Screening key long non-coding RNAs in early-stage colon adenocarcinoma by RNA-sequencing

Epigenomics. 2018 Sep;10(9):1215-1228. doi: 10.2217/epi-2017-0155. Epub 2018 Sep 5.

Abstract

Aim: We aim to identify the key long noncoding RNAs (lncRNAs) in early-stage colon adenocarcinoma (COAD).

Patients & methods: Compared with colonic intraepithelial neoplasia, differentially expressed lncRNAs (DElncRNAs) in early-stage COAD were obtained by RNA-sequencing. Our previous work has obtained the differentially expressed mRNAs and miRNAs (DEmRNAs and DEmiRNAs) in early-stage COAD. DEmiRNA-DElncRNA-DEmRNA interaction analysis and functional annotation were performed. Validation of expression and receiver-operating characteristic analyses were performed based on The Cancer Genome Atlas.

Results: Seventy-nine significantly DElncRNAs in early-stage COAD were obtained. MiR-153-3p-TUG1-DAPK1/ARNT2/KLK3/PLD1/SMAD2 and miR-153-3p-SNHG17-COL11A1/IGFBP3/KLF6 interactions were associated with early-stage COAD. Five DElncRNAs (ELFN1-AS1, LINC01234, SNHG17, UCA1 and LOC101929549) involved in early-stage COAD with potential diagnostic value.

Conclusion: LncRNAs involve in early-stage COAD by interaction with COAD-regulated genes and miRNAs.

Keywords: RNA-sequencing; biomarker; colonic intraepithelial neoplasia; early-stage colon adenocarcinoma; long noncoding RNA (lncRNA); mRNA; miRNA.

MeSH terms

  • Adenocarcinoma / diagnosis*
  • Adenocarcinoma / genetics
  • Biomarkers, Tumor / genetics*
  • Colonic Neoplasms / diagnosis*
  • Colonic Neoplasms / genetics
  • Computational Biology
  • Databases, Genetic
  • Early Detection of Cancer / methods*
  • Gene Expression Profiling
  • Gene Expression Regulation, Neoplastic
  • Gene Regulatory Networks
  • Humans
  • MicroRNAs / genetics
  • RNA, Long Noncoding / genetics*
  • RNA, Messenger / genetics
  • Sequence Analysis, RNA / methods

Substances

  • Biomarkers, Tumor
  • MicroRNAs
  • RNA, Long Noncoding
  • RNA, Messenger