Transcription Factor Driven Gene Regulation in COVID-19 Patients
SARS-CoV-2 and its many variants have caused a worldwide emergency. Host cells colonised by SARS-CoV-2 present a significantly different gene expression landscape. As expected, this is particularly true for genes that directly interact with virus proteins. Thus, understanding the role that transcrip...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-05-01
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| Series: | Viruses |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1999-4915/15/5/1188 |
| _version_ | 1827739922068406272 |
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| author | Daniele Santoni Nimisha Ghosh Carlo Derelitto Indrajit Saha |
| author_facet | Daniele Santoni Nimisha Ghosh Carlo Derelitto Indrajit Saha |
| author_sort | Daniele Santoni |
| collection | DOAJ |
| description | SARS-CoV-2 and its many variants have caused a worldwide emergency. Host cells colonised by SARS-CoV-2 present a significantly different gene expression landscape. As expected, this is particularly true for genes that directly interact with virus proteins. Thus, understanding the role that transcription factors can play in driving differential regulation in patients affected by COVID-19 is a focal point to unveil virus infection. In this regard, we have identified 19 transcription factors which are predicted to target human proteins interacting with Spike glycoprotein of SARS-CoV-2. Transcriptomics RNA-Seq data derived from 13 human organs are used to analyse expression correlation between identified transcription factors and related target genes in both COVID-19 patients and healthy individuals. This resulted in the identification of transcription factors showing the most relevant impact in terms of most evident differential correlation between COVID-19 patients and healthy individuals. This analysis has also identified five organs such as the blood, heart, lung, nasopharynx and respiratory tract in which a major effect of differential regulation mediated by transcription factors is observed. These organs are also known to be affected by COVID-19, thereby providing consistency to our analysis. Furthermore, 31 key human genes differentially regulated by the transcription factors in the five organs are identified and the corresponding KEGG pathways and GO enrichment are also reported. Finally, the drugs targeting those 31 genes are also put forth. This in silico study explores the effects of transcription factors on human genes interacting with Spike glycoprotein of SARS-CoV-2 and intends to provide new insights to inhibit the virus infection. |
| first_indexed | 2024-03-11T03:14:44Z |
| format | Article |
| id | doaj.art-c580f768d27e4825a501f5b537fd464d |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-11T03:14:44Z |
| publishDate | 2023-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-c580f768d27e4825a501f5b537fd464d2023-11-18T03:40:14ZengMDPI AGViruses1999-49152023-05-01155118810.3390/v15051188Transcription Factor Driven Gene Regulation in COVID-19 PatientsDaniele Santoni0Nimisha Ghosh1Carlo Derelitto2Indrajit Saha3Institute for System Analysis and Computer Science “Antonio Ruberti”, National Research Council of Italy, 00185 Rome, ItalyFaculty of Mathematics, Informatics and Mechanics, University of Warsaw, 02-097 Warsaw, PolandInstitute for System Analysis and Computer Science “Antonio Ruberti”, National Research Council of Italy, 00185 Rome, ItalyDepartment of Computer Science and Engineering, National Institute of Technical Teachers’ Training and Research, Kolkata 700106, IndiaSARS-CoV-2 and its many variants have caused a worldwide emergency. Host cells colonised by SARS-CoV-2 present a significantly different gene expression landscape. As expected, this is particularly true for genes that directly interact with virus proteins. Thus, understanding the role that transcription factors can play in driving differential regulation in patients affected by COVID-19 is a focal point to unveil virus infection. In this regard, we have identified 19 transcription factors which are predicted to target human proteins interacting with Spike glycoprotein of SARS-CoV-2. Transcriptomics RNA-Seq data derived from 13 human organs are used to analyse expression correlation between identified transcription factors and related target genes in both COVID-19 patients and healthy individuals. This resulted in the identification of transcription factors showing the most relevant impact in terms of most evident differential correlation between COVID-19 patients and healthy individuals. This analysis has also identified five organs such as the blood, heart, lung, nasopharynx and respiratory tract in which a major effect of differential regulation mediated by transcription factors is observed. These organs are also known to be affected by COVID-19, thereby providing consistency to our analysis. Furthermore, 31 key human genes differentially regulated by the transcription factors in the five organs are identified and the corresponding KEGG pathways and GO enrichment are also reported. Finally, the drugs targeting those 31 genes are also put forth. This in silico study explores the effects of transcription factors on human genes interacting with Spike glycoprotein of SARS-CoV-2 and intends to provide new insights to inhibit the virus infection.https://www.mdpi.com/1999-4915/15/5/1188COVID-19drug repurposingRNA-Seq expressionSARS-CoV-2transcription factors |
| spellingShingle | Daniele Santoni Nimisha Ghosh Carlo Derelitto Indrajit Saha Transcription Factor Driven Gene Regulation in COVID-19 Patients Viruses COVID-19 drug repurposing RNA-Seq expression SARS-CoV-2 transcription factors |
| title | Transcription Factor Driven Gene Regulation in COVID-19 Patients |
| title_full | Transcription Factor Driven Gene Regulation in COVID-19 Patients |
| title_fullStr | Transcription Factor Driven Gene Regulation in COVID-19 Patients |
| title_full_unstemmed | Transcription Factor Driven Gene Regulation in COVID-19 Patients |
| title_short | Transcription Factor Driven Gene Regulation in COVID-19 Patients |
| title_sort | transcription factor driven gene regulation in covid 19 patients |
| topic | COVID-19 drug repurposing RNA-Seq expression SARS-CoV-2 transcription factors |
| url | https://www.mdpi.com/1999-4915/15/5/1188 |
| work_keys_str_mv | AT danielesantoni transcriptionfactordrivengeneregulationincovid19patients AT nimishaghosh transcriptionfactordrivengeneregulationincovid19patients AT carloderelitto transcriptionfactordrivengeneregulationincovid19patients AT indrajitsaha transcriptionfactordrivengeneregulationincovid19patients |