Integrated whole transcriptome and small RNA analysis revealed multiple regulatory networks in colorectal cancer

Abstract Colorectal cancer (CRC) remains a global disease burden and a leading cause of cancer related deaths worldwide. The identification of aberrantly expressed messenger RNA (mRNA), long non-coding RNA (lncRNA), and microRNA (miRNA), and the resulting molecular interactions and signaling network...

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Autores principales:	Hibah Shaath, Salman M. Toor, Mohamed Abu Nada, Eyad Elkord, Nehad M. Alajez
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/5025821479a044d1898187bf8e055c68
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spelling	oai:doaj.org-article:5025821479a044d1898187bf8e055c682021-12-02T18:30:46ZIntegrated whole transcriptome and small RNA analysis revealed multiple regulatory networks in colorectal cancer10.1038/s41598-021-93531-y2045-2322https://doaj.org/article/5025821479a044d1898187bf8e055c682021-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-93531-yhttps://doaj.org/toc/2045-2322Abstract Colorectal cancer (CRC) remains a global disease burden and a leading cause of cancer related deaths worldwide. The identification of aberrantly expressed messenger RNA (mRNA), long non-coding RNA (lncRNA), and microRNA (miRNA), and the resulting molecular interactions and signaling networks is essential for better understanding of CRC, identification of novel diagnostic biomarkers and potential development of therapeutic interventions. Herein, we performed microRNA (miRNA) sequencing on fifteen CRC and their non-tumor adjacent tissues and whole transcriptome RNA-Seq on six paired samples from the same cohort and identified alterations in miRNA, mRNA, and lncRNA expression. Computational analyses using Ingenuity Pathway Analysis (IPA) identified multiple activated signaling networks in CRC, including ERBB2, RABL6, FOXM1, and NFKB networks, while functional annotation highlighted activation of cell proliferation and migration as the hallmark of CRC. IPA in combination with in silico prediction algorithms and experimentally validated databases gave insight into the complex associations and interactions between downregulated miRNAs and upregulated mRNAs in CRC and vice versa. Additionally, potential interaction between differentially expressed lncRNAs such as H19, SNHG5, and GATA2-AS1 with multiple miRNAs has been revealed. Taken together, our data provides thorough analysis of dysregulated protein-coding and non-coding RNAs in CRC highlighting numerous associations and regulatory networks thus providing better understanding of CRC.Hibah ShaathSalman M. ToorMohamed Abu NadaEyad ElkordNehad M. AlajezNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Hibah Shaath Salman M. Toor Mohamed Abu Nada Eyad Elkord Nehad M. Alajez Integrated whole transcriptome and small RNA analysis revealed multiple regulatory networks in colorectal cancer
description	Abstract Colorectal cancer (CRC) remains a global disease burden and a leading cause of cancer related deaths worldwide. The identification of aberrantly expressed messenger RNA (mRNA), long non-coding RNA (lncRNA), and microRNA (miRNA), and the resulting molecular interactions and signaling networks is essential for better understanding of CRC, identification of novel diagnostic biomarkers and potential development of therapeutic interventions. Herein, we performed microRNA (miRNA) sequencing on fifteen CRC and their non-tumor adjacent tissues and whole transcriptome RNA-Seq on six paired samples from the same cohort and identified alterations in miRNA, mRNA, and lncRNA expression. Computational analyses using Ingenuity Pathway Analysis (IPA) identified multiple activated signaling networks in CRC, including ERBB2, RABL6, FOXM1, and NFKB networks, while functional annotation highlighted activation of cell proliferation and migration as the hallmark of CRC. IPA in combination with in silico prediction algorithms and experimentally validated databases gave insight into the complex associations and interactions between downregulated miRNAs and upregulated mRNAs in CRC and vice versa. Additionally, potential interaction between differentially expressed lncRNAs such as H19, SNHG5, and GATA2-AS1 with multiple miRNAs has been revealed. Taken together, our data provides thorough analysis of dysregulated protein-coding and non-coding RNAs in CRC highlighting numerous associations and regulatory networks thus providing better understanding of CRC.
format	article
author	Hibah Shaath Salman M. Toor Mohamed Abu Nada Eyad Elkord Nehad M. Alajez
author_facet	Hibah Shaath Salman M. Toor Mohamed Abu Nada Eyad Elkord Nehad M. Alajez
author_sort	Hibah Shaath
title	Integrated whole transcriptome and small RNA analysis revealed multiple regulatory networks in colorectal cancer
title_short	Integrated whole transcriptome and small RNA analysis revealed multiple regulatory networks in colorectal cancer
title_full	Integrated whole transcriptome and small RNA analysis revealed multiple regulatory networks in colorectal cancer
title_fullStr	Integrated whole transcriptome and small RNA analysis revealed multiple regulatory networks in colorectal cancer
title_full_unstemmed	Integrated whole transcriptome and small RNA analysis revealed multiple regulatory networks in colorectal cancer
title_sort	integrated whole transcriptome and small rna analysis revealed multiple regulatory networks in colorectal cancer
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/5025821479a044d1898187bf8e055c68
work_keys_str_mv	AT hibahshaath integratedwholetranscriptomeandsmallrnaanalysisrevealedmultipleregulatorynetworksincolorectalcancer AT salmanmtoor integratedwholetranscriptomeandsmallrnaanalysisrevealedmultipleregulatorynetworksincolorectalcancer AT mohamedabunada integratedwholetranscriptomeandsmallrnaanalysisrevealedmultipleregulatorynetworksincolorectalcancer AT eyadelkord integratedwholetranscriptomeandsmallrnaanalysisrevealedmultipleregulatorynetworksincolorectalcancer AT nehadmalajez integratedwholetranscriptomeandsmallrnaanalysisrevealedmultipleregulatorynetworksincolorectalcancer
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Integrated whole transcriptome and small RNA analysis revealed multiple regulatory networks in colorectal cancer

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