1
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Plaça DR, Fonseca DLM, Marques AHC, Zaki Pour S, Usuda JN, Baiocchi GC, Prado CADS, Salgado RC, Filgueiras IS, Freire PP, Rocha V, Camara NOS, Catar R, Moll G, Jurisica I, Calich VLG, Giil LM, Rivino L, Ochs HD, Cabral-Miranda G, Schimke LF, Cabral-Marques O. Immunological signatures unveiled by integrative systems vaccinology characterization of dengue vaccination trials and natural infection. Front Immunol 2024; 15:1282754. [PMID: 38444851 PMCID: PMC10912564 DOI: 10.3389/fimmu.2024.1282754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/31/2024] [Indexed: 03/07/2024] Open
Abstract
Introduction Dengue virus infection is a global health problem lacking specific therapy, requiring an improved understanding of DENV immunity and vaccine responses. Considering the recent emerging of new dengue vaccines, here we performed an integrative systems vaccinology characterization of molecular signatures triggered by the natural DENV infection (NDI) and attenuated dengue virus infection models (DVTs). Methods and results We analyzed 955 samples of transcriptomic datasets of patients with NDI and attenuated dengue virus infection trials (DVT1, DVT2, and DVT3) using a systems vaccinology approach. Differential expression analysis identified 237 common differentially expressed genes (DEGs) between DVTs and NDI. Among them, 28 and 60 DEGs were up or downregulated by dengue vaccination during DVT2 and DVT3, respectively, with 20 DEGs intersecting across all three DVTs. Enriched biological processes of these genes included type I/II interferon signaling, cytokine regulation, apoptosis, and T-cell differentiation. Principal component analysis based on 20 common DEGs (overlapping between DVTs and our NDI validation dataset) distinguished dengue patients by disease severity, particularly in the late acute phase. Machine learning analysis ranked the ten most critical predictors of disease severity in NDI, crucial for the anti-viral immune response. Conclusion This work provides insights into the NDI and vaccine-induced overlapping immune response and suggests molecular markers (e.g., IFIT5, ISG15, and HERC5) for anti-dengue-specific therapies and effective vaccination development.
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Affiliation(s)
- Desirée Rodrigues Plaça
- Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Dennyson Leandro M. Fonseca
- Interunit Postgraduate Program on Bioinformatics, Institute of Mathematics and Statistics (IME), University of Sao Paulo (USP), Sao Paulo, SP, Brazil
| | - Alexandre H. C. Marques
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Shahab Zaki Pour
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Júlia Nakanishi Usuda
- Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Gabriela Crispim Baiocchi
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Caroline Aliane de Souza Prado
- Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Ranieri Coelho Salgado
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Igor Salerno Filgueiras
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Paula Paccielli Freire
- Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Vanderson Rocha
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31), Department of Hematology and Cell Therapy, Hospital das Clínicas, Faculdade de Medicina, University of São Paulo, São Paulo, Brazil
- Instituto D’Or de Ensino e Pesquisa, São Paulo, Brazil
- Fundação Pró-Sangue-Hemocentro de São Paulo, São Paulo, Brazil
- Department of Hematology, Churchill Hospital, University of Oxford, Oxford, United Kingdom
| | - Niels Olsen Saraiva Camara
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Rusan Catar
- Department of Nephrology and Internal Intensive Care Medicine, Charité University Hospital, Berlin, Germany
| | - Guido Moll
- Department of Nephrology and Internal Intensive Care Medicine, Charité University Hospital, Berlin, Germany
- Berlin Institute of Health (BIH) Center for Regenerative Therapies (BCRT) and Berlin-Brandenburg School for Regenerative Therapies (BSRT), Charité Universitätsmedizin Berlin, Berlin, Germany
| | - 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, Canada
- Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, ON, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Vera Lúcia Garcia Calich
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Lasse M. Giil
- Department of Internal Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway
| | - Laura Rivino
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
- Emerging Infectious Diseases, Duke-National University of Singapore (NUS) Medical School, Singapore, Singapore
| | - Hans D. Ochs
- Department of Pediatrics, University of Washington School of Medicine, and Seattle Children’s Research Institute, Seattle, WA, United States
| | - Gustavo Cabral-Miranda
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Lena F. Schimke
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
- Department of Medicine, Division of Molecular Medicine, Laboratory of Medical Investigation 29, University of São Paulo School of Medicine, Berlin, Germany
- Network of Immunity in Infection, Malignancy, Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), São Paulo, SP, Brazil
| | - Otavio Cabral-Marques
- Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
- Interunit Postgraduate Program on Bioinformatics, Institute of Mathematics and Statistics (IME), University of Sao Paulo (USP), Sao Paulo, SP, Brazil
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
- Instituto D’Or de Ensino e Pesquisa, São Paulo, Brazil
- Department of Medicine, Division of Molecular Medicine, Laboratory of Medical Investigation 29, University of São Paulo School of Medicine, Berlin, Germany
- Network of Immunity in Infection, Malignancy, Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), São Paulo, SP, Brazil
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2
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Hoving D, Marques AHC, Huisman W, Nosoh BA, de Kroon AC, van Hengel ORJ, Wu BR, Steenbergen RAM, van Helden PM, Urban BC, Dhar N, Ferreira DM, Kwatra G, Hokke CH, Jochems SP. Combinatorial multimer staining and spectral flow cytometry facilitate quantification and characterization of polysaccharide-specific B cell immunity. Commun Biol 2023; 6:1095. [PMID: 37898698 PMCID: PMC10613281 DOI: 10.1038/s42003-023-05444-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 10/11/2023] [Indexed: 10/30/2023] Open
Abstract
Bacterial capsular polysaccharides are important vaccine immunogens. However, the study of polysaccharide-specific immune responses has been hindered by technical restrictions. Here, we developed and validated a high-throughput method to analyse antigen-specific B cells using combinatorial staining with fluorescently-labelled capsular polysaccharide multimers. Concurrent staining of 25 cellular markers further enables the in-depth characterization of polysaccharide-specific cells. We used this assay to simultaneously analyse 14 Streptococcus pneumoniae or 5 Streptococcus agalactiae serotype-specific B cell populations. The phenotype of polysaccharide-specific B cells was associated with serotype specificity, vaccination history and donor population. For example, we observed a link between non-class switched (IgM+) memory B cells and vaccine-inefficient S. pneumoniae serotypes 1 and 3. Moreover, B cells had increased activation in donors from South Africa, which has high-incidence of S. agalactiae invasive disease, compared to Dutch donors. This assay allows for the characterization of heterogeneity in B cell immunity that may underlie immunization efficacy.
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Affiliation(s)
- Dennis Hoving
- Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands.
| | - Alexandre H C Marques
- Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Wesley Huisman
- Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Beckley A Nosoh
- Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Alicia C de Kroon
- Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Oscar R J van Hengel
- Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Bing-Ru Wu
- Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Rosanne A M Steenbergen
- Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Britta C Urban
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
- Oxford Vaccine Group, University of Oxford, Oxford, UK
| | - Nisha Dhar
- Vaccines & Infectious Diseases Analytics, University of Witwatersrand, Johannesburg, South Africa
| | - Daniela M Ferreira
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
- Oxford Vaccine Group, University of Oxford, Oxford, UK
| | - Gaurav Kwatra
- Vaccines & Infectious Diseases Analytics, University of Witwatersrand, Johannesburg, South Africa
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
| | - Cornelis H Hokke
- Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Simon P Jochems
- Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands.
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3
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Fonseca DLM, Filgueiras IS, Marques AHC, Vojdani E, Halpert G, Ostrinski Y, Baiocchi GC, Plaça DR, Freire PP, Pour SZ, Moll G, Catar R, Lavi YB, Silverberg JI, Zimmerman J, Cabral-Miranda G, Carvalho RF, Khan TA, Heidecke H, Dalmolin RJS, Luchessi AD, Ochs HD, Schimke LF, Amital H, Riemekasten G, Zyskind I, Rosenberg AZ, Vojdani A, Shoenfeld Y, Cabral-Marques O. Severe COVID-19 patients exhibit elevated levels of autoantibodies targeting cardiolipin and platelet glycoprotein with age: a systems biology approach. NPJ Aging 2023; 9:21. [PMID: 37620330 PMCID: PMC10449916 DOI: 10.1038/s41514-023-00118-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 07/12/2023] [Indexed: 08/26/2023]
Abstract
Age is a significant risk factor for the coronavirus disease 2019 (COVID-19) severity due to immunosenescence and certain age-dependent medical conditions (e.g., obesity, cardiovascular disorder, and chronic respiratory disease). However, despite the well-known influence of age on autoantibody biology in health and disease, its impact on the risk of developing severe COVID-19 remains poorly explored. Here, we performed a cross-sectional study of autoantibodies directed against 58 targets associated with autoimmune diseases in 159 individuals with different COVID-19 severity (71 mild, 61 moderate, and 27 with severe symptoms) and 73 healthy controls. We found that the natural production of autoantibodies increases with age and is exacerbated by SARS-CoV-2 infection, mostly in severe COVID-19 patients. Multiple linear regression analysis showed that severe COVID-19 patients have a significant age-associated increase of autoantibody levels against 16 targets (e.g., amyloid β peptide, β catenin, cardiolipin, claudin, enteric nerve, fibulin, insulin receptor a, and platelet glycoprotein). Principal component analysis with spectrum decomposition and hierarchical clustering analysis based on these autoantibodies indicated an age-dependent stratification of severe COVID-19 patients. Random forest analysis ranked autoantibodies targeting cardiolipin, claudin, and platelet glycoprotein as the three most crucial autoantibodies for the stratification of severe COVID-19 patients ≥50 years of age. Follow-up analysis using binomial logistic regression found that anti-cardiolipin and anti-platelet glycoprotein autoantibodies significantly increased the likelihood of developing a severe COVID-19 phenotype with aging. These findings provide key insights to explain why aging increases the chance of developing more severe COVID-19 phenotypes.
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Affiliation(s)
- Dennyson Leandro M Fonseca
- Interunit Postgraduate Program on Bioinformatics, Institute of Mathematics and Statistics (IME), University of Sao Paulo (USP), Sao Paulo, SP, Brazil.
| | - Igor Salerno Filgueiras
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Alexandre H C Marques
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Elroy Vojdani
- Regenera Medical 11860 Wilshire Blvd., Ste. 301, Los Angeles, CA, 90025, USA
| | - Gilad Halpert
- Ariel University, Ari'el, Israel
- Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Israel
- Saint Petersburg State University Russia, Saint Petersburg, Russia
| | - Yuri Ostrinski
- Ariel University, Ari'el, Israel
- Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Israel
- Saint Petersburg State University Russia, Saint Petersburg, Russia
| | - Gabriela Crispim Baiocchi
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Desirée Rodrigues Plaça
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Paula P Freire
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Shahab Zaki Pour
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, 05508-000, Brazil
| | - Guido Moll
- Departament of Nephrology and Internal Intensive Care Medicine, Charité University Hospital, Berlin, Germany
| | - Rusan Catar
- Departament of Nephrology and Internal Intensive Care Medicine, Charité University Hospital, Berlin, Germany
| | - Yael Bublil Lavi
- Scakler faculty of medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jonathan I Silverberg
- Department of Dermatology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | | | - Gustavo Cabral-Miranda
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Robson F Carvalho
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Taj Ali Khan
- Institute of Pathology and Diagnostic Medicine, Khyber Medical University, Peshawar, Pakistan
| | - Harald Heidecke
- CellTrend Gesellschaft mit beschränkter Haftung (GmbH), Luckenwalde, Germany
| | - Rodrigo J S Dalmolin
- Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte, Natal, Brazil
- Department of Biochemistry, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Andre Ducati Luchessi
- Department of Clinical and Toxicological Analyses, Federal University of Rio Grande do Norte, R.N., Natal, Brazil
| | - Hans D Ochs
- Department of Pediatrics, University of Washington School of Medicine, and Seattle Children's Research Institute, Seattle, WA, USA
| | - Lena F Schimke
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Howard Amital
- Ariel University, Ari'el, Israel
- Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Israel
- Department of Medicine B, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Gabriela Riemekasten
- Department of Rheumatology, University Medical Center Schleswig-Holstein Campus Lübeck, Lübeck, Germany
| | - Israel Zyskind
- Maimonides Medical Center, Brooklyn, NY, USA
- Department of Pediatrics, NYU Langone Medical Center, New York, NY, USA
| | - Avi Z Rosenberg
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Aristo Vojdani
- Department of Immunology, Immunosciences Laboratory, Inc., Los Angeles, CA, USA
- Cyrex Laboratories, LLC 2602 S. 24th St., Phoenix, AZ, 85034, USA
| | - Yehuda Shoenfeld
- Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Israel
| | - Otavio Cabral-Marques
- Interunit Postgraduate Program on Bioinformatics, Institute of Mathematics and Statistics (IME), University of Sao Paulo (USP), Sao Paulo, SP, Brazil.
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.
- Department of Pharmacy and Postgraduate Program of Health and Science, Federal University of Rio Grande do Norte, Natal, Brazil.
- Department of Medicine, Division of Molecular Medicine, University of São Paulo School of Medicine, São Paulo, Brazil.
- Laboratory of Medical Investigation 29, University of São Paulo School of Medicine, São Paulo, Brazil.
- Network of Immunity in Infection, Malignancy, Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), São Paulo, SP, Brazil.
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4
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Usuda JN, Plaça DR, Fonseca DLM, Marques AHC, Filgueiras IS, Chaves VGB, Adri AS, Torrentes-Carvalho A, Hirata MH, Freire PP, Catar R, Cabral-Miranda G, Schimke LF, Moll G, Cabral-Marques O. Interferome signature dynamics during the anti-dengue immune response: a systems biology characterization. Front Immunol 2023; 14:1243516. [PMID: 37638052 PMCID: PMC10449254 DOI: 10.3389/fimmu.2023.1243516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023] Open
Abstract
Dengue virus (DENV) infection manifests as a febrile illness with three distinct phases: early acute, late acute, and convalescent. Dengue can result in clinical manifestations with different degrees of severity, dengue fever, dengue hemorrhagic fever, and dengue shock syndrome. Interferons (IFNs) are antiviral cytokines central to the anti-DENV immune response. Notably, the distinct global signature of type I, II, and III interferon-regulated genes (the interferome) remains uncharacterized in dengue patients to date. Therefore, we performed an in-depth cross-study for the integrative analysis of transcriptome data related to DENV infection. Our systems biology analysis shows that the anti-dengue immune response is characterized by the modulation of numerous interferon-regulated genes (IRGs) enriching, for instance, cytokine-mediated signaling (e.g., type I and II IFNs) and chemotaxis, which is then followed by a transcriptional wave of genes associated with cell cycle, also regulated by the IFN cascade. The adjunct analysis of disease stratification potential, followed by a transcriptional meta-analysis of the interferome, indicated genes such as IFI27, ISG15, and CYBRD1 as potential suitable biomarkers of disease severity. Thus, this study characterizes the landscape of the interferome signature in DENV infection, indicating that interferome dynamics are a crucial and central part of the anti-dengue immune response.
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Affiliation(s)
- Júlia Nakanishi Usuda
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Desirée Rodrigues Plaça
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Dennyson Leandro M. Fonseca
- Interunit PostGraduate Program on Bioinformatics, Institute of Mathematics and Statistics, University of São Paulo, São Paulo, Brazil
| | - Alexandre H. C. Marques
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Igor Salerno Filgueiras
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Victor Gabriel Bastos Chaves
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Anny Silva Adri
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Mario Hiroyuki Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Paula Paccielli Freire
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Rusan Catar
- Departament of Nephrology and Internal Intensive Care Medicine, Charité University Hospital, Berlin, Germany
| | - Gustavo Cabral-Miranda
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Lena F. Schimke
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Department of Medicine, Division of Molecular Medicine, University of São Paulo School of Medicine, São Paulo, Brazil
- Laboratory of Medical Investigation 29, University of São Paulo School of Medicine, São Paulo, Brazil
| | - Guido Moll
- Departament of Nephrology and Internal Intensive Care Medicine, Charité University Hospital, Berlin, Germany
| | - Otavio Cabral-Marques
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Interunit PostGraduate Program on Bioinformatics, Institute of Mathematics and Statistics, University of São Paulo, São Paulo, Brazil
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Department of Medicine, Division of Molecular Medicine, University of São Paulo School of Medicine, São Paulo, Brazil
- Laboratory of Medical Investigation 29, University of São Paulo School of Medicine, São Paulo, Brazil
- Network of Immunity in Infection, Malignancy, Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), São Paulo, SP, Brazil
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5
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Baiocchi GC, Vojdani A, Rosenberg AZ, Vojdani E, Halpert G, Ostrinski Y, Zyskind I, Filgueiras IS, Schimke LF, Marques AHC, Giil LM, Lavi YB, Silverberg JI, Zimmerman J, Hill DA, Thornton A, Kim M, De Vito R, Fonseca DLM, Plaça DR, Freire PP, Camara NOS, Calich VLG, Scheibenbogen C, Heidecke H, Lattin MT, Ochs HD, Riemekasten G, Amital H, Shoenfeld Y, Cabral-Marques O. Cross-sectional analysis reveals autoantibody signatures associated with COVID-19 severity. J Med Virol 2023; 95:e28538. [PMID: 36722456 DOI: 10.1002/jmv.28538] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 02/02/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is associated with increased levels of autoantibodies targeting immunological proteins such as cytokines and chemokines. Reports further indicate that COVID-19 patients may develop a broad spectrum of autoimmune diseases due to reasons not fully understood. Even so, the landscape of autoantibodies induced by SARS-CoV-2 infection remains uncharted territory. To gain more insight, we carried out a comprehensive assessment of autoantibodies known to be linked to diverse autoimmune diseases observed in COVID-19 patients in a cohort of 231 individuals, of which 161 were COVID-19 patients (72 with mild, 61 moderate, and 28 with severe disease) and 70 were healthy controls. Dysregulated IgG and IgA autoantibody signatures, characterized mainly by elevated concentrations, occurred predominantly in patients with moderate or severe COVID-19 infection. Autoantibody levels often accompanied anti-SARS-CoV-2 antibody concentrations while stratifying COVID-19 severity as indicated by random forest and principal component analyses. Furthermore, while young versus elderly COVID-19 patients showed only slight differences in autoantibody levels, elderly patients with severe disease presented higher IgG autoantibody concentrations than young individuals with severe COVID-19. This work maps the intersection of COVID-19 and autoimmunity by demonstrating the dysregulation of multiple autoantibodies triggered during SARS-CoV-2 infection. Thus, this cross-sectional study suggests that SARS-CoV-2 infection induces autoantibody signatures associated with COVID-19 severity and several autoantibodies that can be used as biomarkers of COVID-19 severity, indicating autoantibodies as potential therapeutical targets for these patients.
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Affiliation(s)
- Gabriela C Baiocchi
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Aristo Vojdani
- Immunosciences Laboratory, Inc., Department of Immunology, Los Angeles, California, USA.,Cyrex Laboratories, Phoenix, Arizona, USA
| | - Avi Z Rosenberg
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Gilad Halpert
- Ariel University, Ariel, Israel.,Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Israel.,Saint Petersburg State University Russia, St Petersburg, Russia
| | - Yuri Ostrinski
- Ariel University, Ariel, Israel.,Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Israel.,Saint Petersburg State University Russia, St Petersburg, Russia
| | - Israel Zyskind
- Department of Pediatrics, NYU Langone Medical Center, New York, New York, USA.,Maimonides Medical Center, Brooklyn, New York, USA
| | - Igor S Filgueiras
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Lena F Schimke
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Alexandre H C Marques
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Lasse M Giil
- Department of Internal Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway
| | - Yael B Lavi
- Department of Chemistry Ben Gurion University Beer-Sheva, Beer-Sheva, Israel
| | - Jonathan I Silverberg
- Department of Dermatology, George Washington University School of Medicine and Health Sciences, Washington, USA
| | | | | | | | - Myungjin Kim
- Data Science Initiative at Brown University, Providence, Rhode Island, USA
| | - Roberta De Vito
- Department of Biostatistics and the Data Science Initiative at Brown University, Providence, Rhode Island, USA
| | - Dennyson L M Fonseca
- Interunit Postgraduate Program on Bioinformatics, Institute of Mathematics and Statistics (IME), University of Sao Paulo (USP), Sao Paulo, Brazil
| | - Desireé R Plaça
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, São Paulo, Brazil
| | - Paula P Freire
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Niels O S Camara
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Vera L G Calich
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Carmen Scheibenbogen
- Institute for Medical Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Harald Heidecke
- CellTrend Gesellschaft mit beschränkter Haftung (GmbH), Luckenwalde, Germany
| | - Miriam T Lattin
- Department of Biology, Yeshiva University, Manhatten, New York, USA
| | - Hans D Ochs
- Department of Pediatrics, University of Washington School of Medicine, and Seattle Children's Research Institute, Seattle, Washington, USA
| | - Gabriela Riemekasten
- Department of Rheumatology, University Medical Center Schleswig-Holstein Campus Lübeck, Lübeck, Germany
| | - Howard Amital
- Ariel University, Ariel, Israel.,Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Israel.,Department of Medicine B, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Yehuda Shoenfeld
- Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Israel.,Saint Petersburg State University Russia, St Petersburg, Russia
| | - Otavio Cabral-Marques
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Interunit Postgraduate Program on Bioinformatics, Institute of Mathematics and Statistics (IME), University of Sao Paulo (USP), Sao Paulo, Brazil.,Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, São Paulo, Brazil.,Department of Pharmacy and Postgraduate Program of Health and Science, Federal University of Rio Grande do Norte, Natal, Brazil.,Department of Medicine, Division of Molecular Medicine, University of São Paulo School of Medicine, Baltimore, USA.,Laboratory of Medical Investigation 29, University of São Paulo School of Medicine, São Paulo, Brazil
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6
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Prado CADS, Fonseca DLM, Singh Y, Filgueiras IS, Baiocchi GC, Plaça DR, Marques AHC, Dantas-Komatsu RCS, Usuda JN, Freire PP, Salgado RC, Napoleao SMDS, Ramos RN, Rocha V, Zhou G, Catar R, Moll G, Camara NOS, de Miranda GC, Calich VLG, Giil LM, Mishra N, Tran F, Luchessi AD, Nakaya HI, Ochs HD, Jurisica I, Schimke LF, Cabral-Marques O. Integrative systems immunology uncovers molecular networks of the cell cycle that stratify COVID-19 severity. J Med Virol 2023; 95:e28450. [PMID: 36597912 PMCID: PMC10107240 DOI: 10.1002/jmv.28450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/24/2022] [Accepted: 12/28/2022] [Indexed: 01/05/2023]
Abstract
Several perturbations in the number of peripheral blood leukocytes, such as neutrophilia and lymphopenia associated with Coronavirus disease 2019 (COVID-19) severity, point to systemic molecular cell cycle alterations during severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. However, the landscape of cell cycle alterations in COVID-19 remains primarily unexplored. Here, we performed an integrative systems immunology analysis of publicly available proteome and transcriptome data to characterize global changes in the cell cycle signature of COVID-19 patients. We found significantly enriched cell cycle-associated gene co-expression modules and an interconnected network of cell cycle-associated differentially expressed proteins (DEPs) and genes (DEGs) by integrating the molecular data of 1469 individuals (981 SARS-CoV-2 infected patients and 488 controls [either healthy controls or individuals with other respiratory illnesses]). Among these DEPs and DEGs are several cyclins, cell division cycles, cyclin-dependent kinases, and mini-chromosome maintenance proteins. COVID-19 patients partially shared the expression pattern of some cell cycle-associated genes with other respiratory illnesses but exhibited some specific differential features. Notably, the cell cycle signature predominated in the patients' blood leukocytes (B, T, and natural killer cells) and was associated with COVID-19 severity and disease trajectories. These results provide a unique global understanding of distinct alterations in cell cycle-associated molecules in COVID-19 patients, suggesting new putative pathways for therapeutic intervention.
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Affiliation(s)
- Caroline Aliane de Souza Prado
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Dennyson Leandro M Fonseca
- Interunit Postgraduate Program on Bioinformatics, Institute of Mathematics and Statistics (IME), University of Sao Paulo (USP), Sao Paulo, Brazil
| | - Youvika Singh
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Igor Salerno Filgueiras
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Gabriela Crispim Baiocchi
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Desirée Rodrigues Plaça
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Alexandre H C Marques
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Júlia N Usuda
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Paula Paccielli Freire
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Ranieri Coelho Salgado
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Rodrigo Nalio Ramos
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31), Departament of Hematology and Cell Therapy, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, University of São Paulo, São Paulo, Brazil.,Instituto D'Or de Ensino e Pesquisa, Hospital São Luiz, São Paulo, Brazil
| | - Vanderson Rocha
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31), Departament of Hematology and Cell Therapy, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, University of São Paulo, São Paulo, Brazil.,Instituto D'Or de Ensino e Pesquisa, Hospital São Luiz, São Paulo, Brazil.,Fundação Pró-Sangue-Hemocentro de São Paulo, Hospital das Clínicas da Universidade de São Paulo, São Paulo, Brazil.,Department of Hematology, Churchill Hospital, University of Oxford, Oxford, UK
| | - Guangyan Zhou
- Institute of Parasitology, McGill University, Montreal, Quebec, Canada
| | - Rusan Catar
- Department of Nephrology and Internal Intensive Care Medicine, Charité University Hospital, Berlin, Germany
| | - Guido Moll
- Department of Nephrology and Internal Intensive Care Medicine, Charité University Hospital, Berlin, Germany.,Berlin Institute of Health (BIH) and Berlin Center for Regenerative Therapies (BCRT), Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin-Brandenburg School for Regenerative Therapies (BSRT), all Charité Universitätsmedizin Berlin, Berlin, Germany
| | | | - Gustavo Cabral de Miranda
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Vera Lúcia Garcia Calich
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Lasse M Giil
- Department of Internal Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway
| | - Neha Mishra
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Florian Tran
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Kiel, Germany.,Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Andre Ducati Luchessi
- Department of Clinical and Toxicology Analysis, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Helder I Nakaya
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.,Instituto Israelita de Ensino e Pesquisa Albert Einstein, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Hans D Ochs
- Department of Pediatrics, University of Washington School of Medicine and Seattle Children's Research Institute, Seattle, Washington, USA
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, UHN, Toronto, Ontario, Canada.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia.,Departments of Medical Biophysics and Computer Science, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada.,Krembil Research Institute, UHN, Data Science Discovery Centre, Toronto, Ontario, Canada
| | - Lena F Schimke
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Otavio Cabral-Marques
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.,Interunit Postgraduate Program on Bioinformatics, Institute of Mathematics and Statistics (IME), University of Sao Paulo (USP), Sao Paulo, Brazil.,Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Pharmacy and Postgraduate Program of Health and Science, Federal University of Rio Grande do Norte, Natal, Brazil.,Department of Medicine, Division of Molecular Medicine, University of São Paulo School of Medicine, São Paulo, Brazil.,Laboratory of Medical Investigation 29, University of São Paulo School of Medicine, São Paulo, Brazil
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7
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Sotzny F, Filgueiras IS, Kedor C, Freitag H, Wittke K, Bauer S, Sepúlveda N, Mathias da Fonseca DL, Baiocchi GC, Marques AHC, Kim M, Lange T, Plaça DR, Luebber F, Paulus FM, De Vito R, Jurisica I, Schulze-Forster K, Paul F, Bellmann-Strobl J, Rust R, Hoppmann U, Shoenfeld Y, Riemekasten G, Heidecke H, Cabral-Marques O, Scheibenbogen C. Dysregulated autoantibodies targeting vaso- and immunoregulatory receptors in Post COVID Syndrome correlate with symptom severity. Front Immunol 2022; 13:981532. [PMID: 36238301 PMCID: PMC9552223 DOI: 10.3389/fimmu.2022.981532] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Most patients with Post COVID Syndrome (PCS) present with a plethora of symptoms without clear evidence of organ dysfunction. A subset of them fulfills diagnostic criteria of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). Symptom severity of ME/CFS correlates with natural regulatory autoantibody (AAB) levels targeting several G-protein coupled receptors (GPCR). In this exploratory study, we analyzed serum AAB levels against vaso- and immunoregulatory receptors, mostly GPCRs, in 80 PCS patients following mild-to-moderate COVID-19, with 40 of them fulfilling diagnostic criteria of ME/CFS. Healthy seronegative (n=38) and asymptomatic post COVID-19 controls (n=40) were also included in the study as control groups. We found lower levels for various AABs in PCS compared to at least one control group, accompanied by alterations in the correlations among AABs. Classification using random forest indicated AABs targeting ADRB2, STAB1, and ADRA2A as the strongest classifiers (AABs stratifying patients according to disease outcomes) of post COVID-19 outcomes. Several AABs correlated with symptom severity in PCS groups. Remarkably, severity of fatigue and vasomotor symptoms were associated with ADRB2 AAB levels in PCS/ME/CFS patients. Our study identified dysregulation of AAB against various receptors involved in the autonomous nervous system (ANS), vaso-, and immunoregulation and their correlation with symptom severity, pointing to their role in the pathogenesis of PCS.
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Affiliation(s)
- Franziska Sotzny
- Institute for Medical Immunology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
- *Correspondence: Franziska Sotzny, ; Igor Salerno Filgueiras, ; Otavio Cabral-Marques, ; Carmen Scheibenbogen,
| | - Igor Salerno Filgueiras
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- *Correspondence: Franziska Sotzny, ; Igor Salerno Filgueiras, ; Otavio Cabral-Marques, ; Carmen Scheibenbogen,
| | - Claudia Kedor
- Institute for Medical Immunology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Helma Freitag
- Institute for Medical Immunology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Kirsten Wittke
- Institute for Medical Immunology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Sandra Bauer
- Institute for Medical Immunology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Nuno Sepúlveda
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
- CEAUL – Centro de Estatística e Aplicações da Universidade de Lisboa, Lisbon, Portugal
| | | | - Gabriela Crispim Baiocchi
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Alexandre H. C. Marques
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Myungjin Kim
- Data Science Initiative, Brown University, Providence, RI, United States
| | - Tanja Lange
- Department of Rheumatology and Clinical Immunology, University of Lübeck, Lübeck, Germany
| | - Desirée Rodrigues Plaça
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Finn Luebber
- Department of Rheumatology and Clinical Immunology, University of Lübeck, Lübeck, Germany
- Department of Psychiatry and Psychotherapy, University of Lübeck, Lübeck, Germany
| | - Frieder M. Paulus
- Department of Psychiatry and Psychotherapy, University of Lübeck, Lübeck, Germany
| | - Roberta De Vito
- Department of Biostatistics and the Data Science Initiative, Brown University, Providence, RI, United States
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | | | - Friedemann Paul
- Experimental and Clinical Research Center, a cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- NeuroCure Clinical Research Center, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Judith Bellmann-Strobl
- Institute for Medical Immunology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center, a cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Rebekka Rust
- Institute for Medical Immunology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center, a cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Uta Hoppmann
- Institute for Medical Immunology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center, a cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Yehuda Shoenfeld
- Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Affiliated with the Sackler Faculty of Medicine, Tel-Aviv University, Tel-Hashomer, Israel
- Ariel University, Ariel, Israel
| | - Gabriela Riemekasten
- Department of Rheumatology and Clinical Immunology, University of Lübeck, Lübeck, Germany
| | | | - Otavio Cabral-Marques
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Interunit PostGraduate Program on Bioinformatics, Institute of Mathematics and Statistics (IME), University of Sao Paulo, Sao Paulo, Brazil
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Network of Immunity in Infection, Malignancy, and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Sao Paulo, Brazil
- Department of Pharmacy, Federal University of Rio Grande do Norte, Natal, RN, Brazil
- *Correspondence: Franziska Sotzny, ; Igor Salerno Filgueiras, ; Otavio Cabral-Marques, ; Carmen Scheibenbogen,
| | - Carmen Scheibenbogen
- Institute for Medical Immunology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
- *Correspondence: Franziska Sotzny, ; Igor Salerno Filgueiras, ; Otavio Cabral-Marques, ; Carmen Scheibenbogen,
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8
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Cabral-Marques O, Halpert G, Schimke LF, Ostrinski Y, Vojdani A, Baiocchi GC, Freire PP, Filgueiras IS, Zyskind I, Lattin MT, Tran F, Schreiber S, Marques AHC, Plaça DR, Fonseca DLM, Humrich JY, Müller A, Giil LM, Graßhoff H, Schumann A, Hackel A, Junker J, Meyer C, Ochs HD, Lavi YB, Scheibenbogen C, Dechend R, Jurisica I, Schulze-Forster K, Silverberg JI, Amital H, Zimmerman J, Heidecke H, Rosenberg AZ, Riemekasten G, Shoenfeld Y. Autoantibodies targeting GPCRs and RAS-related molecules associate with COVID-19 severity. Nat Commun 2022; 13:1220. [PMID: 35264564 PMCID: PMC8907309 DOI: 10.1038/s41467-022-28905-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 02/16/2022] [Indexed: 12/27/2022] Open
Abstract
COVID-19 shares the feature of autoantibody production with systemic autoimmune diseases. In order to understand the role of these immune globulins in the pathogenesis of the disease, it is important to explore the autoantibody spectra. Here we show, by a cross-sectional study of 246 individuals, that autoantibodies targeting G protein-coupled receptors (GPCR) and RAS-related molecules associate with the clinical severity of COVID-19. Patients with moderate and severe disease are characterized by higher autoantibody levels than healthy controls and those with mild COVID-19 disease. Among the anti-GPCR autoantibodies, machine learning classification identifies the chemokine receptor CXCR3 and the RAS-related molecule AGTR1 as targets for antibodies with the strongest association to disease severity. Besides antibody levels, autoantibody network signatures are also changing in patients with intermediate or high disease severity. Although our current and previous studies identify anti-GPCR antibodies as natural components of human biology, their production is deregulated in COVID-19 and their level and pattern alterations might predict COVID-19 disease severity.
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Affiliation(s)
- Otavio Cabral-Marques
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil.
- Network of Immunity in Infection, Malignancy, and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Sao Paulo, Brazil.
| | - Gilad Halpert
- Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Israel
- Saint Petersburg State University, Saint-Petersburg, Russia
| | - Lena F Schimke
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Yuri Ostrinski
- Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Israel
- Saint Petersburg State University, Saint-Petersburg, Russia
- Ariel University, Ariel, Israel
| | - Aristo Vojdani
- Department of Immunology, Immunosciences Laboratory, Inc., Los Angeles, CA, United States
- Cyrex Laboratories, LLC 2602S. 24th St., Phoenix, AZ, 85034, USA
| | - Gabriela Crispim Baiocchi
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Paula Paccielli Freire
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Igor Salerno Filgueiras
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Israel Zyskind
- Department of Pediatrics, NYU Langone Medical Center, New York, NY, USA
- Maimonides Medical Center, Brooklyn, NY, USA
| | - Miriam T Lattin
- Department of Biology, Yeshiva University, Manhatten, NY, USA
| | - Florian Tran
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - Stefan Schreiber
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - Alexandre H C Marques
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Desirée Rodrigues Plaça
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Dennyson Leandro M Fonseca
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Jens Y Humrich
- Department of Rheumatology, University Medical Center Schleswig-Holstein Campus Lübeck, Lübeck, Germany
| | - Antje Müller
- Department of Rheumatology, University Medical Center Schleswig-Holstein Campus Lübeck, Lübeck, Germany
| | - Lasse M Giil
- Department of Internal Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway
| | - Hanna Graßhoff
- Department of Rheumatology, University Medical Center Schleswig-Holstein Campus Lübeck, Lübeck, Germany
| | - Anja Schumann
- Department of Rheumatology, University Medical Center Schleswig-Holstein Campus Lübeck, Lübeck, Germany
| | - Alexander Hackel
- Department of Rheumatology, University Medical Center Schleswig-Holstein Campus Lübeck, Lübeck, Germany
| | - Juliane Junker
- CellTrend Gesellschaft mit beschränkter Haftung (GmbH), Luckenwalde, Germany
| | - Carlotta Meyer
- CellTrend Gesellschaft mit beschränkter Haftung (GmbH), Luckenwalde, Germany
| | - Hans D Ochs
- Department of Pediatrics, University of Washington School of Medicine, and Seattle Children's Research Institute, Seattle, WA, USA
| | - Yael Bublil Lavi
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Carmen Scheibenbogen
- Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Ralf Dechend
- Experimental and Clinical Research Center, a collaboration of Max Delbruck Center for Molecular Medicine and Charité Universitätsmedizin, and HELIOS Clinic, Department of Cardiology and Nephrology, Berlin, 13125, Germany
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, UHN; Data Science Discovery Centre, Krembil Research Institute, UHN, Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Kai Schulze-Forster
- CellTrend Gesellschaft mit beschränkter Haftung (GmbH), Luckenwalde, Germany
| | - Jonathan I Silverberg
- School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
| | - Howard Amital
- Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Department of Medicine B, Sheba Medical Center, Tel Hashomer, Israel
| | | | - Harry Heidecke
- CellTrend Gesellschaft mit beschränkter Haftung (GmbH), Luckenwalde, Germany
| | - Avi Z Rosenberg
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Gabriela Riemekasten
- Department of Rheumatology, University Medical Center Schleswig-Holstein Campus Lübeck, Lübeck, Germany.
| | - Yehuda Shoenfeld
- Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Israel.
- Saint Petersburg State University, Saint-Petersburg, Russia.
- Ariel University, Ariel, Israel.
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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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