Recently, a wealth of data have been accumulating on the role of long non-coding RNAs (lncRNAs) in the fine-tuning of mRNA expression. Four new lncRNAs, namely, TMEM92-AS1, FAM222A-AS, TXLNB, and ...lnc-CCL28, were identified as differentially expressed in ovarian tumors using deep machine learning. The levels of lnc-CCL28 transcripts in both tumors and normal tissue samples were sufficient for further analysis by RT-PCR. In addition, the promising ovarian cancer biomarkers, lncRNAs LINC00152, NEAT1 and SNHG17 were added to RT-PCR analysis. For the first time, an increase in the level of lnc-CCL28 and SNHG17 lncRNAs was found in ovarian tumors, and the overexpression of LINC00152 and NEAT1 was confirmed. It seems that lnc-CCL28 is involved in carcinogenesis and, in particular, in ovarian cancer progression. Overexpression of LINC00152 and lnc-CCL28 was significantly associated with the later stages and metastasis.
The study was designed to determine genes of microRNAs hypermethylated in malignant ovarian tumors and to select new diagnostic and prognostic markers of the disease and effective system of markers. ...Using methyl-specific PCR and a representative sample of 54 ovarian cancer specimens, we determined 5 microRNA genes (
MIR-34b/c
,
MIR-9-1
,
MIR-124-3
,
MIR-129-2
, and
MIR-107
) hypermethylated in the majority of tumor samples in comparison with paired samples of histologically unchanged tissue (48-57%
vs
. 4-19%,
p
<0.001). Using ROC-analysis, we selected an effective system of 4 markers for diagnosis of ovarian cancer (
MIR-9-1
,
MIR-124-3
,
MIR-129-2
, and
MIR-107
) characterized by high sensitivity and specificity (up to 87-94% at AUC=0.92) relative to the conventional norm (54 paired samples of histologically unchanged tissue) and absolute norm (18 ovarian tissue samples from subjects who died from non-tumor diseases). It was also shown that methylation of
MIR-129-2
,
MIR-9-1
, and
MIR-34b/c
genes is significantly (
p
<0.01) correlated with the clinical stage or the presence of metastases. The results indicate that epigenetic modifications of the studied microRNA genes are involved in the pathogenesis and progression of ovarian cancer and attest to their diagnostic and prognostic potential.
Methylation of CpG-islands in promoter regions as well as interaction of miRNAs with messenger RNAs of target genes are related to multilayer mechanisms regulating gene expression. The goal of this ...study was to assess a possibility for miRNA gene methylation to influence indirectly activation of their target genes in lung tumors. By using a unified collection of samples of non-small cell lung cancer, it was demonstrated that elevated levels of mRNA for
RHOA
and
NKIRAS1
genes were significantly (Spearman rank correlation,
P
< 10
−11
) associated both with loss of methylation in their CpG-islands and methylation in a number of miRNA genes, which, according to the miRWalk database, were predicted to possess regulatory functions. Novel potential regulatory miRNAs for
RHOA
(miR-9-1/-3, -34b/c, -129-2, -125b-1, -375, -1258) and
NKIRAS1
(miR-34b/c, -129-2, -125b-1, -193a, -124a-1/-2/-3, -212, -132) genes in lung cancer were identified.
It is known that microRNAs (miRNAs) are able to dynamically regulate gene expression. At the same time, methylation can reduce expression of miRNA encoding genes and, therefore, reduce their ...inhibitory effects on mRNAs of target genes, including those of oncogenes, that promoting the development of tumors of different localization. The role of miRNA hypermethylation in the pathogenesis of ovarian cancer is not completely understood; so we conducted a search for new hypermethylated and potentially suppressor miRNA genes in ovarian tumors. Four new miRNA genes (
MIR-107
,
MIR-130b
,
MIR-203a
,
MIR-1258
) commonly hypermethylated (28‒52% ) in tumor tissues vs 4‒7% in paired histologically normal tissues,
p
< 0.01, were identified in a representative set of 54 ovarian cancer samples using methylation-specific PCR. It was shown that hypermethylation of
MIR-130b
,
MIR-203a
, and
MIR-1258
genes is significantly (
p
≤ 0.05) associated with metastasis of ovarian cancer. These results suggest the involvement of four miRNAs (miR-107, miR-130b, miR-203a, and miR-1258) and hypermethylation of their encoding genes in the pathogenesis of ovarian cancer.
MicroRNAs play an important role in the regulation of expression of many genes involved in cancer pathogenesis. One of the causes of miRNA level deregulation in tumors is the methylation of CpG ...islands in the promoter regions of the genes that encode them. Hypermethylation may lead to the suppression of miRNA gene expression and, as a consequence, to a decrease in their inhibitory effect on target gene mRNAs. A search for new miRNA genes hypermethylated in breast cancer has been carried out in the present study. The methylation of five miRNA genes associated with breast cancer (miR-132, miR-1258, miR-107, miR-130b, miR-137) has been as studied using a representative set of 41 breast cancer samples by methylation-specific PCR. Three new genes,
MIR-132, MIR-137
and
MIR-1258
, with a high frequency of hypermethylation (41, 37 and 34%, respectively) have been identified in breast cancer. The methylation of these genes in the breast tissues of ten donors without cancer pathology in anamnesis was only found in single cases. These results enable the involvement of three miRNAs (miR-132, miR-137, miR-1258) and the methylation of the genes that encode them in the pathogenesis of breast cancer to be suggested.
miRNA genes play an important role in cancer pathogenesis, while they may be suppressed by hypermethylation. Here, we assess the diagnostic potential of a group of hypermethylated miRNA genes (
...MIR-124-1
,
MIR-124-3
,
MIR-125B-1
,
MIR-127
,
MIR-132
,
MIR-193a
, and
MIR-34b
/
c
) in a representative set of 70 breast cancer samples and 17 breast tissue samples from deceased donors with no malignancies. For these seven genes, the methylation status is determined using the methylation-specific PCR. Methylation reached 26–76% in tumor specimens, 1‒27% in paired considered normal breast tissues, and 0–18% in breast tissue from deceased donors. By quantitative RT-PCR, reduced expression levels of the investigated miRNAs are detected, with a negative correlation of expression levels with gene hypermethylation. Combinations of three or four hypermethylation biomarkers, namely,
MIR-124-1
,
MIR-125B-1
,
MIR-127
, and
MIR-34b
/
c
are found suitable for breast cancer diagnostics; with sensitivity (76‒93%), specificity (88‒100%), and AUC (0.88‒0.94). Notably, the
MIR-127
gene was hypermethylated only in the tumor samples of patients with metastases, and, therefore, should be tested as a marker of breast cancer dissemination. These findings may lead to improvement in the management of breast cancer.
It is known that microRNAs (miRNAs) are able to dynamically regulate gene expression. At the same time, methylation can reduce expression of miRNA encoding genes and, therefore, reduce their ...inhibitory effects on mRNAs of target genes, including those of oncogenes, that promoting the development of tumors of different localization. The role of miRNA hypermethylation in the pathogenesis of ovarian cancer is not completely understood; so we conducted a search for new hypermethylated and potentially suppressor miRNA genes in ovarian tumors. Four new miRNA genes (MIR-107, MIR-130b, MIR-203a, MIR-1258) commonly hypermethylated (28-52%) in tumor tissues vs 4-7% in paired histologically normal tissues, p < 0.01, were identified in a representative set of 54 ovarian cancer samples using methylation-specific PCR. It was shown that hypermethylation of MIR-130b, MIR-203a, and MIR-1258 genes is significantly (p < 0.05) associated with metastasis of ovarian cancer. These results suggest the involvement of four miRNAs (miR-107, miR-130b, miR-203a, and miR-1258) and hypermethylation of their encoding genes in the pathogenesis of ovarian cancer.
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.
Objectives. Lung cancer, representing a difficult-to-diagnose heterogeneous malignant neoplasm, is characterized by an asymptomatic course up to late stages, a high incidence of adverse outcomes, and ...a high probability of metastasis. Its most common form is non-small cell lung cancer (NSCLC). Recent studies have demonstrated a significant role of non-coding RNAs—in particular, microRNAs—in the development of NSCLC. MicroRNAs, which function as post-transcriptional regulators of the expression of protein-coding genes, including those associated with oncogenesis, are involved in the processes of cell proliferation, differentiation, and apoptosis. One of the approaches for regulating the expression of microRNAs themselves is to change the methylation of the CpG island adjacent to the microRNA gene or overlapping it. It has been shown that microRNA genes are several times more likely to undergo methylation than protein-coding genes. The aim of the present work is to study changes in the level of methylation of a number of microRNA genes and compile a potential panel of markers for the diagnosis and prognosis of NSCLC. Methods. Samples of NSCLC tumors were collected and clinically characterized at the Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, Moscow, Russia. High-molecular-weight DNA was isolated from tissues using a standard method. The level of methylation was analyzed using bisulfite conversion of DNA and quantitative methyl-specific polymerase chain reaction with real-time detection. The significance of differences between the studied groups was assessed by the nonparametric Mann–Whitney U test for independent samples. Differences were considered significant at p < 0.05. Results. The analysis of methylation levels of microRNA genes revealed a significant ( p < 0.05) increase in the methylation level of eight microRNA genes: MIR124-1/2/3, MIR125В-1, MIR129-2, MIR137, MIR375, MIR1258, and MIR339 ( p < 0.01, false discovery rate ≤ 0.25). On the basis of receiver operating characteristic analysis, a panel of markers is proposed for the diagnosis of NSCLC according to the nature of methylation of the studied microRNA genes in the tumor and in the normal tissue. Conclusions. Our results, which contribute to the understanding of molecular mechanisms involved in NSCLC development, can be used in the development of new diagnostic and prognostic approaches in clinical oncology.
Recently, more and more data have been accumulating indicating the role of long noncoding 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. Using a sample of 93 OC samples, real-time methylation specific PCR showed a statistically significant (
p
< 0.05) increase in the level of methylation in tumors. Moreover, for the genes
LINC00472
,
LINC00886
,
SNHG17
, and
TUG1
, hypermethylation in OC was detected for the first time. Five genes (except
SNHG17
) showed a further increase in methylation levels at a more advanced stage, and four 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.
