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Alexovič M, Bondarchuk T, Uličná C, Sabo J. Blood proteomics of COVID-19 infection: An update. Clin Chim Acta 2024; 562:119881. [PMID: 39033952 DOI: 10.1016/j.cca.2024.119881] [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: 05/10/2024] [Revised: 07/15/2024] [Accepted: 07/17/2024] [Indexed: 07/23/2024]
Abstract
Despite significant progress in understanding SARS-CoV-2 and its impact, a deeper comprehension of the molecular changes in the host following infection is still lacking. Proteomic analysis of COVID-19 infected patients can provide valuable data about the events and mechanisms related to the initial, progression, and terminal stages of the disease. Such information can lead to better prevention, treatment, and convalescence strategies. In this review, we discuss blood proteomic studies based on mass spectrometry in COVID-19 patients. The analysis focuses on various blood components including plasma, platelets, serum, red blood cells, and peripheral blood mononuclear cells. Scientific papers published since 2022 are covered, with approaches categorised based on whether they use in-gel, in-solution, or on-beads/on-filter digestion modes. Additionally, candidate protein biomarkers related to COVID-19 are surveyed and discussed.
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Affiliation(s)
- Michal Alexovič
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P.J. Šafárik in Košice, 04011, Košice, Slovakia.
| | - Tetiana Bondarchuk
- Institute of Molecular Biology and Genetics of NAS of Ukraine, 03143, Kyiv, Ukraine
| | - Csilla Uličná
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P.J. Šafárik in Košice, 04011, Košice, Slovakia; University Library, University of Prešov, 08001, Prešov, Slovakia
| | - Ján Sabo
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P.J. Šafárik in Košice, 04011, Košice, Slovakia
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Zhao L, Bian W, Shang Y, Zhi H, Ma X, He Y, Yu W, Liu C, Xu Y, Gong P, Gao Z. Plasma proteome analysis and validation of patients with community-acquired pneumonia: A cohort study. Proteomics Clin Appl 2024; 18:e202300069. [PMID: 38332320 DOI: 10.1002/prca.202300069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 12/16/2023] [Accepted: 12/21/2023] [Indexed: 02/10/2024]
Abstract
PURPOSE This study aimed to investigate the diagnostic potential of plasma biomarkers of community-acquired pneumonia (CAP) and their severity grading. EXPERIMENTAL DESIGN Plasma proteomes from cohort I (n = 32) with CAP were analyzed by data-independent acquisition mass spectrometry (MS). MetaboAnalyst 5.0 was used to statistically evaluate significant differences in proteins from different samples, and demographic and clinical data were recorded for all enrolled patients. Cohort II (n = 80) was used to validate candidate biomarkers. Plasma protein levels were determined using quantitative enzyme-linked immunosorbent assay (ELISA). Correlations were assessed using Pearson's correlation coefficient. A receiver operating characteristic curve was used to verify the association between the variables, CAP diagnosis, and prognosis. RESULTS 121 differentially expressed proteins (DEPs) were obtained between CAP and controls. These DEPs were mainly aggregated in pathways of phagosome(hsa04145) and complement and coagulation cascades (hsa04610). No significant differential proteins were detected in bacterial, viral, and mixed infection groups. The plasma levels of fetuin-A, alpha-1-antichymotrypsin (AACT), α1-acid glycoprotein (A1AG), and S100A8/S100A9 heterodimers detected by ELISA were consistent with those of MS. AACT, A1AG, S100A8/S100A9 heterodimer, and fetuin-A can potentially be used as diagnostic predictors, and fetuin-A and AACT are potential predictors of SCAP. CONCLUSIONS AND CLINICAL RELEVANCE Plasma protein profiling can successfully identify potential biomarkers for CAP diagnosis and disease severity assessment. These biomarkers should be further studied for their clinical application.
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Affiliation(s)
- Lili Zhao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Wenjie Bian
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Ying Shang
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Hui Zhi
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Xinqian Ma
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Yukun He
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Wenyi Yu
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Chunyu Liu
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Yu Xu
- Department of Respiratory and Critical Care Medicine, Beijing Jishuitan Hospital, Beijing, China
| | - Pihua Gong
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Zhancheng Gao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
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Rosario-Rodríguez LJ, Cantres-Rosario YM, Carrasquillo-Carrión K, Rosa-Díaz A, Rodríguez-De Jesús AE, Rivera-Nieves V, Tosado-Rodríguez EL, Méndez LB, Roche-Lima A, Bertrán J, Meléndez LM. Plasma Proteins Associated with COVID-19 Severity in Puerto Rico. Int J Mol Sci 2024; 25:5426. [PMID: 38791465 PMCID: PMC11121485 DOI: 10.3390/ijms25105426] [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: 04/07/2024] [Revised: 05/10/2024] [Accepted: 05/12/2024] [Indexed: 05/26/2024] Open
Abstract
Viral strains, age, and host factors are associated with variable immune responses against SARS-CoV-2 and disease severity. Puerto Ricans have a genetic mixture of races: European, African, and Native American. We hypothesized that unique host proteins/pathways are associated with COVID-19 disease severity in Puerto Rico. Following IRB approval, a total of 95 unvaccinated men and women aged 21-71 years old were recruited in Puerto Rico from 2020-2021. Plasma samples were collected from COVID-19-positive subjects (n = 39) and COVID-19-negative individuals (n = 56) during acute disease. COVID-19-positive individuals were stratified based on symptomatology as follows: mild (n = 18), moderate (n = 13), and severe (n = 8). Quantitative proteomics was performed in plasma samples using tandem mass tag (TMT) labeling. Labeled peptides were subjected to LC/MS/MS and analyzed by Proteome Discoverer (version 2.5), Limma software (version 3.41.15), and Ingenuity Pathways Analysis (IPA, version 22.0.2). Cytokines were quantified using a human cytokine array. Proteomics analyses of severely affected COVID-19-positive individuals revealed 58 differentially expressed proteins. Cadherin-13, which participates in synaptogenesis, was downregulated in severe patients and validated by ELISA. Cytokine immunoassay showed that TNF-α levels decreased with disease severity. This study uncovers potential host predictors of COVID-19 severity and new avenues for treatment in Puerto Ricans.
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Affiliation(s)
- Lester J. Rosario-Rodríguez
- Department of Microbiology and Medical Zoology, University of Puerto Rico, Medical Sciences Campus, San Juan 00935, Puerto Rico;
| | - Yadira M. Cantres-Rosario
- Translational Proteomics Center, Research Capacity Core, Center for Collaborative Research in Health Disparities, University of Puerto Rico, Medical Sciences Campus, San Juan 00935, Puerto Rico; (Y.M.C.-R.); (A.E.R.-D.J.)
| | - Kelvin Carrasquillo-Carrión
- Integrated Informatics, Research Capacity Core, Center for Collaborative Research in Health Disparities, University of Puerto Rico, Medical Sciences Campus, San Juan 00935, Puerto Rico; (K.C.-C.); (E.L.T.-R.); (A.R.-L.)
| | - Alexandra Rosa-Díaz
- Interdisciplinary Studies, Natural Sciences, University of Puerto Rico, Río Piedras Campus, San Juan 00925, Puerto Rico; (A.R.-D.); (V.R.-N.)
| | - Ana E. Rodríguez-De Jesús
- Translational Proteomics Center, Research Capacity Core, Center for Collaborative Research in Health Disparities, University of Puerto Rico, Medical Sciences Campus, San Juan 00935, Puerto Rico; (Y.M.C.-R.); (A.E.R.-D.J.)
| | - Verónica Rivera-Nieves
- Interdisciplinary Studies, Natural Sciences, University of Puerto Rico, Río Piedras Campus, San Juan 00925, Puerto Rico; (A.R.-D.); (V.R.-N.)
| | - Eduardo L. Tosado-Rodríguez
- Integrated Informatics, Research Capacity Core, Center for Collaborative Research in Health Disparities, University of Puerto Rico, Medical Sciences Campus, San Juan 00935, Puerto Rico; (K.C.-C.); (E.L.T.-R.); (A.R.-L.)
| | - Loyda B. Méndez
- Department of Science & Technology, Ana G. Mendez University, Carolina 00928, Puerto Rico;
| | - Abiel Roche-Lima
- Integrated Informatics, Research Capacity Core, Center for Collaborative Research in Health Disparities, University of Puerto Rico, Medical Sciences Campus, San Juan 00935, Puerto Rico; (K.C.-C.); (E.L.T.-R.); (A.R.-L.)
| | - Jorge Bertrán
- Infectious Diseases, Auxilio Mutuo Hospital, San Juan 00919, Puerto Rico;
| | - Loyda M. Meléndez
- Department of Microbiology and Medical Zoology, University of Puerto Rico, Medical Sciences Campus, San Juan 00935, Puerto Rico;
- Translational Proteomics Center, Research Capacity Core, Center for Collaborative Research in Health Disparities, University of Puerto Rico, Medical Sciences Campus, San Juan 00935, Puerto Rico; (Y.M.C.-R.); (A.E.R.-D.J.)
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Luz IS, Takaya R, Ribeiro DG, Castro MS, Fontes W. Proteomics: Unraveling the Cross Talk Between Innate Immunity and Disease Pathophysiology, Diagnostics, and Treatment Options. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1443:221-242. [PMID: 38409424 DOI: 10.1007/978-3-031-50624-6_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Inflammation is crucial in diseases, and proteins play a key role in the interplay between innate immunity and pathology. This review explores how proteomics helps understanding this relationship, focusing on diagnosis and treatment. We explore the dynamic innate response and the significance of proteomic techniques in deciphering the complex network of proteins involved in prevalent diseases, including infections, cancer, autoimmune and neurodegenerative disorders. Proteomics identifies key proteins in host-pathogen interactions, shedding light on infection mechanisms and inflammation. These discoveries hold promise for diagnostic tools, therapies, and vaccines. In cancer research, proteomics reveals innate signatures associated with tumor development, immune evasion, and therapeutic response. Additionally, proteomic analysis has unveiled autoantigens and dysregulation of the innate immune system in autoimmunity, offering opportunities for early diagnosis, disease monitoring, and new therapeutic targets. Moreover, proteomic analysis has identified altered protein expression patterns in neurodegenerative diseases like Alzheimer's and Parkinson's, providing insights into potential therapeutic strategies. Proteomics of the innate immune system provides a comprehensive understanding of disease mechanisms, identifies biomarkers, and enables effective interventions in various diseases. Despite still in its early stages, this approach holds great promise to revolutionize innate immunity research and significantly improve patient outcomes across a wide range of diseases.
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Affiliation(s)
- Isabelle Souza Luz
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasília, Federal District, Brazil
| | - Raquel Takaya
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasília, Federal District, Brazil
| | - Daiane Gonzaga Ribeiro
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasília, Federal District, Brazil
| | - Mariana S Castro
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasília, Federal District, Brazil
| | - Wagner Fontes
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasília, Federal District, Brazil.
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