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Профилактика и лечение COVID-19 с позиций постгеномного фармакологического анализа. Систематический компьютерный анализ 290 000 научных статей по COVID-19
© ООО «КОНСИЛИУМ МЕДИКУМ», 2024 г.
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Torshin IYu, Gromova OA, Chuchalin AG. Prevention and treatment of COVID-19 based on post-genomic pharmacological analysis: Systematic computer analysis of 290,000 scientific articles on COVID-19. Terapevticheskii Arkhiv (Ter. Arkh.). 2024;96(3):205–211. DOI: 10.26442/00403660.2024.03.202635
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Ключевые слова: коронавирусы, иммунитет, системная биология, биоинформатика, интеллектуальный анализ данных
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The COVID-19 pandemic has highlighted pressing challenges in biomedical research methodology. It has become obvious that the rapid and effective development of treatments for “new” viral infections is impossible without the coordination of interdisciplinary research and in-depth analysis of data obtained within the framework of the post-genomic paradigm. Presents the results of a systematic computer analysis of 290,000 scientific articles on COVID-19, with an emphasis on the results of post-genomic studies of SARS-CoV-2. The futility of the overly simplified approach, which considers only one “most important receptor protein”, only one “key virus gene”, etc., is shown. It is shown how post-genomic technologies will make it possible to find informative biomarkers of severe coronavirus infection, including those based on complex immune disorders associated with COVID-19.
Keywords: coronaviruses, immunity, systems biology, bioinformatics, data mining
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DOI:10.17749/2070-4909/farmakoekonomika.2021.078
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15. Rostamzadeh F, Najafipour H, Yazdani R, et al. Changes in serum levels of apelin and nitric oxide in hospitalized patients with COVID-19: association with hypertension, diabetes, obesity, and severity of disease. Eur J Med Res. 2022;27(1):243. DOI:10.1186/s40001-022-00852-3
16. Hua-Huy T, Gunther S, Lorut C, et al. Distal Lung Inflammation Assessed by Alveolar Concentration of Nitric Oxide Is an Individualised Biomarker of Severe COVID-19 Pneumonia. J Pers Med. 2022;12(10):1631. DOI:10.3390/jpm12101631
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21. Bicakcioglu M, Kalkan S, Duzenci D, et al. Inhaled nitric oxide as rescue therapy in severe ARDS cases due to COVID-19 pneumonia: a single center experience. Eur Rev Med Pharmacol Sci. 2023;27(13):6422-8. DOI:10.26355/eurrev_202307_33002
22. Mekontso Dessap A, Papazian L, Schaller M, et al. Inhaled nitric oxide in patients with acute respiratory distress syndrome caused by COVID-19: treatment modalities, clinical response, and outcomes. Ann Intensive Care. 2023;13(1):57. DOI:10.1186/s13613-023-01150-9
23. Arunachalam PS, Wimmers F, Mok CKP, et al. Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans. Science.
2020;369(6508):1210-20. DOI:10.1126/science.abc6261
24. Mathew D, Giles JR, Baxter AE, et al; UPenn COVID Processing Unit. Deep immune profiling of COVID-19 patients reveals distinct immunotypes with therapeutic implications. Science. 2020;369(6508):eabc8511. DOI:10.1126/science.abc8511
25. Ren X, Wen W, Fan X, et al. COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas. Cell. 2021;184(7):1895-913.e19. DOI:10.1016/j.cell.2021.01.053
26. Sindel A, Taylor T, Chesney A, et al. Hematopoietic stem cell mobilization following PD-1 blockade: Cytokine release syndrome after transplantation managed with ascorbic acid. Eur J Haematol. 2019;103(2):134-6. DOI:10.1111/ejh.13248
27. Лила А.М., Громова О.А., Торшин И.Ю., и др. Молекулярные эффекты хондрогарда при остеоартрите и грыжах межпозвоночного диска. Неврология, нейропсихиатрия, психосоматика. 2017;9(3):88-97 [Lila AM, Gromova OA, Torshin IYu. Molecular effects of chondroguard in osteoarthritis and herniated discs. Neurology, Neuropsychiatry, Psychosomatics. 2017;9(3):88-97 (in Russian)]. DOI:10.14412/2074-2711-2017-3-88-97
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1. Torshin IYu. Bioinformatics in the Post-Genomic Era: The Role of Biophysics. New York: Nova Biomedical Books, 2006.
2. Torshin IYu. Sensing the change from molecular genetics to personalized medicine (Bioinformatics in the Post-Genomic Era). Ed. OA Gromova. New York: Nova Biomedical Books, 2009.
3. Peng H, Chen Z, Wang Y, et al. Systematic Review and Pharmacological Considerations for Chloroquine and Its Analogs in the Treatment for COVID-19. Front Pharmacol. 2020;11:554172. DOI:10.3389/fphar.2020.554172
4. Torshin IYu, Gromova OA, Chuchalin AG, Zhuravlev YuI. Chemoreactome Screening of Pharmaceutical Effects On SARS-CoV-2 and Human Virome to Help Decide on Drug-Based COVID-19 Therapy. Farmakoekonomika. Sovremennaia Farmakoekonomika i Farmakoepidemiologiia. 2021;14(2):191-211 (in Russian).
DOI:10.17749/2070-4909/farmakoekonomika.2021.078
5. Danser AHJ, Epstein M, Batlle D. Renin-Angiotensin System Blockers and the COVID-19 Pandemic: At Present There Is No Evidence to Abandon Renin-Angiotensin System Blockers. Hypertension. 2020;75(6):1382-5. DOI:10.1161/HYPERTENSIONAHA.120.15082
6. Torshin IIu, Gromova OA. Mikronutrienty protiv koronavirusov. Vchera, segodnia, zavtra. Pod red. AG Chuchalina. Moscow: GEOTAR-Media, 2023 (in Russian).
7. Torshin IYu, Rudakov KV. On metric spaces arising during formalization of problems of recognition and classification. Part 2: Density properties. Pattern Recognition and Image Analysis. 2016;26(3):483-96. DOI:10.1134/S1054661816030202
8. Griffin G, Hewison M, Hopkin J, et al. Perspective: Vitamin D supplementation prevents rickets and acute respiratory infections when given as daily maintenance but not as intermittent bolus: implications for COVID-19. Clin Med (Lond). 2021;21(2):e144-9. DOI:10.7861/clinmed.2021-0035
9. Cobre AF, Stremel DP, Noleto GR, et al. Diagnosis and prediction of COVID-19 severity: can biochemical tests and machine learning be used as prognostic indicators? Comput Biol Med. 2021;134:104531. DOI:10.1016/j.compbiomed.2021.104531
10. Al-Nesf MAY, Abdesselem HB, Bensmail I, et al. Prognostic tools and candidate drugs based on plasma proteomics of patients with severe COVID-19 complications. Nat Commun. 2022;13(1):946. DOI:10.1038/s41467-022-28639-4
11. COvid-19 Multi-omics Blood ATlas (COMBAT) Consortium. A blood atlas of COVID-19 defines hallmarks of disease severity and specificity. Cell. 2022;185(5):916-38.e58. DOI:10.1016/j.cell.2022.01.012
12. Shen B, Yi X, Sun Y, et al. Proteomic and Metabolomic Characterization of COVID-19 Patient Sera. Cell. 2020;182(1):59-72.e15. DOI:10.1016/j.cell.2020.05.032
13. Chuchalin AG. A role of nitric oxide for the modern clinical practice: A scientific report at the 5th Pan-Russian Congress on pulmonary hypertension, December 13, 2017. Pulmonologiya. 2018;28(4):503-11 (in Russian). DOI:10.18093/0869-0189-2018-28-4-503-511
14. Mikuteit M, Baskal S, Klawitter S, et al. Amino acids, post-translational modifications, nitric oxide, and oxidative stress in serum and urine of long COVID and ex COVID human subjects. Amino Acids. 2023;55(9):1173-88. DOI:10.1007/s00726-023-03305-1
15. Rostamzadeh F, Najafipour H, Yazdani R, et al. Changes in serum levels of apelin and nitric oxide in hospitalized patients with COVID-19: association with hypertension, diabetes, obesity, and severity of disease. Eur J Med Res. 2022;27(1):243. DOI:10.1186/s40001-022-00852-3
16. Hua-Huy T, Gunther S, Lorut C, et al. Distal Lung Inflammation Assessed by Alveolar Concentration of Nitric Oxide Is an Individualised Biomarker of Severe COVID-19 Pneumonia. J Pers Med. 2022;12(10):1631. DOI:10.3390/jpm12101631
17. Shtabnitskiy VA, Chuchalin AG. Causes of non-responding to inhaled nitric oxide for respiratory distress-syndrome. The Bulletin of Contemporary Clinical Medicine. 2014;7(3):39-44 (in Russian).
18. Truong TT, Shogenova LV, Selemir VD, Chuchalin AG. Effects of inhaled nitric oxide in chronic obstructive pulmonary disease patients with hypercapnic respiratory failure and pulmonary hypertension. Pulmonologiya. 2022;32(2):216-25 (in Russian). DOI:10.18093/0869-0189-2022-32-2-216-225
19. Mandal SM. Nitric oxide mediated hypoxia dynamics in COVID-19. Nitric Oxide. 2023;133:18-21. DOI:10.1016/j.niox.2023.02.002
20. Barh D, Tiwari S, Weener ME, et al. Multi-omics-based identification of SARS-CoV-2 infection biology and candidate drugs against COVID-19. Comput Biol Med. 2020;126:104051. DOI:10.1016/j.compbiomed.2020.104051
21. Bicakcioglu M, Kalkan S, Duzenci D, et al. Inhaled nitric oxide as rescue therapy in severe ARDS cases due to COVID-19 pneumonia: a single center experience. Eur Rev Med Pharmacol Sci. 2023;27(13):6422-8. DOI:10.26355/eurrev_202307_33002
22. Mekontso Dessap A, Papazian L, Schaller M, et al. Inhaled nitric oxide in patients with acute respiratory distress syndrome caused by COVID-19: treatment modalities, clinical response, and outcomes. Ann Intensive Care. 2023;13(1):57. DOI:10.1186/s13613-023-01150-9
23. Arunachalam PS, Wimmers F, Mok CKP, et al. Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans. Science.
2020;369(6508):1210-20. DOI:10.1126/science.abc6261
24. Mathew D, Giles JR, Baxter AE, et al; UPenn COVID Processing Unit. Deep immune profiling of COVID-19 patients reveals distinct immunotypes with therapeutic implications. Science. 2020;369(6508):eabc8511. DOI:10.1126/science.abc8511
25. Ren X, Wen W, Fan X, et al. COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas. Cell. 2021;184(7):1895-913.e19. DOI:10.1016/j.cell.2021.01.053
26. Sindel A, Taylor T, Chesney A, et al. Hematopoietic stem cell mobilization following PD-1 blockade: Cytokine release syndrome after transplantation managed with ascorbic acid. Eur J Haematol. 2019;103(2):134-6. DOI:10.1111/ejh.13248
27. Lila AM, Gromova OA, Torshin IYu. Molecular effects of chondroguard in osteoarthritis and herniated discs. Neurology, Neuropsychiatry, Psychosomatics. 2017;9(3):88-97 (in Russian). DOI:10.14412/2074-2711-2017-3-88-97
1ФГУ «Федеральный исследовательский центр „Информатика и управление“ Российской академии наук», Москва, Россия;
2ФГАОУ ВО «Российский национальный исследовательский медицинский университет им. Н.И. Пирогова» Минздрава России, Москва, Россия
*unesco.gromova@gmail.com
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Ivan Yu. Torshin1, Olga A. Gromova*1, Alexander G. Chuchalin2
1Federal Research Center “Computer Science and Control” of the Russian Academy of Sciences, Moscow, Russia;
2Pirogov Russian National Research Medical University, Moscow, Russia
*unesco.gromova@gmail.com