Proteomics and Informatics for Understanding Phases and Identifying Biomarkers in COVID-19 Disease

Whetton, Anthony D.; Preston, George W.; Abubeker, Semira; Geifman, Nophar

doi:10.1021/acs.jproteome.0c00326

Cited by 70 publications

(79 citation statements)

References 97 publications

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“…Over the past several months, proteomic and metabolomic profiles of peripheral blood samples have been investigated to correlate disease severity of COVID-19 with certain proteins and lipids. 54 , 55 Details can be found elsewhere.…”

Section: Discussionmentioning

confidence: 99%

Fast Screening and Primary Diagnosis of COVID-19 by ATR–FT-IR

et al. 2021

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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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Section: Discussionmentioning

confidence: 99%

Fast Screening and Primary Diagnosis of COVID-19 by ATR–FT-IR

et al. 2021

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“…In fact, proteomic methods allowed the characterization and understanding of SARS-CoV during the severe acute respiratory syndrome (SARS) outbreak in 2003, enabling the description of virus protein sequences and antigenic virus proteins and the identification of ACE2 as the human receptor for SARS-CoV (Krokhin et al, 2003;Li et al, 2003;Ying et al, 2004). Consequently, the application of proteomic workflows may be highly beneficial to increase our understanding of the pathogenesis of COVID-19, to identify potential therapeutic targets, and even to develop fast and effective diagnostic tests (Struwe et al, 2020;Whetton et al, 2020). In this mini-review, we focus on different proteomic methodologies currently used to decipher novel SARS-CoV-2 targets and potential COVID-19 biomarkers ( Table 1).…”

Section: Introductionmentioning

confidence: 99%

Proteomics Insights Into the Molecular Basis of SARS-CoV-2 Infection: What We Can Learn From the Human Olfactory Axis

et al. 2020

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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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“…While our approach did find some associations in our mined COVID-19 corpus, our data mining in Coronavirus- and other related lung-damaging diseases as a proxy for COVID-19 produced valid comparators in terms of drug targeting and an overview of molecular cellular pathology. We recently performed an analysis of protein biomarkers in COVID-19 [ 30 ]; this labour-intensive approach produced similar data to the methodology we describe here. Thus, we have created a paradigm for such research which is easy to use and apply, and demonstrated its utility.…”

Section: Discussionmentioning

confidence: 99%

A consideration of publication-derived immune-related associations in Coronavirus and related lung damaging diseases

Geifman

Whetton

2020

J Transl Med

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Background The severe acute respiratory syndrome virus SARS-CoV-2, a close relative of the SARS-CoV virus, is the cause of the recent COVID-19 pandemic affecting, to date, over 14 million individuals across the globe and demonstrating relatively high rates of infection and mortality. A third virus, the H5N1, responsible for avian influenza, has caused infection with some clinical similarities to those in COVID-19 infections. Cytokines, small proteins that modulate immune responses, have been directly implicated in some of the severe responses seen in COVID-19 patients, e.g. cytokine storms. Understanding the immune processes related to COVID-19, and other similar infections, could help identify diagnostic markers and therapeutic targets. Methods Here we examine data of cytokine, immune cell types, and disease associations captured from biomedical literature associated with COVID-19, Coronavirus in general, SARS, and H5N1 influenza, with the objective of identifying potentially useful relationships and areas for future research. Results Cytokine and cell-type associations captured from Medical Subject Heading (MeSH) terms linked to thousands of PubMed records, has identified differing patterns of associations between the four corpuses of publications (COVID-19, Coronavirus, SARS, or H5N1 influenza). Clustering of cytokine-disease co-occurrences in the context of Coronavirus has identified compelling clusters of co-morbidities and symptoms, some of which already known to be linked to COVID-19. Finally, network analysis identified sub-networks of cytokines and immune cell types associated with different manifestations, co-morbidities and symptoms of Coronavirus, SARS, and H5N1. Conclusion Systematic review of research in medicine is essential to facilitate evidence-based choices about health interventions. In a fast moving pandemic the approach taken here will identify trends and enable rapid comparison to the literature of related diseases.

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Proteomics and Informatics for Understanding Phases and Identifying Biomarkers in COVID-19 Disease

Cited by 70 publications

References 97 publications

Fast Screening and Primary Diagnosis of COVID-19 by ATR–FT-IR

Fast Screening and Primary Diagnosis of COVID-19 by ATR–FT-IR

Proteomics Insights Into the Molecular Basis of SARS-CoV-2 Infection: What We Can Learn From the Human Olfactory Axis

A consideration of publication-derived immune-related associations in Coronavirus and related lung damaging diseases

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