Identification of key lncRNAs in the carcinogenesis and progression of colon adenocarcinoma by co-expression network analysis
- PMID: 30430631
- DOI: 10.1002/jcb.27940
Identification of key lncRNAs in the carcinogenesis and progression of colon adenocarcinoma by co-expression network analysis
Abstract
Colon adenocarcinoma (COAD) is one of the most common cancers, and its carcinogenesis and progression is influenced by multiple long non-coding RNAs (lncRNA), especially through the miRNA sponge effect. In this study, more than 4000 lncRNAs were re-annotated from the microarray datasets through probe sequence mapping to obtain reliable lncRNA expression profiles. As a systems biology method for describing the correlation patterns among genes across microarray samples, weighted gene co-expression network analysis was conducted to identify lncRNA modules associated with the five stepwise stages from normal colonic samples to COAD (n = 94). In the most relevant module (R2 = -0.78, P = 4E-20), four hub lncRNAs were identified (CTD-2396E7.11, PCGF5, RP11-33O4.1, and RP11-164P12.5). Then, these four hub lncRNAs were validated using two other independent datasets including GSE20916 (n = 145) and GSE39582 (n = 552). The results indicated that all hub lncRNAs were significantly negatively correlated with the three-stage colonic carcinogenesis, as well as TNM stages in COAD (one-way analysis of variance P < 0.05). Kaplan-Meier survival curve showed that patients with higher expression of each hub lncRNA had a significantly higher overall survival rate and lower relapse risk (log-rank P < 0.05). In conclusion, through co-expression analysis, we identified and validated four key lncRNAs in association with the carcinogenesis and progression of COAD, and these lncRNAs might have important clinical implications for improving the risk stratification, therapeutic decision and prognosis prediction in COAD patients.
Keywords: carcinogenesis; colon adenocarcinoma (COAD); lncRNAs; progression; weighted gene co-expression network analysis (WGCNA).
© 2018 Wiley Periodicals, Inc.
Similar articles
-
The tale of SOX2: Focusing on lncRNA regulation in cancer progression and therapy.Life Sci. 2024 May 1;344:122576. doi: 10.1016/j.lfs.2024.122576. Epub 2024 Mar 14. Life Sci. 2024. PMID: 38492918 Review.
-
Long non-coding RNAs in recurrent ovarian cancer: Theranostic perspectives.Cancer Lett. 2021 Apr 1;502:97-107. doi: 10.1016/j.canlet.2020.12.042. Epub 2021 Jan 8. Cancer Lett. 2021. PMID: 33429007 Review.
-
Identification of hub genes and construction of transcriptional regulatory network for the progression of colon adenocarcinoma hub genes and TF regulatory network of colon adenocarcinoma.J Cell Physiol. 2020 Mar;235(3):2037-2048. doi: 10.1002/jcp.29067. Epub 2019 Oct 14. J Cell Physiol. 2020. PMID: 31612481 Free PMC article.
-
Identification of long noncoding RNAs biomarkers for diagnosis and prognosis in patients with colon adenocarcinoma.J Cell Biochem. 2019 Mar;120(3):4121-4131. doi: 10.1002/jcb.27697. Epub 2018 Sep 30. J Cell Biochem. 2019. PMID: 30269368
-
Analysis of lncRNA-Associated ceRNA Network Reveals Potential lncRNA Biomarkers in Human Colon Adenocarcinoma.Cell Physiol Biochem. 2018;49(5):1778-1791. doi: 10.1159/000493623. Epub 2018 Sep 19. Cell Physiol Biochem. 2018. PMID: 30231249
Cited by
-
A human stomach cell type transcriptome atlas.BMC Biol. 2024 Feb 14;22(1):36. doi: 10.1186/s12915-024-01812-5. BMC Biol. 2024. PMID: 38355543 Free PMC article.
-
Interactions Networks for Primary Heart Sarcomas.Cancers (Basel). 2021 Aug 1;13(15):3882. doi: 10.3390/cancers13153882. Cancers (Basel). 2021. PMID: 34359782 Free PMC article.
-
LncRNA AC079630.4 expression associated with the progression and prognosis in lung cancer.Aging (Albany NY). 2021 Jul 19;13(14):18658-18668. doi: 10.18632/aging.203310. Epub 2021 Jul 19. Aging (Albany NY). 2021. PMID: 34282054 Free PMC article.
-
Identification of Hub Genes and Construction of a Transcriptional Regulatory Network Associated With Tumor Recurrence in Colorectal Cancer by Weighted Gene Co-expression Network Analysis.Front Genet. 2021 Apr 7;12:649752. doi: 10.3389/fgene.2021.649752. eCollection 2021. Front Genet. 2021. PMID: 33897765 Free PMC article.
-
Identification of key lncRNAs in the tumorigenesis of intraductal pancreatic mucinous neoplasm by coexpression network analysis.Cancer Med. 2020 Jun;9(11):3840-3851. doi: 10.1002/cam4.2927. Epub 2020 Apr 2. Cancer Med. 2020. PMID: 32239802 Free PMC article.
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Research Materials