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Whole-Transcriptome Sequencing Identifies Key Differentially Expressed mRNAs, miRNAs, lncRNAs, and circRNAs Associated with CHOL
- Source :
- Molecular Therapy: Nucleic Acids, Vol 21, Iss, Pp 592-603 (2020), Molecular Therapy. Nucleic Acids
- Publication Year :
- 2020
- Publisher :
- Elsevier BV, 2020.
-
Abstract
- 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.<br />Graphical Abstract<br />The whole-transcriptome sequencing data of cholangiocarcinoma (CHOL) were systematically evaluated to gain more insights into the transcriptomic landscape and molecular mechanism of this cancer.
- Subjects :
- 0301 basic medicine
Spliceosome
miR-144-3p
Competing endogenous RNA
lcsh:RM1-950
ceRNA
Computational biology
Protein degradation
Biology
Article
Transcriptome
03 medical and health sciences
lcsh:Therapeutics. Pharmacology
030104 developmental biology
0302 clinical medicine
Downregulation and upregulation
030220 oncology & carcinogenesis
Drug Discovery
microRNA
RNA splicing
Molecular Medicine
DEG
CHOL
spliceosome
Gene
Subjects
Details
- ISSN :
- 21622531
- Volume :
- 21
- Database :
- OpenAIRE
- Journal :
- Molecular Therapy - Nucleic Acids
- Accession number :
- edsair.doi.dedup.....4c3e20f5eac0f32cfda6498679152707
- Full Text :
- https://doi.org/10.1016/j.omtn.2020.06.025