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Burdennyy AM, Filippova EA, Khodyrev DS, Pronina IV, Lukina SS, Ivanova NA, Kazubskaya TP, Loginov VI, Braga EA. Optimized Marker System for Early Diagnosis of Breast Cancer. Bull Exp Biol Med 2021; 172:57-62. [PMID: 34791555 DOI: 10.1007/s10517-021-05331-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Indexed: 11/30/2022]
Abstract
Changes in the methylation levels of 21 microRNA genes in 91 breast cancer samples in comparison with paired samples of histologically unchanged tissue were studied by quantitative methylation-specific PCR. For 19 microRNA genes, a significant increase in the methylation level in tumors in comparison with normal tissues was shown (Mann-Whitney test). When considering the data for breast cancer samples only from patients with clinical stages I and II (59samples), 17 genes with a significantly increased level of methylation were identified. Increased methylation level for 11 genes (MIR124-1, MIR124-3, MIR125B-1, MIR127, MIR129-2, MIR132, MIR137, MIR193a, MIR34B/C, MIR375, and MIR9-1) compared to the paired norm was highly significant (p<0.001, FDR=0.01). The ROC analysis was used to optimize a set of markers for diagnosing breast cancer at the early stages consisting of 4 microRNA genes: MIR125B1, MIR127, MIR1258, and MIR132; the system is characterized by 100% specificity, 85% sensitivity, and AUC=0.924. Importantly, 100% specificity eliminates false positive results. Detection of methylation of at least one of the 4 genes of this set is sufficient to classify the patient's sample as breast cancer.
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Affiliation(s)
- A M Burdennyy
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia.
| | - E A Filippova
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia
| | - D S Khodyrev
- Federal Research Clinical Center of Specialized Types of Medical Care and Medical Technologies, Federal Medial-Biological Agency of Russia, Moscow, Russia
| | - I V Pronina
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia
| | - S S Lukina
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia
| | - N A Ivanova
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia
| | - T P Kazubskaya
- N. N. Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - V I Loginov
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia
| | - E A Braga
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia
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Sun H, Fan G, Deng C, Wu L. miR‐4429 sensitized cervical cancer cells to irradiation by targeting RAD51. J Cell Physiol 2019; 235:185-193. [PMID: 31190335 DOI: 10.1002/jcp.28957] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 05/21/2019] [Accepted: 05/22/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Hongbo Sun
- Department of Gynecology and Obstetrics Beijing ChuiYangLiu Hospital Beijing China
| | - Guimei Fan
- Department of Gynecology and Obstetrics Shanxian Central Hospital Heze Shandong China
| | - Chunxia Deng
- Department of Gynecology and Obstetrics Beijing ChuiYangLiu Hospital Beijing China
| | - Lin Wu
- Department of Gynecology and Obstetrics Xi'an XD Group Hospital Xi'an Shaanxi China
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Braga EA, Fridman MV, Loginov VI, Dmitriev AA, Morozov SG. Molecular Mechanisms in Clear Cell Renal Cell Carcinoma: Role of miRNAs and Hypermethylated miRNA Genes in Crucial Oncogenic Pathways and Processes. Front Genet 2019; 10:320. [PMID: 31110513 PMCID: PMC6499217 DOI: 10.3389/fgene.2019.00320] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 03/22/2019] [Indexed: 12/13/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the third most common urological cancer, and it has the highest mortality rate. The increasing drug resistance of metastatic ccRCC has resulted in the search for new biomarkers. Epigenetic regulatory mechanisms, such as genome-wide DNA methylation and inhibition of protein translation by interaction of microRNA (miRNA) with its target messenger RNA (mRNA), are deeply involved in the pathogenesis of human cancers, including ccRCC, and may be used in its diagnosis and prognosis. Here, we review oncogenic and oncosuppressive miRNAs, their putative target genes, and the crucial pathways they are involved in. The contradictory behavior of a number of miRNAs, such as suppressive and anti-metastatic miRNAs with oncogenic potential (for example, miR-99a, miR-106a, miR-125b, miR-144, miR-203, miR-378), is examined. miRNAs that contribute mostly to important pathways and processes in ccRCC, for instance, PI3K/AKT/mTOR, Wnt-β, histone modification, and chromatin remodeling, are discussed in detail. We also separately consider their participation in crucial oncogenic processes, such as hypoxia and angiogenesis, metastasis, and epithelial-mesenchymal transition (EMT). The review also considers the interactions of long non-coding RNAs (lncRNAs) and miRNAs of significance in ccRCC. Recent advances in the understanding of the role of hypermethylated miRNA genes in ccRCC and their usefulness as biomarkers are reviewed based on our own data and those available in the literature. Finally, new data and perspectives concerning the clinical applications of miRNAs in the diagnosis, prognosis, and treatment of ccRCC are discussed.
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Affiliation(s)
| | - Marina V. Fridman
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Vitaly I. Loginov
- Institute of General Pathology and Pathophysiology, Moscow, Russia
- Research Center of Medical Genetics, Moscow, Russia
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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Pan H, Hong Y, Yu B, Li L, Zhang X. miR-4429 Inhibits Tumor Progression and Epithelial-Mesenchymal Transition Via Targeting CDK6 in Clear Cell Renal Cell Carcinoma. Cancer Biother Radiopharm 2019; 34:334-341. [PMID: 30844301 DOI: 10.1089/cbr.2018.2697] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background: Clear cell renal cell carcinoma (ccRCC), as the commonest type among renal cell cancers, is featured with easy relapse and metastasis. Despite mounting achievements on its treatment and diagnosis, the identification of new biomarkers remains urgent. Purposes: Present study aimed to explore the role of microRNA-4429 (miR-4429) in ccRCC. Methods: The expression of miR-4429 and cyclin-dependent kinase 6 (CDK6) was evaluated by real-time polymerase chain reaction and Western blot. Cell proliferation, migration and invasion was evaluated by MTT and transwell assays. The interaction between miR-4429 and CDK6 was assessed by luciferase reporter assay. Prognostic significance of miR-4429 was evaluated by Kaplan-Meier analysis. Correlation between miR-4429 and CDK6 was determined by Spearman's correlation analysis. Results: Firstly, the downregulation of miR-4429 and upregulation of CDK6 in ccRCC tissues and cells were uncovered by quantitative real-time polymerase chain reaction. The prognostic significance of miR-4429 in ccRCC patients was proved by Kaplan-Meier analysis. Gain- and loss-of-function assays validated the suppressive effect of miR-4429 on cell proliferation, migration, invasion, as well as epithelial-mesenchymal transition (EMT) progression. The interaction between miR-4429 and CDK6 was predicted by bioinformatics tool and confirmed by luciferase reporter assay. And the negative expression correlation between miR-4429 and CDK6 was verified by Spearman's correlation analysis. Rescue assays confirmed the role of miR-4429/CDK6 in proliferation, metastasis and EMT progression in ccRCC. Conclusions: Present study revealed that miR-4429 suppressed ccRCC tumor progression and EMT by targeting CDK6.
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Affiliation(s)
- Hong Pan
- 1 Department of Nephropathy, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - Yejing Hong
- 1 Department of Nephropathy, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - Biying Yu
- 1 Department of Nephropathy, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - Li Li
- 1 Department of Nephropathy, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - Xiaojian Zhang
- 2 Department of Internal Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
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Loginov VI, Burdennyy AM, Filippova EA, Pronina IV, Kazubskaya TP, Kushlinsky DN, Ermilova VD, Rykov SV, Khodyrev DS, Braga EA. Hypermethylation of miR-107, miR-130b, miR-203a, miR-1258 Genes Associated with Ovarian Cancer Development and Metastasis. Mol Biol 2018. [DOI: 10.1134/s0026893318050102] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Novel miRNA genes deregulated by aberrant methylation in ovarian carcinoma are involved in metastasis. Gene 2018; 662:28-36. [DOI: 10.1016/j.gene.2018.04.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 03/28/2018] [Accepted: 04/04/2018] [Indexed: 02/06/2023]
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Pronina IV, Klimov EA, Burdennyy AM, Beresneva EV, Fridman MV, Ermilova VD, Kazubskaya TP, Karpukhin AV, Braga EA, Loginov VI. 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. Mol Biol 2017. [DOI: 10.1134/s0026893316060169] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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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 2015; 576:483-91. [PMID: 26519551 DOI: 10.1016/j.gene.2015.10.059] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 10/14/2015] [Accepted: 10/25/2015] [Indexed: 01/05/2023]
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.
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Ben Dhiab M, Ziadi S, Louhichi T, Ben Gacem R, Ksiaa F, Trimeche M. Investigation of miR9-1, miR9-2 and miR9-3 Methylation in Hodgkin Lymphoma. Pathobiology 2015; 82:195-202. [PMID: 26337487 DOI: 10.1159/000432402] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 05/15/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND miR9 is an important tumor suppressor microRNA regulated by DNA methylation in various types of cancers. METHODS We analyzed the methylation status of the 3 members of the miR9 family in 58 cases of Hodgkin lymphoma (HL) in comparison to 15 reactive lymph nodes. We also assessed the relationships between miR9 methylation and Epstein-Barr virus (EBV) infection and several clinicopathological parameters. RESULTS We found that 84.5% of HL cases had a methylation in at least 1 of the 3 loci of miR9, whereas none of the nontumoral samples was methylated. The highest rate of methylation was found in miR9-2 (5q14.3) in 74.1% of the HL cases, followed by miR9-3 (15q26.1) in 56.9% and miR9-1 (1q22) in only 8.6% (p < 0.001). The promoter methylation of miR9-3 was more frequent in patients older than 15 years than in children (p = 0.02) and among women rather than men (p = 0.02). However, no significant correlation was found between miR9 methylation and EBV infection. CONCLUSION These results indicate that miR9 methylation, especially miR9-2, is a frequent event in HL and may be involved in HL pathogenesis, irrespective of EBV infection.
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Affiliation(s)
- Myriam Ben Dhiab
- Department of Pathology, Farhat Hached University Hospital, Sousse, Tunisia
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Braga EA, Khodyrev DS, Loginov VI, Pronina IV, Senchenko VN, Dmitriev AA, Kubatiev AA, Kushlinskii NE. Methylation in the regulation of the expression of chromosome 3 and microRNA genes in clear-cell renal cell carcinomas. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415050026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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