostics (Basel) 2022; 12:diagnostics12061440. [PMID: 35741250 PMCID: PMC9221995 DOI: 10.3390/diagnostics12061440] [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: 04/16/2022] [Revised: 05/28/2022] [Accepted: 06/09/2022] [Indexed: 11/23/2022] Open
Abstract
Onchocerciasis is a Neglected Tropical Disease that has a significant socioeconomic impact, especially in Sub-Saharan Africa. Numerous reports indicate that the Expanded Special Project for the Elimination of Neglected Tropical Diseases needs novel diagnostic tools before achieving its goal of successful elimination of onchocerciasis in Africa. The current diagnostic tests are either invasive, insensitive, or not applicable in the field and about 25% of persons infected cannot mount immune responses against the single antigen used in the only approved Ov-16 serological test. In the quest to identify novel biomarkers that can be used to certify that a patient is free from the disease, evaluate the progress of elimination programmes, and conduct post elimination surveillances, mass spectrometric analysis of Onchocerca volvulus crude extract revealed that 1392 proteins are expressed in the adult and microfilariae stages of the parasite. Computational analysis predicted six of the proteins as O. volvulus potential diagnostic targets. Linear B-epitopes were predicted from the six proteins and used to construct a multiepitope antigen (OvMCBL02). Serological analysis revealed that the OvMCBL02 test significantly differentiated between serum samples of onchocerciasis patients from the Kombone Health Area in the South West Region of Cameroon (n = 63) and control serum samples from Rwanda (n = 29) and Europe (n = 26) as well as between serum samples from the onchocerciasis hyperendemic region of Kombone Health Area (n = 63) and the hypoendemic region of Bandjoun Health District (n = 54). Interestingly, the test did not cross-react with serum samples from patients suffering from related nematode infections, thereby suggesting that further characterization of the OvMCBL02 multiepitope antigen will render it an additional member of the diagnostic toolbox for the elimination of onchocerciasis.
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Affiliation(s)
- Bernis Neneyoh Yengo
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Buea, Buea P.O. Box 63, Cameroon; (B.N.Y.); (C.M.S.); (N.E.Y.); (R.A.S.)
| | - Cabirou Mounchili Shintouo
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Buea, Buea P.O. Box 63, Cameroon; (B.N.Y.); (C.M.S.); (N.E.Y.); (R.A.S.)
- Department of Gerontology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium;
- Frailty in Ageing Research Group, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - An Hotterbeekx
- Global Health Institute, University of Antwerp, 2610 Antwerp, Belgium; (A.H.); (R.C.)
- Molecular Pathology Group, Laboratory of Cell biology and Histology, University of Antwerp, 2610 Antwerp, Belgium
| | - Ntang Emmaculate Yaah
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Buea, Buea P.O. Box 63, Cameroon; (B.N.Y.); (C.M.S.); (N.E.Y.); (R.A.S.)
| | - Robert Adamu Shey
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Buea, Buea P.O. Box 63, Cameroon; (B.N.Y.); (C.M.S.); (N.E.Y.); (R.A.S.)
| | - Jusal Quanico
- Center for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium; (J.Q.); (G.B.)
| | - Geert Baggerman
- Center for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium; (J.Q.); (G.B.)
| | - Lawrence Ayong
- Malaria Research Unit, Centre Pasteur Cameroon, Yaoundé P.O. Box 1274, Cameroon;
| | - Luc Vanhamme
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM, Gosselies Campus, Université Libre de Bruxelles, 1070 Brussels, Belgium; (L.V.); (J.S.)
| | - Rose Njemini
- Department of Gerontology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium;
- Frailty in Ageing Research Group, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Jacob Souopgui
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM, Gosselies Campus, Université Libre de Bruxelles, 1070 Brussels, Belgium; (L.V.); (J.S.)
| | - Robert Colebunders
- Global Health Institute, University of Antwerp, 2610 Antwerp, Belgium; (A.H.); (R.C.)
| | - Stephen Mbigha Ghogomu
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Buea, Buea P.O. Box 63, Cameroon; (B.N.Y.); (C.M.S.); (N.E.Y.); (R.A.S.)
- Correspondence: ; Tel.: +237-6-7845-5646
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Ndolo SM, Zachariah M, Molefi L, Phaladze N, Sichilongo KF. Mass spectrometry based metabolomics for small molecule metabolites mining and confirmation as potential biomarkers for schistosomiasis - case of the Okavango Delta communities in Botswana. Expert Rev Proteomics 2021; 19:61-71. [PMID: 34846232 DOI: 10.1080/14789450.2021.2012454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Metabolomics for identifying schistosomiasis biomarkers in noninvasive samples at various infection stages is being actively explored. The literature on the traditional detection of schistosomiasis in human specimens is well documented. However, state-of-the-art technologies based on mass spectrometry have simplified the use of biomarkers for diagnostics. This review examines methods currently in use for the metabolomics of small molecules using separation science and mass spectrometry. AREA COVERED This article highlights the evolution of traditional diagnostic methods for schistosomiasis based on inter alia microscopy, immunology, and polymerase chain reaction. An exhaustive literature search of metabolite mining, focusing on separation science and mass spectrometry, is presented. A comparative analysis of mass spectrometry methods was undertaken, including a projection for the future. EXPERT COMMENTARY Mass spectrometry metabolomics for schistosomiasis will lead to biomarker discovery for noninvasive human samples. These biomarkers, together with those from other neglected tropical diseases, such as malaria and sleeping sickness, could be incorporated as arrays on a single biosensor chip and inserted into smartphones, in order to improve surveillance, monitoring, and management.
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Affiliation(s)
- Sedireng M Ndolo
- College of Open Schooling, Botswana Open University, Gaborone Regional Campus, Gaborone, Botswana
| | - Matshediso Zachariah
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Lebotse Molefi
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Nthabiseng Phaladze
- School of Nursing, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Kwenga F Sichilongo
- Chemistry Department, Faculty of Science, University of Botswana, Gaborone, Botswana
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Lagatie O, Njumbe Ediage E, Van Roosbroeck D, Van Asten S, Verheyen A, Batsa Debrah L, Debrah A, Odiere MR, T’Kindt R, Dumont E, Sandra K, Dillen L, Verhaeghe T, Vreeken R, Cuyckens F, Stuyver LJ. Multimodal biomarker discovery for active Onchocerca volvulus infection. PLoS Negl Trop Dis 2021; 15:e0009999. [PMID: 34843471 PMCID: PMC8659328 DOI: 10.1371/journal.pntd.0009999] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 12/09/2021] [Accepted: 11/16/2021] [Indexed: 11/19/2022] Open
Abstract
The neglected tropical disease onchocerciasis, or river blindness, is caused by infection with the filarial nematode Onchocerca volvulus. Current estimates indicate that 17 million people are infected worldwide, the majority of them living in Africa. Today there are no non-invasive tests available that can detect ongoing infection, and that can be used for effective monitoring of elimination programs. In addition, to enable pharmacodynamic studies with novel macrofilaricide drug candidates, surrogate endpoints and efficacy biomarkers are needed but are non-existent. We describe the use of a multimodal untargeted mass spectrometry-based approach (metabolomics and lipidomics) to identify onchocerciasis-associated metabolites in urine and plasma, and of specific lipid features in plasma of infected individuals (O. volvulus infected cases: 68 individuals with palpable nodules; lymphatic filariasis cases: 8 individuals; non-endemic controls: 20 individuals). This work resulted in the identification of elevated concentrations of the plasma metabolites inosine and hypoxanthine as biomarkers for filarial infection, and of the urine metabolite cis-cinnamoylglycine (CCG) as biomarker for O. volvulus. During the targeted validation study, metabolite-specific cutoffs were determined (inosine: 34.2 ng/ml; hypoxanthine: 1380 ng/ml; CCG: 29.7 ng/ml) and sensitivity and specificity profiles were established. Subsequent evaluation of these biomarkers in a non-endemic population from a different geographical region invalidated the urine metabolite CCG as biomarker for O. volvulus. The plasma metabolites inosine and hypoxanthine were confirmed as biomarkers for filarial infection. With the availability of targeted LC-MS procedures, the full potential of these 2 biomarkers in macrofilaricide clinical trials, MDA efficacy surveys, and epidemiological transmission studies can be investigated. Today’s diagnosis of infection with the filarial parasite Onchocerca volvulus mainly depends on the microscopic analysis of skin biopsies and serological testing. The work presented here describes the use of multiple mass spectrometry-based screening methods (metabolomics and lipidomics) to search for biomarkers indicative of infection with Onchocerca volvulus. This resulted in the identification of elevated concentrations of the plasma metabolites inosine and hypoxanthine as biomarkers for filarial infection, and of the urine metabolite cis-cinnamoylglycine as biomarker for O. volvulus. Further evaluation of these biomarkers in a geographically distinct non-endemic population however invalidated the use of urine cis-cinnamoylglycine. These findings are of utmost importance as it not only opens new avenues in the development of non-invasive diagnostic tools for filarial infections, but also emphasizes the need for evaluation and validation of newly discovered biomarkers in different populations from different geographies.
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Affiliation(s)
- Ole Lagatie
- J&J Global Public Health, Janssen R&D, Beerse, Belgium
- * E-mail:
| | | | | | | | - Ann Verheyen
- J&J Global Public Health, Janssen R&D, Beerse, Belgium
| | - Linda Batsa Debrah
- Department of Clinical Microbiology, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Alex Debrah
- Faculty of Allied Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Maurice R. Odiere
- Kenya Medical Research Institute, Centre for Global Health Research, Kisumu, Kenya
| | - Ruben T’Kindt
- Research Institute for Chromatography (RIC), Kortrijk, Belgium
| | - Emmie Dumont
- Research Institute for Chromatography (RIC), Kortrijk, Belgium
| | - Koen Sandra
- Research Institute for Chromatography (RIC), Kortrijk, Belgium
| | - Lieve Dillen
- Discovery Sciences, Janssen R&D, Beerse, Belgium
| | | | - Rob Vreeken
- Discovery Sciences, Janssen R&D, Beerse, Belgium
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Urine metabolites for the identification of Onchocerca volvulus infections in patients from Cameroon. Parasit Vectors 2021; 14:397. [PMID: 34380554 PMCID: PMC8359580 DOI: 10.1186/s13071-021-04893-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/24/2021] [Indexed: 11/10/2022] Open
Abstract
Background The tropical disease onchocerciasis (river blindness), caused by Onchocerca volvulus filarial nematodes, is targeted for elimination by mass treatment with nematocidal and antimicrobial drugs. Diagnosis of O. volvulus infections is based on counts of skin-borne microfilariae, but additional diagnostic tools, e.g. worm- or host-derived small RNAs, proteins or metabolites, are required for high-throughput screening. N-acetyltyramine-O,β-glucuronide (NATOG) was suggested as a biomarker for onchocerciasis but its viability as diagnostic tool has been challenged. Methods We performed a screening program of urine samples from individuals from Cameroon infected with O. volvulus, Loa loa, Mansonella perstans or a combination thereof. Urine metabolites were measured by liquid chromatography–mass spectrometry (LC-MS). Principle component analysis (PCA) revealed that onchocerciasis causes complex changes of the urine metabolome. Results The mean NATOG content was elevated in urine of O. volvulus-infected compared with non-infected individuals, but NATOG levels showed considerable variation. However, 13.8% of all O. volvulus-infected individuals had high NATOG levels never reached by individuals without filarial infections or only infected with L. loa or M. perstans. Therefore, the identification of individuals with high NATOG levels might be used to screen for the elimination of onchocerciasis after mass drug application. Additional metabolites, including a compound identified as cinnamoylglycine, had high PC1/PC2 loadings in the data set. Mean levels of cinnamoylglycine were increased in O. volvulus-infected individuals, and 17.2% of all O. volvulus individuals had elevated cinnamoylglycine levels not reached by the controls. Conclusions On an individual level, NATOG alone had poor discriminative power distinguishing infected from non-infected individuals. However, 13.8% of all O. volvulus-infected individuals had NATOG levels never reached by individuals without filarial infections or infected with only L. loa or M. perstans. Discrimination of O. volvulus infections from controls or individuals suffering from multiple infections was improved by the measurement of additional metabolites, e.g. cinnamoylglycine. Thus, measuring a combination of urine metabolites may provide a way to assess onchocerciasis on the population level. This provides the possibility to design a strategy for large-scale onchocerciasis epidemiological screening programs based on urine rather than invasive techniques. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-021-04893-1.
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Zhu M, Du X, Xu H, Yang S, Wang C, Zhu Y, Zhang T, Zhao W. Metabolic profiling of liver and faeces in mice infected with echinococcosis. Parasit Vectors 2021; 14:324. [PMID: 34127037 PMCID: PMC8201681 DOI: 10.1186/s13071-021-04807-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/25/2021] [Indexed: 12/13/2022] Open
Abstract
Background Echinococcosis is a severe zoonotic parasitic disease which severely affects the health of the hosts. The diagnosis of echinococcosis depends mainly on imaging examination. However, the patient is often in the late stage of the disease when the symptoms appear, thus limiting the early diagnosis of echinococcosis. The treatment and prognosis of the patients are hampered because of long-term asymptomatic latency. Metabolomics is a new discipline developed in the late 1990s. It reflects a series of biological responses in pathophysiological processes by demonstrating the changes in metabolism under the influence of internal and external factors. When the organism is invaded by pathogens, the alteration in the characteristics of metabolites in cells becomes extremely sensitive. Here, we used a metabolomics approach involving liquid chromatography coupled with tandem mass spectrometry (LC–MS/MS) to determine the molecular mechanism of cystic echinococcosis (CE) and to develop an effective method for CE diagnosis. Methods Twenty 8-week-old female BALB/c mice were divided into normal and Echinococcus granulosus infection groups. To develop the E. granulosus infection model, mice were infected with protoscoleces. Six weeks later, the abdomens of the mice showed significant bulging. An LC–MS/MS system-based metabolomics approach was used to analyse the liver and faeces to reveal the metabolic profiles of mice with echinococcosis. Results We found that the metabolism of nucleotides, alkaloids, amino acids, amides, and organic acids in mice is closely interrelated with E. granulosus infection. In the liver, the metabolic pathways of tyrosine and tryptophan biosynthesis; phenylalanine, valine, leucine and isoleucine biosynthesis; and phenylalanine metabolism were notably associated with the occurrence and development of hydatid disease, and in the faeces, pantothenate and CoA biosynthesis are thought to be closely associated with the development of CE. Conclusion The metabolomics approach used in this study provides a reference for a highly sensitive and specific diagnostic and screening method for echinococcosis. Graphic Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-021-04807-1.
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Affiliation(s)
- Mingxing Zhu
- Center of Scientific Technology of Ningxia Medical University, Yinchuan, 750004, Ningxia Hui Autonomous Region, People's Republic of China.,Key Laboratory of Hydatid Disease of Ningxia Medical University, Yinchuan, 750004, Ningxia Hui Autonomous Region, People's Republic of China.,School of Basic Medical Science of Ningxia Medical University, Yinchuan, 750004, Ningxia Hui Autonomous Region, People's Republic of China
| | - Xiancai Du
- Key Laboratory of Hydatid Disease of Ningxia Medical University, Yinchuan, 750004, Ningxia Hui Autonomous Region, People's Republic of China.,School of Basic Medical Science of Ningxia Medical University, Yinchuan, 750004, Ningxia Hui Autonomous Region, People's Republic of China
| | - Hongxia Xu
- Center of Scientific Technology of Ningxia Medical University, Yinchuan, 750004, Ningxia Hui Autonomous Region, People's Republic of China.,Key Laboratory of Hydatid Disease of Ningxia Medical University, Yinchuan, 750004, Ningxia Hui Autonomous Region, People's Republic of China
| | - Songhao Yang
- Key Laboratory of Hydatid Disease of Ningxia Medical University, Yinchuan, 750004, Ningxia Hui Autonomous Region, People's Republic of China.,School of Basic Medical Science of Ningxia Medical University, Yinchuan, 750004, Ningxia Hui Autonomous Region, People's Republic of China
| | - Chan Wang
- Key Laboratory of Hydatid Disease of Ningxia Medical University, Yinchuan, 750004, Ningxia Hui Autonomous Region, People's Republic of China.,School of Basic Medical Science of Ningxia Medical University, Yinchuan, 750004, Ningxia Hui Autonomous Region, People's Republic of China
| | - Yazhou Zhu
- Key Laboratory of Hydatid Disease of Ningxia Medical University, Yinchuan, 750004, Ningxia Hui Autonomous Region, People's Republic of China.,School of Basic Medical Science of Ningxia Medical University, Yinchuan, 750004, Ningxia Hui Autonomous Region, People's Republic of China
| | - Tingrui Zhang
- Key Laboratory of Hydatid Disease of Ningxia Medical University, Yinchuan, 750004, Ningxia Hui Autonomous Region, People's Republic of China.,School of Basic Medical Science of Ningxia Medical University, Yinchuan, 750004, Ningxia Hui Autonomous Region, People's Republic of China
| | - Wei Zhao
- Center of Scientific Technology of Ningxia Medical University, Yinchuan, 750004, Ningxia Hui Autonomous Region, People's Republic of China. .,Key Laboratory of Hydatid Disease of Ningxia Medical University, Yinchuan, 750004, Ningxia Hui Autonomous Region, People's Republic of China.
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9
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Brattig NW, Cheke RA, Garms R. Onchocerciasis (river blindness) - more than a century of research and control. Acta Trop 2021; 218:105677. [PMID: 32857984 DOI: 10.1016/j.actatropica.2020.105677] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 08/06/2020] [Accepted: 08/21/2020] [Indexed: 12/14/2022]
Abstract
This review summarises more than a century of research on onchocerciasis, also known as river blindness, and its control. River blindness is an infection caused by the tissue filaria Onchocerca volvulus affecting the skin, subcutaneous tissue and eyes and leading to blindness in a minority of infected persons. The parasite is transmitted by its intermediate hosts Simulium spp. which breed in rivers. Featured are history and milestones in onchocerciasis research and control, state-of-the-art data on the parasite, its endobacteria Wolbachia, on the vectors, previous and current prevalence of the infection, its diagnostics, the interaction between the parasite and its host, immune responses and the pathology of onchocerciasis. Detailed information is documented on the time course of control programmes in the afflicted countries in Africa and the Americas, a long road from previous programmes to current successes in control of the transmission of this infectious disease. By development, adjustment and optimization of the control measures, transmission by the vector has been interrupted in foci of countries in the Americas, in Uganda, in Sudan and elsewhere, followed by onchocerciasis eliminations. The current state and future perspectives for control, elimination and eradication within the next 20-30 years are described and discussed. This review contributes to a deeper comprehension of this disease by a tissue-dwelling filaria and it will be helpful in efforts to control and eliminate other filarial infections.
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10
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Vanhamme L, Souopgui J, Ghogomu S, Ngale Njume F. The Functional Parasitic Worm Secretome: Mapping the Place of Onchocerca volvulus Excretory Secretory Products. Pathogens 2020; 9:pathogens9110975. [PMID: 33238479 PMCID: PMC7709020 DOI: 10.3390/pathogens9110975] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 01/15/2023] Open
Abstract
Nematodes constitute a very successful phylum, especially in terms of parasitism. Inside their mammalian hosts, parasitic nematodes mainly dwell in the digestive tract (geohelminths) or in the vascular system (filariae). One of their main characteristics is their long sojourn inside the body where they are accessible to the immune system. Several strategies are used by parasites in order to counteract the immune attacks. One of them is the expression of molecules interfering with the function of the immune system. Excretory-secretory products (ESPs) pertain to this category. This is, however, not their only biological function, as they seem also involved in other mechanisms such as pathogenicity or parasitic cycle (molting, for example). We will mainly focus on filariae ESPs with an emphasis on data available regarding Onchocerca volvulus, but we will also refer to a few relevant/illustrative examples related to other worm categories when necessary (geohelminth nematodes, trematodes or cestodes). We first present Onchocerca volvulus, mainly focusing on the aspects of this organism that seem relevant when it comes to ESPs: life cycle, manifestations of the sickness, immunosuppression, diagnosis and treatment. We then elaborate on the function and use of ESPs in these aspects.
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Affiliation(s)
- Luc Vanhamme
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM, Université Libre de Bruxelles, Rue des Professeurs Jeener et Brachet 12, 6041 Gosselies, Belgium; (J.S.); (F.N.N.)
- Correspondence:
| | - Jacob Souopgui
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM, Université Libre de Bruxelles, Rue des Professeurs Jeener et Brachet 12, 6041 Gosselies, Belgium; (J.S.); (F.N.N.)
| | - Stephen Ghogomu
- Molecular and Cell Biology Laboratory, Biotechnology Unit, University of Buea, Buea P.O Box 63, Cameroon;
| | - Ferdinand Ngale Njume
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM, Université Libre de Bruxelles, Rue des Professeurs Jeener et Brachet 12, 6041 Gosselies, Belgium; (J.S.); (F.N.N.)
- Molecular and Cell Biology Laboratory, Biotechnology Unit, University of Buea, Buea P.O Box 63, Cameroon;
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11
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Ritler D, Rufener R, Li JV, Kämpfer U, Müller J, Bühr C, Schürch S, Lundström-Stadelmann B. In vitro metabolomic footprint of the Echinococcus multilocularis metacestode. Sci Rep 2019; 9:19438. [PMID: 31857639 PMCID: PMC6923418 DOI: 10.1038/s41598-019-56073-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/04/2019] [Indexed: 12/17/2022] Open
Abstract
Alveolar echinococcosis (AE) is a zoonotic disease that is deadly if left untreated. AE is caused by the larval metacestode stage of the cestode Echinococcus multilocularis. Better knowledge on the host-parasite interface could yield novel targets for improvement of the treatment against AE. We analyzed culture media incubated with in vitro grown E. multilocularis metacestodes by 1H nuclear magnetic resonance spectroscopy to identify the unknown metabolic footprint of the parasite. Moreover, we quantitatively analyzed all amino acids, acetate, glucose, lactate, and succinate in time-course experiments using liquid chromatography and enzymatic assays. The E. multilocularis metacestodes consumed glucose and, surprisingly, threonine and produced succinate, acetate, and alanine as major fermentation products. The metabolic composition of vesicle fluid (VF) from in vitro grown E. multilocularis metacestodes was different from parasite-incubated culture medium with respect to the abundance, but not the spectrum, of metabolites, and some metabolites, in particular amino acids, accumulated in the VF. Overall, this study presents the first characterization of the in vitro metabolic footprint of E. multilocularis metacestodes and VF composition, and it provides the basis for analyses of potentially targetable pathways for future drug development.
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Affiliation(s)
- Dominic Ritler
- Institute of Parasitology, Department of Infectious Disease and Pathobiology, Vetsuisse Bern, University of Bern, Bern, Switzerland
| | - Reto Rufener
- Institute of Parasitology, Department of Infectious Disease and Pathobiology, Vetsuisse Bern, University of Bern, Bern, Switzerland
| | - Jia V Li
- Division of Systems and Digestive Medicine, Department of Surgery & Cancer, Imperial College London, London, United Kingdom
| | - Urs Kämpfer
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Joachim Müller
- Institute of Parasitology, Department of Infectious Disease and Pathobiology, Vetsuisse Bern, University of Bern, Bern, Switzerland
| | - Claudia Bühr
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Stefan Schürch
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Britta Lundström-Stadelmann
- Institute of Parasitology, Department of Infectious Disease and Pathobiology, Vetsuisse Bern, University of Bern, Bern, Switzerland.
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12
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Naouma H, Pataky TC. A comparison of random-field-theory and false-discovery-rate inference results in the analysis of registered one-dimensional biomechanical datasets. PeerJ 2019; 7:e8189. [PMID: 31844582 PMCID: PMC6910120 DOI: 10.7717/peerj.8189] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/11/2019] [Indexed: 01/01/2023] Open
Abstract
Background The inflation of falsely rejected hypotheses associated with multiple hypothesis testing is seen as a threat to the knowledge base in the scientific literature. One of the most recently developed statistical constructs to deal with this problem is the false discovery rate (FDR), which aims to control the proportion of the falsely rejected null hypotheses among those that are rejected. FDR has been applied to a variety of problems, especially for the analysis of 3-D brain images in the field of Neuroimaging, where the predominant form of statistical inference involves the more conventional control of false positives, through Gaussian random field theory (RFT). In this study we considered FDR and RFT as alternative methods for handling multiple testing in the analysis of 1-D continuum data. The field of biomechanics has recently adopted RFT, but to our knowledge FDR has not previously been used to analyze 1-D biomechanical data, nor has there been a consideration of how FDR vs. RFT can affect biomechanical interpretations. Methods We reanalyzed a variety of publicly available experimental datasets to understand the characteristics which contribute to the convergence and divergence of RFT and FDR results. We also ran a variety of numerical simulations involving smooth, random Gaussian 1-D data, with and without true signal, to provide complementary explanations for the experimental results. Results Our results suggest that RFT and FDR thresholds (the critical test statistic value used to judge statistical significance) were qualitatively identical for many experimental datasets, but were highly dissimilar for others, involving non-trivial changes in data interpretation. Simulation results clarified that RFT and FDR thresholds converge as the true signal weakens and diverge when the signal is broad in terms of the proportion of the continuum size it occupies. Results also showed that, while sample size affected the relation between RFT and FDR results for small sample sizes (<15), this relation was stable for larger sample sizes, wherein only the nature of the true signal was important. Discussion RFT and FDR thresholds are both computationally efficient because both are parametric, but only FDR has the ability to adapt to the signal features of particular datasets, wherein the threshold lowers with signal strength for a gain in sensitivity. Additional advantages and limitations of these two techniques as discussed further. This article is accompanied by freely available software for implementing FDR analyses involving 1-D data and scripts to replicate our results.
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Affiliation(s)
- Hanaa Naouma
- Bioengineering Course/Graduate School of Science and Technology, Shinshu University, Ueda, Nagano, Japan.,Department of Human Health Sciences/Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Todd C Pataky
- Department of Human Health Sciences/Graduate School of Medicine, Kyoto University, Kyoto, Japan
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13
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Surendran Nair M, Yao D, Chen C, Pieters M. Serum metabolite markers of early Mycoplasma hyopneumoniae infection in pigs. Vet Res 2019; 50:98. [PMID: 31771624 PMCID: PMC6878661 DOI: 10.1186/s13567-019-0715-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/23/2019] [Indexed: 01/22/2023] Open
Abstract
Mycoplasma hyopneumoniae, the primary pathogenic bacterium causing enzootic pneumonia, significantly affects worldwide swine production. The infection is usually persistent and bacterial identification and isolation of M. hyopneumoniae in clinical samples are challenging due to the fastidious requirements for its growth. Hence, new practical surveillance tools that improve or complement existing diagnostics on M. hyopneumoniae are desirable, especially in early infection. The objective of this study was to identify potential metabolite markers of early M. hyopneumoniae infection in pigs through metabolomics analysis. Samples obtained from pigs in a previous M. hyopneumoniae experimental infection were used in this study. Briefly, two pigs served as mock inoculated controls and ten pigs were intra-tracheally inoculated with M. hyopneumoniae. Sera, laryngeal swabs (LS), and tracheo-bronchial lavage fluid (TBLF) were collected from all pigs at 0, 2, 5, 9, 14, 21 and 28 days post-inoculation (dpi). Bronchial swabs (BS) were collected post-mortem at 28 dpi. Mycoplasma hyopneumoniae infection was confirmed by PCR in LS, TBLF and BS. Serum metabolites were profiled using high-resolution liquid chromatography-mass spectrometry (LC-MS) analysis. Metabolite markers were identified by structural analysis following multivariate analysis of LC-MS data. The results showed that M. hyopneumoniae infection time-dependently altered the serum levels of selective amino acids and fatty acids. α-Aminobutyric acid and long-chain fatty acids were markedly increased at 14 and 21 dpi in inoculated pigs (p < 0.05). These results indicated that M. hyopneumoniae infection caused systemic changes in host metabolism, warranting further studies to determine underlying biochemical and physiological mechanisms responsible for the observed changes.
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Affiliation(s)
- Meera Surendran Nair
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN 55108 USA
| | - Dan Yao
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN 55018 USA
| | - Chi Chen
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN 55018 USA
| | - Maria Pieters
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN 55108 USA
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14
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Wangchuk P, Kouremenos K, Eichenberger RM, Pearson M, Susianto A, Wishart DS, McConville MJ, Loukas A. Metabolomic profiling of the excretory-secretory products of hookworm and whipworm. Metabolomics 2019; 15:101. [PMID: 31254203 DOI: 10.1007/s11306-019-1561-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 06/20/2019] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Soil-transmitted helminths infect billions of people, livestock and companion animals worldwide, and chronic infections with these nematodes represent a major health burden in many developing countries. On the other hand, complete elimination of parasitic helminths and other infectious pathogens has been implicated with rising rates of autoimmune and allergic disorders in developed countries. Given the enormous health impact of these parasites, it is surprising how little is known about the non-protein small metabolites of the excretory-secretory products (ESP), including their composition and pharmacological properties. OBJECTIVES We sought proof-of-concept that Nippostrongylus brasiliensis and Trichuris muris, rodent models of two of the most important human soil-transmitted helminths, secrete small metabolites and that some of these metabolites may have specific pharmacological functions. METHODS N. brasiliensis and T. muris ESP were collected from adult worms and filtered using a 10 kDa cut-off membrane to produce excretory-secretory metabolites (ESM). The ESM were analysed using targeted gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry for polar and non-polar small metabolites. RESULTS ESM from both N. brasiliensis and T. muris contained small molecules. A total of 54 small molecules (38 polar metabolites and 16 fatty acids) were identified, 36 known polar metabolites from N. brasiliensis and 35 from T. muris. A literature review of the identified compounds revealed that 17 of them have various demonstrated pharmacological activities. CONCLUSION N. brasiliensis and T. muris secrete polar and non-polar small molecules with as many as 17 metabolites known to exhibit various pharmacological activities.
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Affiliation(s)
- Phurpa Wangchuk
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Building E4, McGregor Rd, Smithfield, Cairns, QLD, 4878, Australia.
| | - Konstantinos Kouremenos
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, VIC, 3010, Australia
| | - Ramon M Eichenberger
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Building E4, McGregor Rd, Smithfield, Cairns, QLD, 4878, Australia
- Institute of Parasitology, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 266a, 8057, Zurich, Switzerland
| | - Mark Pearson
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Building E4, McGregor Rd, Smithfield, Cairns, QLD, 4878, Australia
| | - Atik Susianto
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Building E4, McGregor Rd, Smithfield, Cairns, QLD, 4878, Australia
| | - David S Wishart
- Department of Biological Science, University of Alberta, Edmonton, AB, Canada
| | - Malcolm J McConville
- Department of Biochemistry and Molecular Biology, University of Melbourne, 30 Flemington Road, Parkville, VIC, 3010, Australia
| | - Alex Loukas
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Building E4, McGregor Rd, Smithfield, Cairns, QLD, 4878, Australia.
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15
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Silvestre R, Torrado E. Metabolomic-Based Methods in Diagnosis and Monitoring Infection Progression. EXPERIENTIA SUPPLEMENTUM (2012) 2019; 109:283-315. [PMID: 30535603 PMCID: PMC7124096 DOI: 10.1007/978-3-319-74932-7_7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A robust biomarker screening and validation is crucial for overcoming the current limits in the clinical management of infectious diseases. In this chapter, a general workflow for metabolomics is summarized. Subsequently, an overview of the major contributions of this omics science to the field of biomarkers of infectious diseases is discussed. Different approaches using a variety of analytical platforms can be distinguished to unveil the key metabolites for the diagnosis, prognosis, response to treatment and susceptibility for infectious diseases. To allow the implementation of such biomarkers into the clinics, the performance of large-scale studies employing solid validation criteria becomes essential. Focusing on the etiological agents and after an extensive review of the field, we present a comprehensive revision of the main metabolic biomarkers of viral, bacterial, fungal, and parasitic diseases. Finally, we discussed several articles which show the strongest validation criteria. Following these research avenues, precious clinical resources will be revealed, allowing for reduced misdiagnosis, more efficient therapies, and affordable costs, ultimately leading to a better patient management.
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Affiliation(s)
- Ricardo Silvestre
- Life and Health Sciences Research Institute, University of Minho, Braga, Portugal
| | - Egídio Torrado
- Life and Health Sciences Research Institute, University of Minho, Braga, Portugal
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16
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Lagatie O, Verheyen A, Nijs E, Batsa Debrah L, Debrah YA, Stuyver LJ. Performance evaluation of 3 serodiagnostic peptide epitopes and the derived multi-epitope peptide OvNMP-48 for detection of Onchocerca volvulus infection. Parasitol Res 2019; 118:2263-2270. [PMID: 31089811 PMCID: PMC6611744 DOI: 10.1007/s00436-019-06345-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 04/30/2019] [Indexed: 02/04/2023]
Abstract
Current diagnostic tools to determine infection with the helminth parasite Onchocerca volvulus have limited performance characteristics. In previous studies, a proteome-wide screen was conducted to identify linear epitopes in this parasite’s proteome, resulting in the discovery of 1110 antigenic peptide fragments. Here, we investigated three of these peptides using peptide ELISA’s and evaluated their sensitivity and specificity. Epitope mapping was performed, and peptides were constructed that contained only the minimal epitope, flanked by a linker. Investigation of the performance of these minimal epitope peptides demonstrated that all three of them have a specificity (as defined by lack of response in non-helminth-infected individuals) of 100%, low cross-reactivity (5.6%, 5.6%, and 9.3%, respectively), but low sensitivity (36.9%, 46.5%, and 41.2%, respectively). Some cross-reactivity was observed in samples from individuals infected with soil-transmitted helminths or Brugia malayi. Combining these three minimal epitopes in a single peptide, called OvNMP-48, resulted in a performance that exceeded the sum of the individual epitopes, with a sensitivity of 76.0%, a specificity of 97.4%, and a cross-reactivity of 11.1%. Cross-reactivity was observed in some STH and Brugia malayi-infected individuals. This work opens the opportunity to start exploring how these novel linear epitope markers might become part of the O. volvulus diagnostic toolbox.
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Affiliation(s)
- Ole Lagatie
- Global Public Health, Janssen R&D, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Ann Verheyen
- Global Public Health, Janssen R&D, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Erik Nijs
- Global Public Health, Janssen R&D, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Linda Batsa Debrah
- Kumasi Centre for Collaborative Research into Tropical medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Yaw A Debrah
- Faculty of Allied Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Lieven J Stuyver
- Global Public Health, Janssen R&D, Turnhoutseweg 30, 2340, Beerse, Belgium
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17
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A pilot study of the effect of phospholipid curcumin on serum metabolomic profile in patients with non-alcoholic fatty liver disease: a randomized, double-blind, placebo-controlled trial. Eur J Clin Nutr 2019; 73:1224-1235. [PMID: 30647436 DOI: 10.1038/s41430-018-0386-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 12/17/2018] [Accepted: 12/17/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND/OBJECTIVES Curcumin, a natural polyphenol compound in the spice turmeric, has been found to have potent anti-oxidative and anti-inflammatory activity. Curcumin may treat non-alcoholic fatty liver disease (NAFLD) through its beneficial effects on biomarkers of oxidative stress (OS) and inflammation, which are considered as two feature of this disease. However, the effects of curcumin on NAFLD have been remained poorly understood. This investigation evaluated the effects of administrating curcumin on metabolic status in NAFLD patients. SUBJECTS/METHODS Fifty-eight NAFLD patients participated in a randomized, double-blind, placebo-controlled parallel design of study. The subjects were allocated randomly into two groups, which either received 250 mg phospholipid curcumin or placebo, one capsule per day for a period of 8 weeks. Fasting blood samples were taken from each subject at the start and end of the study period. Subsequently, metabolomics analysis was performed for serum samples using NMR. RESULTS Compared with the placebo, supplementing phospholipid curcumin resulted in significant decreases in serum including 3- methyl-2-oxovaleric acid, 3-hydroxyisobutyrate, kynurenine, succinate, citrate, α-ketoglutarate, methylamine, trimethylamine, hippurate, indoxyl sulfate, chenodeoxycholic acid, taurocholic acid, and lithocholic acid. This profile of metabolic biomarkers could distinguish effectively NAFLD subjects who were treated with curcumin and placebo groups, achieving value of 0.99 for an area under receiver operating characteristic curve (AUC). CONCLUSIONS Characterizing the serum metabolic profile of the patients with NAFLD at the end of the intervention using NMR-based metabolomics method indicated that the targets of curcumin treatment included some amino acids, TCA cycle, bile acids, and gut microbiota.
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18
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Shirey RJ, Globisch D, Eubanks LM, Hixon MS, Janda KD. Noninvasive Urine Biomarker Lateral Flow Immunoassay for Monitoring Active Onchocerciasis. ACS Infect Dis 2018; 4:1423-1431. [PMID: 30141624 PMCID: PMC6189908 DOI: 10.1021/acsinfecdis.8b00163] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The parasitic disease onchocerciasis is the second leading cause of preventable blindness, afflicting more than 18 million people worldwide. Despite an available treatment, ivermectin, and control efforts by the World Health Organization, onchocerciasis remains a burden in many regions. With an estimated 120 million people living in areas at risk of infection, efforts are now shifting from prevention to surveillance and elimination. The lack of a robust, point-of-care diagnostic for an active Onchocerca infection has been a limiting factor in these efforts. Previously, we reported the discovery of the biomarker N-acetyl-tyramine- O-glucuronide (NATOG) in human urine samples and its ability to track treatment progression between medicated patients relative to placebo; we also established its capability to monitor disease burden in a jird model. NATOG is a human-produced metabolite of tyramine, which itself is produced as a nematode neurotransmitter. The ability of NATOG to distinguish between active and past infection overcomes the limitations of antibody biomarkers and PCR methodologies. Lateral flow immunoassay (LFIA) diagnostics offer the versatility and simplicity to be employed in the field and are inexpensive enough to be utilized in large-scale screening efforts. Herein, we report the development and assessment of a NATOG-based urine LFIA for onchocerciasis, which accurately identified 85% of analyzed patient samples ( N = 27).
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Affiliation(s)
- Ryan J. Shirey
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- Department of Immunology, The Skaggs Institute for Chemical Biology, The Worm Institute of Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey, La Jolla, California 92037, United States
| | - Daniel Globisch
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- Department of Immunology, The Skaggs Institute for Chemical Biology, The Worm Institute of Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey, La Jolla, California 92037, United States
| | - Lisa M. Eubanks
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- Department of Immunology, The Skaggs Institute for Chemical Biology, The Worm Institute of Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey, La Jolla, California 92037, United States
| | - Mark S. Hixon
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- Department of Immunology, The Skaggs Institute for Chemical Biology, The Worm Institute of Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey, La Jolla, California 92037, United States
| | - Kim D. Janda
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- Department of Immunology, The Skaggs Institute for Chemical Biology, The Worm Institute of Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey, La Jolla, California 92037, United States
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Murdoch ME. Onchodermatitis: Where Are We Now? Trop Med Infect Dis 2018; 3:E94. [PMID: 30274490 PMCID: PMC6160948 DOI: 10.3390/tropicalmed3030094] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 08/27/2018] [Accepted: 08/28/2018] [Indexed: 02/07/2023] Open
Abstract
Onchocerciasis causes debilitating pruritus and rashes as well as visual impairment and blindness. Prior to control measures, eye disease was particularly prominent in savanna areas of sub-Saharan Africa whilst skin disease was more common across rainforest regions of tropical Africa. Mass drug distribution with ivermectin is changing the global scene of onchocerciasis. There has been successful progressive elimination in Central and Southern American countries and the World Health Organization has set a target for elimination in Africa of 2025. This literature review was conducted to examine progress regarding onchocercal skin disease. PubMed searches were performed using keywords 'onchocerciasis', 'onchodermatitis' and 'onchocercal skin disease' over the past eight years. Articles in English, or with an English abstract, were assessed for relevance, including any pertinent references within the articles. Recent progress in awareness of, understanding and treatment of onchocercal skin disease is reviewed with particular emphasis on publications within the past five years. The global burden of onchodermatitis is progressively reducing and is no longer seen in children in many formerly endemic foci.
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Affiliation(s)
- Michele E Murdoch
- Department of Dermatology, West Herts Hospitals NHS Trust, Vicarage Road, Watford, Hertfordshire WD18 0HB, UK.
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Unnasch TR, Golden A, Cama V, Cantey PT. Diagnostics for onchocerciasis in the era of elimination. Int Health 2018; 10:i20-i26. [PMID: 29471336 PMCID: PMC5881263 DOI: 10.1093/inthealth/ihx047] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 10/19/2017] [Accepted: 11/06/2017] [Indexed: 12/31/2022] Open
Abstract
In the past few years, efforts to eliminate onchocerciasis from Africa have intensified. These efforts are primarily based on the mass distribution of the anti-helminthic drug Mectizan™ (ivermectin). This program has led to the development of new guidelines by the World Health Organization for the verification that transmission has been suppressed and eventually eliminated. The requirements of diagnostic tools for this purpose differ in many ways from tests used to diagnose infection in individuals. In this review, we summarize the progress that has been made to identify diagnostics that meet the specialized requirements needed to verify onchocerciasis elimination, discuss why these tests were selected and summarize the needs that still exist to complete the arsenal of diagnostic tools that will be useful as the goal of elimination is achieved.
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Affiliation(s)
- Thomas R Unnasch
- Center for Global Health Infectious Disease Research, College of Public Health, University of South Florida, 3720 Spectrum Blvd., Suite 304, Tampa, FL 33612, USA
| | | | - Vitaliano Cama
- Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GAUSA
| | - Paul T Cantey
- Department of Control of Neglected Tropical Diseases, World Health Organization, Geneva, Switzerland
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Zhang R, Qin Q, Liu B, Qiao L. TiO2-Assisted Laser Desorption/Ionization Mass Spectrometry for Rapid Profiling of Candidate Metabolite Biomarkers from Antimicrobial-Resistant Bacteria. Anal Chem 2018; 90:3863-3870. [PMID: 29461808 DOI: 10.1021/acs.analchem.7b04565] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rutan Zhang
- Department of Chemistry, Shanghai Stomatological Hospital, Fudan University, Shanghai 200000, China
| | - Qin Qin
- The Second Military Medical University, Changhai Hospital, Shanghai 200433, China
| | - Baohong Liu
- Department of Chemistry, Shanghai Stomatological Hospital, Fudan University, Shanghai 200000, China
| | - Liang Qiao
- Department of Chemistry, Shanghai Stomatological Hospital, Fudan University, Shanghai 200000, China
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22
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Recent advances in the applications of metabolomics in eye research. Anal Chim Acta 2018; 1037:28-40. [PMID: 30292303 DOI: 10.1016/j.aca.2018.01.060] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 01/26/2018] [Accepted: 01/29/2018] [Indexed: 11/21/2022]
Abstract
Metabolomics, the identification and quantitation of metabolites in a system, have been applied to identify new biomarkers or elucidate disease mechanism. In this review, we discussed the application of metabolomics in several ocular diseases and recent developments in metabolomics regarding tear fluids analysis, data acquisition and processing.
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O-5S quantitative real-time PCR: a new diagnostic tool for laboratory confirmation of human onchocerciasis. Parasit Vectors 2017; 10:451. [PMID: 28969662 PMCID: PMC5625774 DOI: 10.1186/s13071-017-2382-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 09/17/2017] [Indexed: 12/01/2022] Open
Abstract
Background Onchocerciasis is a parasitic disease caused by the filarial nematode Onchocerca volvulus. In endemic areas, the diagnosis is commonly confirmed by microscopic examination of skin snip samples, though this technique is considered to have low sensitivity. The available melting-curve based quantitative real-time PCR (qPCR) using degenerated primers targeting the O-150 repeat of O. volvulus was considered insufficient for confirming the individual diagnosis, especially in elimination studies. This study aimed to improve detection of O. volvulus DNA in clinical samples through the development of a highly sensitive qPCR assay. Methods A novel hydrolysis probe based qPCR assay was designed targeting the specific sequence of the O. volvulus O-5S rRNA gene. A total of 200 clinically suspected onchocerciasis cases were included from Goma district in South-west Ethiopia, from October 2012 through May 2013. Skin snip samples were collected and subjected to microscopy, O-150 qPCR, and the novel O-5S qPCR. Results Among the 200 individuals, 133 patients tested positive (positivity rate of 66.5%) and 67 negative by O-5S qPCR, 74 tested positive by microscopy (37.0%) and 78 tested positive by O-150 qPCR (39.0%). Among the 133 O-5S qPCR positive individuals, microscopy and O-150 qPCR detected 55.6 and 59.4% patients, respectively, implying a higher sensitivity of O-5S qPCR than microscopy and O-150 qPCR. None of the 67 individuals who tested negative by O-5S qPCR tested positive by microscopy or O-150 qPCR, implying 100% specificity of the newly designed O-5S qPCR assay. Conclusions The novel O-5S qPCR assay is more sensitive than both microscopic examination and the existing O-150 qPCR for the detection of O. volvulus from skin snip samples. The newly designed assay is an important step towards appropriate individual diagnosis and control of onchocerciasis. Electronic supplementary material The online version of this article (10.1186/s13071-017-2382-3) contains supplementary material, which is available to authorized users.
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Wewer V, Makepeace BL, Tanya VN, Peisker H, Pfarr K, Hoerauf A, Dörmann P. Lipid profiling of the filarial nematodes Onchocerca volvulus, Onchocerca ochengi and Litomosoides sigmodontis reveals the accumulation of nematode-specific ether phospholipids in the host. Int J Parasitol 2017; 47:903-912. [PMID: 28743489 PMCID: PMC5716430 DOI: 10.1016/j.ijpara.2017.06.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 06/20/2017] [Accepted: 06/21/2017] [Indexed: 01/21/2023]
Abstract
Onchocerciasis is an infectious disease caused by filarial nematodes. Three different filarial nematodes infecting cattle, humans and jirds were studied. Phospholipids in nematodes and hosts were determined by mass spectrometry. Filaria-specific ether phosphatidylethanolamine (PE) lipids accumulate in the host. These ether PE lipids could serve as potential biomarkers for onchocerciasis.
Onchocerciasis, a neglected tropical disease prevalent in western and central Africa, is a major health problem and has been targeted for elimination. The causative agent for this disease is the human parasite Onchocerca volvulus. Onchocerca ochengi and Litomosoides sigmodontis, infectious agents of cattle and rodents, respectively, serve as model organisms to study filarial nematode infections. Biomarkers to determine infection without the use of painful skin biopsies and microscopic identification of larval worms are needed and their discovery is facilitated by an improved knowledge of parasite-specific metabolites. In addition to proteins and nucleic acids, lipids may be suitable candidates for filarial biomarkers that are currently underexplored. To fill this gap, we present the phospholipid profile of the filarial nematodes O. ochengi, O. volvulus and L. sigmodontis. Direct infusion quadrupole time-of-flight (Q-TOF) mass spectrometry was employed to analyze the composition of phospholipids and their molecular species in the three nematode species. Analysis of the phospholipid profiles of plasma or serum of uninfected and infected hosts showed that nematode-specific phospholipids were below detection limits. However, several phospholipids, in particular ether lipids of phosphatidylethanolamine (PE), were abundant in O. ochengi worms and in bovine nodule fluid, suggesting that these phospholipids might be released from O. ochengi into the host, and could serve as potential biomarkers.
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Affiliation(s)
- Vera Wewer
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany
| | - Benjamin L Makepeace
- Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, UK
| | - Vincent N Tanya
- Institut de Recherche Agricole pour le Développement, Regional Centre of Wakwa, BP65 Ngaoundéré, Cameroon
| | - Helga Peisker
- Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, Karlrobert-Kreiten-Str. 13, 53115 Bonn, Germany
| | - Kenneth Pfarr
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany; German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany..
| | - Achim Hoerauf
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany; German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany..
| | - Peter Dörmann
- Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, Karlrobert-Kreiten-Str. 13, 53115 Bonn, Germany.
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Bennuru S, Lustigman S, Abraham D, Nutman TB. Metabolite profiling of infection-associated metabolic markers of onchocerciasis. Mol Biochem Parasitol 2017; 215:58-69. [PMID: 28188804 PMCID: PMC5474354 DOI: 10.1016/j.molbiopara.2017.01.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 01/25/2017] [Accepted: 01/28/2017] [Indexed: 11/30/2022]
Abstract
The global efforts for onchocerciasis elimination may require additional tools (safe micro and macrofilaricidal drugs, vaccines and biomarkers) as elimination efforts move toward the "end game". Efforts toward the identification of suitable biomarkers have focused on specific protein(s) and/or nucleic acids, but metabolites present an alternative option as they have limited half-lives and are the result of combinatorial effects. In comparison to previously used methodology of LC-MS for metabolomic approaches, we used a non-targeted capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS) to analyze the serum metabolic profiles of Ov-infected and -uninfected individuals (n=20). We identified 286 known metabolites (167 in the cation mode and 119 in the anion mode). In addition, putative metabolites were identified based on KEGG (51), HMDB (37) and HMT (6) databases. One hundred ten of these putative metabolites were quantified based on peak areas of internal standards and their ability to be mapped to known pathways (primary-, carbon-, lipid-, amino acid-, nucleotide and coenzyme-metabolism). Multivariate analysis demonstrated clustering and segregation of some of these metabolites to either the infected or control groups. The levels of serotonin, hypoxanthine, pipecolic acid and inosine were significantly elevated in those with onchocerciasis, whereas the levels of glycerophosphocholine, choline and adenine were significantly lower. This non-targeted metabolomic approach provides a global view of the metabolic variations that occur during Ov infection and thus allow the discovery of key metabolites (and associated pathways) that may serve as useful biomarkers in human onchocerciasis.
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Affiliation(s)
| | | | | | - Thomas B Nutman
- Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD, USA
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26
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Yap TWC, Leow AHR, Azmi AN, Callahan DL, Perez-Perez GI, Loke MF, Goh KL, Vadivelu J. Global Fecal and Plasma Metabolic Dynamics Related to Helicobacter pylori Eradication. Front Microbiol 2017; 8:536. [PMID: 28424674 PMCID: PMC5371670 DOI: 10.3389/fmicb.2017.00536] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/14/2017] [Indexed: 12/20/2022] Open
Abstract
Background:Helicobacter pylori colonizes the gastric mucosa of more than half of the world's population. There is increasing evidence H. pylori protects against the development of obesity and childhood asthma/allergies in which the development of these diseases coincide with transient dysbiosis. However, the mechanism underlying the association of H. pylori eradication with human metabolic and immunological disorders is not well-established. In this study, we aimed to investigate the local and systemic effects of H. pylori eradication through untargeted fecal lipidomics and plasma metabolomics approaches by liquid chromatography mass spectrometry (LC-MS). Results: Our study revealed that eradication of H. pylori eradication (i.e., loss of H. pylori and/or H. pylori eradication therapy) changed many global metabolite/lipid features, with the majority being down-regulated. Our findings primarily show that H. pylori eradication affects the host energy and lipid metabolism which may eventually lead to the development of metabolic disorders. Conclusion: These predictive metabolic signatures of metabolic and immunological disorders following H. pylori eradication can provide insights into dynamic local and systemic metabolism related to H. pylori eradication in modulating human health.
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Affiliation(s)
- Theresa Wan-Chen Yap
- Department of Medical Microbiology, Faculty of Medicine, University of MalayaKuala Lumpur, Malaysia
| | - Alex Hwong-Ruey Leow
- Department of Medicine, Faculty of Medicine, University of MalayaKuala Lumpur, Malaysia
| | - Ahmad Najib Azmi
- Department of Medicine, Faculty of Medicine, University of MalayaKuala Lumpur, Malaysia.,Faculty of Medicine and Health Sciences, Universiti Sains Islam MalaysiaKuala Lumpur, Malaysia
| | - Damien L Callahan
- Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences, Deakin UniversityGeelong, VIC, Australia
| | - Guillermo I Perez-Perez
- Department of Medicine, New York University School of MedicineNew York, NY, USA.,Department of Microbiology, New York University School of MedicineNew York, NY, USA
| | - Mun-Fai Loke
- Department of Medical Microbiology, Faculty of Medicine, University of MalayaKuala Lumpur, Malaysia.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of SingaporeSingapore, Singapore
| | - Khean-Lee Goh
- Department of Medicine, Faculty of Medicine, University of MalayaKuala Lumpur, Malaysia
| | - Jamuna Vadivelu
- Department of Medical Microbiology, Faculty of Medicine, University of MalayaKuala Lumpur, Malaysia
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27
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Lagatie O, Batsa Debrah L, Debrah A, Stuyver LJ. Plasma-derived parasitic microRNAs have insufficient concentrations to be used as diagnostic biomarker for detection of Onchocerca volvulus infection or treatment monitoring using LNA-based RT-qPCR. Parasitol Res 2017; 116:1013-1022. [PMID: 28111713 PMCID: PMC5313568 DOI: 10.1007/s00436-017-5382-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 01/16/2017] [Indexed: 01/30/2023]
Abstract
River blindness, caused by infection with the filarial nematode Onchocerca volvulus, is a neglected tropical disease affecting millions of people. There is a clear need for diagnostic tools capable of identifying infected patients, but that can also be used for monitoring disease progression and treatment efficacy. Plasma-derived parasitic microRNAs have been suggested as potential candidates for such diagnostic tools. We have investigated whether these parasitic microRNAs are present in sufficient quantity in plasma of Onchocerca-infected patients to be used as a diagnostic biomarker for detection of O. volvulus infection or treatment monitoring. Plasma samples were collected from different sources (23 nodule-positive individuals and 20 microfilaridermic individuals), microRNAs (miRNAs) were extracted using Qiagen miRNeasy kit, and a set of 17 parasitic miRNAs was evaluated on these miRNA extracts using miRCURY Locked Nucleic Acid (LNA) Universal RT microRNA PCR system. Of the 17 miRNAs evaluated, only 7 miRNAs were found to show detectable signal in a number of samples: bma-miR-236-1, bma-miR-71, ov-miR71-22nt, ov-miR-71-23nt, ov-miR-100d, ov-bantam-a, and ov-miR-87-3p. Subsequent melting curve analysis, however, indicated that the signals observed for ov-miR-71 variants and ov-miR-87-3p are non-specific. The other miRNAs only showed positive signal in one or few samples with Cq values just below the cutoff. Our data indicate that parasitic miRNAs are not present in circulation at a sufficiently high level to be used as biomarker for O. volvulus infection or treatment monitoring using LNA-based RT-qPCR analysis.
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Affiliation(s)
- Ole Lagatie
- Janssen Diagnostics, Janssen R&D, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Linda Batsa Debrah
- Kumasi Centre for Collaborative Research, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Alex Debrah
- Faculty of Allied Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Lieven J Stuyver
- Janssen Diagnostics, Janssen R&D, Turnhoutseweg 30, 2340, Beerse, Belgium
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Trivedi DK, Hollywood KA, Goodacre R. Metabolomics for the masses: The future of metabolomics in a personalized world. NEW HORIZONS IN TRANSLATIONAL MEDICINE 2017; 3:294-305. [PMID: 29094062 PMCID: PMC5653644 DOI: 10.1016/j.nhtm.2017.06.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 06/02/2017] [Accepted: 06/02/2017] [Indexed: 02/07/2023]
Abstract
Current clinical practices focus on a small number of biochemical directly related to the pathophysiology with patients and thus only describe a very limited metabolome of a patient and fail to consider the interations of these small molecules. This lack of extended information may prevent clinicians from making the best possible therapeutic interventions in sufficient time to improve patient care. Various post-genomics '('omic)' approaches have been used for therapeutic interventions previously. Metabolomics now a well-established'omics approach, has been widely adopted as a novel approach for biomarker discovery and in tandem with genomics (especially SNPs and GWAS) has the potential for providing systemic understanding of the underlying causes of pathology. In this review, we discuss the relevance of metabolomics approaches in clinical sciences and its potential for biomarker discovery which may help guide clinical interventions. Although a powerful and potentially high throughput approach for biomarker discovery at the molecular level, true translation of metabolomics into clinics is an extremely slow process. Quicker adaptation of biomarkers discovered using metabolomics can be possible with novel portable and wearable technologies aided by clever data mining, as well as deep learning and artificial intelligence; we shall also discuss this with an eye to the future of precision medicine where metabolomics can be delivered to the masses.
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Affiliation(s)
| | | | - Royston Goodacre
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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29
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Vincent IM, Daly R, Courtioux B, Cattanach AM, Biéler S, Ndung’u JM, Bisser S, Barrett MP. Metabolomics Identifies Multiple Candidate Biomarkers to Diagnose and Stage Human African Trypanosomiasis. PLoS Negl Trop Dis 2016; 10:e0005140. [PMID: 27941966 PMCID: PMC5152828 DOI: 10.1371/journal.pntd.0005140] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/26/2016] [Indexed: 12/01/2022] Open
Abstract
Treatment for human African trypanosomiasis is dependent on the species of trypanosome causing the disease and the stage of the disease (stage 1 defined by parasites being present in blood and lymphatics whilst for stage 2, parasites are found beyond the blood-brain barrier in the cerebrospinal fluid (CSF)). Currently, staging relies upon detecting the very low number of parasites or elevated white blood cell numbers in CSF. Improved staging is desirable, as is the elimination of the need for lumbar puncture. Here we use metabolomics to probe samples of CSF, plasma and urine from 40 Angolan patients infected with Trypanosoma brucei gambiense, at different disease stages. Urine samples provided no robust markers indicative of infection or stage of infection due to inherent variability in urine concentrations. Biomarkers in CSF were able to distinguish patients at stage 1 or advanced stage 2 with absolute specificity. Eleven metabolites clearly distinguished the stage in most patients and two of these (neopterin and 5-hydroxytryptophan) showed 100% specificity and sensitivity between our stage 1 and advanced stage 2 samples. Neopterin is an inflammatory biomarker previously shown in CSF of stage 2 but not stage 1 patients. 5-hydroxytryptophan is an important metabolite in the serotonin synthetic pathway, the key pathway in determining somnolence, thus offering a possible link to the eponymous symptoms of “sleeping sickness”. Plasma also yielded several biomarkers clearly indicative of the presence (87% sensitivity and 95% specificity) and stage of disease (92% sensitivity and 81% specificity). A logistic regression model including these metabolites showed clear separation of patients being either at stage 1 or advanced stage 2 or indeed diseased (both stages) versus control. Human African trypanosomiasis, also known as sleeping sickness, is a parasitic disease that affects people in sub-Saharan Africa. There are two stages of the infection. The first stage involves parasites proliferating in the bloodstream following introduction via the bite of an infected tsetse fly. The second, more serious stage, involves parasite invasion and proliferation within the central nervous system causing characteristic disturbances to the patients’ sleep wake patterns and progressive appearance of other neurological signs, including walking disabilities behaviour changes, abnormal movements, incontinence, then ultimately coma and death. Drugs are available to treat both stages of the disease, but the drugs for stage 2 disease have serious side effects and must be administered in hospital settings. Stage determination is thus a key element for disease management. Currently staging involves microscopic evaluation of CSF following a lumbar puncture. Here, we have analysed the metabolome of CSF, blood and urine of patients to seek biomarkers to stage the disease based on these biofluids. CSF and blood fluids were found to have distinctive metabolic biomarkers and when several of these metabolites are combined, a sensitive and robust discriminatory staging test can be developed. Some CSF metabolic markers relate to brain inflammation, whilst others may be related to somnolence associated with the disease in stage 2 patients, which may also help in understanding disease progression. Interestingly, distinctive biomarkers were also found in plasma, potentially abrogating the need for diagnostic lumbar punctures in the future.
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Affiliation(s)
- Isabel M. Vincent
- Wellcome Trust Centre of Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Rónán Daly
- Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Bertrand Courtioux
- INSERM U1094, Tropical Neuroepidemiology, Limoges, France; Université de Limoges, Institute of Neuroepidemiology and Tropical Neurology, Limoges, France
| | - Amy M. Cattanach
- Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Sylvain Biéler
- Foundation for Innovative New Diagnostics, Geneva, Switzerland
| | | | - Sylvie Bisser
- INSERM U1094, Tropical Neuroepidemiology, Limoges, France; Université de Limoges, Institute of Neuroepidemiology and Tropical Neurology, Limoges, France
- * E-mail: (MPB); (SBis)
| | - Michael P. Barrett
- Wellcome Trust Centre of Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- * E-mail: (MPB); (SBis)
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30
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Lagatie O, Merino M, Batsa Debrah L, Debrah AY, Stuyver LJ. An isothermal DNA amplification method for detection of Onchocerca volvulus infection in skin biopsies. Parasit Vectors 2016; 9:624. [PMID: 27906100 PMCID: PMC5134125 DOI: 10.1186/s13071-016-1913-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/24/2016] [Indexed: 12/20/2022] Open
Abstract
Background Diagnostic procedures for the diagnosis of infection with the nematode parasite Onchocerca volvulus are currently based on the microscopic detection of microfilariae in skin biopsies. Alternative approaches based on amplification of parasitic DNA in these skin biopsies are currently being explored. Mostly this is based on the detection of the O-150 repeat sequence using PCR based techniques. Methods An isothermal, loop-mediated amplification method has been designed using the mitochondrial O. volvulus cox1 gene as a target. Results Analysis of dilution series of synthetic DNA containing the targeted sequence show a non-linear dose-response curve, as is usually the case for isothermal amplification methods. Evaluation of cross-reactivity with the heterologous sequence from the closely related parasites Wuchereria bancrofti, Loa loa and Brugia malayi demonstrated strong specificity, as none of these sequences was amplified. The assay however amplified both O. volvulus and O. ochengi DNA, but with a different melting point that can be used to discriminate between the species. Evaluation of this assay in a set of skin snip biopsies collected in an endemic area in Ghana showed a high correlation with O-150 qPCR and also demonstrated a similar sensitivity. Compared to qPCR, LAMP had a sensitivity of 88.2% and a specificity of 99.2%. Conclusions We have developed a sensitive and specific loop-mediated amplification method for detection of O. volvulus DNA in skin biopsies that is capable of providing results within 30 min. Electronic supplementary material The online version of this article (doi:10.1186/s13071-016-1913-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ole Lagatie
- Janssen Diagnostics, Janssen R&D, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Michelle Merino
- Janssen Diagnostics, Janssen R&D, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Linda Batsa Debrah
- Kumasi Centre for Collaborative Research into Tropical medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Alexander Y Debrah
- Faculty of Allied Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Lieven J Stuyver
- Janssen Diagnostics, Janssen R&D, Turnhoutseweg 30, 2340, Beerse, Belgium
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Lagatie O, Njumbe Ediage E, Batsa Debrah L, Diels L, Nolten C, Vinken P, Debrah A, Dillen L, Silber S, Stuyver LJ. Evaluation of the diagnostic potential of urinary N-Acetyltyramine-O,β-glucuronide (NATOG) as diagnostic biomarker for Onchocerca volvulus infection. Parasit Vectors 2016; 9:302. [PMID: 27216752 PMCID: PMC4877973 DOI: 10.1186/s13071-016-1582-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/10/2016] [Indexed: 12/14/2022] Open
Abstract
Background Onchocerciasis, also known as river blindness is one of the neglected tropical diseases affecting millions of people, mainly in sub-Saharan Africa and is caused by the filarial nematode Onchocerca volvulus. Efforts to eliminate this disease are ongoing and are based on mass drug administration programs with the microfilaricide ivermectin. In order to monitor the efficacy of these programs, there is an unmet need for diagnostic tools capable of identifying infected patients. We have investigated the diagnostic potential of urinary N-acetyltyramine-O,β-glucuronide (NATOG), which is a promising O. volvulus specific biomarker previously identified by urine metabolome analysis. Methods A liquid chromatography tandem mass spectrometry (LC-MS/MS) method was used to assess the stability characteristics of NATOG and to evaluate the levels of NATOG in study samples. An LC-fluorescence method was also developed. Results Stability characteristics of NATOG were investigated and shown to be ideally suited for use in tropical settings. Also, an easy and more accessible method based on liquid chromatography coupled to fluorescence detection was developed and shown to have the necessary sensitivity (limit of quantification 1 μM). Furthermore, we have evaluated the levels of NATOG in a population of 98 nodule-positive individuals from Ghana with no or low levels of microfilaria in the skin and compared them with the levels observed in different control groups (endemic controls (n = 50), non-endemic controls (n = 18) and lymphatic filariasis (n = 51). Only a few (5 %) of nodule-positive individuals showed an increased level (> 10 μM) of NATOG and there was no statistical difference between the nodule-positive individuals and the control groups (P > 0.05). Conclusions Results of the present study indicate the limited potential of NATOG as a diagnostic biomarker for O. volvulus infection in amicrofilaridermic individuals. Electronic supplementary material The online version of this article (doi:10.1186/s13071-016-1582-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ole Lagatie
- Janssen Diagnostics, Janssen R&D, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | | | - Linda Batsa Debrah
- Kumasi Centre for Collaborative Research, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Luc Diels
- Bioanalysis, Janssen R&D, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Christ Nolten
- Neuroscience, Janssen R&D, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Petra Vinken
- Toxicology, Janssen R&D, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Alex Debrah
- Faculty of Allied Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Lieve Dillen
- Bioanalysis, Janssen R&D, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Steven Silber
- Janssen Global Public Health, Janssen R&D, 12 W Sunset Ave, Philadelphia, PA, 19118, USA
| | - Lieven J Stuyver
- Janssen Diagnostics, Janssen R&D, Turnhoutseweg 30, 2340, Beerse, Belgium
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Xu H, Zhang L, Kang H, Zhang J, Liu J, Liu S. Serum Metabonomics of Mild Acute Pancreatitis. J Clin Lab Anal 2016; 30:990-998. [PMID: 27169745 DOI: 10.1002/jcla.21969] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 12/03/2015] [Accepted: 01/09/2016] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Mild acute pancreatitis (MAP) is a common acute abdominal disease, and exhibits rising incidence in recent decades. As an important component of systemic biology, metabonomics is a new discipline developed following genomics and proteomics. In this study, the objective was to analyze the serum metabonomics of patients with MAP, aiming to screen metabolic markers with potential diagnostic values. METHODS An analysis platform with ultra performance liquid chromatography-high-resolution mass spectrometry was used to screen the difference metabolites related to MAP diagnosis and disease course monitoring. RESULTS A total of 432 endogenous metabolites were screened out from 122 serum samples, and 49 difference metabolites were verified, among which 12 difference metabolites were identified by nonparametric test. After material identification, eight metabolites exhibited reliable results, and their levels in MAP serum were higher than those in healthy serum. Four metabolites exhibited gradual downward trend with treatment process going on, and the differences were statistically significant (P < 0.05). CONCLUSION Metabonomic analysis has revealed eight metabolites with potential diagnostic values toward MAP, among which four metabolites can be used to monitor the disease course.
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Affiliation(s)
- Hongmin Xu
- Department of Clinical Laboratory, Tianjin Third Central Hospital, Tianjin, China
| | - Lei Zhang
- Department of Clinical Laboratory, Tianjin Third Central Hospital, Tianjin, China
| | - Huan Kang
- Department of Clinical Laboratory, Tianjin Third Central Hospital, Tianjin, China
| | - Jiandong Zhang
- Department of Clinical Laboratory, Tianjin Third Central Hospital, Tianjin, China
| | - Jie Liu
- Department of Clinical Laboratory, Tianjin Third Central Hospital, Tianjin, China
| | - Shuye Liu
- Department of Clinical Laboratory, Tianjin Third Central Hospital, Tianjin, China.
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Koen N, Du Preez I, Loots DT. Metabolomics and Personalized Medicine. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2015; 102:53-78. [PMID: 26827602 DOI: 10.1016/bs.apcsb.2015.09.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Current clinical practice strongly relies on the prognosis, diagnosis, and treatment of diseases using methods determined and averaged for the specific diseased cohort/population. Although this approach complies positively with most patients, misdiagnosis, treatment failure, relapse, and adverse drug effects are common occurrences in many individuals, which subsequently hamper the control and eradication of a number of diseases. These incidences can be explained by individual variation in the genome, transcriptome, proteome, and metabolome of a patient. Various "omics" approaches have investigated the influence of these factors on a molecular level, with the intention of developing personalized approaches to disease diagnosis and treatment. Metabolomics, the newest addition to the "omics" domain and the closest to the observed phenotype, reflects changes occurring at all molecular levels, as well as influences resulting from other internal and external factors. By comparing the metabolite profiles of two or more disease phenotypes, metabolomics can be applied to identify biomarkers related to the perturbation being investigated. These biomarkers can, in turn, be used to develop personalized prognostic, diagnostic, and treatment approaches, and can also be applied to the monitoring of disease progression, treatment efficacy, predisposition to drug-related side effects, and potential relapse. In this review, we discuss the contributions that metabolomics has made, and can potentially still make, towards the field of personalized medicine.
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Affiliation(s)
- Nadia Koen
- School for Physical and Chemical Sciences, Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Ilse Du Preez
- School for Physical and Chemical Sciences, Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Du Toit Loots
- School for Physical and Chemical Sciences, Human Metabolomics, North-West University, Potchefstroom, South Africa.
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From sample treatment to biomarker discovery: A tutorial for untargeted metabolomics based on GC-(EI)-Q-MS. Anal Chim Acta 2015; 900:21-35. [PMID: 26572836 DOI: 10.1016/j.aca.2015.10.001] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 09/29/2015] [Accepted: 10/08/2015] [Indexed: 12/24/2022]
Abstract
This tutorial provides a comprehensive description of the GC-MS-based untargeted metabolomics workflow including: ethical approval requirement, sample collection and storage, equipment maintenance and setup, sample treatment, monitoring of analytical variability, data pre-processing including deconvolution by free software such as AMDIS, data processing, statistical analysis and validation, detection of outliers and biological interpretation of the results. For each stage tricks will be suggested, pitfalls will be highlighted and advice will be provided on how to get the best from this methodology and technique. In addition, a step-by-step procedure and an example of our in-house library have been included in the supplementary material to lead the user through the concepts described herein. As a case study, an interesting example from one of our experiments at CEMBIO Research Centre is described, presenting an example of the use of this ready-to use protocol for identification of a metabolite that was not previously included in Fiehn commercial target library.
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Preidis GA, Hotez PJ. The newest "omics"--metagenomics and metabolomics--enter the battle against the neglected tropical diseases. PLoS Negl Trop Dis 2015; 9:e0003382. [PMID: 25675250 PMCID: PMC4326130 DOI: 10.1371/journal.pntd.0003382] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Geoffrey A. Preidis
- Section of Gastroenterology, Hepatology & Nutrition, Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, Texas, United States of America
- * E-mail:
| | - Peter J. Hotez
- National School of Tropical Medicine, Department of Pediatrics and Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Sabin Vaccine Institute and Texas Children’s Hospital Center for Vaccine Development, Houston, Texas, United States of America
- James A. Baker III Institute for Public Policy, Rice University, Houston, Texas, United States of America
- Department of Biology, Baylor University, Waco, Texas, United States of America
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Kim DH, Achcar F, Breitling R, Burgess KE, Barrett MP. LC-MS-based absolute metabolite quantification: application to metabolic flux measurement in trypanosomes. Metabolomics 2015; 11:1721-1732. [PMID: 26491423 PMCID: PMC4605981 DOI: 10.1007/s11306-015-0827-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/25/2015] [Indexed: 01/15/2023]
Abstract
Human African trypanosomiasis is a neglected tropical disease caused by the protozoan parasite, Trypanosoma brucei. In the mammalian bloodstream, the trypanosome's metabolism differs significantly from that of its host. For example, the parasite relies exclusively on glycolysis for energy source. Recently, computational and mathematical models of trypanosome metabolism have been generated to assist in understanding the parasite metabolism with the aim of facilitating drug development. Optimisation of these models requires quantitative information, including metabolite concentrations and/or metabolic fluxes that have been hitherto unavailable on a large scale. Here, we have implemented an LC-MS-based method that allows large scale quantification of metabolite levels by using U-13C-labelled E.coli extracts as internal standards. Known amounts of labelled E. coli extract were added into the parasite samples, as well as calibration standards, and used to obtain calibration curves enabling us to convert intensities into concentrations. This method allowed us to reliably quantify the changes of 43 intracellular metabolites and 32 extracellular metabolites in the medium over time. Based on the absolute quantification, we were able to compute consumption and production fluxes. These quantitative data can now be used to optimise computational models of parasite metabolism.
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Affiliation(s)
- Dong-Hyun Kim
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA UK
- Centre for Analytical Bioscience, School of Pharmacy, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Fiona Achcar
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA UK
| | - Rainer Breitling
- Manchester Centre of Synthetic Biology for Fine and Speciality Chemicals, Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, M1 7DN UK
| | - Karl E. Burgess
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, G61 1QH UK
| | - Michael P. Barrett
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA UK
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, G61 1QH UK
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Trivedi DK, Iles RK. Do not just do it, do it right: urinary metabolomics -establishing clinically relevant baselines. Biomed Chromatogr 2014; 28:1491-501. [DOI: 10.1002/bmc.3219] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 03/17/2014] [Accepted: 03/25/2014] [Indexed: 12/11/2022]
Affiliation(s)
- Drupad K. Trivedi
- Eric Leonard Kruse Foundation for Health Research; Manchester UK
- Manchester Institute of Biotechnology and School of Chemistry; University of Manchester; M1 7DN UK
| | - Ray K. Iles
- Eric Leonard Kruse Foundation for Health Research; Manchester UK
- MAP Diagnostic Ltd; Ely Cambridgeshire UK
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Current practice of liquid chromatography–mass spectrometry in metabolomics and metabonomics. J Pharm Biomed Anal 2014; 87:12-25. [DOI: 10.1016/j.jpba.2013.06.032] [Citation(s) in RCA: 280] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 06/26/2013] [Accepted: 06/29/2013] [Indexed: 02/06/2023]
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Mozzi F, Ortiz ME, Bleckwedel J, De Vuyst L, Pescuma M. Metabolomics as a tool for the comprehensive understanding of fermented and functional foods with lactic acid bacteria. Food Res Int 2013. [DOI: 10.1016/j.foodres.2012.11.010] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Godzien J, Ciborowski M, Angulo S, Barbas C. From numbers to a biological sense: How the strategy chosen for metabolomics data treatment may affect final results. A practical example based on urine fingerprints obtained by LC-MS. Electrophoresis 2013; 34:2812-26. [PMID: 23775708 DOI: 10.1002/elps.201300053] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 04/08/2013] [Accepted: 05/08/2013] [Indexed: 01/05/2023]
Abstract
Application of high-throughput technologies in metabolomics studies increases the quantity of data obtained, which in turn imposes several problems during data analysis. Correctly and clearly addressed biological question and comprehensive knowledge about data structure and properties are definitely necessary to select proper chemometric tools. However, there is a broad range of chemometric tools available for use with metabolomics data, which makes this choice challenging. Precisely performed data treatment enables valuable extraction of information and its proper interpretation. The effect of an error made at an early stage will be enhanced throughout the later stages, which in combination with other errors made at each step can accumulate and significantly affect the data interpretation. Moreover, adequate application of these tools may help not only to detect, but sometimes also to correct, biological, analytical, or methodological errors, which may affect truthfulness of obtained results. This report presents steps and tools used for LC-MS based metabolomics data extraction, reduction, and visualization. Following such steps as data reprocessing, data pretreatment, data treatment, and data revision, authors want to show how to extract valuable information and how to avoid misinterpretation of results obtained. The purpose of this work was to emphasize problematic characteristics of metabolomics data and the necessity for their attentive and precise treatment. The dataset used to illustrate metabolomics data properties and to illustrate major data treatment challenges was obtained utilizing an animal model of control and diabetic rats, both with and without rosemary treatment. Urine samples were fingerprinted employing LC-QTOF-MS.
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Affiliation(s)
- Joanna Godzien
- CEMBIO (Center for Metabolomics and Bioanalysis) Facultad de Farmacia, Universidad San Pablo CEU, Campus Monteprincipe, Madrid, Spain; Department of Molecular Biology, Faculty of Biotechnology and Environment Sciences, The John Paul II Catholic University of Lublin, Lublin, Poland
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Amaral JJ, Antunes LCM, de Macedo CS, Mattos KA, Han J, Pan J, Candéa ALP, Henriques MDGMO, Ribeiro-Alves M, Borchers CH, Sarno EN, Bozza PT, Finlay BB, Pessolani MCV. Metabonomics reveals drastic changes in anti-inflammatory/pro-resolving polyunsaturated fatty acids-derived lipid mediators in leprosy disease. PLoS Negl Trop Dis 2013; 7:e2381. [PMID: 23967366 PMCID: PMC3744420 DOI: 10.1371/journal.pntd.0002381] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 07/07/2013] [Indexed: 12/20/2022] Open
Abstract
Despite considerable efforts over the last decades, our understanding of leprosy pathogenesis remains limited. The complex interplay between pathogens and hosts has profound effects on host metabolism. To explore the metabolic perturbations associated with leprosy, we analyzed the serum metabolome of leprosy patients. Samples collected from lepromatous and tuberculoid patients before and immediately after the conclusion of multidrug therapy (MDT) were subjected to high-throughput metabolic profiling. Our results show marked metabolic alterations during leprosy that subside at the conclusion of MDT. Pathways showing the highest modulation were related to polyunsaturated fatty acid (PUFA) metabolism, with emphasis on anti-inflammatory, pro-resolving omega-3 fatty acids. These results were confirmed by eicosanoid measurements through enzyme-linked immunoassays. Corroborating the repertoire of metabolites altered in sera, metabonomic analysis of skin specimens revealed alterations in the levels of lipids derived from lipase activity, including PUFAs, suggesting a high lipid turnover in highly-infected lesions. Our data suggest that omega-6 and omega-3, PUFA-derived, pro-resolving lipid mediators contribute to reduced tissue damage irrespectively of pathogen burden during leprosy disease. Our results demonstrate the utility of a comprehensive metabonomic approach for identifying potential contributors to disease pathology that may facilitate the development of more targeted treatments for leprosy and other inflammatory diseases. Leprosy is caused by a mycobacterium that has a predilection for the skin and nerve cells, and the disease is treated with a combination of antibiotics (multidrug therapy, MDT). Nerve damage caused by the infection may lead to permanent disabilities, and can happen even during MDT and subsequent to patient release. Therefore, a more comprehensive understanding of the interaction between the leprosy bacillus and humans is mandatory in order to develop new tools for better disease control and management. Aiming to understand more about the effects of leprosy on human metabolism, we analyzed the chemical composition of sera from leprosy patients before and after MDT. Our results show that specific classes of molecules are affected by the infection, and that MDT can partially reverse these effects. In particular, lipids related to polyunsaturated fatty acid metabolism and known to play a role in the host's defense mechanisms were highly affected during the disease. A complete understanding of all the steps in this process may open new avenues for leprosy treatment with consequent prevention of neuropathy.
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Affiliation(s)
- Julio J. Amaral
- Laboratório de Microbiologia Celular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Biologia, Instituto Nacional de Metrologia, Qualidade e Tecnologia, Rio de Janeiro, Brazil
| | - Luis Caetano M. Antunes
- Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
- Escola Nacional de Saúde Pública Sergio Arouca, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Cristiana S. de Macedo
- Laboratório de Microbiologia Celular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Katherine A. Mattos
- Laboratório de Microbiologia Celular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Jun Han
- University of Victoria – Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada
| | - Jingxi Pan
- University of Victoria – Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada
| | - André L. P. Candéa
- Laboratório de Farmacologia Aplicada, Farmanguinhos, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | - Marcelo Ribeiro-Alves
- Laboratório de Pesquisa em Farmacogenética, Instituto de Pesquisa Clínica Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Christoph H. Borchers
- University of Victoria – Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada
| | - Euzenir N. Sarno
- Laboratório de Hanseníase, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Patrícia T. Bozza
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - B. Brett Finlay
- Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Maria Cristina V. Pessolani
- Laboratório de Microbiologia Celular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- * E-mail:
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Barry MA, Simon GG, Mistry N, Hotez PJ. Global trends in neglected tropical disease control and elimination: impact on child health. Arch Dis Child 2013; 98:635-41. [PMID: 23793132 DOI: 10.1136/archdischild-2012-302338] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The neglected tropical diseases (NTDs) are a group of 17 lesser known chronic infections which predominantly affect poor and disenfranchised communities. There are a number of NTDs that cause significant global morbidity in children, including the three major soil transmitted helminth (STH) infections (ascariasis, trichuriasis and hookworm infection), schistosomiasis and trachoma. These NTDs, together with lymphatic filariasis and onchocerciasis, are currently being targeted for global control and elimination through mass drug administration (MDA) campaigns. They represent the most common NTDs and share significant geographical overlap. Additionally, many individuals are polyparasitised with more than a single NTD. Integrated NTD control and elimination MDA programmes offer safe and efficacious treatments for all seven NTDs. However, the current global level of MDA coverage for the leading childhood NTDs, that is, STH infections, schistosomiasis and trachoma, remains well under 50%. Limiting factors for global coverage include insufficient global financial support, drug donation capacity of pharmaceutical companies and targeting school age children to the exclusion of other age groups in need of treatment, such as preschool age children. There is also a need for development of novel prevention and treatment modalities, such as next-generation small molecule drugs and vaccines. Efforts are underway to harness the momentum of a 2012 London Declaration on NTDs and a 2013 World Health Assembly (WHA) resolution as a means to control or in some cases eliminate by 2020 these NTDs that affect children worldwide.
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Affiliation(s)
- Meagan A Barry
- Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX 77030, USA.
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Onchocerca volvulus-neurotransmitter tyramine is a biomarker for river blindness. Proc Natl Acad Sci U S A 2013; 110:4218-23. [PMID: 23440222 DOI: 10.1073/pnas.1221969110] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Onchocerciasis, also known as "river blindness", is a neglected tropical disease infecting millions of people mainly in Africa and the Middle East but also in South America and Central America. Disease infectivity initiates from the filarial parasitic nematode Onchocerca volvulus, which is transmitted by the blackfly vector Simulium sp. carrying infectious third-stage larvae. Ivermectin has controlled transmission of microfilariae, with an African Program elimination target date of 2025. However, there is currently no point-of-care diagnostic that can distinguish the burden of infection--including active and/or past infection--and enable the elimination program to be effectively monitored. Here, we describe how liquid chromatography-MS-based urine metabolome analysis can be exploited for the identification of a unique biomarker, N-acetyltyramine-O,β-glucuronide (NATOG), a neurotransmitter-derived secretion metabolite from O. volvulus. The regulation of this tyramine neurotransmitter was found to be linked to patient disease infection, including the controversial antibiotic doxycycline treatment that has been shown to both sterilize and kill adult female worms. Further clues to its regulation have been elucidated through biosynthetic pathway determination within the nematode and its human host. Our results demonstrate that NATOG tracks O. volvulus metabolism in both worms and humans, and thus can be considered a host-specific biomarker for onchocerciasis progression. Liquid chromatography-MS-based urine metabolome analysis discovery of NATOG not only has broad implications for a noninvasive host-specific onchocerciasis diagnostic but provides a basis for the metabolome mining of other neglected tropical diseases for the discovery of distinct biomarkers and monitoring of disease progression.
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Watson DG. A rough guide to metabolite identification using high resolution liquid chromatography mass spectrometry in metabolomic profiling in metazoans. Comput Struct Biotechnol J 2013; 4:e201301005. [PMID: 24688687 PMCID: PMC3962115 DOI: 10.5936/csbj.201301005] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 01/28/2013] [Accepted: 02/08/2013] [Indexed: 12/15/2022] Open
Abstract
Compound identification in mass spectrometry based metabolomics can be a problem but sometimes the problem seems to be presented in an over complicated way. The current review focuses on metazoans where the range of metabolites is more restricted than for example in plants. The focus is on liquid chromatography with high resolution mass spectrometry where it is proposed that most of the problems in compound identification relate to structural isomers rather than to isobaric compounds. Thus many of the problems faced relate to separation of isomers, which is usually required even if fragmentation is used to support structural identification. Many papers report the use of MS/MS or MS2 as an adjunct to the identification of known metabolites but there a few examples in metabolomics studies of metazoans of complete structure elucidation of novel metabolites or metabolites where no authentic standards are available for comparison.
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Affiliation(s)
- David G Watson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, 161, Cathedral Street, Glasgow G4 0RE, United Kingdom
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Zhang J, Wei S, Liu L, Nagana Gowda G, Bonney P, Stewart J, Knapp DW, Raftery D. NMR-based metabolomics study of canine bladder cancer. Biochim Biophys Acta Mol Basis Dis 2012; 1822:1807-14. [DOI: 10.1016/j.bbadis.2012.08.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 07/14/2012] [Accepted: 08/02/2012] [Indexed: 12/12/2022]
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Chen J, Zhou L, Zhang X, Lu X, Cao R, Xu C, Xu G. Urinary hydrophilic and hydrophobic metabolic profiling based on liquid chromatography-mass spectrometry methods: Differential metabolite discovery specific to ovarian cancer. Electrophoresis 2012; 33:3361-9. [DOI: 10.1002/elps.201200140] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 05/11/2012] [Accepted: 05/25/2012] [Indexed: 11/11/2022]
Affiliation(s)
- Jing Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian; P.R. China
| | - Lina Zhou
- CAS Key Laboratory of Separation Science for Analytical Chemistry; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian; P.R. China
| | | | - Xin Lu
- CAS Key Laboratory of Separation Science for Analytical Chemistry; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian; P.R. China
| | - Rui Cao
- Department of the Obstetrics and Gynecology Hospital of Dalian; Dalian Medical University; Dalian; P.R. China
| | | | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian; P.R. China
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Abstract
Metabolomics has a special place among other 'omics' disciplines (genomics, transcriptomics and proteomics) as it describes the most dynamic level of biological regulation and, as such, provides the most direct reflection of the physiological status of an organism. Quick development of the analytical technologies in the first place - MS and NMR - has enabled the metabolomics analysis of such complex biological phenomena as host-pathogen interactions in the development of infection. In this review, an overview of the metabolomics studies of infectious diseases carried out on human material is provided. The relevant papers on the metabolomics of human infectious diseases are comprehensively summarized in a table, including, for example, information on the study design, number of subjects, employed technology and metabolic discriminator. Future considerations, such as importance of the time-resolved study designs and the embedment of metabolomics in large-scale epidemiological studies are discussed.
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Zhang A, Sun H, Wang X. Saliva Metabolomics Opens Door to Biomarker Discovery, Disease Diagnosis, and Treatment. Appl Biochem Biotechnol 2012; 168:1718-27. [DOI: 10.1007/s12010-012-9891-5] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2012] [Accepted: 08/31/2012] [Indexed: 12/31/2022]
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Zhang A, Sun H, Wang X. Serum metabolomics as a novel diagnostic approach for disease: a systematic review. Anal Bioanal Chem 2012; 404:1239-45. [DOI: 10.1007/s00216-012-6117-1] [Citation(s) in RCA: 163] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 05/05/2012] [Accepted: 05/15/2012] [Indexed: 01/19/2023]
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