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López-Ayllón BD, Marin S, Fernández MF, García-García T, Fernández-Rodríguez R, de Lucas-Rius A, Redondo N, Mendoza-García L, Foguet C, Grigas J, Calvet A, Villalba JM, Gómez MJR, Megías D, Mandracchia B, Luque D, Lozano JJ, Calvo C, Herrán UM, Thomson TM, Garrido JJ, Cascante M, Montoya M. Metabolic and mitochondria alterations induced by SARS-CoV-2 accessory proteins ORF3a, ORF9b, ORF9c and ORF10. J Med Virol 2024; 96:e29752. [PMID: 38949191 DOI: 10.1002/jmv.29752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 06/07/2024] [Accepted: 06/08/2024] [Indexed: 07/02/2024]
Abstract
Antiviral signaling, immune response and cell metabolism are dysregulated by SARS-CoV-2, the causative agent of COVID-19. Here, we show that SARS-CoV-2 accessory proteins ORF3a, ORF9b, ORF9c and ORF10 induce a significant mitochondrial and metabolic reprogramming in A549 lung epithelial cells. While ORF9b, ORF9c and ORF10 induced largely overlapping transcriptomes, ORF3a induced a distinct transcriptome, including the downregulation of numerous genes with critical roles in mitochondrial function and morphology. On the other hand, all four ORFs altered mitochondrial dynamics and function, but only ORF3a and ORF9c induced a marked alteration in mitochondrial cristae structure. Genome-Scale Metabolic Models identified both metabolic flux reprogramming features both shared across all accessory proteins and specific for each accessory protein. Notably, a downregulated amino acid metabolism was observed in ORF9b, ORF9c and ORF10, while an upregulated lipid metabolism was distinctly induced by ORF3a. These findings reveal metabolic dependencies and vulnerabilities prompted by SARS-CoV-2 accessory proteins that may be exploited to identify new targets for intervention.
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Affiliation(s)
- Blanca D López-Ayllón
- Viral Immunology Lab, Molecular Biomedicine Department, BICS Unit. Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Silvia Marin
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, Spain
- CIBER of Hepatic and Digestive Diseases (CIBEREHD), Institute of Health Carlos III (ISCIII), Madrid, Spain
- Institute of Biomedicine of University of Barcelona (IBUB), University of Barcelona (UB), Barcelona, Spain
| | - Marco Fariñas Fernández
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, Spain
- Department of Biomedical Laboratory Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Tránsito García-García
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research, Institute of Córdoba (IMIBIC), Córdoba, Spain
| | - Raúl Fernández-Rodríguez
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research, Institute of Córdoba (IMIBIC), Córdoba, Spain
| | - Ana de Lucas-Rius
- Viral Immunology Lab, Molecular Biomedicine Department, BICS Unit. Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Natalia Redondo
- Unit of Infectious Diseases, University Hospital '12 de Octubre', Institute for Health Research Hospital '12 de Octubre' (imas12), Madrid, Spain
- Centre for Biomedical Research Network on Infectious Diseases (CIBERINFEC), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Laura Mendoza-García
- Viral Immunology Lab, Molecular Biomedicine Department, BICS Unit. Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Carles Foguet
- British Heart Foundation Cardiovascular Epidemiology Unit and Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Juozas Grigas
- Laboratory of Immunology, Department of Anatomy and Physiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Institute of Microbiology and Virology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Alba Calvet
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, Spain
- Institute of Biomedicine of University of Barcelona (IBUB), University of Barcelona (UB), Barcelona, Spain
| | - José Manuel Villalba
- Department of Cell Biology, Physiology and Immunology, Agrifood Campus of International Excellence, University of Córdoba, Córdoba, Spain
| | - María Josefa Rodríguez Gómez
- Scientific-Technical Central Units, Instituto de Salud Carlos III (ISCIII), Majadahonda, Spain
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Diego Megías
- Scientific-Technical Central Units, Instituto de Salud Carlos III (ISCIII), Majadahonda, Spain
| | - Biagio Mandracchia
- Scientific-Technical Central Units, Instituto de Salud Carlos III (ISCIII), Majadahonda, Spain
- ETSI Telecommunication, University of Valladolid, Valladolid, Spain
| | - Daniel Luque
- Scientific-Technical Central Units, Instituto de Salud Carlos III (ISCIII), Majadahonda, Spain
- Electron Microscope Unit, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, Australia
- School of Biomedical Sciences, University of New South Wales, Sydney, Australia
| | - Juan José Lozano
- CIBER of Hepatic and Digestive Diseases (CIBEREHD), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Cristina Calvo
- Barcelona Institute for Molecular Biology (IBMB-CSIC), Barcelona, Spain
| | - Unai Merino Herrán
- Viral Immunology Lab, Molecular Biomedicine Department, BICS Unit. Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Timothy M Thomson
- CIBER of Hepatic and Digestive Diseases (CIBEREHD), Institute of Health Carlos III (ISCIII), Madrid, Spain
- Barcelona Institute for Molecular Biology (IBMB-CSIC), Barcelona, Spain
- Translational Research and Computational Biology Laboratory, Faculty of Science and Engineering, Peruvian University Cayetano Heredia, Lima, Perú
| | - Juan J Garrido
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research, Institute of Córdoba (IMIBIC), Córdoba, Spain
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, Spain
- CIBER of Hepatic and Digestive Diseases (CIBEREHD), Institute of Health Carlos III (ISCIII), Madrid, Spain
- Institute of Biomedicine of University of Barcelona (IBUB), University of Barcelona (UB), Barcelona, Spain
| | - María Montoya
- Viral Immunology Lab, Molecular Biomedicine Department, BICS Unit. Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
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Taufer CR, da Silva J, Rampelotto PH. The Influence of Probiotic Lactobacilli on COVID-19 and the Microbiota. Nutrients 2024; 16:1350. [PMID: 38732597 PMCID: PMC11085918 DOI: 10.3390/nu16091350] [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: 03/07/2024] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 05/13/2024] Open
Abstract
This comprehensive review explores the potential of using lactobacilli as a probiotic in the management of COVID-19. Our findings suggest that lactobacilli show promise in reducing the risk of death, gastrointestinal and overall symptoms, and respiratory failure, as well as in lowering cytokines and inflammatory markers associated with the disease. The molecular mechanisms by which lactobacilli protect against COVID-19 and other viral infections may be related to the reduction in inflammation, modulation of the immune response, and direct interaction with viruses to produce antiviral substances. However, the selected studies demonstrate the presence of mixed findings for various clinical, biochemical, hematological, and immunological parameters, which may be attributed to methodological differences among studies. We highlight the importance of clearly describing randomization processes to minimize bias and caution against small sample sizes and inappropriate statistical tests that could lead to errors. This review offers valuable insights into the therapeutic potential of lactobacilli in the context of COVID-19 and identifies avenues for further research and applications. These findings hold promise for the development of novel approaches to managing COVID-19 and warrant further investigation into the potential benefits of lactobacilli in combating the disease.
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Affiliation(s)
- Clarissa Reginato Taufer
- Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| | - Juliana da Silva
- Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
- Graduate Program in Health and Human Development, Universidade La Salle, Canoas 92010-000, Brazil
| | - Pabulo Henrique Rampelotto
- Bioinformatics and Biostatistics Core Facility, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
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3
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Lei H. Hypoxia and Activation of Neutrophil Degranulation-Related Genes in the Peripheral Blood of COVID-19 Patients. Viruses 2024; 16:201. [PMID: 38399976 PMCID: PMC10891603 DOI: 10.3390/v16020201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 01/20/2024] [Accepted: 01/21/2024] [Indexed: 02/25/2024] Open
Abstract
Severe COVID-19 is characterized by systematic hyper-inflammation and subsequent damage to various organs. Therefore, it is critical to trace this cascade of hyper-inflammation. Blood transcriptome has been routinely utilized in the interrogation of host immune response in COVID-19 and other infectious conditions. In this study, consensus gene dysregulation in the blood was obtained from 13 independent transcriptome studies on COVID-19. Among the up-regulated genes, the most prominent functional categories were neutrophil degranulation and cell cycle, which is clearly different from the classical activation of interferon signaling pathway in seasonal flu. As for the potential upstream causal factors of the atypical gene dysregulation, systemic hypoxia was further examined because it is much more widely reported in COVID-19 than that in seasonal flu. It was found that both physiological and pathological hypoxia can induce activation of neutrophil degranulation-related genes in the blood. Furthermore, COVID-19 patients with different requirement for oxygen intervention showed distinctive levels of gene expression related to neutrophil degranulation in the whole blood, which was validated in isolated neutrophils. Thus, activation of neutrophil degranulation-related genes in the blood of COVID-19 could be partially attributed to hypoxia. Interestingly, similar pattern was also observed in H1N1 infection (the cause of Spanish flu) and several other severe respiratory viral infections. As for the molecular mechanism, both HIF-dependent and HIF-independent pathways have been examined. Since the activation of neutrophil degranulation-related genes is highly correlated with disease severity in COVID-19, early detection of hypoxia and active intervention may prevent further activation of neutrophil degranulation-related genes and other harmful downstream hyper-inflammation. This common mechanism is applicable to current and future pandemic as well as the severe form of common respiratory infection.
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Affiliation(s)
- Hongxing Lei
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China; ; Tel.: +86-010-84097276
- Cunji Medical School, University of Chinese Academy of Sciences, Beijing 101408, China
- Center of Alzheimer’s Disease, Beijing Institute for Brain Disorders, Beijing 100069, China
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4
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Krchlíková V, Lotke R, Haußmann I, Reinišová M, Kučerová D, Pecnová Ľ, Ungrová L, Hejnar J, Sauter D, Elleder D. Independent loss events of a functional tetherin gene in galliform birds. J Virol 2023; 97:e0080323. [PMID: 37712707 PMCID: PMC10617486 DOI: 10.1128/jvi.00803-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 07/19/2023] [Indexed: 09/16/2023] Open
Abstract
IMPORTANCE Birds represent important hosts for numerous viruses, including zoonotic viruses and pathogens with the potential to cause major economic losses to the poultry industry. Viral replication and transmission can be inhibited or blocked by the action of antiviral restriction factors (RFs) encoded by the host. One well-characterized RF is tetherin, a protein that directly blocks the release of newly formed viral particles from infected cells. Here, we describe the evolutionary loss of a functional tetherin gene in two galliform birds, turkey (Meleagris gallopavo) and Mikado pheasant (Syrmaticus mikado). Moreover, we demonstrate that the structurally related protein TMCC(aT) exerts antiviral activity in several birds, albeit by a mechanism different from that of tetherin. The evolutionary scenario described here represents the first documented loss-of-tetherin cases in vertebrates.
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Affiliation(s)
- Veronika Krchlíková
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Rishikesh Lotke
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Isabell Haußmann
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Markéta Reinišová
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Dana Kučerová
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ľubomíra Pecnová
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Lenka Ungrová
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jiří Hejnar
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Daniel Sauter
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Daniel Elleder
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
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5
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Breno M, Noris M, Rubis N, Parvanova AI, Martinetti D, Gamba S, Liguori L, Mele C, Piras R, Orisio S, Valoti E, Alberti M, Diadei O, Bresin E, Rigoldi M, Prandini S, Gamba T, Stucchi N, Carrara F, Daina E, Benigni A, Remuzzi G. A GWAS in the pandemic epicenter highlights the severe COVID-19 risk locus introgressed by Neanderthals. iScience 2023; 26:107629. [PMID: 37731612 PMCID: PMC10507134 DOI: 10.1016/j.isci.2023.107629] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/29/2023] [Accepted: 08/11/2023] [Indexed: 09/22/2023] Open
Abstract
Large GWAS indicated that genetic factors influence the response to SARS-CoV-2. However, sex, age, concomitant diseases, differences in ancestry, and uneven exposure to the virus impacted the interpretation of data. We aimed to perform a GWAS of COVID-19 outcome in a homogeneous population who experienced a high exposure to the virus and with a known infection status. We recruited inhabitants of Bergamo province-that in spring 2020 was the epicenter of the SARS-Cov-2 pandemic in Europe-via an online questionnaire followed by personal interviews. Cases and controls were matched by age, sex and risk factors. We genotyped 1195 individuals and replicated the association at the 3p21.31 locus with severity, but with a stronger effect size that further increased in gravely ill patients. Transcriptome-wide association study highlighted eQTLs for LZTFL1 and CCR9. We also identified 17 loci not previously reported, suggestive for an association with either COVID-19 severity or susceptibility.
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Affiliation(s)
- Matteo Breno
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Marina Noris
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Nadia Rubis
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Aneliya Ilieva Parvanova
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Davide Martinetti
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Sara Gamba
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Lucia Liguori
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Caterina Mele
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Rossella Piras
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Silvia Orisio
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Elisabetta Valoti
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Marta Alberti
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Olimpia Diadei
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Elena Bresin
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Miriam Rigoldi
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Silvia Prandini
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Tiziano Gamba
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Nadia Stucchi
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Fabiola Carrara
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Erica Daina
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Ariela Benigni
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Giuseppe Remuzzi
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
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Viasus D, Nonell L, Restrepo C, Figueroa F, Donado-Mazarrón C, Carratalà J. A Systematic Review of Gene Expression Studies in Critically Ill Patients with Sepsis and Community-Acquired Pneumonia. Biomedicines 2023; 11:2755. [PMID: 37893128 PMCID: PMC10604146 DOI: 10.3390/biomedicines11102755] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/14/2023] [Accepted: 10/08/2023] [Indexed: 10/29/2023] Open
Abstract
(1) Background: Sepsis is present in nearly 90% of critically ill patients with community-acquired pneumonia (CAP). This systematic review updates the information on studies that have assessed gene expression profiles in critically ill septic patients with CAP. (2) Methods: We searched for studies that satisfied the following criteria: (a) expression profile in critically ill patients with sepsis due to CAP, (b) presence of a control group, and (c) adult patients. Over-representation analysis was performed with clusterProfiler using the Hallmark and Reactome collections. (3) Results: A total of 4312 differentially expressed genes (DEGs) and sRNAs were included in the enrichment analysis. In the Hallmark collection, genes regulated by nuclear factor kappa B in response to tumor necrosis factor, genes upregulated by signal transducer and activator of transcription 5 in response to interleukin 2 stimulation, genes upregulated in response to interferon-gamma, genes defining the inflammatory response, a subgroup of genes regulated by MYC-version 1 (v1), and genes upregulated during transplant rejection were significantly enriched in critically ill septic patients with CAP. Moreover, 88 pathways were identified in the Reactome database. (4) Conclusions: This study summarizes the reported DEGs in critically ill septic patients with CAP and investigates their functional implications. The results highlight the complexity of immune responses during CAP.
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Affiliation(s)
- Diego Viasus
- Department of Medicine, Division of Health Sciences, Universidad del Norte and Hospital Universidad del Norte, Barranquilla 081001, Colombia
| | - Lara Nonell
- Departament de Biociències, Universitat de Vic—Universitat Central de Catalunya, 08500 Barcelona, Spain;
| | - Carlos Restrepo
- Department of Medicine, Division of Health Sciences, Universidad del Norte and Hospital Universidad del Norte, Barranquilla 081001, Colombia
| | - Fabian Figueroa
- Department of Medicine, Division of Health Sciences, Universidad del Norte and Hospital Universidad del Norte, Barranquilla 081001, Colombia
| | - Carla Donado-Mazarrón
- Department of Infectious Diseases, Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), University of Barcelona, 08907 Barcelona, Spain;
| | - Jordi Carratalà
- Department of Infectious Diseases, Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), University of Barcelona, 08907 Barcelona, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
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7
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Alqutami F, Hachim M, Hodgman C, Atiomo W. Transcriptomic analysis identifies four novel receptors potentially linking endometrial cancer with polycystic ovary syndrome and generates a transcriptomic atlas. Oncotarget 2023; 14:825-835. [PMID: 37737665 PMCID: PMC10515731 DOI: 10.18632/oncotarget.28513] [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: 04/03/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023] Open
Abstract
Polycystic Ovary Syndrome (PCOS) is associated with a 3 to 4-fold increased risk of endometrial cancer (EC), but molecular mechanisms are unclear. Upregulation of the IGF1 gene in PCOS endometrium may increase EC risk, but this is uncertain. We aimed to investigate links between EC and PCOS, by analysing publicly available transcriptomic data. The NCBI Gene Expression Omnibus was used to identify relevant studies. Differentially expressed genes (DEGs) were identified and analysed using Metascape to identify pathways of interest. PCOS DEGs that encode proteins secreted into blood were identified using the Human Protein Atlas blood protein database. EC DEGs that are cellular receptors were identified using EcoTyper. These were intersected to identify which EC receptors interact with PCOS secreted proteins. Seven receptors were identified in EC but only PTPRF, ITGA2, ITGA3 and ITGB4 genes were expressed on epithelial cells. Pathway enrichment of these genes showed that the major and common pathway involved was that of the PI3K-AKT signalling pathway which was consistent with a link between PCOS and EC. However, IGF1 was down regulated in PCOS and EC. These findings hold significant promise for improving our understanding of mechanistic pathways leading to EC in PCOS.
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Affiliation(s)
- Fatma Alqutami
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Healthcare City, Dubai, UAE
| | - Mahmood Hachim
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Healthcare City, Dubai, UAE
| | - Charlie Hodgman
- School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
| | - William Atiomo
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Healthcare City, Dubai, UAE
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8
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Banerjee U, Chunchanur S, R A, Balaji KN, Singh A, Chakravortty D, Chandra N. Systems-level profiling of early peripheral host-response landscape variations across COVID-19 severity states in an Indian cohort. Genes Immun 2023; 24:183-193. [PMID: 37438430 DOI: 10.1038/s41435-023-00210-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 06/25/2023] [Accepted: 06/28/2023] [Indexed: 07/14/2023]
Abstract
Host immune response to COVID-19 plays a significant role in regulating disease severity. Although big data analysis has provided significant insights into the host biology of COVID-19 across the world, very few such studies have been performed in the Indian population. This study utilizes a transcriptome-integrated network analysis approach to compare the immune responses between asymptomatic or mild and moderate-severe COVID-19 patients in an Indian cohort. An immune suppression phenotype is observed in the early stages of moderate-severe COVID-19 manifestation. A number of pathways are identified that play crucial roles in the host control of the disease such as the type I interferon response and classical complement pathway which show different activity levels across the severity spectrum. This study also identifies two transcription factors, IRF7 and ESR1, to be important in regulating the severity of COVID-19. Overall this study provides a deep understanding of the peripheral immune landscape in the COVID-19 severity spectrum in the Indian genetic background and opens up future research avenues to compare immune responses across global populations.
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Affiliation(s)
- Ushashi Banerjee
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Sneha Chunchanur
- Bangalore Medical College and Research Institute (BMCRI), Bengaluru, India
| | - Ambica R
- Bangalore Medical College and Research Institute (BMCRI), Bengaluru, India
| | | | - Amit Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Center for Infectious Disease Research, Indian Institute of Science, Bengaluru, India
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Center for Infectious Disease Research, Indian Institute of Science, Bengaluru, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India.
- Center for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, India.
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Mucosal Gene Expression in Response to SARS-CoV-2 Is Associated with Viral Load. J Virol 2023; 97:e0147822. [PMID: 36656015 PMCID: PMC9973040 DOI: 10.1128/jvi.01478-22] [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] [Indexed: 01/20/2023] Open
Abstract
Little is known about the relationships between symptomatic early severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral load and upper airway mucosal gene expression and immune response. To examine the association of symptomatic SARS-CoV-2 early viral load with upper airway mucosal gene expression, we profiled the host mucosal transcriptome from nasopharyngeal swab samples from 68 adults with symptomatic, mild-to-moderate coronavirus disease 19 (COVID-19). We measured SARS-CoV-2 viral load using reverse transcription-quantitative PCR (RT-qPCR). We then examined the association of SARS-CoV-2 viral load with upper airway mucosal immune response. We detected SARS-CoV-2 in all samples and recovered >80% of the genome from 95% of the samples from symptomatic COVID-19 adults. The respiratory virome was dominated by SARS-CoV-2, with limited codetection of other respiratory viruses, with the human Rhinovirus C being identified in 4 (6%) samples. This limited codetection of other respiratory viral pathogens may be due to the implementation of public health measures, like social distancing and masking practices. We observed a significant positive correlation between SARS-CoV-2 viral load and interferon signaling (OAS2, OAS3, IFIT1, UPS18, ISG15, ISG20, IFITM1, and OASL), chemokine signaling (CXCL10 and CXCL11), and adaptive immune system (IFITM1, CD300E, and SIGLEC1) genes in symptomatic, mild-to-moderate COVID-19 adults, when adjusting for age, sex, and race. Interestingly, the expression levels of most of these genes plateaued at a cycle threshold (CT) value of ~25. Overall, our data show that the early nasal mucosal immune response to SARS-CoV-2 infection is viral load dependent, potentially modifying COVID-19 outcomes. IMPORTANCE Several prior studies have shown that SARS-CoV-2 viral load can predict the likelihood of disease spread and severity. A higher detectable SARS-CoV-2 plasma viral load was associated with worse respiratory disease severity. However, the relationship between SARS-CoV-2 viral load, airway mucosal gene expression, and immune response remains elusive. We profiled the nasal mucosal transcriptome from nasal samples collected from adults infected with SARS-CoV-2 during spring 2020 with mild-to-moderate symptoms using a comprehensive metatranscriptomics method. We observed a positive correlation between SARS-CoV-2 viral load, interferon signaling, chemokine signaling, and adaptive immune system in adults with COVID-19. Our data suggest that early nasal mucosal immune response to SARS-CoV-2 infection was viral load dependent and may modify COVID-19 outcomes.
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10
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Context-Specific Genome-Scale Metabolic Modelling and Its Application to the Analysis of COVID-19 Metabolic Signatures. Metabolites 2023; 13:metabo13010126. [PMID: 36677051 PMCID: PMC9866716 DOI: 10.3390/metabo13010126] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/27/2022] [Accepted: 01/10/2023] [Indexed: 01/19/2023] Open
Abstract
Genome-scale metabolic models (GEMs) have found numerous applications in different domains, ranging from biotechnology to systems medicine. Herein, we overview the most popular algorithms for the automated reconstruction of context-specific GEMs using high-throughput experimental data. Moreover, we describe different datasets applied in the process, and protocols that can be used to further automate the model reconstruction and validation. Finally, we describe recent COVID-19 applications of context-specific GEMs, focusing on the analysis of metabolic implications, identification of biomarkers and potential drug targets.
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11
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Lio CT, Grabert G, Louadi Z, Fenn A, Baumbach J, Kacprowski T, List M, Tsoy O. Systematic analysis of alternative splicing in time course data using Spycone. Bioinformatics 2022; 39:6965022. [PMID: 36579860 PMCID: PMC9831059 DOI: 10.1093/bioinformatics/btac846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 11/16/2022] [Accepted: 12/28/2022] [Indexed: 12/30/2022] Open
Abstract
MOTIVATION During disease progression or organism development, alternative splicing may lead to isoform switches that demonstrate similar temporal patterns and reflect the alternative splicing co-regulation of such genes. Tools for dynamic process analysis usually neglect alternative splicing. RESULTS Here, we propose Spycone, a splicing-aware framework for time course data analysis. Spycone exploits a novel IS detection algorithm and offers downstream analysis such as network and gene set enrichment. We demonstrate the performance of Spycone using simulated and real-world data of SARS-CoV-2 infection. AVAILABILITY AND IMPLEMENTATION The Spycone package is available as a PyPI package. The source code of Spycone is available under the GPLv3 license at https://github.com/yollct/spycone and the documentation at https://spycone.readthedocs.io/en/latest/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Chit Tong Lio
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, Hamburg 22607, Germany,Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Gordon Grabert
- Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics of Technische Universität Braunschweig and Hannover Medical School, Braunschweig 38106, Germany,Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, Braunschweig 38106, Germany
| | - Zakaria Louadi
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, Hamburg 22607, Germany,Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Amit Fenn
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, Hamburg 22607, Germany,Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, Hamburg 22607, Germany,Institute of Mathematics and Computer Science, University of Southern Denmark, Odense 5000, Denmark
| | - Tim Kacprowski
- Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics of Technische Universität Braunschweig and Hannover Medical School, Braunschweig 38106, Germany,Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, Braunschweig 38106, Germany
| | | | - Olga Tsoy
- To whom correspondence should be addressed.
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Rajagopala SV, Strickland BA, Pakala SB, Kimura KS, Shilts MH, Rosas-Salazar C, Brown HM, Freeman MH, Wessinger BC, Gupta V, Phillips E, Mallal SA, Turner JH, Das SR. Mucosal gene expression in response to SARS-CoV-2 is associated with early viral load. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.08.23.504908. [PMID: 36052371 PMCID: PMC9435401 DOI: 10.1101/2022.08.23.504908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Little is known about the relationships between symptomatic early-time SARS-CoV-2 viral load and upper airway mucosal gene expression and immune response. To examine the association of symptomatic SARS-CoV-2 early viral load with upper airway mucosal gene expression, we profiled the host mucosal transcriptome from nasopharyngeal swab samples from 68 adults with symptomatic, mild-to-moderate COVID-19. We measured SARS-CoV-2 viral load using qRT-PCR. We then examined the association of SARS-CoV-2 viral load with upper airway mucosal immune response. We detected SARS-CoV-2 in all samples and recovered >80% of the genome from 85% of the samples from symptomatic COVID-19 adults. The respiratory virome was dominated by SARS-CoV-2, with limited co-detection of common respiratory viruses i.e., only the human Rhinovirus (HRV) being identified in 6% of the samples. We observed a significant positive correlation between SARS-CoV-2 viral load and interferon signaling (OAS2, OAS3, IFIT1, UPS18, ISG15, ISG20, IFITM1, and OASL), chemokine signaling (CXCL10 and CXCL11), and adaptive immune system (IFITM1, CD300E, and SIGLEC1) genes in symptomatic, mild-to-moderate COVID-19 adults, when adjusted for age, sex and race. Interestingly, the expression levels of most of these genes plateaued at a CT value of ~25. Overall, our data shows that early nasal mucosal immune response to SARS-CoV-2 infection is viral load dependent, which potentially could modify COVID-19 outcomes. AUTHOR SUMMARY Several prior studies have shown that SARS-CoV-2 viral load can predict the likelihood of disease spread and severity. A higher detectable SARS-CoV-2 plasma viral load was associated with worse respiratory disease severity. However, the relationship between SARS-CoV-2 viral load and airway mucosal gene expression and immune response remains elusive. We profiled the nasal mucosal transcriptome from nasal samples collected from adults infected with SARS-CoV-2 during Spring 2020 with mild-to-moderate symptoms using a comprehensive metatranscriptomics method. We observed a positive correlation between SARS-CoV-2 viral load with interferon signaling, chemokine signaling, and adaptive immune system in adults with COVID-19. Our data suggest that early nasal mucosal immune response to SARS-CoV-2 infection was viral load-dependent and may modify COVID-19 outcomes.
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Affiliation(s)
| | - Britton A. Strickland
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN,Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Suman B. Pakala
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Kyle S. Kimura
- Department of Otolaryngology, Vanderbilt University Medical Center, Nashville, TN
| | - Meghan H. Shilts
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | | | - Hunter M. Brown
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Michael H. Freeman
- Department of Otolaryngology, Vanderbilt University Medical Center, Nashville, TN
| | | | - Veerain Gupta
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Elizabeth Phillips
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Simon A. Mallal
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Justin H. Turner
- Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Suman R. Das
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN,Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA,Department of Otolaryngology, Vanderbilt University Medical Center, Nashville, TN
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13
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Rhoades R, Solomon S, Johnson C, Teng S. Impact of SARS-CoV-2 on Host Factors Involved in Mental Disorders. Front Microbiol 2022; 13:845559. [PMID: 35444632 PMCID: PMC9014212 DOI: 10.3389/fmicb.2022.845559] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 02/14/2022] [Indexed: 11/23/2022] Open
Abstract
COVID-19, caused by SARS-CoV-2, is a systemic illness due to its multiorgan effects in patients. The disease has a detrimental impact on respiratory and cardiovascular systems. One early symptom of infection is anosmia or lack of smell; this implicates the involvement of the olfactory bulb in COVID-19 disease and provides a route into the central nervous system. However, little is known about how SARS-CoV-2 affects neurological or psychological symptoms. SARS-CoV-2 exploits host receptors that converge on pathways that impact psychological symptoms. This systemic review discusses the ways involved by coronavirus infection and their impact on mental health disorders. We begin by briefly introducing the history of coronaviruses, followed by an overview of the essential proteins to viral entry. Then, we discuss the downstream effects of viral entry on host proteins. Finally, we review the literature on host factors that are known to play critical roles in neuropsychiatric symptoms and mental diseases and discuss how COVID-19 could impact mental health globally. Our review details the host factors and pathways involved in the cellular mechanisms, such as systemic inflammation, that play a significant role in the development of neuropsychological symptoms stemming from COVID-19 infection.
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Affiliation(s)
- Raina Rhoades
- Department of Biology, Howard University, Washington, DC, United States
| | - Sarah Solomon
- Department of Biology, Howard University, Washington, DC, United States
| | - Christina Johnson
- Department of Biology, Howard University, Washington, DC, United States
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14
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Schimke LF, Marques AHC, Baiocchi GC, de Souza Prado CA, Fonseca DLM, Freire PP, Rodrigues Plaça D, Salerno Filgueiras I, Coelho Salgado R, Jansen-Marques G, Rocha Oliveira AE, Peron JPS, Cabral-Miranda G, Barbuto JAM, Camara NOS, Calich VLG, Ochs HD, Condino-Neto A, Overmyer KA, Coon JJ, Balnis J, Jaitovich A, Schulte-Schrepping J, Ulas T, Schultze JL, Nakaya HI, Jurisica I, Cabral-Marques O. Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States. Cells 2022; 11:cells11050847. [PMID: 35269470 PMCID: PMC8909161 DOI: 10.3390/cells11050847] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 02/06/2023] Open
Abstract
Severe COVID-19 patients present a clinical and laboratory overlap with other hyperinflammatory conditions such as hemophagocytic lymphohistiocytosis (HLH). However, the underlying mechanisms of these conditions remain to be explored. Here, we investigated the transcriptome of 1596 individuals, including patients with COVID-19 in comparison to healthy controls, other acute inflammatory states (HLH, multisystem inflammatory syndrome in children [MIS-C], Kawasaki disease [KD]), and different respiratory infections (seasonal coronavirus, influenza, bacterial pneumonia). We observed that COVID-19 and HLH share immunological pathways (cytokine/chemokine signaling and neutrophil-mediated immune responses), including gene signatures that stratify COVID-19 patients admitted to the intensive care unit (ICU) and COVID-19_nonICU patients. Of note, among the common differentially expressed genes (DEG), there is a cluster of neutrophil-associated genes that reflects a generalized hyperinflammatory state since it is also dysregulated in patients with KD and bacterial pneumonia. These genes are dysregulated at the protein level across several COVID-19 studies and form an interconnected network with differentially expressed plasma proteins that point to neutrophil hyperactivation in COVID-19 patients admitted to the intensive care unit. scRNAseq analysis indicated that these genes are specifically upregulated across different leukocyte populations, including lymphocyte subsets and immature neutrophils. Artificial intelligence modeling confirmed the strong association of these genes with COVID-19 severity. Thus, our work indicates putative therapeutic pathways for intervention.
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Affiliation(s)
- Lena F. Schimke
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
- Correspondence: (L.F.S.); (O.C.-M.); Tel.: +55-11-943661555 (L.F.S.); +55-11-974642022 (O.C.-M.)
| | - Alexandre H. C. Marques
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
| | - Gabriela Crispim Baiocchi
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
| | - Caroline Aliane de Souza Prado
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (C.A.d.S.P.); (D.L.M.F.); (D.R.P.); (A.E.R.O.); (H.I.N.)
| | - Dennyson Leandro M. Fonseca
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (C.A.d.S.P.); (D.L.M.F.); (D.R.P.); (A.E.R.O.); (H.I.N.)
| | - Paula Paccielli Freire
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
| | - Desirée Rodrigues Plaça
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (C.A.d.S.P.); (D.L.M.F.); (D.R.P.); (A.E.R.O.); (H.I.N.)
| | - Igor Salerno Filgueiras
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
| | - Ranieri Coelho Salgado
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
| | - Gabriel Jansen-Marques
- Information Systems, School of Arts, Sciences and Humanities, University of Sao Paulo, São Paulo 03828-000, Brazil;
| | - Antonio Edson Rocha Oliveira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (C.A.d.S.P.); (D.L.M.F.); (D.R.P.); (A.E.R.O.); (H.I.N.)
| | - Jean Pierre Schatzmann Peron
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
| | - Gustavo Cabral-Miranda
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
| | - José Alexandre Marzagão Barbuto
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
- Laboratory of Medical Investigation in Pathogenesis, Targeted Therapy in Onco-Immuno-Hematology (LIM-31), Department of Hematology, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo 05403-000, Brazil
| | - Niels Olsen Saraiva Camara
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
| | - Vera Lúcia Garcia Calich
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
| | - Hans D. Ochs
- Department of Pediatrics, Seattle Children’s Research Institute, University of Washington School of Medicine, Seattle, WA 98101, USA;
| | - Antonio Condino-Neto
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
| | - Katherine A. Overmyer
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; (K.A.O.); (J.J.C.)
- Morgridge Institute for Research, Madison, WI 53562, USA
| | - Joshua J. Coon
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; (K.A.O.); (J.J.C.)
- Morgridge Institute for Research, Madison, WI 53562, USA
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53506, USA
- Department of Chemistry, University of Wisconsin, Madison, WI 53506, USA
| | - Joseph Balnis
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY 12208, USA; (J.B.); (A.J.)
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| | - Ariel Jaitovich
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY 12208, USA; (J.B.); (A.J.)
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| | - Jonas Schulte-Schrepping
- Life and Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany; (J.S.-S.); (J.L.S.)
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), University of Bonn, 53127 Bonn, Germany;
| | - Thomas Ulas
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), University of Bonn, 53127 Bonn, Germany;
- German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE, University of Bonn, 53127 Bonn, Germany
| | - Joachim L. Schultze
- Life and Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany; (J.S.-S.); (J.L.S.)
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), University of Bonn, 53127 Bonn, Germany;
- German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE, University of Bonn, 53127 Bonn, Germany
| | - Helder I. Nakaya
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (C.A.d.S.P.); (D.L.M.F.); (D.R.P.); (A.E.R.O.); (H.I.N.)
- Hospital Israelita Albert Einstein, São Paulo 05652-900, Brazil
- Scientific Platform Pasteur, University of São Paulo, São Paulo 05508-020, Brazil
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada;
- Departments of Medical Biophysics and Computer Science, Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1L7, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, 845 10 Bratislava, Slovakia
| | - Otávio Cabral-Marques
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (C.A.d.S.P.); (D.L.M.F.); (D.R.P.); (A.E.R.O.); (H.I.N.)
- Network of Immunity in Infection, Malignancy, Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), São Paulo 05508-000, Brazil
- Correspondence: (L.F.S.); (O.C.-M.); Tel.: +55-11-943661555 (L.F.S.); +55-11-974642022 (O.C.-M.)
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