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Genome‐wide analysis of long noncoding RNA (lncRNA) expression in colorectal cancer tissues from patients with liver metastasis
The liver is the most frequent site of metastasis in colorectal cancer (CRC), in which long noncoding RNAs (lncRNAs) may play a crucial role. In this study, we performed a genome‐wide analysis of lncRNA expression to identify novel targets for the further study of liver metastasis in CRC. Samples ob...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4867661/ https://www.ncbi.nlm.nih.gov/pubmed/27165481 http://dx.doi.org/10.1002/cam4.738 |
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author | Chen, Dong Sun, Qiang Cheng, Xiaofei Zhang, Lufei Song, Wei Zhou, Dongkai Lin, Jianjiang Wang, Weilin |
author_facet | Chen, Dong Sun, Qiang Cheng, Xiaofei Zhang, Lufei Song, Wei Zhou, Dongkai Lin, Jianjiang Wang, Weilin |
author_sort | Chen, Dong |
collection | PubMed |
description | The liver is the most frequent site of metastasis in colorectal cancer (CRC), in which long noncoding RNAs (lncRNAs) may play a crucial role. In this study, we performed a genome‐wide analysis of lncRNA expression to identify novel targets for the further study of liver metastasis in CRC. Samples obtained from CRC patients were analyzed using Arraystar human 8 × 60K lncRNA/mRNA v3.0 microarrays chips to find differentially expressed lncRNAs and mRNAs. The results were confirmed by quantitative reverse transcription‐polymerase chain reaction (qRT‐PCR). The differentially expressed lncRNAs and mRNAs were identified through fold change filtering. Gene ontology (GO) and pathway analyses were performed using standard enrichment computational methods. In the CRC tissues from patients with liver metastasis, 2636 lncRNAs were differentially expressed, including 1600 up‐regulated and 1036 down‐regulated over two‐fold compared with the CRC tissues without metastasis. Among the 1584 differentially expressed mRNAs, 548 were up‐regulated and 1036 down‐regulated. GO and pathway analysis of the up‐regulated and down‐regulated mRNAs yielded different results. The up‐regulated mRNAs were associated with single‐organism process (biological process), membrane part (cellular component), and transporter activity (molecular function), whereas the down‐regulated mRNAs were associated with cellular process, membrane, and binding, respectively. In the pathway analysis, 27 gene pathways associated with the up‐regulated mRNAs and 51 gene pathways associated with the down‐regulated mRNAs were targeted. The significant changes in NQO2 (NM_000904) mRNA and six associated lncRNAs were selected for validation by qRT‐PCR. Aberrantly expressed lncRNAs may play an important role in the liver metastasis of CRC. The further study can provide useful insights into the biology and, ultimately, the prevention of liver metastasis. |
format | Online Article Text |
id | pubmed-4867661 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-48676612016-05-31 Genome‐wide analysis of long noncoding RNA (lncRNA) expression in colorectal cancer tissues from patients with liver metastasis Chen, Dong Sun, Qiang Cheng, Xiaofei Zhang, Lufei Song, Wei Zhou, Dongkai Lin, Jianjiang Wang, Weilin Cancer Med Cancer Biology The liver is the most frequent site of metastasis in colorectal cancer (CRC), in which long noncoding RNAs (lncRNAs) may play a crucial role. In this study, we performed a genome‐wide analysis of lncRNA expression to identify novel targets for the further study of liver metastasis in CRC. Samples obtained from CRC patients were analyzed using Arraystar human 8 × 60K lncRNA/mRNA v3.0 microarrays chips to find differentially expressed lncRNAs and mRNAs. The results were confirmed by quantitative reverse transcription‐polymerase chain reaction (qRT‐PCR). The differentially expressed lncRNAs and mRNAs were identified through fold change filtering. Gene ontology (GO) and pathway analyses were performed using standard enrichment computational methods. In the CRC tissues from patients with liver metastasis, 2636 lncRNAs were differentially expressed, including 1600 up‐regulated and 1036 down‐regulated over two‐fold compared with the CRC tissues without metastasis. Among the 1584 differentially expressed mRNAs, 548 were up‐regulated and 1036 down‐regulated. GO and pathway analysis of the up‐regulated and down‐regulated mRNAs yielded different results. The up‐regulated mRNAs were associated with single‐organism process (biological process), membrane part (cellular component), and transporter activity (molecular function), whereas the down‐regulated mRNAs were associated with cellular process, membrane, and binding, respectively. In the pathway analysis, 27 gene pathways associated with the up‐regulated mRNAs and 51 gene pathways associated with the down‐regulated mRNAs were targeted. The significant changes in NQO2 (NM_000904) mRNA and six associated lncRNAs were selected for validation by qRT‐PCR. Aberrantly expressed lncRNAs may play an important role in the liver metastasis of CRC. The further study can provide useful insights into the biology and, ultimately, the prevention of liver metastasis. John Wiley and Sons Inc. 2016-05-11 /pmc/articles/PMC4867661/ /pubmed/27165481 http://dx.doi.org/10.1002/cam4.738 Text en © 2016 The Authors. Cancer Medicine published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution (http://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Cancer Biology Chen, Dong Sun, Qiang Cheng, Xiaofei Zhang, Lufei Song, Wei Zhou, Dongkai Lin, Jianjiang Wang, Weilin Genome‐wide analysis of long noncoding RNA (lncRNA) expression in colorectal cancer tissues from patients with liver metastasis |
title | Genome‐wide analysis of long noncoding RNA (lncRNA) expression in colorectal cancer tissues from patients with liver metastasis |
title_full | Genome‐wide analysis of long noncoding RNA (lncRNA) expression in colorectal cancer tissues from patients with liver metastasis |
title_fullStr | Genome‐wide analysis of long noncoding RNA (lncRNA) expression in colorectal cancer tissues from patients with liver metastasis |
title_full_unstemmed | Genome‐wide analysis of long noncoding RNA (lncRNA) expression in colorectal cancer tissues from patients with liver metastasis |
title_short | Genome‐wide analysis of long noncoding RNA (lncRNA) expression in colorectal cancer tissues from patients with liver metastasis |
title_sort | genome‐wide analysis of long noncoding rna (lncrna) expression in colorectal cancer tissues from patients with liver metastasis |
topic | Cancer Biology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4867661/ https://www.ncbi.nlm.nih.gov/pubmed/27165481 http://dx.doi.org/10.1002/cam4.738 |
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