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Identification of key differentially expressed genes in SARS-CoV-2 using RNA-seq analysis with a systems biology approach

COVID-19 is associated with dysregulation of several genes and signaling pathways. Based on the importance of expression profiling in identification of the pathogenesis of COVID-19 and proposing novel therapies for this disorder, we have employed an in silico approach to find differentially expresse...

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Autores principales: Safarzadeh, Arash, Mahmud Hussen, Bashdar, Taheri, Mohammad, Ghafouri-Fard, Soudeh, Hajiesmaeili, Mohammadreza
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Author(s). Published by Elsevier Ltd. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10036311/
https://www.ncbi.nlm.nih.gov/pubmed/37018908
http://dx.doi.org/10.1016/j.cyto.2023.156187
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author Safarzadeh, Arash
Mahmud Hussen, Bashdar
Taheri, Mohammad
Ghafouri-Fard, Soudeh
Hajiesmaeili, Mohammadreza
author_facet Safarzadeh, Arash
Mahmud Hussen, Bashdar
Taheri, Mohammad
Ghafouri-Fard, Soudeh
Hajiesmaeili, Mohammadreza
author_sort Safarzadeh, Arash
collection PubMed
description COVID-19 is associated with dysregulation of several genes and signaling pathways. Based on the importance of expression profiling in identification of the pathogenesis of COVID-19 and proposing novel therapies for this disorder, we have employed an in silico approach to find differentially expressed genes between COVID-19 patients and healthy controls and their relevance with cellular functions and signaling pathways. We obtained 630 DEmRNAs, including 486 down-regulated DEGs (such as CCL3 and RSAD2) and 144 up-regulated DEGs (such as RHO and IQCA1L), and 15 DElncRNAs, including 9 down-regulated DElncRNAs (such as PELATON and LINC01506) and 6 up-regulated DElncRNAs (such as AJUBA-DT and FALEC). The PPI network of DEGs showed the presence of a number immune-related genes such as those coding for HLA molecules and interferon regulatory factors. Taken together, these results highlight the importance of immune-related genes and pathways in the pathogenesis of COVID-19 and suggest novel targets for treatment of this disorder.
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spelling pubmed-100363112023-03-24 Identification of key differentially expressed genes in SARS-CoV-2 using RNA-seq analysis with a systems biology approach Safarzadeh, Arash Mahmud Hussen, Bashdar Taheri, Mohammad Ghafouri-Fard, Soudeh Hajiesmaeili, Mohammadreza Cytokine Article COVID-19 is associated with dysregulation of several genes and signaling pathways. Based on the importance of expression profiling in identification of the pathogenesis of COVID-19 and proposing novel therapies for this disorder, we have employed an in silico approach to find differentially expressed genes between COVID-19 patients and healthy controls and their relevance with cellular functions and signaling pathways. We obtained 630 DEmRNAs, including 486 down-regulated DEGs (such as CCL3 and RSAD2) and 144 up-regulated DEGs (such as RHO and IQCA1L), and 15 DElncRNAs, including 9 down-regulated DElncRNAs (such as PELATON and LINC01506) and 6 up-regulated DElncRNAs (such as AJUBA-DT and FALEC). The PPI network of DEGs showed the presence of a number immune-related genes such as those coding for HLA molecules and interferon regulatory factors. Taken together, these results highlight the importance of immune-related genes and pathways in the pathogenesis of COVID-19 and suggest novel targets for treatment of this disorder. The Author(s). Published by Elsevier Ltd. 2023-06 2023-03-24 /pmc/articles/PMC10036311/ /pubmed/37018908 http://dx.doi.org/10.1016/j.cyto.2023.156187 Text en © 2023 The Author(s) Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.
spellingShingle Article
Safarzadeh, Arash
Mahmud Hussen, Bashdar
Taheri, Mohammad
Ghafouri-Fard, Soudeh
Hajiesmaeili, Mohammadreza
Identification of key differentially expressed genes in SARS-CoV-2 using RNA-seq analysis with a systems biology approach
title Identification of key differentially expressed genes in SARS-CoV-2 using RNA-seq analysis with a systems biology approach
title_full Identification of key differentially expressed genes in SARS-CoV-2 using RNA-seq analysis with a systems biology approach
title_fullStr Identification of key differentially expressed genes in SARS-CoV-2 using RNA-seq analysis with a systems biology approach
title_full_unstemmed Identification of key differentially expressed genes in SARS-CoV-2 using RNA-seq analysis with a systems biology approach
title_short Identification of key differentially expressed genes in SARS-CoV-2 using RNA-seq analysis with a systems biology approach
title_sort identification of key differentially expressed genes in sars-cov-2 using rna-seq analysis with a systems biology approach
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10036311/
https://www.ncbi.nlm.nih.gov/pubmed/37018908
http://dx.doi.org/10.1016/j.cyto.2023.156187
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