Hypermethylation in Ovarian Cancer of Long Non-Coding RNA Genes: HOTAIR, GAS5, LINC00472, LINC00886, TUG1

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Abstract

Recently, more and more data have been accumulating indicating the role of long non-coding RNAs (lncRNAs) in the regulation of biological processes in cells, as well as in the mechanisms of cancer development and progression. Aberrant methylation of promoter regions of both protein genes and lncRNA genes can disrupt their expression and functional activity. Using bioinformatics databases, six lncRNA genes (GAS5, HOTAIR, LINC00472, LINC00886, SNHG17 and TUG1) with CpG islands, differentially expressed and presumably hypermethylated in tumors of patients with ovarian cancer (OC) were selected. A statistically significant (p < 0.05) increase in the methylation level in tumours was demonstrated in a sample of 93 OC specimens using methylation-specific real-time PCR assay. Moreover, for the genes LINC00472, LINC00886, SNHG17 and TUG1, hypermethylation in OC was detected for the first time. 5 genes (except SNHG17) showed a further increase in methylation levels at a more advanced stage, and 4 genes (except SNHG17 and LINC00886) showed a significant association with metastasis. Using real-time RT-PCR, differential changes in the expression level of the GAS5, HOTAIR, SNHG17 and TUG1 genes and a significant correlation of methylation with expression for the GAS5 gene were shown. Thus, hypermethylation associated with the progression and/or development of OC was detected for six lncRNA genes, which is important for elucidating the epigenetic processes involved in the pathogenesis of OC and can be used as new biomarkers of OC.

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About the authors

A. M. Burdyonny

Institute of General Pathology and Pathophysiology

Author for correspondence.
Email: burdennyy@gmail.com
Russian Federation, Moscow

S. S. Lukina

Institute of General Pathology and Pathophysiology

Email: burdennyy@gmail.com
Russian Federation, Moscow

L. A. Uroshlev

Vavilov Institute of General Genetics of the Russian Academy of Sciences

Email: burdennyy@gmail.com
Russian Federation, Moscow

E. A. Filippova

Institute of General Pathology and Pathophysiology

Email: burdennyy@gmail.com
Russian Federation, Moscow

I. V. Pronina

Institute of General Pathology and Pathophysiology

Email: burdennyy@gmail.com
Russian Federation, Moscow

M. V. Fridman

Vavilov Institute of General Genetics of the Russian Academy of Sciences

Email: burdennyy@gmail.com
Russian Federation, Moscow

K. I. Zhordania

Blokhin National Medical Research Center of Oncology

Email: burdennyy@gmail.com
Russian Federation, Moscow

T. P. Kazubskaya

Blokhin National Medical Research Center of Oncology

Email: burdennyy@gmail.com
Russian Federation, Moscow

N. E. Kushlinsky

Blokhin National Medical Research Center of Oncology

Email: burdennyy@gmail.com
Russian Federation, Moscow

V. I. Loginov

Institute of General Pathology and Pathophysiology

Email: burdennyy@gmail.com
Russian Federation, Moscow

E. A. Braga

Institute of General Pathology and Pathophysiology; Research Centre for Medical Genetics

Email: eleonora10_45@mail.ru
Russian Federation, Moscow; Moscow

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2. Fig. 1. Comparison of methylation levels of six dnRNA genes (GAS5, HOTAIR, LINC00472, LINC00886, SNHG17 and TUG1) in 93 RN tumour samples and in 75 paired samples of conditional normal; calculated using the non-parametric Mann-Whitney criterion, shown as a heat map

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3. Fig. 2. Increased methylation levels of five dnRNA genes (GAS5, HOTAIR, LINC00472, LINC00886 and TUG1) at later clinical stages (III-IV (51 samples) vs. I-II (42 samples)). On the abscissa axis, disease stage

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4. Fig. 3. Increased dnRNA gene methylation level (GAS5, HOTAIR, LINC00472, TUG1) in primary tumours of RN patients with metastases (56 samples) compared to tumour samples of patients without metastases (37 samples). Abscissa axis - presence or absence of metastases

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5. Fig. 4. Expression level change profile of GAS5, HOTAIR, SNHG17 and TUG1 dnRNA expression levels in a sample of 36-53 RN samples relative to the conditional normal range

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6. Fig. 5. Negative correlation between changes in methylation levels and GAS5 gene expression (in 53 paired RN samples); Spearman's correlation coefficient is plotted: rs = -0.47, p < 0.001

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