1
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Ghini V, Vieri W, Celli T, Pecchioli V, Boccia N, Alonso-Vásquez T, Pelagatti L, Fondi M, Luchinat C, Bertini L, Vannucchi V, Landini G, Turano P. COVID-19: A complex disease with a unique metabolic signature. PLoS Pathog 2023; 19:e1011787. [PMID: 37943960 PMCID: PMC10662774 DOI: 10.1371/journal.ppat.1011787] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 11/21/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023] Open
Abstract
Plasma of COVID-19 patients contains a strong metabolomic/lipoproteomic signature, revealed by the NMR analysis of a cohort of >500 patients sampled during various waves of COVID-19 infection, corresponding to the spread of different variants, and having different vaccination status. This composite signature highlights common traits of the SARS-CoV-2 infection. The most dysregulated molecules display concentration trends that scale with disease severity and might serve as prognostic markers for fatal events. Metabolomics evidence is then used as input data for a sex-specific multi-organ metabolic model. This reconstruction provides a comprehensive view of the impact of COVID-19 on the entire human metabolism. The human (male and female) metabolic network is strongly impacted by the disease to an extent dictated by its severity. A marked metabolic reprogramming at the level of many organs indicates an increase in the generic energetic demand of the organism following infection. Sex-specific modulation of immune response is also suggested.
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Affiliation(s)
- Veronica Ghini
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino Florence, Italy
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Florence, Italy
| | - Walter Vieri
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino Florence, Italy
- Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Tommaso Celli
- Internal Medicine, Santa Maria Nuova Hospital, Florence, Florence, Italy
| | - Valentina Pecchioli
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino Florence, Italy
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Florence, Italy
| | - Nunzia Boccia
- Internal Medicine, Santa Maria Nuova Hospital, Florence, Florence, Italy
| | - Tania Alonso-Vásquez
- Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Lorenzo Pelagatti
- Internal Medicine, Santa Maria Nuova Hospital, Florence, Florence, Italy
| | - Marco Fondi
- Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Claudio Luchinat
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino Florence, Italy
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Florence, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Sesto Fiorentino Florence, Italy
| | - Laura Bertini
- Internal Medicine, Santa Maria Nuova Hospital, Florence, Florence, Italy
| | - Vieri Vannucchi
- Internal Medicine, Santa Maria Nuova Hospital, Florence, Florence, Italy
| | - Giancarlo Landini
- Internal Medicine, Santa Maria Nuova Hospital, Florence, Florence, Italy
| | - Paola Turano
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino Florence, Italy
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Florence, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Sesto Fiorentino Florence, Italy
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2
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Druzak S, Iffrig E, Roberts BR, Zhang T, Fibben KS, Sakurai Y, Verkerke HP, Rostad CA, Chahroudi A, Schneider F, Wong AKH, Roberts AM, Chandler JD, Kim SO, Mosunjac M, Mosunjac M, Geller R, Albizua I, Stowell SR, Arthur CM, Anderson EJ, Ivanova AA, Ahn J, Liu X, Maner-Smith K, Bowen T, Paiardini M, Bosinger SE, Roback JD, Kulpa DA, Silvestri G, Lam WA, Ortlund EA, Maier CL. Multiplatform analyses reveal distinct drivers of systemic pathogenesis in adult versus pediatric severe acute COVID-19. Nat Commun 2023; 14:1638. [PMID: 37015925 PMCID: PMC10073144 DOI: 10.1038/s41467-023-37269-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 03/08/2023] [Indexed: 04/06/2023] Open
Abstract
The pathogenesis of multi-organ dysfunction associated with severe acute SARS-CoV-2 infection remains poorly understood. Endothelial damage and microvascular thrombosis have been identified as drivers of COVID-19 severity, yet the mechanisms underlying these processes remain elusive. Here we show alterations in fluid shear stress-responsive pathways in critically ill COVID-19 adults as compared to non-COVID critically ill adults using a multiomics approach. Mechanistic in-vitro studies, using microvasculature-on-chip devices, reveal that plasma from critically ill COVID-19 adults induces fibrinogen-dependent red blood cell aggregation that mechanically damages the microvascular glycocalyx. This mechanism appears unique to COVID-19, as plasma from non-COVID sepsis patients demonstrates greater red blood cell membrane stiffness but induces less significant alterations in overall blood rheology. Multiomics analyses in pediatric patients with acute COVID-19 or the post-infectious multi-inflammatory syndrome in children (MIS-C) demonstrate little overlap in plasma cytokine and metabolite changes compared to adult COVID-19 patients. Instead, pediatric acute COVID-19 and MIS-C patients show alterations strongly associated with cytokine upregulation. These findings link high fibrinogen and red blood cell aggregation with endotheliopathy in adult COVID-19 patients and highlight differences in the key mediators of pathogenesis between adult and pediatric populations.
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Grants
- T32 GM142617 NIGMS NIH HHS
- P51 OD011132 NIH HHS
- R35 HL145000 NHLBI NIH HHS
- K99 HL150626 NHLBI NIH HHS
- T32 GM135060 NIGMS NIH HHS
- F31 DK126435 NIDDK NIH HHS
- R01 DK115213 NIDDK NIH HHS
- R38 AI140299 NIAID NIH HHS
- A F31 training fellowship from the National Institutes of Health National Institute of Diabetes and Digestive and Kidney Diseases (NIH/NIDDK), F31DK126435, supported S.A.D during the duration of this work. Stimulating Access to Research in Residency of the National Institutes of Health under Award Number R38AI140299 supported E.I. R35HL145000 supported E.I, Y.S, K.S.F and W.A.L. National Institutes of Health National Heart, Lung, and Blood Institute (NIH/NHLBI) HL150658, awarded to J.D.C. A training grant supported by the Biochemistry and Cell Developmental Biology program (BCDB) at Emory university, T32GM135060-02S1, to S.O.K. NIH/NIDDK Grant R01-DK115213 and Winship Synergy Award to E.A.O. NIH/NHLBI K99 HL150626-01 awarded to C.L.M. The lipidomics and metabolomics experiments were supported by the Emory Integrated Metabolomics and Lipidomics Core, which is subsidized by the Emory University School of Medicine and is one of the Emory Integrated Core Facilities.
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Affiliation(s)
- Samuel Druzak
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Elizabeth Iffrig
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Blaine R Roberts
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Tiantian Zhang
- Emory Integrated Metabolomics and Lipidomics Core, Emory University School of Medicine, Atlanta, GA, USA
| | - Kirby S Fibben
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Yumiko Sakurai
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Hans P Verkerke
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Christina A Rostad
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Ann Chahroudi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Frank Schneider
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Andrew Kam Ho Wong
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Emory National Primate Research Center, Atlanta, GA, USA
| | - Anne M Roberts
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Joshua D Chandler
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Susan O Kim
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Mario Mosunjac
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Marina Mosunjac
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Rachel Geller
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Georgia Bureau of Investigation, Decatur, GA, USA
| | - Igor Albizua
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Sean R Stowell
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Connie M Arthur
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Evan J Anderson
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Anna A Ivanova
- Emory Integrated Metabolomics and Lipidomics Core, Emory University School of Medicine, Atlanta, GA, USA
| | - Jun Ahn
- Emory Integrated Metabolomics and Lipidomics Core, Emory University School of Medicine, Atlanta, GA, USA
| | - Xueyun Liu
- Emory Integrated Metabolomics and Lipidomics Core, Emory University School of Medicine, Atlanta, GA, USA
| | - Kristal Maner-Smith
- Emory Integrated Metabolomics and Lipidomics Core, Emory University School of Medicine, Atlanta, GA, USA
| | - Thomas Bowen
- Emory Integrated Metabolomics and Lipidomics Core, Emory University School of Medicine, Atlanta, GA, USA
| | - Mirko Paiardini
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Emory National Primate Research Center, Atlanta, GA, USA
| | - Steve E Bosinger
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Emory National Primate Research Center, Atlanta, GA, USA
- Emory Vaccine Center, Atlanta, GA, USA
| | - John D Roback
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Deanna A Kulpa
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Emory National Primate Research Center, Atlanta, GA, USA
- Center for AIDS Research, Emory University, Atlanta, GA, USA
| | - Guido Silvestri
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Emory National Primate Research Center, Atlanta, GA, USA
- Emory Vaccine Center, Atlanta, GA, USA
- Center for AIDS Research, Emory University, Atlanta, GA, USA
| | - Wilbur A Lam
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
- Children's Healthcare of Atlanta, Atlanta, GA, USA.
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA.
- Emory Integrated Metabolomics and Lipidomics Core, Emory University School of Medicine, Atlanta, GA, USA.
| | - Cheryl L Maier
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA.
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3
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Shakiba MH, Gemünd I, Beyer M, Bonaguro L. Lung T cell response in COVID-19. Front Immunol 2023; 14:1108716. [PMID: 36875071 PMCID: PMC9977798 DOI: 10.3389/fimmu.2023.1108716] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/06/2023] [Indexed: 02/18/2023] Open
Abstract
The COVID-19 pandemic has shown the potentially devastating impact of novel respiratory infections worldwide. Insightful data obtained in the last years have shed light on the pathophysiology of SARS-CoV-2 infection and the role of the inflammatory response in driving both the resolution of the disease and uncontrolled deleterious inflammatory status in severe cases. In this mini-review, we cover some important aspects of the role of T cells in COVID-19 with a special focus on the local response in the lung. We focus on the reported T cell phenotypes in mild, moderate, and severe COVID-19, focusing on lung inflammation and on both the protective and damaging roles of the T cell response, also highlighting the open questions in the field.
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Affiliation(s)
- Mehrnoush Hadaddzadeh Shakiba
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- Immunogenomics and Neurodegeneration, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Ioanna Gemünd
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC, Australia
| | - Marc Beyer
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- Immunogenomics and Neurodegeneration, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) and University of Bonn, Bonn, Germany
| | - Lorenzo Bonaguro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
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4
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Batra R, Uni R, Akchurin OM, Alvarez-Mulett S, Gómez-Escobar LG, Patino E, Hoffman KL, Simmons W, Whalen W, Chetnik K, Buyukozkan M, Benedetti E, Suhre K, Schenck E, Cho SJ, Choi AMK, Schmidt F, Choi ME, Krumsiek J. Urine-based multi-omic comparative analysis of COVID-19 and bacterial sepsis-induced ARDS. Mol Med 2023; 29:13. [PMID: 36703108 PMCID: PMC9879238 DOI: 10.1186/s10020-023-00609-6] [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: 09/29/2022] [Accepted: 01/11/2023] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Acute respiratory distress syndrome (ARDS), a life-threatening condition during critical illness, is a common complication of COVID-19. It can originate from various disease etiologies, including severe infections, major injury, or inhalation of irritants. ARDS poses substantial clinical challenges due to a lack of etiology-specific therapies, multisystem involvement, and heterogeneous, poor patient outcomes. A molecular comparison of ARDS groups holds the potential to reveal common and distinct mechanisms underlying ARDS pathogenesis. METHODS We performed a comparative analysis of urine-based metabolomics and proteomics profiles from COVID-19 ARDS patients (n = 42) and bacterial sepsis-induced ARDS patients (n = 17). To this end, we used two different approaches, first we compared the molecular omics profiles between ARDS groups, and second, we correlated clinical manifestations within each group with the omics profiles. RESULTS The comparison of the two ARDS etiologies identified 150 metabolites and 70 proteins that were differentially abundant between the two groups. Based on these findings, we interrogated the interplay of cell adhesion/extracellular matrix molecules, inflammation, and mitochondrial dysfunction in ARDS pathogenesis through a multi-omic network approach. Moreover, we identified a proteomic signature associated with mortality in COVID-19 ARDS patients, which contained several proteins that had previously been implicated in clinical manifestations frequently linked with ARDS pathogenesis. CONCLUSION In summary, our results provide evidence for significant molecular differences in ARDS patients from different etiologies and a potential synergy of extracellular matrix molecules, inflammation, and mitochondrial dysfunction in ARDS pathogenesis. The proteomic mortality signature should be further investigated in future studies to develop prediction models for COVID-19 patient outcomes.
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Affiliation(s)
- Richa Batra
- grid.5386.8000000041936877XDepartment of Physiology and Biophysics, Institute for Computational Biomedicine, Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021 USA
| | - Rie Uni
- Division of Nephrology and Hypertension, Joan and Sanford I. Weill Department of Medicine, New York, NY USA
| | - Oleh M. Akchurin
- grid.5386.8000000041936877XDivision of Pediatric Nephrology, Department of Pediatrics, Weill Cornell Medicine, New York, NY USA ,grid.413734.60000 0000 8499 1112New York-Presbyterian Hospital, New York, NY USA
| | - Sergio Alvarez-Mulett
- grid.5386.8000000041936877XDivision of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY USA
| | - Luis G. Gómez-Escobar
- grid.5386.8000000041936877XDivision of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY USA
| | - Edwin Patino
- Division of Nephrology and Hypertension, Joan and Sanford I. Weill Department of Medicine, New York, NY USA
| | - Katherine L. Hoffman
- grid.5386.8000000041936877XDivision of Biostatistics, Department of Population Health Sciences, Weill Cornell Medicine, New York, NY USA
| | - Will Simmons
- grid.5386.8000000041936877XDivision of Biostatistics, Department of Population Health Sciences, Weill Cornell Medicine, New York, NY USA
| | - William Whalen
- grid.5386.8000000041936877XDivision of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY USA
| | - Kelsey Chetnik
- grid.5386.8000000041936877XDepartment of Physiology and Biophysics, Institute for Computational Biomedicine, Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021 USA
| | - Mustafa Buyukozkan
- grid.5386.8000000041936877XDepartment of Physiology and Biophysics, Institute for Computational Biomedicine, Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021 USA
| | - Elisa Benedetti
- grid.5386.8000000041936877XDepartment of Physiology and Biophysics, Institute for Computational Biomedicine, Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021 USA
| | - Karsten Suhre
- grid.418818.c0000 0001 0516 2170Bioinformatics Core, Weill Cornell Medicine –Qatar, Qatar Foundation, Doha, Qatar
| | - Edward Schenck
- grid.5386.8000000041936877XDivision of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY USA
| | - Soo Jung Cho
- grid.5386.8000000041936877XDivision of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY USA
| | - Augustine M. K. Choi
- grid.5386.8000000041936877XDivision of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY USA
| | - Frank Schmidt
- Proteomics Core, Weill Cornell Medicine -Qatar, Qatar Foundation, Doha, Qatar.
| | - Mary E. Choi
- Division of Nephrology and Hypertension, Joan and Sanford I. Weill Department of Medicine, New York, NY USA
| | - Jan Krumsiek
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, 10021, USA.
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5
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Brandwijk RJMGE, Michels MAHM, van Rossum M, de Nooijer AH, Nilsson PH, de Bruin WCC, Toonen EJM. Pitfalls in complement analysis: A systematic literature review of assessing complement activation. Front Immunol 2022; 13:1007102. [PMID: 36330514 PMCID: PMC9623276 DOI: 10.3389/fimmu.2022.1007102] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Background The complement system is an essential component of our innate defense and plays a vital role in the pathogenesis of many diseases. Assessment of complement activation is critical in monitoring both disease progression and response to therapy. Complement analysis requires accurate and standardized sampling and assay procedures, which has proven to be challenging. Objective We performed a systematic analysis of the current methods used to assess complement components and reviewed whether the identified studies performed their complement measurements according to the recommended practice regarding pre-analytical sample handling and assay technique. Results are supplemented with own data regarding the assessment of key complement biomarkers to illustrate the importance of accurate sampling and measuring of complement components. Methods A literature search using the Pubmed/MEDLINE database was performed focusing on studies measuring the key complement components C3, C5 and/or their split products and/or the soluble variant of the terminal C5b-9 complement complex (sTCC) in human blood samples that were published between February 2017 and February 2022. The identified studies were reviewed whether they had used the correct sample type and techniques for their analyses. Results A total of 92 out of 376 studies were selected for full-text analysis. Forty-five studies (49%) were identified as using the correct sample type and techniques for their complement analyses, while 25 studies (27%) did not use the correct sample type or technique. For 22 studies (24%), it was not specified which sample type was used. Conclusion A substantial part of the reviewed studies did not use the appropriate sample type for assessing complement activation or did not mention which sample type was used. This deviation from the standardized procedure can lead to misinterpretation of complement biomarker levels and hampers proper comparison of complement measurements between studies. Therefore, this study underlines the necessity of general guidelines for accurate and standardized complement analysis
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Affiliation(s)
| | - Marloes A. H. M. Michels
- Radboud Institute for Molecular Life Sciences, Department of Pediatric Nephrology, Amalia Children’s Hospital, Radboud University Medical Center, Nijmegen, Netherlands
| | - Mara van Rossum
- R&D Department, Hycult Biotechnology b.v., Uden, Netherlands
| | - Aline H. de Nooijer
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Per H. Nilsson
- Department of Immunology, University of Oslo and Oslo University Hospital Rikshospitalet, Oslo, Norway
- Linnaeus Centre for Biomaterials Chemistry, Linnaeus University, Kalmar, Sweden
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, Sweden
| | | | - Erik J. M. Toonen
- R&D Department, Hycult Biotechnology b.v., Uden, Netherlands
- *Correspondence: Erik J. M. Toonen,
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6
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Agrati C, Carsetti R, Bordoni V, Sacchi A, Quintarelli C, Locatelli F, Ippolito G, Capobianchi MR. The immune response as a double-edged sword: the lesson learnt during the COVID-19 pandemic. Immunology 2022; 167:287-302. [PMID: 35971810 PMCID: PMC9538066 DOI: 10.1111/imm.13564] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/06/2022] [Indexed: 11/29/2022] Open
Abstract
The COVID‐19 pandemic has represented an unprecedented challenge for the humanity, and scientists around the world provided a huge effort to elucidate critical aspects in the fight against the pathogen, useful in designing public health strategies, vaccines and therapeutic approaches. One of the first pieces of evidence characterizing the SARS‐CoV‐2 infection has been its breadth of clinical presentation, ranging from asymptomatic to severe/deadly disease, and the indication of the key role played by the immune response in influencing disease severity. This review is aimed at summarizing what the SARS‐CoV‐2 infection taught us about the immune response, highlighting its features of a double‐edged sword mediating both protective and pathogenic processes. We will discuss the protective role of soluble and cellular innate immunity and the detrimental power of a hyper‐inflammation‐shaped immune response, resulting in tissue injury and immunothrombotic events. We will review the importance of B‐ and T‐cell immunity in reducing the clinical severity and their ability to cross‐recognize viral variants.
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Affiliation(s)
- Chiara Agrati
- Laboratory of Cellular Immunology, INMI L. Spallanzani, IRCCS
| | - Rita Carsetti
- B cell laboratory, Immunology Research Area, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Alessandra Sacchi
- Molecular Virology and antimicrobial immunity Laboratory, Department of Science, Roma Tre University, Rome, Italy
| | - Concetta Quintarelli
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy.,Department of Hematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children Hospital, IRCCS
| | - Franco Locatelli
- Department of Hematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children Hospital, IRCCS.,Department of Pediatrics, Catholic University of Sacred Heart, Rome, Italy
| | - Giuseppe Ippolito
- General Directorate for Research and Health Innovation, Italian Ministry of Health
| | - Maria R Capobianchi
- Sacro Cuore Don Calabria Hospital IRCCS, Negrar di Valpolicella (Verona).,Saint Camillus International University of Health Sciences, Rome
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7
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Spick M, Lewis HM, Frampas CF, Longman K, Costa C, Stewart A, Dunn-Walters D, Greener D, Evetts G, Wilde MJ, Sinclair E, Barran PE, Skene DJ, Bailey MJ. An integrated analysis and comparison of serum, saliva and sebum for COVID-19 metabolomics. Sci Rep 2022; 12:11867. [PMID: 35831456 PMCID: PMC9278322 DOI: 10.1038/s41598-022-16123-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/05/2022] [Indexed: 12/15/2022] Open
Abstract
The majority of metabolomics studies to date have utilised blood serum or plasma, biofluids that do not necessarily address the full range of patient pathologies. Here, correlations between serum metabolites, salivary metabolites and sebum lipids are studied for the first time. 83 COVID-19 positive and negative hospitalised participants provided blood serum alongside saliva and sebum samples for analysis by liquid chromatography mass spectrometry. Widespread alterations to serum-sebum lipid relationships were observed in COVID-19 positive participants versus negative controls. There was also a marked correlation between sebum lipids and the immunostimulatory hormone dehydroepiandrosterone sulphate in the COVID-19 positive cohort. The biofluids analysed herein were also compared in terms of their ability to differentiate COVID-19 positive participants from controls; serum performed best by multivariate analysis (sensitivity and specificity of 0.97), with the dominant changes in triglyceride and bile acid levels, concordant with other studies identifying dyslipidemia as a hallmark of COVID-19 infection. Sebum performed well (sensitivity 0.92; specificity 0.84), with saliva performing worst (sensitivity 0.78; specificity 0.83). These findings show that alterations to skin lipid profiles coincide with dyslipidaemia in serum. The work also signposts the potential for integrated biofluid analyses to provide insight into the whole-body atlas of pathophysiological conditions.
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Affiliation(s)
- Matt Spick
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - Holly-May Lewis
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - Cecile F Frampas
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, GU2 7XH, UK
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - Katie Longman
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - Catia Costa
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, GU2 7XH, UK
- Surrey Ion Beam Centre, University of Surrey, Guildford, GU2 7XH, UK
| | - Alexander Stewart
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - Deborah Dunn-Walters
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - Danni Greener
- Frimley Park Hospital, Frimley Health NHS Trust, Frimley, GU16 7UJ, UK
| | - George Evetts
- Frimley Park Hospital, Frimley Health NHS Trust, Frimley, GU16 7UJ, UK
| | - Michael J Wilde
- School of Geography, Earth and Environmental Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
| | - Eleanor Sinclair
- Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Perdita E Barran
- Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Debra J Skene
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - Melanie J Bailey
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, GU2 7XH, UK.
- Surrey Ion Beam Centre, University of Surrey, Guildford, GU2 7XH, UK.
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Hu Y, Rehawi G, Moyon L, Gerstner N, Ogris C, Knauer-Arloth J, Bittner F, Marsico A, Mueller NS. Network Embedding Across Multiple Tissues and Data Modalities Elucidates the Context of Host Factors Important for COVID-19 Infection. Front Genet 2022; 13:909714. [PMID: 35903362 PMCID: PMC9315940 DOI: 10.3389/fgene.2022.909714] [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: 03/31/2022] [Accepted: 06/06/2022] [Indexed: 11/30/2022] Open
Abstract
COVID-19 is a heterogeneous disease caused by SARS-CoV-2. Aside from infections of the lungs, the disease can spread throughout the body and damage many other tissues, leading to multiorgan failure in severe cases. The highly variable symptom severity is influenced by genetic predispositions and preexisting diseases which have not been investigated in a large-scale multimodal manner. We present a holistic analysis framework, setting previously reported COVID-19 genes in context with prepandemic data, such as gene expression patterns across multiple tissues, polygenetic predispositions, and patient diseases, which are putative comorbidities of COVID-19. First, we generate a multimodal network using the prior-based network inference method KiMONo. We then embed the network to generate a meaningful lower-dimensional representation of the data. The input data are obtained via the Genotype-Tissue Expression project (GTEx), containing expression data from a range of tissues with genomic and phenotypic information of over 900 patients and 50 tissues. The generated network consists of nodes, that is, genes and polygenic risk scores (PRS) for several diseases/phenotypes, as well as for COVID-19 severity and hospitalization, and links between them if they are statistically associated in a regularized linear model by feature selection. Applying network embedding on the generated multimodal network allows us to perform efficient network analysis by identifying nodes close by in a lower-dimensional space that correspond to entities which are statistically linked. By determining the similarity between COVID-19 genes and other nodes through embedding, we identify disease associations to tissues, like the brain and gut. We also find strong associations between COVID-19 genes and various diseases such as ischemic heart disease, cerebrovascular disease, and hypertension. Moreover, we find evidence linking PTPN6 to a range of comorbidities along with the genetic predisposition of COVID-19, suggesting that this kinase is a central player in severe cases of COVID-19. In conclusion, our holistic network inference coupled with network embedding of multimodal data enables the contextualization of COVID-19-associated genes with respect to tissues, disease states, and genetic risk factors. Such contextualization can be exploited to further elucidate the biological importance of known and novel genes for severity of the disease in patients.
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Affiliation(s)
- Yue Hu
- Computational Health Department, Helmholtz Center Munich, Neuherberg, Germany
- Informatics 12 Chair of Bioinformatics, Technical University Munich, Garching, Germany
| | - Ghalia Rehawi
- Computational Health Department, Helmholtz Center Munich, Neuherberg, Germany
- Translational Research in Psychiatry, MaxPlanck Institute of Psychiatry, Munich, Germany
| | - Lambert Moyon
- Computational Health Department, Helmholtz Center Munich, Neuherberg, Germany
| | - Nathalie Gerstner
- Computational Health Department, Helmholtz Center Munich, Neuherberg, Germany
- Translational Research in Psychiatry, MaxPlanck Institute of Psychiatry, Munich, Germany
| | - Christoph Ogris
- Computational Health Department, Helmholtz Center Munich, Neuherberg, Germany
| | - Janine Knauer-Arloth
- Computational Health Department, Helmholtz Center Munich, Neuherberg, Germany
- Translational Research in Psychiatry, MaxPlanck Institute of Psychiatry, Munich, Germany
| | | | - Annalisa Marsico
- Computational Health Department, Helmholtz Center Munich, Neuherberg, Germany
| | - Nikola S. Mueller
- Computational Health Department, Helmholtz Center Munich, Neuherberg, Germany
- knowing01 GmbH, Munich, Germany
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9
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Liu P, Fang M, Luo Y, Zheng F, Jin Y, Cheng F, Zhu H, Jin X. Rare Variants in Inborn Errors of Immunity Genes Associated With Covid-19 Severity. Front Cell Infect Microbiol 2022; 12:888582. [PMID: 35694544 PMCID: PMC9184678 DOI: 10.3389/fcimb.2022.888582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/21/2022] [Indexed: 01/08/2023] Open
Abstract
Host genetic factors have been shown to play an important role in SARS-CoV-2 infection and the course of Covid-19 disease. The genetic contributions of common variants influencing Covid-19 susceptibility and severity have been extensively studied in diverse populations. However, the studies of rare genetic defects arising from inborn errors of immunity (IEI) are relatively few, especially in the Chinese population. To fill this gap, we used a deeply sequenced dataset of nearly 500 patients, all of Chinese descent, to investigate putative functional rare variants. Specifically, we annotated rare variants in our call set and selected likely deleterious missense (LDM) and high-confidence predicted loss-of-function (HC-pLoF) variants. Further, we analyzed LDM and HC-pLoF variants between non-severe and severe Covid-19 patients by (a) performing gene- and pathway-level association analyses, (b) testing the number of mutations in previously reported genes mapped from LDM and HC-pLoF variants, and (c) uncovering candidate genes via protein-protein interaction (PPI) network analysis of Covid-19-related genes and genes defined from LDM and HC-pLoF variants. From our analyses, we found that (a) pathways Tuberculosis (hsa:05152), Primary Immunodeficiency (hsa:05340), and Influenza A (hsa:05164) showed significant enrichment in severe patients compared to the non-severe ones, (b) HC-pLoF mutations were enriched in Covid-19-related genes in severe patients, and (c) several candidate genes, such as IL12RB1, TBK1, TLR3, and IFNGR2, are uncovered by PPI network analysis and worth further investigation. These regions generally play an essential role in regulating antiviral innate immunity responses to foreign pathogens and in responding to many inflammatory diseases. We believe that our identified candidate genes/pathways can be potentially used as Covid-19 diagnostic markers and help distinguish patients at higher risk.
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Affiliation(s)
- Panhong Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Beijing Genomeics Institute At Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Mingyan Fang
- Beijing Genomeics Institute At Shenzhen, BGI-Shenzhen, Shenzhen, China
- Beijing Genomeics Institute In Singapore, BGI-Singapore, Singapore, Singapore
| | - Yuxue Luo
- Beijing Genomeics Institute At Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Fang Zheng
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yan Jin
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fanjun Cheng
- Department of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huanhuan Zhu
- Beijing Genomeics Institute At Shenzhen, BGI-Shenzhen, Shenzhen, China
- *Correspondence: Xin Jin, ; Huanhuan Zhu,
| | - Xin Jin
- Beijing Genomeics Institute At Shenzhen, BGI-Shenzhen, Shenzhen, China
- Beijing Genomeics Institute In Singapore, BGI-Singapore, Singapore, Singapore
- School of Medicine, South China University of Technology, Guangzhou, China
- *Correspondence: Xin Jin, ; Huanhuan Zhu,
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10
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Farroni C, Picchianti-Diamanti A, Aiello A, Nicastri E, Laganà B, Agrati C, Castilletti C, Meschi S, Colavita F, Cuzzi G, Casetti R, Grassi G, Petrone L, Vanini V, Salmi A, Repele F, Altera AMG, Maffongelli G, Corpolongo A, Salemi S, Di Rosa R, Nalli G, Sesti G, Vaia F, Puro V, Goletti D. Kinetics of the B- and T-Cell Immune Responses After 6 Months From SARS-CoV-2 mRNA Vaccination in Patients With Rheumatoid Arthritis. Front Immunol 2022; 13:846753. [PMID: 35309297 PMCID: PMC8924958 DOI: 10.3389/fimmu.2022.846753] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/02/2022] [Indexed: 12/16/2022] Open
Abstract
ObjectiveTo assess the kinetics of the humoral and cell-mediated responses after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination in rheumatoid arthritis (RA) patients treated with different immunosuppressive therapies.MethodsFollowing vaccine completed schedule, health care workers (HCWs, n = 49) and RA patients (n = 35) were enrolled at 5 weeks (T1) and 6 months (T6) after the first dose of BNT162b2-mRNA vaccination. Serological response was assessed by quantifying anti-receptor-binding domain (RBD)-specific immunoglobulin G (IgG) and SARS-CoV-2 neutralizing antibodies, while cell-mediated response was assessed by a whole-blood test quantifying the interferon (IFN)-γ response to spike peptides. B-cell phenotype and IFN-γ-specific T-cell responses were evaluated by flow cytometry.ResultsAfter 6 months, anti-RBD antibodies were still detectable in 91.4% of RA patients, although we observed a significant reduction of the titer in patients under Cytotoxic T-Lymphocyte Antigen 4 (CTLA-4)-Ig [median: 16.4 binding antibody units (BAU)/ml, interquartile range (IQR): 11.3–44.3, p < 0.0001] or tumor necrosis factor (TNF)-α inhibitors (median: 26.5 BAU/ml, IQR: 14.9–108.8, p = 0.0034) compared to controls (median: 152.7 BAU/ml, IQR: 89.3–260.3). All peripheral memory B-cell (MBC) subpopulations, in particular, the switched IgG+ MBCs (CD19+CD27+IgD-IgM-IgG+), were significantly reduced in RA subjects under CTLA-4-Ig compared to those in HCWs (p = 0.0012). In RA patients, a significantly reduced anti-RBD IgG titer was observed at T6 vs. T1, mainly in those treated with CTLA-4-Ig (p = 0.002), interleukin (IL)-6 inhibitors (p = 0.015), and disease-modifying antirheumatic drugs (DMARDs) ± corticosteroids (CCSs) (p = 0.015). In contrast, a weak nonsignificant reduction of the T-cell response was reported at T6 vs. T1. T-cell response was found in 65.7% of the RA patients at T6, with lower significant magnitude in patients under CTLA-4-Ig compared to HCWs (p < 0.0001). The SARS-CoV-2 IFN-γ-S-specific T-cell response was mainly detected in the CD4+ T-cell compartment.ConclusionsIn this study, in RA patients after 6 months from COVID-19 vaccination, we show the kinetics, waning, and impairment of the humoral and, to a less extent, of the T-cell response. Similarly, a reduction of the specific response was also observed in the controls. Therefore, based on these results, a booster dose of the vaccine is crucial to increase the specific immune response regardless of the immunosuppressive therapy.
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Affiliation(s)
- Chiara Farroni
- Translational Research Unit, National Institute for Infectious Diseases Lazzaro Spallanzani-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Andrea Picchianti-Diamanti
- Department of Clinical and Molecular Medicine, “Sapienza” University, S. Andrea University Hospital, Rome, Italy
| | - Alessandra Aiello
- Translational Research Unit, National Institute for Infectious Diseases Lazzaro Spallanzani-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Emanuele Nicastri
- Clinical Division of Infectious Diseases, National Institute for Infectious Diseases Lazzaro Spallanzani-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Bruno Laganà
- Department of Clinical and Molecular Medicine, “Sapienza” University, S. Andrea University Hospital, Rome, Italy
| | - Chiara Agrati
- Laboratory of Cellular Immunology, National Institute for Infectious Diseases Lazzaro Spallanzani-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Concetta Castilletti
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Silvia Meschi
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Francesca Colavita
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Gilda Cuzzi
- Translational Research Unit, National Institute for Infectious Diseases Lazzaro Spallanzani-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Rita Casetti
- Laboratory of Cellular Immunology, National Institute for Infectious Diseases Lazzaro Spallanzani-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Germana Grassi
- Laboratory of Cellular Immunology, National Institute for Infectious Diseases Lazzaro Spallanzani-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Linda Petrone
- Translational Research Unit, National Institute for Infectious Diseases Lazzaro Spallanzani-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Valentina Vanini
- Translational Research Unit, National Institute for Infectious Diseases Lazzaro Spallanzani-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- Unità Operativa Semplice (UOS) Professioni Sanitarie Tecniche, National Institute for Infectious Diseases Lazzaro Spallanzani-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Andrea Salmi
- Translational Research Unit, National Institute for Infectious Diseases Lazzaro Spallanzani-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Federica Repele
- Translational Research Unit, National Institute for Infectious Diseases Lazzaro Spallanzani-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Anna Maria Gerarda Altera
- Translational Research Unit, National Institute for Infectious Diseases Lazzaro Spallanzani-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Gaetano Maffongelli
- Clinical Division of Infectious Diseases, National Institute for Infectious Diseases Lazzaro Spallanzani-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Angela Corpolongo
- Clinical Division of Infectious Diseases, National Institute for Infectious Diseases Lazzaro Spallanzani-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Simonetta Salemi
- Department of Clinical and Molecular Medicine, “Sapienza” University, S. Andrea University Hospital, Rome, Italy
| | - Roberta Di Rosa
- Department of Clinical and Molecular Medicine, “Sapienza” University, S. Andrea University Hospital, Rome, Italy
| | - Gabriele Nalli
- Department of Clinical and Molecular Medicine, “Sapienza” University, S. Andrea University Hospital, Rome, Italy
| | - Giorgio Sesti
- Department of Clinical and Molecular Medicine, “Sapienza” University, S. Andrea University Hospital, Rome, Italy
| | - Francesco Vaia
- Unità Operativa Complessa (UOC) Direzione Sanitaria, National Institute for Infectious Diseases Lazzaro Spallanzani-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Vincenzo Puro
- Unità Operativa Complessa (UOC) Emerging Infections and Centro di Riferimento AIDS (CRAIDS), National Institute for Infectious Diseases Lazzaro Spallanzani-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Delia Goletti
- Translational Research Unit, National Institute for Infectious Diseases Lazzaro Spallanzani-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- *Correspondence: Delia Goletti,
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Wu X, Li W, Luo Z, Chen Y. The molecular mechanism of Ligusticum wallichii for improving idiopathic pulmonary fibrosis: A network pharmacology and molecular docking study. Medicine (Baltimore) 2022; 101:e28787. [PMID: 35147109 PMCID: PMC8830865 DOI: 10.1097/md.0000000000028787] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/21/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND At present, there was no evidence that any drugs other than lung transplantation can effectively treat Idiopathic Pulmonary Fibrosis (IPF). Ligusticum wallichii, or Chinese name Chuan xiong has been widely used in different fibrosis fields. Our aim is to use network pharmacology and molecular docking to explore the pharmacological mechanism of the Traditional Chinese medicine (TCM) Ligusticum wallichii to improve IPF. MATERIALS AND METHODS The main chemical components and targets of Ligusticum wallichii were obtained from TCMSP, Swiss Target Prediction and Phammapper databases, and the targets were uniformly regulated in the Uniprot protein database after the combination. The main targets of IPF were obtained through Gencards, OMIM, TTD and DRUGBANK databases, and protein interaction analysis was carried out by using String to build PPI network. Metascape platform was used to analyze its involved biological processes and pathways, and Cytoscape3.8.2 software was used to construct "component-IPF target-pathway" network. And molecular docking verification was conducted through Auto Dock software. RESULTS The active ingredients of Ligusticum wallichii were Myricanone, Wallichilide, Perlolyrine, Senkyunone, Mandenol, Sitosterol and FA. The core targets for it to improve IPF were MAPK1, MAPK14, SRC, BCL2L1, MDM2, PTGS2, TGFB2, F2, MMP2, MMP9, and so on. The molecular docking verification showed that the molecular docking affinity of the core active compounds in Ligusticum wallichii (Myricanone, wallichilide, Perlolyrine) was <0 with MAPK1, MAPK14, and SRC. Perlolyrine has the strongest molecular docking ability, and its docking ability with SRC (-6.59 kJ/mol) is particularly prominent. Its biological pathway to improve IPF was mainly acted on the pathways in cancer, proteoglycans in cancer, and endocrine resistance, etc. CONCLUSIONS This study preliminarily identified the various molecular targets and multiple pathways of Ligusticum wallichii to improve IPF.
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