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Demicheva E, Dordiuk V, Polanco Espino F, Ushenin K, Aboushanab S, Shevyrin V, Buhler A, Mukhlynina E, Solovyova O, Danilova I, Kovaleva E. Advances in Mass Spectrometry-Based Blood Metabolomics Profiling for Non-Cancer Diseases: A Comprehensive Review. Metabolites 2024; 14:54. [PMID: 38248857 PMCID: PMC10820779 DOI: 10.3390/metabo14010054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/05/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
Blood metabolomics profiling using mass spectrometry has emerged as a powerful approach for investigating non-cancer diseases and understanding their underlying metabolic alterations. Blood, as a readily accessible physiological fluid, contains a diverse repertoire of metabolites derived from various physiological systems. Mass spectrometry offers a universal and precise analytical platform for the comprehensive analysis of blood metabolites, encompassing proteins, lipids, peptides, glycans, and immunoglobulins. In this comprehensive review, we present an overview of the research landscape in mass spectrometry-based blood metabolomics profiling. While the field of metabolomics research is primarily focused on cancer, this review specifically highlights studies related to non-cancer diseases, aiming to bring attention to valuable research that often remains overshadowed. Employing natural language processing methods, we processed 507 articles to provide insights into the application of metabolomic studies for specific diseases and physiological systems. The review encompasses a wide range of non-cancer diseases, with emphasis on cardiovascular disease, reproductive disease, diabetes, inflammation, and immunodeficiency states. By analyzing blood samples, researchers gain valuable insights into the metabolic perturbations associated with these diseases, potentially leading to the identification of novel biomarkers and the development of personalized therapeutic approaches. Furthermore, we provide a comprehensive overview of various mass spectrometry approaches utilized in blood metabolomics research, including GC-MS, LC-MS, and others discussing their advantages and limitations. To enhance the scope, we propose including recent review articles supporting the applicability of GC×GC-MS for metabolomics-based studies. This addition will contribute to a more exhaustive understanding of the available analytical techniques. The Integration of mass spectrometry-based blood profiling into clinical practice holds promise for improving disease diagnosis, treatment monitoring, and patient outcomes. By unraveling the complex metabolic alterations associated with non-cancer diseases, researchers and healthcare professionals can pave the way for precision medicine and personalized therapeutic interventions. Continuous advancements in mass spectrometry technology and data analysis methods will further enhance the potential of blood metabolomics profiling in non-cancer diseases, facilitating its translation from the laboratory to routine clinical application.
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Affiliation(s)
- Ekaterina Demicheva
- Institute of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620075, Russia; (V.D.); (F.P.E.); (K.U.); (A.B.); (E.M.); (O.S.); (I.D.)
- Institute of Immunology and Physiology of the Ural Branch of the Russian Academy of Sciences, Ekaterinburg 620049, Russia
| | - Vladislav Dordiuk
- Institute of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620075, Russia; (V.D.); (F.P.E.); (K.U.); (A.B.); (E.M.); (O.S.); (I.D.)
| | - Fernando Polanco Espino
- Institute of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620075, Russia; (V.D.); (F.P.E.); (K.U.); (A.B.); (E.M.); (O.S.); (I.D.)
| | - Konstantin Ushenin
- Institute of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620075, Russia; (V.D.); (F.P.E.); (K.U.); (A.B.); (E.M.); (O.S.); (I.D.)
- Autonomous Non-Profit Organization Artificial Intelligence Research Institute (AIRI), Moscow 105064, Russia
| | - Saied Aboushanab
- Institute of Chemical Engineering, Ural Federal University, Ekaterinburg 620002, Russia; (S.A.); (V.S.); (E.K.)
| | - Vadim Shevyrin
- Institute of Chemical Engineering, Ural Federal University, Ekaterinburg 620002, Russia; (S.A.); (V.S.); (E.K.)
| | - Aleksey Buhler
- Institute of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620075, Russia; (V.D.); (F.P.E.); (K.U.); (A.B.); (E.M.); (O.S.); (I.D.)
| | - Elena Mukhlynina
- Institute of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620075, Russia; (V.D.); (F.P.E.); (K.U.); (A.B.); (E.M.); (O.S.); (I.D.)
- Institute of Immunology and Physiology of the Ural Branch of the Russian Academy of Sciences, Ekaterinburg 620049, Russia
| | - Olga Solovyova
- Institute of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620075, Russia; (V.D.); (F.P.E.); (K.U.); (A.B.); (E.M.); (O.S.); (I.D.)
- Institute of Immunology and Physiology of the Ural Branch of the Russian Academy of Sciences, Ekaterinburg 620049, Russia
| | - Irina Danilova
- Institute of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620075, Russia; (V.D.); (F.P.E.); (K.U.); (A.B.); (E.M.); (O.S.); (I.D.)
- Institute of Immunology and Physiology of the Ural Branch of the Russian Academy of Sciences, Ekaterinburg 620049, Russia
| | - Elena Kovaleva
- Institute of Chemical Engineering, Ural Federal University, Ekaterinburg 620002, Russia; (S.A.); (V.S.); (E.K.)
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Wang YY, Zhen C, Hu W, Huang HH, Li YJ, Zhou MJ, Li J, Fu YL, Zhang P, Li XY, Yang T, Song JW, Fan X, Zou J, Meng SR, Qin YQ, Jiao YM, Xu R, Zhang JY, Zhou CB, Yuan JH, Huang L, Shi M, Cheng L, Wang FS, Zhang C. Elevated glutamate impedes anti-HIV-1 CD8 + T cell responses in HIV-1-infected individuals on antiretroviral therapy. Commun Biol 2023; 6:696. [PMID: 37419968 PMCID: PMC10328948 DOI: 10.1038/s42003-023-04975-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 05/24/2023] [Indexed: 07/09/2023] Open
Abstract
CD8 + T cells are essential for long-lasting HIV-1 control and have been harnessed to develop therapeutic and preventive approaches for people living with HIV-1 (PLWH). HIV-1 infection induces marked metabolic alterations. However, it is unclear whether these changes affect the anti-HIV function of CD8 + T cells. Here, we show that PLWH exhibit higher levels of plasma glutamate than healthy controls. In PLWH, glutamate levels positively correlate with HIV-1 reservoir and negatively correlate with the anti-HIV function of CD8 + T cells. Single-cell metabolic modeling reveals glutamate metabolism is surprisingly robust in virtual memory CD8 + T cells (TVM). We further confirmed that glutamate inhibits TVM cells function via the mTORC1 pathway in vitro. Our findings reveal an association between metabolic plasticity and CD8 + T cell-mediated HIV control, suggesting that glutamate metabolism can be exploited as a therapeutic target for the reversion of anti-HIV CD8 + T cell function in PLWH.
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Affiliation(s)
- You-Yuan Wang
- Medical School of Chinese PLA, Beijing, China
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Cheng Zhen
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Wei Hu
- Department of Emergency, Fifth Medical Center of Chinese PLA Hospital, Beijing, China
| | - Hui-Huang Huang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Yan-Jun Li
- Guangxi AIDS Clinical Treatment Centre, The Fourth People's Hospital of Nanning, Nanning, China
| | - Ming-Ju Zhou
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Jing Li
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Yu-Long Fu
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Peng Zhang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Xiao-Yu Li
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Tao Yang
- Medical School of Chinese PLA, Beijing, China
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Jin-Wen Song
- Medical School of Chinese PLA, Beijing, China
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Xing Fan
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Jun Zou
- Guangxi AIDS Clinical Treatment Centre, The Fourth People's Hospital of Nanning, Nanning, China
| | - Si-Run Meng
- Guangxi AIDS Clinical Treatment Centre, The Fourth People's Hospital of Nanning, Nanning, China
| | - Ya-Qin Qin
- Guangxi AIDS Clinical Treatment Centre, The Fourth People's Hospital of Nanning, Nanning, China
| | - Yan-Mei Jiao
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Ruonan Xu
- Medical School of Chinese PLA, Beijing, China
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Ji-Yuan Zhang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Chun-Bao Zhou
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Jin-Hong Yuan
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Lei Huang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Ming Shi
- Medical School of Chinese PLA, Beijing, China
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Liang Cheng
- Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Fu-Sheng Wang
- Medical School of Chinese PLA, Beijing, China.
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China.
- Guangxi AIDS Clinical Treatment Centre, The Fourth People's Hospital of Nanning, Nanning, China.
| | - Chao Zhang
- Medical School of Chinese PLA, Beijing, China.
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China.
- Guangxi AIDS Clinical Treatment Centre, The Fourth People's Hospital of Nanning, Nanning, China.
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Svensson Akusjärvi S, Krishnan S, Ambikan AT, Mikaeloff F, Munusamy Ponnan S, Vesterbacka J, Lourda M, Nowak P, Sönnerborg A, Neogi U. Role of myeloid cells in system-level immunometabolic dysregulation during prolonged successful HIV-1 treatment. AIDS 2023; 37:1023-1033. [PMID: 36779490 PMCID: PMC10155691 DOI: 10.1097/qad.0000000000003512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/19/2023] [Accepted: 02/01/2023] [Indexed: 02/14/2023]
Abstract
OBJECTIVE Why people with HIV-1 on ART (PWH ART ) display convoluted metabolism and immune cell functions during prolonged suppressive therapy is not well evaluated. In this study, we aimed to address this question using multiomics methodologies to investigate immunological and metabolic differences between PWH ART and HIV-1 negative individuals (HC). DESIGN Cross-sectional study. METHODS Untargeted and targeted metabolomics was performed using gas and liquid chromatography/mass spectrometry, and targeted proteomics using Olink inflammation panel on plasma samples. The cellular metabolic state was further investigated using flow cytometry and intracellular metabolic measurement in single-cell populations isolated by EasySep cell isolation. Finally, flow cytometry was performed for deep-immunophenotyping of mononuclear phagocytes. RESULTS We detected increased levels of glutamate, lactate, and pyruvate by plasma metabolomics and increased inflammatory markers (e.g. CCL20 and CCL7) in PWH ART compared to HC. The metabolite transporter detection by flow cytometry in T cells and monocytes indicated an increased expression of glucose transporter 1 (Glut1) and monocarboxylate transporter 1 (MCT-1) in PWH ART . Single cell-type metabolite measurement identified decreased glucose, glutamate, and lactate in monocytic cell populations in PWH ART . Deep-immunophenotyping of myeloid cell lineages subpopulations showed no difference in cell frequency, but expression levels of CCR5 were increased on classical monocytes and some dendritic cells. CONCLUSIONS Our data thus suggest that the myeloid cell populations potentially contribute significantly to the modulated metabolic environment during suppressive HIV-1 infection.
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Affiliation(s)
- Sara Svensson Akusjärvi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
| | - Shuba Krishnan
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
| | - Anoop T. Ambikan
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
| | - Flora Mikaeloff
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
| | - Sivasankaran Munusamy Ponnan
- HIV Vaccine Trials Network, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Centre, Seattle, USA
| | - Jan Vesterbacka
- Department of Medicine Huddinge (MedH), Karolinska Institutet, Stockholm
| | - Magda Lourda
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, ANA Futura, Campus Flemingsberg
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Piotr Nowak
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
- Department of Medicine Huddinge (MedH), Karolinska Institutet, Stockholm
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
- Department of Medicine Huddinge (MedH), Karolinska Institutet, Stockholm
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
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Mikaeloff F, Gelpi M, Benfeitas R, Knudsen AD, Vestad B, Høgh J, Hov JR, Benfield T, Murray D, Giske CG, Mardinoglu A, Trøseid M, Nielsen SD, Neogi U. Network-based multi-omics integration reveals metabolic at-risk profile within treated HIV-infection. eLife 2023; 12:82785. [PMID: 36794912 PMCID: PMC10017104 DOI: 10.7554/elife.82785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 02/15/2023] [Indexed: 02/17/2023] Open
Abstract
Multiomics technologies improve the biological understanding of health status in people living with HIV on antiretroviral therapy (PWH). Still, a systematic and in-depth characterization of metabolic risk profile during successful long-term treatment is lacking. Here, we used multi-omics (plasma lipidomic, metabolomic, and fecal 16 S microbiome) data-driven stratification and characterization to identify the metabolic at-risk profile within PWH. Through network analysis and similarity network fusion (SNF), we identified three groups of PWH (SNF-1-3): healthy (HC)-like (SNF-1), mild at-risk (SNF-3), and severe at-risk (SNF-2). The PWH in the SNF-2 (45%) had a severe at-risk metabolic profile with increased visceral adipose tissue, BMI, higher incidence of metabolic syndrome (MetS), and increased di- and triglycerides despite having higher CD4+ T-cell counts than the other two clusters. However, the HC-like and the severe at-risk group had a similar metabolic profile differing from HIV-negative controls (HNC), with dysregulation of amino acid metabolism. At the microbiome profile, the HC-like group had a lower α-diversity, a lower proportion of men having sex with men (MSM) and was enriched in Bacteroides. In contrast, in at-risk groups, there was an increase in Prevotella, with a high proportion of MSM, which could potentially lead to higher systemic inflammation and increased cardiometabolic risk profile. The multi-omics integrative analysis also revealed a complex microbial interplay of the microbiome-associated metabolites in PWH. Those severely at-risk clusters may benefit from personalized medicine and lifestyle intervention to improve their dysregulated metabolic traits, aiming to achieve healthier aging.
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Affiliation(s)
- Flora Mikaeloff
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska InstituteStockholmSweden
| | - Marco Gelpi
- Copenhagen University Hospital RigshospitaletCopenhagenDenmark
| | - Rui Benfeitas
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
| | | | - Beate Vestad
- Research Institute of Internal Medicine, Oslo University Hospital RikshospitaletOsloNorway
- Norwegian PSC Research Center, Oslo University Hospital RikshospitaletOsloNorway
| | - Julie Høgh
- Copenhagen University Hospital RigshospitaletCopenhagenDenmark
| | - Johannes R Hov
- Research Institute of Internal Medicine, Oslo University Hospital RikshospitaletOsloNorway
- Norwegian PSC Research Center, Oslo University Hospital RikshospitaletOsloNorway
- Institute of Clinical Medicine, University of OsloOsloNorway
| | - Thomas Benfield
- Department of Infectious Diseases, Copenhagen University Hospital – Amager and HvidovreHvidovreDenmark
| | - Daniel Murray
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of CopenhagenCopenhagenDenmark
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska InstitutetStockholmSweden
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH - Royal Institute of TechnologyStockholmSweden
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College LondonLondonUnited Kingdom
| | - Marius Trøseid
- Research Institute of Internal Medicine, Oslo University Hospital RikshospitaletOsloNorway
- Institute of Clinical MedicineOsloNorway
| | | | - Ujjwal Neogi
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska InstituteStockholmSweden
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Akusjärvi SS, Neogi U. Biological Aging in People Living with HIV on Successful Antiretroviral Therapy: Do They Age Faster? Curr HIV/AIDS Rep 2023. [PMID: 36695947 DOI: 10.1007/s11904-023-00646-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2023] [Indexed: 01/26/2023]
Abstract
PURPOSE OF REVIEW In the absence of a prophylactic/therapeutic vaccine or cure, the most amazing achievement in the battle against HIV was the discovery of effective, well-tolerated combination antiretroviral therapy (cART). The primary research question remains whether PLWH on prolonged successful therapy has accelerated, premature, or accentuated biological aging. In this review, we discuss the current understanding of the immunometabolic profile in PLWH, potentially associated with biological aging, and a better understanding of the mechanisms and temporal dynamics of biological aging in PLWH. RECENT FINDINGS Biological aging, defined by the epigenetic alterations analyzed by the DNA methylation pattern, has been reported in PLWH with cART that points towards epigenetic age acceleration. The hastened development of specific clinical geriatric syndromes like cardiovascular diseases, metabolic syndrome, cancers, liver diseases, neurocognitive diseases, persistent low-grade inflammation, and a shift toward glutamate metabolism in PLWH may potentiate a metabolic profile at-risk for accelerated aging.
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Isaguliants MG, Trotsenko I, Buonaguro FM. An overview of "Chronic viral infection and cancer, openings for vaccines" virtual symposium of the TechVac Network - December 16-17, 2021. Infect Agent Cancer 2022; 17:28. [PMID: 35804391 PMCID: PMC9263434 DOI: 10.1186/s13027-022-00436-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2022] [Indexed: 11/10/2022] Open
Abstract
This is a report on the research activities currently ongoing in virology, oncology and virus-associated cancers and possibilities of their treatment and prevention by vaccines and immunotherapies as outlined at the symposium “Chronic viral infection and cancer, openings for vaccines” virtually held on December 16–17, 2021. Experts from the various disciplines involved in the study of the complex relationships between solid tumors and viruses met to discuss recent developments in the field and to report their personal contributions to the specified topics. Secondary end point was to sustain the TECHVAC Network established in 2016 as a multidisciplinary work group specifically devoted to development of vaccines and immunotherapies against chronic viral infections and associated cancers, with the aim to identify areas of common interest, promote research cooperation, establish collaborative cross-border programs and projects, and to coordinate clinical and research activities.
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Affiliation(s)
- Maria G Isaguliants
- Riga Stradins University, Riga, Latvia. .,Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Ivan Trotsenko
- Peoples Friendship University of Russia (RUDN University), Moscow, Russia
| | - Franco M Buonaguro
- Molecular Biology and Viral Oncology, Department of Experimental Oncology, Istituto Nazionale Tumori Fond Pascale, Naples, Italy.
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Ambikan AT, Svensson-Akusjärvi S, Krishnan S, Sperk M, Nowak P, Vesterbacka J, Sönnerborg A, Benfeitas R, Neogi U. Genome-scale metabolic models for natural and long-term drug-induced viral control in HIV infection. Life Sci Alliance 2022; 5:5/9/e202201405. [PMID: 35537851 PMCID: PMC9095731 DOI: 10.26508/lsa.202201405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/02/2022] [Accepted: 05/02/2022] [Indexed: 12/21/2022] Open
Abstract
A system-level up-regulation of OXPHOS and glycolysis could play a role in latent reservoir dynamics and immunosenescence in HIV-1–infected individuals with long-term successful therapy. Genome-scale metabolic models (GSMMs) can provide novel insights into metabolic reprogramming during disease progression and therapeutic interventions. We developed a context-specific system-level GSMM of people living with HIV (PLWH) using global RNA sequencing data from PBMCs with suppressive viremia either by natural (elite controllers, PLWHEC) or drug-induced (PLWHART) control. This GSMM was compared with HIV-negative controls (HC) to provide a comprehensive systems-level metabo-transcriptomic characterization. Transcriptomic analysis identified up-regulation of oxidative phosphorylation as a characteristic of PLWHART, differentiating them from PLWHEC with dysregulated complexes I, III, and IV. The flux balance analysis identified altered flux in several intermediates of glycolysis including pyruvate, α-ketoglutarate, and glutamate, among others, in PLWHART. The in vitro pharmacological inhibition of OXPHOS complexes in a latent lymphocytic cell model (J-Lat 10.6) suggested a role for complex IV in latency reversal and immunosenescence. Furthermore, inhibition of complexes I/III/IV induced apoptosis, collectively indicating their contribution to reservoir dynamics.
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Affiliation(s)
- Anoop T Ambikan
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
| | - Sara Svensson-Akusjärvi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
| | - Shuba Krishnan
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
| | - Maike Sperk
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
| | - Piotr Nowak
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Campus Flemingsberg, Stockholm, Sweden.,Department of Medicine, Huddinge (MedH), Karolinska Institutet, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
| | - Jan Vesterbacka
- Department of Medicine, Huddinge (MedH), Karolinska Institutet, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Campus Flemingsberg, Stockholm, Sweden.,Department of Medicine, Huddinge (MedH), Karolinska Institutet, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
| | - Rui Benfeitas
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Campus Flemingsberg, Stockholm, Sweden .,Manipal Institute of Virology (MIV), Manipal Academy of Higher Education, Manipal, Karnataka, India
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8
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Allen CNS, Arjona SP, Santerre M, Sawaya BE. Hallmarks of Metabolic Reprogramming and Their Role in Viral Pathogenesis. Viruses 2022; 14:602. [PMID: 35337009 PMCID: PMC8955778 DOI: 10.3390/v14030602] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 02/07/2023] Open
Abstract
Metabolic reprogramming is a hallmark of cancer and has proven to be critical in viral infections. Metabolic reprogramming provides the cell with energy and biomass for large-scale biosynthesis. Based on studies of the cellular changes that contribute to metabolic reprogramming, seven main hallmarks can be identified: (1) increased glycolysis and lactic acid, (2) increased glutaminolysis, (3) increased pentose phosphate pathway, (4) mitochondrial changes, (5) increased lipid metabolism, (6) changes in amino acid metabolism, and (7) changes in other biosynthetic and bioenergetic pathways. Viruses depend on metabolic reprogramming to increase biomass to fuel viral genome replication and production of new virions. Viruses take advantage of the non-metabolic effects of metabolic reprogramming, creating an anti-apoptotic environment and evading the immune system. Other non-metabolic effects can negatively affect cellular function. Understanding the role metabolic reprogramming plays in viral pathogenesis may provide better therapeutic targets for antivirals.
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9
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Olund Villumsen S, Benfeitas R, Knudsen AD, Gelpi M, Høgh J, Thomsen MT, Murray D, Ullum H, Neogi U, Nielsen SD. Integrative Lipidomics and Metabolomics for System-Level Understanding of the Metabolic Syndrome in Long-Term Treated HIV-Infected Individuals. Front Immunol 2022; 12:742736. [PMID: 35095835 PMCID: PMC8791652 DOI: 10.3389/fimmu.2021.742736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 12/22/2021] [Indexed: 11/23/2022] Open
Abstract
People living with HIV (PLWH) require life-long anti-retroviral treatment and often present with comorbidities such as metabolic syndrome (MetS). Systematic lipidomic characterization and its association with the metabolism are currently missing. We included 100 PLWH with MetS and 100 without MetS from the Copenhagen Comorbidity in HIV Infection (COCOMO) cohort to examine whether and how lipidome profiles are associated with MetS in PLWH. We combined several standard biostatistical, machine learning, and network analysis techniques to investigate the lipidome systematically and comprehensively and its association with clinical parameters. Additionally, we generated weighted lipid-metabolite networks to understand the relationship between lipidomic profiles with those metabolites associated with MetS in PLWH. The lipidomic dataset consisted of 917 lipid species including 602 glycerolipids, 228 glycerophospholipids, 61 sphingolipids, and 26 steroids. With a consensus approach using four different statistical and machine learning methods, we observed 13 differentially abundant lipids between PLWH without MetS and PLWH with MetS, which mainly belongs to diacylglyceride (DAG, n = 2) and triacylglyceride (TAG, n = 11). The comprehensive network integration of the lipidomics and metabolomics data suggested interactions between specific glycerolipids' structural composition patterns and key metabolites involved in glutamate metabolism. Further integration of the clinical data with metabolomics and lipidomics resulted in the association of visceral adipose tissue (VAT) and exposure to earlier generations of antiretroviral therapy (ART). Our integrative omics data indicated disruption of glutamate and fatty acid metabolism, suggesting their involvement in the pathogenesis of PLWH with MetS. Alterations in the lipid homeostasis and glutaminolysis need clinical interventions to prevent accelerated aging in PLWH with MetS.
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Affiliation(s)
- Sofie Olund Villumsen
- Department of Infectious Diseases, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Rui Benfeitas
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Andreas Dehlbæk Knudsen
- Department of Infectious Diseases, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Marco Gelpi
- Department of Infectious Diseases, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Julie Høgh
- Department of Infectious Diseases, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Magda Teresa Thomsen
- Department of Infectious Diseases, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Daniel Murray
- Personalized Medicine of Infectious Complications in Immune Deficiency (PERSIMUNE), Rigshospitalet, Copenhagen, Denmark
| | - Henrik Ullum
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Ujjwal Neogi
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Stockholm, Sweden
- Manipal Institute of Virology (MIV), Manipal Academy of Higher Education, Manipal, India
| | - Susanne Dam Nielsen
- Department of Infectious Diseases, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
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Mikaeloff F, Svensson Akusjärvi S, Ikomey GM, Krishnan S, Sperk M, Gupta S, Magdaleno GDV, Escós A, Lyonga E, Okomo MC, Tagne CT, Babu H, Lorson CL, Végvári Á, Banerjea AC, Kele J, Hanna LE, Singh K, de Magalhães JP, Benfeitas R, Neogi U. Trans cohort metabolic reprogramming towards glutaminolysis in long-term successfully treated HIV-infection. Commun Biol 2022; 5:27. [PMID: 35017663 PMCID: PMC8752762 DOI: 10.1038/s42003-021-02985-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/16/2021] [Indexed: 12/20/2022] Open
Abstract
Despite successful combination antiretroviral therapy (cART), persistent low-grade immune activation together with inflammation and toxic antiretroviral drugs can lead to long-lasting metabolic flexibility and adaptation in people living with HIV (PLWH). Our study investigated alterations in the plasma metabolic profiles by comparing PLWH on long-term cART(>5 years) and matched HIV-negative controls (HC) in two cohorts from low- and middle-income countries (LMIC), Cameroon, and India, respectively, to understand the system-level dysregulation in HIV-infection. Using untargeted and targeted LC-MS/MS-based metabolic profiling and applying advanced system biology methods, an altered amino acid metabolism, more specifically to glutaminolysis in PLWH than HC were reported. A significantly lower level of neurosteroids was observed in both cohorts and could potentiate neurological impairments in PLWH. Further, modulation of cellular glutaminolysis promoted increased cell death and latency reversal in pre-monocytic HIV-1 latent cell model U1, which may be essential for the clearance of the inducible reservoir in HIV-integrated cells.
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Affiliation(s)
- Flora Mikaeloff
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
| | - Sara Svensson Akusjärvi
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
| | - George Mondinde Ikomey
- Center for the Study and Control of Communicable Diseases (CSCCD), Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, P.O. Box. 8445, Yaoundé, Cameroon
- Department of Microbiology, Haematology, Parasitology and Infectious Disease, Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, Yaoundé, Cameroon
| | - Shuba Krishnan
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
| | - Maike Sperk
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
| | - Soham Gupta
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
| | - Gustavo Daniel Vega Magdaleno
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Alejandra Escós
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
| | - Emilia Lyonga
- Center for the Study and Control of Communicable Diseases (CSCCD), Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, P.O. Box. 8445, Yaoundé, Cameroon
- Department of Microbiology, Haematology, Parasitology and Infectious Disease, Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, Yaoundé, Cameroon
| | - Marie Claire Okomo
- Center for the Study and Control of Communicable Diseases (CSCCD), Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, P.O. Box. 8445, Yaoundé, Cameroon
- Department of Microbiology, Haematology, Parasitology and Infectious Disease, Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, Yaoundé, Cameroon
| | - Claude Tayou Tagne
- Department of Microbiology, Haematology, Parasitology and Infectious Disease, Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, Yaoundé, Cameroon
| | - Hemalatha Babu
- Department of HIV/AIDS, National Institute for Research in Tuberculosis, ICMR, Chennai, 600031, India
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory Vaccine Center, Emory University, Atlanta, GA, 30329, USA
| | - Christian L Lorson
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, 65211, USA
| | - Ákos Végvári
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Akhil C Banerjea
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | - Julianna Kele
- Department of Physiology and Pharmacology, Neurovascular Biology and Health, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Luke Elizabeth Hanna
- Department of HIV/AIDS, National Institute for Research in Tuberculosis, ICMR, Chennai, 600031, India
| | - Kamal Singh
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, 65211, USA
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Rui Benfeitas
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, S-10691, Stockholm, Sweden
| | - Ujjwal Neogi
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm, Sweden.
- Manipal Institute of Virology (MIV), Manipal Academy of Higher Education, Manipal, Karnataka, India.
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