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Whole-Transcriptome Sequencing Identifies Key Differentially Expressed mRNAs, miRNAs, lncRNAs, and circRNAs Associated with CHOL

To systematically evaluate the whole-transcriptome sequencing data of cholangiocarcinoma (CHOL) to gain more insights into the transcriptomic landscape and molecular mechanism of this cancer, we performed whole-transcriptome sequencing based on the tumorous (C) and their corresponding non-tumorous a...

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Autores principales: Chu, Kai-Jian, Ma, Yu-Shui, Jiang, Xiao-Hui, Wu, Ting-Miao, Wu, Zhi-Jun, Li, Zhi-Zhen, Wang, Jing-Han, Gao, Qing-Xiang, Yi, Bin, Shi, Yi, Wang, Hui-Min, Gu, Li-Peng, Zhang, Su-Qing, Wang, Gao-Ren, Liu, Ji-Bin, Fu, Da, Jiang, Xiao-Qing
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Society of Gene & Cell Therapy 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7390861/
https://www.ncbi.nlm.nih.gov/pubmed/32721879
http://dx.doi.org/10.1016/j.omtn.2020.06.025
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author Chu, Kai-Jian
Ma, Yu-Shui
Jiang, Xiao-Hui
Wu, Ting-Miao
Wu, Zhi-Jun
Li, Zhi-Zhen
Wang, Jing-Han
Gao, Qing-Xiang
Yi, Bin
Shi, Yi
Wang, Hui-Min
Gu, Li-Peng
Zhang, Su-Qing
Wang, Gao-Ren
Liu, Ji-Bin
Fu, Da
Jiang, Xiao-Qing
author_facet Chu, Kai-Jian
Ma, Yu-Shui
Jiang, Xiao-Hui
Wu, Ting-Miao
Wu, Zhi-Jun
Li, Zhi-Zhen
Wang, Jing-Han
Gao, Qing-Xiang
Yi, Bin
Shi, Yi
Wang, Hui-Min
Gu, Li-Peng
Zhang, Su-Qing
Wang, Gao-Ren
Liu, Ji-Bin
Fu, Da
Jiang, Xiao-Qing
author_sort Chu, Kai-Jian
collection PubMed
description To systematically evaluate the whole-transcriptome sequencing data of cholangiocarcinoma (CHOL) to gain more insights into the transcriptomic landscape and molecular mechanism of this cancer, we performed whole-transcriptome sequencing based on the tumorous (C) and their corresponding non-tumorous adjacent to the tumors (CP) from eight CHOL patients. Subsequently, differential expression analysis was performed on the C and CP groups, followed by functional interaction prediction analysis to investigate gene-regulatory circuits in CHOL. In addition, The Cancer Genome Atlas (TCGA) for CHOL data was used to validate the results. In total, 2,895 differentially expressed messenger RNAs (dif-mRNAs), 56 differentially expressed microRNAs (dif-miRNAs), 151 differentially expressed long non-coding RNAs (dif-lncRNAs), and 110 differentially expressed circular RNAs (dif-circRNAs) were found in CHOL samples compared with controls. Enrichment analysis on those differentially expressed genes (DEGs) related to miRNA, lncRNA, and circRNA also identified the function of spliceosome. The downregulated hsa-miR-144-3p were significantly enriched in the competing endogenous RNA (ceRNA) complex network, which also included 7 upregulated and 13 downregulated circRNAs, 7 upregulated lncRNAs, and 90 upregulated and 40 downregulated mRNAs. Moreover, most of the DEGs and a few of the miRNAs (such as hsa-miR-144-3p) were successfully validated by TCGA data. The genes involved in RNA splicing and protein degradation processes and miR-144-3p may play fundamental roles in the pathogenesis of CHOL.
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spelling pubmed-73908612020-08-07 Whole-Transcriptome Sequencing Identifies Key Differentially Expressed mRNAs, miRNAs, lncRNAs, and circRNAs Associated with CHOL Chu, Kai-Jian Ma, Yu-Shui Jiang, Xiao-Hui Wu, Ting-Miao Wu, Zhi-Jun Li, Zhi-Zhen Wang, Jing-Han Gao, Qing-Xiang Yi, Bin Shi, Yi Wang, Hui-Min Gu, Li-Peng Zhang, Su-Qing Wang, Gao-Ren Liu, Ji-Bin Fu, Da Jiang, Xiao-Qing Mol Ther Nucleic Acids Article To systematically evaluate the whole-transcriptome sequencing data of cholangiocarcinoma (CHOL) to gain more insights into the transcriptomic landscape and molecular mechanism of this cancer, we performed whole-transcriptome sequencing based on the tumorous (C) and their corresponding non-tumorous adjacent to the tumors (CP) from eight CHOL patients. Subsequently, differential expression analysis was performed on the C and CP groups, followed by functional interaction prediction analysis to investigate gene-regulatory circuits in CHOL. In addition, The Cancer Genome Atlas (TCGA) for CHOL data was used to validate the results. In total, 2,895 differentially expressed messenger RNAs (dif-mRNAs), 56 differentially expressed microRNAs (dif-miRNAs), 151 differentially expressed long non-coding RNAs (dif-lncRNAs), and 110 differentially expressed circular RNAs (dif-circRNAs) were found in CHOL samples compared with controls. Enrichment analysis on those differentially expressed genes (DEGs) related to miRNA, lncRNA, and circRNA also identified the function of spliceosome. The downregulated hsa-miR-144-3p were significantly enriched in the competing endogenous RNA (ceRNA) complex network, which also included 7 upregulated and 13 downregulated circRNAs, 7 upregulated lncRNAs, and 90 upregulated and 40 downregulated mRNAs. Moreover, most of the DEGs and a few of the miRNAs (such as hsa-miR-144-3p) were successfully validated by TCGA data. The genes involved in RNA splicing and protein degradation processes and miR-144-3p may play fundamental roles in the pathogenesis of CHOL. American Society of Gene & Cell Therapy 2020-06-27 /pmc/articles/PMC7390861/ /pubmed/32721879 http://dx.doi.org/10.1016/j.omtn.2020.06.025 Text en © 2020 The Author(s) http://creativecommons.org/licenses/by-nc-nd/4.0/ This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Article
Chu, Kai-Jian
Ma, Yu-Shui
Jiang, Xiao-Hui
Wu, Ting-Miao
Wu, Zhi-Jun
Li, Zhi-Zhen
Wang, Jing-Han
Gao, Qing-Xiang
Yi, Bin
Shi, Yi
Wang, Hui-Min
Gu, Li-Peng
Zhang, Su-Qing
Wang, Gao-Ren
Liu, Ji-Bin
Fu, Da
Jiang, Xiao-Qing
Whole-Transcriptome Sequencing Identifies Key Differentially Expressed mRNAs, miRNAs, lncRNAs, and circRNAs Associated with CHOL
title Whole-Transcriptome Sequencing Identifies Key Differentially Expressed mRNAs, miRNAs, lncRNAs, and circRNAs Associated with CHOL
title_full Whole-Transcriptome Sequencing Identifies Key Differentially Expressed mRNAs, miRNAs, lncRNAs, and circRNAs Associated with CHOL
title_fullStr Whole-Transcriptome Sequencing Identifies Key Differentially Expressed mRNAs, miRNAs, lncRNAs, and circRNAs Associated with CHOL
title_full_unstemmed Whole-Transcriptome Sequencing Identifies Key Differentially Expressed mRNAs, miRNAs, lncRNAs, and circRNAs Associated with CHOL
title_short Whole-Transcriptome Sequencing Identifies Key Differentially Expressed mRNAs, miRNAs, lncRNAs, and circRNAs Associated with CHOL
title_sort whole-transcriptome sequencing identifies key differentially expressed mrnas, mirnas, lncrnas, and circrnas associated with chol
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7390861/
https://www.ncbi.nlm.nih.gov/pubmed/32721879
http://dx.doi.org/10.1016/j.omtn.2020.06.025
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