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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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Camelo ALM, Zamora Obando HR, Rocha I, Dias AC, Mesquita ADS, Simionato AVC. COVID-19 and Comorbidities: What Has Been Unveiled by Metabolomics? Metabolites 2024; 14:195. [PMID: 38668323 PMCID: PMC11051775 DOI: 10.3390/metabo14040195] [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: 01/18/2024] [Revised: 03/14/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
The COVID-19 pandemic has brought about diverse impacts on the global population. Individuals with comorbidities were more susceptible to the severe symptoms caused by the virus. Within the crisis scenario, metabolomics represents a potential area of science capable of providing relevant information for understanding the metabolic pathways associated with the intricate interaction between the viral disease and previous comorbidities. This work aims to provide a comprehensive description of the scientific production pertaining to metabolomics within the specific context of COVID-19 and comorbidities, while highlighting promising areas for exploration by those interested in the subject. In this review, we highlighted the studies of metabolomics that indicated a variety of metabolites associated with comorbidities and COVID-19. Furthermore, we observed that the understanding of the metabolic processes involved between comorbidities and COVID-19 is limited due to the urgent need to report disease outcomes in individuals with comorbidities. The overlap of two or more comorbidities associated with the severity of COVID-19 hinders the comprehension of the significance of each condition. Most identified studies are observational, with a restricted number of patients, due to challenges in sample collection amidst the emergent situation.
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Affiliation(s)
- André Luiz Melo Camelo
- Laboratory of Analysis of Biomolecules Tiselius, Department of Analytical Chemistry, Institute of Chemistry, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-970, São Paulo, Brazil; (A.L.M.C.); (H.R.Z.O.); (I.R.); (A.C.D.); (A.d.S.M.)
| | - Hans Rolando Zamora Obando
- Laboratory of Analysis of Biomolecules Tiselius, Department of Analytical Chemistry, Institute of Chemistry, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-970, São Paulo, Brazil; (A.L.M.C.); (H.R.Z.O.); (I.R.); (A.C.D.); (A.d.S.M.)
| | - Isabela Rocha
- Laboratory of Analysis of Biomolecules Tiselius, Department of Analytical Chemistry, Institute of Chemistry, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-970, São Paulo, Brazil; (A.L.M.C.); (H.R.Z.O.); (I.R.); (A.C.D.); (A.d.S.M.)
| | - Aline Cristina Dias
- Laboratory of Analysis of Biomolecules Tiselius, Department of Analytical Chemistry, Institute of Chemistry, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-970, São Paulo, Brazil; (A.L.M.C.); (H.R.Z.O.); (I.R.); (A.C.D.); (A.d.S.M.)
| | - Alessandra de Sousa Mesquita
- Laboratory of Analysis of Biomolecules Tiselius, Department of Analytical Chemistry, Institute of Chemistry, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-970, São Paulo, Brazil; (A.L.M.C.); (H.R.Z.O.); (I.R.); (A.C.D.); (A.d.S.M.)
| | - Ana Valéria Colnaghi Simionato
- Laboratory of Analysis of Biomolecules Tiselius, Department of Analytical Chemistry, Institute of Chemistry, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-970, São Paulo, Brazil; (A.L.M.C.); (H.R.Z.O.); (I.R.); (A.C.D.); (A.d.S.M.)
- National Institute of Science and Technology for Bioanalytics—INCTBio, Institute of Chemistry, Universidade Estadual de (UNICAMP), Campinas 13083-970, São Paulo, Brazil
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Ahmed FF, Das AD, Sumi MJ, Islam MZ, Rahman MS, Rashid MH, Alyami SA, Alotaibi N, Azad AKM, Moni MA. Identification of genetic biomarkers, drug targets and agents for respiratory diseases utilising integrated bioinformatics approaches. Sci Rep 2023; 13:19072. [PMID: 37925496 PMCID: PMC10625598 DOI: 10.1038/s41598-023-46455-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 11/01/2023] [Indexed: 11/06/2023] Open
Abstract
Respiratory diseases (RD) are significant public health burdens and malignant diseases worldwide. However, the RD-related biological information and interconnection still need to be better understood. Thus, this study aims to detect common differential genes and potential hub genes (HubGs), emphasizing their actions, signaling pathways, regulatory biomarkers for diagnosing RD and candidate drugs for treating RD. In this paper we used integrated bioinformatics approaches (such as, gene ontology (GO) and KEGG pathway enrichment analysis, molecular docking, molecular dynamic simulation and network-based molecular interaction analysis). We discovered 73 common DEGs (CDEGs) and ten HubGs (ATAD2B, PPP1CB, FOXO1, AKT3, BCR, PDE4D, ITGB1, PCBP2, CD44 and SMARCA2). Several significant functions and signaling pathways were strongly related to RD. We recognized six transcription factor (TF) proteins (FOXC1, GATA2, FOXL1, YY1, POU2F2 and HINFP) and five microRNAs (hsa-mir-218-5p, hsa-mir-335-5p, hsa-mir-16-5p, hsa-mir-106b-5p and hsa-mir-15b-5p) as the important transcription and post-transcription regulators of RD. Ten HubGs and six major TF proteins were considered drug-specific receptors. Their binding energy analysis study was carried out with the 63 drug agents detected from network analysis. Finally, the five complexes (the PDE4D-benzo[a]pyrene, SMARCA2-benzo[a]pyrene, HINFP-benzo[a]pyrene, CD44-ketotifen and ATAD2B-ponatinib) were selected for RD based on their strong binding affinity scores and stable performance as the most probable repurposable protein-drug complexes. We believe our findings will give readers, wet-lab scientists, and pharmaceuticals a thorough grasp of the biology behind RD.
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Affiliation(s)
- Fee Faysal Ahmed
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.
| | - Arnob Dip Das
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Mst Joynab Sumi
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md Zohurul Islam
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
- High Performance Computing (HPC) Laboratory, Department of Mathematics, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
- Bioinformatics and Microbial Biotechnology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md Harun Rashid
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Salem A Alyami
- Department of Mathematics and Statistics, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), 13318, Riyadh, Saudi Arabia
| | - Naif Alotaibi
- Department of Mathematics and Statistics, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), 13318, Riyadh, Saudi Arabia
| | - A K M Azad
- Department of Mathematics and Statistics, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), 13318, Riyadh, Saudi Arabia
| | - Mohammad Ali Moni
- Artificial Intelligence and Data Science, School of Health and Rehabilitation Sciences, Faculty of Health and Behavioural Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
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Cai X, Yang R, Shi W, Cai Y, Ma Z. Exploration of the common pathogenic link between COVID-19 and diabetic foot ulcers: An in silico approach. Health Sci Rep 2023; 6:e1686. [PMID: 37936615 PMCID: PMC10626003 DOI: 10.1002/hsr2.1686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/09/2023] [Accepted: 10/23/2023] [Indexed: 11/09/2023] Open
Abstract
Background and Aims The Coronavirus Disease-19 (COVID-19) is posing an ongoing threat to human health. Patients of diabetic foot ulcer (DFU) are susceptible to COVID-19-induced adverse outcomes. Nevertheless, investigations into their mutual molecular mechanisms have been limited to date. In the present work, we tried to uncover the shared pathogenesis and regulatory gene targets of COVID-19 and DFU. Methods In this study, we chose GSE161281 as the COVID-19 data set, which contained severe acute respiratory syndrome coronavirus 2 infected human induced embryonic stem cell-derived peripheral neurons (n = 2) with uninfected controls (n = 2). The GSE134431 designated as the DFU data set, comprising full-thickness DFU (n = 13) and diabetic foot skin (n = 8) samples from diabetic patients. The differential expressed genes (DEGs) were identified from GSE161281 and GSE134431, and the common DEGs between COVID-19 and DFU were extracted. Multifactor regulatory network and co-expression network of the common DEGs were analyzed, along with candidate drug prediction. Results Altogether, six common DEGs (dickkopf-related protein 1 [DKK1], serine proteinase inhibitor A3 [SERPINA3], ras homolog family member D [RHOD], myelin protein zero like 3 [MPZL3], Claudin-11 [CLDN11], and epidermal growth factor receptor pathway substrate 8-like 1 [EPS8L1]) were found between COVID-19 and DFU. Functional analyses indicated that pathways of apoptotic and Wnt signaling may contribute to progression of COVID-19. Gene co-expression network implied the shared pathways of immune regulation and cytokine response participated collectively in the development of DFU and COVID-19. A multifactor regulatory network was constructed integrating the corresponding microRNAs (miRNAs) and transcription factors. Additionally, we proposed potential drug objects for the combined therapy. Conclusion Our study revealed the shared molecular mechanisms underlying COVID-19 and DFU. The identified pivotal targets and common pathways can provide new perspectives for further research and assist the development of management strategies in patients of DFU complicated with COVID-19.
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Affiliation(s)
- Xueyao Cai
- Department of Burn and Plastic SurgeryDongguan Tungwah HospitalDongguanChina
| | - Ruijin Yang
- Department of Burn and Plastic SurgeryDongguan Tungwah HospitalDongguanChina
| | - Wenjun Shi
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yuchen Cai
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Zhengzheng Ma
- Department of Burn and Plastic SurgeryDongguan Tungwah HospitalDongguanChina
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Hanson BA, Visvabharathy L, Orban ZS, Jimenez M, Batra A, Liotta EM, DeLisle RK, Klausner JD, Cohen P, Padhye AS, Tachas G, Koralnik IJ. Plasma proteomics show altered inflammatory and mitochondrial proteins in patients with neurologic symptoms of post-acute sequelae of SARS-CoV-2 infection. Brain Behav Immun 2023; 114:462-474. [PMID: 37704012 PMCID: PMC10718560 DOI: 10.1016/j.bbi.2023.08.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/17/2023] [Accepted: 08/26/2023] [Indexed: 09/15/2023] Open
Abstract
Persistent symptoms of COVID-19 survivors constitute long COVID syndrome, also called post-acute sequelae of SARS-CoV-2 infection (PASC). Neurologic manifestations of PASC (Neuro-PASC) are particularly debilitating, long lasting, and poorly understood. To gain insight into the pathogenesis of PASC, we leveraged a well-characterized group of Neuro-PASC (NP) patients seen at our Neuro-COVID-19 clinic who had mild acute COVID-19 and never required hospitalization to investigate their plasma proteome. Using the SomaLogic platform, SomaScan, the plasma concentration of >7000 proteins was measured from 92 unvaccinated individuals, including 48 NP patients, 20 COVID-19 convalescents (CC) without lingering symptoms, and 24 unexposed healthy controls (HC) to interrogate underlying pathobiology and potential biomarkers of PASC. We analyzed the plasma proteome based on post-COVID-19 status, neurologic and non-neurologic symptoms, as well as subjective and objective standardized tests for changes in quality-of-life (QoL) and cognition associated with Neuro-PASC. The plasma proteome of NP patients differed from CC and HC subjects more substantially than post-COVID-19 groups (NP and CC combined) differed from HC. Proteomic differences in NP patients 3-9 months following acute COVID-19 showed alterations in inflammatory proteins and pathways relative to CC and HC subjects. Proteomic associations with Neuro-PASC symptoms of brain fog and fatigue included changes in markers of DNA repair, oxidative stress, and neutrophil degranulation. Furthermore, we discovered a correlation between NP patients lower subjective impression of recovery to pre-COVID-19 baseline with an increase in the concentration of the oxidative phosphorylation protein COX7A1, which was also associated with neurologic symptoms and fatigue, as well as impairment in QoL and cognitive dysfunction. Finally, we identified other oxidative phosphorylation-associated proteins correlating with central nervous system symptoms. Our results suggest ongoing inflammatory changes and mitochondrial involvement in Neuro-PASC and pave the way for biomarker validation for use in monitoring and development of therapeutic intervention for this debilitating condition.
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Affiliation(s)
- Barbara A Hanson
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Lavanya Visvabharathy
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Zachary S Orban
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Millenia Jimenez
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ayush Batra
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Eric M Liotta
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | | | - Jeffrey D Klausner
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Pinchas Cohen
- The Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | | | - George Tachas
- Antisense Therapeutics Limited, Toorak, Victoria, Australia
| | - Igor J Koralnik
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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Halder A, Biswas D, Chauhan A, Saha A, Auromahima S, Yadav D, Nissa MU, Iyer G, Parihari S, Sharma G, Epari S, Shetty P, Moiyadi A, Ball GR, Srivastava S. A large-scale targeted proteomics of serum and tissue shows the utility of classifying high grade and low grade meningioma tumors. Clin Proteomics 2023; 20:41. [PMID: 37770851 PMCID: PMC10540342 DOI: 10.1186/s12014-023-09426-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/21/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND Meningiomas are the most prevalent primary brain tumors. Due to their increasing burden on healthcare, meningiomas have become a pivot of translational research globally. Despite many studies in the field of discovery proteomics, the identification of grade-specific markers for meningioma is still a paradox and requires thorough investigation. The potential of the reported markers in different studies needs further verification in large and independent sample cohorts to identify the best set of markers with a better clinical perspective. METHODS A total of 53 fresh frozen tumor tissue and 51 serum samples were acquired from meningioma patients respectively along with healthy controls, to validate the prospect of reported differentially expressed proteins and claimed markers of Meningioma mined from numerous manuscripts and knowledgebases. A small subset of Glioma/Glioblastoma samples were also included to investigate inter-tumor segregation. Furthermore, a simple Machine Learning (ML) based analysis was performed to evaluate the classification accuracy of the list of proteins. RESULTS A list of 15 proteins from tissue and 12 proteins from serum were found to be the best segregator using a feature selection-based machine learning strategy with an accuracy of around 80% in predicting low grade (WHO grade I) and high grade (WHO grade II and WHO grade III) meningiomas. In addition, the discriminant analysis could also unveil the complexity of meningioma grading from a segregation pattern, which leads to the understanding of transition phases between the grades. CONCLUSIONS The identified list of validated markers could play an instrumental role in the classification of meningioma as well as provide novel clinical perspectives in regard to prognosis and therapeutic targets.
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Affiliation(s)
- Ankit Halder
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Deeptarup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Aparna Chauhan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Adrita Saha
- Motilal Nehru National Institute of Technology, Allahabad, 211004, UP, India
| | - Shreeman Auromahima
- Department of Bioscience & Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Deeksha Yadav
- CSIR-Institute of Genomics and Integrative Biology, Sukhdev Vihar, New Delhi, 110025, India
| | - Mehar Un Nissa
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - Gayatri Iyer
- Koita Centre for Digital Health, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Shashwati Parihari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Gautam Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Sridhar Epari
- Department of Pathology, Tata Memorial Centre, Mumbai, India
| | - Prakash Shetty
- Department of Neurosurgery, Tata Memorial Centre, Mumbai, India
| | | | - Graham Roy Ball
- Medical Technology Research Centre, Anglia Ruskin University, Cambridge Campus, East Rd, Cambridge, CB1 1PT, UK
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 185 Berry St., Suite 290, San Francisco, CA, 94107, USA.
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Babačić H, Christ W, Araújo JE, Mermelekas G, Sharma N, Tynell J, García M, Varnaite R, Asgeirsson H, Glans H, Lehtiö J, Gredmark-Russ S, Klingström J, Pernemalm M. Comprehensive proteomics and meta-analysis of COVID-19 host response. Nat Commun 2023; 14:5921. [PMID: 37739942 PMCID: PMC10516886 DOI: 10.1038/s41467-023-41159-z] [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: 11/09/2022] [Accepted: 08/24/2023] [Indexed: 09/24/2023] Open
Abstract
COVID-19 is characterised by systemic immunological perturbations in the human body, which can lead to multi-organ damage. Many of these processes are considered to be mediated by the blood. Therefore, to better understand the systemic host response to SARS-CoV-2 infection, we performed systematic analyses of the circulating, soluble proteins in the blood through global proteomics by mass-spectrometry (MS) proteomics. Here, we show that a large part of the soluble blood proteome is altered in COVID-19, among them elevated levels of interferon-induced and proteasomal proteins. Some proteins that have alternating levels in human cells after a SARS-CoV-2 infection in vitro and in different organs of COVID-19 patients are deregulated in the blood, suggesting shared infection-related changes.The availability of different public proteomic resources on soluble blood proteome alterations leaves uncertainty about the change of a given protein during COVID-19. Hence, we performed a systematic review and meta-analysis of MS global proteomics studies of soluble blood proteomes, including up to 1706 individuals (1039 COVID-19 patients), to provide concluding estimates for the alteration of 1517 soluble blood proteins in COVID-19. Finally, based on the meta-analysis we developed CoViMAPP, an open-access resource for effect sizes of alterations and diagnostic potential of soluble blood proteins in COVID-19, which is publicly available for the research, clinical, and academic community.
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Affiliation(s)
- Haris Babačić
- Science for Life Laboratory and Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden.
| | - Wanda Christ
- Centre for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - José Eduardo Araújo
- Science for Life Laboratory and Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Georgios Mermelekas
- Science for Life Laboratory and Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Nidhi Sharma
- Science for Life Laboratory and Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Janne Tynell
- Centre for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Marina García
- Centre for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Renata Varnaite
- Centre for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Hilmir Asgeirsson
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Hedvig Glans
- Centre for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Janne Lehtiö
- Science for Life Laboratory and Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Sara Gredmark-Russ
- Centre for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå, Sweden
| | - Jonas Klingström
- Centre for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
- Division of Molecular Medicine and Virology (MMV), Department of Biomedical and Clinical Sciences (BKV), Linköping University, Linköping, Sweden
| | - Maria Pernemalm
- Science for Life Laboratory and Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden.
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8
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Zhang F, Luna A, Tan T, Chen Y, Sander C, Guo T. COVIDpro: Database for Mining Protein Dysregulation in Patients with COVID-19. J Proteome Res 2023; 22:2847-2859. [PMID: 37555633 DOI: 10.1021/acs.jproteome.3c00092] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
The ongoing pandemic of the coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 still has limited treatment options. Our understanding of the molecular dysregulations that occur in response to infection remains incomplete. We developed a web application COVIDpro (https://www.guomics.com/covidPro/) that includes proteomics data obtained from 41 original studies conducted in 32 hospitals worldwide, involving 3077 patients and covering 19 types of clinical specimens, predominantly plasma and serum. The data set encompasses 53 protein expression matrices, comprising a total of 5434 samples and 14,403 unique proteins. We identified a panel of proteins that exhibit significant dysregulation, enabling the classification of COVID-19 patients into severe and non-severe disease categories. The proteomic signatures achieved promising results in distinguishing severe cases, with a mean area under the curve of 0.87 and accuracy of 0.80 across five independent test sets. COVIDpro serves as a valuable resource for testing hypotheses and exploring potential targets for novel treatments in COVID-19 patients.
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Affiliation(s)
- Fangfei Zhang
- Fudan University, 220 Handan Road, Shanghai 200433, China
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province 310024, China
- Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang 310030, China
| | - Augustin Luna
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Broad Institute of MIT and Harvard, Cambridge, Cambridge, Massachusetts 02142, United States
| | - Tingting Tan
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province 310024, China
- Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang 310030, China
| | - Yingdan Chen
- Westlake Omics (Hangzhou) Biotechnology Company Limited, Hangzhou, Zhejiang Province 310024, China
| | - Chris Sander
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Broad Institute of MIT and Harvard, Cambridge, Cambridge, Massachusetts 02142, United States
| | - Tiannan Guo
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province 310024, China
- Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang 310030, China
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Wolny M, Rozanova S, Knabbe C, Pfeiffer K, Barkovits K, Marcus K, Birschmann I. Changes in the Proteome of Platelets from Patients with Critical Progression of COVID-19. Cells 2023; 12:2191. [PMID: 37681923 PMCID: PMC10486756 DOI: 10.3390/cells12172191] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/09/2023] Open
Abstract
Platelets, the smallest cells in human blood, known for their role in primary hemostasis, are also able to interact with pathogens and play a crucial role in the immune response. In severe coronavirus disease 2019 (COVID-19) cases, platelets become overactivated, resulting in the release of granules, exacerbating inflammation and contributing to the cytokine storm. This study aims to further elucidate the role of platelets in COVID-19 progression and to identify predictive biomarkers for disease outcomes. A comparative proteome analysis of highly purified platelets from critically diseased COVID-19 patients with different outcomes (survivors and non-survivors) and age- and sex-matched controls was performed. Platelets from critically diseased COVID-19 patients exhibited significant changes in the levels of proteins associated with protein folding. In addition, a number of proteins with isomerase activity were found to be more highly abundant in patient samples, apparently exerting an influence on platelet activity via the non-genomic properties of the glucocorticoid receptor (GR) and the nuclear factor κ-light-chain-enhancer of activated B cells (NFκB). Moreover, carbonic anhydrase 1 (CA-1) was found to be a candidate biomarker in platelets, showing a significant increase in COVID-19 patients.
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Affiliation(s)
- Monika Wolny
- Institut für Laboratoriums- und Transfusionsmedizin, Herz- und Diabeteszentrum NRW, Universitätsklinik der Ruhr-Universität Bochum, 32545 Bad Oeynhausen, Germany
| | - Svitlana Rozanova
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany
- Medical Proteome Analysis, Center for Protein Diagnostics (ProDi), Ruhr-University Bochum, 44801 Bochum, Germany
| | - Cornelius Knabbe
- Institut für Laboratoriums- und Transfusionsmedizin, Herz- und Diabeteszentrum NRW, Universitätsklinik der Ruhr-Universität Bochum, 32545 Bad Oeynhausen, Germany
| | - Kathy Pfeiffer
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany
- Medical Proteome Analysis, Center for Protein Diagnostics (ProDi), Ruhr-University Bochum, 44801 Bochum, Germany
| | - Katalin Barkovits
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany
- Medical Proteome Analysis, Center for Protein Diagnostics (ProDi), Ruhr-University Bochum, 44801 Bochum, Germany
| | - Katrin Marcus
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany
- Medical Proteome Analysis, Center for Protein Diagnostics (ProDi), Ruhr-University Bochum, 44801 Bochum, Germany
| | - Ingvild Birschmann
- Institut für Laboratoriums- und Transfusionsmedizin, Herz- und Diabeteszentrum NRW, Universitätsklinik der Ruhr-Universität Bochum, 32545 Bad Oeynhausen, Germany
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10
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di Flora DC, Dionizio A, Pereira HABS, Garbieri TF, Grizzo LT, Dionisio TJ, Leite ADL, Silva-Costa LC, Buzalaf NR, Reis FN, Pereira VBR, Rosa DMC, Dos Santos CF, Buzalaf MAR. Analysis of Plasma Proteins Involved in Inflammation, Immune Response/Complement System, and Blood Coagulation upon Admission of COVID-19 Patients to Hospital May Help to Predict the Prognosis of the Disease. Cells 2023; 12:1601. [PMID: 37371071 DOI: 10.3390/cells12121601] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
The development of new approaches allowing for the early assessment of COVID-19 cases that are likely to become critical and the discovery of new therapeutic targets are urgently required. In this prospective cohort study, we performed proteomic and laboratory profiling of plasma from 163 COVID-19 patients admitted to Bauru State Hospital (Brazil) between 4 May 2020 and 4 July 2020. Plasma samples were collected upon admission for routine laboratory analyses and shotgun quantitative label-free proteomics. Based on the course of the disease, the patients were divided into three groups: (a) mild (n = 76) and (b) severe (n = 56) symptoms, whose patients were discharged without or with admission to an intensive care unit (ICU), respectively, and (c) critical (n = 31), a group consisting of patients who died after admission to an ICU. Based on our data, potential therapies for COVID-19 should target proteins involved in inflammation, the immune response and complement system, and blood coagulation. Other proteins that could potentially be employed in therapies against COVID-19 but that so far have not been associated with the disease are CD5L, VDBP, A1BG, C4BPA, PGLYRP2, SERPINC1, and APOH. Targeting these proteins' pathways might constitute potential new therapies or biomarkers of prognosis of the disease.
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Affiliation(s)
- Daniele Castro di Flora
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru 17012-901, Brazil
- Therapy and Diagnosis Unit, Bauru State Hospital, Bauru 17033-360, Brazil
| | - Aline Dionizio
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru 17012-901, Brazil
| | | | - Thais Francini Garbieri
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru 17012-901, Brazil
| | - Larissa Tercilia Grizzo
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru 17012-901, Brazil
| | - Thiago José Dionisio
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru 17012-901, Brazil
| | - Aline de Lima Leite
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68503, USA
| | - Licia C Silva-Costa
- Laboratory of Neuroproteomics, Institute of Biology, Department of Biochemistry and Tissue Biology, University of Campinas, Campinas 13083-862, Brazil
| | - Nathalia Rabelo Buzalaf
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru 17012-901, Brazil
| | - Fernanda Navas Reis
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru 17012-901, Brazil
| | | | | | - Carlos Ferreira Dos Santos
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru 17012-901, Brazil
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11
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Rajoria S, Halder A, Tarnekar I, Pal P, Bansal P, Srivastava S. Detection of Mutant Peptides of SARS-CoV-2 Variants by LC/MS in the DDA Approach Using an In-House Database. J Proteome Res 2023; 22:1816-1827. [PMID: 37093804 PMCID: PMC10152398 DOI: 10.1021/acs.jproteome.2c00819] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Indexed: 04/25/2023]
Abstract
Equipped with a dramatically high mutation rate, which happens to be a signature of RNA viruses, SARS-CoV-2 trampled across the globe infecting individuals of all ages and ethnicities. As the variants of concern (VOC) loomed large, definitive detection of SARS-CoV-2 strains became a matter of utmost importance in epidemiological and clinical research. Besides, unveiling the disease pathogenesis at the molecular level and deciphering the therapeutic targets became key priorities since the emergence of the pandemic. Mass spectrometry has been largely used in this regard. A critical part of mass spectrometric analyses is the proteome database required for the identification of peptides. Presently, the mutational information on proteins available on SARS-CoV-2 databases cannot be used to analyze data extracted from mass spectrometers. Hence, we developed the novel Mutant Peptide Database (MPD) for the mass spectrometry (MS)-based identification of mutated peptides, which contains information from 11 proteins of SARS-CoV-2 from a total of 21,549 SARS-CoV-2 variants across different regions of India. The database was validated using clinical samples, and its applicability was also demonstrated with the mutated peptides extracted from the literature. We believe that MPD will support broad-spectrum MS-based studies like viral detection, disease pathogenesis, and therapeutics with respect to SARS-CoV-2 and its variants.
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Affiliation(s)
- Sakshi Rajoria
- Department of Biosciences and Bioengineering,
Indian Institute of Technology Bombay, Mumbai 400076,
India
| | - Ankit Halder
- Department of Biosciences and Bioengineering,
Indian Institute of Technology Bombay, Mumbai 400076,
India
| | - Ishita Tarnekar
- Thadomal Shahani Engineering
College, P.G. Kher Marg T.P.S III, Bandra West, Mumbai 400050,
India
| | - Pracheta Pal
- Department of Life Sciences, Presidency
University, 86/1 College Street, Kolkata 700073, West Bengal,
India
| | - Prakhar Bansal
- Department of Electrical Engineering,
Indian Institute of Technology Bombay, Mumbai 400076,
India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering,
Indian Institute of Technology Bombay, Mumbai 400076,
India
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12
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Siegel PM, Barta BA, Orlean L, Steenbuck ID, Cosenza-Contreras M, Wengenmayer T, Trummer G, Wolf D, Westermann D, Schilling O, Diehl P. The serum proteome of VA-ECMO patients changes over time and allows differentiation of survivors and non-survivors: an observational study. J Transl Med 2023; 21:319. [PMID: 37173738 PMCID: PMC10176307 DOI: 10.1186/s12967-023-04174-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/30/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Veno-arterial extracorporeal membrane oxygenation (VA-ECMO) is applied in patients with refractory hemodynamic failure. Exposure of blood components to high shear stress and the large extracorporeal surfaces in the ECMO circuit trigger a complex inflammatory response syndrome and coagulopathy which are believed to worsen the already poor prognosis of these patients. Mass spectrometry-based proteomics allow a detailed characterization of the serum proteome as it provides the identity and concentration of large numbers of individual proteins at the same time. In this study, we aimed to characterize the serum proteome of patients receiving VA-ECMO. METHODS Serum samples were collected on day 1 and day 3 after initiation of VA-ECMO. Samples underwent immunoaffinity based depletion for the 14 most abundant serum proteins, in-solution digestion and PreOmics clean-up. A spectral library was built with multiple measurements of a master-mix sample using variable mass windows. Individual samples were measured in data independent acquisition (DIA) mode. Raw files were analyzed by DIA-neural network. Unique proteins were log transformed and quantile normalized. Differential expression analysis was conducted with the LIMMA-R package. ROAST was applied to generate gene ontology enrichment analyses. RESULTS Fourteen VA-ECMO patients and six healthy controls were recruited. Seven patients survived. Three hundred and fifty-one unique proteins were identified. One hundred and thirty-seven proteins were differentially expressed between VA-ECMO patients and controls. One hundred and forty-five proteins were differentially expressed on day 3 compared to day 1. Many of the differentially expressed proteins were involved in coagulation and the inflammatory response. The serum proteomes of survivors and non-survivors on day 3 differed from each other according to partial least-squares discriminant analysis (PLS-DA) and 48 proteins were differentially expressed. Many of these proteins have also been ascribed to processes in coagulation and inflammation (e.g., Factor IX, Protein-C, Kallikrein, SERPINA10, SEMA4B, Complement C3, Complement Factor D and MASP-1). CONCLUSION The serum proteome of VA-ECMO patients displays major changes compared to controls and changes from day 1 until day 3. Many changes in the serum proteome are related to inflammation and coagulation. Survivors and non-survivors can be differentiated according to their serum proteomes using PLS-DA analysis on day 3. Our results build the basis for future studies using mass-spectrometry based serum proteomics as a tool to identify novel prognostic biomarkers. TRIAL REGISTRATION DRKS00011106.
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Affiliation(s)
- Patrick Malcolm Siegel
- Department of Cardiology and Angiology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Bálint András Barta
- Institute for Surgical Pathology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lukas Orlean
- Department of Cardiology and Angiology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ines Derya Steenbuck
- Department of Cardiology and Angiology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Institute for Surgical Pathology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Miguel Cosenza-Contreras
- Institute for Surgical Pathology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tobias Wengenmayer
- Interdisciplinary Medical Intensive Care (IMIT), Medical Center, University of Freiburg, Freiburg, Germany
| | - Georg Trummer
- Department of Cardiovascular Surgery, Medical Center, University of Freiburg, Freiburg, Germany
| | - Dennis Wolf
- Department of Cardiology and Angiology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dirk Westermann
- Department of Cardiology and Angiology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Oliver Schilling
- Institute for Surgical Pathology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Philipp Diehl
- Department of Cardiology and Angiology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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13
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Challenges and Opportunities in Clinical Diagnostic Routine of Envenomation Using Blood Plasma Proteomics. Toxins (Basel) 2023; 15:toxins15030180. [PMID: 36977071 PMCID: PMC10056359 DOI: 10.3390/toxins15030180] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 03/02/2023] Open
Abstract
Specific and sensitive tools for the diagnosis and monitoring of accidents by venomous animals are urgently needed. Several diagnostic and monitoring assays have been developed; however, they have not yet reached the clinic. This has resulted in late diagnoses, which represents one of the main causes of progression from mild to severe disease. Human blood is a protein-rich biological fluid that is routinely collected in hospital settings for diagnostic purposes, which can translate research progress from the laboratory to the clinic. Although it is a limited view, blood plasma proteins provide information about the clinical picture of envenomation. Proteome disturbances in response to envenomation by venomous animals have been identified, allowing mass spectrometry (MS)-based plasma proteomics to emerge as a tool in a range of clinical diagnostics and disease management that can be applied to cases of venomous animal envenomation. Here, we provide a review of the state of the art on routine laboratory diagnoses of envenomation by snakes, scorpions, bees, and spiders, as well as a review of the diagnostic methods and the challenges encountered. We present the state of the art on clinical proteomics as the standardization of procedures to be performed within and between research laboratories, favoring a more excellent peptide coverage of candidate proteins for biomarkers. Therefore, the selection of a sample type and method of preparation should be very specific and based on the discovery of biomarkers in specific approaches. However, the sample collection protocol (e.g., collection tube type) and the processing procedure of the sample (e.g., clotting temperature, time allowed for clotting, and anticoagulant used) are equally important to eliminate any bias.
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14
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Acharjee A, Ray A, Salkar A, Bihani S, Tuckley C, Shastri J, Agrawal S, Duttagupta S, Srivastava S. Humoral Immune Response Profile of COVID-19 Reveals Severity and Variant-Specific Epitopes: Lessons from SARS-CoV-2 Peptide Microarray. Viruses 2023; 15:248. [PMID: 36680289 PMCID: PMC9866125 DOI: 10.3390/v15010248] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/12/2023] [Accepted: 01/14/2023] [Indexed: 01/18/2023] Open
Abstract
The amaranthine scale of the COVID-19 pandemic and unpredictable disease severity is of grave concern. Serological diagnostic aids are an excellent choice for clinicians for rapid and easy prognosis of the disease. To this end, we studied the humoral immune response to SARS-CoV-2 infection to map immunogenic regions in the SARS-CoV-2 proteome at amino acid resolution using a high-density SARS-CoV-2 proteome peptide microarray. The microarray has 4932 overlapping peptides printed in duplicates spanning the entire SARS-CoV-2 proteome. We found 204 and 676 immunogenic peptides against IgA and IgG, corresponding to 137 and 412 IgA and IgG epitopes, respectively. Of these, 6 and 307 epitopes could discriminate between disease severity. The emergence of variants has added to the complexity of the disease. Using the mutation panel available, we could detect 5 and 10 immunogenic peptides against IgA and IgG with mutations belonging to SAR-CoV-2 variants. The study revealed severity-based epitopes that could be presented as potential prognostic serological markers. Further, the mutant epitope immunogenicity could indicate the putative use of these markers for diagnosing variants responsible for the infection.
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Affiliation(s)
- Arup Acharjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Arka Ray
- Centre for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Akanksha Salkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Surbhi Bihani
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Chaitanya Tuckley
- Centre for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai 400076, India
| | | | - Sachee Agrawal
- Kasturba Hospital for Infectious Diseases, Mumbai 400011, India
| | - Siddhartha Duttagupta
- Department of Electrical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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15
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SERPINA3: Stimulator or Inhibitor of Pathological Changes. Biomedicines 2023; 11:biomedicines11010156. [PMID: 36672665 PMCID: PMC9856089 DOI: 10.3390/biomedicines11010156] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
SERPINA3, also called α-1-antichymotrypsin (AACT, ACT), is one of the inhibitors of serine proteases, one of which is cathepsin G. As an acute-phase protein secreted into the plasma by liver cells, it plays an important role in the anti-inflammatory response and antiviral response. Elevated levels of SERPINA3 have been observed in heart failure and neurological diseases such as Alzheimer's disease or Creutzfeldt-Jakob disease. Many studies have shown increased expression levels of the SERPINA3 gene in various types of cancer, such as glioblastoma, colorectal cancer, endometrial cancer, breast cancer, or melanoma. In this case, the SERPINA3 protein is associated with an antiapoptotic function implemented by adjusting the PI3K/AKT or MAPK/ERK 1/2 signal pathways. However, the functions of the SERPINA3 protein are still only partially understood, mainly in the context of cancerogenesis, so it seems necessary to summarize the available information and describe its mechanism of action. In particular, we sought to amass the existing body of research focusing on the description of the underlying mechanisms of various diseases not related to cancer. Our goal was to present an overview of the correct function of SERPINA3 as part of the defense system, which unfortunately easily becomes the "Fifth Column" and begins to support processes of destruction.
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16
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Ranathunge C, Patel SS, Pinky L, Correll VL, Chen S, Semmes OJ, Armstrong RK, Combs CD, Nyalwidhe JO. promor: a comprehensive R package for label-free proteomics data analysis and predictive modeling. BIOINFORMATICS ADVANCES 2023; 3:vbad025. [PMID: 36922981 PMCID: PMC10010602 DOI: 10.1093/bioadv/vbad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 02/22/2023] [Accepted: 03/06/2023] [Indexed: 03/09/2023]
Abstract
Summary We present promor, a comprehensive, user-friendly R package that streamlines label-free quantification proteomics data analysis and building machine learning-based predictive models with top protein candidates. Availability and implementation promor is freely available as an open source R package on the Comprehensive R Archive Network (CRAN) (https://CRAN.R-project.org/package=promor) and distributed under the Lesser General Public License (version 2.1 or later). Development version of promor is maintained on GitHub (https://github.com/caranathunge/promor) and additional documentation and tutorials are provided on the package website (https://caranathunge.github.io/promor/). Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Chathurani Ranathunge
- Eastern Virginia Medical School, School of Health Professions, Norfolk, VA 23501, USA
| | - Sagar S Patel
- Eastern Virginia Medical School, School of Health Professions, Norfolk, VA 23501, USA
| | - Lubna Pinky
- Eastern Virginia Medical School, School of Health Professions, Norfolk, VA 23501, USA
| | - Vanessa L Correll
- The Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA 23501, USA
| | - Shimin Chen
- The Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA 23501, USA
| | - O John Semmes
- The Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA 23501, USA
| | - Robert K Armstrong
- Eastern Virginia Medical School, School of Health Professions, Norfolk, VA 23501, USA.,Sentara Center for Simulation and Immersive Learning, Eastern Virginia Medical School, Norfolk, VA 23501, USA
| | - C Donald Combs
- Eastern Virginia Medical School, School of Health Professions, Norfolk, VA 23501, USA
| | - Julius O Nyalwidhe
- The Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA 23501, USA
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17
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Rajoria S, Nair D, Suvarna K, Pai MGJ, Salkar A, Palanivel V, Verma A, Barpanda A, Awasthi G, Doshi H, Dhara V, Burli A, Agrawal S, Shrivastav O, Shastri J, Srivastava S. Proteomic Investigation of COVID-19 Severity During the Tsunamic Second Wave in Mumbai. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1412:175-195. [PMID: 37378767 DOI: 10.1007/978-3-031-28012-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Maharashtra was severely affected during the noxious second wave of COVID-19, with the highest number of cases recorded across India. The emergence of new symptoms and dysregulation of multiple organs resulted in high disease severity during the second wave which led to increased difficulties in understanding the molecular mechanisms behind the disease pathology. Exploring the underlying factors can help to relieve the burden on the medical communities to some extent by prioritizing the patients and, at the same time, opening avenues for improved treatments. In the current study, we have performed a mass-spectrometry-based proteomic analysis to investigate the disease pathology using nasopharyngeal swab samples collected from the COVID-19 patients in the Mumbai region of Maharashtra over the period of March-June 2021, the peak of the second wave. A total of 59 patients, including 32 non-severe and 27 severe cases, were considered for this proteomic study. We identified 23 differentially regulated proteins in severe patients as a host response to infection. In addition to the previously identified innate mechanisms of neutrophil and platelet degranulation, this study revealed significant alterations of anti-microbial peptide pathways in severe conditions, illustrating its role in the severity of the infectious strain of COVID-19 during the second wave. Furthermore, myeloperoxidase, cathepsin G, and profilin-1 were identified as potential therapeutic targets of the FDA-approved drugs dabrafenib, ZINC4097343, and ritonavir. This study has enlightened the role of the anti-microbial peptide pathway associated with the second wave in India and proposed its importance in potential therapeutics for COVID-19.
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Affiliation(s)
- Sakshi Rajoria
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Divya Nair
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Kruthi Suvarna
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Medha Gayathri J Pai
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Akanksha Salkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Viswanthram Palanivel
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Ayushi Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Abhilash Barpanda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Gaurav Awasthi
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Hastyn Doshi
- Department of Computer Science, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Vivek Dhara
- Department of Mechanical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Ananya Burli
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sachee Agrawal
- Kasturba Hospital for Infectious Diseases, Chinchpokli, Mumbai, Maharashtra, India
| | - Om Shrivastav
- Kasturba Hospital for Infectious Diseases, Chinchpokli, Mumbai, Maharashtra, India
| | - Jayanthi Shastri
- Kasturba Hospital for Infectious Diseases, Chinchpokli, Mumbai, Maharashtra, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.
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Li C, Yue L, Ju Y, Wang J, Chen M, Lu H, Liu S, Liu T, Wang J, Hu X, Tuohetaerbaike B, Wen H, Zhang W, Xu S, Jiang C, Chen F. Serum Proteomic Analysis for New Types of Long-Term Persistent COVID-19 Patients in Wuhan. Microbiol Spectr 2022; 10:e0127022. [PMID: 36314975 PMCID: PMC9784772 DOI: 10.1128/spectrum.01270-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 10/07/2022] [Indexed: 12/24/2022] Open
Abstract
The emergence of a new type of COVID-19 patients, who were retested positive after hospital discharge with long-term persistent SARS-CoV-2 infection but without COVID-19 clinical symptoms (hereinafter, LTPPs), poses novel challenges to COVID-19 treatment and prevention. Why was there such a contradictory phenomenon in LTPPs? To explore the mechanism underlying this phenomenon, we performed quantitative proteomic analyses using the sera of 12 LTPPs (Wuhan Pulmonary Hospital), with the longest carrying history of 132 days, and mainly focused on 7 LTPPs without hypertension (LTPPs-NH). The results showed differential serum protein profiles between LTPPs/LTPPs-NH and health controls. Further analysis identified 174 differentially-expressed-proteins (DEPs) for LTPPs, and 165 DEPs for LTPPs-NH, most of which were shared. GO and KEGG analyses for these DEPs revealed significant enrichment of "coagulation" and "immune response" in both LTPPs and LTPPs-NH. A unity of contradictory genotypes in the 2 aspects were then observed: some DEPs showed the same dysregulated expressed trend as that previously reported for patients in the acute phase of COVID-19, which might be caused by long-term stimulation of persistent SARS-CoV-2 infection in LTPPs, further preventing them from complete elimination; in contrast, some DEPs showed the opposite expression trend in expression, so as to retain control of COVID-19 clinical symptoms in LTPPs. Overall, the contrary effects of these DEPs worked together to maintain the balance of LTPPs, further endowing their contradictory steady-state with long-term persistent SARS-CoV-2 infection but without symptoms. Additionally, our study revealed some potential therapeutic targets of COVID-19. Further studies on these are warranted. IMPORTANCE This study reported a new type of COVID-19 patients and explored the underlying molecular mechanism by quantitative proteomic analyses. DEPs were significantly enriched in "coagulation" and "immune response". Importantly, we identified 7 "coagulation system"- and 9 "immune response"-related DEPs, the expression levels of which were consistent with those previously reported for patients in the acute phase of COVID-19, which appeared to play a role in avoiding the complete elimination of SARS-CoV-2 in LTPPs. On the contrary, 6 "coagulation system"- and 5 "immune response"-related DEPs showed the opposite trend in expression. The 11 inconsistent serum proteins seem to play a key role in the fight against long-term persistent SARS-CoV-2 infection, further retaining control of COVID-19 clinical symptom of LTPPs. The 26 proteins can serve as potential therapeutic targets and are thus valuable for the treatment of LTPPs; further studies on them are warranted.
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Affiliation(s)
- Cuidan Li
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, China
| | - Liya Yue
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, China
| | - Yingjiao Ju
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Wang
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mengfan Chen
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hao Lu
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Sitong Liu
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tao Liu
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing Wang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, Xinjiang, China
| | - Xin Hu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, Xinjiang, China
| | - Bahetibieke Tuohetaerbaike
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, Xinjiang, China
| | - Hao Wen
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, Xinjiang, China
| | - Wenbao Zhang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, Xinjiang, China
| | - Sihong Xu
- Division II of In Vitro Diagnostics for Infectious Diseases, Institute for In Vitro Diagnostics Control, National Institutes for Food and Drug Control, Beijing, China
| | - Chunlai Jiang
- National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun, China
| | - Fei Chen
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, Xinjiang, China
- Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing, China
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Hausburg MA, Williams JS, Banton KL, Mains CW, Roshon M, Bar-Or D. C1 esterase inhibitor-mediated immunosuppression in COVID-19: Friend or foe? CLINICAL IMMUNOLOGY COMMUNICATIONS 2022; 2:83-90. [PMID: 38013973 PMCID: PMC9068237 DOI: 10.1016/j.clicom.2022.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/03/2022] [Accepted: 05/03/2022] [Indexed: 10/10/2023]
Abstract
From asymptomatic to severe, SARS-CoV-2, causative agent of COVID-19, elicits varying disease severities. Moreover, understanding innate and adaptive immune responses to SARS-CoV-2 is imperative since variants such as Omicron negatively impact adaptive antibody neutralization. Severe COVID-19 is, in part, associated with aberrant activation of complement and Factor XII (FXIIa), initiator of contact system activation. Paradoxically, a protein that inhibits the three known pathways of complement activation and FXIIa, C1 esterase inhibitor (C1-INH), is increased in COVID-19 patient plasma and is associated with disease severity. Here we review the role of C1-INH in the regulation of innate and adaptive immune responses. Additionally, we contextualize regulation of C1-INH and SERPING1, the gene encoding C1-INH, by other pathogens and SARS viruses and propose that viral proteins bind to C1-INH to inhibit its function in severe COVID-19. Finally, we review the current clinical trials and published results of exogenous C1-INH treatment in COVID-19 patients.
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Key Words
- C1 esterase inhibitor
- C1 esterase inhibitor, C1-INH
- C1-INH
- COVID-19
- Complement
- FXII
- Inflammation
- Middle East respiratory syndrome coronavirus, MERS-CoV
- Mycobacterium tuberculosis, Mtb
- Severe acute respiratory syndrome coronavirus, SARS-CoV
- acquired C1-INH deficiency, AEE
- activated plasma kallikrein, PKa
- antibody-mediated rejection, AMR
- bradykinin, BK
- contact system, CS
- coronavirus disease 2019, COVID-19
- exogenous C1-INH, exC1-INH
- hereditary angioedema, HAE
- high-molecular-weight kininogen, HK
- human immunodeficiency virus, HIV
- interferon, IFN
- interleukin, IL
- ischemia/reperfusion injury, IRI
- mannose-binding lectin, MBL
- prekallikrein, PK
- recombinant C1-INH, rhC1-INH
- serine protease inhibitor, serpin
- tuberculosis, TB
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Affiliation(s)
- Melissa A Hausburg
- Department of Trauma Research, Swedish Medical Center, 501 E. Hampden, Englewood, CO 80113, USA
- Department of Trauma Research, St. Anthony Hospital, 11600 W 2nd Pl, Lakewood, CO 80228, USA
- Department of Trauma Research, Penrose Hospital, 2222 N Nevada Ave, Colorado Springs, CO 80907, USA
| | - Jason S Williams
- Department of Trauma Research, Swedish Medical Center, 501 E. Hampden, Englewood, CO 80113, USA
- Department of Trauma Research, St. Anthony Hospital, 11600 W 2nd Pl, Lakewood, CO 80228, USA
- Department of Trauma Research, Penrose Hospital, 2222 N Nevada Ave, Colorado Springs, CO 80907, USA
| | - Kaysie L Banton
- Department of Trauma Research, Swedish Medical Center, 501 E. Hampden, Englewood, CO 80113, USA
| | - Charles W Mains
- Centura Health Trauma Systems, Centura Health, 9100 E Mineral Circle, Centennial, CO 80112, USA
| | - Michael Roshon
- Centura Health Trauma Systems, Centura Health, 9100 E Mineral Circle, Centennial, CO 80112, USA
- Department of Emergency Services, Penrose Hospital, 2222 N Nevada Ave, Colorado Springs, CO 80907, USA
| | - David Bar-Or
- Department of Trauma Research, Swedish Medical Center, 501 E. Hampden, Englewood, CO 80113, USA
- Department of Trauma Research, St. Anthony Hospital, 11600 W 2nd Pl, Lakewood, CO 80228, USA
- Department of Trauma Research, Penrose Hospital, 2222 N Nevada Ave, Colorado Springs, CO 80907, USA
- Department of Molecular Biology, Rocky Vista University, 8401 S Chambers Rd, Parker, CO 80134, USA
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20
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Rajoria S, Nissa MU, Suvarna K, Khatri H, Srivastava S. Multiomics Data Analysis Workflow to Assess Severity in Longitudinal Plasma Samples of COVID-19 Patients. Data Brief 2022; 46:108765. [PMCID: PMC9678393 DOI: 10.1016/j.dib.2022.108765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/31/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022] Open
Abstract
Elucidation of molecular markers related to the mounted immune response is crucial for the understanding of disease pathogenesis. In this article, we present the mass-spectrometry-based metabolomic and proteomic data of blood plasma of COVID-19 patients collected at two-time points, which showed a transition from non-severe to severe conditions during these time points. Metabolites were extracted and subjected to mass spectrometric analysis using the Q-Exactive mass spectrometer. For proteomic analysis, depleted plasma samples were tryptic digested and subjected to mass spectrometry analysis. The expression of a few significant targeted proteins was also validated by employing the targeted proteomic approach of multiple reaction monitoring (MRM). Integrative pathway analysis was performed with the significant proteins to obtain biological insights into disease severity. For discussion and more information on the dataset creation, please refer to the related full-length article [1].
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21
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Heterologous expression of hAID in E. coli leads to the production of a splice isoform of AID: hAIDδC, a mystery to be explored. Protein Expr Purif 2022; 199:106149. [PMID: 35952962 DOI: 10.1016/j.pep.2022.106149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 11/21/2022]
Abstract
Activation-induced cytidine deaminase (AID) is a key player that initiates antibody diversification in activated B-cell. AID mediates somatic hypermutation (SHM) and class switch recombination (CSR) via the deamination of cytosine to uracil at the Ig locus, resulting in the production of high-affinity antibodies. AID is predominantly restricted to Ig genes, whereas off-targeting of AID leads to lymphocyte-related malignancies. Interestingly, apart from FL-AID other splice isoforms of AID are highly expressed in the lymphocyte malignancies. In our study, we found that the heterologous expression of hAID-FL in E. coli cells produced two induced bands of hAID as demonstrated by SDS-PAGE and western blotting. Remarkably, peptide mapping data predicted that one band is hAID-FL and the other is its splice isoform, hAIDδE4a. To get an insight into why E. coli cells expressed hAID-FL and hAID variant, we mutated the 5' and 3' splice site of a putative intron of hAID, but it failed to produce only hAID-FL. Incidentally, hAID expressed with fusion partners also displayed two bands, and peptide mapping data strongly suggest that besides hAID-FL, the lower band showed a significant number of amino acids missing towards the C-terminal domain (named as hAIDδC). Our results are the first report to show that expression of recombinant hAID alone or irrespective of solubilization tags in E. coli cells produced hAID-FL and hAIDδC. It will be fascinating to explore the potential mechanism underlying the expression of hAIDδC from recombinant hAID plasmid in E. coli cells.
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22
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Tierney AL, Alali WM, Scott T, Rees-Unwin KS, Clark SJ, Unwin RD. Levels of soluble complement regulators predict severity of COVID-19 symptoms. Front Immunol 2022; 13:1032331. [PMID: 36330526 PMCID: PMC9624227 DOI: 10.3389/fimmu.2022.1032331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 09/26/2022] [Indexed: 12/15/2022] Open
Abstract
The SARS-CoV-2 virus continues to cause significant morbidity and mortality worldwide from COVID-19. One of the major challenges of patient management is the broad range of symptoms observed. While the majority of individuals experience relatively mild disease, a significant minority of patients require hospitalisation, with COVID-19 still proving fatal for some. As such, there remains a desperate need to better understand what drives this severe disease, both in terms of the underlying biology, but also to potentially predict at diagnosis which patients are likely to require further interventions, thus enabling better outcomes for both patients and healthcare systems. Several lines of evidence have pointed to dysregulation of the complement cascade as a major factor in severe COVID-19 outcomes. How this is underpinned mechanistically is not known. Here, we have focussed on the role of the soluble complement regulators Complement Factor H (FH), its splice variant Factor H-like 1 (FHL-1) and five Factor H-Related proteins (FHR1-5). Using a targeted mass spectrometry approach, we quantified these proteins in a cohort of 188 plasma samples from controls and SARS-CoV-2 patients taken at diagnosis. This analysis revealed significant elevations in all FHR proteins, but not FH, in patients with more severe disease, particularly FHR2 and FHR5 (FHR2: 1.97-fold, p<0.0001; FHR5: 2.4-fold, p<0.0001). Furthermore, for a subset of 77 SARS-CoV-2 +ve patients we also analysed time course samples taken approximately 28 days post-diagnosis. Here, we see complement regulator levels drop in all individuals with asymptomatic or mild disease, but regulators remain high in those with more severe outcomes, with elevations in FHR2 over baseline levels in this group. These data support the hypothesis that elevation of circulating levels of the FHR family of proteins could predict disease severity in COVID-19 patients, and that the duration of elevation (or lack of immune activation resolution) may be partly responsible for driving poor outcomes in COVID-19.
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Affiliation(s)
- Anna L. Tierney
- Division of Cardiovascular Sciences, School of Medicine, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Stoller Biomarker Discovery Centre and Division of Cancer Sciences, School of Medicine, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Wajd Mohammed Alali
- Stoller Biomarker Discovery Centre and Division of Cancer Sciences, School of Medicine, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Thomas Scott
- Stoller Biomarker Discovery Centre and Division of Cancer Sciences, School of Medicine, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Karen S. Rees-Unwin
- Stoller Biomarker Discovery Centre and Division of Cancer Sciences, School of Medicine, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | | | - Simon J. Clark
- Institute for Opthalmic Research is based at Eberhard Karls University of Tubingen, Tubingen, BW, Germany
- University Eye Clinic, Eberhard Karls University of Tubingen, Tubingen, BW, Germany
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, United Kingdom
| | - Richard D. Unwin
- Stoller Biomarker Discovery Centre and Division of Cancer Sciences, School of Medicine, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
- *Correspondence: Richard D. Unwin,
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23
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Zhang F, Luna A, Tan T, Chen Y, Sander C, Guo T. COVIDpro: Database for mining protein dysregulation in patients with COVID-19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.09.27.509819. [PMID: 36203550 PMCID: PMC9536031 DOI: 10.1101/2022.09.27.509819] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Background The ongoing pandemic of the coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) still has limited treatment options partially due to our incomplete understanding of the molecular dysregulations of the COVID-19 patients. We aimed to generate a repository and data analysis tools to examine the modulated proteins underlying COVID-19 patients for the discovery of potential therapeutic targets and diagnostic biomarkers. Methods We built a web server containing proteomic expression data from COVID-19 patients with a toolset for user-friendly data analysis and visualization. The web resource covers expert-curated proteomic data from COVID-19 patients published before May 2022. The data were collected from ProteomeXchange and from select publications via PubMed searches and aggregated into a comprehensive dataset. Protein expression by disease subgroups across projects was compared by examining differentially expressed proteins. We also visualize differentially expressed pathways and proteins. Moreover, circulating proteins that differentiated severe cases were nominated as predictive biomarkers. Findings We built and maintain a web server COVIDpro ( https://www.guomics.com/covidPro/ ) containing proteomics data generated by 41 original studies from 32 hospitals worldwide, with data from 3077 patients covering 19 types of clinical specimens, the majority from plasma and sera. 53 protein expression matrices were collected, for a total of 5434 samples and 14,403 unique proteins. Our analyses showed that the lipopolysaccharide-binding protein, as identified in the majority of the studies, was highly expressed in the blood samples of patients with severe disease. A panel of significantly dysregulated proteins was identified to separate patients with severe disease from non-severe disease. Classification of severe disease based on these proteomic signatures on five test sets reached a mean AUC of 0.87 and ACC of 0.80. Interpretation COVIDpro is an online database with an integrated analysis toolkit. It is a unique and valuable resource for testing hypotheses and identifying proteins or pathways that could be targeted by new treatments of COVID-19 patients. Funding National Key R&D Program of China: Key PDPM technologies (2021YFA1301602, 2021YFA1301601, 2021YFA1301603), Zhejiang Provincial Natural Science Foundation for Distinguished Young Scholars (LR19C050001), Hangzhou Agriculture and Society Advancement Program (20190101A04), National Natural Science Foundation of China (81972492) and National Science Fund for Young Scholars (21904107), National Resource for Network Biology (NRNB) from the National Institute of General Medical Sciences (NIGMS-P41 GM103504). Research in context Evidence before this study: Although an increasing number of therapies against COVID-19 are being developed, they are still insufficient, especially with the rise of new variants of concern. This is partially due to our incomplete understanding of the disease’s mechanisms. As data have been collected worldwide, several questions are now worth addressing via meta-analyses. Most COVID-19 drugs function by targeting or affecting proteins. Effectiveness and resistance to therapeutics can be effectively assessed via protein measurements. Empowered by mass spectrometry-based proteomics, protein expression has been characterized in a variety of patient specimens, including body fluids (e.g., serum, plasma, urea) and tissue (i.e., formalin-fixed and paraffin-embedded (FFPE)). We expert-curated proteomic expression data from COVID-19 patients published before May 2022, from the largest proteomic data repository ProteomeXhange as well as from literature search engines. Using this resource, a COVID-19 proteome meta-analysis could provide useful insights into the mechanisms of the disease and identify new potential drug targets.Added value of this study: We integrated many published datasets from patients with COVID-19 from 11 nations, with over 3000 patients and more than 5434 proteome measurements. We collected these datasets in an online database, and generated a toolbox to easily explore, analyze, and visualize the data. Next, we used the database and its associated toolbox to identify new proteins of diagnostic and therapeutic value for COVID-19 treatment. In particular, we identified a set of significantly dysregulated proteins for distinguishing severe from non-severe patients using serum samples.Implications of all the available evidence: COVIDpro will support the navigation and analysis of patterns of dysregulated proteins in various COVID-19 clinical specimens for identification and verification of protein biomarkers and potential therapeutic targets.
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24
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Cavalcante JS, Borges da Silva WRG, de Oliveira LA, Brito IMC, Muller KS, J Vidal IS, Dos Santos LD, Jorge RJB, Almeida C, de Lima Bicho C. Blood plasma proteome alteration after local tissue damage induced by Bothrops erythromelas snake venom in mice. J Proteomics 2022; 269:104742. [PMID: 36174952 DOI: 10.1016/j.jprot.2022.104742] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 09/03/2022] [Accepted: 09/22/2022] [Indexed: 11/26/2022]
Abstract
Snakes of the genus Bothrops are responsible the most snakebites in the Brazil, causing a diverse and complex pathophysiological condition. Bothrops erythromelas is the main specie of medical relevance found in the Caatinga from the Brazilian Northeast region. The pathophysiological effects involving B. erythromelas snakebite as well as the organism reaction in response to this envenomation are not so explored. Thus, edema was induced in mice paws using 2.5 μg or 5.0 μg of B. erythromelas venom, and the percentage of edema was measured. Plasma was collected 30 minutes after the envenomation-induced in mice and analyzed by mass spectrometry. It was identified a total of 112 common plasma proteins differentially abundant among experimental groups, which are involved with the complement system and coagulation cascades, oxidative stress, neutrophil degranulation, platelets degranulation and inflammatory response. Apolipoprotein A1 (Apoa), serum amyloid protein A-4 (Saa4), adiponectin (Adipoq) showed up-regulated in mice plasma after injection of venom, while fibulin (Fbln1), factor XII (F12) and vitamin K-dependent protein Z (Proz) showed down-regulated. The results indicate a protein pattern of thrombo-inflammation to the B. erythromelas snakebite, evidencing potential biomarkers for monitoring this snakebite, new therapeutic targets and its correlations with the degree of envenomation once showed modulations in the abundance among the different groups according to the amount of venom injected into the mice.
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Affiliation(s)
- Joeliton S Cavalcante
- Graduate Program in Tropical Diseases, Botucatu Medical School (FMB), São Paulo University (UNESP - Univ Estadual Paulista), Botucatu, São Paulo, Brazil.
| | - Weslley Ruan G Borges da Silva
- Department of Biology, Center of Biological and Health Sciences, Paraíba State University (UEPB), Campina Grande, Paraíba, Brazil
| | - Laudicéia Alves de Oliveira
- Graduate Program in Tropical Diseases, Botucatu Medical School (FMB), São Paulo University (UNESP - Univ Estadual Paulista), Botucatu, São Paulo, Brazil
| | - Ingrid Mayara C Brito
- Graduate Program in Tropical Diseases, Botucatu Medical School (FMB), São Paulo University (UNESP - Univ Estadual Paulista), Botucatu, São Paulo, Brazil
| | - Kevin S Muller
- Institute of Biosciences, São Paulo University (UNESP - Univ Estadual Paulista), Botucatu, São Paulo, Brazil
| | - Ivynna Suellen J Vidal
- Graduate Program in Translational Medicine, Drug Research and Development Center, Federal University of Ceará (UFC), Fortaleza, Ceará, Brazil
| | - Lucilene Delazari Dos Santos
- Graduate Program in Tropical Diseases, Botucatu Medical School (FMB), São Paulo University (UNESP - Univ Estadual Paulista), Botucatu, São Paulo, Brazil; Biotechnology Institute (IBTEC), São Paulo University (UNESP - Univ Estadual Paulista), Botucatu, São Paulo, Brazil
| | - Roberta Jeane Bezerra Jorge
- Drug Research and Development Center, Federal University of Ceará (UFC), Fortaleza, Ceará, Brazil; Department of Physiology and Pharmacology, School of Medicine, Federal University of Ceará (UFC), Fortaleza, Ceará, Brazil
| | - Cayo Almeida
- Center of Mathematics, Computing Sciences and Cognition, Federal University of ABC, São Paulo, SP, Brazil
| | - Carla de Lima Bicho
- Department of Biology, Center of Biological and Health Sciences, Paraíba State University (UEPB), Campina Grande, Paraíba, Brazil
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25
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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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26
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Shi B, Ye H, Heidari AA, Zheng L, Hu Z, Chen H, Turabieh H, Mafarja M, Wu P. Analysis of COVID-19 severity from the perspective of coagulation index using evolutionary machine learning with enhanced brain storm optimization. JOURNAL OF KING SAUD UNIVERSITY. COMPUTER AND INFORMATION SCIENCES 2022; 34:4874-4887. [PMID: 38620699 PMCID: PMC8483978 DOI: 10.1016/j.jksuci.2021.09.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 09/14/2021] [Accepted: 09/18/2021] [Indexed: 01/11/2023]
Abstract
Coronavirus 2019 (COVID-19) is an extreme acute respiratory syndrome. Early diagnosis and accurate assessment of COVID-19 are not available, resulting in ineffective therapeutic therapy. This study designs an effective intelligence framework to early recognition and discrimination of COVID-19 severity from the perspective of coagulation indexes. The framework is proposed by integrating an enhanced new stochastic optimizer, a brain storm optimizing algorithm (EBSO), with an evolutionary machine learning algorithm called EBSO-SVM. Fast convergence and low risk of the local stagnant can be guaranteed for EBSO with added by Harris hawks optimization (HHO), and its property is verified on 23 benchmarks. Then, the EBSO is utilized to perform parameter optimization and feature selection simultaneously for support vector machine (SVM), and the presented EBSO-SVM early recognition and discrimination of COVID-19 severity in terms of coagulation indexes using COVID-19 clinical data. The classification performance of the EBSO-SVM is very promising, reaching 91.9195% accuracy, 90.529% Matthews correlation coefficient, 90.9912% Sensitivity and 88.5705% Specificity on COVID-19. Compared with other existing state-of-the-art methods, the EBSO-SVM in this paper still shows obvious advantages in multiple metrics. The statistical results demonstrate that the proposed EBSO-SVM shows predictive properties for all metrics and higher stability, which can be treated as a computer-aided technique for analysis of COVID-19 severity from the perspective of coagulation.
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Affiliation(s)
- Beibei Shi
- Affiliated People's Hospital of Jiangsu University, 8 Dianli Road, Zhenjiang, Jiangsu 212000, China
- Department of Public Health, International College, Krirk University, Bangkok 10220, Thailand
| | - Hua Ye
- Department of Pulmonary and Critical Care Medicine, Affiliated Yueqing Hospital, Wenzhou Medical University, Yueqing 325600, China
| | - Ali Asghar Heidari
- College of Computer Science and Artificial Intelligence, Wenzhou University, Wenzhou 325035, China
| | - Long Zheng
- Department of Pulmonary and Critical Care Medicine, Affiliated Yueqing Hospital, Wenzhou Medical University, Yueqing 325600, China
| | - Zhongyi Hu
- College of Computer Science and Artificial Intelligence, Wenzhou University, Wenzhou 325035, China
| | - Huiling Chen
- College of Computer Science and Artificial Intelligence, Wenzhou University, Wenzhou 325035, China
- Institute of Big Data and Information Technology, Wenzhou University, Wenzhou 325035, China
| | - Hamza Turabieh
- Department of Information Technology, College of Computers and Information Technology, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Majdi Mafarja
- Department of Computer Science, Birzeit University, P.O. Box 14, West Bank, Palestine
| | - Peiliang Wu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
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Richard VR, Gaither C, Popp R, Chaplygina D, Brzhozovskiy A, Kononikhin A, Mohammed Y, Zahedi RP, Nikolaev EN, Borchers CH. Early Prediction of COVID-19 Patient Survival by Targeted Plasma Multi-Omics and Machine Learning. Mol Cell Proteomics 2022; 21:100277. [PMID: 35931319 PMCID: PMC9345792 DOI: 10.1016/j.mcpro.2022.100277] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 07/05/2022] [Accepted: 07/27/2022] [Indexed: 01/18/2023] Open
Abstract
The recent surge of coronavirus disease 2019 (COVID-19) hospitalizations severely challenges healthcare systems around the globe and has increased the demand for reliable tests predictive of disease severity and mortality. Using multiplexed targeted mass spectrometry assays on a robust triple quadrupole MS setup which is available in many clinical laboratories, we determined the precise concentrations of hundreds of proteins and metabolites in plasma from hospitalized COVID-19 patients. We observed a clear distinction between COVID-19 patients and controls and, strikingly, a significant difference between survivors and nonsurvivors. With increasing length of hospitalization, the survivors' samples showed a trend toward normal concentrations, indicating a potential sensitive readout of treatment success. Building a machine learning multi-omic model that considers the concentrations of 10 proteins and five metabolites, we could predict patient survival with 92% accuracy (area under the receiver operating characteristic curve: 0.97) on the day of hospitalization. Hence, our standardized assays represent a unique opportunity for the early stratification of hospitalized COVID-19 patients.
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Key Words
- acd, acid citrate dextrose
- acn, acetonitrile
- auc, area under the receiver operating characteristic curve
- bqc19, biobanque quebecoise de la covid-19
- bsa, bovine serum albumin covid-19
- cptac, clinical proteomic tumor analysis consortium
- dtt, dithiothreitol
- fa, formic acid
- fdr, false discovery rate
- icu, intensive care unit
- lc/mrm-ms, liquid chromatography/multiple reaction monitoring mass spectrometry
- lc-ms, liquid chromatography-mass spectrometry
- lloq, lower limit of quantitation
- lysopc, lysophosphatidylcholine
- maldi, matrix-assisted laser desorption ionization
- meoh, methanol
- ms, mass spectrometry
- pbs, phosphatase buffered saline
- pcr, polymerase chain reaction
- pitc, phenylisothiocyanate
- qc, quality control
- rp-uhplc, reversed phase ultrahigh performance liquid chromatography
- sis, stable-isotope-labeled internal standard
- spe, solid-phase extraction
- svm, support vector machine
- trishcl, tris (hydroxymethyl) aminomethane hydrochloride
- uniprot, the universal protein resource
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Affiliation(s)
- Vincent R. Richard
- Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, McGill University, Montreal, Quebec, Canada
| | | | | | - Daria Chaplygina
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Alexander Brzhozovskiy
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Alexey Kononikhin
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Yassene Mohammed
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands,Genome BC Proteomics Centre, University of Victoria, Victoria, Canada
| | - René P. Zahedi
- Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, McGill University, Montreal, Quebec, Canada,Manitoba Centre for Proteomics & Systems Biology, John Buhler Research Centre, University of Manitoba, Winnipeg, Canada,Department of Internal Medicine, University of Manitoba, Winnipeg, Canada
| | - Evgeny N. Nikolaev
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Christoph H. Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, McGill University, Montreal, Quebec, Canada,Gerald Bronfman Department of Oncology, Division of Experimental Medicine, Lady Davis Institute for Medical Research, McGill University, Montreal, Canada,Department of Pathology, McGill University, Montreal, Canada,For correspondence: Christoph H. Borchers
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Ghanem M, Brown SJ, EAT Mohamed A, Fuller HR. A Meta-summary and Bioinformatic Analysis Identified Interleukin 6 as a Master Regulator of COVID-19 Severity Biomarkers. Cytokine 2022; 159:156011. [PMID: 36067713 PMCID: PMC9420723 DOI: 10.1016/j.cyto.2022.156011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 07/22/2022] [Accepted: 08/16/2022] [Indexed: 12/15/2022]
Abstract
With the rising demand for improved COVID-19 disease monitoring and prognostic markers, studies have aimed to identify biomarkers using a range of screening methods. However, the selection of biomarkers for validation from large datasets may result in potentially important biomarkers being overlooked when datasets are considered in isolation. Here, we have utilized a meta-summary approach to investigate COVID-19 biomarker datasets to identify conserved biomarkers of COVID-19 severity. This approach identified a panel of 17 proteins that showed a consistent direction of change across two or more datasets. Furthermore, bioinformatics analysis of these proteins highlighted a range of enriched biological processes that include inflammatory responses and compromised integrity of physiological systems including cardiovascular, neurological, and metabolic. A panel of upstream regulators of the COVID-19 severity biomarkers were identified, including chemical compounds currently under investigation for COVID-19 treatment. One of the upstream regulators, interleukin 6 (IL6), was identified as a “master regulator” of the severity biomarkers. COVID-19 disease severity is intensified due to the extreme viral immunological reaction that results in increased inflammatory biomarkers and cytokine storm. Since IL6 is the primary stimulator of cytokines, it could be used independently as a biomarker in determining COVID-19 disease progression, in addition to a potential therapeutic approach targeting IL6. The array of upstream regulators of the severity biomarkers identified here serve as attractive candidates for the development of new therapeutic approaches to treating COVID-19. In addition, the findings from this study highlight COVID-19 severity biomarkers which represent promising, robust biomarkers for future validation studies for their use in defining and monitoring disease severity and patient prognosis.
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Nuñez E, Orera I, Carmona-Rodríguez L, Paño JR, Vázquez J, Corrales FJ. Mapping the Serum Proteome of COVID-19 Patients; Guidance for Severity Assessment. Biomedicines 2022; 10:biomedicines10071690. [PMID: 35884998 PMCID: PMC9313396 DOI: 10.3390/biomedicines10071690] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/28/2022] [Accepted: 07/04/2022] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), whose outbreak in 2019 led to an ongoing pandemic with devastating consequences for the global economy and human health. According to the World Health Organization, COVID-19 has affected more than 481 million people worldwide, with 6 million confirmed deaths. The joint efforts of the scientific community have undoubtedly increased the pace of production of COVID-19 vaccines, but there is still so much uncharted ground to cover regarding the mechanisms of SARS-CoV-2 infection, replication and host response. These issues can be approached by proteomics with unprecedented capacity paving the way for the development of more efficient strategies for patient care. In this study, we present a deep proteome analysis that has been performed on a cohort of 72 COVID-19 patients aiming to identify serum proteins assessing the dynamics of the disease at different age ranges. A panel of 53 proteins that participate in several functions such as acute-phase response and inflammation, blood coagulation, cell adhesion, complement cascade, endocytosis, immune response, oxidative stress and tissue injury, have been correlated with patient severity, suggesting a molecular basis for their clinical stratification. Eighteen protein candidates were further validated by targeted proteomics in an independent cohort of 84 patients including a group of individuals that had satisfactorily resolved SARS-CoV-2 infection. Remarkably, all protein alterations were normalized 100 days after leaving the hospital, which further supports the reliability of the selected proteins as hallmarks of COVID-19 progression and grading. The optimized protein panel may prove its value for optimal severity assessment as well as in the follow up of COVID-19 patients.
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Affiliation(s)
- Estefanía Nuñez
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain;
- Cardiovascular Proteomics Laboratory, Centro Nacional de Enfermedades Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - Irene Orera
- Proteomics Research Core Facility, Instituto Aragonés de Ciencias de la Salud (IACS), 50009 Zaragoza, Spain;
| | | | - José Ramón Paño
- Division of Infectious Diseases, Hospital Clínico Universitario, IIS Aragón, Ciberinfec, 50009 Zaragoza, Spain;
| | - Jesús Vázquez
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain;
- Cardiovascular Proteomics Laboratory, Centro Nacional de Enfermedades Cardiovasculares (CNIC), 28029 Madrid, Spain
- Correspondence: (J.V.); (F.J.C.)
| | - Fernando J. Corrales
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología (CSIC), 28049 Madrid, Spain;
- Correspondence: (J.V.); (F.J.C.)
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30
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Ghosh S, Parikh S, Nissa MU, Acharjee A, Singh A, Patwa D, Makwana P, Athalye A, Barpanda A, Laloraya M, Srivastava S, Parikh F. Semen Proteomics of COVID-19 Convalescent Men Reveals Disruption of Key Biological Pathways Relevant to Male Reproductive Function. ACS OMEGA 2022; 7:8601-8612. [PMID: 35309488 PMCID: PMC8928495 DOI: 10.1021/acsomega.1c06551] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 02/22/2022] [Indexed: 05/09/2023]
Abstract
A considerable section of males suffered from COVID-19, with many experiencing long-term repercussions. Recovered males have been documented to have compromised fertility, albeit the mechanisms remain unclear. We investigated the impact of COVID-19 on semen proteome following complete clinical recovery using mass spectrometry. A label-free quantitative proteomics study involved 10 healthy fertile subjects and 17 COVID-19-recovered men. With 1% false discovery rate and >1 unique peptide stringency, MaxQuant analysis found 1099 proteins and 8503 peptides. Of the 48 differentially expressed proteins between the healthy and COVID-19-recovered groups, 21 proteins were downregulated and 27 were upregulated in COVID-19-recovered males. The major pathways involved in reproductive functions, such as sperm-oocyte recognition, testosterone response, cell motility regulation, adhesion regulation, extracellular matrix adhesion, and endopeptidase activity, were downregulated in COVID-19-recovered patients according to bioinformatics analysis. Furthermore, the targeted approach revealed significant downregulation of semenogelin 1 and prosaposin, two proteins related to male fertility. Therefore, we demonstrate the alteration of semen proteome in response to COVID-19, thus disrupting the male reproductive function despite the patient's clinical remission. Hence, to understand fertility-related biological processes triggered by this infection, a protracted evaluation of the consequences of COVID-19 in recovered men is warranted.
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Affiliation(s)
- Susmita Ghosh
- Proteomics
Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India
| | - Swapneil Parikh
- Molecular
Laboratory, Kasturba Hospital for Infectious
Diseases, Mumbai 400011, India
| | - Mehar Un Nissa
- Proteomics
Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India
| | - Arup Acharjee
- Proteomics
Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India
| | - Avinash Singh
- Proteomics
Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India
| | - Dhruv Patwa
- Department
of Chemical Engineering, Indian Institute
of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India
| | - Prashant Makwana
- Jaslok-FertilTree
International Centre, Department of Assisted Reproduction and Genetics, Jaslok Hospital and Research Centre, 8th Floor, Dr. G, Pedder Road, Mumbai 400026, Maharashtra, India
| | - Arundhati Athalye
- Jaslok-FertilTree
International Centre, Department of Assisted Reproduction and Genetics, Jaslok Hospital and Research Centre, 8th Floor, Dr. G, Pedder Road, Mumbai 400026, Maharashtra, India
| | - Abhilash Barpanda
- Proteomics
Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India
| | - Malini Laloraya
- Division
of Molecular Reproduction, Rajiv Gandhi
Centre for Biotechnology, Thycaud P.O.,
Poojappura, Thiruvananthapuram 695014, Kerala, India
| | - Sanjeeva Srivastava
- Proteomics
Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India
| | - Firuza Parikh
- Jaslok-FertilTree
International Centre, Department of Assisted Reproduction and Genetics, Jaslok Hospital and Research Centre, 8th Floor, Dr. G, Pedder Road, Mumbai 400026, Maharashtra, India
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COVID-19 Drug Repurposing: A Network-Based Framework for Exploring Biomedical Literature and Clinical Trials for Possible Treatments. Pharmaceutics 2022; 14:pharmaceutics14030567. [PMID: 35335943 PMCID: PMC8955179 DOI: 10.3390/pharmaceutics14030567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/25/2022] [Accepted: 02/25/2022] [Indexed: 12/24/2022] Open
Abstract
Background: With the Coronavirus becoming a new reality of our world, global efforts continue to seek answers to many questions regarding the spread, variants, vaccinations, and medications. Particularly, with the emergence of several strains (e.g., Delta, Omicron), vaccines will need further development to offer complete protection against the new variants. It is critical to identify antiviral treatments while the development of vaccines continues. In this regard, the repurposing of already FDA-approved drugs remains a major effort. In this paper, we investigate the hypothesis that a combination of FDA-approved drugs may be considered as a candidate for COVID-19 treatment if (1) there exists an evidence in the COVID-19 biomedical literature that suggests such a combination, and (2) there is match in the clinical trials space that validates this drug combination. Methods: We present a computational framework that is designed for detecting drug combinations, using the following components (a) a Text-mining module: to extract drug names from the abstract section of the biomedical publications and the intervention/treatment sections of clinical trial records. (b) a network model constructed from the drug names and their associations, (c) a clique similarity algorithm to identify candidate drug treatments. Result and Conclusions: Our framework has identified treatments in the form of two, three, or four drug combinations (e.g., hydroxychloroquine, doxycycline, and azithromycin). The identifications of the various treatment candidates provided sufficient evidence that supports the trustworthiness of our hypothesis.
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32
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Acharjee A, Stephen Kingsly J, Kamat M, Kurlawala V, Chakraborty A, Vyas P, Vaishnav R, Srivastava S. Rise of the SARS-CoV-2 Variants: can proteomics be the silver bullet? Expert Rev Proteomics 2022; 19:197-212. [PMID: 35655386 DOI: 10.1080/14789450.2022.2085564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION The challenges posed by emergent strains of SARS-CoV-2 need to be tackled by contemporary scientific approaches, with proteomics playing a significant role. AREAS COVERED In this review, we provide a brief synthesis of the impact of proteomics technologies in elucidating disease pathogenesis and classifiers for the prognosis of COVID-19 and propose proteomics methodologies that could play a crucial role in understanding emerging variants and their altered disease pathology. From aiding the design of novel drug candidates to facilitating the identification of T cell vaccine targets, we have discussed the impact of proteomics methods in COVID-19 research. Techniques varied as mass spectrometry, single-cell proteomics, multiplexed ELISA arrays, high-density proteome arrays, surface plasmon resonance, immunopeptidomics, and in silico docking studies that have helped augment the fight against existing diseases were useful in preparing us to tackle SARS-CoV-2 variants. We also propose an action plan for a pipeline to combat emerging pandemics using proteomics technology by adopting uniform standard operating procedures and unified data analysis paradigms. EXPERT OPINION The knowledge about the use of diverse proteomics approaches for COVID-19 investigation will provide a framework for future basic research, better infectious disease prevention strategies, improved diagnostics, and targeted therapeutics.
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Affiliation(s)
- Arup Acharjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | | | - Madhura Kamat
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be University), Mumbai, India
| | - Vishakha Kurlawala
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be University), Mumbai, India
| | | | - Priyanka Vyas
- Department of Biotechnology and Botany, Mahila PG Mahavidyalaya, J. N. V University, Jodhpur, India
| | - Radhika Vaishnav
- Department of Life Sciences, Ivy Tech Community College, Indianapolis, Indiana, USA
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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33
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Lazari LC, Zerbinati RM, Rosa-Fernandes L, Santiago VF, Rosa KF, Angeli CB, Schwab G, Palmieri M, Sarmento DJS, Marinho CRF, Almeida JD, To K, Giannecchini S, Wrenger C, Sabino EC, Martinho H, Lindoso JAL, Durigon EL, Braz-Silva PH, Palmisano G. MALDI-TOF mass spectrometry of saliva samples as a prognostic tool for COVID-19. J Oral Microbiol 2022; 14:2043651. [PMID: 35251522 PMCID: PMC8890567 DOI: 10.1080/20002297.2022.2043651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Background Methods Results Conclusion
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Affiliation(s)
- Lucas C. Lazari
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Rodrigo M. Zerbinati
- Laboratory of Virology (LIM-52-HC-FMUSP), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Livia Rosa-Fernandes
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Veronica Feijoli Santiago
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Klaise F. Rosa
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Claudia B. Angeli
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Gabriela Schwab
- Laboratory of Virology (LIM-52-HC-FMUSP), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Michelle Palmieri
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Dmitry J. S. Sarmento
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Claudio R. F. Marinho
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Janete Dias Almeida
- Department of Biosciences and Oral Diagnosis, Institute of Science and Technology, São Paulo State University, São José dos Campos, Brazil
| | - Kelvin To
- State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Carol Yu Centre for Infection, Li KaShing Faculty of Medicine of the University of Hong Kong, Hong Kong, Special Administrative Region, China
| | - Simone Giannecchini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Ester C. Sabino
- Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Herculano Martinho
- Centro de Ciencias Naturais e Humanas, Universidade Federal do ABC, Santo André, Brazil
| | - José A. L. Lindoso
- Institute of Infectious Diseases Emílio Ribas, São Paulo, Brazil
- Laboratory of Protozoology (LIM-49-HC-FMUSP), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
- Department of Infectious Diseases, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Edison L. Durigon
- Laboratory of Clinical and Molecular Virology, Department of Microbiology, ICB, University of São Paulo, São Paulo, Brazil
| | - Paulo H. Braz-Silva
- Laboratory of Virology (LIM-52-HC-FMUSP), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
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Hasankhani A, Bahrami A, Sheybani N, Aria B, Hemati B, Fatehi F, Ghaem Maghami Farahani H, Javanmard G, Rezaee M, Kastelic JP, Barkema HW. Differential Co-Expression Network Analysis Reveals Key Hub-High Traffic Genes as Potential Therapeutic Targets for COVID-19 Pandemic. Front Immunol 2022; 12:789317. [PMID: 34975885 PMCID: PMC8714803 DOI: 10.3389/fimmu.2021.789317] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/26/2021] [Indexed: 01/08/2023] Open
Abstract
Background The recent emergence of COVID-19, rapid worldwide spread, and incomplete knowledge of molecular mechanisms underlying SARS-CoV-2 infection have limited development of therapeutic strategies. Our objective was to systematically investigate molecular regulatory mechanisms of COVID-19, using a combination of high throughput RNA-sequencing-based transcriptomics and systems biology approaches. Methods RNA-Seq data from peripheral blood mononuclear cells (PBMCs) of healthy persons, mild and severe 17 COVID-19 patients were analyzed to generate a gene expression matrix. Weighted gene co-expression network analysis (WGCNA) was used to identify co-expression modules in healthy samples as a reference set. For differential co-expression network analysis, module preservation and module-trait relationships approaches were used to identify key modules. Then, protein-protein interaction (PPI) networks, based on co-expressed hub genes, were constructed to identify hub genes/TFs with the highest information transfer (hub-high traffic genes) within candidate modules. Results Based on differential co-expression network analysis, connectivity patterns and network density, 72% (15 of 21) of modules identified in healthy samples were altered by SARS-CoV-2 infection. Therefore, SARS-CoV-2 caused systemic perturbations in host biological gene networks. In functional enrichment analysis, among 15 non-preserved modules and two significant highly-correlated modules (identified by MTRs), 9 modules were directly related to the host immune response and COVID-19 immunopathogenesis. Intriguingly, systemic investigation of SARS-CoV-2 infection identified signaling pathways and key genes/proteins associated with COVID-19's main hallmarks, e.g., cytokine storm, respiratory distress syndrome (ARDS), acute lung injury (ALI), lymphopenia, coagulation disorders, thrombosis, and pregnancy complications, as well as comorbidities associated with COVID-19, e.g., asthma, diabetic complications, cardiovascular diseases (CVDs), liver disorders and acute kidney injury (AKI). Topological analysis with betweenness centrality (BC) identified 290 hub-high traffic genes, central in both co-expression and PPI networks. We also identified several transcriptional regulatory factors, including NFKB1, HIF1A, AHR, and TP53, with important immunoregulatory roles in SARS-CoV-2 infection. Moreover, several hub-high traffic genes, including IL6, IL1B, IL10, TNF, SOCS1, SOCS3, ICAM1, PTEN, RHOA, GDI2, SUMO1, CASP1, IRAK3, HSPA5, ADRB2, PRF1, GZMB, OASL, CCL5, HSP90AA1, HSPD1, IFNG, MAPK1, RAB5A, and TNFRSF1A had the highest rates of information transfer in 9 candidate modules and central roles in COVID-19 immunopathogenesis. Conclusion This study provides comprehensive information on molecular mechanisms of SARS-CoV-2-host interactions and identifies several hub-high traffic genes as promising therapeutic targets for the COVID-19 pandemic.
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Affiliation(s)
- Aliakbar Hasankhani
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Abolfazl Bahrami
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran.,Biomedical Center for Systems Biology Science Munich, Ludwig-Maximilians-University, Munich, Germany
| | - Negin Sheybani
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | - Behzad Aria
- Department of Physical Education and Sports Science, School of Psychology and Educational Sciences, Yazd University, Yazd, Iran
| | - Behzad Hemati
- Biotechnology Research Center, Karaj Branch, Islamic Azad University, Karaj, Iran
| | - Farhang Fatehi
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | | | - Ghazaleh Javanmard
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Mahsa Rezaee
- Department of Medical Mycology, School of Medical Science, Tarbiat Modares University, Tehran, Iran
| | - John P Kastelic
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Herman W Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
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35
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Zhang Y, Cai X, Ge W, Wang D, Zhu G, Qian L, Xiang N, Yue L, Liang S, Zhang F, Wang J, Zhou K, Zheng Y, Lin M, Sun T, Lu R, Zhang C, Xu L, Sun Y, Zhou X, Yu J, Lyu M, Shen B, Zhu H, Xu J, Zhu Y, Guo T. Potential Use of Serum Proteomics for Monitoring COVID-19 Progression to Complement RT-PCR Detection. J Proteome Res 2022; 21:90-100. [PMID: 34783559 PMCID: PMC8610005 DOI: 10.1021/acs.jproteome.1c00525] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Indexed: 12/18/2022]
Abstract
RT-PCR is the primary method to diagnose COVID-19 and is also used to monitor the disease course. This approach, however, suffers from false negatives due to RNA instability and poses a high risk to medical practitioners. Here, we investigated the potential of using serum proteomics to predict viral nucleic acid positivity during COVID-19. We analyzed the proteome of 275 inactivated serum samples from 54 out of 144 COVID-19 patients and shortlisted 42 regulated proteins in the severe group and 12 in the non-severe group. Using these regulated proteins and several key clinical indexes, including days after symptoms onset, platelet counts, and magnesium, we developed two machine learning models to predict nucleic acid positivity, with an AUC of 0.94 in severe cases and 0.89 in non-severe cases, respectively. Our data suggest the potential of using a serum protein-based machine learning model to monitor COVID-19 progression, thus complementing swab RT-PCR tests. More efforts are required to promote this approach into clinical practice since mass spectrometry-based protein measurement is not currently widely accessible in clinic.
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Affiliation(s)
- Ying Zhang
- Taizhou Hospital of Zhejiang Province
Affiliated to Wenzhou Medical University, Linhai, Zhejiang 317000,
China
| | - Xue Cai
- Key Laboratory of Structural Biology of Zhejiang
Province, School of Life Sciences, Westlake University, Xihu
District, Hangzhou, Zhejiang 310000, China
- Center for Infectious Disease Research,
Westlake Laboratory of Life Sciences and Biomedicine, Xihu
District, Hangzhou, Zhejiang 310000, China
- Institute of Basic Medical Sciences,
Westlake Institute for Advanced Study, Xihu District,
Hangzhou, Zhejiang 310000, China
| | - Weigang Ge
- Key Laboratory of Structural Biology of Zhejiang
Province, School of Life Sciences, Westlake University, Xihu
District, Hangzhou, Zhejiang 310000, China
- Center for Infectious Disease Research,
Westlake Laboratory of Life Sciences and Biomedicine, Xihu
District, Hangzhou, Zhejiang 310000, China
- Institute of Basic Medical Sciences,
Westlake Institute for Advanced Study, Xihu District,
Hangzhou, Zhejiang 310000, China
- Westlake Omics (Hangzhou) Biotechnology
Co., Ltd., No.1, Yunmeng Road, Cloud Town, Xihu District, Hangzhou,
Zhejiang 310000, China
| | - Donglian Wang
- Taizhou Hospital of Zhejiang Province
Affiliated to Wenzhou Medical University, Linhai, Zhejiang 317000,
China
| | - Guangjun Zhu
- Taizhou Hospital of Zhejiang Province
Affiliated to Wenzhou Medical University, Linhai, Zhejiang 317000,
China
| | - Liujia Qian
- Key Laboratory of Structural Biology of Zhejiang
Province, School of Life Sciences, Westlake University, Xihu
District, Hangzhou, Zhejiang 310000, China
- Center for Infectious Disease Research,
Westlake Laboratory of Life Sciences and Biomedicine, Xihu
District, Hangzhou, Zhejiang 310000, China
- Institute of Basic Medical Sciences,
Westlake Institute for Advanced Study, Xihu District,
Hangzhou, Zhejiang 310000, China
| | - Nan Xiang
- Key Laboratory of Structural Biology of Zhejiang
Province, School of Life Sciences, Westlake University, Xihu
District, Hangzhou, Zhejiang 310000, China
- Center for Infectious Disease Research,
Westlake Laboratory of Life Sciences and Biomedicine, Xihu
District, Hangzhou, Zhejiang 310000, China
- Institute of Basic Medical Sciences,
Westlake Institute for Advanced Study, Xihu District,
Hangzhou, Zhejiang 310000, China
- Westlake Omics (Hangzhou) Biotechnology
Co., Ltd., No.1, Yunmeng Road, Cloud Town, Xihu District, Hangzhou,
Zhejiang 310000, China
| | - Liang Yue
- Key Laboratory of Structural Biology of Zhejiang
Province, School of Life Sciences, Westlake University, Xihu
District, Hangzhou, Zhejiang 310000, China
- Center for Infectious Disease Research,
Westlake Laboratory of Life Sciences and Biomedicine, Xihu
District, Hangzhou, Zhejiang 310000, China
- Institute of Basic Medical Sciences,
Westlake Institute for Advanced Study, Xihu District,
Hangzhou, Zhejiang 310000, China
| | - Shuang Liang
- Key Laboratory of Structural Biology of Zhejiang
Province, School of Life Sciences, Westlake University, Xihu
District, Hangzhou, Zhejiang 310000, China
- Center for Infectious Disease Research,
Westlake Laboratory of Life Sciences and Biomedicine, Xihu
District, Hangzhou, Zhejiang 310000, China
- Institute of Basic Medical Sciences,
Westlake Institute for Advanced Study, Xihu District,
Hangzhou, Zhejiang 310000, China
| | - Fangfei Zhang
- Key Laboratory of Structural Biology of Zhejiang
Province, School of Life Sciences, Westlake University, Xihu
District, Hangzhou, Zhejiang 310000, China
- Center for Infectious Disease Research,
Westlake Laboratory of Life Sciences and Biomedicine, Xihu
District, Hangzhou, Zhejiang 310000, China
- Institute of Basic Medical Sciences,
Westlake Institute for Advanced Study, Xihu District,
Hangzhou, Zhejiang 310000, China
| | - Jing Wang
- Taizhou Hospital of Zhejiang Province
Affiliated to Wenzhou Medical University, Linhai, Zhejiang 317000,
China
| | - Kai Zhou
- Taizhou Hospital of Zhejiang Province
Affiliated to Wenzhou Medical University, Linhai, Zhejiang 317000,
China
| | - Yufen Zheng
- Taizhou Hospital of Zhejiang Province
Affiliated to Wenzhou Medical University, Linhai, Zhejiang 317000,
China
| | - Minjie Lin
- Taizhou Hospital of Zhejiang Province
Affiliated to Wenzhou Medical University, Linhai, Zhejiang 317000,
China
| | - Tong Sun
- Taizhou Hospital of Zhejiang Province
Affiliated to Wenzhou Medical University, Linhai, Zhejiang 317000,
China
| | - Ruyue Lu
- Taizhou Hospital of Zhejiang Province
Affiliated to Wenzhou Medical University, Linhai, Zhejiang 317000,
China
| | - Chao Zhang
- Taizhou Hospital of Zhejiang Province
Affiliated to Wenzhou Medical University, Linhai, Zhejiang 317000,
China
| | - Luang Xu
- Key Laboratory of Structural Biology of Zhejiang
Province, School of Life Sciences, Westlake University, Xihu
District, Hangzhou, Zhejiang 310000, China
- Center for Infectious Disease Research,
Westlake Laboratory of Life Sciences and Biomedicine, Xihu
District, Hangzhou, Zhejiang 310000, China
- Institute of Basic Medical Sciences,
Westlake Institute for Advanced Study, Xihu District,
Hangzhou, Zhejiang 310000, China
| | - Yaoting Sun
- Key Laboratory of Structural Biology of Zhejiang
Province, School of Life Sciences, Westlake University, Xihu
District, Hangzhou, Zhejiang 310000, China
- Center for Infectious Disease Research,
Westlake Laboratory of Life Sciences and Biomedicine, Xihu
District, Hangzhou, Zhejiang 310000, China
- Institute of Basic Medical Sciences,
Westlake Institute for Advanced Study, Xihu District,
Hangzhou, Zhejiang 310000, China
| | - Xiaoxu Zhou
- Key Laboratory of Structural Biology of Zhejiang
Province, School of Life Sciences, Westlake University, Xihu
District, Hangzhou, Zhejiang 310000, China
- Institute of Basic Medical Sciences,
Westlake Institute for Advanced Study, Xihu District,
Hangzhou, Zhejiang 310000, China
| | - Jing Yu
- Key Laboratory of Structural Biology of Zhejiang
Province, School of Life Sciences, Westlake University, Xihu
District, Hangzhou, Zhejiang 310000, China
- Center for Infectious Disease Research,
Westlake Laboratory of Life Sciences and Biomedicine, Xihu
District, Hangzhou, Zhejiang 310000, China
- Institute of Basic Medical Sciences,
Westlake Institute for Advanced Study, Xihu District,
Hangzhou, Zhejiang 310000, China
| | - Mengge Lyu
- Key Laboratory of Structural Biology of Zhejiang
Province, School of Life Sciences, Westlake University, Xihu
District, Hangzhou, Zhejiang 310000, China
- Center for Infectious Disease Research,
Westlake Laboratory of Life Sciences and Biomedicine, Xihu
District, Hangzhou, Zhejiang 310000, China
- Institute of Basic Medical Sciences,
Westlake Institute for Advanced Study, Xihu District,
Hangzhou, Zhejiang 310000, China
| | - Bo Shen
- Taizhou Hospital of Zhejiang Province
Affiliated to Wenzhou Medical University, Linhai, Zhejiang 317000,
China
| | - Hongguo Zhu
- Taizhou Hospital of Zhejiang Province
Affiliated to Wenzhou Medical University, Linhai, Zhejiang 317000,
China
| | - Jiaqin Xu
- Taizhou Hospital of Zhejiang Province
Affiliated to Wenzhou Medical University, Linhai, Zhejiang 317000,
China
| | - Yi Zhu
- Key Laboratory of Structural Biology of Zhejiang
Province, School of Life Sciences, Westlake University, Xihu
District, Hangzhou, Zhejiang 310000, China
- Center for Infectious Disease Research,
Westlake Laboratory of Life Sciences and Biomedicine, Xihu
District, Hangzhou, Zhejiang 310000, China
- Institute of Basic Medical Sciences,
Westlake Institute for Advanced Study, Xihu District,
Hangzhou, Zhejiang 310000, China
| | - Tiannan Guo
- Key Laboratory of Structural Biology of Zhejiang
Province, School of Life Sciences, Westlake University, Xihu
District, Hangzhou, Zhejiang 310000, China
- Center for Infectious Disease Research,
Westlake Laboratory of Life Sciences and Biomedicine, Xihu
District, Hangzhou, Zhejiang 310000, China
- Institute of Basic Medical Sciences,
Westlake Institute for Advanced Study, Xihu District,
Hangzhou, Zhejiang 310000, China
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36
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Guest PC, Zahedipour F, Majeed M, Jamialahmadi T, Sahebkar A. Multiplex Technologies in COVID-19 Research, Diagnostics, and Prognostics: Battling the Pandemic. Methods Mol Biol 2022; 2511:3-20. [PMID: 35838948 DOI: 10.1007/978-1-0716-2395-4_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Due to continuous technical developments and new insights into the high complexity of infectious diseases such as COVID-19, there is an increasing need for multiplex biomarkers to aid clinical management and support the development of new drugs and vaccines. COVID-19 disease requires rapid diagnosis and stratification to enable the most appropriate treatment course for the best possible outcomes for patients. In addition, these tests should be rapid, specific, and sensitive. They should rule out other potential causes of illness with simultaneous testing for other diseases. Elevated levels of specific biomarkers can be used to establish severity risks of chronic diseases so that patients can be provided the proper medication at the right time. This review describes the state-of-the-art technologies in proteomics, transcriptomics, and metabolomics, for multiplex biomarker approaches in COVID-19 research.
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Affiliation(s)
- Paul C Guest
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Fatemeh Zahedipour
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Tannaz Jamialahmadi
- Surgical Oncology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Nutrition, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- School of Medicine, The University of Western Australia, Perth, Australia.
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37
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Mukherjee A, Verma A, Bihani S, Burli A, Mantri K, Srivastava S. Proteomics advances towards developing SARS-CoV-2 therapeutics using in silico drug repurposing approaches. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 39:1-12. [PMID: 34906319 PMCID: PMC8222565 DOI: 10.1016/j.ddtec.2021.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/21/2021] [Accepted: 06/11/2021] [Indexed: 12/12/2022]
Abstract
Standing amidst the COVID-19 pandemic, we have faced major medical and economic crisis in recent times which remains to be an unresolved issue till date. Although the scientific community has made significant progress towards diagnosis and understanding the disease; however, effective therapeutics are still lacking. Several omics-based studies, especially proteomics and interactomics, have contributed significantly in terms of identifying biomarker panels that can potentially be used for the disease prognosis. This has also paved the way to identify the targets for drug repurposing as a therapeutic alternative. US Food and Drug Administration (FDA) has set in motion more than 500 drug development programs on an emergency basis, most of them are focusing on repurposed drugs. Remdesivir is one such success of a robust and quick drug repurposing approach. The advancements in omics-based technologies has allowed to explore altered host proteins, which were earlier restricted to only SARS-CoV-2 protein signatures. In this article, we have reviewed major contributions of proteomics and interactomics techniques towards identifying therapeutic targets for COVID-19. Furthermore, in-silico molecular docking approaches to streamline potential drug candidates are also discussed.
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Affiliation(s)
- Amrita Mukherjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Ayushi Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Surbhi Bihani
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Ananya Burli
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Krishi Mantri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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38
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Suvarna K, Salkar A, Palanivel V, Bankar R, Banerjee N, Gayathri J Pai M, Srivastava A, Singh A, Khatri H, Agrawal S, Shrivastav O, Shastri J, Srivastava S. A Multi-omics Longitudinal Study Reveals Alteration of the Leukocyte Activation Pathway in COVID-19 Patients. J Proteome Res 2021; 20:4667-4680. [PMID: 34379420 PMCID: PMC8370121 DOI: 10.1021/acs.jproteome.1c00215] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Indexed: 12/24/2022]
Abstract
Severe coronavirus disease 2019 (COVID-19) infection may lead to lung injury, multi-organ failure, and eventually death. Cytokine storm due to excess cytokine production has been associated with fatality in severe infections. However, the specific molecular signatures associated with the elevated immune response are yet to be elucidated. We performed a mass-spectrometry-based proteomic and metabolomic analysis of COVID-19 plasma samples collected at two time points. Using Orbitrap Fusion LC-MS/MS-based label-free proteomic analysis, we identified around 10 significant proteins, 32 significant peptides, and 5 metabolites that were dysregulated at the severe time points. Few of these proteins identified by quantitative proteomics were validated using the multiple reaction monitoring (MRM) assay. Integrated pathway analysis using distinct proteomic and metabolomic signatures revealed alterations in complement and coagulation cascade, platelet aggregation, myeloid leukocyte activation pathway, and arginine metabolism. Further, we highlight the role of leukocyte activation and arginine metabolism in COVID-19 pathogenesis and targeting these pathways for COVID-19 therapeutics.
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Affiliation(s)
- Kruthi Suvarna
- Department of Biosciences and Bioengineering,
Indian Institute of Technology Bombay, Powai, Mumbai 400076,
India
| | - Akanksha Salkar
- Department of Biosciences and Bioengineering,
Indian Institute of Technology Bombay, Powai, Mumbai 400076,
India
| | - Viswanthram Palanivel
- Department of Biosciences and Bioengineering,
Indian Institute of Technology Bombay, Powai, Mumbai 400076,
India
| | - Renuka Bankar
- Department of Biosciences and Bioengineering,
Indian Institute of Technology Bombay, Powai, Mumbai 400076,
India
| | - Nirjhar Banerjee
- Department of Biosciences and Bioengineering,
Indian Institute of Technology Bombay, Powai, Mumbai 400076,
India
| | - Medha Gayathri J Pai
- Department of Biosciences and Bioengineering,
Indian Institute of Technology Bombay, Powai, Mumbai 400076,
India
| | - Alisha Srivastava
- Department of Biosciences and Bioengineering,
Indian Institute of Technology Bombay, Powai, Mumbai 400076,
India
- University of Delhi, New
Delhi, Delhi 110021, India
| | - Avinash Singh
- Department of Biosciences and Bioengineering,
Indian Institute of Technology Bombay, Powai, Mumbai 400076,
India
| | - Harsh Khatri
- Department of Biosciences and Bioengineering,
Indian Institute of Technology Bombay, Powai, Mumbai 400076,
India
| | - Sachee Agrawal
- Kasturba Hospital for Infectious
Diseases, Chinchpokli, Mumbai, Maharashtra 400034,
India
| | - Om Shrivastav
- Kasturba Hospital for Infectious
Diseases, Chinchpokli, Mumbai, Maharashtra 400034,
India
| | - Jayanthi Shastri
- Kasturba Hospital for Infectious
Diseases, Chinchpokli, Mumbai, Maharashtra 400034,
India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering,
Indian Institute of Technology Bombay, Powai, Mumbai 400076,
India
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39
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Correa Rojo A, Heylen D, Aerts J, Thas O, Hooyberghs J, Ertaylan G, Valkenborg D. Towards Building a Quantitative Proteomics Toolbox in Precision Medicine: A Mini-Review. Front Physiol 2021; 12:723510. [PMID: 34512391 PMCID: PMC8427610 DOI: 10.3389/fphys.2021.723510] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/05/2021] [Indexed: 12/26/2022] Open
Abstract
Precision medicine as a framework for disease diagnosis, treatment, and prevention at the molecular level has entered clinical practice. From the start, genetics has been an indispensable tool to understand and stratify the biology of chronic and complex diseases in precision medicine. However, with the advances in biomedical and omics technologies, quantitative proteomics is emerging as a powerful technology complementing genetics. Quantitative proteomics provide insight about the dynamic behaviour of proteins as they represent intermediate phenotypes. They provide direct biological insights into physiological patterns, while genetics accounting for baseline characteristics. Additionally, it opens a wide range of applications in clinical diagnostics, treatment stratification, and drug discovery. In this mini-review, we discuss the current status of quantitative proteomics in precision medicine including the available technologies and common methods to analyze quantitative proteomics data. Furthermore, we highlight the current challenges to put quantitative proteomics into clinical settings and provide a perspective to integrate proteomics data with genomics data for future applications in precision medicine.
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Affiliation(s)
- Alejandro Correa Rojo
- Data Science Institute, Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Hasselt University, Diepenbeek, Belgium.,Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Dries Heylen
- Data Science Institute, Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Hasselt University, Diepenbeek, Belgium.,Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Jan Aerts
- Data Science Institute, Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Hasselt University, Diepenbeek, Belgium
| | - Olivier Thas
- Data Science Institute, Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Hasselt University, Diepenbeek, Belgium.,Department of Applied Mathematics, Computer Science and Statistics, Faculty of Sciences, Ghent University, Ghent, Belgium.,National Institute for Applied Statistics Research Australia (NIASRA), Wollongong, NSW, Australia
| | - Jef Hooyberghs
- Flemish Institute for Technological Research (VITO), Mol, Belgium.,Theoretical Physics, Data Science Institute, Hasselt University, Diepenbeek, Belgium
| | - Gökhan Ertaylan
- Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Dirk Valkenborg
- Data Science Institute, Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Hasselt University, Diepenbeek, Belgium
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