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Patel MA, Daley M, Van Nynatten LR, Slessarev M, Cepinskas G, Fraser DD. A reduced proteomic signature in critically ill Covid-19 patients determined with plasma antibody micro-array and machine learning. Clin Proteomics 2024; 21:33. [PMID: 38760690 PMCID: PMC11100131 DOI: 10.1186/s12014-024-09488-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 05/06/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND COVID-19 is a complex, multi-system disease with varying severity and symptoms. Identifying changes in critically ill COVID-19 patients' proteomes enables a better understanding of markers associated with susceptibility, symptoms, and treatment. We performed plasma antibody microarray and machine learning analyses to identify novel proteins of COVID-19. METHODS A case-control study comparing the concentration of 2000 plasma proteins in age- and sex-matched COVID-19 inpatients, non-COVID-19 sepsis controls, and healthy control subjects. Machine learning was used to identify a unique proteome signature in COVID-19 patients. Protein expression was correlated with clinically relevant variables and analyzed for temporal changes over hospitalization days 1, 3, 7, and 10. Expert-curated protein expression information was analyzed with Natural language processing (NLP) to determine organ- and cell-specific expression. RESULTS Machine learning identified a 28-protein model that accurately differentiated COVID-19 patients from ICU non-COVID-19 patients (accuracy = 0.89, AUC = 1.00, F1 = 0.89) and healthy controls (accuracy = 0.89, AUC = 1.00, F1 = 0.88). An optimal nine-protein model (PF4V1, NUCB1, CrkL, SerpinD1, Fen1, GATA-4, ProSAAS, PARK7, and NET1) maintained high classification ability. Specific proteins correlated with hemoglobin, coagulation factors, hypertension, and high-flow nasal cannula intervention (P < 0.01). Time-course analysis of the 28 leading proteins demonstrated no significant temporal changes within the COVID-19 cohort. NLP analysis identified multi-system expression of the key proteins, with the digestive and nervous systems being the leading systems. CONCLUSIONS The plasma proteome of critically ill COVID-19 patients was distinguishable from that of non-COVID-19 sepsis controls and healthy control subjects. The leading 28 proteins and their subset of 9 proteins yielded accurate classification models and are expressed in multiple organ systems. The identified COVID-19 proteomic signature helps elucidate COVID-19 pathophysiology and may guide future COVID-19 treatment development.
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Affiliation(s)
- Maitray A Patel
- Epidemiology and Biostatistics, Western University, London, ON, N6A 3K7, Canada
| | - Mark Daley
- Epidemiology and Biostatistics, Western University, London, ON, N6A 3K7, Canada
- Computer Science, Western University, London, ON, N6A 3K7, Canada
| | | | - Marat Slessarev
- Medicine, Western University, London, ON, N6A 3K7, Canada
- Lawson Health Research Institute, London, ON, N6C 2R5, Canada
| | - Gediminas Cepinskas
- Lawson Health Research Institute, London, ON, N6C 2R5, Canada
- Medical Biophysics, Western University, London, ON, N6A 3K7, Canada
| | - Douglas D Fraser
- Lawson Health Research Institute, London, ON, N6C 2R5, Canada.
- Children's Health Research Institute, London, ON, N6C 4V3, Canada.
- Pediatrics, Western University, London, ON, N6A 3K7, Canada.
- Clinical Neurological Sciences, Western University, London, ON, N6A 3K7, Canada.
- Physiology & Pharmacology, Western University, London, ON, N6A 3K7, Canada.
- London Health Sciences Centre, 800 Commissioners Road East, London, ON, N6A 5W9, Canada.
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Patel MA, Fraser DD, Daley M, Cepinskas G, Veraldi N, Grazioli S. The plasma proteome differentiates the multisystem inflammatory syndrome in children (MIS-C) from children with SARS-CoV-2 negative sepsis. Mol Med 2024; 30:51. [PMID: 38632526 PMCID: PMC11022403 DOI: 10.1186/s10020-024-00806-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 03/09/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND The Multi-System Inflammatory Syndrome in Children (MIS-C) can develop several weeks after SARS-CoV-2 infection and requires a distinct treatment protocol. Distinguishing MIS-C from SARS-CoV-2 negative sepsis (SCNS) patients is important to quickly institute the correct therapies. We performed targeted proteomics and machine learning analysis to identify novel plasma proteins of MIS-C for early disease recognition. METHODS A case-control study comparing the expression of 2,870 unique blood proteins in MIS-C versus SCNS patients, measured using proximity extension assays. The 2,870 proteins were reduced in number with either feature selection alone or with a prior COMBAT-Seq batch effect adjustment. The leading proteins were correlated with demographic and clinical variables. Organ system and cell type expression patterns were analyzed with Natural Language Processing (NLP). RESULTS The cohorts were well-balanced for age and sex. Of the 2,870 unique blood proteins, 58 proteins were identified with feature selection (FDR-adjusted P < 0.005, P < 0.0001; accuracy = 0.96, AUC = 1.00, F1 = 0.95), and 15 proteins were identified with a COMBAT-Seq batch effect adjusted feature selection (FDR-adjusted P < 0.05, P < 0.0001; accuracy = 0.92, AUC = 1.00, F1 = 0.89). All of the latter 15 proteins were present in the former 58-protein model. Several proteins were correlated with illness severity scores, length of stay, and interventions (LTA4H, PTN, PPBP, and EGF; P < 0.001). NLP analysis highlighted the multi-system nature of MIS-C, with the 58-protein set expressed in all organ systems; the highest levels of expression were found in the digestive system. The cell types most involved included leukocytes not yet determined, lymphocytes, macrophages, and platelets. CONCLUSIONS The plasma proteome of MIS-C patients was distinct from that of SCNS. The key proteins demonstrated expression in all organ systems and most cell types. The unique proteomic signature identified in MIS-C patients could aid future diagnostic and therapeutic advancements, as well as predict hospital length of stays, interventions, and mortality risks.
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Affiliation(s)
- Maitray A Patel
- Epidemiology and Biostatistics, Western University, N6A 3K7, London, ON, Canada
| | - Douglas D Fraser
- Lawson Health Research Institute, N6C 2R5, London, ON, Canada.
- Children's Health Research Institute, N6C 4V3, London, ON, Canada.
- Pediatrics, Western University, N6A 3K7, London, ON, Canada.
- Clinical Neurological Sciences, Western University, N6A 3K7, London, ON, Canada.
- Physiology & Pharmacology, Western University, N6A 3K7, London, ON, Canada.
- London Health Sciences Centre, Room C2-C82, 800 Commissioners Road East, N6A 5W9, London, ON, Canada.
| | - Mark Daley
- Epidemiology and Biostatistics, Western University, N6A 3K7, London, ON, Canada
- Computer Science, Western University, N6A 3K7, London, ON, Canada
| | - Gediminas Cepinskas
- Lawson Health Research Institute, N6C 2R5, London, ON, Canada
- Medical Biophysics, Western University, N6A 3K7, London, ON, Canada
| | - Noemi Veraldi
- Department of Pediatrics, Gynaecology and Obstetrics, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Serge Grazioli
- Department of Pediatrics, Gynaecology and Obstetrics, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of Neonatal and Pediatric Intensive Care, Department of Child, Woman, and Adolescent Medicine, Geneva University Hospitals, Geneva, Switzerland
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Viderman D, Kotov A, Popov M, Abdildin Y. Machine and deep learning methods for clinical outcome prediction based on physiological data of COVID-19 patients: a scoping review. Int J Med Inform 2024; 182:105308. [PMID: 38091862 DOI: 10.1016/j.ijmedinf.2023.105308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/20/2023] [Accepted: 12/03/2023] [Indexed: 01/07/2024]
Abstract
INTRODUCTION Since the beginning of the COVID-19 pandemic, numerous machine and deep learning (MDL) methods have been proposed in the literature to analyze patient physiological data. The objective of this review is to summarize various aspects of these methods and assess their practical utility for predicting various clinical outcomes. METHODS We searched PubMed, Scopus, and Cochrane Library, screened and selected the studies matching the inclusion criteria. The clinical analysis focused on the characteristics of the patient cohorts in the studies included in this review, the specific tasks in the context of the COVID-19 pandemic that machine and deep learning methods were used for, and their practical limitations. The technical analysis focused on the details of specific MDL methods and their performance. RESULTS Analysis of the 48 selected studies revealed that the majority (∼54 %) of them examined the application of MDL methods for the prediction of survival/mortality-related patient outcomes, while a smaller fraction (∼13 %) of studies also examined applications to the prediction of patients' physiological outcomes and hospital resource utilization. 21 % of the studies examined the application of MDL methods to multiple clinical tasks. Machine and deep learning methods have been shown to be effective at predicting several outcomes of COVID-19 patients, such as disease severity, complications, intensive care unit (ICU) transfer, and mortality. MDL methods also achieved high accuracy in predicting the required number of ICU beds and ventilators. CONCLUSION Machine and deep learning methods have been shown to be valuable tools for predicting disease severity, organ dysfunction and failure, patient outcomes, and hospital resource utilization during the COVID-19 pandemic. The discovered knowledge and our conclusions and recommendations can also be useful to healthcare professionals and artificial intelligence researchers in managing future pandemics.
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Affiliation(s)
- Dmitriy Viderman
- Department of Surgery, School of Medicine, Nazarbayev University, Astana, Kazakhstan; Department of Anesthesiology, Intensive Care, and Pain Medicine, National Research Oncology Center, Astana, Kazakhstan.
| | - Alexander Kotov
- Department of Computer Science, College of Engineering, Wayne State University, Detroit, USA.
| | - Maxim Popov
- Department of Computer Science, School of Engineering and Digital Sciences, Nazarbayev University, Astana, Kazakhstan.
| | - Yerkin Abdildin
- Department of Mechanical and Aerospace Engineering, School of Engineering and Digital Sciences, Nazarbayev University, Astana, Kazakhstan.
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Hernández-Caravaca I, Moros-Nicolás C, González-Brusi L, Romero de Ávila MJ, De Paco Matallana C, Pelegrín P, Castaño-Molina MÁ, Díaz-Meca L, Sánchez-Romero J, Martínez-Alarcón L, Avilés M, Izquierdo-Rico MJ. Colostrum Features of Active and Recovered COVID-19 Patients Revealed Using Next-Generation Proteomics Technique, SWATH-MS. CHILDREN (BASEL, SWITZERLAND) 2023; 10:1423. [PMID: 37628421 PMCID: PMC10453012 DOI: 10.3390/children10081423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023]
Abstract
Colostrum performs nutritional, anti-inflammatory and anti-infective functions and promotes immune system formation and organ development. The new coronavirus, SARS-CoV-2, has generated concerns about viral transmission through human milk, with a lack of evidence about human milk's protective effects against the infection. This study aimed at analyzing presence of the virus and at identifying the protein expression profile of human colostrum in active and COVID-19-recovered patients. Colostrum samples were collected from women with COVID-19 (n = 3), women recently recovered from the infection (n = 4), and non-infected women (n = 5). The samples were analyzed by means of RT-qPCR to determine presence of the virus and using SWATH-MS for proteomic analysis. Proteomic results were then analyzed using bioinformatic methods. The viral tests were negative for SARS-CoV-2 in the colostrum from COVID-19 patients. The proteomic analysis identified 301 common proteins in all samples analyzed. Nineteen proteins were upregulated and 7 were downregulated in the COVID-19 group versus the control samples, whereas 18 were upregulated and 7 were downregulated when comparing the COVID-19 group to the recovered group. Eleven proteins were biomarkers of active COVID-19 infection. Ten were upregulated: ACTN1, CD36, FAM3B, GPRC5B, IGHA2, IGK, PLTP, RAC1, SDCBP and SERPINF1, and one was downregulated: PSAP. These proteins are mainly related to immunity, inflammatory response and protein transport. In conclusion, the results of this study suggest that colostrum is not a vehicle for mother-to-child SARS-CoV-2 transmission. Moreover, the colostrum's proteome of active and recuperated patients indicate that it could provide immune benefits to infants.
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Affiliation(s)
- Iván Hernández-Caravaca
- Department of Community Nursing, Preventive Medicine and Public Health and History of Science, Campus de Sant Vicent del Raspeig, University of Alicante, 03690 Alicante, Spain;
- Instituto Murciano de Investigación Biosanitaria Pascual Parrilla (IMIB), Campus de Ciencias de la Salud, 30120 Murcia, Spain; (C.M.-N.); (L.G.-B.); (C.D.P.M.); (P.P.); (L.D.-M.); (L.M.-A.); (M.A.)
| | - Carla Moros-Nicolás
- Instituto Murciano de Investigación Biosanitaria Pascual Parrilla (IMIB), Campus de Ciencias de la Salud, 30120 Murcia, Spain; (C.M.-N.); (L.G.-B.); (C.D.P.M.); (P.P.); (L.D.-M.); (L.M.-A.); (M.A.)
- Departamento de Biología Celular e Histología, Facultad de Medicina, Universidad de Murcia, Campus Mare Nostrum (CMN), 30120 Murcia, Spain;
| | - Leopoldo González-Brusi
- Instituto Murciano de Investigación Biosanitaria Pascual Parrilla (IMIB), Campus de Ciencias de la Salud, 30120 Murcia, Spain; (C.M.-N.); (L.G.-B.); (C.D.P.M.); (P.P.); (L.D.-M.); (L.M.-A.); (M.A.)
- Departamento de Biología Celular e Histología, Facultad de Medicina, Universidad de Murcia, Campus Mare Nostrum (CMN), 30120 Murcia, Spain;
| | - Mª José Romero de Ávila
- Departamento de Biología Celular e Histología, Facultad de Medicina, Universidad de Murcia, Campus Mare Nostrum (CMN), 30120 Murcia, Spain;
| | - Catalina De Paco Matallana
- Instituto Murciano de Investigación Biosanitaria Pascual Parrilla (IMIB), Campus de Ciencias de la Salud, 30120 Murcia, Spain; (C.M.-N.); (L.G.-B.); (C.D.P.M.); (P.P.); (L.D.-M.); (L.M.-A.); (M.A.)
- Servicio de Obstetricia y Ginecología, Hospital Clínico Universitario Virgen de la Arrixaca, 30120 Murcia, Spain;
| | - Pablo Pelegrín
- Instituto Murciano de Investigación Biosanitaria Pascual Parrilla (IMIB), Campus de Ciencias de la Salud, 30120 Murcia, Spain; (C.M.-N.); (L.G.-B.); (C.D.P.M.); (P.P.); (L.D.-M.); (L.M.-A.); (M.A.)
- Departamento de Bioquímica y Biología Molecular “B” e Inmunología, Facultad de Medicina, Universidad de Murcia, Campus Mare Nostrum (CMN), 30120 Murcia, Spain
| | - María Ángeles Castaño-Molina
- Servicio de Obstetricia y Ginecología, Hospital Clínico Universitario Virgen de la Arrixaca, 30120 Murcia, Spain;
- Departamento de Enfermería, Facultad de Enfermería, Universidad de Murcia, Campus Mare Nostrum (CMN), 30120 Murcia, Spain
| | - Lucía Díaz-Meca
- Instituto Murciano de Investigación Biosanitaria Pascual Parrilla (IMIB), Campus de Ciencias de la Salud, 30120 Murcia, Spain; (C.M.-N.); (L.G.-B.); (C.D.P.M.); (P.P.); (L.D.-M.); (L.M.-A.); (M.A.)
- Servicio de Obstetricia y Ginecología, Hospital Clínico Universitario Virgen de la Arrixaca, 30120 Murcia, Spain;
| | - Javier Sánchez-Romero
- Instituto Murciano de Investigación Biosanitaria Pascual Parrilla (IMIB), Campus de Ciencias de la Salud, 30120 Murcia, Spain; (C.M.-N.); (L.G.-B.); (C.D.P.M.); (P.P.); (L.D.-M.); (L.M.-A.); (M.A.)
- Servicio de Obstetricia y Ginecología, Hospital Clínico Universitario Virgen de la Arrixaca, 30120 Murcia, Spain;
| | - Laura Martínez-Alarcón
- Instituto Murciano de Investigación Biosanitaria Pascual Parrilla (IMIB), Campus de Ciencias de la Salud, 30120 Murcia, Spain; (C.M.-N.); (L.G.-B.); (C.D.P.M.); (P.P.); (L.D.-M.); (L.M.-A.); (M.A.)
- Departamento de Enfermería, Facultad de Enfermería, Universidad de Murcia, Campus Mare Nostrum (CMN), 30120 Murcia, Spain
- Unit, Department of Surgery, Virgen de la Arrixaca University Hospital, 30120 Murcia, Spain
| | - Manuel Avilés
- Instituto Murciano de Investigación Biosanitaria Pascual Parrilla (IMIB), Campus de Ciencias de la Salud, 30120 Murcia, Spain; (C.M.-N.); (L.G.-B.); (C.D.P.M.); (P.P.); (L.D.-M.); (L.M.-A.); (M.A.)
- Departamento de Biología Celular e Histología, Facultad de Medicina, Universidad de Murcia, Campus Mare Nostrum (CMN), 30120 Murcia, Spain;
| | - Mª José Izquierdo-Rico
- Instituto Murciano de Investigación Biosanitaria Pascual Parrilla (IMIB), Campus de Ciencias de la Salud, 30120 Murcia, Spain; (C.M.-N.); (L.G.-B.); (C.D.P.M.); (P.P.); (L.D.-M.); (L.M.-A.); (M.A.)
- Departamento de Biología Celular e Histología, Facultad de Medicina, Universidad de Murcia, Campus Mare Nostrum (CMN), 30120 Murcia, Spain;
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Iosef C, Knauer MJ, Nicholson M, Van Nynatten LR, Cepinskas G, Draghici S, Han VKM, Fraser DD. Plasma proteome of Long-COVID patients indicates HIF-mediated vasculo-proliferative disease with impact on brain and heart function. J Transl Med 2023; 21:377. [PMID: 37301958 PMCID: PMC10257382 DOI: 10.1186/s12967-023-04149-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/25/2023] [Indexed: 06/12/2023] Open
Abstract
AIMS Long-COVID occurs after SARS-CoV-2 infection and results in diverse, prolonged symptoms. The present study aimed to unveil potential mechanisms, and to inform prognosis and treatment. METHODS Plasma proteome from Long-COVID outpatients was analyzed in comparison to matched acutely ill COVID-19 (mild and severe) inpatients and healthy control subjects. The expression of 3072 protein biomarkers was determined with proximity extension assays and then deconvoluted with multiple bioinformatics tools into both cell types and signaling mechanisms, as well as organ specificity. RESULTS Compared to age- and sex-matched acutely ill COVID-19 inpatients and healthy control subjects, Long-COVID outpatients showed natural killer cell redistribution with a dominant resting phenotype, as opposed to active, and neutrophils that formed extracellular traps. This potential resetting of cell phenotypes was reflected in prospective vascular events mediated by both angiopoietin-1 (ANGPT1) and vascular-endothelial growth factor-A (VEGFA). Several markers (ANGPT1, VEGFA, CCR7, CD56, citrullinated histone 3, elastase) were validated by serological methods in additional patient cohorts. Signaling of transforming growth factor-β1 with probable connections to elevated EP/p300 suggested vascular inflammation and tumor necrosis factor-α driven pathways. In addition, a vascular proliferative state associated with hypoxia inducible factor 1 pathway suggested progression from acute COVID-19 to Long-COVID. The vasculo-proliferative process predicted in Long-COVID might contribute to changes in the organ-specific proteome reflective of neurologic and cardiometabolic dysfunction. CONCLUSIONS Taken together, our findings point to a vasculo-proliferative process in Long-COVID that is likely initiated either prior hypoxia (localized or systemic) and/or stimulatory factors (i.e., cytokines, chemokines, growth factors, angiotensin, etc). Analyses of the plasma proteome, used as a surrogate for cellular signaling, unveiled potential organ-specific prognostic biomarkers and therapeutic targets.
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Affiliation(s)
- Cristiana Iosef
- Children's Health Research Institute, Victoria Research Laboratories, 800 Commissioners Road East, London, ON, N6C 2V5, Canada.
| | - Michael J Knauer
- Department of Pathology and Laboratory Medicine, London, ON, N6A 5C1, Canada
| | - Michael Nicholson
- Department of Medicine, Western University, London, ON, N6A 5C1, Canada
| | | | - Gediminas Cepinskas
- Lawson Health Research Institute, London, ON, N6C 2R5, Canada
- Department of Medical Biophysics, Western University, London, ON, N6A 5C1, Canada
| | - Sorin Draghici
- Department of Computer Science College of Engineering, Wayne State University, Ann Arbor, MI, 48202, USA
- Advaita Bioinformatics, Ann Arbor, 48105-2552, USA
- National Science Foundation, Alexandria, VA, 22314, USA
| | - Victor K M Han
- Children's Health Research Institute, Victoria Research Laboratories, 800 Commissioners Road East, London, ON, N6C 2V5, Canada
- Department of Pediatrics, Western University, London, ON, N6A 5C1, Canada
| | - Douglas D Fraser
- Children's Health Research Institute, Victoria Research Laboratories, 800 Commissioners Road East, London, ON, N6C 2V5, Canada.
- Lawson Health Research Institute, London, ON, N6C 2R5, Canada.
- Department of Pediatrics, Western University, London, ON, N6A 5C1, Canada.
- Department of Physiology & Pharmacology, Western University, London, ON, N6A 5C1, Canada.
- Department of Clinical Neurological Sciences, Western University, London, ON, N6A 5C1, Canada.
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Rombauts A, Bódalo Torruella M, Abelenda-Alonso G, Perera-Bel J, Ferrer-Salvador A, Acedo-Terrades A, Gabarrós-Subirà M, Oriol I, Gudiol C, Nonell L, Carratalà J. Dynamics of Gene Expression Profiling and Identification of High-Risk Patients for Severe COVID-19. Biomedicines 2023; 11:biomedicines11051348. [PMID: 37239019 DOI: 10.3390/biomedicines11051348] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/28/2023] [Accepted: 05/01/2023] [Indexed: 05/28/2023] Open
Abstract
The clinical manifestations of SARS-CoV-2 infection vary widely, from asymptomatic infection to the development of acute respiratory distress syndrome (ARDS) and death. The host response elicited by SARS-CoV-2 plays a key role in determining the clinical outcome. We hypothesized that determining the dynamic whole blood transcriptomic profile of hospitalized adult COVID-19 patients and characterizing the subgroup that develops severe disease and ARDS would broaden our understanding of the heterogeneity in clinical outcomes. We recruited 60 hospitalized patients with RT-PCR-confirmed SARS-CoV-2 infection, among whom 19 developed ARDS. Peripheral blood was collected using PAXGene RNA tubes within 24 h of admission and on day 7. There were 2572 differently expressed genes in patients with ARDS at baseline and 1149 at day 7. We found a dysregulated inflammatory response in COVID-19 ARDS patients, with an increased expression of genes related to pro-inflammatory molecules and neutrophil and macrophage activation at admission, in addition to an immune regulation loss. This led, in turn, to a higher expression of genes related to reactive oxygen species, protein polyubiquitination, and metalloproteinases in the latter stages. Some of the most significant differences in gene expression found between patients with and without ARDS corresponded to long non-coding RNA involved in epigenetic control.
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Affiliation(s)
- Alexander Rombauts
- Department of Infectious Diseases, Hospital Universitari de Bellvitge-IDIBELL, 08908 Barcelona, Spain
| | | | - Gabriela Abelenda-Alonso
- Department of Infectious Diseases, Hospital Universitari de Bellvitge-IDIBELL, 08908 Barcelona, Spain
| | - Júlia Perera-Bel
- MARGenomics, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain
| | - Anna Ferrer-Salvador
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | | | - Maria Gabarrós-Subirà
- MARGenomics, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain
| | - Isabel Oriol
- Department of Infectious Diseases, Hospital Universitari de Bellvitge-IDIBELL, 08908 Barcelona, Spain
| | - Carlota Gudiol
- Department of Infectious Diseases, Hospital Universitari de Bellvitge-IDIBELL, 08908 Barcelona, Spain
- Department of Medicine, Universitat de Barcelona, 08007 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Lara Nonell
- MARGenomics, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain
| | - Jordi Carratalà
- Department of Infectious Diseases, Hospital Universitari de Bellvitge-IDIBELL, 08908 Barcelona, Spain
- Department of Medicine, Universitat de Barcelona, 08007 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
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Patel MA, Knauer MJ, Nicholson M, Daley M, Van Nynatten LR, Cepinskas G, Fraser DD. Organ and cell-specific biomarkers of Long-COVID identified with targeted proteomics and machine learning. Mol Med 2023; 29:26. [PMID: 36809921 PMCID: PMC9942653 DOI: 10.1186/s10020-023-00610-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/13/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Survivors of acute COVID-19 often suffer prolonged, diffuse symptoms post-infection, referred to as "Long-COVID". A lack of Long-COVID biomarkers and pathophysiological mechanisms limits effective diagnosis, treatment and disease surveillance. We performed targeted proteomics and machine learning analyses to identify novel blood biomarkers of Long-COVID. METHODS A case-control study comparing the expression of 2925 unique blood proteins in Long-COVID outpatients versus COVID-19 inpatients and healthy control subjects. Targeted proteomics was accomplished with proximity extension assays, and machine learning was used to identify the most important proteins for identifying Long-COVID patients. Organ system and cell type expression patterns were identified with Natural Language Processing (NLP) of the UniProt Knowledgebase. RESULTS Machine learning analysis identified 119 relevant proteins for differentiating Long-COVID outpatients (Bonferonni corrected P < 0.01). Protein combinations were narrowed down to two optimal models, with nine and five proteins each, and with both having excellent sensitivity and specificity for Long-COVID status (AUC = 1.00, F1 = 1.00). NLP expression analysis highlighted the diffuse organ system involvement in Long-COVID, as well as the involved cell types, including leukocytes and platelets, as key components associated with Long-COVID. CONCLUSIONS Proteomic analysis of plasma from Long-COVID patients identified 119 highly relevant proteins and two optimal models with nine and five proteins, respectively. The identified proteins reflected widespread organ and cell type expression. Optimal protein models, as well as individual proteins, hold the potential for accurate diagnosis of Long-COVID and targeted therapeutics.
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Affiliation(s)
- Maitray A Patel
- Epidemiology and Biostatistics, Western University, London, ON, N6A 3K7, Canada
| | - Michael J Knauer
- Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | | | - Mark Daley
- Epidemiology and Biostatistics, Western University, London, ON, N6A 3K7, Canada.,Computer Science, Western University, London, ON, N6A 3K7, Canada
| | | | - Gediminas Cepinskas
- Lawson Health Research Institute, London, ON, N6C 2R5, Canada.,Medical Biophysics, Western University, London, ON, N6A 3K7, Canada
| | - Douglas D Fraser
- Lawson Health Research Institute, London, ON, N6C 2R5, Canada. .,Children's Health Research Institute, London, ON, N6C 4V3, Canada. .,Pediatrics, Western University, London, ON, N6A 3K7, Canada. .,Clinical Neurological Sciences, Western University, London, ON, N6A 3K7, Canada. .,Physiology and Pharmacology, Western University, London, ON, N6A 3K7, Canada. .,Room C2-C82, London Health Sciences Centre, 800 Commissioners Road East, London, ON, N6A 5W9, Canada.
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Cardiovascular and Renal Comorbidities Included into Neural Networks Predict the Outcome in COVID-19 Patients Admitted to an Intensive Care Unit: Three-Center, Cross-Validation, Age- and Sex-Matched Study. J Cardiovasc Dev Dis 2023; 10:jcdd10020039. [PMID: 36826535 PMCID: PMC9967447 DOI: 10.3390/jcdd10020039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/16/2023] [Accepted: 01/19/2023] [Indexed: 01/25/2023] Open
Abstract
Here, we performed a multicenter, age- and sex-matched study to compare the efficiency of various machine learning algorithms in the prediction of COVID-19 fatal outcomes and to develop sensitive, specific, and robust artificial intelligence tools for the prompt triage of patients with severe COVID-19 in the intensive care unit setting. In a challenge against other established machine learning algorithms (decision trees, random forests, extra trees, neural networks, k-nearest neighbors, and gradient boosting: XGBoost, LightGBM, and CatBoost) and multivariate logistic regression as a reference, neural networks demonstrated the highest sensitivity, sufficient specificity, and excellent robustness. Further, neural networks based on coronary artery disease/chronic heart failure, stage 3-5 chronic kidney disease, blood urea nitrogen, and C-reactive protein as the predictors exceeded 90% sensitivity and 80% specificity, reaching AUROC of 0.866 at primary cross-validation and 0.849 at secondary cross-validation on virtual samples generated by the bootstrapping procedure. These results underscore the impact of cardiovascular and renal comorbidities in the context of thrombotic complications characteristic of severe COVID-19. As aforementioned predictors can be obtained from the case histories or are inexpensive to be measured at admission to the intensive care unit, we suggest this predictor composition is useful for the triage of critically ill COVID-19 patients.
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9
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Van Nynatten LR, Slessarev M, Martin CM, Leligdowicz A, Miller MR, Patel MA, Daley M, Patterson EK, Cepinskas G, Fraser DD. Novel plasma protein biomarkers from critically ill sepsis patients. Clin Proteomics 2022; 19:50. [PMID: 36572854 PMCID: PMC9792322 DOI: 10.1186/s12014-022-09389-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/09/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Despite the high morbidity and mortality associated with sepsis, the relationship between the plasma proteome and clinical outcome is poorly understood. In this study, we used targeted plasma proteomics to identify novel biomarkers of sepsis in critically ill patients. METHODS Blood was obtained from 15 critically ill patients with suspected/confirmed sepsis (Sepsis-3.0 criteria) on intensive care unit (ICU) Day-1 and Day-3, as well as age- and sex-matched 15 healthy control subjects. A total of 1161 plasma proteins were measured with proximal extension assays. Promising sepsis biomarkers were narrowed with machine learning and then correlated with relevant clinical and laboratory variables. RESULTS The median age for critically ill sepsis patients was 56 (IQR 51-61) years. The median MODS and SOFA values were 7 (IQR 5.0-8.0) and 7 (IQR 5.0-9.0) on ICU Day-1, and 4 (IQR 3.5-7.0) and 6 (IQR 3.5-7.0) on ICU Day-3, respectively. Targeted proteomics, together with feature selection, identified the leading proteins that distinguished sepsis patients from healthy control subjects with ≥ 90% classification accuracy; 25 proteins on ICU Day-1 and 26 proteins on ICU Day-3 (6 proteins overlapped both ICU days; PRTN3, UPAR, GDF8, NTRK3, WFDC2 and CXCL13). Only 7 of the leading proteins changed significantly between ICU Day-1 and Day-3 (IL10, CCL23, TGFα1, ST2, VSIG4, CNTN5, and ITGAV; P < 0.01). Significant correlations were observed between a variety of patient clinical/laboratory variables and the expression of 15 proteins on ICU Day-1 and 14 proteins on ICU Day-3 (P < 0.05). CONCLUSIONS Targeted proteomics with feature selection identified proteins altered in critically ill sepsis patients relative to healthy control subjects. Correlations between protein expression and clinical/laboratory variables were identified, each providing pathophysiological insight. Our exploratory data provide a rationale for further hypothesis-driven sepsis research.
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Affiliation(s)
| | - Marat Slessarev
- grid.39381.300000 0004 1936 8884Medicine, Western University, London, ON Canada ,grid.415847.b0000 0001 0556 2414Lawson Health Research Institute, London, ON Canada
| | - Claudio M. Martin
- grid.39381.300000 0004 1936 8884Medicine, Western University, London, ON Canada ,grid.415847.b0000 0001 0556 2414Lawson Health Research Institute, London, ON Canada
| | - Aleks Leligdowicz
- grid.39381.300000 0004 1936 8884Medicine, Western University, London, ON Canada ,grid.415847.b0000 0001 0556 2414Lawson Health Research Institute, London, ON Canada
| | - Michael R. Miller
- grid.415847.b0000 0001 0556 2414Lawson Health Research Institute, London, ON Canada ,grid.39381.300000 0004 1936 8884Pediatrics, Western University, London, ON Canada
| | - Maitray A. Patel
- grid.39381.300000 0004 1936 8884Computer Science, Western University, London, ON N6A 3K7 Canada
| | - Mark Daley
- grid.415847.b0000 0001 0556 2414Lawson Health Research Institute, London, ON Canada ,grid.39381.300000 0004 1936 8884Computer Science, Western University, London, ON N6A 3K7 Canada ,grid.494618.6The Vector Institute for Artificial Intelligence, Toronto, ON M5G 1M1 Canada
| | - Eric K. Patterson
- grid.415847.b0000 0001 0556 2414Lawson Health Research Institute, London, ON Canada
| | - Gediminas Cepinskas
- grid.415847.b0000 0001 0556 2414Lawson Health Research Institute, London, ON Canada ,grid.39381.300000 0004 1936 8884Medical Biophysics, Western University, London, ON N6A 3K7 Canada
| | - Douglas D. Fraser
- grid.415847.b0000 0001 0556 2414Lawson Health Research Institute, London, ON Canada ,grid.39381.300000 0004 1936 8884Pediatrics, Western University, London, ON Canada ,grid.39381.300000 0004 1936 8884Clinical Neurological Sciences, Western University, London, ON Canada ,grid.39381.300000 0004 1936 8884Physiology and Pharmacology, Western University, London, ON Canada ,grid.412745.10000 0000 9132 1600London Health Sciences Centre, Room C2-C82, 800 Commissioners Road East, London, ON N6A 5W9 Canada
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10
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Iosef C, Martin CM, Slessarev M, Gillio‐Meina C, Cepinskas G, Han VKM, Fraser DD. COVID-19 plasma proteome reveals novel temporal and cell-specific signatures for disease severity and high-precision disease management. J Cell Mol Med 2022; 27:141-157. [PMID: 36537107 PMCID: PMC9806290 DOI: 10.1111/jcmm.17622] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/19/2022] [Accepted: 10/23/2022] [Indexed: 12/31/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a systemic inflammatory condition with high mortality that may benefit from personalized medicine and high-precision approaches. COVID-19 patient plasma was analysed with targeted proteomics of 1161 proteins. Patients were monitored from Days 1 to 10 of their intensive care unit (ICU) stay. Age- and gender-matched COVID-19-negative sepsis ICU patients and healthy subjects were examined as controls. Proteomic data were resolved using both cell-specific annotation and deep-analysis for functional enrichment. COVID-19 caused extensive remodelling of the plasma microenvironment associated with a relative immunosuppressive milieu between ICU Days 3-7, and characterized by extensive organ damage. COVID-19 resulted in (1) reduced antigen presentation and B/T-cell function, (2) increased repurposed neutrophils and M1-type macrophages, (3) relatively immature or disrupted endothelia and fibroblasts with a defined secretome, and (4) reactive myeloid lines. Extracellular matrix changes identified in COVID-19 plasma could represent impaired immune cell homing and programmed cell death. The major functional modules disrupted in COVID-19 were exaggerated in patients with fatal outcome. Taken together, these findings provide systems-level insight into the mechanisms of COVID-19 inflammation and identify potential prognostic biomarkers. Therapeutic strategies could be tailored to the immune response of severely ill patients.
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Affiliation(s)
| | - Claudio M. Martin
- Lawson Health Research InstituteLondonOntarioCanada,Department of MedicineWestern UniversityLondonOntarioCanada
| | - Marat Slessarev
- Lawson Health Research InstituteLondonOntarioCanada,Department of MedicineWestern UniversityLondonOntarioCanada
| | | | - Gediminas Cepinskas
- Lawson Health Research InstituteLondonOntarioCanada,Department of Medical BiophysicsWestern UniversityLondonOntarioCanada
| | - Victor K. M. Han
- Children's Health research InstituteLondonOntarioCanada,Department of PediatricsWestern UniversityLondonOntarioCanada
| | - Douglas D. Fraser
- Children's Health research InstituteLondonOntarioCanada,Lawson Health Research InstituteLondonOntarioCanada,Department of PediatricsWestern UniversityLondonOntarioCanada,Department of Physiology & PharmacologyWestern UniversityLondonOntarioCanada,Department of Clinical Neurological SciencesWestern UniversityLondonOntarioCanada
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11
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Cui M, Cheng C, Zhang L. High-throughput proteomics: a methodological mini-review. J Transl Med 2022; 102:1170-1181. [PMID: 36775443 PMCID: PMC9362039 DOI: 10.1038/s41374-022-00830-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 07/06/2022] [Accepted: 07/10/2022] [Indexed: 11/15/2022] Open
Abstract
Proteomics plays a vital role in biomedical research in the post-genomic era. With the technological revolution and emerging computational and statistic models, proteomic methodology has evolved rapidly in the past decade and shed light on solving complicated biomedical problems. Here, we summarize scientific research and clinical practice of existing and emerging high-throughput proteomics approaches, including mass spectrometry, protein pathway array, next-generation tissue microarrays, single-cell proteomics, single-molecule proteomics, Luminex, Simoa and Olink Proteomics. We also discuss important computational methods and statistical algorithms that can maximize the mining of proteomic data with clinical and/or other 'omics data. Various principles and precautions are provided for better utilization of these tools. In summary, the advances in high-throughput proteomics will not only help better understand the molecular mechanisms of pathogenesis, but also to identify the signature signaling networks of specific diseases. Thus, modern proteomics have a range of potential applications in basic research, prognostic oncology, precision medicine, and drug discovery.
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Affiliation(s)
- Miao Cui
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Pathology, Mount Sinai West, New York, NY, USA
| | - Chao Cheng
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, Houston, TX, USA. .,Department of Medicine, Baylor College of Medicine, Houston, TX, USA. .,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
| | - Lanjing Zhang
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA. .,Department of Pathology, Princeton Medical Center, Plainsboro, NJ, USA. .,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA. .,Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ, USA.
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12
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Patel MA, Knauer MJ, Nicholson M, Daley M, Van Nynatten LR, Martin C, Patterson EK, Cepinskas G, Seney SL, Dobretzberger V, Miholits M, Webb B, Fraser DD. Elevated vascular transformation blood biomarkers in Long-COVID indicate angiogenesis as a key pathophysiological mechanism. Mol Med 2022; 28:122. [PMID: 36217108 PMCID: PMC9549814 DOI: 10.1186/s10020-022-00548-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/17/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Long-COVID is characterized by prolonged, diffuse symptoms months after acute COVID-19. Accurate diagnosis and targeted therapies for Long-COVID are lacking. We investigated vascular transformation biomarkers in Long-COVID patients. METHODS A case-control study utilizing Long-COVID patients, one to six months (median 98.5 days) post-infection, with multiplex immunoassay measurement of sixteen blood biomarkers of vascular transformation, including ANG-1, P-SEL, MMP-1, VE-Cad, Syn-1, Endoglin, PECAM-1, VEGF-A, ICAM-1, VLA-4, E-SEL, thrombomodulin, VEGF-R2, VEGF-R3, VCAM-1 and VEGF-D. RESULTS Fourteen vasculature transformation blood biomarkers were significantly elevated in Long-COVID outpatients, versus acutely ill COVID-19 inpatients and healthy controls subjects (P < 0.05). A unique two biomarker profile consisting of ANG-1/P-SEL was developed with machine learning, providing a classification accuracy for Long-COVID status of 96%. Individually, ANG-1 and P-SEL had excellent sensitivity and specificity for Long-COVID status (AUC = 1.00, P < 0.0001; validated in a secondary cohort). Specific to Long-COVID, ANG-1 levels were associated with female sex and a lack of disease interventions at follow-up (P < 0.05). CONCLUSIONS Long-COVID patients suffer prolonged, diffuse symptoms and poorer health. Vascular transformation blood biomarkers were significantly elevated in Long-COVID, with angiogenesis markers (ANG-1/P-SEL) providing classification accuracy of 96%. Vascular transformation blood biomarkers hold potential for diagnostics, and modulators of angiogenesis may have therapeutic efficacy.
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Affiliation(s)
- Maitray A Patel
- Epidemiology and Biostatistics, Western University, London, ON, N6A 3K7, Canada
| | - Michael J Knauer
- Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | | | - Mark Daley
- Epidemiology and Biostatistics, Western University, London, ON, N6A 3K7, Canada.,Computer Science, Western University, London, ON, N6A 3K7, Canada
| | | | - Claudio Martin
- Medicine, Western University, London, ON, N6A 3K7, Canada.,Lawson Health Research Institute, London, ON, N6C 2R5, Canada
| | | | - Gediminas Cepinskas
- Lawson Health Research Institute, London, ON, N6C 2R5, Canada.,Medical Biophysics, Western University, London, ON, N6A 3K7, Canada
| | - Shannon L Seney
- Lawson Health Research Institute, London, ON, N6C 2R5, Canada
| | | | | | - Brian Webb
- Thermo Fisher Scientific, Rockford, IL, USA
| | - Douglas D Fraser
- Lawson Health Research Institute, London, ON, N6C 2R5, Canada. .,Pediatrics, Western University, London, ON, N6A 3K7, Canada. .,Clinical Neurological Sciences, Western University, London, ON, N6A 3K7, Canada. .,Physiology and Pharmacology, Western University, London, ON, N6A 3K7, Canada. .,London Health Sciences Centre, Room C2-C82, 800 Commissioners Road East, London, ON, N6A 5W9, Canada.
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13
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COVID-19 Salivary Protein Profile: Unravelling Molecular Aspects of SARS-CoV-2 Infection. J Clin Med 2022; 11:jcm11195571. [PMID: 36233441 PMCID: PMC9570692 DOI: 10.3390/jcm11195571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 09/16/2022] [Accepted: 09/17/2022] [Indexed: 11/18/2022] Open
Abstract
COVID-19 is the most impacting global pandemic of all time, with over 600 million infected and 6.5 million deaths worldwide, in addition to an unprecedented economic impact. Despite the many advances in scientific knowledge about the disease, much remains to be clarified about the molecular alterations induced by SARS-CoV-2 infection. In this work, we present a hybrid proteomics and in silico interactomics strategy to establish a COVID-19 salivary protein profile. Data are available via ProteomeXchange with identifier PXD036571. The differential proteome was narrowed down by the Partial Least-Squares Discriminant Analysis and enrichment analysis was performed with FunRich. In parallel, OralInt was used to determine interspecies Protein-Protein Interactions between humans and SARS-CoV-2. Five dysregulated biological processes were identified in the COVID-19 proteome profile: Apoptosis, Energy Pathways, Immune Response, Protein Metabolism and Transport. We identified 10 proteins (KLK 11, IMPA2, ANXA7, PLP2, IGLV2-11, IGHV3-43D, IGKV2-24, TMEM165, VSIG10 and PHB2) that had never been associated with SARS-CoV-2 infection, representing new evidence of the impact of COVID-19. Interactomics analysis showed viral influence on the host immune response, mainly through interaction with the degranulation of neutrophils. The virus alters the host’s energy metabolism and interferes with apoptosis mechanisms.
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14
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Caillet C, Stofberg ML, Muleya V, Shonhai A, Zininga T. Host cell stress response as a predictor of COVID-19 infectivity and disease progression. Front Mol Biosci 2022; 9:938099. [PMID: 36032680 PMCID: PMC9411049 DOI: 10.3389/fmolb.2022.938099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022] Open
Abstract
The coronavirus disease (COVID-19) caused by a coronavirus identified in December 2019 has caused a global pandemic. COVID-19 was declared a pandemic in March 2020 and has led to more than 6.3 million deaths. The pandemic has disrupted world travel, economies, and lifestyles worldwide. Although vaccination has been an effective tool to reduce the severity and spread of the disease there is a need for more concerted approaches to fighting the disease. COVID-19 is characterised as a severe acute respiratory syndrome . The severity of the disease is associated with a battery of comorbidities such as cardiovascular diseases, cancer, chronic lung disease, and renal disease. These underlying diseases are associated with general cellular stress. Thus, COVID-19 exacerbates outcomes of the underlying conditions. Consequently, coronavirus infection and the various underlying conditions converge to present a combined strain on the cellular response. While the host response to the stress is primarily intended to be of benefit, the outcomes are occasionally unpredictable because the cellular stress response is a function of complex factors. This review discusses the role of the host stress response as a convergent point for COVID-19 and several non-communicable diseases. We further discuss the merits of targeting the host stress response to manage the clinical outcomes of COVID-19.
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Affiliation(s)
- Celine Caillet
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
| | | | - Victor Muleya
- Department of Biochemistry, Midlands State University, Gweru, Zimbabwe
| | - Addmore Shonhai
- Department of Biochemistry and Microbiology, University of Venda, Thohoyandou, South Africa
| | - Tawanda Zininga
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
- *Correspondence: Tawanda Zininga,
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15
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Ura B, Capaci V, Aloisio M, Di Lorenzo G, Romano F, Ricci G, Monasta L. A Targeted Proteomics Approach for Screening Serum Biomarkers Observed in the Early Stage of Type I Endometrial Cancer. Biomedicines 2022; 10:biomedicines10081857. [PMID: 36009404 PMCID: PMC9405144 DOI: 10.3390/biomedicines10081857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/22/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022] Open
Abstract
Endometrial cancer (EC) is the most common gynecologic malignancy, and it arises in the inner part of the uterus. Identification of serum biomarkers is essential for diagnosing the disease at an early stage. In this study, we selected 44 healthy controls and 44 type I EC at tumor stage 1, and we used the Immuno-oncology panel and the Target 96 Oncology III panel to simultaneously detect the levels of 92 cancer-related proteins in serum, using a proximity extension assay. By applying this methodology, we identified 20 proteins, associated with the outcome at binary logistic regression, with a p-value below 0.01 for the first panel and 24 proteins with a p-value below 0.02 for the second one. The final multivariate logistic regression model, combining proteins from the two panels, generated a model with a sensitivity of 97.67% and a specificity of 83.72%. These results support the use of the proposed algorithm after a validation phase.
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Affiliation(s)
- Blendi Ura
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 34137 Trieste, Italy; (V.C.); (M.A.); (G.D.L.); (F.R.); (G.R.); (L.M.)
- Correspondence:
| | - Valeria Capaci
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 34137 Trieste, Italy; (V.C.); (M.A.); (G.D.L.); (F.R.); (G.R.); (L.M.)
| | - Michelangelo Aloisio
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 34137 Trieste, Italy; (V.C.); (M.A.); (G.D.L.); (F.R.); (G.R.); (L.M.)
| | - Giovanni Di Lorenzo
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 34137 Trieste, Italy; (V.C.); (M.A.); (G.D.L.); (F.R.); (G.R.); (L.M.)
| | - Federico Romano
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 34137 Trieste, Italy; (V.C.); (M.A.); (G.D.L.); (F.R.); (G.R.); (L.M.)
| | - Giuseppe Ricci
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 34137 Trieste, Italy; (V.C.); (M.A.); (G.D.L.); (F.R.); (G.R.); (L.M.)
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34129 Trieste, Italy
| | - Lorenzo Monasta
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 34137 Trieste, Italy; (V.C.); (M.A.); (G.D.L.); (F.R.); (G.R.); (L.M.)
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16
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Ward B, Yombi JC, Balligand JL, Cani PD, Collet JF, de Greef J, Dewulf JP, Gatto L, Haufroid V, Jodogne S, Kabamba B, Pyr dit Ruys S, Vertommen D, Elens L, Belkhir L. HYGIEIA: HYpothesizing the Genesis of Infectious Diseases and Epidemics through an Integrated Systems Biology Approach. Viruses 2022; 14:v14071373. [PMID: 35891354 PMCID: PMC9318602 DOI: 10.3390/v14071373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/13/2022] [Accepted: 06/21/2022] [Indexed: 12/13/2022] Open
Abstract
More than two years on, the COVID-19 pandemic continues to wreak havoc around the world and has battle-tested the pandemic-situation responses of all major global governments. Two key areas of investigation that are still unclear are: the molecular mechanisms that lead to heterogenic patient outcomes, and the causes of Post COVID condition (AKA Long-COVID). In this paper, we introduce the HYGIEIA project, designed to respond to the enormous challenges of the COVID-19 pandemic through a multi-omic approach supported by network medicine. It is hoped that in addition to investigating COVID-19, the logistics deployed within this project will be applicable to other infectious agents, pandemic-type situations, and also other complex, non-infectious diseases. Here, we first look at previous research into COVID-19 in the context of the proteome, metabolome, transcriptome, microbiome, host genome, and viral genome. We then discuss a proposed methodology for a large-scale multi-omic longitudinal study to investigate the aforementioned biological strata through high-throughput sequencing (HTS) and mass-spectrometry (MS) technologies. Lastly, we discuss how a network medicine approach can be used to analyze the data and make meaningful discoveries, with the final aim being the translation of these discoveries into the clinics to improve patient care.
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Affiliation(s)
- Bradley Ward
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (B.W.); (S.P.d.R.)
- Louvain Center for Toxicology and Applied Pharmacology (LTAP), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.d.G.); (J.P.D.); (V.H.)
| | - Jean Cyr Yombi
- Department of Internal Medicine, Cliniques Universitaires Saint-Luc, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Jean-Luc Balligand
- WELBIO (Walloon Excellence in Life Sciences and Biotechnology), Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Experimentale et Clinique (IREC), Cliniques Universitaires Saint-Luc, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Patrice D. Cani
- WELBIO (Walloon Excellence in Life Sciences and Biotechnology), Metabolism and Nutrition Research Group, Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Jean-François Collet
- WELBIO (Walloon Excellence in Life Sciences and Biotechnology), de Duve Institute, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Julien de Greef
- Louvain Center for Toxicology and Applied Pharmacology (LTAP), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.d.G.); (J.P.D.); (V.H.)
- Department of Internal Medicine, Cliniques Universitaires Saint-Luc, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Joseph P. Dewulf
- Louvain Center for Toxicology and Applied Pharmacology (LTAP), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.d.G.); (J.P.D.); (V.H.)
- Department of Laboratory Medicine, Cliniques Universitaires Saint-Luc, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
- Department of Biochemistry, de Duve Institute, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Laurent Gatto
- Computational Biology and Bioinformatics Unit (CBIO), de Duve Institute, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Vincent Haufroid
- Louvain Center for Toxicology and Applied Pharmacology (LTAP), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.d.G.); (J.P.D.); (V.H.)
- Department of Laboratory Medicine, Cliniques Universitaires Saint-Luc, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Sébastien Jodogne
- Computer Science and Engineering Department (INGI), Institute of Information and Communication Technologies, Electronics and Applied Mathematics (ICTEAM), UCLouvain, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium;
| | - Benoît Kabamba
- Department of Laboratory Medicine, Cliniques Universitaires Saint-Luc, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
- Pôle de Microbiologie, Institut de Recherche Expérimentale et Clinique, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Sébastien Pyr dit Ruys
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (B.W.); (S.P.d.R.)
| | - Didier Vertommen
- De Duve Institute, and MASSPROT Platform, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Laure Elens
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (B.W.); (S.P.d.R.)
- Louvain Center for Toxicology and Applied Pharmacology (LTAP), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.d.G.); (J.P.D.); (V.H.)
- Correspondence: (L.E.); (L.B.)
| | - Leïla Belkhir
- Louvain Center for Toxicology and Applied Pharmacology (LTAP), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.d.G.); (J.P.D.); (V.H.)
- Department of Internal Medicine, Cliniques Universitaires Saint-Luc, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
- Correspondence: (L.E.); (L.B.)
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17
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IGF1R acts as a cancer-promoting factor in the tumor microenvironment facilitating lung metastasis implantation and progression. Oncogene 2022; 41:3625-3639. [PMID: 35688943 PMCID: PMC9184253 DOI: 10.1038/s41388-022-02376-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 05/27/2022] [Accepted: 06/01/2022] [Indexed: 11/08/2022]
Abstract
Given the long-term ineffectiveness of current therapies and late-stage diagnoses, lung cancer is a leading cause of malignant diseases. Tumor progression is influenced by cancer cell interactions with the tumor microenvironment (TME). Insulin-like growth factor 1 receptor (IGF1R) was reported to affect the TME; however, the role of IGF1R in lung TME has not been investigated. First, we assessed IGF1R genomic alterations and expression in NSCLC patient tissue samples, as well as IGF1R serum levels. Next, we performed tumor heterotopic transplantation and pulmonary metastases in IGF1R-deficient mice using melanoma and Lewis lung carcinoma (LLC) cells. Herein we report increased amplification and mRNA expression, as well as increased protein expression (IGF1R/p-IGF1R) and IGF1R levels in tumor samples and serum from NSCLC patients, respectively. Moreover, IGF1R deficiency in mice reduced tumor growth, proliferation, inflammation and vascularization, and increased apoptosis after tumor heterotopic transplantation. Following induction of lung metastasis, IGF1R-deficient lungs also demonstrated a reduced tumor burden, and decreased expression of tumor progression markers, p-IGF1R and p-ERK1/2. Additionally, IGF1R-deficient lungs showed increased apoptosis and diminished proliferation, vascularization, EMT and fibrosis, along with attenuated inflammation and immunosuppression. Accordingly, IGF1R deficiency decreased expression of p-IGF1R in blood vessels, fibroblasts, tumor-associated macrophages and FOXP3+ tumor-infiltrating lymphocytes. Our results demonstrate that IGF1R promotes metastatic tumor initiation and progression in lung TME. Furthermore, our research indicates that IGF1R could be a potential biomarker for early prediction of drug response and clinical evolution in NSCLC patients.
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18
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Qi P, Huang M, Li T. Screening the Potential Biomarkers of COVID-19-Related Thrombosis Through Bioinformatics Analysis. Front Genet 2022; 13:889348. [PMID: 35692833 PMCID: PMC9174658 DOI: 10.3389/fgene.2022.889348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/09/2022] [Indexed: 11/30/2022] Open
Abstract
A high proportion of critically ill patients with coronavirus disease 2019 (COVID-19) experience thrombosis, and there is a strong correlation between anticoagulant therapy and the COVID-19 survival rate, indicating that common COVID-19 and thrombosis targets have potential therapeutic value for severe COVID-19.Gene expression profiling data were downloaded from Gene Expression Omnibus (GEO), and common differentially expressed genes (co-DEGs) were identified. The potential biological functions of these co-DEGs were explored by functional enrichment analysis, and protein–protein interaction (PPI) networks were constructed to elucidate the molecular mechanisms of the co-DEGs. Finally, hub genes in the co-DEG network were identified, and correlation analysis was performed.We identified 8320 upregulated genes and 7651 downregulated genes from blood samples of COVID-19 patients and 368 upregulated genes and 240 downregulated genes from blood samples of thrombosis patients. The enriched cellular component terms were mainly related to cytosolic ribosomes and ribosomal subunits. The enriched molecular function terms were mainly related to structural constituents of ribosomes and electron transfer activity. Construction of the PPI network and identification of hub genes ultimately confirmed that RPS7, IGF1R, DICER1, ERH, MCTS1, and TNPO1 were jointly upregulated hub genes, and FLNA and PXN were jointly downregulated hub genes.The identification of novel potential biomarkers provides new options for treating COVID-19-related thrombosis and reducing the rate of severe COVID-19.
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Affiliation(s)
- Peng Qi
- Department of Emergency, First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Mengjie Huang
- Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Tanshi Li
- Department of Emergency, First Medical Center of Chinese PLA General Hospital, Beijing, China
- *Correspondence: Tanshi Li,
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19
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Prognostic tools and candidate drugs based on plasma proteomics of patients with severe COVID-19 complications. Nat Commun 2022; 13:946. [PMID: 35177642 PMCID: PMC8854716 DOI: 10.1038/s41467-022-28639-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 01/26/2022] [Indexed: 12/12/2022] Open
Abstract
COVID-19 complications still present a huge burden on healthcare systems and warrant predictive risk models to triage patients and inform early intervention. Here, we profile 893 plasma proteins from 50 severe and 50 mild-moderate COVID-19 patients, and 50 healthy controls, and show that 375 proteins are differentially expressed in the plasma of severe COVID-19 patients. These differentially expressed plasma proteins are implicated in the pathogenesis of COVID-19 and present targets for candidate drugs to prevent or treat severe complications. Based on the plasma proteomics and clinical lab tests, we also report a 12-plasma protein signature and a model of seven routine clinical tests that validate in an independent cohort as early risk predictors of COVID-19 severity and patient survival. The risk predictors and candidate drugs described in our study can be used and developed for personalized management of SARS-CoV-2 infected patients. Prognostic markers for patients with COVID-19 are of critical importance in determining the course of SARS-CoV-2 infection and patient handling. Here the authors determine and apply a prognostic proteomic panel for risk and drug prediction in the management of SARS-CoV-2 infected patients.
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20
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Amiri-Dashatan N, Koushki M, Rezaei-Tavirani M. Mass Spectrometry-Based Proteomics Research to Fight COVID-19: An Expert Review on Hopes and Challenges. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:19-34. [PMID: 35005991 DOI: 10.1089/omi.2021.0182] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The COVID-19 pandemic caused by the severe acute respiratory syndrome (SARS)-CoV-2 infection is a systemic disease and a major planetary health burden. While SARS-CoV-2 impacts host biology extensively, our knowledge of these alterations from a systems perspective remains incomplete. Moreover, there is currently only a limited description of this systemic disease. For precision diagnosis and treatment of SARS-CoV-2, multiomics technologies and systems science research offer significant prospects. This expert review offers a critical analysis of the prospects and challenges of the emerging mass spectrometry-based proteomics approaches to the study of COVID-19 as seen through a systems medicine lens. We also discuss the ways in which proteomics is poised to offer hope for diagnostics and therapeutics innovation on SARS-CoV-2 infection as the disease transitions from a pandemic to an endemic disease, and thus further challenging the health systems and services worldwide in the coming decade. Proteomics is an important high-throughput technology platform to achieve a functional overview of the ways in which COVID-19 changes host biology, and hence, can help identify possible points of entry for innovation in medicines and vaccines, among others.
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Affiliation(s)
- Nasrin Amiri-Dashatan
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Zanjan Metabolic Diseases Research Center, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mehdi Koushki
- Department of Clinical Biochemistry, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
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21
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Wik L, Nordberg N, Broberg J, Björkesten J, Assarsson E, Henriksson S, Grundberg I, Pettersson E, Westerberg C, Liljeroth E, Falck A, Lundberg M. Proximity Extension Assay in Combination with Next-Generation Sequencing for High-throughput Proteome-wide Analysis. Mol Cell Proteomics 2021; 20:100168. [PMID: 34715355 PMCID: PMC8633680 DOI: 10.1016/j.mcpro.2021.100168] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 10/14/2021] [Accepted: 10/21/2021] [Indexed: 01/21/2023] Open
Abstract
Understanding the dynamics of the human proteome is crucial for developing biomarkers to be used as measurable indicators for disease severity and progression, patient stratification, and drug development. The Proximity Extension Assay (PEA) is a technology that translates protein information into actionable knowledge by linking protein-specific antibodies to DNA-encoded tags. In this report we demonstrate how we have combined the unique PEA technology with an innovative and automated sample preparation and high-throughput sequencing readout enabling parallel measurement of nearly 1500 proteins in 96 samples generating close to 150,000 data points per run. This advancement will have a major impact on the discovery of new biomarkers for disease prediction and prognosis and contribute to the development of the rapidly evolving fields of wellness monitoring and precision medicine.
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22
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McArdle A, Washington KE, Chazarin Orgel B, Binek A, Manalo DM, Rivas A, Ayres M, Pandey R, Phebus C, Raedschelders K, Fert-Bober J, Van Eyk JE. Discovery Proteomics for COVID-19: Where We Are Now. J Proteome Res 2021; 20:4627-4639. [PMID: 34550702 PMCID: PMC8482317 DOI: 10.1021/acs.jproteome.1c00475] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Indexed: 02/07/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible coronavirus responsible for the pandemic coronavirus disease 2019 (COVID-19), which has had a devastating impact on society. Here, we summarize proteomic research that has helped elucidate hallmark proteins associated with the disease with respect to both short- and long-term diagnosis and prognosis. Additionally, we review the highly variable humoral response associated with COVID-19 and the increased risk of autoimmunity.
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Affiliation(s)
- Angela McArdle
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Kirstin E. Washington
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Blandine Chazarin Orgel
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Aleksandra Binek
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Danica-Mae Manalo
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Alejandro Rivas
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Matthew Ayres
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Rakhi Pandey
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Connor Phebus
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Koen Raedschelders
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Justyna Fert-Bober
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
- Department
of Cardiology, Smidt Heart Institute, Cedars-Sinai
Medical Center, Los Angeles, California 90048, United States
| | - Jennifer E. Van Eyk
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
- Department
of Cardiology, Smidt Heart Institute, Cedars-Sinai
Medical Center, Los Angeles, California 90048, United States
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23
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Lorkiewicz P, Waszkiewicz N. Biomarkers of Post-COVID Depression. J Clin Med 2021; 10:4142. [PMID: 34575258 PMCID: PMC8470902 DOI: 10.3390/jcm10184142] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/04/2021] [Accepted: 09/10/2021] [Indexed: 02/06/2023] Open
Abstract
The COVID-19 pandemic is spreading around the world and 187 million people have already been affected. One of its after-effects is post-COVID depression, which, according to the latest data, affects up to 40% of people who have had SARS-CoV-2 infection. A very important issue for the mental health of the general population is to look for the causes of this complication and its biomarkers. This will help in faster diagnosis and effective treatment of the affected patients. In our work, we focused on the search for major depressive disorder (MDD) biomarkers, which are also present in COVID-19 patients and may influence the development of post-COVID depression. For this purpose, we searched PubMed, Scopus and Google Scholar scientific literature databases using keywords such as 'COVID-19', 'SARS-CoV-2', 'depression', 'post-COVID', 'biomarkers' and others. Among the biomarkers found, the most important that were frequently described are increased levels of interleukin 6 (IL-6), soluble interleukin 6 receptor (sIL-6R), interleukin 1 β (IL-1β), tumor necrosis factor α (TNF-α), interferon gamma (IFN-γ), interleukin 10 (IL-10), interleukin 2 (IL-2), soluble interleukin 2 receptor (sIL-2R), C-reactive protein (CRP), Monocyte Chemoattractant Protein-1 (MCP-1), serum amyloid a (SAA1) and metabolites of the kynurenine pathway, as well as decreased brain derived neurotrophic factor (BDNF) and tryptophan (TRP). The biomarkers identified by us indicate the etiopathogenesis of post-COVID depression analogous to the leading inflammatory hypothesis of MDD.
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Affiliation(s)
- Piotr Lorkiewicz
- Department of Psychiatry, Medical University of Bialystok, Plac Brodowicza 1, 16-070 Choroszcz, Poland;
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24
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Alfaro-Arnedo E, López IP, Piñeiro-Hermida S, Ucero ÁC, González-Barcala FJ, Salgado FJ, Pichel JG. IGF1R as a Potential Pharmacological Target in Allergic Asthma. Biomedicines 2021; 9:biomedicines9080912. [PMID: 34440118 PMCID: PMC8389607 DOI: 10.3390/biomedicines9080912] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 07/22/2021] [Accepted: 07/24/2021] [Indexed: 12/21/2022] Open
Abstract
Background: Asthma is a chronic lung disease characterized by reversible airflow obstruction, airway hyperresponsiveness (AHR), mucus overproduction and inflammation. Although Insulin-like growth factor 1 receptor (IGF1R) was found to be involved in asthma, its pharmacological inhibition has not previously been investigated in this pathology. We aimed to determine if therapeutic targeting of IGF1R ameliorates allergic airway inflammation in a murine model of asthma. Methods: C57BL/6J mice were challenged by house dust mite (HDM) extract or PBS for four weeks and therapeutically treated with the IGF1R tyrosine kinase inhibitor (TKI) NVP-ADW742 (NVP) once allergic phenotype was established. Results: Lungs of HDM-challenged mice exhibited a significant increase in phospho-IGF1R levels, incremented AHR, airway remodeling, eosinophilia and allergic inflammation, as well as altered pulmonary surfactant expression, all of being these parameters counteracted by NVP treatment. HDM-challenged lungs also displayed augmented expression of the IGF1R signaling mediator p-ERK1/2, which was greatly reduced upon treatment with NVP. Conclusions: Our results demonstrate that IGF1R could be considered a potential pharmacological target in murine HDM-induced asthma and a candidate biomarker in allergic asthma.
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Affiliation(s)
- Elvira Alfaro-Arnedo
- Lung Cancer and Respiratory Diseases Unit, Center for Biomedical Research of La Rioja (CIBIR), Fundación Rioja Salud, 26006 Logroño, Spain; (E.A.-A.); (I.P.L.)
| | - Icíar P. López
- Lung Cancer and Respiratory Diseases Unit, Center for Biomedical Research of La Rioja (CIBIR), Fundación Rioja Salud, 26006 Logroño, Spain; (E.A.-A.); (I.P.L.)
| | - Sergio Piñeiro-Hermida
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre (CNIO), 28029 Madrid, Spain;
| | - Álvaro C. Ucero
- Thoracic Oncology, Research Institute Hospital 12 de Octubre, 28041 Madrid, Spain;
- Department of Physiology, Faculty of Medicine, Complutense University, 28040 Madrid, Spain
| | - Francisco J. González-Barcala
- Department of Respiratory Medicine, University Hospital of Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain;
- Health Research Institute of Santiago de Compostela (FIDIS), 15706 Santiago de Compostela, Spain
- Spanish Biomedical Research Networking Centre-CIBERES, 15706 Santiago de Compostela, Spain
| | - Francisco J. Salgado
- Department of Biochemistry and Molecular Biology, Faculty of Biology-Biological Research Centre (CIBUS), Universidad de Santiago de Compostela, 15706 Santiago de Compostela, Spain;
| | - José G. Pichel
- Lung Cancer and Respiratory Diseases Unit, Center for Biomedical Research of La Rioja (CIBIR), Fundación Rioja Salud, 26006 Logroño, Spain; (E.A.-A.); (I.P.L.)
- Spanish Biomedical Research Networking Centre-CIBERES, 15706 Santiago de Compostela, Spain
- Correspondence: ; Tel.: +34-638-056-014
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25
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Fraser DD, Chen M, Ren A, Miller MR, Martin C, Daley M, Diamandis EP, Prassas I. Novel severe traumatic brain injury blood outcome biomarkers identified with proximity extension assay. Clin Chem Lab Med 2021; 59:1662-1669. [PMID: 34144643 DOI: 10.1515/cclm-2021-0103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/28/2021] [Indexed: 01/04/2023]
Abstract
OBJECTIVES Severe traumatic brain injury (sTBI) patients suffer high mortality. Accurate prognostic biomarkers have not been identified. In this exploratory study, we performed targeted proteomics on plasma obtained from sTBI patients to identify potential outcome biomarkers. METHODS Blood sample was collected from patients admitted to the ICU suffering a sTBI, using standardized clinical and computerized tomography (CT) imaging criteria. Age- and sex-matched healthy control subjects and sTBI patients were enrolled. Targeted proteomics was performed on plasma with proximity extension assays (1,161 proteins). RESULTS Cohorts were well-balanced for age and sex. The majority of sTBI patients were injured in motor vehicle collisions and the most frequent head CT finding was subarachnoid hemorrhage. Mortality rate for sTBI patients was 40%. Feature selection identified the top performing 15 proteins for identifying sTBI patients from healthy control subjects with a classification accuracy of 100%. The sTBI proteome was dominated by markers of vascular pathology, immunity/inflammation, cell survival and macrophage/microglia activation. Receiver operating characteristic (ROC) curve analyses demonstrated areas-under-the-curves (AUC) for identifying sTBI that ranged from 0.870-1.000 (p≤0.005). When mortality was used as outcome, ROC curve analyses identified the top 3 proteins as Willebrand factor (vWF), Wnt inhibitory factor-1 (WIF-1), and colony stimulating factor-1 (CSF-1). Combining vWF with either WIF-1 or CSF-1 resulted in excellent mortality prediction with AUC of 1.000 for both combinations (p=0.011). CONCLUSIONS Targeted proteomics with feature classification and selection distinguished sTBI patients from matched healthy control subjects. Two protein combinations were identified that accurately predicted sTBI patient mortality. Our exploratory findings require confirmation in larger sTBI patient populations.
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Affiliation(s)
- Douglas D Fraser
- Lawson Health Research Institute, London, ON, Canada.,Pediatrics, Western University, London, ON, Canada.,Clinical Neurological Sciences, Western University, London, ON, Canada.,Physiology and Pharmacology, Western University, London, ON, Canada.,NeuroLytixs Inc., Toronto, ON, Canada
| | - Michelle Chen
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Annie Ren
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Michael R Miller
- Lawson Health Research Institute, London, ON, Canada.,Pediatrics, Western University, London, ON, Canada
| | | | - Mark Daley
- Lawson Health Research Institute, London, ON, Canada
| | - Eleftherios P Diamandis
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada.,Clinical Biochemistry, University Health Network, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Ioannis Prassas
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
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26
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Juneja GK, Castelo M, Yeh CH, Cerroni SE, Hansen BE, Chessum JE, Abraham J, Cani E, Dwivedi DJ, Fraser DD, Slessarev M, Martin C, McGilvray S, Gross PL, Liaw PC, Weitz JI, Kim PY. Biomarkers of coagulation, endothelial function, and fibrinolysis in critically ill patients with COVID-19: A single-center prospective longitudinal study. J Thromb Haemost 2021; 19:1546-1557. [PMID: 33826233 PMCID: PMC8250276 DOI: 10.1111/jth.15327] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 03/26/2021] [Accepted: 03/30/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND Immunothrombosis and coagulopathy in the lung microvasculature may lead to lung injury and disease progression in coronavirus disease 2019 (COVID-19). We aim to identify biomarkers of coagulation, endothelial function, and fibrinolysis that are associated with disease severity and may have prognostic potential. METHODS We performed a single-center prospective study of 14 adult COVID-19(+) intensive care unit patients who were age- and sex-matched to 14 COVID-19(-) intensive care unit patients, and healthy controls. Daily blood draws, clinical data, and patient characteristics were collected. Baseline values for 10 biomarkers of interest were compared between the three groups, and visualized using Fisher's linear discriminant function. Linear repeated-measures mixed models were used to screen biomarkers for associations with mortality. Selected biomarkers were further explored and entered into an unsupervised longitudinal clustering machine learning algorithm to identify trends and targets that may be used for future predictive modelling efforts. RESULTS Elevated D-dimer was the strongest contributor in distinguishing COVID-19 status; however, D-dimer was not associated with survival. Variable selection identified clot lysis time, and antigen levels of soluble thrombomodulin (sTM), plasminogen activator inhibitor-1 (PAI-1), and plasminogen as biomarkers associated with death. Longitudinal multivariate k-means clustering on these biomarkers alone identified two clusters of COVID-19(+) patients: low (30%) and high (100%) mortality groups. Biomarker trajectories that characterized the high mortality cluster were higher clot lysis times (inhibited fibrinolysis), higher sTM and PAI-1 levels, and lower plasminogen levels. CONCLUSIONS Longitudinal trajectories of clot lysis time, sTM, PAI-1, and plasminogen may have predictive ability for mortality in COVID-19.
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Affiliation(s)
- Ganeem K Juneja
- Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, Canada
- Department of Medical Sciences, McMaster University, Hamilton, ON, Canada
| | - Matthew Castelo
- Department of Surgery, University of Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Calvin H Yeh
- Department of Medicine, Division of Emergency Medicine, University of Toronto, Toronto, ON, Canada
| | - Samantha E Cerroni
- Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Bettina E Hansen
- Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - James E Chessum
- Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, Canada
- Department of Medical Sciences, McMaster University, Hamilton, ON, Canada
| | - Joel Abraham
- Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, Canada
- Department of Medical Sciences, McMaster University, Hamilton, ON, Canada
| | - Erblin Cani
- Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, Canada
- Department of Medical Sciences, McMaster University, Hamilton, ON, Canada
| | - Dhruva J Dwivedi
- Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Douglas D Fraser
- Lawson Health Research Institute, London, ON, Canada
- Pediatrics, Western University, London, ON, Canada
- Clinical Neurological Sciences, Western University, London, ON, Canada
- Physiology & Pharmacology, Western University, London, ON, Canada
| | - Marat Slessarev
- Lawson Health Research Institute, London, ON, Canada
- Medicine, Western University, London, ON, Canada
| | - Claudio Martin
- Lawson Health Research Institute, London, ON, Canada
- Medicine, Western University, London, ON, Canada
| | - Scott McGilvray
- Department of Medicine, Division of Emergency Medicine, University of Toronto, Toronto, ON, Canada
| | - Peter L Gross
- Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Patricia C Liaw
- Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Jeffrey I Weitz
- Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Paul Y Kim
- Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
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27
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Filbin MR, Mehta A, Schneider AM, Kays KR, Guess JR, Gentili M, Fenyves BG, Charland NC, Gonye AL, Gushterova I, Khanna HK, LaSalle TJ, Lavin-Parsons KM, Lilley BM, Lodenstein CL, Manakongtreecheep K, Margolin JD, McKaig BN, Rojas-Lopez M, Russo BC, Sharma N, Tantivit J, Thomas MF, Gerszten RE, Heimberg GS, Hoover PJ, Lieb DJ, Lin B, Ngo D, Pelka K, Reyes M, Smillie CS, Waghray A, Wood TE, Zajac AS, Jennings LL, Grundberg I, Bhattacharyya RP, Parry BA, Villani AC, Sade-Feldman M, Hacohen N, Goldberg MB. Longitudinal proteomic analysis of severe COVID-19 reveals survival-associated signatures, tissue-specific cell death, and cell-cell interactions. Cell Rep Med 2021; 2:100287. [PMID: 33969320 PMCID: PMC8091031 DOI: 10.1016/j.xcrm.2021.100287] [Citation(s) in RCA: 142] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/08/2021] [Accepted: 04/23/2021] [Indexed: 02/06/2023]
Abstract
Mechanisms underlying severe coronavirus disease 2019 (COVID-19) disease remain poorly understood. We analyze several thousand plasma proteins longitudinally in 306 COVID-19 patients and 78 symptomatic controls, uncovering immune and non-immune proteins linked to COVID-19. Deconvolution of our plasma proteome data using published scRNA-seq datasets reveals contributions from circulating immune and tissue cells. Sixteen percent of patients display reduced inflammation yet comparably poor outcomes. Comparison of patients who died to severely ill survivors identifies dynamic immune-cell-derived and tissue-associated proteins associated with survival, including exocrine pancreatic proteases. Using derived tissue-specific and cell-type-specific intracellular death signatures, cellular angiotensin-converting enzyme 2 (ACE2) expression, and our data, we infer whether organ damage resulted from direct or indirect effects of infection. We propose a model in which interactions among myeloid, epithelial, and T cells drive tissue damage. These datasets provide important insights and a rich resource for analysis of mechanisms of severe COVID-19 disease.
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Affiliation(s)
- Michael R. Filbin
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Emergency Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Arnav Mehta
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Alexis M. Schneider
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kyle R. Kays
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Matteo Gentili
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Bánk G. Fenyves
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Emergency Medicine, Semmelweis University, Budapest, Hungary
| | - Nicole C. Charland
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Anna L.K. Gonye
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Irena Gushterova
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Hargun K. Khanna
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Thomas J. LaSalle
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Brendan M. Lilley
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Carl L. Lodenstein
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kasidet Manakongtreecheep
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Justin D. Margolin
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Brenna N. McKaig
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Maricarmen Rojas-Lopez
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Brian C. Russo
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Nihaarika Sharma
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jessica Tantivit
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Molly F. Thomas
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Robert E. Gerszten
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- CardioVascular Institute, Department of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Graham S. Heimberg
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Paul J. Hoover
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - David J. Lieb
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Brian Lin
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Regenerative Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Debby Ngo
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Karin Pelka
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Miguel Reyes
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Christopher S. Smillie
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Avinash Waghray
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Regenerative Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Thomas E. Wood
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Amanda S. Zajac
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | | | | | - Roby P. Bhattacharyya
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Blair Alden Parry
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Alexandra-Chloé Villani
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Moshe Sade-Feldman
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nir Hacohen
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Marcia B. Goldberg
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
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28
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Critically Ill COVID-19 Patients Exhibit Anti-SARS-CoV-2 Serological Responses. PATHOPHYSIOLOGY 2021; 28:212-223. [PMID: 35366258 PMCID: PMC8830473 DOI: 10.3390/pathophysiology28020014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 12/16/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, is a global health care emergency. Anti-SARS-CoV-2 serological profiling of critically ill COVID-19 patients was performed to determine their humoral response. Blood was collected from critically ill ICU patients, either COVID-19 positive (+) or COVID-19 negative (−), to measure anti-SARS-CoV-2 immunoglobulins: IgM; IgA; IgG; and Total Ig (combined IgM/IgA/IgG). Cohorts were similar, with the exception that COVID-19+ patients had a greater body mass indexes, developed bilateral pneumonias more frequently and suffered increased hypoxia when compared to COVID-19- patients (p < 0.05). The mortality rate for COVID-19+ patients was 50%. COVID-19 status could be determined by anti-SARS-CoV-2 serological responses with excellent classification accuracies on ICU day 1 (89%); ICU day 3 (96%); and ICU days 7 and 10 (100%). The importance of each Ig isotype for determining COVID-19 status on combined ICU days 1 and 3 was: Total Ig, 43%; IgM, 27%; IgA, 24% and IgG, 6%. Peak serological responses for each Ig isotype occurred on different ICU days (IgM day 13 > IgA day 17 > IgG persistently increased), with the Total Ig peaking at approximately ICU day 18. Those COVID-19+ patients who died had earlier or similar peaks in IgA and Total Ig in their ICU stay when compared to patients who survived (p < 0.005). Critically ill COVID-19 patients exhibit anti-SARS-CoV-2 serological responses, including those COVID-19 patients who ultimately died, suggesting that blunted serological responses did not contribute to mortality. Serological profiling of critically ill COVID-19 patients may aid disease surveillance, patient cohorting and help guide antibody therapies such as convalescent plasma.
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29
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Rastogi S. Ayurveda co-interventions have supported complete recovery in Severe COVID- 19 infection with a Chest Severity Score 18/25: A Case Report. J Ayurveda Integr Med 2021; 13:100417. [PMID: 33727768 PMCID: PMC7953452 DOI: 10.1016/j.jaim.2021.02.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/13/2021] [Accepted: 02/27/2021] [Indexed: 12/30/2022] Open
Abstract
Severe COVID-19 infection requiring oxygen support is reported to have high mortality. Chest Severity Score evaluated through CT scan has a predictive value about future outcomes in such cases. Score value ∼18 is predicted to have poor outcomes. We are presenting here a case of severe COVID-19 with all predictors suggestive of a bad prognosis including IL-6, D-Dimer, Ferritin and CRP in addition to 18/25 Chest Severity Score. Initially treated under ICU care at a tertiary care COVID hospital for about 14days, the patient was intervened with Ayurveda on his own insistence seeing the unsatisfactory improvements. Ayurveda intervention for 19 days along with standard ICU care resulted in complete clinical recovery of the patient besides the correction of biomarker levels. Rapid clinical and biochemical correction in this severe COVID-19 case against all odds is highly significant and warrants an urgent search for possibility of instituting the integrative management strategies for all those treated in an allopathic facility. This case also advocates an early institution of Ayurveda interventions in COVID-19 in order to prevent deterioration leading to complications.
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Affiliation(s)
- Sanjeev Rastogi
- Department of Kaya Chikitsa, State Ayurvedic College and Hospital, Lucknow University, Lucknow, 226003, India
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30
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Fraser DD, Cepinskas G, Slessarev M, Martin CM, Daley M, Patel MA, Miller MR, Patterson EK, O'Gorman DB, Gill SE, Oehler S, Miholits M, Webb B. Detection and Profiling of Human Coronavirus Immunoglobulins in Critically Ill Coronavirus Disease 2019 Patients. Crit Care Explor 2021; 3:e0369. [PMID: 33786445 PMCID: PMC7994038 DOI: 10.1097/cce.0000000000000369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVES Coronavirus disease 2019 continues to spread worldwide with high levels of morbidity and mortality. We performed anticoronavirus immunoglobulin G profiling of critically ill coronavirus disease 2019 patients to better define their underlying humoral response. DESIGN Blood was collected at predetermined ICU days to measure immunoglobulin G with a research multiplex assay against four severe acute respiratory syndrome coronavirus 2 proteins/subunits and against all six additionally known human coronaviruses. SETTING Tertiary care ICU and academic laboratory. SUBJECTS ICU patients suspected of being infected with severe acute respiratory syndrome coronavirus 2 had blood collected until either polymerase chain reaction testing was confirmed negative on ICU day 3 (coronavirus disease 2019 negative) or until death or discharge if the patient tested polymerase chain reaction positive (coronavirus disease 2019 positive). INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS Age- and sex-matched healthy controls and ICU patients who were either coronavirus disease 2019 positive or coronavirus disease 2019 negative were enrolled. Cohorts were well-balanced with the exception that coronavirus disease 2019 positive patients had greater body mass indexes, presented with bilateral pneumonias more frequently, and suffered lower Pao2:Fio2 ratios, when compared with coronavirus disease 2019 negative patients (p < 0.05). Mortality rate for coronavirus disease 2019 positive patients was 50%. On ICU days 1-3, anti-severe acute respiratory syndrome coronavirus 2 immunoglobulin G was significantly elevated in coronavirus disease 2019 positive patients, as compared to both healthy control subjects and coronavirus disease 2019 negative patients (p < 0.001). Weak severe acute respiratory syndrome coronavirus immunoglobulin G serologic responses were also detected, but not other coronavirus subtypes. The four anti-severe acute respiratory syndrome coronavirus 2 immunoglobulin G were maximal by ICU day 3, with all four anti-severe acute respiratory syndrome coronavirus 2 immunoglobulin G providing excellent diagnostic potential (severe acute respiratory syndrome coronavirus 2 Spike 1 protein immunoglobulin G, area under the curve 1.0, p < 0.0005; severe acute respiratory syndrome coronavirus receptor binding domain immunoglobulin G, area under the curve, 0.93-1.0; p ≤ 0.0001; severe acute respiratory syndrome coronavirus 2 Spike proteins immunoglobulin G, area under the curve, 1.0; p < 0.0001; severe acute respiratory syndrome coronavirus 2 Nucleocapsid protein immunoglobulin G area under the curve, 0.90-0.95; p ≤ 0.0003). Anti-severe acute respiratory syndrome coronavirus 2 immunoglobulin G increased and/or plateaued over 10 ICU days. CONCLUSIONS Critically ill coronavirus disease 2019 patients exhibited anti-severe acute respiratory syndrome coronavirus 2 immunoglobulin G, whereas serologic responses to non-severe acute respiratory syndrome coronavirus 2 antigens were weak or absent. Detection of human coronavirus immunoglobulin G against the different immunogenic structural proteins/subunits with multiplex assays may be useful for pathogen identification, patient cohorting, and guiding convalescent plasma therapy.
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Affiliation(s)
- Douglas D Fraser
- Lawson Health Research Institute, London, ON, Canada
- Pediatrics, Western University, London, ON, Canada
- Clinical Neurological Sciences, Western University, London, ON, Canada
- Physiology & Pharmacology, Western University, London, ON, Canada
| | - Gediminas Cepinskas
- Lawson Health Research Institute, London, ON, Canada
- Medical Biophysics, Western University, London, ON, Canada
| | - Marat Slessarev
- Lawson Health Research Institute, London, ON, Canada
- Medicine, Western University, London, ON, Canada
| | - Claudio M Martin
- Lawson Health Research Institute, London, ON, Canada
- Medicine, Western University, London, ON, Canada
| | - Mark Daley
- Lawson Health Research Institute, London, ON, Canada
- Computer Science, Western University, London, ON, Canada
- The Vector Institute for Artificial Intelligence, Toronto, ON, Canada
| | | | - Michael R Miller
- Lawson Health Research Institute, London, ON, Canada
- Pediatrics, Western University, London, ON, Canada
| | | | - David B O'Gorman
- Lawson Health Research Institute, London, ON, Canada
- Surgery, Western University, London, ON, Canada
- Biochemistry, Western University, London, ON, Canada
| | - Sean E Gill
- Lawson Health Research Institute, London, ON, Canada
- Physiology & Pharmacology, Western University, London, ON, Canada
- Medicine, Western University, London, ON, Canada
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31
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Fraser DD, Patterson EK, Daley M, Cepinskas G. Case Report: Inflammation and Endothelial Injury Profiling of COVID-19 Pediatric Multisystem Inflammatory Syndrome (MIS-C). Front Pediatr 2021; 9:597926. [PMID: 33898353 PMCID: PMC8060468 DOI: 10.3389/fped.2021.597926] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 03/09/2021] [Indexed: 12/26/2022] Open
Abstract
Introduction: COVID-19 is associated with a novel multi-system inflammatory syndrome that shares some characteristics with Kawasaki's Disease. The syndrome manifestation is delayed relative to COVID-19 onset, with a spectrum of clinical severity. Clinical signs may include persistent fever, gastrointestinal symptoms, cardiac inflammation and/or shock. Case Presentation: We measured 59 inflammatory and endothelial injury plasma analytes in an adolescent girl that presented with malaise, fever, cough, strawberry tongue and jaundice. Her COVID-19 status was positive with detection of 2 SARS-CoV-2 viral genes using polymerase chain reaction. She was treated with intravenous immunoglobulin prior to blood draw, but our plasma measurements suggested a unique analyte expression pattern associated with inflammation, endothelial injury and microvascular glycocalyx degradation. Conclusions: COVID-19 is associated with a multi-system inflammatory syndrome and a unique inflammatory and endothelial injury signature. Summary: Analyte markers of inflammation and endothelial cell injury might serve as putative biomarkers and/or be investigated further as potential therapeutic targets.
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Affiliation(s)
- Douglas D Fraser
- Lawson Health Research Institute, London, ON, Canada.,Pediatrics, Western University, London, ON, Canada
| | | | - Mark Daley
- Lawson Health Research Institute, London, ON, Canada.,Computer Science, Western University, London, ON, Canada
| | - Gediminas Cepinskas
- Lawson Health Research Institute, London, ON, Canada.,Medical Biophysics, Western University, London, ON, Canada
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32
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Ilias I, Diamantopoulos A, Botoula E, Athanasiou N, Zacharis A, Tsipilis S, Jahaj E, Vassiliou AG, Vassiliadi DA, Kotanidou A, Tsagarakis S, Dimopoulou I. Covid-19 and Growth Hormone/Insulin-Like Growth Factor 1: Study in Critically and Non-Critically Ill Patients. Front Endocrinol (Lausanne) 2021; 12:644055. [PMID: 34220703 PMCID: PMC8242942 DOI: 10.3389/fendo.2021.644055] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 05/28/2021] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE We aimed to measure insulin-like growth factor 1 (IGF1) and growth hormone (GH) in critically and non-critically ill patients with Covid-19 and assess them vis-a-vis clinical and laboratory parameters and prognostic tools. SUBJECTS AND METHODS We included patients who were admitted to the wards or the ICU of the largest Covid-19 referral hospital in Greece; patients with non-Covid-19 pneumonia served as controls. Apart from the routine laboratory work-up for Covid-19 we measured GH and IGF1 (and calculated normalized IGF-1 values as standard deviation scores; SDS), after blood sampling upon admission to the wards or the ICU. RESULTS We studied 209 critically and non-critically ill patients with Covid-19 and 39 control patients. Patients with Covid-19 who were ICU non-survivors were older and presented with a worse hematological/biochemical profile (including white blood cell count, troponin, glucose, aminotransferases and lactate dehydrogenase) compared to ICU survivors or Covid-19 survivors in the wards. Overall, IGF-1 SDS was higher in Covid-19 survivors compared to non-survivors (-0.96 ± 1.89 vs -2.05 ± 2.48, respectively, p=0.030). No significant differences were noted in GH between the groups. Nevertheless, in critically ill patients with Covid-19, the prognostic value of IGF-1 (raw data), IGF-1 (SDS) and GH for survival/non-survival was on a par with that of APACHE II and SOFA (with a marginal difference between GH and SOFA). CONCLUSION In conclusion, our findings suggest that there might be an association between low IGF1 (and possibly GH) and poor outcome in patients with Covid-19.
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Affiliation(s)
- Ioannis Ilias
- Department of Endocrinology, Diabetes and Metabolism, Elena Venizelou Hospital, Athens, Greece
- *Correspondence: Ioannis Ilias,
| | | | - Efthymia Botoula
- Department of Endocrinology, Diabetes and Metabolism, Evagelismos Hospital, Athens, Greece
| | - Nikolaos Athanasiou
- First Department of Critical Care Medicine & Pulmonary Services, Medical School of National & Kapodistrian University of Athens, Evagelismos Hospital, Athens, Greece
| | - Alexandros Zacharis
- First Department of Critical Care Medicine & Pulmonary Services, Medical School of National & Kapodistrian University of Athens, Evagelismos Hospital, Athens, Greece
| | | | - Edison Jahaj
- First Department of Critical Care Medicine & Pulmonary Services, Medical School of National & Kapodistrian University of Athens, Evagelismos Hospital, Athens, Greece
| | - Alice G. Vassiliou
- First Department of Critical Care Medicine & Pulmonary Services, Medical School of National & Kapodistrian University of Athens, Evagelismos Hospital, Athens, Greece
| | - Dimitra A. Vassiliadi
- Department of Endocrinology, Diabetes and Metabolism, Evagelismos Hospital, Athens, Greece
| | - Anastasia Kotanidou
- First Department of Critical Care Medicine & Pulmonary Services, Medical School of National & Kapodistrian University of Athens, Evagelismos Hospital, Athens, Greece
| | - Stylianos Tsagarakis
- Department of Endocrinology, Diabetes and Metabolism, Evagelismos Hospital, Athens, Greece
| | - Ioanna Dimopoulou
- First Department of Critical Care Medicine & Pulmonary Services, Medical School of National & Kapodistrian University of Athens, Evagelismos Hospital, Athens, Greece
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33
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Gill SE, Dos Santos CC, O'Gorman DB, Carter DE, Patterson EK, Slessarev M, Martin C, Daley M, Miller MR, Cepinskas G, Fraser DD. Transcriptional profiling of leukocytes in critically ill COVID19 patients: implications for interferon response and coagulation. Intensive Care Med Exp 2020; 8:75. [PMID: 33306162 PMCID: PMC7729690 DOI: 10.1186/s40635-020-00361-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/19/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND COVID19 is caused by the SARS-CoV-2 virus and has been associated with severe inflammation leading to organ dysfunction and mortality. Our aim was to profile the transcriptome in leukocytes from critically ill patients positive for COVID19 compared to those negative for COVID19 to better understand the COVID19-associated host response. For these studies, all patients admitted to our tertiary care intensive care unit (ICU) suspected of being infected with SARS-CoV-2, using standardized hospital screening methodologies, had blood samples collected at the time of admission to the ICU. Transcriptome profiling of leukocytes via ribonucleic acid sequencing (RNAseq) was then performed and differentially expressed genes as well as significantly enriched gene sets were identified. RESULTS We enrolled seven COVID19 + (PCR positive, 2 SARS-CoV-2 genes) and seven age- and sex-matched COVID19- (PCR negative) control ICU patients. Cohorts were well-balanced with the exception that COVID19- patients had significantly higher total white blood cell counts and circulating neutrophils and COVID19 + patients were more likely to suffer bilateral pneumonia. The mortality rate for this cohort of COVID19 + ICU patients was 29%. As indicated by both single-gene based and gene set (GSEA) approaches, the major disease-specific transcriptional responses of leukocytes in critically ill COVID19 + ICU patients were: (i) a robust overrepresentation of interferon-related gene expression; (ii) a marked decrease in the transcriptional level of genes contributing to general protein synthesis and bioenergy metabolism; and (iii) the dysregulated expression of genes associated with coagulation, platelet function, complement activation, and tumour necrosis factor/interleukin 6 signalling. CONCLUSIONS Our findings demonstrate that critically ill COVID19 + patients on day 1 of admission to the ICU display a unique leukocyte transcriptional profile that distinguishes them from COVID19- patients, providing guidance for future targeted studies exploring novel prognostic and therapeutic aspects of COVID19.
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Affiliation(s)
- Sean E Gill
- Lawson Health Research Institute, London, ON, Canada. .,Physiology and Pharmacology, Western University, London, ON, Canada. .,Medicine, Western University, London, ON, Canada. .,Victoria Research Labs, Room A6-134, 800 Commissioners Road East, London, ON, N6A 5W9, Canada.
| | - Claudia C Dos Santos
- Interdepartmental Division of Critical Care Medicine and Keenan Center for Biomedical Research of St. Michael's Hospital, University of Toronto, Toronto, ON, Canada
| | - David B O'Gorman
- Lawson Health Research Institute, London, ON, Canada.,Biochemistry, Western University, London, ON, Canada
| | - David E Carter
- London Regional Genomics Centre, Western University, London, ON, Canada
| | | | - Marat Slessarev
- Lawson Health Research Institute, London, ON, Canada.,Medicine, Western University, London, ON, Canada
| | - Claudio Martin
- Lawson Health Research Institute, London, ON, Canada.,Medicine, Western University, London, ON, Canada
| | - Mark Daley
- Lawson Health Research Institute, London, ON, Canada.,Computer Science, Western University, London, ON, Canada
| | - Michael R Miller
- Lawson Health Research Institute, London, ON, Canada.,Pediatrics, Western University, London, ON, Canada
| | - Gediminas Cepinskas
- Lawson Health Research Institute, London, ON, Canada.,Medical Biophysics, Western University, London, ON, Canada
| | - Douglas D Fraser
- Lawson Health Research Institute, London, ON, Canada. .,Physiology and Pharmacology, Western University, London, ON, Canada. .,Pediatrics, Western University, London, ON, Canada. .,London Health Sciences Centre, Room C2-C82, 800 Commissioners Road East, London, ON, N6A 5W9, Canada.
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34
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Asim M, Sathian B, Banerjee I, Robinson J. A contemporary insight of metabolomics approach for COVID-19: Potential for novel therapeutic and diagnostic targets. Nepal J Epidemiol 2020; 10:923-927. [PMID: 33495710 PMCID: PMC7812325 DOI: 10.3126/nje.v10i4.33964] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 12/30/2020] [Accepted: 12/31/2020] [Indexed: 12/12/2022] Open
Abstract
The Coronavirus disease 2019 (COVID-19) pandemic is caused by rapidly spreading pathogenic virus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), that affects vast majority of population worldwide. Although, around 80% of the cases had mild infection but still remaining 20% had developed respiratory failure and dysfunction of other organs that necessitate urgent oxygen therapy or specific interventions. Therefore, it is imperative to establish novel prognostic approaches to screen patients at high-risk of developing severe complications. The primary focus of current research for COVID-19 is to discover safe and efficacious vaccine for prevention and effective treatment for better management of the patients to overcome the pandemic. To achieve this goal, it is imperative to have better understanding of the molecular pathways involved in the pathophysiology and progression of severe COVID-19. The surge for reliable diagnostics and therapeutics targets for COVID-19 highlighted the great potential of high-throughput approach like metabolomics which may enable the development of personalized medicine.
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Affiliation(s)
- Mohammad Asim
- Surgery Department, Trauma Surgery, Hamad General Hospital, Doha, Qatar
| | - Brijesh Sathian
- Geriatrics and long term care Department, Rumailah Hospital, Hamad Medical Corporation, Doha, Qatar
- Centre for Midwifery, Maternal and Perinatal Health, Bournemouth University, Bournemouth, England, United Kingdom
| | | | - Jared Robinson
- Sir Seewoosagur Ramgoolam Medical College, Belle Rive, Mauritius
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35
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Filbin MR, Mehta A, Schneider AM, Kays KR, Guess JR, Gentili M, Fenyves BG, Charland NC, Gonye ALK, Gushterova I, Khanna HK, LaSalle TJ, Lavin-Parsons KM, Lilly BM, Lodenstein CL, Manakongtreecheep K, Margolin JD, McKaig BN, Rojas-Lopez M, Russo BC, Sharma N, Tantivit J, Thomas MF, Gerszten RE, Heimberg GS, Hoover PJ, Lieb DJ, Lin B, Ngo D, Pelka K, Reyes M, Smillie CS, Waghray A, Wood TE, Zajac AS, Jennings LL, Grundberg I, Bhattacharyya RP, Parry BA, Villani AC, Sade-Feldman M, Hacohen N, Goldberg MB. Plasma proteomics reveals tissue-specific cell death and mediators of cell-cell interactions in severe COVID-19 patients. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.11.02.365536. [PMID: 33173871 PMCID: PMC7654866 DOI: 10.1101/2020.11.02.365536] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
COVID-19 has caused over 1 million deaths globally, yet the cellular mechanisms underlying severe disease remain poorly understood. By analyzing several thousand plasma proteins in 306 COVID-19 patients and 78 symptomatic controls over serial timepoints using two complementary approaches, we uncover COVID-19 host immune and non-immune proteins not previously linked to this disease. Integration of plasma proteomics with nine published scRNAseq datasets shows that SARS-CoV-2 infection upregulates monocyte/macrophage, plasmablast, and T cell effector proteins. By comparing patients who died to severely ill patients who survived, we identify dynamic immunomodulatory and tissue-associated proteins associated with survival, providing insights into which host responses are beneficial and which are detrimental to survival. We identify intracellular death signatures from specific tissues and cell types, and by associating these with angiotensin converting enzyme 2 (ACE2) expression, we map tissue damage associated with severe disease and propose which damage results from direct viral infection rather than from indirect effects of illness. We find that disease severity in lung tissue is driven by myeloid cell phenotypes and cell-cell interactions with lung epithelial cells and T cells. Based on these results, we propose a model of immune and epithelial cell interactions that drive cell-type specific and tissue-specific damage in severe COVID-19.
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Anticytokine Therapies in Severe Coronavirus Disease 2019 Should Be Informed by Detailed Inflammatory Profiling and Specific Therapeutic Targets. Crit Care Explor 2020; 2:e0246. [PMID: 33134941 PMCID: PMC7566861 DOI: 10.1097/cce.0000000000000246] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Fraser DD, Slessarev M, Martin CM, Daley M, Patel MA, Miller MR, Patterson EK, O'Gorman DB, Gill SE, Wishart DS, Mandal R, Cepinskas G. Metabolomics Profiling of Critically Ill Coronavirus Disease 2019 Patients: Identification of Diagnostic and Prognostic Biomarkers. Crit Care Explor 2020; 2:e0272. [PMID: 33134953 PMCID: PMC7587450 DOI: 10.1097/cce.0000000000000272] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES Coronavirus disease 2019 continues to spread rapidly with high mortality. We performed metabolomics profiling of critically ill coronavirus disease 2019 patients to understand better the underlying pathologic processes and pathways, and to identify potential diagnostic/prognostic biomarkers. DESIGN Blood was collected at predetermined ICU days to measure the plasma concentrations of 162 metabolites using both direct injection-liquid chromatography-tandem mass spectrometry and proton nuclear magnetic resonance. SETTING Tertiary-care ICU and academic laboratory. SUBJECTS Patients admitted to the ICU suspected of being infected with severe acute respiratory syndrome coronavirus 2, using standardized hospital screening methodologies, had blood samples collected until either testing was confirmed negative on ICU day 3 (coronavirus disease 2019 negative) or until ICU day 10 if the patient tested positive (coronavirus disease 2019 positive). INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS Age- and sex-matched healthy controls and ICU patients that were either coronavirus disease 2019 positive or coronavirus disease 2019 negative were enrolled. Cohorts were well balanced with the exception that coronavirus disease 2019 positive patients suffered bilateral pneumonia more frequently than coronavirus disease 2019 negative patients. Mortality rate for coronavirus disease 2019 positive ICU patients was 40%. Feature selection identified the top-performing metabolites for identifying coronavirus disease 2019 positive patients from healthy control subjects and was dominated by increased kynurenine and decreased arginine, sarcosine, and lysophosphatidylcholines. Arginine/kynurenine ratio alone provided 100% classification accuracy between coronavirus disease 2019 positive patients and healthy control subjects (p = 0.0002). When comparing the metabolomes between coronavirus disease 2019 positive and coronavirus disease 2019 negative patients, kynurenine was the dominant metabolite and the arginine/kynurenine ratio provided 98% classification accuracy (p = 0.005). Feature selection identified creatinine as the top metabolite for predicting coronavirus disease 2019-associated mortality on both ICU days 1 and 3, and both creatinine and creatinine/arginine ratio accurately predicted coronavirus disease 2019-associated death with 100% accuracy (p = 0.01). CONCLUSIONS Metabolomics profiling with feature classification easily distinguished both healthy control subjects and coronavirus disease 2019 negative patients from coronavirus disease 2019 positive patients. Arginine/kynurenine ratio accurately identified coronavirus disease 2019 status, whereas creatinine/arginine ratio accurately predicted coronavirus disease 2019-associated death. Administration of tryptophan (kynurenine precursor), arginine, sarcosine, and/or lysophosphatidylcholines may be considered as potential adjunctive therapies.
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Affiliation(s)
- Douglas D Fraser
- Lawson Health Research Institute, London, ON, Canada
- Department of Pediatrics, Western University, London, ON, Canada
- Department of Clinical Neurological Sciences, Western University, London, ON, Canada
- Department of Physiology and Pharmacology, Western University, London, ON, Canada
| | - Marat Slessarev
- Lawson Health Research Institute, London, ON, Canada
- Department of Medicine, Western University, London, ON, Canada
| | - Claudio M Martin
- Lawson Health Research Institute, London, ON, Canada
- Department of Medicine, Western University, London, ON, Canada
| | - Mark Daley
- Lawson Health Research Institute, London, ON, Canada
- Department of Computer Science, Western University, London, ON, Canada
- Vector Institute for Artificial Intelligence, Toronto, ON, Canada
| | - Maitray A Patel
- Department of Computer Science, Western University, London, ON, Canada
| | - Michael R Miller
- Lawson Health Research Institute, London, ON, Canada
- Department of Pediatrics, Western University, London, ON, Canada
| | | | - David B O'Gorman
- Lawson Health Research Institute, London, ON, Canada
- Department of Surgery, Western University, London, ON, Canada
- Department of Biochemistry, Western University, London, ON, Canada
| | - Sean E Gill
- Lawson Health Research Institute, London, ON, Canada
- Department of Physiology and Pharmacology, Western University, London, ON, Canada
- Department of Medicine, Western University, London, ON, Canada
| | - David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- The Metabolomics Innovation Centre, Edmonton, AB, Canada
| | - Rupasri Mandal
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- The Metabolomics Innovation Centre, Edmonton, AB, Canada
| | - Gediminas Cepinskas
- Lawson Health Research Institute, London, ON, Canada
- Department of Medical Biophysics, Western University, London, ON, Canada
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Endothelial Injury and Glycocalyx Degradation in Critically Ill Coronavirus Disease 2019 Patients: Implications for Microvascular Platelet Aggregation. Crit Care Explor 2020; 2:e0194. [PMID: 32904031 PMCID: PMC7449254 DOI: 10.1097/cce.0000000000000194] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Objectives Coronavirus disease 2019 is caused by the novel severe acute respiratory syndrome coronavirus 2 virus. Patients admitted to the ICU suffer from microvascular thrombosis, which may contribute to mortality. Our aim was to profile plasma thrombotic factors and endothelial injury markers in critically ill coronavirus disease 2019 ICU patients to help understand their thrombotic mechanisms. Design Daily blood coagulation and thrombotic factor profiling with immunoassays and in vitro experiments on human pulmonary microvascular endothelial cells. Setting Tertiary care ICU and academic laboratory. Subjects All patients admitted to the ICU suspected of being infected with severe acute respiratory syndrome coronavirus 2, using standardized hospital screening methodologies, had daily blood samples collected until testing was confirmed coronavirus disease 2019 negative on either ICU day 3 or ICU day 7 if the patient was coronavirus disease 2019 positive. Interventions None. Measurement and Main Results Age- and sex-matched healthy control subjects and ICU patients that were either coronavirus disease 2019 positive or coronavirus disease 2019 negative were enrolled. Cohorts were well balanced with the exception that coronavirus disease 2019 positive patients were more likely than coronavirus disease 2019 negative patients to suffer bilateral pneumonia. Mortality rate for coronavirus disease 2019 positive ICU patients was 40%. Compared with healthy control subjects, coronavirus disease 2019 positive patients had higher plasma von Willebrand factor (p < 0.001) and glycocalyx-degradation products (chondroitin sulfate and syndecan-1; p < 0.01). When compared with coronavirus disease 2019 negative patients, coronavirus disease 2019 positive patients had persistently higher soluble P-selectin, hyaluronic acid, and syndecan-1 (p < 0.05), particularly on ICU day 3 and thereafter. Thrombosis profiling on ICU days 1-3 predicted coronavirus disease 2019 status with 85% accuracy and patient mortality with 86% accuracy. Surface hyaluronic acid removal from human pulmonary microvascular endothelial cells with hyaluronidase treatment resulted in depressed nitric oxide, an instigating mechanism for platelet adhesion to the microvascular endothelium. Conclusions Thrombosis profiling identified endothelial activation and glycocalyx degradation in coronavirus disease 2019 positive patients. Our data suggest that medications to protect and/or restore the endothelial glycocalyx, as well as platelet inhibitors, should be considered for further study.
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