Expression profile analysis of long non-coding RNA associated with vincristine resistance in colon cancer cells by next-generation sequencing

• Published in: Gene 2015-11, Vol.572 (1), p.79-86
• Main Authors: Sun, Qiu-Li, Zhao, Chun-Peng, Wang, Tian-Yun, Hao, Xiao-Bo, Wang, Xiao-Yin, Zhang, Xi, Li, Yi-Chun
• Format: Article
• Language: English
• Subjects: Cell Line, Tumor; Colon cancer; Colonic Neoplasms - drug therapy; Colonic Neoplasms - genetics; Colonic Neoplasms - metabolism; Drug resistance; Drug Resistance, Neoplasm - genetics; Gene Expression Profiling; Gene Ontology; HCT-8; High-Throughput Nucleotide Sequencing; Humans; lncRNA; Next-generation sequencing; RNA, Long Noncoding - genetics; RNA, Long Noncoding - metabolism; RNA, Neoplasm - genetics; RNA, Neoplasm - metabolism; Sequence Analysis, RNA; Vincristine - pharmacology
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2015.06.087

Vincristine (VCR) is widely used in tumor treatment. However, long-term use of this drug can make tumor cells resistant to it. Furthermore, the mechanisms underlying resistance development are unclear. The aim of this study was to investigate the long non-coding RNAs (lncRNAs) associated with colon cancer drug resistance using next-generation sequencing. A cDNA library of HCT-8 VCR-resistant colon cancer cell was established through PCR amplification. Using HiSeq 2500 sequencing and bioinformatic methods, we identified lncRNAs showing different expression levels in drug-resistant and non-resistant cells, and constructed expression profiles of the lncRNA differences. The pretreatment of data was quality controlled using FastQC software. Transcription of lncRNA was calculated using Fragments Per Kilobase of transcript per Million fragments mapped (FPKM). To reveal the potential functions of these lncRNAs, we applied GO analysis to study the differentially expressed lncRNAs. Total transcript number was higher in resistant cells than in non-resistant colon cancer cells, and high-quality transcripts constituted the major portion of the total. In addition, 121 transcripts showed significantly different expression in VCR-resistant and non-resistant cells. Of these, we observed 23 up-regulated and 20 down-regulated lncRNAs (fold change >10.0). This is the first report of the expression profile of lncRNA of VCR-resistant colon cancer cells. Abnormal lncRNA expression was associated with VCR resistance in colon cancer cells and these expression differences may play a key role in VCR resistance of these cells. •LncRNAs associated with colon cancer drug resistance were investigated.•LncRNA expression was investigated using next-generation sequencing.•Abnormal lncRNA expression was associated with VCR resistance in colon cancer cells.