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Functional Long Noncoding RNAs (lncRNAs) in Clear Cell Kidney Carcinoma Revealed by Reconstruction and Comprehensive Analysis of the lncRNA-miRNA-mRNA Regulatory Network.
Med Sci Monit. 2018 Nov 16; 24:8250-8263.MS

Abstract

BACKGROUND

A variety of treatment strategies have been developed for clear cell kidney carcinoma (KIRC); however, there is still a need for effective therapeutic targets and prognostic molecular biomarkers. Given that long noncoding RNAs (lncRNAs) has been emerging as an important regulator in tumorigenesis, we explored potential functional lncRNAs in KIRC by comprehensively analyzing the lncRNA-miRNA-mRNA regulatory network with bioinformatics processing tools. MATERIAL AND

METHODS

RNA-seq/miRNA-seq data of KIRC in The Cancer Genome Atlas (TCGA) were obtained and analyzed. The "edgeR" package in R software was used to identify differentially expressed lncRNAs (DElncRNAs, differentially expressed long noncoding RNAs), miRNAs (DEmiRNAs, differentially expressed micro RNAs), and mRNAs (DEmRNAs, differentially expressed messenger RNAs) in KIRC and normal samples. A global triple network was conducted based on the competing endogenous RNA (ceRNA) theory, and survival analysis was conducted by "survival" package in R software.

RESULTS

A total of 4246 DElncRNAs, 179 DEmiRNAs, and 5758 DEmRNAs were identified, among which a subset of them (321 lncRNAs, 26 miRNAs, and 1068 mRNAs) were found to constitute a global ceRNA network in KIRC. Four lncRNAs (ENTPD3-AS1, FGD5-AS1, LIFR-AS1, and UBAC2-AS1) were revealed to be potential therapeutic targets as well as prognostic biomarkers of KIRC by our extensive functional analysis.

CONCLUSIONS

We reported here the identification of functional lncRNAs in KIRC via a TCGA data-based bioinformatics analysis. We believe that this study might contribute to improving the comprehension of the lncRNA-mediated ceRNA regulatory mechanisms in the tumorigenesis of KIRC. Meanwhile, our results suggested that 4 lncRNAs might act as potential therapeutic targets or candidate prognostic biomarkers in KIRC.

Authors+Show Affiliations

Fujian Provincial Key Laboratory of Transplant Biology, Department of Urology, Fuzhou Dongfang Hospital, Xiamen University, Fuzhou, Fujian, China (mainland).Fujian Provincial Key Laboratory of Transplant Biology, Department of Urology, Fuzhou Dongfang Hospital, Xiamen University, Fuzhou, Fujian, China (mainland).Fujian Provincial Key Laboratory of Transplant Biology, Department of Urology, Fuzhou Dongfang Hospital, Xiamen University, Fuzhou, Fujian, China (mainland).Fujian Provincial Key Laboratory of Transplant Biology, Department of Urology, Fuzhou Dongfang Hospital, Xiamen University, Fuzhou, Fujian, China (mainland).Fujian Provincial Key Laboratory of Transplant Biology, Department of Urology, Fuzhou Dongfang Hospital, Xiamen University, Fuzhou, Fujian, China (mainland).Fujian Provincial Key Laboratory of Transplant Biology, Department of Urology, Fuzhou Dongfang Hospital, Xiamen University, Fuzhou, Fujian, China (mainland).Fujian Provincial Key Laboratory of Transplant Biology, Department of Urology, Fuzhou Dongfang Hospital, Xiamen University, Fuzhou, Fujian, China (mainland).Fujian Provincial Key Laboratory of Transplant Biology, Department of Urology, Fuzhou Dongfang Hospital, Xiamen University, Fuzhou, Fujian, China (mainland).Fujian Provincial Key Laboratory of Transplant Biology, Department of Urology, Fuzhou Dongfang Hospital, Xiamen University, Fuzhou, Fujian, China (mainland).Fujian Provincial Key Laboratory of Transplant Biology, Department of Urology, Fuzhou Dongfang Hospital, Xiamen University, Fuzhou, Fujian,, China (mainland).Fujian Provincial Key Laboratory of Transplant Biology, Department of Urology, Fuzhou Dongfang Hospital, Xiamen University, Fuzhou, Fujian, China (mainland).

Pub Type(s)

Journal Article

Language

eng

PubMed ID

30444862

Citation

Zhu, Hehuan, et al. "Functional Long Noncoding RNAs (lncRNAs) in Clear Cell Kidney Carcinoma Revealed By Reconstruction and Comprehensive Analysis of the lncRNA-miRNA-mRNA Regulatory Network." Medical Science Monitor : International Medical Journal of Experimental and Clinical Research, vol. 24, 2018, pp. 8250-8263.
Zhu H, Lu J, Zhao H, et al. Functional Long Noncoding RNAs (lncRNAs) in Clear Cell Kidney Carcinoma Revealed by Reconstruction and Comprehensive Analysis of the lncRNA-miRNA-mRNA Regulatory Network. Med Sci Monit. 2018;24:8250-8263.
Zhu, H., Lu, J., Zhao, H., Chen, Z., Cui, Q., Lin, Z., Wang, X., Wang, J., Dong, H., Wang, S., & Tan, J. (2018). Functional Long Noncoding RNAs (lncRNAs) in Clear Cell Kidney Carcinoma Revealed by Reconstruction and Comprehensive Analysis of the lncRNA-miRNA-mRNA Regulatory Network. Medical Science Monitor : International Medical Journal of Experimental and Clinical Research, 24, 8250-8263. https://doi.org/10.12659/MSM.910773
Zhu H, et al. Functional Long Noncoding RNAs (lncRNAs) in Clear Cell Kidney Carcinoma Revealed By Reconstruction and Comprehensive Analysis of the lncRNA-miRNA-mRNA Regulatory Network. Med Sci Monit. 2018 Nov 16;24:8250-8263. PubMed PMID: 30444862.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Functional Long Noncoding RNAs (lncRNAs) in Clear Cell Kidney Carcinoma Revealed by Reconstruction and Comprehensive Analysis of the lncRNA-miRNA-mRNA Regulatory Network. AU - Zhu,Hehuan, AU - Lu,Jun, AU - Zhao,Hu, AU - Chen,Zhan, AU - Cui,Qiang, AU - Lin,Zhiwen, AU - Wang,Xuyang, AU - Wang,Jie, AU - Dong,Huiyue, AU - Wang,Shuiliang, AU - Tan,Jianming, Y1 - 2018/11/16/ PY - 2018/11/17/entrez PY - 2018/11/18/pubmed PY - 2019/1/19/medline SP - 8250 EP - 8263 JF - Medical science monitor : international medical journal of experimental and clinical research JO - Med. Sci. Monit. VL - 24 N2 - BACKGROUND A variety of treatment strategies have been developed for clear cell kidney carcinoma (KIRC); however, there is still a need for effective therapeutic targets and prognostic molecular biomarkers. Given that long noncoding RNAs (lncRNAs) has been emerging as an important regulator in tumorigenesis, we explored potential functional lncRNAs in KIRC by comprehensively analyzing the lncRNA-miRNA-mRNA regulatory network with bioinformatics processing tools. MATERIAL AND METHODS RNA-seq/miRNA-seq data of KIRC in The Cancer Genome Atlas (TCGA) were obtained and analyzed. The "edgeR" package in R software was used to identify differentially expressed lncRNAs (DElncRNAs, differentially expressed long noncoding RNAs), miRNAs (DEmiRNAs, differentially expressed micro RNAs), and mRNAs (DEmRNAs, differentially expressed messenger RNAs) in KIRC and normal samples. A global triple network was conducted based on the competing endogenous RNA (ceRNA) theory, and survival analysis was conducted by "survival" package in R software. RESULTS A total of 4246 DElncRNAs, 179 DEmiRNAs, and 5758 DEmRNAs were identified, among which a subset of them (321 lncRNAs, 26 miRNAs, and 1068 mRNAs) were found to constitute a global ceRNA network in KIRC. Four lncRNAs (ENTPD3-AS1, FGD5-AS1, LIFR-AS1, and UBAC2-AS1) were revealed to be potential therapeutic targets as well as prognostic biomarkers of KIRC by our extensive functional analysis. CONCLUSIONS We reported here the identification of functional lncRNAs in KIRC via a TCGA data-based bioinformatics analysis. We believe that this study might contribute to improving the comprehension of the lncRNA-mediated ceRNA regulatory mechanisms in the tumorigenesis of KIRC. Meanwhile, our results suggested that 4 lncRNAs might act as potential therapeutic targets or candidate prognostic biomarkers in KIRC. SN - 1643-3750 UR - https://www.unboundmedicine.com/medline/citation/30444862/Functional_Long_Noncoding_RNAs__lncRNAs__in_Clear_Cell_Kidney_Carcinoma_Revealed_by_Reconstruction_and_Comprehensive_Analysis_of_the_lncRNA_miRNA_mRNA_Regulatory_Network_ L2 - https://www.medscimonit.com/download/index/idArt/910773 DB - PRIME DP - Unbound Medicine ER -