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Identification of RNA Expression Profiles in Thyroid Cancer to Construct a Competing Endogenous RNA (ceRNA) Network of mRNAs, Long Noncoding RNAs (lncRNAs), and microRNAs (miRNAs).
Med Sci Monit. 2019 Feb 12; 25:1140-1154.MS

Abstract

BACKGROUND

The aims of this study were to use RNA expression profile bioinformatics data from cases of thyroid cancer from the Cancer Genome Atlas (TCGA), the Kyoto Encyclopedia of Genes and Genomes (KEGG), and the Gene Ontology (GO) databases to construct a competing endogenous RNA (ceRNA) network of mRNAs, long noncoding RNAs (lncRNAs), and microRNAs (miRNAs). MATERIAL AND

METHODS

TCGA provided RNA profiles from 515 thyroid cancer tissues and 56 normal thyroid tissues. The DESeq R package analyzed high-throughput sequencing data on differentially expressed RNAs. GO and KEGG pathway analysis used the DAVID 6.8 and the ClusterProfile R package. Kaplan-Meier survival statistics and Cox regression analysis were performed. The thyroid cancer ceRNA network was constructed based on the miRDB, miRTarBase, and TargetScan databases.

RESULTS

There were 1,098 mRNAs associated with thyroid cancer; 101 mRNAs were associated with overall survival (OS). Multivariate analysis developed a risk scoring system that identified seven signature mRNAs, with a discriminative value of 0.88, determined by receiver operating characteristic (ROC) curve analysis. A ceRNA network included 13 mRNAs, 31 lncRNAs, and seven miRNAs. Four out of the 31 lncRNAs and all miRNAs were down-regulated, and the remaining RNAs were upregulated. Two lncRNAs (MIR1281A2HG and OPCML-IT1) and one miRNA (miR-184) were significantly associated with OS in patients with thyroid cancer.

CONCLUSIONS

Differential RNA expression profiling in thyroid cancer was used to construct a ceRNA network of mRNAs, lncRNAs, and miRNAs that showed potential in evaluating prognosis.

Authors+Show Affiliations

Department of Endocrinology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China (mainland).Harbin Medical University, Harbin, Heilongjiang, China (mainland).Department of Public Health Sciences, Stockholm University, Stockholm, Sweden.Department of Nursing, The Hospital of Heilongjiang Province, Harbin, Heilongjiang, China (mainland).

Pub Type(s)

Journal Article

Language

eng

PubMed ID

30745559

Citation

Xu, Yuanxin, et al. "Identification of RNA Expression Profiles in Thyroid Cancer to Construct a Competing Endogenous RNA (ceRNA) Network of mRNAs, Long Noncoding RNAs (lncRNAs), and microRNAs (miRNAs)." Medical Science Monitor : International Medical Journal of Experimental and Clinical Research, vol. 25, 2019, pp. 1140-1154.
Xu Y, Chen J, Yang Z, et al. Identification of RNA Expression Profiles in Thyroid Cancer to Construct a Competing Endogenous RNA (ceRNA) Network of mRNAs, Long Noncoding RNAs (lncRNAs), and microRNAs (miRNAs). Med Sci Monit. 2019;25:1140-1154.
Xu, Y., Chen, J., Yang, Z., & Xu, L. (2019). Identification of RNA Expression Profiles in Thyroid Cancer to Construct a Competing Endogenous RNA (ceRNA) Network of mRNAs, Long Noncoding RNAs (lncRNAs), and microRNAs (miRNAs). Medical Science Monitor : International Medical Journal of Experimental and Clinical Research, 25, 1140-1154. https://doi.org/10.12659/MSM.912450
Xu Y, et al. Identification of RNA Expression Profiles in Thyroid Cancer to Construct a Competing Endogenous RNA (ceRNA) Network of mRNAs, Long Noncoding RNAs (lncRNAs), and microRNAs (miRNAs). Med Sci Monit. 2019 Feb 12;25:1140-1154. PubMed PMID: 30745559.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Identification of RNA Expression Profiles in Thyroid Cancer to Construct a Competing Endogenous RNA (ceRNA) Network of mRNAs, Long Noncoding RNAs (lncRNAs), and microRNAs (miRNAs). AU - Xu,Yuanxin, AU - Chen,Jiuwei, AU - Yang,Zhihui, AU - Xu,Lihua, Y1 - 2019/02/12/ PY - 2019/2/13/entrez PY - 2019/2/13/pubmed PY - 2019/4/30/medline SP - 1140 EP - 1154 JF - Medical science monitor : international medical journal of experimental and clinical research JO - Med. Sci. Monit. VL - 25 N2 - BACKGROUND The aims of this study were to use RNA expression profile bioinformatics data from cases of thyroid cancer from the Cancer Genome Atlas (TCGA), the Kyoto Encyclopedia of Genes and Genomes (KEGG), and the Gene Ontology (GO) databases to construct a competing endogenous RNA (ceRNA) network of mRNAs, long noncoding RNAs (lncRNAs), and microRNAs (miRNAs). MATERIAL AND METHODS TCGA provided RNA profiles from 515 thyroid cancer tissues and 56 normal thyroid tissues. The DESeq R package analyzed high-throughput sequencing data on differentially expressed RNAs. GO and KEGG pathway analysis used the DAVID 6.8 and the ClusterProfile R package. Kaplan-Meier survival statistics and Cox regression analysis were performed. The thyroid cancer ceRNA network was constructed based on the miRDB, miRTarBase, and TargetScan databases. RESULTS There were 1,098 mRNAs associated with thyroid cancer; 101 mRNAs were associated with overall survival (OS). Multivariate analysis developed a risk scoring system that identified seven signature mRNAs, with a discriminative value of 0.88, determined by receiver operating characteristic (ROC) curve analysis. A ceRNA network included 13 mRNAs, 31 lncRNAs, and seven miRNAs. Four out of the 31 lncRNAs and all miRNAs were down-regulated, and the remaining RNAs were upregulated. Two lncRNAs (MIR1281A2HG and OPCML-IT1) and one miRNA (miR-184) were significantly associated with OS in patients with thyroid cancer. CONCLUSIONS Differential RNA expression profiling in thyroid cancer was used to construct a ceRNA network of mRNAs, lncRNAs, and miRNAs that showed potential in evaluating prognosis. SN - 1643-3750 UR - https://www.unboundmedicine.com/medline/citation/30745559/Identification_of_RNA_Expression_Profiles_in_Thyroid_Cancer_to_Construct_a_Competing_Endogenous_RNA__ceRNA__Network_of_mRNAs_Long_Noncoding_RNAs__lncRNAs__and_microRNAs__miRNAs__ L2 - https://www.medscimonit.com/download/index/idArt/912450 DB - PRIME DP - Unbound Medicine ER -