Expression and DNA methylation alterations of seven cancer-associated 3p genes and their predicted regulator miRNAs (miR-129-2, miR-9-1) in breast and ovarian cancers

Irina V Pronina; Vitaly I Loginov; Alexey M Burdennyy; Marina V Fridman; Tatiana P Kazubskaya; Alexey A Dmitriev; Eleonora A Braga

doi:10.1016/j.gene.2015.10.059

Expression and DNA methylation alterations of seven cancer-associated 3p genes and their predicted regulator miRNAs (miR-129-2, miR-9-1) in breast and ovarian cancers

Gene. 2016 Jan 15;576(1 Pt 3):483-91. doi: 10.1016/j.gene.2015.10.059. Epub 2015 Oct 28.

Authors

Irina V Pronina¹, Vitaly I Loginov¹, Alexey M Burdennyy¹, Marina V Fridman¹, Tatiana P Kazubskaya², Alexey A Dmitriev³, Eleonora A Braga⁴

Affiliations

¹ Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia\
² Blokhin Cancer Research Center, 115478 Moscow, Russia.
³ Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
⁴ Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia\. Electronic address: eleonora10_45@mail.ru.

PMID: 26519551
DOI: 10.1016/j.gene.2015.10.059

Abstract

The methylation of promoter CpG islands and interactions between microRNAs (miRNAs) and messenger RNAs (mRNAs) of target genes are considered two crucial epigenetic mechanisms for inducing gene and pathway deregulation in tumors. Here, the expression levels of seven cancer-associated 3p genes (RASSF1(isoform A), RARB(isoform 2), SEMA3B, RHOA, GPX1, NKIRAS1, and CHL1) and their predicted regulator miRNAs (miR-129-2, miR-9-1) were analyzed in breast (BC, 40 samples) and ovarian (OC, 14 samples) cancers using RT-PCR and qPCR. We first revealed a negative correlation between the level of the miR-129-2 precursor and RASSF1(A) and GPX1 mRNA levels in BC (Spearman's correlation coefficient (rs) was − 0.26 in both cases). Similar results were observed for the miR-129-2 precursor and the RASSF1(A), GPX1, RARB(2), and CHL1 genes in OC (rs was in the range − 0.48 to − 0.54). Using methylation-specific PCR, a significant correlation was shown between promoter hypermethylation and the down-regulation of the RASSF1(A), GPX1, RARB(2), SEMA3B, MIR-129-2, and MIR-9-1 genes in BC (rs = 0.41 to 0.75) and of the RASSF1(A) gene in OC (rs = 0.67). We first demonstrated a high hypermethylation frequency of MIR-129-2 and SEMA3B (up to 45 to 48%) in both BC (69 samples) and OC (41 samples). Moreover, we observed a positive correlation between the hypermethylation of MIR-129-2 and the up-regulation of the RASSF1(A) and GPX1 genes in BC (rs = 0.38 and 0.42, respectively). QPCR analysis of the expression of RASSF1(A) and mature miR-129-2 in additional BC sample set (24 samples) revealed a negative correlation between them (rs = − 0.41) that strengthened the results obtained during the analysis of miR-129-2 precursor level. In summary, the obtained data indicate the involvement of methylation in the down-regulation of the studied coding and miRNA genes and suggest the involvement of miR-129-2 in the deregulation of RASSF1(A) via a direct interaction or/and mediators in common pathways (according to KEGG, Gene Ontology (FDR < 0.01), and GeneCards data) in the examined gynecological tumors.

Keywords: Cancer-associated genes; Deregulation of gene expression; Epigenetic mechanisms; Methylation of promoter CpG islands; MiRNA target genes; MiRNA–mRNA interaction pairs.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Breast Neoplasms / genetics*
Chromosomes, Human, Pair 3*
DNA Methylation*
Female
Humans
MicroRNAs / genetics*
Neoplasms / genetics*
Ovarian Neoplasms / genetics*

Substances

MIRN92 microRNA, human
MicroRNAs
Mirn129 microRNA, human