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Agamah FE, Ederveen THA, Skelton M, Martin DP, Chimusa ER, ’t Hoen PAC. Network-based integrative multi-omics approach reveals biosignatures specific to COVID-19 disease phases. Front Mol Biosci 2024; 11:1393240. [PMID: 39040605 PMCID: PMC11260748 DOI: 10.3389/fmolb.2024.1393240] [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: 02/28/2024] [Accepted: 05/22/2024] [Indexed: 07/24/2024] Open
Abstract
Background COVID-19 disease is characterized by a spectrum of disease phases (mild, moderate, and severe). Each disease phase is marked by changes in omics profiles with corresponding changes in the expression of features (biosignatures). However, integrative analysis of multiple omics data from different experiments across studies to investigate biosignatures at various disease phases is limited. Exploring an integrative multi-omics profile analysis through a network approach could be used to determine biosignatures associated with specific disease phases and enable the examination of the relationships between the biosignatures. Aim To identify and characterize biosignatures underlying various COVID-19 disease phases in an integrative multi-omics data analysis. Method We leveraged a multi-omics network-based approach to integrate transcriptomics, metabolomics, proteomics, and lipidomics data. The World Health Organization Ordinal Scale WHO Ordinal Scale was used as a disease severity reference to harmonize COVID-19 patient metadata across two studies with independent data. A unified COVID-19 knowledge graph was constructed by assembling a disease-specific interactome from the literature and databases. Disease-state specific omics-graphs were constructed by integrating multi-omics data with the unified COVID-19 knowledge graph. We expanded on the network layers of multiXrank, a random walk with restart on multilayer network algorithm, to explore disease state omics-specific graphs and perform enrichment analysis. Results Network analysis revealed the biosignatures involved in inducing chemokines and inflammatory responses as hubs in the severe and moderate disease phases. We observed distinct biosignatures between severe and moderate disease phases as compared to mild-moderate and mild-severe disease phases. Mild COVID-19 cases were characterized by a unique biosignature comprising C-C Motif Chemokine Ligand 4 (CCL4), and Interferon Regulatory Factor 1 (IRF1). Hepatocyte Growth Factor (HGF), Matrix Metallopeptidase 12 (MMP12), Interleukin 10 (IL10), Nuclear Factor Kappa B Subunit 1 (NFKB1), and suberoylcarnitine form hubs in the omics network that characterizes the moderate disease state. The severe cases were marked by biosignatures such as Signal Transducer and Activator of Transcription 1 (STAT1), Superoxide Dismutase 2 (SOD2), HGF, taurine, lysophosphatidylcholine, diacylglycerol, triglycerides, and sphingomyelin that characterize the disease state. Conclusion This study identified both biosignatures of different omics types enriched in disease-related pathways and their associated interactions (such as protein-protein, protein-transcript, protein-metabolite, transcript-metabolite, and lipid-lipid interactions) that are unique to mild, moderate, and severe COVID-19 disease states. These biosignatures include molecular features that underlie the observed clinical heterogeneity of COVID-19 and emphasize the need for disease-phase-specific treatment strategies. The approach implemented here can be used to find associations between transcripts, proteins, lipids, and metabolites in other diseases.
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Affiliation(s)
- Francis E. Agamah
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Thomas H. A. Ederveen
- Department of Medical BioSciences, Radboud University Medical Center Nijmegen, Nijmegen, Netherlands
| | - Michelle Skelton
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Darren P. Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Emile R. Chimusa
- Department of Applied Science, Faculty of Health and Life Sciences, Northumbria University, Newcastle, United Kingdom
| | - Peter A. C. ’t Hoen
- Department of Medical BioSciences, Radboud University Medical Center Nijmegen, Nijmegen, Netherlands
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Ji X, Ji HL. Metabolic signatures of acute respiratory distress syndrome: COVID versus non-COVID. Am J Physiol Lung Cell Mol Physiol 2024; 326:L596-L603. [PMID: 38469648 DOI: 10.1152/ajplung.00266.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 03/02/2024] [Accepted: 03/05/2024] [Indexed: 03/13/2024] Open
Abstract
Acute respiratory distress syndrome (ARDS) is a fatal pulmonary disorder characterized by severe hypoxia and inflammation. ARDS is commonly triggered by systemic and pulmonary infections, with bacteria and viruses. Notable pathogens include Pseudomonas aeruginosa, Streptococcus aureus, Enterobacter species, coronaviruses, influenza viruses, and herpesviruses. COVID-19 ARDS represents the latest etiological phenotype of the disease. The pathogenesis of ARDS caused by bacteria and viruses exhibits variations in host immune responses and lung mesenchymal injury. We postulate that the systemic and pulmonary metabolomics profiles of ARDS induced by COVID-19 pathogens may exhibit distinctions compared with those induced by other infectious agents. This review aims to compare metabolic signatures in blood and lung specimens specifically within the context of ARDS. Both prevalent and phenotype-specific metabolomic signatures, including but not limited to glycolysis, ketone body production, lipid oxidation, and dysregulation of the kynurenine pathways, were thoroughly examined in this review. The distinctions in metabolic signatures between COVID-19 and non-COVID ARDS have the potential to reveal new biomarkers, elucidate pathogenic mechanisms, identify druggable targets, and facilitate differential diagnosis in the future.
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Affiliation(s)
- Xiangming Ji
- Department of Nutrition, Georgia State University, Atlanta, Georgia, United States
| | - Hong-Long Ji
- Burn and Shock Trauma Research Institute, Stritch School of Medicine, Loyola University Chicago Health Sciences Division, Maywood, Illinois, United States
- Department of Surgery, Stritch School of Medicine, Loyola University Chicago Health Sciences Division, Maywood, Illinois, United States
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Mwangi VI, Netto RLA, Borba MGS, Santos GF, Lima GS, Machado LS, Yakubu MN, Val FFA, Sampaio VS, Sartim MA, Koolen HHF, Costa AG, Toméi MCM, Guimarães TP, Chaves AR, Vaz BG, Lacerda MVG, Monteiro WM, Gardinassi LG, Melo GC. Methylprednisolone therapy induces differential metabolic trajectories in severe COVID-19 patients. mSystems 2023; 8:e0072623. [PMID: 37874139 PMCID: PMC10734516 DOI: 10.1128/msystems.00726-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/17/2023] [Indexed: 10/25/2023] Open
Abstract
IMPORTANCE The SARS-CoV-2 virus infection in humans induces significant inflammatory and systemic reactions and complications of which corticosteroids like methylprednisolone have been recommended as treatment. Our understanding of the metabolic and metabolomic pathway dysregulations while using intravenous corticosteroids in COVID-19 is limited. This study will help enlighten the metabolic and metabolomic pathway dysregulations underlying high daily doses of intravenous methylprednisolone in COVID-19 patients compared to those receiving placebo. The information on key metabolites and pathways identified in this study together with the crosstalk with the inflammation and biochemistry components may be used, in the future, to leverage the use of methylprednisolone in any future pandemics from the coronavirus family.
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Affiliation(s)
- Victor I. Mwangi
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
| | - Rebeca L. A. Netto
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
| | - Mayla G. S. Borba
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
- Fundação de Medicina Tropical Heitor Vieira Dourado (FMT-HVD), Manaus, Amazonas, Brazil
| | - Gabriel F. Santos
- Laboratório de Cromatografia e Espectrometria de Massas, Instituto de Química, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Gesiane S. Lima
- Laboratório de Cromatografia e Espectrometria de Massas, Instituto de Química, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Lucas S. Machado
- Laboratório de Cromatografia e Espectrometria de Massas, Instituto de Química, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Michael N. Yakubu
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
| | - Fernando F. A. Val
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
- Fundação de Medicina Tropical Heitor Vieira Dourado (FMT-HVD), Manaus, Amazonas, Brazil
- Programa de Pós-Graduação em Ciência da Saúde, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brazil
- Programa de Pós-Graduação em Ciências do Movimento Humano, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brazil
| | - Vanderson S. Sampaio
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
- Fundação de Medicina Tropical Heitor Vieira Dourado (FMT-HVD), Manaus, Amazonas, Brazil
- Instituto Todos pela Saúde, São Paulo, São Paulo, Brazil
| | - Marco A. Sartim
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
- Fundação de Medicina Tropical Heitor Vieira Dourado (FMT-HVD), Manaus, Amazonas, Brazil
- Pró-reitoria de Pesquisa e Pós-graduação, Universidade Nilton Lins, Manaus, Amazonas, Brazil
| | - Hector H. F. Koolen
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
- Grupo de Pesquisa em Metabolômica e Espectrometria de Massas, Universidade do Estado do Amazonas, Manaus, Amazonas, Brazil
| | - Allyson G. Costa
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
- Fundação de Medicina Tropical Heitor Vieira Dourado (FMT-HVD), Manaus, Amazonas, Brazil
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brazil
- Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus, Amazonas, Brazil
- Escola de Enfermagem de Manaus, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brazil
- Programa de Pós-graduação em Ciências Aplicadas à Hematologia (PPGH-UEA/HEMOAM), Manaus, Amazonas, Brazil
| | - Maria C. M. Toméi
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás (UFG), Goiânia, Goiás, Brazil
| | - Tiago P. Guimarães
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás (UFG), Goiânia, Goiás, Brazil
| | - Andrea R. Chaves
- Laboratório de Cromatografia e Espectrometria de Massas, Instituto de Química, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Boniek G. Vaz
- Laboratório de Cromatografia e Espectrometria de Massas, Instituto de Química, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Marcus V. G. Lacerda
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
- Fundação de Medicina Tropical Heitor Vieira Dourado (FMT-HVD), Manaus, Amazonas, Brazil
- Instituto Leônidas & Maria Deane/Fundação Oswaldo Cruz (ILMD/Fiocruz Amazônia), Manaus, Amazonas, Brazil
| | - Wuelton M. Monteiro
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
- Fundação de Medicina Tropical Heitor Vieira Dourado (FMT-HVD), Manaus, Amazonas, Brazil
| | - Luiz G. Gardinassi
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás (UFG), Goiânia, Goiás, Brazil
| | - Gisely C. Melo
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
- Fundação de Medicina Tropical Heitor Vieira Dourado (FMT-HVD), Manaus, Amazonas, Brazil
- Programa de Pós-graduação em Ciências Aplicadas à Hematologia (PPGH-UEA/HEMOAM), Manaus, Amazonas, Brazil
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Palermo A, Li S, Ten Hoeve J, Chellappa A, Morris A, Dillon B, Ma F, Wang Y, Cao E, Shabane B, Acín-Perez R, Petcherski A, Lusis AJ, Hazen S, Shirihai OS, Pellegrini M, Arumugaswami V, Graeber TG, Deb A. A ketogenic diet can mitigate SARS-CoV-2 induced systemic reprogramming and inflammation. Commun Biol 2023; 6:1115. [PMID: 37923961 PMCID: PMC10624922 DOI: 10.1038/s42003-023-05478-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/17/2023] [Indexed: 11/06/2023] Open
Abstract
The ketogenic diet (KD) has demonstrated benefits in numerous clinical studies and animal models of disease in modulating the immune response and promoting a systemic anti-inflammatory state. Here we investigate the effects of a KD on systemic toxicity in mice following SARS-CoV-2 infection. Our data indicate that under KD, SARS-CoV-2 reduces weight loss with overall improved animal survival. Muted multi-organ transcriptional reprogramming and metabolism rewiring suggest that a KD initiates and mitigates systemic changes induced by the virus. We observed reduced metalloproteases and increased inflammatory homeostatic protein transcription in the heart, with decreased serum pro-inflammatory cytokines (i.e., TNF-α, IL-15, IL-22, G-CSF, M-CSF, MCP-1), metabolic markers of inflammation (i.e., kynurenine/tryptophane ratio), and inflammatory prostaglandins, indicative of reduced systemic inflammation in animals infected under a KD. Taken together, these data suggest that a KD can alter the transcriptional and metabolic response in animals following SARS-CoV-2 infection with improved mice health, reduced inflammation, and restored amino acid, nucleotide, lipid, and energy currency metabolism.
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Affiliation(s)
- Amelia Palermo
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- California Nanosystems Institute, University of California, Los Angeles, CA, 90095, USA
- UCLA Metabolomics Center, University of California, Los Angeles, CA, 90095, USA
- Crump Institute for Molecular Imaging, University of California, Los Angeles, CA, 90095, USA
| | - Shen Li
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- UCLA Cardiovascular Research Theme, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Department of Molecular, Cell and Developmental Biology, Division of Life Sciences, University of California, Los Angeles, CA, 90095, USA
- Eli & Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA
- Department of Genetics, David Geffen School of Medicine, Los Angeles, CA, 90095, USA
| | - Johanna Ten Hoeve
- California Nanosystems Institute, University of California, Los Angeles, CA, 90095, USA
- UCLA Metabolomics Center, University of California, Los Angeles, CA, 90095, USA
- Crump Institute for Molecular Imaging, University of California, Los Angeles, CA, 90095, USA
| | - Akshay Chellappa
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Alexandra Morris
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Barbara Dillon
- Department of Environment, Health and Safety, University of California, Los Angeles, CA, 90095, USA
| | - Feiyang Ma
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Yijie Wang
- UCLA Cardiovascular Research Theme, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Department of Molecular, Cell and Developmental Biology, Division of Life Sciences, University of California, Los Angeles, CA, 90095, USA
- Eli & Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA
- Department of Genetics, David Geffen School of Medicine, Los Angeles, CA, 90095, USA
| | - Edward Cao
- UCLA Cardiovascular Research Theme, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Department of Molecular, Cell and Developmental Biology, Division of Life Sciences, University of California, Los Angeles, CA, 90095, USA
- Eli & Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA
- Department of Genetics, David Geffen School of Medicine, Los Angeles, CA, 90095, USA
| | - Byourak Shabane
- Department of Medicine, Endocrinology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Rebeca Acín-Perez
- Department of Medicine, Endocrinology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Anton Petcherski
- Department of Medicine, Endocrinology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - A Jake Lusis
- California Nanosystems Institute, University of California, Los Angeles, CA, 90095, USA
- UCLA Cardiovascular Research Theme, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Stanley Hazen
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Orian S Shirihai
- California Nanosystems Institute, University of California, Los Angeles, CA, 90095, USA
- Department of Medicine, Endocrinology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, Division of Life Sciences, University of California, Los Angeles, CA, 90095, USA
- Eli & Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA
| | - Vaithilingaraja Arumugaswami
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Eli & Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, 90095, USA
| | - Thomas G Graeber
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
- California Nanosystems Institute, University of California, Los Angeles, CA, 90095, USA.
- UCLA Metabolomics Center, University of California, Los Angeles, CA, 90095, USA.
- Crump Institute for Molecular Imaging, University of California, Los Angeles, CA, 90095, USA.
- Eli & Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, 90095, USA.
| | - Arjun Deb
- California Nanosystems Institute, University of California, Los Angeles, CA, 90095, USA.
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
- UCLA Cardiovascular Research Theme, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
- Department of Molecular, Cell and Developmental Biology, Division of Life Sciences, University of California, Los Angeles, CA, 90095, USA.
- Eli & Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, 90095, USA.
- Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA.
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Ghini V, Meoni G, Vignoli A, Di Cesare F, Tenori L, Turano P, Luchinat C. Fingerprinting and profiling in metabolomics of biosamples. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2023; 138-139:105-135. [PMID: 38065666 DOI: 10.1016/j.pnmrs.2023.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/13/2023] [Accepted: 10/15/2023] [Indexed: 12/18/2023]
Abstract
This review focuses on metabolomics from an NMR point of view. It attempts to cover the broad scope of metabolomics and describes the NMR experiments that are most suitable for each sample type. It is addressed not only to NMR specialists, but to all researchers who wish to approach metabolomics with a clear idea of what they wish to achieve but not necessarily with a deep knowledge of NMR. For this reason, some technical parts may seem a bit naïve to the experts. The review starts by describing standard metabolomics procedures, which imply the use of a dedicated 600 MHz instrument and of four properly standardized 1D experiments. Standardization is a must if one wants to directly compare NMR results obtained in different labs. A brief mention is also made of standardized pre-analytical procedures, which are even more essential. Attention is paid to the distinction between fingerprinting and profiling, and the advantages and disadvantages of fingerprinting are clarified. This aspect is often not fully appreciated. Then profiling, and the associated problems of signal assignment and quantitation, are discussed. We also describe less conventional approaches, such as the use of different magnetic fields, the use of signal enhancement techniques to increase sensitivity, and the potential of field-shuttling NMR. A few examples of biomedical applications are also given, again with the focus on NMR techniques that are most suitable to achieve each particular goal, including a description of the most common heteronuclear experiments. Finally, the growing applications of metabolomics to foodstuffs are described.
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Affiliation(s)
- Veronica Ghini
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Gaia Meoni
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Alessia Vignoli
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Francesca Di Cesare
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Leonardo Tenori
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, Italy
| | - Paola Turano
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, Italy.
| | - Claudio Luchinat
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, Italy; Giotto Biotech S.r.l., Sesto Fiorentino, Italy.
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6
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El-Derany MO, Hanna DMF, Youshia J, Elmowafy E, Farag MA, Azab SS. Metabolomics-directed nanotechnology in viral diseases management: COVID-19 a case study. Pharmacol Rep 2023; 75:1045-1065. [PMID: 37587394 PMCID: PMC10539420 DOI: 10.1007/s43440-023-00517-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 07/28/2023] [Accepted: 07/28/2023] [Indexed: 08/18/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently regarded as the twenty-first century's plague accounting for coronavirus disease 2019 (COVID-19). Besides its reported symptoms affecting the respiratory tract, it was found to alter several metabolic pathways inside the body. Nanoparticles proved to combat viral infections including COVID-19 to demonstrate great success in developing vaccines based on mRNA technology. However, various types of nanoparticles can affect the host metabolome. Considering the increasing proportion of nano-based vaccines, this review compiles and analyses how COVID-19 and nanoparticles affect lipids, amino acids, and carbohydrates metabolism. A search was conducted on PubMed, ScienceDirect, Web of Science for available information on the interrelationship between metabolomics and immunity in the context of SARS-CoV-2 infection and the effect of nanoparticles on metabolite levels. It was clear that SARS-CoV-2 disrupted several pathways to ensure a sufficient supply of its building blocks to facilitate its replication. Such information can help in developing treatment strategies against viral infections and COVID-19 based on interventions that overcome these metabolic changes. Furthermore, it showed that even drug-free nanoparticles can exert an influence on biological systems as evidenced by metabolomics.
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Affiliation(s)
- Marwa O El-Derany
- Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Diana M F Hanna
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Ain Shams University, 11566, Cairo, Egypt
| | - John Youshia
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Enas Elmowafy
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Mohamed A Farag
- Pharmacognosy Department, College of Pharmacy, Cairo University, Kasr El-Aini St., P.B. 11562, Cairo, Egypt
| | - Samar S Azab
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Ain Shams University, 11566, Cairo, Egypt.
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7
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Farooqui AA, Farooqui T, Sun GY, Lin TN, Teh DBL, Ong WY. COVID-19, Blood Lipid Changes, and Thrombosis. Biomedicines 2023; 11:biomedicines11041181. [PMID: 37189799 DOI: 10.3390/biomedicines11041181] [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: 03/13/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 05/17/2023] Open
Abstract
Although there is increasing evidence that oxidative stress and inflammation induced by COVID-19 may contribute to increased risk and severity of thromboses, the underlying mechanism(s) remain to be understood. The purpose of this review is to highlight the role of blood lipids in association with thrombosis events observed in COVID-19 patients. Among different types of phospholipases A2 that target cell membrane phospholipids, there is increasing focus on the inflammatory secretory phospholipase A2 IIA (sPLA2-IIA), which is associated with the severity of COVID-19. Analysis indicates increased sPLA2-IIA levels together with eicosanoids in the sera of COVID patients. sPLA2 could metabolise phospholipids in platelets, erythrocytes, and endothelial cells to produce arachidonic acid (ARA) and lysophospholipids. Arachidonic acid in platelets is metabolised to prostaglandin H2 and thromboxane A2, known for their pro-coagulation and vasoconstrictive properties. Lysophospholipids, such as lysophosphatidylcholine, could be metabolised by autotaxin (ATX) and further converted to lysophosphatidic acid (LPA). Increased ATX has been found in the serum of patients with COVID-19, and LPA has recently been found to induce NETosis, a clotting mechanism triggered by the release of extracellular fibres from neutrophils and a key feature of the COVID-19 hypercoagulable state. PLA2 could also catalyse the formation of platelet activating factor (PAF) from membrane ether phospholipids. Many of the above lipid mediators are increased in the blood of patients with COVID-19. Together, findings from analyses of blood lipids in COVID-19 patients suggest an important role for metabolites of sPLA2-IIA in COVID-19-associated coagulopathy (CAC).
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Affiliation(s)
- Akhlaq A Farooqui
- Department of Molecular and Cellular Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Tahira Farooqui
- Department of Molecular and Cellular Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Grace Y Sun
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Teng-Nan Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11929, Taiwan
| | - Daniel B L Teh
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119260, Singapore
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119260, Singapore
- Neurobiology Research Programme, Life Sciences Institute, National University of Singapore, Singapore 119260, Singapore
| | - Wei-Yi Ong
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119260, Singapore
- Neurobiology Research Programme, Life Sciences Institute, National University of Singapore, Singapore 119260, Singapore
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8
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Alomair BM, Al-Kuraishy HM, Al-Gareeb AI, Al-Buhadily AK, Alexiou A, Papadakis M, Alshammari MA, Saad HM, Batiha GES. Mixed storm in SARS-CoV-2 infection: A narrative review and new term in the Covid-19 era. Immun Inflamm Dis 2023; 11:e838. [PMID: 37102645 PMCID: PMC10132185 DOI: 10.1002/iid3.838] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/28/2023] Open
Abstract
Coronavirus disease 2019 (Covid-19) is caused by a novel severe acute respiratory syndrome coronavirus virus type 2 (SARS-CoV-2) leading to the global pandemic worldwide. Systemic complications in Covid-19 are mainly related to the direct SARS-CoV-2 cytopathic effects, associated hyperinflammation, hypercytokinemia, and the development of cytokine storm (CS). As well, Covid-19 complications are developed due to the propagation of oxidative and thrombotic events which may progress to a severe state called oxidative storm and thrombotic storm (TS), respectively. In addition, inflammatory and lipid storms are also developed in Covid-19 due to the activation of inflammatory cells and the release of bioactive lipids correspondingly. Therefore, the present narrative review aimed to elucidate the interrelated relationship between different storm types in Covid-19 and the development of the mixed storm (MS). In conclusion, SARS-CoV-2 infection induces various storm types including CS, inflammatory storm, lipid storm, TS and oxidative storm. These storms are not developing alone since there is a close relationship between them. Therefore, the MS seems to be more appropriate to be related to severe Covid-19 than CS, since it develops in Covid-19 due to the intricate interface between reactive oxygen species, proinflammatory cytokines, complement activation, coagulation disorders, and activated inflammatory signaling pathway.
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Affiliation(s)
- Basil Mohammed Alomair
- Department of Medicine, College of Medicine, Internal Medicine and Endocrinology, Jouf University, Al-Jouf, Saudi Arabia
| | - Hayder M Al-Kuraishy
- Department of Clinical Pharmacology and Medicine, College of Medicine, Al-Mustansiriya University, Baghdad, Iraq
| | - Ali I Al-Gareeb
- Department of Clinical Pharmacology and Medicine, College of Medicine, Al-Mustansiriya University, Baghdad, Iraq
| | - Ali K Al-Buhadily
- Department of Clinical Pharmacology, Medicine, and Therapeutic, Medical Faculty, College of Medicine, Al-Mustansiriyah University, Baghdad, Iraq
| | - Athanasios Alexiou
- Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, New South Wales, Australia
- AFNP Med, Wien, Austria
| | - Marios Papadakis
- Department of Surgery II, University Hospital Witten-Herdecke, University of Witten-Herdecke, Wuppertal, Germany
| | - Majed Ayed Alshammari
- Department of Medicine, Prince Mohammed Bin Abdulaziz Medical City, Sakaka, Al-Jouf, Saudi Arabia
| | - Hebatallah M Saad
- Department of Pathology, Faculty of Veterinary Medicine, Matrouh University, Marsa, Matruh, Egypt
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
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9
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Qiu S, Cai Y, Yao H, Lin C, Xie Y, Tang S, Zhang A. Small molecule metabolites: discovery of biomarkers and therapeutic targets. Signal Transduct Target Ther 2023; 8:132. [PMID: 36941259 PMCID: PMC10026263 DOI: 10.1038/s41392-023-01399-3] [Citation(s) in RCA: 105] [Impact Index Per Article: 105.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/22/2023] Open
Abstract
Metabolic abnormalities lead to the dysfunction of metabolic pathways and metabolite accumulation or deficiency which is well-recognized hallmarks of diseases. Metabolite signatures that have close proximity to subject's phenotypic informative dimension, are useful for predicting diagnosis and prognosis of diseases as well as monitoring treatments. The lack of early biomarkers could lead to poor diagnosis and serious outcomes. Therefore, noninvasive diagnosis and monitoring methods with high specificity and selectivity are desperately needed. Small molecule metabolites-based metabolomics has become a specialized tool for metabolic biomarker and pathway analysis, for revealing possible mechanisms of human various diseases and deciphering therapeutic potentials. It could help identify functional biomarkers related to phenotypic variation and delineate biochemical pathways changes as early indicators of pathological dysfunction and damage prior to disease development. Recently, scientists have established a large number of metabolic profiles to reveal the underlying mechanisms and metabolic networks for therapeutic target exploration in biomedicine. This review summarized the metabolic analysis on the potential value of small-molecule candidate metabolites as biomarkers with clinical events, which may lead to better diagnosis, prognosis, drug screening and treatment. We also discuss challenges that need to be addressed to fuel the next wave of breakthroughs.
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Affiliation(s)
- Shi Qiu
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China
| | - Ying Cai
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Hong Yao
- First Affiliated Hospital, Harbin Medical University, Harbin, 150081, China
| | - Chunsheng Lin
- Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin, 150001, China
| | - Yiqiang Xie
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
| | - Songqi Tang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
| | - Aihua Zhang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, 150040, China.
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10
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Gardinassi LG, Servian CDP, Lima GDS, dos Anjos DCC, Gomes Junior AR, Guilarde AO, Borges MASB, dos Santos GF, Moraes BGN, Silva JMM, Masson LC, de Souza FP, da Silva RR, de Araújo GL, Rodrigues MF, da Silva LC, Meira S, Fiaccadori FS, Souza M, Romão PRT, Spadafora Ferreira M, Coelho V, Chaves AR, Simas RC, Vaz BG, Fonseca SG. Integrated Metabolic and Inflammatory Signatures Associated with Severity of, Fatality of, and Recovery from COVID-19. Microbiol Spectr 2023; 11:e0219422. [PMID: 36852984 PMCID: PMC10100880 DOI: 10.1128/spectrum.02194-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 02/04/2023] [Indexed: 03/01/2023] Open
Abstract
Severe manifestations of coronavirus disease 2019 (COVID-19) and mortality have been associated with physiological alterations that provide insights into the pathogenesis of the disease. Moreover, factors that drive recovery from COVID-19 can be explored to identify correlates of protection. The cellular metabolism represents a potential target to improve survival upon severe disease, but the associations between the metabolism and the inflammatory response during COVID-19 are not well defined. We analyzed blood laboratorial parameters, cytokines, and metabolomes of 150 individuals with mild to severe disease, of which 33 progressed to a fatal outcome. A subset of 20 individuals was followed up after hospital discharge and recovery from acute disease. We used hierarchical community networks to integrate metabolomics profiles with cytokines and markers of inflammation, coagulation, and tissue damage. Infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) promotes significant alterations in the plasma metabolome, whose activity varies according to disease severity and correlates with oxygen saturation. Differential metabolism underlying death was marked by amino acids and related metabolites, such as glutamate, glutamyl-glutamate, and oxoproline, and lipids, including progesterone, phosphocholine, and lysophosphatidylcholines (lysoPCs). Individuals who recovered from severe disease displayed persistent alterations enriched for metabolism of purines and phosphatidylinositol phosphate and glycolysis. Recovery of mild disease was associated with vitamin E metabolism. Data integration shows that the metabolic response is a hub connecting other biological features during disease and recovery. Infection by SARS-CoV-2 induces concerted activity of metabolic and inflammatory responses that depend on disease severity and collectively predict clinical outcomes of COVID-19. IMPORTANCE COVID-19 is characterized by diverse clinical outcomes that include asymptomatic to mild manifestations or severe disease and death. Infection by SARS-CoV-2 activates inflammatory and metabolic responses that drive protection or pathology. How inflammation and metabolism communicate during COVID-19 is not well defined. We used high-resolution mass spectrometry to investigate small biochemical compounds (<1,500 Da) in plasma of individuals with COVID-19 and controls. Age, sex, and comorbidities have a profound effect on the plasma metabolites of individuals with COVID-19, but we identified significant activity of pathways and metabolites related to amino acids, lipids, nucleotides, and vitamins determined by disease severity, survival outcome, and recovery. Furthermore, we identified metabolites associated with acute-phase proteins and coagulation factors, which collectively identify individuals with severe disease or individuals who died of severe COVID-19. Our study suggests that manipulating specific metabolic pathways can be explored to prevent hyperinflammation, organ dysfunction, and death.
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Affiliation(s)
- Luiz Gustavo Gardinassi
- Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Carolina do Prado Servian
- Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Gesiane da Silva Lima
- Laboratório de Cromatografia e Espectrometria de Massas, Instituto de Química, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Déborah Carolina Carvalho dos Anjos
- Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Antonio Roberto Gomes Junior
- Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Adriana Oliveira Guilarde
- Departamento de Medicina Tropical e Dermatologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Moara Alves Santa Bárbara Borges
- Departamento de Medicina Tropical e Dermatologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Gabriel Franco dos Santos
- Laboratório de Cromatografia e Espectrometria de Massas, Instituto de Química, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | | | - João Marcos Maia Silva
- Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Letícia Carrijo Masson
- Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Flávia Pereira de Souza
- Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Rodolfo Rodrigues da Silva
- Laboratório de Cromatografia e Espectrometria de Massas, Instituto de Química, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Giovanna Lopes de Araújo
- Laboratório de Cromatografia e Espectrometria de Massas, Instituto de Química, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Marcella Ferreira Rodrigues
- Laboratório de Cromatografia e Espectrometria de Massas, Instituto de Química, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Lidya Cardozo da Silva
- Laboratório de Cromatografia e Espectrometria de Massas, Instituto de Química, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Sueli Meira
- Laboratório Prof Margarida Dobler Komma, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Fabiola Souza Fiaccadori
- Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Menira Souza
- Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Pedro Roosevelt Torres Romão
- Laboratório de Imunologia Celular e Molecular, Programa de Pós-Graduação em Ciências da Saúde, Programa de Pós-Graduação em Ciências da Reabilitação, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Verônica Coelho
- Laboratório de Imunologia, Instituto do Coração, Faculdade de Medicina, Universidade de São Paulo, São Paulo, São Paulo, Brazil
- Laboratório de Histocompatibilidade e Imunidade Celular, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, São Paulo, Brazil
- Instituto de Investigação em Imunologia, Instituto Nacional de Ciências e Tecnologia, São Paulo, São Paulo, Brazil
| | - Andréa Rodrigues Chaves
- Laboratório de Cromatografia e Espectrometria de Massas, Instituto de Química, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Rosineide Costa Simas
- Laboratório de Cromatografia e Espectrometria de Massas, Instituto de Química, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Boniek Gontijo Vaz
- Laboratório de Cromatografia e Espectrometria de Massas, Instituto de Química, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Simone Gonçalves Fonseca
- Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
- Instituto de Investigação em Imunologia, Instituto Nacional de Ciências e Tecnologia, São Paulo, São Paulo, Brazil
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11
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Bourgin M, Durand S, Kroemer G. Diagnostic, Prognostic and Mechanistic Biomarkers of COVID-19 Identified by Mass Spectrometric Metabolomics. Metabolites 2023; 13:metabo13030342. [PMID: 36984782 PMCID: PMC10056171 DOI: 10.3390/metabo13030342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/14/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
A number of studies have assessed the impact of SARS-CoV-2 infection and COVID-19 severity on the metabolome of exhaled air, saliva, plasma, and urine to identify diagnostic and prognostic biomarkers. In spite of the richness of the literature, there is no consensus about the utility of metabolomic analyses for the management of COVID-19, calling for a critical assessment of the literature. We identified mass spectrometric metabolomic studies on specimens from SARS-CoV2-infected patients and subjected them to a cross-study comparison. We compared the clinical design, technical aspects, and statistical analyses of published studies with the purpose to identify the most relevant biomarkers. Several among the metabolites that are under- or overrepresented in the plasma from patients with COVID-19 may directly contribute to excessive inflammatory reactions and deficient immune control of SARS-CoV2, hence unraveling important mechanistic connections between whole-body metabolism and the course of the disease. Altogether, it appears that mass spectrometric approaches have a high potential for biomarker discovery, especially if they are subjected to methodological standardization.
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Affiliation(s)
- Mélanie Bourgin
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, 94805 Villejuif, France
- Centre de Recherche des Cordeliers, Equipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, 75005 Paris, France
- Correspondence:
| | - Sylvère Durand
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, 94805 Villejuif, France
- Centre de Recherche des Cordeliers, Equipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, 75005 Paris, France
| | - Guido Kroemer
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, 94805 Villejuif, France
- Centre de Recherche des Cordeliers, Equipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, 75005 Paris, France
- Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, AP-HP, 75610 Paris, France
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12
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Murali R, Wanjari UR, Mukherjee AG, Gopalakrishnan AV, Kannampuzha S, Namachivayam A, Madhyastha H, Renu K, Ganesan R. Crosstalk between COVID-19 Infection and Kidney Diseases: A Review on the Metabolomic Approaches. Vaccines (Basel) 2023; 11:vaccines11020489. [PMID: 36851366 PMCID: PMC9959335 DOI: 10.3390/vaccines11020489] [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: 01/15/2023] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19, a respiratory disorder. Various organ injuries have been reported in response to this virus, including kidney injury and, in particular, kidney tubular injury. It has been discovered that infection with the virus does not only cause new kidney disease but also increases treatment difficulty and mortality rates in people with kidney diseases. In individuals hospitalized with COVID-19, urinary metabolites from several metabolic pathways are used to distinguish between patients with acute kidney injury (AKI) and those without. This review summarizes the pathogenesis, pathophysiology, treatment strategies, and role of metabolomics in relation to AKI in COVID-19 patients. Metabolomics is likely to play a greater role in predicting outcomes for patients with kidney disease and COVID-19 with varying levels of severity in the near future as data on metabolic profiles expand rapidly. Here, we also discuss the correlation between COVID-19 and kidney diseases and the available metabolomics approaches.
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Affiliation(s)
- Reshma Murali
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Uddesh Ramesh Wanjari
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Anirban Goutam Mukherjee
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Abilash Valsala Gopalakrishnan
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
- Correspondence: (A.V.G.); (R.G.)
| | - Sandra Kannampuzha
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Arunraj Namachivayam
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Harishkumar Madhyastha
- Department of Cardiovascular Physiology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Kaviyarasi Renu
- Center of Molecular Medicine and Diagnostics (COMMAND), Department of Biochemistry, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, Tamil Nadu, India
| | - Raja Ganesan
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
- Correspondence: (A.V.G.); (R.G.)
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13
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Bruzzone C, Conde R, Embade N, Mato JM, Millet O. Metabolomics as a powerful tool for diagnostic, pronostic and drug intervention analysis in COVID-19. Front Mol Biosci 2023; 10:1111482. [PMID: 36876049 PMCID: PMC9975567 DOI: 10.3389/fmolb.2023.1111482] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/06/2023] [Indexed: 02/17/2023] Open
Abstract
COVID-19 currently represents one of the major health challenges worldwide. Albeit its infectious character, with onset affectation mainly at the respiratory track, it is clear that the pathophysiology of COVID-19 has a systemic character, ultimately affecting many organs. This feature enables the possibility of investigating SARS-CoV-2 infection using multi-omic techniques, including metabolomic studies by chromatography coupled to mass spectrometry or by nuclear magnetic resonance (NMR) spectroscopy. Here we review the extensive literature on metabolomics in COVID-19, that unraveled many aspects of the disease including: a characteristic metabotipic signature associated to COVID-19, discrimination of patients according to severity, effect of drugs and vaccination treatments and the characterization of the natural history of the metabolic evolution associated to the disease, from the infection onset to full recovery or long-term and long sequelae of COVID.
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Affiliation(s)
- Chiara Bruzzone
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bilbao, Bizkaia, Spain
| | - Ricardo Conde
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bilbao, Bizkaia, Spain
| | - Nieves Embade
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bilbao, Bizkaia, Spain
| | - José M Mato
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bilbao, Bizkaia, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Oscar Millet
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bilbao, Bizkaia, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
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