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Comprehensive analysis of microarray expression profiles of circRNAs and lncRNAs with associated co-expression networks in human colorectal cancer

Increasing data demonstrate that circular RNAs (circRNAs) and long non-coding RNAs (lncRNAs) play important roles in tumorigenesis. However, the mechanisms in colorectal cancer (CRC) remain unclear. Here, hundreds of significantly expressed circRNAs, and thousands of lncRNAs as well as mRNAs were id...

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Autores principales: Tian, Yan, Xu, Yu, Wang, Huawei, Shu, Ruo, Sun, Liang, Zeng, Yujian, Gong, Fangyou, Lei, Yi, Wang, Kunhua, Luo, Huayou
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer Berlin Heidelberg 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6394731/
https://www.ncbi.nlm.nih.gov/pubmed/30446877
http://dx.doi.org/10.1007/s10142-018-0641-9
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author Tian, Yan
Xu, Yu
Wang, Huawei
Shu, Ruo
Sun, Liang
Zeng, Yujian
Gong, Fangyou
Lei, Yi
Wang, Kunhua
Luo, Huayou
author_facet Tian, Yan
Xu, Yu
Wang, Huawei
Shu, Ruo
Sun, Liang
Zeng, Yujian
Gong, Fangyou
Lei, Yi
Wang, Kunhua
Luo, Huayou
author_sort Tian, Yan
collection PubMed
description Increasing data demonstrate that circular RNAs (circRNAs) and long non-coding RNAs (lncRNAs) play important roles in tumorigenesis. However, the mechanisms in colorectal cancer (CRC) remain unclear. Here, hundreds of significantly expressed circRNAs, and thousands of lncRNAs as well as mRNAs were identified. By qRT-PCR, one abnormal circRNA, lncRNA, and three mRNAs were verified in 24 pairs of tissues and blood samples, respectively. Then, by GO analysis, we found that the gene expression profile of linear counterparts of upregulated circRNAs in human CRC tissues preferred positive regulation of GTPase activity, cellular protein metabolic process, and protein binding, while that of downregulated circRNAs of CRC preferred positive regulation of cellular metabolic process, acetyl-CoA metabolic process, and protein kinase C activity. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that p53 signaling pathway was an important pathway in upregulated protein-coding genes, whereas cyclic guanosine monophosphate-protein kinase G (cGMP–PKG) signaling pathway was the top enriched KEGG pathway for downregulated transcripts. Furthermore, lncRNA–mRNA co-expression analysis demonstrated that downregulated lncRNA uc001tma.3 was negatively with CDC45 and positively with ELOVL4, BVES, FLNA, and HSPB8, while upregulated lncRNA NR_110882 was positively with FZD2. In addition, lncRNA–transcription factor (TF) co-expression analysis showed that the most relevant TFs were forkhead box protein A1 (FOXA1), transcription initiation factor TFIID submint 7 (TAF7), and adenovirus early region 1A(E1A)-associated protein p300 (EP300). Our findings offer a fresh view on circRNAs and lncRNAs and provide the foundation for further study on the potential roles of circRNAs and lncRNAs in colorectal cancer. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10142-018-0641-9) contains supplementary material, which is available to authorized users.
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spelling pubmed-63947312019-03-15 Comprehensive analysis of microarray expression profiles of circRNAs and lncRNAs with associated co-expression networks in human colorectal cancer Tian, Yan Xu, Yu Wang, Huawei Shu, Ruo Sun, Liang Zeng, Yujian Gong, Fangyou Lei, Yi Wang, Kunhua Luo, Huayou Funct Integr Genomics Original Article Increasing data demonstrate that circular RNAs (circRNAs) and long non-coding RNAs (lncRNAs) play important roles in tumorigenesis. However, the mechanisms in colorectal cancer (CRC) remain unclear. Here, hundreds of significantly expressed circRNAs, and thousands of lncRNAs as well as mRNAs were identified. By qRT-PCR, one abnormal circRNA, lncRNA, and three mRNAs were verified in 24 pairs of tissues and blood samples, respectively. Then, by GO analysis, we found that the gene expression profile of linear counterparts of upregulated circRNAs in human CRC tissues preferred positive regulation of GTPase activity, cellular protein metabolic process, and protein binding, while that of downregulated circRNAs of CRC preferred positive regulation of cellular metabolic process, acetyl-CoA metabolic process, and protein kinase C activity. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that p53 signaling pathway was an important pathway in upregulated protein-coding genes, whereas cyclic guanosine monophosphate-protein kinase G (cGMP–PKG) signaling pathway was the top enriched KEGG pathway for downregulated transcripts. Furthermore, lncRNA–mRNA co-expression analysis demonstrated that downregulated lncRNA uc001tma.3 was negatively with CDC45 and positively with ELOVL4, BVES, FLNA, and HSPB8, while upregulated lncRNA NR_110882 was positively with FZD2. In addition, lncRNA–transcription factor (TF) co-expression analysis showed that the most relevant TFs were forkhead box protein A1 (FOXA1), transcription initiation factor TFIID submint 7 (TAF7), and adenovirus early region 1A(E1A)-associated protein p300 (EP300). Our findings offer a fresh view on circRNAs and lncRNAs and provide the foundation for further study on the potential roles of circRNAs and lncRNAs in colorectal cancer. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10142-018-0641-9) contains supplementary material, which is available to authorized users. Springer Berlin Heidelberg 2018-11-16 2019 /pmc/articles/PMC6394731/ /pubmed/30446877 http://dx.doi.org/10.1007/s10142-018-0641-9 Text en © The Author(s) 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
spellingShingle Original Article
Tian, Yan
Xu, Yu
Wang, Huawei
Shu, Ruo
Sun, Liang
Zeng, Yujian
Gong, Fangyou
Lei, Yi
Wang, Kunhua
Luo, Huayou
Comprehensive analysis of microarray expression profiles of circRNAs and lncRNAs with associated co-expression networks in human colorectal cancer
title Comprehensive analysis of microarray expression profiles of circRNAs and lncRNAs with associated co-expression networks in human colorectal cancer
title_full Comprehensive analysis of microarray expression profiles of circRNAs and lncRNAs with associated co-expression networks in human colorectal cancer
title_fullStr Comprehensive analysis of microarray expression profiles of circRNAs and lncRNAs with associated co-expression networks in human colorectal cancer
title_full_unstemmed Comprehensive analysis of microarray expression profiles of circRNAs and lncRNAs with associated co-expression networks in human colorectal cancer
title_short Comprehensive analysis of microarray expression profiles of circRNAs and lncRNAs with associated co-expression networks in human colorectal cancer
title_sort comprehensive analysis of microarray expression profiles of circrnas and lncrnas with associated co-expression networks in human colorectal cancer
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6394731/
https://www.ncbi.nlm.nih.gov/pubmed/30446877
http://dx.doi.org/10.1007/s10142-018-0641-9
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