Methylation of the genes for the microRNAs miR-129-2 and miR-9-1, changes in their expression, and activation of their potential target genes in clear cell renal cell carcinoma

Methylation of promoter CpG islands and microRNA (miRNA) interactions with mRNAs of target genes are epigenetic mechanisms that play a crucial role in deregulation of gene expression and signaling pathways in tumors. Altered expression of six chromosome 3p genes ( RARB(2), SEMA3B, RHOA, GPX1, NKIRAS...

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Published in:Molecular biology (New York) 2017, Vol.51 (1), p.61-71
Main Authors: Pronina, I. V., Klimov, E. A., Burdennyy, A. M., Beresneva, E. V., Fridman, M. V., Ermilova, V. D., Kazubskaya, T. P., Karpukhin, A. V., Braga, E. A., Loginov, V. I.
Format: Article
Language:English
Subjects:
Biochemistry
Biomedical and Life Sciences
DNA methylation
Epigenetics
Gene expression
Human Genetics
Kidney cancer
Life Sciences
MicroRNAs
Molecular Cell Biology
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Summary:Methylation of promoter CpG islands and microRNA (miRNA) interactions with mRNAs of target genes are epigenetic mechanisms that play a crucial role in deregulation of gene expression and signaling pathways in tumors. Altered expression of six chromosome 3p genes ( RARB(2), SEMA3B, RHOA, GPX1, NKIRAS1 , and CHL1 ) and two miRNA genes ( MIR-129-2 and MIR-9-1 ) was observed in primary clear cell renal cell carcinomas (ccRCCs, 31–48 samples) by RT-PCR and qPCR. Significant downregulation ( p < 0.05, Fisher’s exact test) was observed for SEMA3B, NKIRAS1, and CHL1 ; and differential expression, for the other chromosome 3p and miRNA genes. Methylation-specific PCR with primers to RARB(2), SEMA3B, MIR-129-2 , and MIR-9-1 showed that their methylation frequency was significantly ( p < 0.05, Fisher’s exact test) elevated in the ccRCC samples. Significant correlations between promoter methylation and expression were confirmed for SEMA3B and observed for the first time for RARB(2), GPX1 , and MIR-129-2 in ccRCC (Spearman’s correlation coefficient r s ranging 0.31–0.60, p < 0.05). The MIR-129-2 and RARB(2) methylation frequencies significantly correlated with ccRCC progression. MIR-129-2 methylation correlated with upregulation of RARB(2), RHOA, NKIRAS1, and CHL1 ( r s ranging 0.35–0.53, p < 0.05). The findings implicate methylation in regulating RARB(2), SEMA3B, GPX1 , and MIR-129-2 and indicate that miR-129-2 and methylation of its gene affect RARB(2), RHOA, NKIRAS1 , and CHL1 expression.
ISSN:0026-8933
1608-3245
DOI:10.1134/S0026893316060169