Integrated whole transcriptome and small RNA analysis revealed multiple regulatory networks in colorectal cancer
<div><p>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 signal...
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2021
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| _version_ | 1864513516698861568 |
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| author | Hibah Shaath (5599658) |
| author2 | Salman M. Toor (8854751) Mohamed Abu Nada (17766021) Eyad Elkord (5396390) Nehad M. Alajez (7397276) |
| author2_role | author author author author |
| author_facet | Hibah Shaath (5599658) Salman M. Toor (8854751) Mohamed Abu Nada (17766021) Eyad Elkord (5396390) Nehad M. Alajez (7397276) |
| author_role | author |
| dc.creator.none.fl_str_mv | Hibah Shaath (5599658) Salman M. Toor (8854751) Mohamed Abu Nada (17766021) Eyad Elkord (5396390) Nehad M. Alajez (7397276) |
| dc.date.none.fl_str_mv | 2021-07-14T03:00:00Z |
| dc.identifier.none.fl_str_mv | 10.1038/s41598-021-93531-y |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/journal_contribution/Integrated_whole_transcriptome_and_small_RNA_analysis_revealed_multiple_regulatory_networks_in_colorectal_cancer/25771131 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biomedical and clinical sciences Oncology and carcinogenesis Colorectal cancer (CRC) Aberrantly expressed RNAs Messenger RNA (mRNA) Long non-coding RNA (lncRNA) MicroRNA (miRNA) Molecular interactions Signaling networks Diagnostic biomarkers |
| dc.title.none.fl_str_mv | Integrated whole transcriptome and small RNA analysis revealed multiple regulatory networks in colorectal cancer |
| dc.type.none.fl_str_mv | Text Journal contribution info:eu-repo/semantics/publishedVersion text contribution to journal |
| description | <div><p>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.</p><p> </p></div><h2>Other Information</h2> <p> Published in: Scientific Reports<br> License: <a href="https://creativecommons.org/licenses/by/4.0" target="_blank">https://creativecommons.org/licenses/by/4.0</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1038/s41598-021-93531-y" target="_blank">https://dx.doi.org/10.1038/s41598-021-93531-y</a></p> |
| eu_rights_str_mv | openAccess |
| id | Manara2_480680de8eec49a85cbf7e13f6756ca7 |
| identifier_str_mv | 10.1038/s41598-021-93531-y |
| network_acronym_str | Manara2 |
| network_name_str | Manara2 |
| oai_identifier_str | oai:figshare.com:article/25771131 |
| publishDate | 2021 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Integrated whole transcriptome and small RNA analysis revealed multiple regulatory networks in colorectal cancerHibah Shaath (5599658)Salman M. Toor (8854751)Mohamed Abu Nada (17766021)Eyad Elkord (5396390)Nehad M. Alajez (7397276)Biomedical and clinical sciencesOncology and carcinogenesisColorectal cancer (CRC)Aberrantly expressed RNAsMessenger RNA (mRNA)Long non-coding RNA (lncRNA)MicroRNA (miRNA)Molecular interactionsSignaling networksDiagnostic biomarkers<div><p>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.</p><p> </p></div><h2>Other Information</h2> <p> Published in: Scientific Reports<br> License: <a href="https://creativecommons.org/licenses/by/4.0" target="_blank">https://creativecommons.org/licenses/by/4.0</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1038/s41598-021-93531-y" target="_blank">https://dx.doi.org/10.1038/s41598-021-93531-y</a></p>2021-07-14T03:00:00ZTextJournal contributioninfo:eu-repo/semantics/publishedVersiontextcontribution to journal10.1038/s41598-021-93531-yhttps://figshare.com/articles/journal_contribution/Integrated_whole_transcriptome_and_small_RNA_analysis_revealed_multiple_regulatory_networks_in_colorectal_cancer/25771131CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/257711312021-07-14T03:00:00Z |
| spellingShingle | Integrated whole transcriptome and small RNA analysis revealed multiple regulatory networks in colorectal cancer Hibah Shaath (5599658) Biomedical and clinical sciences Oncology and carcinogenesis Colorectal cancer (CRC) Aberrantly expressed RNAs Messenger RNA (mRNA) Long non-coding RNA (lncRNA) MicroRNA (miRNA) Molecular interactions Signaling networks Diagnostic biomarkers |
| status_str | publishedVersion |
| title | 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_short | 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 |
| topic | Biomedical and clinical sciences Oncology and carcinogenesis Colorectal cancer (CRC) Aberrantly expressed RNAs Messenger RNA (mRNA) Long non-coding RNA (lncRNA) MicroRNA (miRNA) Molecular interactions Signaling networks Diagnostic biomarkers |