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Transcriptome sequencing of lncRNA, miRNA, mRNA and interaction network constructing in coronary heart disease
BACKGROUND: Non-coding RNA has been shown to participate in numerous biological and pathological processes and has attracted increasing attention in recent years. Recent studies have demonstrated that long non-coding RNA and micro RNA can interact through various mechanisms to regulate mRNA. Yet the...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6708182/ https://www.ncbi.nlm.nih.gov/pubmed/31443660 http://dx.doi.org/10.1186/s12920-019-0570-z |
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author | Liao, Jiangquan Wang, Jie Liu, Yongmei Li, Jun Duan, Lian |
author_facet | Liao, Jiangquan Wang, Jie Liu, Yongmei Li, Jun Duan, Lian |
author_sort | Liao, Jiangquan |
collection | PubMed |
description | BACKGROUND: Non-coding RNA has been shown to participate in numerous biological and pathological processes and has attracted increasing attention in recent years. Recent studies have demonstrated that long non-coding RNA and micro RNA can interact through various mechanisms to regulate mRNA. Yet the gene-gene interaction has not been investigated in coronary heart disease (CHD). METHODS: High throughput sequencing were used to identify differentially expressed (DE) lncRNA, miRNA, and mRNA profiles between CHD and healthy control. Gene Oncology (GO), KEGG enrichment analysis were performed. Gene-gene interaction network were constructed and pivotal genes were screened out. Lentivirus-induced shRNA infection and qRT-PCR were performed to validated the gene-gene interactions. RESULTS: A total of 62 lncRNAs, 332 miRNAs and 366 mRNAs were differentially expressed between CHD and healthy control. GO and KEGG analysis show that immune related molecular mechanisms and biological processes play a role in CHD. The gene-gene interaction network were constructed and visualized based on Pearson correlation coefficients and starBase database. 6 miRNAs in the network were significantly correlated to left ventricular ejection fraction, total choleterol and homocysteine. 2 lncRNAs (CTA-384D8.35 and CTB-114C7.4 (refseq entry LOC100128059)), 1 miRNA (miR-4497), and 1 mRNA (NR4A1) were the pivotal genes. Lentivirus-induced shRNA infection and qRT-PCR had validated the pivotal gene-gene interactions. CONCLUSIONS: These results have shown the potential of lncRNA, miRNA, and mRNA as clinical biomarkers and in elucidating pathological mechanisms of CHD from a transcriptomic perspective. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12920-019-0570-z) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6708182 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-67081822019-08-28 Transcriptome sequencing of lncRNA, miRNA, mRNA and interaction network constructing in coronary heart disease Liao, Jiangquan Wang, Jie Liu, Yongmei Li, Jun Duan, Lian BMC Med Genomics Research Article BACKGROUND: Non-coding RNA has been shown to participate in numerous biological and pathological processes and has attracted increasing attention in recent years. Recent studies have demonstrated that long non-coding RNA and micro RNA can interact through various mechanisms to regulate mRNA. Yet the gene-gene interaction has not been investigated in coronary heart disease (CHD). METHODS: High throughput sequencing were used to identify differentially expressed (DE) lncRNA, miRNA, and mRNA profiles between CHD and healthy control. Gene Oncology (GO), KEGG enrichment analysis were performed. Gene-gene interaction network were constructed and pivotal genes were screened out. Lentivirus-induced shRNA infection and qRT-PCR were performed to validated the gene-gene interactions. RESULTS: A total of 62 lncRNAs, 332 miRNAs and 366 mRNAs were differentially expressed between CHD and healthy control. GO and KEGG analysis show that immune related molecular mechanisms and biological processes play a role in CHD. The gene-gene interaction network were constructed and visualized based on Pearson correlation coefficients and starBase database. 6 miRNAs in the network were significantly correlated to left ventricular ejection fraction, total choleterol and homocysteine. 2 lncRNAs (CTA-384D8.35 and CTB-114C7.4 (refseq entry LOC100128059)), 1 miRNA (miR-4497), and 1 mRNA (NR4A1) were the pivotal genes. Lentivirus-induced shRNA infection and qRT-PCR had validated the pivotal gene-gene interactions. CONCLUSIONS: These results have shown the potential of lncRNA, miRNA, and mRNA as clinical biomarkers and in elucidating pathological mechanisms of CHD from a transcriptomic perspective. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12920-019-0570-z) contains supplementary material, which is available to authorized users. BioMed Central 2019-08-23 /pmc/articles/PMC6708182/ /pubmed/31443660 http://dx.doi.org/10.1186/s12920-019-0570-z Text en © The Author(s). 2019 Open AccessThis 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. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Liao, Jiangquan Wang, Jie Liu, Yongmei Li, Jun Duan, Lian Transcriptome sequencing of lncRNA, miRNA, mRNA and interaction network constructing in coronary heart disease |
title | Transcriptome sequencing of lncRNA, miRNA, mRNA and interaction network constructing in coronary heart disease |
title_full | Transcriptome sequencing of lncRNA, miRNA, mRNA and interaction network constructing in coronary heart disease |
title_fullStr | Transcriptome sequencing of lncRNA, miRNA, mRNA and interaction network constructing in coronary heart disease |
title_full_unstemmed | Transcriptome sequencing of lncRNA, miRNA, mRNA and interaction network constructing in coronary heart disease |
title_short | Transcriptome sequencing of lncRNA, miRNA, mRNA and interaction network constructing in coronary heart disease |
title_sort | transcriptome sequencing of lncrna, mirna, mrna and interaction network constructing in coronary heart disease |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6708182/ https://www.ncbi.nlm.nih.gov/pubmed/31443660 http://dx.doi.org/10.1186/s12920-019-0570-z |
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