Dysregulation of Long Non-coding RNAs in Glioblastoma Multiforme and Their Study Through Use of Modern Molecular-Genetic Approaches
Authors:
M. Večeřa 1; J. Šána 1; R. Bútová 1; Š. Reguli 2; M. Hermanová 3; L. Křen 4; R. Lipina 2; M. Smrčka 5; O. Slabý 1
Authors‘ workplace:
CEITEC – Středoevropský technologický institut, MU, Brno
1; Neurochirurgická klinika LF UO a FN Ostrava
2; I. patologicko-anatomický ústav, LF MU a FN u sv. Anny v Brně
3; Ústav patologie, LF MU a FN Brno
4; Neurochirurgická klinika LF MU a FN Brno
5
Published in:
Klin Onkol 2018; 31(Supplementum1): 168-170
Category:
Article
Overview
Background:
Glioblastoma (GBM) is the most frequent primary brain tumor characterized by an unfavourable prognosis despite multimodal therapy. Therefore, a lot of efforts and financial resources are dedicated to the research of new therapeutic targets and prognostic or predictive biomarkers. Long non-coding RNAs (lncRNAs) are regulators of gene expression which play a significant role in GBM pathology and, thus, present promising candidates.
Material and Methods:
Our study included 14 patients with GBM and 8 patients with intractable epilepsy from whom we acquired brain tissues during surgical intervention. Ribosomal RNA depleted RNA was used for sequencing by NextSeq 500 instrument (Illumina). Statistical analysis evaluated 24,087 protein-coding and 8,414 non-coding RNAs and their sequential variants with non-zero reads per kilobase per million mapped reads (RPKM) at least in one sample. CLC Genomic Workbench was used for the alignment and target counts. Targeted downregulation of up-regulated ZFAS1, one of the identified lncRNA, level has been carried out by the transient transfection of specific small interfering RNA (siRNA) in GBM stable cell lines (A172, U87MG, T98G). The success of transfection and viability were analyzed in vitro using quantitative real time polymerase chain reaction and MTT assay, resp.
Results:
Statistical analysis has revealed 274 (p < 0.01) dysregulated lncRNAs in GBMs in comparison with non-tumor brain tissues. Moreover, the results have showed 489 dysregulated mRNAs (p < 0.0001) and 26 mRNAs (p < 0.000001). Transfection of ZFAS1 inhibitor led to successful downregulation of ZFAS1 expression level, although it did not have a significant effect on proliferation of GBM cells.
Conclusion:
We described a significant dysregulation of lncRNAs and mRNAs in GBM tissue in comparison with non-tumor tissue. We also succesfully decreased expression level of ZFAS1, which in turn, however, had no impact on the viability of GBM cell lines.
Key words:
glioblastoma – long non-coding RNA – next-generation sequencing
The authors declare they have no potential conflicts of interest concerning drugs, products, or services used in the study.
The Editorial Board declares that the manuscript met the ICMJE recommendation for biomedical papers.
This tudy was supported by Ministry of Health of the Czech Republic, grant No. 15-33158A. All rights reserved.
Submitted:
19. 3. 2018
Accepted:
10. 4. 2018
Sources
1. Delgado-López PD, Corrales-García EM. Survival in glioblastoma: a review on the impact of treatment modalities. Clin Transl Oncol 2016; 18 (11): 1062–1071. doi: 10.1007/s12094-016-1497-x.
2. Stupp R, Hegi ME, Mason WP et al. Effects of radiotherapy with concomitant and adjuvant temozolomide versus radiotherapy alone on survival in glioblastoma in a randomised phase III study: 5-year analysis of the EORTC-NCIC trial. Lancet Oncol 2009; 10 (5): 459–466. doi: 10.1016/S1470-2045 (09) 70025-7.
3. Lakomy R, Fadrus P, Slampa P et al. Multimodal treatment of glioblastoma multiforme: results of 86 consecutive patients diagnosed in period 2003–2009. Klin Onkol 2011; 24 (2): 112–120.
4. Ohgaki H, Kleihues P. The definition of primary and secondary glioblastoma. Clin Cancer Res 2013; 19 (4): 764–772. doi: 10.1158/1078-0432.CCR-12-3002.
5. Verhaak RG, Hoadley KA, Purdom E et al. Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell 2010; 17 (1): 98–110. doi: 10.1016/j.ccr.2009.12.020.
6. Agnihotri S, Gajadhar AS, Ternamian C et al. Alkylpurine-DNA-N-glycosylase confers resistance to temozolomide in xenograft models of glioblastoma multiforme and is associated with poor survival in patients. J Clin Invest 2012; 122 (1): 253–266. doi: 10.1172/JCI59334.
7. Lee SY. Temozolomide resistance in glioblastoma multiforme. Genes Dis 2016; 3: 198–210. doi: 10.1016/j.gendis.2016.04.007.
8. Sanson M, Marie Y, Paris S et al. Isocitrate dehydrogenase 1 codon 132 mutation is an important prognostic biomarker in gliomas. J Clin Oncol 2009; 27 (25): 4150–4154. doi: 10.1200/JCO.2009.21.9832.
9. Iyer MK, Niknafs YS, Malik R et al. The landscape of long noncoding RNAs in the human transcriptome. Nat Genet 2015; 47 (3): 199–208. doi: 10.1038/ng.3192.
10. Derrien T, Johnson R, Bussotti G et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 2012; 22 (9): 1775–1789. doi: 10.1101/gr.132159.111.
11. Zhang XQ, Sun S, Lam KF et al. A long non-coding RNA signature in glioblastoma multiforme predicts survival. Neurobiol Dis 2013; 58: 123–131. doi: 10.1016/j.nbd.2013.05.011.
12. Zhang XQ, Kiang KM, Wang YC et al. IDH1 mutation-associated long non-coding RNA expression profile changes in glioma. J Neurooncol 2015; 125 (2): 253–263. doi: 10.1007/s11060-015-1916-9.
13. Wang Q, Zhang J, Liu Y et al. A novel cell cycle-associated lncRNA, HOXA11-AS, is transcribed from the 5-prime end of the HOXA transcript and is a biomarker of progression in glioma. Cancer Lett 2016; 373 (2): 251–259. doi: 10.1016/j.canlet.2016.01.039.
14. Wang P, Ren Z, Sun P. Overexpression of the long non-coding RNA MEG3 impairs in vitro glioma cell proliferation. J Cell Biochem 2012; 113 (6): 1868–1874. doi: 10.1002/jcb.24055.
Labels
Paediatric clinical oncology Surgery Clinical oncologyArticle was published in
Clinical Oncology
2018 Issue Supplementum1
Most read in this issue
- MicroRNA Analysis for Extramedullary Multiple Myeloma Relapse
- Flow Cytometric Analysis of Nucleoside Transporters Activity in Chemoresistant Prostate Cancer Model
- A Development and Overview of the Use of Chemotherapy and the Role of Radiotherapy and Surgery in Patients with Newly Diagnosed Pancreatic Tumor and Cancer in the Current 5-year Center Practice
- Can Analysis of Cellular Lipidome Contribute to Discrimination of Tumour and Non-tumour Colon Cells?