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Jiang RW, Marin LM, Jaroch K, Zhou W, Siqueira WL, Pawliszyn J. Proteomic Analysis of Human Saliva via Solid-Phase Microextraction Coupled with Liquid Chromatography-Mass Spectrometry. Anal Chem 2024; 96:5363-5367. [PMID: 38535996 DOI: 10.1021/acs.analchem.4c00307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Proteomics of human saliva samples was achieved for the first time via biocompatible solid-phase microextraction (bio-SPME) devices. Upon introduction of a porogen to a conventional C18 coating, porous C18/polyacrylonitrile (PAN) SPME blades were able to extract peptides up to 3.0 kDa and more peptides than commercial SPME blades. Following Trypsin digestion, salivary proteomic analysis was achieved via SPME-LC-MS/MS. Seven endogenous proteins were consistently identified in all saliva samples via bio-SPME. Taking advantage of this strategy, untargeted peptidomics was applied for the comparison of saliva samples between healthy and SARS-CoV-2 positive individuals. The results showed clear peptidomic differences between the viral and healthy saliva samples. This proof-of-concept study demonstrates the potential of bio-SPME-LC-MS/MS for peptidomics and proteomics in biomedical applications.
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Affiliation(s)
- Runshan W Jiang
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Lina M Marin
- College of Dentistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Karol Jaroch
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- Department of Pharmacodynamics and Molecular Pharmacology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz 85-089, Poland
| | - Wei Zhou
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Walter L Siqueira
- College of Dentistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Janusz Pawliszyn
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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2
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Brazaca LC, Imamura AH, Blasques RV, Camargo JR, Janegitz BC, Carrilho E. The use of biological fluids in microfluidic paper-based analytical devices (μPADs): Recent advances, challenges and future perspectives. Biosens Bioelectron 2024; 246:115846. [PMID: 38006702 DOI: 10.1016/j.bios.2023.115846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 11/27/2023]
Abstract
The use of microfluidic paper-based analytical devices (μPADs) for aiding medical diagnosis is a growing trend in the literature mainly due to their low cost, easy use, simple manufacturing, and great potential for application in low-resource settings. Many important biomarkers (proteins, ions, lipids, hormones, DNA, RNA, drugs, whole cells, and more) and biofluids are available for precise detection and diagnosis. We have reviewed the advances μPADs in medical diagnostics have achieved in the last few years, focusing on the most common human biofluids (whole blood/plasma, sweat, urine, tears, and saliva). The challenges of detecting specific biomarkers in each sample are discussed, along with innovative techniques that overcome such limitations. Finally, the difficulties of commercializing μPADs are considered, and future trends are presented, including wearable devices and integrating multiple steps in a single platform.
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Affiliation(s)
- Laís Canniatti Brazaca
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP, 13566-590, Brazil.
| | - Amanda Hikari Imamura
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP, 13566-590, Brazil; Instituto Nacional de Ciência e Tecnologia de Bioanalítica-INCTBio, Campinas, SP, 13083-970, Brazil
| | - Rodrigo Vieira Blasques
- Departamento de Ciências da Natureza, Matemática e Educação, Universidade Federal de São Carlos, Araras, SP, 13600-970, Brazil
| | - Jéssica Rocha Camargo
- Departamento de Ciências da Natureza, Matemática e Educação, Universidade Federal de São Carlos, Araras, SP, 13600-970, Brazil
| | - Bruno Campos Janegitz
- Departamento de Ciências da Natureza, Matemática e Educação, Universidade Federal de São Carlos, Araras, SP, 13600-970, Brazil
| | - Emanuel Carrilho
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP, 13566-590, Brazil; Instituto Nacional de Ciência e Tecnologia de Bioanalítica-INCTBio, Campinas, SP, 13083-970, Brazil
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Abdullah M, Ali A, Usman M, Naz A, Qureshi JA, Bajaber MA, Zhang X. Post COVID-19 complications and follow up biomarkers. NANOSCALE ADVANCES 2023; 5:5705-5716. [PMID: 37881715 PMCID: PMC10597564 DOI: 10.1039/d3na00342f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/11/2023] [Indexed: 10/27/2023]
Abstract
Millions of people were infected by the coronavirus disease (COVID-19) epidemic, which left a huge burden on the care of post COVID-19 survivors around the globe. The self-reported COVID-19 symptoms were experienced by an estimated 1.3 million people in the United Kingdom (2% of the population), and these symptoms persisted for about 4 weeks from the beginning of the infection. The symptoms most frequently reported were exhaustion, shortness of breath, muscular discomfort, joint pain, headache, cough, chest pain, cognitive impairment, memory loss, anxiety, sleep difficulties, diarrhea, and a decreased sense of smell and taste in post-COVID-19 affected people. The post COVID-19 complications were frequently related to the respiratory, cardiac, nervous, psychological and musculoskeletal systems. The lungs, liver, kidneys, heart, brain and other organs had been impaired by hypoxia and inflammation in post COVID-19 individuals. The upregulation of substance "P" (SP) and various cytokines such as tumor necrosis factor-alpha (TNF-α), interleukin 6 (IL-6), interleukin 10 (IL-10), interleukin 1 beta (IL-1β), angiotensin-converting enzyme 2 (ACE2) and chemokine C-C motif ligand 3 (CCL3) has muddled respiratory, cardiac, neuropsychiatric, dermatological, endocrine, musculoskeletal, gastrointestinal, renal and genitourinary complications in post COVID-19 people. To prevent these complications from worsening, it was therefore important to study how these biomarkers were upregulated and block their receptors.
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Affiliation(s)
- Muhammad Abdullah
- Institute of Molecular Biology and Biotechnology, University of Lahore Pakistan
| | - Amjed Ali
- University Institute of Physical Therapy, University of Lahore Pakistan
| | - Muhammad Usman
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University Xuzhou China
| | - Anam Naz
- Institute of Molecular Biology and Biotechnology, University of Lahore Pakistan
| | - Javed Anver Qureshi
- Institute of Molecular Biology and Biotechnology, University of Lahore Pakistan
| | - Majed A Bajaber
- Department of Chemistry, Faculty of Science, King Khalid University P.O. Box 9004 Abha 61413 Saudi Arabia
| | - Xiao Zhang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University Xuzhou China
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4
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Freeman SL, Oliveira ASF, Gallio AE, Rosa A, Simitakou MK, Arthur CJ, Mulholland AJ, Cherepanov P, Raven EL. Heme binding to the SARS-CoV-2 spike glycoprotein. J Biol Chem 2023; 299:105014. [PMID: 37414149 PMCID: PMC10416065 DOI: 10.1016/j.jbc.2023.105014] [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] [Received: 04/11/2023] [Revised: 06/12/2023] [Accepted: 07/01/2023] [Indexed: 07/08/2023] Open
Abstract
The target for humoral immunity, SARS-CoV-2 spike glycoprotein, has become the focus of vaccine research and development. Previous work demonstrated that the N-terminal domain (NTD) of SARS-CoV-2 spike binds biliverdin-a product of heme catabolism-causing a strong allosteric effect on the activity of a subset of neutralizing antibodies. Herein, we show that the spike glycoprotein is also able to bind heme (KD = 0.5 ± 0.2 μM). Molecular modeling indicated that the heme group fits well within the same pocket on the SARS-CoV-2 spike NTD. Lined by aromatic and hydrophobic residues (W104, V126, I129, F192, F194, I203, and L226), the pocket provides a suitable environment to stabilize the hydrophobic heme. Mutagenesis of N121 has a substantive effect on heme binding (KD = 3000 ± 220 μM), confirming the pocket as a major heme binding location of the viral glycoprotein. Coupled oxidation experiments in the presence of ascorbate indicated that the SARS-CoV-2 glycoprotein can catalyze the slow conversion of heme to biliverdin. The heme trapping and oxidation activities of the spike may allow the virus to reduce levels of free heme during infection to facilitate evasion of the adaptive and innate immunity.
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Affiliation(s)
- Samuel L Freeman
- School of Chemistry, Cantock's Close, University of Bristol, Bristol, United Kingdom
| | - A Sofia F Oliveira
- School of Chemistry, Cantock's Close, University of Bristol, Bristol, United Kingdom
| | - Andrea E Gallio
- School of Chemistry, Cantock's Close, University of Bristol, Bristol, United Kingdom
| | - Annachiara Rosa
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Maria K Simitakou
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Christopher J Arthur
- School of Chemistry, Cantock's Close, University of Bristol, Bristol, United Kingdom
| | - Adrian J Mulholland
- School of Chemistry, Cantock's Close, University of Bristol, Bristol, United Kingdom
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom; Department of Infectious Disease, St-Mary's Campus, Imperial College London, United Kingdom.
| | - Emma L Raven
- School of Chemistry, Cantock's Close, University of Bristol, Bristol, United Kingdom.
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Robinson JP, Ostafe R, Iyengar SN, Rajwa B, Fischer R. Flow Cytometry: The Next Revolution. Cells 2023; 12:1875. [PMID: 37508539 PMCID: PMC10378642 DOI: 10.3390/cells12141875] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/06/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Unmasking the subtleties of the immune system requires both a comprehensive knowledge base and the ability to interrogate that system with intimate sensitivity. That task, to a considerable extent, has been handled by an iterative expansion in flow cytometry methods, both in technological capability and also in accompanying advances in informatics. As the field of fluorescence-based cytomics matured, it reached a technological barrier at around 30 parameter analyses, which stalled the field until spectral flow cytometry created a fundamental transformation that will likely lead to the potential of 100 simultaneous parameter analyses within a few years. The simultaneous advance in informatics has now become a watershed moment for the field as it competes with mature systematic approaches such as genomics and proteomics, allowing cytomics to take a seat at the multi-omics table. In addition, recent technological advances try to combine the speed of flow systems with other detection methods, in addition to fluorescence alone, which will make flow-based instruments even more indispensable in any biological laboratory. This paper outlines current approaches in cell analysis and detection methods, discusses traditional and microfluidic sorting approaches as well as next-generation instruments, and provides an early look at future opportunities that are likely to arise.
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Affiliation(s)
- J Paul Robinson
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Raluca Ostafe
- Molecular Evolution, Protein Engineering and Production Facility (PI4D), Purdue University, West Lafayette, IN 47907, USA
| | | | - Bartek Rajwa
- Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA
| | - Rainer Fischer
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute of Inflammation, Immunology and Infectious Diseases, Purdue University, West Lafayette, IN 47907, USA
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Gajula SNR, Khairnar AS, Jock P, Kumari N, Pratima K, Munjal V, Kalan P, Sonti R. LC-MS/MS: A sensitive and selective analytical technique to detect COVID-19 protein biomarkers in the early disease stage. Expert Rev Proteomics 2023; 20:5-18. [PMID: 36919634 DOI: 10.1080/14789450.2023.2191845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
INTRODUCTION The COVID-19 outbreak has put enormous pressure on the scientific community to detect infection rapidly, identify the status of disease severity, and provide an immediate vaccine/drug for the treatment. Relying on immunoassay and a real-time reverse transcription polymerase chain reaction (rRT-PCR) led to many false-negative and false-positive reports. Therefore, detecting biomarkers is an alternative and reliable approach for determining the infection, its severity, and disease progression. Recent advances in liquid chromatography and mass spectrometry (LC-MS/MS) enable the protein biomarkers even at low concentrations, thus facilitating clinicians to monitor the treatment in hospitals. AREAS COVERED This review highlights the role of LC-MS/MS in identifying protein biomarkers and discusses the clinically significant protein biomarkers such as Serum amyloid A, Interleukin-6, C-Reactive Protein, Lactate dehydrogenase, D-dimer, cardiac troponin, ferritin, Alanine transaminase, Aspartate transaminase, gelsolin and galectin-3-binding protein in COVID-19, and their analysis by LC-MS/MS in the early stage. EXPERT OPINION Clinical doctors monitor significant biomarkers to understand, stratify, and treat patients according to disease severity. Knowledge of clinically significant COVID-19 protein biomarkers is critical not only for COVID-19 caused by the coronavirus but also to prepare us for future pandemics of other diseases in detecting by LC-MS/MS at the early stages.
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Affiliation(s)
- Siva Nageswara Rao Gajula
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Balanagar, India
| | - Ankita Sahebrao Khairnar
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Balanagar, India
| | - Pallavi Jock
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Balanagar, India
| | - Nikita Kumari
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Balanagar, India
| | - Kendre Pratima
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Balanagar, India
| | - Vijay Munjal
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Balanagar, India
| | - Pavan Kalan
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Balanagar, India
| | - Rajesh Sonti
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Balanagar, India
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7
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Fang C, Ma Y. Peripheral Blood Genes Crosstalk between COVID-19 and Sepsis. Int J Mol Sci 2023; 24:ijms24032591. [PMID: 36768914 PMCID: PMC9916586 DOI: 10.3390/ijms24032591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 01/21/2023] [Accepted: 01/24/2023] [Indexed: 01/31/2023] Open
Abstract
Severe coronavirus disease 2019 (COVID-19) has led to a rapid increase in death rates all over the world. Sepsis is a life-threatening disease associated with a dysregulated host immune response. It has been shown that COVID-19 shares many similarities with sepsis in many aspects. However, the molecular mechanisms underlying sepsis and COVID-19 are not well understood. The aim of this study was to identify common transcriptional signatures, regulators, and pathways between COVID-19 and sepsis, which may provide a new direction for the treatment of COVID-19 and sepsis. First, COVID-19 blood gene expression profile (GSE179850) data and sepsis blood expression profile (GSE134347) data were obtained from GEO. Then, we intersected the differentially expressed genes (DEG) from these two datasets to obtain common DEGs. Finally, the common DEGs were used for functional enrichment analysis, transcription factor and miRNA prediction, pathway analysis, and candidate drug analysis. A total of 307 common DEGs were identified between the sepsis and COVID-19 datasets. Protein-protein interactions (PPIs) were constructed using the STRING database. Subsequently, hub genes were identified based on PPI networks. In addition, we performed GO functional analysis and KEGG pathway analysis of common DEGs, and found a common association between sepsis and COVID-19. Finally, we identified transcription factor-gene interaction, DEGs-miRNA co-regulatory networks, and protein-drug interaction, respectively. Through ROC analysis, we identified 10 central hub genes as potential biomarkers. In this study, we identified SARS-CoV-2 infection as a high risk factor for sepsis. Our study may provide a potential therapeutic direction for the treatment of COVID-19 patients suffering from sepsis.
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Clemente-Suárez VJ, Bustamante-Sanchez Á, Tornero-Aguilera JF, Ruisoto P, Mielgo-Ayuso J. Inflammation in COVID-19 and the Effects of Non-Pharmacological Interventions during the Pandemic: A Review. Int J Mol Sci 2022; 23:ijms232415584. [PMID: 36555231 PMCID: PMC9779440 DOI: 10.3390/ijms232415584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/25/2022] [Accepted: 12/04/2022] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the coronavirus disease 2019 (COVID-19) pandemic that hit the health systems worldwide hard, causing a collapse of healthcare systems. One of the main problems of this new virus is the high inflammatory response it provokes, which is the cause of much of the symptoms. Different pharmacological approaches tried to stop the advance of the pandemic, but it seems that only vaccines are the solution. In this line, different nonpharmacological approaches have been made in order to improve symptomatology, contagion, and spread of COVID-19, the principal factors being the physical activity, nutrition, physiotherapy, psychology, and life patterns. The SARS-CoV-2 virus produces a disproportionate inflammatory response in the organism of the guest and causes complications in this that can end the life of the patient. It has been possible to see how different nonpharmacological interventions based on physical activity, nutritional, psychological, and physical therapy, and lifestyle changes can be functional tools to treat this inflammation. Thus, in the present review, we aim to provide an overview of the role of inflammation in COVID-19 and the nonpharmacological interventions related to it.
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Affiliation(s)
- Vicente Javier Clemente-Suárez
- Faculty of Sports Sciences, Universidad Europea de Madrid, Tajo Street, s/n, 28670 Madrid, Spain
- Research Center in Applied Combat (CESCA), 45007 Toledo, Spain
- Correspondence:
| | | | - José Francisco Tornero-Aguilera
- Faculty of Sports Sciences, Universidad Europea de Madrid, Tajo Street, s/n, 28670 Madrid, Spain
- Research Center in Applied Combat (CESCA), 45007 Toledo, Spain
| | - Pablo Ruisoto
- Department of Health Sciences, Public University of Navarre, 31006 Pamplona, Spain
| | - Juan Mielgo-Ayuso
- Department of Health Sciences, Faculty of Health Sciences, University of Burgos, 09001 Burgos, Spain
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He J, Zhou L, Huang G, Shen J, Chen W, Wang C, Kim A, Zhang Z, Cheng W, Dai S, Ding F, Chen P. Enhanced Label-Free Nanoplasmonic Cytokine Detection in SARS-CoV-2 Induced Inflammation Using Rationally Designed Peptide Aptamer. ACS APPLIED MATERIALS & INTERFACES 2022; 14:48464-48475. [PMID: 36281943 PMCID: PMC9627400 DOI: 10.1021/acsami.2c14748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/13/2022] [Indexed: 06/12/2023]
Abstract
Rapid and precise serum cytokine quantification provides immense clinical significance in monitoring the immune status of patients in rapidly evolving infectious/inflammatory disorders, examplified by the ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. However, real-time information on predictive cytokine biomarkers to guide targetable immune pathways in pathogenic inflammation is critically lacking, because of the insufficient detection range and detection limit in current label-free cytokine immunoassays. In this work, we report a highly sensitive localized surface plasmon resonance imaging (LSPRi) immunoassay for label-free Interleukin 6 (IL-6) detection utilizing rationally designed peptide aptamers as the capture interface. Benefiting from its characteristically smaller dimension and direct functionalization on the sensing surface via Au-S bonding, the peptide-aptamer-based LSPRi immunoassay achieved enhanced label-free serum IL-6 detection with a record-breaking limit of detection down to 4.6 pg/mL, and a wide dynamic range of ∼6 orders of magnitude (values from 4.6 to 1 × 106 pg/mL were observed). The immunoassay was validated in vitro for label-free analysis of SARS-CoV-2 induced inflammation, and further applied in rapid quantification of serum IL-6 profiles in COVID-19 patients. Our peptide aptamer LSPRi immunoassay demonstrates great potency in label-free cytokine detection with unprecedented sensing capability to provide accurate and timely interpretation of the inflammatory status and disease progression, and determination of prognosis.
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Affiliation(s)
- Jiacheng He
- Materials Research and Education Center, Auburn University, Auburn, Alabama36849, United States
| | - Lang Zhou
- Materials Research and Education Center, Auburn University, Auburn, Alabama36849, United States
| | - Gangtong Huang
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina29634, United States
| | - Jialiang Shen
- Materials Research and Education Center, Auburn University, Auburn, Alabama36849, United States
| | - Wu Chen
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, Alabama36849, United States
| | - Chuanyu Wang
- Materials Research and Education Center, Auburn University, Auburn, Alabama36849, United States
| | - Albert Kim
- Center for Medicine, Health, and Society, Vanderbilt University, Nashville, Tennessee37235, United States
| | - Zhuoyu Zhang
- Department of Mechanical and Aerospace Engineering, New York University, Brooklyn, New York11201, United States
- Department of Biomedical Engineering, New York University, Brooklyn, New York11201, United States
| | - Weiqiang Cheng
- Department of Mechanical and Aerospace Engineering, New York University, Brooklyn, New York11201, United States
- Department of Biomedical Engineering, New York University, Brooklyn, New York11201, United States
| | - Siyuan Dai
- Materials Research and Education Center, Auburn University, Auburn, Alabama36849, United States
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina29634, United States
| | - Pengyu Chen
- Materials Research and Education Center, Auburn University, Auburn, Alabama36849, United States
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10
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He B, Huang Z, Huang C, Nice EC. Clinical applications of plasma proteomics and peptidomics: Towards precision medicine. Proteomics Clin Appl 2022; 16:e2100097. [PMID: 35490333 DOI: 10.1002/prca.202100097] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/16/2022] [Accepted: 04/28/2022] [Indexed: 02/05/2023]
Abstract
In the context of precision medicine, disease treatment requires individualized strategies based on the underlying molecular characteristics to overcome therapeutic challenges posed by heterogeneity. For this purpose, it is essential to develop new biomarkers to diagnose, stratify, or possibly prevent diseases. Plasma is an available source of biomarkers that greatly reflects the physiological and pathological conditions of the body. An increasing number of studies are focusing on proteins and peptides, including many involving the Human Proteome Project (HPP) of the Human Proteome Organization (HUPO), and proteomics and peptidomics techniques are emerging as critical tools for developing novel precision medicine preventative measures. Excitingly, the emerging plasma proteomics and peptidomics toolbox exhibits a huge potential for studying pathogenesis of diseases (e.g., COVID-19 and cancer), identifying valuable biomarkers and improving clinical management. However, the enormous complexity and wide dynamic range of plasma proteins makes plasma proteome profiling challenging. Herein, we summarize the recent advances in plasma proteomics and peptidomics with a focus on their emerging roles in COVID-19 and cancer research, aiming to emphasize the significance of plasma proteomics and peptidomics in clinical applications and precision medicine.
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Affiliation(s)
- Bo He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China
| | - Zhao Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China.,Department of Pharmacology, and Provincial Key Laboratory of Pathophysiology in Ningbo University School of Medicine, Ningbo, Zhejiang, China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
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11
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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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12
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Baros-Steyl SS, Al Heialy S, Semreen AH, Semreen MH, Blackburn JM, Soares NC. A review of mass spectrometry-based analyses to understand COVID-19 convalescent plasma mechanisms of action. Proteomics 2022; 22:e2200118. [PMID: 35809024 PMCID: PMC9349457 DOI: 10.1002/pmic.202200118] [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: 03/21/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 01/08/2023]
Abstract
The spread of coronavirus disease 2019 (COVID‐19) viral pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has become a worldwide pandemic claiming several thousands of lives worldwide. During this pandemic, several studies reported the use of COVID‐19 convalescent plasma (CCP) from recovered patients to treat severely or critically ill patients. Although this historical and empirical treatment holds immense potential as a first line of response against eventual future unforeseen viral epidemics, there are several concerns regarding the efficacy and safety of this approach. This critical review aims to pinpoint the possible role of mass spectrometry‐based analysis in the identification of unique molecular component proteins, peptides, and metabolites of CCP that explains the therapeutic mechanism of action against COVID‐19. Additionally, the text critically reviews the potential application of mass spectrometry approaches in the search for novel plasma biomarkers that may enable a rapid and accurate assessment of the safety and efficacy of CCP. Considering the relative low‐cost value involved in the CCP therapy, this proposed line of research represents a tangible scientific challenge that will be translated into clinical practice and help save several thousand lives around the world, specifically in low‐ and middle‐income countries.
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Affiliation(s)
- Seanantha S Baros-Steyl
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Saba Al Heialy
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.,Meakin-Christie Laboratories, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Ahlam H Semreen
- College of Pharmacy-Department of Medicinal Chemistry, University of Sharjah, United Arab Emirates.,Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Mohammad H Semreen
- College of Pharmacy-Department of Medicinal Chemistry, University of Sharjah, United Arab Emirates.,Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Jonathan M Blackburn
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Nelson C Soares
- College of Pharmacy-Department of Medicinal Chemistry, University of Sharjah, United Arab Emirates.,Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
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13
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Mohammed Y, Goodlett DR, Cheng MP, Vinh DC, Lee TC, Mcgeer A, Sweet D, Tran K, Lee T, Murthy S, Boyd JH, Singer J, Walley KR, Patrick DM, Quan C, Ismail S, Amar L, Pal A, Bassawon R, Fesdekjian L, Gou K, Lamontagne F, Marshall J, Haljan G, Fowler R, Winston BW, Russell JA. Longitudinal Plasma Proteomics Analysis Reveals Novel Candidate Biomarkers in Acute COVID-19. J Proteome Res 2022; 21:975-992. [PMID: 35143212 PMCID: PMC8864781 DOI: 10.1021/acs.jproteome.1c00863] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Indexed: 12/15/2022]
Abstract
The host response to COVID-19 pathophysiology over the first few days of infection remains largely unclear, especially the mechanisms in the blood compartment. We report on a longitudinal proteomic analysis of acute-phase COVID-19 patients, for which we used blood plasma, multiple reaction monitoring with internal standards, and data-independent acquisition. We measured samples on admission for 49 patients, of which 21 had additional samples on days 2, 4, 7, and 14 after admission. We also measured 30 externally obtained samples from healthy individuals for comparison at baseline. The 31 proteins differentiated in abundance between acute COVID-19 patients and healthy controls belonged to acute inflammatory response, complement activation, regulation of inflammatory response, and regulation of protein activation cascade. The longitudinal analysis showed distinct profiles revealing increased levels of multiple lipid-associated functions, a rapid decrease followed by recovery for complement activation, humoral immune response, and acute inflammatory response-related proteins, and level fluctuation in the regulation of smooth muscle cell proliferation, secretory mechanisms, and platelet degranulation. Three proteins were differentiated between survivors and nonsurvivors. Finally, increased levels of fructose-bisphosphate aldolase B were determined in patients with exposure to angiotensin receptor blockers versus decreased levels in those exposed to angiotensin-converting enzyme inhibitors. Data are available via ProteomeXchange PXD029437.
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Affiliation(s)
- Yassene Mohammed
- Genome BC Proteomics Centre, University
of Victoria, Victoria V8Z 5N3, British Columbia,
Canada
- Center for Proteomics and Metabolomics,
Leiden University Medical Center, Leiden 2333 ZA,
Netherlands
| | - David R. Goodlett
- Genome BC Proteomics Centre, University
of Victoria, Victoria V8Z 5N3, British Columbia,
Canada
- Department of Biochemistry and Microbiology,
University of Victoria, Victoria V8W 2Y2, British Columbia,
Canada
- International Centre for Cancer Vaccine Science,
University of Gdansk, Gdansk 80-822, European Union,
Poland
| | - Matthew P. Cheng
- Division of Infectious Diseases (Department of
Medicine), Division of Medical Microbiology (Department of Pathology and Laboratory
Medicine), McGill University Health Centre, Montreal H4A 3J1,
Quebec, Canada
| | - Donald C. Vinh
- Division of Infectious Diseases (Department of
Medicine), Division of Medical Microbiology (Department of Pathology and Laboratory
Medicine), McGill University Health Centre, Montreal H4A 3J1,
Quebec, Canada
| | - Todd C. Lee
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | - Allison Mcgeer
- Mt. Sinai Hospital and University of
Toronto, University Avenue, Toronto M5G 1X5, Ontario,
Canada
| | - David Sweet
- Division of Critical Care Medicine, Department of
Emergency Medicine, Vancouver General Hospital and University of British
Columbia, Vancouver V5Z 1M9, British Columbia,
Canada
| | - Karen Tran
- Division of General Internal Medicine,
Vancouver General Hospital and University of British
Columbia, Vancouver V5Z 1M9, British Columbia,
Canada
| | - Terry Lee
- Centre for Health Evaluation and Outcome Science
(CHEOS), St. Paul’s Hospital, University of British
Columbia, 1081 Burrard Street, Vancouver V6Z 1Y6, British Columbia,
Canada
| | - Srinivas Murthy
- BC Children’s Hospital,
University of British Columbia, Vancouver V6H 3N1, British Columbia,
Canada
| | - John H. Boyd
- Centre for Heart Lung Innovation, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
- Division of Critical Care Medicine, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
| | - Joel Singer
- Centre for Health Evaluation and Outcome Science
(CHEOS), St. Paul’s Hospital, University of British
Columbia, 1081 Burrard Street, Vancouver V6Z 1Y6, British Columbia,
Canada
| | - Keith R. Walley
- Centre for Heart Lung Innovation, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
- Division of Critical Care Medicine, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
| | - David M. Patrick
- British Columbia Centre for Disease
Control (BCCDC) and University of British Columbia, Vancouver V5Z 4R4,
British Columbia, Canada
| | - Curtis Quan
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | - Sara Ismail
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | - Laetitia Amar
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | - Aditya Pal
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | - Rayhaan Bassawon
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | - Lara Fesdekjian
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | - Karine Gou
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | | | - John Marshall
- Department of Surgery, St.
Michael’s Hospital, Toronto M5B 1W8, Ontario,
Canada
| | - Greg Haljan
- Division of Critical Care, Surrey
Memorial Hospital and University of British Columbia, Surrey V3V 1Z2,
British Columbia, Canada
| | - Robert Fowler
- Sunnybrook Health Sciences
Centre, Toronto M4N 3M5, Ontario, Canada
| | - Brent W. Winston
- Departments of Critical Care Medicine, Medicine and
Biochemistry and Molecular Biology, University of Calgary,
Calgary T2N 4N1, Alberta, Canada
| | - James A. Russell
- Centre for Heart Lung Innovation, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
- Division of Critical Care Medicine, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
| | - ARBs CORONA I
- Genome BC Proteomics Centre, University
of Victoria, Victoria V8Z 5N3, British Columbia,
Canada
- Center for Proteomics and Metabolomics,
Leiden University Medical Center, Leiden 2333 ZA,
Netherlands
- Department of Biochemistry and Microbiology,
University of Victoria, Victoria V8W 2Y2, British Columbia,
Canada
- International Centre for Cancer Vaccine Science,
University of Gdansk, Gdansk 80-822, European Union,
Poland
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
- Mt. Sinai Hospital and University of
Toronto, University Avenue, Toronto M5G 1X5, Ontario,
Canada
- Division of Critical Care Medicine, Department of
Emergency Medicine, Vancouver General Hospital and University of British
Columbia, Vancouver V5Z 1M9, British Columbia,
Canada
- Division of General Internal Medicine,
Vancouver General Hospital and University of British
Columbia, Vancouver V5Z 1M9, British Columbia,
Canada
- Centre for Health Evaluation and Outcome Science
(CHEOS), St. Paul’s Hospital, University of British
Columbia, 1081 Burrard Street, Vancouver V6Z 1Y6, British Columbia,
Canada
- BC Children’s Hospital,
University of British Columbia, Vancouver V6H 3N1, British Columbia,
Canada
- Centre for Heart Lung Innovation, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
- Division of Critical Care Medicine, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
- British Columbia Centre for Disease
Control (BCCDC) and University of British Columbia, Vancouver V5Z 4R4,
British Columbia, Canada
- University of Sherbrooke,
Sherbrooke J1K 2R1, Quebec, Canada
- Department of Surgery, St.
Michael’s Hospital, Toronto M5B 1W8, Ontario,
Canada
- Division of Critical Care, Surrey
Memorial Hospital and University of British Columbia, Surrey V3V 1Z2,
British Columbia, Canada
- Sunnybrook Health Sciences
Centre, Toronto M4N 3M5, Ontario, Canada
- Departments of Critical Care Medicine, Medicine and
Biochemistry and Molecular Biology, University of Calgary,
Calgary T2N 4N1, Alberta, Canada
- Division of Infectious Diseases (Department of
Medicine), Division of Medical Microbiology (Department of Pathology and Laboratory
Medicine), McGill University Health Centre, Montreal H4A 3J1,
Quebec, Canada
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14
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Hua Y, Ma J, Li D, Wang R. DNA-Based Biosensors for the Biochemical Analysis: A Review. BIOSENSORS 2022; 12:bios12030183. [PMID: 35323453 PMCID: PMC8945906 DOI: 10.3390/bios12030183] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/09/2022] [Accepted: 03/16/2022] [Indexed: 05/21/2023]
Abstract
In recent years, DNA-based biosensors have shown great potential as the candidate of the next generation biomedical detection device due to their robust chemical properties and customizable biosensing functions. Compared with the conventional biosensors, the DNA-based biosensors have advantages such as wider detection targets, more durable lifetime, and lower production cost. Additionally, the ingenious DNA structures can control the signal conduction near the biosensor surface, which could significantly improve the performance of biosensors. In order to show a big picture of the DNA biosensor's advantages, this article reviews the background knowledge and recent advances of DNA-based biosensors, including the functional DNA strands-based biosensors, DNA hybridization-based biosensors, and DNA templated biosensors. Then, the challenges and future directions of DNA-based biosensors are discussed and proposed.
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15
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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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16
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Biomarker candidates for progression and clinical management of COVID-19 associated pneumonia at time of admission. Sci Rep 2022; 12:640. [PMID: 35022497 PMCID: PMC8755735 DOI: 10.1038/s41598-021-04683-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/08/2021] [Indexed: 12/20/2022] Open
Abstract
COVID-19 pathophysiology is currently not fully understood, reliable prognostic factors remain elusive, and few specific therapeutic strategies have been proposed. In this scenario, availability of biomarkers is a priority. MS-based Proteomics techniques were used to profile the proteome of 81 plasma samples extracted in four consecutive days from 23 hospitalized COVID-19 associated pneumonia patients. Samples from 10 subjects that reached a critical condition during their hospital stay and 10 matched non-severe controls were drawn before the administration of any COVID-19 specific treatment and used to identify potential biomarkers of COVID-19 prognosis. Additionally, we compared the proteome of five patients before and after glucocorticoids and tocilizumab treatment, to assess the changes induced by the therapy on our selected candidates. Forty-two proteins were differentially expressed between patients' evolution groups at 10% FDR. Twelve proteins showed lower levels in critical patients (fold-changes 1.20–3.58), of which OAS3 and COG5 found their expression increased after COVID-19 specific therapy. Most of the 30 proteins over-expressed in critical patients (fold-changes 1.17–4.43) were linked to inflammation, coagulation, lipids metabolism, complement or immunoglobulins, and a third of them decreased their expression after treatment. We propose a set of candidate proteins for biomarkers of COVID-19 prognosis at the time of hospital admission. The study design employed is distinctive from previous works and aimed to optimize the chances of the candidates to be validated in confirmatory studies and, eventually, to play a useful role in the clinical practice.
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17
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Validation of the Performance of A1HPV6, a Triage Blood Test for the Early Diagnosis and Prognosis of SARS-CoV-2 Infection. GASTRO HEP ADVANCES 2022; 1:393-402. [PMID: 35174366 PMCID: PMC8818442 DOI: 10.1016/j.gastha.2021.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/29/2021] [Indexed: 11/23/2022]
Abstract
Background and Aims Apolipoprotein A1 (A1) and haptoglobin (HP) serum levels are associated with the spread and severity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We have constructed and validated a multivariable risk calculator (A1HPV6) integrating A1, HP, alpha2-macroglobulin, and gamma glutamyl transferase to improve the performances of virological biomarkers. Methods In a prospective observational study of hospitalized patients with nonsevere SARS-CoV-2 infection, A1HPV6 was constructed in 127 patients and validated in 116. The specificity was assessed in 7482 controls representing the general population. The primary diagnostic endpoint was the area under the receiver operating characteristic curve in patients with positive SARS-CoV-2 PCR. The primary prognostic endpoint was the age-and-sex adjusted risk of A1HPV6 to predict patients with WHO-stage > 4 (W > 4) severity. We assessed the kinetics of the A1HPV6 components in a nonhuman primate model (NHP), from baseline to 7 days (D7) after SARS-CoV-2 infection. Results The area under the receiver operating characteristic curve for A1HPV6 was 0.99 (95% CI 0.97–0.99) in the validation subset, which was not significantly different from that in the construction subset, 0.99 (0.99–0.99; P = .80), like for sensitivity 92% (85–96) vs 94% (88–97; P = .29). A1HPV6 was associated with W > 4, with a significant odds ratio of 1.3 (1.1–1.5; 0.002). In NHP, A1 levels decreased (P < .01) at D2 and normalized at D4; HP levels increased at D2 and peaked at D4. In patients, A1 concentration was very low at D2 vs controls (P < .01) and increased at D14 (P < .01) but was still lower than controls; HP increased at D2 and remained elevated at D14. Conclusion These results validate the diagnostic and prognostic performances of A1HPV6. Similar kinetics of apolipoprotein A1, HP, and alpha-2-macroglobulin were observed in the NHP model. ClinicalTrials.gov number, NCT01927133.
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18
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Pinto G, Illiano A, Ferrucci V, Quarantelli F, Fontanarosa C, Siciliano R, Di Domenico C, Izzo B, Pucci P, Marino G, Zollo M, Amoresano A. Identification of SARS-CoV-2 Proteins from Nasopharyngeal Swabs Probed by Multiple Reaction Monitoring Tandem Mass Spectrometry. ACS OMEGA 2021; 6:34945-34953. [PMID: 34926968 PMCID: PMC8672425 DOI: 10.1021/acsomega.1c05587] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/02/2021] [Indexed: 05/12/2023]
Abstract
Numerous reverse transcription polymerase chain reaction (RT-PCR) tests have emerged over the past year as the gold standard for detecting millions of cases of SARS-CoV-2 reported daily worldwide. However, problems with critical shortages of key reagents such as PCR primers and RNA extraction kits and unpredictable test reliability related to high viral replication cycles have triggered the need for alternative methodologies to PCR to detect specific COVID-19 proteins. Several authors have developed methods based on liquid chromatography with tandem mass spectrometry (LC-MS/MS) to confirm the potential of the technique to detect two major proteins, the spike and the nucleoprotein, of COVID-19. In the present work, an S-Trap mini spin column digestion protocol was used for sample preparation prodromal to LC-MS/MS analysis in multiple reactions monitoring ion mode (MRM) to obtain a comprehensive method capable of detecting different viral proteins. The developed method was applied to n. 81 oro/nasopharyngeal swabs submitted in parallel to quantitative reverse transcription PCR (RT-qPCR) assays to detect RdRP, the S and N genes specific for COVID-19, and the E gene for all Sarbecoviruses, including SARS-CoV-2 (with cycle negativity threshold set to 40). A total of 23 peptides representative of the six specific viral proteins were detected in the monitoring of 128 transitions found to have good ionic currents extracted in clinical samples that reacted differently to the PCR assay. The best instrumental response came from the FLPFQFGR sequence of spike [558-566] peptide used to test the analytical performance of the method that has good sensitivity with a low false-negative rate. Transition monitoring using a targeted MS approach has the great potential to detect the fragmentation reactions of any peptide molecularly defined by a specific amino acid sequence, offering the extensibility of the approach to any viral sequence including derived variants and thus providing insights into the development of new types of clinical diagnostics.
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Affiliation(s)
- Gabriella Pinto
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cinthia 26, 80126 Naples, Italy
- Istituto
Nazionale Biostrutture e Biosistemi-Consorzio Interuniversitario, Viale delle Medaglie d’Oro,
305, 00136 Rome, Italy
| | - Anna Illiano
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cinthia 26, 80126 Naples, Italy
- CEINGE
Advanced Biotechnology, Via Gaetano Salvatore 486, 80145 Naples, Italy
- Istituto
Nazionale Biostrutture e Biosistemi-Consorzio Interuniversitario, Viale delle Medaglie d’Oro,
305, 00136 Rome, Italy
| | - Veronica Ferrucci
- CEINGE
Advanced Biotechnology, Via Gaetano Salvatore 486, 80145 Naples, Italy
- Department
of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, 80145 Naples, Italy
| | | | - Carolina Fontanarosa
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cinthia 26, 80126 Naples, Italy
- Istituto
Nazionale Biostrutture e Biosistemi-Consorzio Interuniversitario, Viale delle Medaglie d’Oro,
305, 00136 Rome, Italy
| | - Roberto Siciliano
- CEINGE
Advanced Biotechnology, Via Gaetano Salvatore 486, 80145 Naples, Italy
| | - Carmela Di Domenico
- CEINGE
Advanced Biotechnology, Via Gaetano Salvatore 486, 80145 Naples, Italy
| | - Barbara Izzo
- CEINGE
Advanced Biotechnology, Via Gaetano Salvatore 486, 80145 Naples, Italy
- Department
of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, 80145 Naples, Italy
| | - Piero Pucci
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cinthia 26, 80126 Naples, Italy
- CEINGE
Advanced Biotechnology, Via Gaetano Salvatore 486, 80145 Naples, Italy
| | - Gennaro Marino
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cinthia 26, 80126 Naples, Italy
| | - Massimo Zollo
- CEINGE
Advanced Biotechnology, Via Gaetano Salvatore 486, 80145 Naples, Italy
- Department
of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, 80145 Naples, Italy
| | - Angela Amoresano
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cinthia 26, 80126 Naples, Italy
- Istituto
Nazionale Biostrutture e Biosistemi-Consorzio Interuniversitario, Viale delle Medaglie d’Oro,
305, 00136 Rome, Italy
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19
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Yang J, Fang W, Wu W, Tian Z, Gao R, Yu L, Chen D, Weng X, Zhu S, Yang C. A Novel Diagnostic Biomarker, PZP, for Detecting Colorectal Cancer in Type 2 Diabetes Mellitus Patients Identified by Serum-Based Mass Spectrometry. Front Mol Biosci 2021; 8:736272. [PMID: 34917649 PMCID: PMC8670180 DOI: 10.3389/fmolb.2021.736272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 11/16/2021] [Indexed: 12/19/2022] Open
Abstract
Background: Growing evidence has confirmed that populations with type 2 diabetes mellitus (T2DM) have an increasing risk of developing colorectal cancer (CRC). Thus, convenient and effective screening strategies for CRC should be developed for the T2DM population to increase the detection rate of CRC. Methods: Twenty serum samples extracted from five healthy participants, five T2DM patients, five CRC patients and five T2DM patients with CRC (T2DM + CRC) were submitted to data-independent acquisition mass spectrometry (DIA-MS) analysis to discover unique differentially altered proteins (DAPs) for CRC in patients with T2DM. Then, the diagnostic value of pregnancy zone protein (PZP) was validated by ELISA analysis in the validated cohort. Results: Based on DIA-MS analysis, we found eight unique proteins specific to T2DM patients with CRC. Among these proteins, four proteins showed different expression between the T2DM + CRC and T2DM groups, and PZP exhibited the largest difference. Next, the diagnostic value of serum PZP was validated by ELISA analysis with an AUC of 0.713. Moreover, the combination of PZP, CA199 and CEA exhibited encouraging diagnostic value, and the AUC reached 0.916. Conclusion: Overall, our current research implied that PZP could be regarded as a newfound serum biomarker for CRC medical diagnosis in T2DM patients.
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Affiliation(s)
- Jiayue Yang
- Department of Endocrinology, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Weigang Fang
- Department of Gastroenterology, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Wenjun Wu
- Department of Endocrinology, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Zhen Tian
- Department of Clinical Laboratory, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Rong Gao
- Department of Clinical Laboratory, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Lu Yu
- Department of Endocrinology, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Dayang Chen
- Department of Gastroenterology, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Xiaohua Weng
- Department of Endocrinology, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Shengwei Zhu
- Department of Endocrinology, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Cheng Yang
- Department of Gastroenterology, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
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20
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Identification of serum prognostic biomarkers of severe COVID-19 using a quantitative proteomic approach. Sci Rep 2021; 11:20638. [PMID: 34667241 PMCID: PMC8526747 DOI: 10.1038/s41598-021-98253-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 09/06/2021] [Indexed: 12/17/2022] Open
Abstract
The COVID-19 pandemic is an unprecedented threat to humanity that has provoked global health concerns. Since the etiopathogenesis of this illness is not fully characterized, the prognostic factors enabling treatment decisions have not been well documented. Accurately predicting the progression of the disease would aid in appropriate patient categorization and thus help determine the best treatment option. Here, we have introduced a proteomic approach utilizing data-independent acquisition mass spectrometry (DIA-MS) to identify the serum proteins that are closely associated with COVID-19 prognosis. Twenty-seven proteins were differentially expressed between severely ill COVID-19 patients with an adverse or favorable prognosis. Ingenuity Pathway Analysis revealed that 15 of the 27 proteins might be regulated by cytokine signaling relevant to interleukin (IL)-1β, IL-6, and tumor necrosis factor (TNF), and their differential expression was implicated in the systemic inflammatory response and in cardiovascular disorders. We further evaluated practical predictors of the clinical prognosis of severe COVID-19 patients. Subsequent ELISA assays revealed that CHI3L1 and IGFALS may serve as highly sensitive prognostic markers. Our findings can help formulate a diagnostic approach for accurately identifying COVID-19 patients with severe disease and for providing appropriate treatment based on their predicted prognosis.
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21
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McArdle A, Washington KE, Chazarin Orgel B, Binek A, Manalo DM, Rivas A, Ayres M, Pandey R, Phebus C, Raedschelders K, Fert-Bober J, Van Eyk JE. Discovery Proteomics for COVID-19: Where We Are Now. J Proteome Res 2021; 20:4627-4639. [PMID: 34550702 PMCID: PMC8482317 DOI: 10.1021/acs.jproteome.1c00475] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Indexed: 02/07/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible coronavirus responsible for the pandemic coronavirus disease 2019 (COVID-19), which has had a devastating impact on society. Here, we summarize proteomic research that has helped elucidate hallmark proteins associated with the disease with respect to both short- and long-term diagnosis and prognosis. Additionally, we review the highly variable humoral response associated with COVID-19 and the increased risk of autoimmunity.
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Affiliation(s)
- Angela McArdle
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Kirstin E. Washington
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Blandine Chazarin Orgel
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Aleksandra Binek
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Danica-Mae Manalo
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Alejandro Rivas
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Matthew Ayres
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Rakhi Pandey
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Connor Phebus
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Koen Raedschelders
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Justyna Fert-Bober
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
- Department
of Cardiology, Smidt Heart Institute, Cedars-Sinai
Medical Center, Los Angeles, California 90048, United States
| | - Jennifer E. Van Eyk
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
- Department
of Cardiology, Smidt Heart Institute, Cedars-Sinai
Medical Center, Los Angeles, California 90048, United States
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22
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Chivte P, LaCasse Z, Seethi VDR, Bharti P, Bland J, Kadkol SS, Gaillard ER. MALDI-ToF protein profiling as a potential rapid diagnostic platform for COVID-19. J Mass Spectrom Adv Clin Lab 2021; 21:31-41. [PMID: 34518823 PMCID: PMC8426322 DOI: 10.1016/j.jmsacl.2021.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 08/27/2021] [Accepted: 09/05/2021] [Indexed: 12/20/2022] Open
Abstract
More than a year after the COVID-19 pandemic was declared, the need still exists for accurate, rapid, inexpensive and non-invasive diagnostic methods that yield high specificity and sensitivity towards the current and newly emerging SARS-CoV-2 strains. Compared to the nasopharyngeal swabs, several studies have established saliva as a more amenable specimen type for early detection of SARS-CoV-2. Considering the limitations and high demand for COVID-19 testing, we employed MALDI-ToF mass spectrometry in the analysis of 60 gargle samples from human donors and compared the resultant spectra against COVID-19 status. Several standards, including isolated human serum immunoglobulins, and controls, such as pre-COVID-19 saliva and heat inactivated SARS-CoV-2 virus, were simultaneously analyzed to provide a relative view of the saliva and viral proteome as they would appear in this workflow. Five potential biomarker peaks were established that demonstrated high concordance with COVID-19 positive individuals. Overall, the agreement of these results with RT-qPCR testing on nasopharyngeal swabs was ≥90% for the studied cohort, which consisted of young and largely asymptomatic student athletes. From a clinical standpoint, the results from this pilot study suggest that MALDI-ToF could be used to develop a relatively rapid and inexpensive COVID-19 assay.
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Key Words
- ACE2, angiotensin-converting enzyme 2
- AUC, area under the curve
- Asymptomatic
- COVID-19 testing
- COVID-19, coronavirus disease 2019
- Ct, cycle threshold, DTT, dithiothreitol
- E Protein, envelope protein
- EUA, emergency use authorization
- FDA, food and drug administration
- IgA, immunoglobulin A
- IgG, immunoglobulin G
- IgM, immunoglobulin M
- Immunoglobulins
- LoD, limit of detection, LC-MS, liquid chromatography mass spectrometry
- M Protein, membrane protein
- MALDI-ToF
- MALDI-ToF MS, matrix-assisted laser desorption/ionization-time of flight mass spectrometry
- N Protein, nucleocapsid protein
- NP, nasopharyngeal
- RBD, receptor binding domain
- RNA, ribonucleic acid
- ROC, receiver operating characteristic, RT-qPCR, reverse transcriptase quantitative polymerase chain reaction
- S Protein, spike protein
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- Saliva
- VEP, viral envelope protein
- WHO, world health organization
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Affiliation(s)
- Prajkta Chivte
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, United States
| | - Zane LaCasse
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, United States
| | | | - Pratool Bharti
- Department of Computer Science, Northern Illinois University, DeKalb, IL 60115, United States
| | - Joshua Bland
- Department of Pathology, University of Illinois at Chicago, Chicago, IL 60612, United States
| | - Shrihari S. Kadkol
- Department of Pathology, University of Illinois at Chicago, Chicago, IL 60612, United States
| | - Elizabeth R. Gaillard
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, United States
- Corresponding author.
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23
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Das JK, Roy S, Guzzi PH. Analyzing host-viral interactome of SARS-CoV-2 for identifying vulnerable host proteins during COVID-19 pathogenesis. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 93:104921. [PMID: 34004362 PMCID: PMC8123524 DOI: 10.1016/j.meegid.2021.104921] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 05/04/2021] [Accepted: 05/07/2021] [Indexed: 02/07/2023]
Abstract
The development of therapeutic targets for COVID-19 relies on understanding the molecular mechanism of pathogenesis. Identifying genes or proteins involved in the infection mechanism is the key to shedding light on the complex molecular mechanisms. The combined effort of many laboratories distributed throughout the world has produced protein and genetic interactions. We integrated available results and obtained a host protein-protein interaction network composed of 1432 human proteins. Next, we performed network centrality analysis to identify critical proteins in the derived network. Finally, we performed a functional enrichment analysis of central proteins. We observed that the identified proteins are primarily associated with several crucial pathways, including cellular process, signaling transduction, neurodegenerative diseases. We focused on the proteins that are involved in human respiratory tract diseases. We highlighted many potential therapeutic targets, including RBX1, HSPA5, ITCH, RAB7A, RAB5A, RAB8A, PSMC5, CAPZB, CANX, IGF2R, and HSPA1A, which are central and also associated with multiple diseases.
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Affiliation(s)
- Jayanta Kumar Das
- Department of Pediatrics, School of Medicine, Johns Hopkins University, MD, USA
| | - Swarup Roy
- Network Reconstruction & Analysis (NetRA) Lab, Department of Computer Applications, Sikkim University, Gangtok, India,Corresponding authors
| | - Pietro Hiram Guzzi
- Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy,Corresponding authors
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24
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Meng Z, Guo S, Zhou Y, Li M, Wang M, Ying B. Applications of laboratory findings in the prevention, diagnosis, treatment, and monitoring of COVID-19. Signal Transduct Target Ther 2021; 6:316. [PMID: 34433805 PMCID: PMC8386162 DOI: 10.1038/s41392-021-00731-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 07/21/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
The worldwide pandemic of coronavirus disease 2019 (COVID-19) presents us with a serious public health crisis. To combat the virus and slow its spread, wider testing is essential. There is a need for more sensitive, specific, and convenient detection methods of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Advanced detection can greatly improve the ability and accuracy of the clinical diagnosis of COVID-19, which is conducive to the early suitable treatment and supports precise prophylaxis. In this article, we combine and present the latest laboratory diagnostic technologies and methods for SARS-CoV-2 to identify the technical characteristics, considerations, biosafety requirements, common problems with testing and interpretation of results, and coping strategies of commonly used testing methods. We highlight the gaps in current diagnostic capacity and propose potential solutions to provide cutting-edge technical support to achieve a more precise diagnosis, treatment, and prevention of COVID-19 and to overcome the difficulties with the normalization of epidemic prevention and control.
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Affiliation(s)
- Zirui Meng
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Shuo Guo
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Yanbing Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Mengjiao Li
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Minjin Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China.
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25
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The Post-Acute Phase of SARS-CoV-2 Infection in Two Macaque Species Is Associated with Signs of Ongoing Virus Replication and Pathology in Pulmonary and Extrapulmonary Tissues. Viruses 2021; 13:v13081673. [PMID: 34452537 PMCID: PMC8402919 DOI: 10.3390/v13081673] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/13/2021] [Accepted: 08/18/2021] [Indexed: 12/21/2022] Open
Abstract
The post-acute phase of SARS-CoV-2 infection was investigated in rhesus (Macaca mulatta) and cynomolgus macaques (Macaca fascicularis). During the acute phase of infection, SARS-CoV-2 was shed via the nose and throat, and viral RNA was occasionally detected in feces. This phase coincided with a transient change in systemic immune activation. Even after the alleged resolution of the infection, computed tomography (CT) and positron emission tomography (PET)-CT revealed pulmonary lesions and activated tracheobronchial lymph nodes in all animals. Post-mortem histological examination of the lung tissue revealed mostly marginal or resolving minimal lesions that were indicative of SARS-CoV-2 infection. Evidence for SARS-CoV-2-induced histopathology was also found in extrapulmonary tissue samples, such as conjunctiva, cervical, and mesenteric lymph nodes. However, 5–6 weeks after SARS-CoV-2 exposure, upon necropsy, viral RNA was still detectable in a wide range of tissue samples in 50% of the macaques and included amongst others the heart, the respiratory tract and surrounding lymph nodes, salivary gland, and conjunctiva. Subgenomic messenger RNA was detected in the lungs and tracheobronchial lymph nodes, indicative of ongoing virus replication during the post-acute phase. These results could be relevant for understanding the long-term consequences of COVID-19 in humans.
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26
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Immunophenotyping assessment in a COVID-19 cohort (IMPACC): A prospective longitudinal study. Sci Immunol 2021; 6:6/62/eabf3733. [PMID: 34376480 PMCID: PMC8713959 DOI: 10.1126/sciimmunol.abf3733] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 08/05/2021] [Indexed: 12/13/2022]
Abstract
The Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC) is a prospective longitudinal study designed to enroll 1000 hospitalized patients with COVID-19 (NCT04378777). IMPACC collects detailed clinical, laboratory, and radiographic data along with longitudinal biologic sampling of blood and respiratory secretions for in-depth testing. Clinical and laboratory data are integrated to identify immunologic, virologic, proteomic, metabolomic, and genomic features of COVID-19–related susceptibility, severity, and disease progression. The goals of IMPACC are to better understand the contributions of pathogen dynamics and host immune responses to the severity and course of COVID-19 and to generate hypotheses for identification of biomarkers and effective therapeutics, including optimal timing of such interventions. In this report, we summarize the IMPACC study design and protocols including clinical criteria and recruitment, multisite standardized sample collection and processing, virologic and immunologic assays, harmonization of assay protocols, high-level analyses, and the data sharing plans.
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27
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Quantification of Changes in Protein Expression Using SWATH Proteomics. Methods Mol Biol 2021. [PMID: 34236656 DOI: 10.1007/978-1-0716-1641-3_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Sequential Window Acquisition of all THeoretical fragment ion spectra (SWATH) is a data independent acquisition mode used to accurately quantify thousands of proteins in a biological sample in a single run. It exploits fast scanning hybrid mass spectrometers to combine accuracy, reproducibility and sensitivity. This method requires the use of ion libraries, a sort of databases of spectral and chromatographic information about the proteins to be quantified. In this chapter, a typical workflow of SWATH experiment is described, from the sample preparation to the analysis of proteomics data.
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28
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Mohapatra S, Sharma N, Mohapatra G, Padhye LP, Mukherji S. Seasonal variation in fluorescence characteristics of dissolved organic matter in wastewater and identification of proteins through HRLC-MS/MS. JOURNAL OF HAZARDOUS MATERIALS 2021; 413:125453. [PMID: 33930968 DOI: 10.1016/j.jhazmat.2021.125453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/21/2021] [Accepted: 02/15/2021] [Indexed: 06/12/2023]
Abstract
In the present study, wastewater samples acquired from five wastewater treatment plants (WWTPs), located in western India were characterized using fluorescence spectroscopy, and resin-based fractionation was conducted to fractionate DOM into hydrophobic and hydrophilic base, acid, and neutral fractions. Among several fractions, the hydrophilic acid (HIA) and hydrophilic neutral (HIN) fractions were present in higher abundance (more than 50% of DOC) compared to the hydrophilic base (HIB) fraction in both influent and effluent wastewater stream obtained from WWTPs. Tryptophan-like and tyrosine-like substances were also abundant in the influent and effluent stream of WWTPs. Further, LC-MS/MS analysis could identify 235 and 288 DOM proteins in the influent and effluent stream of WWTP-1, respectively. These proteins revealed varying percentage of tryptophan and tyrosine residues. The tryptophan residues primarily contributed to protein-like fluorescence in wastewater. The proteins were further classified based on their role in biological processes, location in the cell, and molecular function. Among several proteins, Alzheimer's and Huntington disease biomarkers were identified at WWTP-1. Their presence in the surface water can serve as an early warning system for wastewater-based epidemiology.
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Affiliation(s)
- Sanjeeb Mohapatra
- Environmental Science and Engineering Department (ESED), IIT Bombay, Mumbai, India
| | - Neha Sharma
- Environmental Science and Engineering Department (ESED), IIT Bombay, Mumbai, India
| | | | - Lokesh P Padhye
- Department of Civil and Environmental Engineering, The University of Auckland, New Zealand
| | - Suparna Mukherji
- Environmental Science and Engineering Department (ESED), IIT Bombay, Mumbai, India.
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29
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Messner CB, Demichev V, Bloomfield N, Yu JSL, White M, Kreidl M, Egger AS, Freiwald A, Ivosev G, Wasim F, Zelezniak A, Jürgens L, Suttorp N, Sander LE, Kurth F, Lilley KS, Mülleder M, Tate S, Ralser M. Ultra-fast proteomics with Scanning SWATH. Nat Biotechnol 2021; 39:846-854. [PMID: 33767396 PMCID: PMC7611254 DOI: 10.1038/s41587-021-00860-4] [Citation(s) in RCA: 130] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/18/2021] [Indexed: 01/31/2023]
Abstract
Accurate quantification of the proteome remains challenging for large sample series and longitudinal experiments. We report a data-independent acquisition method, Scanning SWATH, that accelerates mass spectrometric (MS) duty cycles, yielding quantitative proteomes in combination with short gradients and high-flow (800 µl min-1) chromatography. Exploiting a continuous movement of the precursor isolation window to assign precursor masses to tandem mass spectrometry (MS/MS) fragment traces, Scanning SWATH increases precursor identifications by ~70% compared to conventional data-independent acquisition (DIA) methods on 0.5-5-min chromatographic gradients. We demonstrate the application of ultra-fast proteomics in drug mode-of-action screening and plasma proteomics. Scanning SWATH proteomes capture the mode of action of fungistatic azoles and statins. Moreover, we confirm 43 and identify 11 new plasma proteome biomarkers of COVID-19 severity, advancing patient classification and biomarker discovery. Thus, our results demonstrate a substantial acceleration and increased depth in fast proteomic experiments that facilitate proteomic drug screens and clinical studies.
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Affiliation(s)
- Christoph B Messner
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Vadim Demichev
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK
| | | | - Jason S L Yu
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Matthew White
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Marco Kreidl
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Anna-Sophia Egger
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Anja Freiwald
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Core Facility - High Throughput Mass Spectrometry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | | | | | - Aleksej Zelezniak
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Linda Jürgens
- Department of Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Norbert Suttorp
- Department of Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Leif Erik Sander
- Department of Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Florian Kurth
- Department of Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine & I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kathryn S Lilley
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK
| | - Michael Mülleder
- Core Facility - High Throughput Mass Spectrometry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Markus Ralser
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
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30
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Schindell BG, Allardice M, Lockman S, Kindrachuk J. Integrating Proteomics for Facilitating Drug Identification and Repurposing During an Emerging Virus Pandemic. ACS Infect Dis 2021; 7:1303-1316. [PMID: 33319978 DOI: 10.1021/acsinfecdis.0c00579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has disrupted global healthcare and economic systems throughout 2020 with no clear end in sight. While the pandemic continues to have deleterious effects across the globe, mechanisms for disrupting disease transmission have relied on behavioral controls (e.g., social distancing, masks, and hygiene) as there are currently no vaccines approved for use and limited therapeutic options. As this pandemic has demonstrated our vulnerability to newly emerging viruses, there has been strong interest in utilizing proteomics approaches to identify targets for repurposed drugs as novel therapeutic candidates that could be fast-tracked for human use. Building on a previous discussion on the combination of proteomics technologies with clinical data for combating emerging viruses, we discuss how these technologies are being employed for COVID-19 and the current state of knowledge regarding repurposed drugs in these efforts.
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Affiliation(s)
- Brayden G. Schindell
- Laboratory of Emerging and Re-Emerging Viruses, Department of Medical Microbiology & Infectious Diseases, University of Manitoba, Winnipeg R3T 2N2, Canada
| | - Meagan Allardice
- Laboratory of Emerging and Re-Emerging Viruses, Department of Medical Microbiology & Infectious Diseases, University of Manitoba, Winnipeg R3T 2N2, Canada
| | - Sandhini Lockman
- Regenerative Medicine Program, Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg R3T 2N2, Canada
| | - Jason Kindrachuk
- Laboratory of Emerging and Re-Emerging Viruses, Department of Medical Microbiology & Infectious Diseases, University of Manitoba, Winnipeg R3T 2N2, Canada
- Vaccine and Infectious Disease Organization−International Vaccine Centre (VIDO-InterVac, University of Saskatchewan, Saskatoon S7N 5E3, Canada
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31
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Hartl D, de Luca V, Kostikova A, Laramie J, Kennedy S, Ferrero E, Siegel R, Fink M, Ahmed S, Millholland J, Schuhmacher A, Hinder M, Piali L, Roth A. Translational precision medicine: an industry perspective. J Transl Med 2021; 19:245. [PMID: 34090480 PMCID: PMC8179706 DOI: 10.1186/s12967-021-02910-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/25/2021] [Indexed: 02/08/2023] Open
Abstract
In the era of precision medicine, digital technologies and artificial intelligence, drug discovery and development face unprecedented opportunities for product and business model innovation, fundamentally changing the traditional approach of how drugs are discovered, developed and marketed. Critical to this transformation is the adoption of new technologies in the drug development process, catalyzing the transition from serendipity-driven to data-driven medicine. This paradigm shift comes with a need for both translation and precision, leading to a modern Translational Precision Medicine approach to drug discovery and development. Key components of Translational Precision Medicine are multi-omics profiling, digital biomarkers, model-based data integration, artificial intelligence, biomarker-guided trial designs and patient-centric companion diagnostics. In this review, we summarize and critically discuss the potential and challenges of Translational Precision Medicine from a cross-industry perspective.
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Affiliation(s)
- Dominik Hartl
- Novartis Institutes for BioMedical Research, Basel, Switzerland.
- Department of Pediatrics I, University of Tübingen, Tübingen, Germany.
| | - Valeria de Luca
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Anna Kostikova
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Jason Laramie
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Scott Kennedy
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Enrico Ferrero
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Richard Siegel
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Martin Fink
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | | | | | - Markus Hinder
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Luca Piali
- Roche Innovation Center Basel, Basel, Switzerland
| | - Adrian Roth
- Roche Innovation Center Basel, Basel, Switzerland
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32
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Praissman JL, Wells L. Proteomics-Based Insights Into the SARS-CoV-2-Mediated COVID-19 Pandemic: A Review of the First Year of Research. Mol Cell Proteomics 2021; 20:100103. [PMID: 34089862 PMCID: PMC8176883 DOI: 10.1016/j.mcpro.2021.100103] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 05/24/2021] [Indexed: 02/08/2023] Open
Abstract
In late 2019, a virus subsequently named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in China and led to a worldwide pandemic of the disease termed coronavirus disease 2019. The global health threat posed by this pandemic led to an extremely rapid and robust mobilization of the scientific and medical communities as evidenced by the publication of more than 10,000 peer-reviewed articles and thousands of preprints in the first year of the pandemic alone. With the publication of the initial genome sequence of SARS-CoV-2, the proteomics community immediately joined this effort publishing, to date, more than 100 peer-reviewed proteomics studies and submitting many more preprints to preprint servers. In this review, we focus on peer-reviewed articles published on the proteome, glycoproteome, and glycome of SARS-CoV-2. At a basic level, proteomic studies provide valuable information on quantitative aspects of viral infection course; information on the identities, sites, and microheterogeneity of post-translational modifications; and, information on protein-protein interactions. At a biological systems level, these studies elucidate host cell and tissue responses, characterize antibodies and other immune system factors in infection, suggest biomarkers that may be useful for diagnosis and disease-course monitoring, and help in the development or repurposing of potential therapeutics. Here, we summarize results from selected early studies to provide a perspective on the current rapidly evolving literature.
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Affiliation(s)
- Jeremy L Praissman
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Lance Wells
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA.
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International COVID-19 thrombosis biomarkers colloquium: COVID-19 diagnostic tests. J Thromb Thrombolysis 2021; 52:992-998. [PMID: 34021852 PMCID: PMC8140326 DOI: 10.1007/s11239-021-02465-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/26/2021] [Indexed: 01/20/2023]
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Lee JS, Han D, Kim SY, Hong KH, Jang MJ, Kim MJ, Kim YG, Park JH, Cho SI, Park WB, Lee KB, Shin HS, Oh HS, Kim TS, Park SS, Seong MW. Longitudinal proteomic profiling provides insights into host response and proteome dynamics in COVID-19 progression. Proteomics 2021; 21:e2000278. [PMID: 33945677 PMCID: PMC8206655 DOI: 10.1002/pmic.202000278] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 03/25/2021] [Accepted: 03/30/2021] [Indexed: 11/21/2022]
Abstract
In managing patients with coronavirus disease 2019 (COVID‐19), early identification of those at high risk and real‐time monitoring of disease progression to severe COVID‐19 is a major challenge. We aimed to identify potential early prognostic protein markers and to expand understanding of proteome dynamics during clinical progression of the disease. We performed in‐depth proteome profiling on 137 sera, longitudinally collected from 25 patients with COVID‐19 (non‐severe patients, n = 13; patients who progressed to severe COVID‐19, n = 12). We identified 11 potential biomarkers, including the novel markers IGLV3‐19 and BNC2, as early potential prognostic indicators of severe COVID‐19. These potential biomarkers are mainly involved in biological processes associated with humoral immune response, interferon signalling, acute phase response, lipid metabolism, and platelet degranulation. We further revealed that the longitudinal changes of 40 proteins persistently increased or decreased as the disease progressed to severe COVID‐19. These 40 potential biomarkers could effectively reflect the clinical progression of the disease. Our findings provide some new insights into host response to SARS‐CoV‐2 infection, which are valuable for understanding of COVID‐19 disease progression. This study also identified potential biomarkers that could be further validated, which may support better predicting and monitoring progression to severe COVID‐19.
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Affiliation(s)
- Jee-Soo Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Dohyun Han
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - So Yeon Kim
- Department of Laboratory Medicine, National Medical Center, Seoul, South Korea
| | - Ki Ho Hong
- Department of Laboratory Medicine, Seoul Medical Center, Seoul, South Korea
| | - Myoung-Jin Jang
- Medical Research Collaborating Center, Seoul National University Hospital
| | - Man Jin Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Young-Gon Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Jae Hyeon Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Wan Beom Park
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Kyung Bok Lee
- Department of Statistics, Seoul National University, Seoul, South Korea
| | - Ho Seob Shin
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Hyeon Sae Oh
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Taek Soo Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
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Hopp MT, Domingo-Fernández D, Gadiya Y, Detzel MS, Graf R, Schmalohr BF, Kodamullil AT, Imhof D, Hofmann-Apitius M. Linking COVID-19 and Heme-Driven Pathophysiologies: A Combined Computational-Experimental Approach. Biomolecules 2021; 11:biom11050644. [PMID: 33925394 PMCID: PMC8147026 DOI: 10.3390/biom11050644] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 01/08/2023] Open
Abstract
The SARS-CoV-2 outbreak was declared a worldwide pandemic in 2020. Infection triggers the respiratory tract disease COVID-19, which is accompanied by serious changes in clinical biomarkers such as hemoglobin and interleukins. The same parameters are altered during hemolysis, which is characterized by an increase in labile heme. We present two computational–experimental approaches aimed at analyzing a potential link between heme-related and COVID-19 pathophysiologies. Herein, we performed a detailed analysis of the common pathways induced by heme and SARS-CoV-2 by superimposition of knowledge graphs covering heme biology and COVID-19 pathophysiology. Focus was laid on inflammatory pathways and distinct biomarkers as the linking elements. In a second approach, four COVID-19-related proteins, the host cell proteins ACE2 and TMPRSS2 as well as the viral proteins 7a and S protein were computationally analyzed as potential heme-binding proteins with an experimental validation. The results contribute to the understanding of the progression of COVID-19 infections in patients with different clinical backgrounds and may allow for a more individual diagnosis and therapy in the future.
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Affiliation(s)
- Marie-Thérèse Hopp
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany; (M.-T.H.); (M.S.D.); (R.G.); (B.F.S.)
| | - Daniel Domingo-Fernández
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, D-53757 Sankt Augustin, Germany; (D.D.-F.); (Y.G.); (A.T.K.)
- Enveda Biosciences, Inc., San Francisco, CA 94080, USA
| | - Yojana Gadiya
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, D-53757 Sankt Augustin, Germany; (D.D.-F.); (Y.G.); (A.T.K.)
| | - Milena S. Detzel
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany; (M.-T.H.); (M.S.D.); (R.G.); (B.F.S.)
| | - Regina Graf
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany; (M.-T.H.); (M.S.D.); (R.G.); (B.F.S.)
| | - Benjamin F. Schmalohr
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany; (M.-T.H.); (M.S.D.); (R.G.); (B.F.S.)
| | - Alpha T. Kodamullil
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, D-53757 Sankt Augustin, Germany; (D.D.-F.); (Y.G.); (A.T.K.)
- Causality Biomodels, Kinfra Hi-Tech Park, Kalamassery, Cochin, Kerala 683503, India
| | - Diana Imhof
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany; (M.-T.H.); (M.S.D.); (R.G.); (B.F.S.)
- Correspondence: (D.I.); (M.H.-A.)
| | - Martin Hofmann-Apitius
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, D-53757 Sankt Augustin, Germany; (D.D.-F.); (Y.G.); (A.T.K.)
- Correspondence: (D.I.); (M.H.-A.)
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36
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Li C, Revote J, Ramarathinam SH, Chung SZ, Croft NP, Scull KE, Huang Z, Ayala R, Braun A, Mifsud NA, Illing PT, Faridi P, Purcell AW. Resourcing, annotating, and analysing synthetic peptides of SARS-CoV-2 for immunopeptidomics and other immunological studies. Proteomics 2021; 21:e2100036. [PMID: 33811468 PMCID: PMC8250278 DOI: 10.1002/pmic.202100036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/15/2021] [Accepted: 03/15/2021] [Indexed: 12/27/2022]
Abstract
SARS‐CoV‐2 has caused a significant ongoing pandemic worldwide. A number of studies have examined the T cell mediated immune responses against SARS‐CoV‐2, identifying potential T cell epitopes derived from the SARS‐CoV‐2 proteome. Such studies will aid in identifying targets for vaccination and immune monitoring. In this study, we applied tandem mass spectrometry and proteomic techniques to a library of ∼40,000 synthetic peptides, in order to generate a large dataset of SARS‐CoV‐2 derived peptide MS/MS spectra. On this basis, we built an online knowledgebase, termed virusMS (https://virusms.erc.monash.edu/), to document, annotate and analyse these synthetic peptides and their spectral information. VirusMS incorporates a user‐friendly interface to facilitate searching, browsing and downloading the database content. Detailed annotations of the peptides, including experimental information, peptide modifications, predicted peptide‐HLA (human leukocyte antigen) binding affinities, and peptide MS/MS spectral data, are provided in virusMS.
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Affiliation(s)
- Chen Li
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jerico Revote
- Monash Bioinformatics Platform, Monash University, Melbourne, Victoria, Australia
| | - Sri H Ramarathinam
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Shan Zou Chung
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Nathan P Croft
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Katherine E Scull
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Ziyi Huang
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Rochelle Ayala
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Asolina Braun
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Nicole A Mifsud
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Patricia T Illing
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Pouya Faridi
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
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Zamanian-Azodi M, Arjmand B, Razzaghi M, Rezaei Tavirani M, Ahmadzadeh A, Rostaminejad M. Platelet and Haemostasis are the Main Targets in Severe Cases of COVID-19 Infection; a System Biology Study. ARCHIVES OF ACADEMIC EMERGENCY MEDICINE 2021; 9:e27. [PMID: 34027422 PMCID: PMC8126352 DOI: 10.22037/aaem.v9i1.1108] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Introduction: Many proteomics-based and bioinformatics-based efforts are made to detect the molecular mechanism of COVID-19 infection. Identification of the main protein targets and pathways of severe cases of COVID-19 infection is the aim of this study. Methods: Published differentially expressed proteins were screened and the significant proteins were investigated via protein-protein interaction network using Cytoscape software V. 3.7.2 and STRING database. The studied proteins were assessed via action map analysis to determine the relationship between individual proteins using CluePedia. The related biological terms were investigated using ClueGO and the terms were clustered and discussed. Results: Among the 35 queried proteins, six of them (FGA, FGB, FGG, and FGl1 plus TLN1 and THBS1) were identified as critical proteins. A total of 38 biological terms, clustered in 4 groups, were introduced as the affected terms. “Platelet degranulation” and “hereditary factor I deficiency disease” were introduced as the main class of the terms disturbed by COVID-19 virus. Conclusion: It can be concluded that platelet damage and disturbed haemostasis could be the main targets in severe cases of coronavirus infection. It is vital to follow patients’ condition by examining the introduced critical differentially expressed proteins (DEPs).
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Affiliation(s)
- Mona Zamanian-Azodi
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Babak Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Razzaghi
- Laser Application in Medical Sciences Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mostafa Rezaei Tavirani
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Ahmadzadeh
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Rostaminejad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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38
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Bittremieux W, Adams C, Laukens K, Dorrestein PC, Bandeira N. Open Science Resources for the Mass Spectrometry-Based Analysis of SARS-CoV-2. J Proteome Res 2021; 20:1464-1475. [PMID: 33605735 DOI: 10.1021/acs.jproteome.0c00929] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The SARS-CoV-2 virus is the causative agent of the 2020 pandemic leading to the COVID-19 respiratory disease. With many scientific and humanitarian efforts ongoing to develop diagnostic tests, vaccines, and treatments for COVID-19, and to prevent the spread of SARS-CoV-2, mass spectrometry research, including proteomics, is playing a role in determining the biology of this viral infection. Proteomics studies are starting to lead to an understanding of the roles of viral and host proteins during SARS-CoV-2 infection, their protein-protein interactions, and post-translational modifications. This is beginning to provide insights into potential therapeutic targets or diagnostic strategies that can be used to reduce the long-term burden of the pandemic. However, the extraordinary situation caused by the global pandemic is also highlighting the need to improve mass spectrometry data and workflow sharing. We therefore describe freely available data and computational resources that can facilitate and assist the mass spectrometry-based analysis of SARS-CoV-2. We exemplify this by reanalyzing a virus-host interactome data set to detect protein-protein interactions and identify host proteins that could potentially be used as targets for drug repurposing.
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Affiliation(s)
- Wout Bittremieux
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla 92093, California, United States.,Department of Computer Science, University of Antwerp, Antwerp 2020, Belgium
| | - Charlotte Adams
- Department of Computer Science, University of Antwerp, Antwerp 2020, Belgium
| | - Kris Laukens
- Department of Computer Science, University of Antwerp, Antwerp 2020, Belgium
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla 92093, California, United States
| | - Nuno Bandeira
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla 92093, California, United States.,Department of Computer Science and Engineering, University of California San Diego, La Jolla 92093, California, United States
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39
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Thuy-Boun PS, Mehta S, Gruening B, McGowan T, Nguyen A, Rajczewski A, Johnson JE, Griffin TJ, Wolan DW, Jagtap PD. Metaproteomics Analysis of SARS-CoV-2-Infected Patient Samples Reveals Presence of Potential Coinfecting Microorganisms. J Proteome Res 2021; 20:1451-1454. [PMID: 33393790 PMCID: PMC7805602 DOI: 10.1021/acs.jproteome.0c00822] [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: 10/15/2020] [Indexed: 01/06/2023]
Abstract
In this Letter, we reanalyze published mass spectrometry data sets of clinical samples with a focus on determining the coinfection status of individuals infected with SARS-CoV-2 coronavirus. We demonstrate the use of ComPIL 2.0 software along with a metaproteomics workflow within the Galaxy platform to detect cohabitating potential pathogens in COVID-19 patients using mass spectrometry-based analysis. From a sample collected from gargling solutions, we detected Streptococcus pneumoniae (opportunistic and multidrug-resistant pathogen) and Lactobacillus rhamnosus (a probiotic component) along with SARS-Cov-2. We could also detect Pseudomonas sps. Bc-h from COVID-19 positive samples and Acinetobacter ursingii and Pseudomonas monteilii from COVID-19 negative samples collected from oro- and nasopharyngeal samples. We believe that the early detection and characterization of coinfections by using metaproteomics from COVID-19 patients will potentially impact the diagnosis and treatment of patients affected by SARS-CoV-2 infection.
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Affiliation(s)
| | | | - Bjoern Gruening
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg im Breisgau, Germany
| | | | - An Nguyen
- University of Minnesota, Minneapolis, MN, USA
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40
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Zhang L, Xiao M, Wang Y, Peng S, Chen Y, Zhang D, Zhang D, Guo Y, Wang X, Luo H, Zhou Q, Xu Y. Fast Screening and Primary Diagnosis of COVID-19 by ATR-FT-IR. Anal Chem 2021; 93:2191-2199. [PMID: 33427452 PMCID: PMC7805601 DOI: 10.1021/acs.analchem.0c04049] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/18/2020] [Indexed: 12/21/2022]
Abstract
The outbreak of coronavirus disease 2019 (COVID-19) has led to substantial infections and mortality around the world. Fast screening and diagnosis are thus crucial for quick isolation and clinical intervention. In this work, we showed that attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FT-IR) can be a primary diagnostic tool for COVID-19 as a supplement to in-use techniques. It requires only a small volume (∼3 μL) of the serum sample and a shorter detection time (several minutes). The distinct spectral differences and the separability between normal control and COVID-19 were investigated using multivariate and statistical analysis. Results showed that ATR-FT-IR coupled with partial least squares discriminant analysis was effective to differentiate COVID-19 from normal controls and some common respiratory viral infections or inflammation, with the area under the receiver operating characteristic curve (AUROC) of 0.9561 (95% CI: 0.9071-0.9774). Several serum constituents including, but not just, antibodies and serum phospholipids could be reflected on the infrared spectra, serving as "chemical fingerprints" and accounting for good model performances.
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Affiliation(s)
- Liyang Zhang
- Department of Electrical Engineering,
Tsinghua University, Beijing 100084,
China
| | - Meng Xiao
- Department of Laboratory Medicine,
Peking Union Medical College Hospital, Peking Union Medical College,
Chinese Academy of Medical Sciences,
Beijing 100730, China
| | - Yao Wang
- Department of Laboratory Medicine,
Peking Union Medical College Hospital, Peking Union Medical College,
Chinese Academy of Medical Sciences,
Beijing 100730, China
| | - Siqi Peng
- Department of Electrical Engineering,
Tsinghua University, Beijing 100084,
China
| | - Yu Chen
- Department of Laboratory Medicine,
Peking Union Medical College Hospital, Peking Union Medical College,
Chinese Academy of Medical Sciences,
Beijing 100730, China
| | - Dong Zhang
- Department of Laboratory Medicine,
Peking Union Medical College Hospital, Peking Union Medical College,
Chinese Academy of Medical Sciences,
Beijing 100730, China
| | - Dongheyu Zhang
- Department of Electrical Engineering,
Tsinghua University, Beijing 100084,
China
| | - Yuntao Guo
- Department of Electrical Engineering,
Tsinghua University, Beijing 100084,
China
| | - Xinxin Wang
- Department of Electrical Engineering,
Tsinghua University, Beijing 100084,
China
| | - Haiyun Luo
- Department of Electrical Engineering,
Tsinghua University, Beijing 100084,
China
| | - Qun Zhou
- Department of Chemistry, Key Laboratory
of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of
Education), Tsinghua University, Beijing
100084, China
| | - Yingchun Xu
- Department of Laboratory Medicine,
Peking Union Medical College Hospital, Peking Union Medical College,
Chinese Academy of Medical Sciences,
Beijing 100730, China
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41
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Zhang L, Xiao M, Wang Y, Peng S, Chen Y, Zhang D, Zhang D, Guo Y, Wang X, Luo H, Zhou Q, Xu Y. Fast Screening and Primary Diagnosis of COVID-19 by ATR-FT-IR. Anal Chem 2021; 93:2191-2199. [PMID: 33427452 DOI: 10.1021/acs.analchem.0c0404910.1021/acs.analchem.0c04049.s001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The outbreak of coronavirus disease 2019 (COVID-19) has led to substantial infections and mortality around the world. Fast screening and diagnosis are thus crucial for quick isolation and clinical intervention. In this work, we showed that attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FT-IR) can be a primary diagnostic tool for COVID-19 as a supplement to in-use techniques. It requires only a small volume (∼3 μL) of the serum sample and a shorter detection time (several minutes). The distinct spectral differences and the separability between normal control and COVID-19 were investigated using multivariate and statistical analysis. Results showed that ATR-FT-IR coupled with partial least squares discriminant analysis was effective to differentiate COVID-19 from normal controls and some common respiratory viral infections or inflammation, with the area under the receiver operating characteristic curve (AUROC) of 0.9561 (95% CI: 0.9071-0.9774). Several serum constituents including, but not just, antibodies and serum phospholipids could be reflected on the infrared spectra, serving as "chemical fingerprints" and accounting for good model performances.
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Affiliation(s)
- Liyang Zhang
- Department of Electrical Engineering, Tsinghua University, Beijing 100084, China
| | - Meng Xiao
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Yao Wang
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Siqi Peng
- Department of Electrical Engineering, Tsinghua University, Beijing 100084, China
| | - Yu Chen
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Dong Zhang
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Dongheyu Zhang
- Department of Electrical Engineering, Tsinghua University, Beijing 100084, China
| | - Yuntao Guo
- Department of Electrical Engineering, Tsinghua University, Beijing 100084, China
| | - Xinxin Wang
- Department of Electrical Engineering, Tsinghua University, Beijing 100084, China
| | - Haiyun Luo
- Department of Electrical Engineering, Tsinghua University, Beijing 100084, China
| | - Qun Zhou
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Yingchun Xu
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
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42
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Gowri A, Ashwin Kumar N, Suresh Anand BS. Recent advances in nanomaterials based biosensors for point of care (PoC) diagnosis of Covid-19 - A minireview. Trends Analyt Chem 2021; 137:116205. [PMID: 33531721 PMCID: PMC7842193 DOI: 10.1016/j.trac.2021.116205] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Early diagnosis and ultrahigh sample throughput screening are the need of the hour to control the geological spread of the COVID-19 pandemic. Traditional laboratory tests such as enzyme-linked immunosorbent assay (ELISA), reverse transcription polymerase chain reaction (RT-PCR) and computed tomography are implemented for the detection of COVID-19. However, they are limited by the laborious sample collection and processing procedures, longer wait time for test results and skilled technicians to operate sophisticated facilities. In this context, the point of care (PoC) diagnostic platform has proven to be the prospective approach in addressing the abovementioned challenges. This review emphasizes the mechanism of viral infection spread detailing the host-virus interaction, pathophysiology, and the recent advances in the development of affordable PoC diagnostic platforms for rapid and accurate diagnosis of COVID-19. First, the well-established optical and electrochemical biosensors are discussed. Subsequently, the recent advances in the development of PoC biosensors, including lateral flow immunoassays and other emerging techniques, are highlighted. Finally, a focus on integrating nanotechnology with wearables and smartphones to develop smart nanobiosensors is outlined, which could promote COVID-19 diagnosis accessible to both individuals and the mass population at patient care.
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Affiliation(s)
- Annasamy Gowri
- Department of Biomedical Engineering, Vel Tech Research Park, Vel Tech Rangarajan Dr.Sagunthala R & D Institute of Science and Technology, Avadi, Chennai 600 062, Tamil Nadu, India
| | - N Ashwin Kumar
- Department of Biomedical Engineering, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur 603203, Tamil Nadu, India
| | - B S Suresh Anand
- Department of Biomedical Engineering, Rajalakshmi Engineering College, Thandalam, Chennai 602 105, Tamil Nadu, India
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43
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Mir JM, Khan MW, Shalla AH, Maurya RC. A Nonclinical Spectroscopic Approach for Diagnosing Covid-19: A Concise Perspective. JOURNAL OF APPLIED SPECTROSCOPY 2021; 88:765-771. [PMID: 34538886 PMCID: PMC8435118 DOI: 10.1007/s10812-021-01238-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Indexed: 05/08/2023]
Abstract
With the COVID-19 outbreak, many challenges are posed before the scientific world to curb this pandemic. The diagnostic testing, treatment, and vaccine development for this infection caught the scientific community's immediate attention. Currently, despite the global proliferation of COVID-19 vaccination, the specific treatment for this disease is yet unknown. Meanwhile, COVID-19 detection or diagnosis using polymerase chain reaction (PCR)-based me hods is expensive and less reliable. Moreover, this technique needs much time to furnish the results. Thus, the elaboration of a highly sensitive and fast method of COVID-19 diagnostics is of great importance. The spectroscopic approach is herein suggested as an efficient detection methodology for COVID-19 diagnosis, particularly Raman spectroscopy, infrared spectroscopy, and mass spectrometry.
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Affiliation(s)
- J. M. Mir
- Department of Chemistry, Islamic University of Science and Technology-Awantipora, J&K, Awantipora, 192122 India
- Coordination, Metallopharmaceutical and Computational Chemistry Laboratory, Department of PG Studies and Research in Chemistry and Pharmacy, RD University, Jabalpur, MP India
| | - M. W. Khan
- Coordination, Metallopharmaceutical and Computational Chemistry Laboratory, Department of PG Studies and Research in Chemistry and Pharmacy, RD University, Jabalpur, MP India
| | - A. H. Shalla
- Department of Chemistry, Islamic University of Science and Technology-Awantipora, J&K, Awantipora, 192122 India
| | - R. C. Maurya
- Coordination, Metallopharmaceutical and Computational Chemistry Laboratory, Department of PG Studies and Research in Chemistry and Pharmacy, RD University, Jabalpur, MP India
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44
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Al-kuraishy HM, Al-Gareeb AI, Alblihed M, Cruz-Martins N, Batiha GES. COVID-19 and Risk of Acute Ischemic Stroke and Acute Lung Injury in Patients With Type II Diabetes Mellitus: The Anti-inflammatory Role of Metformin. Front Med (Lausanne) 2021; 8:644295. [PMID: 33718411 PMCID: PMC7944640 DOI: 10.3389/fmed.2021.644295] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 01/22/2021] [Indexed: 12/14/2022] Open
Abstract
Background: Coronavirus disease 19 (COVID-19) is regarded as an independent risk factor for acute ischemic stroke (AIS) due to the induction of endothelial dysfunction, coagulopathy, cytokine storm, and plaque instability. Method: In this retrospective cohort study, a total of 42 COVID-19 patients with type 2 diabetes mellitus (T2DM) who presented with AIS within 1 week of displaying COVID-19 symptoms were recruited. According to the current anti-DM pharmacotherapy, patients were divided into two groups: a Metformin group of T2DM patients with COVID-19 and AIS on metformin therapy (850 mg, 3 times daily (n = 22), and a Non-metformin group of T2DM patients with COVID-19 and AIS under another anti-DM pharmacotherapy like glibenclamide and pioglitazone (n = 20). Anthropometric, biochemical, and radiological data were evaluated. Results: Ferritin serum level was lower in metformin-treated patients compared to non-metformin treated patients (365.93 ± 17.41 vs. 475.92 ± 22.78 ng/mL, p = 0.0001). CRP, LDH, and D-dimer serum levels were also lowered in metformin-treated patients compared to non-metformin treated patients (p = 0.0001). In addition, lung CT scan scores of COVID-19 patients was 30.62 ± 10.64 for metformin and 36.31 ± 5.03 for non-metformin treated patients. Conclusion: Metformin therapy in T2DM patients was linked to a lower risk of AIS during COVID-19. Further studies are needed to observe the link between AIS in COVID-19 diabetic patients and metformin therapy.
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Affiliation(s)
- Hayder M. Al-kuraishy
- Department of Clinical Pharmacology and Medicine, College of Medicine, Al-Mustansiriyia University, Baghdad, Iraq
| | - Ali I. Al-Gareeb
- Department of Clinical Pharmacology and Medicine, College of Medicine, Al-Mustansiriyia University, Baghdad, Iraq
| | - M. Alblihed
- Department of Microbiology, College of Medicine, Taif University, Taif, Saudi Arabia
| | - Natália Cruz-Martins
- Faculty of Medicine, University of Porto, Porto, Portugal
- Institute for Research and Innovation in Health (i3S), University of Porto, Porto, Portugal
- Laboratory of Neuropsychophysiology, Faculty of Psychology and Education Sciences, University of Porto, Porto, Portugal
- *Correspondence: Natália Cruz-Martins
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
- Gaber El-Saber Batiha
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45
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Ng TI, Dorr PK, Krishnan P, Cohen DE, Rhee S, Wang SX, Ruzek MC, Mensa FJ, Kati WM. Biomarkers for the clinical development of antiviral therapies. CYTOMETRY. PART B, CLINICAL CYTOMETRY 2021; 100:19-32. [PMID: 34542933 DOI: 10.1002/cyto.b.21974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/23/2020] [Accepted: 11/17/2020] [Indexed: 06/13/2023]
Abstract
With the morbidity and mortality associated with the COVID-19 pandemic that we are witnessing this year, the risks posed by emerging viral diseases to global health are all too obvious. This pandemic highlights the importance of antiviral drug discovery, which targets emerging viral pathogens, as well as existing pathogenic viruses that undergo continuous evolution. Drug discovery and development is a long and resource intensive process; however, the use of biomarkers can accelerate clinical development of antivirals by providing information regarding diagnosis of specific viral infections, status of infection, potential safety parameters, and antiviral responses. In clinical practice, many of the biomarkers initially utilized to support clinical development are also used for patient care. While viral load is a standard and essential biomarker used to detect the desired viral suppression induced by an antiviral agent, it has become apparent that additional biomarkers, whether related to the virus, the host or as a consequence of the drug's mechanistic effects, are also important for monitoring clinical outcomes associated with an antiviral therapy. This review summarizes the biomarkers used in the clinical development (as well as in clinical practice, where appropriate) of antiviral therapies for hepatitis C virus, hepatitis B virus, human immunodeficiency virus, and severe acute respiratory syndrome coronavirus 2.
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Affiliation(s)
- Teresa I Ng
- Virology Drug Discovery, AbbVie Inc., North Chicago, Illinois, USA
| | - Patrick K Dorr
- General Medicine and Virology, AbbVie Inc., North Chicago, Illinois, USA
| | - Preethi Krishnan
- Virology Drug Discovery, AbbVie Inc., North Chicago, Illinois, USA
| | - Daniel E Cohen
- General Medicine and Virology, AbbVie Inc., North Chicago, Illinois, USA
| | - Susan Rhee
- General Medicine and Virology, AbbVie Inc., North Chicago, Illinois, USA
| | - Stanley X Wang
- General Medicine and Virology, AbbVie Inc., North Chicago, Illinois, USA
| | - Melanie C Ruzek
- Translational Immunology, AbbVie Inc., Worcester, Massachusetts, USA
| | - Federico J Mensa
- General Medicine and Virology, AbbVie Inc., North Chicago, Illinois, USA
| | - Warren M Kati
- Virology Drug Discovery, AbbVie Inc., North Chicago, Illinois, USA
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46
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Park J, Kim H, Kim SY, Kim Y, Lee JS, Dan K, Seong MW, Han D. In-depth blood proteome profiling analysis revealed distinct functional characteristics of plasma proteins between severe and non-severe COVID-19 patients. Sci Rep 2020; 10:22418. [PMID: 33376242 PMCID: PMC7772338 DOI: 10.1038/s41598-020-80120-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 12/15/2020] [Indexed: 01/08/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected over forty million patients worldwide. Although most coronavirus disease 2019 (COVID-19) patients have a good prognosis, some develop severe illness. Markers that define disease severity or predict clinical outcome need to be urgently developed as the mortality rate in critical cases is approximately 61.5%. In the present study, we performed in-depth proteome profiling of undepleted plasma from eight COVID-19 patients. Quantitative proteomic analysis using the BoxCar method revealed that 91 out of 1222 quantified proteins were differentially expressed depending on the severity of COVID-19. Importantly, we found 76 proteins, previously not reported, which could be novel prognostic biomarker candidates. Our plasma proteome signatures captured the host response to SARS-CoV-2 infection, thereby highlighting the role of neutrophil activation, complement activation, platelet function, and T cell suppression as well as proinflammatory factors upstream and downstream of interleukin-6, interleukin-1B, and tumor necrosis factor. Consequently, this study supports the development of blood biomarkers and potential therapeutic targets to aid clinical decision-making and subsequently improve prognosis of COVID-19.
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Affiliation(s)
- Joonho Park
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, 71 Daehak-ro, Seoul, Republic of Korea
| | - Hyeyoon Kim
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, 71 Daehak-ro, Seoul, Republic of Korea
| | - So Yeon Kim
- Department of Laboratory Medicine, National Medical Center, Seoul, Korea
| | - Yeonjae Kim
- Department of Infectious Disease, National Medical Center, Seoul, Korea
| | - Jee-Soo Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Seoul, Republic of Korea
| | - Kisoon Dan
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, 71 Daehak-ro, Seoul, Republic of Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Seoul, Republic of Korea.
| | - Dohyun Han
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, 71 Daehak-ro, Seoul, Republic of Korea.
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47
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Syal K. Guidelines on newly identified limitations of diagnostic tools for COVID-19 and consequences. J Med Virol 2020; 93:1837-1842. [PMID: 33200414 PMCID: PMC7753543 DOI: 10.1002/jmv.26673] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/05/2020] [Accepted: 11/12/2020] [Indexed: 01/07/2023]
Abstract
Coronavirus disease 2019 (COVID-19) caused by coronavirus has spread worldwide and has become the deadliest pandemic of the 21st century. Such rapid spread is predominantly attributed to the poor diagnosis and its asymptomatic transmission. In the absence of treatment regime, timely diagnosis is the best available remedy that can restrict its spread. An early diagnosis of COVID-19 is critical for determining the line of treatment and preventing long term complications in the infected subject. Unfortunately, available rapid antigen and antibody kits are known to be erroneous whereas reverse transcription polymerase chain reaction based tests are expensive, viral load dependent and at times inconclusive. In current scenario, the false-negative results imposed a major risk to the individual patient care and also to the efforts for containing the spread at the population level, where as false positives are traumatic for families and can lead to improper treatment resulting in severe complications. In this article, the limitations of available diagnostic procedures have been elaborated and plausible combination approach has been advised.
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Affiliation(s)
- Kirtimaan Syal
- Department of Biological Sciences, BITS-Pilani, Telangana, India
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48
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Grenga L, Armengaud J. Proteomics in the COVID-19 Battlefield: First Semester Check-Up. Proteomics 2020; 21:e2000198. [PMID: 33236484 PMCID: PMC7744874 DOI: 10.1002/pmic.202000198] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/09/2020] [Indexed: 12/11/2022]
Abstract
Proteomics offers a wide collection of methodologies to study biological systems at the finest granularity. Faced with COVID‐19, the most worrying pandemic in a century, proteomics researchers have made significant progress in understanding how the causative virus hijacks the host's cellular machinery and multiplies exponentially, how the disease can be diagnosed, and how it develops, as well as its severity predicted. Numerous cellular targets of potential interest for the development of new antiviral drugs have been documented. Here, the most striking results obtained in the proteomics field over this first semester of the pandemic are presented. The molecular machinery of SARS‐CoV‐2 is much more complex than initially believed, as many post‐translational modifications can occur, leading to a myriad of proteoforms and a broad heterogeneity of viral particles. The interplay of protein–protein interactions, protein abundances, and post‐translational modifications has yet to be fully documented to provide a full picture of this intriguing but lethal biological threat. Proteomics has the potential to provide rapid detection of the SARS‐CoV‐2 virus by mass spectrometry proteotyping, and to further increase the knowledge of severe respiratory syndrome COVID‐19 and its long‐term health consequences.
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Affiliation(s)
- Lucia Grenga
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Ceze, F-30200, France
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Ceze, F-30200, France
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49
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Affiliation(s)
- Suman S. Thakur
- Proteomics and Cell Signaling, Lab
W110, Centre for Cellular & Molecular
Biology, Habsiguda, Uppal
Road, Hyderabad 500 007, Telangana, India
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50
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Lachén-Montes M, Corrales FJ, Fernández-Irigoyen J, Santamaría E. Proteomics Insights Into the Molecular Basis of SARS-CoV-2 Infection: What We Can Learn From the Human Olfactory Axis. Front Microbiol 2020; 11:2101. [PMID: 33071996 PMCID: PMC7536310 DOI: 10.3389/fmicb.2020.02101] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 08/10/2020] [Indexed: 12/12/2022] Open
Abstract
Like other RNA viruses, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replicates in host cells, continuously modulating the molecular environment. It encodes 28 multifunctional proteins that induce an imbalance in the metabolic and proteostatic homeostasis in infected cells. Recently, proteomic approaches have allowed the evaluation of the impact of SARS-CoV-2 infection in human cells. Here, we discuss the current use of proteomics in three major application areas: (i) virus-protein interactomics, (ii) differential proteotyping to map the virus-induced changes in different cell types, and (iii) diagnostic methods for coronavirus infectious disease 2019 (COVID-19). Since the nasal cavity is one of the entry sites for SARS-CoV-2, we will also discuss the potential application of olfactory proteomics to provide novel insights into the olfactory dysfunction triggered by SARS-CoV-2 in patients with COVID-19.
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Affiliation(s)
- Mercedes Lachén-Montes
- Clinical Neuroproteomics Unit, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
- Proteored-Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Fernando J. Corrales
- Proteored-Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Proteomics Unit, National Centre for Biotechnology, Madrid, Spain
| | - Joaquín Fernández-Irigoyen
- Clinical Neuroproteomics Unit, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
- Proteored-Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
- Proteored-Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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