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Профилактика и лечение COVID-19 с позиций постгеномного фармакологического анализа. Систематический компьютерный анализ 290 000 научных статей по COVID-19 - Журнал Терапевтический архив №3 Вопросы пульмонологии 2024
Профилактика и лечение COVID-19 с позиций постгеномного фармакологического анализа. Систематический компьютерный анализ 290 000 научных статей по COVID-19
Торшин И.Ю., Громова О.А., Чучалин А.Г. Профилактика и лечение COVID-19 с позиций постгеномного фармакологического анализа. Систематический компьютерный анализ 290 000 научных статей по COVID-19. Терапевтический архив. 2024;96(3):205–211. DOI: 10.26442/00403660.2024.03.202635
© ООО «КОНСИЛИУМ МЕДИКУМ», 2024 г.
© ООО «КОНСИЛИУМ МЕДИКУМ», 2024 г.
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Аннотация
Пандемия COVID-19 указала на насущные проблемы в методологии биомедицинских исследований. Стало очевидно, что быстрая и эффективная разработка средств лечения «новых» вирусных инфекций невозможна без координации междисциплинарных исследований и углубленного анализа данных, получаемых в рамках постгеномной парадигмы. Представлены результаты систематического компьютерного анализа 290 тыс. научных статей по COVID-19 с акцентом на результаты постгеномных исследований SARS-CoV-2. Показана бесперспективность сверхупрощенного подхода, в котором рассматривается только один «наиважнейший белок-рецептор», только один «ключевой ген вируса» и т.п. Постгеномные технологии позволят находить информативные биомаркеры тяжелого течения коронавирусной инфекции, в том числе основанные на комплексных нарушениях иммунитета, ассоциированных с COVID-19.
Ключевые слова: коронавирусы, иммунитет, системная биология, биоинформатика, интеллектуальный анализ данных
Keywords: coronaviruses, immunity, systems biology, bioinformatics, data mining
Ключевые слова: коронавирусы, иммунитет, системная биология, биоинформатика, интеллектуальный анализ данных
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Keywords: coronaviruses, immunity, systems biology, bioinformatics, data mining
Полный текст
Список литературы
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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
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2020;369(6508):1210-20. DOI:10.1126/science.abc6261
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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
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
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. Торшин И.Ю., Громова О.А., Чучалин А.Г., Журавлев Ю.И. Хемореактомный скрининг воздействия фармакологических препаратов на SARS-CoV-2 и виром человека как информационная основа для принятия решений по фармакотерапии COVID-19. Фармакоэкономика. Современная фармакоэкономика и фармакоэпидемиология. 2021;14(2):191-211 [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. Торшин И.Ю., Громова О.А. Микронутриенты против коронавирусов. Вчера, сегодня, завтра. Под ред. А.Г. Чучалина. М.: ГЭОТАР-Медиа, 2023 [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. Чучалин А.Г. Роль оксида азота в современной клинической практике: научный доклад на V Всероссийском конгрессе «Легочная гипертензия» (13 декабря 2017 г.). Пульмонология. 2018;28(4):503-11 [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. Штабницкий В.А., Чучалин А.Г. Причины отсутствия ответа на ингаляционный оксид азота у больных острым респираторным дистресс-синдромом. Вестник современной клинической медицины. 2014;7(3):39-44 [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. Чыонг Т.Т., Шогенова Л.В., Селемир С.Д., Чучалин А.Г. Эффекты ингаляционного оксида азота у пациентов с хронической обструктивной болезнью легких с гиперкапнической дыхательной недостаточностью и легочной гипертензией. Пульмонология. 2022;32(2):216-25 [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
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Авторы
И.Ю. Торшин1, О.А. Громова*1, А.Г. Чучалин2
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
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
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
________________________________________________
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
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