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Guo Y, Wang W, Yu Y, Sun X, Zhang B, Wang Y, Cao J, Wen S, Wang X, Li Y, Cai S, Wu R, Duan W, Xia W, Wei F, Duan J, Dong H, Guo S, Zhang F, Sun Z, Huang X. Crosstalk between human immunodeficiency virus infection and salivary bacterial function in men who have sex with men. Front Cell Infect Microbiol 2024; 14:1341545. [PMID: 38779561 PMCID: PMC11109444 DOI: 10.3389/fcimb.2024.1341545] [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: 11/20/2023] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Background Engaging in anal sexual intercourse markedly increases the risk of developing HIV among men who have sex with men (MSM); oral sexual activities tend to uniquely introduce gut-derived microbes to salivary microbiota, which, combined with an individual's positive HIV status, may greatly perturb oral microecology. However, till date, only a few published studies have addressed this aspect. Methods Based on 16S rRNA sequencing data of bacterial taxa, MicroPITA picks representative samples for metagenomic analysis, effectively revealing how the development and progression of the HIV disease influences oral microbiota in MSM. Therefore, we collected samples from 11 HIV-negative and 44 HIV-positive MSM subjects (stage 0 was defined by HIV RNA positivity, but negative or indeterminate antibody status; stages 1, 2, and 3 were defined by CD4+ T lymphocyte counts ≥ 500, 200-499, and ≤ 200 or opportunistic infection) and selected 25 representative saliva samples (5 cases/stage) using MicroPITA. Metagenomic sequencing analysis were performed to explore whether positive HIV status changes salivary bacterial KEGG function and metabolic pathway in MSM. Results The core functions of oral microbiota were maintained across each of the five groups, including metabolism, genetic and environmental information processing. All HIV-positive groups displayed KEGG functions of abnormal proliferation, most prominently at stage 0, and others related to metabolism. Clustering relationship analysis tentatively identified functional relationships between groups, with bacterial function being more similar between stage 0-control groups and stage 1-2 groups, whereas the stage 3 group exhibited large functional changes. Although we identified most metabolic pathways as being common to all five groups, several unique pathways formed clusters for certain groups; the stage 0 group had several, while the stage 2 and 3 groups had few, such clusters. The abundance of K03046 was positively correlated with CD4 counts. Conclusion As HIV progresses, salivary bacterial function and metabolic pathways in MSM progressively changes, which may be related to HIV promoting abnormal energy metabolism and exacerbate pathogen virulence. Further, infection and drug resistance of acute stage and immune cell destruction of AIDS stage were abnormally increased, predicting an increased risk for MSM individuals to develop systemic and oral diseases.
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Affiliation(s)
- Ying Guo
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Wenjing Wang
- Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Yixi Yu
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Xintong Sun
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Baojin Zhang
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Yan Wang
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Jie Cao
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Shuo Wen
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Xin Wang
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Yuchen Li
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Siyu Cai
- Center for Clinical Epidemiology and Evidence-Based Medicine, Beijing Children’s Hospital, Capital Medical University, Beijing, China
| | - Ruojun Wu
- Harvard School of Dental Medicine, Boston, MA, United States
| | - Wenshan Duan
- Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Wei Xia
- Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Feili Wei
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Junyi Duan
- Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Haozhi Dong
- Department of Stomatology, Beijing Daxing District Hospital of Integrated Chinese and Western Medicine, Beijing, China
| | - Shan Guo
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Fengqiu Zhang
- Department of Periodontology, Beijing Stomatological Hospital, Capital Medical University, Beijing, China
| | - Zheng Sun
- Department of Oral Medicine, Beijing Stomatological Hospital, Capital Medical University, Beijing, China
| | - Xiaojie Huang
- Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
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2
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Frias MA, Pagano S, Bararpour N, Sidibé J, Kamau F, Fétaud-Lapierre V, Hudson P, Thomas A, Lecour S, Strijdom H, Vuilleumier N. People living with HIV display increased anti-apolipoprotein A1 auto-antibodies, inflammation, and kynurenine metabolites: a case-control study. Front Cardiovasc Med 2024; 11:1343361. [PMID: 38414919 PMCID: PMC10896987 DOI: 10.3389/fcvm.2024.1343361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/25/2024] [Indexed: 02/29/2024] Open
Abstract
Objective This study aimed to study the relationship between auto-antibodies against apolipoprotein A1 (anti-apoA1 IgG), human immunodeficiency virus (HIV) infection, anti-retroviral therapy (ART), and the tryptophan pathways in HIV-related cardiovascular disease. Design This case-control study conducted in South Africa consisted of control volunteers (n = 50), people living with HIV (PLWH) on ART (n = 50), and untreated PLWH (n = 44). Cardiovascular risk scores were determined, vascular measures were performed, and an extensive biochemical characterisation (routine, metabolomic, and inflammatory systemic profiles) was performed. Methods Anti-apoA1 IgG levels were assessed by an in-house ELISA. Inflammatory biomarkers were measured with the Meso Scale Discovery® platform, and kynurenine pathway metabolites were assessed using targeted metabolomic profiling conducted by liquid chromatography-multiple reaction monitoring/mass spectrometry (LC-MRM/MS). Results Cardiovascular risk scores and vascular measures exhibited similarities across the three groups, while important differences were observed in systemic inflammatory and tryptophan pathways. Anti-apoA1 IgG seropositivity rates were 15%, 40%, and 70% in control volunteers, PLWH ART-treated, and PLWH ART-naïve, respectively. Circulating anti-apoA1 IgG levels were significantly negatively associated with CD4+ cell counts and positively associated with viremia and pro-inflammatory biomarkers (IFNγ, TNFα, MIPα, ICAM-1, VCAM-1). While circulating anti-apoA1 IgG levels were associated with increased levels of kynurenine in both control volunteers and PLWH, the kynurenine/tryptophan ratio was significantly increased in PLWH ART-treated. Conclusion HIV infection increases the humoral response against apoA1, which is associated with established HIV severity criteria and kynurenine pathway activation.
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Affiliation(s)
- Miguel A. Frias
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals, Geneva, Switzerland
- Department of Medical Specialties, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Sabrina Pagano
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals, Geneva, Switzerland
- Department of Medical Specialties, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Nasim Bararpour
- Faculty Unit of Toxicology, CURML, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- Department of Genetics, Stanford University, Stanford, CA, United States
- Stanford Center for Genomics and Personalized Medicine, Stanford, CA, United States
| | - Jonathan Sidibé
- Faculty Unit of Toxicology, CURML, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Festus Kamau
- Centre for Cardiometabolic Research in Africa, Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Vanessa Fétaud-Lapierre
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals, Geneva, Switzerland
- Department of Medical Specialties, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Peter Hudson
- Cape Heart Institute, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Aurélien Thomas
- Faculty Unit of Toxicology, CURML, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- Unit of Forensic Toxicology and Chemistry, CURML, Lausanne and Geneva University Hospitals, Lausanne, Geneva, Switzerland
| | - Sandrine Lecour
- Cape Heart Institute, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Hans Strijdom
- Centre for Cardiometabolic Research in Africa, Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Nicolas Vuilleumier
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals, Geneva, Switzerland
- Department of Medical Specialties, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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3
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Grootveld M, Page G, Bhogadia M, Hunwin K, Edgar M. Updates and Original Case Studies Focused on the NMR-Linked Metabolomics Analysis of Human Oral Fluids Part III: Implementations for the Diagnosis of Non-Cancerous Disorders, Both Oral and Systemic. Metabolites 2023; 13:metabo13010066. [PMID: 36676991 PMCID: PMC9864626 DOI: 10.3390/metabo13010066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/03/2023] Open
Abstract
This communication represents Part III of our series of reports based on the applications of human saliva as a useful and conveniently collectable medium for the discovery, identification and monitoring of biomarkers, which are of some merit for the diagnosis of human diseases. Such biomarkers, or others reflecting the dysfunction of specific disease-associated metabolic pathways, may also be employed for the prognostic pathological tracking of these diseases. Part I of this series set the experimental and logistical groundwork for this report, and the preceding paper, Part II, featured the applications of newly developed metabolomics technologies to the diagnosis and severity grading of human cancer conditions, both oral and systemic. Clearly, there are many benefits, both scientific and economic, associated with the donation of human saliva samples (usually as whole mouth saliva) from humans consenting to and participating in investigations focused on the discovery of biomolecular markers of diseases. These include usually non-invasive collection protocols, relatively low cost when compared against blood sample collection, and no requirement for clinical supervision during collection episodes. This paper is centred on the employment and value of 'state-of-the-art' metabolomics technologies to the diagnosis and prognosis of a wide range of non-cancerous human diseases. Firstly, these include common oral diseases such as periodontal diseases (from type 1 (gingivitis) to type 4 (advanced periodontitis)), and dental caries. Secondly, a wide range of extra-oral (systemic) conditions are covered, most notably diabetes types 1 and 2, cardiovascular and neurological diseases, and Sjögren's syndrome, along with a series of viral infections, e.g., pharyngitis, influenza, HIV and COVID-19. Since the authors' major research interests lie in the area of the principles and applications of NMR-linked metabolomics techniques, many, but not all, of the studies reviewed were conducted using these technologies, with special attention being given to recommended protocols for their operation and management, for example, satisfactory experimental model designs; sample collection and laboratory processing techniques; the selection of sample-specific NMR pulse sequences for saliva analysis; and strategies available for the confirmation of resonance assignments for both endogenous and exogenous molecules in this biofluid. This article also features an original case study, which is focussed on the use of NMR-based salivary metabolomics techniques to provide some key biomarkers for the diagnosis of pharyngitis, and an example of how to 'police' such studies and to recognise participants who perceive that they actually have this disorder but do not from their metabolic profiles and multivariate analysis pattern-based clusterings. The biochemical and clinical significance of these multidimensional metabolomics investigations are discussed in detail.
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Li SY, Yin LB, Ding HB, Liu M, Lv JN, Li JQ, Wang J, Tang T, Fu YJ, Jiang YJ, Zhang ZN, Shang H. Altered lipid metabolites accelerate early dysfunction of T cells in HIV-infected rapid progressors by impairing mitochondrial function. Front Immunol 2023; 14:1106881. [PMID: 36875092 PMCID: PMC9981933 DOI: 10.3389/fimmu.2023.1106881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/27/2023] [Indexed: 02/19/2023] Open
Abstract
The complex mechanism of immune-system damage in HIV infection is incompletely understood. HIV-infected "rapid progressors" (RPs) have severe damage to the immune system early in HIV infection, which provides a "magnified" opportunity to study the interaction between HIV and the immune system. In this study, forty-four early HIV-infected patients (documented HIV acquisition within the previous 6 months) were enrolled. By study the plasma of 23 RPs (CD4+ T-cell count < 350 cells/µl within 1 year of infection) and 21 "normal progressors" (NPs; CD4+ T-cell count > 500 cells/μl after 1 year of infection), eleven lipid metabolites were identified that could distinguish most of the RPs from NPs using an unsupervised clustering method. Among them, the long chain fatty acid eicosenoate significantly inhibited the proliferation and secretion of cytokines and induced TIM-3 expression in CD4+ and CD8+ T cells. Eicosenoate also increased levels of reactive oxygen species (ROS) and decreased oxygen consumption rate (OCR) and mitochondrial mass in T cells, indicating impairment in mitochondrial function. In addition, we found that eicosenoate induced p53 expression in T cells, and inhibition of p53 effectively decreased mitochondrial ROS in T cells. More importantly, treatment of T cells with the mitochondrial-targeting antioxidant mito-TEMPO restored eicosenoate-induced T-cell functional impairment. These data suggest that the lipid metabolite eicosenoate inhibits immune T-cell function by increasing mitochondrial ROS by inducing p53 transcription. Our results provide a new mechanism of metabolite regulation of effector T-cell function and provides a potential therapeutic target for restoring T-cell function during HIV infection.
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Affiliation(s)
- Si-Yao Li
- National Health Commission (NHC) Key Laboratory of Acquired Immunodeficiency Syndrome (AIDS) Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Units of Medical Laboratory, Chinese Academy of Medical Sciences, Shenyang, China
| | - Lin-Bo Yin
- National Health Commission (NHC) Key Laboratory of Acquired Immunodeficiency Syndrome (AIDS) Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Department of Clinical Laboratory, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Liaoning, China
| | - Hai-Bo Ding
- National Health Commission (NHC) Key Laboratory of Acquired Immunodeficiency Syndrome (AIDS) Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Units of Medical Laboratory, Chinese Academy of Medical Sciences, Shenyang, China
| | - Mei Liu
- National Health Commission (NHC) Key Laboratory of Acquired Immunodeficiency Syndrome (AIDS) Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China.,Units of Medical Laboratory, Chinese Academy of Medical Sciences, Shenyang, China
| | - Jun-Nan Lv
- National Health Commission (NHC) Key Laboratory of Acquired Immunodeficiency Syndrome (AIDS) Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Units of Medical Laboratory, Chinese Academy of Medical Sciences, Shenyang, China
| | - Jia-Qi Li
- National Health Commission (NHC) Key Laboratory of Acquired Immunodeficiency Syndrome (AIDS) Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Units of Medical Laboratory, Chinese Academy of Medical Sciences, Shenyang, China
| | - Jing Wang
- National Health Commission (NHC) Key Laboratory of Acquired Immunodeficiency Syndrome (AIDS) Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Units of Medical Laboratory, Chinese Academy of Medical Sciences, Shenyang, China
| | - Tian Tang
- National Health Commission (NHC) Key Laboratory of Acquired Immunodeficiency Syndrome (AIDS) Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Units of Medical Laboratory, Chinese Academy of Medical Sciences, Shenyang, China
| | - Ya-Jing Fu
- National Health Commission (NHC) Key Laboratory of Acquired Immunodeficiency Syndrome (AIDS) Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Units of Medical Laboratory, Chinese Academy of Medical Sciences, Shenyang, China
| | - Yong-Jun Jiang
- National Health Commission (NHC) Key Laboratory of Acquired Immunodeficiency Syndrome (AIDS) Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Units of Medical Laboratory, Chinese Academy of Medical Sciences, Shenyang, China
| | - Zi-Ning Zhang
- National Health Commission (NHC) Key Laboratory of Acquired Immunodeficiency Syndrome (AIDS) Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Units of Medical Laboratory, Chinese Academy of Medical Sciences, Shenyang, China
| | - Hong Shang
- National Health Commission (NHC) Key Laboratory of Acquired Immunodeficiency Syndrome (AIDS) Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Units of Medical Laboratory, Chinese Academy of Medical Sciences, Shenyang, China
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5
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Andresen C, Boch T, Gegner HM, Mechtel N, Narr A, Birgin E, Rasbach E, Rahbari N, Trumpp A, Poschet G, Hübschmann D. Comparison of extraction methods for intracellular metabolomics of human tissues. Front Mol Biosci 2022; 9:932261. [PMID: 36090025 PMCID: PMC9461704 DOI: 10.3389/fmolb.2022.932261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/12/2022] [Indexed: 11/16/2022] Open
Abstract
Analyses of metabolic compounds inside cells or tissues provide high information content since they represent the endpoint of biological information flow and are a snapshot of the integration of many regulatory processes. However, quantification of the abundance of metabolites requires their careful extraction. We present a comprehensive study comparing ten extraction protocols in four human sample types (liver tissue, bone marrow, HL60, and HEK cells) aiming to detect and quantify up to 630 metabolites of different chemical classes. We show that the extraction efficiency and repeatability are highly variable across protocols, tissues, and chemical classes of metabolites. We used different quality metrics including the limit of detection and variability between replicates as well as the sum of concentrations as a global estimate of analytical repeatability of the extraction. The coverage of extracted metabolites depends on the used solvents, which has implications for the design of measurements of different sample types and metabolic compounds of interest. The benchmark dataset can be explored in an easy-to-use, interactive, and flexible online resource (R/shiny app MetaboExtract: http://www.metaboextract.shiny.dkfz.de) for context-specific selection of the optimal extraction method. Furthermore, data processing and conversion functionality underlying the shiny app are accessible as an R package: https://cran.r-project.org/package=MetAlyzer.
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Affiliation(s)
- Carolin Andresen
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
- Division of Stem Cells and Cancer, German Cancer Research Center and DKFZ-ZMBH Alliance, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Tobias Boch
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
- Division of Stem Cells and Cancer, German Cancer Research Center and DKFZ-ZMBH Alliance, Heidelberg, Germany
- Division of Personalized Medical Oncology, German Cancer Research Center, Heidelberg, Germany
- Department of Personalized Oncology, University Hospital Mannheim, University of Heidelberg, Mannheim, Germany
- DKFZ-Hector Cancer Institute at the University Medical Center Mannheim, Mannheim, Germany
| | - Hagen M. Gegner
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Nils Mechtel
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Andreas Narr
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
- Division of Stem Cells and Cancer, German Cancer Research Center and DKFZ-ZMBH Alliance, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Emrullah Birgin
- Department of Surgery, Medical Faculty Mannheim, Universitätsmedizin Mannheim, Heidelberg University, Mannheim, Germany
| | - Erik Rasbach
- Department of Surgery, Medical Faculty Mannheim, Universitätsmedizin Mannheim, Heidelberg University, Mannheim, Germany
| | - Nuh Rahbari
- Department of Surgery, Medical Faculty Mannheim, Universitätsmedizin Mannheim, Heidelberg University, Mannheim, Germany
| | - Andreas Trumpp
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
- Division of Stem Cells and Cancer, German Cancer Research Center and DKFZ-ZMBH Alliance, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Gernot Poschet
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Daniel Hübschmann
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Computational Oncology, Molecular Diagnostics Program, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- *Correspondence: Daniel Hübschmann,
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6
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Liebenberg C, Luies L, Williams AA. Metabolomics as a Tool to Investigate HIV/TB Co-Infection. Front Mol Biosci 2021; 8:692823. [PMID: 34746228 PMCID: PMC8565463 DOI: 10.3389/fmolb.2021.692823] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 10/04/2021] [Indexed: 12/28/2022] Open
Abstract
The HIV/AIDS (human immunodeficiency virus/acquired immunodeficiency syndrome) and tuberculosis (TB) pandemics are perpetuated by a significant global burden of HIV/TB co-infection. The synergy between HIV and Mycobacterium tuberculosis (Mtb) during co-infection of a host is well established. While this synergy is known to be driven by immunological deterioration, the metabolic mechanisms thereof remain poorly understood. Metabolomics has been applied to study various aspects of HIV and Mtb infection separately, yielding insights into infection- and treatment-induced metabolic adaptations experienced by the host. Despite the contributions that metabolomics has made to the field, this approach has not yet been systematically applied to characterize the HIV/TB co-infected state. Considering that limited HIV/TB co-infection metabolomics studies have been published to date, this review briefly summarizes what is known regarding the HIV/TB co-infection synergism from a conventional and metabolomics perspective. It then explores metabolomics as a tool for the improved characterization of HIV/TB co-infection in the context of previously published human-related HIV infection and TB investigations, respectively as well as for addressing the gaps in existing knowledge based on the similarities and deviating trends reported in these HIV infection and TB studies.
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7
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Gabazana Z, Sitole L. Raman-based metabonomics unravels metabolic changes related to a first-line tenofovir-based treatment in a small cohort of South African HIV-infected patients. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 248:119256. [PMID: 33310612 DOI: 10.1016/j.saa.2020.119256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/28/2020] [Accepted: 11/26/2020] [Indexed: 06/12/2023]
Abstract
In addition to immunological disorders, human immunodeficiency virus (HIV) also causes metabolic abnormalities. Though successful in viral suppression and immune restoration, continued use of antiretroviral therapy (ART) has also been linked to the development of several metabolic ailments. Currently, the only clinical markers used to manage and monitor the development of HIV-induced metabolic disorders, disease progression as well as observing individual's response to antiviral treatment are CD4 count, viral loads and several other single variable colometric assays. Despite the common use of these clinical markers, these markers remain unreliable and limited in the ability to monitor the development of metabolic disorders as well as monitor treatment response. Given these limitations, it is imperative to discover and develop reliable biological markers for overall HIV disease management. Here, Raman spectroscopy was used to profile metabolic changes in the plasma of 22 HIV+ receiving a first-line tenofovir-based combination antiretroviral therapy compared to their 8 HIV+ ART- and 10 HIV- counterparts. Multivariate statistical analysis was performed in order to classify the samples into their respective groups and to identify significantly altered metabolites between the control and experimental groups. Orthogonal Projections to Latent Structures Discriminant Analysis (OPLS-DA) discriminant analysis identified significant differences (p < 0.05) in 9 different metabolites. Alterations were identified in spectral regions associated with glucose (1124 cm-1), lipids/phospholipids (1116 cm-1, 1098 cm-1, 1077 cm-1), proteins (1120 cm-1), nucleic acids (1081 cm-1) and phenylalanine (1103 cm-1). Pathway analysis also revealed 3 significantly altered pathways. This study presented the reproducible nature of Raman spectroscopy in distinguishing between HIV-infected (treated and untreated) and uninfected blood plasma and allowed for the detection and identification of treatment induced metabolite changes. The results obtained in the study may, therefore, give insights into understanding the metabolic effect of HIV therapy.
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Affiliation(s)
- Zikhona Gabazana
- Department of Biochemistry, University of Johannesburg, PO Box 524, Auckland Park, Johannesburg 2006, South Africa
| | - Lungile Sitole
- Department of Biochemistry, University of Johannesburg, PO Box 524, Auckland Park, Johannesburg 2006, South Africa.
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8
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Gómez-Archila LG, Palomino-Schätzlein M, Zapata-Builes W, Galeano E. Development of an optimized method for processing peripheral blood mononuclear cells for 1H-nuclear magnetic resonance-based metabolomic profiling. PLoS One 2021; 16:e0247668. [PMID: 33630921 PMCID: PMC7906414 DOI: 10.1371/journal.pone.0247668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 02/11/2021] [Indexed: 01/04/2023] Open
Abstract
Human peripheral blood mononuclear cells (PBMCs) are part of the innate and adaptive immune system, and form a critical interface between both systems. Studying the metabolic profile of PBMC could provide valuable information about the response to pathogens, toxins or cancer, the detection of drug toxicity, in drug discovery and cell replacement therapy. The primary purpose of this study was to develop an improved processing method for PBMCs metabolomic profiling with nuclear magnetic resonance (NMR) spectroscopy. To this end, an experimental design was applied to develop an alternative method to process PBMCs at low concentrations. The design included the isolation of PBMCs from the whole blood of four different volunteers, of whom 27 cell samples were processed by two different techniques for quenching and extraction of metabolites: a traditional one using organic solvents and an alternative one employing a high-intensity ultrasound probe, the latter with a variation that includes the use of deproteinizing filters. Finally, all the samples were characterized by 1H-NMR and the metabolomic profiles were compared by the method. As a result, two new methods for PBMCs processing, called Ultrasound Method (UM) and Ultrasound and Ultrafiltration Method (UUM), are described and compared to the Folch Method (FM), which is the standard protocol for extracting metabolites from cell samples. We found that UM and UUM were superior to FM in terms of sensitivity, processing time, spectrum quality, amount of identifiable, quantifiable metabolites and reproducibility.
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Affiliation(s)
- León Gabriel Gómez-Archila
- Grupo de Investigación en Sustancias Bioactivas, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia (UdeA), Medellín, Colombia
| | | | - Wildeman Zapata-Builes
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia (UdeA), Medellín, Colombia
- Grupo Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medelín, Colombia
| | - Elkin Galeano
- Grupo de Investigación en Sustancias Bioactivas, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia (UdeA), Medellín, Colombia
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Diray-Arce J, Conti MG, Petrova B, Kanarek N, Angelidou A, Levy O. Integrative Metabolomics to Identify Molecular Signatures of Responses to Vaccines and Infections. Metabolites 2020; 10:E492. [PMID: 33266347 PMCID: PMC7760881 DOI: 10.3390/metabo10120492] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/24/2020] [Accepted: 11/30/2020] [Indexed: 12/16/2022] Open
Abstract
Approaches to the identification of metabolites have progressed from early biochemical pathway evaluation to modern high-dimensional metabolomics, a powerful tool to identify and characterize biomarkers of health and disease. In addition to its relevance to classic metabolic diseases, metabolomics has been key to the emergence of immunometabolism, an important area of study, as leukocytes generate and are impacted by key metabolites important to innate and adaptive immunity. Herein, we discuss the metabolomic signatures and pathways perturbed by the activation of the human immune system during infection and vaccination. For example, infection induces changes in lipid (e.g., free fatty acids, sphingolipids, and lysophosphatidylcholines) and amino acid pathways (e.g., tryptophan, serine, and threonine), while vaccination can trigger changes in carbohydrate and bile acid pathways. Amino acid, carbohydrate, lipid, and nucleotide metabolism is relevant to immunity and is perturbed by both infections and vaccinations. Metabolomics holds substantial promise to provide fresh insight into the molecular mechanisms underlying the host immune response. Its integration with other systems biology platforms will enhance studies of human health and disease.
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Affiliation(s)
- Joann Diray-Arce
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA 02115, USA; (M.G.C.); (A.A.)
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; (B.P.); (N.K.)
| | - Maria Giulia Conti
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA 02115, USA; (M.G.C.); (A.A.)
- Department of Maternal and Child Health, Sapienza University of Rome, 5, 00185 Rome, Italy
| | - Boryana Petrova
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; (B.P.); (N.K.)
- Department of Pathology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Naama Kanarek
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; (B.P.); (N.K.)
- Department of Pathology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Asimenia Angelidou
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA 02115, USA; (M.G.C.); (A.A.)
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; (B.P.); (N.K.)
- Department of Neonatology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Ofer Levy
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA 02115, USA; (M.G.C.); (A.A.)
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; (B.P.); (N.K.)
- Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA
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10
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Cognitive Effects of a Ketogenic Diet on Neurocognitive Impairment in Adults Aging With HIV: A Pilot Study. J Assoc Nurses AIDS Care 2020; 31:312-324. [PMID: 31725105 PMCID: PMC7883774 DOI: 10.1097/jnc.0000000000000110] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We assessed a ketogenic diet (KD) intervention protocol and the cognitive effects of KD in older adults with HIV-associated neurocognitive impairment. Adults older than 50 years and living with HIV and mild-to-moderate neurocognitive impairment were randomized to either a KD or a patient-choice diet for 12 weeks followed by a 6-week washout period. A neurocognitive battery was administered at baseline, Week 12, and Week 18. Paired t tests compared groups at baseline, and multivariate analyses of covariance were used to assess between-group differences on primary outcome variables at Weeks 12 and 18. We enrolled 17 participants, and 14 completed the study. No between-group baseline differences were noted. The KD group demonstrated improved executive function and speed of processing at Week 12, which were negated after participants resumed their usual diets. Our study supports the potential efficacy of a KD for the treatment of HIV-associated neurocognitive impairment.
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11
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Boyd A, Boccara F, Meynard JL, Ichou F, Bastard JP, Fellahi S, Samri A, Sauce D, Haddour N, Autran B, Cohen A, Girard PM, Capeau J. Serum Tryptophan-Derived Quinolinate and Indole-3-Acetate Are Associated With Carotid Intima-Media Thickness and its Evolution in HIV-Infected Treated Adults. Open Forum Infect Dis 2019; 6:ofz516. [PMID: 31890722 PMCID: PMC6929253 DOI: 10.1093/ofid/ofz516] [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: 10/25/2019] [Accepted: 12/05/2019] [Indexed: 11/14/2022] Open
Abstract
Background HIV-infected individuals undergoing effective antiretroviral therapy (ART) present an increased risk of atherosclerotic cardiovascular disease. We identified serum metabolites associated with carotid intima-media thickness (c-IMT) and its evolution. Methods One hundred forty-three hydrophilic serum metabolites were measured by ultraperformance liquid chromatography coupled with high-resolution mass spectrometry in 49 HIV+ ART+, 48 HIV+ ART-naïve and 50 HIV-negative, age-matched, never-smoking male triads. Metabolites differentially altered between groups ("features") were defined as having a Benjamini-Hochberg-adjusted P value <.05 from a t test and >0.25 log2 absolute mean fold change in metabolite levels. c-IMT was measured across 12 sites at inclusion in all individuals and at the carotid artery (cca) after a median of 5.1 years in 32 HIV+ ART+ individuals. The difference in c-IMT (cross-sectional analysis) and slope of cca-IMT regression/progression per year (longitudinal analysis) for each log10 (area) increase in metabolite level were estimated with linear regression. Results Compared with HIV-, metabolite features of HIV+ ART+ were increased N6,N6,N6-trimethyl-L-lysine and decreased ferulate and 5-hydroxy-L-tryptophan, whereas features of HIV+ ART-naïve were increased malate, kynurenine, 2-oxoglutarate, and indole-3-acetate and decreased succinate and 5-hydroxy-L-tryptophan. In HIV+ ART+ individuals, quinolinate and/or indole-3-acetate were positively associated with c-IMT (P < .03), cca-IMT (P < .03), and cca-IMT progression (P < .008). These associations were not observed in HIV+ ART-naïve or HIV-negative individuals. In HIV+ ART+ individuals, the metabolites xanthosine and uridine, from nucleotide metabolism, and g-butyrobetaine, from lysine/dietary choline degradation, were also positively or negatively associated with c-IMT and/or cca-IMT (all P < .01), but not its evolution. Conclusions In these highly selected HIV-positive ART-controlled males, 2 novel metabolites derived from tryptophan catabolism, indole-3-acetate and quinolinate, were associated with c-IMT and its progression.
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Affiliation(s)
- Anders Boyd
- Inserm UMR_S1136, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), Paris, France
| | - Franck Boccara
- Department of Cardiology, AP-HP, Hôpital Saint-Antoine, Paris, France.,Faculty of Medicine, Sorbonne Université, Inserm UMR_S938, ICAN, Paris, France
| | - Jean-Luc Meynard
- Department of Infectious Diseases, APHP, Hôpital Saint-Antoine, Paris, France
| | - Farid Ichou
- Institute of Cardiometabolism and Nutrition, ICAN, ICANalytics, Paris, France
| | - Jean-Philippe Bastard
- Faculty of Medicine, Sorbonne Université, Inserm UMR_S938, ICAN, Paris, France.,Department of Biochemistry, APHP, Hôpital Tenon, Paris, France
| | - Soraya Fellahi
- Faculty of Medicine, Sorbonne Université, Inserm UMR_S938, ICAN, Paris, France.,Department of Biochemistry, APHP, Hôpital Tenon, Paris, France
| | - Assia Samri
- Sorbonne Université, INSERM U1135, Centre d'Immunologie et des Maladies Infectieuses, Paris, France
| | - Delphine Sauce
- Sorbonne Université, INSERM U1135, Centre d'Immunologie et des Maladies Infectieuses, Paris, France
| | - Nabila Haddour
- Department of Cardiology, AP-HP, Hôpital Saint-Antoine, Paris, France
| | - Brigitte Autran
- Sorbonne Université, INSERM U1135, Centre d'Immunologie et des Maladies Infectieuses, Paris, France
| | - Ariel Cohen
- Department of Cardiology, AP-HP, Hôpital Saint-Antoine, Paris, France
| | - Pierre-Marie Girard
- Inserm UMR_S1136, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), Paris, France.,Department of Infectious Diseases, APHP, Hôpital Saint-Antoine, Paris, France
| | - Jacqueline Capeau
- Faculty of Medicine, Sorbonne Université, Inserm UMR_S938, ICAN, Paris, France
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12
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Naseer K, Saleem M, Ali S, Mirza B, Qazi J. Identification of new spectral signatures from hepatitis C virus infected human sera. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 222:117181. [PMID: 31202032 DOI: 10.1016/j.saa.2019.117181] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 05/01/2019] [Accepted: 05/26/2019] [Indexed: 05/27/2023]
Abstract
Hepatitis C virus (HCV) infection is one of the leading causes of morbidity and mortality worldwide. Mortality linked with HCV infection can be lowered with effective and prompt diagnosis in early stages of infection. In this study potential of Raman spectroscopy to differentiate between healthy and HCV infected serum samples was investigated. Clear differences were observed in the Raman spectra of HCV infected and healthy sera samples. Using the analysis of variance (ANOVA) and t-test (p < 0.001) on Raman spectra of diseased and healthy samples, we observed eleven unique Raman bands at 676, 825, 853, 936, 1029, 1105, 1155, 1305, 1620, 1654 and 1757 cm-1 associated with only HCV infected sera and have not been reported in earlier studies. In addition, six Raman bands at 556, 585, 716, 815, 1273 and 1142 cm-1were observed in healthy sera only. Three Raman bands at 1330, 1526 and 1572 cm-1 were observed in both type of samples but their intensity was drastically reduced in diseased samples. Various multivariate analysis techniques were employed to demonstrate the robustness of the results. We employed multivariate and unsupervised principal component analysis (PCA) in conjunction with supervised classification linear discriminant analysis (LDA), using ten-fold jackknife cross-validation, in order to develop effective diagnostic algorithm technique (PCA-LDA). Our PCA-LDA model yielded sufficient sensitivity and specificity i.e. correctly identified all infected samples included in this study. Ours results indicate that these unique Raman bands have the potential to be used as biomarkers for optical diagnosis of HCV infection.
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Affiliation(s)
- Khulla Naseer
- Faculty of Biological Sciences, Qauid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Saleem
- Agri. & Biophotonics Division, National Institute of Laser and Optronics (NILOP), Lehtrar Road, Islamabad, Pakistan
| | - Safdar Ali
- Directorate General National Repository, P.O. Box 1175, Islamabad, Pakistan
| | - Bushra Mirza
- Faculty of Biological Sciences, Qauid-i-Azam University, Islamabad, Pakistan
| | - Javaria Qazi
- Faculty of Biological Sciences, Qauid-i-Azam University, Islamabad, Pakistan.
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13
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Sitole LJ, Tugizimana F, Meyer D. Multi-platform metabonomics unravel amino acids as markers of HIV/combination antiretroviral therapy-induced oxidative stress. J Pharm Biomed Anal 2019; 176:112796. [PMID: 31398507 DOI: 10.1016/j.jpba.2019.112796] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 07/29/2019] [Indexed: 01/14/2023]
Abstract
Infection by the human immunodeficiency virus (HIV) elicits an immune response wherein neutrophils produce reactive oxygen species (ROS) to defend against pathogen invasion. Consequently, disproportionate levels of ROS in relation to antioxidants lead to oxidative stress (OS), which plays a key role in HIV disease progression and pathogenesis. There is a close relationship between oxidative stress status and HIV infection/progression, both separately and in the presence of combination antiretroviral therapy (cART). Biomarkers of oxidative stress present an additional means of monitoring HIV disease progression and/or management. Thus, the objective of this study was to apply untargeted nuclear magnetic resonance (NMR)-based metabonomics followed by targeted quantitative gas chromatography-mass spectrometry (GC/MS) analyses to identify predictors of oxidative stress in HIV infected individuals, with or without cART. Untargeted NMR-based metabonomics allowed a global profiling of metabolic perturbations in HIV-infected sera. The cohort consisted of 21 HIV-negative control subjects (HIV-) and 113 HIV-infected individuals, of which 100 were on cART. Significant differences in metabolic features corresponding to changes in glucose, lipids, phenylalanine, glutamic acid, aspartic acid and branched amino acids were observed, which point to oxidative stress and insulin resistance. To further confirm oxidative stress, targeted GC/MS-based metabonomics, performed in succession, allowed for a quantitative description of a total of 9 oxidative stress-related metabolites. Significant up-regulation of aspartic acid, phenylalanine and glutamic acid were observed in the HIV-infected cohorts as compared to controls. Tryptophan and tyrosine were down-regulated whereas cystine levels were increased in HIV-infected and untreated individuals as compared to both HIV treated and negative control subjects. Pathway analysis also revealed 11 metabolic pathways to be significantly altered by infection and/or treatment. These pathways included aminoacyl-tRNA biosynthesis, nitrogen metabolism and phenylalanine, tyrosine and tryptophan biosynthesis. This pilot study demonstrated the use of multiplatform metabonomic strategies to elucidate metabolic markers that would be essential in predicting HIV/cART-induced oxidative stress. This could aid and contribute in HIV treatment and management programmes.
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Affiliation(s)
- Lungile J Sitole
- Department of Biochemistry, University of Johannesburg, Johannesburg 2006, South Africa.
| | - Fidele Tugizimana
- Department of Biochemistry, University of Johannesburg, Johannesburg 2006, South Africa
| | - Debra Meyer
- Department of Biochemistry, University of Johannesburg, Johannesburg 2006, South Africa
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14
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Glutaminolysis and lipoproteins are key factors in late immune recovery in successfully treated HIV-infected patients. Clin Sci (Lond) 2019; 133:997-1010. [PMID: 30952809 DOI: 10.1042/cs20190111] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 12/19/2022]
Abstract
The immunological, biochemical and molecular mechanisms associated with poor immune recovery are far from known, and metabolomic profiling offers additional value to traditional soluble markers. Here, we present novel and relevant data that could contribute to better understanding of the molecular mechanisms preceding a discordant response and HIV progression under suppressive combined antiretroviral therapy (cART). Integrated data from nuclear magnetic resonance (NMR)-based lipoprotein profiles, mass spectrometry (MS)-based metabolomics and soluble plasma biomarkers help to build prognostic and immunological progression tools that enable the differentiation of HIV-infected subjects based on their immune recovery status after 96 weeks of suppressive cART. The metabolomic signature of ART-naïve HIV subjects with a subsequent late immune recovery is the expression of pro-inflammatory molecules and glutaminolysis, which is likely related to elevate T-cell turnover in these patients. The knowledge about how these metabolic pathways are interconnected and regulated provides new targets for future therapeutic interventions not only in HIV infection but also in other metabolic disorders such as human cancers where glutaminolysis is the alternative pathway for energy production in tumor cells to meet their requirement of rapid proliferation.
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15
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Zhou YJ, Li LS, Sun JL, Guan K, Wei JF. 1H NMR-based metabolomic study of metabolic profiling for pollinosis. World Allergy Organ J 2019; 12:100005. [PMID: 30937130 PMCID: PMC6439407 DOI: 10.1016/j.waojou.2018.11.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/13/2018] [Accepted: 11/28/2018] [Indexed: 01/07/2023] Open
Abstract
Background Allergic rhinitis is the main symptom of pollinosis, relieved by non-specific treatment universally. This study aimed to find the changes of serum metabolites between the seizure and remission periods of pollinosis and provide assistance in the diagnosis and/or therapy. Methods Metabonomics based on 1H nuclear magnetic resonance (NMR) was used to study the 37 serum samples of pollinosis patients. Results We believed that the decreased levels of isoleutine, leutine, valine, 3-hydroxybutyric acid, allo-threonine, alanine, methionine, glutamine, lysine, glycine, l-tyrosine, histidine, phenylalanine, lactate, acetate, O-acetylcholine, creatine and creatinine and the increased level of N-acetylglutamine at the seizure stage were statistically significant. Conclusions Pollinosis could change the metabolic profiles of energy, amino acid and lipid in patients, which might be the diagnosis and/or prognosis markers for hay fever patients.
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Key Words
- Amino acid
- Energy
- FIDs, free induction decay
- Lipid metabolism
- Metabonomics
- NMR, nuclear magnetic resonance
- OPLS-DA, orthogonal partial least squares discriminant analysis
- OSC-PLS-DA, orthogonal signal correction-partial least squares discriminant analysis
- PBS, phosphate buffer solution
- PCA, principle component analysis
- Pollinosis
- SD, standard deviation
- SIT, allergen-specific immunotherapy
- SLE, systemic lupus erythematosus
- TCA, tricarboxylic acid cycle
- TSP, 3-trimethylsilyl-propionic acid
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Affiliation(s)
- Yan-Jun Zhou
- Department of Allergy, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan Wangfujing Dongcheng District, Dongcheng, Beijing, 100730, PR China.,Research Division of Clinical Pharmacology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, PR China
| | - Li-Sha Li
- Department of Allergy, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan Wangfujing Dongcheng District, Dongcheng, Beijing, 100730, PR China.,Beijing Key Laboratory of Precision Medicine for Diagnosis and Treatment on Allergic Diseases, Beijing 100730, PR China
| | - Jin-Lu Sun
- Department of Allergy, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan Wangfujing Dongcheng District, Dongcheng, Beijing, 100730, PR China.,Beijing Key Laboratory of Precision Medicine for Diagnosis and Treatment on Allergic Diseases, Beijing 100730, PR China
| | - Kai Guan
- Department of Allergy, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan Wangfujing Dongcheng District, Dongcheng, Beijing, 100730, PR China.,Beijing Key Laboratory of Precision Medicine for Diagnosis and Treatment on Allergic Diseases, Beijing 100730, PR China
| | - Ji-Fu Wei
- Research Division of Clinical Pharmacology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, PR China
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16
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Williams AA, Sitole LJ, Meyer D. HIV/HAART-associated oxidative stress is detectable by metabonomics. MOLECULAR BIOSYSTEMS 2018; 13:2202-2217. [PMID: 28920117 DOI: 10.1039/c7mb00336f] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Chronic human immunodeficiency virus (HIV) infection, separately and in combination with highly active antiretroviral therapy (HAART) is closely associated with oxidative stress (OS). Most studies demonstrating redox imbalances in HIV-infected individuals have done so using conventional biochemical methodologies. The limited simultaneous detection of multiple OS markers within one sample is a major drawback of these methodologies and can be addressed through the use of metabonomics. HIV-metabonomic studies utilizing biofluids from HAART cohorts as the investigative source, are on the increase. Data from many of these studies identified metabolic markers indicative of HIV-induced OS, usually as an outcome of an untargeted metabonomics study. Untargeted studies cast a wide net for any and all detectable metabolites in complex mixtures. Given the prevalence of OS during HIV infection and antiviral treatment, it is perhaps not surprising that indicators of this malady would become evident during metabolite identification. At times, targeted studies for specific (non-OS) metabolites would also yield OS markers as an outcome. This review examines the findings of these studies by first providing the necessary background information on OS and the main ways in which free radicals/reactive oxygen species (ROS) produced during OS, cause biomolecular damage. This is followed by information on the biomarkers which come about as a result of free radical damage and the techniques used for assaying these stress indicators. The established links between elevated ROS and lowered antioxidants during HIV infection and the subsequent use of HAART is then presented followed by a review of the OS markers detected in HIV metabonomic studies to date. We identify gaps in HIV/HAART-associated OS research and finally suggest how these research gaps can be addressed through metabonomic analysis, specifically targeting the multiple markers of HIV-induced OS.
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Affiliation(s)
- Aurelia A Williams
- Human Metabolomics, North-West University, Private Bag X6001, Box 269, Potchefstroom, 2531, South Africa
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17
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Zeolitic imidazolate framework-based biosensor for detection of HIV-1 DNA. Anal Biochem 2018; 546:5-9. [DOI: 10.1016/j.ab.2018.01.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/16/2018] [Accepted: 01/19/2018] [Indexed: 01/11/2023]
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18
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A baseline metabolomic signature is associated with immunological CD4+ T-cell recovery after 36 months of antiretroviral therapy in HIV-infected patients. AIDS 2018; 32:565-573. [PMID: 29280761 PMCID: PMC5844590 DOI: 10.1097/qad.0000000000001730] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Objectives: Poor immunological recovery in treated HIV-infected patients is associated with greater morbidity and mortality. To date, predictive biomarkers of this incomplete immune reconstitution have not been established. We aimed to identify a baseline metabolomic signature associated with a poor immunological recovery after antiretroviral therapy (ART) to envisage the underlying mechanistic pathways that influence the treatment response. Design: This was a multicentre, prospective cohort study in ART-naive and a pre-ART low nadir (<200 cells/μl) HIV-infected patients (n = 64). Methods: We obtained clinical data and metabolomic profiles for each individual, in which low molecular weight metabolites, lipids and lipoproteins (including particle concentrations and sizes) were measured by NMR spectroscopy. Immunological recovery was defined as reaching CD4+ T-cell count at least 250 cells/μl after 36 months of virologically successful ART. We used univariate comparisons, Random Forest test and receiver-operating characteristic curves to identify and evaluate the predictive factors of immunological recovery after treatment. Results: HIV-infected patients with a baseline metabolic pattern characterized by high levels of large high density lipoprotein (HDL) particles, HDL cholesterol and larger sizes of low density lipoprotein particles had a better immunological recovery after treatment. Conversely, patients with high ratios of non-HDL lipoprotein particles did not experience this full recovery. Medium very-low-density lipoprotein particles and glucose increased the classification power of the multivariate model despite not showing any significant differences between the two groups. Conclusion: In HIV-infected patients, a baseline healthier metabolomic profile is related to a better response to ART where the lipoprotein profile, mainly large HDL particles, may play a key role.
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19
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Manchester M, Anand A. Metabolomics: Strategies to Define the Role of Metabolism in Virus Infection and Pathogenesis. Adv Virus Res 2017; 98:57-81. [PMID: 28433052 DOI: 10.1016/bs.aivir.2017.02.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Metabolomics is an analytical profiling technique for measuring and comparing large numbers of metabolites present in biological samples. Combining high-throughput analytical chemistry and multivariate data analysis, metabolomics offers a window on metabolic mechanisms. Because they intimately utilize and often rewire host metabolism, viruses are an excellent choice to study by metabolomics techniques. Studies of the effects of viruses on metabolism during replication in vitro and infection in animal models or human subjects have provided novel insights into these networks and provided new targets for therapy and biomarker development. Identifying the common metabolic pathways utilized by viruses has the potential to reveal those that can be targeted by broad-spectrum antiviral and vaccine approaches.
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Affiliation(s)
- Marianne Manchester
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland.
| | - Anisha Anand
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
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20
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Ludwig KR, Hummon AB. Mass spectrometry for the discovery of biomarkers of sepsis. MOLECULAR BIOSYSTEMS 2017; 13:648-664. [PMID: 28207922 PMCID: PMC5373965 DOI: 10.1039/c6mb00656f] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Sepsis is a serious medical condition that occurs in 30% of patients in intensive care units (ICUs). Early detection of sepsis is key to prevent its progression to severe sepsis and septic shock, which can cause organ failure and death. Diagnostic criteria for sepsis are nonspecific and hinder a timely diagnosis in patients. Therefore, there is currently a large effort to detect biomarkers that can aid physicians in the diagnosis and prognosis of sepsis. Mass spectrometry is often the method of choice to detect metabolomic and proteomic changes that occur during sepsis progression. These "omics" strategies allow for untargeted profiling of thousands of metabolites and proteins from human biological samples obtained from septic patients. Differential expression of or modifications to these metabolites and proteins can provide a more reliable source of diagnostic biomarkers for sepsis. Here, we focus on the current knowledge of biomarkers of sepsis and discuss the various mass spectrometric technologies used in their detection. We consider studies of the metabolome and proteome and summarize information regarding potential biomarkers in both general and neonatal sepsis.
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Affiliation(s)
- Katelyn R Ludwig
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA.
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA.
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21
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Nanoflow-Nanospray Mass Spectrometry Metabolomics Reveals Disruption of the Urinary Metabolite Profiles of HIV-Positive Patients on Combination Antiretroviral Therapy. J Acquir Immune Defic Syndr 2017; 74:e45-e53. [DOI: 10.1097/qai.0000000000001159] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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22
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Han F, Li G, Dai S, Huang J. Genome-wide metabolic model to improve understanding of CD4+ T cell metabolism, immunometabolism and application in drug design. MOLECULAR BIOSYSTEMS 2016; 12:431-43. [DOI: 10.1039/c5mb00480b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Model-based investigation of the metabolism and immunometabolism of CD4+ T cells (CD4T1670) and the application of CD4T1670 in drug development.
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Affiliation(s)
- Feifei Han
- State Key Laboratory of Genetic Resources and Evolution
- Kunming Institute of Zoology
- Chinese Academy of Sciences
- Kunming
- China
| | - Gonghua Li
- State Key Laboratory of Genetic Resources and Evolution
- Kunming Institute of Zoology
- Chinese Academy of Sciences
- Kunming
- China
| | - Shaoxing Dai
- State Key Laboratory of Genetic Resources and Evolution
- Kunming Institute of Zoology
- Chinese Academy of Sciences
- Kunming
- China
| | - Jingfei Huang
- State Key Laboratory of Genetic Resources and Evolution
- Kunming Institute of Zoology
- Chinese Academy of Sciences
- Kunming
- China
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23
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McKnight TR, Yoshihara HAI, Sitole LJ, Martin JN, Steffens F, Meyer D. A combined chemometric and quantitative NMR analysis of HIV/AIDS serum discloses metabolic alterations associated with disease status. MOLECULAR BIOSYSTEMS 2015; 10:2889-97. [PMID: 25105420 DOI: 10.1039/c4mb00347k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Individuals infected with the human immunodeficiency virus (HIV) often suffer from concomitant metabolic complications. Treatment with antiretroviral therapy has also been shown to alter the metabolism of patients. Although chemometric analysis of nuclear magnetic resonance (NMR) spectra of human sera can distinguish normal sera (HIVneg) from HIV-infected sera (HIVpos) and sera from HIV-infected patients on antiretroviral therapy (ART), quantitative analysis of the discriminating metabolites and their relationship to disease status has yet to be determined. The objectives of the study were to analyze NMR spectra of HIVneg, HIVpos, and ART serum samples with a combination of chemometric and quantitative methods and to compare the NMR data with disease status as measured by viral load and CD4 count. High-resolution magic angle spinning (HRMAS) NMR spectroscopy was performed on HIVneg (N = 10), HIVpos (N = 10), and ART (N = 10) serum samples. Chemometric linear discriminant analysis classified the three groups of spectra with 100% accuracy. Concentrations of 12 metabolites were determined with a semi-parametric metabolite quantification method named high-resolution quantum estimation (HR-QUEST). CD4 count was directly associated with alanine (p = 0.008), and inversely correlated with both glutamine (p = 0.017) and glucose (p = 0.022) concentrations. A multivariate linear model using alanine, glutamine and glucose as covariates demonstrated an association with CD4 count (p = 0.038). The combined chemometric and quantitative analysis of the data disclosed previously unknown associations between specific metabolites and disease status. The observed associations with CD4 count are consistent with metabolic disorders that are commonly seen in HIV-infected patients.
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Affiliation(s)
- Tracy R McKnight
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, CA, USA
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Gostner JM, Becker K, Kurz K, Fuchs D. Disturbed Amino Acid Metabolism in HIV: Association with Neuropsychiatric Symptoms. Front Psychiatry 2015; 6:97. [PMID: 26236243 PMCID: PMC4500866 DOI: 10.3389/fpsyt.2015.00097] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Accepted: 06/17/2015] [Indexed: 12/31/2022] Open
Abstract
Blood levels of the amino acid phenylalanine, as well as of the tryptophan breakdown product kynurenine, are found to be elevated in human immunodeficiency virus type 1 (HIV-1)-infected patients. Both essential amino acids, tryptophan and phenylalanine, are important precursor molecules for neurotransmitter biosynthesis. Thus, dysregulated amino acid metabolism may be related to disease-associated neuropsychiatric symptoms, such as development of depression, fatigue, and cognitive impairment. Increased phenylalanine/tyrosine and kynurenine/tryptophan ratios are associated with immune activation in patients with HIV-1 infection and decrease upon effective antiretroviral therapy. Recent large-scale metabolic studies have confirmed the crucial involvement of tryptophan and phenylalanine metabolism in HIV-associated disease. Herein, we summarize the current status of the role of tryptophan and phenylalanine metabolism in HIV disease and discuss how inflammatory stress-associated dysregulation of amino acid metabolism may be part of the pathophysiology of common HIV-associated neuropsychiatric conditions.
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Affiliation(s)
- Johanna M Gostner
- Division of Medical Biochemistry, Biocenter, Medical University of Innsbruck , Innsbruck , Austria
| | - Kathrin Becker
- Division of Biological Chemistry, Biocenter, Medical University of Innsbruck , Innsbruck , Austria
| | - Katharina Kurz
- Department of Internal Medicine VI, Medical University of Innsbruck , Innsbruck , Austria
| | - Dietmar Fuchs
- Division of Biological Chemistry, Biocenter, Medical University of Innsbruck , Innsbruck , Austria
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Glutamate and lipid metabolic perturbation in the hippocampi of asymptomatic borna disease virus-infected horses. PLoS One 2014; 9:e99752. [PMID: 24956478 PMCID: PMC4067290 DOI: 10.1371/journal.pone.0099752] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 05/19/2014] [Indexed: 11/19/2022] Open
Abstract
Borna disease virus (BDV) is a neurotropic, enveloped, non-segmented, negative-stranded RNA virus that infects a wide variety of vertebrate species from birds to humans across a broad global geographic distribution. Animal symptomatology range from asymptomatic infection to behavioral abnormalities to acute meningoencephalitis. Asymptomatic BDV infection has been shown to be more frequent than conventionally estimated. However, the molecular mechanism(s) underyling asymptomatic BDV infection remain largely unknown. Here, based on real-time quantitative PCR and Western blotting, a total of 18 horse hippocampi were divided into BDV-infected (n = 8) and non-infected control (n = 10) groups. A gas chromatography coupled with mass spectrometry (GC-MS) metabolomic approach, in conjunction with multivariate statistical analysis, was used to characterize the hippocampal metabolic changes associated with asymptomatic BDV infection. Multivariate statistical analysis showed a significant discrimination between the BDV-infected and control groups. BDV-infected hippocampi were characterized by lower levels of D-myo-inositol-1-phosphate, glutamate, phosphoethanolamine, heptadecanoic acid, and linoleic acid in combination with a higher level of ammonia. These differential metabolites are primarily involved in glutamate and lipid metabolism. These finding provide an improved understanding of hippocampal changes associated with asymptomatic BDV infection.
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Sitole L, Steffens F, Krüger TPJ, Meyer D. Mid-ATR-FTIR spectroscopic profiling of HIV/AIDS sera for novel systems diagnostics in global health. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:513-23. [PMID: 24937213 DOI: 10.1089/omi.2013.0157] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Global health, whether in developed or developing countries, is in need of robust systems diagnostics for major diseases, such as HIV/AIDS, impacting the world populations. Fourier transform Infrared (FTIR) spectroscopy of serum is a quick and reagent-free methodology with which to analyze metabolic alterations such as those caused by disease or treatment. In this study, Attenuated Total Reflectance Fourier-Transform (ATR-FTIR) Spectroscopy was investigated as a means of distinguishing HIV-infected treatment-experienced (HIV(pos) ART(pos), n=39) and HIV-infected-treatment-naïve (HIV(pos) ART(neg), n=16) subjects from uninfected control subjects (n=30). Multivariate pattern recognition techniques, including partial least squares discriminant analysis (PLS-DA) and orthogonal partial least squares discriminant analysis (OPLS-DA), successfully distinguished sample classes, while univariate approaches identified significant differences (p<0.05) after Benjamini-Hochberg corrections. OPLS-DA discriminated between all groups with sensitivity, specificity, and accuracy of >90%. Compared to uninfected controls, HIV(pos) ART(pos) and HIV(pos) ART(neg) subjects displayed significant differences in spectral regions linked to lipids/fatty acids (3010 cm(-1)), carbohydrates (1299 cm(-1); 1498 cm(-1)), glucose (1035 cm(-1)), and proteins (1600 cm(-1); 1652 cm(-1)). These are all molecules shown by conventional biochemical analysis to be affected by HIV/ART interference. The biofluid metabolomics approach applied here successfully differentiated global metabolic profiles of HIV-infected patients and uninfected controls and detected potential biomarkers for development into indicators of host response to treatment and/or disease progression. Our findings therefore contribute to ongoing efforts for capacity-building in global health for robust omics science and systems diagnostics towards major diseases impacting population health.
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Affiliation(s)
- Lungile Sitole
- 1 Department of Biochemistry, University of Pretoria , Pretoria, South Africa
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Duarte IF, Diaz SO, Gil AM. NMR metabolomics of human blood and urine in disease research. J Pharm Biomed Anal 2014; 93:17-26. [DOI: 10.1016/j.jpba.2013.09.025] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 09/16/2013] [Accepted: 09/24/2013] [Indexed: 02/06/2023]
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Zhu Y, Cong W, Shen L, Wei H, Wang Y, Wang L, Ruan K, Wu F, Feng Y. Fecal metabonomic study of a polysaccharide, MDG-1 from Ophiopogon japonicus on diabetic mice based on gas chromatography/time-of-flight mass spectrometry (GC TOF/MS). ACTA ACUST UNITED AC 2014; 10:304-12. [DOI: 10.1039/c3mb70392d] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Abstract
PURPOSE OF REVIEW Activation of the immune system only occurs when stimulated cells generate sufficient energy to support their growth and proliferation. Moreover, efficient HIV-1 infection requires that CD4(+) T cells meet the energy demands involved in completing the different steps of the virus life cycle. In this review, we highlight recent studies revealing the importance of nutrient fuels, nucleotide metabolism and the oxygen microenvironment in regulating HIV-1 infection, T-cell differentiation and the generation of HIV-1-specific immune responses. RECENT FINDINGS Glucose uptake via the Glut1 glucose transporter is required for efficient HIV-1 infection of CD4(+) lymphocytes. Other nutrients can also be used as sources of energy and their utilization conditions the differentiation of CD4(+) T cells to distinct effector fates. The conversion of ATP to adenosine inhibits HIV-specific effector cells and the hydrolysis of dNTPs by SAMHD1 restricts infection. Furthermore, oxygen concentration modulates metabolic status, thereby altering T-cell differentiation and potential to mediate a specific immune response. SUMMARY The availability and use of energy resources in fluctuating environments regulate T-cell function and susceptibility to HIV-1 infection. Identification of the targets coordinating the selected metabolic pathways will advance new strategic avenues for controlling HIV-1 disease progression.
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Stollar V, Mensah V, Adams S, Li ML. Evolution of Sindbis virus with a low-methionine-resistant phenotype is dependent both on a pre-existing mutation and on the methionine concentration in the medium. PLoS One 2013; 8:e60504. [PMID: 23544150 PMCID: PMC3609753 DOI: 10.1371/journal.pone.0060504] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 02/27/2013] [Indexed: 11/30/2022] Open
Abstract
SVlm21 is a mutant of Sindbis virus which was isolated by serial passage of virus in mosquito cells maintained in low-methionine medium; it therefore has a low-methionine-resistant (LMR) phenotype. This phenotype requires mutations at nts 319 and 321; these mutations result in Arg to Leu and Ser to Cys changes at positions 87 and 88 respectively in the viral methyl transferase, nsP1. To better understand the genesis of SVlm21, we carried out serial passages of viruses having only one of these amino acid changes, but in mosquito cells maintained in normal methionine-medium. Whether the passage was begun with SV319 or with SV321, the dominant virus population which emerged always acquired the second SVlm21 amino acid change. However, when the passage was begun with virus having neither the nt 319 or the nt321 mutation, even after many passages neither of these mutations was seen in the passaged virus population. Virus with the LMR phenotype emerged earlier when the virus encoded a wild-type RDRP (passage 4) rather than the mutant RDRP encoded by SVpzf (passage 7). When the methionine concentration in the medium of mosquito cells was increased to 250 µM, more than 20 passages were required until the LMR phenotype predominated. Competition experiments were carried out to compare the relative fitness of SVlm21, SVwt, SV319 and SV321 to each other. Our results indicated that SVlm21 was dominant to SVwt, as well as to both SV319 and SV321. However, SV319 and SV321 were able to co-exist with SVwt implying that in these mixed infection the presence of SVwt inhibited the emergence of SVlm21. Finally, our experiments highlight how a virus population by mutation and selection can adapt to the intracellular concentration of a simple metabolite, S-adenosylmethionine.
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Affiliation(s)
- Victor Stollar
- Department of Biochemistry and Molecular Biology, UMDNJ-Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
- The Cancer Institute of New Jersey, New Brunswick, New Jersey, United States of America
| | - Virginia Mensah
- Department of Biochemistry and Molecular Biology, UMDNJ-Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
| | - Sandra Adams
- Department of Biology and Molecular Biology, Montclair State University, Montclair, New Jersey, United States of America
| | - Mei-Ling Li
- Department of Biochemistry and Molecular Biology, UMDNJ-Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
- * E-mail:
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Li ZC, Lai YH, Chen LL, Chen C, Xie Y, Dai Z, Zou XY. Identifying subcellular localizations of mammalian protein complexes based on graph theory with a random forest algorithm. MOLECULAR BIOSYSTEMS 2013; 9:658-67. [DOI: 10.1039/c3mb25451h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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