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Kugler S, Hahnefeld L, Kloka JA, Ginzel S, Nürenberg-Goloub E, Zinn S, Vehreschild MJ, Zacharowski K, Lindau S, Ullrich E, Burmeister J, Kohlhammer J, Schwäble J, Gurke R, Dorochow E, Bennett A, Dauth S, Campe J, Knape T, Laux V, Kannt A, Köhm M, Geisslinger G, Resch E, Behrens F. Short-term predictor for COVID-19 severity from a longitudinal multi-omics study for practical application in intensive care units. Talanta 2024; 268:125295. [PMID: 37866305 DOI: 10.1016/j.talanta.2023.125295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 10/24/2023]
Abstract
BACKGROUND The COVID-19 pandemic challenged the management of technical and human resources in intensive care units (ICU) across the world. Several long-term predictors for COVID-19 disease progression have been discovered. However, predictors to support short-term planning of resources and medication that can be translated to future pandemics are still missing. A workflow was established to identify a predictor for short-term COVID-19 disease progression in the acute phase of intensive care patients to support clinical decision-making. METHODS Thirty-two patients with SARS-CoV-2 infection were recruited on admission to the ICU and clinical data collected. During their hospitalization, plasma samples were acquired from each patient on multiple occasions, excepting one patient for which only one time point was possible, and the proteome (Inflammation, Immune Response and Organ Damage panels from Olink® Target 96), metabolome and lipidome (flow injection analysis and liquid chromatography-mass spectrometry) analyzed for each sample. Patient visits were grouped according to changes in disease severity based on their respiratory and organ function, and evaluated using a combination of statistical analysis and machine learning. The resulting short-term predictor from this multi-omics approach was compared to the human assessment of disease progression. Furthermore, the potential markers were compared to the baseline levels of 50 healthy subjects with no known SARS-CoV-2 or other viral infections. RESULTS A total of 124 clinical parameters, 271 proteins and 782 unique metabolites and lipids were assessed. The dimensionality of the dataset was reduced, selecting 47 from the 1177 parameters available following down-selection, to build the machine learning model. Subsequently, two proteins (C-C motif chemokine 7 (CCL7) and carbonic anhydrase 14 (CA14)) and one lipid (hexosylceramide 18:2; O2/20:0) were linked to disease progression in the studied SARS-CoV-2 infections. Thus, a predictor delivering the prognosis of an upcoming worsening of the patient's condition up to five days in advance with a reasonable accuracy (79 % three days prior to event, 84 % four to five days prior to event) was found. Interestingly, the predictor's performance was complementary to the clinicians' capabilities to foresee a worsening of a patient. CONCLUSION This study presents a workflow to identify omics-based biomarkers to support clinical decision-making and resource management in the ICU. This was successfully applied to develop a short-term predictor for aggravation of COVID-19 symptoms. The applied methods can be adapted for future small cohort studies.
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Affiliation(s)
- Sabine Kugler
- Fraunhofer Cluster of Excellence Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Fraunhofer Institute for Intelligent Analysis and Information Systems IAIS, Schloss Birlinghoven 1, St. Augustin, Germany
| | - Lisa Hahnefeld
- Fraunhofer Cluster of Excellence Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Goethe University Frankfurt, University Hospital, Institute of Clinical Pharmacology, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany.
| | - Jan Andreas Kloka
- Goethe University Frankfurt, University Hospital, Clinic for Anesthesiology, Intensive Care Medicine and Pain Therapy, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Sebastian Ginzel
- Fraunhofer Cluster of Excellence Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Fraunhofer Institute for Intelligent Analysis and Information Systems IAIS, Schloss Birlinghoven 1, St. Augustin, Germany
| | - Elina Nürenberg-Goloub
- Goethe University Frankfurt, University Hospital, Clinic for Anesthesiology, Intensive Care Medicine and Pain Therapy, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Sebastian Zinn
- Goethe University Frankfurt, University Hospital, Clinic for Anesthesiology, Intensive Care Medicine and Pain Therapy, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany; Fraunhofer Leistungszentrum TheraNova, Theodor-Stern-Kai 6, 60596, Frankfurt am Main, Germany
| | - Maria Jgt Vehreschild
- Goethe University Frankfurt, University Hospital, Department of Internal Medicine, Infectious Diseases, 60590, Frankfurt am Main, Germany
| | - Kai Zacharowski
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Goethe University Frankfurt, University Hospital, Clinic for Anesthesiology, Intensive Care Medicine and Pain Therapy, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Simone Lindau
- Goethe University Frankfurt, University Hospital, Clinic for Anesthesiology, Intensive Care Medicine and Pain Therapy, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Evelyn Ullrich
- University Cancer Center Frankfurt (UCT), University Hospital, Goethe University Frankfurt, Frankfurt, Germany; Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany; Goethe University Frankfurt, Department of Pediatrics, Experimental Immunology and Cell Therapy, Frankfurt, Germany
| | - Jan Burmeister
- Fraunhofer Institute for Computer Graphics Research IGD, Darmstadt, Germany
| | - Jörn Kohlhammer
- Fraunhofer Institute for Computer Graphics Research IGD, Darmstadt, Germany
| | - Joachim Schwäble
- Goethe University Frankfurt, University Hospital, Institute of Transfusion Medicine and Immunohematology, German Red Cross Blood Transfusion Service Baden-Württemberg, Frankfurt, Germany
| | - Robert Gurke
- Fraunhofer Cluster of Excellence Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Goethe University Frankfurt, University Hospital, Institute of Clinical Pharmacology, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Erika Dorochow
- Goethe University Frankfurt, University Hospital, Institute of Clinical Pharmacology, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Alexandre Bennett
- Fraunhofer Cluster of Excellence Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Stephanie Dauth
- Fraunhofer Cluster of Excellence Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Julia Campe
- Goethe University Frankfurt, Department of Pediatrics, Experimental Immunology and Cell Therapy, Frankfurt, Germany; Goethe University Frankfurt, Biological Sciences, Frankfurt am Main, Germany
| | - Tilo Knape
- Fraunhofer Cluster of Excellence Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Volker Laux
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Aimo Kannt
- Fraunhofer Cluster of Excellence Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Fraunhofer Leistungszentrum TheraNova, Theodor-Stern-Kai 6, 60596, Frankfurt am Main, Germany
| | - Michaela Köhm
- Fraunhofer Cluster of Excellence Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Goethe University Frankfurt, University Hospital, Rheumatology, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Gerd Geisslinger
- Fraunhofer Cluster of Excellence Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Goethe University Frankfurt, University Hospital, Institute of Clinical Pharmacology, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Eduard Resch
- Fraunhofer Cluster of Excellence Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Frank Behrens
- Fraunhofer Cluster of Excellence Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany; Goethe University Frankfurt, University Hospital, Rheumatology, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
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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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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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Spectroscopic methods for COVID-19 detection and early diagnosis. Virol J 2022; 19:152. [PMID: 36138463 PMCID: PMC9502632 DOI: 10.1186/s12985-022-01867-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 08/16/2022] [Indexed: 11/10/2022] Open
Abstract
The coronavirus pandemic is a worldwide hazard that poses a threat to millions of individuals throughout the world. This pandemic is caused by the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), which was initially identified in Wuhan, China's Hubei provincial capital, and has since spread throughout the world. According to the World Health Organization's Weekly Epidemiological Update, there were more than 250 million documented cases of coronavirus infections globally, with five million fatalities. Early detection of coronavirus does not only reduce the spread of the virus, but it also increases the chance of curing the infection. Spectroscopic techniques have been widely used in the early detection and diagnosis of COVID-19 using Raman, Infrared, mass spectrometry and fluorescence spectroscopy. In this review, the reported spectroscopic methods for COVID-19 detection were discussed with emphasis on the practical aspects, limitations and applications.
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Serum metabolomic abnormalities in survivors of non-severe COVID-19. Heliyon 2022; 8:e10473. [PMID: 36065322 PMCID: PMC9433334 DOI: 10.1016/j.heliyon.2022.e10473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/25/2022] [Accepted: 08/23/2022] [Indexed: 11/23/2022] Open
Abstract
Metabolic reprogramming is a distinctive characteristic of SARS-CoV-2 infection, which refers to metabolic changes in hosts triggered by viruses for their survival and spread. It is current urgent to understand the metabolic health status of COVID-19 survivors and its association with long-term health consequences of infection, especially for the predominant non-severe patients. Herein, we show systemic metabolic signatures of survivors of non-severe COVID-19 from Wuhan, China at six months after discharge using metabolomics approaches. The serum amino acids, organic acids, purine, fatty acids and lipid metabolism were still abnormal in the survivors, but the kynurenine pathway and the level of itaconic acid have returned to normal. These metabolic abnormalities are associated with liver injury, mental health, energy production, and inflammatory responses. Our findings identify and highlight the metabolic abnormalities in survivors of non-severe COVID-19, which provide information on biomarkers and therapeutic targets of infection and cues for post-hospital care and intervention strategies centered on metabolism reprogramming.
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Bordbar MM, Samadinia H, Sheini A, Aboonajmi J, Javid M, Sharghi H, Ghanei M, Bagheri H. Non-invasive detection of COVID-19 using a microfluidic-based colorimetric sensor array sensitive to urinary metabolites. Mikrochim Acta 2022; 189:316. [PMID: 35927498 PMCID: PMC9361914 DOI: 10.1007/s00604-022-05423-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/15/2022] [Indexed: 01/17/2023]
Abstract
A colorimetric sensor array designed on a paper substrate with a microfluidic structure has been developed. This array is capable of detecting COVID-19 disease by tracking metabolites of urine samples. In order to determine minor metabolic changes, various colorimetric receptors consisting of gold and silver nanoparticles, metalloporphyrins, metal ion complexes, and pH-sensitive indicators are used in the array structure. By injecting a small volume of the urine sample, the color pattern of the sensor changes after 7 min, which can be observed visually. The color changes of the receptors (recorded by a scanner) are subsequently calculated by image analysis software and displayed as a color difference map. This study has been performed on 130 volunteers, including 60 patients infected by COVID-19, 55 healthy controls, and 15 cured individuals. The resulting array provides a fingerprint response for each category due to the differences in the metabolic profile of the urine sample. The principal component analysis-discriminant analysis confirms that the assay sensitivity to the correctly detected patient, healthy, and cured participants is equal to 73.3%, 74.5%, and 66.6%, respectively. Apart from COVID-19, other diseases such as chronic kidney disease, liver disorder, and diabetes may be detectable by the proposed sensor. However, this performance of the sensor must be tested in the studies with a larger sample size. These results show the possible feasibility of the sensor as a suitable alternative to costly and time-consuming standard methods for rapid detection and control of viral and bacterial infectious diseases and metabolic disorders.
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Affiliation(s)
- Mohammad Mahdi Bordbar
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Hosein Samadinia
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Azarmidokht Sheini
- Department of Mechanical Engineering, Shohadaye Hoveizeh Campus of Technology, Shahid Chamran University of Ahvaz, Dashte Azadegan, Khuzestan, Iran
| | - Jasem Aboonajmi
- Department of Chemistry, College of Sciences, Shiraz University, Shiraz, Iran
| | - Mohammad Javid
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Hashem Sharghi
- Department of Chemistry, College of Sciences, Shiraz University, Shiraz, Iran
| | - Mostafa Ghanei
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Hasan Bagheri
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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Cheudjeu A. The SARS-CoV-2 Entry Inhibition Mechanisms of Serine Protease Inhibitors, OM-85, Heparin and Soluble HS Might Be Linked to HS Attachment Sites. Molecules 2022; 27:molecules27061947. [PMID: 35335311 PMCID: PMC8954261 DOI: 10.3390/molecules27061947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 11/16/2022] Open
Abstract
This article discusses the importance of D-xylose for fighting viruses (especially SARS-CoV-2) that use core proteins as receptors at the cell surface, by providing additional supporting facts that these viruses probably bind at HS/CS attachment sites (i.e., the hydroxyl groups of Ser/Thr residues of the core proteins intended to receive the D-xylose molecules to initiate the HS/CS chains). Essentially, the additional supporting facts, are: some anterior studies on the binding sites of exogenous heparin and soluble HS on the core proteins, the inhibition of the viral entry by pre-incubation of cells with heparin, and additionally, corroborating studies about the mechanism leading to type 2 diabetes during viral infection. We then discuss the mechanism by which serine protease inhibitors inhibit SARS-CoV-2 entry. The biosynthesis of heparan sulfate (HS), chondroitin sulfate (CS), dermatan sulfate (DS), and heparin (Hep) is initiated not only by D-xylose derived from uridine diphosphate (UDP)-xylose, but also bioactive D-xylose molecules, even in situations where cells were previously treated with GAG inhibitors. This property of D-xylose shown by previous anterior studies helped in the explanation of the mechanism leading to type 2 diabetes during SARS-CoV-2 infection. This explanation is completed here by a preliminary estimation of xyloside GAGs (HS/CS/DS/Hep) in the body, and with other previous studies helping to corroborate the mechanism by which the D-xylose exhibits its antiglycaemic properties and the mechanism leading to type 2 diabetes during SARS-CoV-2 infection. This paper also discusses the confirmatory studies of regarding the correlation between D-xylose and COVID-19 severity.
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Staufer O, Gupta K, Hernandez Bücher JE, Kohler F, Sigl C, Singh G, Vasileiou K, Yagüe Relimpio A, Macher M, Fabritz S, Dietz H, Cavalcanti Adam EA, Schaffitzel C, Ruggieri A, Platzman I, Berger I, Spatz JP. Synthetic virions reveal fatty acid-coupled adaptive immunogenicity of SARS-CoV-2 spike glycoprotein. Nat Commun 2022; 13:868. [PMID: 35165285 PMCID: PMC8844029 DOI: 10.1038/s41467-022-28446-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 01/24/2022] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV-2 infection is a major global public health concern with incompletely understood pathogenesis. The SARS-CoV-2 spike (S) glycoprotein comprises a highly conserved free fatty acid binding pocket (FABP) with unknown function and evolutionary selection advantage1,2. Deciphering FABP impact on COVID-19 progression is challenged by the heterogenous nature and large molecular variability of live virus. Here we create synthetic minimal virions (MiniVs) of wild-type and mutant SARS-CoV-2 with precise molecular composition and programmable complexity by bottom-up assembly. MiniV-based systematic assessment of S free fatty acid (FFA) binding reveals that FABP functions as an allosteric regulatory site enabling adaptation of SARS-CoV-2 immunogenicity to inflammation states via binding of pro-inflammatory FFAs. This is achieved by regulation of the S open-to-close equilibrium and the exposure of both, the receptor binding domain (RBD) and the SARS-CoV-2 RGD motif that is responsible for integrin co-receptor engagement. We find that the FDA-approved drugs vitamin K and dexamethasone modulate S-based cell binding in an FABP-like manner. In inflammatory FFA environments, neutralizing immunoglobulins from human convalescent COVID-19 donors lose neutralization activity. Empowered by our MiniV technology, we suggest a conserved mechanism by which SARS-CoV-2 dynamically couples its immunogenicity to the host immune response. Staufer et al. provide a protocol for preparation of synthetic minimal virions (MiniV) of SARS-CoV-2, mimicking viral structure and allowing for precise investigation of receptor binding mechanism. They find that the highly conserved free fatty acid binding pocket (FABP) can function as an allosteric regulator, enabling adaptation of immunogenicity via binding of proinflammatory free fatty acids and mediating the spike open to-closed equilibrium.
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Lu LY, Feng PH, Yu MS, Chen MC, Lin AJH, Chen JL, Yu LHL. Current utilization of interferon alpha for the treatment of coronavirus disease 2019: A comprehensive review. Cytokine Growth Factor Rev 2022; 63:34-43. [PMID: 35115233 PMCID: PMC8755267 DOI: 10.1016/j.cytogfr.2022.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/03/2022] [Accepted: 01/06/2022] [Indexed: 12/14/2022]
Abstract
Recent studies have identified an association between perturbed type I interferon (IFN) responses and the severity of coronavirus disease 2019 (COVID-19). IFNα intervention may normalize the dysregulated innate immunity of COVID-19. However, details regarding its utilization and therapeutic evidence have yet to be systematically evaluated. The aim of this comprehensive review was to summarize the current utilization of IFNα for COVID-19 treatment and to explore the evidence on safety and efficacy. A comprehensive review of clinical studies in the literature prior to December 1st, 2021, was performed to identify the current utilization of IFNα, which included details on the route of administration, the number of patients who received the treatment, the severity at the initiation of treatment, age range, the time from the onset of symptoms to treatment, dose, frequency, and duration as well as safety and efficacy. Encouragingly, no evidence was found against the safety of IFNα treatment for COVID-19. Early intervention, either within five days from the onset of symptoms or at hospital admission, confers better clinical outcomes, whereas late intervention may result in prolonged hospitalization.
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Affiliation(s)
- Ling-Ying Lu
- Division of Allergy, Immunology, and Rheumatology, Department of Medicine, Kaohsiung Veterans General Hospital, No.386, Dazhong 1st Rd., Zuoying District, Kaohsiung City, Taiwan
| | - Po-Hao Feng
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, No. 291, Zhongzheng Rd, Zhonghe District, New Taipei City, Taiwan,Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, No. 250, Wuxing Street, Xinyi District, Taipei City, Taiwan
| | - Ming-Sun Yu
- Division of Hematology, Conde S. Januário Hospital, Estrada do Visconde de São Januário, Macau, China
| | - Min-Chi Chen
- Graduate Institute of Biomedical Sciences, Chang Gung University, No. 259, Wenhua 1st Road, Guishan District, Taoyuan City, Taiwan
| | - Alex Jia-Hong Lin
- Medical Affairs Department, Panco Healthcare Co., Ltd., a PharmaEssentia Company, 2F-5 No. 3 Park Street, Nangang District, Taipei, Taiwan
| | - Justin L. Chen
- Medical Affairs Department, Panco Healthcare Co., Ltd., a PharmaEssentia Company, 2F-5 No. 3 Park Street, Nangang District, Taipei, Taiwan
| | - Lennex Hsueh-Lin Yu
- Medical Affairs Department, Panco Healthcare Co., Ltd., a PharmaEssentia Company, 2F-5 No. 3 Park Street, Nangang District, Taipei, Taiwan,Corresponding author
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10
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Valdés A, Moreno LO, Rello SR, Orduña A, Bernardo D, Cifuentes A. Metabolomics study of COVID-19 patients in four different clinical stages. Sci Rep 2022; 12:1650. [PMID: 35102215 PMCID: PMC8803913 DOI: 10.1038/s41598-022-05667-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 12/13/2021] [Indexed: 12/22/2022] Open
Abstract
SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is the coronavirus strain causing the respiratory pandemic COVID-19 (coronavirus disease 2019). To understand the pathobiology of SARS-CoV-2 in humans it is necessary to unravel the metabolic changes that are produced in the individuals once the infection has taken place. The goal of this work is to provide new information about the altered biomolecule profile and with that the altered biological pathways of patients in different clinical situations due to SARS-CoV-2 infection. This is done via metabolomics using HPLC-QTOF-MS analysis of plasma samples at COVID-diagnose from a total of 145 adult patients, divided into different clinical stages based on their subsequent clinical outcome (25 negative controls (non-COVID); 28 positive patients with asymptomatic disease not requiring hospitalization; 27 positive patients with mild disease defined by a total time in hospital lower than 10 days; 36 positive patients with severe disease defined by a total time in hospital over 20 days and/or admission at the ICU; and 29 positive patients with fatal outcome or deceased). Moreover, follow up samples between 2 and 3 months after hospital discharge were also obtained from the hospitalized patients with mild prognosis. The final goal of this work is to provide biomarkers that can help to better understand how the COVID-19 illness evolves and to predict how a patient could progress based on the metabolites profile of plasma obtained at an early stage of the infection. In the present work, several metabolites were found as potential biomarkers to distinguish between the end-stage and the early-stage (or non-COVID) disease groups. These metabolites are mainly involved in the metabolism of carnitines, ketone bodies, fatty acids, lysophosphatidylcholines/phosphatidylcholines, tryptophan, bile acids and purines, but also omeprazole. In addition, the levels of several of these metabolites decreased to "normal" values at hospital discharge, suggesting some of them as early prognosis biomarkers in COVID-19 at diagnose.
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Affiliation(s)
- Alberto Valdés
- Laboratory of Foodomics, Institute of Food Science Research, CIAL, CSIC, Nicolás Cabrera 9, 28049, Madrid, Spain
| | - Lorena Ortega Moreno
- Dpt. Medicina, Universidad Autónoma de Madrid, Madrid, Spain
- Instituto de Investigación Sanitaria Hospital Universitario de La Princesa, Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBERehd), Barcelona, Spain
| | - Silvia Rojo Rello
- Servicio de Microbiología, Hospital Clínico Universitario de Valladolid, 47004, Valladolid, Spain
| | - Antonio Orduña
- Servicio de Microbiología, Hospital Clínico Universitario de Valladolid, 47004, Valladolid, Spain
- Departamento de Microbiología, Universidad de Valladolid, Valladolid, Spain
| | - David Bernardo
- Centro de Investigación Biomédica en Red (CIBERehd), Barcelona, Spain
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular (IBGM), Universidad de Valladolid-CSIC, Valladolid, Spain
| | - Alejandro Cifuentes
- Laboratory of Foodomics, Institute of Food Science Research, CIAL, CSIC, Nicolás Cabrera 9, 28049, Madrid, Spain.
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11
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Shekhawat JK, Banerjee M. OUP accepted manuscript. J Appl Lab Med 2022; 7:1175-1188. [PMID: 35723351 PMCID: PMC9278167 DOI: 10.1093/jalm/jfac040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/21/2022] [Indexed: 12/04/2022]
Abstract
Background COVID-19 is a highly contagious respiratory disease that can be transmitted through human exhaled breath. It has caused immense loss and has challenged the healthcare sector. It has affected the economy of countries and thereby affected numerous sectors. Analysis of human breath samples is an attractive strategy for rapid diagnosis of COVID-19 by monitoring breath biomarkers. Content Breath collection is a noninvasive process. Various technologies are employed for detection of breath biomarkers like mass spectrometry, biosensors, artificial learning, and machine learning. These tools have low turnaround time, robustness, and provide onsite results. Also, MS-based approaches are promising tools with high speed, specificity, sensitivity, reproducibility, and broader coverage, as well as its coupling with various chromatographic separation techniques providing better clinical and biochemical understanding of COVID-19 using breath samples. Summary Herein, we have tried to review the MS-based approaches as well as other techniques used for the analysis of breath samples for COVID-19 diagnosis. We have also highlighted the different breath analyzers being developed for COVID-19 detection.
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Affiliation(s)
- Jyoti Kanwar Shekhawat
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur-342005, Rajasthan, India
| | - Mithu Banerjee
- Address correspondence to this author at: AIIMS, Road, MI Phase-2, Basni, Jodhpur, Rajasthan, India—342005. E-mail:
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12
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Phenylalanine and COVID-19: Tracking disease severity markers. Int Immunopharmacol 2021; 101:108313. [PMID: 34741868 PMCID: PMC8559801 DOI: 10.1016/j.intimp.2021.108313] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/15/2021] [Accepted: 10/24/2021] [Indexed: 12/13/2022]
Abstract
Background Although there are several severity
predictors for COVID-19, none are specific. Serum levels of phenylalanine
were recently associated with increased inflammation, higher SOFA scores,
ICU admission, and mortality rates among non-COVID-19 patients. Here, we
investigated the relationship between phenylalanine and inflammatory
markers in adults with COVID-19. Methods We assessed adults with COVID-19 at
hospital admission for clinical and laboratory data. Nuclear magnetic
resonance spectroscopy measured serum levels of phenylalanine and other
amino acids of its metabolomic pathway. Flow Cytometry measured serum
levels of IL-2, IL-4, IL-6, Il-10, TNF-α, and IFN-γ. Linear regression
models adjusted for potential confounders assessed the relationship
between serum levels of phenylalanine and inflammatory
cytokines. Results Phenylalanine and tyrosine were
significantly lower in mild disease as compared to moderate and severe
groups. Linear regression models showed that phenylalanine is
independently and positively associated with disease severity regardless
of the cytokine analyzed and after adjustment for potential confounders.
In addition, mild cases showed consistently lower serum phenylalanine
levels within the first ten days from disease onset to hospital
admission. Conclusions Phenylalanine is a marker of disease
severity. This association is independent of the time between the onset
of symptoms and the magnitude of the inflammatory state.
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13
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Bourgin M, Derosa L, Silva CAC, Goubet AG, Dubuisson A, Danlos FX, Grajeda-Iglesias C, Cerbone L, Geraud A, Laparra A, Aprahamian F, Nirmalathasan N, Madeo F, Zitvogel L, Kroemer G, Durand S. Circulating acetylated polyamines correlate with Covid-19 severity in cancer patients. Aging (Albany NY) 2021; 13:20860-20885. [PMID: 34517343 PMCID: PMC8457559 DOI: 10.18632/aging.203525] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/02/2021] [Indexed: 12/18/2022]
Abstract
Cancer patients are particularly susceptible to the development of severe Covid-19, prompting us to investigate the serum metabolome of 204 cancer patients enrolled in the ONCOVID trial. We previously described that the immunosuppressive tryptophan/kynurenine metabolite anthranilic acid correlates with poor prognosis in non-cancer patients. In cancer patients, we observed an elevation of anthranilic acid at baseline (without Covid-19 diagnosis) and no further increase with mild or severe Covid-19. We found that, in cancer patients, Covid-19 severity was associated with the depletion of two bacterial metabolites, indole-3-proprionate and 3-phenylproprionate, that both positively correlated with the levels of several inflammatory cytokines. Most importantly, we observed that the levels of acetylated polyamines (in particular N1-acetylspermidine, N1,N8-diacetylspermidine and N1,N12-diacetylspermine), alone or in aggregate, were elevated in severe Covid-19 cancer patients requiring hospitalization as compared to uninfected cancer patients or cancer patients with mild Covid-19. N1-acetylspermidine and N1,N8-diacetylspermidine were also increased in patients exhibiting prolonged viral shedding (>40 days). An abundant literature indicates that such acetylated polyamines increase in the serum from patients with cancer, cardiovascular disease or neurodegeneration, associated with poor prognosis. Our present work supports the contention that acetylated polyamines are associated with severe Covid-19, both in the general population and in patients with malignant disease. Severe Covid-19 is characterized by a specific metabolomic signature suggestive of the overactivation of spermine/spermidine N1-acetyl transferase-1 (SAT1), which catalyzes the first step of polyamine catabolism.
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Affiliation(s)
- Mélanie Bourgin
- Gustave Roussy Comprehensive Cancer Institute, Villejuif 94805, France
- Centre de Recherche des Cordeliers, Equipe Labellisée par la Ligue Contre le Cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris 75006, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif 94805, France
| | - Lisa Derosa
- Gustave Roussy Comprehensive Cancer Institute, Villejuif 94805, France
- Inserm U1015, Villejuif 94805, France
- Center of Clinical Investigations in Biotherapies of Cancer (Biotheris), Villejuif 94805, France
| | - Carolina Alves Costa Silva
- Gustave Roussy Comprehensive Cancer Institute, Villejuif 94805, France
- Inserm U1015, Villejuif 94805, France
- Center of Clinical Investigations in Biotherapies of Cancer (Biotheris), Villejuif 94805, France
- Faculty of Medicine, Université Paris Saclay, Le Kremlin-Bicêtre 94270, France
| | - Anne-Gaëlle Goubet
- Gustave Roussy Comprehensive Cancer Institute, Villejuif 94805, France
- Inserm U1015, Villejuif 94805, France
- Center of Clinical Investigations in Biotherapies of Cancer (Biotheris), Villejuif 94805, France
- Faculty of Medicine, Université Paris Saclay, Le Kremlin-Bicêtre 94270, France
| | - Agathe Dubuisson
- Gustave Roussy Comprehensive Cancer Institute, Villejuif 94805, France
- Inserm U1015, Villejuif 94805, France
| | - François-Xavier Danlos
- Gustave Roussy Comprehensive Cancer Institute, Villejuif 94805, France
- Faculty of Medicine, Université Paris Saclay, Le Kremlin-Bicêtre 94270, France
| | - Claudia Grajeda-Iglesias
- Gustave Roussy Comprehensive Cancer Institute, Villejuif 94805, France
- Centre de Recherche des Cordeliers, Equipe Labellisée par la Ligue Contre le Cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris 75006, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif 94805, France
| | - Luigi Cerbone
- Cancer Medicine Department, Gustave Roussy, Villejuif 94805, France
- Inserm U981, Villejuif 94805, France
| | - Arthur Geraud
- Department of Drug Development (DITEP), Gustave Roussy, Villejuif 94805, France
- Cancer Medicine Department, Gustave Roussy, Villejuif 94805, France
| | - Ariane Laparra
- Department of Drug Development (DITEP), Gustave Roussy, Villejuif 94805, France
| | - Fanny Aprahamian
- Gustave Roussy Comprehensive Cancer Institute, Villejuif 94805, France
- Centre de Recherche des Cordeliers, Equipe Labellisée par la Ligue Contre le Cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris 75006, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif 94805, France
| | - Nitharsshini Nirmalathasan
- Gustave Roussy Comprehensive Cancer Institute, Villejuif 94805, France
- Centre de Recherche des Cordeliers, Equipe Labellisée par la Ligue Contre le Cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris 75006, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif 94805, France
| | - Frank Madeo
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz 8010, Austria
- BioTechMed-Graz, Graz 8010, Austria
- Field of Excellence BioHealth, University of Graz, Graz 8010, Austria
| | - Laurence Zitvogel
- Gustave Roussy Comprehensive Cancer Institute, Villejuif 94805, France
- Inserm U1015, Villejuif 94805, France
- Center of Clinical Investigations in Biotherapies of Cancer (Biotheris), Villejuif 94805, France
- Faculty of Medicine, Université Paris Saclay, Le Kremlin-Bicêtre 94270, France
| | - Guido Kroemer
- Gustave Roussy Comprehensive Cancer Institute, Villejuif 94805, France
- Centre de Recherche des Cordeliers, Equipe Labellisée par la Ligue Contre le Cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris 75006, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif 94805, France
- Pôle De Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris 75015, France
| | - Sylvère Durand
- Gustave Roussy Comprehensive Cancer Institute, Villejuif 94805, France
- Centre de Recherche des Cordeliers, Equipe Labellisée par la Ligue Contre le Cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris 75006, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif 94805, France
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14
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D’Alessandro A, Thomas T, Akpan IJ, Reisz JA, Cendali FI, Gamboni F, Nemkov T, Thangaraju K, Katneni U, Tanaka K, Kahn S, Wei AZ, Valk JE, Hudson KE, Roh D, Moriconi C, Zimring JC, Hod EA, Spitalnik SL, Buehler PW, Francis RO. Biological and Clinical Factors Contributing to the Metabolic Heterogeneity of Hospitalized Patients with and without COVID-19. Cells 2021; 10:2293. [PMID: 34571942 PMCID: PMC8467961 DOI: 10.3390/cells10092293] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/24/2021] [Accepted: 08/31/2021] [Indexed: 12/26/2022] Open
Abstract
The Corona Virus Disease 2019 (COVID-19) pandemic represents an ongoing worldwide challenge. The present large study sought to understand independent and overlapping metabolic features of samples from acutely ill patients (n = 831) that tested positive (n = 543) or negative (n = 288) for COVID-19. High-throughput metabolomics analyses were complemented with antigen and enzymatic activity assays on plasma from acutely ill patients collected while in the emergency department, at admission, or during hospitalization. Lipidomics analyses were also performed on COVID-19-positive or -negative subjects with the lowest and highest body mass index (n = 60/group). Significant changes in amino acid and fatty acid/acylcarnitine metabolism emerged as highly relevant markers of disease severity, progression, and prognosis as a function of biological and clinical variables in these patients. Further, machine learning models were trained by entering all metabolomics and clinical data from half of the COVID-19 patient cohort and then tested on the other half, yielding ~78% prediction accuracy. Finally, the extensive amount of information accumulated in this large, prospective, observational study provides a foundation for mechanistic follow-up studies and data sharing opportunities, which will advance our understanding of the characteristics of the plasma metabolism in COVID-19 and other acute critical illnesses.
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Affiliation(s)
- Angelo D’Alessandro
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado Denver, Aurora, CO 80045, USA; (J.A.R.); (F.I.C.); (F.G.); (T.N.)
| | - Tiffany Thomas
- Department of Pathology & Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; (T.T.); (J.E.V.); (K.E.H.); (C.M.); (E.A.H.); (S.L.S.); (R.O.F.)
| | - Imo J. Akpan
- Division of Hematology/Oncology, Department of Medicine, Irving Medical Center, Columbia University, New York, NY 10032, USA; (I.J.A.); (S.K.); (A.Z.W.)
| | - Julie A. Reisz
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado Denver, Aurora, CO 80045, USA; (J.A.R.); (F.I.C.); (F.G.); (T.N.)
| | - Francesca I. Cendali
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado Denver, Aurora, CO 80045, USA; (J.A.R.); (F.I.C.); (F.G.); (T.N.)
| | - Fabia Gamboni
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado Denver, Aurora, CO 80045, USA; (J.A.R.); (F.I.C.); (F.G.); (T.N.)
| | - Travis Nemkov
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado Denver, Aurora, CO 80045, USA; (J.A.R.); (F.I.C.); (F.G.); (T.N.)
| | - Kiruphagaran Thangaraju
- Center for Blood Oxygen Transport, Department of Pathology, Department of Pediatrics, University of Maryland, Baltimore, MD 21201, USA; (K.T.); (U.K.); (P.W.B.)
| | - Upendra Katneni
- Center for Blood Oxygen Transport, Department of Pathology, Department of Pediatrics, University of Maryland, Baltimore, MD 21201, USA; (K.T.); (U.K.); (P.W.B.)
| | - Kenichi Tanaka
- Department of Anesthesiology, University of Maryland, Baltimore, MD 21201, USA;
- Department of Anesthesiology, University of Oklahoma College of Medicine, Oklahoma City, OK 73126-0901, USA
| | - Stacie Kahn
- Division of Hematology/Oncology, Department of Medicine, Irving Medical Center, Columbia University, New York, NY 10032, USA; (I.J.A.); (S.K.); (A.Z.W.)
| | - Alexander Z. Wei
- Division of Hematology/Oncology, Department of Medicine, Irving Medical Center, Columbia University, New York, NY 10032, USA; (I.J.A.); (S.K.); (A.Z.W.)
| | - Jacob E. Valk
- Department of Pathology & Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; (T.T.); (J.E.V.); (K.E.H.); (C.M.); (E.A.H.); (S.L.S.); (R.O.F.)
| | - Krystalyn E. Hudson
- Department of Pathology & Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; (T.T.); (J.E.V.); (K.E.H.); (C.M.); (E.A.H.); (S.L.S.); (R.O.F.)
| | - David Roh
- Department of Neurology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA;
| | - Chiara Moriconi
- Department of Pathology & Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; (T.T.); (J.E.V.); (K.E.H.); (C.M.); (E.A.H.); (S.L.S.); (R.O.F.)
| | - James C. Zimring
- Department of Pathology, University of Virginia, Charlottesville, VA 22903, USA;
| | - Eldad A. Hod
- Department of Pathology & Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; (T.T.); (J.E.V.); (K.E.H.); (C.M.); (E.A.H.); (S.L.S.); (R.O.F.)
| | - Steven L. Spitalnik
- Department of Pathology & Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; (T.T.); (J.E.V.); (K.E.H.); (C.M.); (E.A.H.); (S.L.S.); (R.O.F.)
| | - Paul W. Buehler
- Center for Blood Oxygen Transport, Department of Pathology, Department of Pediatrics, University of Maryland, Baltimore, MD 21201, USA; (K.T.); (U.K.); (P.W.B.)
| | - Richard O. Francis
- Department of Pathology & Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; (T.T.); (J.E.V.); (K.E.H.); (C.M.); (E.A.H.); (S.L.S.); (R.O.F.)
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15
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Yuan ZC, Hu B. Mass Spectrometry-Based Human Breath Analysis: Towards COVID-19 Diagnosis and Research. JOURNAL OF ANALYSIS AND TESTING 2021; 5:287-297. [PMID: 34422436 PMCID: PMC8364943 DOI: 10.1007/s41664-021-00194-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/25/2021] [Indexed: 12/12/2022]
Abstract
COVID-19 is a highly contagious respiratory disease that can be infected through human exhaled breath. Human breath analysis is an attractive strategy for rapid diagnosis of COVID-19 in a non-invasive way by monitoring breath biomarkers. Mass spectrometry (MS)-based approaches offer a promising analytical platform for human breath analysis due to their high speed, specificity, sensitivity, reproducibility, and broad coverage, as well as its versatile coupling methods with different chromatographic separation, and thus can lead to a better understanding of the clinical and biochemical processes of COVID-19. Herein, we try to review the developments and applications of MS-based approaches for multidimensional analysis of COVID-19 breath samples, including metabolites, proteins, microorganisms, and elements. New features of breath sampling and analysis are highlighted. Prospects and challenges on MS-based breath analysis related to COVID-19 diagnosis and study are discussed.
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Affiliation(s)
- Zi-Cheng Yuan
- Guangdong Provincial Engineering Research Center for On-line Source Apportionment System of Air Pollution, Institute of Mass Spectrometry and Atmospheric Environment, Jinan University, Guangzhou, 510632 China
| | - Bin Hu
- Guangdong Provincial Engineering Research Center for On-line Source Apportionment System of Air Pollution, Institute of Mass Spectrometry and Atmospheric Environment, Jinan University, Guangzhou, 510632 China
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D'Alessandro A, Akpan I, Thomas T, Reisz J, Cendali F, Gamboni F, Nemkov T, Thangaraju K, Katneni U, Tanaka K, Kahn S, Wei A, Valk J, Hudson K, Roh D, Moriconi C, Zimring J, Hod E, Spitalnik S, Buehler P, Francis R. Biological and Clinical Factors contributing to the Metabolic Heterogeneity of Hospitalized Patients with and without COVID-19. RESEARCH SQUARE 2021:rs.3.rs-480167. [PMID: 34013258 PMCID: PMC8132252 DOI: 10.21203/rs.3.rs-480167/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The Corona Virus Disease 2019 (COVID-19) pandemic represents an ongoing worldwide challenge. Exploratory studies evaluating the impact of COVID-19 infection on the plasma metabolome have been performed, often with small numbers of patients, and with or without relevant control data; however, determining the impact of biological and clinical variables remains critical to understanding potential markers of disease severity and progression. The present large study, including relevant controls, sought to understand independent and overlapping metabolic features of samples from acutely ill patients (n = 831), testing positive (n = 543) or negative (n = 288) for COVID-19. High-throughput metabolomics analyses were complemented with antigen and enzymatic activity assays on 831 plasma samples from acutely ill patients while in the emergency department, at admission, and during hospitalization. We then performed additional lipidomics analyses of the 60 subjects with the lowest and highest body mass index, either COVID-19 positive or negative. Omics data were correlated to detailed data on patient characteristics and clinical laboratory assays measuring coagulation, hematology and chemistry analytes. Significant changes in arginine/proline/citrulline, tryptophan/indole/kynurenine, fatty acid and acyl-carnitine metabolism emerged as highly relevant markers of disease severity, progression and prognosis as a function of biological and clinical variables in these patients. Further, machine learning models were trained by entering all metabolomics and clinical data from half of the COVID-19 patient cohort and then tested on the other half yielding ~ 78% prediction accuracy. Finally, the extensive amount of information accumulated in this large, prospective, observational study provides a foundation for follow-up mechanistic studies and data sharing opportunities, which will advance our understanding of the characteristics of the plasma metabolism in COVID-19 and other acute critical illnesses.
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Affiliation(s)
| | - Imo Akpan
- Columbia University Irving Medical Center
| | | | | | | | | | - Travis Nemkov
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver
| | | | | | | | | | | | - Jacob Valk
- Columbia University Irving Medical Center
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