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Gil-Manso S, Herrero-Quevedo D, Carbonell D, Martínez-Bonet M, Bernaldo-de-Quirós E, Kennedy-Batalla R, Gallego-Valle J, López-Esteban R, Blázquez-López E, Miguens-Blanco I, Correa-Rocha R, Gomez-Verdejo V, Pion M. Multidimensional analysis of immune cells from COVID-19 patients identified cell subsets associated with the severity at hospital admission. PLoS Pathog 2023; 19:e1011432. [PMID: 37311004 PMCID: PMC10263360 DOI: 10.1371/journal.ppat.1011432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 05/18/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND SARS-CoV-2 emerged as a new coronavirus causing COVID-19, and it has been responsible for more than 760 million cases and 6.8 million deaths worldwide until March 2023. Although infected individuals could be asymptomatic, other patients presented heterogeneity and a wide range of symptoms. Therefore, identifying those infected individuals and being able to classify them according to their expected severity could help target health efforts more effectively. METHODOLOGY/PRINCIPAL FINDINGS Therefore, we wanted to develop a machine learning model to predict those who will develop severe disease at the moment of hospital admission. We recruited 75 individuals and analysed innate and adaptive immune system subsets by flow cytometry. Also, we collected clinical and biochemical information. The objective of the study was to leverage machine learning techniques to identify clinical features associated with disease severity progression. Additionally, the study sought to elucidate the specific cellular subsets involved in the disease following the onset of symptoms. Among the several machine learning models tested, we found that the Elastic Net model was the better to predict the severity score according to a modified WHO classification. This model was able to predict the severity score of 72 out of 75 individuals. Besides, all the machine learning models revealed that CD38+ Treg and CD16+ CD56neg HLA-DR+ NK cells were highly correlated with the severity. CONCLUSIONS/SIGNIFICANCE The Elastic Net model could stratify the uninfected individuals and the COVID-19 patients from asymptomatic to severe COVID-19 patients. On the other hand, these cellular subsets presented here could help to understand better the induction and progression of the symptoms in COVID-19 individuals.
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Affiliation(s)
- Sergio Gil-Manso
- Advanced ImmunoRegulation Group, Gregorio Marañón Health Research Institute (IiSGM), General University Hospital Gregorio Marañón, Madrid, Spain
| | - Diego Herrero-Quevedo
- Signal Processing and Communications Department, University Carlos III de Madrid, Leganés, Madrid, Spain
| | - Diego Carbonell
- Department of Hematology, General University Hospital Gregorio Marañón (HGUGM), Madrid, Spain
- Gregorio Marañón Health Research Institute (IiSGM), Madrid, Spain
| | - Marta Martínez-Bonet
- Laboratory of Immune-Regulation, Gregorio Marañón Health Research Institute (IiSGM), General University Hospital Gregorio Marañón, Madrid, Spain
| | - Esther Bernaldo-de-Quirós
- Laboratory of Immune-Regulation, Gregorio Marañón Health Research Institute (IiSGM), General University Hospital Gregorio Marañón, Madrid, Spain
| | - Rebeca Kennedy-Batalla
- Laboratory of Immune-Regulation, Gregorio Marañón Health Research Institute (IiSGM), General University Hospital Gregorio Marañón, Madrid, Spain
| | - Jorge Gallego-Valle
- Advanced ImmunoRegulation Group, Gregorio Marañón Health Research Institute (IiSGM), General University Hospital Gregorio Marañón, Madrid, Spain
| | - Rocío López-Esteban
- Laboratory of Immune-Regulation, Gregorio Marañón Health Research Institute (IiSGM), General University Hospital Gregorio Marañón, Madrid, Spain
| | - Elena Blázquez-López
- Gastroenterology—Digestive Service, General University Hospital Gregorio Marañón, Network of Hepatic and Digestive Diseases (CIBEREHD), Carlos III Health Institute (ISCIII), Madrid, Spain
| | - Iria Miguens-Blanco
- Emergency Department, General University Hospital Gregorio Marañón, Madrid, Spain
| | - Rafael Correa-Rocha
- Laboratory of Immune-Regulation, Gregorio Marañón Health Research Institute (IiSGM), General University Hospital Gregorio Marañón, Madrid, Spain
| | - Vanessa Gomez-Verdejo
- Signal Processing and Communications Department, University Carlos III de Madrid, Leganés, Madrid, Spain
| | - Marjorie Pion
- Advanced ImmunoRegulation Group, Gregorio Marañón Health Research Institute (IiSGM), General University Hospital Gregorio Marañón, Madrid, Spain
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Gil-Manso S, Miguens Blanco I, Motyka B, Halpin A, López-Esteban R, Pérez-Fernández VA, Carbonell D, López-Fernández LA, West L, Correa-Rocha R, Pion M. ABO blood group is involved in the quality of the specific immune response anti-SARS-CoV-2. Virulence 2022; 13:30-45. [PMID: 34967260 PMCID: PMC9794011 DOI: 10.1080/21505594.2021.2019959] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Since December 2019, the coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread throughout the world. To eradicate it, it is crucial to acquire a strong and long-lasting anti-SARS-CoV-2 immunity, by either natural infection or vaccination. We collected blood samples 12-305 days after positive polymerase chain reactions (PCRs) from 35 recovered individuals infected by SARS-CoV-2. Peripheral blood mononuclear cells were stimulated with SARS-CoV-2-derived peptide pools, such as the spike (S), nucleocapsid (N) and membrane (M) proteins, and we quantified anti-S immunoglobulins in plasma. After 10 months post-infection, we observed a sustained SARS-CoV-2-specific CD4+ T-cell response directed against M-protein, but responses against S- or N-proteins were lost over time. Besides, we demonstrated that O-group individuals presented significantly lower frequencies of specific CD4+ T-cell responses against Pep-M than non O-group individuals. The non O-group subjects also needed longer to clear the virus, and they lost cellular immune responses over time, compared to the O-group individuals, who showed a persistent specific immune response against SARS-CoV-2. Therefore, the S-specific immune response was lost over time, and individual factors might determine the sustainability of the body's defenses, which must be considered in the future design of vaccines to achieve continuous anti-SARS-CoV-2 immunity.
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Affiliation(s)
- Sergio Gil-Manso
- Laboratory of Immune- Gregorio Marañón Health Research Institute (IiSGM), Gregorio Marañón University General Hospital, Madrid, Spain
| | - Iria Miguens Blanco
- Department of Emergency, Gregorio Marañón University General Hospital, Madrid, Spain
| | - Bruce Motyka
- Department of Pediatrics, Alberta Transplant Institute and Canadian Donation and Transplantation Research Program; University of Alberta, Edmonton, Alberta, Canada
| | - Anne Halpin
- Department of Pediatrics, Alberta Transplant Institute and Canadian Donation and Transplantation Research Program; University of Alberta, Edmonton, Alberta, Canada,Laboratory Medicine & Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Rocío López-Esteban
- Laboratory of Immune- Gregorio Marañón Health Research Institute (IiSGM), Gregorio Marañón University General Hospital, Madrid, Spain
| | - Verónica Astrid Pérez-Fernández
- Laboratory of Immune- Gregorio Marañón Health Research Institute (IiSGM), Gregorio Marañón University General Hospital, Madrid, Spain
| | - Diego Carbonell
- Laboratory of Immune- Gregorio Marañón Health Research Institute (IiSGM), Gregorio Marañón University General Hospital, Madrid, Spain,Department of Hematology, Gregorio Marañón University General Hospital, Madrid, Spain
| | - Luis Andrés López-Fernández
- Service of Pharmacy, Gregorio Marañón Health Research Institute (IiSGM), Gregorio Marañón University General Hospital, Spanish Clinical Research Network (SCReN), Madrid, Spain
| | - Lori West
- Department of Pediatrics, Alberta Transplant Institute and Canadian Donation and Transplantation Research Program; University of Alberta, Edmonton, Alberta, Canada,Medical Microbiology & Immunology, Surgery, and Laboratory Medicine & Pathology; University of Alberta, Edmonton, Alberta, Canada
| | - Rafael Correa-Rocha
- Laboratory of Immune- Gregorio Marañón Health Research Institute (IiSGM), Gregorio Marañón University General Hospital, Madrid, Spain,CONTACT Rafael Correa-Rocha
| | - Marjorie Pion
- Laboratory of Immune- Gregorio Marañón Health Research Institute (IiSGM), Gregorio Marañón University General Hospital, Madrid, Spain,Marjorie Pion
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Gil-Manso S, Carbonell D, Pérez-Fernández VA, López-Esteban R, Alonso R, Muñoz P, Ochando J, Sánchez-Arcilla I, Bellón JM, Correa-Rocha R, Pion M. Cellular and Humoral Responses Follow-up for 8 Months after Vaccination with mRNA-Based Anti-SARS-CoV-2 Vaccines. Biomedicines 2022; 10:biomedicines10071676. [PMID: 35884980 PMCID: PMC9312914 DOI: 10.3390/biomedicines10071676] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/01/2022] [Accepted: 07/09/2022] [Indexed: 11/16/2022] Open
Abstract
Vaccination against SARS-CoV-2 has become the main method of reducing mortality and severity of COVID-19. This work aims to study the evolution of the cellular and humoral responses conferred by two mRNA vaccines after two doses against SARS-CoV-2. On days 30 and 240 after the second dose of both vaccines, the anti-S antibodies in plasma were evaluated from 82 volunteers vaccinated with BNT162b2 and 68 vaccinated with mRNA-1273. Peripheral blood was stimulated with peptides encompassing the entire SARS-CoV-2 Spike sequence. IgG Anti-S antibodies (humoral) were quantified on plasma, and inflammatory cytokines (cellular) were measured after stimulation. We observed a higher response (both humoral and cellular) with the mRNA-1273 vaccine. Stratifying by age and gender, differences between vaccines were observed, especially in women under 48 and men over 48 years old. Therefore, this work could help to set up a vaccination strategy that could be applied to confer maximum immunity.
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Affiliation(s)
- Sergio Gil-Manso
- Advanced Immunoregulation Group, Gregorio Marañón Health Research Institute (IiSGM), Gregorio Marañón University General Hospital, 28009 Madrid, Spain; (S.G.-M.); (D.C.); (V.A.P.-F.)
| | - Diego Carbonell
- Advanced Immunoregulation Group, Gregorio Marañón Health Research Institute (IiSGM), Gregorio Marañón University General Hospital, 28009 Madrid, Spain; (S.G.-M.); (D.C.); (V.A.P.-F.)
- Department of Hematology, Gregorio Marañón Health Research Institute (IiSGM), Gregorio Marañón University General Hospital, 28009 Madrid, Spain
| | - Verónica Astrid Pérez-Fernández
- Advanced Immunoregulation Group, Gregorio Marañón Health Research Institute (IiSGM), Gregorio Marañón University General Hospital, 28009 Madrid, Spain; (S.G.-M.); (D.C.); (V.A.P.-F.)
| | - Rocío López-Esteban
- Laboratory of Immune-Regulation, Gregorio Marañón Health Research Institute (IiSGM), Gregorio Marañón University General Hospital, 28009 Madrid, Spain; (R.L.-E.); (R.C.-R.)
| | - Roberto Alonso
- Department of Clinical Microbiology and Infectious Diseases, Gregorio Marañón University General Hospital, 28009 Madrid, Spain; (R.A.); (P.M.)
- School of Medicine, Complutense University of Madrid, 28040 Madrid, Spain
| | - Patricia Muñoz
- Department of Clinical Microbiology and Infectious Diseases, Gregorio Marañón University General Hospital, 28009 Madrid, Spain; (R.A.); (P.M.)
- School of Medicine, Complutense University of Madrid, 28040 Madrid, Spain
| | - Jordi Ochando
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
- National Centre of Microbiology, Carlos III Health Institute, 28222 Madrid, Spain
| | - Ignacio Sánchez-Arcilla
- Department of Occupational Risk Prevention, Gregorio Marañón University General Hospital, 28009 Madrid, Spain;
| | - Jose M Bellón
- Department of Biostatistics, Gregorio Marañón Health Research Institute (IiSGM), Gregorio Marañón University General Hospital, 28009 Madrid, Spain;
| | - Rafael Correa-Rocha
- Laboratory of Immune-Regulation, Gregorio Marañón Health Research Institute (IiSGM), Gregorio Marañón University General Hospital, 28009 Madrid, Spain; (R.L.-E.); (R.C.-R.)
| | - Marjorie Pion
- Advanced Immunoregulation Group, Gregorio Marañón Health Research Institute (IiSGM), Gregorio Marañón University General Hospital, 28009 Madrid, Spain; (S.G.-M.); (D.C.); (V.A.P.-F.)
- Correspondence: ; Tel.: +34-664-43-44-02
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Bernaldo-de-Quirós E, Cózar B, López-Esteban R, Clemente M, Gil-Jaurena JM, Pardo C, Pita A, Pérez-Caballero R, Camino M, Gil N, Fernández-Santos ME, Suarez S, Pion M, Martínez-Bonet M, Correa-Rocha R. A Novel GMP Protocol to Produce High-Quality Treg Cells From the Pediatric Thymic Tissue to Be Employed as Cellular Therapy. Front Immunol 2022; 13:893576. [PMID: 35651624 PMCID: PMC9148974 DOI: 10.3389/fimmu.2022.893576] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 03/10/2022] [Accepted: 04/19/2022] [Indexed: 12/13/2022] Open
Abstract
Due to their suppressive capacity, the adoptive transfer of regulatory T cells (Treg) has acquired a growing interest in controlling exacerbated inflammatory responses. Limited Treg recovery and reduced quality remain the main obstacles in most current protocols where differentiated Treg are obtained from adult peripheral blood. An alternate Treg source is umbilical cord blood, a promising source of Treg cells due to the higher frequency of naïve Treg and lower frequency of memory T cells present in the fetus’ blood. However, the Treg number isolated from cord blood remains limiting. Human thymuses routinely discarded during pediatric cardiac surgeries to access the retrosternal operative field has been recently proposed as a novel source of Treg for cellular therapy. This strategy overcomes the main limitations of current Treg sources, allowing the obtention of very high numbers of undifferentiated Treg. We have developed a novel good manufacturing practice (GMP) protocol to obtain large Treg amounts, with very high purity and suppressive capacity, from the pediatric thymus (named hereafter thyTreg). The total amount of thyTreg obtained at the end of the procedure, after a short-term culture of 7 days, reach an average of 1,757 x106 (range 50 x 106 – 13,649 x 106) cells from a single thymus. The thyTreg product obtained with our protocol shows very high viability (mean 93.25%; range 83.35% – 97.97%), very high purity (mean 92.89%; range 70.10% – 98.41% of CD25+FOXP3+ cells), stability under proinflammatory conditions and a very high suppressive capacity (inhibiting in more than 75% the proliferation of activated CD4+ and CD8+ T cells in vitro at a thyTreg:responder cells ratio of 1:1). Our thyTreg product has been approved by the Spanish Drug Agency (AEMPS) to be administered as cell therapy. We are recruiting patients in the first-in-human phase I/II clinical trial worldwide that evaluates the safety, feasibility, and efficacy of autologous thyTreg administration in children undergoing heart transplantation (NCT04924491). The high quality and amount of thyTreg and the differential features of the final product obtained with our protocol allow preparing hundreds of doses from a single thymus with improved therapeutic properties, which can be cryopreserved and could open the possibility of an “off-the-shelf” allogeneic use in another individual.
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Affiliation(s)
| | - Beatriz Cózar
- Laboratory of Immune-Regulation, Gregorio Marañón Health Research Institute (IISGM), Madrid, Spain
| | - Rocío López-Esteban
- Laboratory of Immune-Regulation, Gregorio Marañón Health Research Institute (IISGM), Madrid, Spain
| | - Maribel Clemente
- Cell Culture Unit, Gregorio Marañón Health Research Institute (IISGM), Madrid, Spain
| | | | - Carlos Pardo
- Pediatric Cardiac Surgery Unit, Hospital Materno Infantil Gregorio Marañón, Madrid, Spain
| | - Ana Pita
- Pediatric Cardiac Surgery Unit, Hospital Materno Infantil Gregorio Marañón, Madrid, Spain
| | - Ramón Pérez-Caballero
- Pediatric Cardiac Surgery Unit, Hospital Materno Infantil Gregorio Marañón, Madrid, Spain
| | - Manuela Camino
- Pediatric Heart Transplant Unit, Hospital Materno Infantil Gregorio Marañón, Madrid, Spain
| | - Nuria Gil
- Pediatric Heart Transplant Unit, Hospital Materno Infantil Gregorio Marañón, Madrid, Spain
| | | | - Susana Suarez
- Cell Production Unit, Gregorio Marañón Health Research Institute (IISGM), Madrid, Spain
| | - Marjorie Pion
- Laboratory of Immune-Regulation, Gregorio Marañón Health Research Institute (IISGM), Madrid, Spain
| | - Marta Martínez-Bonet
- Laboratory of Immune-Regulation, Gregorio Marañón Health Research Institute (IISGM), Madrid, Spain
- *Correspondence: Rafael Correa-Rocha, ; Marta Martínez-Bonet,
| | - Rafael Correa-Rocha
- Laboratory of Immune-Regulation, Gregorio Marañón Health Research Institute (IISGM), Madrid, Spain
- *Correspondence: Rafael Correa-Rocha, ; Marta Martínez-Bonet,
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Gil-Manso S, Miguens Blanco I, López-Esteban R, Carbonell D, López-Fernández LA, West L, Correa-Rocha R, Pion M. Comprehensive Flow Cytometry Profiling of the Immune System in COVID-19 Convalescent Individuals. Front Immunol 2022; 12:793142. [PMID: 35069575 PMCID: PMC8771913 DOI: 10.3389/fimmu.2021.793142] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 10/11/2021] [Accepted: 12/15/2021] [Indexed: 12/13/2022] Open
Abstract
SARS-CoV-2 has infected more than 200 million people worldwide, with more than 4 million associated deaths. Although more than 80% of infected people develop asymptomatic or mild COVID-19, SARS-CoV-2 can induce a profound dysregulation of the immune system. Therefore, it is important to investigate whether clinically recovered individuals present immune sequelae. The potential presence of a long-term dysregulation of the immune system could constitute a risk factor for re-infection and the development of other pathologies. Here, we performed a deep analysis of the immune system in 35 COVID-19 recovered individuals previously infected with SARS-CoV-2 compared to 16 healthy donors, by flow cytometry. Samples from COVID-19 individuals were analysed from 12 days to 305 days post-infection. We observed that, 10 months post-infection, recovered COVID-19 patients presented alterations in the values of some T-cell, B-cell, and innate cell subsets compared to healthy controls. Moreover, we found in recovered COVID-19 individuals increased levels of circulating follicular helper type 1 (cTfh1), plasmablast/plasma cells, and follicular dendritic cells (foDC), which could indicate that the Tfh-B-foDC axis might be functional to produce specific immunoglobulins 10 months post-infection. The presence of this axis and the immune system alterations could constitute prognosis markers and could play an important role in potential re-infection or the presence of long-term symptoms in some individuals.
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Affiliation(s)
- Sergio Gil-Manso
- Laboratory of Immune-Regulation, Gregorio Marañón Health Research Institute (IiSGM), Gregorio Marañón University General Hospital, Madrid, Spain
| | - Iria Miguens Blanco
- Department of Emergency, Gregorio Marañón University General Hospital, Madrid, Spain
| | - Rocío López-Esteban
- Laboratory of Immune-Regulation, Gregorio Marañón Health Research Institute (IiSGM), Gregorio Marañón University General Hospital, Madrid, Spain
| | - Diego Carbonell
- Laboratory of Immune-Regulation, Gregorio Marañón Health Research Institute (IiSGM), Gregorio Marañón University General Hospital, Madrid, Spain
- Department of Hematology, Gregorio Marañón Health Research Institute (IiSGM), Gregorio Marañón University General Hospital, Madrid, Spain
| | - Luis Andrés López-Fernández
- Service of Pharmacy, Gregorio Marañón Health Research Institute (IiSGM), Gregorio Marañón University General Hospital, Madrid, Spain
| | - Lori West
- Department of Pediatrics, Alberta Transplant Institute and Canadian Donation and Transplantation Research Program, University of Alberta, Edmonton, AB, Canada
- Department of Medical Microbiology & Immunology, Alberta Transplant Institute and Canadian Donation and Transplantation Research Program, University of Alberta, Edmonton, AB, Canada
- Department of Surgery, Alberta Transplant Institute and Canadian Donation and Transplantation Research Program, University of Alberta, Edmonton, AB, Canada
- Department of Laboratory Medicine & Pathology, Alberta Transplant Institute and Canadian Donation and Transplantation Research Program, University of Alberta, Edmonton, AB, Canada
| | - Rafael Correa-Rocha
- Laboratory of Immune-Regulation, Gregorio Marañón Health Research Institute (IiSGM), Gregorio Marañón University General Hospital, Madrid, Spain
| | - Marjorie Pion
- Laboratory of Immune-Regulation, Gregorio Marañón Health Research Institute (IiSGM), Gregorio Marañón University General Hospital, Madrid, Spain
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