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A Competing Endogenous RNA Network Reveals Novel Potential lncRNA, miRNA, and mRNA Biomarkers in the Prognosis of Human Colon Adenocarcinoma.
J Surg Res. 2019 03; 235:22-33.JS

Abstract

BACKGROUND

Accumulating evidence indicated that long noncoding RNAs (lncRNAs) have a wide range of biological functions and may play significant roles in tumorigenesis and progression. However, the understanding of its functions and related competitive endogenous RNAs (ceRNAs) networks is much less than that of protein-coding genes, particularly in colon adenocarcinoma.

METHODS

We comprehensively analyzed the sequencing data of protein-coding and noncoding RNAs in colon adenocarcinoma patients from The Cancer Genome Atlas (TCGA) database. Next, we constructed colon adenocarcinoma-specific ceRNA network and evaluated the effect of these RNAs on overall survival (OS) for colon adenocarcinoma patients.

RESULTS

Totally, 1138 differentially expressed lncRNAs (DElncRNAs), 245 microRNAs (DEmiRNAs), and 2081 mRNAs (DEmRNAs) were identified using a threshold of |log2FoldChange| >2.0 and adjusted P-value < 0.01. Subsequently, a colon adenocarcinoma-specific ceRNA network was successfully established with133 DElncRNAs, 29 DEmiRNAs, and 55 DEmRNAs. Among ceRNA network, seven DElncRNAs (AL590483.1, AP004609.1, ARHGEF26-AS1, HOX transcript antisense RNA (HOTAIR), ITCH-IT1, KCNQ1OT1, and LINC00491), four DEmiRNAs (hsa-mir-143, hsa-mir-183, hsa-mir-216a, and hsa-mir-424), and six DEmRNAs (FJX1, TPM2, ULBP2, PDCD4, PLAU, and SERPINE1) significantly correlated with OS (all P-value < 0.05). Notably, several interactions were highlighted in the ceRNA network, such as "KCNQ1OT1-hsa-mir-183-PDCD4", "KCNQ1OT1-hsa-mir-424-TPM2", "HOTAIR-hsa-mir-143-SERPINE1", and "ARHGEF26-AS1-hsa-mir-143-SERPINE1".

CONCLUSIONS

These findings reveal several molecules might be novel important prognostic factors and potential treatment targets for colon adenocarcinoma. In addition, these observations contribute to a more comprehensive understanding of lncRNA-related ceRNA network and provide novel strategies for subsequent functional studies of lncRNAs in colon adenocarcinoma.

Authors+Show Affiliations

Second Clinical Medical College, Lanzhou University, Lanzhou, Gansu, P.R. China; Department of General Surgery, Lanzhou General Hospital of Chinese People's Liberation Army, Lanzhou, Gansu, P.R. China.Second Clinical Medical College, Lanzhou University, Lanzhou, Gansu, P.R. China; Department of General Surgery, Lanzhou General Hospital of Chinese People's Liberation Army, Lanzhou, Gansu, P.R. China.Second Clinical Medical College, Lanzhou University, Lanzhou, Gansu, P.R. China; Department of General Surgery, Lanzhou General Hospital of Chinese People's Liberation Army, Lanzhou, Gansu, P.R. China.Second Clinical Medical College, Lanzhou University, Lanzhou, Gansu, P.R. China; Department of General Surgery, Lanzhou General Hospital of Chinese People's Liberation Army, Lanzhou, Gansu, P.R. China.Second Clinical Medical College, Lanzhou University, Lanzhou, Gansu, P.R. China; Department of General Surgery, Lanzhou General Hospital of Chinese People's Liberation Army, Lanzhou, Gansu, P.R. China.Second Clinical Medical College, Lanzhou University, Lanzhou, Gansu, P.R. China. Electronic address: liym@lzu.edu.cn.Second Clinical Medical College, Lanzhou University, Lanzhou, Gansu, P.R. China.Second Clinical Medical College, Lanzhou University, Lanzhou, Gansu, P.R. China; Department of General Surgery, Lanzhou General Hospital of Chinese People's Liberation Army, Lanzhou, Gansu, P.R. China. Electronic address: liuhongbin999@163.com.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

30691798

Citation

Wang, Wen-Jie, et al. "A Competing Endogenous RNA Network Reveals Novel Potential lncRNA, miRNA, and mRNA Biomarkers in the Prognosis of Human Colon Adenocarcinoma." The Journal of Surgical Research, vol. 235, 2019, pp. 22-33.
Wang WJ, Li HT, Yu JP, et al. A Competing Endogenous RNA Network Reveals Novel Potential lncRNA, miRNA, and mRNA Biomarkers in the Prognosis of Human Colon Adenocarcinoma. J Surg Res. 2019;235:22-33.
Wang, W. J., Li, H. T., Yu, J. P., Han, X. P., Xu, Z. P., Li, Y. M., Jiao, Z. Y., & Liu, H. B. (2019). A Competing Endogenous RNA Network Reveals Novel Potential lncRNA, miRNA, and mRNA Biomarkers in the Prognosis of Human Colon Adenocarcinoma. The Journal of Surgical Research, 235, 22-33. https://doi.org/10.1016/j.jss.2018.09.053
Wang WJ, et al. A Competing Endogenous RNA Network Reveals Novel Potential lncRNA, miRNA, and mRNA Biomarkers in the Prognosis of Human Colon Adenocarcinoma. J Surg Res. 2019;235:22-33. PubMed PMID: 30691798.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A Competing Endogenous RNA Network Reveals Novel Potential lncRNA, miRNA, and mRNA Biomarkers in the Prognosis of Human Colon Adenocarcinoma. AU - Wang,Wen-Jie, AU - Li,Hong-Tao, AU - Yu,Jian-Ping, AU - Han,Xiao-Peng, AU - Xu,Zi-Peng, AU - Li,Yu-Min, AU - Jiao,Zuo-Yi, AU - Liu,Hong-Bin, Y1 - 2018/10/23/ PY - 2018/06/26/received PY - 2018/08/21/revised PY - 2018/09/13/accepted PY - 2019/1/30/entrez PY - 2019/1/30/pubmed PY - 2019/11/19/medline KW - Colon adenocarcinoma KW - Competing endogenous RNA network KW - Long noncoding RNAs KW - Prognosis KW - mRNA KW - microRNAs SP - 22 EP - 33 JF - The Journal of surgical research JO - J. Surg. Res. VL - 235 N2 - BACKGROUND: Accumulating evidence indicated that long noncoding RNAs (lncRNAs) have a wide range of biological functions and may play significant roles in tumorigenesis and progression. However, the understanding of its functions and related competitive endogenous RNAs (ceRNAs) networks is much less than that of protein-coding genes, particularly in colon adenocarcinoma. METHODS: We comprehensively analyzed the sequencing data of protein-coding and noncoding RNAs in colon adenocarcinoma patients from The Cancer Genome Atlas (TCGA) database. Next, we constructed colon adenocarcinoma-specific ceRNA network and evaluated the effect of these RNAs on overall survival (OS) for colon adenocarcinoma patients. RESULTS: Totally, 1138 differentially expressed lncRNAs (DElncRNAs), 245 microRNAs (DEmiRNAs), and 2081 mRNAs (DEmRNAs) were identified using a threshold of |log2FoldChange| >2.0 and adjusted P-value < 0.01. Subsequently, a colon adenocarcinoma-specific ceRNA network was successfully established with133 DElncRNAs, 29 DEmiRNAs, and 55 DEmRNAs. Among ceRNA network, seven DElncRNAs (AL590483.1, AP004609.1, ARHGEF26-AS1, HOX transcript antisense RNA (HOTAIR), ITCH-IT1, KCNQ1OT1, and LINC00491), four DEmiRNAs (hsa-mir-143, hsa-mir-183, hsa-mir-216a, and hsa-mir-424), and six DEmRNAs (FJX1, TPM2, ULBP2, PDCD4, PLAU, and SERPINE1) significantly correlated with OS (all P-value < 0.05). Notably, several interactions were highlighted in the ceRNA network, such as "KCNQ1OT1-hsa-mir-183-PDCD4", "KCNQ1OT1-hsa-mir-424-TPM2", "HOTAIR-hsa-mir-143-SERPINE1", and "ARHGEF26-AS1-hsa-mir-143-SERPINE1". CONCLUSIONS: These findings reveal several molecules might be novel important prognostic factors and potential treatment targets for colon adenocarcinoma. In addition, these observations contribute to a more comprehensive understanding of lncRNA-related ceRNA network and provide novel strategies for subsequent functional studies of lncRNAs in colon adenocarcinoma. SN - 1095-8673 UR - https://www.unboundmedicine.com/medline/citation/30691798/A_Competing_Endogenous_RNA_Network_Reveals_Novel_Potential_lncRNA_miRNA_and_mRNA_Biomarkers_in_the_Prognosis_of_Human_Colon_Adenocarcinoma_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0022-4804(18)30675-9 DB - PRIME DP - Unbound Medicine ER -