Proteomic insights into SARS-CoV-2 infection mechanisms, diagnosis, therapies and prognostic monitoring methods

Yu, Shengman; Li, Xiaoyan; Xin, Zhuoyuan; Sun, Li‐Zhong; Shi, Jingwei

doi:10.3389/fimmu.2022.923387

Cited by 12 publications

(5 citation statements)

References 85 publications

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“…Current understanding of COVID-19 pathophysiology needs further development to determine the role of the immune response against the SARS-CoV-2 infection and in the variability of clinical symptoms. Since the COVID-19 outbreak, several studies demonstrated that proteomics is a powerful tool for identifying biomarkers and characterizing COVID-19 pathophysiology [5,[35][36][37][38][39]. For instance, the LC-MS/MS proteomics analysis of COVID-19 patients' plasma combined with machine learning determined an 11-protein signature with a potential biomarker application and with a capacity to predict COVID-19 outcomes [35].…”

Section: Discussionmentioning

confidence: 99%

“…Despite great advances in COVID-19 research, a deeper understanding of COVID-19 immunopathology, especially in patients with pre-existing comorbidities, and the determination of specific COVID-19 biomarkers, is urgently needed [4]. Importantly, proteomics approaches can provide novel insights into the protein changes caused by the SARS-CoV-2 infection, at the cellular and systemic levels, to identify the drivers of the pathogenesis [5]. In fact, the proteomics characterization of COVID-19 patients' plasma is a non-invasive strategy that can reflect the disease status and determine potential biomarkers associated with the pathophysiological mechanisms of the SARS-CoV-2 infection.…”

Section: Introductionmentioning

confidence: 99%

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Plasma Proteomics Elucidated a Protein Signature in COVID-19 Patients with Comorbidities and Early-Diagnosis Biomarkers

Urbiola-Salvador,

Lima de Souza,

Macur

et al. 2024

Biomedicines

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Despite great scientific efforts, deep understanding of coronavirus-19 disease (COVID-19) immunopathology and clinical biomarkers remains a challenge. Pre-existing comorbidities increase the mortality rate and aggravate the exacerbated immune response against the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection, which can result in more severe symptoms as well as long-COVID and post-COVID complications. In this study, we applied proteomics analysis of plasma samples from 28 patients with SARS-CoV-2, with and without pre-existing comorbidities, as well as their corresponding controls to determine the systemic protein changes caused by the SARS-CoV-2 infection. As a result, the protein signature shared amongst COVID-19 patients with comorbidities was revealed to be characterized by alterations in the coagulation and complement pathways, acute-phase response proteins, tissue damage and remodeling, as well as cholesterol metabolism. These altered proteins may play a relevant role in COVID-19 pathophysiology. Moreover, several novel potential biomarkers for early diagnosis of the SARS-CoV-2 infection were detected, such as increased levels of keratin K22E, extracellular matrix protein-1 (ECM1), and acute-phase response protein α-2-antiplasmin (A2AP). Importantly, elevated A2AP may contribute to persistent clotting complications associated with the long-COVID syndrome in patients with comorbidities. This study provides new insights into COVID-19 pathogenesis and proposes novel potential biomarkers for early diagnosis that could be facilitated for clinical application by further validation studies.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Plasma Proteomics Elucidated a Protein Signature in COVID-19 Patients with Comorbidities and Early-Diagnosis Biomarkers

Urbiola-Salvador,

Lima de Souza,

Macur

et al. 2024

Biomedicines

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“…They serve as an alternative to the traditional measurement of a single unique marker in both normal and pathological conditions. This approach significantly enhances the sensitivity and specificity of the analysis, and it has been utilized in a number of studies (4)(5)(6)(7).…”

Section: Introductionmentioning

confidence: 99%

Evaluation of serum and urine biomarkers for severe COVID-19

Shansky,

Yanushevich,

Gospodarik

et al. 2024

Front. Med.

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IntroductionThe new coronavirus disease, COVID-19, poses complex challenges exacerbated by several factors, with respiratory tissue lesions being notably significant among them. Consequently, there is a pressing need to identify informative biological markers that can indicate the severity of the disease. Several studies have highlighted the involvement of proteins such as APOA1, XPNPEP2, ORP150, CUBN, HCII, and CREB3L3 in these respiratory tissue lesions. However, there is a lack of information regarding antibodies to these proteins in the human body, which could potentially serve as valuable diagnostic markers for COVID-19. Simultaneously, it is relevant to select biological fluids that can be obtained without invasive procedures. Urine is one such fluid, but its effect on clinical laboratory analysis is not yet fully understood due to lack of study on its composition.MethodsMethods used in this study are as follows: total serum protein analysis; ELISA on moderate and severe COVID-19 patients’ serum and urine; bioinformatic methods: ROC analysis, PCA, SVM.Results and discussionThe levels of antiAPOA1, antiXPNPEP2, antiORP150, antiCUBN, antiHCII, and antiCREB3L3 exhibit gradual fluctuations ranging from moderate to severe in both the serum and urine of COVID-19 patients. However, the diagnostic value of individual anti-protein antibodies is low, in both blood serum and urine. On the contrary, joint detection of these antibodies in patients’ serum significantly increases the diagnostic value as demonstrated by the results of principal component analysis (PCA) and support vector machine (SVM). The non-linear regression model achieved an accuracy of 0.833. Furthermore, PCA aided in identifying serum protein markers that have the greatest impact on patient group discrimination. The study revealed that serum serves as a superior analyte for describing protein quantification due to its consistent composition and lack of organic salts and drug residues, which can otherwise affect protein stability.

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“…It is precisely this complex clinical spectrum and the need for personalized medical care that have led the scientific community to focus on the discovery of a diagnostic and prognostic signature of COVID-19 through multi-omics approaches [ 3 ]. Proteomic workflow has been applied to the elucidation of the interaction between the COVID-19 virus and host proteins by mainly using cross-linking and liquid chromatography-tandem mass spectrometry (LC-MS/MS) techniques [ 4 , 5 , 6 , 7 , 8 ]. Equally important, however, have been the characterization of the proteomic profile of host cells infected by SARS-CoV-2 and the comprehension of the virus-driven alterations of metabolic homeostasis in positive patients [ 6 , 9 , 10 , 11 , 12 , 13 , 14 ].…”

Section: Introductionmentioning

confidence: 99%

“…Proteomic workflow has been applied to the elucidation of the interaction between the COVID-19 virus and host proteins by mainly using cross-linking and liquid chromatography-tandem mass spectrometry (LC-MS/MS) techniques [ 4 , 5 , 6 , 7 , 8 ]. Equally important, however, have been the characterization of the proteomic profile of host cells infected by SARS-CoV-2 and the comprehension of the virus-driven alterations of metabolic homeostasis in positive patients [ 6 , 9 , 10 , 11 , 12 , 13 , 14 ]. Metabolomics, as well, helped get an insight into the pathophysiological alterations related to SARS-CoV-2 infection, since changes in the metabolomic profile have been deepened both in severe and mild infected cohorts, aiming to predict the disease course.…”

Section: Introductionmentioning

confidence: 99%

Circulating Peptidome Is Strongly Altered in COVID-19 Patients

Baldanzi

Purghè

Ragnoli

et al. 2023

IJERPH

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Whilst the impact of coronavirus disease 2019 (COVID-19) on the host proteome, metabolome, and lipidome has been largely investigated in different bio-fluids, to date, the circulating peptidome remains unexplored. Thus, the present study aimed to apply an untargeted peptidomic approach to provide insight into alterations of circulating peptides in the development and severity of SARS-CoV-2 infection. The circulating peptidome from COVID-19 severe and mildly symptomatic patients and negative controls was characterized using LC-MS/MS analysis for identification and quantification purposes. Database search and statistical analysis allowed a complete characterization of the plasma peptidome and the detection of the most significant modulated peptides that were impacted by the infection. Our results highlighted not only that peptide abundance inversely correlates with disease severity, but also the involvement of biomolecules belonging to inflammatory, immune-response, and coagulation proteins/processes. Moreover, our data suggested a possible involvement of changes in protein degradation patterns. In the present research, for the first time, the untargeted peptidomic approach enabled the identification of circulating peptides potentially playing a crucial role in the progression of COVID-19.

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Proteomic insights into SARS-CoV-2 infection mechanisms, diagnosis, therapies and prognostic monitoring methods

Cited by 12 publications

References 85 publications

Plasma Proteomics Elucidated a Protein Signature in COVID-19 Patients with Comorbidities and Early-Diagnosis Biomarkers

Plasma Proteomics Elucidated a Protein Signature in COVID-19 Patients with Comorbidities and Early-Diagnosis Biomarkers

Evaluation of serum and urine biomarkers for severe COVID-19

Circulating Peptidome Is Strongly Altered in COVID-19 Patients

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