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Comprehensive Analysis of Differentially Expressed Profiles of lncRNAs/mRNAs and miRNAs with Associated ceRNA Networks in Triple-Negative Breast Cancer.
Cell Physiol Biochem. 2018; 50(2):473-488.CP

Abstract

BACKGROUND/AIMS

Triple-negative breast cancer (TNBC) is a subtype of highly malignant breast cancer with poor prognosis. Growing evidence indicates that Long noncoding RNAs (lncRNAs) play important regulatory roles in the development and progression of a variety of cancers including breast cancer. However, the underlying mechanisms remain largely unknown.

METHODS

Here, we compared the expression profiles of mRNAs, lncRNAs and miRNAs between 111 TNBC tissues and 104 non-cancerous tissues utilizing RNA-Seq Data from The Cancer Genome Atlas (TCGA). Gene Ontology and KEGG pathway enrichment analyses were executed to investigate the principal functions of the significantly dysregulated mRNAs. Moreover, Kaplan-Meier survival analyses were performed to determine the effects of differentially expressed lncRNAs/mRNAs/miRNAs on overall survival. Subsequently, we constructed a competing endogenous RNA (ceRNA) network, which included 66 dysregulated lncRNAs, 24 miRNAs and 55 mRNAs. The four dysregulated lncRNAs, three aberrantly expressed miRNAs and four mRNAs were confirmed in the ceRNA network by qRT-PCR in 30 pairs of samples, respectively.

RESULTS

A total of 1441 lncRNAs, 114 miRNA and 2501 mRNAs were found to be differentially expressed in TNBC tissues compared with controls. 109 lncRNAs and 124 mRNAs might serve as prognostic signature for patients with TNBC according to the survival analysis. Functional analysis revealed that 19 mRNAs in the ceRNA network were enriched in 17 cancer-related pathways.

CONCLUSION

Taken together, we identified novel lncRNAs/miRNAs which may serve as potential biomarkers to predict the survival and therapeutic targets for TNBC patients based on a large-scale sample. More importantly, we constructed the ceRNA network of TNBC, which provides valuable information to further explore the molecular mechanism underlying tumorigenesis and development of TNBC.

Authors+Show Affiliations

Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, China.Department of Endocrine and breast surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, China.Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, China.Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, China.Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, China.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

30308479

Citation

Yang, Rui, et al. "Comprehensive Analysis of Differentially Expressed Profiles of lncRNAs/mRNAs and miRNAs With Associated ceRNA Networks in Triple-Negative Breast Cancer." Cellular Physiology and Biochemistry : International Journal of Experimental Cellular Physiology, Biochemistry, and Pharmacology, vol. 50, no. 2, 2018, pp. 473-488.
Yang R, Xing L, Wang M, et al. Comprehensive Analysis of Differentially Expressed Profiles of lncRNAs/mRNAs and miRNAs with Associated ceRNA Networks in Triple-Negative Breast Cancer. Cell Physiol Biochem. 2018;50(2):473-488.
Yang, R., Xing, L., Wang, M., Chi, H., Zhang, L., & Chen, J. (2018). Comprehensive Analysis of Differentially Expressed Profiles of lncRNAs/mRNAs and miRNAs with Associated ceRNA Networks in Triple-Negative Breast Cancer. Cellular Physiology and Biochemistry : International Journal of Experimental Cellular Physiology, Biochemistry, and Pharmacology, 50(2), 473-488. https://doi.org/10.1159/000494162
Yang R, et al. Comprehensive Analysis of Differentially Expressed Profiles of lncRNAs/mRNAs and miRNAs With Associated ceRNA Networks in Triple-Negative Breast Cancer. Cell Physiol Biochem. 2018;50(2):473-488. PubMed PMID: 30308479.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Comprehensive Analysis of Differentially Expressed Profiles of lncRNAs/mRNAs and miRNAs with Associated ceRNA Networks in Triple-Negative Breast Cancer. AU - Yang,Rui, AU - Xing,Lei, AU - Wang,Min, AU - Chi,Hong, AU - Zhang,Luyu, AU - Chen,Junxia, Y1 - 2018/10/11/ PY - 2018/01/29/received PY - 2018/10/02/accepted PY - 2018/10/12/pubmed PY - 2018/11/6/medline PY - 2018/10/12/entrez KW - Expression profiles KW - Triple-negative breast cancer KW - ceRNA KW - lncRNA KW - miRNA SP - 473 EP - 488 JF - Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology JO - Cell Physiol Biochem VL - 50 IS - 2 N2 - BACKGROUND/AIMS: Triple-negative breast cancer (TNBC) is a subtype of highly malignant breast cancer with poor prognosis. Growing evidence indicates that Long noncoding RNAs (lncRNAs) play important regulatory roles in the development and progression of a variety of cancers including breast cancer. However, the underlying mechanisms remain largely unknown. METHODS: Here, we compared the expression profiles of mRNAs, lncRNAs and miRNAs between 111 TNBC tissues and 104 non-cancerous tissues utilizing RNA-Seq Data from The Cancer Genome Atlas (TCGA). Gene Ontology and KEGG pathway enrichment analyses were executed to investigate the principal functions of the significantly dysregulated mRNAs. Moreover, Kaplan-Meier survival analyses were performed to determine the effects of differentially expressed lncRNAs/mRNAs/miRNAs on overall survival. Subsequently, we constructed a competing endogenous RNA (ceRNA) network, which included 66 dysregulated lncRNAs, 24 miRNAs and 55 mRNAs. The four dysregulated lncRNAs, three aberrantly expressed miRNAs and four mRNAs were confirmed in the ceRNA network by qRT-PCR in 30 pairs of samples, respectively. RESULTS: A total of 1441 lncRNAs, 114 miRNA and 2501 mRNAs were found to be differentially expressed in TNBC tissues compared with controls. 109 lncRNAs and 124 mRNAs might serve as prognostic signature for patients with TNBC according to the survival analysis. Functional analysis revealed that 19 mRNAs in the ceRNA network were enriched in 17 cancer-related pathways. CONCLUSION: Taken together, we identified novel lncRNAs/miRNAs which may serve as potential biomarkers to predict the survival and therapeutic targets for TNBC patients based on a large-scale sample. More importantly, we constructed the ceRNA network of TNBC, which provides valuable information to further explore the molecular mechanism underlying tumorigenesis and development of TNBC. SN - 1421-9778 UR - https://www.unboundmedicine.com/medline/citation/30308479/Comprehensive_Analysis_of_Differentially_Expressed_Profiles_of_lncRNAs/mRNAs_and_miRNAs_with_Associated_ceRNA_Networks_in_Triple_Negative_Breast_Cancer_ DB - PRIME DP - Unbound Medicine ER -