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Rossi K, Ruiz-Ferrando A, Akl DF, Abalos VG, Heras-Domingo J, Graux R, Hai X, Lu J, Garcia-Gasulla D, López N, Pérez-Ramírez J, Mitchell S. Quantitative Description of Metal Center Organization and Interactions in Single-Atom Catalysts. Adv Mater 2024; 36:e2307991. [PMID: 37757786 DOI: 10.1002/adma.202307991] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/22/2023] [Indexed: 09/29/2023]
Abstract
Ultra-high-density single-atom catalysts (UHD-SACs) present unique opportunities for harnessing cooperative effects between neighboring metal centers. However, the lack of tools to establish correlations between the density, types, and arrangements of isolated metal atoms and the support surface properties hinders efforts to engineer advanced material architectures. Here, this work precisely describes the metal center organization in various mono- and multimetallic UHD-SACs based on nitrogen-doped carbon (NC) supports by coupling transmission electron microscopy with tailored machine-learning methods (released as a user-friendly web app) and density functional theory simulations. This approach quantifies the non-negligible presence of multimers with increasing atom density, characterizes the size and shape of these low-nuclearity clusters, and identifies surface atom density criteria to ensure isolation. Further, it provides previously inaccessible experimental insights into coordination site arrangements in the NC host, uncovering a repulsive interaction that influences the disordered distribution of metal centers in UHD-SACs. This observation holds in multimetallic systems, where chemically-specific analysis quantifies the degree of intermixing. These fundamental insights into the materials chemistry of single-atom catalysts are crucial for designing catalytic systems with superior reactivity.
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Affiliation(s)
- Kevin Rossi
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1, Zurich, 8093, Switzerland
| | - Andrea Ruiz-Ferrando
- Institute of Chemical Research of Catalonia, Avenida Països Catalans 16, Tarragona, 43007, Spain
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Carrer de Marcellí Domingo 1, Tarragona, 43007, Spain
| | - Dario Faust Akl
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1, Zurich, 8093, Switzerland
| | | | - Javier Heras-Domingo
- Institute of Chemical Research of Catalonia, Avenida Països Catalans 16, Tarragona, 43007, Spain
| | - Romain Graux
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Route Cantonale, Lausanne, 1015, Switzerland
| | - Xiao Hai
- Department of Chemistry, National University of Singapore, Science Drive 3, Singapore, 117543, Singapore
| | - Jiong Lu
- Department of Chemistry, National University of Singapore, Science Drive 3, Singapore, 117543, Singapore
- Centre for Advanced 2D Materials and Graphene Research Centre, National University of Singapore, Science Drive 2, Singapore, 117546, Singapore
- Institute for Functional Intelligent Materials, National University of Singapore, Science Drive 2, Singapore, 117544, Singapore
| | - Dario Garcia-Gasulla
- Barcelona Supercomputing Center, Plaça d'Eusebi Güell 1-3, Barcelona, 08034, Spain
| | - Nuria López
- Institute of Chemical Research of Catalonia, Avenida Països Catalans 16, Tarragona, 43007, Spain
| | - Javier Pérez-Ramírez
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1, Zurich, 8093, Switzerland
| | - Sharon Mitchell
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1, Zurich, 8093, Switzerland
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Cilloniz C, Motos A, Canseco J, Peñasco Y, Ricart P, Abril E, García JMG, Ortiz AB, Mateo NG, Sánchez-Miralles Á, Franco N, Riera J, Ferrer R, Bustamante-Munguira E, Caballero J, Gándara AMDL, Sancho S, Masclans JR, Urrelo-Cerrón L, Carbonell N, Socías L, Barberà C, Lorente JA, Rodríguez ÓP, Menéndez R, de Gonzalo-Calvo D, Ceccato A, Fernandez-Barat L, Garcia-Gasulla D, Gabarrus A, Garcia-Vidal C, Moreno A, Barbé F, Miro JM, Torres A. Clinical Outcomes of Critical COVID-19 in HIV-Infected Adults: A Propensity Score Matched Analysis. Arch Bronconeumol 2023; 59:772-778. [PMID: 37661559 DOI: 10.1016/j.arbres.2023.07.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 09/05/2023]
Affiliation(s)
- Catia Cilloniz
- CIBER of Respiratory Diseases (CIBERES), Madrid, Spain; August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Spain; University of Barcelona, Spain; Faculty of Health Sciences, Continental University, Huancayo, Peru.
| | - Anna Motos
- CIBER of Respiratory Diseases (CIBERES), Madrid, Spain; August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Spain; University of Barcelona, Spain
| | - Joan Canseco
- CIBER of Respiratory Diseases (CIBERES), Madrid, Spain; August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Spain
| | - Yhivian Peñasco
- Intensive Medicine Department, Hospital Universitario Marqués of Valdecilla, Santander, Spain
| | - Pilar Ricart
- Intensive Medicine Department, Hospital Universitari Germans Trias, Badalona, Spain
| | - Elena Abril
- Hospital Universitario Torrejón, Madrid, Spain
| | | | - Aaron Blandino Ortiz
- Intensive Care Department, Hospital Universitario Ramón y Cajal, Madrid, Spain; Universidad de Alcalá, Madrid, Spain
| | - Nadia García Mateo
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca (IBSAL), Paseo de San Vicente, Salamanca, Spain
| | | | | | - Jordi Riera
- Intensive Care Department, Vall d'Hebron Hospital Universitari, SODIR Research Group, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Ricard Ferrer
- Intensive Care Department, Vall d'Hebron Hospital Universitari, SODIR Research Group, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | | | - Jesús Caballero
- Critical Care Department, Hospital Universitari Arnau de Vilanova, IRBLleida, Lleida, Spain
| | | | - Susana Sancho
- Critical Care Department, Hospital Universitario y Politecnico de La Fe, Valencia, Spain
| | - Joan-Ramon Masclans
- Critical Care Department, Hospital del Mar, Critical Illness Research Group (GREPAC), Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain; Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | | | - Nieves Carbonell
- Intensive Care Unit, Hospital Clinico Universitario de Valencia, Spain
| | - Lorenzo Socías
- Intensive Care Unit, Hospital Son Llàtzer, Palma de Mallorca, Illes Balears, Spain
| | | | - José A Lorente
- CIBER of Respiratory Diseases (CIBERES), Madrid, Spain; Hospital Universitario de Getafe, Madrid, Spain
| | - Óscar Peñuelas Rodríguez
- CIBER of Respiratory Diseases (CIBERES), Madrid, Spain; Hospital Universitario de Getafe, Madrid, Spain
| | - Rosario Menéndez
- CIBER of Respiratory Diseases (CIBERES), Madrid, Spain; Pulmonology Service, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - David de Gonzalo-Calvo
- CIBER of Respiratory Diseases (CIBERES), Madrid, Spain; Hospital Santa Maria, IRBLleida, Lleida, Spain
| | - Adrian Ceccato
- CIBER of Respiratory Diseases (CIBERES), Madrid, Spain; Critical Care Center, ParcTaulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí I3PT, Sabadell, Spain; Intensive Care Unit, Hospital Universitari Sagrat Cor, Grupo Quironsalud, Barcelona, Spain
| | - Laia Fernandez-Barat
- CIBER of Respiratory Diseases (CIBERES), Madrid, Spain; August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Spain; University of Barcelona, Spain
| | | | - Albert Gabarrus
- CIBER of Respiratory Diseases (CIBERES), Madrid, Spain; August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Spain
| | - Carolina Garcia-Vidal
- Department of Infectious Diseases, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Asunción Moreno
- Department of Infectious Diseases, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Ferran Barbé
- CIBER of Respiratory Diseases (CIBERES), Madrid, Spain; Pulmonary Department, Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Spain
| | - José M Miro
- Department of Infectious Diseases, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain.
| | - Antoni Torres
- CIBER of Respiratory Diseases (CIBERES), Madrid, Spain; August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Spain; University of Barcelona, Spain; Pulmonology Department, Hospital Clinic of Barcelona, Spain
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3
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de Gonzalo-Calvo D, Molinero M, Benítez ID, Perez-Pons M, García-Mateo N, Ortega A, Postigo T, García-Hidalgo MC, Belmonte T, Rodríguez-Muñoz C, González J, Torres G, Gort-Paniello C, Moncusí-Moix A, Estella Á, Tamayo Lomas L, Martínez de la Gándara A, Socias L, Peñasco Y, de la Torre MDC, Bustamante-Munguira E, Gallego Curto E, Martínez Varela I, Martin Delgado MC, Vidal-Cortés P, López Messa J, Pérez-García F, Caballero J, Añón JM, Loza-Vázquez A, Carbonell N, Marin-Corral J, Jorge García RN, Barberà C, Ceccato A, Fernández-Barat L, Ferrer R, Garcia-Gasulla D, Lorente-Balanza JÁ, Menéndez R, Motos A, Peñuelas O, Riera J, Bermejo-Martin JF, Torres A, Barbé F. A blood microRNA classifier for the prediction of ICU mortality in COVID-19 patients: a multicenter validation study. Respir Res 2023; 24:159. [PMID: 37328754 DOI: 10.1186/s12931-023-02462-x] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 05/25/2023] [Indexed: 06/18/2023] Open
Abstract
BACKGROUND The identification of critically ill COVID-19 patients at risk of fatal outcomes remains a challenge. Here, we first validated candidate microRNAs (miRNAs) as biomarkers for clinical decision-making in critically ill patients. Second, we constructed a blood miRNA classifier for the early prediction of adverse outcomes in the ICU. METHODS This was a multicenter, observational and retrospective/prospective study including 503 critically ill patients admitted to the ICU from 19 hospitals. qPCR assays were performed in plasma samples collected within the first 48 h upon admission. A 16-miRNA panel was designed based on recently published data from our group. RESULTS Nine miRNAs were validated as biomarkers of all-cause in-ICU mortality in the independent cohort of critically ill patients (FDR < 0.05). Cox regression analysis revealed that low expression levels of eight miRNAs were associated with a higher risk of death (HR from 1.56 to 2.61). LASSO regression for variable selection was used to construct a miRNA classifier. A 4-blood miRNA signature composed of miR-16-5p, miR-192-5p, miR-323a-3p and miR-451a predicts the risk of all-cause in-ICU mortality (HR 2.5). Kaplan‒Meier analysis confirmed these findings. The miRNA signature provides a significant increase in the prognostic capacity of conventional scores, APACHE-II (C-index 0.71, DeLong test p-value 0.055) and SOFA (C-index 0.67, DeLong test p-value 0.001), and a risk model based on clinical predictors (C-index 0.74, DeLong test-p-value 0.035). For 28-day and 90-day mortality, the classifier also improved the prognostic value of APACHE-II, SOFA and the clinical model. The association between the classifier and mortality persisted even after multivariable adjustment. The functional analysis reported biological pathways involved in SARS-CoV infection and inflammatory, fibrotic and transcriptional pathways. CONCLUSIONS A blood miRNA classifier improves the early prediction of fatal outcomes in critically ill COVID-19 patients.
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Affiliation(s)
- David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Marta Molinero
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Iván D Benítez
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Manel Perez-Pons
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Nadia García-Mateo
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de Salud de Castilla y León, Salamanca, Spain
| | - Alicia Ortega
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de Salud de Castilla y León, Salamanca, Spain
| | - Tamara Postigo
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de Salud de Castilla y León, Salamanca, Spain
| | - María C García-Hidalgo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Thalia Belmonte
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Carlos Rodríguez-Muñoz
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Jessica González
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Gerard Torres
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Clara Gort-Paniello
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Anna Moncusí-Moix
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Ángel Estella
- Department of Medicine, Intensive Care Unit University Hospital of Jerez, University of Cádiz, INIBiCA, Cádiz, Spain
| | - Luis Tamayo Lomas
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Critical Care Department, Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain
| | | | - Lorenzo Socias
- Intensive Care Unit, Hospital Son Llàtzer, Palma de Mallorca, Illes Balears, Spain
| | - Yhivian Peñasco
- Servicio de Medicina Intensiva, Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - Maria Del Carmen de la Torre
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Servei de Medicina Intensiva, Hospital de Mataró (Consorci Sanitari del Maresme), Mataró, Spain
| | - Elena Bustamante-Munguira
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Department of Intensive Care Medicine, Hospital Clínico Universitario Valladolid, Valladolid, Spain
| | - Elena Gallego Curto
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Unidad de Cuidados Intensivos, Hospital Universitario San Pedro de Alcántara, Cáceres, Spain
| | | | | | - Pablo Vidal-Cortés
- Intensive Care Unit, Complexo Hospitalario Universitario de Ourense, Ourense, Spain
| | | | - Felipe Pérez-García
- Servicio de Microbiología Clínica, Facultad de Medicina, Departamento de Biomedicina y Biotecnología, Hospital Universitario Príncipe de Asturias - Universidad de Alcalá, Madrid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Caballero
- Grup de Recerca Medicina Intensiva, Intensive Care Department Hospital, Universitari Arnau de Vilanova, Lleida, Spain
| | - José M Añón
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Servicio de Medicina Intensiva. Hospital Universitario La Paz, IdiPAZ, Madrid, Spain
| | - Ana Loza-Vázquez
- Unidad de Medicina Intensiva, Hospital Universitario Virgen de Valme, Seville, Spain
| | - Nieves Carbonell
- Intensive Care Unit, Hospital Clínico y Universitario de Valencia, Valencia, Spain
| | | | | | - Carmen Barberà
- Intensive Care Department, University Hospital Santa María, IRBLleida, Lleida, Spain
| | - Adrián Ceccato
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Laia Fernández-Barat
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Ricard Ferrer
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Intensive Care Department, SODIR Research Group, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | | | - Jose Ángel Lorente-Balanza
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Hospital Universitario de Getafe, Madrid, Spain
- Dep. of Medicine, Universidad Europea, Madrid, Spain
- Dep. of Bioengineering, Universidad Carlos III, Madrid, Spain
| | - Rosario Menéndez
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Pulmonology Service, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Ana Motos
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Oscar Peñuelas
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Hospital Universitario de Getafe, Madrid, Spain
| | - Jordi Riera
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Intensive Care Department, SODIR Research Group, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Jesús F Bermejo-Martin
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de Salud de Castilla y León, Salamanca, Spain
- Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain
| | - Antoni Torres
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Ferran Barbé
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.
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4
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González J, de Batlle J, Benítez ID, Torres G, Santisteve S, Targa AD, Gort-Paniello C, Moncusí-Moix A, Aguilà M, Seck F, Ceccato A, Ferrer R, Motos A, Riera J, Fernández L, Menéndez R, Lorente JÁ, Peñuelas O, Garcia-Gasulla D, Peñasco Y, Ricart P, Abril Palomares E, Aguilera L, Rodríguez A, Boado Varela MV, Beteré B, Pozo-Laderas JC, Solé-Violan J, Salvador-Adell I, Novo MA, Barberán J, Amaya Villar R, Garnacho-Montero J, Gómez JM, Blandino Ortiz A, Tamayo Lomas L, Úbeda A, Catalán-González M, Sánchez-Miralles A, Martínez Varela I, Jorge García RN, Franco N, Gumucio-Sanguino VD, Bustamante-Munguira E, Valdivia LJ, Caballero J, Gallego E, Rodríguez C, Castellanos-Ortega Á, Trenado J, Marin-Corral J, Albaiceta GM, de la Torre MDC, Loza-Vázquez A, Vidal P, Añón JM, Carbajales Pérez C, Sagredo V, Carbonell N, Socias L, Barberà C, Estella A, Diaz E, de Gonzalo-Calvo D, Torres A, Barbé F. Key Factors Associated With Pulmonary Sequelae in the Follow-Up of Critically Ill COVID-19 Patients. Arch Bronconeumol 2023; 59:205-215. [PMID: 36690515 PMCID: PMC9824938 DOI: 10.1016/j.arbres.2022.12.017] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/09/2023]
Abstract
INTRODUCTION Critical COVID-19 survivors have a high risk of respiratory sequelae. Therefore, we aimed to identify key factors associated with altered lung function and CT scan abnormalities at a follow-up visit in a cohort of critical COVID-19 survivors. METHODS Multicenter ambispective observational study in 52 Spanish intensive care units. Up to 1327 PCR-confirmed critical COVID-19 patients had sociodemographic, anthropometric, comorbidity and lifestyle characteristics collected at hospital admission; clinical and biological parameters throughout hospital stay; and, lung function and CT scan at a follow-up visit. RESULTS The median [p25-p75] time from discharge to follow-up was 3.57 [2.77-4.92] months. Median age was 60 [53-67] years, 27.8% women. The mean (SD) percentage of predicted diffusing lung capacity for carbon monoxide (DLCO) at follow-up was 72.02 (18.33)% predicted, with 66% of patients having DLCO<80% and 24% having DLCO<60%. CT scan showed persistent pulmonary infiltrates, fibrotic lesions, and emphysema in 33%, 25% and 6% of patients, respectively. Key variables associated with DLCO<60% were chronic lung disease (CLD) (OR: 1.86 (1.18-2.92)), duration of invasive mechanical ventilation (IMV) (OR: 1.56 (1.37-1.77)), age (OR [per-1-SD] (95%CI): 1.39 (1.18-1.63)), urea (OR: 1.16 (0.97-1.39)) and estimated glomerular filtration rate at ICU admission (OR: 0.88 (0.73-1.06)). Bacterial pneumonia (1.62 (1.11-2.35)) and duration of ventilation (NIMV (1.23 (1.06-1.42), IMV (1.21 (1.01-1.45)) and prone positioning (1.17 (0.98-1.39)) were associated with fibrotic lesions. CONCLUSION Age and CLD, reflecting patients' baseline vulnerability, and markers of COVID-19 severity, such as duration of IMV and renal failure, were key factors associated with impaired DLCO and CT abnormalities.
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Affiliation(s)
- Jessica González
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Jordi de Batlle
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Iván D. Benítez
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Gerard Torres
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Sally Santisteve
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Adriano D.S. Targa
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Clara Gort-Paniello
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Anna Moncusí-Moix
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Maria Aguilà
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Fatty Seck
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Adrián Ceccato
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Critical Care Center, ParcTaulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí I3PT, Sabadell, Spain
| | - Ricard Ferrer
- Intensive Care Department, Vall d’Hebron Hospital Universitari, SODIR Research Group, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Anna Motos
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Department of Pneumology, Hospital Clinic of Barcelona, August Pi i Sunyer Biomedical Research Institute – IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Jordi Riera
- Intensive Care Department, Vall d’Hebron Hospital Universitari, SODIR Research Group, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Laia Fernández
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Department of Pneumology, Hospital Clinic of Barcelona, August Pi i Sunyer Biomedical Research Institute – IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Rosario Menéndez
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Pulmonology Service, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - José Ángel Lorente
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Hospital Universitario de Getafe, Madrid, Spain
| | - Oscar Peñuelas
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Hospital Universitario de Getafe, Madrid, Spain
| | | | - Yhivian Peñasco
- Servicio de Medicina Intensiva, Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - Pilar Ricart
- Servei de Medicina Intensiva, Hospital Universitari Germans Trias, Badalona, Spain
| | | | - Luciano Aguilera
- Servicio de Anestesiología y Reanimación, Hospital Universitario Basurto, Bilbao, Spain
| | | | | | - Belén Beteré
- Servicio de Análisis Clínicos, Hospital Universitario Príncipe de Asturias, Alcalá de Henares, Spain
| | - Juan Carlos Pozo-Laderas
- UGC-Medicina Intensiva, Hospital Universitario Reina Sofia, Instituto Maimonides IMIBIC, Córdoba, Spain
| | - Jordi Solé-Violan
- Critical Care Department, Hospital Dr. Negrín Gran Canaria, Universidad Fernando Pessoa, Las Palmas, Gran Canaria, Canarias, Spain
| | | | - Mariana Andrea Novo
- Servei de Medicina Intensiva, Hospital Universitari Son Espases, Palma de Mallorca, Illes Balears, Spain
| | - José Barberán
- Hospital Universitario HM Montepríncipe, Universidad San Pablo-CEU, Madrid, Spain
| | - Rosario Amaya Villar
- Intensive Care Clinical Unit, Hospital Universitario Virgen de Rocío, Sevilla, Spain
| | - José Garnacho-Montero
- Intensive Care Clinical Unit, Hospital Universitario Virgen Macarena, Sevilla, Spain
| | - José M. Gómez
- Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Aaron Blandino Ortiz
- Servicio de Medicina Intensiva, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Luis Tamayo Lomas
- Critical Care Department, Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain
| | - Alejandro Úbeda
- Servicio de Medicina Intensiva, Hospital Punta de Europa, Algeciras, Spain
| | | | | | | | | | | | - Víctor D. Gumucio-Sanguino
- Department of Intensive Care, Hospital Universitari de Bellvitge, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Spain
| | | | | | - Jesús Caballero
- Critical Care Department, Hospital Universitari Arnau de Vilanova, IRBLleida, Lleida, Spain
| | - Elena Gallego
- Unidad de Cuidados Intensivos, Hospital Universitario San Pedro de Alcántara, Cáceres, Spain
| | | | | | - Josep Trenado
- Servicio de Medicina Intensiva, Hospital Universitario Mútua de Terrassa, Terrassa, Barcelona, Spain
| | | | - Guillermo M. Albaiceta
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Departamento de Biología Funcional, Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Instituto de Investigación Sanitaria del Principado de Asturias, Hospital Central de Asturias, Oviedo, Spain
| | | | - Ana Loza-Vázquez
- Unidad de Medicina Intensiva, Hospital Universitario Virgen de Valme, Sevilla, Spain
| | - Pablo Vidal
- Complexo Hospitalario Universitario de Ourense, Ourense, Spain
| | - Jose M. Añón
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Servicio de Medicina Intensiva, Hospital Universitario La Paz, IdiPAZ, Madrid, Spain
| | | | | | - Nieves Carbonell
- Intensive Care Unit, Hospital Clínico y Universitario de Valencia, Valencia, Spain
| | - Lorenzo Socias
- Intensive Care Unit, Hospital Son Llàtzer, Palma de Mallorca, Illes Balears, Spain
| | | | - Angel Estella
- Intensive Care Unit, University Hospital of Jerez, Medicine Department University of Cadiz, INiBICA, Spain
| | - Emili Diaz
- Department of Medicine, Universitat Autònoma de Barcelona (UAB), Critical Care Department, Corporació Sanitària Parc Taulí, Sabadell, Barcelona, Spain
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Antoni Torres
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Department of Pneumology, Hospital Clinic of Barcelona, August Pi i Sunyer Biomedical Research Institute – IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Ferran Barbé
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Corresponding author
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5
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García-Hidalgo MC, González J, Benítez ID, Carmona P, Santisteve S, Pérez-Pons M, Moncusí-Moix A, Gort-Paniello C, Rodríguez-Jara F, Molinero M, Belmonte T, Torres G, Labarca G, Nova-Lamperti E, Caballero J, Bermejo-Martin JF, Ceccato A, Fernández-Barat L, Ferrer R, Garcia-Gasulla D, Menéndez R, Motos A, Peñuelas O, Riera J, Torres A, Barbé F, de Gonzalo-Calvo D. Identification of circulating microRNA profiles associated with pulmonary function and radiologic features in survivors of SARS-CoV-2-induced ARDS. Emerg Microbes Infect 2022; 11:1537-1549. [PMID: 35603455 PMCID: PMC9176679 DOI: 10.1080/22221751.2022.2081615] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
There is a limited understanding of the pathophysiology of postacute pulmonary sequelae in severe COVID-19. The aim of current study was to define the circulating microRNA (miRNA) profiles associated with pulmonary function and radiologic features in survivors of SARS-CoV-2-induced ARDS. The study included patients who developed ARDS secondary to SARS-CoV-2 infection (n = 167) and a group of infected patients who did not develop ARDS (n = 33). Patients were evaluated 3 months after hospital discharge. The follow-up included a complete pulmonary evaluation and chest computed tomography. Plasma miRNA profiling was performed using RT-qPCR. Random forest was used to construct miRNA signatures associated with lung diffusing capacity for carbon monoxide (DLCO) and total severity score (TSS). Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses were conducted. DLCO < 80% predicted was observed in 81.8% of the patients. TSS showed a median [P25;P75] of 5 [2;8]. The miRNA model associated with DLCO comprised miR-17-5p, miR-27a-3p, miR-126-3p, miR-146a-5p and miR-495-3p. Concerning radiologic features, a miRNA signature composed by miR-9-5p, miR-21-5p, miR-24-3p and miR-221-3p correlated with TSS values. These associations were not observed in the non-ARDS group. KEGG pathway and GO enrichment analyses provided evidence of molecular mechanisms related not only to profibrotic or anti-inflammatory states but also to cell death, immune response, hypoxia, vascularization, coagulation and viral infection. In conclusion, diffusing capacity and radiological features in survivors from SARS-CoV-2-induced ARDS are associated with specific miRNA profiles. These findings provide novel insights into the possible molecular pathways underlying the pathogenesis of pulmonary sequelae. Trial registration:ClinicalTrials.gov identifier: NCT04457505.. Trial registration:ISRCTN.org identifier: ISRCTN16865246..
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Affiliation(s)
- María C García-Hidalgo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Jessica González
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Iván D Benítez
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Paola Carmona
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Sally Santisteve
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Manel Pérez-Pons
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Anna Moncusí-Moix
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Clara Gort-Paniello
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Fátima Rodríguez-Jara
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Marta Molinero
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Thalia Belmonte
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Gerard Torres
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Gonzalo Labarca
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, Universidad de Concepcion, Concepcion, Chile.,Internal Medicine Unit, Complejo Asistencial Dr. Víctor Ríos Ruiz, Los Ángeles, Chile
| | - Estefania Nova-Lamperti
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, Universidad de Concepcion, Concepcion, Chile
| | - Jesús Caballero
- Grup de Recerca Medicina Intensiva, Intensive Care Department Hospital Universitari Arnau de Vilanova, IRBLleida, Lleida, Spain
| | - Jesús F Bermejo-Martin
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Adrián Ceccato
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Laia Fernández-Barat
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona; IDIBAPS, Barcelona, Spain
| | - Ricard Ferrer
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Intensive Care Department, Vall d'Hebron Hospital Universitari. SODIR Research Group, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | | | - Rosario Menéndez
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Pulmonology Service, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Ana Motos
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona; IDIBAPS, Barcelona, Spain
| | - Oscar Peñuelas
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Hospital Universitario de Getafe, Madrid, Spain
| | - Jordi Riera
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Intensive Care Department, Vall d'Hebron Hospital Universitari. SODIR Research Group, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Antoni Torres
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Pneumology Department, Clinic Institute of Thorax (ICT), Hospital Clinic of Barcelona - Insitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - ICREA, University of Barcelona (UB), Barcelona, Spain
| | - Ferran Barbé
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
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- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
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6
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García-Hidalgo MC, Peláez R, González J, Santisteve S, Benítez ID, Molinero M, Perez-Pons M, Belmonte T, Torres G, Moncusí-Moix A, Gort-Paniello C, Aguilà M, Seck F, Carmona P, Caballero J, Barberà C, Ceccato A, Fernández-Barat L, Ferrer R, Garcia-Gasulla D, Lorente-Balanza JÁ, Menéndez R, Motos A, Peñuelas O, Riera J, Bermejo-Martin JF, Torres A, Barbé F, de Gonzalo-Calvo D, Larráyoz IM. Genome-wide transcriptional profiling of pulmonary functional sequelae in ARDS- secondary to SARS-CoV-2 infection. Biomed Pharmacother 2022; 154:113617. [PMID: 36058144 PMCID: PMC9424524 DOI: 10.1016/j.biopha.2022.113617] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/18/2022] [Accepted: 08/27/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Up to 80% of patients surviving acute respiratory distress syndrome (ARDS) secondary to SARS-CoV-2 infection present persistent anomalies in pulmonary function after hospital discharge. There is a limited understanding of the mechanistic pathways linked to post-acute pulmonary sequelae. AIM To identify the molecular underpinnings associated with severe lung diffusion involvement in survivors of SARS-CoV-2-induced ARDS. METHODS Survivors attended to a complete pulmonary evaluation 3 months after hospital discharge. RNA sequencing (RNA-seq) was performed using Illumina technology in whole-blood samples from 50 patients with moderate to severe diffusion impairment (DLCO<60%) and age- and sex-matched individuals with mild-normal lung function (DLCO≥60%). A transcriptomic signature for optimal classification was constructed using random forest. Transcriptomic data were analyzed for biological pathway enrichment, cellular deconvolution, cell/tissue-specific gene expression and candidate drugs. RESULTS RNA-seq identified 1357 differentially expressed transcripts. A model composed of 14 mRNAs allowed the optimal discrimination of survivors with severe diffusion impairment (AUC=0.979). Hallmarks of lung sequelae involved cell death signaling, cytoskeleton reorganization, cell growth and differentiation and the immune response. Resting natural killer (NK) cells were the most important immune cell subtype for the prediction of severe diffusion impairment. Components of the signature correlated with neutrophil, lymphocyte and monocyte counts. A variable expression profile of the transcripts was observed in lung cell subtypes and bodily tissues. One upregulated gene, TUBB4A, constitutes a target for FDA-approved drugs. CONCLUSIONS This work defines the transcriptional programme associated with post-acute pulmonary sequelae and provides novel insights for targeted interventions and biomarker development.
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Affiliation(s)
- María C. García-Hidalgo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Rafael Peláez
- Biomarkers and Molecular Signaling Group, Neurodegenerative Diseases Area Center for Biomedical Research of La Rioja, CIBIR, Logroño, Spain
| | - Jessica González
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Sally Santisteve
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Iván D. Benítez
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Marta Molinero
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Manel Perez-Pons
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Thalía Belmonte
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Gerard Torres
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Anna Moncusí-Moix
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Clara Gort-Paniello
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Maria Aguilà
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Faty Seck
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Paola Carmona
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Jesús Caballero
- Grup de Recerca Medicina Intensiva, Intensive Care Department Hospital Universitari Arnau de Vilanova, Lleida, Spain
| | - Carme Barberà
- Intensive Care Department, University Hospital Santa María, IRBLleida, Lleida, Spain
| | - Adrián Ceccato
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Hospital Universitari Sagrat Cor, Barcelona, Spain
| | - Laia Fernández-Barat
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Servei de Pneumologia, Hospital Clinic; Universitat de Barcelona; IDIBAPS, Barcelona, Spain
| | - Ricard Ferrer
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Intensive Care Department, Vall d’Hebron Hospital Universitari. SODIR Research Group, Vall d’Hebron Institut de Recerca (VHIR), Spain
| | | | - Jose Ángel Lorente-Balanza
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Hospital Universitario de Getafe, Madrid, Spain
| | - Rosario Menéndez
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Pulmonology Service, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Ana Motos
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Servei de Pneumologia, Hospital Clinic; Universitat de Barcelona; IDIBAPS, Barcelona, Spain
| | - Oscar Peñuelas
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Hospital Universitario de Getafe, Madrid, Spain
| | - Jordi Riera
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Intensive Care Department, Vall d’Hebron Hospital Universitari. SODIR Research Group, Vall d’Hebron Institut de Recerca (VHIR), Spain
| | - Jesús F. Bermejo-Martin
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Antoni Torres
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Pneumology Department, Clinic Institute of Thorax (ICT), Hospital Clinic of Barcelona, Insitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), ICREA, University of Barcelona (UB), Barcelona, Spain
| | - Ferran Barbé
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Correspondence to: Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Avda. Alcalde Rovira Roure 80, Lleida 25198, Spain
| | - Ignacio M. Larráyoz
- Biomarkers and Molecular Signaling Group, Neurodegenerative Diseases Area Center for Biomedical Research of La Rioja, CIBIR, Logroño, Spain,GRUPAC, Department of Nursing, University of La Rioja, Logroño, Spain,Correspondence to: Biomarkers and Molecular Signaling Group, Neurodegenerative Diseases Area, Center for Biomedical Research of La Rioja, CIBIR. C. Piqueras, 98, Logroño 26006, Spain
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7
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Molinero M, Gómez S, Benítez ID, Vengoechea JJ, González J, Polanco D, Gort-Paniello C, Moncusí-Moix A, García-Hidalgo MC, Perez-Pons M, Belmonte T, Torres G, Caballero J, Barberà C, Ayestarán Rota JI, Socías Crespí L, Ceccato A, Fernández-Barat L, Ferrer R, Garcia-Gasulla D, Lorente-Balanza JÁ, Menéndez R, Motos A, Peñuelas O, Riera J, Torres A, Barbé F, de Gonzalo-Calvo D. Multiplex protein profiling of bronchial aspirates reveals disease-, mortality- and respiratory sequelae-associated signatures in critically ill patients with ARDS secondary to SARS-CoV-2 infection. Front Immunol 2022; 13:942443. [PMID: 35967328 PMCID: PMC9373836 DOI: 10.3389/fimmu.2022.942443] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Introduction Bronchial aspirates (BAS) obtained during invasive mechanical ventilation (IMV) constitutes a useful tool for molecular phenotyping and decision making. Aim To identify the proteomic determinants associated with disease pathogenesis, all-cause mortality and respiratory sequelae in BAS samples from critically ill patients with SARS-CoV-2-induced ARDS. Methods Multicenter study including 74 critically ill patients with COVID-19 and non-COVID-19 ARDS. BAS were obtained by bronchoaspiration after IMV initiation. Three hundred sixty-four proteins were quantified using proximity extension assay (PEA) technology. Random forest models were used to assess predictor importance. Results After adjusting for confounding factors, CST5, NADK, SRPK2 and TGF-α were differentially detected in COVID-19 and non-COVID-19 patients. In random forest models for COVID-19, CST5, DPP7, NADK, KYAT1 and TYMP showed the highest variable importance. In COVID-19 patients, reduced levels of ENTPD2 and PTN were observed in nonsurvivors of ICU stay, even after adjustment. AGR2, NQO2, IL-1α, OSM and TRAIL showed the strongest associations with in-ICU mortality and were used to construct a protein-based prediction model. Kaplan-Meier curves revealed a clear separation in mortality risk between subgroups of PTN, ENTPD2 and the prediction model. Cox regression models supported these findings. In survivors, the levels of FCRL1, NTF4 and THOP1 in BAS samples obtained during the ICU stay correlated with lung function (i.e., DLCO levels) 3 months after hospital discharge. Similarly, Flt3L and THOP1 levels were correlated with radiological features (i.e., TSS). These proteins are expressed in immune and nonimmune lung cells. Poor host response to viral infectivity and an inappropriate reparative mechanism seem to be linked with the pathogenesis of the disease and fatal outcomes, respectively. Conclusion BAS proteomics identified novel factors associated with the pathology of SARS-CoV-2-induced ARDS and its adverse outcomes. BAS-based protein testing emerges as a novel tool for risk assessment in the ICU.
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Affiliation(s)
- Marta Molinero
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Silvia Gómez
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Iván D Benítez
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - J J Vengoechea
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Jessica González
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Dinora Polanco
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Clara Gort-Paniello
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Anna Moncusí-Moix
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - María C García-Hidalgo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Manel Perez-Pons
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Thalía Belmonte
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Gerard Torres
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Jesús Caballero
- Intensive Care Department, University Hospital Arnau de Vilanova, IRBLleida, Lleida, Spain
| | - Carme Barberà
- Intensive Care Department, University Hospital Santa María, IRBLleida, Lleida, Spain
| | - Jose Ignacio Ayestarán Rota
- Intensive Care Unit, Son Espases University Hospital, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | | | - Adrián Ceccato
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Laia Fernández-Barat
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Ricard Ferrer
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Intensive Care Department, Vall d'Hebron Hospital Universitari. SODIR Research Group, Vall d'Hebron Institut de Recerca VHIR), Barcelona, Spain
| | | | - Jose Ángel Lorente-Balanza
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Hospital Universitario de Getafe, Madrid, Spain
| | - Rosario Menéndez
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Pulmonology Service, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Ana Motos
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Oscar Peñuelas
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Hospital Universitario de Getafe, Madrid, Spain
| | - Jordi Riera
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Intensive Care Department, Vall d'Hebron Hospital Universitari. SODIR Research Group, Vall d'Hebron Institut de Recerca VHIR), Barcelona, Spain
| | - Antoni Torres
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Ferran Barbé
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
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8
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Benítez ID, de Batlle J, Torres G, González J, de Gonzalo-Calvo D, Targa AD, Gort-Paniello C, Moncusí-Moix A, Ceccato A, Fernández-Barat L, Ferrer R, Garcia-Gasulla D, Menéndez R, Motos A, Peñuelas O, Riera J, Bermejo-Martin JF, Peñasco Y, Ricart P, Martin Delgado MC, Aguilera L, Rodríguez A, Boado Varela MV, Suarez-Sipmann F, Pozo-Laderas JC, Solé-Violan J, Nieto M, Novo MA, Barberán J, Amaya Villar R, Garnacho-Montero J, García-Garmendia JL, Gómez JM, Lorente JÁ, Blandino Ortiz A, Tamayo Lomas L, López-Ramos E, Úbeda A, Catalán-González M, Sánchez-Miralles A, Martínez Varela I, Jorge García RN, Franco N, Gumucio-Sanguino VD, Huerta Garcia A, Bustamante-Munguira E, Valdivia LJ, Caballero J, Gallego E, Martínez de la Gándara A, Castellanos-Ortega Á, Trenado J, Marin-Corral J, Albaiceta GM, de la Torre MDC, Loza-Vázquez A, Vidal P, Lopez Messa J, Añón JM, Carbajales Pérez C, Sagredo V, Bofill N, Carbonell N, Socias L, Barberà C, Estella A, Valledor Mendez M, Diaz E, López Lago A, Torres A, Barbé F. Prognostic implications of comorbidity patterns in critically ill COVID-19 patients: A multicenter, observational study. Lancet Reg Health Eur 2022; 18:100422. [PMID: 35655660 PMCID: PMC9148543 DOI: 10.1016/j.lanepe.2022.100422] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Background The clinical heterogeneity of COVID-19 suggests the existence of different phenotypes with prognostic implications. We aimed to analyze comorbidity patterns in critically ill COVID-19 patients and assess their impact on in-hospital outcomes, response to treatment and sequelae. Methods Multicenter prospective/retrospective observational study in intensive care units of 55 Spanish hospitals. 5866 PCR-confirmed COVID-19 patients had comorbidities recorded at hospital admission; clinical and biological parameters, in-hospital procedures and complications throughout the stay; and, clinical complications, persistent symptoms and sequelae at 3 and 6 months. Findings Latent class analysis identified 3 phenotypes using training and test subcohorts: low-morbidity (n=3385; 58%), younger and with few comorbidities; high-morbidity (n=2074; 35%), with high comorbid burden; and renal-morbidity (n=407; 7%), with chronic kidney disease (CKD), high comorbidity burden and the worst oxygenation profile. Renal-morbidity and high-morbidity had more in-hospital complications and higher mortality risk than low-morbidity (adjusted HR (95% CI): 1.57 (1.34-1.84) and 1.16 (1.05-1.28), respectively). Corticosteroids, but not tocilizumab, were associated with lower mortality risk (HR (95% CI) 0.76 (0.63-0.93)), especially in renal-morbidity and high-morbidity. Renal-morbidity and high-morbidity showed the worst lung function throughout the follow-up, with renal-morbidity having the highest risk of infectious complications (6%), emergency visits (29%) or hospital readmissions (14%) at 6 months (p<0.01). Interpretation Comorbidity-based phenotypes were identified and associated with different expression of in-hospital complications, mortality, treatment response, and sequelae, with CKD playing a major role. This could help clinicians in day-to-day decision making including the management of post-discharge COVID-19 sequelae. Funding ISCIII, UNESPA, CIBERES, FEDER, ESF.
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9
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García-Hidalgo MC, González J, Benítez ID, Carmona P, Santisteve S, Moncusí-Moix A, Gort-Paniello C, Rodríguez-Jara F, Molinero M, Perez-Pons M, Torres G, Caballero J, Barberà C, Tedim AP, Almansa R, Ceccato A, Fernández-Barat L, Ferrer R, Garcia-Gasulla D, Menéndez R, Motos A, Peñuelas O, Riera J, Bermejo-Martin JF, Torres A, Barbé F, de Gonzalo-Calvo D. Proteomic profiling of lung diffusion impairment in the recovery stage of SARS-CoV-2-induced ARDS. Clin Transl Med 2022; 12:e838. [PMID: 35538880 PMCID: PMC9091985 DOI: 10.1002/ctm2.838] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/04/2022] [Accepted: 04/08/2022] [Indexed: 12/19/2022] Open
Affiliation(s)
- María C García-Hidalgo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Jessica González
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Iván D Benítez
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Paola Carmona
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Sally Santisteve
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Anna Moncusí-Moix
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Clara Gort-Paniello
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Fátima Rodríguez-Jara
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Marta Molinero
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Manel Perez-Pons
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Gerard Torres
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Jesús Caballero
- Intensive Care Department, University Hospital Arnau de Vilanova, IRBLleida, Lleida, Spain
| | - Carme Barberà
- Intensive Care Department, University Hospital Santa María, IRBLleida, Lleida, Spain
| | - Ana P Tedim
- Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Raquel Almansa
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Adrián Ceccato
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Laia Fernández-Barat
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Ricard Ferrer
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Intensive Care Department, Vall d'Hebron Hospital Universitari, SODIR Research Group, Vall d'Hebron Institut de Recerca (VHIR), Spain
| | | | - Rosario Menéndez
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Pulmonology Service, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Ana Motos
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Oscar Peñuelas
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Hospital Universitario de Getafe, Madrid, Spain
| | - Jordi Riera
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Intensive Care Department, Vall d'Hebron Hospital Universitari, SODIR Research Group, Vall d'Hebron Institut de Recerca (VHIR), Spain
| | - Jesús F Bermejo-Martin
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Antoni Torres
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Ferran Barbé
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
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10
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Mitchell S, Parés F, Faust Akl D, Collins SM, Kepaptsoglou DM, Ramasse QM, Garcia-Gasulla D, Pérez-Ramírez J, López N. Automated Image Analysis for Single-Atom Detection in Catalytic Materials by Transmission Electron Microscopy. J Am Chem Soc 2022; 144:8018-8029. [PMID: 35333043 DOI: 10.1021/jacs.1c12466] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Single-atom catalytic sites may have existed in all supported transition metal catalysts since their first application. Yet, interest in the design of single-atom heterogeneous catalysts (SACs) only really grew when advances in transmission electron microscopy (TEM) permitted direct confirmation of metal site isolation. While atomic-resolution imaging remains a central characterization tool, poor statistical significance, reproducibility, and interoperability limit its scope for deriving robust characteristics about these frontier catalytic materials. Here, we introduce a customized deep-learning method for automated atom detection in image analysis, a rate-limiting step toward high-throughput TEM. Platinum atoms stabilized on a functionalized carbon support with a challenging irregular three-dimensional morphology serve as a practically relevant test system with promising scope in thermo- and electrochemical applications. The model detects over 20,000 atomic positions for the statistical analysis of important properties for establishing structure-performance relations over nanostructured catalysts, like the surface density, proximity, clustering extent, and dispersion uniformity of supported metal species. Good performance obtained on direct application of the model to an iron SAC based on carbon nitride demonstrates its generalizability for single-atom detection on carbon-related materials. The approach establishes a route to integrate artificial intelligence into routine TEM workflows. It accelerates image processing times by orders of magnitude and reduces human bias by providing an uncertainty analysis that is not readily quantifiable in manual atom identification, improving standardization and scalability.
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Affiliation(s)
- Sharon Mitchell
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
| | - Ferran Parés
- Barcelona Supercomputing Center (BSC), Plaça d'Eusebi Güell 1-3, 08034 Barcelona, Spain
| | - Dario Faust Akl
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
| | - Sean M Collins
- School of Chemical and Process Engineering and School of Chemistry, University of Leeds, Leeds LS2 9JT, U.K
| | - Demie M Kepaptsoglou
- SuperSTEM Laboratory, SciTech Daresbury Campus, Daresbury WA4 4AD, U.K.,Department of Physics, University of York, Heslington, York YO10 5DD, U.K
| | - Quentin M Ramasse
- SuperSTEM Laboratory, SciTech Daresbury Campus, Daresbury WA4 4AD, U.K.,School of Chemical and Process Engineering and School of Physics, University of Leeds, Leeds LS2 9JT, U.K
| | - Dario Garcia-Gasulla
- Barcelona Supercomputing Center (BSC), Plaça d'Eusebi Güell 1-3, 08034 Barcelona, Spain
| | - Javier Pérez-Ramírez
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
| | - Núria López
- Institute of Chemical Research of Catalonia and The Barcelona Institute of Science and Technology, 43007 Tarragona, Spain
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11
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Molinero M, Benítez ID, González J, Gort-Paniello C, Moncusí-Moix A, Rodríguez-Jara F, García-Hidalgo MC, Torres G, Vengoechea JJ, Gómez S, Cabo R, Caballero J, Bermejo-Martin JF, Ceccato A, Fernández-Barat L, Ferrer R, Garcia-Gasulla D, Menéndez R, Motos A, Peñuelas O, Riera J, Torres A, Barbé F, de Gonzalo-Calvo D. Bronchial Aspirate-Based Profiling Identifies MicroRNA Signatures Associated With COVID-19 and Fatal Disease in Critically Ill Patients. Front Med (Lausanne) 2022; 8:756517. [PMID: 35186962 PMCID: PMC8850692 DOI: 10.3389/fmed.2021.756517] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 08/10/2021] [Accepted: 12/28/2021] [Indexed: 12/22/2022] Open
Abstract
Background The pathophysiology of COVID-19-related critical illness is not completely understood. Here, we analyzed the microRNA (miRNA) profile of bronchial aspirate (BAS) samples from COVID-19 and non-COVID-19 patients admitted to the ICU to identify prognostic biomarkers of fatal outcomes and to define molecular pathways involved in the disease and adverse events. Methods Two patient populations were included (n = 89): (i) a study population composed of critically ill COVID-19 and non-COVID-19 patients; (ii) a prospective study cohort composed of COVID-19 survivors and non-survivors among patients assisted by invasive mechanical ventilation (IMV). BAS samples were obtained by bronchoaspiration during the ICU stay. The miRNA profile was analyzed using RT-qPCR. Detailed biomarker and bioinformatics analyses were performed. Results The deregulation in five miRNA ratios (miR-122-5p/miR-199a-5p, miR-125a-5p/miR-133a-3p, miR-155-5p/miR-486-5p, miR-214-3p/miR-222-3p, and miR-221-3p/miR-27a-3p) was observed when COVID-19 and non-COVID-19 patients were compared. In addition, five miRNA ratios segregated between ICU survivors and nonsurvivors (miR-1-3p/miR-124-3p, miR-125b-5p/miR-34a-5p, miR-126-3p/miR-16-5p, miR-199a-5p/miR-9-5p, and miR-221-3p/miR-491-5p). Through multivariable analysis, we constructed a miRNA ratio-based prediction model for ICU mortality that optimized the best combination of miRNA ratios (miR-125b-5p/miR-34a-5p, miR-199a-5p/miR-9-5p, and miR-221-3p/miR-491-5p). The model (AUC 0.85) and the miR-199a-5p/miR-9-5p ratio (AUC 0.80) showed an optimal discrimination value and outperformed the best clinical predictor for ICU mortality (days from first symptoms to IMV initiation, AUC 0.73). The survival analysis confirmed the usefulness of the miRNA ratio model and the individual ratio to identify patients at high risk of fatal outcomes following IMV initiation. Functional enrichment analyses identified pathological mechanisms implicated in fibrosis, coagulation, viral infections, immune responses and inflammation. Conclusions COVID-19 induces a specific miRNA signature in BAS from critically ill patients. In addition, specific miRNA ratios in BAS samples hold individual and collective potential to improve risk-based patient stratification following IMV initiation in COVID-19-related critical illness. The biological role of the host miRNA profiles may allow a better understanding of the different pathological axes of the disease.
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Affiliation(s)
- Marta Molinero
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Iván D. Benítez
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Jessica González
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Clara Gort-Paniello
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Anna Moncusí-Moix
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Fátima Rodríguez-Jara
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - María C. García-Hidalgo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Gerard Torres
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - J. J. Vengoechea
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Silvia Gómez
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Ramón Cabo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Jesús Caballero
- Intensive Care Department, University Hospital Arnau de Vilanova, IRBLleida, Lleida, Spain
| | - Jesús F. Bermejo-Martin
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Adrián Ceccato
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Laia Fernández-Barat
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Ricard Ferrer
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Intensive Care Department, Vall d'Hebron Hospital Universitari, SODIR Research Group, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | | | - Rosario Menéndez
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Pulmonology Service, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Ana Motos
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Oscar Peñuelas
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Hospital Universitario de Getafe, Madrid, Spain
| | - Jordi Riera
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Intensive Care Department, Vall d'Hebron Hospital Universitari, SODIR Research Group, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Antoni Torres
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Ferran Barbé
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- *Correspondence: David de Gonzalo-Calvo
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12
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de Gonzalo-Calvo D, Benítez ID, Pinilla L, Carratalá A, Moncusí-Moix A, Gort-Paniello C, Molinero M, González J, Torres G, Bernal M, Pico S, Almansa R, Jorge N, Ortega A, Bustamante-Munguira E, Gómez JM, González-Rivera M, Micheloud D, Ryan P, Martinez A, Tamayo L, Aldecoa C, Ferrer R, Ceccato A, Fernández-Barat L, Motos A, Riera J, Menéndez R, Garcia-Gasulla D, Peñuelas O, Torres A, Bermejo-Martin JF, Barbé F. Circulating microRNA profiles predict the severity of COVID-19 in hospitalized patients. Transl Res 2021; 236:147-159. [PMID: 34048985 PMCID: PMC8149473 DOI: 10.1016/j.trsl.2021.05.004] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/04/2021] [Accepted: 05/20/2021] [Indexed: 12/13/2022]
Abstract
We aimed to examine the circulating microRNA (miRNA) profile of hospitalized COVID-19 patients and evaluate its potential as a source of biomarkers for the management of the disease. This was an observational and multicenter study that included 84 patients with a positive nasopharyngeal swab Polymerase chain reaction (PCR) test for SARS-CoV-2 recruited during the first pandemic wave in Spain (March-June 2020). Patients were stratified according to disease severity: hospitalized patients admitted to the clinical wards without requiring critical care and patients admitted to the intensive care unit (ICU). An additional study was completed including ICU nonsurvivors and survivors. Plasma miRNA profiling was performed using reverse transcription polymerase quantitative chain reaction (RT-qPCR). Predictive models were constructed using least absolute shrinkage and selection operator (LASSO) regression. Ten circulating miRNAs were dysregulated in ICU patients compared to ward patients. LASSO analysis identified a signature of three miRNAs (miR-148a-3p, miR-451a and miR-486-5p) that distinguishes between ICU and ward patients [AUC (95% CI) = 0.89 (0.81-0.97)]. Among critically ill patients, six miRNAs were downregulated between nonsurvivors and survivors. A signature based on two miRNAs (miR-192-5p and miR-323a-3p) differentiated ICU nonsurvivors from survivors [AUC (95% CI) = 0.80 (0.64-0.96)]. The discriminatory potential of the signature was higher than that observed for laboratory parameters such as leukocyte counts, C-reactive protein (CRP) or D-dimer [maximum AUC (95% CI) for these variables = 0.73 (0.55-0.92)]. miRNA levels were correlated with the duration of ICU stay. Specific circulating miRNA profiles are associated with the severity of COVID-19. Plasma miRNA signatures emerge as a novel tool to assist in the early prediction of vital status deterioration among ICU patients.
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Key Words
- auc, area under the roc curve
- crp, c-reactive protein
- cq, quantification cycle
- icu, intensive care unit
- lasso, least absolute shrinkage and selection operator
- ldh, lactate dehydrogenase
- mirna, microrna
- mse, mean square error
- ncrna, noncoding rna
- pca, principal component analysis
- roc, receiver operating characteristic
- rt, reverse transcription
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Affiliation(s)
- David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Iván D Benítez
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Lucía Pinilla
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Amara Carratalá
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Anna Moncusí-Moix
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Clara Gort-Paniello
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Marta Molinero
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Jessica González
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, Lleida, Spain
| | - Gerard Torres
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - María Bernal
- Laboratory Medicine Department, University Hospital Arnau de Vilanova, Lleida, Spain
| | - Silvia Pico
- Laboratory Medicine Department, University Hospital Arnau de Vilanova, Lleida, Spain
| | - Raquel Almansa
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Noelia Jorge
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Alicia Ortega
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | | | | | | | | | - Pablo Ryan
- Hospital Universitario Infanta Leonor, Madrid, Spain
| | | | - Luis Tamayo
- Hospital Universitario Río Hortega, Valladolid, Spain
| | - César Aldecoa
- Hospital Universitario Río Hortega, Valladolid, Spain
| | - Ricard Ferrer
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Intensive Care Department, Vall d'Hebron Hospital Universitari. SODIR Research Group, Vall d'Hebron Institut de Recerca (VHIR), Spain
| | - Adrián Ceccato
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Laia Fernández-Barat
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Servei de Pneumologia, Hospital Clinic. Universitat de Barcelona. IDIBAPS, Barcelona, Spain
| | - Ana Motos
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Servei de Pneumologia, Hospital Clinic. Universitat de Barcelona. IDIBAPS, Barcelona, Spain
| | - Jordi Riera
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Intensive Care Department, Vall d'Hebron Hospital Universitari. SODIR Research Group, Vall d'Hebron Institut de Recerca (VHIR), Spain
| | - Rosario Menéndez
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Pulmonology Service, University and Polytechnic Hospital La Fe, Valencia, Spain
| | | | - Oscar Peñuelas
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Hospital Universitario de Getafe, Madrid, Spain
| | - Antoni Torres
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Servei de Pneumologia, Hospital Clinic. Universitat de Barcelona. IDIBAPS, Barcelona, Spain
| | - Jesús F Bermejo-Martin
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Ferran Barbé
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.
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Cortés U, Cortés A, Garcia-Gasulla D, Pérez-Arnal R, Álvarez-Napagao S, Àlvarez E. The ethical use of high-performance computing and artificial intelligence: fighting COVID-19 at Barcelona Supercomputing Center. AI Ethics 2021; 2:325-340. [PMID: 34790948 PMCID: PMC8101339 DOI: 10.1007/s43681-021-00056-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/15/2021] [Indexed: 10/24/2022]
Abstract
The COVID-19 pandemic has created an extraordinary medical, economic and humanitarian emergency. Artificial intelligence, in combination with other digital technologies, is being used as a tool to support the fight against the viral pandemic that has affected the entire world since the beginning of 2020. Barcelona Supercomputing Center collaborates in the battle against the coronavirus in different areas: the application of bioinformatics for the research on the virus and its possible treatments, the use of artificial intelligence, natural language processing and big data techniques to analyse the spread and impact of the pandemic, and the use of the MareNostrum 4 supercomputer to enable massive analysis on COVID-19 data. Many of these activities have included the use of personal and sensitive data of citizens, which, even during a pandemic, should be treated and handled with care. In this work we discuss our approach based on an ethical, transparent and fair use of this information, an approach aligned with the guidelines proposed by the European Union.
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Affiliation(s)
- Ulises Cortés
- Universitat Politècnica de Catalunya, Edifici Omega 205, Jordi Girona 29, 08034 Barcelona, Spain.,Barcelona Supercomputing Center, Edifici Omega 201, Jordi Girona 1 and 3, 08034 Barcelona, Spain
| | - Atia Cortés
- Barcelona Supercomputing Center, Edifici Omega 201, Jordi Girona 1 and 3, 08034 Barcelona, Spain
| | - Dario Garcia-Gasulla
- Barcelona Supercomputing Center, Edifici Omega 201, Jordi Girona 1 and 3, 08034 Barcelona, Spain
| | - Raquel Pérez-Arnal
- Barcelona Supercomputing Center, Edifici Omega 201, Jordi Girona 1 and 3, 08034 Barcelona, Spain
| | - Sergio Álvarez-Napagao
- Barcelona Supercomputing Center, Edifici Omega 201, Jordi Girona 1 and 3, 08034 Barcelona, Spain
| | - Enric Àlvarez
- Universitat Politècnica de Catalunya, Edifici Omega 205, Jordi Girona 29, 08034 Barcelona, Spain
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González J, Benítez ID, Carmona P, Santisteve S, Monge A, Moncusí-Moix A, Gort-Paniello C, Pinilla L, Carratalá A, Zuil M, Ferrer R, Ceccato A, Fernández L, Motos A, Riera J, Menéndez R, Garcia-Gasulla D, Peñuelas O, Bermejo-Martin JF, Labarca G, Caballero J, Torres G, de Gonzalo-Calvo D, Torres A, Barbé F. Pulmonary Function and Radiologic Features in Survivors of Critical COVID-19: A 3-Month Prospective Cohort. Chest 2021; 160:187-198. [PMID: 33676998 PMCID: PMC7930807 DOI: 10.1016/j.chest.2021.02.062] [Citation(s) in RCA: 144] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 02/12/2021] [Accepted: 02/25/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND More than 20% of hospitalized patients with COVID-19 demonstrate ARDS requiring ICU admission. The long-term respiratory sequelae in such patients remain unclear. RESEARCH QUESTION What are the major long-term pulmonary sequelae in critical patients who survive COVID-19? STUDY DESIGN AND METHODS Consecutive patients with COVID-19 requiring ICU admission were recruited and evaluated 3 months after hospitalization discharge. The follow-up comprised symptom and quality of life, anxiety and depression questionnaires, pulmonary function tests, exercise test (6-min walking test [6MWT]), and chest CT imaging. RESULTS One hundred twenty-five patients admitted to the ICU with ARDS secondary to COVID-19 were recruited between March and June 2020. At the 3-month follow-up, 62 patients were available for pulmonary evaluation. The most frequent symptoms were dyspnea (46.7%) and cough (34.4%). Eighty-two percent of patients showed a lung diffusing capacity of less than 80%. The median distance in the 6MWT was 400 m (interquartile range, 362-440 m). CT scans showed abnormal results in 70.2% of patients, demonstrating reticular lesions in 49.1% and fibrotic patterns in 21.1%. Patients with more severe alterations on chest CT scan showed worse pulmonary function and presented more degrees of desaturation in the 6MWT. Factors associated with the severity of lung damage on chest CT scan were age and length of invasive mechanical ventilation during the ICU stay. INTERPRETATION Three months after hospital discharge, pulmonary structural abnormalities and functional impairment are highly prevalent in patients with ARDS secondary to COVID-19 who required an ICU stay. Pulmonary evaluation should be considered for all critical COVID-19 survivors 3 months after discharge.
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Affiliation(s)
- Jessica González
- Pulmonary Department, Hospital Universitari Arnau de Vilanova and Santa Maria, Lleida, Spain; Translational Research in Respiratory Medicine Group (TRRM), Lleida, Spain; Lleida Biomedical Research Institute (IRBLleida), Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Iván D Benítez
- Translational Research in Respiratory Medicine Group (TRRM), Lleida, Spain; Lleida Biomedical Research Institute (IRBLleida), Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Paola Carmona
- Pulmonary Department, Hospital Universitari Arnau de Vilanova and Santa Maria, Lleida, Spain; Translational Research in Respiratory Medicine Group (TRRM), Lleida, Spain; Lleida Biomedical Research Institute (IRBLleida), Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Sally Santisteve
- Pulmonary Department, Hospital Universitari Arnau de Vilanova and Santa Maria, Lleida, Spain; Translational Research in Respiratory Medicine Group (TRRM), Lleida, Spain; Lleida Biomedical Research Institute (IRBLleida), Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Aida Monge
- Pulmonary Department, Hospital Universitari Arnau de Vilanova and Santa Maria, Lleida, Spain; Translational Research in Respiratory Medicine Group (TRRM), Lleida, Spain; Lleida Biomedical Research Institute (IRBLleida), Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Anna Moncusí-Moix
- Translational Research in Respiratory Medicine Group (TRRM), Lleida, Spain; Lleida Biomedical Research Institute (IRBLleida), Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Clara Gort-Paniello
- Translational Research in Respiratory Medicine Group (TRRM), Lleida, Spain; Lleida Biomedical Research Institute (IRBLleida), Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Lucía Pinilla
- Translational Research in Respiratory Medicine Group (TRRM), Lleida, Spain; Lleida Biomedical Research Institute (IRBLleida), Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Amara Carratalá
- Translational Research in Respiratory Medicine Group (TRRM), Lleida, Spain; Lleida Biomedical Research Institute (IRBLleida), Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - María Zuil
- Pulmonary Department, Hospital Universitari Arnau de Vilanova and Santa Maria, Lleida, Spain; Translational Research in Respiratory Medicine Group (TRRM), Lleida, Spain; Lleida Biomedical Research Institute (IRBLleida), Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Ricard Ferrer
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Intensive Care Department, Vall d'Hebron Hospital Universitari. SODIR Research Group, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Adrián Ceccato
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Laia Fernández
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Pulmonary Department, Hospital Clinic, Universitat de Barcelona, IDIBAPS, ICREA, Barcelona, Spain
| | - Ana Motos
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Pulmonary Department, Hospital Clinic, Universitat de Barcelona, IDIBAPS, ICREA, Barcelona, Spain
| | - Jordi Riera
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Intensive Care Department, Vall d'Hebron Hospital Universitari. SODIR Research Group, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Rosario Menéndez
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Pulmonary Department, University and Polytechnic Hospital La Fe, Valencia, Spain
| | | | - Oscar Peñuelas
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Hospital Universitario de Getafe, Madrid, Spain
| | - Jesús F Bermejo-Martin
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Gonzalo Labarca
- Faculty of Medicine, Faculty of Pharmacy, University of Concepcion, Concepción, Chile; Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, University of Concepcion, Concepción, Chile
| | - Jesus Caballero
- Intensive Care Department, Hospital Universitari Arnau de Vilanova and Santa Maria, Lleida, Spain
| | - Gerard Torres
- Pulmonary Department, Hospital Universitari Arnau de Vilanova and Santa Maria, Lleida, Spain; Translational Research in Respiratory Medicine Group (TRRM), Lleida, Spain; Lleida Biomedical Research Institute (IRBLleida), Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine Group (TRRM), Lleida, Spain; Lleida Biomedical Research Institute (IRBLleida), Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Antoni Torres
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Pulmonary Department, Hospital Clinic, Universitat de Barcelona, IDIBAPS, ICREA, Barcelona, Spain
| | - Ferran Barbé
- Pulmonary Department, Hospital Universitari Arnau de Vilanova and Santa Maria, Lleida, Spain; Translational Research in Respiratory Medicine Group (TRRM), Lleida, Spain; Lleida Biomedical Research Institute (IRBLleida), Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.
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Garcia-Gasulla D, Parés F, Vilalta A, Moreno J, Ayguadé E, Labarta J, Cortés U, Suzumura T. On the Behavior of Convolutional Nets for Feature Extraction. J ARTIF INTELL RES 2018. [DOI: 10.1613/jair.5756] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Deep neural networks are representation learning techniques. During training, a deep net is capable of generating a descriptive language of unprecedented size and detail in machine learning. Extracting the descriptive language coded within a trained CNN model (in the case of image data), and reusing it for other purposes is a field of interest, as it provides access to the visual descriptors previously learnt by the CNN after processing millions of images, without requiring an expensive training phase. Contributions to this field (commonly known as feature representation transfer or transfer learning) have been purely empirical so far, extracting all CNN features from a single layer close to the output and testing their performance by feeding them to a classifier. This approach has provided consistent results, although its relevance is limited to classification tasks. In a completely different approach, in this paper we statistically measure the discriminative power of every single feature found within a deep CNN, when used for characterizing every class of 11 datasets. We seek to provide new insights into the behavior of CNN features, particularly the ones from convolutional layers, as this can be relevant for their application to knowledge representation and reasoning. Our results confirm that low and middle level features may behave differently to high level features, but only under certain conditions. We find that all CNN features can be used for knowledge representation purposes both by their presence or by their absence, doubling the information a single CNN feature may provide. We also study how much noise these features may include, and propose a thresholding approach to discard most of it. All these insights have a direct application to the generation of CNN embedding spaces.
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Garcia-Gasulla D, Ayguadé E, Labarta J, Béjar J, Cortés U, Suzumura T, Chen R. A visual embedding for the unsupervised extraction of abstract semantics. COGN SYST RES 2017. [DOI: 10.1016/j.cogsys.2016.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Abstract
Nowadays Web services are one of the most commonly used technologies for distributed system integration and interoperability. Recently, a new communication technique called WebSockets has appeared for implementing Web services that offer a true server-push mechanism. In this paper we present a system based on it to manage agent communications, and we motivate its use in an Assistive Technologies use case. A new WebSocket Message Transport Protocol is described and an implementation for the Jade platform is presented. Subscription based agent interaction for the use case is presented, along with a comparison between WebSocket and HTTP Message Transport Protocols.
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Affiliation(s)
- Hannu Järvinen
- Department of Media Technology, Aalto University School of Science, P.O. Box 15400, Aalto, 00076, Finland
| | - Dario Garcia-Gasulla
- Departament de Llenguatges i Sistemes Informàtics, Universitat Politècnica de Catalunya (BarcelonaTech-UPC), C/Jordi Girona 1-3, Office K2M-201, Barcelona, E-08034, Spain
| | - Ulises Cortés
- Departament de Llenguatges i Sistemes Informàtics, Universitat Politècnica de Catalunya (BarcelonaTech-UPC), C/Jordi Girona 1-3, Office K2M-202d, Barcelona, E-08034, Spain
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