Novel interferon-sensitive genes unveiled by correlation-driven gene selection and systems biology

Abstract Interferons (IFNs) are key cytokines involved in alerting the immune system to viral infection. After IFN stimulation, cellular transcriptional profile critically changes, leading to the expression of several IFN stimulated genes (ISGs) that exert a wide variety of antiviral activities. Des...

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Autores principales:	Cristina Cheroni, Lara Manganaro, Lorena Donnici, Valeria Bevilacqua, Raoul J. P. Bonnal, Riccardo L. Rossi, Raffaele De Francesco
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e7ea4f5c876b42c19f3dfa4679c5eca3
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spelling	oai:doaj.org-article:e7ea4f5c876b42c19f3dfa4679c5eca32021-12-02T17:41:18ZNovel interferon-sensitive genes unveiled by correlation-driven gene selection and systems biology10.1038/s41598-021-97258-82045-2322https://doaj.org/article/e7ea4f5c876b42c19f3dfa4679c5eca32021-09-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-97258-8https://doaj.org/toc/2045-2322Abstract Interferons (IFNs) are key cytokines involved in alerting the immune system to viral infection. After IFN stimulation, cellular transcriptional profile critically changes, leading to the expression of several IFN stimulated genes (ISGs) that exert a wide variety of antiviral activities. Despite many ISGs have been already identified, a comprehensive network of coding and non-coding genes with a central role in IFN-response still needs to be elucidated. We performed a global RNA-Seq transcriptome profile of the HCV permissive human hepatoma cell line Huh7.5 and its parental cell line Huh7, upon IFN treatment, to define a network of genes whose coordinated modulation plays a central role in IFN-response. Our study adds molecular actors, coding and non-coding genes, to the complex molecular network underlying IFN-response and shows how systems biology approaches, such as correlation networks, network’s topology and gene ontology analyses can be leveraged to this aim.Cristina CheroniLara ManganaroLorena DonniciValeria BevilacquaRaoul J. P. BonnalRiccardo L. RossiRaffaele De FrancescoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-15 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Cristina Cheroni Lara Manganaro Lorena Donnici Valeria Bevilacqua Raoul J. P. Bonnal Riccardo L. Rossi Raffaele De Francesco Novel interferon-sensitive genes unveiled by correlation-driven gene selection and systems biology
description	Abstract Interferons (IFNs) are key cytokines involved in alerting the immune system to viral infection. After IFN stimulation, cellular transcriptional profile critically changes, leading to the expression of several IFN stimulated genes (ISGs) that exert a wide variety of antiviral activities. Despite many ISGs have been already identified, a comprehensive network of coding and non-coding genes with a central role in IFN-response still needs to be elucidated. We performed a global RNA-Seq transcriptome profile of the HCV permissive human hepatoma cell line Huh7.5 and its parental cell line Huh7, upon IFN treatment, to define a network of genes whose coordinated modulation plays a central role in IFN-response. Our study adds molecular actors, coding and non-coding genes, to the complex molecular network underlying IFN-response and shows how systems biology approaches, such as correlation networks, network’s topology and gene ontology analyses can be leveraged to this aim.
format	article
author	Cristina Cheroni Lara Manganaro Lorena Donnici Valeria Bevilacqua Raoul J. P. Bonnal Riccardo L. Rossi Raffaele De Francesco
author_facet	Cristina Cheroni Lara Manganaro Lorena Donnici Valeria Bevilacqua Raoul J. P. Bonnal Riccardo L. Rossi Raffaele De Francesco
author_sort	Cristina Cheroni
title	Novel interferon-sensitive genes unveiled by correlation-driven gene selection and systems biology
title_short	Novel interferon-sensitive genes unveiled by correlation-driven gene selection and systems biology
title_full	Novel interferon-sensitive genes unveiled by correlation-driven gene selection and systems biology
title_fullStr	Novel interferon-sensitive genes unveiled by correlation-driven gene selection and systems biology
title_full_unstemmed	Novel interferon-sensitive genes unveiled by correlation-driven gene selection and systems biology
title_sort	novel interferon-sensitive genes unveiled by correlation-driven gene selection and systems biology
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/e7ea4f5c876b42c19f3dfa4679c5eca3
work_keys_str_mv	AT cristinacheroni novelinterferonsensitivegenesunveiledbycorrelationdrivengeneselectionandsystemsbiology AT laramanganaro novelinterferonsensitivegenesunveiledbycorrelationdrivengeneselectionandsystemsbiology AT lorenadonnici novelinterferonsensitivegenesunveiledbycorrelationdrivengeneselectionandsystemsbiology AT valeriabevilacqua novelinterferonsensitivegenesunveiledbycorrelationdrivengeneselectionandsystemsbiology AT raouljpbonnal novelinterferonsensitivegenesunveiledbycorrelationdrivengeneselectionandsystemsbiology AT riccardolrossi novelinterferonsensitivegenesunveiledbycorrelationdrivengeneselectionandsystemsbiology AT raffaeledefrancesco novelinterferonsensitivegenesunveiledbycorrelationdrivengeneselectionandsystemsbiology
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Novel interferon-sensitive genes unveiled by correlation-driven gene selection and systems biology

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