Tissue-specific pathway activities: A retrospective analysis in COVID-19 patients
The ACE2 receptors essential for SARS-CoV-2 infections are expressed not only in the lung but also in many other tissues in the human body. To better understand the disease mechanisms and progression, it is essential to understand how the virus affects and alters molecular pathways in the different...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-09-01
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| Series: | Frontiers in Immunology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2022.963357/full |
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| author | Nhung Pham Nhung Pham Finterly Hu Finterly Hu Chris T. Evelo Chris T. Evelo Martina Kutmon Martina Kutmon |
| author_facet | Nhung Pham Nhung Pham Finterly Hu Finterly Hu Chris T. Evelo Chris T. Evelo Martina Kutmon Martina Kutmon |
| author_sort | Nhung Pham |
| collection | DOAJ |
| description | The ACE2 receptors essential for SARS-CoV-2 infections are expressed not only in the lung but also in many other tissues in the human body. To better understand the disease mechanisms and progression, it is essential to understand how the virus affects and alters molecular pathways in the different affected tissues. In this study, we mapped the proteomics data obtained from Nie X. et al. (2021) to the pathway models of the COVID-19 Disease Map project and WikiPathways. The differences in pathway activities between COVID-19 and non-COVID-19 patients were calculated using the Wilcoxon test. As a result, 46% (5,235) of the detected proteins were found to be present in at least one pathway. Only a few pathways were altered in multiple tissues. As an example, the Kinin-Kallikrein pathway, an important inflammation regulatory pathway, was found to be less active in the lung, spleen, testis, and thyroid. We can confirm previously reported changes in COVID-19 patients such as the change in cholesterol, linolenic acid, and arachidonic acid metabolism, complement, and coagulation pathways in most tissues. Of all the tissues, we found the thyroid to be the organ with the most changed pathways. In this tissue, lipid pathways, energy pathways, and many COVID-19 specific pathways such as RAS and bradykinin pathways, thrombosis, and anticoagulation have altered activities in COVID-19 patients. Concluding, our results highlight the systemic nature of COVID-19 and the effect on other tissues besides the lung. |
| first_indexed | 2024-04-11T09:58:59Z |
| format | Article |
| id | doaj.art-fc7aff5e6c1c43d683e0e629f87c5ef6 |
| institution | Directory Open Access Journal |
| issn | 1664-3224 |
| language | English |
| last_indexed | 2024-04-11T09:58:59Z |
| publishDate | 2022-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Immunology |
| spelling | doaj.art-fc7aff5e6c1c43d683e0e629f87c5ef62022-12-22T04:30:29ZengFrontiers Media S.A.Frontiers in Immunology1664-32242022-09-011310.3389/fimmu.2022.963357963357Tissue-specific pathway activities: A retrospective analysis in COVID-19 patientsNhung Pham0Nhung Pham1Finterly Hu2Finterly Hu3Chris T. Evelo4Chris T. Evelo5Martina Kutmon6Martina Kutmon7Department of Bioinformatics (BiGCaT), School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, NetherlandsMaastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, NetherlandsDepartment of Bioinformatics (BiGCaT), School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, NetherlandsMaastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, NetherlandsDepartment of Bioinformatics (BiGCaT), School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, NetherlandsMaastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, NetherlandsDepartment of Bioinformatics (BiGCaT), School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, NetherlandsMaastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, NetherlandsThe ACE2 receptors essential for SARS-CoV-2 infections are expressed not only in the lung but also in many other tissues in the human body. To better understand the disease mechanisms and progression, it is essential to understand how the virus affects and alters molecular pathways in the different affected tissues. In this study, we mapped the proteomics data obtained from Nie X. et al. (2021) to the pathway models of the COVID-19 Disease Map project and WikiPathways. The differences in pathway activities between COVID-19 and non-COVID-19 patients were calculated using the Wilcoxon test. As a result, 46% (5,235) of the detected proteins were found to be present in at least one pathway. Only a few pathways were altered in multiple tissues. As an example, the Kinin-Kallikrein pathway, an important inflammation regulatory pathway, was found to be less active in the lung, spleen, testis, and thyroid. We can confirm previously reported changes in COVID-19 patients such as the change in cholesterol, linolenic acid, and arachidonic acid metabolism, complement, and coagulation pathways in most tissues. Of all the tissues, we found the thyroid to be the organ with the most changed pathways. In this tissue, lipid pathways, energy pathways, and many COVID-19 specific pathways such as RAS and bradykinin pathways, thrombosis, and anticoagulation have altered activities in COVID-19 patients. Concluding, our results highlight the systemic nature of COVID-19 and the effect on other tissues besides the lung.https://www.frontiersin.org/articles/10.3389/fimmu.2022.963357/fullSARS-CoV-2tissue-specific proteomics datapathway activityWikiPathwaysCOVID-19 |
| spellingShingle | Nhung Pham Nhung Pham Finterly Hu Finterly Hu Chris T. Evelo Chris T. Evelo Martina Kutmon Martina Kutmon Tissue-specific pathway activities: A retrospective analysis in COVID-19 patients Frontiers in Immunology SARS-CoV-2 tissue-specific proteomics data pathway activity WikiPathways COVID-19 |
| title | Tissue-specific pathway activities: A retrospective analysis in COVID-19 patients |
| title_full | Tissue-specific pathway activities: A retrospective analysis in COVID-19 patients |
| title_fullStr | Tissue-specific pathway activities: A retrospective analysis in COVID-19 patients |
| title_full_unstemmed | Tissue-specific pathway activities: A retrospective analysis in COVID-19 patients |
| title_short | Tissue-specific pathway activities: A retrospective analysis in COVID-19 patients |
| title_sort | tissue specific pathway activities a retrospective analysis in covid 19 patients |
| topic | SARS-CoV-2 tissue-specific proteomics data pathway activity WikiPathways COVID-19 |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2022.963357/full |
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