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Metabolites
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COVIDomics: Metabolomic Views on COVID-19 and Related Diseases
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COVIDomics: Metabolomic Views on COVID-19 and Related Diseases

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Advances in Metabolomics".

Deadline for manuscript submissions: closed (20 December 2023) | Viewed by 26447

Special Issue Editors

Dr. Michele Costanzo

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Guest Editor
Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Via S. Pansini 5, 80131 Napoli, Italy
Interests: metabolomics; lipidomics; proteomics; systems biology; data analysis
Special Issues, Collections and Topics in MDPI journals
Dr. Lucia Santorelli

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Guest Editor
Department of Oncology and Hematology-Oncology, University of Milano, 20122 Milan, Italy
Interests: functional proteomics; oncoproteomics; biomarkers; biopsy; DNA metabolism
Special Issues, Collections and Topics in MDPI journals
Dr. Armando Cevenini

E-Mail Website
Guest Editor
Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Via S. Pansini 5, 80131 Napoli, Italy
Interests: biochemistry; molecular biology; cell biology; metabolomics; nanomedicine

Special Issue Information

Dear Colleagues,

The COVID-19 pandemic has amplified the efforts made by the scientific community in adopting several large-scale omics investigations (COVIDomics), with the common intent of combatting COVID-19. Amongst the main purposes of such investigations are the development of methods for a prompt diagnosis, the prediction of patient outcomes, and fishing suitable therapeutic targets to demolish SARS-CoV-2 infection. Furthermore, the current emergency has shed light on already known immune, infectious, and inflammatory diseases, stressing the importance of investigating the immune system and related disturbacies. In this scenario, COVIDomics, and metabolomics/lipidomics in particular, may provide an explanation to many still-unsolved questions. In fact, the contributions and pragmaticity offered by metabolomics and lipidomics in any field of research is nowadays widely acknowledged. Metabolomics can boost the theoretical and practical knowledge of a biological context by identifying and quantifying thousands of metabolites present in a multitude of samples, revealing the ultimate metabolic signature of a pathological condition.

This Special Issue of Metabolites will publish works in the form of original research articles, reviews, or shorter perspective articles on all the aspects related to COVID-19. Metabolomics and lipidomics approaches should be strongly emphasized. Accordingly, new insights into sample preparation, instrument settings, and data analysis will be highly considered.

Dr. Michele Costanzo
Dr. Lucia Santorelli
Dr. Armando Cevenini
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Metabolites is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Metabolomics
  • Lipidomics
  • COVID-19
  • Therapy
  • Immunity
  • Integrative medicine
  • Clinical epidemiology
  • System biology

Published Papers (6 papers)

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Research

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14 pages, 1443 KiB  
Article
Changes in the Urine Metabolomic Profile in Patients Recovering from Severe COVID-19
by Robert Rosolanka, Peter Liptak, Eva Baranovicova, Anna Bobcakova, Robert Vysehradsky, Martin Duricek, Andrea Kapinova, Dana Dvorska, Zuzana Dankova, Katarina Simekova, Jan Lehotsky, Erika Halasova and Peter Banovcin
Metabolites 2023, 13(3), 364; https://doi.org/10.3390/metabo13030364 - 28 Feb 2023
Cited by 3 | Viewed by 1226
Abstract
Metabolomics is a relatively new research area that focuses mostly on the profiling of selected molecules and metabolites within the organism. A SARS-CoV-2 infection itself can lead to major disturbances in the metabolite profile of the infected individuals. The aim of this study [...] Read more.
Metabolomics is a relatively new research area that focuses mostly on the profiling of selected molecules and metabolites within the organism. A SARS-CoV-2 infection itself can lead to major disturbances in the metabolite profile of the infected individuals. The aim of this study was to analyze metabolomic changes in the urine of patients during the acute phase of COVID-19 and approximately one month after infection in the recovery period. We discuss the observed changes in relation to the alterations resulting from changes in the blood plasma metabolome, as described in our previous study. The metabolome analysis was performed using NMR spectroscopy from the urine of patients and controls. The urine samples were collected at three timepoints, namely upon hospital admission, during hospitalization, and after discharge from the hospital. The acute COVID-19 phase induced massive alterations in the metabolic composition of urine was linked with various changes taking place in the organism. Discriminatory analyses showed the feasibility of successful discrimination of COVID-19 patients from healthy controls based on urinary metabolite levels, with the highest significance assigned to citrate, Hippurate, and pyruvate. Our results show that the metabolomic changes persist one month after the acute phase and that the organism is not fully recovered. Full article
(This article belongs to the Special Issue COVIDomics: Metabolomic Views on COVID-19 and Related Diseases)
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22 pages, 7994 KiB  
Article
The Discovery of Potential SARS-CoV-2 Natural Inhibitors among 4924 African Metabolites Targeting the Papain-like Protease: A Multi-Phase In Silico Approach
by Eslam B. Elkaeed, Mohamed M. Khalifa, Bshra A. Alsfouk, Aisha A. Alsfouk, Abdul-Aziz M. M. El-Attar, Ibrahim H. Eissa and Ahmed M. Metwaly
Metabolites 2022, 12(11), 1122; https://doi.org/10.3390/metabo12111122 - 16 Nov 2022
Cited by 4 | Viewed by 1584
Abstract
Four compounds, hippacine, 4,2′-dihydroxy-4′-methoxychalcone, 2′,5′-dihydroxy-4-methoxychalcone, and wighteone, were selected from 4924 African natural metabolites as potential inhibitors against SARS-CoV-2 papain-like protease (PLpro, PDB ID: 3E9S). A multi-phased in silico approach was employed to select the most similar metabolites to the co-crystallized ligand ( [...] Read more.
Four compounds, hippacine, 4,2′-dihydroxy-4′-methoxychalcone, 2′,5′-dihydroxy-4-methoxychalcone, and wighteone, were selected from 4924 African natural metabolites as potential inhibitors against SARS-CoV-2 papain-like protease (PLpro, PDB ID: 3E9S). A multi-phased in silico approach was employed to select the most similar metabolites to the co-crystallized ligand (TTT) of the PLpro through molecular fingerprints and structural similarity studies. Followingly, to examine the binding of the selected metabolites with the PLpro (molecular docking. Further, to confirm this binding through molecular dynamics simulations. Finally, in silico ADMET and toxicity studies were carried out to prefer the most convenient compounds and their drug-likeness. The obtained results could be a weapon in the battle against COVID-19 via more in vitro and in vivo studies. Full article
(This article belongs to the Special Issue COVIDomics: Metabolomic Views on COVID-19 and Related Diseases)
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16 pages, 2707 KiB  
Article
Signatures of Mitochondrial Dysfunction and Impaired Fatty Acid Metabolism in Plasma of Patients with Post-Acute Sequelae of COVID-19 (PASC)
by Vamsi P. Guntur, Travis Nemkov, Esther de Boer, Michael P. Mohning, David Baraghoshi, Francesca I. Cendali, Inigo San-Millán, Irina Petrache and Angelo D’Alessandro
Metabolites 2022, 12(11), 1026; https://doi.org/10.3390/metabo12111026 - 26 Oct 2022
Cited by 55 | Viewed by 15069
Abstract
Exercise intolerance is a major manifestation of post-acute sequelae of severe acute respiratory syndrome coronavirus infection (PASC, or “long-COVID”). Exercise intolerance in PASC is associated with higher arterial blood lactate accumulation and lower fatty acid oxidation rates during graded exercise tests to volitional [...] Read more.
Exercise intolerance is a major manifestation of post-acute sequelae of severe acute respiratory syndrome coronavirus infection (PASC, or “long-COVID”). Exercise intolerance in PASC is associated with higher arterial blood lactate accumulation and lower fatty acid oxidation rates during graded exercise tests to volitional exertion, suggesting altered metabolism and mitochondrial dysfunction. It remains unclear whether the profound disturbances in metabolism that have been identified in plasma from patients suffering from acute coronavirus disease 2019 (COVID-19) are also present in PASC. To bridge this gap, individuals with a history of previous acute COVID-19 infection that did not require hospitalization were enrolled at National Jewish Health (Denver, CO, USA) and were grouped into those that developed PASC (n = 29) and those that fully recovered (n = 16). Plasma samples from the two groups were analyzed via mass spectrometry-based untargeted metabolomics and compared against plasma metabolic profiles of healthy control individuals (n = 30). Observational demographic and clinical data were retrospectively abstracted from the medical record. Compared to plasma of healthy controls or individuals who recovered from COVID-19, PASC plasma exhibited significantly higher free- and carnitine-conjugated mono-, poly-, and highly unsaturated fatty acids, accompanied by markedly lower levels of mono-, di- and tricarboxylates (pyruvate, lactate, citrate, succinate, and malate), polyamines (spermine) and taurine. Plasma from individuals who fully recovered from COVID-19 exhibited an intermediary metabolic phenotype, with milder disturbances in fatty acid metabolism and higher levels of spermine and taurine. Of note, depletion of tryptophan—a hallmark of disease severity in COVID-19—is not normalized in PASC patients, despite normalization of kynurenine levels—a tryptophan metabolite that predicts mortality in hospitalized COVID-19 patients. In conclusion, PASC plasma metabolites are indicative of altered fatty acid metabolism and dysfunctional mitochondria-dependent lipid catabolism. These metabolic profiles obtained at rest are consistent with previously reported mitochondrial dysfunction during exercise, and may pave the way for therapeutic intervention focused on restoring mitochondrial fat-burning capacity. Full article
(This article belongs to the Special Issue COVIDomics: Metabolomic Views on COVID-19 and Related Diseases)
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14 pages, 890 KiB  
Article
Persistence of Metabolomic Changes in Patients during Post-COVID Phase: A Prospective, Observational Study
by Peter Liptak, Eva Baranovicova, Robert Rosolanka, Katarina Simekova, Anna Bobcakova, Robert Vysehradsky, Martin Duricek, Zuzana Dankova, Andrea Kapinova, Dana Dvorska, Erika Halasova and Peter Banovcin
Metabolites 2022, 12(7), 641; https://doi.org/10.3390/metabo12070641 - 13 Jul 2022
Cited by 11 | Viewed by 1959
Abstract
Several relatively recently published studies have shown changes in plasma metabolites in various viral diseases such as Zika, Dengue, RSV or SARS-CoV-1. The aim of this study was to analyze the metabolome profile of patients during acute COVID-19 approximately one month after the [...] Read more.
Several relatively recently published studies have shown changes in plasma metabolites in various viral diseases such as Zika, Dengue, RSV or SARS-CoV-1. The aim of this study was to analyze the metabolome profile of patients during acute COVID-19 approximately one month after the acute infection and to compare these results with healthy (SARS-CoV-2-negative) controls. The metabolome analysis was performed by NMR spectroscopy from the peripheral blood of patients and controls. The blood samples were collected on 3 different occasions (at admission, during hospitalization and on control visit after discharge from the hospital). When comparing sample groups (based on the date of acquisition) to controls, there is an indicative shift in metabolomics features based on the time passed after the first sample was taken towards controls. Based on the random forest algorithm, there is a strong discriminatory predictive value between controls and different sample groups (AUC equals 1 for controls versus samples taken at admission, Mathew correlation coefficient equals 1). Significant metabolomic changes persist in patients more than a month after acute SARS-CoV-2 infection. The random forest algorithm shows very strong discrimination (almost ideal) when comparing metabolite levels of patients in two various stages of disease and during the recovery period compared to SARS-CoV-2-negative controls. Full article
(This article belongs to the Special Issue COVIDomics: Metabolomic Views on COVID-19 and Related Diseases)
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17 pages, 2805 KiB  
Article
Human Serum Metabolites as Potential Mediators from Type 2 Diabetes and Obesity to COVID-19 Severity and Susceptibility: Evidence from Mendelian Randomization Study
by Chuiguo Huang, Mai Shi, Hongjiang Wu, Andrea O. Y. Luk, Juliana C. N. Chan and Ronald C. W. Ma
Metabolites 2022, 12(7), 598; https://doi.org/10.3390/metabo12070598 - 27 Jun 2022
Cited by 6 | Viewed by 2899
Abstract
Obesity, type 2 diabetes (T2D), and severe coronavirus disease 2019 (COVID-19) are closely associated. The aim of this study was to elucidate the casual and mediating relationships of human serum metabolites on the pathways from obesity/T2D to COVID-19 using Mendelian randomization (MR) techniques. [...] Read more.
Obesity, type 2 diabetes (T2D), and severe coronavirus disease 2019 (COVID-19) are closely associated. The aim of this study was to elucidate the casual and mediating relationships of human serum metabolites on the pathways from obesity/T2D to COVID-19 using Mendelian randomization (MR) techniques. We performed two-sample MR to study the causal effects of 309 metabolites on COVID-19 severity and susceptibility, based on summary statistics from genome-wide association studies (GWAS) of metabolites (n = 7824), COVID-19 phenotypes (n = 2,586,691), and obesity (n = 322,154)/T2D traits (n = 898,130). We conducted two-sample network MR analysis to determine the mediating metabolites on the causal path from obesity/T2D to COVID-19 phenotypes. We used multivariable MR analysis (MVMR) to discover causal metabolites independent of body mass index (BMI). Our MR analysis yielded four causal metabolites that increased the risk of severe COVID-19, including 2-stearoylglycerophosphocholine (OR 2.15; 95% CI 1.48–3.11), decanoylcarnitine (OR 1.32; 95% CI 1.17–1.50), thymol sulfate (OR 1.20; 95% CI 1.10–1.30), and bradykinin-des-arg(9) (OR 1.09; 95% CI 1.05–1.13). One significant mediator, gamma-glutamyltyrosine, lay on the causal path from T2D/obesity to severe COVID-19, with 16.67% (0.64%, 32.70%) and 6.32% (1.76%, 10.87%) increased risk, respectively, per one-standard deviation increment of genetically predicted T2D and BMI. Our comprehensive MR analyses identified credible causative metabolites, mediators of T2D and obesity, and obesity-independent causative metabolites for severe COVID-19. These biomarkers provide a novel basis for mechanistic studies for risk assessment, prognostication, and therapeutic purposes in COVID-19. Full article
(This article belongs to the Special Issue COVIDomics: Metabolomic Views on COVID-19 and Related Diseases)
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Review

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22 pages, 1176 KiB  
Review
Diagnostic, Prognostic and Mechanistic Biomarkers of COVID-19 Identified by Mass Spectrometric Metabolomics
by Mélanie Bourgin, Sylvère Durand and Guido Kroemer
Metabolites 2023, 13(3), 342; https://doi.org/10.3390/metabo13030342 - 24 Feb 2023
Cited by 3 | Viewed by 2394
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue COVIDomics: Metabolomic Views on COVID-19 and Related Diseases)
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