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Abyadeh M, Mirshahvaladi S, Kashani SA, Paulo JA, Amirkhani A, Mehryab F, Seydi H, Moradpour N, Jodeiryjabarzade S, Mirzaei M, Gupta V, Shekari F, Salekdeh GH. Proteomic profiling of mesenchymal stem cell-derived extracellular vesicles: Impact of isolation methods on protein cargo. JOURNAL OF EXTRACELLULAR BIOLOGY 2024; 3:e159. [PMID: 38947171 PMCID: PMC11212298 DOI: 10.1002/jex2.159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/01/2024] [Accepted: 05/15/2024] [Indexed: 07/02/2024]
Abstract
Extracellular vesicles (EVs) are nanosized vesicles with a lipid bilayer that are secreted by cells and play a critical role in cell-to-cell communication. Despite the promising reports regarding their diagnostic and therapeutic potential, the utilization of EVs in the clinical setting is limited due to insufficient information about their cargo and a lack of standardization in isolation and analysis methods. Considering protein cargos in EVs as key contributors to their therapeutic potency, we conducted a tandem mass tag (TMT) quantitative proteomics analysis of three subpopulations of mesenchymal stem cell (MSC)-derived EVs obtained through three different isolation techniques: ultracentrifugation (UC), high-speed centrifugation (HS), and ultracentrifugation on sucrose cushion (SU). Subsequently, we checked EV marker expression, size distribution, and morphological characterization, followed by bioinformatic analysis. The bioinformatic analysis of the proteome results revealed that these subpopulations exhibit distinct molecular and functional characteristics. The choice of isolation method impacts the proteome of isolated EVs by isolating different subpopulations of EVs. Specifically, EVs isolated through the high-speed centrifugation (HS) method exhibited a higher abundance of ribosomal and mitochondrial proteins. Functional apoptosis assays comparing isolated mitochondria with EVs isolated through different methods revealed that HS-EVs, but not other EVs, induced early apoptosis in cancer cells. On the other hand, EVs isolated using the sucrose cushion (SU) and ultracentrifugation (UC) methods demonstrated a higher abundance of proteins primarily involved in the immune response, cell-cell interactions and extracellular matrix interactions. Our analyses unveil notable disparities in proteins and associated biological functions among EV subpopulations, underscoring the importance of meticulously selecting isolation methods and resultant EV subpopulations based on the intended application.
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Affiliation(s)
- Morteza Abyadeh
- Department of Stem Cells and Developmental Biology, Cell Science Research CenterRoyan Institute for Stem Cell Biology and Technology, ACECRTehranIran
| | - Shahab Mirshahvaladi
- Macquarie Medical School, School of MedicineHealth and Human Sciences, Macquarie UniversitySydneyNew South WalesAustralia
| | - Sara Assar Kashani
- Department of Stem Cells and Developmental Biology, Cell Science Research CenterRoyan Institute for Stem Cell Biology and Technology, ACECRTehranIran
- Motor Neuron Disease Research Centre, Faculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Joao A. Paulo
- Department of Cell BiologyHarvard Medical SchoolBostonMassachusettsUSA
| | - Ardeshir Amirkhani
- Australian Proteome Analysis FacilityMacquarie UniversitySydneyNew South WalesAustralia
| | - Fatemeh Mehryab
- Advanced Therapy Medicinal Product Technology Development Center, Cell Science Research CenterRoyan Institute for Stem Cell Biology and Technology, ACECRTehranIran
| | - Homeyra Seydi
- Advanced Therapy Medicinal Product Technology Development Center, Cell Science Research CenterRoyan Institute for Stem Cell Biology and Technology, ACECRTehranIran
- Department of BiologyUniversity of Science and CultureTehranIran
| | | | | | - Mehdi Mirzaei
- Macquarie Medical School, School of MedicineHealth and Human Sciences, Macquarie UniversitySydneyNew South WalesAustralia
| | - Vivek Gupta
- Macquarie Medical School, School of MedicineHealth and Human Sciences, Macquarie UniversitySydneyNew South WalesAustralia
| | - Faezeh Shekari
- Department of Stem Cells and Developmental Biology, Cell Science Research CenterRoyan Institute for Stem Cell Biology and Technology, ACECRTehranIran
- Advanced Therapy Medicinal Product Technology Development Center, Cell Science Research CenterRoyan Institute for Stem Cell Biology and Technology, ACECRTehranIran
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Di Ciaula A, Liberale L, Portincasa P, Khalil M, Galerati I, Farella I, Noto A, JohnBritto S, Moriero M, Michelauz C, Frè F, Olivero C, Bertolotto M, Montecucco F, Carbone F, Bonfrate L. Neutrophil degranulation, endothelial and metabolic dysfunction in unvaccinated long COVID patients. Eur J Clin Invest 2024; 54:e14155. [PMID: 38226472 DOI: 10.1111/eci.14155] [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: 09/12/2023] [Revised: 12/03/2023] [Accepted: 12/06/2023] [Indexed: 01/17/2024]
Abstract
BACKGROUND Long COVID symptoms are widely diffused and have a poorly understood pathophysiology, with possible involvement of inflammatory cytokines. MATERIALS AND METHODS A prospective follow-up study involved 385 unvaccinated patients, started 1 month after SARS-CoV-2 infection and continued for up to 12 months. We compared circulating biomarkers of neutrophil degranulation, endothelial and metabolic dysfunction in subjects with long COVID symptoms and in asymptomatic post-COVID controls. RESULTS The highest occurrence of symptoms (71%) was after 3 months from the infection, decreasing to 62.3% and 29.4% at 6 and 12 months, respectively. Compared to controls, long COVID patients had increased levels of the neutrophilic degranulation indices MMP-8 and MPO, of endothelial dysfunction indices L-selectin and P-selectin. Among indices of metabolic dysfunction, leptin levels were higher in long COVID patients than in controls. CONCLUSION In unvaccinated patients, symptoms may persist up to 1 year after acute COVID infection, with increased indices of neutrophil degranulation, endothelial and metabolic dysfunction. The clinical implications of specific inflammatory biomarkers require further attention, especially in individuals with fatigue and long COVID-linked cognitive dysfunctions.
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Affiliation(s)
- Agostino Di Ciaula
- Clinica Medica "A. Murri", Division of Internal Medicine, Department of Preventive and Regenerative Medicine and Ionian Area (DiMePrev-J), University of Bari Aldo Moro, Bari, Italy
| | - Luca Liberale
- First Clinic of Internal Medicine, Department of Internal Medicine, University of Genoa, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino Genoa-Italian Cardiovascular Network, Genoa, Italy
| | - Piero Portincasa
- Clinica Medica "A. Murri", Division of Internal Medicine, Department of Preventive and Regenerative Medicine and Ionian Area (DiMePrev-J), University of Bari Aldo Moro, Bari, Italy
| | - Mohamad Khalil
- Clinica Medica "A. Murri", Division of Internal Medicine, Department of Preventive and Regenerative Medicine and Ionian Area (DiMePrev-J), University of Bari Aldo Moro, Bari, Italy
| | - Ilaria Galerati
- Clinica Medica "A. Murri", Division of Internal Medicine, Department of Preventive and Regenerative Medicine and Ionian Area (DiMePrev-J), University of Bari Aldo Moro, Bari, Italy
| | - Ilaria Farella
- Clinica Medica "A. Murri", Division of Internal Medicine, Department of Preventive and Regenerative Medicine and Ionian Area (DiMePrev-J), University of Bari Aldo Moro, Bari, Italy
| | - Antonino Noto
- Clinica Medica "A. Murri", Division of Internal Medicine, Department of Preventive and Regenerative Medicine and Ionian Area (DiMePrev-J), University of Bari Aldo Moro, Bari, Italy
| | - Stephy JohnBritto
- Clinica Medica "A. Murri", Division of Internal Medicine, Department of Preventive and Regenerative Medicine and Ionian Area (DiMePrev-J), University of Bari Aldo Moro, Bari, Italy
| | - Margherita Moriero
- First Clinic of Internal Medicine, Department of Internal Medicine, University of Genoa, Genoa, Italy
| | - Cristina Michelauz
- First Clinic of Internal Medicine, Department of Internal Medicine, University of Genoa, Genoa, Italy
| | - Federica Frè
- First Clinic of Internal Medicine, Department of Internal Medicine, University of Genoa, Genoa, Italy
| | - Chiara Olivero
- First Clinic of Internal Medicine, Department of Internal Medicine, University of Genoa, Genoa, Italy
| | - Maria Bertolotto
- First Clinic of Internal Medicine, Department of Internal Medicine, University of Genoa, Genoa, Italy
| | - Fabrizio Montecucco
- First Clinic of Internal Medicine, Department of Internal Medicine, University of Genoa, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino Genoa-Italian Cardiovascular Network, Genoa, Italy
| | - Federico Carbone
- First Clinic of Internal Medicine, Department of Internal Medicine, University of Genoa, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino Genoa-Italian Cardiovascular Network, Genoa, Italy
| | - Leonilde Bonfrate
- Clinica Medica "A. Murri", Division of Internal Medicine, Department of Preventive and Regenerative Medicine and Ionian Area (DiMePrev-J), University of Bari Aldo Moro, Bari, Italy
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3
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Singh MS, Pyati A, Rubi RD, Subramanian R, Muley VY, Ansari MA, Yellaboina S. Systems-wide view of host-pathogen interactions across COVID-19 severities using integrated omics analysis. iScience 2024; 27:109087. [PMID: 38384846 PMCID: PMC10879696 DOI: 10.1016/j.isci.2024.109087] [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: 09/11/2023] [Revised: 11/07/2023] [Accepted: 01/29/2024] [Indexed: 02/23/2024] Open
Abstract
The mechanisms explaining the variability in COVID-19 clinical manifestations (mild, moderate, and severe) are not fully understood. To identify key gene expression markers linked to disease severity, we employed an integrated approach, combining host-pathogen protein-protein interaction data and viral-induced host gene expression data. We analyzed an RNA-seq dataset from peripheral blood mononuclear cells across 12 projects representing the spectrum of disease severity. We identified genes showing differential expression across mild, moderate, and severe conditions. Enrichment analysis of the pathways in host proteins targeted by each of the SARS-CoV-2 proteins revealed a strong association with processes related to ribosomal biogenesis, translation, and translocation. Interestingly, most of these pathways and associated cellular machinery, including ribosomal biogenesis, ribosomal proteins, and translation, were upregulated in mild conditions but downregulated in severe cases. This suggests that COVID-19 exhibits a paradoxical host response, boosting host/viral translation in mild cases but slowing it in severe cases.
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Affiliation(s)
- Mairembam Stelin Singh
- Department of Biochemistry, SCLS, Jamia Hamdard, New Delhi, India
- Department of Zoology, Rajiv Gandhi University, Itanagar, Arunachal Pradesh, India
| | - Anand Pyati
- All India Institute of Medical Sciences, Bibinagar, Hyderabad, Telangana 508126, India
| | - R. Devika Rubi
- Department of Computer Science and Engineering, Keshav Memorial Institute of Technology, Hyderabad, Telangana State, India
| | - Rajasekaran Subramanian
- Department of Computer Science and Engineering, Keshav Memorial Institute of Technology, Hyderabad, Telangana State, India
| | | | - Mairaj Ahmed Ansari
- Department of Biotechnology, SCLS, Jamia Hamdard, New Delhi, India
- Centre for Virology, SIST, Jamia Hamdard, New Delhi, India
| | - Sailu Yellaboina
- All India Institute of Medical Sciences, Bibinagar, Hyderabad, Telangana 508126, India
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Rajoria S, Kavuru SR, Pyda HS, Bihani S, Borishetty D, Biswas D, Prajapati J, Paladi H, Srivastava S. CoVProt: Toward a Mass Spectrometry Data Portal for COVID-19 Proteomics Research and Development. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:24-31. [PMID: 38193774 DOI: 10.1089/omi.2023.0274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has wreaked havoc globally. Beyond the pandemic, the long-term effects of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus in multiple organ systems are yet to be deciphered. This calls for continued systems science research. Moreover, the host response to SARS-CoV-2 varies person-to-person and gives rise to different degrees of morbidity and mortality. Mass spectrometry (MS) has been a proven asset in studies of the SARS-CoV-2 from an omics systems science lens. To strengthen the proteomics research dedicated to COVID-19, we introduce here a web-based portal, CoVProt. The portal is work in progress and aims for a comprehensive curation of MS-based proteomics data of COVID-19 clinical samples for deep proteomic investigations, data visualization, and easy data accessibility for life sciences innovations and planetary health research community. Currently, CoVProt contains information on 2725 different proteins and 37,125 different peptides from six data sets covering a total of 202 clinical samples. Moreover, all pertinent data sets extracted from the literature have been reanalyzed using a common analysis pipeline developed by combining multiple tools. Going forward, we anticipate that the CoVProt portal will also provide access to the clinical parameters of the patients. The CoVProt (v1.0) portal addresses an existing significant gap to study COVID-19 host proteomics, which, to the best of our knowledge, is the first effort in this direction. We believe that CoVProt is poised to make contributions as a community resource for proteomic applications and aims to broadly support clinical studies to facilitate the discovery of COVID-19 biomarkers and therapeutics with translational potential.
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Affiliation(s)
- Sakshi Rajoria
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Sai Rohith Kavuru
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Hari Sundar Pyda
- Department of Chemical Engineering, Institute of Chemical Technology, Mumbai- Indian Oil Odisha Campus, Bhubaneswar, India
| | - Surbhi Bihani
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Dhanush Borishetty
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Deeptrup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Jeel Prajapati
- Department of Biotechnology and Bioengineering, Institute of Advanced Research, Gandhinagar, India
| | - Harshith Paladi
- Department of Computer Science, School of Computing, SASTRA Deemed to be University, Thanjavur, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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Bihani S, Gupta A, Mehta S, Rajczewski AT, Johnson J, Borishetty D, Griffin TJ, Srivastava S, Jagtap PD. Metaproteomic Analysis of Nasopharyngeal Swab Samples to Identify Microbial Peptides in COVID-19 Patients. J Proteome Res 2023; 22:2608-2619. [PMID: 37450889 DOI: 10.1021/acs.jproteome.3c00040] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
During the COVID-19 pandemic, impaired immunity and medical interventions resulted in cases of secondary infections. The clinical difficulties and dangers associated with secondary infections in patients necessitate the exploration of their microbiome. Metaproteomics is a powerful approach to study the taxonomic composition and functional status of the microbiome under study. In this study, the mass spectrometry (MS)-based data of nasopharyngeal swab samples from COVID-19 patients was used to investigate the metaproteome. We have established a robust bioinformatics workflow within the Galaxy platform, which includes (a) generation of a tailored database of the common respiratory tract pathogens, (b) database search using multiple search algorithms, and (c) verification of the detected microbial peptides. The microbial peptides detected in this study, belong to several opportunistic pathogens such as Streptococcus pneumoniae, Klebsiella pneumoniae, Rhizopus microsporus, and Syncephalastrum racemosum. Microbial proteins with a role in stress response, gene expression, and DNA repair were found to be upregulated in severe patients compared to negative patients. Using parallel reaction monitoring (PRM), we confirmed some of the microbial peptides in fresh clinical samples. MS-based clinical metaproteomics can serve as a powerful tool for detection and characterization of potential pathogens, which can significantly impact the diagnosis and treatment of patients.
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Affiliation(s)
- Surbhi Bihani
- Department of Bioscience and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
| | - Aryan Gupta
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
| | - Subina Mehta
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 7-129 MCB, 420 Washington Ave SE, Minneapolis, Minnesota 55455, United States
| | - Andrew T Rajczewski
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 7-129 MCB, 420 Washington Ave SE, Minneapolis, Minnesota 55455, United States
| | - James Johnson
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Dhanush Borishetty
- Department of Bioscience and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
| | - Timothy J Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 7-129 MCB, 420 Washington Ave SE, Minneapolis, Minnesota 55455, United States
| | - Sanjeeva Srivastava
- Department of Bioscience and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
| | - Pratik D Jagtap
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 7-129 MCB, 420 Washington Ave SE, Minneapolis, Minnesota 55455, United States
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Liu C, Zhang Y, Gao X, Wang G. Identification of cell subpopulations associated with disease phenotypes from scRNA-seq data using PACSI. BMC Biol 2023; 21:159. [PMID: 37468850 PMCID: PMC10354926 DOI: 10.1186/s12915-023-01658-3] [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: 03/21/2023] [Accepted: 07/03/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Single-cell RNA sequencing (scRNA-seq) has revolutionized the transcriptomics field by advancing analyses from tissue-level to cell-level resolution. Despite the great advances in the development of computational methods for various steps of scRNA-seq analyses, one major bottleneck of the existing technologies remains in identifying the molecular relationship between disease phenotype and cell subpopulations, where "disease phenotype" refers to the clinical characteristics of each patient sample, and subpopulation refer to groups of single cells, which often do not correspond to clusters identified by standard single-cell clustering analysis. Here, we present PACSI, a method aimed at distinguishing cell subpopulations associated with disease phenotypes at the single-cell level. RESULTS PACSI takes advantage of the topological properties of biological networks to introduce a proximity-based measure that quantifies the correlation between each cell and the disease phenotype of interest. Applied to simulated data and four case studies, PACSI accurately identified cells associated with disease phenotypes such as diagnosis, prognosis, and response to immunotherapy. In addition, we demonstrated that PACSI can also be applied to spatial transcriptomics data and successfully label spots that are associated with poor survival of breast carcinoma. CONCLUSIONS PACSI is an efficient method to identify cell subpopulations associated with disease phenotypes. Our research shows that it has a broad range of applications in revealing mechanistic and clinical insights of diseases.
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Affiliation(s)
- Chonghui Liu
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
- College of Computer and Control Engineering, Northeast Forestry University, Harbin, 150040, China
| | - Yan Zhang
- Department of Ophthalmology, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Xin Gao
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
- KAUST Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia.
| | - Guohua Wang
- College of Computer and Control Engineering, Northeast Forestry University, Harbin, 150040, China.
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, 150001, China.
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Abyadeh M, Yadav VK, Kaya A. Common molecular signatures between coronavirus infection and Alzheimer's disease reveal targets for drug development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544970. [PMID: 37398415 PMCID: PMC10312734 DOI: 10.1101/2023.06.14.544970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Cognitive decline has been reported as a common consequence of COVID-19, and studies have suggested a link between COVID-19 infection and Alzheimer's disease (AD). However, the molecular mechanisms underlying this association remain unclear. To shed light on this link, we conducted an integrated genomic analysis using a novel Robust Rank Aggregation method to identify common transcriptional signatures of the frontal cortex, a critical area for cognitive function, between individuals with AD and COVID-19. We then performed various analyses, including the KEGG pathway, GO ontology, protein-protein interaction, hub gene, gene-miRNA, and gene-transcription factor interaction analyses to identify molecular components of biological pathways that are associated with AD in the brain also show similar changes in severe COVID-19. Our findings revealed the molecular mechanisms underpinning the association between COVID-19 infection and AD development and identified several genes, miRNAs, and TFs that may be targeted for therapeutic purposes. However, further research is needed to investigate the diagnostic and therapeutic applications of these findings.
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Affiliation(s)
- Morteza Abyadeh
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284 USA
| | - Vijay K. Yadav
- Department of Genetics and Development, Columbia University, New York, NY, USA
| | - Alaattin Kaya
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284 USA
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8
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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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9
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Liang Z, Zheng X, Wang Y, Chu K, Gao Y. Using system biology and bioinformatics to identify the influences of COVID-19 co-infection with influenza virus on COPD. Funct Integr Genomics 2023; 23:175. [PMID: 37221323 DOI: 10.1007/s10142-023-01091-3] [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: 04/10/2023] [Revised: 05/07/2023] [Accepted: 05/09/2023] [Indexed: 05/25/2023]
Abstract
Coronavirus disease 2019 (COVID-19) has speedily increased mortality globally. Although they are risk factors for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), less is known about the common molecular mechanisms behind COVID-19, influenza virus A (IAV), and chronic obstructive pulmonary disease (COPD). This research used bioinformatics and systems biology to find possible medications for treating COVID-19, IAV, and COPD via identifying differentially expressed genes (DEGs) from gene expression datasets (GSE171110, GSE76925, GSE106986, and GSE185576). A total of 78 DEGs were subjected to functional enrichment, pathway analysis, protein-protein interaction (PPI) network construct, hub gene extraction, and other potentially relevant disorders. Then, DEGs were discovered in networks including transcription factor (TF)-gene connections, protein-drug interactions, and DEG-microRNA (miRNA) coregulatory networks by using NetworkAnalyst. The top 12 hub genes were MPO, MMP9, CD8A, HP, ELANE, CD5, CR2, PLA2G7, PIK3R1, SLAMF1, PEX3, and TNFRSF17. We found that 44 TFs-genes, as well as 118 miRNAs, are directly linked to hub genes. Additionally, we searched the Drug Signatures Database (DSigDB) and identified 10 drugs that could potentially treat COVID-19, IAV, and COPD. Therefore, we evaluated the top 12 hub genes that could be promising DEGs for targeted therapy for SARS-CoV-2 and identified several prospective medications that may benefit COPD patients with COVID-19 and IAV co-infection.
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Affiliation(s)
- Zihao Liang
- Clinical Research Center, the Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xudong Zheng
- Department of Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yuan Wang
- Clinical Research Center, the Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Kai Chu
- Department of Vaccine Clinical Evaluation, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, China.
| | - Yanan Gao
- Department of Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
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Banerjee A, Halder A, Jadhav P, Sarkar A, Hole A, Shastri JS, Agrawal S, Chilakapati MK, Srivastava S. SARS-CoV-2 severity classification from plasma sample using confocal Raman spectroscopy. JOURNAL OF RAMAN SPECTROSCOPY : JRS 2023; 54:124-132. [PMID: 36713977 PMCID: PMC9874663 DOI: 10.1002/jrs.6461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/05/2022] [Accepted: 10/10/2022] [Indexed: 06/18/2023]
Abstract
The world is on the brink of facing coronavirus's (COVID-19) fourth wave as the mutant forms of viruses are escaping neutralizing antibodies in spite of being vaccinated. As we have already witnessed that it has encumbered our health system, with hospitals swamped with infected patients observed during the viral outbreak. Rapid triage of patients infected with SARS-CoV-2 is required during hospitalization to prioritize and provide the best point of care. Traditional diagnostics techniques such as RT-PCR and clinical parameters such as symptoms, comorbidities, sex and age are not enough to identify the severity of patients. Here, we investigated the potential of confocal Raman microspectroscopy as a powerful tool to generate an expeditious blood-based test for the classification of COVID-19 disease severity using 65 patients plasma samples from cohorts infected with SARS-CoV-2. We designed an easy manageable blood test where we used a small volume (8 μl) of inactivated whole plasma samples from infected patients without any extra solvent usage in plasma processing. Raman spectra of plasma samples were acquired and multivariate exploratory analysis PC-LDA (principal component based linear discriminant analysis) was used to build a model, which segregated the severe from the non-severe COVID-19 group with a sensitivity of 83.87%, specificity of 70.60% and classification efficiency of 76.92%. Among the bands expressed in both the cohorts, the study led to the identification of Raman fingerprint regions corresponding to lipids (1661, 1742), proteins amide I and amide III (1555, 1247), proteins (Phe) (1006, 1034), and nucleic acids (760) to be differentially expressed in severe COVID-19 patient's samples. In summary, the current study exhibits the potential of confocal Raman to generate simple, rapid, and less expensive blood tests to triage the severity of patients infected with SARS-CoV-2.
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Affiliation(s)
- Arghya Banerjee
- Department of Biosciences and BioengineeringIndian Institute of Technology BombayMumbaiIndia
| | - Ankit Halder
- Department of Biosciences and BioengineeringIndian Institute of Technology BombayMumbaiIndia
| | - Priyanka Jadhav
- Advanced Centre for Treatment Research and Education in Cancer (ACTREC)Tata Memorial Centre (TMC)Navi MumbaiIndia
- Homi Bhabha National InstituteTraining School Complex, Anushakti NagarMumbaiIndia
| | - Anushka Sarkar
- Department of Life SciencesPresidency University (Main Campus)KolkataIndia
| | - Arti Hole
- Advanced Centre for Treatment Research and Education in Cancer (ACTREC)Tata Memorial Centre (TMC)Navi MumbaiIndia
| | | | | | - Murali Krishna Chilakapati
- Advanced Centre for Treatment Research and Education in Cancer (ACTREC)Tata Memorial Centre (TMC)Navi MumbaiIndia
| | - Sanjeeva Srivastava
- Department of Biosciences and BioengineeringIndian Institute of Technology BombayMumbaiIndia
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11
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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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12
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Abyadeh M, Yadav VK, Kaya A. Common Molecular Signatures Between Coronavirus Infection and Alzheimer's Disease Reveal Targets for Drug Development. J Alzheimers Dis 2023; 95:995-1011. [PMID: 37638446 DOI: 10.3233/jad-230684] [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] [Indexed: 08/29/2023]
Abstract
BACKGROUND Cognitive decline is a common consequence of COVID-19, and studies suggest a link between COVID-19 and Alzheimer's disease (AD). However, the molecular mechanisms underlying this association remain unclear. OBJECTIVE To understand the potential molecular mechanisms underlying the association between COVID-19 and AD development, and identify the potential genetic targets for pharmaceutical approaches to reduce the risk or delay the development of COVID-19-related neurological pathologies. METHODS We analyzed transcriptome datasets of 638 brain samples using a novel Robust Rank Aggregation method, followed by functional enrichment, protein-protein, hub genes, gene-miRNA, and gene-transcription factor (TF) interaction analyses to identify molecular markers altered in AD and COVID-19 infected brains. RESULTS Our analyses of frontal cortex from COVID-19 and AD patients identified commonly altered genes, miRNAs and TFs. Functional enrichment and hub gene analysis of these molecular changes revealed commonly altered pathways, including downregulation of the cyclic adenosine monophosphate (cAMP) signaling and taurine and hypotaurine metabolism, alongside upregulation of neuroinflammatory pathways. Furthermore, gene-miRNA and gene-TF network analyses provided potential up- and downstream regulators of identified pathways. CONCLUSION We found that downregulation of cAMP signaling pathway, taurine metabolisms, and upregulation of neuroinflammatory related pathways are commonly altered in AD and COVID-19 pathogenesis, and may make COVID-19 patients more susceptible to cognitive decline and AD. We also identified genetic targets, regulating these pathways that can be targeted pharmaceutically to reduce the risk or delay the development of COVID-19-related neurological pathologies and AD.
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Affiliation(s)
- Morteza Abyadeh
- Department of Biology, Virginia Common wealth University, Richmond, VA, USA
| | - Vijay K Yadav
- Department of Genetics and Development, Columbia University, New York, NY, USA
| | - Alaattin Kaya
- Department of Biology, Virginia Common wealth University, Richmond, VA, USA
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13
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Ciccosanti F, Antonioli M, Sacchi A, Notari S, Farina A, Beccacece A, Fusto M, Vergori A, D'Offizi G, Taglietti F, Antinori A, Nicastri E, Marchioni L, Palmieri F, Ippolito G, Piacentini M, Agrati C, Fimia GM. Proteomic analysis identifies a signature of disease severity in the plasma of COVID-19 pneumonia patients associated to neutrophil, platelet and complement activation. Clin Proteomics 2022; 19:38. [PMID: 36348270 PMCID: PMC9641302 DOI: 10.1186/s12014-022-09377-7] [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: 06/13/2022] [Accepted: 10/26/2022] [Indexed: 11/10/2022] Open
Abstract
Most patients infected with SARS-CoV-2 display mild symptoms with good prognosis, while 20% of patients suffer from severe viral pneumonia and up to 5% may require intensive care unit (ICU) admission due to severe acute respiratory syndrome, which could be accompanied by multiorgan failure.Plasma proteomics provide valuable and unbiased information about disease progression and therapeutic candidates. Recent proteomic studies have identified molecular changes in plasma of COVID-19 patients that implied significant dysregulation of several aspects of the inflammatory response accompanied by a general metabolic suppression. However, which of these plasma alterations are associated with disease severity remains only partly characterized.A known limitation of proteomic studies of plasma samples is the large difference in the macromolecule abundance, with concentration spanning at least 10 orders of magnitude. To improve the coverage of plasma contents, we performed a deep proteomic analysis of plasma from 10 COVID-19 patients with severe/fatal pneumonia compared to 10 COVID-19 patients with pneumonia who did not require ICU admission (non-ICU). To this aim, plasma samples were first depleted of the most abundant proteins, trypsin digested and peptides subjected to a high pH reversed-phase peptide fractionation before LC-MS analysis.These results highlighted an increase of proteins involved in neutrophil and platelet activity and acute phase response, which is significantly higher in severe/fatal COVID-19 patients when compared to non-ICU ones. Importantly, these changes are associated with a selective induction of complement cascade factors in severe/fatal COVID-19 patients. Data are available via ProteomeXchange with identifier PXD036491. Among these alterations, we confirmed by ELISA that higher levels of the neutrophil granule proteins DEFA3 and LCN2 are present in COVID-19 patients requiring ICU admission when compared to non-ICU and healthy donors.Altogether, our study provided an in-depth view of plasma proteome changes that occur in COVID-19 patients in relation to disease severity, which can be helpful to identify therapeutic strategies to improve the disease outcome.
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Affiliation(s)
- Fabiola Ciccosanti
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Manuela Antonioli
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Alessandra Sacchi
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Stefania Notari
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Anna Farina
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Alessia Beccacece
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Marisa Fusto
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Alessandra Vergori
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Gianpiero D'Offizi
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Fabrizio Taglietti
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Andrea Antinori
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Emanuele Nicastri
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Luisa Marchioni
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Fabrizio Palmieri
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Giuseppe Ippolito
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
- General Directorate for Research and Health Innovation, Italian Ministry of Health, Rome, Italy
| | - Mauro Piacentini
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Chiara Agrati
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy.
- Department of Hematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children Hospital, IRCCS, Rome, Italy.
| | - Gian Maria Fimia
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy.
- Department of Molecular Medicine, University of Rome "Sapienza", Rome, Italy.
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14
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Cavalcante LTDF, da Fonseca GC, Amado Leon LA, Salvio AL, Brustolini OJ, Gerber AL, Guimarães APDC, Marques CAB, Fernandes RA, Ramos Filho CHF, Kader RL, Pimentel Amaro M, da Costa Gonçalves JP, Vieira Alves-Leon S, Vasconcelos ATR. Buffy Coat Transcriptomic Analysis Reveals Alterations in Host Cell Protein Synthesis and Cell Cycle in Severe COVID-19 Patients. Int J Mol Sci 2022; 23:13588. [PMID: 36362378 PMCID: PMC9659271 DOI: 10.3390/ijms232113588] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 11/25/2023] Open
Abstract
Transcriptome studies have reported the dysregulation of cell cycle-related genes and the global inhibition of host mRNA translation in COVID-19 cases. However, the key genes and cellular mechanisms that are most affected by the severe outcome of this disease remain unclear. For this work, the RNA-seq approach was used to study the differential expression in buffy coat cells of two groups of people infected with SARS-CoV-2: (a) Mild, with mild symptoms; and (b) SARS (Severe Acute Respiratory Syndrome), who were admitted to the intensive care unit with the severe COVID-19 outcome. Transcriptomic analysis revealed 1009 up-regulated and 501 down-regulated genes in the SARS group, with 10% of both being composed of long non-coding RNA. Ribosome and cell cycle pathways were enriched among down-regulated genes. The most connected proteins among the differentially expressed genes involved transport dysregulation, proteasome degradation, interferon response, cytokinesis failure, and host translation inhibition. Furthermore, interactome analysis showed Fibrillarin to be one of the key genes affected by SARS-CoV-2. This protein interacts directly with the N protein and long non-coding RNAs affecting transcription, translation, and ribosomal processes. This work reveals a group of dysregulated processes, including translation and cell cycle, as key pathways altered in severe COVID-19 outcomes.
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Affiliation(s)
| | | | - Luciane Almeida Amado Leon
- Laboratório de Desenvolvimento Tecnológico em Virologia, Instituto Oswaldo Cruz/FIOCRUZ, Rio de Janeiro 21040-360, Brazil
| | - Andreza Lemos Salvio
- Laboratório de Neurociências Translacional, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro 20211-040, Brazil
| | - Otávio José Brustolini
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro 25651-076, Brazil
| | - Alexandra Lehmkuhl Gerber
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro 25651-076, Brazil
| | - Ana Paula de Campos Guimarães
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro 25651-076, Brazil
| | - Carla Augusta Barreto Marques
- Laboratório de Neurociências Translacional, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro 20211-040, Brazil
- Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-617, Brazil
| | - Renan Amphilophio Fernandes
- Laboratório de Neurociências Translacional, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro 20211-040, Brazil
| | | | - Rafael Lopes Kader
- Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-617, Brazil
| | - Marisa Pimentel Amaro
- Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-617, Brazil
| | - João Paulo da Costa Gonçalves
- Laboratório de Neurociências Translacional, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro 20211-040, Brazil
- Yale New Haven Hospital, New Haven, CT 06510, USA
| | - Soniza Vieira Alves-Leon
- Laboratório de Neurociências Translacional, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro 20211-040, Brazil
- Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-617, Brazil
| | - Ana Tereza Ribeiro Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro 25651-076, Brazil
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15
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Mehta S, Carvalho VM, Rajczewski AT, Pible O, Grüning BA, Johnson JE, Wagner R, Armengaud J, Griffin TJ, Jagtap PD. Catching the Wave: Detecting Strain-Specific SARS-CoV-2 Peptides in Clinical Samples Collected during Infection Waves from Diverse Geographical Locations. Viruses 2022; 14:2205. [PMID: 36298760 PMCID: PMC9609567 DOI: 10.3390/v14102205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/05/2022] Open
Abstract
The Coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resulted in a major health crisis worldwide with its continuously emerging new strains, resulting in new viral variants that drive "waves" of infection. PCR or antigen detection assays have been routinely used to detect clinical infections; however, the emergence of these newer strains has presented challenges in detection. One of the alternatives has been to detect and characterize variant-specific peptide sequences from viral proteins using mass spectrometry (MS)-based methods. MS methods can potentially help in both diagnostics and vaccine development by understanding the dynamic changes in the viral proteome associated with specific strains and infection waves. In this study, we developed an accessible, flexible, and shareable bioinformatics workflow that was implemented in the Galaxy Platform to detect variant-specific peptide sequences from MS data derived from the clinical samples. We demonstrated the utility of the workflow by characterizing published clinical data from across the world during various pandemic waves. Our analysis identified six SARS-CoV-2 variant-specific peptides suitable for confident detection by MS in commonly collected clinical samples.
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Affiliation(s)
- Subina Mehta
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Andrew T. Rajczewski
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Olivier Pible
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, 30200 Bagnols-sur-Cèze, France
| | - Björn A. Grüning
- Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany
| | - James E. Johnson
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Reid Wagner
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, 30200 Bagnols-sur-Cèze, France
| | - Timothy J. Griffin
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Pratik D. Jagtap
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
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16
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Noninvasive nasopharyngeal proteomics of COVID-19 patient identify abnormalities related to complement and coagulation cascade and mucosal immune system. PLoS One 2022; 17:e0274228. [PMID: 36094909 PMCID: PMC9467311 DOI: 10.1371/journal.pone.0274228] [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: 06/20/2022] [Accepted: 08/23/2022] [Indexed: 11/25/2022] Open
Abstract
Serum or plasma have been the primary focus of proteomics studies for COVID-19 to identity biomarkers and potential drug targets. The nasal mucosal environment which consists of lipids, mucosal immune cells, and nasal proteome, has been largely neglected but later revealed to have critical role combating SARS-CoV-2 infection. We present a bottom-up proteomics investigation of the host response to SARS-CoV-2 infection in the nasopharyngeal environment, featuring a noninvasive approach using proteins in nasopharyngeal swabs collected from groups of 76 SARS-CoV-2 positive and 76 negative patients. Results showed that 31 significantly down-regulated and 6 up-regulated proteins were identified (p < 0.05, log2 FC > 1.3) in SARS-CoV-2 positive patient samples as compared to the negatives; these proteins carry potential value as markers for the early detection of COVID-19, disease monitoring, as well as be drug targets. The down-regulation of coagulation factor 5 indicates a thrombotic abnormality in COVID-19 patients and the decreased IgG4 suggests an abnormal immune response at the point of entry in human nasopharyngeal environment, which is in consistent with KEGG and GO pathway analysis. Our study also demonstrated that mass spectrometry proteomics analysis of nasopharyngeal swabs can be used as a powerful early approach to evaluate host response to SARS-CoV-2 viral infection.
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17
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Lai G, Liu H, Deng J, Li K, Xie B. A Novel 3-Gene Signature for Identifying COVID-19 Patients Based on Bioinformatics and Machine Learning. Genes (Basel) 2022; 13:genes13091602. [PMID: 36140771 PMCID: PMC9498787 DOI: 10.3390/genes13091602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/29/2022] [Accepted: 09/06/2022] [Indexed: 12/15/2022] Open
Abstract
Although many biomarkers associated with coronavirus disease 2019 (COVID-19) were found, a novel signature relevant to immune cells has not been developed. In this work, the “CIBERSORT” algorithm was used to assess the fraction of immune infiltrating cells in GSE152641 and GSE171110. Key modules associated with important immune cells were selected by the “WGCNA” package. The “GO” enrichment analysis was used to reveal the biological function associated with COVID-19. The “Boruta” algorithm was used to screen candidate genes, and the “LASSO” algorithm was used for collinearity reduction. A novel gene signature was developed based on multivariate logistic regression analysis. Subsequently, M0 macrophages (PRAUC = 0.948 in GSE152641 and PRAUC = 0.981 in GSE171110) and neutrophils (PRAUC = 0.892 in GSE152641 and PRAUC = 0.960 in GSE171110) were considered as important immune cells. Forty-three intersected genes from two modules were selected, which mainly participated in some immune-related activities. Finally, a three-gene signature comprising CLEC4D, DUSP13, and UNC5A that can accurately distinguish COVID-19 patients and healthy controls in three datasets was constructed. The ROCAUC was 0.974 in the training set, 0.946 in the internal test set, and 0.709 in the external test set. In conclusion, we constructed a three-gene signature to identify COVID-19, and CLEC4D, DUSP13, and UNC5A may be potential biomarkers for COVID-19 patients.
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18
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Zhang N, Wang S, Wong CC. Proteomics research of SARS-CoV-2 and COVID-19 disease. MEDICAL REVIEW (BERLIN, GERMANY) 2022; 2:427-445. [PMID: 37724330 PMCID: PMC10388787 DOI: 10.1515/mr-2022-0016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 07/06/2022] [Indexed: 09/20/2023]
Abstract
Currently, coronavirus disease 2019 (COVID-19) is still spreading in a global scale, exerting a massive health and socioeconomic crisis. Deep insights into the molecular functions of the viral proteins and the pathogenesis of this infectious disease are urgently needed. In this review, we comprehensively describe the proteome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and summarize their protein interaction map with host cells. In the protein interaction network between the virus and the host, a total of 787 host prey proteins that appeared in at least two studies or were verified by co-immunoprecipitation experiments. Together with 29 viral proteins, a network of 1762 proximal interactions were observed. We also review the proteomics results of COVID-19 patients and proved that SARS-CoV-2 hijacked the host's translation system, post-translation modification system, and energy supply system via viral proteins, resulting in various immune disorders, multiple cardiomyopathies, and cholesterol metabolism diseases.
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Affiliation(s)
- Nan Zhang
- Department of Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, USA
- Center for Cancer Metabolism, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Siyuan Wang
- Department of Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Catherine C.L. Wong
- Department of Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
- Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing, P. R. China
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19
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Banerjee A, Pai MGJ, Singh A, Nissa MU, Srivastava S. Mass spectrometry and proteome analysis to identify SARS-CoV-2 protein from COVID-19 patient swab samples. STAR Protoc 2022; 3:101177. [PMID: 35233542 PMCID: PMC8808698 DOI: 10.1016/j.xpro.2022.101177] [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] [Indexed: 12/01/2022] Open
Abstract
With new emerging SARS-CoV-2 strains and their increased pathogenicity, diagnosis has become more challenging. Molecular diagnosis often involves the use of nasopharyngeal swabs and subsequent real-time PCR-based tests. Although this test is the gold standard, it has several limitations; therefore, more complementary assays are required. This protocol describes how to identify SARS-CoV-2 protein from patients' nasopharyngeal swab samples. We first introduce the approach of label-free quantitative proteomics. We then detail target verification by triple quadrupole mass spectrometry (MS)-based targeted proteomics. For complete details on the use and execution of this profile, please refer to Bankar et al. (2021). A protocol for identification of SARS-CoV-2 protein from patients' swab samples Sequential steps involved in proteomic sample preparation are elaborated Detailed procedure for MS-based targeted proteomic verification is presented A detailed presentation of workflow for label-free and targeted data analyses
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20
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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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21
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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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22
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Shrivastava S, Chelluboina S, Jedge P, Doke P, Palkar S, Mishra AC, Arankalle VA. Elevated Levels of Neutrophil Activated Proteins, Alpha-Defensins (DEFA1), Calprotectin (S100A8/A9) and Myeloperoxidase (MPO) Are Associated With Disease Severity in COVID-19 Patients. Front Cell Infect Microbiol 2021; 11:751232. [PMID: 34746027 PMCID: PMC8566808 DOI: 10.3389/fcimb.2021.751232] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 10/08/2021] [Indexed: 12/29/2022] Open
Abstract
Understanding of the basis for severity and fatal outcome of SARS-CoV-2 infection is of paramount importance for developing therapeutic options and identification of prognostic markers. So far, accumulation of neutrophils and increased levels of pro-inflammatory cytokines are associated with disease severity in COVID-19 patients. In this study, we aimed to compare circulatory levels of neutrophil secretory proteins, alpha-defensins (DEFA1), calprotectin (S100A8/A9), and myeloperoxidase (MPO) in COVID-19 patients with different clinical presentations. We studied 19 healthy subjects, 63 COVID-19 patients with mild (n=32) and severe (n=31) disease, 23 asymptomatic individuals identified through contact tracing programme and 23 recovering patients (1-4 months post-disease). At the time of disease presentation, serum levels of DEFA1 were significantly higher in patients with mild (mean230 ± 17, p<0.0001) and severe (mean452 ± 46, p<0.0001) disease respectively in comparison to healthy subjects (mean113 ± 11). S100A8/A9 proteins were significantly higher in COVID-19 patients (p<0.0001) irrespective of disease severity. The levels of DEFA1, S100A8/A9 and MPO reduced to normal in recovering patients and comparable to healthy subjects. Surprisingly, DEFA1 levels were higher in severe than mild patients in first week of onset of disease (p=0.004). Odds-ratio analysis showed that DEFA1 could act as potential biomarker in predicting disease severity (OR=11.34). In addition, levels of DEFA1 and S100A8/A9 were significantly higher in patients with fatal outcome (p=0.004 and p=0.03) respectively. The rise in DEFA1 levels was independent of secondary infections. In conclusion, our data suggest that induction of elevated levels of alpha-defensins and S100A8/A9 is associated with poor disease outcome in COVID-19 patients.
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Affiliation(s)
- Shubham Shrivastava
- Department of Communicable Diseases, Interactive Research School for Health Affairs (IRSHA), Bharati Vidyapeeth (Deemed to be University), Pune, India
| | - Shweta Chelluboina
- Department of Communicable Diseases, Interactive Research School for Health Affairs (IRSHA), Bharati Vidyapeeth (Deemed to be University), Pune, India
| | - Prashant Jedge
- Department of Critical Care Medicine, Bharati Vidyapeeth (Deemed to be University) Medical College, Pune, India
| | - Purwa Doke
- Department of Medicine, Bharati Vidyapeeth (Deemed to be University) Medical College, Pune, India
| | - Sonali Palkar
- Department of Community Medicine, Bharati Vidyapeeth (Deemed to be University) Medical College, Pune, India
| | - Akhilesh Chandra Mishra
- Department of Communicable Diseases, Interactive Research School for Health Affairs (IRSHA), Bharati Vidyapeeth (Deemed to be University), Pune, India
| | - Vidya A. Arankalle
- Department of Communicable Diseases, Interactive Research School for Health Affairs (IRSHA), Bharati Vidyapeeth (Deemed to be University), Pune, India
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23
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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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24
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Rajczewski AT, Mehta S, Nguyen DDA, Grüning B, Johnson JE, McGowan T, Griffin TJ, Jagtap PD. A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19). Clin Proteomics 2021; 18:15. [PMID: 33971807 PMCID: PMC8107781 DOI: 10.1186/s12014-021-09321-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/01/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The Coronavirus Disease 2019 (COVID-19) global pandemic has had a profound, lasting impact on the world's population. A key aspect to providing care for those with COVID-19 and checking its further spread is early and accurate diagnosis of infection, which has been generally done via methods for amplifying and detecting viral RNA molecules. Detection and quantitation of peptides using targeted mass spectrometry-based strategies has been proposed as an alternative diagnostic tool due to direct detection of molecular indicators from non-invasively collected samples as well as the potential for high-throughput analysis in a clinical setting; many studies have revealed the presence of viral peptides within easily accessed patient samples. However, evidence suggests that some viral peptides could serve as better indicators of COVID-19 infection status than others, due to potential misidentification of peptides derived from human host proteins, poor spectral quality, high limits of detection etc. METHODS: In this study we have compiled a list of 636 peptides identified from Sudden Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) samples, including from in vitro and clinical sources. These datasets were rigorously analyzed using automated, Galaxy-based workflows containing tools such as PepQuery, BLAST-P, and the Multi-omic Visualization Platform as well as the open-source tools MetaTryp and Proteomics Data Viewer (PDV). RESULTS Using PepQuery for confirming peptide spectrum matches, we were able to narrow down the 639-peptide possibilities to 87 peptides that were most robustly detected and specific to the SARS-CoV-2 virus. The specificity of these sequences to coronavirus taxa was confirmed using Unipept and BLAST-P. Through stringent p-value cutoff combined with manual verification of peptide spectrum match quality, 4 peptides derived from the nucleocapsid phosphoprotein and membrane protein were found to be most robustly detected across all cell culture and clinical samples, including those collected non-invasively. CONCLUSION We propose that these peptides would be of the most value for clinical proteomics applications seeking to detect COVID-19 from patient samples. We also contend that samples harvested from the upper respiratory tract and oral cavity have the highest potential for diagnosis of SARS-CoV-2 infection from easily collected patient samples using mass spectrometry-based proteomics assays.
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Affiliation(s)
- Andrew T Rajczewski
- Department of Biochemistry, Molecular and Cell Biology Building, University of Minnesota, 420 Washington Ave SE 7-129, Minneapolis, MN, 55455, USA
| | - Subina Mehta
- Department of Biochemistry, Molecular and Cell Biology Building, University of Minnesota, 420 Washington Ave SE 7-129, Minneapolis, MN, 55455, USA
| | - Dinh Duy An Nguyen
- Department of Biochemistry, Molecular and Cell Biology Building, University of Minnesota, 420 Washington Ave SE 7-129, Minneapolis, MN, 55455, USA
| | - Björn Grüning
- Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - James E Johnson
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Thomas McGowan
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Timothy J Griffin
- Department of Biochemistry, Molecular and Cell Biology Building, University of Minnesota, 420 Washington Ave SE 7-129, Minneapolis, MN, 55455, USA
| | - Pratik D Jagtap
- Department of Biochemistry, Molecular and Cell Biology Building, University of Minnesota, 420 Washington Ave SE 7-129, Minneapolis, MN, 55455, USA.
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25
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Yadav R, Acharjee A, Salkar A, Bankar R, Palanivel V, Agrawal S, Shastri J, Sabnis SV, Srivastava S. Mumbai mayhem of COVID-19 pandemic reveals important factors that influence susceptibility to infection. EClinicalMedicine 2021; 35:100841. [PMID: 33937730 PMCID: PMC8068776 DOI: 10.1016/j.eclinm.2021.100841] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND COVID-19 severity is disproportionately high in the elderly and people with comorbidities. However, other factors that predispose individuals to increased chances of infection are unclear. METHODS Data from 18,600 people screened for COVID-19 in Mumbai during the outbreak's initial phase, March 7 to June 30, 2020, were used to assess risk factors associated with COVID-19 using the odds ratio analysis. FINDINGS Males aged ≥60 years having both diabetes and hypertension were at the highest risk of COVID-19 infection (M vs. F OR=2.5, 95% CI=1.34-4.67, p = 0.0049). People having both diabetes and hypertension in ≥20 years (OR=4.11, 95% CI=3.26-5.20, p <0.0001), diabetes and hypertension independently in 20-39 (OR=4.13, 95% CI=2.22-7.70, p <0.0001, OR=4.32, 95% CI=2.10-8.88, p = 0.0001) and ≥60 years (OR=2.69, 95% CI=1.87-3.87, p <0.0001, OR=2.03, 95% CI=1.46-2.82, p <0.0001), chronic renal disease in 20-39 years (OR=5.38, 95% CI=1.91-15.09, p = 0.0007) age groups had significantly higher risk of COVID-19 infection than those without comorbidity. Quarantined people had significantly lower positive odds (OR=0.59, 95% CI=0.53-0.66, p <0.001) than non-quarantined people. INTERPRETATION Our research indicates that the risk of getting COVID-19 disease is not equal. When considering sex, age, and comorbidity together, we found that males aged ≥60 years and having both diabetes and hypertension had a significantly high risk of COVID-19 infection. Therefore, remedial measures such as vaccination programs should be prioritized for at-risk individuals. FUNDING SERB, India: SB/S1/COVID-2/2020 and Seed grant RD/0520-IRCCHC0-006 from IRCC, IIT Bombay.
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Affiliation(s)
- Radha Yadav
- Department of Mathematics, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Arup Acharjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Akanksha Salkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Renuka Bankar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Viswanthram Palanivel
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Sachee Agrawal
- Kasturba Hospital for Infectious Diseases, Chinchpokli, Mumbai, Maharashtra 400034, India
| | - Jayanthi Shastri
- Kasturba Hospital for Infectious Diseases, Chinchpokli, Mumbai, Maharashtra 400034, India
| | - Sanjeev V. Sabnis
- Department of Mathematics, 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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