دورية أكاديمية
Transcriptome from Paired Samples Improves the Power of Comprehensive COVID-19 Host-Viral Characterization
| العنوان: | Transcriptome from Paired Samples Improves the Power of Comprehensive COVID-19 Host-Viral Characterization |
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| المؤلفون: | Ognjen Milicevic, Ana Loncar, Dzihan Abazovic, Marija Vukcevic, Dragana Despot, Tatjana Djukic, Vladimir Djukic, Andjela Milovanovic, Nikola Panic, Nemanja Plecic, Ana Banko |
| المصدر: | International Journal of Molecular Sciences, Vol 24, Iss 17, p 13125 (2023) |
| بيانات النشر: | MDPI AG, 2023. |
| سنة النشر: | 2023 |
| المجموعة: | LCC:Biology (General) LCC:Chemistry |
| مصطلحات موضوعية: | transcriptome, metagenomics, COVID-19, therapeutics, pairing, differential expression (DEG), Biology (General), QH301-705.5, Chemistry, QD1-999 |
| الوصف: | Previous transcriptome profiling studies showed significantly upregulated genes and altered biological pathways in acute COVID-19. However, changes in the transcriptional signatures during a defined time frame are not yet examined and described. The aims of this study included viral metagenomics and evaluation of the total expression in time-matched and tissue-matched paired COVID-19 samples with the analysis of the host splicing profile to reveal potential therapeutic targets. Prospective analysis of paired nasopharyngeal swabs (NPS) and blood (BL) samples from 18 COVID-19 patients with acute and resolved infection performed using Kallisto, Suppa2, Centrifuge, EdgeR, PantherDB, and L1000CDS2 tools. In NPS, we discovered 6 genes with changed splicing and 40 differentially expressed genes (DEG) that yielded 88 altered pathways. Blood samples yielded 15 alternatively spliced genes. Although the unpaired DEG analysis failed, pairing identified 78 genes and 242 altered pathways with meaningful clinical interpretation and new candidate drug combinations with up to 65% overlap. Metagenomics analyses showed SARS-CoV-2 dominance during and after the acute infection, with a significant reduction in NPS (0.008 vs. 0.002, p = 0.019). Even though both NPS and BL give meaningful insights into expression changes, this is the first demonstration of how the power of blood analysis is vastly maximized by pairing. The obtained results essentially showed that pairing is a determinant between a failed and a comprehensive study. Finally, the bioinformatics results prove to be a comprehensive tool for full-action insights, drug development, and infectious disease research when designed properly. |
| نوع الوثيقة: | article |
| وصف الملف: | electronic resource |
| اللغة: | English |
| تدمد: | 1422-0067 1661-6596 |
| العلاقة: | https://www.mdpi.com/1422-0067/24/17/13125Test; https://doaj.org/toc/1661-6596Test; https://doaj.org/toc/1422-0067Test |
| DOI: | 10.3390/ijms241713125 |
| الوصول الحر: | https://doaj.org/article/fea4e662011a45da9940c4ba95de7126Test |
| رقم الانضمام: | edsdoj.fea4e662011a45da9940c4ba95de7126 |
| قاعدة البيانات: | Directory of Open Access Journals |
Full Text Finder | تدمد: | 14220067 16616596 |
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| DOI: | 10.3390/ijms241713125 |