Aim: The goal of this study is to identify differentially methylated (DM) loci associated with long noncoding RNA (lncRNA)/mRNA expression in non-small-cell lung cancer (NSCLC).
Materials & methods: Microarrays were used to interrogate genome-wide methylation and expression of lncRNA/mRNA in NSCLC.
Results: We identified 113,644 DM loci between tumors and adjacent tissues. Among them, 26,310 DM loci were associated with 1685 differentially expressed genes, and 839 genes had significant correlations between methylation and expression, of which 26 hypermethylated loci in transcription start site 200 were correlated with low gene expression. We validated the correlations between methylation and expression in five genes (CDO1, C2orf40, SCARF1, ZFP106 and IFFO1) using pyrosequencing and quantitative polymerase chain reaction. We also found significant correlations between lncRNAs and mRNAs, and validated four of the correlations with quantitative polymerase chain reaction.
Conclusion: Integrated analysis of genome-wide DNA methylation and lncRNA/mRNA expression allows us to identify new DM loci-correlated with gene expression in NSCLC.
Keywords: genome-wide methylation; long noncoding RNA; lung cancer; microarray expression.
Genome-wide analysis of long noncoding RNA (lncRNA) expression in hepatoblastoma tissues.PLoS One. 2014 Jan 17;9(1):e85599. doi: 10.1371/journal.pone.0085599. eCollection 2014. PLoS One. 2014. PMID: 24465615 Free PMC article.
Study on expression of lncRNA RGMB-AS1 and repulsive guidance molecule b in non-small cell lung cancer.Diagn Pathol. 2015 Jun 9;10:63. doi: 10.1186/s13000-015-0297-x. Diagn Pathol. 2015. PMID: 26055877 Free PMC article.
Aberrant expression of long noncoding RNAs in cumulus cells isolated from PCOS patients.J Assist Reprod Genet. 2016 Jan;33(1):111-21. doi: 10.1007/s10815-015-0630-z. Epub 2015 Dec 9. J Assist Reprod Genet. 2016. PMID: 26650608 Free PMC article.
Global DNA methylation profiling reveals new insights into epigenetically deregulated protein coding and long noncoding RNAs in CLL.Clin Epigenetics. 2016 Oct 12;8:106. doi: 10.1186/s13148-016-0274-6. eCollection 2016. Clin Epigenetics. 2016. PMID: 27777635 Free PMC article.
Integrative analysis identified mediation effects of lncRNAs on the correlations between methylation and mRNA.Int J Biochem Cell Biol. 2018 Nov;104:66-72. doi: 10.1016/j.biocel.2018.09.005. Epub 2018 Sep 15. Int J Biochem Cell Biol. 2018. PMID: 30227253
Cited by 2 articles
Long non-coding RNA cartilage injury-related promotes malignancy in bladder cancer.Oncol Lett. 2018 Mar;15(3):3049-3055. doi: 10.3892/ol.2017.7678. Epub 2017 Dec 21. Oncol Lett. 2018. PMID: 29435036 Free PMC article.
Evaluation of Post-Mortem Effects on Global Brain DNA Methylation and Hydroxymethylation.Basic Clin Pharmacol Toxicol. 2018 Feb;122(2):208-213. doi: 10.1111/bcpt.12875. Epub 2017 Nov 13. Basic Clin Pharmacol Toxicol. 2018. PMID: 28834189 Free PMC article.