A Comprehensive Overview of Proteomics Approach for COVID 19: New Perspectives in Target Therapy Strategies

Overview

Journal J Proteins Proteom

Date 2020 Nov 9

PMID 33162722

Citations 10

Authors

Rashmi Rana

Vaishnavi Rathi

Nirmal Kumar Ganguly

Affiliations

Soon will be listed here.

Abstract

World Health Organisation declared COVID-19 a pandemic on March 11, 2020. It was temporarily named as 2019-nCoV then subsequently named as COVID-19 virus. A coronavirus is a group of viruses, known to be zoonotic, causing illness ranging from acute to mild respiratory infections. These are spherical or pleomorphic enveloped particles containing positive sense RNA. The virus enters host cells, its uncoated genetic material transcribes, and translates. Since it has started spreading rapidly, protective measures have been taken all over the world. However, its transmission has been proved to be unstoppable and the absence of an effective drug makes the situation worse. The scientific community has gone all-out to discover and develop a possible vaccine or a competent antiviral drug. Other domains of biological sciences that promise effective results and target somewhat stable entities that are proteins, could be very useful in this time of crisis. Proteomics and metabolomics are the vast fields that are equipped with sufficient technologies to face this challenge. Various protein separation and identification techniques are available which facilitates the analysis of various types of interactions among proteins and their evolutionary lineages. The presented review aims at confronting the question: 'how proteomics can help in tackling SARS-CoV-2?' It deals with the role of upcoming proteome technology in these pandemic situations and discusses the proteomics approach towards the COVID-19 dilemma.

Citing Articles

Proteomics research of SARS-CoV-2 and COVID-19 disease.

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An update on SARS-CoV-2 immunization and future directions.

Rana R, Kant R, Kumra T, Gupta S, Rana D, Ganguly N Front Pharmacol. 2023; 14:1125305.

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BIRCH: An Automated Workflow for Evaluation, Correction, and Visualization of Batch Effect in Bottom-Up Mass Spectrometry-Based Proteomics Data.

Sundararaman N, Bhat A, Venkatraman V, Binek A, Dwight Z, Ariyasinghe N J Proteome Res. 2023; 22(2):471-481.

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SARS-CoV-2-positive patients display considerable differences in proteome diversity in urine, nasopharyngeal, gargle solution and bronchoalveolar lavage fluid samples.

Okendo J, Musanabaganwa C, Mwangi P, Nyaga M, Onywera H PLoS One. 2022; 17(8):e0271870.

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Systematic review with meta-analysis of diagnostic test accuracy for COVID-19 by mass spectrometry.

Spick M, Lewis H, Wilde M, Hopley C, Huggett J, Bailey M Metabolism. 2021; 126:154922.

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References

Ren Y, He Q, Fan J, Jones B, Zhou Y, Xie Y . The use of proteomics in the discovery of serum biomarkers from patients with severe acute respiratory syndrome. Proteomics. 2004; 4(11):3477-84. PMC: 7167722. DOI: 10.1002/pmic.200400897. View

Bruning A, Aatola H, Toivola H, Ikonen N, Savolainen-Kopra C, Blomqvist S . Rapid detection and monitoring of human coronavirus infections. New Microbes New Infect. 2018; 24:52-55. PMC: 5986163. DOI: 10.1016/j.nmni.2018.04.007. View

von Eggeling F, Gawriljuk A, Fiedler W, Ernst G, Claussen U, Klose J . Fluorescent dual colour 2D-protein gel electrophoresis for rapid detection of differences in protein pattern with standard image analysis software. Int J Mol Med. 2001; 8(4):373-7. DOI: 10.3892/ijmm.8.4.373. View

Wang H, Wu X, Zhang X, Hou X, Liang T, Wang D . SARS-CoV-2 Proteome Microarray for Mapping COVID-19 Antibody Interactions at Amino Acid Resolution. ACS Cent Sci. 2020; 6(12):2238-2249. PMC: 7586461. DOI: 10.1021/acscentsci.0c00742. View

Mahajan M, Bhattacharjya S . NMR structures and localization of the potential fusion peptides and the pre-transmembrane region of SARS-CoV: Implications in membrane fusion. Biochim Biophys Acta. 2014; 1848(2):721-30. PMC: 7094234. DOI: 10.1016/j.bbamem.2014.11.025. View

Wu Z, McGoogan J . Characteristics of and Important Lessons From the Coronavirus Disease 2019 (COVID-19) Outbreak in China: Summary of a Report of 72 314 Cases From the Chinese Center for Disease Control and Prevention. JAMA. 2020; 323(13):1239-1242. DOI: 10.1001/jama.2020.2648. View

Lim M, Elenitoba-Johnson K . Proteomics in pathology research. Lab Invest. 2004; 84(10):1227-44. DOI: 10.1038/labinvest.3700167. View

Chan J, Yuan S, Kok K, To K, Chu H, Yang J . A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. Lancet. 2020; 395(10223):514-523. PMC: 7159286. DOI: 10.1016/S0140-6736(20)30154-9. View

Zhou P, Yang X, Wang X, Hu B, Zhang L, Zhang W . A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020; 579(7798):270-273. PMC: 7095418. DOI: 10.1038/s41586-020-2012-7. View

10.

Hoffmann P, Ji H, Moritz R, Connolly L, Frecklington D, Layton M . Continuous free-flow electrophoresis separation of cytosolic proteins from the human colon carcinoma cell line LIM 1215: a non two-dimensional gel electrophoresis-based proteome analysis strategy. Proteomics. 2001; 1(7):807-18. DOI: 10.1002/1615-9861(200107)1:7<807::AID-PROT807>3.0.CO;2-6. View

11.

Jacquemier J, Ginestier C, Rougemont J, Bardou V, Charafe-Jauffret E, Geneix J . Protein expression profiling identifies subclasses of breast cancer and predicts prognosis. Cancer Res. 2005; 65(3):767-79. View

12.

Seike M, Kondo T, Fujii K, Yamada T, Gemma A, Kudoh S . Proteomic signature of human cancer cells. Proteomics. 2004; 4(9):2776-88. DOI: 10.1002/pmic.200300795. View

13.

Tonge R, Shaw J, Middleton B, Rowlinson R, Rayner S, Young J . Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology. Proteomics. 2001; 1(3):377-96. DOI: 10.1002/1615-9861(200103)1:3<377::AID-PROT377>3.0.CO;2-6. View

14.

Pang R, Poon T, Chan K, Lee N, Chiu R, Tong Y . Serum proteomic fingerprints of adult patients with severe acute respiratory syndrome. Clin Chem. 2006; 52(3):421-9. PMC: 7108167. DOI: 10.1373/clinchem.2005.061689. View

15.

Eickhoff H, Konthur Z, Lueking A, Lehrach H, Walter G, Nordhoff E . Protein array technology: the tool to bridge genomics and proteomics. Adv Biochem Eng Biotechnol. 2002; 77:103-12. DOI: 10.1007/3-540-45713-5_6. View

16.

Liotta L, Espina V, Mehta A, Calvert V, Rosenblatt K, Geho D . Protein microarrays: meeting analytical challenges for clinical applications. Cancer Cell. 2003; 3(4):317-25. DOI: 10.1016/s1535-6108(03)00086-2. View

17.

Bjellqvist B, Ek K, Righetti P, Gianazza E, Gorg A, Westermeier R . Isoelectric focusing in immobilized pH gradients: principle, methodology and some applications. J Biochem Biophys Methods. 1982; 6(4):317-39. DOI: 10.1016/0165-022x(82)90013-6. View

18.

Qiu M, Shi Y, Guo Z, Chen Z, He R, Chen R . Antibody responses to individual proteins of SARS coronavirus and their neutralization activities. Microbes Infect. 2005; 7(5-6):882-9. PMC: 7110836. DOI: 10.1016/j.micinf.2005.02.006. View

19.

Zhu N, Zhang D, Wang W, Li X, Yang B, Song J . A Novel Coronavirus from Patients with Pneumonia in China, 2019. N Engl J Med. 2020; 382(8):727-733. PMC: 7092803. DOI: 10.1056/NEJMoa2001017. View

20.

Appelberg S, Gupta S, Akusjarvi S, Ambikan A, Mikaeloff F, Saccon E . Dysregulation in Akt/mTOR/HIF-1 signaling identified by proteo-transcriptomics of SARS-CoV-2 infected cells. Emerg Microbes Infect. 2020; 9(1):1748-1760. PMC: 7473213. DOI: 10.1080/22221751.2020.1799723. View