PhD Scientific Days 2018

Budapest, April 19–20, 2018

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

Kalmár, Alexandra

Alexandra Kalmár1, Zsófia Brigitta Nagy1, Orsolya Galamb2, Barnabás Wichmann2, Barbara Kinga Barták1, Gábor Valcz2, Krisztina Szigeti1, Zsolt Tulassay2, Péter Igaz2, Béla Molnár2

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Text of the abstract

Introduction: Long 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.
Aims: We aimed the perform whole genomic lncRNA expression profiling and the analysis of underlying functional interactions of aberrantly expressed lncRNAs.
Methods: lncRNA expression levels were analyzed 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 analyzed using miRNA 3.0 Array. Comprehensive lncRNA-mRNA coexpression pattern analysis was also performed.
Results: According 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 tumors, 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).
Conclusion: The defined lncRNA sets (e.g. CCAT1, UCA1) may have a regulatory role in adenoma and CRC development and in tumor 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.

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New National Excellence Program of the Ministry of Human Capacities
Young Researcher I grant (ÚNKP-17-4-I-SE-56)