PO-377 Whole transcriptome analysis reveals colorectal cancer-associated long non-coding RNAs including UCA1 already dysregulated in colorectal adenomas

Abstract

IntroductionLong non-coding RNAs (lncRNAs) play role in colorectal cancer (CRC) development, however, lncRNA expression profile in colorectal adenomas and CRC and its relation to the epigenetic regulatory system still remain incomplete.Material and methodsWe aimed the perform whole genomic lncRNA expression profiling and the analysis of underlying functional interactions of aberrantly expressed lncRNAs. lncRNA expression levels were analysed on 60 colonic biopsy samples (20 CRCs, 20 adenomas, 20 normals) by Human Transcriptome Array (HTA) 2.0. Expression alteration of certain candidates was verified by qPCR. Furthermore, in silico validation was performed on HGU133 Plus 2.0 array data and also on TCGA COAD dataset. miRNA targets of lncRNAs were predicted with the miRCODE algorithm and miRNA expression was analysed using miRNA 3.0 Array. Comprehensive lncRNA-mRNA coexpression pattern analysis was also performed.Results and discussionsAccording to HTA results in adenomas 12 lncRNAs (e.g. LINC00278) were upregulated and 6 lncRNAs (e.g. RP11.747D18.1) were downregulated compared to normals, while in CRCs 1 lncRNA (UCA1) was overexpressed and 8 lncRNAs (e.g. LINC00350) were underexpressed compared to adenomas (p<0.05; −2≥Fc≥2). In CRC samples 8 lncRNAs (e.g. AC123023.1) were overexpressed and 9 lncRNAs (e.g. RP13-497K6.1) were downregulated compared to normals. 42% of lncRNAs upregulated in CRC samples showed elevated expression (p<0.05) already in adenomas (e.g. overexpressed CCAT1, downregulated LINC01133). In line with aberrant expression of certain lncRNAs in tumours, miRNA and mRNA targets’ expression showed systematic alterations, e.g. UCA1 upregulation in CRC samples in parallel with miR-1 downregulation accompanied by CMET target mRNA overexpression (p<0.05).ConclusionThe defined lncRNA sets (e.g. CCAT1, UCA1) may have a regulatory role in adenoma and CRC development and in tumour cell growth pathways. A subset of CRC-associated lncRNAs showed significant differential expression in precancerous samples, that raise the possibility to develop potential adenoma-specific markers and achieve early detection of colon lesions.