Comprehensive analysis of differentially expressed profiles of lncRNAs and construction of miR-133b mediated ceRNA network in colorectal cancer

Objective. To screen some RNAs that correlated with colorectal cancer (CRC). Methods. Differentially expressed miRNAs, lncRNAs, and mRNAs between cancer tissues and normal tissues in CRC were identified using data from the Gene Expression Omnibus (GEO) database. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and protein-protein interactions (PPIs) were performed to do the functional enrichment analysis. And a lncRNA-miRNA-mRNA network was constructed which correlated with CRC. RNAs in this network were subjected to analyze the relationship with the patient prognosis. Results. A total of 688, 241, and 103 differentially expressed genes (diff-mRNA), diff-lncRNA, and diff-miRNA were obtained between cancer tissues and normal tissues. A total of 315 edges were obtained in the ceRNA network. lncRNA RP11-108K3.2 and mRNA ONECUT2 correlated with prognosis. Conclusion. The identified RNAs and constructed ceRNA network could provide great sources for the researches of therapy of the CRC. And the lncRNA RP11-108K3.2 and mRNA ONECUT2 may serve as a novel prognostic predictor of CRC.

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Comprehensive Analysis of the Expression Profiles of Long Non-Coding RNAs with Associated ceRNA Network Involved in the Colon Cancer Staging and Progression

Scientific Reports ◽

10.1038/s41598-019-52883-2 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 5

Author(s):

Meini Wu ◽

Wenliang Li ◽

Fengchang Huang ◽

Jing Sun ◽

Kang ping Li ◽

...

Keyword(s):

Colon Cancer ◽

Expression Profiles ◽

Comprehensive Analysis ◽

Differentially Expressed ◽

Stage Iii ◽

Aberrant Expression ◽

Normal Tissues ◽

Cerna Network ◽

Tumor Tissues ◽

Non Coding Rnas

AbstractLong non-coding RNAs (lncRNAs) act as competing endogenous RNAs (ceRNAs) to compete with microRNAs (miRNAs) in cancer occurrence and development. However, the differential expression of RNAs and their ceRNA network during the development of colon cancer (CC) remains unclear. This study was aimed at comprehensive analysis of the lncRNAs and their ceRNA networks associated with CC. Whole transcriptome sequencing was performed on colorectal and adjacent normal tissues at different pathological stages. Forty-nine lncRNAs were differently expressed between the CC tissues and their adjacent normal tissues at all stages. Aberrant expression of lncRNA CDKN2B-AS1 and lncRNA MIR4435-2HG was confirmed by TCGA database. Moreover, 14 lncRNAs were differentially expressed between early and advance stages of the tumor tissues, and 117 miRNAs were specifically expressed in stage III & IV. Weighted gene co-expression network analysis of 17105 differently expressed mRNAs revealed that the mRNAs shown in module pink, midnight blue, black, and light cyan were related to TNM and pathological stage, and that these mRNAs were enriched in cancer related functions and pathways. As DElncRNA showed a trend of change similar to that of the DEmRNA and opposite to that of DEmiRNA, ceRNA network was constructed with 3 DEmiRNAs, 5 DElncRNAs, and 130 DEmRNAs. Real time PCR revealed that expression of MEG3 was decreased in the tumor tissues belonging to stage III and IV as compared to that in stage I. Moreover, hsa-miR-324-5p was upregulated, while FGFR3, PLCB4, and IKBKB were downregulated in the tumor tissues as compared to that in the adjacent normal tissues. Thus, this study revealed differentially expressed lncRNA between different stages of CC as well as suggested that lncRNA CDKN2B-AS1, MIR4435-2HG, and MEG3 may act as diagnostic biomarkers for the development of CC.

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Integrated Analysis of Circular RNA Associated Cerna Network Reveals Potential CircRNA Biomarkers in Human Breast Cancer

10.21203/rs.3.rs-90865/v1 ◽

2020 ◽

Author(s):

Hui Shen ◽

Huan Pan ◽

Jianju Lu ◽

Jianfen Shen ◽

Longsheng Xu ◽

...

Keyword(s):

Breast Cancer ◽

Survival Analysis ◽

Correlation Analysis ◽

Mrna Expression ◽

Circular Rna ◽

Comprehensive Analysis ◽

Differentially Expressed ◽

Hub Genes ◽

Cerna Network ◽

Competitive Endogenous Rna

Abstract BackgroundThere is increasing evidence that circular RNA (circRNA) is closely related to tumorigenesis and cancer progression. circRNA has been identified as a sponge of microRNA (miRNA) in a competitive endogenous RNA (ceRNA) network and is involved in the regulation of mRNA expression. However, the roles of cancer specific circRNAs in circRNA-related ceRNA network of breast cancer (BRCA) are still unclear. This study aims to construct a ceRNA network associated with circRNA and to explore new therapeutic and prognostic targets and biomarkers for breast cancer.MethodsWe downloaded the circRNA expression profile of BRCA from Gene Expression Omnibus (GEO) microarray datasets and downloaded the miRNA and mRNA expression profiles of BRCA from The Cancer Genome Atlas (TCGA) database, these data were included in the study for comprehensive analysis. Differentially expressed mRNAs (DEmRNAs), differentially expressed miRNAs (DEmiRNAs) and differentially expressed circRNAs (DEcircRNAs) were identified and a competitive endogenous RNA (ceRNA) regulatory network was constructed based on circRNA–miRNA pairs and miRNA–mRNA pairs. Gene ontology and pathway enrichment analysis were performed on mRNAs regulated by circRNAs in ceRNA networks. Survival analysis and correlation analysis of all mRNAs and miRNAs in the ceRNA network were performed. The STRING search tool was used to predict the interaction between proteins, and the hub genes were screened by the MCODE plugin in Cytoscape.ResultsA total of 72 DEcircRNAs, 158 DEmiRNAs and 2762 DE mRNAs were identified. The constructed ceRNA network contains 60 circRNA-miRNA pairs and 140 miRNA-mRNA pairs, including 40 circRNAs, 30 miRNAs and 100 mRNAs. Functional enrichment indicated that DEmRNAs regulated by DEcircRNAs in ceRNA networks were significantly enriched in PI3K-Akt signaling pathway, MicroRNAs in cancer and Proteoglycans in cancer. Survival analysis and correlation analysis of all mRNAs and miRNAs in the ceRNA network showed that a total of 13 mRNAs and 6 miRNAs were significantly associated with overall survival, and 48 miRNA-mRNA interaction pairs had a significant negative correlation. A PPI network was established and 21 hub genes were determined from the network. After comprehensive analysis, four potential ceRNA regulatory axes were constructed based on three circRNAs, two miRNAs, and three mRNAs.ConclusionsThis study provides an effective bioinformatics basis for further understanding the molecular mechanisms and predictions of breast cancer. A better understanding of the circRNA-related ceRNA network in BRCA will help identify potential biomarkers for diagnosis and prognosis.

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Comprehensive Analysis of Competing Endogenous RNA (ceRNA) Network Based on RNAs Differentially Expressed in Lung Adenocarcinoma Using The Cancer Genome Atlas (TCGA) Database

Medical Science Monitor ◽

10.12659/msm.922676 ◽

2020 ◽

Vol 26 ◽

Author(s):

Huaihui Tang ◽

Zhongshuai Wang ◽

Qianqian Shao ◽

Yue Wang ◽

Qingshan Yang

Keyword(s):

Lung Adenocarcinoma ◽

Comprehensive Analysis ◽

Cancer Genome ◽

The Cancer Genome Atlas ◽

Differentially Expressed ◽

Competing Endogenous Rna ◽

Cerna Network ◽

Cancer Genome Atlas ◽

Genome Atlas

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Comprehensive Analysis of Differentially Expressed circRNAs Reveals a Colorectal Cancer-Related ceRNA Network

Computational and Mathematical Methods in Medicine ◽

10.1155/2020/7159340 ◽

2020 ◽

Vol 2020 ◽

pp. 1-14

Author(s):

Feng Que ◽

Hua Wang ◽

Yi Luo ◽

Li Cui ◽

Lanfu Wei ◽

...

Keyword(s):

Colorectal Cancer ◽

Cell Cycle Progression ◽

Cancer Prognosis ◽

Differentially Expressed ◽

Sequencing Technology ◽

Cycle Progression ◽

Normal Tissues ◽

Metabolism Regulation ◽

Cerna Network ◽

Very High

The morbidity and mortality of colorectal cancer (CRC) remained to be very high worldwide. Recently, circRNAs had been revealed to have a crucial role in cancer prognosis and progression. Numerous researches have shown that RNA sequencing technology and in silico method were widely used to identify pathogenic mechanisms and uncover promising targets for diagnosis and therapy. In this study, these methods were analyzed to obtain differentially expressed circRNAs (DECs). We identified upregulated 316 circRNAs and reduced 76 circRNAs in CRC samples, in comparison with those in normal tissues. In addition, a competitive endogenous network of circRNA-miRNA-mRNA was established to predict the mechanisms of circRNAs. Bioinformatics analysis revealed that these circRNAs participated in metabolism regulation and cell cycle progression. Of note, we observed the hub genes and miRNAs in this ceRNA network were associated with the survival time in CRC. We think this study could provide potential prognostic biomarkers and targets for CRC.

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Construction of ceRNA co-expression network and screening of molecular targets in colorectal cancer

10.21203/rs.2.17910/v1 ◽

2019 ◽

Author(s):

Hui Zhao ◽

Zhanwei Wang ◽

Xi Yang ◽

Jin Liu ◽

Jing Zhuang ◽

...

Keyword(s):

Colorectal Cancer ◽

Protein Interactions ◽

Enrichment Analysis ◽

Gene Expression Omnibus ◽

Differentially Expressed ◽

Protein Protein Interactions ◽

Normal Tissues ◽

Cerna Network ◽

Using Data ◽

Cancer Tissues

Abstract Objective to screen some RNAs that correlated with colorectal cancer (CRC).Methods Differentially expressed miRNAs, lncRNAs, and mRNAs between cancer tissues and normal tissues in CRC were identified using data from the Gene Expression Omnibus (GEO) database. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and protein-protein interactions (PPIs) were performed to do the functioal enrichment analysis. And a lncRNA-miRNA-mRNA network was constructed wich correlated with CRC. RNAs in this network were subjecte to analyze the relationship with the patient prognosis.Results A total of 688, 241, and 103 differentially expressed genes (diff-mRNA), diff-lncRNA, and diff-miRNA were obtained. between cancer tissues and normal tissues. A total of 315 edges were obtained in the ceRNA network. lncRNA RP11-108K3.2 and mRNA ONECUT2 correlated with prognosis.Conclusion The identified RNAs and constructed ceRNA network could provide great sources for the reasearches of therapy the CRC. And the lncRNA RP11-108K3.2 and mRNA ONECUT2 may serve novel prognostic predictor of CRC.

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