Abstract 990: Key tumor growth controlling long non-coding RNA (lncRNA) expression alterations in the colorectal adenoma-carcinoma sequence
Authors: Kalmar Alexandra , Nagy Zsofia B. , Galamb Orsolya , Wichmann Barnabas , Bartak Barbara K. , Tulassay Zsolt , Molnar Bela 
Published: July 2016

Background: Long non-coding RNAs may play role in colorectal cancer (CRC) development, however, lncRNA expression profile in the colorectal adenoma-carcinoma sequence (C-ACS) and its relation to the complex epigenetic regulation system still remain incomplete.

Aims: We aimed the whole genomic lncRNA expression profiling with up- and downstream epigenetic analyses of the C-ACS in order to explore the underlying mechanisms and consequences of aberrantly expressed lncRNAs.

Materials&methods: lncRNA expression levels were analyzed on 60 colonic biopsy samples (20 CRCs, 20 adenomas, 20 normals) by Human Transcriptome Array (HTA) 2.0 (Affymetrix). Data analysis was perfomed using Expression Console and Transcriptome Analysis Console. Expression of certain candidates was verified in silico on HGU133 Plus 2.0 array data and also by qRT-PCR. DNA methylation status of lncRNA promoter regions was studied by methyl-capture sequencing. miRNA targets of lncRNAs were predicted with miRCODE algorithm and miRNA expression was analysed using GeneChip miRNA 3.0 Array. In the respective regulatory networks mRNA expression changes were also evaluated on the basis of the above-mentioned whole genome expression arrays.

Results: According to HTA results analyzing 40.914 non-coding transcripts on whole genome level, in adenomas 12 lncRNAs (e.g. CCAT1, LINC00278) were significantly upregulated and 6 lncRNAs (e.g.FLJ22763, RP11.747D18.1) were downregulated compared to the healthy controls, while in CRC samples 1 lncRNA (UCA1) was overexpressed and 8 lncRNAs (e.g. LINC00350, LINC00261) were underexpressed compared to adenomas (p&lt;0.05; -2≥Fold change≥2). In CRC samples 8 lncRNAs (e.g. MACC1, AC123023.1) were upregulated and 11 lncRNAs (e.g. RP13-497K6.1) were downregulated compared to normal controls. Furthermore, 42% of lncRNAs upregulated in CRC samples showed significantly elevated expression (p&lt;0.05) already in adenoma samples (e.g. LINC350, CCAT1 were upregulated and LINC01133, FLJ22763 were downregulated compared to healthy controls). Promoter DNA methylation showed inverse relation with lncRNA expression along the C-ACS (e.g. CCAT1). In line with aberrant lncRNA expression in tumors, miRNA and mRNA targets’ expression showed systematic alterations, e.g. UCA1 upregulation in CRC samples in parallel with miR-1 downregulation accompanied by MET proto-oncogene target mRNA overexpression (p&lt;0.05).

Conclusion: The defined lncRNA sets (including MACC1, CCAT1, UCA1) have a central regulatory role in colorectal adenoma development and in tumor cell growth pathways. The underlying DNA methylation changes and miRNA and mRNA target expression alterations were proven using whole genomic array technologies. The identified lncRNA candidate sets can be further investigated as early diagnostic biomarkers and as potential therapeutic molecular targets for CRC.

Citation Format: Alexandra Kalmar, Zsofia B. Nagy, Orsolya Galamb, Barnabas Wichmann, Barbara K. Bartak, Zsolt Tulassay, Bela Molnar. Key tumor growth controlling long non-coding RNA (lncRNA) expression alterations in the colorectal adenoma-carcinoma sequence. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 990.